Characterization of New SNPs - Dr Amy Yasko

A Molecular Approach to Health Care Characterization of New SNPs Panel I and Panel II H62H COMT L136L MTRR S175L H595Y maoA

MTR

I1259V

MTR

R52G

MTRR

A919G (A66G)

MTRR

S175L

gene name

amino acid change

MTRR

S257T

AHCY

L318L

MTRR

L333V

AHCY

K214R

MTRR

K350A

AHCY

L125L

MTRR

R415T

AHCY

L135T

MTRR

P450R

AHCY

R38W

MTRR

A515V

CBS

Y233Y (C699T)

MTRR

H595Y

CBS

A360A

MTHFR

CBS

N212N

E429A (A1298C)

COMT

Q73Q

MTHFR

A222V (C677T)

COMT

L136L

MTHFR

F435F

COMT

V158M

MTHFR

E423D

COMT

H62H

NOS

D298E

COMT

P149L

SUOX

L300L

COMT

V92M

SUOX

S370S

COMT

A96V

VDR

Bsm/Taq

COMT

A72S

VDR

Taq

MAO A

R297R

VDR

Fok

MTR

A919G (A2756G)

ACE

Del 16

COMT 1 aga ggt gct ttg aag atg ccg gag gcc ccg cct ctg ctg ttg gca gct gtg ttg ctg ggc 61 ctg gtg ctg ctg gtg gtg ctg ctg ctg ctt ctg agg cac tgg ggc tgg ggc ctg tgc ctt 121 atc ggc tgg aac gag ttc atc ctg cag ccc atc cac aac ctg ctc atg ggt gac acc aag 181 gag cag cgc atc ctg aac cat/c gtg ctg cag cat gcg gag ccc ggg aac gca cag agc gtg 241 ctg gag gcc att gac acc tac tgc gag cag aag gag tgg gcc atg aac gtg ggc gac aag 301 aaa ggc aag atc gtg gac gcc gtg att cag gag cac cag ccc tcc gtg ctg ctg gag ctg 361 ggg gcc tac tgt ggc tac tca gct gtg cgc atg gcc cgc ctg ctg tca cca ggg gcg agg 421 ctc/g atc acc atc gag atc aac ccc gac tgt gcc gcc atc acc cag cgg atg gtg gat ttc 481 gct ggc g/atg aag gac aag gtc acc ctt gtg gtt gga gcg tcc cag gac atc atc ccc cag 541 ctg aag aag aag tat gat gtg gac aca ctg gac atg gtc ttc ctc gac cac tgg aag gac 601 cgg tac ctg ccg gac acg ctt ctc ttg gag gaa tgt ggc ctg ctg cgg aag ggg aca gtg 661 cta ctg gct gac aac gtg atc tgc cca ggt gcg cca gac ttc cta gca cac gtg cgc ggg 721 agc agc tgc ttt gag tgc aca cac tac caa tcg ttc ctg gaa tac agg gag gtg gtg gac 781 ggc ctg gag aag gcc atc tac aag ggc cca ggc agc gaa gca ggg ccc tga ctg ccc ccc 841 cgg ccc ccc tct cgg gct ctc tca ccc agc ctg

COMT

COMT

COMT

COMT

COMT

COMT

I. Tinoco, Jr. In Appendix 1 of:The RNA World (R. F. Gesteland, J. F. Atkins, Eds.), Cold Spring Harbor Laboratory Press, 1993, pp. 603-607.

COMT

COMT V158M decreased activity H62H decreased activity L136L increased activity

MTRR

MTRR

MTRR

MTRR

MTRR

MTRR

MTRR

MTRR

MTRR

MTRR

MTRR

MTRR

MTRR

MTRR

MTRR H595Y version 2 close up shorter construct

MTRR

MTRR

MTRR

MTRR

MTRR

MTRR A66G decreased activity S175L increased activity H595Y decreased activity

serotonin maoA + +

5 HIAA

Serotonin-mediated inhibitory postsynaptic potential in guinea-pig prepositus hypoglossi and feedback inhibition by serotonin DH Bobker and JT Williams

Intracellular recordings were made from neurones of the nucleus prepositus hypoglossi (PH) in slices of guinea-pig brain. Focal stimulation evoked an inhibitory postsynaptic potential (IPSP) that was typically 10-25 mV in amplitude and 1 s in duration. The IPSP reversal potential showed a Nernstian dependence on the external potassium concentration ([K+]o). 2. Spiperone blocked the IPSP with an IC50 of 40 nM, while ketanserin and (-)sulpiride had no effect. Cocaine (1 microM) prolonged the IPSP half-duration by 157%, and increased the amplitude by 28%. 3. 5-Hydroxytryptamine (5-HT, serotonin) hyperpolarized PH cells with an EC50 of 8.5 microM in control, and 135 nM in cocaine (10 microM). 8-Hydroxy-2-(di-n-propylamino)-tetralin (8OH-DPAT) also hyperpolarized PH cells with an EC50 of 16 nM, although the maximal effect was only 81% of the maximum 5-HT hyperpolarization. Spiperone produced a parallel, right shift of the 5-HT concentrationresponse curve; Schild analysis gave a Kd of 10 nM. Application of 5-HT to neurones voltage-clamped near their resting potential (about -55 mV) caused an outward current and an increase in membrane conductance. 4. The amplitude of the IPSP was reversibly decreased by non- hyperpolarizing concentrations of 5-HT and by the 5-HT1 receptor agonists 1-(m-trifluoromethylphenyl)piperazine (TFMPP) and 1-(3- chlorophenyl)piperazine (mCPP). The IC50 values for the latter two compounds were 50 nM and 1.5 microM, respectively; the maximal effect was a 90% inhibition. Neither compound affected the membrane potential nor changed the hyperpolarization induced by 5-HT. Quipizine competitively antagonized TFMPP with an estimated Kd of 165 nM. 5. When trains of stimuli were applied, an inhibition of the IPSP was observed following the first stimulus. At a frequency of 1 Hz, the inhibition was approximately 75%. This frequency-dependent 'run-down' of the IPSP was markedly attenuated by pre-treatment with TFMPP (1 microM). 6. It is concluded that the IPSP in PH cells is caused by 5-HT acting on 5- HT1A receptors to activate a potassium conductance. The release of 5-HT can be inhibited by activation of a presynaptic 5-HT1D receptor. This presynaptic receptor appears to be at least partly responsible for the run-down phenomenon, and may be involved in the physiological regulation of 5-HT synaptic transmission.

CBS no mutation

CBS C699T

A Molecular Approach to Health Care Biochemical Results that are Influenced by Nutrigenomic Results DNA Based Nutritional Testing and RNA Based Nutrition

How mutations can cause changes in the biochemical pathways and affect the results of biochemical tests

Example Elevated Beta alanine and Carnosine

Beta alanine may either be excreted or incorporated into the brain and muscle dipeptides, carnosine ( histidine/ beta alanine) and anserine (methylhistidine/ beta alanine)

http://www-medlib.med.utah.edu/NetBiochem/pupyr/pupy11.gif

Thymidine=5 methyl uracil

Pyrimidine catabolism leads to beta-alanine and beta aminoisobutyrate

Example Elevated Beta alanine and beta aminoisobutyrate

The elevations in beta amino isobutyrate and anserine can be produced by excess uridine that is not processed to thymidine due to lack of methyl groups.

Implication is that both taurine and β alanine have inhibitory actions and may block GABA transport.

Implication is that mutations in GAT1 can occur such that taurine and β alanine can inhibit GABA transport at all four transporters.

Example Elevated oxaloacetate

With decreased ammonia, arginine from the urea cycle is available to produce creatinine. This can cause increased levels of asparatate. Asparate can then feed into the Krebs cycle to increase the level of oxaloacetate. Aspartate can also result in elevated beta alanine. Beta alanine leads to increased levels of carnosine and anserine.

Urea cycle

aspartate

β alanine

Carnosine

arginine

Anserine

Oxaloacetate in Krebs cycle

creatinine

Example Decreased oxaloacetate and Increased hydroxybutyrate

Hydroxybutyrate

oxaloacetate

Elevated ammonia requires more urea cycle function, depleting oxaloacetate from the Krebs cycle. Imbalances in oxaloacetate can lead to an increased level of hydroxybutyrate.

Hydroxymethylglutarate

Example Elevated 8 hydroxy 2 deoxyguanosine

DNA damage 8-hydroxy-2-deoxyguanosine

EntryR04858

Reaction

Name S-Adenosyl-L-methionine:DNA (cytosine-5-)-methyltransferase Definition S-Adenosyl-L-methionine + Cytosine (in DNA) S-Adenosyl-L-homocysteine + 5-Methylcytosine (in DNA) EquationC00019 + C05522 C00021 + C05523 RPairRP: A00004 C00019_C00021 main RP: A04473 C05522_C05523 main RP: A08326 C00019_C05523 trans PathwayPATH: rn00271 Methionine metabolism SAH + cytosine-methyl group SAMe to cytosine

Implication that in order to reconvert SAH to SAMe you lose DNA methylation. Implies should add SAMe???

Example Elevated Sarcosine

If there are mutations in MTR and/or MTRR, with support for the BHMT pathway increases in sarcosine and glycine may occur

creatinine kinase

B2

As creatinine decreases sarcosine can be seen to increase.

creatinine kinase

rhodiola

B2 Rhodiola inhibits creatinine kinase. The use of rhodiola may lead to increased levels of sarcosine and glycine on amino acid tests.

Example Decreased tyrosinase

Use of tyrosinase for dopamine synthesis due to decreased TH activity may result in paler skin, light hair and eye color.

A typical form of Albinism is due to the inability to convert DOPA to the various melanin pigments ordinarily found in the skin. Defective of tyrosinase in melanocytes

Example Elevated phenylalanine

Lack of BH4 due to A1298C mutations or CBS up regulations may look similar to PKU in terms of build up of intermediates.

BH4

Phenylketonuria (PKU) is a metabolic disease that involves a defect of phenylalanine hydroxylase. As a result of this defect, phenyalanine is metabolized to phenylpyruvic acid in alternative pathway that is characterizied by accumulation of Phenylalanine and its by-product Phenylpyruvic Acid in the blood.

Example Elevated phenylacetate phenyl lactate phenylethylamine

BH4

There are two routes by which the excess Phe can be metabolized: oxidation to tyrosine (the normal and main route for degradation of Phe, and the normal route for biosynthesis of Tyr), and transamination to phenylpyruvate and subsequent further metabolism (a minor route, which comes to the fore when the main route is blocked).

Example Black secretions

Deposits of black secretions have been observed in some children with CBS up regulations using lipid/sulfur based detoxification.

Alkaptonuria is a metabolic disease characterized by the accumulation of Homogentistic Acid (formerly known as Alkapton) in the urine. Exposure of homogentisic acid to light results in darkening, thus producing the characteristic "black diaper" disease.

Example Elevated FIGLU and elevated methylhistidine

histidine

β alanine

1 methyl histidine

urocanate

histamine

carnosine 4 imidazolone 5 propionate anserine

FIGLU

tetrahydrofolate

If there is not sufficient THF then FIGLU as well as histidine can accumulate glutamate

Example Elevated hippuric

Lack of BH4 can lead to elevations in phenylalanine.

Increased phenylalanine can lead to increased hippuric.

Nature. 1961 Jan 7;189:63-4. Formation of hippuric acid from phenylalanine labelled with carbon-14 in phenylketonuric subjects. GRUEMER HD. PMID: 13709187 [PubMed - OLDMEDLINE for Pre1966]

Example Elevated Taurine

CBS

Level of cysteine

pyroglutamate

Example Elevated Methionine sulfoxide

Example Elevated Branced chain amino acids

Figure 44-1. Major pathways of branched-chain amino acid metabolism. Maple syrup urine disease is caused by a congenital deficiency of reaction 2. Many of the primary organic acidurias, for example, isovaleric acidemia and methylmalonic acidemia, are referable to inherited defects of enzymes involved in the oxidation of organic acids derived from the branched-chain amino acids. Enzymes: 1, branched-chain amino acid transaminase; 2, branched-chain amino acid decarboxylase; 3, isovaleryl-CoA dehydrogenase; 4, glycine-N-acylase; 5, 3-methylcrotonyl-CoA carboxylase; 6, crotonase; 7, 3-methylglutaconyl-CoA hydratase; 8, 3 OH-3-methylglutaryl-CoA lyase; 9, 2-ketothiolase; 10, isobutyryl-CoA dehydrogenase; 11, propionyl-CoA carboxylase; 12, methylmalonyl-CoA mutase; 13, 3-OH-isobutyryl-CoA deacylase. TPP, thiamine pyrophosphate; LipA, lipoic acid; ETF, electron transfer flavoprotein; AdoB12, adenosylcobalamin; IVA, isovaleric acid; IVG, isovalerylglycine; TCA, tricarboxylic acid.

Example Elevated Glutamine

X X X

Example Distinctive Odors

An unusual odor can be particularly helpful in several disorders:

Odor

Disorder

Musty

phenylketonuria

Cabbage

tyrosinemia*

maple syrup

maple syrup urine disease

sweaty feet

**isovaleric acidemia, glutaric acidemia type II

*High levels of methionine probably result from the inhibition of S-adenosylmethionine synthetase by the metabolites of tyrosine breakdown, fumarylacetoacetic acid, maleylacetoacetic acid, fumarylacetone and fumarylacetone glutathione. **Isovaleric acid is a breakdown product of leucine

Odors related to foods and diseases: Some diseases have been described as having characteristic odors. Patients with diphtheria have a "sweetish" odor, those in a diabetic coma smell "fruity," yellow fever patients smell like a "butcher shop," scurvy gives a "putrid" odor and scrofula the odor of "stale beer," while those with typhoid fever have an odor like "fresh-baked brown bread." It is said that nurses in the past confidently diagnosed enteric fever by sniffing the armpits.10 By intelligent use of the sense of smell, an astute clinician may make a presumptive diagnosis of a rare metabolic disorder and institute life-saving therapy while awaiting laboratory confirmation. There is a group of disorders in metabolism that lead to unusual odors of the body or urine; they are individually rare, but collectively they make up a sizable portion of acute life-threatening illnesses of infancy.11 a. The characteristic odor of phenylketonuria has been described as "musty," "wolflike," "barny," "mousy," "horsey," and "stale sweaty locker-room towels."10,11,12 b. In maple syrup urine disease, the odor is described as "caramel-like," "malty," or like "maple syrup."10 It was determined that 4,5-dimethyl-3-hydroxy-2[5H]-furanone (sotolone), a well-known flavor impact compound also present in fenugreek, lovage and buckwheat honey13, is responsible for the characteristic odor in the urine of affected individuals. The common name given to the disease is thus quite appropriate, as maple syrup also contains sotolone.14 Ingestion of fenugreek (a leguminous herb cultivated in southern Europe, northern Africa and India) resulted in a false suspicion of maple syrup urine disease when the doctor noticed the characteristic smell of the patient's urine. It has been reported where the patient was given fenugreek tea15 or a folk remedy containing the plant.16 Also, false suspicion arose when the ingestion of fenugreek by mothers in labor resulted in a maple syrup-like odor in their newborn infants.17 c. Oast-house syndrome (or Oasthouse urine disease or Methionine malabsorption syndrome), which has some resemblances to phenylketonuria, presents with a distinctive dried malt or hops (as in breweries), dried celery or yeast odor.10,11

Odors related to foods and diseases: d. Individuals with hypermethioninemia have been variously described as having a "fishy," "sweet and fruity," "rancid butter" or "boiled cabbage" odor.10 It has been suggested that tyrosinosis-tyrosinemia (or rancid butter syndrome) which presents with a strong offensive odor resembling that of rancid butter is the same as hypermethioninemia.11 e. Isovaleric acidemia (or sweaty feet syndrome) often presents with a "cheesy" or "sweaty feet" odor.10,11 f. Trimethylaminuria (TMAuria) (also known as fish malodor syndrome or fish odor syndrome) is an uncommon disorder that causes an accumulation and massive excretion of the volatile tertiary amine trimethylamine (TMA) in the urine and other bodily fluids (sweat, expired air, saliva, vaginal secretions and other bodily secretions).18,19,20 (This should not be confused with the fishy odor present in Trichomonas vaginitis. This odor is as a result of anaerobic organisms.) The disease produces a powerful aroma of rotting fish, and this causes the affected person to have an offensive body odor.18,21 Trimethylamine is derived from the intestinal bacterial degradation of foods rich in choline (egg yolk, liver, etc.) and carnitine. TMA is also formed by reduction of TMA-oxide present in high concentrations in marine fish.20,22 TMA is normally oxidized by the liver into odorless trimethylamine N-oxide and then excreted in the urine. This oxidization is defective in TMA-uria. The above foods can exacerbate the condition. Dietary adjustments can reduce the excretion of trimethylamine and may reduce the odour.22 g. Cat's urine syndrome has neurological symptoms resembling Werdnig-Hoffman's disease, and the patient's urine has a cat urine-like odor.11 h. Diabetic keto-acidosis induces a characteristic odor on the breath that has been described as "sweet" or "fruity."11

compiled by Karen du Plessis B.Sc. Diet.

D. References 1. Mitchell SC. Asparagus and malodorous urine. Br J Clin Pharmacol 1989 May;27(5):641-2. 2. Richer C, Decker N, Belin J, Imbs JL, Montastruc JL, Giudicelli JF. Odorous urine in man after asparagus. Br J Clin Pharmacol 1989 May;27(5):640-1. 3. White RH. Occurrence of S-methyl thioesters in urines of humans after they have eaten asparagus. Science 1975 Sep 5;189(4205):810-11. 4. Mitchell SC. Food idiosyncrasies: beetroot and asparagus. Drug Metab Dispos 2001;29:539-43. 5. Mitchell SC, Waring RH, Land D, Thorpe WV. Odorous urine following asparagus ingestion in man. Experientia 1987 Apr 15;43(4):382-3. 6. Hoffenberg L. A note on polymorphism: the ability to smell urinary metabolites of asparagus. Diastema 1983;11:37-8. 7. Lison M, Blondheim SH, Melmed RN. A polymorphism of the ability to smell urinary metabolites of asparagus. Br Med J 1980 Dec 20-27;281(6256):1676-8. 8. Waring RH, Mitchell SC, Fenwick GR. The chemical nature of the urinary odour produced by man after asparagus ingestion. Xenobiotica 1987 Nov;17(11):1363-71. 9. Gearhart HL, Pierce SK, Payne-Bose D. Volatile organic components in human urine after ingestion of asparagus. Clin Chem 1977 Oct;23(10):1941. 10. Cone TE Jr. Diagnosis and treatment: some diseases, syndromes, and conditions associated with an unusual odor. Pediatrics 1968 May;41(5):993-5. 11. Mace JW, Goodman SI, Centerwall WR, Chinnock RF. The child with an unusual odor. A clinical resume. Clin Pediatr (Phila) 1976 Jan;15(1):57-62. 12. Beers MH, Berkow R. The Merck Manual of Diagnosis and Therapy Seventeenth edition. Merck Research Laboratories, NJ, 1999.

D. References 13. Zhou Q, Wintersteen CL, Cadwallader KR. Identification and quantification of aroma-active components that contribute to the distinct malty flavor of buckwheat honey. J Agric Food Chem 2002 Mar 27;50(7):2016-21. 14. Podebrad F, Heil M, Reichert S, Mosandl A, Sewell AC, Bohles H. 4,5-dimethyl-3-hydroxy-2[5H]furanone (sotolone)--the odour of maple syrup urine disease. J Inherit Metab Dis 1999 Apr;22(2):10714. 15. Sewell AC, Mosandl A, Bohles H. False diagnosis of maple syrup urine disease owing to ingestion of herbal tea. N Engl J Med 1999 Sep 2;341(10):769. 16. Bartley GB, Hilty MD, Andreson BD, Clairmont AC, Maschke SP. "Maple-syrup" urine odor due to fenugreek ingestion. N Engl J Med 1981 Aug 20;305(8):467. 17. Korman SH, Cohen E, Preminger A. Pseudo-maple syrup urine disease due to maternal prenatal ingestion of fenugreek. J Paediatr Child Health 2001 Aug;37(4):403-4. 18. Mitchell SC, Smith RL. Trimethylaminuria: the fish malodor syndrome. Drug Metab Dispos 2001 Apr;29(4 Pt 2):517-21. 19. Treacy E, Johnson D, Pitt JJ, Danks DM. Trimethylaminuria, fish odour syndrome: a new method of detection and response to treatment with metronidazole. J Inherit Metab Dis 1995;18(3):306-12. 20. Sela BA, Trau H, Spira A. [Trimethylaminuria: fish-odor syndrome] Harefuah 1993 Feb 1;124(3):138-9, 183. 21. Akerman BR, Lemass H, Chow LM, Lambert DM, Greenberg C, Bibeau C, Mamer OA, Treacy EP. Trimethylaminuria is caused by mutations of the FMO3 gene in a North American cohort. Mol Genet Metab 1999 Sep;68(1):24-31. 22. Rehman HU. Fish odor syndrome. Postgrad Med J 1999 Aug;75(886):451-2. 23. Bartoshuk LM, Lee CH, Scarpellino R. Sweet taste of water induced by artichoke (Cynara scolymus). Science 1972;178(64):988-90.

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RNA

Boston Conference, August 2004, DVD Phoenix Conference, April 2005, DVD Heal Your Body Naturally, book RNA Educational Starter Package