Systems Genetics Analysis of Gene-by-Environment Interactions in Human Cells

American Journal of Human Genetics

Volumn 86, Issue 3, 2010, Pages 399-410

  Romanoski, Casey E ^a   Lee, Sangderk ^a   Kim, Michelle J ^a   Ingram Drake, Leslie ^a   Plaisier, Christopher L ^b   Yordanova, Roumyana ^c   Tilford, Charles ^c   Guan, Bo ^c   He, Aiqing ^c   Gargalovic, Peter S ^c   Kirchgessner, Todd G ^c   Berliner, Judith A ^a   Lusis, Aldons J ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^c BRISTOL MYERS SQUIBB   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

1 PALMITOYL 2 ARACHIDONOYL SN GLYCERO 3 PHOSPHATIDYLCHOLINE; MESSENGER RNA; PHOSPHATIDYLCHOLINE; PHOSPHOLIPID; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

ARTICLE; CARDIOVASCULAR DISEASE; CELL LINE; CONTROLLED STUDY; DISEASE PREDISPOSITION; ENDOPLASMIC RETICULUM STRESS; ENDOTHELIUM CELL; ENVIRONMENT; GENE CONTROL; GENE EXPRESSION; GENE INTERACTION; GENE LOCUS; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC TRAIT; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOME; GENOTYPE; HUMAN; HUMAN CELL; INFLAMMATION; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM;

CELL LINE; ENDOTHELIAL CELLS; ENVIRONMENT; FEMALE; GENE EXPRESSION REGULATION; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MALE; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHOSPHATIDYLCHOLINES; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; RNA, SMALL INTERFERING; SYSTEMS BIOLOGY; TRANSCRIPTION, GENETIC;

EID: 77649236340     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ajhg.2010.02.002     Document Type: Article

References (57)

1. Ioannidis J.P., Thomas G., and Daly M.J. Validating, augmenting and refining genome-wide association signals. Nat. Rev. Genet. 10 (2009) 318-329
2. Hardy J., and Singleton A. Genomewide association studies and human disease. N. Engl. J. Med. 360 (2009) 1759-1768
3. Talmud P.J. Gene-environment interaction and its impact on coronary heart disease risk. Nutr. Metab. Cardiovasc. Dis. 17 (2007) 148-152
4. Caspi A., Sugden K., Moffitt T.E., Taylor A., Craig I.W., Harrington H., McClay J., Mill J., Martin J., Braithwaite A., and Poulton R. Influence of life stress on depression: Moderation by a polymorphism in the 5-HTT gene. Science 301 (2003) 386-389
5. Mackay T.F., Stone E.A., and Ayroles J.F. The genetics of quantitative traits: Challenges and prospects. Nat. Rev. Genet. 10 (2009) 565-577
6. Ulrich C.M., Kampman E., Bigler J., Schwartz S.M., Chen C., Bostick R., Fosdick L., Beresford S.A., Yasui Y., and Potter J.D. Colorectal adenomas and the C677T MTHFR polymorphism: Evidence for gene-environment interaction?. Cancer Epidemiol. Biomarkers Prev. 8 (1999) 659-668
7. Perlstein E.O., Ruderfer D.M., Roberts D.C., Schreiber S.L., and Kruglyak L. Genetic basis of individual differences in the response to small-molecule drugs in yeast. Nat. Genet. 39 (2007) 496-502
8. Smith E.N., and Kruglyak L. Gene-environment interaction in yeast gene expression. PLoS Biol. 6 (2008) e83
9. Li Y., Alvarez O.A., Gutteling E.W., Tijsterman M., Fu J., Riksen J.A., Hazendonk E., Prins P., Plasterk R.H., Jansen R.C., et al. Mapping determinants of gene expression plasticity by genetical genomics in C. elegans. PLoS Genet. 2 (2006) e222
10. Smirnov D.A., Morley M., Shin E., Spielman R.S., and Cheung V.G. Genetic analysis of radiation-induced changes in human gene expression. Nature 459 (2009) 587-591
11. Lusis A.J. Atherosclerosis. Nature 407 (2000) 233-241
12. Berliner J.A., and Watson A.D. A role for oxidized phospholipids in atherosclerosis. N. Engl. J. Med. 353 (2005) 9-11
13. Gargalovic P.S., Imura M., Zhang B., Gharavi N.M., Clark M.J., Pagnon J., Yang W.P., He A., Truong A., Patel S., et al. Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids. Proc. Natl. Acad. Sci. USA 103 (2006) 12741-12746
14. Navab M., Hough G.P., Stevenson L.W., Drinkwater D.C., Laks H., and Fogelman A.M. Monocyte migration into the subendothelial space of a coculture of adult human aortic endothelial and smooth muscle cells. J. Clin. Invest. 82 (1988) 1853-1863
15. Watson A.D., Leitinger N., Navab M., Faull K.F., Hörkkö S., Witztum J.L., Palinski W., Schwenke D., Salomon R.G., Sha W., et al. Structural identification by mass spectrometry of oxidized phospholipids in minimally oxidized low density lipoprotein that induce monocyte/endothelial interactions and evidence for their presence in vivo. J. Biol. Chem. 272 (1997) 13597-13607
16. Johnson W.E., Li C., and Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8 (2007) 118-127
17. Bolstad B.M., Irizarry R.A., Astrand M., and Speed T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19 (2003) 185-193
18. Irizarry R.A., Bolstad B.M., Collin F., Cope L.M., Hobbs B., and Speed T.P. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31 (2003) e15
19. Zhang J., Finney R.P., Clifford R.J., Derr L.K., and Buetow K.H. Detecting false expression signals in high-density oligonucleotide arrays by an in silico approach. Genomics 85 (2005) 297-308
20. Cheung V.G., Spielman R.S., Ewens K.G., Weber T.M., Morley M., and Burdick J.T. Mapping determinants of human gene expression by regional and genome-wide association. Nature 437 (2005) 1365-1369
21. Morley M., Molony C.M., Weber T.M., Devlin J.L., Ewens K.G., Spielman R.S., and Cheung V.G. Genetic analysis of genome-wide variation in human gene expression. Nature 430 (2004) 743-747
22. Gargalovic P.S., Gharavi N.M., Clark M.J., Pagnon J., Yang W.P., He A., Truong A., Baruch-Oren T., Berliner J.A., Kirchgessner T.G., and Lusis A.J. The unfolded protein response is an important regulator of inflammatory genes in endothelial cells. Arterioscler. Thromb. Vasc. Biol. 26 (2006) 2490-2496
23. Mungrue I.N., Pagnon J., Kohannim O., Gargalovic P.S., and Lusis A.J. CHAC1/MGC4504 is a novel proapoptotic component of the unfolded protein response, downstream of the ATF4-ATF3-CHOP cascade. J. Immunol. 182 (2009) 466-476
24. Korn J.M., Kuruvilla F.G., McCarroll S.A., Wysoker A., Nemesh J., Cawley S., Hubbell E., Veitch J., Collins P.J., Darvishi K., et al. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat. Genet. 40 (2008) 1253-1260
25. Purcell S., Neale B., Todd-Brown K., Thomas L., Ferreira M.A., Bender D., Maller J., Sklar P., de Bakker P.I., Daly M.J., and Sham P.C. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81 (2007) 559-575
26. Hochberg Y.B.Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B Stat. Methodol. 57 (1995) 289-300
27. Duggal P., Gillanders E.M., Holmes T.N., and Bailey-Wilson J.E. Establishing an adjusted p-value threshold to control the family-wide type 1 error in genome wide association studies. BMC Genomics 9 (2008) 516
28. Rockman M.V., and Kruglyak L. Genetics of global gene expression. Nat. Rev. Genet. 7 (2006) 862-872
29. Emilsson V., Thorleifsson G., Zhang B., Leonardson A.S., Zink F., Zhu J., Carlson S., Helgason A., Walters G.B., Gunnarsdottir S., et al. Genetics of gene expression and its effect on disease. Nature 452 (2008) 423-428
30. Göring H.H., Curran J.E., Johnson M.P., Dyer T.D., Charlesworth J., Cole S.A., Jowett J.B., Abraham L.J., Rainwater D.L., Comuzzie A.G., et al. Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nat. Genet. 39 (2007) 1208-1216
31. Veyrieras J.B., Kudaravalli S., Kim S.Y., Dermitzakis E.T., Gilad Y., Stephens M., and Pritchard J.K. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet. 4 (2008) e1000214
32. Su N., and Kilberg M.S. C/EBP homology protein (CHOP) interacts with activating transcription factor 4 (ATF4) and negatively regulates the stress-dependent induction of the asparagine synthetase gene. J. Biol. Chem. 283 (2008) 35106-35117
33. Lee J.I., Dominy Jr. J.E., Sikalidis A.K., Hirschberger L.L., Wang W., and Stipanuk M.H. HepG2/C3A cells respond to cysteine deprivation by induction of the amino acid deprivation/integrated stress response pathway. Physiol. Genomics 33 (2008) 218-229
34. Ohoka N., Yoshii S., Hattori T., Onozaki K., and Hayashi H. TRB3, a novel ER stress-inducible gene, is induced via ATF4-CHOP pathway and is involved in cell death. EMBO J. 24 (2005) 1243-1255
35. Oskolkova O.V., Afonyushkin T., Leitner A., von Schlieffen E., Gargalovic P.S., Lusis A.J., Binder B.R., and Bochkov V.N. ATF4-dependent transcription is a key mechanism in VEGF up-regulation by oxidized phospholipids: Critical role of oxidized sn-2 residues in activation of unfolded protein response. Blood 112 (2008) 330-339
36. Jousse C., Deval C., Maurin A.C., Parry L., Chérasse Y., Chaveroux C., Lefloch R., Lenormand P., Bruhat A., and Fafournoux P. TRB3 inhibits the transcriptional activation of stress-regulated genes by a negative feedback on the ATF4 pathway. J. Biol. Chem. 282 (2007) 15851-15861
37. Dimas A.S., Deutsch S., Stranger B.E., Montgomery S.B., Borel C., Attar-Cohen H., Ingle C., Beazley C., Gutierrez Arcelus M., Sekowska M., et al. Common regulatory variation impacts gene expression in a cell type-dependent manner. Science 325 (2009) 1246-1250
38. Dixon A.L., Liang L., Moffatt M.F., Chen W., Heath S., Wong K.C., Taylor J., Burnett E., Gut I., Farrall M., et al. A genome-wide association study of global gene expression. Nat. Genet. 39 (2007) 1202-1207
39. Stranger B.E., Nica A.C., Forrest M.S., Dimas A., Bird C.P., Beazley C., Ingle C.E., Dunning M., Flicek P., Koller D., et al. Population genomics of human gene expression. Nat. Genet. 39 (2007) 1217-1224
40. Myers A.J., Gibbs J.R., Webster J.A., Rohrer K., Zhao A., Marlowe L., Kaleem M., Leung D., Bryden L., Nath P., et al. A survey of genetic human cortical gene expression. Nat. Genet. 39 (2007) 1494-1499
41. Grundberg E., Kwan T., Ge B., Lam K.C., Koka V., Kindmark A., Mallmin H., Dias J., Verlaan D.J., Ouimet M., et al. Population genomics in a disease targeted primary cell model. Genome Res. 19 (2009) 1942-1952
42. Schadt E.E., Molony C., Chudin E., Hao K., Yang X., Lum P.Y., Kasarskis A., Zhang B., Wang S., Suver C., et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol. 6 (2008) e107
43. Joo H.Y., Zhai L., Yang C., Nie S., Erdjument-Bromage H., Tempst P., Chang C., and Wang H. Regulation of cell cycle progression and gene expression by H2A deubiquitination. Nature 449 (2007) 1068-1072
44. Cai S.Y., Babbitt R.W., and Marchesi V.T. A mutant deubiquitinating enzyme (Ubp-M) associates with mitotic chromosomes and blocks cell division. Proc. Natl. Acad. Sci. USA 96 (1999) 2828-2833
45. Visel A., Rubin E.M., and Pennacchio L.A. Genomic views of distant-acting enhancers. Nature 461 (2009) 199-205
46. Helgadottir A., Thorleifsson G., Manolescu A., Gretarsdottir S., Blondal T., Jonasdottir A., Jonasdottir A., Sigurdsson A., Baker A., Palsson A., et al. A common variant on chromosome 9p21 affects the risk of myocardial infarction. Science 316 (2007) 1491-1493
47. McPherson R., Pertsemlidis A., Kavaslar N., Stewart A., Roberts R., Cox D.R., Hinds D.A., Pennacchio L.A., Tybjaerg-Hansen A., Folsom A.R., et al. A common allele on chromosome 9 associated with coronary heart disease. Science 316 (2007) 1488-1491
48. Choy E., Yelensky R., Bonakdar S., Plenge R.M., Saxena R., De Jager P.L., Shaw S.Y., Wolfish C.S., Slavik J.M., Cotsapas C., et al. Genetic analysis of human traits in vitro: Drug response and gene expression in lymphoblastoid cell lines. PLoS Genet. 4 (2008) e1000287
49. Pastinen T., Ge B., and Hudson T.J. Influence of human genome polymorphism on gene expression. Hum. Mol. Genet. 15 Spec No 1 (2006) R9-R16
50. Leitinger N. Oxidized phospholipids as modulators of inflammation in atherosclerosis. Curr. Opin. Lipidol. 14 (2003) 421-430
51. Drake T.A., Hannani K., Fei H.H., Lavi S., and Berliner J.A. Minimally oxidized low-density lipoprotein induces tissue factor expression in cultured human endothelial cells. Am. J. Pathol. 138 (1991) 601-607
52. Birukova A.A., Chatchavalvanich S., Oskolkova O., Bochkov V.N., and Birukov K.G. Signaling pathways involved in OxPAPC-induced pulmonary endothelial barrier protection. Microvasc. Res. 73 (2007) 173-181
53. Vasques E., Almeida A.L., Noya V., D'Alegria B., Marathe G., McIntyre T.M., Tibiriçá E., Bozza P.T., Silva A.R., and Castro-Faria-Neto H.C. Impairment of endothelium-dependent aorta relaxation by phospholipid components of oxidized low-density lipoprotein. Endothelium 13 (2006) 1-8
54. Bochkov V.N., Philippova M., Oskolkova O., Kadl A., Furnkranz A., Karabeg E., Afonyushkin T., Gruber F., Breuss J., Minchenko A., et al. Oxidized phospholipids stimulate angiogenesis via autocrine mechanisms, implicating a novel role for lipid oxidation in the evolution of atherosclerotic lesions. Circ. Res. 99 (2006) 900-908
55. Lee S., Li R., Kim B., Palvolgyi R., Ho T., Yang Q.Z., Xu J., Szeto W.L., Honda H., and Berliner J.A. Ox-PAPC activation of PMET system increases expression of heme oxygenase-1 in human aortic endothelial cell. J. Lipid Res. 50 (2009) 265-274
56. Fahmi S., Yang C., Esmail S., Hobbs H.H., and Cohen J.C. Functional characterization of genetic variants in NPC1L1 supports the sequencing extremes strategy to identify complex trait genes. Hum. Mol. Genet. 17 (2008) 2101-2107
57. Cordell H.J. Genome-wide association studies: Detecting gene-gene interactions that underlie human diseases. Nat. Rev. Genet. 10 (2009) 392-404