We sought to identify susceptibility genes for high-grade serous ovarian cancer (HGSOC) by performing a transcriptome-wide association study of gene expression and splice junction usage in HGSOC-relevant tissue types (N = 2,169) and the largest genome-wide association study available for HGSOC (N = 13,037 cases and 40,941 controls). We identified 25 transcriptome-wide association study significant genes, 7 at the junction level only, including LRRC46 at 19q21.32, (P = 1 × 10−9), CHMP4C at 8q21 (P = 2 × 10−11) and a PRC1 junction at 15q26 (P = 7 × 10−9). In vitro assays for CHMP4C showed that the associated variant induces allele-specific exon inclusion (P = 0.0024). Functional screens in HGSOC cell lines found evidence of essentiality for three of the new genes we identified: HAUS6, KANSL1 and PRC1, with the latter comparable to MYC. Our study implicates at least one target gene for 6 out of 13 distinct genome-wide association study regions, identifying 23 new candidate susceptibility genes for HGSOC.
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Code, documentation for all methods and all trained TWAS models for all genes and splice variants have been made available on the TWAS/FUSION website (http://gusevlab.org/projects/fusion/). Full TWAS association statistics have been made available in an interactive database available at http://www.twas-hub.org..
Jones, M. R., Kamara, D., Karlan, B. Y., Pharoah, P. D. P. & Gayther, S. A. Genetic epidemiology of ovarian cancer and prospects for polygenic risk prediction. Gynecol. Oncol. 147, 705–713 (2017).
Lawrenson, K. et al. Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus. Nat. Commun. 7, 12675 (2016).
Lawrenson, K. et al. Cis-eQTL analysis and functional validation of candidate susceptibility genes for high-grade serous ovarian cancer. Nat. Commun. 6, 8234 (2015).
Song, H. et al. A genome-wide association study identifies a new ovarian cancer susceptibility locus on 9p22.2. Nat. Genet. 41, 996–1000 (2009).
Bolton, K. L. et al. Common variants at 19p13 are associated with susceptibility to ovarian cancer. Nat. Genet. 42, 880–884 (2010).
Pharoah, P. D. P. et al. GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer. Nat. Genet. 45, 362–370 (2013).
Phelan, C. M. et al. Identification of 12 new susceptibility loci for different histotypes of epithelial ovarian cancer. Nat. Genet. 49, 680–691 (2017).
Kelemen, L. E. et al. Genome-wide significant risk associations for mucinous ovarian carcinoma. Nat. Genet. 47, 888–897 (2015).
Kar, S. P. et al. Genome-wide meta-analyses of breast, ovarian, and prostate cancer association studies identify multiple new susceptibility loci shared by at least two cancer types. Cancer Discov. 6, 1052–1067 (2016).
Chen, K. et al. Genome-wide association study identifies new susceptibility loci for epithelial ovarian cancer in Han Chinese women. Nat. Commun. 5, 4682 (2014).
Kuchenbaecker, K. B. et al. Identification of six new susceptibility loci for invasive epithelial ovarian cancer. Nat. Genet. 47, 164–171 (2015).
Bojesen, S. E. et al. Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer. Nat. Genet. 45, 371–384 (2013).
Goode, E. L. et al. A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24. Nat. Genet. 42, 874–879 (2010).
Li, Q. et al. Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types. Hum. Mol. Genet. 23, 5294–5302 (2014).
Li, Q. et al. Integrative eQTL-based analyses reveal the biology of breast cancer risk loci. Cell 152, 633–641 (2013).
Mancuso, N. et al. Integrating gene expression with summary association statistics to identify genes associated with 30 complex traits. Am. J. Hum. Genet. 100, 473–487 (2017).
Gusev, A. et al. Integrative approaches for large-scale transcriptome-wide association studies. Nat. Genet. 48, 245–252 (2016).
Zhu, Z. et al. Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. Nat. Genet. 48, 481–487 (2016).
Xu, Z., Wu, C., Wei, P. & Pan, W. A powerful framework for integrating eQTL and GWAS summary data. Genetics 207, 893–902 (2017).
Gamazon, E. R. et al. A gene-based association method for mapping traits using reference transcriptome data. Nat. Genet. 47, 1091–1098 (2015).
Wainberg, M. et al. Opportunities and challenges for transcriptome-wide association studies. Nat. Genet. 51, 592–599 (2019).
Meyers, R. M. et al. Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells. Nat. Genet. 49, 1779–1784 (2017).
Leeper, K. et al. Pathologic findings in prophylactic oophorectomy specimens in high-risk women. Gynecol. Oncol. 87, 52–56 (2002).
Paley, P. J. et al. Occult cancer of the fallopian tube in BRCA-1 germline mutation carriers at prophylactic oophorectomy: a case for recommending hysterectomy at surgical prophylaxis. Gynecol. Oncol. 80, 176–180 (2001).
Carcangiu, M. L. et al. Atypical epithelial proliferation in fallopian tubes in prophylactic salpingo-oophorectomy specimens from BRCA1 and BRCA2 germline mutation carriers. Int. J. Gynecol. Pathol. 23, 35–40 (2004).
Callahan, M. J. et al. Primary fallopian tube malignancies in BRCA-positive women undergoing surgery for ovarian cancer risk reduction. J. Clin. Oncol. 25, 3985–3990 (2007).
Gilks, C. B. et al. Incidental nonuterine high-grade serous carcinomas arise in the fallopian tube in most cases: further evidence for the tubal origin of high-grade serous carcinomas. Am. J. Surg. Pathol. 39, 357–364 (2015).
Auersperg, N. et al. Expression of two mucin antigens in cultured human ovarian surface epithelium: influence of a family history of ovarian cancer. Am. J. Obstet. Gynecol. 173, 558–565 (1995).
Dyck, H. G. et al. Autonomy of the epithelial phenotype in human ovarian surface epithelium: changes with neoplastic progression and with a family history of ovarian cancer. Int. J. Cancer 69, 429–436 (1996).
He, Q.-Y. et al. Proteomic analysis of a preneoplastic phenotype in ovarian surface epithelial cells derived from prophylactic oophorectomies. Gynecol. Oncol. 98, 68–76 (2005).
Casey, M. J. et al. Histology of prophylactically removed ovaries from BRCA1 and BRCA2 mutation carriers compared with noncarriers in hereditary breast ovarian cancer syndrome kindreds. Gynecol. Oncol. 78, 278–287 (2000).
Lu, K. H. et al. Occult ovarian tumors in women with BRCA1 or BRCA2 mutations undergoing prophylactic oophorectomy. J. Clin. Oncol. 18, 2728–2732 (2000).
Adler, E., Mhawech-Fauceglia, P., Gayther, S. A. & Lawrenson, K. PAX8 expression in ovarian surface epithelial cells. Hum. Pathol. 46, 948–956 (2015).
Bell, D. et al. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609–615 (2011).
Ross-Adams, H. et al. HNF1B variants associate with promoter methylation and regulate gene networks activated in prostate and ovarian cancer. Oncotarget 7, 74734–74746 (2016).
Aguet, F. et al. Genetic effects on gene expression across human tissues. Nature 550, 204–213 (2017).
Permuth-Wey, J. et al. Identification and molecular characterization of a new ovarian cancer susceptibility locus at 17q21.31. Nat. Commun. 4, 1627 (2013).
Goecks, J. et al. Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines. Cancer Med. 4, 392–403 (2015).
Giambartolomei, C. et al. Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS Genet. 10, e1004383 (2014).
Michailidou, K. et al. Association analysis identifies 65 new breast cancer risk loci. Nature 551, 92–94 (2017).
Schumacher, F. R. et al. Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci. Nat. Genet. 50, 928–936 (2018).
Reyes-González, J. M. et al. Targeting c-MYC in platinum-resistant ovarian cancer. Mol. Cancer Ther. 14, 2260–2269 (2015).
Baskin, R. et al. Functional analysis of the 11q23.3 glioma susceptibility locus implicates PHLDB1 and DDX6 in glioma susceptibility. Sci. Rep. 5, 17367 (2015).
French, J. D. et al. Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers. Am. J. Hum. Genet. 92, 489–503 (2013).
Pasquali, L. et al. Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants. Nat. Genet. 46, 136–143 (2014).
Fujita, K. et al. Proteomic analysis of urinary extracellular vesicles from high Gleason score prostate cancer. Sci. Rep. 7, 42961 (2017).
Nikolova, D. N. et al. Genome-wide gene expression profiles of ovarian carcinoma: identification of molecular targets for the treatment of ovarian carcinoma. Mol. Med. Rep. 2, 365–384 (2009).
Lu, Y. et al. A transcriptome-wide association study among 97,898 women to identify candidate susceptibility genes for epithelial ovarian cancer risk. Cancer Res. 78, 5419–5430 (2018).
Lawrenson, K. et al. In vitro three-dimensional modelling of human ovarian surface epithelial cells. Cell Prolif. 42, 385–393 (2009).
Karst, A. M., Levanon, K. & Drapkin, R. Modeling high-grade serous ovarian carcinogenesis from the fallopian tube. Proc. Natl Acad. Sci. USA 108, 7547–7552 (2011).
Ardlie, K. G. et al. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348, 648–660 (2015).
Stegle, O., Parts, L., Piipari, M., Winn, J. & Durbin, R. Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nat. Protoc. 7, 500–507 (2012).
Aran, D., Sirota, M. & Butte, A. J. Systematic pan-cancer analysis of tumour purity. Nat. Commun. 6, 8971 (2015).
Haseman, J. K. & Elston, R. C. The investigation of linkage between a quantitative trait and a marker locus. Behav. Genet. 2, 3–19 (1972).
Yang, J., Lee, S. H., Goddard, M. E. & Visscher, P. M. GCTA: a tool for genome-wide complex trait analysis. Am. J. Hum. Genet. 88, 76–82 (2011).
Falconer, D. S. & Mackay, T. F. C. Introduction to Quantitative Genetics 4th edn (Pearson Prentice Hall, 1996).
Wheeler, H. E. et al. Survey of the heritability and sparse architecture of gene expression traits across human tissues. PLoS Genet. 12, e1006423 (2016).
Yang, J. et al. Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits. Nat. Genet. 44, 369–375 (2012).
Li, N. F. et al. A modified medium that significantly improves the growth of human normal ovarian surface epithelial (OSE) cells in vitro. Lab. Invest. 84, 923–931 (2004).
Hsiao, Y.-H. E. et al. Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins. Genome Res. 26, 440–450 (2016).
Buckley, M. et al. Enhancer scanning to locate regulatory regions in genomic loci. Nat. Protoc. 11, 46–60 (2016).
Lawrenson, K. et al. Senescent fibroblasts promote neoplastic transformation of partially transformed ovarian epithelial cells in a three-dimensional model of early stage ovarian cancer. Neoplasia 12, 317–325 (2010).
This work was supported by multiple grants: an NIH/NCI R21 award (grant no. CA22007801); an NIH/NCI U19 award as part of the Genetic Mechanisms in Oncology (GAME-ON) consortium (grant no. CA148112); an NIH/NCI R01 award (grant no. CA211707); an NIH/NCI R01 award (grant no. CA207456); an NIH/NCI R01 award (grant no. CA204954); and an NIH/NCI R01 award (grant no. CA227237). S.A.G. is additionally supported by the Barth Family Chair in Cancer Genetics at Cedars-Sinai Medical Center. K.L. is supported in part by a K99/R00 Pathway to Independence Award from the NIH (grant no. R00CA184415) and institutional support from the Samuel Oschin Comprehensive Cancer Institute at Cedars-Sinai Medical Center. H.N. and M.A.S.F. are supported by grant nos. 2015/07925-5 and 2017/08211-1 from São Paulo Research Foundation. H.N. is also supported by an institutional grant (Henry Ford Hospital, A30935). This work was supported in part by the Ovarian Cancer Research Fund Alliance Program Project Development Grant (grant no. 373356; Co-Evolution of Epithelial Ovarian Cancer and Tumor Stroma). Additional support for this work came from NIH/NCI grant nos. 1R01CA211707 and 1R01CA207456 and Ovarian Cancer Research Foundation award no. 258807. The results shown in this article are in part based on data generated by the TCGA Research Network (http://cancergenome.nih.gov/). Some of the normal tissue specimens were collected as part of the USC Jean Richardson Gynecologic Tissue and Fluid Repository, which is supported by a grant from the USC Department of Obstetrics & Gynecology and the NCT Cancer Center Shared Grant award no. P30 CA014089 (to the Norris Comprehensive Cancer Center). A.G. is supported by R01-CA227237 and the Claudia Adams Barr Award. B.P. is supported by R01-HG009120, R21-CA220078 and U01-CA194393.
The authors declare no conflicts of interest.
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Gusev, A., Lawrenson, K., Lin, X. et al. A transcriptome-wide association study of high-grade serous epithelial ovarian cancer identifies new susceptibility genes and splice variants. Nat Genet 51, 815–823 (2019). https://doi.org/10.1038/s41588-019-0395-x
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