Population-based in vitro hazard and concentration-response assessment of chemicals: The 1000 genomes high-throughput screening study

Environmental Health Perspectives

Volumn 123, Issue 5, 2015, Pages 458-466

  Abdo, Nour ^a   Xia, Menghang ^b   Brown, Chad C ^c   Kosyk, Oksana ^a   Huang, Ruili ^b   Sakamuru, Srilatha ^b   Zhou, Yi Hui ^c   Jack, John R ^c   Gallins, Paul ^d   Xia, Kai ^d   Li, Yun ^d,e   Chiu, Weihsueh A ^f   Motsinger Reif, Alison A ^c   Austin, Christopher P ^b   Tice, Raymond R ^g   Rusyn, Ivan ^a   Wright, Fred A ^c  

^a University of North Carolina at Chapel Hill   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c NORTH CAROLINA STATE UNIVERSITY   (United States)

^d UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^e University of North Carolina at Chapel Hill   (United States)

^f U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

^g NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMAN; PROCEDURES; RISK ASSESSMENT; TOXICITY TESTING; TUMOR CELL LINE;

CELL LINE, TUMOR; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; RISK ASSESSMENT; TOXICITY TESTS;

EID: 84929478944     PISSN: 00916765     EISSN: 15529924     Source Type: Journal    
DOI: 10.1289/ehp.1408775     Document Type: Article

References (53)

1. 1000 Genomes Project Consortium. 2012. An integrated map of genetic variation from 1,092 human genomes. Nature 491:56-65.
2. Abecasis GR, Cherny SS, Cookson WO, Cardon LR. 2002. Merlin—rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 30:97-101.
3. Aksoy P, Zhu MJ, Kalari KR, Moon I, Pelleymounter LL, Eckloff BW, et al. 2009. Cytosolic 5’nucleotidase III (NT5C3): gene sequence variation and functional genomics. Pharmacogenet Genomics 19:567-576.
4. Almasy L, Blangero J. 1998. Multipoint quantitativetrait linkage analysis in general pedigrees. Am J Hum Genet 62:1198-1211.
5. Brown CC, Havener TM, Medina MW, Auman JT, Mangravite LM, Krauss RM, et al. 2012a. A genome-wide association analysis of temozolomide response using lymphoblastoid cell lines shows a clinically relevant association with MGMT. Pharmacogenet Genomics 22:796-802.
6. Brown CC, Havener TM, Medina MW, Jack JR, Krauss RM, McLeod HL, et al. 2014. Genome-wide association and pharmacological profiling of 29 anticancer agents using lymphoblastoid cell lines. Pharmacogenomics 15:137-146.
7. Brown CC, Havener TM, Medina MW, Krauss RM, McLeod HL, Motsinger-Reif AA. 2012b. Multivariate methods and software for association mapping in dose-response genome-wide association studies. BioData Min 5:21; doi:10.1186/1756-0381-5-21.
8. Choy E, Yelensky R, Bonakdar S, Plenge RM, Saxena R, De Jager PL, et al. 2008. Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet 4:e1000287; doi:10.1371/journal.pgen.1000287.
9. Collins FS, Gray GM, Bucher JR. 2008. Toxicology. Transforming environmental health protection. Science 319:906-907.
10. DeGorter MK, Xia CQ, Yang JJ, Kim RB. 2012. Drug transporters in drug efficacy and toxicity. Annu Rev Pharmacol Toxicol 52:249-273.
11. Drayton RM, Dudziec E, Peter S, Bertz S, Hartmann A, Bryant HE, et al. 2014. Reduced expression of miRNA-27a modulates cisplatin resistance in bladder cancer by targeting the cystine/glutamate exchanger SLC7A11. Clin Cancer Res 20:1990-2000.
12. Fridley BL, Batzler A, Li L, Li F, Matimba A, Jenkins GD, et al. 2011. Gene set analysis of purine and pyrimidine antimetabolites cancer therapies. Pharmacogenet Genomics 21:701-712.
13. Gamazon ER, Huang RS, Cox NJ, Dolan ME. 2010. Chemotherapeutic drug susceptibility associated SNPs are enriched in expression quantitative trait loci. Proc Natl Acad Sci USA 107:9287-9292.
14. Gamazon ER, Skol AD, Perera MA. 2012. The limits of genome-wide methods for pharmacogenomic testing. Pharmacogenet Genomics 22:261-272.
15. Ginsberg G, Smolenski S, Neafsey P, Hattis D, Walker K, Guyton KZ, et al. 2009. The influence of genetic polymorphisms on population variability in six xenobiotic-metabolizing enzymes. J Toxicol Environ Health B Crit Rev 12:307-333.
16. Goldstein DB. 2009. Common genetic variation and human traits. N Engl J Med 360:1696-1698.
17. Huang R, Southall N, Cho MH, Xia M, Inglese J, Austin CP. 2008. Characterization of diversity in toxicity mechanism using in vitro cytotoxicity assays in quantitative high throughput screening. Chem Res Toxicol 21:659-667.
18. Huang RS, Gamazon ER, Ziliak D, Wen Y, Im HK, Zhang W, et al. 2011. Population differences in microRNA expression and biological implications. RNA Biol 8:692-701.
19. Huang RS, Kistner EO, Bleibel WK, Shukla SJ, Dolan ME. 2007. Effect of population and gender on chemotherapeutic agent-induced cytotoxicity. Mol Cancer Ther 6:31-36.
20. Huang Y, Dai Z, Barbacioru C, Sadée W. 2005. Cystineglutamate transporter SLC7A11 in cancer chemosensitivity and chemoresistance. Cancer Res 65:7446-7454.
21. Innocenti F, Mirkov S, Nagasubramanian R, Ramírez J, Liu W, Bleibel WK, et al. 2009. The Werner’s syndrome 4330T>C (Cys1367Arg) gene variant does not affect the in vitro cytotoxicity of topoisomerase inhibitors and platinum compounds. Cancer Chemother Pharmacol 63:881-887.
22. IPCS (International Programme on Chemical Safety). 2005. Chemical-Specific Adjustment Factors for Interspecies Differences in Human Variability: Guidance Document for Use of Data in Dose/Concentration-Response Assessment. Harmonization Project Document No. 2. Geneva:World Health Organization. Available: http://apps.who.int/iris/bitstream/10665/43294/1/9241546786_eng.pdf?ua=1 [accessed 3 April 2015].
23. IPCS (International Programme on Chemical Safety). 2014. Guidance Document on Evaluating and Expressing Uncertainty in Hazard Characterization. Harmonization Project Document 11. Geneva:World Health Organization. Available: http://www.who.int/ipcs/methods/harmonization/uncertainty_in_hazard_characterization.pdf?ua=1 [accessed 3 April 2015].
24. Januchowski R, Zawierucha P, Andrzejewska M, Rucinski M, Zabel M. 2013. Microarray-based detection and expression analysis of ABC and SLC transporters in drug-resistant ovarian cancer cell lines. Biomed Pharmacother 67:240-245.
25. Judson RS, Kavlock RJ, Setzer RW, Hubal EA, Martin MT, Knudsen TB, et al. 2011. Estimating toxicity-related biological pathway altering doses for high-throughput chemical risk assessment. Chem Res Toxicol 24:451-462.
26. Kinoshita H, Okabe H, Beppu T, Chikamoto A, Hayashi H, Imai K, et al. 2013. Cystine/glutamic acid transporter is a novel marker for predicting poor survival in patients with hepatocellular carcinoma. Oncol Rep 29:685-689.
27. Kulkarni H, Goring HH, Diego V, Cole S, Walder KR, Collier GR, et al. 2012. Association of differential gene expression with imatinib mesylate and omacetaxine mepesuccinate toxicity in lymphoblastoid cell lines. BMC Med Genomics 5:37; doi:10.1186/1755-8794-5-37.
28. Li L, Fridley B, Kalari K, Jenkins G, Batzler A, Safgren S, et al. 2008. Gemcitabine and cytosine arabinoside cytotoxicity: association with lymphoblastoid cell expression. Cancer Res 68:7050-7058.
29. Li L, Fridley BL, Kalari K, Jenkins G, Batzler A, Weinshilboum RM, et al. 2009. Gemcitabine and arabinosylcytosin pharmacogenomics: genomewide association and drug response biomarkers. PLoS One 4:e7765; doi:10.1371/journal.pone.0007765.
30. Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR. 2010. MACH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 34:816-834.
31. Lo M, Wang YZ, Gout PW. 2008. The xc- cystine/ glutamate antiporter: a potential target for therapy of cancer and other diseases. J Cell Physiol 215:593-602.
32. Lock EF, Abdo N, Huang R, Xia M, Kosyk O, O’Shea SH, et al. 2012. Quantitative high-throughput screening for chemical toxicity in a population-based in vitro model. Toxicol Sci 126:578-588.
33. Motaghed M, Al-Hassan FM, Hamid SS. 2014. Thymoquinone regulates gene expression levels in the estrogen metabolic and interferon pathways in MCF7 breast cancer cells. Int J Mol Med 33:8-16.
34. Neubig RR, Spedding M, Kenakin T, Christopoulos A. 2003. International Union of Pharmacology Committee on Receptor Nomenclature and Drug Classification. XXXVIII. Update on terms and symbols in quantitative pharmacology. Pharmacol Rev 55:597-606.
35. Njiaju UO, Gamazon ER, Gorsic LK, Delaney SM, Wheeler HE, Im HK, et al. 2012. Whole-genome studies identify solute carrier transporters in cellular susceptibility to paclitaxel. Pharmacogenet Genomics 22:498-507.
36. O’Donnell PH, Gamazon E, Zhang W, Stark AL, Kistner- Griffin EO, Huang RS, et al. 2010. Population differences in platinum toxicity as a means to identify novel genetic susceptibility variants. Pharmacogenet Genomics 20:327-337.
37. O’Shea SH, Schwarz J, Kosyk O, Ross PK, Ha MJ, Wright FA, et al. 2011. In vitro screening for population variability in chemical toxicity. Toxicol Sci 119:398-407.
38. Peters EJ, Motsinger-Reif A, Havener TM, Everitt L, Hardison NE, Watson VG, et al. 2011. Pharmacogenomic characterization of US FDA-approved cytotoxic drugs. Pharmacogenomics 12:1407-1415.
39. Pham AN, Blower PE, Alvarado O, Ravula R, Gout PW, Huang Y. 2010. Pharmacogenomic approach reveals a role for the xc - cystine/glutamate antiporter in growth and celastrol resistance of glioma cell lines. J Pharmacol Exp Ther 332:949-958.
40. Pillai KC. 1955. Some new test criteria in multivariate analysis. Ann Math Stat 26:117-121.
41. R Core Team. 2012. R: A Language and Environment for Statistical Computing. Vienna, Austria:R Foundation for Statistical Computing. Available: http://www.R-project.org [accessed 8 September 2013].
42. Rusyn I, Daston GP. 2010. Computational toxicology: realizing the promise of the toxicity testing in the 21st century. Environ Health Perspect 118:1047-1050; doi:10.1289/ehp.1001925.
43. Sand S, Ringblom J, Hakansson H, Öberg M. 2012. The point of transition on the dose-effect curve as a reference point in the evaluation of in vitro toxicity data. J Appl Toxicol 32:843-849.
44. Schaid DJ, Sinnwell JP, Jenkins GD, McDonnell SK, Ingle JN, Kubo M, et al. 2012. Using the gene ontology to scan multilevel gene sets for associations in genome wide association studies. Genet Epidemiol 36:3-16.
45. Stark AL, Zhang W, Mi S, Duan S, O’Donnell PH, Huang RS, et al. 2010. Heritable and non-genetic factors as variables of pharmacologic phenotypes in lymphoblastoid cell lines. Pharmacogenomics J 10:505-512.
46. Tice RR, Austin CP, Kavlock RJ, Bucher JR. 2013. Improving the human hazard characterization of chemicals: a Tox21 update. Environ Health Perspect 121:756-765; doi:10.1289/ehp.1205784.
47. van den Oord EJ, Sullivan PF. 2003. False discoveries and models for gene discovery. Trends Genet 19:537-542.
48. Wheeler HE, Dolan ME. 2012. Lymphoblastoid cell lines in pharmacogenomic discovery and clinical translation. Pharmacogenomics 13:55-70.
49. Wheeler HE, Gamazon ER, Stark AL, O’Donnell PH, Gorsic LK, Huang RS, et al. 2013. Genome-wide meta-analysis identifies variants associated with platinating agent susceptibility across populations. Pharmacogenomics J 13:35-43.
50. Wheeler HE, Gorsic LK, Welsh M, Stark AL, Gamazon ER, Cox NJ, et al. 2011. Genome-wide local ancestry approach identifies genes and variants associated with chemotherapeutic susceptibility in African Americans. PLoS One 6:e21920; doi:10.1371/journal.pone.0021920.
51. Xia M, Huang R, Witt KL, Southall N, Fostel J, Cho MH, et al. 2008. Compound cytotoxicity profiling using quantitative high-throughput screening. Environ Health Perspect 116:284-291; doi:10.1289/ehp.10727.
52. Yang J, Lee SH, Goddard ME, Visscher PM. 2011. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet 88:76-82.
53. Zeise L, Bois FY, Chiu WA, Hattis D, Rusyn I, Guyton KZ. 2013. Addressing human variability in nextgeneration human health risk assessments of environmental chemicals. Environ Health Perspect 121:23-31; doi:10.1289/ehp.1205687.