Phenotype prediction of deleterious nonsynonymous single nucleotide polymorphisms in human alcohol metabolism-related genes: A bioinformatics study

Alcohol

Volumn 44, Issue 5, 2010, Pages 425-438

  Wang, Lin Lin ^a   Yang, An Kui ^b,c   Li, Yong ^a   Liu, Jun Ping ^d   Zhou, Shu Feng ^e  

^a PEKING UNIVERSITY HEALTH SCIENCE CENTER   (China)

^b SUN YAT SEN UNIVERSITY   (China)

^c SUN YAT SEN UNIVERSITY CANCER CENTER   (China)

^d MONASH UNIVERSITY   (Australia)

^e RMIT UNIVERSITY   (Australia)

Author keywords

Alcohol metabolism; Bioinformatics; Phenotype; Single nucleotide polymorphisms

Indexed keywords

ALCOHOL DEHYDROGENASE; ALCOHOL DEHYDROGENASE 1A; ALCOHOL DEHYDROGENASE 1B; ALCOHOL DEHYDROGENASE 1C; ALCOHOL DEHYDROGENASE 4; ALCOHOL DEHYDROGENASE 5; ALCOHOL DEHYDROGENASE 6; ALCOHOL DEHYDROGENASE 7; ALDEHYDE DEHYDROGENASE 16A1; ALDEHYDE DEHYDROGENASE 18A1; ALDEHYDE DEHYDROGENASE 1A1; ALDEHYDE DEHYDROGENASE 1A2; ALDEHYDE DEHYDROGENASE 1A3; ALDEHYDE DEHYDROGENASE 1B1; ALDEHYDE DEHYDROGENASE 1L1; ALDEHYDE DEHYDROGENASE 1L2; ALDEHYDE DEHYDROGENASE 3A1; ALDEHYDE DEHYDROGENASE 3A2; ALDEHYDE DEHYDROGENASE 3B1; ALDEHYDE DEHYDROGENASE 3B2; ALDEHYDE DEHYDROGENASE 4A1; ALDEHYDE DEHYDROGENASE 5A1; ALDEHYDE DEHYDROGENASE 6A1; ALDEHYDE DEHYDROGENASE 7A1; ALDEHYDE DEHYDROGENASE 8A1; ALDEHYDE DEHYDROGENASE 9A1; ALDEHYDE DEHYDROGENASE FE1; ALDEHYDE DEHYDROGENASE ISOENZYME 2; CYTOCHROME P450 2E1; UNCLASSIFIED DRUG;

ACCURACY; ALCOHOL METABOLISM; ALGORITHM; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; DISEASE PREDISPOSITION; ENZYME ACTIVITY; HUMAN; INFORMATION PROCESSING; INFORMATION RETRIEVAL; NUCLEOTIDE SEQUENCE; PHENOTYPE; PREDICTION; PROTEIN ANALYSIS; PROTEIN FUNCTION; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; SITE DIRECTED MUTAGENESIS; UNINDEXED SEQUENCE; VALIDITY;

ALCOHOL DEHYDROGENASE; ALCOHOL-RELATED DISORDERS; ALDEHYDE DEHYDROGENASE; AMINO ACID SUBSTITUTION; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; ETHANOL; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; HUMANS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 77956182739     PISSN: 07418329     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.alcohol.2010.05.009     Document Type: Article

References (53)

1. Akaboshi S., Hogema B.M., Novelletto A., Malaspina P., Salomons G.S., Maropoulos G.D., et al. Mutational spectrum of the succinate semialdehyde dehydrogenase (ALDH5A1) gene and functional analysis of 27 novel disease-causing mutations in patients with SSADH deficiency. Hum. Mutat. 2003, 22:442-450.
2. Aoki N., Suzuki H., Ito K., Ito M. A novel point mutation of the FALDH gene in a Japanese family with Sjogren-Larsson syndrome. J. Invest. Dermatol. 2000, 114:1065-1066.
3. Aoshima T., Kajita M., Sekido Y., Ishiguro Y., Tsuge I., Kimura M., et al. Mutation analysis in a patient with succinic semialdehyde dehydrogenase deficiency: a compound heterozygote with 103-121del and 1460T > A of the ALDH5A1 gene. Hum. Hered. 2002, 53:42-44.
4. Asakage T., Yokoyama A., Haneda T., Yamazaki M., Muto M., Yokoyama T., et al. Genetic polymorphisms of alcohol and aldehyde dehydrogenases, and drinking, smoking and diet in Japanese men with oral and pharyngeal squamous cell carcinoma. Carcinogenesis 2007, 28:865-874.
5. Boonyaphiphat P., Thongsuksai P., Sriplung H., Puttawibul P. Lifestyle habits and genetic susceptibility and the risk of esophageal cancer in the Thai population. Cancer Lett. 2002, 186:193-199.
6. Buervenich S., Carmine A., Galter D., Shahabi H.N., Johnels B., Holmberg B., et al. A rare truncating mutation in ADH1C (G78Stop) shows significant association with Parkinson disease in a large international sample. Arch. Neurol. 2005, 62:74-78.
7. Burnell J.C., Carr L.G., Dwulet F.E., Edenberg H.J., Li T.K., Bosron W.F. The human β-3 alcohol dehydrogenase subunit differs from β-1 by a Cys for Arg-369 substitution which decreases NAD(H) binding. Biochem. Biophys. Res. Commun. 1987, 146:1127-1133.
8. Cargill M., Altshuler D., Ireland J., Sklar P., Ardlie K., Patil N., et al. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 1999, 22:231-238.
9. Chai Y.G., Oh D.Y., Chung E.K., Kim G.S., Kim L., Lee Y.S., et al. Alcohol and aldehyde dehydrogenase polymorphisms in men with type I and type II alcoholism. Am. J. Psychiatry 2005, 162:1003-1005.
10. Chen Y.C., Peng G.S., Wang M.F., Tsao T.P., Yin S.J. Polymorphism of ethanol-metabolism genes and alcoholism: correlation of allelic variations with the pharmacokinetic and pharmacodynamic consequences. Chem. Biol. Interact. 2009, 178:2-7.
11. Chen Y.J., Chen C., Wu D.C., Lee C.H., Wu C.I., Lee J.M., et al. Interactive effects of lifetime alcohol consumption and alcohol and aldehyde dehydrogenase polymorphisms on esophageal cancer risks. Int. J. Cancer 2006, 119:2827-2831.
12. Cichoz-Lach H., Partycka J., Nesina I., Celinski K., Slomka M., Wojcierowski J. Alcohol dehydrogenase and aldehyde dehydrogenase gene polymorphism in alcohol liver cirrhosis and alcohol chronic pancreatitis among Polish individuals. Scand. J. Gastroenterol. 2007, 42:493-498.
13. Das U.G., Cronk C.E., Martier S.S., Simpson P.M., McCarver D.G. Alcohol dehydrogenase 2*3 affects alterations in offspring facial morphology associated with maternal ethanol intake in pregnancy. Alcohol Clin. Exp. Res. 2004, 28:1598-1606.
14. De Laurenzi V., Rogers G.R., Hamrock D.J., Marekov L.N., Steinert P.M., Compton J.G., et al. Sjogren-Larsson syndrome is caused by mutations in the fatty aldehyde dehydrogenase gene. Nat. Genet. 1996, 12:52-57.
15. Druesne-Pecollo N., Tehard B., Mallet Y., Gerber M., Norat T., Hercberg S., et al. Alcohol and genetic polymorphisms: effect on risk of alcohol-related cancer. Lancet Oncol. 2009, 10:173-180.
16. Eng M.Y., Luczak S.E., Wall T.L. ALDH2, ADH1B, and ADH1C genotypes in Asians: a literature review. Alcohol Res. Health 2007, 30:22-27.
17. Eriksson C.J. The role of acetaldehyde in the actions of alcohol (update 2000). Alcohol Clin. Exp. Res. 2001, 25:15S-32S.
18. Hiraki A., Matsuo K., Wakai K., Suzuki T., Hasegawa Y., Tajima K. Gene-gene and gene-environment interactions between alcohol drinking habit and polymorphisms in alcohol-metabolizing enzyme genes and the risk of head and neck cancer in Japan. Cancer Sci. 2007, 98:1087-1091.
19. Hurley T., Edenberg H., Li T. Pharmacogenomics of Alcoholism 2002, Wiley-VCH, Weinheim, Germany.
20. Hu Y., Hakkola J., Oscarson M., Ingelman-Sundberg M. Structural and functional characterization of the 5'-flanking region of the rat and human cytochrome P450 2E1 genes: identification of a polymorphic repeat in the human gene. Biochem. Biophys. Res. Commun. 1999, 263:286-293.
21. Hu Y., Oscarson M., Johansson I., Yue Q.Y., Dahl M.L., Tabone M., et al. Genetic polymorphism of human CYP2E1: characterization of two variant alleles. Mol. Pharmacol. 1997, 51:370-376.
22. Jacobson S.W., Carr L.G., Croxford J., Sokol R.J., Li T.K., Jacobson J.L. Protective effects of the alcohol dehydrogenase-ADH1B allele in children exposed to alcohol during pregnancy. J. Pediatr. 2006, 148:30-37.
23. Liu J., Lewohl J.M., Harris R.A., Dodd P.R., Mayfield R.D. Altered gene expression profiles in the frontal cortex of cirrhotic alcoholics. Alcohol Clin. Exp. Res. 2007, 31:1460-1466.
24. Malaspina P., Picklo M.J., Jakobs C., Snead O.C., Gibson K.M. Comparative genomics of aldehyde dehydrogenase 5A1 (succinate semialdehyde dehydrogenase) and accumulation of γ-hydroxybutyrate associated with its deficiency. Hum. Genomics 2009, 3:106-120.
25. Marchitti S.A., Brocker C., Stagos D., Vasiliou V. Non-P450 aldehyde oxidizing enzymes: the aldehyde dehydrogenase superfamily. Expert Opin. Drug Metab. Toxicol. 2008, 4:697-720.
26. Nadeau J.H. Single nucleotide polymorphisms: tackling complexity. Nature 2002, 420:517-518.
27. Neafsey P., Ginsberg G., Hattis D., Johns D.O., Guyton K.Z., Sonawane B. Genetic polymorphism in CYP2E1: population distribution of CYP2E1 activity. J. Toxicol. Environ. Health B Crit. Rev. 2009, 12:362-388.
28. Ng P.C., Henikoff S. Predicting deleterious amino acid substitutions. Genome Res. 2001, 11:863-874.
29. Ng P.C., Henikoff S. Accounting for human polymorphisms predicted to affect protein function. Genome Res. 2002, 12:436-446.
30. Ng P.C., Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003, 31:3812-3814.
31. Ng P.C., Henikoff S. Predicting the effects of amino acid substitutions on protein function. Annu. Rev. Genomics Hum. Genet. 2006, 7:61-80.
32. Peng G.S., Yin S.J. Effect of the allelic variants of aldehyde dehydrogenase ALDH2*2 and alcohol dehydrogenase ADH1B*2 on blood acetaldehyde concentrations. Hum. Genomics 2009, 3:121-127.
33. Quertemont E. Genetic polymorphism in ethanol metabolism: acetaldehyde contribution to alcohol abuse and alcoholism. Mol. Psychiatry 2004, 9:570-581.
34. Ramensky V., Bork P., Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res. 2002, 30:3894-3900.
35. Rizzo W.B., Carney G., Lin Z. The molecular basis of Sjogren-Larsson syndrome: mutation analysis of the fatty aldehyde dehydrogenase gene. Am. J. Hum. Genet. 1999, 65:1547-1560.
36. 2A receptors. Pharmacol. Res. 2001, 43:179-183.
37. Sillen A., Anton-Lamprecht I., Braun-Quentin C., Kraus C.S., Sayli B.S., Ayuso C., et al. Spectrum of mutations and sequence variants in the FALDH gene in patients with Sjogren-Larsson syndrome. Hum. Mutat. 1998, 12:377-384.
38. Sillen A., Jagell S., Wadelius C. A missense mutation in the FALDH gene identified in Sjogren-Larsson syndrome patients originating from the northern part of Sweden. Hum. Genet. 1997, 100:201-203.
39. Stenson P.D., Ball E., Howells K., Phillips A., Mort M., Cooper D.N. Human Gene Mutation Database: towards a comprehensive central mutation database. J. Med. Genet. 2008, 45:124-126.
40. Stenson P.D., Ball E.V., Mort M., Phillips A.D., Shiel J.A., Thomas N.S., et al. Human Gene Mutation Database (HGMD): 2003 update. Hum. Mutat. 2003, 21:577-581.
41. Suzuki Y., Ando F., Ohsawa I., Shimokata H., Ohta S. Association of alcohol dehydrogenase 2*1 allele with liver damage and insulin concentration in the Japanese. J. Hum. Genet. 2006, 51:31-37.
42. Vasiliou V., Pappa A., Estey T. Role of human aldehyde dehydrogenases in endobiotic and xenobiotic metabolism. Drug Metab. Rev. 2004, 36:279-299.
43. Vaswani M., Prasad P., Kapur S. Association of ADH1B and ALDH2 gene polymorphisms with alcohol dependence: a pilot study from India. Hum. Genomics 2009, 3:213-220.
44. Wall T.L., Shea S.H., Luczak S.E., Cook T.A., Carr L.G. Genetic associations of alcohol dehydrogenase with alcohol use disorders and endophenotypes in white college students. J. Abnorm. Psychol. 2005, 114:456-465.
45. Wang L.L., Li Y., Zhou S.F. A bioinformatics approach for the phenotype prediction of nonsynonymous single nucleotide polymorphisms in human cytochromes P450. Drug Metab. Dispos. 2009, 37:977-991.
46. Warren K.R., Li T.K. Genetic polymorphisms: impact on the risk of fetal alcohol spectrum disorders. Birth Defects Res. A Clin. Mol. Teratol. 2005, 73:195-203.
47. Xi T., Jones I.M., Mohrenweiser H.W. Many amino acid substitution variants identified in DNA repair genes during human population screenings are predicted to impact protein function. Genomics 2004, 83:970-979.
48. Xu C.F., Lewis K., Cantone K.L., Khan P., Donnelly C., White N., et al. Effectiveness of computational methods in haplotype prediction. Hum. Genet. 2002, 110:148-156.
49. Xu Y.L., Carr L.G., Bosron W.F., Li T.K., Edenberg H.J. Genotyping of human alcohol dehydrogenases at the ADH2 and ADH3 loci following DNA sequence amplification. Genomics 1988, 2:209-214.
50. Yang S.J., Wang H.Y., Li X.Q., Du H.Z., Zheng C.J., Chen H.G., et al. Genetic polymorphisms of ADH2 and ALDH2 association with esophageal cancer risk in southwest China. World J. Gastroenterol. 2007, 13:5760-5764.
51. Yatsenko A.N., Shroyer N.F., Lewis R.A., Lupski J.R. Late-onset Stargardt disease is associated with missense mutations that map outside known functional regions of ABCR (ABCA4). Hum. Genet. 2001, 108:346-355.
52. Yoshida A., Huang I.Y., Ikawa M. Molecular abnormality of an inactive aldehyde dehydrogenase variant commonly found in Orientals. Proc. Natl. Acad. Sci. U S A 1984, 81:258-261.
53. Yu C., Li Y., Chen W., Yue M. Genotype of ethanol metabolizing enzyme genes by oligonucleotide microarray in alcoholic liver disease in Chinese people. Chin. Med. J. (Engl) 2002, 115:1085-1087.