Functional evaluation of genetic variants associated with endometriosis near GREB1

Human Reproduction

Volumn 30, Issue 5, 2015, Pages 1263-1275

  Fung, Jenny N ^a   Holdsworth Carson, Sarah J ^b   Sapkota, Yadav ^a   Zhao, Zhen Zhen ^a   Jones, Lincoln ^a   Girling, Jane E ^b   Paiva, Premila ^b   Healey, Martin ^b   Nyholt, Dale R ^a   Rogers, Peter A W ^b   Montgomery, Grant W ^a  

^a QIMR BERGHOFER MEDICAL RESEARCH INSTITUTE   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

endometriosis; eQTLs; GREB1; GWAS

Indexed keywords

MESSENGER RNA; GREB1 PROTEIN, HUMAN; TUMOR PROTEIN;

ALLELE; AMINO ACID SUBSTITUTION; ARTICLE; BIOCHEMICAL EQUIPMENT; BIOINFORMATICS; CHROMOSOME 2P; COMPUTER MODEL; COMPUTER PREDICTION; CONTROLLED STUDY; ENDOMETRIOSIS; ENDOMETRIUM; EPISTASIS; EPITHELIUM CELL; EXON; FEMALE; GENE EXPRESSION; GENE FREQUENCY; GENETIC ASSOCIATION; GENETIC RISK; GENETIC VARIABILITY; GENOTYPE; GROWTH REGULATION BY ESTROGEN IN BREAST CANCER 1 GENE; HAPLOTYPE; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; INTRON; MAJOR CLINICAL STUDY; MENSTRUAL CYCLE; PATHOPHYSIOLOGY; PHENOTYPE; PROTEIN EXPRESSION; QUANTITATIVE TRAIT LOCUS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RISK ASSESSMENT; SINGLE NUCLEOTIDE POLYMORPHISM; STROMA CELL; TRANSCRIPTION REGULATION; WESTERN BLOTTING; BIOLOGY; CHROMOSOME MAP; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PATHOLOGY;

CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; ENDOMETRIOSIS; ENDOMETRIUM; FEMALE; GENE EXPRESSION REGULATION; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; IMMUNOHISTOCHEMISTRY; NEOPLASM PROTEINS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

EID: 84929751231     PISSN: 02681161     EISSN: 14602350     Source Type: Journal    
DOI: 10.1093/humrep/dev051     Document Type: Article

References (47)

1. Barlow WE. Robust variance estimation for the case-cohort design. Biometrics 1994;50:1064-1072.
2. Bergqvist A, Ekman R, Ljungberg O. Binding of estrogen and progesterone to human endometrium in the different phases of the menstrual cycle. A histochemical study. Am J Clin Pathol 1985;83:444-449.
3. Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S et al. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res 2012; 22:1790-1797.
4. Burney R, Giudice L. Pathogenesis and pathophysiology of endometriosis. Fertil Steril 2012;98:511-519.
5. Bush D, Evans S, Vancaillie T. The Pelvic Pain Report. Australia: The Pelvic Pain Steering Committee, 2011.
6. Culley L, Law C, Hudson N, Denny E, Mitchell H, Baumgarten M, Raine-Fenning N. The social and psychological impact of endometriosis on women's lives: a critical narrative review. Hum Reprod Update 2013; 19:625-639.
7. Deschenes J, Bourdeau V, White JH, Mader S. Regulation of GREB1 transcription by estrogen receptor alpha through a multipartite enhancer spread over 20 kb of upstream flanking sequences. J Biol Chem 2007;282:17335-17339.
8. Encode-project-consortium. An integrated encyclopedia ofDNAelements in the human genome. Nature 2012;489:57-74.
9. Freedman ML, Monteiro AN, Gayther SA, Coetzee GA, Risch A, Plass C, Casey G, De Biasi M, Carlson C, Duggan D et al. Principles for the post-GWAS functional characterization of cancer risk loci. Nat Genet 2011;43:513-518.
10. Ghosh MG, Thompson DA, Weigel RJ. PDZK1 and GREB1 are estrogen-regulated genes expressed in hormone-responsive breast cancer1, 2. Cancer Res 2000;60:6367-6375.
11. Haynes BP, Viale G, Galimberti V, Rotmensz N, Gibelli B, A'hern R, Smith IE, Dowsett M. Expression of key oestrogen-regulated genes differs substantially across the menstrual cycle in oestrogen receptor-positive primary breast cancer. Breast Cancer Res Treat 2013;138:157-165.
12. Hickey M, Ballard K, Farquhar C. Endometriosis. Br Med J 2014;348:1-9.
13. Hnatyszyn HJ, Liu M, Hilger A, Herbert L, Gomez-Fernandez CR, Jorda M, Thomas D, Rae JM, El-Ashry D, Lippman ME. Correlation of GREB1 mRNA with protein expression in breast cancer: validation of a novel GREB1 monoclonal antibody. Breast Cancer Res Treat 2010;122:371-380.
14. Holdsworth-Carson SJ, Zaitseva M, Vollenhoven BJ, Rogers PA. Clonality of smooth muscle and fibroblast cell populations isolated fromhuman fibroid and myometrial tissues. Mol Hum Reprod 2014;20:250-259.
15. Kennedy S, Mardon H, Barlow D. Familial endometriosis. J Assist Reprod Genet 1995;12:32-34.
16. Kohl M. SLqPCR: Functions for Analysis of Real-Time Quantitative PCR Data at SIRS-Lab GmbH. Jena, Germany: SIRS-Lab GmbH, 2007.
17. Lappalainen T, Sammeth M, Friedlander MR, t Hoen PA, Monlong J, Rivas MA, Gonzalez-Porta M, Kurbatova N, Griebel T, Ferreira PG et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 2013;501:506-511.
18. Li Y, Willer C, Sanna S, Abecasis G. Genotype imputation. Annu Rev Genomics Hum Genet 2009;10:387-406.
19. Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 2010;34:816-834.
20. Luong HT, Painter JN, Shakhbazov K, Chapman B, Henders AK, Powell JE, Nyholt DR, Montgomery GW. Fine mapping of variants associated with endometriosis in the WNT4 region on chromosome 1p36. Int J Mol Epidemiol Genet 2013;4:193-206.
21. Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J et al. Systematic localization of common disease-Associated variation in regulatory DNA. Science 2012;337:1190-1195.
22. Moen MH, Magnus P. The familial risk of endometriosis. Acta Obstet Gynecol Scand 1993;72:560-564.
23. Mohammed H, D Santos C, Serandour AA, Ali HR, Brown GD, Atkins A, Rueda OM, Holmes KA, Theodorou V, Robinson JL et al. Endogenous purification reveals GREB1 as a key estrogen receptor regulatory factor. Cell Rep 2013;3:342-349.
24. Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, Spielman RS, Cheung VG. Genetic analysis of genome-wide variation in human gene expression. Nature 2004;430:743-747.
25. Nyholt DR, Low SK, Anderson CA, Painter JN, Uno S, Morris AP, Macgregor S, Gordon SD, Henders AK, Martin NG et al. Genome-wide association meta-Analysis identifies new endometriosis risk loci. Nat Genet 2012;44:1355-1359.
26. Painter JN, Anderson CA, Nyholt DR, Macgregor S, Lin J, Lee SH, Lambert A, ZhaoZZ, Roseman F, GuoQetal.Genome-wideassociation studyidentifies a locus at 7p15.2 associated with endometriosis. Nat Genet 2011;43:51-54.
27. Pellegrini C, Gori I, Achtari C, Hornung D, Chardonnens E, Wunder D, Fiche M, Canny GO. The expression of estrogen receptors as well as GREB1, c-MYC, and cyclin D1, estrogen-regulated genes implicated in proliferation, is increased in peritoneal endometriosis. Fertil Steril 2012; 98:1200-1208.
28. Phillips JE, Corces VG. CTCF: master weaver of the genome. Cell 2009; 137:1194-1211.
29. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, De Bakker PI, Daly MJ et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007;81:559-575.
30. Rae JM, Johnson MD, Scheys JO, Cordero KE, Larios JM, Lippman ME. GREB 1 is a critical regulator of hormone dependent breast cancer growth. Breast Cancer Res Treat 2005;92:141-149.
31. Rahmioglu N, Nyholt DR, Morris AP, Missmer SA, Montgomery GW, Zondervan KT. Genetic variants underlying risk of endometriosis: insights from meta-Analysis of eight genome-wide association and replication datasets. Hum Reprod Update 2014;20:702-716.
32. Ross-Innes CS, Brown GD, Carroll JS. A co-ordinated interaction between CTCF and ER in breast cancer cells. BMC Genomics 2011;12:593.
33. Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature 2012;489:109-113.
34. SapkotaY, LowSK, Attia J, Gordon SD, HendersAK, Holliday EG, Macgregor S, MartinNG, McevoyM, MorrisAP et al. Association between endometriosis and the interleukin 1A (IL1A) locus. Hum Reprod 2015;30:239-248.
35. Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Linking disease associations with regulatory information in the human genome. Genome Res 2012;22:1748-1759.
36. Sun J, Nawaz Z, Slingerland JM. Long-range activation of GREB1 by estrogen receptor via three distal consensus estrogen-responsive elements in breast cancer cells. Mol Endocrinol 2007;21:2651-2662.
37. Treloar SA, O'connor DT, O'connor VM, Martin NG. Genetic influences on endometriosis in an Australian twin sample. Fertil Steril 1999;71:701-710.
38. Treloar S, Hadfield R, Montgomery G, Lambert A, Wicks J, Barlow DH, O'connor DT, Kennedy S. The International Endogene Study: a collection of families for genetic research in endometriosis. Fertil Steril 2002;78:679-685.
39. Uno S, Zembutsu H, Hirasawa A, Takahashi A, Kubo M, Akahane T, Aoki D, Kamatani N, Hirata K, Nakamura Y. A genome-wide association study identifies genetic variants in the CDKN2BAS locus associated with endometriosis in Japanese. Nat Genet 2010;42:707-710.
40. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F. Accurate normalization of real-Time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002;3:RESEARCH0034.
41. Vercellini P, BarbaraG, Abbiati A, Somigliana E, Vigano P, Fedele L. Repetitive surgery for recurrent symptomatic endometriosis:What todo?. Eur J Obstet Gynecol Reprod Biol 2009;146:15-21.
42. Westra HJ, Peters MJ, Esko T, Yaghootkar H, Schurmann C, Kettunen J, Christiansen MW, Fairfax BP, Schramm K, Powell JE et al. Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat Genet 2013;45:1238-1243.
43. Williams RL. A note on robust variance estimation for cluster-correlated data. Biometrics 2000;56:645-646.
44. Zaitseva M, Holdsworth-Carson SJ, Waldrip L, Nevzorova J, Martelotto L, Vollenhoven BJ, Rogers PA. Aberrant expression and regulation of NR2F2 and CTNNB1 in uterine fibroids. Reproduction 2013;146: 91-102.
45. Zhang Y, Liang J, Li Y, Xuan C, Wang F, Wang D, Shi L, Zhang D, Shang Y. CCCTC-binding factor acts upstream of FOXA1 and demarcates the genomic response to estrogen. J Biol Chem 2010;285:28604-28613.
46. Zhao ZZ, Nyholt DR, Le L, Martin NG, James MR, Treloar SA, Montgomery GW. KRAS variation and risk of endometriosis. Mol Hum Reprod 2006;12:671-676.
47. Zighelboim I, Mutch DG, Knapp A, Ding L, Xie M, Cohn DE, Goodfellow PJ. High frequency strand slippage mutations in CTCF in MSI-positive endometrial cancers. Hum Mutat 2014;35:63-65.