sabre center investigators

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Sandler Asthma Basic REsearch Center! University of California, San Francisco! !

Progress Report! Year 14! April 2013!

Innate Lymphoid Cells in Asthma!

Figure Legend: Lung slices from mice before and after allergen challenge were imaged using three-channel multiphoton microscopy. Animals contain a red fluorescent marker introduced into the interleukin-5 gene, which reveals IL-5-producing innate lymphoid cells organized at airway branchpoints that respond to provocation by activating cytokine expression. IL-5 is critical for recruiting and sustaining eosinophils, a central cell type seen in allergic asthma. Image courtesy of Emily Thornton, Steve Van Dyken, Jesse Nussbaum from the laboratories of Drs. Krummel and Locksley.

TABLE OF CONTENTS Mission Statement Overview Summary of Accomplishments Executive Committee: Members and Functions Scientific Advisory Board Mitchell Kronenberg, Ph.D. Philippa Marrack, Ph.D Christopher Wilson, M.D. SABRE Center Investigators Richard Locksley, M.D., Ph.D. Christopher Allen, Ph.D. K. Mark Ansel, Ph.D. Limin Liu, Ph.D. Jeoung-Sook Shin, Ph.D. Core Facilities Mouse Physiology and Morphology Functional Genomics Genetics Cell Sorting and Analysis Microscopy Asthma Related Research Projects Evolving Microenvironments in Airway Inflammation NIAID Asthma and Allergic Diseases Cooperative Research Center Contributions to Relevant Scientific Activities Publications Supported by the Sandler Asthma Basic Research Center Looking to the Future Biographical Sketches

Mission Statement The Sandler Asthma Basic Research Center (SABRE Center) at UCSF is an investigative unit dedicated to basic discovery in asthma research. The SABRE Center is nucleated by a small group of five basic scientists who are supported by advanced technology cores and linked with the larger scientific community through Center Grants and Program Project Grants focused around asthma research. Strong linkage with the Airway Clinical Research Center at UCSF has enabled increasing focus on human studies. Regular seminars promote additional integration of the SABRE Center into the more extended UCSF research community to facilitate collaboration and to increase awareness for needs in fundamental discovery in asthma research. Founded in 1999, the SABRE Center is made possible by the generous support of the Sandler Foundation.

Summary of Accomplishments over the Past Year The SABRE Center is evolving into a successful research enterprise within the greater UCSF scientific community. Notable benchmarks achieved this year include: (1) the award of an NIH Director’s New Innovator Award to Chris Allen, the SABRE Center UCSF Fellow, who was recruited to stay at UCSF on the faculty as a member of the Cardiovascular Research Institute, where he will continue his work as a SABRE Center member; (2) the first full year of funding of the SABRE Center Program Project grant to study the role of innate lymphoid cells in human asthma using patients accrued from the Airway Clinical Research Center; (3) the successful renewal of the NIH NIAID Asthma and Allergic Diseases Cooperative Research Center to continue investigations of cytokine regulation of airway smooth muscle contraction; (4) the successful organization and planning of a Keystone Symposium in January 2013 devoted to recent advanced in Type 2 Immunity and Pathogenic Processes in Asthma in Santa Fe, New Mexico, that drew over 250 scientists together; and (5) continued successes in obtaining extramural funding and publishing high impact manuscripts in competitive journals. Increasingly, these studies have begun to work with and focus on human patients and materials and the interactions with our clinical colleagues in the Pulmonary Division continue to strengthen with the establishment of the Airway Clinical Research Center. We look forward to ongoing successes in the coming year as we continue with our mission to conquer asthma.

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Overview – 2013 Richard M. Locksley, M.D. The SABRE Center consists of the Director, Dr. Locksley, three full-time faculty, Drs. Ansel, Liu and Shin, and one UCSF Fellow, Dr. Allen, who has just completed his five year appointment and has been recruited to join the faculty. In turn, these investigators now support 10 postdoctoral trainees, 9 graduate students in Immunology and Biomedical Sciences, and 3 professional staff. Dr. Chapman, the former head of the Pulmonary Division at UCSF, works in contiguous space. His interests focus on lung inflammation and fibrosis, which overlap the interests of the SABRE Center. The SABRE Center maintains close working relationships with the Airway Clinical Research Center (ACRC) under the leadership of Dr. John Fahy, who has become a member of the Executive Board. The fruits of this collaborative effort resulted in the first NIH Program Project Grant awarded to SABRE investigators beginning in 2012, with a major focus centered on human patients and tissues as organized through the ACRC. The SABRE Center has evolved into a self-standing research addition to the UCSF campus with the capacity to contribute to our understanding of this important human disease. We will review the individual investigators and their progress, followed by an overview of the constituents of the Center, a brief discussion of achievements and finally a look at the extramural grants that have been obtained to support these activities. Investigators Dr. Ansel is working to understand the gene expression pathways that mediate differentiation and regulation of cell fate and function in allergy, particularly asthma. His focus remains on microRNAs, transcription factors and epigenetics as critical executioners of these pathways. He continues to push new technologies relevant to his studies, including a method for assessing microRNA targets by demonstrating their associations with the miRISC processing complex, an analysis which could greatly spur the field. He published 4 manuscripts in 2012-13 as senior author and contributed to a fifth; an additional manuscript is under revision at Nature Immunology and describes the role of a specific microRNA, miR-17~92, in follicular T cell differentiation. He is building increasing excitement over his discoveries in the field as evidenced by recognition of his early achievements through solid publications and enhanced amounts of extramural grant support. He was asked to write a review on RNA regulation of the immune system for Nature Reviews Immunology and to organize an issue of Immunological Reviews on the subject, attesting to his recognition by leaders in the field. Dr. Ansel participated in several national and international scientific conferences related to his expertise, including talks in Japan and Korea. Based on studies completed with his 3-year Dana Foundation Award, Mark received his first R01 funded grant from the National Heart, Lung and Blood Institute of the NIH to pursue collaborations with Dr. Prescott Woodruff in the Airway Clinical Research Center, bringing in $1,796,403 in direct research dollars over a five year period. Dr. Ansel also was a participating Principal Investigator as part of the first Program Project Grant among SABRE Investigators from the NIH. This grant began funding in July 2012 at a total level of approximately

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$1,575,000 per year over the next 5 years. In recognition of his outstanding accomplishments as a young investigator, Dr. Ansel was awarded a Leukemia & Lymphoma Society Scholar Award, resulting in approximately $525,000 in direct costs from 2012-2017. He has a U19 application under consideration that involves a concerted effort towards understanding microRNA biogenesis and regulation in immune cells using allergic immunity as a template. Personnel in the Ansel laboratory include two graduate students, with one supported by National Science Foundation Predoctoral Research Fellowship and one a recipient of an HHMI Graduate Education in Medical Science (GEMS) Training Program Award to pursue translational studies in asthma patients in collaboration with Dr. Fahy in the Airway Clinical Research Center. The postdoctoral fellow is supported by a Swiss National Fellowship. Dr. Ansel’s first student graduated and is doing a postdoctoral fellowship. He is actively pursuing studies using materials collected from patients with asthma in the Airway Clinical Research Center. He is collaborating in studies with the Functional Genomics Core, the Animal Physiology Core and the Flow Cytometry Core. He collaborates with multiple other investigators in the SABRE Center. In recognition of Dr. Ansel’s success to date, the Department of Microbiology & Immunology has submitted his materials for consideration of early advancement to Associate Professor. Dr. Liu is pursuing the mechanisms that control the targeting and turnover of nitric oxide, an important airway and blood vessel relaxant. Work in his postdoctoral training identified the enzyme GSNOR as an important molecule regulating nitrosylation and nitric oxide turnover in tissues, and this molecule has become an important target in asthma, although it will be critical to first identify potential toxicities that might be associated with inhibiting this pathway. During his studies at UCSF, Dr. Liu identified an important role for GSNOR in protecting liver cells from genotoxic stress. He went on to identify the mechanism as linked to the nitrosative inactivation of a DNA alkyltransferase involved in DNA repair. He continues to address the role of GSNOR in immune pathways related to asthma in a collaborative publication with Dr. Krummel in the Imaging Core and in on-going but incomplete studies addressing cell-specific deletion of GSNOR in different lung cell populations in order to pinpoint the origin of GSNOR amenable to therapeutic intervention in asthma. He is actively attempting to identify the targets of protein nitrosylation potentially impacted by this pathway. He had two manuscripts related to GSNOR in publication over the past year and two additional manuscripts submitted. He has been working recently with Dr. Steven An to define direct roles for GSNOR in airway smooth muscle cell contraction and relaxation pathways. Dr. Liu is working collaboratively with individuals in the Functional Genomics, Genetics and Flow Cytometry Cores. He presented his work at both national and international scientific meetings. Dr. Liu is supported by an R01 and P01 on which he participates. These grants, which contribute over $475,000 direct costs per year, are from the National Cancer Institute of the NIH and study aspects of oncogenesis mediated by GSNOR deficiency, an important issue that must be addressed in order to sustain interest in this enzyme as a viable asthma therapeutic target. He has three postdocs in his laboratory. He continues to work to develop sufficient preliminary and published information on the role of GSNOR in smooth muscle contraction in order to pursue this as an asthma-related source of NIH funding. Dr. Liu was promoted to Associate Professor,

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effective July 2012, thus becoming the first SABRE Center recruit to achieve academic tenure at UCSF. Dr. Shin studies dendritic cell maturation and antigen processing, which represent an extension of her postdoctoral training where she described a novel pathway affecting the turnover of surface complexes of major histocompatibility-peptide complexes at the surface of the dendritic cells, a process which was regulated by ubiquitination. She is continuing studies of dendritic cells with an emphasis on cells collected from the human lung. She published a manuscript addressing the role of ubiquitination in controlling MHC class II surface distribution on antigen presenting cells. A manuscript describing the unexpected finding that IgE receptor on dendritic cells promotes serum IgE clearance, was reviewed positively at the Journal of Clinical Investigation and is under revision. A third manuscript describing the role of ubiquitination in the process of dendritic cell of thymic regulatory T cells was reviewed positively and is being revised for the Journal of Experimental Medicine. Two additional manuscripts are in preparation. She was invited to present her work at a Keystone Meeting on Dendritic Cell Biology. Dr. Shin supports her laboratory with two young investigator awards from the Cancer Research Institute and from the American Heart Association. She is re-submitting an R01 to the NIH for the next deadline after closely missing the payline on her first submission. She received a UCSF School of Medicine Bridge Fund Award, which is awarded to individuals whose grants are felt most likely to succeed if given support for re-submission, at the start of 2013. Dr. Shin has established close collaborations with pulmonary physicians in the Airway Clinical Research Center – Drs. Paul Wolters, Prescott Woodruff and John Fahy – to obtain freshly dissected human lung tissues from transplant procedures and samples of biopsies and cell lavages from asthma patients and individuals with idiopathic pulmonary fibrosis. She is also using humanized transgenic mice with human FcεRI expressed on mouse cells in a pattern resembling its expression in humans (developed in the Kinet lab at Harvard). Dr. Shin works closely with the Airway Clinical Research Center, the Flow Cytometry Core and the Imaging Center. She currently has a graduate student, two postdoctoral trainees and a technician in her laboratory. Dr. Allen began 5 years ago as a UCSF Fellow and is the first member of the UCSF Fellows Program (http://biochemistry.ucsf.edu/~ucsffellows/current.html) who was selected to work on a specific human disease, in this case, asthma. Dr. Allen combines skills in cellular and molecular immunology with optical imaging capacities that have powered new insights in allergic inflammation. His primary research focuses on understanding the mechanisms by which highaffinity IgE-producing B cells and plasma cells are produced. Surprisingly, this remains a poorly understood pathway of fundamental importance to the pathogenesis of allergy and asthma. Dr. Allen published some of his initial findings in a report in Immunity reporting his discovery that IgE heavy chains inherently drive movement of B cells out of germinal centers, a process that may serve to limit somatic hypermutation and thus affinity. This finding will drive new hypotheses regarding mechanisms by which some allergic individuals develop high-affinity IgE, and constitute major efforts of his laboratory. His generation of an IgE reporter mouse that permits the efficient tracking of IgE-switched B cells constitutes an important technical advance

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for the field. He was invited to two Keystone meetings to present his findings. He continues to work closely with other investigators in the SABRE Center as he optimizes lung and immune cell imaging technologies that are applicable to broader use by other investigators on campus. Dr. Allen has attracted substantial new extramural funding to support his studies. This includes an NIH R01 that will focus on imaging of basophils in tissues in situ and an NIH Director’s New Innovator Award, fewer than 8% of which were funded in the last year. Together, these awards, both for 5 years duration, will bring in over $500K in direct costs to support his lab over the coming year. In recognition of these accomplishments, Dr. Allen was recruited to the Cardiovascular Research Institute (CVRI) at UCSF, where he joined the UCSF faculty as an Assistant Professor in the Department of Anatomy in 2013. He remains committed to investigations into the basic pathogenesis of asthma. Dr. Allen will continue to be a member of SABRE, and will continue to participate in monthly and quarterly meetings with SABRE investigators on the Parnassus site. Core Activities An integral component of the SABRE Center has been support and guidance for advanced technology cores. The specific workings of these Cores and their achievements are detailed elsewhere in this report. The SABRE Center contributes to cores in Mouse Physiology (which provides both acute and chronic mouse models of allergic lung inflammation, including challenge with model antigens, fungal antigens and house dust mite antigens), Functional Genomics, Genetics, Flow Cytometry and Imaging, including video, two-photon, confocal and total internal reflection instruments. Our largest monetary support goes to the Mouse Physiology and the Genetics Cores, which support small animal models and the collection of cohorts of carefully phenotyped families with asthma, respectively, in order to meet specialized needs of importance to asthma investigators. These cores continue to attract substantial use among investigators across the campus as well as scientists in related fields, including inflammation, genetics and stem cell biology. The Animal Core contributed to 5 AAF studies from non-UCSF investigators over the past year and helped train investigators at the University of Arizona and at Virginia Commonwealth who have started to center such studies at those universities. The Genetics Core has procured very large cohorts of Latino and African American families afflicted with asthma for use genetic studies, and continues to participate in a number of multiinstitutional studies for genome-wide investigations and gene replicative studies. Dr. Burchard, the Core Director, has attained national prominence in recognition of this highly annotated cohort. The remaining cores are supported by smaller amounts of funding, typically to core directors and operators or to help support maintenance contracts for equipment, costs that are difficult to recover through recharge or other mechanisms. The Imaging Core has made large technical strides in providing optical support for live lung and lymph node imaging. SABRE funding is concentrated on developing novel technologies to enhance live imaging capacity, to establish site-specific photo-ablation technology and to extend imaging capacity to sections of human lung. Participation in the Imaging Center has grown to support over 166 users involving 66 Principle Investigators from 26 different Department or Organized Research Units at UCSF. Substantial training of new users and software development to support these new technologies is

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an ongoing part of the mission. Thus, in a relatively short time, the Imaging Core has become an integral and productive component of the scientific community at UCSF. The Functional Genomics Core, led by Dr. David Erle, has used SABRE support to enable improved technologies for high throughput sequencing, CHIP-seq, microRNA profiling and RNAseq. This has proven particularly useful in Dr. Ansel’s studies in identifying important regulatory RNAs involved in T cell fate and effector function. SABRE support for these technology cores has been leveraged to attract NIH funding: the Animal Physiology Core is additionally supported by technical core funds from NIAID Asthma and Allergic Disease Cooperative Research Center (Sheppard, Krummel, Woodruff, Erle) and the Imaging Core is additionally supported by technical core funds supported by a PPG from NHLBI to assess the microenvironments induced by lung inflammation (Caughey, Krummel, McDonald). In each case, funds from the SABRE Innovative Grants program initiated projects that led to the organization and support for these programmatic awards, indicative of the leverage enabled by a focused efforts from relatively small groups of investigators. Support for the Flow Cytometry Core, which is largely self-supported and self-operated, is restricted to financial help with maintenance contracts, data base management and emergency laser failure, issues that are incompletely covered through recharge or grant-based mechanisms. These Cores achieve substantial leverage of resources, and over the past 2 years contributed to at least 12 successfully funded extramural grants, 7 postdoctoral fellowships and over 40 peerreviewed manuscripts. Recharge systems have been set in place for the Functional Genomics Core, the Mouse Physiology Core and the Flow Cytometry Core, and these are constantly reassessed to ensure that fiscal accountability is maintained such that these services are not only sustained, but enhanced by upgrading and enabling new technologies.

Airway Clinical Research Center The Airway Clinical Research Center (ACRC) (see Figure) is a customized space of 3500 sq ft. located on the 13th floor of the UCSF Medical Center. The Airway Center comprises 5 separate testing rooms for history and physical examination, phlebotomy, allergen skin tests, spirometry and methacholine challenge. This center also has a research bronchoscopy suite, a sample processing lab, and administrative space for twelve research coordinators and six research fellows. All of this space is dedicated to clinical research in airway disease; there is no clinical patient activity in this space. The Airway Clinical Research Center has fully equipped exam rooms for conducting pulmonary function testing, research bronchoscopy, participant interviews and specimen collection and processing.

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The ACRC is equipped to see patients and collect tissue specimens quickly and efficiently. The following instruments are currently on site. Spirometers: Eight spirometers (Jaeger Masterscope (2), nSpire HDpft 1000 (1), Sensormedics VMax22 (1), Medgraphics CPFS/D Spirometer (2), nSpire KoKo PFT (2). Bronchoscopy equipment: Pentax Fiberoptic Bronchoscope Model #EB-1530T3 (2), Pentax Processor Model #EPM-3500, Welch Allyn ProPaq CS vital signs monitor. Sputum Induction: Devilbiss UltraNeb 99 ultrasonic nebulizer (2), Nouvag UltraNeb ultrasonic nebulizer (2), NuAire NU-810-SPEC Biohood sputum induction booths (2). Biospecimen Processing room: Smith Kline Beecham VanGuard V6500 centrifuge, Fisher Scientific centrifuge Model #228, Thermo Shandon Cytospin 4 cytocentrifuge, Reichert hemocytometer (2), Eppendorf 5810R refrigerated centrifuge, Lab Companion B5-06 shaking water bath, Fisher Scientific specimen refrigerator #97-915-1, Frigidaire refrigerator/freezer for medication storage, Sanyo -80 freezer MDF-U53VA, Sanyo -80 freezer MDF-U73VC, Forma Class II A2 Biological Safety Cabinet, TLS2200 Thermal Labeling System, barcode reader (2), Van Guard microscope. Other: Devilbiss PulmoAide compressor nebulizer (Rooms 1333, 1329A, 1329E), IsoTemp 205 water bath, Fisher Scientific Stereomaster Zoom Microscope Model #12-562-1, Niox Mino nitric oxide (NO) monitor, ECG machines (2) HP Pagewriter Xli and Burdick Eclipse LE, Nellcor pulse oximeter (2), Welch Allyn Sure Temp Plus (2), SM DSM-2 micro-dosimeter, Salter Labs Dosimeter (2), Tanita Scale, stadiometer, Bedfont Micro+ Smokerlyzer carbon monoxide (CO) monitors (2), Omron HEM-907XL blood pressure monitor. The ACRC has 12 research coordinators, a part time nurse, and a data manager. The model for these staff is that individual coordinators take ownership of specific research studies and

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manage that study in terms of recruitment, study visits, and biospecimen handling. Weekly meeting of Airway Research Center staff and faculty involve presentations of specific projects and administrative and quality assurance meeting focused on compliance with local, state, and federal regulations governing research in human subjects. The ACRC enables approximately 1200 subject visits per year. The ACRC supports four large NIH research programs that involve multicenter network collaborations in asthma and COPD, thus supporting large numbers of patient visits per year: (i) AsthmaNet - U10 HL098107 (Boushey, Lazarus, Cabana [Pediatrics]) (ii) Severe Asthma Research Program (SARP) - 1U10HL109146-01 (Fahy). (iii) COPD Clinical Research Network (CCRN) (Lazarus) (iv) SPIROMICS (Woodruff) - N01-08-08, The goal of this study is to identify sub-populations and intermediate outcome measures in COPD (chronic obstructive pulmonary disease) through a large multi-center longitudinal study. The Center also supports the clinical components of multiple other NIH awards involved with various aspects of the SABRE Center, including: (i) 1P01HL107202 (Fahy) 8/1/12 - 6/30/17 NIH/NHLBI. Program Project Grant. Innate and Adaptive Immune Responses in Th2-high Asthma. Fahy, Ansel, Woodruff, Locksley. (ii) 2U19AI077439-06 (Sheppard) 4/1/13 - 3/31/18 NIH/NIAID. Asthma and Allergic Diseases Cooperative Research Centers (AADCRC). IL-13 and IL-17 dynamics in the asthmatic airway - Sheppard, Woodruff, Krummel, Erle. (ii) 5R01 HL080414-05 (Fahy) 7/1/5-5/31/15 NIH/NHLBI. Protein carbohydrate interactions in the pathophysiology of acute asthma exacerbations. (iii) Inner City Asthma Consortium (Boushey) – a part of NIH Asthma-Net. (iv) 1P50HL107191-01 (Fahy) 4/1/11- 3/31/13 NIH/NHLBI. Preventing fucose-dependent binding of aspergillus and pseudomonas to lung mucin (v) 1 R01 HL097591 (Woodruff, PG) 7/1/09 - 06/30/13 NIH/NHLBI. Role of Th2 and non-Th2 Inflammation in Airway Smooth Muscle Remodeling in Asthma. In addition to NIH grants, the ACRC is a resource for industry supported clinical research in

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airway disease at UCSF. Recent industry sponsors have included Genentech, Boehringer Ingelheim, and Roche and research alliances with Gilead and Pfizer are pending. The hope is to expand this aspect of SABRE-industry interactions as a platform for successful movement of target identification and pathophysiology onwards to drug and therapeutic development pathways. SABRE Center core scientists and the Director meet quarterly with Dr. Fahy and colleagues to further communication, planning and collaborative investigations of human asthma patients. Each of the core scientists is already involved in ongoing or planned investigations with translational physician scientists in the ACRC, confirming that this will serve as an important integrative unit for translational interests of the SABRE Center. There is also a monthly research conference for SABRE/ACRC investigators at the Parnassus site to promote interactions and collaborations. Successful competition for extramural support Evidence-based metrics for success will be important in leveraging continuing support in the future, including from philanthropic entities. Fund-raising will require evidence for metrics of success, including our capacity to attract extramural research dollars to the community, to contribute high-impact papers that establish novel paradigms in the asthma research arena, to attract new investigators into the field and, ultimately, to drive the discovery of new therapies that affect the disease. Although therapeutic discoveries will take time, we believe we can point to successes in these evidence-based metric achievements over this past year. Since the initial recruitment of Dr. Liu and the additions of Drs. Ansel, Shin and Allen, we have seen a steady climb in the amounts of external funds accrued by the core five SABRE investigators in support of their research efforts. This has occurred despite the difficult funding climate, and attests to the capacity of the Center to serve as a nidus for successful asthma basic research. As demonstrated by our ability to obtain a Program Project this year by capitalizing on the access and expertise of colleagues in the Airway Clinical Research Center, we believe that building multicomponent research teams to take on difficult problems associated with asthma will prove a successful strategy for maintaining this funding momentum.

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Growth in accumulated extramural funds by the five core SABRE investigators In addition, activities related to the SABRE Center resulted in publication of numerous manuscripts and contributions to many successfully awarded grants and fellowships of various types to investigators at UCSF. These are catalogued in the individual Core and Program Reports. Highlighted SABRE Center-supported papers with impact on asthma-related research in 2012-13 Cheng LE, K Hartman, A Roers, MF Krummel, RM Locksley. 2013. Perivascular mast cell dynamically probe cutaneous blood vessels to capture IgE. Immunity 38:166-175. Although cross-linking of IgE bound to high-affinity receptors on mast cells and basophils has been associated with the acute pathology of allergy and asthma, the mechanism by which tissue mast cells acquire serum IgE remains unclear. Using molecularly designed reagents and live tissue imaging, this manuscript demonstrates that mast cells positioned along small cutaneous blood vessels can extend elongated cellular processes between endothelial capillary cells into the blood stream, where they can extract IgE directly upon binding to surface IgE receptors. Efforts are underway to discover the molecular determinants of this probing behavior in hopes of uncovering new strategies for blocking this process that is central to allergic hypersensitivity. Seumois G, P Vijayanand, CJ Eisley, N Omran, L Kalinke, M North, AP Ganesan, LJ Simpson, N Hunkapiller, F Moltzahn, PG Woodruff, JV Fahy, DJ Erle, R Djukanovic, R Blelloch, KM

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Ansel. 2012. An integrated nano-scale approach to profile miRNAs in limited clinical samples. Am J Clin Exp Immunol 1:70-89. Clinical research is limited by the amounts of material and the heterogeneity of specimens available for study. Standardized methods applicable to analysis of small amounts of material are needed. The manuscript demonstrates a flow cytometric and nano-scale quantitative reverse polymerase chain reaction method that is capable of accurately and reproducibly measuring microRNAs from as few as 100 cells collected in bronchial biopsy specimens from asthma patients obtained in the UCSF Airway Clinical Research Center. The study provides methods that should be applicable to other complex human diseases. Kudo M, AC Melton, C Chen, MB Engler, KE Huang, X Ren, Y Wang, X Berstein, JT Li, K Atabai, X Huang, D Sheppard. 2012. IL-17A produced by αβ T cells drives airway hyperresponsiveness in mice and enhances mouse and human airway smooth muscle contraction. Nature Medicine 18:547-54. The role of IL-17, a cytokine that serves to attract neutrophils to sites of inflammation, in asthma is of increasing interest as clinicians begin to understand non-allergic forms of asthma. Using both mouse and human tissues, the authors here show that IL-17A produced by CD4 T cells in the lung can directly mediate airway smooth muscle hyper-contractility and expose a mechanism related to smooth muscle myosin responsiveness. This study will drive much interest in understanding whether targeting this cytokine or these cells may comprise a therapeutic strategy in some patients with non-allergic asthma. Thornton EE, Looney MR, O Bose, D Sen, D Sheppard, RM Locksley, X Huang, MF Krummel. 2012. Spatiotemporally separated antigen uptake by alveolar dendritic cells and airway presentation to T cells in the lung. J Exp Med 209:1183-1199. How allergens are sampled and processed in the airways is not currently understood. Using genetically altered mice with fluorescent cells and two-photon intravital imaging of the lung, this manuscript demonstrates that inhaled antigens are collected by probing dendritic cells in distal airway spaces, but these cells then migrate proximally to present processed antigen to T cells at branch points along the conducting airways. This finding contributes to our understanding of the pathologic processes that center the pathology of asthma on the conducting airways rather than the more distal air-exchange portions of the lung. Yang Z, BM Sullivan, CDC Allen. 2012. Fluorescent in vivo detection reveals that IgE+ B cells are restrained by an intrinsic cell fate predisposition. Immunity 36:857-72. Despite the importance of IgE in mediating manifestations of atopy, methods for studying the B cells that produce IgE were lacking, thus precluding the examination of this pathway as a potential strategy for intervention. The authors devised a knockin reporter mouse strain that reveals cells that have productively switched the immunoglobulin locus to produce IgE. After confirming that they can now isolate and image IgE-producing B cells in vitro, the authors make the unexpected observation that IgE B cells mature in germinal centers, in contrast to prior dogma, but that expression of a successfully rearranged IgE BCR leads to immediate upregulation of Blimp-1 and egress from the germinal center to become a memory B cell or plasma cell. This study reveals a cell-intrinsic mechanism that serves to limit the extent of

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somatic hypermutation, and hence affinity maturation, which occurs once a B cell expresses IgE. The possibility that patients with severe atopy might dysregulate this highly controlled pathway is being explored. Organization of the body of this Annual Report As in prior years, we will organize this report by reviewing the SABRE Center activities and updating the core technologies that focus on asthma-related research. We will summarize our interactions with other campus asthma-oriented research projects and provide listings of the seminar speakers of conferences to which we lend support. We will follow this with a listing of the newly funded, pending or submitted grants and publications since the prior annual reports that reflect support from the many SABRE Center activities. We will summarize the Financial Report for the Program. Finally, we will outline the strategies for the coming years and append the current biographical summaries of the members, awardees and participants in the SABRE Center at UCSF. We wish to thank the Sandler family for their vision and support in creating and sustaining the SABRE Center. Support for high-risk, open-ended, basic science is difficult to procure in the current funding and fiscal climate. As noted in the overview above, we can identify many examples where support from the SABRE Center has been leveraged greatly to achieve substantial gains for the scientific and academic study of asthma at UCSF. We are most grateful for the Sandlers’ continued support.

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Executive Committee Richard M. Locksley, M.D. The goals of the SABRE Center are to drive innovation in basic asthma research. We approach this goal by establishing a core basic science group dedicated to the study of asthma, by promoting access to state-of-the-art technologies required to drive the research, by integrating their accomplishments across the greater UCSF campus, and by creating opportunities for interactions with translational and clinical investigators studying asthma patients. The Committee includes Dr. John Fahy, the Director of the Airway Clinical Research Center at UCSF, who continues to facilitate interactions between SABRE members and the activities of the Clinical Research Center. The Executive Committee is constituted to provide the Director with counsel regarding issues of scope, direction and execution. The Executive Committee played a major role in the recruiting faculty to the SABRE Center and provides oversight in sustaining progress towards the overall goals of the Center. SABRE Center Executive Committee Members Richard Locksley, M.D., Professor Director, SABRE Center Departments of Medicine and Microbiology/Immunology Homer Boushey, M.D., Professor Department of Medicine Hal Chapman, M.D., Professor Department of Medicine John V. Fahy, M.D., Professor Department of Medicine William Seaman, M.D., Professor Department of Medicine Dean Sheppard, M.D., Professor Department of Medicine Art Weiss, M.D., Ph.D., Professor Departments of Medicine and Microbiology/Immunology Zena Werb, Ph.D., Professor Department of Anatomy

Sandler Asthma Basic REsearch Center

Scientific Advisory Board

                                             

SCIENTIFIC ADVISORY BOARD

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Sandler Asthma Basic REsearch Center

Mitchell Kronenberg, Ph.D. President and Scientific Director LIAI - La Jolla Institute for Allergy & Immunology Mitchell Kronenberg was appointed President of the La Jolla Institute for Allergy and Immunology in September 2003. He is responsible for the overall administration of physical resources, finances and space at the Institute; and works with the Institute’s board of directors, faculty, and executive management to develop and implement strategic plans for shaping the Institute’s future. In addition to his duties as LIAI’s chief executive officer, Dr. Kronenberg serves as Scientific Director of the Institute and Head of the Division of Developmental Immunology. He conducts an active research program on the development of the immune system and the pathogenesis of autoimmune disease, and is a world-renowned expert in the fields of mucosal and innate immunity. Dr. Kronenberg graduated with a bachelor’s degree in biochemistry from Columbia University, and earned his Ph.D. from the California Institute of Technology (Caltech) in 1983. He stayed on at Caltech as a postdoctoral fellow, and joined the faculty of the UCLA School of Medicine in 1986, serving first as Assistant, and later as Associate and full Professor. In 1997, he moved to LIAI to head the Division of Developmental Immunology. He also is an Adjunct Professor of Biology at the University of California, San Diego. Dr. Kronenberg is the co-author of more than 215 scientific publications and holds six research grants from the U.S. National Institutes of Health (NIH). He has served on a number of grant review panels for NIH and other private medical research agencies, and is on the editorial board of four scientific journals. He is the winner of the Richard Dwyer award for cancer research (UCLA) and has been the Kroc Professor of Medicine at the University of California, Davis, and the Wellcome Foundation visiting Professor at Harvard University.

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Sandler Asthma Basic REsearch Center

Philippa (Pippa) Marrack, Ph.D. Professor of Molecular Biology and Immunology Vice Chair, Department of Immunology National Jewish Medical and Research Center, Denver Professor at the Health Sciences Center, University of Colorado Research Investigator at the Howard Hughes Medical Institute, USA As one of the world’s leading research scientists investigating T cells, the family of cells that help the body fight off disease, Dr. Marrack’s work has led to a greater understanding of their role in the immune system. Born in the United Kingdom, Philippa Marrack earned her undergraduate and doctoral degrees in biological sciences from the University of Cambridge. She left the UK in 1971 to do postdoctoral work in the USA, where she has lived and worked ever since, initially at the University of California, and then at the University of Rochester. Since 1979, she has been based in Denver, Colorado, where she is now a research investigator at the Howard Hughes Medical Institute, Vice Chair of the Department of Immunology and Professor at National Jewish Medical and Research Center, and Professor at the University of Colorado’s Health Sciences Center. During her career, Philippa Marrack has published more than 300 peer-reviewed journal articles and she has served on the editorial boards of numerous journals, including Cell, Science, and the Journal of Immunology. Amongst her many honors are the Royal Society’s Wellcome Foundation Prize (1990), the Paul Ehrlich and Ludwig Darmtsädter Prize (1993) and the Louisa Gross Horwitz Prize (1995). She has served on various panels and boards for the American Cancer Society, the U.S. National Institutes of Health, and the Burroughs Wellcome Fund. She was the President of the American Association of Immunologists in 2000-2001, and is currently the President of the International Union of Immunological Societies.

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Sandler Asthma Basic REsearch Center

Christopher Wilson, M.D. Director, Global Health Discovery Program, Gates Foundation Dr. Chris Wilson, Director of the Global Health Discovery program, leads a team that targets fundamental scientific and technological advances in global health that could lead to new ways to prevent, treat, and diagnose disease. Wilson joined the foundation in 2009 as Deputy Director, Vaccine Discovery and Human Biology, Global Health Discovery. Wilson is a pediatrician and immunologist. He joined the faculty at the University of Washington in 1979 in the Infectious Diseases Division of the Department of Pediatrics and later served as head of the Division of Infectious Diseases, Immunology and Rheumatology. In 1989, he became one of the founding faculty members in the new Department of Immunology, and served as Chairman of the Department of Immunology and head of the graduate program in immunology from 1999-2009. He has also served on a number of national advisory panels, including the Institute of Medicine Vaccine Safety Review Committee (2001-2004) and the National Advisory Council on Child Health and Human Development, NICHD, NIH, and he co-chaired the NIAID US Immunodeficiency Network Pilot Grant Review Committee. He is an elected fellow of the American Association for the Advancement of Science. Wilson received a bachelor’s degree from the University of California, Irvine and a medical degree from UCLA. He trained in pediatrics at Boston Children’s Hospital /Harvard Medical School, served in the US Public Health Service, and then was a postdoctoral fellow in infectious diseases while performing immunology research at Stanford University.

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Sandler Asthma Basic REsearch Center

SABRE CENTER INVESTIGATORS

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Sandler Asthma Basic REsearch Center

Richard M. Locksley, M.D. Professor, Departments of Medicine and Microbiology & Immunology Investigator, Howard Hughes Medical Institute UCSF 513 Parnassus Avenue Medical Sciences, S-1032B, Box 0795 San Francisco, CA 94143-0795 Tel: 415-476-3087 Fax: 415-502-5081 Website: Cancer Center Immunology Graduate Program Pulmonary & Critical Care Division Howard Hughes Medical Institute Virology & Microbial Pathogenesis Dr. Locksley is the Director of the Sandler Asthma Basic Research Center (SABRE) and a Howard Hughes Medical Institute Investigator. He is a Professor in the Departments of Medicine and Microbiology & Immunology. He received his undergraduate degree in biochemistry from Harvard and his M.D. from the University of Rochester. After completing his residency at UCSF, he trained in infectious diseases at the University of Washington. Prior to his position as director of the SABRE Center, Dr. Locksley served 18 years as the Chief of the Division of Infectious Diseases at UCSF Medical Center. Dr. Locksley is a fellow of the American Academy of Arts and Sciences. Dr. Locksley's laboratory focuses on mechanisms by which the immune system becomes organized in stereotyped ways against discrete types of challenges. This involves the differentiation of naïve helper T cells to distinct types of subsets that produce different kinds of cytokines, key effector molecules of the immune system. In turn, these different T cells subsets work with different kinds of innate cells, including neutrophils, eosinophils, macrophages and others, to mediate immunity. Properly executed, such responses mediate protection against infectious organisms or repair of damaged tissues, but, when dysregulated, these immune responses lead to disease, including asthma. Dr. Locksley’s laboratory investigates immunity using mice genetically engineered to report cytokines expressed during the different types of immune responses. This approach reveals the shared expression of important cytokines by both innate and adaptive immune cells. Using these methods, the laboratory participated in recent discoveries of innate lymphoid type 2 cells, which represent a previously unstudied cell now implicated in allergic immunity. The laboratory also revealed a novel mechanism by which cutaneous mast cells capture IgE from blood. The laboratory continues to study the role of chitin, a structural component of many allergens – including dust mites, cockroaches, shellfish and molds – as well as helminthes, in inducing infiltration of cells

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Sandler Asthma Basic REsearch Center involved in allergy into tissues, and to pursue recent finding connecting the cells of allergic immunity with metabolic pathways involved in vertebrate homeostasis. Representative Publications 1. Reese TA, H-E Liang, AM Tager, AD Luster, N van Rooijen, D Voehringer, RM Locksley. 2007. Chitin induces accumulation in tissue of innate immune cells associated with allergy. Nature 447:92-6. 2. Reinhardt RL, HE Liang, RM Locksley. 2009. Cytokine-secreting follicular T cells shape the antibody repertoire. Nature Immunol 10:385-393. 3. Sullivan BM, RM Locksley. 2009. Basophils: a nonredundant contributor to host immunity. Immunity 30:12-20. 4. Siebold MA, TA Reese, S Choudhry, MT Salam, K Beckman, C Egn, A Atakilit, K Meade, M Lenoir, HG Watson, S Thyne, R Kumar, KB Weiss, LC Grammar, P Avila, RP Schleimer, JV Fahy, J Rodriguez-Santana, W Rodriguez-Cintron, RG Boot, D Sheppard, FD Gilliland, RM Locksley, EG Burchard. 2009. Differential enzymatic activity of common haplotypic versions of the human acidic mammalian chitinase protein. J Biol Chem 284:19650-8. 5. Locksley RM. 2010. Asthma and allergic inflammation. Cell 140:777-83. 6. Price AE, HE Liang, BM Sullivan, RL Reinhardt, CJ Eisley, EJ Erle, RM Locksley. 2010. Systemically dispersed innate IL-13-expressing cells in type 2 immunity. Proc Natl Acad Sci USA 107:11489-94. 7. Wu D, AB Molofsky, HE Liang, RR Ricardo-Gonzalez, HA Jouihan, JK Bando, A Chawla, RM Locksley. 2011. Eosinophils sustain adipose alternatively activated macrophages associated with glucose homeostasis. Science 332:243-7. 8. Sullivan BM, H-E Liang, JK Bando, D Wu, LE Cheng, JK McKerrow, CDC Allen, RM Locksley. 2011. Genetic analysis of basophil function in vivo. Nature Immunol 12:527-35. 9. Nguyen KD, Y Qui, X Cui, YP Sharon Goh, J Mwangi, T David, L Mukundan, F Brombacher, RM Locksley, A Chawla. 2011. Alternatively activated macrophages produce catecholamines to sustain adaptive thermogenesis. Nature 480:104-8. 10. Liang H-E, RL Reinhardt, JK Bando, BM Sullivan, I-C Ho, RM Locksley. 2011. Divergent expression patterns of IL-4 and IL-13 define unique functions in allergic immunity. Nature Immunol 13:58-66. 11. Cheng LE, K Hartmann, A Roers, MF Krummel, RM Locksley. 2013. Perivascular mast cells dynamically probe cutaneous blood vessels to capture IgE. Immunity 38:166-75. 12. Van Dyken SJ, RM Locksley. 2013. Interleukin-4- and interleukin-13-mediated alternatively activated macrophages: role in homeostasis and disease. Annu Rev Immunol 31:317-43. 13. Molofsky AB, JC Nussbaum H-E Liang, SJ Van Dyken, LE Cheng, A Mohapatra, A Chawla, RM Locksley. 2013. Innate lymphoid type 2 cells (ILC2) sustain visceral adipose tissue eosinophils and alternatively activated macrophages. J Exp Med (in press).

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Christopher D. C. Allen, Ph.D. Assistant Professor Cardiovascular Research Institute Departments of Anatomy and Microbiology and Immunology Sandler Asthma Basic Research Center 513 Parnassus Ave. Box 0414, HSE-205A San Francisco, CA 94143-0414 Tel: 415-476-5178 Fax: 415-502-4995 Dr. Allen is an Investigator of the Cardiovascular Research Institute and an Assistant Professor in the Departments of Anatomy and Microbiology and Immunology at UCSF. He completed his B.S. in Biology at MIT, and then his Ph.D. at UCSF in the Biomedical Sciences Graduate Program in the laboratory of Jason Cyster, with the support of a Howard Hughes Medical Institute Predoctoral Fellowship. Dr. Allen was then selected as the first Sandler-Newmann Foundation UCSF Fellow in Asthma Research, giving him the opportunity to attain principal investigator status and to develop an independent research program in asthma immediately after obtaining his Ph.D. He was recently hired into a tenure-track Assistant Professor position at UCSF. Dr. Allen’s research in the SABRE center focuses on the cellular immune response in asthma. He is using his expertise in cutting-edge two-photon microscopy to visualize interactions among cells in the lungs as well as in lymphoid organs that ‘prime’ cells for immune responses in the respiratory tract. A particular emphasis of his research is on the development and function of IgE antibodies that contribute to allergic responses. IgE has been shown to be important in human asthma, yet little is known about the events leading to IgE production after inhaling allergen. The major goals of the research are to: 1) Develop innovative new mouse models of asthma that will be useful for studies of IgE antibody responses to inhaled allergens. 2) Define the early events leading to allergic sensitization and IgE antibody production after inhalation of allergen. 3) Characterize the interactions among inflammatory cells in the lung in asthma and define the features of the microenvironments in which these interactions occur. Publications 1. Allen C.D.C., Ansel K.M., Low C., Lesley R., Tamamura H., Fujii N. Cyster J.G. (2004). Germinal center dark and light zone organization is mediated by CXCR4 and CXCR5. Nature Immunology, 5(9), 943-952. 2. Chen T.T., Li L., Chung D.H., Allen C.D.C., Torti S.V., Torti F.M., Cyster J.G., Chen C.Y., Brodsky F.M., Niemi E.C., Nakamura M.C., Seaman W.E., Daws

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Sandler Asthma Basic REsearch Center M.R. (2005). TIM-2 is expressed on B cells and in liver and kidney and is a receptor for H-ferritin endocytosis. The Journal of Experimental Medicine, 202(7), 955-965. 3. Allen C.D.C., Okada T., Tang H.L., Cyster J.G. (2007). Imaging of germinal center selection events during affinity maturation. Science, 315(5811), 528-531. 4. *Allen C.D.C., *Okada T., *Cyster J.G. (2007). Germinal-center organization and cellular dynamics. Immunity 27(2), 190-202. *co-corresponding author. PMCID: PMC2242846. 5. Haynes N.M., Allen C.D.C., Lesley R., Ansel K.M., Killeen N., and Cyster J.G. (2007). Role of CXCR5 and CCR7 in follicular Th cell positioning and appearance of a programmed cell death gene-1High germinal center-associated subpopulation. The Journal of Immunology, 179(8), 5099-5108. 6. *Allen C.D.C., *Cyster J.G. (2008). Follicular dendritic cell networks of primary follicles and germinal centers: phenotype and function. Seminars in Immunology 20(1), 14-25. *co-corresponding author PMCID: PMC2366796. 7. Beltman J.B., Allen C.D.C., Cyster J.G., de Boer R.J. (2011). B cells within germinal centers migrate preferentially from dark to light zone. Proceedings of the National Academy of Sciences, 108(21), 8755-8760. PMCID: PMC3102384 8. Green J.A., Suzuki K., Cho B., Willison L.D., Palmer D., Allen C.D.C., Schmidt T.H., Xu Y., Proia R.L., Coughlin S.R., Cyster J.G. (2011). The sphingosine 1phosphate receptor S1P2 maintains the homeostasis of germinal center B cells and promotes niche confinement. Nature Immunology, 12(7), 672-680. PMCID: PMC3158008. 9. Sullivan B.M., Liang H.E., Bando J.K., Wu D., Cheng L.E., McKerrow J.K., *Allen C.D.C., *Locksley R.M. (2011). Genetic analysis of basophil function in vivo. Nature Immunology, 12(6), 527-535. *co-corresponding author. PMCID: PMC3271435. 10. Steiner D.F., Thomas M.F., Hu J.K., Yang Z., Babiarz J.E., Allen C.D.C., Matloubian M., Blelloch R., Ansel K.M. (2011). MicroRNA-29 Regulates T-Box Transcription Factors and Interferon-γ Production in Helper T Cells. Immunity, 35(2), 169-181. PMCID: PMC3361370. 11. Yang Z., Sullivan B.M., Allen C.D.C. (2012). Fluorescent in vivo detection reveals that IgE+ B cells are restrained by an intrinsic cell fate predisposition. Immunity, 36(5), 857-872.

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K. Mark Ansel, Ph.D. Assistant Professor, Department of Microbiology & Immunology Sandler Asthma Basic Research Center of UCSF 513 Parnassus Avenue UCSF Box 0414, HSE-201H San Francisco, CA 94143 Tel: 415-476-5368 Fax: 415-502-4995 Websites: Ansel Lab [http://ansel.ucsf.edu] Biomedical Sciences Graduate Program [http://www.ucsf.edu/bms/faculty/ansel.html] Immunology Graduate Program [http://www.ucsf.edu/immuno/faculty/ansel.html] Dr. Mark Ansel is an Assistant Professor in the Department of Microbiology & Immunology. He completed a B.S. in biochemistry at Virginia Tech, a Ph.D. in Biomedical Sciences at UCSF, and postdoctoral training at the Immune Disease Institute at Harvard Medical School. His laboratory in the Sandler Asthma Basic Research Center focuses on the regulation of gene expression in the immune system. MicroRNAs (miRNA), transcription factors, and epigenetic regulation shape the gene expression programs that determine cell identity and function. The Ansel lab studies how these molecular mechanisms work together to control lymphocyte development, differentiation, and function in immunity. We use in vitro cell differentiation systems, mouse genetics, disease models, and gene expression analyses in cells from human clinical samples to unravel the regulatory networks that underlie immunity and immune pathology, especially allergy and asthma. Our primary experimental system is the differentiation of helper T cells, the central coordinators of adaptive immune responses. Upon immune activation, naïve CD4+ T cells can differentiate into several different helper T cell effectors subtypes (e.g. Th1, Th2, Th17, iTreg, Tfh, etc.). These lineages are defined by their characteristic gene expression programs and mediate distinct immune functions. As such, proper regulation of the lineage decisions of helper T cells critically determines the development of protective immunity against a great diversity of pathogens, and improper or exaggerated responses contribute to the development and pathology of autoimmune diseases, chronic inflammation, allergy, and asthma. We and many others have documented how these gene expression programs are controlled by external factors from other cells and the environment, inducible and lineage-specific transcription factors, the cis-regulatory DNA elements to which they bind, and epigenetic modifications that constrain chromatin accessibility at those sites. Active projects in the laboratory aim to determine the function of individual miRNAs in regulating helper T cell differentiation and immune function, and the regulation of the miRNA pathway itself during immune responses. Naive CD4+ T cells that cannot

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Sandler Asthma Basic REsearch Center produce any miRNAs exhibit reduced cell division and survival in response to immune stimuli. Surprisingly, they also undergo rapid unrestrained differentiation into effector cells. We have developed a screening technology that allows us to rapidly determine which specific miRNAs regulate each of these T cell behaviors, and a high throughput nanoscaled pipeline for determining miRNA expression patterns in small clinical samples, including sorted T cell subsets from the airways of human asthmatic subjects. In addition, we discovered that T cells rapidly reset their miRNA repertoire upon activation. This process that involves ubiquitination and degradation of Argonaute proteins, but the signaling mechanisms and the fate of associated miRNAs remains unknown. This rapid change in miRNA expression may be important to allow T cells to change their gene expression programs and develop effector functions. Lab Objectives 1) To define the molecular mechanisms that control miRNA homeostasis, and determine how the miRNA repertoire is so dramatically remodeled during T cell activation. 2) To characterize the function of individual miRNAs that regulate T cell differentiation and immune effector functions. 3) To examine the helper T cells in the blood and inflamed lungs of asthma patients for differences in functional effector subset representation and the expression of miRNAs that may contribute to their pathogenic properties in human asthma. Selected Publications 1. Baumjohann D, Clingan JM, de Kouchkovsky D, Bannard O, Bluestone JA, Matloubian M, Ansel KM#, Jeker LT#. The microRNA cluster miR-17~92 is essential for follicular helper T cell differentiation. Under revision at Nat Immunol (#corresponding authors) 2. Ansel KM. RNA Regulation in the Immune System. Immunol Rev. in press 3. Bronevetsky Y, Ansel KM. Regulation of miRNA biogenesis and function in the immmune system. Immunol Rev. in press 4. Bronevetsky Y, Villarino AV, Eisley C, Barbeau R, Barczak A, Heinz GA, Kremmer E, Heissmeyer V, McManus MT, Erle DJ, Rao A, Ansel KM. T cell activation induces proteasomal degradation of Argonaute and rapid remodeling of the microRNA repertoire. J Exp Med. 210:417-32 (2013) 5. Seumois G, Vijayanand P, Eisley CJ, Omran N, Kalinke L, North M, Ganesan AP, Simpson LJ, Hunkapiller N, Moltzahn F, Woodruff PG, Fahy JV, Erle DJ, Djukanovic R, Blelloch R, Ansel KM: An integrated nano-scale approach to profile miRNAs in limited clinical samples. Am J Clin Exp Immunol. 1:70-89 (2012) 6. Hoefig KP, Rath N, Heinz GA, Wolf C, Dameris J, Schepers A, Kremmer E, Ansel KM, Heissmeyer V. Eri1 degrades the stem-loop of oligouridylated histone mRNAs to induce replication-dependent decay. Nat Struct Mol Biol. 20:73-81 (2013) 7. Solberg OD, Ostrin EJ, Love MI, Peng JC, Bhakta NR, Hou L, Nguyen C, Solon M, Nguyen C, Barczak AJ, Zlock LT, Blagev DP, Finkbeiner WE, Ansel KM,

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Sandler Asthma Basic REsearch Center Arron JR, Erle DJ, Woodruff PG. Airway Epithelial miRNA Expression is Altered in Asthma. Am J Respir Crit Care Med. 186:965-74 (2012) 8. Thomas MF, Abdul-Wajid S, Panduro M, Babiarz JE, Rajaram M, Woodruff P, Lanier LL, Heissmeyer V, Ansel KM. Eri1 regulates microRNA homeostasis and mouse lymphocyte development and anti-viral function. Blood. 120:130-42 (2012) 9. Vijayanand P, Seumois G, Simpson LJ, Abdul-Wajid S, Baumjohann D, Panduro M, Huang X, Interlandi J, Djuretic IM, Brown DR, Sharpe AH, Rao A, Ansel KM. Interleukin-4 Production by Follicular Helper T Cells Requires the Conserved Il4 Enhancer Hypersensitivity Site V. Immunity 36:175-87 (2012). 10. Baumjohann D, Okada T, Ansel KM. Cutting Edge: Distinct Waves of BCL6 Expression during T Follicular Helper Cell Development. J Immunol.187:2089-92 (2011) 11. Steiner DF, Thomas MF, Hu JK, Yang Z, Babiarz JE, Allen CD, Matloubian M, Blelloch R, Ansel KM. MicroRNA-29 Regulates T-Box Transcription Factors and Interferon-γ Production in Helper T Cells. Immunity 35:169-81 (2011) 12. Sofi MH, Qiao Y, Ansel KM, Kubo M, Chang CH. Induction and Maintenance of IL-4 Expression Are Regulated Differently by the 3' Enhancer in CD4 T Cells. J. Immunol. 186:2792-9 (2011) 13. Thomas MF, Ansel KM. Construction of small RNA cDNA libraries for deep sequencing. Methods Mol Biol. 667:93-111 (2010) 14. Ansel KM*, Pastor WA, Rath N, Lapan AD, Glasmacher E, Wolf C, Smith LC, Papadopoulou N, Lamperti E, Tahiliani M, Ellwart JW, Shi Y, Kremmer E, Rao A, Heissmeyer V*. Mouse ERI-1 interacts with the ribosome and catalyzes 5.8S rRNA processing. Nat Struct Mol Biol. 15:523-30 (2008) (*corresponding authors) 15. Thai TH, Calado DP, Casola S, Ansel KM, Xiao C, Xue Y, Murphy A, Frendewey D, Valenzuela D, Kutok JL, Schmidt-Supprian M, Rajewsky N, Yancopoulos G, Rao A, Rajewsky K. Regulation of the germinal center response by microRNA-155. Science 316:604-8 (2007) 16. Djuretic IM, Levanon D, Negreanu V, Groner Y, Rao A, Ansel KM. T-bet and Runx3 cooperate to activate Ifng and silence Il4 in Th1 cells. Nat Immunol. 8:145-53 (2007) 17. Ansel KM, Djuretic I, Tanasa B, Rao A. Regulation of Th2 differentiation and the IL4 locus. Annu Rev Immunol. 24:607-56 (2006) 18. *Monticelli S, *Ansel KM, *Xiao C, *Socci ND, Krichevsky AM, Thai, T-H, Rajewsky N, Marks DS, Sander C, Rajewsky K, Rao A, Kosik KS. MicroRNA profiling of the murine hematopoietic system. Genome Biol. 6:R71 (2005) 19. *Muljo SA, *Ansel KM, *Kanellopoulou C, Livingston DM, Rao A, Rajewsky K. Aberrant T cell differentiation in the absence of Dicer. J Exp Med. 202:261-9 (2005). 20. Ansel KM, Greenwald RJ, Agarwal SA, Bassing CH, Monticelli S, Interlandi J, Djuretic IM, Lee DU, Sharpe AH, Alt FW, Rao A. Deletion of a conserved Il4 silencer impairs Th1-mediated autoimmunity. Nat Immunol. 5:1251-9 (2004).

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Limin Liu, Ph.D. Associate Professor, Department of Microbiology/Immunology Sandler Asthma Basic Research Center University of California San Francisco 513 Parnassus Ave. HSE 201J, Box 0414 San Francisco, CA 94143-0414 Tel: 415-476-1466 Fax: 415-476-8201 email: [email protected] Dr. Limin Liu is an Associate Professor in the Department of Microbiology & Immunology. He obtained his B.S. in Biology from University of Science and Technology of China and his Ph.D. in Molecular Biology from University of Missouri. He did postdoctoral research on the biology of nitric oxide (NO) at Duke University Medical Center. Dr. Liu’s laboratory focuses on enzymatic deactivation of NO bioactivity and its role in asthma and other diseases. NO plays important roles in virtually every biological system. NO regulates functions of numerous proteins through S-nitrosylation, the covalent addition of NO to cysteine thiol. Through the study of S-nitroso-glutathione reductase (GSNOR), the key protein for denitrosylation in cells, Dr. Liu and colleagues have demonstrated that S-nitrosylation and its deactivation exert critical functions in systematic inflammation, asthma, cancer, and many other physiological and pathological processes. GSNOR and asthma It has been demonstrated with GSNOR-deficient (GSNOR-/-) mice that increased S-nitrosylation from GSNOR deficiency in a model of allergic asthma does not affect immune responses but abolishes airway hyperresponsiveness. Dr. Liu’s laboratory is investigating the mechanism of S-nitrosylation-dependent protection to understand a key question in asthma: How do allergic immune responses cause airway hyperresponsiveness? GSNOR and carcinogenesis NO is implicated in tumorigenesis by much circumstantial evidence, but little is known definitively about the mechanisms through which endogenous NO might regulate the behavior of pre-cancerous or cancerous cells. Using GSNOR-/- mice Dr. Liu’s laboratory has discovered that dysregulated S-nitrosylation from GSNOR deficiency inactivates a key DNA repair system and promotes liver cancer (Science Translational Medicine 2:19ra13, 2010). Investigation is underway to expend the findings and to further elucidate molecular mechanisms. New pathways in NO deactivation Dr. Liu and colleagues have demonstrated that GSNOR and flavohemoglobin, the major NO-consuming enzyme, operate together to regulate NO bioactivities and to protect against NO-related toxicity in the yeast Saccharomyces cerevisia. They are employing the yeast model to elucidate the roles of additional, novel genes that are required for protection against NO-related toxicity. Homologue proteins are also investigated in animals.

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Selected Publications 1. Liu L, Yan Y, Zeng M, Zhang J, Hanes MA, Ahearn G, McMahon TJ, Dickfeld T, Marshall HE, Que LG, Stamler JS (2004). Essential roles of S-nitrosothiols in vascular homeostasis and endotoxic shock. Cell 116:617-628. 2. Que LG, Liu L, Yan Y, Whitehead GS, Gavett SH, Schwartz DA, Stamler JS (2005). Protection from experimental asthma by an endogenous bronchodilator. Science 308:1618-1621. 3. Choudhry S, Que LG, Yang Z, Liu L, Eng C, Kim SO, Kumar G, Thyne S, Chapela R, Meade K, Watson HG, LeNoir M, Rodriguez-Santana JR, Rodriguez-Cintron W, Avila PC, Stamler JS, Burchard EG (2010). GSNO Reductase and β2 Adrenergic Receptor Gene-gene Interaction: Bronchodilator Responsiveness to Albuterol. Pharmacogenetics and Genomics 20:351-8. 4. Wei W, Li B, Hanes MA, Kakar S, Chen X, Liu L (2010). Deficiency of SNitrosoglutathione Reductase Impairs DNA Repair and Promotes Hepatocarcinogenesis. Science Translational Medicine 2: 19ra13. 5. Yang Z, Wang Z, Doulias P, Wei W, Ischiropoulos H, Locksley RM, Liu L (2010). Lymphocyte development requires S-nitrosoglutathione reductase. J Immunol, 185:66646669. 6. Wei W, Yang Z, Tang CH, Liu L (2011). Targeted deletion of GSNOR in hepatocytes of mice causes nitrosative inactivation of O6-alkylguanine-DNA alkyltransferase and increased sensitivity to genotoxic diethylnitrosamine. Carcinogenesis 32:973–977. 7. Na B, Huang ZM, Wang Q, Qi ZX, Tian YJ, Lu CC, Yu JW, Hanes MA, Sanjay Kakara S, Huanga EJ, Ou JHJ, Liu L‡,*, and Yen TSB‡,† (2011). Transgenic Expression of Entire Hepatitis B Virus in Mice Induces Hepatocarcinogenesis Independent of Chronic Liver Injury. PLoS One 6:e26240. 8. ‡co-senior author; *Corresponding author; †Deceased August 31, 2009. 9. Tang CH, Wei W, Liu L (2012). Regulation of DNA Repair by S-Nitrosylation. Biochim Biophys Acta 1820:730–735. 10. Ozawa K*, Tsumoto H, Wei W, Tang CH, Komatsubara AT, Kawafune H, Shimizu K, Liu L*, Tsujimoto G (2012). Proteomic analysis of the role of S-nitrosoglutathione reductase in lipopolysaccharide-challenged mice. Proteomics 12, 2024-2035. *Corresponding author. 11. Leung J, Wei W, Liu L (2013). S-nitrosoglutathione reductase deficiency increases mutagenesis from alkylation in mouse liver. Carcinogenesis (in press). 12. Tang CH, Wei W, Hanes MA, Liu L (2013). Hepatocarcinogenesis driven by GSNOR deficiency is prevented by iNOS inhibition. Cancer Research (in press).

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Jeoung-Sook Shin, Ph.D. Assistant Professor, Department of Microbiology & Immunology Sandler Asthma Basic Research Center University of California San Francisco 513 Parnassus Ave, HSE-201 San Francisco, CA 94143-0414 Tel: 415-476-5451 Fax: 415-476-3939 email: jeoung-sook.shin @ ucsf.edu Dr. Jeoung-Sook Shin is an Assistant Professor in the Department of Microbiology & Immunology. She completed her B.S. and M.S. in Chemistry at Seoul National University, Korea. She received her Ph.D. from Duke University and her postdoctoral training at Yale University as a Jane Coffin Childs Memorial Fund Postdoctoral Fellow. The Shin laboratory is interested in understanding the molecular mechanism and function of dendritic cell-mediated antigen presentation. Dr. Shin has previously found that the antigen-presenting molecule MHCII is ubiquitinated by MARCH1 ubiquitin ligase in dendritic cells, and this ubiquitination mediates MHCII endocytosis and lysosomal degradation. Her laboratory has recently found that the costimulatory molecule CD86 is also ubiquitinated by MARCH1 and that this ubiquitination also mediates endocytosis and degradation of CD86. More recently, Dr. Shin’s laboratory has studied the functional role of this ubiquitination. This study indicates that MHCII ubiquitination is required for proper production of regulatory T cells (Tregs) in the thymus. Currently, Dr. Shin is investigating how MHCII ubiquitination contributes to Treg development and whether Tregs generated in MHCII ubiquitination-dependent manner are distinct in their repertoire or function. The Shin laboratory is also interested in understanding the role of the high affinity IgE receptor FceRI expressed in dendritic cells. Although the role of FceRI in the pathogenesis of allergy is well-known, its physiologic role remains unclear. Dr. Shin’s laboratory has recently found that FceRI is constitutively endocytosed and transported to the lysosomes in human dendritic cells and monocytes, and that this FceRI endolysosomal trafficking mediates cellular entry of circulating IgE contributing to serum IgE clearance. These findings suggest that FceRI expressed by dendritic cells and monocytes may play an important role in regulating serum IgE concentration in humans. Her laboratory is currently investigating whether unusually high blood IgE levels found in some human diseases is attributed to the alteration in FceRI endolysosomal trafficking that results circulating IgE not efficiently entering cells but accumulating in the blood. Dr. Shin’s research programs are greatly benefited by many of the excellent core facilities supported by SABRE. Flow cytometry core is being used in a daily basis for most of the projects. Microscopy facility is helping in situ analysis of dendritic cells in human tissues

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Sandler Asthma Basic REsearch Center and also the analysis of protein distribution inside dendritic cells. Mouse physiology core is being used to test the therapeutic potential of human IgE derivative that Dr. Shin has recently found to be immune-regulatory. Selected Publications 1. Shin, JS, Shelburne, CP, Jin, C, LeFurgey, EA, Abraham, SN. Harboring of particulat allergens within secretory compartments by mast cells following IgE/FcεRI-lipid raft mediated phagocytosis, J Immunol. 177:5791-5800, 2006 2. Shin, JS, Ebersold, M, Pypaert, M, Delamarre, L, Hartley, A, and Mellman, I. Surface expression of MHC class II in dendritic cells is controlled by regulated ubiquitination, Nature. 444:115-8, 2006 3. Bloom, O, Unternaehrer, JJ, Jiang, A, Shin, JS, Delamarre, L, Allen, P, and Mellman, I. Spinophilin participates in information transfer at immunological synapses, J Cell Biol. 181:203-11, 2008 4. Baravalle, G, Park, H, McSweeney, M, Ohmura-Hoshino, M, Matsuki, Y, Shin, JS. Ubiquitination of CD86 is a key mechanism in regulating antigen presentation by dendritic cells, J Immunology. 187:2966, 2011 5. Ma, JK, Platt MY, Eastham-Anderson, J, Shin, JS*, and Mellman, I*. MHC class II distribution in dendritic cells and B cells is determined by ubiquitin chain length, PNAS. 109:8820, 2012 6. *Shin, JS and Mellman, I contributed equally to this work

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Core Facilities

                                                           

 

CORE FACILITIES

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Core Facilities

Mouse Physiology and Morphology Core Director: Xiaozhu Huang, M.D. Objective The objective of the Sandler animal physiology and morphology core facility is to provide support to investigators at UCSF and other research institutes for their asthma related research. The core facility has extensive experience in generating and analyzing variety of allergic animal models. Investigators gain insight to the molecular mechanisms of asthma development through either full or partial service provided by the core laboratory. The core also provides training to students, technicians and post-doctoral fellows in techniques relevant to the animal models and their analysis. Accomplishments During the year 2012, the Animal Physiology and Morphology Core provided assistance to many UCSF investigators, including Drs Mark Ansel, Kamran Atabai, Anthony deFranco, David Erle, Xiaozhu Huang, Limin Liu, Steve Nishmura, Jason Rock, Dean Sheppard and Art Weiss for their projects studying airway physiology, immunology, cell and molecular biology and other related areas. The service provided by the core lab has significant impacts on many of these asthma related projects. Dr. Dean Sheppard has been interested in studying biologic role of integrin α9β1, an integrin expressed on airway smooth muscle, in asthma development. The core conducted lung function studies in mice lacking integrin α9β1 specifically in smooth muscle. These mice had increased airway responsiveness in vivo, and loss or inhibition of integrin α9β1 also increased in vitro airway narrowing and airway smooth muscle contraction in murine and human airways. Contraction was enhanced in control airways by the higher-order polyamine spermine or by cellpermeable PIP2, but these interventions had no effect on airways lacking integrin α9β1 or treated with integrin α9β1-blocking antibodies. Enhancement of SSAT activity or knockdown of PIP5K1γ inhibited airway contraction, but only in the presence of functional integrin α9β1. Therefore, integrin α9β1 appears to serve as a brake on airway smooth muscle contraction by recruiting SSAT, which facilitates local catabolism of polyamines and thereby inhibits PIP5K1γ. Targeting key components of this pathway could thus lead to new treatment strategies for asthma. This work has been published in Journal of Clinical Investigation last year. The core assisted Dr. Rosemary Ahnkurst’s group in studying TGFβ activation and signaling in experimental models of allergen-induced asthma as potential therapeutic targets. We show that innate variation within TGFβ1 genetic modifier loci, Tgfbm2 and Tgfbm3, alters disease susceptibility. Specifically, Tgfbm2(129) and Tgfbm3(C57) synergize to reverse accentuated airway hyperresponsiveness caused by low TGFβ1 levels in Tgfb1(+/-) mice of the NIH/OlaHsd strain and the epistatic interaction between Tgfbm2(129) and Tgfbm3(C57) uncouples the inflammatory response to ovalbumin from those of airway remodeling and airway hyperresponsiveness, illustrating independent genetic control of these responses. The study suggests that differential inheritance of genetic variants of Tgfbm genes alters biological responses to reduced TGFβ1 signaling in an experimental asthma model and TGFβ antagonists

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for treatment of lung diseases might therefore give diverse outcomes, dependent on genetic variation. This work resulted in a publication last year in Proc Natl Acad Sci U S A. The animal physiology core also provides assistance to current as well as former AAF awardees for their asthma related studies. Continuing support of their asthma related projects has been appreciated by many former awardees. Dr. Kenneth Rock is one of the former AAF awardees and continues working on asthma related projects. To help solve one of variable allergen related outcomes (Aspergillus induced pulmonary fibrosis) that his group has encountered, the core performed an Aspergillus sensitized and challenged experiment to prove that mice develop significant lung fibrosis using this model. Dr. Rock’s group is currently working on the project with the helpful information provided by the core. In 2012, we continued our efforts in developing more regimens to suit the needs of investigators. One such effort was to use InExpose aerosol machine (Scireq, Canada) for OVA challenges. Our current intra-nasal OVA challenge has been working very well and produces consistent results but it is not the natural route of sensitization and challenge. Some investigators have expressed interest of using aerosol route for challenge. We then tried 1% OVA aerosol challenge according to the literature but failed to achieve allergen-induced phenotype. We are in the process of trying different dosages and have just obtained preliminary data suggesting 6% OVA may be sufficient to produce an allergen-induced airway hyperresponsiveness and lung inflammation. Training and Integration with Sandler Program The core continues to provide training support for lab members whose PIs are interested in adapting the protocols and techniques that are useful for their studies. In 2012, investigators from multiple laboratories (Labs from UCSF- Drs. Jeffery Cox and David Erle; other research institutes - Dr. Michael Daines at University of Arizona, Dr. Daniel Conrad at Virginia Commonwealth University) sent lab members to the core lab in observing the routine performance and getting hands-on experience using the equipment and protocols. Jamie Sturgill and Jennifer Bradley from Virginia Commonwealth University made a special trip to visit us last year. They spent time observing core lab performing experiments and processing routine samples, and obtained protocols used routinely by the core lab. Currently Dr. Conrad’s group has been able to run lung function analysis in the studies of murine models of allergic asthma for their related studies. Core lab follows-up and communicates with former trainees the continues the information exchange that has benefitted studies for both sides. The animal core director attends the weekly UCSF pulmonary conference, monthly SABRE meeting, AAF and ATS annual meetings. This provides direct interaction between the animal core and investigators who are interested in using the core service. The potential experiments can be discussed and oftentimes can be arranged during the interaction. Future Activities We continually try to improve our techniques and develop allergic model regimens so that we may accommodate the investigators needs. As mentioned above, we have been working on

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developing protocol using the aerosol machine for allergen challenge. Our preliminary data suggest that 6% OVA aerosol for 30 minutes once a day for 3 days may produce significant OVA-induced lung function change and lung inflammation. Further study is needed to validate our observation. We still need to improve the consistency and reduce the variability of our house dust mite model. We have been paying close attention to our key equipment. FlexiVent makes the key lung function measurement possible. The machine model we are using has been discontinued and technical service will soon no longer be available. With the continuing support from the SABRE foundation, the animal physiology and microscopy core facility will continue to provide UCSF investigators with high quality service critical to our research community. Grants and Publications: Grant The animal physiology and morphology core continues to work with investigators at UCSF as well as at other research institutes to provide consultations and support letters for their grant applications. Core director generally meets in person (with local investigators) or has phone conversations (with outside institutions) with grant applicants in helping them understand the principles of allergic animal models and carefully discuss the experimental protocols, animal numbers and final outcomes. The AAF applicants very often have not worked with asthma, and some not even with lung disease. For applicants who propose an in vivo animal experiment, a brief description of an allergic animal model will be provided so investigators can incorporate it into their proposals. We not only help investigators funded by NIH, AAF and other grants but also, if they are funded, make commitments to collaborate with investigators who submit proposals. The core staff receive direct salary support from Sandler foundation, NIAID and our recharge system. Publications 1. Gordon ED, Sidhu SS, Wang ZE, Woodruff PG, Yuan S, Solon MC, Conway SJ, Huang X, Locksley RM, Fahy JV. A protective role for periostin and TGF-β in IgE-mediated allergy and airway hyperresponsiveness. Clin Exp Allergy. 2012 Jan; 42(1):144-55. PMID: 22093101 2. Sugimoto K, Kudo M, Sundaram A, Ren X, Huang K, Bernstein X, Wang Y, Raymond

WW, Erle DJ, Abrink M, Caughey GH, Huang X, Sheppard D. The αvβ6 integrin modulates airway hyperresponsiveness in mice by regulating intraepithelial mast cells. J Clin Invest. 2012 Feb 1; 122(2):748-58  

3. Vijayanand P, Seumois G, Simpson LJ, Abdul-Wajid S, Baumjohann D, Panduro M, Huang X, Interlandi J, Djuretic IM, Brown DR, Sharpe AH, Rao A, Ansel KM. Interleukin-4 production by follicular helper T cells requires the conserved Il4 enhancer hypersensitivity site V. Immunity. 2012 Feb 24;36(2):175-87  

4. Makoto Kudo, Andrew C. Melton, Chun Chen, Mary B. Engler, Katherine E. Huang, Xin Ren, Yanli Wang, Xin Bernstein, John T. Li, Kamran Atabai, Xiaozhu Huang, Dean

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Sheppard. IL-17A produced by ab T cells drives airway hyper-responsiveness in mice and enhances mouse and human airway smooth muscle contraction. Nature Medicine. 2012 March 4;18(4)547-54 5. Thornton E, Looney M, Sheppard D, Locksley R, Huang X, Krummel M. Dynamics of antigen capture and presentation revealed by two-photon live imaging in the lung. J Exp Med. 2012 Jun 4;209(6):1183-99 6. Schroeder BW, Verhaeghe C, Park SW, Nguyenvu LT, Huang X, Zhen G, Erle DJ. AGR2 is Induced in Asthma and Promotes Allergen-Induced Mucin Overproduction. Am J Respir Cell Mol Biol. 2012 Aug;47(2):178-85 7. Bhattacharya M, Su G, Su X, Oses-Prieto JA, Li JT, Huang X, Hernandez H, Atakilit A, Burlingame AL, Matthay MA, Sheppard D. IQGAP1 is necessary for pulmonary vascular barrier protection in murine acute lung injury and pneumonia. Am J Physiol Lung Cell Mol Physiol. 2012 Jul 1;303(1):L12-9 8. Chun Chen, Makoto Kudo, Florentine Rutaganira, Hiromi Takano, Candace Lee, Amha Atakilit, Toshimitsu Uede, Paul Wolters, Stephen Liggett, Kevan M. Shokat, Xiaozhu Huang and Dean Sheppard . Integrin α9β1 in airway smooth muscle regulates a novel brake on exaggerated murine and human airway narrowing. JCI 2012 2012 Aug 1;122(8):2916-27 9. Huang F, Zhang H, Wu M, Yang H, Kudo M, Peters CJ, Woodruff PG, Solberg OD, Donne ML, Huang X, Sheppard, Fahy JV, Wolters PJ, Hogan BL, Finkbeiner WE, Li M, Jan YN, Jan LY, Rock JR. Calcium-activated chloride channel TMEM16A modulates mucin secretion and airway smooth muscle contraction. Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16354-9. 10. Julia Freimuth, Frederic F. Clermont, Xiaozhu Huang, Angela De Sapio, Taku Tokuyasu, Dean Sheppard, Rosemary J. Akhurst. Epistatic interactions between Tgfb1 and genetic loci, Tgfbm2 and Tgfbm3, determine susceptibility to an asthmatic stimulus. Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):180

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Functional Genomics Core Director: David J. Erle, M.D. Associate Director: Andrea Barczak Objective To make cutting-edge functional genomics technology readily available for investigators researching questions relevant to basic biology of asthma. Accomplishments Supported projects: We continue to support many investigators studying immunology, airway cell biology, lung development, and other relevant areas. This includes faculty members who participate actively in a range of SABRE activities (including Ansel, Chapman, Erle, Krummel, Seaman, Sheppard, and Woodruff) and AAF-funded investigators (Keoki Williams and Daniel Conrad). Here is a partial listing of relevant projects that have been completed this year or are still in progress: PI

Project (status)

Mark Ansel

Effect of Eri1 on mRNA profile and translation in natural killer cells. Completed.

Mark Ansel

The miR-17~92 cluster regulates TFH cell differentiation. Completed.

Mark Ansel

Empirical determination of miRNA targets with comparative RNA-Seq and PAR-CLIP. In Progress.

Harold Chapman

Beta4 positive AECs vs. B4 negative AECs. Completed.

Harold Chapman

Ephb2/B4 progenitor isolation. Completed.

David Erle

IL-13 and IL-17 responsive microRNAs in the airway epithelium. Completed.

David Erle

RNA-Seq analysis of IL-13 treated airway epithelium. Completed.

Daniel Conrad1*

The Kainic Acid Receptor-ADAM10 Axis in Asthma. In Progress.

Matthew Krummel

Chemotactic circuits in a mouse tumor model. Completed.

Mehrdad Matloubian

Plasmacytoid Dendritic Cell Response to a Viral Infection Completed.

Jason Rock

Gene expression differences between WT and MMP3 KO after pneumonectomy. In Progress.

William Seaman

Microglia expression profile after TBI. Completed.

Dean Sheppard

RNA-Seq analysis of the role of integrin alpha-v in lung and liver fibrosis. In Progress.

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Keoki Williams2*

Pharmacogenomics of asthma. Ongoing.

Asa Wheelock3

COPD and Gender (COSMIC). Completed.

Prescott Woodruff

miRNA profiling in asthma patients. Ongoing.

1

Virginia Commonwealth University, 2Henry Ford Health, 3 Karolinska Institutet, *AAF awardee Personnel Andrea Barczak (manager), Rebecca Barbeau (SRA), and Joshua Pollack (biostatistician) continue to provide outstanding service to core users. In aggregate, they have over 20 years of experience as core staff. New technologies The SABRE functional genomics core is a resource for the UCSF community (and beyond); we collaborate on more than 65 projects per year. SABRE support is critical for development and implementation of new methods. Priority is given to development of methods required for studies requested by SABRE investigators. Although microarrays continue to be a very useful and cost effective method for genome-wide profiling of mRNAs and miRNAs, recent advances in sequencing technology offer substantial advantages over arrays for most global mRNA and miRNA profiling projects. RNA-Seq has superior sensitivity, specificity and reproducibility; offers the potential for novel RNA discovery (especially important for non-coding RNAs); and can be used for analyzing transcript variation (alternative splicing and polyadenylation, allelespecific expression). Supply costs for RNA-Seq continue to drop and are now roughly similar to costs for array experiments. Over the past two years, an increasing number of users have switched to RNA-Seq technologies. We have seen a rise from 2 projects in 2011 to 13 projects in 2012 and anticipate that this trend will continue to grow at a rapid rate. This past year, we have focused the majority of our efforts on implementing the following next generation sequencing services: 1) methods for analysis of partially degraded or FFPE RNA, 2) improving sample throughput for small RNA-Seq and 3) continued development of state-of-the-art methods for analyzing next generation sequencing data. 1) RNA-Seq analysis of degraded RNA: Standard mRNA-Seq library construction methods contain an initial poly(A) RNA selection to remove highly abundant rRNA species before amplification; this method presents a challenge for clinical samples where degradation can be a common problem. We have employed an alternative non-poly(A) based ribosomal depletion method (Ribo-Zero, Epicentre, Inc.) to accommodate samples that have compromised RNA integrity. An additional benefit of this technology is that it recovers the 5’and 3’ ends of both mRNAs and long non-coding RNAs. This is an attractive alternative to standard protocols for investigators who are interested novel gene discovery and expression of lncRNAs. We are currently analyzing data from our first set of ribosomal depleted samples. 2) Improving sample throughput for small RNA-Seq: miRNA expression profiling accounts to approximately 20% of the projects that we process, including studies with Mark Ansel and Prescott Woodruff who are working on determining the miRNA expression patterns that are associated with asthma pathology and response to therapy. Small RNA-Seq library preparation

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protocols require a gel purification based size selection step for each sample library. This process is laborious, time consuming, and not amenable to higher-throughput methods. We have implemented a newer library preparation method that allows us to multiplex libraries before gel purification, which cuts down the turn-around time substantially. Additionally, the ability to multiplex small RNA-Seq libraries significantly decreases the associated costs for the sample preparation and sequencing by up to as much as 50%. To date, we have processed over 24 samples using this new method. 3) Development of data analysis pipelines: RNA-Seq data analysis presents many new challenges including alignment of millions of reads to a reference transcriptome (or genome), assembly of read alignments, and development of new algorithms for normalization and statistical analysis of differential expression. Different tools are required to carry out each step of the analysis and the size and complexity of the datasets make the process computationally expensive and time consuming. This past year our biostatistician, Josh Pollack, has made significant progress towards developing pipelines that incorporate state-of-the-art algorithms from publicly available software, thereby streamlining the process and decreasing the turnaround time. We have implemented these new pipelines, and have analyzed data from both mRNA and miRNA studies. NGS data analysis requires substantial processing power and it was essential for us to acquire a new computer. SABRE funding contributed to the purchase of a 12core workstation with 96 GB of RAM and 6TB of disk storage. Plans for the coming year We have optimized protocols for library generation and other steps in the process and now offer comprehensive RNA-Seq services (including library preparation, coordination of sequencing runs, and data analysis), which relieves investigators of the need to develop and optimize protocols in their own laboratories. We have begun a new initiative to reduce turnaround time for RNA-Seq projects. SABRE support allows us to provide a substantial discount to SABRE investigators and in recognition of this support SABRE projects receive higher priority than nonSABRE projects. We will continue to offer assistance with whole-genome analysis of mRNA and miRNA expression and ChIP analysis. In addition to the array-based analyses offered in previous years, we are encouraging investigators to employ next generation sequencing-based approaches (RNA-Seq, small RNA-Seq, and ChIP-Seq) where appropriate. Further work is planned to implement protocols that will allow the following: 1) analysis of very limited amounts of starting material (starting with as little as 5 ng of total RNA), 2) strand-specific library preparation for analysis of non-coding RNAs and antisense transcription and improved annotation of novel genes, and 3) ChIP-Seq library preparation and analysis. We will also continue to implement state-of-the-art methods for analyzing next generation sequencing data. Short-term goals include the development of pipelines for the following: 1) analysis of differential isoform expression, 2) analysis of non-coding RNAs and 3) implementation of visualization tools to display nextgeneration sequencing data more effectively. Training and Integration with SABRE and AAF programs We provide extensive consultation and training for investigators using the core. We meet with each group (PI and other group members, including students and postdoctoral fellows) to help

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with project planning. We help with grant preparation, sample size determination, appropriate selection of controls, and RNA extraction protocols. We meet with each group again after the initial data analysis to discuss the results and provide guidance about further analysis. When work is being readied for publication, we assist with preparation of figures and tables and submission of the results to a public database (NCBI’s Gene Expression Omnibus [GEO]). The core director attends the monthly UCSF SABRE Research Conference and the annual AAF meeting. This allows many opportunities for raising awareness about the core services among SABRE and AAF investigators. Although we continue to work with other investigators in order to maintain the high volume needed to operate in an economical manner, SABRE projects receive the highest priority. In late 2012, David Erle (contact PI) and Esteban Burchard (co-PI) submitted a K12 proposal in response to an NIH RFA for “Career Development Programs in Omics of Lung Diseases.” 30 UCSF faculty members with expertise in genomics (and other “omics”) and in asthma and other lung diseases agreed to participate. If successful, this proposal will provide salary support for 2 junior faculty K scholars per year to receive training in applying omics technologies to lung diseases. Grants and Publications Grants The core is now supported by SABRE and by a recharge mechanism, which covers labor and reagent costs for projects performed by the core. Core staff members work closely with investigators as they apply for NIH funding via R01 and other mechanisms. The following list includes asthma-related projects supported by the core that received new NIH funding during the last year and projects now applying for additional funding from NIH: PI

Project Number

Title

Ansel, Karl Mark

1R01HL109102-01

Role of miRNAs In Th2-driven Inflammation in Asthma

Chapman, Harold A 1U01HL111054-01

Epithelial Progenitor Cells in Lung Repair and Regeneration

Gerber, Anthony N

1R01 HL109557-01A1

Role of Klf15 in Airway Smooth Muscle and the Response to Glucocorticoids

Pending: Sheppard, Dean

5U19AI077439

Frank, James A

R21 HL111707-01A1

Mechanisms of Initiation and Persistence of Allergic Asthma (funding expected based on impact score of 20 and assurances from NIH program official)

Erle, David J and Burchard, E (multi-PI)

A Claudin-18 Deficiency in the Pathogenesis of Asthma UCSF Career Development Program in

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1K12HL119997-01 Omics of Lung Diseases Arjomandi, Mehrdad VA I21 Respiratory Tract Immune System in Gulf War Illness Planned for submission in early 2013: Rock, Jason

AAF

Tmem16a as a modulator of airway mucin dynamics

Rock, Jason

NIH (R21)

Requirement for spontaneous contractions of the embryonic airway smooth muscle during lung development

Keoki Williams

NIH (R01)

Combined transcriptomics and genomics to find asthma genes in admixed populations (the core has a subcontract to perform RNA-Seq for roughly 800 samples on this grant proposal) The UCSF Clinical and Translational Sciences Institute provided some core funding until July 2011, when CTSI elected not to continue to support any core laboratories. This reduced our nonrecharge funding. Hence continued support from SABRE is critical in allowing us to maintain services and develop new technologies for support of SABRE investigators. Publications Core-supported projects led by SABRE-affiliated faculty: 1. Bronevetsky Y, Villarino A, Eisley C, Barbeau R, Barczak AJ, Tarakhovsky A, Erle DJ, Rao A, Ansel KM. T cell activation induces proteasomal degradation of Argonaute and rapid remodeling of the microRNA repertoire. J Exp Med. In press. 2. Diez D, Goto S, Fahy JV, Erle DJ, Woodruff PG, Wheelock ÅM, Wheelock CE. Network analysis identifies a putative role for the PPAR and type 1 interferon pathways in glucocorticoid actions in asthmatics. BMC Med Genomics. 2012 Jun 19;5:27. 3. Levänen B, Bhakta NR, Paredes PT, Barbeau R, Hiltbrunner S, Pollack JL, Sköld CM, Svartengren, Grunewald J, Gabrielsson S, Eklund A, Larsson, Woodruff PG, David J Erle DJ, Wheelock AM. Altered MicroRNA profiles in Bronchoalveolar Lavage Fluid Exosomes in Asthma J Allergy Clin Immunol. In press. 4. Seumois G, Vijayanand P, Eisley CJ, Omran N, Kalinke L, North M, Ganesan AP, Simpson LJ, Hunkapiller N, Moltzahn F, Woodruff PG, Fahy JV, Erle DJ, Djukanovic R, Blelloch R, Ansel KM. An Integrated nano-scale approach to profile miRNAs in limited clinical samples. Am J Clin Exp Immunol. 2012 Nov 30;1(2):70-89. 5. Solberg OD, Ostrin EJ, Love MI, Peng JC, Bhakta NR, Hou L, Nguyen C, Solon M, Nguyen C, Barczak AJ, Zlock LT, Blagev DP, Finkbeiner WE, Ansel KM, Arron JR, Erle DJ, Woodruff PG. Airway epithelial miRNA expression is altered in asthma. Am J Respir Crit Care Med. 2012 Nov 15;186(10):965-74. 6. Sugimoto K, Kudo M, Sundaram A, Ren X, Huang K, Bernstein X, Wang Y, Raymond WW, Erle DJ, Abrink M, Caughey GH, Huang X, Sheppard D. The αvβ6 integrin modulates airway hyperresponsiveness in mice by regulating intraepithelial mast cells. J Clin Invest. 2012 Feb 1;122(2):748-58.

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7. Thomas MF, Abdul-Wajid S, Panduro M, Babiarz JE, Rajaram M, Woodruff P, Lanier LL, Heissmeyer V, Ansel KM. Eri1 regulates microRNA homeostasis and mouse lymphocyte development and antiviral function. Blood. 2012 Jul 5;120(1):130-42. Under review: Hsieh CL, Kim CC, Ryba BE, Niemi EC, Locksley RM, Liu J, Nakamura MC, Seaman WE. Traumatic brain injury induces unique macrophage subsets. Submitted. Sasse SK, Mailloux CM, Barczak AJ, Wang Q, Jain MK, Haldar SM, Gerber AN. GR and Klf15 regulate gene expression dynamics and integrate signals through feed forward circuitry. In revision. Zhao W, Pollack JL, Blagev D, Erle DJ. Massively parallel mapping of 3’ UTR cis-regulatory elements controlling mRNA stability. Submitted. Other core-supported projects: Broadhurst MJ, Ardeshir A, Kanwar B, Mirpuri J, Gundra UM, Leung JM, Wiens KE, VujkovicCvijin I, Kim CC, Yarovinsky F, Lerche NW, McCune JM, Loke P. Therapeutic helminth infection of macaques with idiopathic chronic diarrhea alters the inflammatory signature and mucosal microbiota of the colon. PLoS Pathog. 2012 Nov;8(11):e1003000. Petrillo LA, Wolf DM, Kapoun AM, Wang NJ, Barczak A, Xiao Y, Korkaya H, Baehner F, Lewicki J, Wicha M, Park JW, Spellman PT, Gray JW, van't Veer L, Esserman LJ. Xenografts faithfully recapitulate breast cancer-specific expression patters of parent primary breast tumors. Breast Cancer Res Treat. 2012 Oct;135(3):913-22. Under review: So AY, Garcia-Flores Y, Minisandram A, Martin A, Taganov K, Boldin M, Baltimore D. Regulation of APC development, immune response, and autoimmunity by Bach1/HO-1 pathway in mice. Blood 2012 Sep 20;120(12):2428-37. Baraban SC, Dinday MT, Hortopan GA. Drug screening for Dravet syndrome using Scn1a zebrafish mutants. Submitted. Hortopan GA and Baraban SC. Morpholino-based knockdown of LIS1 in zebrafish larvae: analysis of seizure activity and differential gene expression using microarrays. Submitted

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Genetics Core Director: Esteban González Burchard, M.D., M.P.H., Professor of Bioengineering & Therapeutic Sciences and Medicine

Vision: We built a multidisciplinary research center and we are taking a comprehensive approach to asthma research. Our approach integrates gene-environment studies with basic biology, population genetics, social and environmental epidemiology. We built a network of “minority serving” providers to recruit well-phenotyped subjects from throughout the U.S. and Puerto Rico. As a result of our efforts we have assembled the largest gene-environment study population of minority children with and without asthma in the U.S. (total sample n = 9,144). Finally, we have recruited two new faculty, Dara Torgerson, Ph.D. and Noah Zaitlen, Ph.D. into the Lung Biology Center. Both scientists are up and coming leaders in their respective fields (described below). We have established the Asthma Genetics Core Facility to facilitate asthma genetic research among Sandler/AAF-sponsored investigators. In keeping with the Mission of the original Sandler-sponsored Asthma Research Program, we have made this resource “Open Source” by having an extensive range of national and international collaborations. We offer investigators a “full service of genetic testing and analyses.” Specifically, we analyze promising candidate genes identified by investigators using biologic material (DNA and plasma) from large wellphenotyped family-based and case-control asthma studies of racially/ethnically diverse subjects. This past year the Genetics Core Facility has focused on three main goals: 1) collaboration 2) well-phenotyped patient recruitment of Latino and African American subjects with and without asthma and 3) faculty recruitment. Accomplishments in 2012: 1) Collaboration: a) UCSF Sandler Program and the AAF: In the era of large “Team Science” the value and importance of collaboration cannot be overstated. We have made the existing cohorts widely available to Sandler sponsored investigators (UCSF Sandler Program and the AAF). The Asthma Genetics Core assists investigators with study design and provides genotyping and expertise with statistical genetic analyses. We also allow our data to be used for replication of promising results from other investigative groups. b) Collaborating Faculty: In 2012 we have collaborated with the following faculty: Ryan Hernandez (UCSF), Carol Ober (Chicago), Kathleen Barnes (John’s Hopkins), Evan Eicher (University of Washington), Jim Gauderman (USC), Charles Rotimi (NIH/NHGRI), Noah Zaitlen (UCSF), Mario Castro (Washington University), L. Keoki Williams (Henry Ford), Fernando Martinez (University of Arizona), Max Seibold (National Jewish), Neil Trivedi (UCSF), Rajesh Kumar (Children’s Memorial Hospital, Chicago), Pedro Avila (Northwestern University), Stephanie London (NIEHS), Scott Weiss (Harvard), and Kathy Giacomini (UCSF). We have contributed our data to national and international consortiums to study asthma, obesity and eczema.

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c) We have generated genome wide association studies (GWAS) data from our study populations and provided our results as in silico replication to supplement initial findings for several Sandler investigators. In addition, we have worked closely with asthma investigators throughout the country to advance the field by collectively working towards testing and replicating novel genetic associations identified from basic science models (animal and human) to GWAS. d) EVE Asthma Consortium: This past year we participated in the NHLBI-sponsored EVE Asthma Consortium, which was published in Nature Genetics. The lead author, Dara Torgerson, was recently recruited to UCSF as an Assistant Professor in the Lung Biology Center. Admixture Mapping Meta-analysis in EVE: Through our work with the EVE Consortium we are currently working on a follow-up to the original GWAS to find additional loci via ancestry association or admixture mapping. We have combined data from the African-American and Hispanic/Latino studies within EVE (9 studies in total), comprising over 7,000 individuals. For all individuals we have estimated local ancestry using LAMP algorithms to have locus-specific ancestry calls for all individuals across the genome. The studies comprise a diverse group of designs including case-control, triobased, and pedigrees. Within this project we have developed novel ancestry imputation methods as well as methods for admixture mapping on large datasets. For replication we have leveraged our study, GALA II, as it is the largest study of asthma with genome-wide data in U.S. minority pediatric populations. We identified SMAD2 as a novel risk factor for asthma in Latino populations. Our results were supported by differential gene expression between children with and without asthma. We did not find the same association in African or European Americans. The manuscript has been approved by all co-authors and will be submitted to Nature Genetics by January 2013. e) Genentech (Joe Aaron): We have entered into a collaboration with Genentech to test the ability to use biomarkers (periostin) and clinical phenotypes to stratify children with asthma into high and low drug responders to Genentech’s new anti-IL13 therapy (Lebrikizumab). f) Gene expression: We are collaborating with Mario Castro (Washington University) and Max Seibold (National Jewish Health Center) to compare gene expression in lung tissue/lavage vs. nasal epithelia vs. peripheral blood. We hypothesize that nasal epithelial tissue gene expression will be a good proxy for gene expression in the lung. If our hypothesis is correct, it will facilitate large scale sampling of nasal epithelial tissue from hundreds of children with and without asthma. 2) Patient Recruitment: We recruited three study populations: 1) the Genetics of Asthma in Latino Americans (GALA I) Study (parent-child trios), a family-based study of Puerto Rican and Mexican children with asthma 2) the Genes-environments & Admixture in Latino Asthmatics (GALA II) Study, a case-control study at 5 urban centers across the U.S. and 3) the Study of African Americans Asthma, Genes & Environments (SAGE), a case-control study in the San Francisco Bay Area. Combined we now have the largest pediatric asthma

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genetic study of Latino and African American pediatric populations in the U.S. (n > 9,144 children with and without asthma). We are continuing to recruit and better characterize children with and without asthma. In collaboration with Genentech we are performing a longitudinal study of asthma treatment and control in a subset of the study population (n~1000). All subjects are extensively well phenotyped. We have detailed clinical measurements (spirometry, maximal bronchodilator response testing, methacholine challenge, skin prick testing, and IgE measurements, exhaled nitric oxide, skin color reflectance), biologic specimens (serum, RNA, DNA and nasal epithelia), geocoded air pollution measures and questionnaire-based information regarding environmental and social risk factors. We have genome-wide data available for all GALA I and II participants. We will combine biomarkers and sub-phenotypes to identify high and low drug responders to anti-IL13 therapy. 3) Faculty Recruitment: We have recruited two young scientists, who have significant research experience in minority populations and asthma genetics. Dara Torgerson, Ph.D. led the largest genomewide meta-analysis of asthma in the U.S., which was published in Nature Genetics. She trained with Drs. Carole Ober and Dan Nicolae of the University of Chicago. We also recruited Dr. Noah Zaitlen from the Harvard University School of Public Health. His expertise is gene-environment interactions and he will apply his theoretical methods to study asthma in minority populations. Financial Support: We have been successful at leveraging Sandler funding with NIH and industry support. The aforementioned efforts are supported by the equivalent of four NIH RO1 grants. Active Grants: 1. 1R01 HL104608-01A1: subcontract ~ $400,000, September 28, 2011-June 30, 2015, PI: Barnes 2. 1P60 MD006902: ~$1 million, August 27, 2012-February 28, 2017. PI, BibbinsDomingo. Project PI: Burchard. Grants under review: 1. K24 - Epigenomics of tobacco exposure on asthma severity among minority children 2. RO1 – Sequencing Candidate Genes Under Admixture Mapping Peaks in Latino Asthmatics. Under review. 3. RO1 - Pharmacogenomics of Bronchodilator Response in Minority Children with Asthma. Scored in the 9th percentile. Pending council review.

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Publications supported by the Strategic Program for Asthma Research and/or the Sandler Family Foundation. 2012 Publications 1. Fejerman, L., Chen, G.K., Eng, C., Huntsman, S., Hu, D., Williams, A., Pasaniuc, B., John, E.M., Via, M., Gignoux, C., Ingles, S., Monroe, K.R., Kolonel, L.N., Torres-Mejía, G., Pérez-Stable, E.J., González Burchard E., Henderson, B.E., Haiman, C.A., Ziv E. (2012) Admixture mapping identifies a locus on 6q25 associated with breast cancer risk in US Latinas. Hum Mol Genet. 2012 Jan 19. 2. Kumar R, Tsai HJ, Hong X, Gignoux C, Pearson C, Ortiz K, Fu M, Pongracic JA, Burchard EG, Bauchner H, Wang X. African ancestry, early life exposures, and respiratory morbidity in early childhood. Clin Exp Allergy. 2012 Feb;42(2):265-74. doi: 10.1111/j.1365-2222.2011.03873.x. Epub 2011 Sep 25. PMID: 22093077 3. Xu H, Cheng C, Devidas M, Pei D, Fan Y, Yang W, Neale G, Scheet P, Burchard EG, Torgerson DG, Eng C, Dean M, Antillon F, Winick NJ, Martin PL, Willman CL, Camitta BM, Reaman GH, Carroll WL, Loh M, Evans WE, Pui CH, Hunger SP, Relling MV, Yang JJ. ARID5B genetic polymorphisms contribute to racial disparities in the incidence and treatment outcome of childhood acute lymphoblastic leukemia. J Clin Oncol. 2012 Mar 1;30(7):751-7. Epub 2012 Jan 30. PMID: 22291082 4. Galanter, J.M., Fernandez, J.C., Gignoux, C.R., Barnholtz-Sloan, J., Fernandez, C., Via, M., Hidalgo-Miranda, A., Contreras, A.V., Uribe Figueroa, L., Raska, P., JimenezSanchez, G., Silva Zolezzi, I., Torres, M., Ruiz Ponte, C., Ruiz, Y., Salas, A., Nguyen, E., Eng, C., Borjas, L., Zabala, W., Barreto, G., Rondón, F., Ibarra, A., Taboada, P., Porras, L., Moreno, F., Bigham,A., Gutierrez, G., Brutsaert, T., León-Velarde, F., Moore, L.G., Vargas, E., Cruz, M., Escobedo, J., Rodriguez-Santana, J., Rodriguez-Cintrón, W., Chapela, R., Ford, J.G., Bustamante, C.D., Seminara, D., Shriver, M.D., Ziv, E., Burchard, E.G., Haile, R., Parra, E., Carracedo, A. for the Latin American Cancer Epidemiology (LACE) Consortium. Development of a Panel of Genome-wide Ancestry Informative Markers to Study Admixture Throughout the Americas. PLoS Genet. 2012 Mar;8(3):e1002554. Epub 2012 Mar 8. PMID: 22412386 5. Avena S, Via M, Ziv E, Pérez-Stable EJ, Gignoux CR, Dejean C, Huntsman S, TorresMejía G, Dutil J, Matta JL, Beckman K, Burchard EG, Parolin ML, Goicoechea A, Acreche N, Boquet M, Ríos Part Mdel C, Fernández V, Rey J, Stern MC, Carnese RF, Fejerman L. Heterogeneity in genetic admixture across different regions of Argentina. PLoS One. 2012;7(4):e34695. 2012 Apr 10. PMID: 22506044 6. Fejerman L, Chen GK, Eng C, Huntsman S, Hu D, Williams A, Pasaniuc B, John EM, Via M, Gignoux C, Ingles S, Monroe KR, Kolonel LN, Torres-Mejía G, Pérez-Stable EJ, Burchard EG, Henderson BE, Haiman CA, Ziv E. Admixture mapping identifies a locus on 6q25 associated with breast cancer risk in US Latinas. Hum Mol Genet. 2012 Apr 15;21(8):1907-17. Epub 2012 Jan 6. PMID: 22228098 7. Kenny EE, Timpson NJ, Sikora M, Yee MC, Moreno-Estrada A, Eng C, Huntsman S,

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Burchard EG, Stoneking M, Bustamante CD, Myles S. Melanesian blond hair is caused by an amino acid change in TYRP1. Science. 2012 May 4;336(6081):554. PMID: 22556244 8. Baran Y, Pasaniuc B, Sankararaman S, Torgerson DG, Gignoux C, Eng C, RodriguezCintron W, Chapela R, Ford JG, Avila PC, Rodriguez-Santana J, Burchard EG, Halperin E. Fast and accurate inference of local ancestry in Latino populations. Bioinformatics. 2012 May 15;28(10):1359-67. Epub 2012 Apr 11. PMID: 22495753 9. Torgerson DG, Capurso D, Ampleford EJ, Li X, Moore WC, Gignoux CR, Hu D, Eng C, Mathias RA, Busse WW, Castro M, Erzurum SC, Fitzpatrick AM, Gaston B, Israel E, Jarjour NN, Teague WG, Wenzel SE, Rodríguez-Santana JR, Rodríguez-Cintrón W, Avila PC, Ford JG, Barnes KC, Burchard EG, Howard TD, Bleecker ER, Meyers DA, Cox NJ, Ober C, Nicolae DL. Genome-wide ancestry association testing identifies a common European variant on 6q14.1 as a risk factor for asthma in African American subjects. J Allergy Clin Immunol. 2012 May 17. PMID: 22607992 10. Oh SS, Tcheurekdjian H, Roth LA, Nguyen EA, Sen S, Galanter JM, Davis A, Farber HJ, Gilliland FD, Kumar R, Avila PC, Brigino-Buenaventura E, Chapela R, Ford JG, LeNoir MA, Lurmann F, Meade K, Serebrisky D, Thyne S, Rodriguez-Cintron W, RodriguezSantana JR, Williams LK, Borrell LN, Burchard EG. Effect of secondhand smoke on asthma control among black and Latino children. J Allergy Clin Immunol (2012). 2012 Jun;129(6):1478-83.e7. Epub 2012 Apr 30. PMID: 22552109 11. Aldrich MC, Kumar R, Colangelo LA, Williams LK, Sen S, Kritchevsky SB, Meibohm B, Galanter J, Hu D, Gignoux CR, Liu Y, Harris TB, Ziv E, Zmuda J, Garcia M, Leak TS, Foreman MG, Smith LJ, Fornage M, Liu K, Burchard EG; for the Health ABC and CARDIA Studies. Genetic Ancestry-Smoking Interactions and Lung Function in African Americans: A Cohort Study. PLoS One. 2012 June;7(6):e39541. Epub 2012 Jun 21. PMID: 22737244 12. Aminuddin F, Akhabir L, Stefanowicz D, Paré PD, Connett JE, Anthonisen NR, Fahy JV, Seibold MA, Burchard EG, Eng C, Gulsvik A, Bakke P, Cho MH, Litonjua A, Lomas DA, Anderson WH, Beaty TH, Crapo JD, Silverman EK, Sandford AJ. Genetic association between human chitinases and lung function in COPD. Hum Genet. 2012 Jul;131(7):1105-14. Epub 2011 Dec 28. PMID: 22200767 13. Torgerson, DG, Gignoux, CR, Galanter, JM, Drake, KA, Roth, LA, Eng C, Huntsman, S, Torres, R, Avila, PC, Chapela, R, Ford, JG, Rodríguez-Santana, JR, Rodríguez-Cintrón, W, Hernandez, RD, and Burchard, EG. Case-control admixture mapping in Latino populations enriches for known asthma-associated genes. Journal of Asthma and Clinical Immunology. J Allergy Clin Immunol. 2012 Jul;130(1):76-82.e12. Epub 2012 Apr 13. PMID: 22502797 14. Nguyen EA, Burchard EG. Asthma Research for All of the United States. Pediatr Allergy Immunol Pulmonol. 2012 Sep;25(3):128-131. PMID: 22970422

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15. Kumar R, Williams LK, Kato A, Peterson EL, Favoreto S Jr, Hulse K, Wang D, Beckman K, Thyne S, Lenoir M, Meade K, Lanfear DE, Levin AM, Favro D, Yang JJ, Weiss K, Boushey HA, Grammer L, Avila PC, Burchard EG, Schleimer R. Genetic variation in B cell-activating factor of the TNF family (BAFF) and asthma exacerbations among African American subjects. J Allergy Clin Immunol. 2012 Oct. Epub 2012 June. PMID: 22728080 16. Myers RA, Himes BE, Gignoux CR, Yang JJ, Gauderman WJ, Rebordosa C, Xie J, Torgerson DG, Levin AM, Baurley J, Graves PE, Mathias RA, Romieu I, Roth LA, Conti D, Avila L, Eng C, Vora H, Lenoir MA, Soto-Quiros M, Liu J, Celedón JC, Farber HJ, Kumar R, Avila PC, Meade K, Serebrisky D, Thyne S, Rodriguez-Cintron W, Rodriguez-Santana JR, Borrell LN, Lemanske RF Jr, Bleecker ER, Meyers DA, London SJ, Barnes KC, Raby BA, Martinez FD, Gilliland FD, Williams LK, Burchard EG, Weiss ST, Nicolae DL, Ober C. Further replication studies of the EVE Consortium meta-analysis identifies 2 asthma risk loci in European Americans. J Allergy Clin Immunol. 2012 Dec;130(6):1294-301. doi: 10.1016/j.jaci.2012.07.054. Epub 2012 Oct 4. 17. Levin AM, Mathias RA, Huang L, Roth LA, Daley D, Myers RA, Himes BE, Romieu I, Yang M, Eng C, Park JE, Zoratti K, Gignoux CR, Torgerson DG, Galanter JM,Huntsman S, Nguyen EA, Becker AB, Chan-Yeung M, Kozyrskyj AL, Kwok PY, Gilliland FD, Gauderman WJ, Bleecker ER, Raby BA, Meyers DA, London SJ,Martinez FD, Weiss ST, Burchard EG, Nicolae DL, Ober C, Barnes KC, Williams LK. A meta-analysis of genome-wide association studies for serum total IgE in diverse study populations. J Allergy Clin Immunol. 2012 Nov 10. doi: 10.1016/j.jaci.2012.10.002. 2012 Nov [Epub ahead of print] Manuscripts currently under review: 1. Rajesh Kumar, Elizabeth A Nguyen, Lindsey A Roth, Sam S Oh,Christopher R Gignoux, Scott Huntsman, Celeste Eng, Andres Moreno-Estrada, Karla Sandoval, Rosenda Peñaloza-Espinosa, Marisol López-López, Pedro C Avila, Harold J Farber, Haig Tcheurekdjian, William Rodriguez-Cintron, Jose R Rodriguez-Santana, Denise Serebrisky, Shannon M Thyne, Keoki Williams, William Klitz, Cheryl Winkler, Carlos D Bustamante, Eliseo J Pérez-Stable, Luisa N Borrell, Esteban G Burchard. Factors associated with degree of atopy in Latino children in a nationwide pediatric sample: The GALA II Study. J Allergy Clin Immunol. (Under 2nd review, December 2013). 2. Joshua M Galanter, Christopher R Gignoux, Dara G Torgerson, Lindsey A Roth, Celeste Eng, Sam S Oh, Elizabeth A Nguyen Scott Huntsman Donglei Hu, Saunak Sen. Adam Davis, Harold J. Farber, Pedro C. Avila, Emerita Brigino-Buenaventura, Michael A. LeNoir, Kelley Meade, Denise Serebrisky, Stephanie London, Frank Gilliland, Fernando Martinez, Luisa N Borrell, William Rodriguez-Cintron, Rajesh Kumar, Jose R. Rodriguez-Santana, Esteban G. Burchard, and the EVE Consortium. Genome-wide association and admixture mapping identify chromosomal regions 17q21 and 6p21 as asthma-associated loci in Latinos. AJRCCM. (Under review December 2013).

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3. Luisa N. Borrell, Elizabeth A. Nguyen, Lindsey A. Roth,Sam S. Oh, Haig Tcheurekdjian,Saunak Sen, Adam Davis, Harold J. Farber, Pedro C. Avila, Emerita Brigino-Buenaventura, Michael A. LeNoir, Fred Lurmann, Kelley Meade, Denise Serebrisky, William Rodriguez-Cintron, Rajesh Kumar, Jose R. Rodriguez-Santana, Shannon Thyne, Esteban G. Burchard. Childhood obesity and asthma control in a diverse sample: Examining age and racial/ethnic differences. AJRCCM. (Submitted for 2nd review January 2013). 4. Chris R Gignoux, Dara G Torgerson, Joshua Galanter, Lindsey A Roth, Celeste Eng, Elizabeth A Nguyen, Scott Huntsman, Sam S Oh,Raskia A Mathias, Adam Davis, Harold J Farber, Pedro C Avila, Emerita Brigino-Buenaventura, Michael A LeNoir, Kelley Meade, Denise Serebrisky, Luisa N Borrell, William Rodriguez-Cintron, Rajesh Kumar, Jose R Rodriguez-Santana, Andres Moreno, Karla Sandoval, Cheryl Winkler, Carlos Bustamante, EVE Collaborators, Carole Ober, Dan Nicholae, Saunak Sen, Kathleen C Barnes, Esteban G Burchard. Meta-analysis of admixture mapping using existing genome-wide association data implicates SMAD2 as a novel asthma-associated locus in Latinos. Nature Genetics. (Submitted January 2013). 5. Katherine A. Drake, Dara G. Torgerson, Christopher R. Gignoux, Joshua M. Galanter, Lindsey A. Roth, Scott Huntsman, Celeste Eng, Sam S. Oh, Sook Wah Yee, Lawrence Lin, Adam Davis, Luisa N. Borrell, Harold J. Farber, Rajesh Kumar, Pedro C. Avila, Emerita Brigino-Buenaventura, Rocio Chapela, Jean G. Ford, Michael A. LeNoir, Fred Lurmann, MS, Kelley Meade, Denise Serebrisky, Shannon Thyne, William RodríguezCintrón, Saunak Sen, José R. Rodríguez-Santana, Kathleen M. Giacomini, and Esteban G. Burchard. A Genome-wide Association Study of Bronchodilator Response in Latinos Implicates Rare Variants. J Allergy Clin Immunol. (Submitted January 2013). 6. Katherine K. Nishimura, Joshua M. Galanter, Lindsey A. Roth, Sam S. Oh, Harold J. Farber, Denise Serebrisky, Rajesh Kumar, Luisa N. Borrell, Emerita BriginoBuenaventura, Adam Davis, Michael A. LeNoir, Kelley Meade, William RodriguezCintron, Pedro C. Avila, Jose R. Rodriguez-Santana, Saunak Sen, Fred Lurmann, John R. Balmes, Esteban G. Burchard. Early Life Exposure to Air Pollution and the Risk of Asthma in Latino and African American Children. ARJCCM. (Submitted January 2013).

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Cell Sorting and Analysis Core Director: Zhien-Wang Objective Flow cytometry is necessary to characterize, purify and separate cell types based on surface characteristics. The objective of this core is to provide technical support and access to highly sophisticated instruments for persons at UCSF performing asthma-related research. Contributions from SABRE Center have been partnered with the Diabetes Center, individual investigator resources and institutional resources to support the space and maintenance of the core largely through an integrated re-charge system. Students and postdocs participate in training in the core at an area where training can be centralized in order to facilitate maintenance and oversight. Accomplishments The Core is located in S1067 in proximity to Dr. Locksley’s laboratory and centrally within the Immunology Program corridor above the SABRE Center space in HSE201. Scheduling is online and suitably trained individuals can access instruments in the core 24 hours a day, 7 days a week. The space offers an array of instrumentation that offers unique capabilities in data acquisition and enhances the depth of technical capacity: Two Beckman-Coulter MoFlo XDP High-Speed sorters with 4-laser, 17-color, 15-parameter capability centered around 488 nm, 532 mm, 561 mm and 647 nm multi-line air-cooled lasers. Two side-by-side instruments has enabled operation by a single individual, thus optimizing use and minimizing cost. Becton-Dickinson Biosciences LSR II Flow Cytometer with 4-laser, 10-color, 12-parameter capability centered around 488 nm OPSL, 637 nm (red), 403 nm (violet) and 535 nm (green) lasers. Total use > 1600 hrs. Becton-Dickinson Biosciences LSR II Flow Cytometer with 4-laser, 10-color, 12-parameter capability centered around 488 nm OPSL, 637 nm (red), 403 nm (violet) and 535 nm (green) lasers is maintained by the core but stationed in HSE201 in the SABRE core space. Total use > 800 hrs. Training and Integration with Sandler Program Use of the core has stabilized over the past 2 years. Over the last 12 months, >45 laboratories at the UCSF Parnassus and Mission Bay campuses have used the facility 2 or more times, with 32 labs over 3 times. In turn, the numbers of users per laboratory has also stabilized at 2.3 users/lab, and reflects use by graduate students and postdocs. Nine of the labs are direct participants in the SABRE Center, and a number of the other users are affiliated investigators examining aspects of

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inflammation and tissue injury of relevance to asthma. All of the core SABRE Center scientists participate in the Sorting Core. Budgetary requests from the SABRE Center are now restricted to acute laser failure and maintenance, as personnel and renewables have all been covered through recharge mechanisms. Grants and Publications Data acquired in the Cell Sorting and Analysis core has contributed to almost a quarter of the publications listed in the bibliography for the current annual report.

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Microscopy Core Managing Director: Kaitlin Corbin Faculty Director: Matthew Krummel, Ph.D. Objective/Mandate The objective of the SABRE Microscopy Core is to advance light-based imaging of the lung and associated tissues. Our core operates under the premise that a critical understanding of diseased tissues and organs such as the asthmatic lung will come with the study of the activities of component players (cell types, effector molecules) in their native environment. We also recognize that many existing imaging methods may require some additional development or elaboration before they can be successfully applied in studies of lung biology. We act both as a repository/resource of imaging technology and expertise and to develop novel technologies. We represent an emerging evolving example of a ‘Co-laboratory’ in which expertise in this active area of scientific progress is shared rather than arbitrarily monetized. Strategic Goals The efforts of this center are being directed toward improved imaging technologies for cells of the normal and allergic lung. In 2013, the core will be trying to advance three specific goals for intravital imaging. Note that in the 2012 period, we have miniaturized and made less-invasive our lung-stabilization rigs, have implemented a new microscope with photoablation and photoactivation capability and have optimized mouse models for imaging increased numbers of cell types at the same time. 1. To provide stabilized access to larger airways and trachea of living mice, using a stabilized gradient- refractive index (GRIN) lens. 2. To develop software processing platforms for converting >100GB datasets into images and parametrized object-based data for rapid scoring of immune and cell-cell dynamics within large and long-time course experiments. 3. To provide improved surgical stabilization to image lungs over many days with repeated visits to the same regions. 4. To extend usage of the human lung imaging method through expanded facility capacity and training/sample processing capabilities and through collaboration with asthma researchers with access to primary biopsy material. 5. To provide ongoing technical and instrumentation support to the UCSF (and beyond) Asthma community in order to put existing and emerging imaging technologies to practical use in the study of asthma.

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Organization The SABRE microscopy core is contained within the Biological Imaging Development Center (BIDC). The larger BIDC is an interdisciplinary center configured to assemble, test, and apply emerging light microscopy techniques and technologies. The BIDC is designed to serve two roles: a conduit for new optical imaging technology & as a site for new technology development. As part of its role as a conduit for new optical imaging technology the BIDC also houses a ‘incubator’ program that helps investigators who are willing to share equipment to have the instrument in a setting where sharing of the instrument is simplified. The SABRE center is currently one of the major supporters for this campus-wide imaging initiative and now holds major ‘stakes’ in confocal and 2-photon instruments in addition to driving key development initiatives. SABRE affiliated labs and investigators enjoy privileged access to both the SABRE microscopy core and the larger BIDC. This center is managed by a managing director (Kaitlin Corbin) under the supervision of a Faculty Director (Max Krummel) and an oversight committee representing many of the key stakeholders on campus. Current Usage Currently there are 208 registered users of the BIDC. These users represent 72 principal investigators or labs. These labs are drawn from 26 departments or organizational units. In 2012, 42 new users from 24 labs were trained. All users received some degree of training on center instruments or image processing stations. Many users are trained on multiple instruments. Most of this training is done on an individual basis and reflects the differences in each users experience, aptitude and project needs. After initial trainings BIDC staff continue to consult and assist with projects on and individual basis. Users are free to ask questions and get assistance as needed-- we don’t charge for our time through recharges and projects are essentially ‘collaborations’. We have specifically trained users from the following labs: Baraban   German   Locksley   Noble   Bluestone   Kajimura   Looney   Ou   Chapman   Klein   Lowell   Shin   Craik   Krummel   McQuillen   Szoka   Debnath   Laird   Muschen   Weaver   Fahy   Lanier   Nishimura   Willenbring   Recent Accomplishments Increased Stability and 24-hours of continuous lung imaging. Using a 3D printer in the facility, purchased with 50% SABRE funds in 2011, we developed a series of protoype stabilization rigs in which only a small incision need be made in order to gain access to the lung. After extensive testing, we found a rig that cams between two ribs and allows for superior survival of animals over long-term imaging. This rig and the associated approaches are being applied to observing the remodeling of the lung that takes place following damage/asthma. It is also suited, and being used for tracking the first hours of clearance of metastatic cancer cells in lung vasculature.

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Photoablation and Photoactivation: In 2012, we extensively tested and subsequently purchased, microscopes with both a single-photon and two-photon ablation lasers that now allow us to purposefully modulate biology in the lung using spots of light. This is being developed as a way to determine which cells are critical for the ongoing biology in allergic lungs. We were able to obtain grant money for this (NIH S10) as a result of preliminary data generated in this SABREfunding facility. Introduction of demo equipment, (see below) and establishment of SOPs and training. This year, we served as a demo site for a Nikon ‘STORM’ microscope as well as the Zeiss &710MP. As with other demos in the past, we negotiated with vendors to ensure that equipment was onsite for at least one month (typically much longer). Space We maintain instruments and development tools in three ‘core’ rooms in Medical Sciences S11 and we also maintain additional microscopes in 6 additional sites throughout the campus, including behind the animal barrier. Funding The following represent some of the lung-related grants which were funded in 2012, in part through our efforts and support: Sheppard/Woodruff/Erle/Krummel: NIH Headley:DoD Postdoctoral ($300K/yr 3 yrs) U01: AADCRC ($7.5M/5 years) Acerbi: Komen Postdoctoral ($60K/yr 3 Maelig PBBR Postdoctoral ($10K/1yr) years) Maelig: DoD Postdoctoral ($300K/yr 3 yrs) Nystul: R01 And these were submitted: Nishimura R01 resubmitted (likely funded) Looney/Krummel R01 submitted P.T. Chuang R01 submitted J.S. Shin R01 submitted

Schneider S10 submitted Werb R01 submitted WErb et al. PPG submitted

Recent publications A number of recent and forthcoming publications, both methodological and research-orientated, have been produced with help of the facility during the past year. These include: 1. Paszek MJ, DuFort CC, Rubashkin MG, Davidson MW, Thorn KS, Liphardt JT, Weaver VM. Scanning angle interference microscopy reveals cell dynamics at the nanoscale. Nat Methods. 2012 Jul 1;9(8):825-7. doi: 10.1038/nmeth.2077. PubMed PMID: 22751201; PubMed Central PMCID: PMC3454456. 2. Zhang Y, Chen YC, Krummel MF, Rosen SD. Autotaxin through lysophosphatidicacid stimulates polarization, motility, and transendothelial migration of naive Tcells. J

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Immunol. 2012 Oct 15;189(8):3914-24. doi: 10.4049/jimmunol.1201604. Epub012 Sep 7. PubMed PMID: 22962684; PubMed Central PMCID: PMC3509168. 3. Caudrillier A, Kessenbrock K, Gilliss BM, Nguyen JX, Marques MB, Monestier M, Toy P, Werb Z, Looney MR. Platelets induce neutrophil extracellular traps in transfusionrelated acute lung injury. J Clin Invest. 2012 Jul 2;122(7):2661-71. doi: 10.1172/JCI61303. Epub 2012 Jun 11. PubMed PMID: 22684106; PubMed Central PMCID: PMC3386815. 4. Beemiller P, Jacobelli J, Krummel MF. Integration of the movement of signaling microclusters with cellular motility in immunological synapses. Nat Immunol. 2012Jul 1;13(8):787-95. doi: 10.1038/ni.2364. PubMed PMID: 22751140. 5. Thornton EE, Looney MR, Bose O, Sen D, Sheppard D, Locksley R, Huang X,Krummel MF. Spatiotemporally separated antigen uptake by alveolar dendritic cells and airway presentation to T cells in the lung. J Exp Med. 2012 Jun 4;209(6):1183-99. doi: 10.1084/jem.20112667. Epub 2012 May 14. PubMed PMID: 22585735; PubMed Central PMCID: PMC3371730. 6. Thornton EE, Krummel MF, Looney MR. Live imaging of the lung. Curr Protoc Cytom. 2012 Apr;Chapter 12:Unit12.28. doi: 10.1002/0471142956.cy1228s60. PubMed PMID: 22470155. 7. Engelhardt JJ, Boldajipour B, Beemiller P, Pandurangi P, Sorensen C, Werb Z, Egeblad M, Krummel MF. Marginating dendritic cells of the tumor microenvironment crosspresent tumor antigens and stably engage tumor-specific T cells. Cancer Cell. 2012 Mar 20;21(3):402-17. doi: 10.1016/j.ccr.2012.01.008. PubMed PMID: 22439936; PubMed Central PMCID: PMC3311997. 8. Gilden JK, Peck S, Chen YC, Krummel MF. The septin cytoskeleton facilitates membrane retraction during motility and blebbing. J Cell Biol. 2012 Jan 9;196(1):103-14. doi: 10.1083/jcb.201105127. PubMed PMID: 22232702; PubMed Central PMCID: PMC3255977. Plans for the Coming Year 1. A major push in the next year will be to implement a stabilized gradient- refractive index (GRIN) lens-based system for real-time analysis of lung trachea and large branching airways. We have obtained two such lenses and have recently completed an assembly for the 6-axis positioning of this as well as the application of mild suction. We will be applying this to model tissues first but then progressing to allergic lungs. 2. The field of intravital imaging in particular has begun to recognize the value of collecting data over vast 3 dimensional spaces over extended time-periods. We have been innovating our highspeed two-photon rigs to accommodate this but have reached a limit in processing. As datasets begin to exceed 100GB per run, loading data into memory, rendering it and processing it to

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quantify data has reached a limit with current tools. Our in-house software programmer, Henry Pinkard, has been developing methods to rapidly parameterize data to reduce complexity for feature-tracking and analysis of cell-cell contacts. This work will expand in 2012. 3. In 2012, we will be taking two steps toward applying subcellular imaging to human tissues directly. First, we are continuing to evolve a ‘live biopsy’ method. Second, we are collaborating with the local and recently funded AADCRC (NIH Asthma consortium) to develop novel protein affinity reagents to specifically label and track key populations within the lung. This work will expand into supporting imaging of bronchial pinch biopsies over the next five years. 4. We plan to continue to provide ongoing technical and instrumentation support to the UCSF (and beyond) Asthma community in order to put existing and emerging imaging technologies to practical use in the study of asthma. Training and Integration with Sandler Program As noted in previous updates, the center aims to provide ongoing technical and instrumentation support to the UCSF (and beyond) Asthma community. Specifically our goal is to put existing and emerging imaging technologies to practical use in the study of asthma. This year, we have specifically undertaken training of Peck and Wong in performing lung-based assays from start to finish so that they may be able to undertake experiments for/with new users that may not have experience with these assays. This is particularly important in some of the more complicated procedures in which technical expertise is critical to the success of the experiment. We have taught live lung imaging techniques to visitors from Michael Cahalan’s lab (UC Irvine) and from Paul Kubes’ lab (University of Calgary). To introduce imaging advances within the wider community, the core also sponsors a recurring pizza-talk at which groups from the Bay Area and beyond present novel imaging technology and advances. Topics this year have included live lung imaging, 3D printing and design, Multidimensional analysis, and in vivo optical imaging. Details can be seen at the website: http://pathology.ucsf.edu/BIDC//seminars.html. Current Equipment Permanent Equipment: 1. Gen1 custom built 2-photon: 4 color 2. Gen2 custom built 2-photon: 5 color 3. *Gen3 custom built 2-photon: 8 color/2 laser (being elaborated with a DMD array for photo-activation/ablation) 4. *Spectral laser scanning confocal microscope (C1Si) 5. Spinning-disk confocal microscope (Yokogawa 4-laser on a Zeiss 200M base) 6. Upright Zeiss microscope set up for fluorescence interference contrast imaging. 7. Zeiss Axiovert 100 timelapse microscope

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Core Facilities

8. IVIS live animal imager (animal colony) 9. Nikon spinning-disk confocal with TIRF and photo-ablation (Wittman) 10. Zeiss Cell Observer with Apotome (Nystul) 11. *Alaris 3D printer 12. Nikon A1R Multiphoton microscope. * Indicates SABRE is a partial owner of this instrument. Additional Equipment hosted on-site in 2012: 1. Zeiss 710 Multi-photon confocal microscope 2. Nikon ‘STORM’ ,microscope. Analysis Computers and Software Platforms: This year, as a result of increased demand, we purchased a third IMARIS license and associated Matlab license and increased our workstations to four, installing a new desk to house this. As part of a cooperative agreement, MDS/Molecular Devices again supplied upgraded keys for PCbased analysis stations for image processing. We have partnered with and will support the following commercial partners who supply working copies of their software as part of the sponsorship program: • MDS/Molecular Devices 'Metamorph' (who are supplying the three offline computers/keys as well as online keys) • Bitplane 'Imaris' (who have subsidized the purchase of software used in the facility). • Solidworks who have supplied 2 discounted software keys for our manufacturing purposes.

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Sandler Asthma Basic REsearch Center  

Asthma Related Research Projects

ASTHMA RELATED RESEARCH PROJECTS

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Sandler Asthma Basic REsearch Center  

Asthma Related Research Projects

Evolving Microenvironments in Airway Inflammation Program Director: George H. Caughey, M.D. Program Project Grant HL024136 is nearing completion of its 33nd year, the third of a planned five years of interdisciplinary study of airway inflammation competitively renewed on May 11, 2010. Each of the component projects focuses on different populations of airway cells and molecules mediating structural changes in the airway accompanying chronic airway inflammation. The Projects are supported by two Cores, one administrative and one scientific (Tools for Analysis of Airway Inflammation). Summary of Advances this Year Project 1: Roles of Peptidases in Chronic Airway Inflammation (Project Leader: G.H. Caughey) One of Project 1’s major achievements was identification of a substrate and spectrophotometric technique allowing direct assay of prostasin activity in living human airway epithelial apical and basolateral surfaces. Using this substrate in conjunction with selective inhibitors, we established that prostasin anchored to the cell surface by a lipid (glycosylphosphatidylinositol) is the major contributor to surface activity. For example, the apical surface of cultured human bronchial epithelial cells expresses 22% of total, extractable, aprotinin-inhibitable, tryptic activity and 16% of prostasin immunoreactivity. Similar results were obtained using cultured cystic fibrosis bronchial cells. Thus, we established that prostasin is present, mature and active on the apical surface of wild type and cystic fibrosis bronchial epithelial cells, where it can be targeted for inhibition via the airway lumen with the goal of inhibiting epithelial Na+ uptake and therapeutically increasing hydration of airway secretions. We also established differences between prostasins (mouse and human) and other surface epithelial tryptic proteases (matriptase and marapsin) in peptide cleavage preferences, inhibitor susceptibility, and modes of membrane anchoring. In contrast to mouse “knockouts” of prostasin and matriptase, a mouse we created that is genetically deficient of marapsin/Prss27 is fully viable, further supporting different roles despite similar high degrees of evolutionary conservation in vertebrate animals. Additional significant progress was made in testing our hypothesis that variations in inheritance of active tryptase genes is common and that inheritance of dysfunctional alleles is protective with respect to asthma phenotypes. Project 2: Imaging T cell Airway Responses during Inflammation (Project Leader: M.F. Krummel) In this year of funding, we established a labeling method for tracking and imaging incoming monocytes using two genetically-encoded fluorescent proteins. We are now tracking in real-time the differentiation of these cells as they move from alveoli towards airways. Our goal is to reveal key checkpoints that might be exploited for modulating asthma severity and this is a direct offshoot of Aim 1 of this proposal. In a second project driven by our Aim 2, we are tracking the site of Th2 differentiation in asthma models. Preliminary data on this front suggests that IL-4 secretion is first found in lung, suggesting that dendritic cell-T cell interactions at that site modulate the response. Related to this, in the coming year, we will complete our study of the relative sites and dynamics of Th2 and regulatory (Treg) cells in asthma models. Finally, we

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Sandler Asthma Basic REsearch Center  

Asthma Related Research Projects

began pilot work to examine interactions of allergic T cells with neurons and neuroendocrine cells in the allergic lung. Project 3: Lymphangiogenesis and Angiogenesis in Airway Inflammation (Project Leader: D.M. McDonald) During the past year, an important focus of Project 3 was to determine the extent and distribution of lymphangiogenesis in the inflamed lung and the principal growth factors that drive it. Studies revealed that lung lymphatics increased 5-fold within 2 weeks after Mycoplasma pulmonis infection in mice. Strikingly, most of the new lymphatics were located within bronchus-associated lymphoid tissue (BALT) around large bronchi, pulmonary arteries, and pulmonary veins. Few lymphatics were located near distal airways or alveoli under normal conditions or in chronic inflammation. By using selective inhibitors of VEGFR2 and VEGFR-3, experiments revealed that VEGFR-3 signaling was the dominant driving mechanism for lymphangiogenesis after M. pulmonis infection. Because VEGF-C and VEGF-D are the principal ligands for VEGFR-3, these growth factors are likely to mediate lymphangiogenesis under these conditions. VEGFR-2 signaling could make a minor contribution, but the underlying mechanism is still under investigation. VEGF-A appears not to have a significant contribution to lymphangiogenesis in the lung in this model. An essential role of VEGFR-3 signaling in lymphangiogenesis in the respiratory tract was also found in a transgenic mouse model, where IL-1b is overexpressed in the epithelium under doxycycline regulation. Here, lymphatic growth was completely blocked by sequestration of the VEGFR3 ligands VEGF-C and VEGF-D. Because of this key involvement of VEGF-C or VEGF-D, the role of IL-1b was explored further by determining the location of IL-1R1 receptor. These were found to be preferentially located on epithelial basal cells and neuroendocrine cells, at least under normal conditions. The identification of factors that link these epithelial targets of IL-1b to the cellular sources of VEGF-C and VEGF-D is underway. Chemokines that recruit macrophages are being explored as candidates. Scientific Core Activities In this year of funding, we generated new and tittered stocks of mycoplasma for use in the three projects and the Core continues to function in performing genotyping of key mouse strains. The Core also has performed and continues to perform confocal and 2-photon imaging experiments in addition to assisting in keeping these instruments maintained and optimized. Personnel funded by this core component have also permitted pilot projects on tryptase and protease functions in airway remodeling, in neuroendocrine cells and in the dynamics of T cell-dendritic-mast cell interactions. In the next year, the core will also contribute to an effort to perform high-resolution intravital imaging of mouse trachea. Training and Integration with the Sandler Program The SABRE Center continues to provide a focus to bring together all of the groups studying fundamental questions relevant to asthma at UCSF. This focus includes a monthly research meeting of investigators with asthma-focused basic research. The Sandler-supported core also provided advice and training in sensitization and challenge protocols for creating mouse models

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Sandler Asthma Basic REsearch Center  

Asthma Related Research Projects

of chronic allergic inflammation and for monitoring changes in airway resistance. It also facilitated sharing of models and advanced imaging technologies. P01 HL024136-supported selected publications (2012-2013) 1. Baluk P, Hogmalm A, Bry M, Alitalo K, Bry K, McDonald DM. Transgenic overexpression of interleukin-1b induces persistent lymphangiogenesis but not angiogenesis in mouse airways. Am J Pathol (in press). 2. Banfi A, von Degenfeld G, Gianni-Barrera R, Reginato S, Merchant MJ, McDonald DM, Blau HM. Therapeutic angiogenesis due to balanced single-vector delivery of VEGF and PDGF-BB. FASEB J 26:2486-97, 2012, PMID 22391130; PMCID PMC3360154. 3. Caughey GH. “Chymases” in Handbook of Proteolytic Enzymes, 3rd edition, Rawlings N and Salvesen G, eds., Elsevier, Oxford, in press. 4. Caughey GH. “Mastins” in Handbook of Proteolytic Enzymes, 3rd edition, Rawlings N and Salvesen G, eds., Elsevier, Oxford, in press. 5. Cheng LE, Hartmann K, Roers A, Krummel MF, Locksley RM. Perivascular mast cells dynamically probe cutaneous blood vessels to capture Immunoglobulin E. Immunity (in press), PMID 23290520. 6. Greenland JR, Jones KD, Hays SR, Golden JA, Urisman A, Jewell NP, Caughey GH, Trivedi NN. Association of large-airway lymphocytic bronchitis with bronchiolitis obliterans syndrome. Am J Resp Crit Care Med, 187:417-23, 2013; PMID 23239157. 7. Nimishakavi S, Besprozvannaya M, Raymond WW, Craik CS, Gruenert DC, Caughey GH. Activity and inhibition of prostasin and matriptase on apical and basolateral surfaces of human airway epithelial cells. Am J Physiol Lung Cell Mol Physiol 303:L97-106, 2012; PMID 22582115. 8. Orsenigo F, Giampietro C, Ferrari A, Corada M, Galaup A, Sigismund S, Ristagno G, Maddaluno L, Young Koh G, Franco D, Kurtcuoglu V, Poulikakos D, Baluk P, McDonald D, Grazia Lampugnani M, Dejana E. Phosphorylation of VE-cadherin is modulated by haemodynamic forces and contributes to the regulation of vascular permeability in vivo. Nat Commun 3:1208, 2012, PMID 23169049; PMCID PMC3514492. 9. Raman K, Caughey GH. “Marapsin” in Handbook of Proteolytic Enzymes, 3rd edition, Rawlings N and Salvesen G, eds., Elsevier, Oxford, 2013. 10. Raman K, Trivedi NN, Raymond WW, Ganesan R, Kirchhofer D, Verghese GM, Craik CS, Schneider EL, Nimishakavi S, Caughey GH. Mutational tail loss is an evolutionary mechanism for liberating marapsins and other type I serine proteases from transmembrane anchors. J Biol Chem, in press. 11. Sennino B, Ishiguro-Oonuma T, Wei Y, Naylor RM, Williamson CW, Bhagwandin V, Tabruyn SP, You WK, Chapman HA, Christensen JG, Aftab DT, McDonald DM. Suppression of tumor invasion and metastasis by concurrent inhibition of c-met and VEGF signaling in pancreatic neuroendocrine tumors. Cancer Discov 2:270-87, 2012, PMID 22585997; PMCID PMC3354652. 12. Sennino B, McDonald DM. Controlling escape from angiogenesis inhibitors. Nat Rev

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Sandler Asthma Basic REsearch Center  

Asthma Related Research Projects

Cancer 12:699-709, 2012, PMID 23001349. 13. Sugimoto K, Kudo M, Sundaram A, Ren X, Huang K, Bernstein X, Wang Y, Raymond WW, Erle DJ, Åbrink M, Caughey GH, Huang X, Sheppard D. The αvβ6 integrin modulates airway hyper-responsiveness in mice by regulating intra-epithelial mast cells. J Clin Invest 122:748-58, 2012; PMID 22232213; PMCID PMC3266785. 14. Thornton EE, Krummel MF, Looney MR. Live Imaging of the Lung. Curr Protoc Cytom Chapter 12:Unit12.28, 2012. 15. Thornton EE, Looney MR, Bose O, Sen D, Sheppard D, Locksley R, Huang X, Krummel MF. Spatiotemporally separated antigen uptake by alveolar dendritic cells and airway presentation to T cells in the lung. J Exp Med 209:1183-99, 2012, PMID 22585735; PMCID PMC3371730. 16. Trivedi NN, Caughey GH. “Human a, b, and d-Tryptases” in Handbook of Proteolytic Enzymes, 3rd edition, Rawlings N and Salvesen G, eds., Elsevier, Oxford, 2013. 17. Trivedi NN, Caughey GH. “g-Tryptases” in Handbook of Proteolytic Enzymes, 3rd edition, Rawlings N and Salvesen G, eds., Elsevier, Oxford, 2013. 18. Xi Y, Wei Y, Sennino B, Ulsamer A, Kwan I, Brumwell AN, Tan K, Aghi MK, McDonald DM, Jablons DM, Chapman HA. Identification of pY654-β-catenin as a critical co-factor in hypoxia-inducible factor-1α signaling and tumor responses to hypoxia. Oncogene 2012 Dec 17. doi: 10.1038/onc.2012.530. [Epub] PMID: 23246962. 19. Xu X, Zhang H, Song Y, Lynch SV, Lowell CA, Wiener-Kronish JP, Caughey GH. Strain-dependent induction of neutrophil histamine production and cell death by Pseudomonas aeruginosa. J Leuk Biol 91:275-84, 2012; PMID 22075928. 20. Yao LC, Baluk P, Srinivasan RS, Oliver G, McDonald DM. Plasticity of button-like junctions in the endothelium of airway lymphatics in development and inflammation. Am J Pathol 180:2561-75, 2012, PMID: 22538088; PMCID: PMC3378913.

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NIAID Asthma and Allergic Disease Cooperative Research Center Principal Investigator, Dean Sheppard Objective The major goal of this multi-project U19 Center Grant is to bring studies using human materials and genetically modified mice together in innovative ways in order to define the overlapping and distinctive roles for the cytokines IL-13 and IL-17 in airway pathology of relevance to human asthma. This U19 was successfully renewed after an initial five year funding period, to extend our total recognition as an AADCRC to 10 years. Specific Aims Over the past decade, work from several centers, including our own, has identified critical roles for the effector cytokines, IL-13 and IL-17, in multiple models of allergic asthma. Recent data demonstrating the effectiveness of IL-13 inhibition in a subset of patients with asthma confirms the importance of this cytokine in the human disease. The demonstration that circulating levels of IL-17 and circulating Th17 cells correlate with asthma severity also support a role for IL-17 in patients. It is now clear that IL-13 and IL-17 can be produced by multiple hematopoietic cells in the airways, but that they exert their major disease-producing effects by acting directly on resident airway cells – principally airway epithelial cells and airway smooth muscle. During the current funding period of this AADCRC, we have used mice engineered to mark cytokineproducing cells to identify key roles for innate helper cells (iH2 cells) and Th2 cells as early and sustained sources of IL-13 in allergic airways. We have also identified an important role for antigen-specific alpha-beta T cells as key effectors of airway hyperresponsiveness and demonstrated that IL-17A released by these cells acts directly on murine (and human) airway smooth muscle to enhance contractility through induction of the small GTPase, RhoA and its effector kinase, ROCK2. Finally, we have identified characteristic mRNA expression signatures and a large number of miRNAs differentially expressed in cytokine-stimulated airway epithelial cells, work that has allowed identification of a subset of patients with asthma (Th2 high) who respond favorably to treatment with IL-13 inhibitors. Work in the current funding period has strongly suggested that IL-13 and IL-17 act locally on airway epithelium and airway smooth muscle, and has pointed to the importance of identifying where and when each cytokine is made and released. It is also clear that we need to know which resident cells are the critical responders, and how these responses are regulated in individual patients. The current renewal is organized around 3 Projects driven by 3 Principle Investigators together with a Clinical Subjects and Biospecimen Core for standardizing the conjoined approaches. There are threee Specific Aims associated with the Grant: 1. To identify critical miRNAs that are differentially expressed in the airway epithelium of patients with asthma at baseline and in response to allergen challenge or corticosteroid treatment, to determine the roles of IL-13 and IL-17 in regulating these miRNAs and to identify miRNAs that mediate cytokine-induced mucous metaplasia. (PI: David Erle) 2. To determine the relative importance of responses of airway smooth muscle and epithelium to IL-17 in the induction of airway hyperresponsiveness and to determine the

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individual and combined effects of IL-13 and IL- 17 on airway smooth muscle contractility and on clinical responses of patients with severe and mild-to-moderate asthma and in response to allergen challenge. (PI: Dean Sheppard) 3. To determine the temporal and spatial dynamics of the interactions of IL-13 and IL-17 producing cells with antigen-presenting cells and with airway epithelium and airway smooth muscle in lung slices from allergen challenged mice and in human airway biopsies from patients with severe and mild-to-moderate asthma and in response to allergen challenge or treatment with corticosteroids. (PI: Matthew Krummel) The proposed studies will draw heavily from our large on-going clinical studies in patients with asthma and from the extensive experience of carefully collecting and utilizing biospecimens from these subjects by Prescott Woodruff, the PI and director of the Clinical Subjects and Biospecimen Core for the Grant. The work will benefit from the extensive experience with microarray and miRNA analysis and the study of mucous metaplasia in human airway epithelium by David Erle, Project Leader of Project 1. We will also benefit from the experience of Dean Sheppard, PI and Project Leader of Project 2 in functional assessment of airway smooth muscle from mice and humans. Finally, we will draw on pioneering approaches to intravital microscopy in lung slices and human airway tissue, developed by Max Krummel, the Project Leader of Project 3. Through our joint efforts, we hope to better understand the dynamics of cytokine release and effects in the asthmatic airway, to develop new strategies to identify clinically relevant sub-phenotypes in asthma, and to develop broadly useful methods to mark and dynamically follow antigen-specific T cell sub-types in readily accessible biopsies from patients with asthma. In addition to addressing the specific important questions raised by this proposal, we expect these methods to be widely useful to investigators in each of the other nationwide Asthma and Allergic Diseases Cooperative Research Centers and to other investigators interested in allergic airway diseases. Training and Integration with the Sandler Center This Center Grant provides training in basic biology and genetics of asthma for approximately post-doctoral fellows and graduate students working in the labs of the project directors. The leaders of each of the Projects and the Core are already actively involved in SABRE. Much of the preliminary data that served as the basis for this successful application was generated at least in part through support from SABRE. The studies using murine models of asthma that supplied preliminary data for project 2 were performed in the SABRE mouse physiology and morphology core and the human genetic studies were performed together with the SABRE human genetics core. Drs. Erle and Krummel, leaders of projects 1 and 3, have each received SABRE Innovative grants in the past that contributed to generation of the preliminary data supporting their project. The infrastructure developed with SABRE participation for the Airway Clinical Research Center provided a critical aspect of support for this grant. This Center grant would not have been likely to succeed without this extensive support from SABRE and thus represents a clear example of leveraging SABRE funds to further enhance research into the basic mechanisms underlying asthma.

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Approved Funding for this Award This program project provides between $1.1 and $1.2 million in direct costs per year for 5 years, with a total indirect and direct over the 5 years of $8,642,948.

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Sandler Asthma Basic REsearch Center

Contributions to Relevant Scientific Activities

                                           

CONTRIBUTIONS TO RELEVANT SCIENTIFIC ACTIVITIES

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Sandler Asthma Basic REsearch Center Immunology Seminar Series 2012-2013 Schedule Mondays, 9am Room: N-217

Date

Speaker

Host

September 10 September 17 September 24 October 1 October 8 October 15 October 22 October 29 November 5 November 12 November 19 November 26 December 3 December10 December 17 January 7 January 14 January 28 February 4 February 11 February 25 March 4 March 11 March 18 March 25 April 1 April 8 April 15 April 22 April 29 May 6 May 13

Amy Weinmann Christopher Garcia Thaddeus Stappenbeck Julie Zikherman Taka Okada Harry Greenberg Markus Müschen Paul Crocker Andre Veillette No Seminar Doreen Cantrell No Seminar Erin Adams Larry Samelson Glenn Dranoff Boris Reizis Mike Dustin Hozefa Bandukwala Emil Unanue Hugh Rosen Patrick Wilson David Underhill Ann Marshak-Rothstein Pam Schwatzberg Victor Engelhard Georg Lauer Judy Lieberman Kees Murre Judith Hellman - UCSF John O’Shea No Seminar Hidde Ploegh

Mark Ansel Lewis Lanier Averil Ma

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Mark Ansel Mike McCune Lowell Jason Cyster Cliff Lowell Art Weiss Frances Brodsky Art Weiss Lewis Lanier Anthony DeFranco Matthew Krummel Anthony DeFranco Jeoung-Sook Shin Matthew Krummel Jason Cyster Cliff Lowell Matthias Wabl Mark Ansel and Averil Ma Mark Anderson Mike McCune Averil Ma Averil Ma Ansel /Ma Art Weiss

Sandler Asthma Basic REsearch Center

UCSF PULMONARY RESEARCH CONFERENCE 2012-2013 Mondays, 5:00 pm - Parnassus HSW-303

Date 09/10/12 09/17/12 09/24/12 10/01/12 10/08/12 10/15/12 10/22/12 10/29/12 11/05/12 11/12/12 11/19/12 11/26/12 12/03/12 12/10/12 12/17/12 12/24/12 12/31/12 01/07/13 01/14/13 01/21/13 01/28/13 02/04/13 02/11/13 02/18/13 02/25/13 03/04/13 03/11/13 03/18/13 03/25/13 04/01/13 04/08/13 04/15/13 04/22/13 04/29/13 05/06/13 05/13/13 05/20/13 05/27/13 06/03/13 06/10/13 06/17/13 06/24/13

Talk 1 (Clinical) Anthony Shum

Talk 2 (Basic) Kamran Atabai

Ted Omachi

Nirav Bhakta

Moderator Luke Davis Dean Sheppard

Erin Gordon

Ed Ostrin

Hal Collard

Madori Kato-Maeda

Suzaynn Schick

Luke Davis

Jon Singer

Eric Seeley

Prescott Woodruff

Christina Yoon

Mike LaFemina

Luke Davis

Yvonne Huang

Aparna Sundaram

Prescott Woodruff

CVRI Retreat (no conf) Stephanie Christenson

Dario Barbone

James Frank

Holiday Neeta Thakur

Dara Torgerson

Mallar Bhattacharya

John Greenland

Shaopeng (Leo) Yuan

Mallar Bhattacharya

Rama Mallampalli, MD (Visiting Professor)

Prescott Woodruff

Nuala Meyer, MD (Assistant Professor from Pennsylvania sponsored by M.Matthay) Michael Matthay Neil Trivedi

Maria Del Mar Del Pino Yanes

Hal Collard

Winter holiday Winter holiday Landon King, MD (Visiting Professor) Charles Everett

Peter Haggie

James Frank Mallar Bhattacharya

Martin Luther King holiday (no conf) Fellows feedback (no conf) Julian Solway, MD (Visiting Professor) Robert Su

Vikash Bhagwandin

Luke Davis (cancel) Paul Wolters Prescott Woodruff

President's Day holiday (no conf) Bruce Levy, MD (Visiting Professor) Payam Nahid Kirsten Kangelaris Elizabeth Fair Chris Gignoux John Metcalfe Noah Zaitlen Misha Agarwal Xiang Xu Sam Oh

Josh Galanter Robert Blount

Luke Bonser Chun Chen Anirban Datta Andrew Vaughan Serpil Erzurum (Visiting Professor) Alexandra Greer Darrell Kotton, MD (Visiting Professor) Binh Diep Marrah Lachowicz-Scroggins Hassan Lemjabbar-Alaoui Mallar Bhattacharya ATS Conf (no conf) Memorial Day holiday (no conf) John Li Katherine Nishimura Fellows feedback (no conf) Year end party

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Luke Davis Hal Collard Hal Collard Paul Wolters Luke Davis Prescott Woodruff Prescott Woodruff James Frank Prescott Woodruff

Mallar Bhattacharya Mallar Bhattacharya

Sandler  Asthma  Basic  REsearch  Center      

 

SABRE Asthma Research Conference Schedule Location: 513 PARNASSUS AVENUE, HSE-1303 2nd Thursday of the Month for 2012 at 4 P.M. 2nd Monday of the Month for 2013 at 3 P.M.

Date

Presenter

9/13/2012

Limin Liu, PhD

10/11/2012

Chris Allen, PhD

11/8/2012

Max Krummel, PhD

12/13/2012

Esteban Burchard, MD, MPH

2/11/2013

Kamran Atabai, MD

3/11/2013

Mark Ansel, PhD

4/8/2013

John Fahy, MD

5/13/2013

Richard Locksley, MD

6/10/2013

Jeoung-Sook Shin, PhD

7/8/2013

David Erle, MD

8/12/2013

Laurence Cheng, MD, PhD

9/9/2013

Herbert DeBroski

10/14/2013

Prescott Woodruff, MD, MPH

11/18/2013

Dean Sheppard, MD

12/9/2013

Chris Allen, PhD

 

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Immunology Seminar Series "Imaging of cross-presenting dendritic cells in the lymph node”

Takaharu  Okada,  Ph.D.   Unit Leader, Research Unit for Immunodynamics Research Center for Allergy & Immunology Riken Japan

Monday,  October  8,  2012   9am,  Parnassus,  N-­‐‑225   Host:  Mark  Ansel  ([email protected])   BROADCAST  |  Mission  Bay,  Genentech  Hall  S-­‐‑271  §  /presentations/live  §  SPONSORS  |  Gladstone  Institute  of  Virology  &   Immunology  §  Rosalind  Russell  Medical  Research  Center  for  Arthritis  §  Sandler  Asthma  Basic  Research  Center,  SABRE  –   INFORMATION  (415)  502-­‐‑1961  http://www.ucsf.edu/immuno  Live  stream  and  archive  available  (UCSF  MyAccess  login  required)    

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Sandler Asthma Basic REsearch Center                                            

 

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Sandler Asthma Basic REsearch Center

Recent and New Publications

                                           

RECENT AND NEW PUBLICATIONS SUPPORTED BY THE SANDLER ASTHMA BASIC RESEARCH CENTER (2011-2013)  

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Christopher C.D. Allen, Ph.D. Beltman JB, Allen CDC, Cyster JG, de Boer RJ (2011). B cells within germinal centers migrate preferentially from dark to light zone. Proceedings of the National Academy of Sciences, 108(21), 8755-8760. PMCID: PMC3102384 Green JA, Suzuki K, Cho B, Willison LD, Palmer D, Allen CDC, Schmidt TH, Xu Y, Proia RL, Coughlin SR, Cyster JG (2011). The sphingosine 1-phosphate receptor S1P2 maintains the homeostasis of germinal center B cells and promotes niche confinement. Nature Immunology, 12(7), 672-680. PMCID: PMC3158008. Sullivan BM, Liang HE, Bando JK, Wu D, Cheng LE, McKerrow JK, *Allen CDC, *Locksley RM (2011). Genetic analysis of basophil function in vivo. Nature Immunology, 12(6), 527-535. *co-corresponding author. NIHMSID352031 Steiner DF, Thomas MF, Hu JK, Yang Z, Babiarz JE, Allen CDC, Matloubian M, Blelloch R, Ansel KM (2011). MicroRNA-29 Regulates T-Box Transcription Factors and Interferon-γ Production in Helper T Cells. Immunity, 35(2), 169-181. Yang Z, Sullivan BM, Allen CDC (2012). Fluorescent in vivo detection reveals that IgE+ B cells are restrained by an intrinsic cell fate predisposition. Immunity, in press, doi:10.1016/j.immuni.2012.02.009 K. Mark Ansel, Ph.D. Baumjohann D, Okada T, Ansel KM. Cutting Edge: Distinct Waves of BCL6 Expression during T Follicular Helper Cell Development. J Immunol.187:2089-92 (2011) Steiner DF, Thomas MF, Hu JK, Yang Z, Babiarz JE, Allen CD, Matloubian M, Blelloch R, Ansel KM. MicroRNA-29 Regulates T-Box Transcription Factors and Interferon-γ Production in Helper T Cells. Immunity 35:169-81 (2011) Sofi MH, Qiao Y, Ansel KM, Kubo M, Chang CH. Induction and Maintenance of IL-4 Expression Are Regulated Differently by the 3' Enhancer in CD4 T Cells. J. Immunol. 186:27929 (2011) Grégory Seumois, Pandurangan Vijayanand, Christopher J Eisley, Nada Omran, Lukas Kalinke, Mai North, Asha P. Ganesan, Laura J Simpson, Nathan Hunkapiller, Fleix Molzahan, Prescott G Woodruff, John V Fahy, David J Erle, Ratka Djukanovic, Robert Blelloch, K Mark Ansel: An integrated nano-scale approach to profile miRNAs in limited clinical samples. Am J Clin Exp Immuol. 1:70-89 (2012) Hoefig KP, Rath N, Heinz GA, Wolf C, Dameris J, Schepers A, Kremmer E, Ansel KM, Heissmeyer V. Eri1 degrades the stem-loop of oligouridylated histone mRNAs to induce replication-dependent decay. Nat Struct Mol Biol. 20:73-81 (2013) Solberg OD, Ostrin EJ, Love MI, Peng JC, Bhakta NR, Hou L, Nguyen C, Solon M, Nguyen C, Barczak AJ, Zlock LT, Blaev DP, Finkbeiner WE, Ansel KM, Arron JR, Erle DJ, Woodruff PG. Airway Epithelial miRNA Expression is Altered in Asthma. Am. J. Respir. Crit. Care Med. 186:965-74 (2012) Thomas MF, Abdul-Wajid S, Panduro M, Babiarz JE, Rajaram M, Woodruff P, Lanier LL, Heissmeyer , Ansel KM. Eri1 regulates microRNA homeostasis and mouse lymphocyte development and anti-viral fuction. Blood. 120:130-42 (2012) Vijayanand P, Seumois G, Simpson LJ, Abdual-Wajid S, Baumjohann D, Panduro M, Huang X, Interlandi J, Djuretic IM, Brown DR, Sharpe AH, Rao A, Ansel KM. Interleukin-4 Production y Follicular Helper T Cells Requires the Conserved Il4 Enhancer Hypersensitivity Site V. Immunity 36:175-87 (2012)

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Thornton EE, MR Looney, O Bose, D Sen, D Sheppard, RM Locksley, X Huang, MF Krummel. 2012. Spatiotemporally separated antigen uptake by alveolar dendritic cells and airway presentation to T cells in the lung. J Exp Med 209:1183-1199. PMC3371730 Price AE, RL Reinhardt, H-E Liang, RM Locksley. 2012. Marking and quantifying IL-17Aproducing cells in vivo. PLoS ONE 7:e39750. PMC3387253 Cheng LE, K Hartmann, A Roers, MF Krummel, RM Locksley. 2013. Perivascular mast cells dynamically probe cutaneous blood vessels to capture IgE. Immunity 38:166-175. PMC in process Oghumu S, R Dong, S Varikuti, T Shawler, T Kampfrath, CA Terrazas, C Lezama-Davila, BMM Ahmer, CC Whitacre, S Rajagopalan, R Locksley, AH Sharpe, AR Sataskar. 2013. Distinct populations of innate CD8 T cells revealed in a CXCR3 reporter mouse. J Immunol (in press). Molofsky AB, JC Nussbaum H-E Liang, SJ Van Dyken, LE Cheng, A Mohapatra, A Chawla, RM Locksley. 2013. Innate lymphoid type 2 cells ILC2) sustain visceral adipose tissue eosinophils and alternatively activated macrophages. J Exp Med (in press). PMC in process Van Dyken SJ, RM Locksley. 2013. Interleukin-4- and interleukin-13-mediated alternatively activated macrophages: roles in homeostasis and disease. Annu Rev Immunol 31:317-43. PMC in process Spits H, D Artis, M Colonna, A Diefenbach, JP Di Santo, G Eberl, S Koyasu, RM Locksley, ANJ McKenzie, RE Mebius, F Powrie, E Vivier. 2013. Innate lymphoid cells – a proposal for a uniform nomenclature. Nature Rev Immunol 13:145-149. PMC in process Heredia JE, L mukundan, FM Chen, AA Mueller, R Deo, RM Locksley, TA Radno, A Chawla. 2013. Type 2 innate signals regulate functionality of fibro/adipogenic progenitors to facilitate muscle regeneration. Cell (in press). William Seaman, M.D. Rebres, RA, Roach TIA, Fraser IDC, Philip F, Moon C, Lin KM, Liu J, Santat L, Cheadle L, Ross EM, Simon MI, Seaman WE: Synergistic Ca2+ responses by Gai- and Gaq-coupled Gprotein-coupled receptors require a single PLCb isoform that is sensitive to both Gbg and Gaq. J Biol Chem 286:1-10, 2011 Dean Sheppard, M.D. Spassov DS, Wong CH, Sergina N, Ahuja D, Fried M, Sheppard D, Moasser MM. A src-driven phosphotyrosine signaling switch determines the anchorage state of epithelial cells. Mol Cell Biol 2011 31:776-82. PMCID: PMC3028653 Su G, Atakilit A, Li T. J, Wu N, Bhattacharya M, Zhu J, Li E, Sun S, Chen R, Su C, Sheppard D. Integrin αvβ3 prevents vascular leak in mice by regulating cortical actin formation in endothelial cells. Am J Resp Crit Care Med 2012 (in press) Kudo M, Melton AC, Chen C, Engler M, Huang KE, Ren X, Wang Y, Bernstein X, Li J, Atabai K, Huang X, Sheppard D. IL-17A produced by ab T cells drives airway smooth muscle contraction. Nature Medicine 2012 (in press). Sugimoto K, Kudo M, Sundaram A, Ren X, Huang K, Bernstein X, Wang Y, Raymond WW, Erle D, Abrink M, Caughey GH, Huang X, Sheppard D. The avb6 integrin modulates airway hyperresponsiveness by regulating intra-epithelial mast cells. J Clin Invest 2012 (in press). Su G, Atakilit A, Li T. J, Wu N, Bhattacharya M, Zhu J, Li E, Sun S, Chen R, Su C, Sheppard D. Integrin αvβ3 prevents vascular leak in mice by regulating cortical actin formation in endothelial cells. Am J Resp Crit Care Med 2012 (in press)

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Giacomini M, Travis M, Sheppard D. Epithelial cells utilize cortical actin/myosin to activate latent TGF-β through integrin αvβ6-dependent physical force. Exp Cell Res 2012 318:716-22. PMID: 22309779. Chen C, Kudo M, Rutaganira F, Takano H, Lee C, Atakilit A, Robinett, KS, Uede T, Wolters P, Shokat KM, Huang X, Sheppard D. Integrin alpha9beta1 in airway smooth muscle regulates a novel brake on exaggerated murine and human airway narrowing J Clin Invest 2012 122:291627 PMID 22772469. Bhattacharya M, Su G, Su X, Oses-Prieto JA, Li JT, Huang X, Hernandez H, Atakilit A, Burlingame AL, Matthay M, Sheppard D. IQGAP1 is necessary for pulmonary vascular barrier protection in murine acute lung injury and pneumonia Am J Physiol: Lung Cell and Mol Biol 2012 303:L12-19 PMID: 22561460. Jeoung-Sook Shin Baravalle, G, Park, H, McSweeney, M, Ohmura-Hoshino, M, Matsuki, Y, Shin, JS. Ubiquitination of CD86 is a key mechanism in regulating antigen presentation by dendritic cells, J Immunology. 187:2966, 2011 Ma JK, Platt MY, Eastham-Anderson J, Shin JS*, and Mellman I*. MHC class II distribution in dendritic cells and B cells is determined by ubiquitin chain length, PNAS. 2012 May 7 [Epub ahead of print] Zhi-En Wang, M.D., M.S. Gordon E, S Sidhu, Z-E Wang, P Woodruff, S Yuan, M Solonm S Conway, X Huang, RM Locksley, J Fahy. 2012. A protective role for periostin and TGF-b in IgE-mediated allergy and airway hyperresponsiveness. Clin Exp Allergy 42: 144-155. PMC3271792 Arthur Weiss, M.D., Ph.D. Limnander A, Depeille P, Freedman TS, Liou J, Leitges M, Kurosaki T, Roose JP, and Weiss A. Stim1, PKCd, and RasGRP proteins set a threshold for pro-apoptotic Erk signaling during B cell development. Nat. Immunol., 12:425-433. 2011. PMID: 21441934 Zhu JW, Doan K, Park J, Chau AH, Zhang H, Lowell CA and Weiss A. Distinct functions of receptor-like tyrosine phosphatases CD45 and CD148 in chemoattractant-mediated neutrophil migration and response to S. aureus infection. Immunity. 35:757-769. 2011. PMID: 22078799 Zikherman J, Doan K, Parameswaran R, Raschke W, and Weiss A. Quantitative differences in CD45 expression unmask functions for CD45 in B-cell development, tolerance and survival. Proc. Natl. Acad. Sci. USA. ePub ahead of print. 2011. PMID: 22135465 Mukherjee S, Zhu J, Zikherman J, Parameswaran R, Kadlecek TA, Wang Q, Au-Yeung B, Ploegh H, Kuriyan J, Das J*, and Weiss A* Monovalent and multivalent ligation of the B cell receptor exhibit differential dependence upon Syk and Src family kinases. Sci. Signal. 2013. Jan 1;6(256):ra1 PMID: 23281368 *co-corresponding authors Zikherman J, Parameswaran R, Hermiston M, and Weiss A. The wedge domain of the receptorlike tyrosine phosphatase CD45 enforces B cell tolerance by regulating substrate specificity. J. Immunol., in press. 2013. Jonathan Weissman, Ph.D. Churchman LS, Weissman JS. (2011) Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature, 469: 368-73. PMID 21248844

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Ingolia NT, Lareau LF, Weissman JS. (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of Mammalian proteomes. Cell, 147: 789-802. PMC3225288 Oh E, Becker AH, Sandikci A, Huber D, Chaba R, Gloge F, Nichols RJ, Typas A, Gross CA, Kramer G, Weissman JS, Bukau B. (2011) Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell, 147: 1295-1308. PMID: 22153074 Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS. (2012) High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science, 335: 552-7. PMID 22194413 Li GW, Oh E, Weissman JS. (2012) The anti-Shine-Dalgamo sequence drives translational pausing and codon choice in bacteria. Nature, 484: 538-41. PMC3338875 Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. (2012) The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nature Protocols, 7: 1534-50. PMID 22836135 Carvunis AR, Rolland T, Wapinski I, Calderwood MA, Yildirim MA, Simonis N, Charloteaux B, Hidalgo CA, Barbette J, Santhanam B, Brar GA, Weissman JS, Regev A, Thierry-Mieg N, Cusick ME, Vidal M. (2012) Proto-genes and de novo gene birth. Nature, 487: 370-4. PMC3401362 Brandman O, Stewart-Ornstein J, Wong D, Larson A, Williams CC, Li GW, Zhou S, King D, Shen PS, Weibezahn J, Dunn JG, Rouskin S, Inada T, Frost A, Weissman JS. (2012) A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress. Cell, 151: 1042-54. PMID 23178123 Stern-Ginossar N, Weisburd B, Michalski A, Le VT, Hein MY, Huang SX, Ma M, Shen B, Qian SB, Hengel H, Mann M, Ingolia NT, Weissman JS. (2012) Decoding human cytomegalovirus. Science, 338: 1088-93. PMID 23180859 Zena Werb, M.D. Hong JS, KJ Greenlee, R Pitchumani, S-H Lee, L-z Song, M Shan, SH Chang, PW Park, C Dong, Z Werb, A Bidani, DB Corry & F Kheradmand (2011). Dual protective mechanisms of matrix metalloproteinases 2 and 9 in immune defense against Streptococcus pneumoniae. J. Immunol. 186:6427-6436. [2011 Apr 20, Epub ahead of print]. PMID: 21508260. Lemieux GA., J Liu, N Mayer, RJ Bainton, K Ashrafi & Z Werb (2011). A whole-organism screen identifies new regulators of fat storage. Nature Chem. Biol. 7: 206-213. [Mar 13. Epub ahead of print]. PMID: 21390037; PMCID: PMC3076723. Phillips JJ, A Ward, E Huillard, A Robinson, DH Lum, M-Y Polley, SD Rosen, DH Rowitch & Z Werb (2012). Heparan sulfate sulfatase SULF2 regulates PDGFRa signaling and growth in malignant glioblastoma. J. Clin. Invest. In press. Engelhardt JE, B Boldajipour, P Beemiller, P Pandurangi, C Sorenson, Z Werb, M Egeblad & MF Krummel. (2011). Marginating dendritic cells of the tumor microenvironment cross-present antigens and stably engage tumor-specific T cells. Cancer Cell. In press. Slorach EM, J Chou & Z Werb (2011). Zeppo1 is a novel metastasis promoter that represses Ecadherin expression and regulates p120-catenin isoform expression and localization. Genes Dev. 25: 471-484. [Epub ahead of print February 11, 2011]. PMCID: PMC3049288. Caudrillier A, K Kessenbrock, BM Gilliss, JX Nguyen, MB Marques, M Monestier, P Toy, Z Werb & MR Looney (2012). Platelets induce neutrophil extracellular traps in transfusion-related acute lung injury. J. Clin. Invest. 122(7):2661–2671. [Epub ahead of print, Jun 11]. PMID:

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22684106; PMCID: PMC3386815. Engelhardt J, B Boldajipour, P Beemiller, P Pandurangi, C Sorenson, Z Werb, M Egeblad & MF Krummel (2012). Marginating dendritic cells of the tumor microenvironment cross-present antigens and stably engage tumor-specific T cells. Cancer Cell. 21:402-417. PMID: 22439936; PMCID: PMC3311997. Littlepage LE, AS Adler, H Kouros-Mehr, G Huang, J Chou, SR Krig, OL Griffith, JE Korkola, K Qu, DA Lawson, Q Xue, MD Sternlicht, GJP Dijkgraaf, P Yaswen, Hope S Rugo, CA Sweeney, CC Collins, JW Gray, HY Chang & Z Werb (2012). The transcription factor ZNF217 is a prognostic biomarker and therapeutic target during breast cancer progression. Cancer Discov. 2:638-651 [Epub June 22]. PMID: 22728437. Nakasone E, HA Askautrud, T Kees, V Plaks, AJ Ewald, MG Rasch, YX Tan, J Qin, M Fein, J Park, P Sinha, MJ Bissell, E Frengen, Z Werb & M Egeblad (2012). Imaging tumor-stroma interactions during chemotherapy reveals microenvironmental contributions to chemoresistance. Cancer Cell. 21:488-503. PMCID: PMC3332002. Phillips JJ, A Ward, E Huillard, A Robinson, DH Lum, MY Polley, SD Rosen, DH Rowitch & Z Werb (2012). Heparan sulfate sulfatase SULF2 regulates PDGFRa signaling and growth in malignant glioblastoma. J. Clin. Invest. 122:911–922 [Epub Feb. 1]. PMID: 22293178; PMCID: PMC3287216. Chou J, JH Lin, A Brenot, JW Kim, S Provot & Z Werb (2013). GATA3 suppresses metastasis and modulates the tumor microenvironment by regulating miR-29 expression. Nat. Cell Biol. In press. Prescott Woodruff Choy DF, Modrek B, Abbas AR, Kummerfeld S, Clark HF, Wu LC, Fedorowicz G, Modrusan Z, Fahy JV, Woodruff PG, Arron JR. Gene expression patterns of th2 inflammation and intercellular communication in asthmatic airways. J Immunol. 2011 Feb 1;186(3):1861-9. Woodruff PG, Albert RK, Bailey WC, Casaburi R, Connett JE, Cooper JAD, Criner GJ, Curtis JL, Dransfield MT, Han MK, Harnden SM, Kim V, Marchetti N, Martinez FJ, McEvoy CE, Niewoehner DE, Reilly JJ, Rice K, Scanlon PD, Scharf SM, Sciurba FC, Washko GR, Lazarus SC for the COPD Clinical Research Network. Randomized Trail of Zileuton for Treatment of COPD Exacerbations Requiring hospitalization. COPD. 2011 Feb:8(1):21-9. PMC Journal – In Process Bhakta NR, Woodruff PG. Human Asthma Phenotypes: From the Clinic, to Cytokines, and Back Again Immunol Rev. 2011 Jul;242(1):220-32. Koth LL, Solberg OD, Peng JC, Bhakta NR, Nguyen DCP, Woodruff PG. Sarcoidosis Blood Transcriptome Reflects Lung Inflammation and Overlaps with Tuberculosis. AM J Respir Crit Care Med. 2011 Aug 18. [Epub ahead of print] Albert RK, Connett J. Bailey WC, Casaburi R, Cooper JAD, Criner GJ, Curtis JL. Dransfield MT, Han MK, Lazarus SC, Make B, Marchetti N. Martinez FJ, Madinger NA, McEvoy C, Niewoehner DE, Porsasz J, Price CS, Reilly J, Scanlon PD, Sciurba FC, Scaharf SM, Washko GR, Woodruff PG, and Anthonisen NR, for the COPD Clinical Research Network. Azithromycin for Prevention of Exacerbations of COPD. N Engl J Med 2011; 365:689-698 Gordon ED, Sidhu SS, Wang ZE, Woodruff PG, Yuan S, Solon MC, Conway SJ, Huang X, Locksley RM, Fahy JV. A protective role for periostin and TGF-β in IgE-mediated allergy and airway hyper-responsiveness. Clin Exp Allergy. 2012 Jan;42(1):144-55.

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Eri1 regulates microRNA homeostasis and mouse lymphocyte development and antiviral function. Thomas MF, Abdul-Wajid S, Panduro M, Babiarz JE, Rajaram M, Woodruff P, Lanier LL, Heissmeyer V, Ansel KM. Blood. 2012 Jul 5;120(1):130-42. Epub 2012 May 21. Jia G, Erickson RW, Choy DF, Mosesova S, Wu LC, Solberg OD, Shikotra A, Carter R, Audusseau S, Hamid Q, Bradding P, Fahy JV, Woodruff PG, Harris JM, Arron JR; Bronchoscopic Exploratory Research Study of Biomarkers in Corticosteroid-refractory Asthma (BOBCAT) Study Group. Periostin is a systemic biomarker of eosinophilic airway inflammation in asthmatic patients. J Allergy Clin Immunol. 2012 Sep;130(3):647-654 Solberg OD, Ostrin EJ, Love MI, Peng JC, Bhakta NR, Hou L, Nguyen C, Solon M, Nguyen C, Barczak AJ, Zlock LT, Blagev DP, Finkbeiner WE, Ansel KM, Arron JR, Erle DJ, Woodruff PG. Airway Epithelial miRNA Expression is Altered in Asthma. Am J Respir Crit Care Med. 2012 Sep 6. [Epub ahead of print] Huang F, Zhang H, Wu M, Yang H, Kudo M, Peters CJ, Woodruff PG, Solberg OD, Donne ML, Huang X, Sheppard D, Fahy JV, Wolters PJ, Hogan BL, Finkbeiner WE, Li M, Jan YN, Jan LY, Rock JR. Calcium-activated chloride channel TMEM16A modulates mucin secretion and airway smooth muscle contraction. Proc Natl Acad Sci USA. 2012 Sep 17. [Epub ahead of print]

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Sandler Asthma Basic REsearch Center                                            

 

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Looking to the Future Richard M. Locksley, M.D. The SABRE Center is evolving into a more mature entity. All but one of the recruited faculty/fellow has obtained R01 NIH funding (the one exception has re-submitted with a very close score and received bridge funding from the School of Medicine based on promise of future success), the first recruit has been promoted to Associate Professor and the second, Mark Ansel, was just put up for promotion this summer. The Fellow, Dr. Allen, was recruited to the faculty at the Cardiovascular Research Institute at Mission Bay and will begin to anchor asthma-related research at that site. The first postdocs and graduate students have left to assume positions after training in the SABRE Center. The SABRE Center is recognized nationally by virtue of participation in each of the major asthma multi-institutional efforts of the NIH, including as a member of AsthmaNet (under the leadership of Homer Boushey), the Severe Asthma Research Program (SARP; under the leadership of John Fahy) and the Asthma and Allergic Diseases Cooperative Research Center Network (under the leadership of Dean Sheppard). Members of the SABRE Center were awarded a Program Project Grant to investigate the role of innate lymphoid cells in human asthma (Fahy, Locksley, Ansel, Woodruff). Extramural funding brought in solely by the 5 core basic investigators has more than doubled over the past 5 years; the totals accrued to the entire program have been leveraged to an even greater extent. The conferences and seminars are well attended and publicized. Thus, by a number of metrics, asthma-centered research is now well established and recognized at UCSF. Given the current political climate, it is likely that continued government support for health sciences will be capped or decline, such that unlimited growth from this sector will not be possible. Although we continue to compete aggressively in this arena, prioritizing research dollars from the Foundation will become increasingly important. Highly successful focused research models from the past, such as Bell Laboratories or the Cavendish laboratory at Cambridge University, reveal several commonalities, including small laboratories with a shared research goal; technological innovation; and an ability to change directions quickly to follow-up new insights. Some of these aspects we share, but re-evaluating our strategies will be an important component for moving forward successfully. Ultimately, the SABRE Center will need to move more comprehensively to studies on human patients utilizing human tissues; will need to capture more individuals like Chris Allen early in science when they can be attracted into the field in a lasting and substantive way; will need to move seamlessly into ‘big science’ technologically-driven fields at low cost, necessitating an interactive and integrated group of scientists; will need to partner with industry in ways to move scientific understanding towards interventional efforts that remain cost-prohibitive for a small Center; and will need to grow an endowed financial base that will enable nimble re-direction and follow-up using competitive priorities to fund shifting emergent needs for equipment, personnel (including visiting scientists) and short-term needs in response to windows of opportunity. Funding fixed Cores may not be an optimal resource allocation, as technology advances, cores become increasingly mainstreamed and publicly available, and costs continue to decrease. In short, with the help of both the Executive Board and the Scientific Advisory Board, the

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SABRE Center will work to develop a Strategic Plan in order to shape the research and financial priorities for the coming decade. Our hope is to continue the trajectory established by the last 5 years on a pathway of increasing success in our mission to understand and ultimately conquer asthma. These challenges we take seriously for the future in order to honor the extraordinary vision of the Sandler family in committing resources to asthma basic research at UCSF. We are most grateful for the opportunity to respond to the challenge and look forward to discoveries that will impact this increasingly prevalent disease of humans.

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Sandler Asthma Basic REsearch Center

Biographical sketches

                                       

BIOGRAPHICAL SKETCHES  

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BIOGRAPHICAL SKETCHES Christopher Allen, Ph.D. K. Mark Ansel, Ph.D. Homer Boushey, M.D. Esteban Burchard, M.D., M.P.H. George Caughey, M.D. Harold Chapman, M.D. Anthony DeFranco, Ph.D. David Erle, M.D. John Fahy, M.D., M.Sc. Xiaozhu Huang, M.D., M.S. Matthew Krummel, Ph.D. Limin Liu, Ph.D. Richard Locksley, M.D. William Seaman, M.D. Dean Sheppard, M.D. Jeoung-Sook Shin, Ph.D Zhi-En Wang, M.D., M.S. Arthur Weiss, M.D., Ph.D. Jonathan Weissman, PhD. Zena Werb, PhD. Prescott Woodruff, M.D., M.P.H.

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BIOGRAPHICAL SKETCH NAME Christopher David Caballero Allen, Ph.D.

POSITION TITLE Sandler-Newmann Foundation UCSF Fellow in Asthma Research

EDUCATION/TRAINING INSTITUTION AND LOCATION

DEGREE

YEAR(s)

FIELD OF STUDY

Massachusetts Institute of Technology University of California, San Francisco University of California, San Francisco

B.S. Ph.D. Postdoctoral aralral

2001 2007 2007

Biology Biomedical Immunology Sciences

Positions and Honors 1998-2000 2000 2001-2007 2007 2007–2012

2012 – Present

1994-1995 1997 1998 1999, 2000 2001 2001 2001–2002

Summer Research Intern, Department of Molecular and Cellular Pharmacology, Isis Pharmaceuticals, Carlsbad, CA Undergraduate Student Researcher, Laboratory of Herman Eisen, Center for Cancer Research, Massachusetts Institute of Technology Graduate Student Researcher, Laboratory of Jason Cyster, Biomedical Sciences Graduate Program and Immunology Graduate Program, University of California, San Francisco, CA Postdoctoral Scholar, Laboratory of Jason Cyster, Department of Microbiology and Immunology, University of California, San Francisco Sandler-Newmann Foundation UCSF Fellow in Asthma Research, Sandler Asthma Basic Research Center and the Department of Microbiology and Immunology, University of California, San Francisco, CA Assistant Professor Cardiovascular Research Institute, Department of Anatomy and Department of Microbiology and Immunology, Sandler Asthma Basic Research Center, University of California, San Francisco National Science Foundation Young Scholars Program Fellowship National Hispanic Scholar San Diego Biotech Employee Development Coalition (BEDC) Scholarship Academic Excellence Award, Office of Minority Education, Massachusetts Institute of Technology Phi Beta Kappa Whitehead Prize in Biomedical Research University of California Regents Fellowship

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2002–2007 2010 2012

Howard Hughes Medical Institute Predoctoral Fellowship Seminars in Immunology Top Cited Article 2008-2010 NIH Director’s New Innovator Award

Selected peer-reviewed publications (in chronological order) 1. Allen C.D.C., Ansel K.M., Low C., Lesley R., Tamamura H., Fujii N. Cyster J.G. (2004). Germinal center dark and light zone organization is mediated by CXCR4 and CXCR5. Nature Immunology, 5(9), 943-952. 2. Chen T.T., Li L., Chung D.H., Allen C.D.C., Torti S.V., Torti F.M., Cyster J.G., Chen C.Y., Brodsky F.M., Niemi E.C., Nakamura M.C., Seaman W.E., Daws M.R. (2005). TIM-2 is expressed on B cells and in liver and kidney and is a receptor for H-ferritin endocytosis. The Journal of Experimental Medicine, 202(7), 955-965. PMC2213179. 3. Allen C.D.C., Okada T., Tang H.L., Cyster J.G. (2007). Imaging of germinal center selection events during affinity maturation. Science, 315(5811), 528-531. 4. *Allen C.D.C., *Okada T., *Cyster J.G. (2007). Germinal-center organization and cellular dynamics. Immunity 27(2), 190-202. *co-corresponding author. PMCID: PMC2242846. 5. Haynes N.M., Allen C.D.C., Lesley R., Ansel K.M., Killeen N., and Cyster J.G. (2007). Role of CXCR5 and CCR7 in follicular Th cell positioning and appearance of a programmed cell death gene-1High germinal center-associated subpopulation. The Journal of Immunology, 179(8), 5099-5108. 6. *Allen C.D.C., *Cyster J.G. (2008). Follicular dendritic cell networks of primary follicles and germinal centers: phenotype and function. Seminars in Immunology 20(1), 14-25. *cocorresponding author PMCID: PMC2366796. 7. Sullivan B.M., Liang H.E., Bando J.K., Wu D., Cheng L.E., McKerrow J.K., *Allen C.D.C., *Locksley R.M. (2011). Genetic analysis of basophil function in vivo. Nature Immunology, 12(6), 527-535. *co-corresponding author. PMCID: 3271435. 8. Beltman J.B., Allen C.D.C., Cyster J.G., de Boer R.J. (2011). B cells within germinal centers migrate preferentially from dark to light zone. Proceedings of the National Academy of Sciences, 108(21), 8755-8760. PMCID: PMC3102384. 9. Green J.A., Suzuki K., Cho B., Willison L.D., Palmer D., Allen C.D.C., Schmidt T.H., Xu Y., Proia R.L., Coughlin S.R., Cyster J.G. (2011). The sphingosine 1-phosphate receptor S1P2 maintains the homeostasis of germinal center B cells and promotes niche confinement. Nature Immunology, 12(7), 672-680. PMCID: PMC3158008. 10. Steiner D.F., Thomas M.F., Hu J.K., Yang Z., Babiarz J.E., Allen C.D.C., Matloubian M., Blelloch R., Ansel K.M. (2011). MicroRNA-29 Regulates T-Box Transcription Factors and Interferon-γ Production in Helper T Cells. Immunity, 35(2), 169-181. PMCD: PMC3361370. 11. Yang Z., Sullivan B.M., Allen C.D.C. (2012). Fluorescent in vivo detection reveals that IgE+ B cells are restrained by an intrinsic cell fate predisposition. Immunity, 36(5), 857-872.

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Research Support Ongoing Research Support 1 DP2 HL117752-01 Allen (PI) 09/30/2012 – 08/31/2017 NIH/NHLBI Cellular interactions in asthma This project is focused on the dynamic communication among inflammatory cells in asthmatic lungs. The major goals of this project are to develop technical approaches to simultaneously visualize multiple different types of inflammatory cells in the lung, followed by characterization of relevant cellular interactions in a combinatorial fashion, and then definition of the stromal microenvironments in which these interactions occur. Role: PI 1 R01 AI103146-01 Allen (PI) 12/01/2012 – 11/30/2017 NIH/NIAID Analysis of basophil function in secondary immune responses The major goal of this project is to determine the functional role of basophils that have captured antigen via IgE antibodies in secondary immune responses. Specifically, this project will determine whether basophils contribute to antigen transport, to the enhancement of adaptive immunity, and to tissue damage and repair. Role: PI Completed Research Support None

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BIOGRAPHICAL SKETCH NAME K. Mark Ansel eRA COMMONS USER NAME

POSITION TITLE Assistant Professor of Microbiology and Immunology

anselm

EDUCATION/TRAINING INSTITUTION AND LOCATION

DEGREE

YEAR(s)

FIELD OF STUDY

Virginia Tech (Blacksburg, VA) University of California, San Francisco Immune Disease Institute, Harvard Medical School

B.S. Ph.D.

1992-1996 1996-2001 2001-2007

Biochemistry Biomedical Sciences Immunology

Positions 2001 – 2005 2005 – 2007 2008 – Present

Postdoctoral Fellow, Immune Disease Institute (p.k.a. Center for Blood Research), Harvard Medical School, Boston, MA Instructor, Department of Pediatrics, Children’s Hospital and Immune Disease Institute (p.k.a. Center for Blood Research), Harvard Medical School, Boston, MA Assistant Professor, Department of Microbiology and Immunology and Sandler Asthma Basic Research Center, University of California San Francisco

Other Experience and Professional Memberships 1998 2006 2007 2011 2011 2012 -

American Association for the Advancement of Science American Association of Immunologists International Cytokine Society Board of Reviewing Editors, Science Signaling International Predoctoral Fellows Review Cmte., Howard Hughes Medical Institute NIH peer review committee: Cellular & Molecular Immunology B, ad hoc reviewer

Awards and Honors 1997 – 2001 2001 – 2004 2005 – 2007 2006

Howard Hughes Medical Institute Predoctoral Fellowship Damon Runyon Cancer Research Fund Postdoctoral Fellowship Leukemia and Lymphoma Society Special Fellow Burroughs Wellcome Career Award in Biomedical Sciences

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2007 2009 2012 2012

International Cytokine Society Outstanding Postdoctoral Fellow Dana Foundation Human Immunology Scholar American Association of Immunologists Young Investigator Travel Award Leukemia & Lymphoma Society Scholar

Selected Peer-reviewed Publications 1. Grégory Seumois, Pandurangan Vijayanand, Christopher J Eisley, Nada Omran, Lukas Kalinke, Mai North, Asha P. Ganesan, Laura J Simpson, Nathan Hunkapiller, Fleix Molzahan, Prescott G Woodruff, John V Fahy, David J Erle, Ratka Djukanovic, Robert Blelloch, K Mark Ansel: An integrated nano-scale approach to profile miRNAs in limited clinical samples. Am J Clin Exp Immuol. 1:70-89 (2012) 2. Hoefig KP, Rath N, Heinz GA, Wolf C, Dameris J, Schepers A, Kremmer E, Ansel KM, Heissmeyer V. Eri1 degrades the stem-loop of oligouridylated histone mRNAs to induce replication-dependent decay. Nat Struct Mol Biol. 20:73-81 (2013) 3. Solberg OD, Ostrin EJ, Love MI, Peng JC, Bhakta NR, Hou L, Nguyen C, Solon M, Nguyen C, Barczak AJ, Zlock LT, Blaev DP, Finkbeiner WE, Ansel KM, Arron JR, Erle DJ, Woodruff PG. Airway Epithelial miRNA Expression is Altered in Asthma. Am. J. Respir. Crit. Care Med. 186:965-74 (2012) 4. Thomas MF, Abdul-Wajid S, Panduro M, Babiarz JE, Rajaram M, Woodruff P, Lanier LL, Heissmeyer , Ansel KM. Eri1 regulates microRNA homeostasis and mouse lymphocyte development and anti-viral fuction. Blood. 120:130-42 (2012) 5. Vijayanand P, Seumois G, Simpson LJ, Abdual-Wajid S, Baumjohann D, Panduro M, Huang X, Interlandi J, Djuretic IM, Brown DR, Sharpe AH, Rao A, Ansel KM. Interleukin-4 Productio y Follicular Helper T Cells Requires the Conserved Il4 Enhancer Hypersensitivity Site V. Immunity 36:175-87 (2012) 6. Baumjohann D, Okada T, Ansel KM. Cutting Edge: Distinct Waves of BCL6 Expression during T Follicular Helper Cell Development. J Immunol.187: 2089-92 (2011) 7. Steiner DF, Thomas MF, Hu JK, Yang Z, Babiarz JE, Allen CD, Matloubian M, Blelloch R, Ansel KM. MicroRNA-29 Regulates T-Box Transcription Factors and Interferon-γ Production in Helper T Cells. Immunity 35:169-81 (2011) 8. Sofi MH, Qiao Y, Ansel KM, Kubo M, Chang CH. Induction and Maintenance of IL-4 Expression Are Regulated Differently by the 3' Enhancer in CD4 T Cells. J. Immunol. 186:2792-9 (2011) 9. Thomas MF, Ansel KM. Construction of small RNA cDNA libraries for deep sequencing. Methods Mol Biol. 667:93-111 (2010) 10. Parameswaran P, Sklan E, Wilkins C, Burgon T, Samuel MA, Lu R, Ansel KM, Heissmeyer V, Einav S, Jackson W, Doukas T, Paranjape S, Polacek C, Barreto dos Santos F, Jalili R, Babrzadeh F, Gharizadeh B, Grimm D, Kay M, Koike S, Sarnow P, Ronaghi M, Ding SW, Harris E, Chow M, Diamond MS, Kirkegaard K, Glenn JS, Fire AZ. Six RNA Viruses and Forty-One Hosts: Viral Small RNAs and Modulation of Small RNA Repertoires in Vertebrate and Invertebrate Systems. PLoS Pathog. 6:e1000764 (2010)

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11. Ansel KM#, Pastor WA, Rath N, Lapan AD, Glasmacher E, Wolf C, Smith LC, Papadopoulou N, Lamperti E, Tahiliani M, Ellwart JW, Shi Y, Kremmer E, Rao A, Heissmeyer V#. Mouse ERI-1 interacts with the ribosome and catalyzes 5.8S rRNA processing. Nat. Struct. Mol. Biol. 15:523-30 (2008) (#corresponding authors, equal contribution) 12. Haynes NM, Allen CD, Lesley R, Ansel KM, Killeen N, Cyster JG. Role of CXCR5 and CCR7 in Follicular Th Cell Positioning and Appearance of a Programmed Cell Death Gene 1 High Germinal Center-Associated Subpopulation. J. Immunol. 179:5099-108 (2007) 13. Thai TH, Calado DP, Casola S, Ansel KM, Xiao C, Xue Y, Murphy A, Frendewey D, Valenzuela D, Kutok JL, Schmidt-Supprian M, Rajewsky N, Yancopoulos G, Rao A, Rajewsky K. Regulation of the germinal center response by microRNA-155. Science 316:604-8 (2007) 14. Djuretic IM, Levanon D, Negreanu V, Groner Y, Rao A, Ansel KM. T-bet and Runx3 cooperate to activate Ifng and silence Il4 in Th1 cells. Nat. Immunol. 8:145-53 (2007) 15. Ansel KM, Djuretic I, Tanasa B, Rao A. Regulation of Th2 differentiation and the IL4 locus. Annu. Rev. Immunol. 24:607-56 (2006) 16. Bronevetsky Y, Villarino AV, Eisley C, Barbeau R, Barczak A, Heinz GA, Kremmer E, Heissmeyer V, McManus MT, Erle DJ, Rao A, Ansel KM. T cell activation induces proteasomal degradation of Argonaute and rapid remodeling of the micro RNA repertoire. J. Exp. Med., in press. 17. Baumjohann D, Clingan JM, de Kouchkovsky D, Bannard O, Bluestone JA, Matloubian M, Ansel KM#, Jeker LT#. The microRNA cluster miR-17-92 is essential for follicular helper T cell differentiation. Under revision at Nature Immunology (#co-corresponding authors). Research Support Ongoing Research Support 1PO1HL107202 Fahy (PI) 8/15/12 – 5-31-17 NIH/NHLBI Innate and adaptive immune responses in Th2-high asthma (PI Dr. John Fahy, co-director UCSF ACRC) Project 2: Role of miRNAs in Th2-Driven inflammation in Asthma (Project Leader Ansel) Project 3: Mechanisms of airway Th2 inflammation in asthma (Project Leader Fahy, Co- project Leader, Ansel). The major goal of this PPG is to elucidate cellular and molecular mechanisms underlying the initiation and maintenance of Th2-high asthma. The goals of Project 2 are to identify miRNAs that regulate helper T cell functions relevant to asthma, to discover asthma associated T cell miRNA expression patterns in clinical samples, and to determine the mRNA targets and in vivo role of miR-29 in mouse model of asthma. My role in aim 3 is immunophenotyping of innate helper type II cells in human asthma. Role: Project 2 Leader, Project 3 co-project leader 1R01HL109102-01 Ansel (PI) 8/1/11 – 6/30/16 NIH/NHLBI Role of miRNAs in Th2-driven inflammation in asthma

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The major goals of this project are to discover asthma-associated T cell miRNA expression patterns in clinical samples, and to identify and characterize the in vivo activity of miRNAs that regulate helper T cell functions relevant to asthma. The project will be conducted in collaboration with co-investigator Dr. Prescott Woodruff, co-director of the UCSF Airway Clinical Research Center. LLS Scholar Award Ansel (PI) 7/1/12 – 6/30/17 Leukemia & Lymphoma Society MicroRNA regulation of lymphocyte growth and effector functions This career development program award would support our research program focus on miRNAs that regulate essential helper T cell functions that contribute to immunity, immunopathology, and immune malignancies. In particular, we aim to identify and characterize miRNAs that regulate helper T cell growth, survival, and cytokine production. Pending Research Support 1R21AI105270 Ansel (PI) 7/1/13 – 6/30/15 NIH/NIAID Molecular mechanisms of Eri1 regulation of antiviral immunity The major goals of this project is to elucidate the molecular mechanisms by which the exoribonuclease Eri1 controls antiviral immune responses mediated by T and NK lymphocytes. Genetic and biochemical approaches will be used to determine the contribution of direct effects on mRNA stability and translation and the indirect effects of Eri1 regulation of microRNA homeostasis. Role: PI 1U19 CA179512 Blelloch (PI) 7/1/13 – 6/30/18 NIH/Director’s Office In Vivo Regulated Release and Function of Extracellular Small RNAs This U19 Center’s long-term goal is to uncover paradigms of extracellular small RNA function in health and disease and apply those paradigms to clinically relevant settings including biomarker discovery and therapeutic intervention. As leader of Project 1, I will conduct studies to test the central hypothesis that immune cells release ex-miRNAs in response to inflammatory stimuli, and that this process is critical for their immune function. Completed Research Support 1R56AI089828-01 Ansel (PI) 9/1/10 – 7/31/11 NIH/NHLBI Regulation of miRNA expression during helper T cell differentiation The goal of these studies is to dissect the mechanisms that govern changes in miRNA expression during the activation of T lymphocytes, and to define how the global regulation of miRNA homeostasis affects T cell activation and immune function.

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Human Immunology Scholars Program Ansel (PI) 2/1/09 – 1/31/12 Dana Foundation MicroRNA regulation of helper T cell function in asthma The major goals of this proposal are to optimize technology for miRNA profiling by qPCR and perform a pilot study of miRNA expression in a small set of clinical samples, to develop a lentiviral miRNA expression library for studies of miRNA function in T cells, and to develop systems for miRNA inhibitor testing in lung explants.

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BIOGRAPHICAL SKETCH NAME Homer A. Boushey, Jr., M.D. eRA COMMONS USER NAME Boushey

POSITION TITLE Professor of Medicine

EDUCATION/TRAINING INSTITUTION AND LOCATION

DEGREE

YEAR(s)

FIELD OF STUDY

Stanford University, Palo Alto, CA University of California, San Fancisco, CA University of California, San Francisco, CA Beth Israel Hospital, Boston, MA Oxford University, Oxford, England

A.B. M.D. Reside ncy Reside ncy Fellow ship

1964 1968 1970 1971 1972

Biology Medicine Internal Medicine Internal Medicine Pulmonary Medicine

Positions and Honors 1974-1981 1981-1987 1986- Present 1987-1989 1989-Present 1989-1995 1996-2009

Assistant Professor of Medicine in Residence, University of California, San Francisco. Associate Professor of Medicine in Residency, University of California, San Francisco. Member, Senior Staff, Cardiovascular Research Institute, University of California, San Francisco Professor of Medicine in Residence, University of California, San Francisco. Professor of Medicine, University of California, San Francisco. Vice Chairman for Clinical Affairs, Department of Medicine, University of California, San Francisco Chief, Allergy/Immunology Division, Department of Medicine, University of California, San Francisco

Medical Licenses and Board Certification California License Number A 023453 American Board of Internal Medicine, June 1972 Subspecialty Board of Pulmonary Medicine, October 1974

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Medical Society Memberships 2003-May 2004

Past-President - American Thoracic Society California Thoracic Society American Federation for Clinical Research American Physiological Society California Academy of Medicine Western Society for Clinical Investigation Western Association of Physicians

Honors and Awards 1964 1967 1964-1968 1968 1977 1988, ’90, ’95, 99, 2000 1993 1993 1996 1997-2000 2000

Phi Beta Kappa AOA Regents' Scholar Gold-Headed Cane Recipient H. J. Kaiser Award for Excellence in Teaching Faculty-Student Teaching Award for "An Outstanding Lecture" Clean Air Award (Education/Research), American Lung Association, San Francisco California Medal, American Lung Association-California UCSF Alumnus of the Year Award Bay Area’s Best Physicians, San Francisco Focus Magazine Medical Student Teaching Award: “An Outstanding Clinical Correlation Lecturer”

Selected peer-reviewed publications (in chronological order) 1. Fahy JV, Wong H, Liu J, Boushey HA. Comparison of samples collected by sputum induction and bronchoscopy from asthmatic and healthy subjects. Am J Respir Crit Care Med 1995;152:53-58. 2. Fahy JV, Kim KW, Liu J, Boushey HA. Prominent neutrophilic inflammation in sputum from subjects with asthma exacerbation. J Allergy Clin Immunol 1995;95(4): 843-852. 3. Drazen JM, Israel E, Boushey HA, Chinchilli VM, Fahy JV, Fish JE, Lazarus SC, Lemanske RF, Martin RJ, Peters SP, Sorkness C, Szefler SJ, for the National Heart, Lung, and Blood Institute’s Asthma Clinical Research Network. Comparison of regularly scheduled with as-needed use of albuterol in mild asthma. N Engl J Med 1996; 335:841- 47. 4. Fahy JV, Fleming HE, Wong HH, Liu JT, Su JQ, Reimann J, Fick RB, Boushey HA. The effect of an anti-IgE monoclonal antibody on the early and late phase responses to allergen inhalation in asthmatic subjects. Am J Respir Crit Care Med 1997; 155:1828-34. 5. Fleming HE, Little FF, Schnurr D, Avila PC, Wong H, Liu J, Yagi S, Boushey HA. Rhinovirus-16 colds in healthy and asthmatic subjects: similar changes in upper and lower airways. Am J Respir Crit Care Med 1999; 160:100-8.

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6. Lazarus S, Boushey H, Fahy J, Chinchilli V, Lemanske R, Sorkness C, Kraft M, Fish J, Peters S, Craig T, Drazen J, Ford J, Israel E, Martin R, Mauger E, Nachman S, Spahn J, Szefler S, and the Asthma Clinical Research Network. A randomized study of longacting beta-agonist in patients with persistent asthma: I. monotherapy? JAMA 2001 May; 23; 285: 2583-93. 7. Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, DeRisi JL. Microarray-based detection and genotyping of viral pathogens. PNAS-2002; 99:1568792. 8. Lopez-Souza N, Dolganov G, Dubin R, Sporer H, Yagi S, Schurr D, Boushey H, et al. Resistance of Differentiated human airway epithelium to infection by rhinovirus. Am J Physiol Lung Cell Mol Physiol. 2004 Feb; 286: L373-81. 9. Boushey HA, Sorkness CA, King TS, Sullivan SD, Fahy JV, Lazarus SC, et al. “Daily versus As-Needed Corticosteroids for Mild Persistent Asthma” New Eng J Med, 2005; 352:1519-28. 10. Stoloff SW, Boushey HA. Severity, Control, and Responsiveness in Asthma. J Allergy Clin Immunol 2006: 117:544-8 (“Rostrum”) 11. Kistler A, Avila PC, Rouskin S, Wang D, Ward T, Yagi S, Schnurr D, Ganem D, DeRisi J, Boushey HA. “Pan-viral screening of respiratory tract infections in asthmatic and nonasthmatic adults reveals unexpected coronavirus and human rhinovirus diversity” J Infect Dis. 2007 Sep 15:196(6):817-25 12. Kistler A, Webster D, Rouskin S, Magrini V, Credle J, Schnurr D, Boushey HA, Mardis E, Li H, DeRisi JL. “Genome-wide diversity and selective pressure in the human rhinovirus.” Virol J. 2007 May 3; 4:40. 13. Huang YJ, Nelson CE, Brodie EL, DeSantis TZ, Baek MS, Liu J, Woyke T, Allaier M, Bristow J, Wiener-Kronish JP, Sutherland ER, King TS, Icitovic N, Martin RJ, Calhoun WJ, Castro M, Denlinger LC, DimangoE, Kraft M, Peters SP, Wasserman SI, Wechsler ME, Boushey HA, and Lynch SV. Airway microbiota andbronchial hyperresponsiveness in patients with sub-optimally controlled asthma. JACI 2011; 127:372-381. 14. Wootton SC, Kim DS, Kondoh Y, Chen E, Lee JS, Song JW, Huh JW, Taniguchi H, Chiu C, Boushey HA, Lancaster LH, Wolters PJ, Derisi J, Ganem D, Collard HR. “Viral Infection in Acute Exacerbation of Idiopathic Pulmonary Fibrosis.” Am J Respir Crit Care Med. 2011 Feb 25 15. Calhoun WJ, Ameredes BT, King TS, Boushey HA. “Comparison of physician-based, biomarker-based, and symptom-based strategies for adjustment of inhaled corticosteroid therapy in adults with asthma: The Basalt Randomized Trial.” JAMA. 2012 Sept 12; 308:987-97.

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Research Support Ongoing Research Support U10 HL098107 (Boushey, HA) 09/30/09-06/30/16 NIH/NHLBI UCSF AsthmaNet Clinical Center The major goals are to serve as a clinical center participating in the conduct of NHLBIsupported multi-center clinical trials of asthma therapies in children and adults with asthma, and to conduct smaller, focused studies of mechanisms of action of asthma therapies, of novel treatments for severe asthma, and of concepts of asthma pathophysiology that could lead to the development of new asthma treatments. Role: Co-Investigator U10 HL0981 (Boushey, HA) 09/30/09-06/30/16 NIH/NHLBI UCSF AsthmaNet Clinical Center The major goals are to serve as a clinical center participating in the conduct of NHLBIsupported multi-center clinical trials of asthma therapies in children and adults with asthma, and to conduct smaller, focused studies of mechanisms of action of asthma therapies, of novel treatments for severe asthma, and of concepts of asthma pathophysiology that could lead to the development of new asthma treatments. Role: Co-Investigator HHS N272200900052C (Boushey, HA) 09/30/09-09/29/14 NIH/NIAID Inner-City Asthma Consortium II / UCSF ICAC-II Basic Science Site The major goal is to serve as a Basic Science Site for the ICAC, enabling examination of relationships of the mirocrobial environment of inner city households, the development of immune function in infancy, and the development of allergic disease, especially asthma, in childhood. Role: Principal Investigator P01 HL070831-06A1 (Lemanske, R) 05/01/08-04/30/13 NIH Rhinovirus Infection and Childhood Asthma The major goals of this study are to apply the Virochip microarray to search for novel viruses in respiratory secretions obtained from children with severe clinical illnesses with the features of a respiratory infection but in whom standard PCR tests have not detected a virus, and further to expand the ViroChip to detect regions of the rhinovirus genome associated with virulence. Role: Co-Investigator 5 U10 HL074204-05 NIH/NHLBI

(Boushey, HA)

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09/15/03-07/31/11

Asthma Clinical Research Network Center at UCSF To link the established clinical research group at the University of California, San Francisco with other clinical research groups in an interactive network conducting collaborative studies of novel therapeutic approaches for asthma and disseminating the findings on optimal management of asthmatic patients to practitioners and other health care professionals. Role: Principal Investigator 5 U10 HL074431-05 (Lazarus, SC) 08/15/03-07/31/11 NIH/NHLBI COPD Clinical Research Network at UCSF HL-03-002 COPD Clinical Research Network The purpose of the NIH-sponsored COPD Clinical Research Network is to evaluate new and existing approaches for the management of COPD and to disseminate the findings of this network to the medical community. Role: Co-Investigator Completed Research Support R01 HL080414-05 (Fahy, JV) 07/01/05-05/31/10 NIH Histoblood group antigens, viruses & asthma The major goals are to understand how expression of histo-blood groups antigens by airway epithelial cells and airway mucins influences susceptibility to asthma exacerbations. Role: CoInvestigator R01 HL080074-01 (Cabana, M) 07/01/04-06/30/10 NIH Trial of Infant Probiotic Exposure on Developing Asthma This trial will measure the effect of a 6-month daily exposure of Lactobacillus, as an infant formula supplement, on immune system and asthma development during the first 3 years of life. Role: Co-Investigator Doris Duke Foundation (Ganem, DE) 10/01/03-6/30/09 Genomics-based Approaches to New Pathogen Discovery in Chronic Human Diseases To use a DNA microarray designed to detect any known virus to explore whether viruses are associated with liver and lung diseases that are currently of unknown etiology. Role: PI AI050496-01 (Boushey, HA) 09/01/01-04/31/06 NIH AI-00-012 Asthma and Allergic Diseases Research Centers -- Rhinoviruses, Epithelial Cells, and Airway Function The purpose of this Program Project Grant is to examine the hypothesis that the nature and intensity of the nasal and bronchial responses to Rhinovirus infection is determined by properties inherent to the infecting strain, and/or properties inherent to the epithelial cells infected. Role: PI

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BIOGRAPHICAL SKETCH NAME Esteban González Burchard, M.D., M.P.H. eRA COMMONS USER NAME Eburchard

POSITION TITLE Professor, Bioengineering & Therapeutic Sciences and Medicine Director, Center on Genes, Environments & Health EDUCATION/TRAINING

INSTITUTION AND LOCATION

DEGREE

San Francisco State University, San Francisco, CA

B.S.

Stanford University School of Medicine, Stanford, CA

M.D.

Harvard School of Public Health, Boston, MA

Certificate

1997

Brigham and Women's Hospital, Boston, MA

Resident

1995-1998

University of California, San Francisco, SF, CA

Fellow

1998-2001

M.P.H.

2001-2002 2005-2006

Stanford University, Stanford, CA University of California, Berkeley

YEAR(s)

FIELD OF STUDY Cellular & Molecular 1984-1990 Biology 1990-1995 Medicine Program in Clinical Effectiveness Internal Medicine Pulmonary & Critical Care Medicine Genetic Epidemiology Epidemiology

Positions and Honors 2001 - 2010 2008 2009 2010 2011 1988, 1989 2005 – 2010 2008 2009 2009 2010 2011

Director, UCSF DNA Bank and Asthma Genetics Core Facility Director, UCSF Center on Genes, Environments & Health Director, UCSF Clinical Pharmacology Training Program Vice Chair, Department of Bioengineering & Therapeutic Sciences, UCSF Professor, Bioengineering & Therapeutic Sciences and Medicine, UCSF National Collegiate Athletic Association (NCAA) Div. II Academic All-American, Wrestling RWJ Amos Medical Faculty Development Award NIH Study Section Member, Genetics of Health and Disease (GHD) American Society of Clinical Investigation (ASCI), inducted member Guest Speaker, Tavis Smiley Show Guest Speaker, NPR’s Science Friday, hosted by Ira Flatow Athletic Hall of Fame, San Francisco State University

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Selected Peer-reviewed Publications (selected from 86 publications) 1. Burchard EG, Ziv E, Coyle N, Lin-Gomez S, Tang H, Karter AJ, Mountain J, PerezStable EJ, Sheppard D, Risch N. (2003) The Importance of Race and Ethnic Background in Biomedical Research and Clinical Practice. N. Engl. J. Med. 348:1077-1192. 2. Burchard EG, Avila PC, Nazario S, Casal J, Torres A, Rodriguez-Santana JR, Toscano M, Senter-Sylvia J, Alioto ME, Salazar M, Gomez I, Fagan JK, Salas J, Lilly C, Matallana H, Ziv E, Castro R, Selman M, Chapela R, Sheppard D, Weiss ST, Ford JG, Boushey HA, Rodriguez-Cintron W, Drazen JM, Silverman EK (2004) Lower Bronchodilator Responsiveness in Puerto Rican than in Mexican Asthmatic Subjects. Am. J. Respir. Crit. Care Med. 169:386-92. 3. Salari K, Choudhry S, Tang H, Naqvi M, Lind D, Avila PC, Coyle NE, Ung N, Nazario S, Casal J, Torres-Palacios A, Clark S, Phong A, Gomez I, Matallana H, Perez-Stable EJ, Shriver MD, Kwok PY, Sheppard D, Rodriguez-Cintron W, Risch NJ, Ziv E, Burchard EG. (2005) Genetic admixture and asthma-related phenotypes in Mexican American and Puerto Rican asthmatics. Genet. Epidemiol. 29:76-86. 4. Burchard EG, Borrell LN, Choudhry S, Naqvi M, Tsai HJ, Rodriguez-Santana JR, Chapela R, Rogers SD, Mei R, Rodriguez-Cintron W, Arena JF, Kittles R, Perez-Stable EJ, Ziv E, Risch N. (2005) Latino Populations: A unique opportunity for the study of race, genetics and social environment in epidemiologic research. Am. J. Public Health 95:2161-8. 5. Tsai HJ, Kho JY, Shaikh N, Choudhry S, Naqvi M, Navarro D, Matallana H, Castro R, Lilly CM, Watson HG, Meade K, Le Noir M, Thyne S, Ziv E, Burchard EG. (2006) Admixture-matched case-control study: A practical approach for genetic association studies in admixed populations. Hum. Genet. 118:626-39. 6. Tang H, Choudhry S, Mei R, Morgan M, Rodriguez-Cintron W, Burchard EG, Risch NJ (2007) Recent genetic selection in the ancestral admixture of Puerto Ricans. Am. J. Hum. Genet. 81:626-33 (PMC1950843). 7. Choudhry S, Taub M, Mei R, Rodriguez-Santana J, Rodriguez-Cintron W, Shriver MD, Ziv E, Risch NJ, Burchard EG (2008) Genome-wide screen for asthma in Puerto Ricans: Evidence for association with 5q23 region. Hum. Genet. 123:455-68 (PMC2664533). 8. Galanter J, Choudhry S, Eng C, Nazario S, Rodriguez-Santana J, Casal J, Torres A, Salas J, Chapela R, Watson HG, Meade K, LeNoir M, Rodriguez-Cintron W, Avila PC, Burchard EG (2008) ORMDL3 gene is associated with asthma in three ethnically diverse populations. Am. J. Resp. Crit. Care Med. 177:1194-200 (PMC2408437). 9. Seibold MA, Reese TA, Choudhry S, Salam MT, Beckman K, Eng C, Atakilit A, Meade K, Lenoir M, Watson HG, Thyne S, Kumar R, Weiss KB, Grammer LC, Avila P, Schleimer RP, Fahy JV, Rodriguez-Santana J, Rodriguez-Cintron W, Boot RG, Sheppard D, Gilliland FD, Locksley RM, Burchard EG (2009) Differential enzymatic activity of common haplotypic versions of the human acidic mammalian chitinase protein. J. Biol. Chem. 284:19650-8 (PMC2740590).

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10. Hancock DB, Romieu I, Shi M, Sienra-Monge JJ, Wu H, Chiu GY, Li H, del RioNavarro BE, Willis-Owens SA, Weiss ST, Raby BA, Gao H, Eng C, Chapela R, Burchard EG, Tang H, Sullivan PF, London SJ (2009) Genome-wide association study implicates chromosome 9q21.31 as a susceptibility locus for asthma in Mexican children. PLoS Genet. 5:e1000623 (PMC2722731). 11. Risch N, Choudhry S, Via M, Basu A, Sebro R, Eng C, Beckman K, Thyne S, Chapela R, Rodriguez-Santana J, Rodriguez-Cintron W, Avila PC, Ziv E, Burchard EG (2009) Ancestry-related assortative mating in Latino populations. Genome Biol. 10:R132. 12. Mathias RA, Grant AV, Rafaels N, Hand T, Gao L, Vergara C, Tsai YJ, Yang M, Campbell M, Foster C, Gao P, Togias A, Hansel NN, Diette G, Adkinson NF, Liu MC, Faruque M, Dunston GM, Watson HR, Bracken MB, Hoh J, Maul P, Maul T, Jedlicka AE, Murray T, Hetmanski JB, Ashworth R, Ongaco CM, Hetrick KN, Doheny KF, Pugh EW, Rotimi CN, Ford J, Eng C, Burchard EG, Sleiman PM, Hakonarson H, Forno E, Raby BA, Weiss ST, Scott AF, Kabesch M, Liang L, Abecasis G, Moffatt MF, Cookson WO, Ruczinski I, Beaty TH, Barnes KC (2010) A genome-wide association study on African-ancestry populations for asthma. J. Allergy Clin. Immunol. 125:336-46. * 13. Kumar R*, Seibold MA*, Aldrich MC*, Williams KL*, Reiner AP, Colangelo L, Galanter J, Gignoux C, Hu D, Sen S, Choudhry S, Peterson EL, Rodriguez-Santana J, Rodriguez-Cintron W, Nalls MA, Leak TS, O'Meara E, Meibohm B, Kritchevsky SB, Li R, Harris TB, Nickerson DA, Fornage M, Enright P, Ziv E, Smith LJ, Liu K, Burchard EG. (2010) Genetic ancestry and lung function predictions. New England Journal of Medicine. 2010 Jul 22;363(4):321-30. Epub 2010 Jul 7. 14. Tcheurekdjian, H.*, Via, M.*, De Giacomo, A., Corvol, H., Eng, C., Thyne, S., Chapela, R., Rodriguez-Cintron, W., Rodriguez-Santana, J., Avila, P.C., González Burchard, E., on behalf of the Genetics of Asthma in Latino Americans (GALA) Study. *These authors contributed equally to this manuscript. ALOX5AP and LTA4H polymorphisms modify augmentation of bronchodilator responsiveness by leukotriene modifiers in Latinos. J Allergy Clin Immunol. 2010 Oct; 126(4):853-8.* 15. Kenny, E.E., Timpson, N.J., Sikora, M., Yee, M.C., Moreno Estrada, A., Eng, C., Huntsman, S., Gonzalez Burchard, E., Stoneking, M., Bustamante, C.D., Myles, S., Blond hair is caused by an amino acid change in TYRP1. Science. 2012 May 4;336(6081):554 Manuscripts in under review

1. Luisa N. Borrell, Elizabeth A. Nguyen, Lindsey A. Roth,Sam S. Oh, Haig Tcheurekdjian,Saunak Sen, Adam Davis, Harold J. Farber, Pedro C. Avila, Emerita Brigino-Buenaventura, Michael A. LeNoir, Fred Lurmann, Kelley Meade, Denise Serebrisky, William Rodriguez-Cintron, Rajesh Kumar, Jose R. Rodriguez-Santana, Shannon Thyne, Esteban G. Burchard. Childhood obesity and asthma control in a diverse sample: Examining age and racial/ethnic differences. AJRCCM. (Under 2nd review January 2013).

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2. Rajesh Kumar, Elizabeth A Nguyen, Lindsey A Roth, Sam S Oh,Christopher R Gignoux, Scott Huntsman, Celeste Eng, Andres Moreno-Estrada, Karla Sandoval, Rosenda Peñaloza-Espinosa, Marisol López-López, Pedro C Avila, Harold J Farber, Haig Tcheurekdjian, William Rodriguez-Cintron, Jose R Rodriguez-Santana, Denise Serebrisky, Shannon M Thyne, Keoki Williams, William Klitz, Cheryl Winkler, Carlos D Bustamante, Eliseo J Pérez-Stable, Luisa N Borrell, Esteban G Burchard. Factors associated with degree of atopy in Latino children in a nationwide pediatric sample: The GALA II Study. J Allergy Clin Immunol. (Under 2nd review, December 2013). 3. Joshua M Galanter, Christopher R Gignoux, Dara G Torgerson, Lindsey A Roth, Celeste Eng, Sam S Oh, Elizabeth A Nguyen Scott Huntsman Donglei Hu, Saunak Sen. Adam Davis, Harold J. Farber, Pedro C. Avila, Emerita Brigino-Buenaventura, Michael A. LeNoir, Kelley Meade, Denise Serebrisky, Stephanie London, Frank Gilliland, Fernando Martinez, Luisa N Borrell, William Rodriguez-Cintron, Rajesh Kumar, Jose R. Rodriguez-Santana, Esteban G. Burchard, and the EVE Consortium. Genome-wide association and admixture mapping identify chromosomal regions 17q21 and 6p21 as asthma-associated loci in Latinos. AJRCCM. (Under review December 2013). 4. Chris R Gignoux, Dara G Torgerson, Joshua Galanter, Lindsey A Roth, Celeste Eng, Elizabeth A Nguyen, Scott Huntsman, Sam S Oh,Raskia A Mathias, Adam Davis, Harold J Farber, Pedro C Avila, Emerita Brigino-Buenaventura, Michael A LeNoir, Kelley Meade, Denise Serebrisky, Luisa N Borrell, William Rodriguez-Cintron, Rajesh Kumar, Jose R Rodriguez-Santana, Andres Moreno, Karla Sandoval, Cheryl Winkler, Carlos Bustamante, EVE Collaborators, Carole Ober, Dan Nicholae, Saunak Sen, Kathleen C Barnes, Esteban G Burchard. Meta-analysis of admixture mapping using existing genome-wide association data implicates SMAD2 as a novel asthma-associated locus in Latinos. Nature Genetics. (Submitted Jan 2013). 5. Katherine A. Drake, Dara G. Torgerson, Christopher R. Gignoux, Joshua M. Galanter, Lindsey A. Roth, Scott Huntsman, Celeste Eng, Sam S. Oh, Sook Wah Yee, Lawrence Lin, Adam Davis, Luisa N. Borrell, Harold J. Farber, Rajesh Kumar, Pedro C. Avila, Emerita Brigino-Buenaventura, Rocio Chapela, Jean G. Ford, Michael A. LeNoir, Fred Lurmann, MS, Kelley Meade, Denise Serebrisky, Shannon Thyne, William RodríguezCintrón, Saunak Sen, José R. Rodríguez-Santana, Kathleen M. Giacomini, and Esteban G. Burchard. A Genome-wide Association Study of Bronchodilator Response in Latinos Implicates Rare Variants. J Allergy Clin Immunol. (Submitted January 2013). 6. Katherine K. Nishimura, Joshua M. Galanter, Lindsey A. Roth, Sam S. Oh, Harold J. Farber, Denise Serebrisky, Rajesh Kumar, Luisa N. Borrell, Emerita BriginoBuenaventura, Adam Davis, Michael A. LeNoir, Kelley Meade, William RodriguezCintron, Pedro C. Avila, Jose R. Rodriguez-Santana, Saunak Sen, Fred Lurmann, John R. Balmes, Esteban G. Burchard. Early Life Exposure to Air Pollution and the Risk of Asthma in Latino and African American Children. ARJCCM. (Submitted January 2013).

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Research Support Ongoing Research Support 1R01 HL104608-01A1 (PI: Barnes) 09/28/2011-6/30/2015 Source: Johns Hopkins University-Subcontract Role: Subcontractor Project title: New Approaches for Empowering Studies of Asthma in Populations of African Descent The major goal of this project is to identify genetic variants specific to African populations. We will sequence Latino and African American samples to design a custom GeneChip for populations with African ancestry. P60 MD006902

(PI: Bibbins-Domingo)

03/01/13-02/28/17

Source: NIH/NIMHD Role: Project PI Program title: Addressing Disparities in Chronic Disease with a Teen and Young Adult Focus Project title: The Genetics of Asthma and Obesity Using Admixture Mapping in Latinos The major goal of this proposal is to identify novel genetic variants associated with both asthma and obesity by deep re-sequencing of candidate regions identified through admixture mapping. R01 ES015794 (PI: Burchard) 9/01/08-5/31/13 Source: NIH/NIEHS Project title: Genes-environments & Admixture in Latino Asthmatics (GALA 2) The major goal of this project is to identify genetic, social and environmental risk factors for asthma among various Latino groups recruited throughout the U.S. R01 HL088133 (PI: Burchard) 3/01/08-2/28/13 Source: NIH/NHLBI Project title: Whole Genome Analyses for Asthma in Latino Populations The major goal of this project is to perform genome-wide association analyses to identify genetic factors associated with asthma and related phenotypes in Puerto Ricans and Mexicans. U19 AI077439 (PI: Sheppard) 04/01/08-03/31/13 Source: NIH/NIAID Role: Project 3 PI Program title: Mechanisms of Initiation and Persistence of Allergic Asthma Project 3 title: Chitinases and TGFb in Human Asthma The goal is to analyze the effects of genetic variation on genes in the TGF beta and Chitinase pathways and their role in the initiation and persistence of asthma across racial and ethnically diverse populations.

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Completed Research (Neal Benowitz, Program PI) 07/01/07-06/30/12 Role on project: Project 7 PI Source: Flight Attendants Medical Research Institute (FAMRI) Program title: UCSF Center of Excellence on Secondhand Smoke Project title: Tobacco Gene–Environment Interactions in African American and Latino Asthmatics. The goal is to identify gene-environment interactions between asthma and secondhand smoke. RC2 HL101651 (Co-PIs: Ober, Nicolae) 09/30/09-09/29/11 NIH/R01 Role on project: Subcontractor The EVE Asthma Genetics Consortium: Building Upon GWAS To replicate the most significant GWAS (meta-analysis) results in >15,000 asthma cases and controls of European American, African American, and U.S. Hispanic ethnicities, resequence 5-10 genes associated with asthma in European Americans but not in African Americans or Hispanics, to study additional asthma-associated phenotypes and examine interactions, and develop methods to facilitate gene discovery. U01 GM61390 (PI:Giacomini) 07/20/05-06/30/10 Role on project: Co-Investigator Source: NIH/NIGMS Program title: Pharmacogenetics of Membrane Transporters Project title: Study of Pharmacogenetics in Ethically Diverse Groups The goal was to develop an ethnically diverse cohort of subjects to participate in pharmacogenetic studies. R01 HL078885 (PI: Burchard) 08/15/05-07/31/10 Source: NIH/NHLBI Project title: Case-control Association Studies and Genetic Confounding The goal was to test and compare methods of detecting and correcting for population stratification.

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BIOGRAPHICAL SKETCH NAME George H. Caughey eRA COMMONS USER NAME gcaughey

POSITION TITLE Professor of Medicine

EDUCATION/TRAINING INSTITUTION AND LOCATION Arizona State University Stanford University School of Medicine Pennsylvania Hospital/UPenn University of California, San Francisco

DEGREE BS MD

YEAR(s)

FIELD OF STUDY

1975 1979 1982 1986

Chemistry Medicine Internal Medicine Pulmonary Medicine

Positions and Honors 1988-92 1988-98 1992-98 199219951996199819992002200420042012-

Assistant Professor, Dept. of Medicine, UCSF Associate Staff, Cardiovascular Research Institute, UCSF Associate Professor, Dept. of Medicine, UCSF Molecular Medicine Program Faculty, UCSF Editorial Board, American Journal of Respiratory Cell and Molecular Biology Member of UCSF Graduate Program in Biomedical Sciences Professor, Dept. of Medicine, UCSF Investigator, Cardiovascular Research Institute, UCSF Member, UCSF Cancer Center and Center for Neurobiology of Digestive Disease Editorial Board, Current Respiratory Medicine Reviews Chief of Pulmonary and Critical Care and Sleep Medicine, San Francisco VA Medical Center Associate Chief of Research and Academic Affairs, Medical Service San Francisco VA Medical Center

Honors and Awards 1974 1975 1986 1992 1992

American Chemical Society Outstanding Undergraduate Award, ASU Phi Beta Kappa and Merck Award in Chemistry, ASU NIH Clinical Investigator Award American Lung Association Career Investigator Award Elected to American Society for Clinical Investigation

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2000 20042010

Elected to American Association of Physicians Julius and Lillian Nadel Endowed Chair of Medicine Elected to Collegium Internationale Allergologicum

Publications in chronological order (selected from 135) 1. Vanderslice P, Ballinger SM, Tam EK, Goldstein SM, Craik CS, Caughey GH. Human mast cell tryptase: multiple cDNAs and genes reveal a multigene protease family. Proc Natl Acad Sci USA 87:3811-5, 1990. 2. Rubinstein I, Nadel JA, Graf PD, Caughey GH. Mast cell chymase potentiates histamine-induced wheal formation in the skin of ragweed-allergic dogs. J Clin Invest 86:555-9, 1990. 3. Ruoss SJ, Hartmann T, Caughey GH. Mast cell tryptase is a mitogen for cultured fibroblasts. J Clin Invest 88:493-9, 1991. 4. Caughey GH, Raymond WW, Bacci E, Lombardy RJ, Tidwell RR. BABIM and related amidines are potent, reversible inhibitors of mast cell tryptases. J Pharmacol Exp Therap 264:676-82, 1993. 5. Caughey GH, Schaumberg TH, Zerweck EH, Butterfield JH, Hanson RD, Silverman GA, Ley TJ. The human mast cell chymase gene (CMA1): mapping to the cathepsin G/granzyme gene cluster and lineage-restricted expression. Genomics 15:614-20, 1993. 6. Fang KC, Raymond WW, Lazarus SC, Caughey GH. Dog mastocytoma cells secrete a 92 kDa gelatinase activated extracellularly by mast cell chymase. J Clin Invest 97:158996, 1996. 7. Fang KC, Raymond WW, Blount JL, Caughey GH. Dog mast cell a-chymase activates progelatinase B by cleaving Phe88-Gln89 and Phe91-Glu92 bonds of the propeptide domain. J Biol Chem 272:25628-35, 1997. 8. Wolters PJ, Raymond WW, Blount JL, Caughey GH. Regulated expression, processing and secretion of dog mast cell dipeptidyl peptidase I. J Biol Chem 273:15514-20, 1998. 9. Pallaoro M, Fejzo MS, Shayesteh L, Blount JL, Caughey GH. Characterization of genes encoding known and novel human tryptases on chromosome 16p13.3. J Biol Chem 274:3355-62, 1999. 10. Ma Y, Longley BJ, Blount JL, Langley K, Caughey GH. Clustering of activating mutations in c-kit’s juxta-membrane coding region in canine mastocytomas. J Invest Dermatol 112:165-70, 1999. 11. Coussens LM, Raymond WW, Bergers G, Behrendtsen O, Werb Z, Caughey GH, Hanahan D Inflammatory mast cells potentiate the angiogenic switch during squamous epithelial carcinogenesis. Genes & Development 13:1382-97, 1999. 12. Caughey GH, Raymond WW, Blount JL. Hau LW-T, Pallaoro M, Wolters PJ, Verghese GM. Characterization of human g-tryptases, novel members of the chromosome 16p mast cell tryptase and prostasin gene families. J Immunol 164:6566-75, 2000. 13. Steinhoff M, Vergnolle N, Young S, Ennes H, Hollenberg MD, Wallace JL, Caughey GH, Williams LM, Geppetti P, Mayer EA, Bunnett NW. Agonists of proteinaseactivated receptor 2 induce inflammation by a neurogenic mechanism. Nature Med 6:151-8, 2000.

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14. Frank BT, Rossall JC, Caughey GH, Fang KC. Mast cell tissue inhibitor of metalloproteinase-1 is cleaved and inactivated extracellularly by a-chymase. J Immunol 166:2783-92, 2001. 15. Wolters PJ, Muilenburg D, Pham CTN, Ley TJ, Caughey GH. Dipeptidylpeptidase I is essential for in vivo activation of mast cell chymases, but not tryptases. J Biol Chem 276:18551-6, 2001. 16. Muilenburg DJ, Raymond WW, Wolters PJ, Caughey GH. Lys40 but not Arg143 influences selectivity of angiotensin conversion by human a-chymase. Biochim Biophys Acta 1596:346-56, 2002. 17. Soto D, Malmsten C, Blount JL, Muilenberg DJ and Caughey GH. Genetic deficiency of human mast cell a-tryptase. Clin Exp Allergy 32:1000-6, 2002. 18. Bhagwandin VJ, Hau L W-T, Mallen-St. Clair J, Wolters PJ, Caughey GH. Structure and activity of pancreasin, a novel tryptic serine peptidase expressed by pancreas. J Biol Chem 278:3363-71, 2003. 19. Reiling KK, Krucinski J, Miercke LJW, Raymond WW, Caughey GH, Stroud RM. Structure of human pro-chymase. Biochemistry 42:2616-24, 2003. 20. Raymond WW, Ruggles Waugh S, Craik CS, Caughey GH. Albumin is a substrate of human chymase: prediction by combinatorial peptide screening and development of a selective inhibitor based on the cleavage site. J Biol Chem 278:34517-24, 2003. 21. Mallen-St. Clair J, Pham CTN, Villalta SA, Caughey GH, Wolters PJ. Mast cell dipeptidyl peptidase I mediates survival from sepsis. J Clin Invest 113:628-34, 2004. 22. Verghese GM, Tong ZY, Bhagwandin V, Caughey GH. Mouse prostasin gene structure, promoter function, and restricted expression in lung and kidney. Am J Respir Cell Mol Biol 30:519-29, 2004. 23. Baluk P, Raymond WW, Ator E, Coussens LM, McDonald DM, Caughey GH. MMP-2 and -9 expression increases in mycoplasma-infected airways but is not required for microvascular remodeling. Am J Physiol 287:L307-17, 2004. 24. Raymond WW, Sommerhoff CP, Caughey GH. Mastin is a gelatinolytic mast cell peptidase resembling a mini-proteasome. Arch Biochem Biophys 435:311-22, 2005. 25. Tong ZY, Illek B, Bhagwandin VK, Verghese GM, Caughey GH. Prostasin, a membrane-anchored serine peptidase, regulates sodium currents in JME/CF15 cells, a cystic fibrosis epithelial cell line. Am J Physiol 287:L928-35, 2004. 26. Wolters PJ, Mallen-St. Clair J, Lewis CC, Villalta SA, Baluk P, Erle DJ, Caughey GH. Tissue-selective mast cell reconstitution and differential lung gene expression in mast cell-deficient KitW-sh/KitW-sh sash mice. Clin Exp Allergy 35:82-8, 2005. 27. Xu X, Golden JA, Dolganov G, Jones KD, Donnelly S, Weaver T, Caughey GH. Transcript signatures of lymphocytic bronchitis in lung allograft biopsies. J Heart Lung Transplant 24:1055-66, 2005. 28. Xu X, Zhang D, Lyubynska N, Wolters PJ, Killeen NP, Baluk P, McDonald DM, Hawgood S, Caughey GH. Mast cells protect mice from mycoplasma pneumonia. Am J Resp Crit Care Med 173:219-25, 2006. 29. Raymond WW, Cruz AC, Caughey GH. Mast cell and neutrophil peptidases attack an inactivation segment in hepatocyte growth factory to generate NK4-like antagonists. J Biol Chem 281:1489-94, 2006.

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30. Caughey GH. Tryptase genetics and anaphylaxis. J Allergy Clin Immunol 117:1411-4, 2006. 31. Mallen-St Clair J, Shi G-P, Sutherland RE, Chapman HA, Caughey GH, Wolters PJ. Cathepsins L and S are not required for activation of dipeptidyl peptidase I in mice. Biol Chem 387:1143-6, 2006. 32. Verghese GM, Gutknecht MF, Caughey GH. Prostasin regulates epithelial monolayer function: cell-specific Gpld1-mediated secretion and role of GPI anchor. Am J Physiol Cell Physiol 291:C1258-70, 2006. 33. Caughey GH. A pulmonary perspective on GASPIDs: Granule-Associated Serine Peptidases of Immune Defense. Curr Resp Med Rev 2:263-77, 2006. 34. Xu X, Zhang D, Zhang H, Wolters PJ, Killeen NP, Sullivan BM, Locksley RM, Lowell CA, Caughey GH. Neutrophil histamine contributes to inflammation in mycoplasma pneumonia. J Exp Med 203:2907-17, 2006. 35. Planès C and Caughey GH. Regulation of the epithelial Na+ channel by peptidases. Curr Top Dev Biol 78:23-46, 2007. 36. Caughey GH. Mast cell tryptases and chymases in inflammation and host defense. Immunol Rev 217:114-54, 2007. 37. Akin C, Soto D, Brittain E, Chhabra A, Schwartz LB, Caughey GH, Metcalfe DD. Tryptase haplotype in mastocytosis: Relationship to disease variant and diagnostic utility of total tryptase levels. Clin Immunol 123:268-71, 2007. 38. Trivedi NN, Tong Q, Raymond WW, Bhagwandin VJ, Caughey GH. Mast cell tryptases changed rapidly during primate speciation and evolved from g-like transmembrane peptidases in ancestral vertebrates. J Immunol 179:6072-9, 2007. 39. Caughey GH. “Mast Cells and Basophils” in Asthma and COPD—Basic Mechanisms and Clinical Management, Barnes PJ, Drazen JM, Rennard S, Thompson NC, eds., Academic Press, London, 2008. 40. Trivedi NN, Raymond WW, Caughey GH. Chimerism, point mutation and truncation dramatically transformed mast cell d tryptases during primate evolution. J Allergy Clin Immunol 121:1262-8, 2008. 41. Caughey GH, Beauchamp J, Schlatter D, Raymond WW, Trivedi NN, Banner D, Mauser H, Fingerle J. Guinea pig chymase is leucine-specific: a novel example of functional plasticity in the chymase/granzyme family of serine peptidases. J Biol Chem 283:1394351, 2008. 42. Raymond WW, Su S, Makarova A, Wilson TM, Carter MC, Metcalfe DD, Caughey GH. a2-Macroglobulin capture allows detection of mast cell chymase in serum and creates a reservoir of angiotensin II-generating activity. J Immunol 182:5770-7, 2009. 43. Innes AL, Carrington SD, Thornton DJ, Kirkham S, Dougherty RH, Raymond WW, Caughey GH, Muller SJ, Fahy JV. Ex vivo sputum analysis reveals impairment of protease-dependent mucus degradation by plasma proteins in acute asthma. Am J Resp Crit Care Med 180:203-10, 2009. 44. Trivedi NN, Tamraz B, Chu C, Kwok PY, Caughey GH. Humans are protected from mast cell tryptase deficiency despite frequent inheritance of loss-of-function mutations. J Allergy Clin Immunol 124:1099-105, 2009.

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45. Trivedi NN and Caughey GH. Mast cell peptidases: chameleons of innate immunity and host defense. Am J Respir Cell Mol Biol 42:257-67, 2010. 46. Dougherty RH, Sidhu SS, Raman K, Solon M, Solberg OD, Caughey GH, Woodruff PG, Fahy JV. Accumulation of intraepithelial mast cells with a unique protease phenotype in Th2-high asthma. J Allergy Clin Immunol, 125:1046-53, 2010. 47. Raymond WW, Trivedi NN, Makarova A, Ray M, Craik CS, Caughey GH. How immune peptidases change specificity: Cathepsin G gained tryptic function but lost efficiency during primate evolution. J Immunol 185:5360-8, 2010. 48. Caughey GH. “Mast cell proteases as protective and inflammatory mediators”, in Mast Cell Biology: Contemporary and Emerging Topics, Gilfillan AM and Metcalfe DD, eds., Landes Bioscience, 2011. 49. Caughey GH. “Protease mediators of anaphylaxis”, in Anaphylaxis and Hypersensitivity Reactions: From Molecular Markers to Rapid Desensitizations, Castells A, ed., Springer Inc., 2011. 50. Xu X, Zhang H, Song Y, Lynch SV, Lowell CA, Wiener-Kronish JP, Caughey GH. Strain-dependent induction of neutrophil histamine production and cell death by Pseudomonas aeruginosa. J Leuk Biol, in press, epub 2011. 51. Sutherland SE. Xu X. Kim SS, Seeley EJ, Caughey GH, Wolters PJ. Parasitic infection improves survival from septic peritonitis by enhancing mast cell responses to bacteria in mice. PLoS One, 6(11):e27564, 2011. 52. Sugimoto K, Kudo M, Sundaram A, Ren X, Huang K, Bernstein X, Wang Y, Raymond WW, Erle DJ, Åbrink M, Caughey GH, Huang X, Sheppard D. The αvβ6 integrin modulates airway hyperresponsiveness in mice by regulating intra-epithelial mast cells. J Clin Invest, in press. 53. Nimishakavi S, Besprozvannaya M, Raymond WW, Craik CS, Gruenert DC, Caughey GH. Activity and inhibition of prostasin and matriptase on apical and basolateral surfaces of human airway epithelial cells. Am J Physiol: Lung Cell Mol Physiol 303:L97-106, 2012. 54. Greenland JR, Jones KD, Hays SR, Golden JA, Urisman A, Jewell NP, Caughey GH, Trivedi NN. Association of large-airway bronchitis with bronchiolitis obliterans syndrome. Am J Respir Crit Care Med, in press

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Research Support Ongoing Research Support "Evolving Microenvironments in Airway Inflammation" Project 1: Roles of Peptidases in Chronic Airway Inflammation; and Administrative Core A Program Director/Project 1 Leader/Core Leader: George H. Caughey Agency: NIH-NHLBI; Type: Program Project P01 HL024136; 05/11/2010-3/30/2015 Project 1 goals are to determine roles of secreted proteases in airway inflammation. “Roles of Mast Cells in Primary Dysfunction of Lung Allografts” Principal Investigator: George H. Caughey Agency: UCSF Nina Ireland Lung Research Program; 01/1/2012-12/31/2013 The goals of this project are to explore roles of mast cells in primary graft dysfunction.

"Alloimmune Monitoring of Lung Transplant Recipients" Principal Investigator: Qizhi Tang; Co-I: George H. Caughey Agency: UCSF Nina Ireland Lung Research Program; 01/1/2013-12/31/2015 The goals of this project are to identify means of predicting and preventing graft dysfunction in lung allograft recipients.

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BIOGRAPHICAL SKETCH NAME Harold A. Chapman, M.D. eRA COMMONS USER NAME Halchapman

POSITION TITLE Professor of Medicine

EDUCATION/TRAINING INSTITUTION AND LOCATION Tulane University University of Alabama School of Medicine

DEGREE

YEAR(s)

M.D.

1968 1972

FIELD OF STUDY Premedical Medicine

Positions and Honors Positions 1972-1975 1975-1977 1978-1979 1979-1985 1985 1985-1999 1992-1999 1992-1999 2000-2008 2000 2000

Residency Training in Internal Medicine, University of Utah Affiliated Hospitals, Salt Lake City, UT Associate Investigator, V.A. Medical Center, Salt Lake City, UT Pulmonary Fellow, University of Utah Affiliated Hospitals, Salt Lake City, UT Assistant Professor of Medicine, University of Utah, Department of Medicine, Salt Lake City, UT Associate Professor of Medicine, University of Utah, Department of Medicine, Salt Lake City UT Associate Professor of Medicine, Harvard Medical School, Department of Medicine, Boston, MA Physician, Brigham and Women's Hospital, Boston, MA Associate Professor of Environmental Health, Harvard School of Public Health, Boston, MA Chief, Division of Pulmonary and Critical Care Medicine, University of California, San Francisco Professor of Medicine, University of California, San Francisco Senior Member, Cardiovascular Research Institute, University of California San Francisco

Honors 1985-1990 1987 1998

Career Investigator Award, American Lung Association American Society for Clinical Investigation American Association of Physicians

119

2001-2011

MERIT Award, NIH/NHLBI Ad Hoc member of various NIH study sections Editorial Board of Journal of Clinical Investigation and Associate Editor, American Journal of Respiratory, Cell, and Molecular Biology.

Selected Peer-reviewed Publications (Selected from ~140) 1. Shi GP, Munger JS, Meara JP, Rich DH, Chapman HA. Molecular cloning and expression of human alveolar macrophage cathepsin S, an elastinolytic cysteine protease. J Biol Chem 1992 15; 267:7258-62. 2. Wei Y, Waltz D, Rao N, Drummond R, Rosenberg S, Chapman HA. Identification of the urokinase receptor as an adhesion receptor for vitronectin. J Biol Chem, 1994; 209:32380-32388. 3. Riese R, Wolf P, Bromme D, Natkin L, Villadangos JA, Ploegh H, and HA Chapman. Essential role for cathepsin S in MHC Class II-associated invariant chain processing and antigen presentation. Immunity 1996;4:357-366. 4. Gelb BD, Shi GP, Chapman HA Jr, Desnick RJ. Pycnodysostosis, a lysosomal disease caused by cathepsin K deficiency. Science 1996; 273:1236-1238. 5. Wei Y, Lukasev M, Simon DI, Bodary SC, Rosenberg S, Doyle MV, Chapman HA. Regulation of integrin function by the urokinase receptor. Science 1996; 273:15511555. 6. Shi GP, Villadangos J, Dranoff G, Ploegh H, Chapman HA. Cathepsin S required for normal MHC class II peptide loading and germinal center development. Immunity, 1999;10:196-206. 7. Tang CH, Lee JW, Galvez MG, Robillard L, Mole SE, Chapman HA. Murine cathepsin F deficiency causes neuronal lipofuscinosis and late-onset neurological disease. Mol Cell Biol. 2006; 26 :2309-16. 8. Kim KK, Kugler MC, Wolters PJ, Robillard L, Galvez MG, Brumwell AN, Sheppard D, Chapman HA. Alveolar epithelial cell mesenchymal transition develops in vivo during pulmonary fibrosis and is regulated by the extracellular matrix. Proc Natl Acad Sci 2006; 103(35):13180-5. Epub 2006 Aug 21 9. Ewald SE, Lee BL, Lau L, Wickliffe KE, Shi GP, Chapman HA, Barton GM. The ectodomain of Toll-like receptor 9 is cleaved to generate a functional receptor. Nature. 2008 Dec 4;456(7222):658-62. 10. Kim KK, Wei Y, Szekeres C, Kugler MC, Wolters PJ, Hill ML, Frank JA, Brumwell AN, Wheeler SE, Kreidberg JA, Chapman HA. Epithelial cell alpha3beta1 integrin links beta-catenin and Smad signaling to promote myofibroblast formation and pulmonary fibrosis. J Clin Invest. 2009 Jan;119(1):213-24. See Commentary same issue. 11. Kim Y, Kugler MC, Wei Y, Kim KK, Li X, Brumwell AN, Chapman HA. Integrin alpha3beta1-dependent beta-catenin phosphorylation links epithelial Smad signaling to cell contacts. J Cell Biol. 2009 Jan 26;184(2):309-22. 12. Chapman HA, Li X, Alexander JP, Brumwell A, Lorizio W, Tan K, Sonnenberg A, Wei Y, Vu T. Integrin α6β4 identifies an adult distal lung epithelial population with

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regenerative potential in mice. J Clin Invest. 2011, 121:2855-62. See Commentary same issue. 13. Ulsamer A, Wei Y, Kim KK, Tan K, Wheeler S, Xi Y, Thies RS, Chapman HA. Axin pathway activity regulates in vivo pY654-b-catenin accumulation and pulmonary fibrosis. J Biol Chem 2012, 287: 5164-5172. 14. Sennino B, Ishiguro-Oonuma T, Wei Y, Naylor RM, Williamson CW, Bhagwandin V, Tabruyn SP, You WK, Chapman HA, Christensen JG, Aftab DR, McDonald DM. Suppression of tumor invasion and metastasis by concurrent inhibition of c-Met and VEGF signaling in pancreatic neuroendocrine tumors. Cancer Discovery 2012, 2:270-287. 15. Xi Y, Wei Y, Sennino, Ulsamer A, Kwan I, Brumwell AN, Tan K, Aghi MK, McDonald DM, Jablons DM, Chapman HA. Identification of pY654-b-catenin as a critical co-factor in hypoxia-inducible factor-1a signaling and tumor responses to hypoxia. Oncogene 2012, Dec 17. doi: 10.1038/onc.2012.530. 16. Smith KR, Dahl HH, Canafoglia L, Andermann E, Damiano J, Morbin M, Franceschetti S, Cossette P, Saftig P, Grötzinger J, Schwake M, Andermann F, Staropoli JF, Sims KB, Mole SE, Alexander NA, Cooper JD, Chapman HA, Carpenter S, Berkovic SF, Bahlo M. Cathepsin F mutations cause type B Kufs disease, an adult-onset neuronal ceroid lipofuscinosis. Human Molecular Genetics 2013, Jan 12. [Epub ahead of print]. Research Support Ongoing Research Support 5 R37 HL67204 (Chapman, HA) No cost extension NIH/NHLBI MERIT AWARD Role of Elastolytic Cathepsins in Emphysema

6/1/2001 – 5/31/2013

The major goal of this project is define the role of cysteine proteases in smoking-related emphysema. The project focuses on pathways of elastase expression in lung mesenchymal cells and on the genetics of emphysema in human subjects with early-onset emphysema and normal alpha-1-antitrypsin. 5 R01 HL44712 (Chapman, HA)

$250,000 per yr direct

Regulation of Integrin Function

1/1/1991 – 12/31/2014

The major goals of this project are to understand the molecular basis and importance of integrin function in promoting TGFb1 signaling and pulmonary fibrosis. The hypothesis that epithelial to mesenchymal transition is an important component of pulmonary fibrosis, and regulated by integrins, is the main idea tested in this grant. 5 R01 CA125564 (Chapman, HA)

No cost extension

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7/1/2007 – 5/31/2013

NIH/NHLBI Urokinase Receptor Integrin Interactions in Lung Cancer The major goals of this project are to define the physical basis of urokiinase receptor beta1 interactions and the influence of these interactions on tumor cell signaling and lung tumor progression. Primary tumor cells from human tumors will be examined for their expression and dependence on urokinase receptors for adhesion and migration. U01 HL111054-01 (Chapman HA, PI) $250,000 per year direct NIH/NHLBI Epithelial Progenitor Cells in Lung Repair and Regeneration 1/1/2012-12/31/2016 The major goals of this project are (1) To define the transcriptional program of heretofore uncharacterized distal airway and alveolar progenitors and test the hypothesis that differential expression of adhesion receptors underlies the capacity of epithelial subtypes to self-organize and promote repair. (2) Define the requirement for neuroendocrine cells (PNECS )and alveolar progenitor cells in maintenance and reconstitution of distal airway and alveolar cells following lung injury. (3) Analyze and further develop a novel, single cell in vivo lung organoid assay in kidney capsules in order to optimize the capacity of adult epithelial progenitor cells to generate functional respiratory units de novo. PO1 HL108794 (Sheppard PI, Chapman HA, project leader) 250,000 per year direct Targeting epithelial cells to treat pulmonary fibrosis. 8/1/2012-7/31/2017 The major goal of this project is to deliver one or more novel therapeutics based on recently identified regulators of EMT in lung epithelial cells for further drug development.

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BIOGRAPHICAL SKETCH NAME Anthony L. DeFranco, Ph.D. eRA COMMONS USER NAME DeFranco

POSITION TITLE Professor, Department of Microbiology & Immunology EDUCATION/TRAINING

INSTITUTION AND LOCATION Harvard University, Cambridge, MA University of California, Berkeley, CA National Institutes of Health, Bethesda, MD

DEGREE

YEAR(s)

A.B. Ph.D. Postdoctoral

6/75 10/79 11/79-8/83

FIELD OF STUDY Biochem. & Molec. Biol. Biochemistry Immunology

Positions and Honors 1972-1975 1976-1979

1998-2004 1999-2009 2012-

Undergraduate research, laboratory of Dr. Jack Strominger. HLA antigens. Graduate research, laboratory of Dr. Daniel E. Koshland, Jr. Bacterial chemotaxis. Postdoctoral research, laboratory of Dr. William E. Paul. B cell activation. Assistant Professor, UCSF, Department of Microbiology & Immunology, Associate Professor, UCSF, Department of Microbiology & Immunology Sabbatical with David Baltimore, Whitehead Insititute, MIT, Cambridge, MA Professor, UCSF, Department of Microbiology & Immunology Sabbatical with Suzanne Cory, Walter and Eliza Hall Institute, Melbourne, Australia Scientific Advisory Board, Abgenix, Inc. Fremont, CA Chairman, Department of Microbiology & Immunology, UCSF Scientific Advisory Board, UCB Celtech, Slough, UK

1974 1975 1975-1978 1979-1982 1993 1994 1997-1998

Dreyfuss Foundation Fellow Phi Beta Kappa, Harvard University NSF Predoctoral Fellow Helen Hay Whitney Postdoctoral Fellow; 2nd Rose Lieberman Lecturer, NIH NIAID Merit Award NIH Fogarty Senior International Award.

1979-1983 1983-1988 1988-1994 1989-1990 1994-present 1997-1998

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Professional Service (selected list) Member Exptl. Immunol. Study Section (1993-97), Chair (1995-1997); NIH grant reviewer, ad hoc (average 3 committees/yr since 2005, including TTT 2008, 2009); J. Immunol. Associate Editor (1986-90), Section Editor (1990-1994), Deputy Editor (1999-2001); Annual Review of Immunology, Editorial Committee for Volumes 9,13, 15, 17 (1991, ‘95, ‘97, ‘99); Current Biology, Editorial Board (1993-99). Lecturer, American Assoc. of Immunologists, Advanced Course 1995-97; Leukemia Society of America, Career Development Program Grant Review Subcommittee (1999-2005); Co-organizer: “B cell Immunobiology and Disease”, a Keystone symposium, 2001. Faculty of 1000 contributor 2001-present (www.facultyof1000.com/start.asp). Selected peer-reviewed publications (in chronological order) Original Research/Peer-reviewed journals (from total of 75 original research publications) 1.

Gold, M.R., D.A. Law and A.L. DeFranco. (1990) Stimulation of protein tyrosine phosphorylation by the B lymphocyte antigen receptor. Nature 345: 810-813. 2. Yu, C.C.K., T.S.B. Yen, C.A. Lowell, and A.L. DeFranco (2001). Lupus-like kidney disease in mice deficient in Src-family protein tyrosine kinases Lyn and Fyn. Curr. Biol. 11:34-38. 3. Gupta, N., B. Wollscheid, J.D. Watts, B. Scheer, R. Aebersold, and A.L. DeFranco (2006). Quantitative proteomic analysis of B cell lipid rafts reveals that ezrin regulates antigen receptor-mediated lipid raft dynamics. Nature Immunol. 7: 625-633. 4. Mamchak, A.A., B.M. Sullivan, B. Hou, L.M. Lee, J.K. Gilden, M.F. Krummel, R.M. Locksley, and A.L. DeFranco (2008). Normal development and activation but altered cytokine production of Fyn-deficient CD4+ T cells. J. Immunol. 181: 5374-5385. PMC2657555 5. Gross, A.J., J.R. Lyandres, A.K. Panigrahi, E.T.L. Prak, and A.L. DeFranco (2009). Developmental acquisition of the Lyn-CD22-SHP-1 inhibitory pathway promotes B Cell tolerance. J. Immunol. 182: 5382-92. PMC2840041 6. Gross, A.J., I. Proekt, and A.L. DeFranco (2011). Elevated BCR signaling and decreased survival of Lyn-deficient transitional and follicular B cells. Eur. J. Immunol. 41: 36453655. PMC in process. 7. Hou, B., P. Saudan, G. Ott, M.L. Wheeler, M. Ji, L. Kuzmich, L.M. Lee, R.L. Coffman, M.F. Bachmann, A. L. DeFranco (2011). Selective utilization of Toll-like receptor and MyD88 signaling in B cells for enhancement of the anti-viral germinal center response. Immunity 34: 375-84. PMC3064721. 8. Scapini, P., Lamagna, C., Hu, Y., Lee, K., Tang, Q., DeFranco, A. L., Lowell, C.A. (2011) B cell-derived IL-10 suppresses inflammatory disease in Lyn-deficient mice. Proc. Natl. Acad Sci. 108: E823-832. PMC3193193 9. Wheeler, M.L., and A.L. DeFranco (2012). Prolonged production of reactive oxygen species in response to BCR stimulation promotes B cell activation and proliferation. J. Immunol. 189: 4405-16. 10. Kirkland, D., A. Benson, J. Mirpuri, R. Pifer, B. Hou, A.L. DeFranco, F. Yarovinsky B cell-intrinsic MyD88 signaling prevents the lethal dissemination of commensal bacteria during colonic damage (2012). Immunity 36: 228-238. PMC3288553.

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Additional recent publications of importance to the field (in chronological order) 11. Nishiya, T. and A.L. DeFranco (2004). Ligand-regulated chimeric receptor approach reveals distinctive subcellular localization and signaling properties of the Toll-like receptors. J. Biol. Chem. 279: 19008-19017. 12. Nishiya, T. Kajita, E., Miwa, S. and A.L. DeFranco (2005). TLR3 and TLR7 are targeted to the same intracellular compartments by distinct regulatory elements. J. Biol. Chem. 280: 37107-17. 13. Hou, B., B. Reizis, and A.L. DeFranco (2008). Toll-like receptors activate innate and adaptive immunity using dendritic cell-dependent and -independent mechanisms. Immunity 29: 272-82. PMC2847796 14. Scapini, P., Y. Hu, C.L. Chu, T.S. Migone, A.L. DeFranco, M.A. Cassatella, and C.A. Lowell (2010). Myeloid cells, BAFF, and IFN-g establish an inflammatory loop that exacerbates autoimmunity in Lyn-deficient mice. J. Exp. Med. 207:1757-73. PMC2916124 15. Hou, B., A. Benson, L. Kuzmich, A.L. DeFranco and F. Yarovinsky (2011). Critical coordination of innate immune defense against Toxoplasma gondii by dendritic cells responding via their Toll-like receptors. Proc. Natl. Acad. Sci. USA 108: 278-283. PMC3017180 Research projects ongoing or completed during the last the three years Active 1. “Regulation of B lymphocyte proliferation by antigen” Principal Investigator: Anthony DeFranco Agency: National Institute for Allergy and Infectious Disease Type: R01 (AI20038-26). Period: 12/1/05-11/30/10 (12/10-11/30/11 no cost extension) The major goals of this project are: 1. Define the roles of ezrin and non-muscle myosins in lipid raft coalescence following BCR stimulation. 2. Define the role of B144, Rho-family GTPases, and non-muscle myosin motors in directing outgrowth of long membrane processes in BCR-stimulated B cells. 3. Determine the mechanism of assembly of the NF-kB signalosome at lipid rafts in mature B cells stimulated through the BCR. 4. Characterize the differences between immature B cells and mature B cells with regard to BCR-induced lipid raft coalescence and assembly of the Carma1/Bcl10 signaling complex. 2. “Cell Type-Specific Roles of TLR Signaling in Immune Responses” Principal Investigator: Anthony DeFranco Agency: NIAID Type: R01 (R01AI0720585-3). Period: 12/1/07-11/30/2012 The major goals of this project are: Aim 1: To define the role of TLR signaling in dendritic cells for initiating adaptive T cell immune responses. Aim 2: To define the role of TLR signaling in phagocytic cells for inducing inflammation and promoting microbial killing during bacterial infection. Aim 3: To define the role of TLR signaling in B lymphocytes for amplifying antibody responses. 3. “Innate Immune Regulation of Inflammation and Adaptive Immunity”

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Program Director: Anthony L. DeFranco. Project #1 “Cellular Basis of TLR Signaling for Mucosal Immune Responses” (A.L. DeFranco, PI) Agency: NIAID Type: P01 (AI078869-02). Period: 7/1/08-6/30/13 The major goals of Project 1 are: Aim 1: To define the role of TLR signaling in dendritic cells for initiating adaptive T cell immune responses to antigen challenge via the airways. Aim 2: To define the role of TLR signaling in immature dendritic cells and in neutrophils and macrophages for innate and adaptive immune responses to fungal cell walls. Aim 3: To define the role of TLR signaling in immature dendritic cells and in neutrophils and macrophages for immune defense against systemic infection with the fungal pathogen Candida albicans. Completed (last 3 years) 1. “Cytoskeleton and Signal Transduction in Host Defense” Principal Investigator: Anthony DeFranco Agency: NIAID Type: R01 (R01 AI35811-11). Period: 12/1/06-1/31/10 The goals of this project are to characterize the functional alterations of L-plastin-deficiency on neutrophil and T cell function (This grant was awarded to Dr. Eric Brown and I became the PI to finish the project when Dr. Brown took a position at Genentech, Inc.).

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BIOGRAPHICAL SKETCH NAME David J. Erle, M.D. eRA COMMONS USER NAME DJERLE

POSITION TITLE Professor of Medicine

EDUCATION/TRAINING INSTITUTION AND LOCATION Harvard College, Cambridge, MA University of California, San Francisco, CA University of California, San Francisco, CA University of California, San Francisco, CA

DEGREE

YEAR(s)

A.B. M.D. Resident Fellow

1980 1984 1984-87 1987-90

FIELD OF STUDY Biochemistry Medicine Internal Medicine Pulmonary Disease

Positions 1984-1987 1987-1988 1988-1990 1990-1992 1990-present 1992-1998 1996-present 1997-2001 1998-2004 1999-present 2000-present 2004-present 2006-2011 Honors 1977 1977, 1978 1984 1990-1993 2008-2012

Resident in Internal Medicine, University of California Hospitals, San Francisco Clinical Pulmonary Fellow, University of California Hospitals, San Francisco Research Fellow, Lung Biology Center and Cardiovascular Research Institute, UCSF Adjunct Assistant Professor of Medicine, UCSF Attending Physician, San Francisco General Hospital Assistant Professor of Medicine in Residence, UCSF Faculty, UCSF Immunology and Biomedical Sciences Graduate Programs UCSF/SFGH General Clinical Research Center (GCRC) Advisory Committee Associate Professor of Medicine, UCSF Investigator, Cardiovascular Research Institute, UCSF Director, Functional Genomics Core Facility, UCSF SABRE Center Professor of Medicine, UCSF Associate Director, UCSF Clinical and Translational Sciences Institute Bioinformatics Program Detur Prize John Harvard Scholarship Alpha Omega Alpha, elected Edward Livingston Trudeau Award of the American Lung Association Member, LCMI Study Section (chair 2010-2012)

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Selected peer-reviewed publications Fifteen most relevant to my role as director of the SABRE Center Functional Genomics Core (all include microarray studies): 1. Kuperman DA, Huang X, Koth LL, Chang GH, Dolganov GM, Zhu Z, Elias JA, Sheppard D, Erle DJ. Direct effects of interleukin-13 on epithelial cells cause airway hyperreactivity and mucus overproduction in asthma. Nat Med 8:885-9, 2002. PMID: 12091879. 2. Barczak A, Rodriguez MW, Hanspers K, Koth LL, Tai YC, Bolstad BM, Speed TP, Erle DJ. Spotted long oligonucleotide arrays for human gene expression analysis. Genome Res 13:1775-85, 2003. PMCID: PMC403751. 3. Woodruff PG, Koth LL, Yang YH, Rodriguez MW, Favoreto S, Dolganov GM, Paquet AC, Erle DJ. A distinctive alveolar macrophage activation state induced by cigarette smoking. Am J Respir Crit Care Med 172:1383-1392, 2005. PMCID: PMC2718436. 4. Kuperman DA, Lewis CC, Woodruff PG, Rodriguez MW, Yang YH, Dolganov GM, Fahy JV, Erle DJ. Dissecting asthma using focused transgenic modeling and functional genomics. J Allergy Clin Immunol 116:305-11, 2005. PMID: 16083784. 5. Woodruff PG, Boushey HA, Dolganov GM, Barker CS, Yang YH, Donnelly S, Ellwanger A, Sidhu SS, Dao-Pick TP, Pantoja C, Erle DJ, Yamamoto KR, Fahy JV. Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids. Proc Natl Acad Sci USA 104:15858-63, 2007. PMCID: PMC2000427. 6. Zhen G, Park SW, Nguyenvu LT, Rodriguez MW, Barbeau R, Paquet AC, Erle DJ. Interleukin-13 and EGF receptor have critical but distinct roles in epithelial cell mucin production. Am J Respir Cell Mol Biol 36(2):244-53, 2007. PMCID: PMC1899314. 7. Lewis CC, Yang JY, Huang X, Banerjee SK, Blackburn MR, Baluk P, McDonald DM, Blackwell TS, Nagabhushanam V, Peters W, Voehringer D, Erle DJ. Disease-specific gene expression profiling in multiple models of lung disease. Am J Respir Crit Care Med 177:376-87, 2008. PMCID: PMC2258439. 8. Park SW, Verhaeghe C, Nguyenvu LT, Barbeau R, Eisley CJ, Nakagami Y, Huang X, Woodruff PG, Fahy JV, Erle DJ. Distinct roles of FOXA2 and FOXA3 in allergic airway disease and asthma. Am J Respir Crit Care Med 180:603-10, 2009. PMCID: PMC2753788. 9. Park SW, Zhen G, Verhaeghe C, Nakagami Y, Nguyenvu LT, Barczak AJ, Killeen N, Erle DJ. The protein disulfide isomerase AGR2 is essential for production of intestinal mucus. Proc Natl Acad Sci USA 106:6950-52009, 2009. PMCID: PMC2678445. 10. Wang BT, Ducker GS, Barczak AJ, Barbeau R, Erle DJ, Shokat KM. The mammalian target of rapamycin regulates cholesterol biosynthetic gene expression and exhibits a rapamycin-resistant transcriptional profile. Proc Natl Acad Sci USA 108:15201-6, 2011. PMCID: PMC3174577. 11. Zhao W, Blagev D, Pollack J, Erle DJ. Toward a systematic understanding of mRNA 3’ untranslated regions. Proc Am Thorac Soc 8:163-6, 2011. PMCID: PMC3131834. 12. Sugimoto K, Kudo M, Sundaram A, Ren X, Huang K, Bernstein X, Wang Y, Raymond WW, Erle DJ, Abrink M, Caughey GH, Huang X, Sheppard D. The αvβ6 integrin modulates airway hyperresponsiveness in mice by regulating intraepithelial mast cells. J Clin Invest 122:748-58, 2012. PMCID: PMC3266785.

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13. Diez D, Goto S, Fahy JV, Erle DJ, Woodruff PG, Wheelock ÅM, Wheelock CE. Network analysis identifies a putative role for the PPAR and type 1 interferon pathways in glucocorticoid actions in asthmatics. BMC Med Genomics 5:27, 2012. PMCID: PMC3408345. 14. Schroeder BW, Verhaeghe C, Park SW, Nguyenvu LT, Huang X, Zhen G, Erle DJ. AGR2 is induced in asthma and promotes allergen-induced mucin overproduction. Am J Respir Cell Mol Biol 47:178-85, 2012. PMCID: PMC3423459. 15. Solberg OD, Ostrin EJ, Love MI, Peng JC, Bhakta NR, Hou L, Nguyen C, Solon M, Nguyen C, Barczak AJ, Zlock LT, Blagev DP, Finkbeiner WE, Ansel KM, Arron JR, Erle DJ*, Woodruff PG*. Airway epithelial miRNA expression is altered in asthma. Am J Respir Crit Care Med 2012 [Epub ahead of print] PubMed PMID: 22955319. * equal contributions. Research Support Active R01 HL099101 (Erle) 01/01/2010-12/31/2013 NIH/NHLBI $247,500 Specialized Molecules with Essential Roles in Mucus Production The major goals of this project are: 1) To analyze AGR2 and AGR3 substrate binding specificity. 2) To determine the in vivo roles of AGR2 and AGR3 in the mouse airway. 3) To analyze the functions of AGR2 and AGR3 in human airway epithelial cells. R21 HL108596 (Erle) 04/06/2011-03/31/2013 NIH/NHLBI $125,000 Micro-RNAs in airway epithelial differentiation and asthma The major goal of this project is to develop tools to determine how selected miRNAs affect airway epithelial cell differentiation and function. P01 HL108794 (PD: Sheppard) 08/09/2012-07/31/2017 NIH/NHLBI $1,666,456 Role: Co-Investigator Program: Targeting Epithelial Cells to Treat Pulmonary Fibrosis This translational program project grant is designed to develop new effective therapies for idiopathic pulmonary fibrosis (IPF). PENDING U19 AI 077439-06 (PD: Sheppard, Project 1 leader: Erle) 04/01/2013-03/31/2018 NIH/NIAID Program: $1,086,097 (priority score: 20, funding expected per NIH program officer) Project 1: $274,962 Program: IL-13 and IL-17 dynamics in the asthmatic airway Project 1: IL-13/17-regulated airway epithelial miRNAs in asthma Overall project goal is to determine how immune cells producing IL-13 and IL-17 specifically modulate contractile responses of airway smooth muscle and the relevance of these pathways to human asthma.

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Completed R21 HG004665 (Erle) 04/01/08-03/31/10 NIH/NHGRI Tools for high-throughput functional analysis of 3’ UTR cis-regulatory elements The major goals of this project were: 1) To optimize the design and implementation of the 3’ UTR high-throughput reporter system. 2) To use the system to identify cis-regulatory elements within a representative group of 3’ UTRs from ENCODE regions of the genome. UL1 RR024131 (PD: McCune) 09/30/06-06/30/11 NIH/NCRR Clinical and Translational Science Institute Role on project: Co-investigator The overall mission of the CTSI is to create an integrated academic home that transforms research and education in clinical investigation and translational science at UCSF and throughout the community. Dr. Erle is a member of the Bioinformatics unit of the CTSI, which supports clinical and translational research and training at UCSF. R01 HL085089 (Erle) 07/21/06-06/30/12 NIH/NHLBI Airway Epithelial Responses to Allergic Inflammation The major goals of this project were: 1) To determine the role of the EGF receptor pathway in the airway epithelial cell response to IL-13. 2) To determine the role of the transcription factor FOXA2 in the airway epithelial cell response to IL-13. 3) To determine how the IL-13inducible epithelial anion exchanger SLC26A4 (Pendrin) contributes to allergic airway disease. 4) To determine how the IL-13-inducible goblet cell-specific secreted protein anterior gradient 2 (AGR2) contributes to allergic airway disease.

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BIOGRAPHICAL SKETCH NAME John Vincent Fahy, M.D., M.Sc. eRA COMMONS USER NAME johnfahy

POSITION TITLE Professor of Medicine in Residence

EDUCATION/TRAINING INSTITUTION AND LOCATION

DEGREE

YEAR(s)

FIELD OF STUDY

University College Dublin

MB BAO BCH Intern Resident Registrar Fellow

1985

Medicine

1985-1986 1986-1989 1988-1999 1989-1993

Medicine and Surgery Internal Medicine Respiratory Medicine Pulmonary/Critical Care Medicine

(doctorate by thesis)

1997

Respiratory Medicine

M.Sc.

(Sabbatical year)

University College Dublin Trinity College Dublin University College Dublin University of California, San Francisco University College Dublin Trinity College Dublin

M.D.

2003

Molecular Medicine

Positions Internship and Residencies 1985 - 1986 1986 - 1988 1988 - 1989 1989 - 1993

Medicine Intern, St Vincent’s Hospital, University College Dublin. Senior House Officer, St James’ Hospital, Trinity College Dublin. Medicine Registrar (pulmonary medicine), St Vincent’s Hospital, University College Dublin. Fellow, Pulmonary and Critical Care Medicine, UCSF.

Academic Appointments 1993 - 1998 1999 - 2005 2005 - Present

Assistant Adjunct Professor of Medicine, UCSF. Associate Professor of Medicine in Residence, UCSF. Professor of Medicine in Residence, UCSF.

Other Experience and Professional Memberships 1993 - Present 2005 - 2006 2006 - Present 2007 - Present 2004 - Present

Member, Steering Committee, NHLBI’s Asthma Clinical Research Network Member, Executive Planning Committee, NHLBI Strategic Plan Director, Airway Clinical Research Center, UCSF. Chair, Data and Safety Monitoring Board for Division of Lung Diseases SCCOR Program Member, Program Committee, Asthma, Inflammation, and Immunology Assembly, ATS.

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2009 - 2010 2009 - Present 2010 - Present

Chair (elected), Program Committee, Asthma, Inflammation, & Immunology Assembly, ATS. Member, Trans NIH Asthma Outcomes Working Group. Member, Scientific Committee, Transatlantic Airway Conference.

Honors 1984 1985 1990 1994 2006

Kirwan Gold Medal and Prize in Ophthalmology, University College Dublin (UCD) Graduated fifth in class of 120 students, UCD Medical School (one of 10 to receive an honors degree). Travelling Studentship in Medicine, National University of Ireland Physician Scientist Award, American College of Chest Physicians. Michael S. Stulbarg Endowed Chair in Pulmonary Medicine, UCSF.

Selected Peer-reviewed Publications 1. Ordoñez CL, Khashayar, R, Wong HH, Ferrando R, Wu R, Hyde DM, Hotchkiss JA, Zhang Y, Novikov A, Dolganov G, Fahy JV. Mild and moderate asthma is associated with goblet cell hyperplasia and abnormalities in mucin gene expression. Am J Resp Crit Care Med 2001;163:517-523. 2. Hays SR, Woodruff PG, Khashayar R, Ferrando RE, Liu J, Fung P, Zhao CQ, Wong HH, Fahy JV. Allergen challenge causes inflammation but not goblet cell degranulation in asthmatic subjects. J Allergy Clin Immunol 2001;108:784-790. 3. Woodruff PG, Boushey HA, Dolganov GM, Barker CS, Yang YH, Donnelly S, Ellwanger A, Sidhu S, Dao-Pick TP, Pantoja C, Erle DJ, Yamamoto KR, Fahy JV. Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids. Proc Natl Acad Sci USA 2007; 104:15858-63. 4. Seibold MA, Donnelly S, Solon M, Innes A, Woodruff PG, Boot R, Burchard EG, Fahy JV. Chitotriosidase is the primary active chitinase in the human lung and is modulated by genotype and disease. J Allergy Clin Immunol. 2008;122:944-950. PMCID: PMC2666777. 5. Innes AL. Carrington SD, David J. Thornton DJ, Kirkham S, Dougherty RH, Raymond WW, Caughey GH, Muller SJ, Fahy JV. Ex vivo sputum analysis reveals impairment of proteasedependent mucus degradation by plasma proteins in acute asthma. Am J Respir Crit Care Med. 2009;180:203-10. PMCID: PMC2724713. 6. Woodruff PG, Modrek M, Choy DF, Guiquan J. Abbas AR, Ellwanger A, Koth LL, Arron JR, Fahy JV. TH2-driven inflammation defines major sub-phenotypes of asthma. Am J Respir Crit Care Med. 2009;180:388-95. 7. Seibold MA, Reese TA, Choudhry S, Salam MT, Beckman K, Eng C, Atakilit A, Meade K, Lenoir M, Watson HG, Thyne S, Kumar R, Weiss KB, Grammer LC, Avila P, Schleimer RP, Fahy JV, Rodriguez-Santana J, Rodriguez-Cintron W, Boot RG, Sheppard D, Gilliland FD, Locksley RM, Burchard EG. Differential enzymatic activity of common haplotypic versions of the human acidic mammalian chitinase protein. J Biol Chem 2009;284:19650-8. 8. Dougherty RH, Sidhu SS, Raman K, Solon M, Solberg OD, Caughey GH, Woodruff PG, Fahy JV. Accumulation of Intra-epithelial Mast Cells with a Unique Protease Phenotype in TH2-high Asthma. J Allergy Clin Immunol. 2010;125:1046-1053. 9. Sukhvinder SS, Yuan S, Innes AL, Kerr S, Woodruff PG, Solon M, Hou L, Muller SL, Fahy JV. Epithelial cell-derived periostin: roles in TGFβ activation, collagen production and collagen elasticity in asthma. Proc Natl Acad Sci USA. 2010;107:14170-5.

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10. Fahy JV, Dickey B. Airway Mucus - Function and Dysfunction. New Engl J of Med. 2010; 2;363:2233-47. 11. Innes AL, Wong McGrath K, Dougherty RH, McCulloch CE, Woodruff PG, Seibold MA, Okamoto KS, Kelsey J. Ingmundson KJ, Solon MC, Carrington SD, Fahy JV. The H Antigen at Epithelial Surfaces is Associated with Susceptibility to Asthma Exacerbation. Am J Respir Crit Care Med. 2011;183:189-94. 12. Choy DF, Modrek B, Abbas AR, Kummerfeld S, Clark HF, Wu LC, Fedorowicz G, Modrusan Z, Fahy JV, Woodruff PG, Arron JR. Gene expression patterns of TH2 inflammation and intercellular communication in asthmatic airways. J Immunol. 2011;186:1861-9. 13. Fahy JV, Locksley RM, The airway epithelium as a regulator of TH2 responses in asthma. American Journal of Respiratory and Critical Care Medicine 2011;184: 390-392. 14. Gordon ED, Sidhu SS, Wang ZE, Woodruff PG, Yuan S, Solon MC, Conway SJ, Huang X, Locksley RM, Fahy JV. A protective role for periostin and TGFβ in IgE-mediated allergy and airway hyperresponsiveness. Clinical and Experimental Allergy 2012;42:144-55. 15. Wong McGrath K, Icitovic N, Boushey HA, Lazarus SC, Sutherland, ER, Chinchilli VM, Fahy JV. A large subgroup of mild moderate asthma is persistently non-eosinophilic. American Journal of Respiratory and Critical Care Medicine. 2012; 185(6):612-9.

Research Support 1P01HL107202 (Fahy, JV) 8/1/12 - 6/30/17 Innate and Adaptive Immune Responses in Th2-high Asthma This PPG will comprehensively investigate the molecular underpinnings of the Th2-high molecular subtype of asthma Role: Overall PPG PI (Project leader for project 3 and Core leader for the Administrative Core and the Human Subjects Core. 1U10HL109146 (Fahy JV) 8/1/2011-7/31/2017 Clinical and Molecular Phenotypes of Severe Asthma This grant was submitted in response to the RFA for Clinical Centers for the Severe Asthma Research program) – a 6-center national program for research into mechanisms of severe asthma. Role: PI 5 R01 HL080414 (Fahy, JV) 7/01/05-05/31/15 Protein carbohydrate interactions in the pathophysiology of acute asthma exacerbations The major goals of this project are to investigate how lectins interact with mucin glycans to cause airway mucus obstruction in acute severe asthma. Role: PI 1P50HL107191 (Fahy, JV) 5/01/11-04/30/13 Preventing fucose-dependent binding of aspergillus and pseudomonas to lung mucin This grant was submitted in response to the RFA for “Centers for Advanced Diagnostics and Experimental Therapeutics (CADET-1)”. Role: PI

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1 U19 A1077439 (Sheppard, D) 4/01/08-3/31/13 NIH/NIAID Mechanisms of Initiation & Persistence of Allergic Asthma; Project 3: Chitinases and TGFβ in human asthma. The goal of this center grant is to examine the role of chitinases and TGFβ pathway genes in asthma. Project 3 specifically focuses on genetic and translational studies of chitinases & TGFβ in asthma. Role: Co-Leader of Project 3 (with Esteban Burchard, M.D.) 1 R01 HL097591 (Woodruff, PG) 7/01/09-06/30/13 NIH/NHLBI Role of Th2 and non-Th2 Inflammation in Airway Smooth Muscle Remodeling in Asthma. This grant supports studies of airway smooth muscle in asthma. Role: Co-investigator

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BIOGRAPHICAL SKETCH NAME Xiaozhu Huang, M.D.

POSITION TITLE Associate Professor EDUCATION

INSTITUTION AND LOCATION

DEGREE

YEAR

FIELD OF STUDY

M.D.

1983

Medicine

M.S.

1988

Pathology

Tongji Medical University, Wuhan, People's Republic of China Tongji Medical University, Wuhan, People's Republic of China

Positions 6/83 to 7/84 8/84 to 8/85

Teaching Assistant, Dept. of Pathology, Tongji Medical University, China Pathology Residence, The First Attached Hospital, Tongji Medical University, China 9/88 to 1/92 Research Assistant, Dept. of Pathology, Tongji Medical University, China 1/92 to 12/95 Postdoctoral Fellow, Dept. of Medicine, Lung Biology Center University of California, San Francisco 1/96 to 6/97 Postgraduate Researcher, Dept. of Medicine, Lung Biology Center University of California, San Francisco 7/97 to 11/99 Assistant Research Molecular Biologist, Dept. of Medicine, Lung Biology Center University of California, San Francisco 12/99 to 6/2005 Assistant Professor, Dept. of Medicine, Lung Biology Center University of California, San Francisco 07/2005 to present Associate Professor, Dept. of Medicine, Lung Biology Center University of California, San Francisco Honors 1989

"Outstanding Teacher" Honor, Department of Pathology, Tongji Medical University 1/1992 to 12/1993 Cheng Research Scholar Award,

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Selected peer-reviewed publications 1. Huang XZ, Chen A, Agrez M, Sheppard D. A point mutation in integrin b6 subunit abolishes both avb6 binding to fibronectin and receptor localization to focal adhesion plaques. Am. J. Respir. Cell Mol. Biol. 1995; 13:245-251. 2. Huang XZ, Wu JF, Cass D, Erle DJ, Corry D, Young SG, Farese RV, Jr., Sheppard D. Inactivation of the integrin b6 subunit gene reveals a role of epithelial integrins in regulating inflammation in the lungs and skin. J. Cell Biol. 1996; 133:921-928. 3. Huang XZ, Wu JF, Zhu W, Pytela R, Sheppard D. Expression of the human integrin b6 subunit in alveolar type II cells and bronchiolar epithelial cells reverses lung inflammation in b6 knockout mice. Am. J. Respir. Cell Mol. Biol. 1998; 19:636-642. 4. Huang XZ, Wu JF, Spong S, Sheppard D. The integrin avb6 is critical for keratinocyte migration on both its known ligand, fibronectin, and on vitronectin. J. Cell Sci. 1998; 111:2189-2195. 5. JS Munger, XZ Huang, H Kawakatsu, MJD Griffiths, SL Dalton, JF Wu, JF Pittet, N Kaminiski, C Garat, MA Matthay, DB Rifkin, D Sheppard. The integrin avb6 binds and activates latent TGFb1: a mechanism for regulating pulmonary inflammation and fibrosis. Cell 1999; 96:319-328. 6. Milner R, Huang XZ, Wu J, Nishimura S, Pytela R, Sheppard D, ffrench-Constant C. Distinct roles for astrocyte avb5 and avb8 integrins in adhesion and migration. J. Cell Sci. 1999; 112: 4271-4279. 7. Huang XZ, Griffiths M, Wu JF, Farese RV, Sheppard D. Normal development, wound healing, and adenovirus susceptibility in b5-deficient mice. Mol. Cell Biol. 2000; 20:755-759. 8. Kaminski N, Allard J, Pittet J-F, Zuo F, Griffiths MJD, Morris D, Huang XZ, Sheppard D, Heller RA. Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and remodeling. Proc. Nat. Acad. Sci. 2000; 97:1778-1783. 9. Huang XZ, Wu JF, Ferrando R, Wang YL, Lee JH, Farese RV, Sheppard D. Fatal Bilateral Chylothorax in Mice Lacking the Integrin a9b1. Mol. Cell Biol. 2000; 20:5208-5215. 10. Pittet JF, Griffiths MJ, Geiser T, Kaminski N, Dalton SL, Huang XZ, Brown LA, Gotwals PJ, Koteliansky VE, Matthay MA, Sheppard D. TGF-beta is a critical mediator of acute lung injury. J Clin Invest. 2001, 107:1537-44. 11. Reynolds LE, Wyder L, Lively JC, Taverna D, Robinson SD, Huang XZ, Sheppard D, Hynes RO, Hodivala-Dilke KM. Enhanced pathological angiogenesis in mice lacking beta3 integrin or beta3 and beta5 integrins. Nat Med. 2002, 8:27-34. 12. Eliceiri BP, Puente XS, Hood JD, Stupack DG, Schlaepfer DD, Huang XZ, Sheppard D, Cheresh DA. Src-mediated coupling of focal adhesion kinase to integrin alpha(v)beta5 in vascular endothelial growth factor signaling. J Cell Biol. 2002, 157:149-60. 13. Kuperman DA, Huang XZ, Koth LL, Chang GH, Dolganov GM, Zhu Z, Elias JA, Sheppard D, Erle DJ. Direct effects of interleukin-13 on epithelial cells cause airway hyperreactivity and mucus overproduction in asthma. Nat Med. 2002, 8:885-9. 14. Knight PA, Wright SH, Brown JK, Huang XZ, Sheppard D, Miller HR. Enteric expression of the integrin alpha(v)beta(6) is essential for nematode-induced mucosal mast cell hyperplasia and expression of the granule chymase, mouse mast cell protease-1. Am J Pathol. 2002, 161:771-9. 15. Morris DG, Huang XZ, Kaminski N, Wang Y, Shapiro SD, Dolganov G, Glick A, Sheppard D. Loss of integrin-mediated TGF-b activation causes Mmp12-dependent

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pulmonary emphysema. Nature 2003, 422:169-73. 16. Nandrot EF, Kim Y, Brodie SE, Huang XZ, Sheppard D, Finnemann SC. Loss of synchronized RPE phagocytosis and age-related blindness in mice lacking avb5 integrin. J Exp Med. 2004, 200:1539-45. 17. Lane NE, Yao W, Nakamura MC, Humphrey MB, Kimmel D, Huang XZ, Sheppard, Ross FP, Teitelbaum SL. Mice lacking the integrin beta5 subunit have accelerated osteoclast maturation and increased activity in the estrogen-deficient state. J Bone Miner Res. 2005, 20:58-66. 18. Kuperman DA, Huang XZ, Nguyenvu L, Hölscher C, Brombacher F, Erle DJ. IL-4 receptor signaling in Clara cells is required for allergen-induced mucus production. J. Immunol. 2005, 175:3746-3752. 19. Atabai K, Fernandez R, Huang X, Ueki I, Kline A, Li Y, Sadatmansoori S, SmithSteinhart C, Zhu W, Pytela R, Werb Z, Sheppard D. Mfge8 Is Critical for Mammary Gland Remodeling during Involution. Mol Biol Cell. 2005, 16:5528-37. 20. Voehringer D, Reese TA, Huang X, Shinkai K, Locksley RM. Type 2 immunity is controlled by IL-4/IL-13 expression in hematopoietic non-eosinophil cells of the innate immune system. J Exp Med. 2006, 203:1435-46. 21. Wang B, Huang X*, Wolters PJ, Sun J, Kitamoto S, Yang M, Riese R, Leng L, Chapman H A., Finn P W., David J R., Bucala R, and Shi GP. Deficiency of Macrophage Migration Inhibitory Factor Impairs Murine Airway Allergic Responses. J Immunol 2006, 177:5779-5784 (* Co-first author) 22. Chen C, Huang X, Sheppard D. ADAM33 is not essential for growth and development and does not modulate allergic asthma in mice. Mol Cell Biol. 2006, 26:6950-6. 23. Chen C, Huang X, Atakilit A, Zhu QS, Corey SJ, Sheppard D. The Integrin alpha9beta1 Contributes to Granulopoiesis by Enhancing Granulocyte ColonyStimulating Factor Receptor Signaling. Immunity. 2006, 25:895-906. 24. Su G, Hodnett M, Wu N, Atakilit A, Kosinski C, Godzich M, Huang XZ, Kim JK, Frank JA, Matthay MA, Sheppard D, Pittet JF. Integrin {alpha}v{beta}5 Regulates Lung Vascular Permeability and Pulmonary Endothelial Barrier Function. Am J Respir Cell Mol Biol. 2007, 36:377-86. 25. Travis MA, Reizis B, Melton AC Masteller E, Tang Q, Proctor J, Wang Y, Bernstein X, Huang X, Riechardt L, Bluestone J, Sheppard D. Loss of integrin avb8 on dendritic cells causes autoimmunity and colitis in mice. Nature 2007; 449:361-365. 26. Horan GS, Wood S, Ona V, Li DJ, Lukashev ME, Weinreb PH, Simon KJ, Hahm K, Allaire NE, Rinaldi NJ, Goyal J, Feghali-Bostwick CA, Matteson EL, O'hara C, Lafyatis R, Davis GS, Huang X, Sheppard D, Violette SM. Partial Inhibition of Integrin {alpha}v{beta}6 Prevents Pulmonary Fibrosis Without Exacerbating Inflammation. Am J Respir Crit Care Med 2008; 177:56-65. 27. Nakagami Y, Favoreto S Jr, Zhen G, Park SW, Nguyenvu LT, Kuperman DA, Dolganov GM, Huang X, Boushey HA, Avila PC, Erle DJ. The epithelial anion transporter pendrin is induced by allergy and rhinovirus infection, regulates airway surface liquid, and increases airway reactivity and inflammation in an asthma model. J Immunol. 2008 Aug 1;181(3):2203-10. 28. Song Y, Pittet JF, Huang X, He H, Lynch SV, Violette SM, Weinreb PH, Horan GS, Carmago A, Sawa Y, Bernstein XL, Wiener-Kronish JP. Role of integrin alphav beta6 in acute lung injury induced by Pseudomonas aeruginosa. Infect Immun. 2008 Jun;76(6):2325-32 29. Caceres AI, Brackmann M, Elia MD, Bessac BF, del Camino D, D'Amours M, Witek JS, Fanger CM, Chong JA, Hayward NJ, Homer RJ, Cohn L, Huang X, Moran MM, Jordt SE.A sensory neuronal ion channel essential for airway inflammation and

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hyperreactivity in asthma.Proc Natl Acad Sci U S A. 2009 Jun 2;106(22):9099-104. 30. Park SW, Verhaeghe C, Nguyenvu LT, Barbeau R, Eisley CJ, Nakagami Y, Huang X, Woodruff PG, Fahy JV, Erle DJ. Distinct Roles of FOXA2 and FOXA3 in Allergic Airway Disease and Asthma. Am J Respir Crit Care Med. 2009 Jul 23. 31. Huang F, Rock JR, Harfe BD, Cheng T, Huang X, Jan YN, Jan LY. Studies on expression and function of the TMEM16A calcium-activated chloride channel. Proc Natl Acad Sci U S A. 2009 Dec 15;106(50):21413-8 32. Frank Kirstein, Horsnell G William, Douglas A Kuperman, Xiaozhu Huang, David J Erle, Andreas L Lopata, Frank Brombacher, Expression of IL-4 Receptor alpha on smooth muscle cells is not necessary for development of experimental allergic asthma. J Allergy Clin Immunol. 2010 Aug;126(2):347-354 33. Li, S. , Chen, Y. , Zhang, S. , More, S.S. , Huang, X. , Giacomini, K.M. Role of Organic Cation Transporter 1, OCT1 in the Pharmacokinetics and Toxicity of cis Diammine(pyridine)chloroplatinum(II) and Oxaliplatin in Mice. Pharm Res. 2010 Nov 23 34. Yu Hua Chow, Xiao Dong Zhu, Li Liu, Barbara Schwartz, Xiaozhu Huang, John Harlan, Lynn M Schnapp. Role of Cdk4 in lymphocyte function and allergen response. Cell Cycle. 2010 Dec 15;9(24):4922-30 35. Masuno K, Haldar SM, Jeyaraj D, Mailloux C, Huang X, Panettieri Jr RA, Jain MK, Gerber AN. Expression Profiling Identifies Klf15 as a Glucocorticoid Target that Regulates Airway Hyperresponsiveness. Am J Respir Cell Mol Biol. 2011 Jan 21 36. Kudo M, Melton AC, Chen C, Engler MB, Huang KE, Ren X, Wang Y, Bernstein X, Li JT, Atabai K, Huang X*, Sheppard D. IL-17A produced by αβ T cells drives airway hyper-responsiveness in mice and enhances mouse and human airway smooth muscle contraction. Nat Med. 2012 Mar 4;18(4):547-54 (*co-authorship) 37. Vijayanand P, Seumois G, Simpson LJ, Abdul-Wajid S, Baumjohann D, Panduro M, Huang X, Interlandi J, Djuretic IM, Brown DR, Sharpe AH, Rao A, Ansel KM. Interleukin-4 production by follicular helper T cells requires the conserved Il4 enhancer hypersensitivity site V. Immunity. 2012 Feb 24;36(2):175-87 38. Thornton E, Looney M, Sheppard D, Locksley R, Huang X, Krummel M. Dynamics of antigen capture and presentation revealed by two-photon live imaging in the lung. J Exp Med. 2012 Jun 4;209(6):1183-99 39. Schroeder BW, Verhaeghe C, Park SW, Nguyenvu LT, Huang X, Zhen G, Erle DJ. AGR2 is Induced in Asthma and Promotes Allergen-Induced Mucin Overproduction. Am J Respir Cell Mol Biol. 2012 Aug;47(2):178-85 40. Bhattacharya M, Su G, Su X, Oses-Prieto JA, Li JT, Huang X, Hernandez H, Atakilit A, Burlingame AL, Matthay MA, Sheppard D. IQGAP1 is necessary for pulmonary vascular barrier protection in murine acute lung injury and pneumonia. Am J Physiol Lung Cell Mol Physiol. 2012 Jul 1;303(1):L12-9 41. Chun Chen, Makoto Kudo, Florentine Rutaganira, Hiromi Takano, Candace Lee, Amha Atakilit, Toshimitsu Uede, Paul Wolters, Stephen Liggett, Kevan M. Shokat, Xiaozhu Huang and Dean Sheppard . Integrin α9β1 in airway smooth muscle regulates a novel brake on exaggerated murine and human airway narrowing. JCI 2012 Aug 1;122(8):2916-27 42. Huang F, Zhang H, Wu M, Yang H, Kudo M, Peters CJ, Woodruff PG, Solberg OD, Donne ML, Huang X, Sheppard, Fahy JV, Wolters PJ, Hogan BL, Finkbeiner WE, Li M, Jan YN, Jan LY, Rock JR. Calcium-activated chloride channel TMEM16A modulates mucin secretion and airway smooth muscle contraction. Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16354-9. 43. Julia Freimuth, Frederic F. Clermont, Xiaozhu Huang, Angela De Sapio, Taku Tokuyasu, Dean Sheppard, Rosemary J. Akhurst. Epistatic interactions between

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Tgfb1 and genetic loci, Tgfbm2 and Tgfbm3, determine susceptibility to an asthmatic stimulus. Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):18042-7 44. Kudo M, Khalifeh Soltani SM, Sakuma SA, McKleroy W, Lee TH, Woodruff PG, Lee JW, Huang K, Chen C, Arjomandi M, Huang X, Atabai K. Mfge8 suppresses airway hyperresponsiveness in asthma by regulating smooth muscle contraction. Proc Natl Acad Sci U S A. 2013 Jan 8;110(2):660 *Equal contribution

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BIOGRAPHICAL SKETCH NAME Matthew Frederick Krummel, Ph.D eRA COMMONS USER NAME Krummel

POSITION TITLE Associate Professor

EDUCATION/TRAINING INSTITUTION AND LOCATION

FIELD OF STUDY

DEGREE

YEAR(s)

University of Illinois at Champaign-Urbana

B.S.

1989

University of California at Berkeley Walter and Eliza Hall Institute, Melbourne Australia Stanford University

Ph.D.

1995

Biology and Chemistry Immunology

1996-1997

Immunology

1997-2001

Immunology

Positions Summer 1987 Summer 1988 1989-1996 1996-1997 1997-2001 2001-2006 July 2006-Present 2006-Present 2012-Present Honors 2009-2012 2005-2010 2004-2007 1997-2000 1996-1997

Summer Undergraduate Research Fellow, UTHSCD Stagiare (Technician) Institut Pasteur, Paris, Unite de Genie Micro-Biologique. Graduate Student and Postdoctoral Fellow, University of California at Berkeley, Department of Molecular and Cell Biology Postdoctoral Fellow, Walter and Eliza Hall Institute, Melbourne Australia Postdoctoral Fellow, Beckman Institute, Stanford University, Stanford, CA Assistant Professor, Department of Pathology, UCSF Associate Professor, Department of Pathology, UCSF Faculty Director, Biological Imaging Development Center, UCSF Professor, Department of Pathology, University of California at San Francisco Fellow of the American Asthma Foundation Leukemia and Lymphoma Foundation, Career Award Investigator Award, Cancer Research Institute. NRSA Postdoctoral Fellowship, National Institutes of Health Postdoctoral Fellowship, Juvenile Diabetes Foundation International

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1998 1987

PATENT: J.P.Allison, D.R.Leach, and M.F. Krummel. Blockade of T Lymphocyte Down-Regulation Associated with CTLA-4 Signaling. US Patent 5,811,097 Summer Undergraduate Research Fellowship, Howard Hughes Medical Institute

Selected Peer-reviewed Publications (out of 51) 1. Krummel MF and Allison JP. 1995. CD28 and CTLA-4 have opposing signals which regulate the response of T cells to stimulation. J. Exp Med. 182, 459-465. PMCID: PMC2192127 2. Krummel MF, Sullivan TJ and Allison JP. 1995. Superantigen responses and costimulation: CD28 and CTLA-4 have opposing effects on T cell expansion In Vitro and In Vivo. Int.Immunol. 8, 101-105. PMCID: 8671638 3. Krummel MF and Allison JP. 1996. CTLA-4 Engagement Inhibits IL-2 Accumulation and Cell Cycle Progression Upon Activation of Resting T cells. J Exp Med 183, 2533-2540. PMCID: PMC2192613 4. Leach, D.R., Krummel MF and Allison JP. 1996. Enhancement of antitumor immunity by CTLA-4 blockade. Science. 271, 1734-1736. PMID: 8596936 5. Krummel MF, Sjaastad MD, Wülfing C and Davis MM. 2000. Differential clustering of CD4 and CD3z during T cell recognition. Science. 289, 1349-1352. PMID: 10958781 6. Jacobelli J, Chmura SA, Buxton DB, Davis MM and Krummel MF. 2004. A single class II myosin modulates T cell motility and stopping, but not synapse assembly. Nature Immunology 5, 531 – 538. PMCID: 15064761 7. Friedman RS Jacobelli J and Krummel MF. 2006. Surface-bound Chemokines Capture and Prime T cells For Synapse Formation. Nature Immunology 7, 1101-8. PMID: 16964261 8. Sabatos CA, Doh J, Chakravarti S, Friedman RS, Pandurangi PG, Tooley AJ, Krummel, MF. 2008. A Synaptic Basis for Paracrine Interleukin-2 Signaling in Activating T cells. Immunity. 29(3): 238-248. PMID: 18674934 9. Tooley AJ, Gilden J, Jacobelli J, Trimble W, Kinoshita M and Krummel MF. 2009. Amoeboid T lymphocytes require the septin cytoskeleton for cortical integrity and persistent motility. Nature Cell Biology. Jan;11(1):17-26. Epub 2008 Nov 30. PMID: 19043408 10. Jacobelli J, Friedman RS, Conti MA, Lennon-Dumenil AM, Piel M, Sorensen CM, Adelstein RS, Krummel MF. Confinement-optimized three-dimensional T cell amoeboid motility is modulated via myosin IIA-regulated adhesions. Nat Immunol. 11: 953-961. PMCID: PMC2943564 11. Friedman RS, Beemiller P, Sorensen CM, Jacobelli J, Krummel MF. 2010. Realtime analysis of T cell receptors in naive cells in vitro and in vivo reveals flexibility in synapse and signaling dynamics. J Exp Med. 11(10):953-61. PMCID: PMC2989766 12. Looney MR, Thornton EE, Sen D, Lamm WJ, Glenny RW, Krummel MF. 2011. Stabilized Imaging of immune surveillance in the mouse lung. Nat Methods. 8(1):91-6. PMCID: PMC3076005 13. Englehardt JE, Boldajipour B, Beemiller P, Werb Z, Pandurangi P, Sorenson C, Egelblad M, Krummel MF. Marginating dendritic cells of the tumor microenvironment cross-present tumor antigens and stably engage tumor-specific T cells. Cancer Cell. 2012 Mar 20;21(3):402-17. doi: 10.1016/j.ccr.2012.01.008. PMCID: PMC3311997

14. Thornton EE, Krummel MF, Looney, M.R. 2012. Live Imaging of the Lung. Curr Protoc Cytom. Apr; Chapter 12:Unit12.28. 15. Thornton EE, Looney MR, Bose O, Sen D, Sheppard D, Locksley R, Huang X, Krummel MF. 2012. Spatiotemporally Separated Antigen Uptake by Alveolar Dendritic Cells and Airway Presentation to T Cells in the Lung. J Exp Med., 209(6):1183-99. Research support Ongoing Research Support 1U01HL111054-01 (Chapman, Chuang, 01/01/12-12/31/16 Krummel, multi-PI) (co-PI) NIH Epithelial Progenitor Cells in Lung Repair and Regeneration: Note: Scored 20 at study section The goal of this project is to image the process of lung repair and regeneration using 2-photon microscopy. Role: co-PI 1U01CA141451 (PI: Krummel) 09/01/09-08/31/14 NIH Collaborative Innate-Adaptive Immune Regulation of Tumor Progression The major goals of this project are Goal 1: Visualize the progression in crosstalk between the innate and adaptive immune response during tumor development using mouse models of luminal and basal breast cancer. Goal 2: Define the specific attractants that regulate immune cell-cell interactions in the tumor. Goal 3: Use mouse models to determine mechanisms of existing and putative immuno- and cytotoxic anti-cancer regimens and to design and test combinatorial therapies based upon this information. Role: co-PI P01 HL024136 (PI: Caughey) 05/11/10-03/31/14 NIH/NHLBI Evolving Microenvironments in Airway Inflammation The aims of this proposal are to identify shifts in antigen-trafficking into APC, the temporal pairing of specific APC with T cell subsets, and the effects of Mycoplasma-mediated inflammation and mast-cell-mediated regulation upon T cell-APC pairing in lung microenvironments. Role: co-PI P01 HL024136 (PI: Caughey) 05/11/10-03/31/14 Core B This Core supports the basic activities of the PPG. Role: co-PI

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1R21CA167601 (PI) 05/01/12-03/31/14 NIH/NCI Defining the First Hours of Lung metastasis using Intravital Live-Imaging This proposal will apply novel intravital imaging of the lung to define the first hours following the arrival of metastatic cells into the mouse lung. As we know very little about why metastatic tumor cells survive in this environment, this represents a major undertaking in determining how to decrease their success. Role: PI R01AI052116 (PI: Krummel) 01/15/12-12/31/17 NIH Myosin Motors in T cell Synapse Formation and Activation The major goals of this project are to analyze MyoIIA regulation during T cell motility and synapse formation. This includes mutational analyses as well as generation and analyses of knockout animals. Role: PI U54 CA163123-01 (Coussens, Krummel, 09/1/12-08/30/13 Van't Veer: multi-PI) (PI (MPI)) NIH/NCI Leukocyte Biomarkers for Predicting Human Breast Cancer Outcome The goal of this project is to identify predictive biomarkers in human breast cancer, using genomic profiling of mouse and human breast cancer infiltrates and correlated analyses of outcome. Role: PI 1R21CA167415-01 (PI) 05/01/12-04/30/14 NIH/NCI Phage-Display Technology to Define and Manipulate Breast Tumor Stroma This proposal will utilize rapid phage-display screening methods to identify novel epitopes on tumor stromal cells. Through a rapid evolution and Fc-tagging method, both diagnostic and therapeutic uses of these reagents will be assessed. This will provide a rapid pipeline between identification of key cell types and their characterization and targeting. Role: PI Completed Research Support R01 CA134622 ARRA (PI: Krummel) 07/17/09-06/30/11 NIH Regulation of T cell Functions by the Breast Cancer Microenvironment The major goals of this project are Aim 1: Define the Nature of the CD8+ T cell response in the microenvironment of a Spontaneous Breast Tumor.

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Aim 2: Define the Nature of Tumor Sampling APCs (TSAPCs), the phenotype and capacity of these cells to activate T cells, and the changes in this population with addition of functional CD8+ T cells. Aim 3: Define the effects of CD4 +T cell subsets, particularly regulatory cells, on CD8 activity in vivo and upon the quantity and phenotype of TSAPCs. Role: PI Fellowship (PI: Krummel) 07/01/05-06/30/10 Leukemia & Lymphoma Society Tumor Suppressors in T cell Synapse Formation and Signaling The major goals of this project are Aim 1. We will determine the role of Septin9/MSF in T cell synapse development, signaling, and proliferative control. Aim 2. We will determine the role of lgl proteins in T cell synapse development, signaling, and proliferative control. Role: PI AAF Fellow (PI: Krummel) 07/01/09-06/30/12 American Asthma Foundation Directing Antigens to Specific APC and T cell subsets in the Lung The major goals of this project are to screen for conditions that bias antigens towards particular antigen presenting cell populations and then to read out, through imaging and functional assays, the resulting T cell responses with the aim of optimizing regulatory interaction pathways. Role: PI

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BIOGRAPHICAL SKETCH NAME Limin Liu, Ph.D. eRA COMMONS USER NAME LIMINLIU

POSITION TITLE Associate Professor

EDUCATION/TRAINING INSTITUTION AND LOCATION University of Science & Technology of China University of Missouri, Columbia, MO Duke University Medical Center

DEGREE

YEAR(s)

B.S. Ph.D.

1986 1995

FIELD OF STUDY Biology Molecular Biology Nitric Oxide Biology

Positions 1996- 1997

Research Associate, Department of Animal Sciences, University of Missouri-Columbia 1997- 2004 Research Associate, Department of Medicine, Division of Pulmonary Medicine, Duke University Medical Center 1998-2003 Research Associate, Howard Hughes Medical Institute, Duke University Medical Center 2005-2012 Assistant Professor, Sandler Center for Basic Research in Asthma, Department of Microbiology and Immunology, University of California San Francisco 2012-Present Associate Professor, Sandler Center for Basic Research in Asthma, Department of Microbiology and Immunology, University of California San Francisco

Honors 1989-1990 1989-1993 1994 2005 2006

Scholarship, Division of Biological Sciences, University of Missouri Predoctoral Fellowship, Molecular Biology Program, University of Missouri New Investigator Award (First Place), Society for the Study of Reproduction (Biology of Reproduction, Vol. 52, pp. 261) Stewart Trust Cancer Research Award Sandler Innovative Research Award

Selected peer-reviewed publications (in chronological order) 1.

Wu WY, Zhao YG and Liu L (1989). Trophic effect of slow nerve on minced fast muscle from newly hatched chicks transplanted into three-week chicks. Chin J Physiol Sci 5:95-97.

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2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16.

17. 18. 19.

Wu WY, Zhao YG, Liu L, Lu DX and Tian, WH (1990). The second stage commitment of chick muscle satellite cells and its relation to the state of innervation. Chin J Physiol Sci 6:19-29. Roberts RM and Liu L (1996). Interferon-ω. In: Aggarawal BB and Gutterman U, eds., Human Cytokines: Handbook for Basic and Clinical Research (II), pp.168-177. Liu L, Leaman DW, Bixby JA and Roberts RM (1996). A type 1 ovine interferon with limited similarity to IFN-α, IFN-ω, and IFN-τ: gene structure, biological properties and unusual species specificity. Biochem Biophys Acta 1294:55-62. Liu L and Roberts RM (1996). Silencing of the gene for the β-subunit of human chorionic gonadotropin by the embryonic transcription factor Oct-3/4. J Biol Chem 271:16683-16689. Liu L, Leaman DW and Roberts RM (1996). The interferon-tau genes of the giraffe, a nonbovid species. J Interferon Cytokine Res 16:949-951. Roberts RM, Liu L and Alexenko A (1997). New and atypical families of type I interferons in mammals: comparative functions, structures and evolutionary relationships. Prog Nucleic Acid Res Mol Biol 56:287-325. Liu L, Leaman DW, Villalta M and Roberts RM (1997). Silencing of the gene for the alpha-subunit of human chorionic gonadotropin by the embryonic transcription factor Oct-3/4. Mol Endocrinol 11:1651-1658. Roberts RM, Liu L, Guo Q, Leaman D and Bixby J (1998) The evolution of type I interferons. J Interferon Cytokine Res 18:805-816. Liu L, Leaman DW and Roberts RM (1998). Possible role of the transcription factor Oct-3/4 in control of human chorionic gonadotropin expression. In: D. Carson, ed., Embryo Implantation: Molecular, Cellular and Clinical Aspects (Serono Symposium), pp.261-270. Mannick JB, Hausladen A, Liu L, Hess DT, Zeng M, Miao QX, Kane LS, Gow AJ, Stamler JS (1999). Fas-induced caspase denitrosylation. Science 284:651-654. Liu L, Stamler JS. (1999) NO: an inhibitor of cell death. Cell Death Differ 6:937-942 Liu L, Zeng M, Stamler JS. (1999) Hemoglobin induction in mouse macrophages. Proc Natl Acad Sci USA 96:6643-6647. Eu JP, Liu L, Zeng M and Stamler JS (2000). An apoptotic model for nitrosative stress. Biochemistry 39:1040-1047. Liu L, Zeng M, Hausladen A, Heitman J, Stamler JS (2000). Protection from nitrosative stress by yeast flavohemoglobin. Proc Natl Acad Sci USA 97:4672-4676. Ealy AD*, Larson SF*, Liu L*, Winkelman GL, Kubisch HM, Alexnko AP, Bixby JA, Roberts RM. (2001) Polymorphic forms of expressed bovine interferon-tau genes: relative transcript abundance during early placental development, promoter sequences of genes and biological activity of protein products. Endocrinology 142:2906-2915. *These authors contributed equally. Liu L, Hausladen A, Zeng M, Loretta Que, Heitman J, Stamler JS (2001). A metabolic enzyme for S-nitrosothiol conserved from bacteria to humans. Nature 410:490-494. Matsumoto A, Comatas KE, Liu L, Stamler JS (2003). Screening for nitric oxide-dependent protein-protein interactions. Science 301:657-661. Jesus-Berrios MD, Liu L, Nussbaum JC, Cox GM, Stamler JS, Heitman J (2003). Enzymes that counteract nitrosative stress promote fungal virulence. Current Biology 13:1963-1968.

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20. 21. 22. 23. 24.

25.

26. 27. 28. 29.

30. 31. 32. 33.

Liu L, Yan Y, Zeng M, Zhang J, Hanes MA, Ahearn G, McMahon TJ, Dickfeld T, Marshall HE, Que LG, Stamler JS (2004). Essential roles of S-nitrosothiols in vascular homeostasis and endotoxic shock. Cell 116:617-628. Que LG, Liu L, Yan Y, Whitehead GS, Gavett SH, Schwartz DA, Stamler JS (2005). Protection from experimental asthma by an endogenous bronchodilator. Science 308:1618-1621. Bang IS, Liu L, Vazquez-Torres A, Crouch ML, Stamler JS, Fang FC (2006). Maintenance of nitric oxide and redox homeostasis by the Salmonella flavohemoglobin Hmp. J Biol Chem 38:28039-28047. Foster MW*, Liu L*, Zeng M, Hess DT, Stamler JS (2009). A Genetic Analysis of Nitrosative Stress. Biochemistry 48:792–799. *Co-first author. Choudhry S, Que LG, Yang Z, Liu L, Eng C, Kim SO, Kumar G, Thyne S, Chapela R, Meade K, Watson HG, LeNoir M, Rodriguez-Santana JR, Rodriguez-Cintron W, Avila PC, Stamler JS, Burchard EG (2010). GSNO Reductase and β2 Adrenergic Receptor Gene-gene Interaction: Bronchodilator Responsiveness to Albuterol. Pharmacogenetics and Genomics 20:351-8. Wei W, Li B, Hanes MA, Kakar S, Chen X, Liu L (2010). Deficiency of S-Nitrosoglutathione Reductase Impairs DNA Repair and Promotes Hepatocarcinogenesis. Science Translational Medicine 2: 19ra13 (PMC3085984). (This paper has been selected and rated by Faculty of 1000 as “Must Read”.) Yang Z, Wang Z, Doulias P, Wei W, Ischiropoulos H, Locksley RM, Liu L (2010). Lymphocyte development requires S-nitrosoglutathione reductase. J Immunol, 185:6664-6669 (PMC3070165). Wei W, Yang Z, Tang CH, Liu L (2011). Targeted deletion of GSNOR in hepatocytes of mice causes nitrosative inactivation of O6-alkylguanine-DNA alkyltransferase and increased sensitivity to genotoxic diethylnitrosamine. Carcinogenesis 32:973–977 (PMC3128557). Lagoda G, Xie Y, Sezen SF, Hurt KJ, Liu L, Musicki B, Burnett AL (2011). FK506 Neuroprotection after Cavernous Nerve Injury is Mediated by Thioredoxin and Glutathione Redox Systems. J Sexual Medicine 8:3325-3334. Na B, Huang ZM, Wang Q, Qi ZX, Tian YJ, Lu CC, Yu JW, Hanes MA, Sanjay Kakara S, Huanga EJ, Ou JHJ, Liu L‡,*, and Yen TSB‡,† (2011). Transgenic Expression of Entire Hepatitis B Virus in Mice Induces Hepatocarcinogenesis Independent of Chronic Liver Injury. PLoS One 6:e26240 (PMC3192172). ‡ co-senior author; *Corresponding author; †Deceased August 31, 2009. Khan O, Headley M, Gerard A, Wei W, Liu L, Krummel MF (2011). Regulation of T cell priming by lymphoid-stromal inducible nitric oxidesynthase. PLoS ONE 6:e26138 (PMC3215700). Tang CH, Wei W, Liu L (2012). Regulation of DNA Repair by S-Nitrosylation. Biochim Biophys Acta 1820:730–735 (PMC3170507; http://dx.doi.org/10.1016/j.bbagen.2011.04.014). Ozawa K*, Tsumoto H, Wei W, Tang CH, Komatsubara AT, Kawafune H, Shimizu K, Liu L*, Tsujimoto G (2012). Proteomic analysis of the role of S-nitrosoglutathione reductase in lipopolysaccharide-challenged mice. Proteomics 12, 2024-2035. *Corresponding author. Leung J, Wei W, Liu L (2013). S-nitrosoglutathione reductase deficiency increases mutagenesis from alkylation in mouse liver. Carcinogenesis (in press).

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34.

Tang CH, Wei W, Hanes MA, Liu L (2013). Hepatocarcinogenesis driven by GSNOR deficiency is prevented by iNOS inhibition. Cancer Research (in press).

Research Support Ongoing Research Support 1 R01 CA122359-01A2 NIH/NCI Liu (PI) 05/01/09-4/30/14 Title: Role of S-nitroso-glutathione Reductase in Hepatocellular Carcinoma The goal of this study is to determine whether GSNOR protects DNA repair proteins and plays a role in liver cancer. Role: PI Completed 1. Innovative Research Award Liu (PI) Sandler Center for Basic Research in Asthma, UCSF Title: Role of GSNOR in Asthma (PI)

1/1/06-6/30/08

2. Pilot-feasibility funding Liu (PI) 6/1/06-5/31/07 UCSF Liver Center Title: Potential Role of S-nitroso-glutathione Reductase in Liver Tumorigenesis (PI) 3. Research Award Liu (PI) 7/1/2007-6/30/2008 Cancer Research Coordinating Committee, UC Title: Role of S-nitroso-glutathione reductase in protection against carcinogenic N-nitrosamines (PI) 4. Research Contract, N30 Pharmaceuticals Liu (PI) 07/01/09-09/30/10 Title: Haplosufficiency of S-nitroso-glutathione Reductase The goal of this study is to test if GSNOR is haplosufficient for protection against nitrosative stress. Role: PI 5 R01 CA055578-14S1 NIH/NCI Pulliam & Liu (PI) 09/30/2009-09/29/2011 Title: Role of PreS2 Mutants in Pathogenesis of Chronic Hepatitis B The goal of this study is to test if GSNOR deficiency functions synergistically with PreS2 Mutants in the pathogenesis of chronic hepatitis B Role: one PI of the double-PI team. 6. 5P01CA123328 J. Ou (PI) 01/01/2010-05/31/2012 Project 2 Title: Hepatic Carcinogenesis Induced By Hepatitis B Virus PreS2 Mutant This project (part of a program project based at the University of Southern California ) examines how the preS2 mutant may interact with other HBV proteins and immunological

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factors in causing HCC and the role of the various mutant products of the preS2 mutant in carcinogenesis Role: PI of Project 2.

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BIOGRAPHICAL SKETCH NAME Richard M. Locksley, M.D. eRA COMMONS USER NAME Locksley

POSITION TITLE Sandler Distinguished Professor, Department of Medicine, University of California, San Francisco EDUCATION/TRAINING

INSTITUTION AND LOCATION

DEGREE

YEAR(s)

FIELD OF STUDY

Harvard College, Cambridge, MA

B.A.

1970

Biochemistry

University of Rochester, Rochester, NY

M.D.

1976

Medicine Resident, Chief Resident Infectious Diseases Fellow

University of California, San Francisco, CA

1976-80

University of Washington, Seattle, WA

1980-83

Positions and Honors 1986-2003 1988-93 1991-94 1994-99 1995-05 1995-01 19971998-01 2002-05 2003-

Chief, Division of Infectious Diseases, UCSF Medical Center, San Francisco, CA Member and Chair (1991-93), Tropical Medicine and Parasitology Study Section, NIH Co-Director, Immunology Section, Biology of Parasitism Course, Woods Hole, MA Chair, Parasitology Pathogenesis Committee, WHO, Geneva Council, Chair (1998), Midwinter Conference of Immunologists, Asilomar Faculty, Association of American Immunology Annual Course, Advanced Immunology Investigator, Howard Hughes Medical Institute, UCSF Member, Chair (2000-01), US-Japan Immunology Board, NIH Council, NIAID, National Institutes of Health Director, Strategic Asthma Basic Research Center, UCSF

Editorial Boards (1999-03)

Immunity, J Clin Invest, Immunology & Cell Biology, Annu Rev Immunol

150

Honors 1991 1994 1992-97 1994 2001-05 2005

American Society for Clinical Investigation Association of American Physicians Burroughs Wellcome Fund Scholar in Molecular Parasitology Bailey K Ashford Medal, American Society Tropical Medicine and Hygiene Ellison Medical Foundation Senior Scholar in Global Infectious Diseases American Academy of Arts & Sciences

Selected peer-reviewed publications (in chronological order) 1. Grunig G, M Warnock, AE Wakil, R Venkayya, F Brombacher, DM Rennick, D Sheppard, M Mohrs, DD Donaldson, RM Locksley, DB Corry. 1998. Requirement for IL-13 independently of IL-4 in experimental asthma. Science 282:2261-63. 2. Loots GG, RM Locksley, CM Blankespoor, Z-E Wang, W Miller, EM Rubin, KA Frazer. 2000. Identification of a coordinate regulator of interleukins 4, 13 and 5 by cross-species sequence comparisons. Science 288:136-40. 3. Grogan JL, M Mohrs, B Harmon, DA Lacy, JW Sedat, RM Locksley. 2001. Early transcription and silencing of cytokine genes underlie polarization of T helper cell subsets. Immunity 14:205-15. 4. Mohrs M, CM Blankespoor, ZE Wang, GG Loots, V Afzal, H Hadeiba, K Shinkai, EM Rubin, RM Locksley. Deletion of a coordinate regulator of type 2 cytokine expression in mice. Nature Immunol 2:842-7, 2001. 5. Mohrs M, K Shinkai, K Mohrs, RM Locksley. Analysis of type 2 immunity in vivo with a biscistronic IL-4 reporter. Immunity 15:303-11, 2001. 6. Shinkai K, M Mohrs, RM Locksley. 2002. Helper T cells regulate type 2 immunity in vivo. Nature 420:825-9. 7. Voehringer D, K Shinkai, RM Locksley. 2004. Type 2 immunity reflects orchestrated recruitment of cells committed to IL-4 production. Immunity 20:267-77. 8. Mohrs K, AE Wakil, N Killeen, RM Locksley, M Mohrs. 2005. A two-step process for cytokine production revealed by IL-4 dual-reporter mice. Immunity 23:419-29. PMC2826320 9. Scheu S, DB Stetson, RL Reinhardt, JH Leber, M Mohrs, RM Locksley. 2006. Activation of the integrated stress response during T helper cell differentiation. Nature Immunol 7:644-51. PMC2629269 10. Voehringer D, TA Reese, X Huang, K Shinkai, RM Locksley. 2006. Type 2 immunity is controlled by IL-4/IL-13 expression in hematopoietic non-eosinophil cells of the innate immune system. J Exp Med 203:1435-46. PMC2118302 11. Reese TA, H-E Liang, AM Tager, AD Luster, N van Rooijen, D Voehringer, RM Locksley. 2007. Chitin induces accumulation in tissue of innate immune cells associated with allergy. Nature 447:92-6. PMC2527589

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12. Reinhardt RL, H-E Liang, RM Locksley. 2009. Cytokine-secreting follicular T cells shape the antibody repertoire. Nature Immunol 10:385-93. PMC2714053 13. Price AE, H-E Liang, BM Sullivan, RL Reinhardt, CJ Eisley, DJ Erle, Grunig G, M Warnock, AE Wakil, R Venkayya, F Brombacher, DM Rennick, D Sheppard, M Mohrs, DD Donaldson, RM Locksley, DB Corry. 1998. Requirement for IL-13 independently of IL-4 in experimental asthma. Science 282:2261-63. 14. Voehringer D, K Shinkai, RM Locksley. 2004. Type 2 immunity reflects orchestrated recruitment of cells committed to IL-4 production. Immunity 20:267-77. 15. Mohrs K, AE Wakil, N Killeen, RM Locksley, M Mohrs. 2005. A two-step process for cytokine production revealed by IL-4 dual-reporter mice. Immunity 23:419-29. MC2826320 16. Price AE, H-E Liang, BM Sullivan, RL Reinhardt, CJ Eisley, DJ Erle, RM Locksley. 2010. Systemically dispersed innate IL-13-producing cells in type 2 immunity. Proc Natl Acad Sci USA 107:11489-94. PMC2895098. 17. Ricardo-Gonzalez RR, A Red Eagle, JI Odegaard, H Jouihan, CR Morel, JE Heredia, L Mukudan, D Wu, RM Locksley, A Chawla. 2010. IL-4/Stat6 immune axis regulates peripheral nutrient metabolism and Insulin sensitivity. Proc Natl Acad Sci USA 107:22617-22. PMC3012500 18. Locksley RM. 2010. Asthma and allergic inflammation. Cell 140:777-83. PMC3134388 19. Wu D, AB Molofsky, H-E Liang, RR Ricardo-Gonzalez, HA Jouihan, JK Bando, A Chawla, RM Locksley. 2011. Eosinophils sustain adipose alternatively activated macrophages associated with glucose homeostasis. Science 332:243-7. PMC3144160 20. Sullivan BM, H-E Liang, JK Bando, D Wu, LE Cheng, JK McKerrow, CDC Allen, RM Locksley. 2011. Genetic analysis of basophil function in vivo. Nat Immunol 12:527-35. PMC3271435 Additional Publications (selected from >150 total) 1. Amiri P, RM Locksley, TG Parslow, MD Sadick, E Rector, D Ritter, JH McKerrow. 1992. Tumor necrosis factor a restores granulomas and induces parasite egg-laying in schistosome-infected SCID mice. Nature 356:604-607. 2. Locksley RM, SL Reiner, F Hatam, DR Littman, N Killeen. 1993. Helper T cells without CD4: control of leishmaniasis in CD4-deficient mice. Science 261:1448-1451. 3. Reiner SL, ZE Wang, F Hatam, P Scott, RM Locksley. 1993. Th1 and Th2 cell antigen receptors in experimental leishmaniasis. Science 259:1457-60. 4. Mougneau E, F Altare, AE Wakil, S Zheng, T Coppola, ZE Wang, R Waldmann, RM Locksley, N Glaichenhaus. 1995. Expression cloning of a protective Leishmania antigen. Science 268:563-566. 5. Fowell DJ, J Magram, CW Turck, N Killeen, RM Locksley. 1997. Impaired Th2 development in the absence of CD4. Immunity 6:559-69. 6. Bix M, Locksley RM. 1998. Independent and epigenetic regulation of the interleukin 4 alleles in CD4+ T cells. Science 281:1352-4.

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7. Bix M., ZE Wang, B Thiel, NJ Schork, RM Locksley. 1998. Genetic regulation of commitment to IL-4 production by a CD4 T cell-intrinsic mechanism. J Exp Med 188:2289-99. 8. Grunig G, M Warnock, AE Wakil, R Venkayya, F Brombacher, DM Rennick, D Sheppard, M Mohrs, DD Symula DJ, KA Frazer, Y Ueda, P Denefle, ME Stevens, Z-E Wang, RM Locksley, EM Rubin. 1999. Functional screening of an asthma QTL in YAC transgenic mice. Nature Genetics 23:241-44. 9. Stetson DB, M Mohrs, V Mallet-Designe, L Teyton, RM Locksley. 2002. Rapid expansion and IL-4 expression by Leishmania-specific naive helper T cells in vivo. Immunity 17:191-200. 10. Fowell DJ, K Shinkai, XC Liao, AM Beebe, RL Coffman, DR Littman, RM Locksley. 1999. Impaired NFATc translocation and failure of Th2 development in itk-deficient CD4 T cells. Immunity 11:399-409. 11. Voehringer D, DB Rosen, LL Lanier, RM Locksley. 2004. CD200R family members represent novel DAP12-associated activating receptors on basophils and mast cells. J Biol Chem 279:54117-23. 12. Kang S-J, H-E Liang, B Reizis, RM Locksley. 2008. Regulation of hierarchical clustering and activation of innate immune cells by dendritic cells. Immunity 29:819-33. NIHMS80422 13. Voehringer D, D Wu, H-E Liang, RM Locksley. 2009. Efficient generation of long-distance conditional alleles using recombineering and a dual selection strategy in replicate plates. BMC Biotechnol 9:69. PMCID: PMC2724507. 2010. 14. Price AE, Liang, H-E, Sullivan BM, Reinhardt, RL, Eisley CJ, Erle, DJ, Locksley RM. 2010. Systemically dispersed innate IL-13-producing cells in type 2 immunity. Proc Natl Acad Sci USA 107(25):11489-94. PMC2895098. 15. Van Dyken SJ, D Garcia, P Porter, X Huang, PJ Quinlan, PD Blanc, DB Corry, RM Locksley. 2011. Fungal chitin from asthma-associated home environments induces eosinophilic lung infiltration. J Immunol 187:2261-2267. PMC3159725 16. Nguyen KD, Y Qui, X Cui, YP Sharon Goh, J Mwangi, T David, L Mukundan, F Brombacher, RM Locksley, A Chawla. 2011. Alternatively activated macrophages produce catecholamines to sustain adaptive thermogenesis. Nature 480:104-108. PMC3371761 17. Liang H-E, RL Reinhardt, JK Bando, BM Sullivan, I-C Ho, RM Locksley. 2011. Divergent expression patterns of IL-4 and IL-13 define unique functions in allergic immunity. Nat Immunol 13:58-66. PMC3242938 18. Gordon E, S Sidhu, Z-E Wang, P Woodruff, S Yuan, M Solon, S Conway, X Huang, RM Locksley, J Fahy. 2012. A protective role for periostin and TGF-b in IgE-mediated allergy and airway hyperresponsiveness. Clin Exp Allergy 42:144-155. PMC3271792 19. Thornton EE, MR Looney, O Bose, D Sen, D Sheppard, RM Locksley, X Huang, MF Krummel. 2012. Spatiotemporally separated antigen uptake by alveolar dendritic cells and airway presentation to T cells in the lung. J Exp Med 209:1183-1199. PMC3371730 20. Price AE, RL Reinhardt, H-E Liang, RM Locksley. 2012. Marking and quantifying IL-17A-producing cells in vivo. PLoS ONE 7:e39750. PMC3387253

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21. Dickgreber N, KJ Farrand, N van Panhuys, DA Knight, ML Chong, S Miranda-Hernandez, AG Baxter, RM Locksley, G Le Gros, IF Hermans. 2012. Immature murine NKT cells pass through a stage of developmentally programmed innate IL-4 secretion. J Leukoc Biol (in press) 22. Cheng LE, K Hartmann, A Roers, MF Krummel, RM Locksley. 2013. Perivascular mast cells dynamically probe cutaneous blood vessels to capture IgE. Immunity 38:166-175. PMC in process 23. Oghumu S, R Dong, S Varikuti, T Shawler, T Kampfrath, CA Terrazas, C Lezama-Davila, BMM Ahmer, CC Whitacre, S Rajagopalan, R Locksley, AH Sharpe, AR Sataskar. 2013. Distinct populations of innate CD8 T cells revealed in a CXCR3 reporter mouse. J Immunol (in press). 24. Molofsky AB, JC Nussbaum H-E Liang, SJ Van Dyken, LE Cheng, A Mohapatra, A Chawla, RM Locksley. 2013. Innate lymphoid type 2 cells ILC2) sustain visceral adipose tissue eosinophils and alternatively activated macrophages. J Exp Med (in press). PMC in process 25. Van Dyken SJ, RM Locksley. 2013. Interleukin-4- and interleukin-13-mediated alternatively activated macrophages: roles in homeostasis and disease. Annu Rev Immunol 31:317-43. PMC in process 26. Spits H, D Artis, M Colonna, A Diefenbach, JP Di Santo, G Eberl, S Koyasu, RM Locksley, ANJ McKenzie, RE Mebius, F Powrie, E Vivier. 2013. Innate lymphoid cells – a proposal for a uniform nomenclature. Nature Rev Immunol 13:145-149. PMC in process 27. Heredia JE, L mukundan, FM Chen, AA Mueller, R Deo, RM Locksley, TA Radno, A Chawla. 2013. Type 2 innate signals regulate functionality of fibro/adipogenic progenitors to facilitate muscle regeneration. Cell (in press). Research Support Active Not assigned Locksley (PI) 10/97-9/12 (budgeted annually) Howard Hughes Medical Institute Activation of Immunity The major goals of this project are to provide new strategies to optimize host defense and vaccines and to treat pathologic immune responses associated with autoimmunity and allergy. Support from HHMI pays Dr. Locksley's salary. R37 AI26918 Locksley (PI) 7/88-3/16 NIH/NIAID Parasite immunity orchestrated by Th2 cells The major goal of this project is to identify the role of basophils and eosinophils required for immunity to parasitic helminths.

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RO1 AI30663 Locksley (PI) 6/08-5/13 NIH/NIAID Initiation of allergic immunity by parasites The major goals of this grant are to understand the mechanism by which chitin in helminthes contributes to eosinophilic inflammation in tissues in response to migrating organisms and eggs. U19 AI077439 Sheppard (PI) 3/08-2/13 NIH/NIAID Mechanisms of initiation and persistence of allergic asthma The major goals of this grant are to understand mechanisms of allergic lung inflammation induced by fungi in murine models and human studies. Role: PI Subproject 1 P01 AI078869 DeFranco (PI) 7/08-6/13 NIH/NIAID Cross-talk between innate and adaptive immune cells in inflammation and autoimmunity The major goals are to assess the role of innate signaling pathways in the induction of mucosal responses to pathogens. Role: PI Subproject 4 P01 AI119944 Fahy (PI) 7/12-6/12 NIH/NHLBI Innate and Adaptive Immune Responses in TH2-High Asthma Project 1: Innate Helper Type-2 Cells in Allergic Lung The goal of this project is to focus on the role of iH2 cells as proximal regulators of TH2 inflammation in the airway. This project proposes to characterize markers for these cells, delineate their role in allergic airway responses and collaborate with investigators in Project 3 to advance understanding of iH2 cells in human asthma. Larry L. Hillblom Center for the immunobiology of type 2 diabetes (Chawla PI, Locksley co-PI) 1/09-12/12 The goal of this project is to understand the inferface between immune cell activation and metabolic disorders. Completed 5-2008-214 Locksley (PI) 12/07-12/08 Juvenile Diabetes Research Foundation Innovative Grants Functional immune cell activation in type 1 diabetes The major goal of this project was to use mice with marker alleles in informative cytokine genes to identify evidence for functionally important cytokine elaboration in mediating peripheral insulin sensitivity.

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BIOGRAPHICAL SKETCH NAME William E. Seaman, M.D. eRA COMMONS USER NAME BSEAMAN

POSITION TITLE Professor of Medicine and of Microbiology and Immunology, UCSF EDUCATION/TRAINING

INSTITUTION AND LOCATION Princeton University, Princeton, NJ Harvard Medical School, Boston, MA Massachusetts General Hospital, Boston, MA Arthritis and Rheumatism Branch, NIAMDD, NIH Bethesda, MD Massachusetts General Hospital, Boston, MA Massachusetts General Hospital, Boston, MA

DEGREE

YEAR(s)

A.B. M.D. Resident

1964 1969 1969-1971

Fellow

1971-1974

Chief Resident Fellow

1974-1975 1976

FIELD OF STUDY English Medicine Internal Medicine Immunology and Rheumatology Medicine Rheumatology

Positions and Honors Academic Positions 1976 - 1984 1978 - Present 1981 - 1992 1984 - 1988 1988 - Present 1992 - 1999 1999 - Present

Assistant Professor of Medicine, University of California San Francisco Staff Physician, San Francisco VA Medical Center Chief, Arthritis/Immunology Section, San Francisco VA Medical Center Associate Professor of Medicine, University of California, San Francisco Professor of Medicine and of Microbiology and Immunology, University of California San Francisco Chief, Medical Service, San Francisco VA Medical Center Chief, Immunology Section, San Francisco VA Medical Center

Other Recent Positions 1999 - Present 1999 - 2003 2000 - 2008 2002 - 2005 2011 – Present

Research Director, American Asthma Foundation NIH Study Section, Experimental Immunology Director, Macrophage Biology Laboratory, Alliance for Cellular Signaling President, Society for Natural Immunity Associate Chair of Medicine for Research, UCSF

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Honors 1964 1969 2007

AB cum laude MD cum laude Master, American College of Rheumatology

Medical and Research Society Memberships and Board Certifications 1973 to Present 1974 1978 1979 to Present 1980 to Present 1984 to Present 1994 to Present 1998 to Present 2001 to Present 2007 to Present 2007 to Present

American College of Rheumatology American Board of Internal Medicine American Board of Rheumatology American Federation for Clinical Research American Association of Immunologist American Society for Clinical Investigation American Association of Physicians Society for Natural Immunity American Association for Cancer Research International Bioiron Society International Society of Neuroimmunology

Editorships 1985-1989 1989-1993 1992-1997 2005 to Present

Associate Editor, Journal of Immunology Section Editor, Journal of Immunology Consulting Editor, Journal of Clinical Investigation Faculty of 1000

15 Selected Peer-Reviewed Publications (of 93) 1. Wofsy D, Seaman WE: Successful treatment of autoimmunity in NZB/NZW mice with monoclonal antibody to L3T4. J Exp Med 161:378-391, 1985. 2. Seaman WE, Eriksson E, Dobrow R, Imboden JB: Inositol trisphosphate is generated by a rat natural killer cell tumor in response to target cells or to cross-linked monoclonal antibody OX-34: possible signaling role for the OX-34 determinant during activation by target cells. Proc Natl Acad Sci USA 84:4239-4243, 1987. 3. Seaman WE, Niemi EC, Stark MR, Goldfien RD, Pollock AS, Imboden JB: Molecular cloning of gp42, a cell-surface molecule that is selectively induced on rat natural killer cells by interleukin-2: Glycolipid membrane anchoring and capacity for transmembrane signaling, J Exp Med. 173:251-260, 1991. 4. Yokoyama WM, Ryan JC, Hunter JJ, Smith HMC, Stark M, Seaman WE. cDNA cloning of mouse NKR-P1 and genetic linkage with Ly-49: Identification of a natural killer gene complex on mouse chromosome VI. J Immunol 147:3229, 1991.

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5. Ryan JC, Turck J, Niemi EC, Yokoyama WM, Seaman WE. Molecular cloning of the NK1.1 antigen, a member of the NKR-P1 family of natural killer cell activation molecules. J Immunol. 149:1631-1635, 1992. 6. Ryan JC, Niemi EC, Nakamura MC, Seaman WE. NKR-P1A is a target-specific receptor that activates natural killer cell cytotoxicity. J Exp Med 181:1911-1915, 1995. 7. Nakamura, MC, Linnemeyer, PA, Niemi EC, Mason L, Ortaldo JR, Ryan JC, Seaman WE. Mouse Ly-49D recognizes H-2Dd and activates natural killer cell cytotoxicity. J Exp Med, 189:493-500, 1999. 8. Nakamura MC, Hayashi S, Niemi EC, Ryan JC, Seaman, WE. Activating Ly-49D and inhibitory Ly-49A NK cell receptors demonstrate distinct requirements for interaction with H2-Dd. J Exp Med 7:192:447-54, 2000. 9. Daws MR, Sullam PM, Niemi EC, Chen TT, Seaman WE. Pattern recognition by TREM-2: binding of anionic ligands. J Immunol. 171:594-9, 2003. 10. Chen TT, Li L, Chung D-H, Allen CDC, Torti SV, Torti FM, Cyster JG, Chen C, Brodsky, FM, Niemi EC, Nakamura MC, Seaman WE, Daws MR. TIM-2 is expressed on B cells and in liver and kidney and it is a receptor for H ferritin endocytosis. J Exp Med. 202:955-65, 2005. 11. Roach TI, Rebres RA, Fraser ID, Decamp DL, Lin KM, Sternweis PC, Simon MI, Seaman WE. Signaling and cross-talk by C5a and UDP in macrophages selectively use PLCbeta3 to regulate intracellular free calcium. J Biol Chem 283(25):17351-61, 2008. 12. N'Diaye EN, Branda CS, Branda SS, Nevarez L, Colonna M, Lowell C, Hamerman JA, Seaman WE. TREM-2 (triggering receptor expressed on myeloid cells 2) is a phagocytic receptor for bacteria. J Cell Biol 184(2):215-23, 2009. 13. Hsieh CL, Koike M, Spusta SC, Niemi E, Yenari M, Nakamura MC, and Seaman WE. A role for TREM2 ligands in the phagocytosis of apoptotic neuronal cells by microglia. J Neurochem 109(4):1144-1156, 2009. 14. Li L, Fang CJ, Ryan JC, Niemi EC, Lebrón JA, Björkman PJ, Arase H, Torti FM, Torti SV, Nakamura MC, Seaman WE. Binding and uptake of H-ferritin is mediated by human transferrin receptor-1. Proc Natl Acad Sci USA. Proc Natl Acad Sci USA 107(8):3505-10, 2010. 15. Rebres, RA, Roach TIA, Fraser IDC, Philip F, Moon C, Lin KM, Liu J, Santat L, Cheadle L, Ross EM, Simon MI, Seaman WE. Synergistic Ca2+ responses by Gai- and Gaq-coupled G-protein-coupled receptors require a single PLCb isoform that is sensitive to both Gbg and Gaq. J Biol Chem 286:1-10, 2011 Research Support Ongoing Research Support Title: The Role of Microglial Subsets in Regulating Brain Injury Agency/Type: Department of Defense PT075679 PI: WE Seaman 7/1/06 to 6/30/2012 Role: Principal Investigator Program: These studies examine the role of microglial subsets in the response to TBI. They examine the hypothesis that microglia, like macrophages may be divided into pro-inflammatory

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vs. reparative subsets, and that injury following TBI may be improved by driving microglia from the former to the latter. Key persons are Christine Hsieh, a postdoctoral fellow, my colleague, Mary Nakamura, MD, and Jialing Liu, PhD, a colleague in Neurosurgery who is expert in TBI. Ongoing Mentored Grant Title: The role of CCR2 and Macrophages in Traumatic Brain Injury Agency/Type: Department of Veterans Affairs PI: Christine Hsieh 1/1/2011 to 12/31/2013 Role: Mentor Program: This is a VA Career Development Award to Christine Hsieh, PhD, a postdoctoral fellow in my laboratory for whom I am the mentor on this award. Dr. Hsieh has been studying traumatic brain injury as part of my DoD grant (above). As part of this work, she showed that TBI results in an influx of macrophage to the brain, and that this influx is primarily dependent on the chemokine receptor, CCR2. This grant has allowed her to study the functional consequences of this response and to develop as an independent investigator. Key persons in addition to Dr. Hsieh and myself include our colleague, Mary Nakamura. Completed support (last 3 years) Title: Role of the Tim-2 Receptor in Immunity and Autoimmunity Agency/Type: NIH RO1 AI061164-01A1 Seaman (PI) 7/1/05 to 3/31/11 Role: Principal Investigator Program: These studies examined the role in immunity and autoimmunity of TIM-2, a receptor expressed on mouse lymphocytes and on liver cells and renal tubule cells

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BIOGRAPHICAL SKETCH NAME Dean Sheppard, M.D. eRA COMMONS USER NAME sheppard

POSITION TITLE Professor of Medicine

EDUCATION/TRAINING INSTITUTION AND LOCATION Harvard College, Cambridge, MA SUNY at Stony Brook, Stony Brook, NY University of Washington, Seattle, WA University of California, San Francisco, San Francisco Positions 2009-Present 1986-Present 1999-2004 1981-1987 1987-1992 1992-Present 1997-2009

DEGREE AB MD Resident Fellow

YEAR(s)

FIELD OF STUDY

6/72 6/75 7/75-6/78 7/78-6/81

Medicine Internal Medicine Pulmonary

Chief, Pulmonary, Critical Care, Allergy and Sleep Division, UCSF Director, Lung Biology Center, University of California, San Francisco Acting Director, Sandler Basic Asthma Research Center, UCSF Assistant Professor of Medicine, University of California, San Francisco Associate Professor of Medicine, University of California, San Francisco Professor of Medicine, University of California, San Francisco Associate Chair for Biomedical Research, Department of Medicine, UCSF

Other Experience Member, NHLBI Program Project Review Committee, 1998-2002, Chair 2000-2002 Member, Lung Injury and Repair Study Section, 2004-2008, Chair 2006-2008 Scientific Advisory Board, Parker B. Francis Foundation 2006-2009 Editorial Board, Journal of Clinical Investigation 2003-present Editorial Board, Clinical and Translational Science 2008-present Associate Editor, American Journal of Respiratory Cell and Molecular Biology 1995-2002 Editorial Board, American Journal of Physiology; Lung Cell and Molecular Biology 1996-2007 Chair, Oversight Committee, NHLBI Lung Tissue Consortium, 2004-present Honors and Awards Elected Member, American Society for Clinical Investigation, 1992 Elected Member, Association of American Physicians, 1995

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Clean Air Award, American Lung Association of California, 1995 Parker B. Francis Lecturer, Aspen Lung Conference, 1996 Lifetime Scientific Achievement Award, American Thoracic Society, 1998 Jerome I. Flance Visiting Professor, Washington University, 2000 Roger Mitchell Lecturer, Aspen Lung Conference, 2001 NIH Merit Award, 2004-2014 Robert Johnston Lecturer, Drexel University, 2005 McClement Lecturer, New York University, 2006 Kass Medal, University of Nebraska, 2007 Amberson Lecturer, American Thoracic Society, 2010 Selected Relevant Publications (from a total 252) 1. Grunig G, Warnock M, Wakil AE, Venkayya R, Brombacher F, Rennick DM, Sheppard D, Mohrs M, Donaldson DD, Locksley RM, Corry DB. Requirement for IL-13 independently of IL-4 in experimental asthma. Science 1998; 282:2261-3.PMID:9856950 2. Munger JS, Huang XZ , Kawakatsu H , Griffiths MJD, Dalton SL, Wu JF, Pittet JF, Kaminiski N, Garat C, Matthay MA, Rifkin DB, Sheppard D. The integrin avb6 binds and activates latent TGFb1: a mechanism for regulating pulmonary inflammation and fibrosis. Cell 1999; 96:319-328.PMID:10025398 3. Kaminski N, Allard J, Pittet J-F, Zuo F, Griffiths MJD, Morris D, Huang XZ, Sheppard D, Heller RA. Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and remodeling. Proc Nat Acad Sci 2000; 97:1778-1783.PMID:10677534 4. Pittet J-F, Griffiths MJD, Geiser T, Kaminski N, Dalton SL, Huang X Brown LAS, Gotwals PJ, Koetiansky VE, Matthay MA, Sheppard D. TGFβ is a critical mediator of acute lung injury. J. Clin Invest 2001; 107:1529-1536. 5. Morris DG, Huang X, Kaminski N, Wang Y, Shapiro SD, Dolganov G, Glick, A, Sheppard D. Loss of integrin avb6-mediated TGFb activation causes Mmp12-dependent emphysema. Nature 2003 422:169-173. PMID: 12634787 6. Chen C, Young BA, Coleman CS, Pegg AE, Sheppard D. Spermidine/Spermine N1-Acetyltransferase specifically binds to the integrin α9 subunit cytoplasmic domain and enhances cell migration J Cell Biol 2004 167:161-170. PMID: 15479742 7. Vlahakis NE, Young BA, Atakilit A, Hawkridge AE, Issaka RB, Boudreau N, Sheppard D. Integrin alpha 9beta 1 directly binds to vascular endothelial growth factor (VEGF)-A and contributes to VEGF-A induced angiogenesis. J Biol Chem. 2007 282:15187-15196. PMID: 17363377 8. Jenkins RG, SuX, Su G, Scotton CJ, Camerer E, Laurent GJ, Davis JE, Chambers RC, Matthay MA, Sheppard D. Ligation of the protease-activated receptor-1 induces αvβ6 integrin-dependent TGFβ activation and promotes acute lung injury. J. Clin Invest 2006 116:1606-1614. 9. Travis MA, Reizis B, Melton AC Masteller E, Tang Q, Proctor J, Wang Y, Bernstein X, Huang X, Riechardt L, Bluestone J, Sheppard D. Loss of integrin αvβ8 on dendritic

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cells causes autoimmunity and colitis in mice. Nature 2007 449:361-365. PMID:17694047 10. Su G, Hodnett M, Wu N, Atakilit A, Kosinski C, Godzich M, Huang XZ, Kim K, Frank JA, Matthay MA, Sheppard D*, Pittet J-F*. Integrin avb5 regulates lung vascular permeability and pulmonary endothelial barrier function Am J Respir Cell Mol Biol 2007 36:377-86 (*denotes equal contributions) PMID:17079779 11. Ganter MT, Roux J, Miyazawa B, Howard M, Frank JA, Su G, Sheppard D, Violette SM, Weinreb PH, Horan GS, Matthay MA, Pittet JF. Interleukin-1β causes acute lung injury via αvβ5 and αvβ6 integrin-dependent mechanism Circ Res 2008 102:804-12. 12. Atabai K, Jame S, Kuo A, Lam M, Dehart G, Xia DD, Azhar N, Werb Z, Sheppard D. Mfge8-mediated collagen endocytosis limits the severity of fibrotic disease J Clin Invest 2009 219:3713-22. PMCID: PMC2786804 13. Melton A, Bailey-Bucktrout SL, Travis MA, Fife BT, Bluestone JA, Sheppard D. avb8 integrin on dendritic cells regulates Th17 cell development and experimental autoimmune encephalomyelitis in mice. J Clin Invest 2010. 120:4436-44. PMCID: PMC2993595 14. Hogmalm A, Sheppard D, Lappalainen U, Bry K. Beta6 integrin subunit deficiency alleviates lung injury in a mouse model of bronchopulmonary dysplasia. Am J Respir Cell Mol Biol 2010 43:88-98. PMCID: PMC2911573 15. Spassov DS, Wong CH, Sergina N, Ahuja D, Fried M, Sheppard D, Moasser MM. A src-driven phosphotyrosine signaling switch determines the anchorage state of epithelial cells. Mol Cell Biol 2011. 31:776-82. PMCID: PMC3028653 16. Su G, Atakilit A, Li T. J, Wu N, Bhattacharya M, Zhu J, Li E, Sun S, Chen R, Su C, Sheppard D. Integrin αvβ3 prevents vascular leak in mice by regulating cortical actin formation in endothelial cells. Am J Resp Crit Care Med 2012 (in press) 17. Kudo M, Melton AC, Chen C, Engler M, Huang KE, Ren X, Wang Y, Bernstein X, Li J, Atabai K, Huang X, Sheppard D. IL-17A produced by ab T cells drives airway smooth muscle contraction. Nature Medicine 2012 (in press). 18. Giacomini M, Travis M, Sheppard D. Epithelial cells utilize cortical actin/myosin to activate latent TGF-β through integrin αvβ6-dependent physical force. Exp Cell Res 2012 318:716-22. PMID: 22309779. 19. Sugimoto K, Kudo M, Sundaram A, Ren X, Huang K, Bernstein X, Wang Y, Raymond WW, Erle D, Abrink M, Caughey GH, Huang X, Sheppard D. The avb6 integrin modulates airway hyperresponsiveness by regulating intra-epithelial mast cells. J Clin Invest 2012 (in press). 20. Chen C, Kudo M, Rutaganira F, Takano H, Lee C, Atakilit A, Robinett, KS, Uede T, Wolters P, Shokat KM, Huang X, Sheppard D. Integrin alpha9beta1 in airway smooth muscle regulates a novel brake on exaggerated murine and human airway narrowing J Clin Invest 2012 122:2916-27 PMID 22772469. 21. Bhattacharya M, Su G, Su X, Oses-Prieto JA, Li JT, Huang X, Hernandez H, Atakilit A, Burlingame AL, Matthay M, Sheppard D. IQGAP1 is necessary for pulmonary vascular barrier protection in murine acute lung injury and pneumonia Am J Physiol: Lung Cell and Mol Biol 2012 303:L12-19 PMID: 22561460.

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Research Support Ongoing R01 HL102292 (Sheppard) 12/03/10-11/30/14 NIH Integrin-mediated Regulation of Airway Smooth Muscle The major goals of this project are to determine the mechanisms by which the alpha9beta1 integrin inhibits the sensitivity of airway smooth muscle to contraction induced by agonists of G protein coupled receptors. R37 HL53949 (Sheppard) 4/1/04-3/31/14 (merit award) NIH In Vivo Functions of Pulmonary Integrins The major goals of this project are to determine the roles of TGFβ1 activation in the induction of lung inflammation and protection from pulmonary fibrosis in integrin β6 subunit null mice. U19 AI077439 (Sheppard) 3/1/08-2/28/13 NIH/NIAID-Project 1 and Core A Mechanisms of Initiation and Pesistence of Allergic Asthma The major goals of this project are to determine the roles of integrin-mediated TGFβ activation in regulating auto-immunity, regulatory T cells and airway hyperresponsiveness after chronic allergen challenge in mice. Scleroderma Research Foundation (Sheppard) 5/1/12-4/30/13 Role of αv integrins in Scleroderma The goals of this project are to determine whether specific integrins expressed on epithelial cells or myofibroblasts could be effective therapeutic targets for treatment of Scleroderma P01 HL108794 (Sheppard) 07/01/2012–6/30/17 NIH/NHLBI- Project 2 and Core A Targeting Epithelial Cells to Treat Pulmonary Fibrosis Overall project goal: This grant will address two critical needs - developing effective treatments for pulmonary fibrosis and better ways to determine if drugs are actually hitting their targets. By targeting specific well-defined pathways, modifying drugs for delivery into the airways, and identifying markers of drug efficacy from readily available sites, we hope to dramatically improve current approaches to treatment of pulmonary fibrosis. T32 HL007185 (Sheppard) NIH/NHLBI Multidisciplinary training program in lung disease Role: Program Co-PI

07/01/2012–6/30/17

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Overall project goal: This is a training grant to train future leaders in basic, clinical and translational pulmonary science Recently completed R01 HL083950 (Sheppard) 4/1/06-3/31/11 NIH/NHLBI Regulations of Pulmonary Vascular Permeability by Integrin AlphaVbeta5 The major goals of this project were: 1) To identify the pathways by which αvβ5 facilitated RhoA activation and contributed to pulmonary vascular permeability. 2) To determine how the integrin β5 subunit contributed to the formation of multi-protein signaling complexes that regulated endothelial permeability. 3) To determine whether the pathways examined in aims 1 and 2 were broadly important in in vivo models of non-cardiogenic pulmonary edema. U19 AI077439-02S1 (Sheppard) 8/15/09-7/31/11 NIH/NIAID (Administrative Supplement Award) Mechanisms of Initiation and Persistence of Allergic Asthma This administrative supplement to our U19 grant had three goals – to develop an assay for measurement of environmental chitin, to replace our outdated tissue processor and process our backlog of fixed murine and human tissues, and to develop multi-plexed, bead based assays for measurements of multiple secreted proteins in small volume samples from human and murine airways. R01 AI024674 (Sheppard) 3/1/06-2/28/10 NIH/NIAID Novel Leukocyte Integrins The major goal of this project was to understand how glycan phosphoatidly inositol anchored proteins influenced the function of Fc and complement receptors on macrophages and dendritic cells. (Sheppard) 6/8/09-12/31/11 University of Edinburgh (Subcontract) The Role of the Alphavbeta8 Integrin in Hepatic Inflammation and Fibrosis The subcontract is to support a postdoctoral fellow, Neil Henderson, to work in Dr. Sheppard’s laboratory. Dr. Henderson was working on the mechanisms of activation of TGF beta in the liver. The major goals of this project are to determine the mechanisms by which the alpha9beta1 integrin inhibits the sensitivity of airway smooth muscle to contraction induced by agonists of G protein coupled receptors.

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BIOGRAPHICAL SKETCH NAME Jeoung-Sook Shin, Ph.D. eRA COMMONS USER NAME SHINJS

POSITION TITLE Assistant Professor

EDUCATION/TRAINING INSTITUTION AND LOCATION Seoul National University, Seoul, Korea Seoul National University, Seoul, Korea Duke University, Durham, NC Duke University, Durham, NC Yale University, New Haven, CT

DEGREE

YEAR(s)

FIELD OF STUDY

BS MS Ph.D. Postdoc Postdoc

1988-1993 1993-1995 1997-2002 2002-2003 2003-2008

Chemistry Biochemistry Pathology Pathology Cell Biology

Professional Positions 1996 2008

Research Associate, Cheong-Am Biotech, Seoul, Korea Assistant Professor, University of California San Francisco, Dept. of Microbiology Immunology & Sandler Asthma Basic Research Center

Honors and Awards 1999 2004 2009 2009

The Best Research Student Award in the Department of Pathology 9th Graduate Student Symposium, Duke University The Jane Coffin Childs Memorial Fund Research Fellowship Award Strategic Innovative Award in Asthma Research Cancer Research Institute Investigator Award

Professional Memberships 2008 - 2009 2010 2011 - Present

American Thoracic Society, member American Society of Cell Biology, member American Association of Immunologists, member

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Selected peer-reviewed publications 1. Shin JS, Gao Z, Abraham SN. Involvement of cellular caveolae in bacterial entry into mast cells, Science. 289:785-8, 2000. 2. Duncan MJ, Shin JS, Abraham SN. Microbial entry through caveolae: variations on a theme. Cell Microbiol. 4: 783-91, 2002 3. Duncan MJ, Lee G, Shin JS, Abraham SN. Bacterial penetration of bladder epithelium through lipid rafts, J Biol Chem. 279: 18944-51, 2004 4. Shin JS, Shelburne CP, Jin C, LeFurgey EA, Abraham SN. Harboring of particulate allergens within secretory compartments by mast cells following IgE/FceRI-lipid raft mediated phagocytosis, J Immunol. 177:5791-5800, 2006 5. Shin JS, Ebersold M, Pypaert M, Delamarre L, Hartley A, and Mellman I. Surface expression of MHC class II in dendritic cells is controlled by regulated ubiquitination, Nature. 444:115-8, 2006 6. Bloom O, Unternaehrer JJ, Jiang A, Shin JS, Delamarre L, Allen P, and Mellman I. Spinophilin participates in information transfer at immunological synapses, J Cell Biol. 181:203-11, 2008 7. Baravalle G, Park H, McSweeney M, Ohmura-Hoshino M, Matsuki Y, Shin JS. Ubiquitination of CD86 is a key mechanism in regulating antigen presentation by dendritic cells, J Immunology. 187:2966, 2011 8. Ma JK, Platt MY, Eastham-Anderson J, Shin JS*, and Mellman I*. MHC class II distribution in dendritic cells and B cells is determined by ubiquitin chain length, PNAS. 2012 May 7 [Epub ahead of print] *Shin JS and Mellman contributed equally to this work. Research Support Cancer Research Institute Investigator Award (PI) 7/1/2009 – 6/30/2013 Cancer Research Institute Mechanism and function of ubiquitin-mediated membrane traffic in dendritic cells The major goals of this project are to identify the molecular mechanism underlying the ubiquitination of MHCII and CD86 and to determine its role in dendritic cell functions. American Heart Association National Scientist Development Award (PI) 7/1/2010 – 6/31/2014 American Heart Association IgE-mediated activation of dendritic cells in the lungs The major goal of this project is to characterize IgE-mediated dendritic cell activation in the lungs using a mouse model. Research Projects Completed During the Last 3 Years American Thoracic Society Research Grant 1/1/2009 – 12/31/2010 American Thoracic Society Role of FcεRI expression on dendritic cells in asthma

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The major goals of this project were to determine the expression of FcRI in human lung dendritic cells and to characterize its role in mediating activation of the cells upon crosslinking. UCSF RAP Academic Senate Pilot Research Award Shin (PI) 1/15/2012 – 1/14/2013 Exploring dendritic cell presentation of IgE-bound antigens in vivo The goal of this project is to determine the tolerogenic role of IgE receptor FceRI expressed by dendritic cells. Role: PI

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BIOGRAPHICAL SKETCH NAME Zhi-En Wang, M.D., M.S. eRA COMMONS USER NAME

POSITION TITLE Research Specialist

EDUCATION/TRAINING INSTITUTION AND LOCATION Xian Medical University, Xian, China Xian Medical University, Xian, China

DEGREE M.D. M.S.

YEAR(s) 12/82 12/85

FIELD OF STUDY Medicine Immunology

Positions and Honors 1986-1987 1987-1989 1989-1990 1990-1991 1991-1994 1994-1997 1997

Research and Teaching Associate, Department of Microbiology and Immunology, Xian University, Xian, China Assistant Researcher and Lecturer, Xian University, Xian China Cheng Scholar and Visiting Scientist, University of California, San Francisco, CA Research Fellow, Temple University School of Medicine, Philadelphia, PA Research Fellow, University of California, San Francisco Department of Medicine Senior Research Associate, Cell Genesys Inc., Foster City, CA Research Specialist II, Howard Hughes Medical Institute (HHMI) San Francisco, CA

Selected Peer-reviewed Publications 1. Sadick, M.D., Holaday, B.J., Heinzel, F.P., Wang, Z. and Locksley, R.M.: Leishmania major-specific CD4+ T cells transferred protective immunity to severe-combine immunodeficient (scid) mice.” The Journal of FASEB, 1990 4(7):1953. 2. Holaday, B.J., Saidck, M.D. Henizel, F.P., Wang, Z. and Locksley, R.M.: Establishment of Th1 and Th2-like cell lines from mice infected with Leishmania major. The Journal of FASEB, 1990 4(7):3046. 3. Holaday, B.J., Saidck, M.D. Henizel, F.P., Wang, Z. and Locksley, R.M.: Reconstitution of Leishmania major scid mice using Th1 and Th2 cell lines. Journal of Immunology, 1991 147(5):1653.

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4. Locksley, R.M., Reiner, S.J., Sadick, M.D., Wang, Z., Heinzel, H.P. and Holaday, B.J.: Evidence for restricted V-D-Jß T cell receptor usage in the Th2 response to Leishmania major. 1991 FASEB J. 5:A1369. 5. Reiner SL, S Zheng, Z Wang, L Stowring, RM Locksley. 1994. Leishmania promastigotes evade IL-12 induction by macrophages and stimulate a broad range of cytokines from CD4 cells during initiation of infection. J Exp Med 179:447-56. 6. Loh, E., Wang, M., Wang, Z., Hyjek, E., and Kozbor, D.: Expression functional g/d T cell receptor recognize tetanus toxin. J of Cellular Biochemistry. 1992 165(D): 67. 7. Kozbor, D., Hyjek, E., Wiaderkiewicz, R., Wang, Z., Wang, M. and Loh, E.: Competitor mRNA fragments for quantitation of cytokine specific transcripts in cell lysates. Molecular Immunology, 1993. 30(1):1. 8. Reiner SL, Z Wang, F Hatam, P Scott, RM Locksley. 1993. Th1 and Th2 cell antigen receptors in experimental leishmaniasis. Science 259:1457-60. 9. Wang Z, SL Reiner, F Hatam, FP Heinzel, J Bouvier, CW Turck, RM Locksley. 1993. Targeted activation of CD8 cells and infection of b2-microglobulin-deficient mice fail to confirm a primary protective role for CD8 cells in experimental leishmaniasis . J Immunol 151:2077-86. 10. Reiner SL, S Zheng, Z Wang, L Stowring, RM Locksley. 1994. Leishmania promastigotes evade IL-12 induction by macrophages and stimulate a broad range of cytokines from CD4 cells during initiation of infection. J Exp Med 179:447-56. 11. Wang ZE, SL Reiner, S Zheng, D Dalton, RM Locksley. 1994. CD4+ effector cells default to the Th2 pathway in IFN-g-deficient mice. J Exp Med 179:1367-71. 12. Wang, Z., Zheng S., Corry D.B., Dalton, D.K., Seder, R.A., Reiner, S.L., and Locksley, R.M.: Interferon-g-dependent effects of interleukin-12 administered during acute or established infection due to Leishmania major. Proc. Natl. Acad. Sci. USA. 1994 91(24):12932-6. 13. Mougneau E, F Altare, AE Wakil, S Zheng, T Coppola, ZE Wang, R Waldmann, RM Locksley, N Glaichenhaus, N. 1995. Expression cloning of a protective Leishmania antigen. Science 268:563-6. 14. Wakil AE, ZE Wang, RM Locksley. 1996. Leishmania major: targeting IL-4 in successful immunomodulation of murine infection. Exp Parasitol 84:214-22. 15. Pingel S, ZE Wang, RM Locksley. 1998. Distribution of protein kinase C isoforms after infection of macrophages with Leishmania major. Infect Immun 66:1795-9. 16. Wakil AE, ZE Wang, JC Ryan, DJ Fowell, RM Locksley. 1998. Interferon gamma derived from CD4(+) T cells is sufficient to mediate helper cell type 1 development. J Exp Med 188:1651-6. 17. Bix, M, ZE Wang, B Thiel, NJ Schork, RM Locksley. 1998. Genetic regulation of commitment to interleukin 4 production by a CD4(+) T cell-intrinsic mechanism. J Exp Med 188:2289-99. 18. Symula DJ, KA Frazer, Y Ueda, P Denefle, ME Stevens, ZE Wang, RM Locksley, EM Rubin. 1999. Functional screening of an asthma QTL in YAC transgenic mice. Nat Genet 23:241-4.

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19. Cretu G, RM Locksley, ZE Wang, EM Rubin, KA Frazer. 2000. Functional analysis of CNS-1 in YAC transgenic mice. Science 288:136-9. 20. Lacy DA, ZE Wang, DJ Symola, C McArthur, EM Rubin, KA Frazer, RM Locksley. 2000. Faithful expression of the human 5q31 cytokine cluster in transgenic mice. J Immunol 164:4569-75. 21. Loots GG, RM Locksley, CM Blankespoor, ZE Wang, W Miller, EM Rubin, KA Frazer. 2000. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288:136-140. 22. Mohrs M, CM Blankespoor, Z Wang, GG Loots, V Afzal, H Hadeiba, K Shinkai, EM Rubin, RM Locksley. 2001. Deletion of a coordinate regulator of type 2 cytokine expression in mice. Nat Immunol 2, 842-7. 23. Grogan JL, ZE Wang, S Stanley, B Harmon, GG Loots, EM Rubin, RM Locksley. 2003. Basal chromatin modification at the IL-4 gene in helper T cells. J Immunol 171:6672-9. 24. Xu M, ZE Wang, RM Locksley. 2004. Innate immune responses in peptidoglycan recognition protein L-deficient mice. Mol Cell Biol 24:7949-57. 25. Reinhardt RL, S Hong, SJ Kang, ZE Wang, RM Locksley. 2006. Visualization of IL-12/23p40 in vivo reveals immunostimulatory dendritic cell migrants that promote Th1 differentiation. J Immunol 177:1618-27. 26. Cheng LE, ZE Wang, RM Locksley. 2010. Murine B cells regulate serum IgE levels in a CD23-dependent manner. J Immunol 185:5040-7. 27. Yang Z, ZE Wang, PT Doulias, W Wei, H Ischiropoulos, RM Locksley, L Liu. 2010. Lymphocyte development requires S-nitrosoglutathione reductase. J Immunol 185:6664-9. 28. Gordon E, S Sidhu, Z-E Wang, P Woodruff, S Yuan, M Solonm S Conway, X Huang, RM Locksley, J Fahy. 2012. A protective role for periostin and TGF-β in IgE-mediated allergy and airway hyperresponsiveness. Clin Exp Allergy 42: 144-155. PMC3271792

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BIOGRAPHICAL SKETCH NAME Arthur Weiss, M.D., Ph.D. eRA COMMONS USER NAME weissa

POSITION TITLE Professor of Medicine and of Microbiology and Immunology EDUCATION/TRAINING

INSTITUTION AND LOCATION University of Chicago University of Chicago

DEGREE

YEAR(s)

Ph.D. M.D.

1978 1979

FIELD OF STUDY Immunology Medicine

Positions and Employment 1979-1980 1980-1982 1982-1984 1982-1985 1984-1985 1985-1989 1985-1989 19871989-1993 1989-1994 1991199219931998-2005 2002-2006 2007-2010

Postdoctoral Fellow, Swiss Institute for Experimental Cancer Research, Lausanne, Switzerland Resident, Department of Medicine, University of California, San Francisco (UCSF) Fellow in Rheumatology/Clinical Immunology, UCSF Associate, Howard Hughes Medical Institute, UCSF Instructor, Department of Medicine, Division of Rheumatology/Clinical Immunology, UCSF Assistant Investigator, Howard Hughes Medical Institute, UCSF Assistant Professor of Medicine, Microbiology and Immunology, UCSF Chief, Division of Rheumatology/Clinical Immunology, Department of Medicine, University of California, San Francisco Associate Professor or Medicine, Microbiology and Immunology, UCSF Associate Investigator, Howard Hughes Medical Institute, UCSF Ephraim P. Engleman Distinguished Professor of Rheumatology, UCSF Professor of Medicine, Microbiology and Immunology, UCSF Investigator, Howard Hughes Medical Institute, UCSF Associate Director, The Rosalind Russell Medical Research Center for Arthritis, UCSF Director, Medical Scientist Training Program (MSTP), UCSF Co-Director, Institute for Molecular Medicine, UCSF

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Other Experience and Professional Memberships 1986-1991 1991 1998-2002 19992000-2002 2003-2010 2008-2009 2005-

Councilor, American Federation for Clinical Research President, Western Region of the American College of Rheumatology Member, Allergy and Immunology Study Section (NIH) Chair, Scientific Advisory Board, American Asthma Foundation Chair, Allergy and Immunology Study Section (NIH) Council, American Association of Immunologists President, American Association of Immunologists Advisory Council, RIKEN Research Center for Allergy & Immunology Yokohama, Japan

Honors 1990 1990 1993 1997 1998 2001 2003 2004 2004 2004 2004 2004 2004 2004 2005 2005 2005 2005 2006 2009 2009 2010 2012 2012

Young Investigator Award, Western Society for Clinical Investigation Henry Kunkel Young Investigator Award, American College of Rheumatology Junior Investigator Award, American Association of Immunologists Lee C. Howley Prize, Arthritis Foundation Forty-First Faculty Research Lecturer, University of California, San Francisco American Association of Immunologist-Huang Foundation Meritorious Career Award Fellow, American Academy of Arts and Sciences Member, National Academy of Sciences Fellow, American Academy of Microbiology Member, Institute of Medicine Distinguished Investigator Award, American College of Rheumatology Walter Bauer Visiting Professor in Rheumatology, Massachusetts General Hospital Bridget Ogilvie Lecture, University of Dundee, Scotland Sue Kim Hansen Lecture, Boston University School of Medicine Dan H. Campbell Memorial Lecture, Midwinter Conference of Immunologists, Asilomar, CA Visiting Professor, Harvard Medical School Rheumatology Division Beirne B. Carter Lecture in Immunology, University of Virginia Dan H. Campbell Memorial Lecture, Midwinter Conference of Immunologists, Asilomar, CA Keynote Speaker, American Association of Immunologists, Advanced Immunology Course Ishizaka Lecture, La Jolla Institute for Allergy and Immunology 46th Charles A. Stuart Memorial Lecture, Brown University Dorothy Baugh Harmon Endowed Lectureship, Oklahoma Medical Research Foundation Lifetime Achievement Award, American Association of Immunologists UCSF Lifetime Achievement in Mentoring Award

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Selected Peer-reviewed Publications (from a total of 207) 1. Deindl S, Kadlecek TA, Brdicka T, Cao X, Weiss A, and Kuriyan. Structural basis for the inhibition of the tyrosine kinase activity of ZAP-70. Cell, 129:735746, 2007. PMID: 17512407 2. Palacios E, Weiss A. Distinct roles for Syk and ZAP-70 during thymic development. J Exp Med. 2007; 204: 1703-15. PMID: 17606633. PMVIF: PMV2118636. 3. Zhu JW, Brdicka T, Katsumoto TR, Lin J, and Weiss A. Structurally distinct phosphatases CD45 and CD148 both regulate B cell and macrophage immunoreceptor signaling. Immunity. 28:183-196. 2008. PMC2265106 4. Hsu L-Y, Tan YX, Xiao Z, Malissen M, and Weiss A. A hypomorphic allele of ZAP-70 reveals a distinct thymic threshold for autoimmune disease versus autoimmune reactivity. J. Exp. Med., 206:2527-2541, 2009. PMC2768860 5. Das J, Ho M, Zikherman J, Govern C, Yang M, Weiss A, Chakraborty AK, Roose JP. Digital signaling and hysteresis characterize Ras activation in lymphoid cells. Cell. 2009; 136337-51. PMCID: PMC2662698. 6. Zikherman J, Hermiston M, Steiner D, Hasegawa K, Chan A and Weiss A. PTPN22 deficiency cooperates with the CD45 E613R allele to break tolerance on a non-autoimmune background. J. Immunol., 182:4093-4106. 2009. PMC2765978 7. Deindl S, Kadlecek TA, Cao X, Kuriyan J, and Weiss A. Stability of an autoinhibitory interface in the structure of the tyrosine kinase ZAP-70 impacts T cell receptor response. Proc. Natl. Acad. Sci. USA 106:20699-20704, 2009. PMC2778580 8. Zikherman J, Jenne C, Watson S, Doan K, Raschke W, Goodnow CC, and Weiss A. The balance between positive and negative regulatory roles of CD45 during T CR signaling varies throughout T cell development. Immunity, 32:342-354. 2010. PMC2865198 9. Phee H, Dzhagalov I, Mollenauer M, Wang Y, Irvine DJ, Robey ., and Weiss A. Regulation of thymocyte positive selection and motility by GIT2. Nat. Immunol., 11:503-511. 2010. PMID: 20431621 10. Au-Yeung BB, Levin SE, Zhang C, Hsu, L-Y, Cheng DA, Killeen N, Shokat K and Weiss A. A genetically selective inhibitor demonstrates a function for the kinase Zap70 in regulatory T cells independent of its catalytic activity. Nat. Immunol., 11:1085-1093. 2010. PMID: 210375 11. Limnander A, Depeille P, Freedman TS, Liou J, Leitges M, Kurosaki T, Roose JP, and Weiss A. Stim1, PKCd, and RasGRP proteins set a threshold for proapoptotic Erk signaling during B cell development. Nat. Immunol., 12:425-433. 2011. PMID: 21441934 12. Zhu JW, Doan K., Park J, Chau AH, Zhang H, Lowell CA, and Weiss A. Distinct functions of receptor-like tyrosine phosphatases CD45 and CD148 in chemoattractant-mediated neutrophil migration and response to S. aureus infection. Immunity. 35:757-769. 2011. PMID: 22078799

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13. Zikherman J, Doan K, Parameswaran R, Raschke W, and Weiss A. Quantitative differences in CD45 expression unmask functions for CD45 in B-cell development, tolerance and survival. Proc. Natl. Acad. Sci. USA. ePub ahead of print. 2011. PMID: 22135465 14. Wei P, Wong WW, Corcoran EE, Peisajovich SG, Weiss A, and Lim WA. Bacterial virulence proteins as tools to synthetically rewire kinase pathways in yeast and immune cells. Nature. 488:384-388. 2012. PMCID: PMC3422413 15. Zikherman, J., Parameswaran, R., and Weiss. A. Endogenous antigen tunes responsiveness of antigen recepor signaling in B cells but not T cells. Nature. 489:160-164. 2012. PMID: 22902503 16. Mukherjee S, Zhu J, Zikherman J, Parameswaran R, Kadlecek TA, Wang Q, AuYeung B, Ploegh H, Kuriyan J, Das J*, and Weiss, A* Monovalent and multivalent ligation of the B cell receptor exhibit differential dependence upon Syk and Src family kinases. Sci. Signal. 2013. Jan 1;6(256):ra1 PMID: 23281368 *co-corresponding authors 17. Zikherman J, Parameswaran R, Hermiston M, and Weiss A. The wedge domain of the receptor-like tyrosine phosphatase CD45 enforces B cell tolerance by regulating substrate specificity. J. Immunol., in press. 2013. Research Support Ongoing Research Support Howard Hughes Medical Institute Weiss (PI) 07/01/85-08/31/12 Cell surface molecules and molecular events involved in human T cell activation The goal is to study cell surface molecules and molecular events involved in T cell activation. HHMI personnel (3 postdocs and 4 technicians) focus on structure of the TCR and the ZAP-70 protein tyrosine kinase. Role: Principal Investigator 1 RC2 AR058947-01 (A.Weiss) 09/25/09-08/31/12 No Cost Extension NIH/NIAMS An allosteric inhibitor of ZAP-70 as a novel therapeutic for autoimmune disease The goals of this project are develop and allosteric inhibitor of ZAP-70 and determine the preclinical utility of a model catalytic inhibitor of ZAP-70 in preclinical models of disease. Role: Principal Investigator 1PO1 AI091580-01 07/15/11-06/30/16 NIH/NIAID (Program Leader A. Weiss) Deconstructing and Reconstructing the T Cell Signaling Network The goals of this project are to understand the molecular mechanims that operate at the plasma membrane to control the specificity, activity and regulation of the TCR signaling mechanisms that lead to protein tyrosine phosphorylation and Ras activity.

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A119632 Weiss (PI) 07/01/12-06/30/14 American College of Rheumatology Identifying antigen-specific T cells in mouse and human arthritis The goals of this grant are to understand how antigen specific T cells are stimulated and to identify and characterize the T cell antigen receptors in mouse and human arthritis. Role: Principal Investigator Completed Research RO1 AI066120 Weiss (PI) 02/15/06-01/31/12 No Cost Extension NIH/NIAID Function of the RPTP CD148 in the Hematopoietic Lineage The goals in this research 1) characterize the developmental, functional, and biochemical consequences of CD148 loss on the T cell lineage, with emphasis on TCR signaling pathways; 2) characterize the developmental, functional and biochemical consequences of the loss CD148 on the B cell lineage, with emphasis on the antigen receptor signaling pathways; and, 3) characterize the biochemical, functional and immunological consequences of inactivating the CD148 gene in myeloid cells on integrin and Fc-receptor dependent pathways. Role: Principal Investigator PO1 AI35297 Abbas (PI) 08/01/0607/31/11 NIH/NIAID Peripheral Tolerance and Autoimmunity Project #3 Regulation of CD45 signaling in tolerance and autoimmunity The goals of this project are to exploit a newly discovered model of autoimmunity caused by a genetic disruption that prevents CD45 dimerization as a model for defects in signaling receptors that interfere with self-tolerance. T cell lineages responsible for autoimmunity and the role of antigen will be defined, and the molecular basis of CD45 regulation of lymphocyte responses and self-tolerance will be examined. Role: Co-Investigator PN2 EY016546 Lim (PI) 08/30/09 NIH

09/01/08-

Cellular Control: Synthetic Signaling/Motility (RMI) The goals of this project are to engineer cells or cell-like molecular assemblies that perform “smart” therapeutic functions: tasks such as tissue repair or “search and deliver” actions to treat microscopic tumors or cardiovascular lesions. Role: Project Principal Investigator

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RO1 AI52127 Goodnow (PI) 09/15/0206/30/07 NIH/NIAID Genes for Tolerance and Immunity Consortium A consortium of investigators will develop and validate screening tests to identify mice with altered immune regulation, and then define the mutant gene, molecular pathways, and cellular processes revealed by each new mouse strain. Role: Co-Investigator

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BIOGRAPHICAL SKETCH NAME Jonathan S. Weissman, Ph.D. eRA COMMONS USER NAME WEISSMAN

POSITION TITLE Professor, University of California San Francisco Investigator, Howard Hughes Medical Institute EDUCATION/TRAINING

INSTITUTION AND LOCATION

DEGREE

YEAR(s)

FIELD OF STUDY

Harvard University Massachusetts Institute of Technology

A.B. Ph.D.

1984-1988 1988-1993

Physics Physics

Positions and Honors 1993 - 1996 1996 - 2000 2000 - 2005 2000 - 2003 2003 - Present 2005 - Present

Postdoctoral Fellow, Yale University, Structural and Biochemical Studies of GroEL Assistant Professor, University of California San Francisco, Departments of Cellular & Molecular Pharmacology, and Biochemistry & Biophysics Assistant Investigator, Howard Hughes Medical Institute Associate Professor, University of California San Francisco, Departments of Cellular & Molecular Pharmacology, and Biochemistry & Biophysics Professor, University of California San Francisco, Departments of Cellular & Molecular Pharmacology, and Biochemistry & Biophysics Investigator, Howard Hughes Medical Institute

Other Experience and Professional Memberships 1999 2001 to Present 2001 - 2003 2002 2002 to Present 2003 to Present 2003 2003 to Present 2004 2005 2004 - 2008 2005 - 2008 2005

Keynote Speaker at Scripps Research Institute Society of Fellows Annual Symposium Associate Editor, Molecular Cell Ad hoc reviewer, CDF-2 NIH study section Organizer, Second International Yeast Prion Symposium Organizer, Cold Spring Harbor Heat Shock Meeting Editorial Board, BMC Cell Biology Burroughs Wellcome Visiting Scholar, University of Chicago Editorial Board, Public Library of Science (PLoS) Biology Organizer, FASEB meeting on Amyloid and Diseases of Misfolding Co-organizer, The Protein Society 19th Annual Meeting Permanent Member, NIH Molecular Biology & Protein Processing Study Section Editorial Board, Molecular Biology of the Cell External Reviewer, Lawrence Berkeley National Lab Physical Biosciences Division

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2005 - 2007 2005 2006 to Present 2006 to Present 2007 to Present 2007 to Present 2008 to Present 2008 to Present 2009 2009 to Present 2009 2009 2009 to Present 2009 2010

Advisory Board NIH on Amyloid Diseases Organizer, Mini-symposium of Quality Control for the Annual American Society of Cell Biology (ASCB) Meeting Member, Yeast Genetics & Molecular Biology Meeting Program Committee Editorial Board, Journal of Molecular Biology Board of Reviewing Editors, Science Scientific Advisory Board, GlycoFi (Merck & Company, Inc.) Scientific Advisor, Merck Research Labs Editorial Board, Cell Program Committee Member, ASCB Editorial Board, Current Opinion in Cell Biology Keynote address at the annual retreat of the Genentech Research Organization Keynote lecture at the annual International Conference on Systems Biology Scientific Advisory Board, Proteostasis Therapeutics Member, NAKFI Steering Committee on Synthetic Biology Member, NIH College of CSR Reviewers

Honors and Awards 1987 1988 1988 1988 1996 1997 2000 2004 2008 2009 2009 2010 2010

Phi Beta Kappa, Harvard University Summa cum laude in Physics, Harvard University Karl Taylor Compton Pre-doctoral Fellowship National Science Foundation Pre-doctoral Fellowship David and Lucile Packard Fellowship Searle Scholars Program Fellowship Assistant Investigator, Howard Hughes Medical Institute Protein Society’s Irving Sigal Young Investigator’s Award Raymond & Beverly Sackler International Prize in Biophysics Alexander M. Cruikshank Lecturer, Gordon Research Conference on Stress Elected to the National Academy of Sciences David Perlman Award Lecturer of the ACS Division of Biochemical Technology (BIOT) Fellow, American Academy of Microbiology

Selected Peer-reviewed Publications (In chronological order; 13 selected of 119 publications) 1. Breslow DK, Cameron DM, Collins SR, Schuldiner M, Stewart-Ornstein J, Newman HW, Braun S, Madhani HD, Krogan NJ, Weissman JS. (2008) A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nat Methods, 5:711-8. PMC2756093 2. Breslow DK, Collins SR, Bodenmiller B, Aebersold R, Simons K, Shevchenko A, Ejsing CS, Weissman JS. (2010) ORM family proteins mediate sphingolipid homeostasis. Nature, 463:1048-53. PMC2877384

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3. Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS. (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 324(5924)218-23. PMC2746483 4. Breslow DK, Weissman JS. (2010) Membranes in Balance: Mechanisms of Sphinogolipid Homeostasis. Mol Cell, 40(2): 267-79. PMC2987644 5. Churchman LS, Weissman JS. (2011) Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature, 469: 368-73. PMID 21248844 6. Ingolia NT, Lareau LF, Weissman JS. (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of Mammalian proteomes. Cell, 147: 789-802. PMC3225288 7. Oh E, Becker AH, Sandikci A, Huber D, Chaba R, Gloge F, Nichols RJ, Typas A, Gross CA, Kramer G, Weissman JS, Bukau B. (2011) Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo. Cell, 147: 1295-1308. PMC3277850 8. Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS. (2012) High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science, 335: 552-7. PMID 22194413 9. Li GW, Oh E, Weissman JS. (2012) The anti-Shine-Dalgamo sequence drives translational pausing and codon choice in bacteria. Nature, 484: 538-41. PMC3338875 10. Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. (2012) The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nature Protocols, 7: 1534-50. PMID 22836135 11. Carvunis AR, Rolland T, Wapinski I, Calderwood MA, Yildirim MA, Simonis N, Charloteaux B, Hidalgo CA, Barbette J, Santhanam B, Brar GA, Weissman JS, Regev A, Thierry-Mieg N, Cusick ME, Vidal M. (2012) Proto-genes and de novo gene birth. Nature, 487: 370-4. PMC3401362 12. Brandman O, Stewart-Ornstein J, Wong D, Larson A, Williams CC, Li GW, Zhou S, King D, Shen PS, Weibezahn J, Dunn JG, Rouskin S, Inada T, Frost A, Weissman JS. (2012) A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress. Cell, 151: 1042-54. PMID 23178123 13. Stern-Ginossar N, Weisburd B, Michalski A, Le VT, Hein MY, Huang SX, Ma M, Shen B, Qian SB, Hengel H, Mann M, Ingolia NT, Weissman JS. (2012) Decoding human cytomegalovirus. Science, 338: 1088-93. PMID 23180859 Research Support Ongoing Research Support No Project Number (Weissman) 10/01/2000-8/31/2017 Howard Hughes Medical Institute Prion-Based Inheritance, Protein Folding, and Analysis of Cellular Systems

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This grant supports our studies of how cells insure that proteins fold into their correct shape, as well as the role of protein misfolding in disease and normal physiology. We are also developing experimental and analytical approaches for exploring the organizational principles of biological systems. Hughes Collaborative Investigator Award -- No Project Number (Weissman) 09/18/2012 08/17/2017 Howard Hughes Medical Institute A combined chemical and genetic approach to explore how chaperone and stress networks maintain the integrity of oncogene-addicted cancer cells P01 AG70770-15 (Prusiner; Weissman Project 2) 04/01/11 - 3/31/16 NIH Molecular Pathogenesis of Age-Dependent CNS Degeneration Specific aims of this project are to 1) identify a novel prion domain in the yeast protein New1p; 2) identify novel prion phenomena; and 3) establish a genetic screen in yeast to study propagation of the mammalian prion protein (PrP). U01 CA168370-01 (McManus) 05/01/12 – 04/30/17 NIH Bay Area Cancer Target Discovery and Development Network The overarching goal of the BACTDDN is to discover and characterize new cancer targets and their modulators, placing them into druggable pathways. Specific aims: 1) develop EXPAND libraries targeting cancer-specific genetic alterations; 2) identify novel drivers that show transforming potential in immortalized primary cells; and 3) produce genetic EMAPs to uncover pathway relationships between candidate drivers. P50 GM073210 (Stroud; Weissman - Key Personnel) 09/01/09 – 08/31/2014 NIH/NIGMS Centers for Innovation in Membrane Protein Production for Structure Determination The goals are to develop approaches that will make the solution of simple membrane protein structures routinely achievable and develop novel methods that can be applied to more complicated membrane proteins containing multiple subunits of the same (homo-oligomers) and different (hetero-oligomers) structure; and to produce and determine structures for complexes that are formed between membrane proteins and their soluble protein partners, small ligands and/or macromolecules. U01 GM098254 (Agard/Walter) 09/2012 - 08/2017 NIH Structural Basis of Protein Homeostasis To obtain structural insights into the mechanism by which unfolded and non-native states are recognized by the cytosolic (Hsp70, TRiC chaperones) and ER (UPR and ERAD pathways) protein homeostasis machineries.

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P50 GM102706-01 (Cate) 09/2012 - 08/2017 NIH Center for RNA Systems Biology This Center aims to use systems biological methods to discover the regulation of mRNA fate controlled by RNA structural elements in pre-mRNAs and mRNAs. No Project Number (Bivona & Weissman) 02/01/2012 - 1/30/2014 California Institute for Quantitative Biosciences Discovery of Rational Companion Targets in Human Lung Cancer The goal is to define rational polytherapies for lung cancer patients through genome-wide RNAi screening. Specific aims of this Rogers Foundation Bridging the Gap Award project are: 1) determine which genes act together to make cancer tumor cells more vulnerable; 2) test drug combinations against these targets; 3) identify additional drug combinations to tackle other subtypes of lung cancers, and expand studies to include different categories of cancer. Completed Research Support Sandler Center for Drug Discovery (Weissman) 11/01/11 - 10/31/2012 Identifying and Characterizing Asiatic Cholera Host Factors Specific aims of this project are: 1) Develop a quantitative functional reporter assay for action of cholera toxin in cell culture; 2) Conduct a comprehensive genome-wide screen for factors affecting cholera toxin action; 3) Validate and characterize the targets in physiological assays for cholera activity. SABRE Center (Weissman) 01/01/09-06/30/11 Sandler Asthma Basic REsearch Center Defining the Function of ORMDL3 and Exploring its Potential Role in Asthma Specific aims of this project are: 1) Define the function of ORM genes in yeast; 2) Characterize the function of the human ORM homolog ORMDL3; 3) Examine the potential role of ORMDL3 in asthma. P0032295 (Weissman) 12/01/09 - 11/30/2010 AFAR (Glenn Foundation for Medical Research) Monitoring the Effects of Aging on Protein Translation Using a ribosome profiling approach pioneered in our lab, we will investigate the impact of aging and the accumulation of misfolded proteins on protein synthesis in a yeast model system. Sandler Center (Weissman and F 01/15/09-01/14/10 Sandler Program in Basic Sciences Defining Roles on N-Glycans in Endopasmic Reticulum-Mediated Quality Control Specific aims of this project are: 1) Biochemical characterization of the putative mannosidase Htm1; and 2) Elucidation of contributions of glycan and misfolded protein components to substrate recognition in late stages of ERAD-L pathway.

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Fight for Mike Program (Weissman) 07/23/07-07/22/09 California Institute for Quantitative Biosciences (QB3) Identification of Factors Important for the Folding of Mammalian Prion Protein The broad goal of our studies is to identify key factors required for folding of the mammalian prion protein.

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BIOGRAPHICAL SKETCH NAME Zena Werb, Ph.D. eRA COMMONS USER NAME werbzena

POSITION TITLE Professor of Anatomy

EDUCATION/TRAINING INSTITUTION AND LOCATION University of Toronto, Toronto, Canada Rockefeller University, New York Strangeways Research Laboratory, Cambridge,

DEGREE B.Sc. Ph.D. Postdoc.

YEAR(s) 06/1966 06/1971 1971-73

FIELD OF STUDY Biochemistry Cell Biology Protein Chemistry

Positions 1973-1975 1975-1976 1976-1980 1979-1980 1980-1983 1983-Present 1985-1986 1998 1999-Present 2006-2008

Research Scientist, Strangeways Res. Lab., Cambridge, United Kingdom Visiting Assistant Professor of Medicine, Dartmouth Medical School, Hanover, NH Assistant Professor Radiobiology, Radiology University of California, San Francisco Assistant Professor Anatomy, University of California San Francisco Associate Professor of Anatomy and Radiology University of California, San Francisco Professor Anatomy, UCSF Visiting Professor, Sir William Dunn School of Pathology University of Oxford, United Kingdom Visiting Professor, Institut Curie, Paris Vice-chair, Dept. of Anatomy, University of California, San Francisco Visiting Professor, Max-Planck Institute for Biochemistry Martinsried, Germany

Other Experience and Professional Memberships Editorial Boards 1983-1985 1982-1987 1985-2004 1990-2001 1999-Present 1999-Present 2000-2009 2001-Present 2001-Present

Journal of Cell Biology American Journal of Physiology Journal of Experimental Medicine Science Matrix Biolog Neoplasia Cell Developmental Cell Cancer Cell

183

2002-2006 2007-2009 2009-Present 2010-Present 2010-Present

Molecular Biology of the Cell Genes & Development Current Opinion in Cell Biology Guest Editor, Proc. National Academy Science, USA Member, Editorial Board, Disease Models and Mechanisms

Professional Memberships 1976-present 1979-present 1967-71 & 1979-present 1988-present 2001-present 2001-present 2004-present

American Society for Cell Biology American Society for Biochemistry and Molecular Biology American Association for the Advancement of Science Society for Developmental Biology American Association for Cancer Research American Society for Matrix Biology International Society for Differentiation

Scientific Leadership 1990-1992 Canada 1991-1995 1992-1995 1993-1995 1994-2001 2001-2003 2001 2002 2003-2005 2003-2006 2005 2007-2009 2007 2008 2008 2008-2010 2009-2012 2010 2011-Present 2011-2016 Honors 1971-1973 1982 1985-1986 1992 1996

Member, Cell and Molecular Biology Panel, National Cancer Institute of Member, Board of Scientific Counselors, NIAMS Council Member, American Society for Cell Biology Council Delegate, Am. Assoc. for the Advancement of Science Member, Scientific Advisory Board, Keystone Symposia Council Member, American Society for Matrix Biology NIH Oncological SS Boundaries Team NIH Biochem SS, ad hoc Council Member, International Society for Matrix Biology Board of Directors, AACR President, American Society for Cell Biology Nominating Committee, AACR Member, NIH ZRG1 ICI–D01 Reviewer, NIH Pioneer Awards Chair, NIH ZRG1 MOSS-A (02) Chair, NIH ICI Study Section Chair, American Academy of Arts and Sciences, Membership Selection Committee Class II, section Co-organizer, CNIO Cancer Symposium on Frontiers in Invasion and Metastasis, Madrid Member, Steering Committee, AACR Council of Scientific Advisors Member, Scientific Advisory Board, Max Planck Institute for Biology of Ageing, Cologne, Germany Fellow, Medical Research Council, Canada R.R. Bensley Memorial Award, American Association of Anatomists Fellow, John Simon Guggenheim Foundation Elected Fellow, American Association for the Advancement of Science FASEB Excellence in Science Award

184

1998 2002 2003 2003 2006-2007 2007 2009 2010 2010 2011

Rotschild/Mayent Fellowship, Institut Curie Elected Member, Institute of Medicine Elected Fellow, American Academy of Arts and Sciences Doctor of Medicine (honoris causa), University of Copenhagen Alexander von Humboldt Foundation (Germany) Research Award E.B. Wilson Medal, American Society for Cell Biology Colin Thomson Memorial Medal, AICR Elected Member, National Academy of Sciences American Society for Cell Biology, Women in Cell Biology Senior Award Zero Breast Cancer 2011 Community Breast Cancer Research Award

Named Lectureships (selected) 2001 2001 2003 2004 2004 2005 2005 2008 2009 2011 2011 2012

44th Faculty Research Lecture Award, University of California, San Francico H.B. Parker Lecture, Pacific Northwest National Lab. Pharmacology Founders’ Seminar, Wayne State University, Detroit, Michigan Schlessinger Lecturer, BIDMC, Harvard Medical School A. S. Wiener Lecture, NY Blood Center Maud L. Menten Lecture, University of Pittsburgh 17th Otto Herz Memorial Lecture, Tel Aviv University, Israel Whitley Lecture, Northwest Developmental Biology Society Suzanne M. Bernier Lecture in Skeletal Biology, University of Western Ontario, London, Canada John H. Blaffer Lecture, M.D. Anderson Cancer Center, University of Texas, Houston TX McAllister Lecture, Pathology Grand Rounds, Yale Medical School, New Haven CT Keynote Lecture, 28th International Association for Breast Cancer Research Breakthrough Breast Cancer Conference, Manchester, UK

Selected Publications 15 Selected Publications (>450 total full publications) 1. Sternlicht MD, A. Lochter, CJ Sympson, B Huey, JP Rougier, JW Gray, D Pinkel, MJ Bissell & Z Werb (1999). The stromal proteinase MMP-3/stromelysin-1 promotes mammary carcinogenesis. Cell. 98: 137-146. PMCID: PMC2853255 2. Coussens LM & Z Werb (2002). Inflammation and cancer. Nature 420:860-867. PMID: 12490959; PMCID: PMC2803035 3. Egeblad MA, J Ewald, HA Askautrud, BE Welm, M Truitt, E Bainbridge, G Peeters, M Krummell & Z Werb (2008). Visualizing stromal cell dynamics in different tumor microenvironments by spinning disk confocal microscopy. Dis. Model. Mech. 1:155-167. PMCID: PMC2562195. 4. Ewald AJ, A Brenot, M Duong, BS Chan & Z Werb (2008). Collective epithelial migration and cell rearrangements drive mammary branching morphogenesis. Dev. Cell. 14:570-581. PMCID: PMC2773823. 5. Kouros-Mehr H, SK Bechis, EM Slorach, LE Littlepage, M Egeblad, AJ Ewald, SY Pai, IC Ho & Z Werb (2008). GATA-3 links tumor differentiation and dissemination in a luminal breast cancer model. Cancer Cell. 13:141-152. PMCID: PMC2262951.

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6. Welm BE, GJP Dijkgraaf, AS Bledau, AL Welm & Z Werb (2008). Lentiviral transduction of stem cells for genetic analysis of mammary development and breast cancer. Cell Stem Cell. 2:90-102. PMCID: PMC2276651. 7. Kessenbrock K, V Plaks & Z Werb (2010). Matrix metalloproteinases: Regulators of the tumor microenvironment. Cell. 141:52-67. PMCID: PMC286205. 8. Littlepage LE, MD Sternlicht, N Rougier, J Phillips, E Gallo, Y Yu, K Williams, A Brenot, JI Gordon & Z Werb (2010). Matrix metalloproteinases contribute distinct roles in neuroendocrine prostate carcinogenesis, metastasis, and angiogenesis progression. Cancer Res. 70:2224-2234 PMID: 20215503; PMCID: PMC2840052. 9. Slorach EM, J Chou & Z Werb (2011). Zeppo1 is a novel metastasis promoter that represses E-cadherin expression and regulates p120-catenin isoform expression and localization. Genes Dev. 25: 471-484. [Epub ahead of print February 11, 2011]. PMCID: PMC3049288. 10. Caudrillier A, K Kessenbrock, BM Gilliss, JX Nguyen, MB Marques, M Monestier, P Toy, Z Werb & MR Looney (2012). Platelets induce neutrophil extracellular traps in transfusion-related acute lung injury. J. Clin. Invest. 122(7):2661–2671. [Epub ahead of print, Jun 11]. PMID: 22684106; PMCID: PMC3386815. 11. Engelhardt J, B Boldajipour, P Beemiller, P Pandurangi, C Sorenson, Z Werb, M Egeblad & MF Krummel (2012). Marginating dendritic cells of the tumor microenvironment cross-present antigens and stably engage tumor-specific T cells. Cancer Cell. 21:402-417. PMID: 22439936; PMCID: PMC3311997. 12. Littlepage LE, AS Adler, H Kouros-Mehr, G Huang, J Chou, SR Krig, OL Griffith, JE Korkola, K Qu, DA Lawson, Q Xue, MD Sternlicht, GJP Dijkgraaf, P Yaswen, Hope S Rugo, CA Sweeney, CC Collins, JW Gray, HY Chang & Z Werb (2012). The transcription factor ZNF217 is a prognostic biomarker and therapeutic target during breast cancer progression. Cancer Discov. 2:638-651 [Epub June 22]. PMID: 22728437. 13. Nakasone E, HA Askautrud, T Kees, V Plaks, AJ Ewald, MG Rasch, YX Tan, J Qin, M Fein, J Park, P Sinha, MJ Bissell, E Frengen, Z Werb & M Egeblad (2012). Imaging tumor-stroma interactions during chemotherapy reveals microenvironmental contributions to chemoresistance. Cancer Cell. 21:488-503. PMCID: PMC3332002. 14. Phillips JJ, A Ward, E Huillard, A Robinson, DH Lum, MY Polley, SD Rosen, DH Rowitch & Z Werb (2012). Heparan sulfate sulfatase SULF2 regulates PDGFRa signaling and growth in malignant glioblastoma. J. Clin. Invest. 122:911–922 [Epub Feb. 1]. PMID: 22293178; PMCID: PMC3287216. 15. Chou J, JH Lin, A Brenot, JW Kim, S Provot & Z Werb (2013). GATA3 suppresses metastasis and modulates the tumor microenvironment by regulating miR-29 expression. Nat. Cell Biol. In press.

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Research Support Ongoing NIH/NCI R01 CA129523-05 Werb (PI) 07/01/08 - 04/30/13 Transcriptional Regulation of Breast Cancer Metastasis This study addresses how GATA-3 regulates the differentiated state of breast tumors. NCI R01 CA057621-20 Werb (PI) 04/15/93 - 05/31/13 Role of Metalloproteinases in Mammary Gland Remodeling This consortium grant between UCSF and LBNL determines functions of ECM-degrading proteinases and inhibitors in mammary epithelium during development. NIH/NIAID P01 AI053194-10 Mostov (PI) 09/30/02 - 08/31/13 Mucosal Immune Barrier in Infection and Inflammation This project studies the role of the inflammatory response in mucosal epithelia. Role: Leader, Project 4 and Core C NIEHS/NCI 5U01 ES019458-03 (Werb, PI) 09/01/10-04/30/15 Environmental Effect on The Mammary Gland Across The Lifespan The major goal of this program is to determine the susceptible times in breast developments and how they are affected by environmental stressors. 17UB-8705-02 California Breast Cancer Research Program (Werb, PI) 09/01/11-08/31/14 Biomarkers for environmental exposures in breast cancer The major goal of this project is to find glycan biomarkers that are induced by exposure to environmental stressors. Completed NIH/NIAMS R01 AR046238-10 Werb (PI) 09/01/99 - 01/31/11 Extracellular Remodeling in Bone Development And Repair This project studied the role of extracellular remodeling in bone development and repair. NCI P01 CA072006-10 Werb (PI) 07/07/03 – 06/30/10 Proteases in Cancer: Biology and Drug Development This program tested new animal models of invasive cancer with antiprotease therapy. Role: Project Leader, Project 3 and Core A NIH/NCI U01 CA105379-05 Hanahan (PI) 09/27/04 - 03/31/09 Immune Enhancement and Therapy in Cancer/ Mouse Models of Human Cancer Consortium This project addressed the immunobiology of carcinogenesis in genetically engineered mouse models Role: Co-I NIH/NIEHS U01 ES012801-07 Hiatt (PI), Werb (PI) 09/29/03 - 07/31/11 This project studied environmental effects on the molecular architecture and function of the mammary gland. Role: PI, Collaborative Project 1

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SU2C-AACR-DT0409-03 Gray, Slamon (Dream team leaders) 10/01/09 - 09/30/12 Stand Up to Cancer-American Association for Cancer Research Dream Team Translational Cancer Research Grant Personalizing Treatment of Metastatic Breast Cancer The goal of this project was to develop xenograft models of human of drug-resistant, metastatic breast cancers to then test therapies selected based on the “omic” features of the metastatic tumors. Role: Dream Team Member

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BIOGRAPHICAL SKETCH NAME Prescott Gurney Woodruff, M.D., M.P.H. eRA COMMONS USER NAME woodruffp

POSITION TITLE Associate Professor of Medicine in Residence

EDUCATION/TRAINING INSTITUTION AND LOCATION Wesleyan University, Middletown, CT Columbia College of Physicians & Surgeons, NY Massachusetts General Hospital Harvard School of Public Health Brigham and Women’s Hospital University of California, San Francisco

DEGREE B.A. M.D. Resident M.P.H. Fellow Fellow

YEAR(s) 6/1989 6/1993 1993-1996 6/1998 1997-1998 1998-2002

FIELD OF STUDY Letters Medicine Internal Medicine Epidemiology Resp Epidemiology Pulmonary/Critical Care

Positions and Honors 1993-1994 1994-1996 1996-1998 1997-1998 1998-2002 2002-2005 2005- 2010 20102012-

Intern in Internal Medicine; Massachusetts General Hospital, Boston, MA Resident in Internal Medicine; Massachusetts General Hospital, Boston, MA Research Fellow, Department of Emergency Medicine; Massachusetts General Hospital, Boston, MA Clinical and Research Fellow, Channing Laboratory, Department of Medicine Brigham and Women’s Hospital, Boston, MA Clinical and Research Fellow, Pulmonary/Critical Care Medicine & Cardiovascular Research Institute, Department of Medicine, University of California San Francisco, San Francisco, CA Assistant Adjunct Professor; University of California San Francisco Assistant Professor in Residence, Pulmonary/Critical Care Medicine, Department of Medicine and CVRI, University of California San Francisco Associate Professor in Residence, Division of Pulmonary and Critical Care Medicine, Department of Medicine and CVRI, University of California San Francisco Vice Chief for Research, Division of Pulmonary, Critical Care, Sleep and Allergy, University of California, San Francisco

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Other Experience and Professional Memberships 200420092011-

Steering Committee, NIH NHLBI COPD Clinical Research Network Steering Committee, NIH NHLBI Spiromics Network Steering Committee, NIH NHLBI Severe Asthma Research Program

Honors 1993 2012

Alpha Omega Alpha, Columbia College of Physicians and Surgeons, NY, NY Elected to membership, American Society of Clinical Investigation

Selected peer-reviewed publications (Selected from 58 peer-reviewed publications) 1. Woodruff PG, Boushey HA, Dolganov GM, Barker CS, Yang YH, Donnelly S, Ellwanger A, Sidhu SS, Dao-Pick TP, Pantoja C, Erle DJ, Yamamoto KR, Fahy JV. Genome-Wide Profiling Identifies Epithelial Cell Genes Associated with Asthma and with Treatment Response to Corticosteroids. Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15858-63. PMCID: PMC2000427 2. Goswami S, Angkasekwinaim P, Shan M, Greenlee KJ, Barranco WT, Polikepahad S, Seryshev A, Redding D, Singh B, Sur S, Woodruff PG, Dong C, Corry DB, Kheradmand F. Divergent Roles for Airway Epithelial MMP7 and Retinoic Acid in Experimental Asthma, Nature Immunology, 2009 May;10(5):496-503. PMID: 19329997 PMC Journal – In Process 3. Woodruff PG, Modrek B, Choy DF, Jia G, Abbas AR, Ellwanger A, Koth LL, Arron JR, and Fahy JV. Th2-driven inflammation defines major sub-phenotypes of asthma. Am J Respir Crit Care Med Sep 1 2009;180(5):388-95. PMCID: PMC2742757 4. Park SW, Verhaeghe C, Nguyenvu LT, Barbeau R, Eisley CJ, Nakagami Y, Huang X, Woodruff PG, Fahy JV, Erle DJ. Roles of FOXA2 and FOXA3 in Allergic Airway Disease and Asthma. Am J Respir Crit Care Med. Jul 23 2009 Oct 1;180(7):603-10. PMCID: PMC2753788 5. Dougherty RH, Sidhu SS, Raman K, Solon M, Solberg OD, Caughey GH, Woodruff PG, Fahy JV. Accumulation of intraepithelial mast cells with a unique protease phenotype in T(H)2-high asthma. J Allergy Clin Immunol. 2010 May;125(5):1046-1053.e8. PMC Journal – In Process 6. Koth LL, Cambier CJ, Ellwanger A, Solon M, Hou L, Lanier LL, Abram CL, Hamerman JA, Woodruff PG. DAP12 is required for macrophage recruitment to the lung in response to cigarette smoke and chemotaxis toward CCL2. J Immunol. 2010 Jun 1;184(11):6522-8. Epub 2010 Apr 26. PMC Journal – In Process 7. Sidhu SS, Yuan S, Innes AL, Woodruff PG, Solon M, Hou L, Muller SJ, and Fahy JV.Epithelial cell-derived periostin: roles in TGFbeta activation, collagen production and collagen gel elasticity in asthma. Proc Natl Acad Sci U S A. 2010 Aug 10;107(32):14170-5. PMCID: PMC2922596

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8. Choy DF, Modrek B, Abbas AR, Kummerfeld S, Clark HF, Wu LC, Fedorowicz G, Modrusan Z, Fahy JV, Woodruff PG, Arron JR. Gene expression patterns of th2 inflammation and intercellular communication in asthmatic airways. J Immunol. 2011 Feb 1;186(3):1861-9. PMC Journal – In Process 9. Gordon ED, Sidhu SS, Wang ZE, Woodruff PG, Yuan S, Solon MC, Conway SJ, Huang X, Locksley RM, Fahy JV. A protective role for periostin and TGF-β in IgE-mediated allergy and airway hyper-responsiveness. Clin Exp Allergy. 2012 Jan;42(1):144-55. 10. Eri1 regulates microRNA homeostasis and mouse lymphocyte development and antiviral function. Thomas MF, Abdul-Wajid S, Panduro M, Babiarz JE, Rajaram M, Woodruff P, Lanier LL, Heissmeyer V, Ansel KM. Blood. 2012 Jul 5;120(1):130-42. Epub 2012 May 21. 11. Jia G, Erickson RW, Choy DF, Mosesova S, Wu LC, Solberg OD, Shikotra A, Carter R, Audusseau S, Hamid Q, Bradding P, Fahy JV, Woodruff PG, Harris JM, Arron JR; Bronchoscopic Exploratory Research Study of Biomarkers in Corticosteroid-refractory Asthma (BOBCAT) Study Group. Periostin is a systemic biomarker of eosinophilic airway inflammation in asthmatic patients. J Allergy Clin Immunol. 2012 Sep;130(3):647-654 12. Solberg OD, Ostrin EJ, Love MI, Peng JC, Bhakta NR, Hou L, Nguyen C, Solon M, Nguyen C, Barczak AJ, Zlock LT, Blagev DP, Finkbeiner WE, Ansel KM, Arron JR, Erle DJ, Woodruff PG. Airway Epithelial miRNA Expression is Altered in Asthma. Am J Respir Crit Care Med. 2012 Sep 6. [Epub ahead of print] 13. Huang F, Zhang H, Wu M, Yang H, Kudo M, Peters CJ, Woodruff PG, Solberg OD, Donne ML, Huang X, Sheppard D, Fahy JV, Wolters PJ, Hogan BL, Finkbeiner WE, Li M, Jan YN, Jan LY, Rock JR. Calcium-activated chloride channel TMEM16A modulates mucin secretion and airway smooth muscle contraction. Proc Natl Acad Sci U S A. 2012 Sep 17. [Epub ahead of print] Research Support ACTIVE R01 HL097591 (Woodruff PG) 7/1/2009 - 6/30/2013 NIH/NHLBI Role of Th2 and non-Th2 Inflammation in Airway Smooth Muscle Remodeling in Asthma The goal of this study is to identify pathways linking Th2-driven inflammation to smooth muscle remodeling. R01 HL095372 (Woodruff PG) 9/24/2008 - 7/31/2012 NIH/NHLBI No cost extension through 7/2013 Molecular Phenotyping of Asthma The goal of this study is to identify and characterize molecular phenotypes of asthma using gene expression profiling, quantitative morphometry and related imaging techniques.

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HHSN268200900014C (Woodruff PG) 2/1/2009 - 1/31/2016 NIH/NHLBI The Spiromics Project: Clinical Center The goal of this study is to identify sub-populations and intermediate outcome measures in COPD through a large multi-center longitudinal study. P01 HL107202 (Fahy JV, Woodruff Core leader) 7/1/12-6/30/17 NIH/NHLBI Innate and Adaptive Immune Responses in Th2 High Asthma To identify the roles of iH2 cells, IL-33 and miRNAs in local immune responses in the lung in asthma. 2U19AI077439-06 (Sheppard D, Woodruff Core Leader, Project Co-I) 4/1/2013-3/31/18 NIH/NIAID IL-13 and IL-17 dynamics in the asthmatic airway To identify the cellular sources, tissue localization and local effects of IL-13 and IL-17 in the lung in asthma. R01 HL114447 (PI: Martinez, subcontract PI: Woodruff) 4/1/2012 - 3/31/2016 NIH/NHLBI Pulmonary bacterial microbiome-epithelial cell interactions in COPD The goal of this study is to establish the lung microbiome in COPD and identify epithelial mucin responses associated with selected pathogens. R21 HL108596 (Erle DJ, Woodruff Co-I) 4/6/2011 - 3/31/2013 NIH/NHLBI Micro-RNAs in Airway Epithelial Differentiation and Asthma The goal of this project is to understand how airway epithelial cell micro-RNAs function and determine how these miRNAs contribute to asthma. U10 HL109146 (Fahy JV, Woodruff Co-I) 7/1/2011 - 6/30/2017 NIH/NHLBI Severe Asthma Research Program The goal of this project is to investigate molecular phenotypes and lectins that regulate mucus viscosity in severe asthma. U10 HL098107 (Boushey HA, Woodruff Co-I) NIH/NHLBI UCSF AsthmaNet Clinical Center Clinical Research Skills Development Core

9/30/2009 - 6/30/2016

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The major goals are to serve as a clinical center participating in the conduct of NHLBI-supported multi-center clinical trials of asthma therapies in children and adults with asthma, Role: Co-Core Leader R01HL110883 ((Kheradmand F, Woodruff sub Co-I) 2/15/2012-1/31/2016 NIH/NHLBI Ancillary T-Cell Based Studies in SPIROMICS The major goals are to determine whether T-cell autoreactivity in COPD is associated with emphysema in cross-sectional and longitudinal human studies (using the Spiromics cohort). U10 RFA-HL-12-013 (Koth LL, Woodruff Co-I) 4/012012 – 3/31/15 NIHI/NHLBI Genomic Phenotyping and Mechanisms in sarcoidosis and AAT To perform genomic and microbiomic human studies to define disease heterogeneity in sarcoidosis and AAT N01 AI90052 (Busse W, Woodruff subcontract) 9/30/2009- 9/29/14 NIH/NIAID Inner City Asthma Consortium (ICAC): Immunologic Approaches to Reduce Asthma” To identify immunological approaches to reduction in asthma prevalence and severity in inner city populations.

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