Gayther, Simon A.

Abstract Background: Little transcriptomic research has compared epithelial ovarian cancer (EOC) histological subtypes. We set out to characterize the transcriptomes of high-grade serous carcinomas (HGSC) and endometrioid carcinomas (EC), which make up around 70% and 20% of EOC tumors, respectively, and have some histopathological similarities. Methods: Fresh frozen tumors from EOC patients seen at the Mayo Clinic (30 EC and 62 HGSC) were used. 1ug RNA riboZero was used for library preparation using the Illumina TruSeq kit and sequenced on a HiSeq 2000 machine. Reads were aligned using TopHat2 followed by quantification of abundances using RSEM and differential expression analysis with edgeR. We analyzed transcriptomes, conducted pathway analyses, and summarized key candidate gene sets. Expressed SNVs (eSNVs) from the RNA-seq data were determined using GATK and RVboost. Results: The analysis found 699 genes with FDR < 1×10-5 for differential expression between HGSC and EC, with most genes being up-regulated in EC. The top most associated genes were TPH1, MAP2K6, KLK2, ADAM23, TESC and TRAF3IP2 (p<10-22). Pathway analysis of the genes up-regulated in EC revealed enrichment of the “basal cell carcinoma signaling pathway” (p = 1.2×10-5). Within 1 Mb of the 25 known EOC risk loci, we observed higher expression in HGSC for RSPO1 and HPSE (p <5×10-7). For genes functionally related to EOC, we observed in HGSC up-regulation (*p < 10-5, ⁁p<0.003) for FOXM1⁁, CDKN2A⁁, CCNE1*, CCND2⁁, PIK3CA*, BRCA2⁁, BIRC5⁁, MMP9⁁, FANCD2⁁, and MAML2⁁. In contrast, we found up-regulation in EC for MDM2*, KLK4*, BCL2⁁, CCND1*, ANXA4*, CDH1⁁, MMP7⁁, and MAML3⁁. We also identified 204 eSNVs (44 non-synonymous) associated with EC v HGSC subtype (p<10-4); this included an exonic TRAF3IP2 eSNV (66% EC, 13% HGSC, p = 4×10-7, chr6:111877117). Discussion: Using one of the largest sets of identically processed fresh-frozen EOC tumors, some patterns emerged among the numerous EC v HGSC transcriptomic differences. TPH1, up-expressed in EC, is regulated by SOX4 which was also up-regulated in EC. Two sets of genes related to Kallikreins serine proteases were differentially expressed, including KLK2 which is known to regulate EGFR and pro-inflammatory cytokines and is regulated by MYC. Lastly, TRAF3IP2 encodes for a protein involved in regulating cytokines through members of the NFKB pathway. Conclusions: These findings suggest important biological insights into one of the rarer EOC histologies and may aid in the development of targeted treatment options. Research is on-going to incorporate additional features (e.g., DNA methylation, copy number) into a “systems biology” framework to better understand the molecular differences between EOC histologies. Citation Format: Brooke L. Fridley, Junqiang Dai, Rama Raghavan, Chen Wang, Pengcheng Lu, Stacey Winham, Madalene Earp, Kate Lawrenson, Simon A. Gayther, Kimberly R. Kalli, Ellen L. Goode. Transcriptome characterization of high grade serous and endometrioid epithelial ovarian cancer tumors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1833.

Abstract Breast, ovarian, and prostate cancers are hormone-related and may have a shared genetic basis, but this has not been investigated systematically by genome-wide association (GWA) studies. Meta-analyses combining the largest GWA meta-analysis data sets for these cancers totaling 112,349 cases and 116,421 controls of European ancestry, all together and in pairs, identified at P < 10−8 seven new cross-cancer loci: three associated with susceptibility to all three cancers (rs17041869/2q13/BCL2L11; rs7937840/11q12/INCENP; rs1469713/19p13/GATAD2A), two breast and ovarian cancer risk loci (rs200182588/9q31/SMC2; rs8037137/15q26/RCCD1), and two breast and prostate cancer risk loci (rs5013329/1p34/NSUN4; rs9375701/6q23/L3MBTL3). Index variants in five additional regions previously associated with only one cancer also showed clear association with a second cancer type. Cell-type–specific expression quantitative trait locus and enhancer–gene interaction annotations suggested target genes with potential cross-cancer roles at the new loci. Pathway analysis revealed significant enrichment of death receptor signaling genes near loci with P < 10−5 in the three-cancer meta-analysis. Significance: We demonstrate that combining large-scale GWA meta-analysis findings across cancer types can identify completely new risk loci common to breast, ovarian, and prostate cancers. We show that the identification of such cross-cancer risk loci has the potential to shed new light on the shared biology underlying these hormone-related cancers. Cancer Discov; 6(9); 1052–67. ©2016 AACR. This article is highlighted in the In This Issue feature, p. 932

Abstract Background: Epithelial Ovarian Cancer (EOC) is a lethal gynecologic malignancy. Mitochondria are cellular organelles that regulate energy metabolism and are the primary source of reactive oxygen species (ROS), which damage both the nuclear and mitochondria DNA (mtDNA), contributing to the pathogenesis of EOC. Previously, we identified statistically significant EOC risk associations with 54 single nucleotide polymorphisms (SNPs) from 11 mitochondria-related genes in a study of 1815 EOC cases and 1900 controls. In this replication study we expand our investigation of mitochondrial metabolism genetic variants and associations with EOC risk and overall survival (OS). Methods: In a discovery set of 3761 EOC cases and 2722 controls, we investigated risk associations in 4200 SNPs from 130 mitochondrial metabolism genes. We genotyped 431 of the most significant SNPs from 86 genes in 14,525 EOC cases and 23,447 controls (of European ancestry) from 43 studies in OCAC using an Illumina Infinium iSelect BeadChip. Risk analyses were conducted using unconditional logistic regression under a log-additive model and adjusted for study site and the first five principal components of population substructure. Both invasive cancers combined and the four main histological subtypes were analyzed. Survival analyses were conducted on the same SNPs using Cox hazards models to estimate hazard ratios (HRs) and 95% CIs considering overall survival in 10,084 cases from 28 OCAC studies. We adjusted for multiple tests using False Discovery Rate q<20%. Results: The strongest evidence of an association for risk of invasive cancers combined and the serous subtype was SNP rs3096 in the pyridoxamine 5'-phosphate oxidase (PNPO) gene (OR=1.08, p=2.8x10-6). In clear cell carcinoma, the strongest association was a missense coding SNP rs28379632 (Ile421Met) in the MT-CYB gene (OR=4.0, p=0.003). For endometrioid cancer rs9330440 in the UNQ6494 gene was most significant (OR=0.89, p=0.001) while rs10267797 in the dihydrolipoamide dehydrogenase (DLD) gene was most significant in the mucinous subtype (OR=1.15, p=0.004). The strongest association with overall survival was mitochondrial transcription termination factor 1 (MTERF) rs2540571 (HR=0.92, p= 0.00011). Conclusion: These results suggest that mitochondrial metabolism gene variants appear to be associated with EOC risk and survival. Citation Format: Ganna Chornokur, Hui-Yi Lin, Alvaro Monteiro, Joellen Schildkraut, Ellen L. Goode, Paul DP Pharoah, Simon A. Gayther, Susan Ramus, Thomas A. Sellers, Catherine M. Phelan. Mitochondrial metabolism gene variants are associated with risk and survival in epithelial ovarian cancer (EOC). [abstract]. In: Proceedings of the AACR Special Conference: Metabolism and Cancer; Jun 7-10, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(1_Suppl):Abstract nr A50.

Abstract Background: Epithelial Ovarian Cancer (EOC) is a lethal gynecologic malignancy and the fifth cause of cancer mortality in women in the US. Normal ovarian physiology is intricately connected to tightly regulated small GTP binding proteins of the Ras superfamily (Ras, Rac, Rho, Rab, Arf, and Ran) which regulate key cellular processes such as signal transduction, cell proliferation, cell motility, and vesicle transport. These proteins function in a highly coordinated manner through signaling cascades and feedback loops within and among the small GTPase subfamilies. We hypothesized that single nucleotide polymorphisms (SNPs) in small GTPase genes are associated with epithelial ovarian cancer (EOC) risk and aberrant expression of these genes correlates with tumor characteristics including overall survival (OS). Methods: In a discovery set of 7931 EOC cases and 9206 controls we investigated 9,356 SNPs from 112 genes, 657 of which showed associations up to the significance level of p<0.05. We genotyped 407 of the most significant SNPs from 112 genes in a combined dataset (discovery and replication) which consisted of 18,736 EOC cases and 23,448 controls (of European ancestry) from 43 studies in the Ovarian Cancer Association Consortium (OCAC), using an Illumina Infinium iSelect BeadChip as part of the Collaborative Oncological Gene-environment Study (COGS). Odds ratios and 95% confidence intervals were calculated using unconditional logistic regression under log-additive models. A False Discovery Rate (FDR) q<0.2 was applied. Pearson's correlation tests were performed on the expression of genes with tumor characteristics and OS in 561 ovarian tumors: serous (n=464); endometrioid (n=52); clear cell carcinoma (n=28) and mucinous (n=17) subtypes. Results: The most significantly associated SNP associations with EOC were: AKAP6 rs1955513, (OR=0.9, p=3.3x10-4) in all invasive; ARGHEF10L rs10788679, (OR=1.05, p=2.6x10-4) in serous; RAB31 rs1166373, (OR=1.25, p=4.0x10-3) in endometrioid; KRAS rs4963872, (OR=1.35, P=4.5x10-4) in mucinous EOC and TNIK rs6780532, (OR=0.88, p=7.7x10-3) in clear cell carcinoma. Increased expression of AKAP6 and TNIK was marginally correlated with advanced EOC stage (p<0.05) while high KRAS expression was correlated with OS (HR=1.18, p=0.038). Conclusions: Genetic variation in the small GTPase genes appears to be associated with ovarian cancer risk and aberrant expression of these genes correlates with tumor characteristics and OS. Citation Format: Hui-Yi Lin, Yin Xiong, Jonathan Tyrer, Douglas C. Marchion, Alvaro NA Monteiro, Andrew Berchuck, Joellen M. Schildkraut, Ellen L. Goode, Susan J. Ramus, Simon A. Gayther, Paul DP Pharoah, Steven A. Narod, Thomas A. Sellers, Catherine M. Phelan. Investigation of small GTPase genes in epithelial ovarian cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr B27.

Abstract Background: Many epithelial ovarian cancer (EOC) risk factors relate to hormone exposure and elevated estrogen levels are associated with obesity in postmenopausal women. Therefore, we hypothesized that gene–environment interactions related to hormone-related risk factors could differ between obese and non-obese women. Methods: We considered interactions between 11,441 SNPs within 80 candidate genes related to hormone biosynthesis and metabolism and insulin-like growth factors with six hormone-related factors (oral contraceptive use, parity, endometriosis, tubal ligation, hormone replacement therapy, and estrogen use) and assessed whether these interactions differed between obese and non-obese women. Interactions were assessed using logistic regression models and data from 14 case–control studies (6,247 cases; 10,379 controls). Histotype-specific analyses were also completed. Results: SNPs in the following candidate genes showed notable interaction: IGF1R (rs41497346, estrogen plus progesterone hormone therapy, histology = all, P = 4.9 × 10−6) and ESR1 (rs12661437, endometriosis, histology = all, P = 1.5 × 10−5). The most notable obesity–gene–hormone risk factor interaction was within INSR (rs113759408, parity, histology = endometrioid, P = 8.8 × 10−6). Conclusions: We have demonstrated the feasibility of assessing multifactor interactions in large genetic epidemiology studies. Follow-up studies are necessary to assess the robustness of our findings for ESR1, CYP11A1, IGF1R, CYP11B1, INSR, and IGFBP2. Future work is needed to develop powerful statistical methods able to detect these complex interactions. Impact: Assessment of multifactor interaction is feasible, and, here, suggests that the relationship between genetic variants within candidate genes and hormone-related risk factors may vary EOC susceptibility. Cancer Epidemiol Biomarkers Prev; 25(5); 780–90. ©2016 AACR.

Abstract Background: While numerous susceptibility loci for epithelial ovarian cancer (EOC) have been identified, few associations have been reported with overall survival. In the absence of common prognostic genetic markers, we hypothesize that rare coding variants may be associated with overall EOC survival and assessed their contribution in two exome-based genotyping projects of the Ovarian Cancer Association Consortium (OCAC). Methods: The primary patient set (Set 1) included 14 independent EOC studies (4,293 patients) and 227,892 variants, and a secondary patient set (Set 2) included six additional EOC studies (1,744 patients) and 114,620 variants. Because power to detect rare variants individually is reduced, gene-level tests were conducted. Sets were analyzed separately at individual variants and by gene, and then combined with meta-analyses (73,203 variants and 13,163 genes overlapped). Results: No individual variant reached genome-wide statistical significance. A SNP previously implicated to be associated with EOC risk and, to a lesser extent, survival, rs8170, showed the strongest evidence of association with survival and similar effect size estimates across sets (Pmeta = 1.1E−6, HRSet1 = 1.17, HRSet2 = 1.14). Rare variants in ATG2B, an autophagy gene important for apoptosis, were significantly associated with survival after multiple testing correction (Pmeta = 1.1E−6; Pcorrected = 0.01). Conclusions: Common variant rs8170 and rare variants in ATG2B may be associated with EOC overall survival, although further study is needed. Impact: This study represents the first exome-wide association study of EOC survival to include rare variant analyses, and suggests that complementary single variant and gene-level analyses in large studies are needed to identify rare variants that warrant follow-up study. Cancer Epidemiol Biomarkers Prev; 25(3); 446–54. ©2016 AACR.

ABSTRACTEpithelial‐mesenchymal transition (EMT) is a process whereby epithelial cells assume mesenchymal characteristics to facilitate cancer metastasis. However, EMT also contributes to the initiation and development of primary tumors. Prior studies that explored the hypothesis that EMT gene variants contribute to epithelial ovarian carcinoma (EOC) risk have been based on small sample sizes and none have sought replication in an independent population. We screened 15,816 single‐nucleotide polymorphisms (SNPs) in 296 genes in a discovery phase using data from a genome‐wide association study of EOC among women of European ancestry (1,947 cases and 2,009 controls) and identified 793 variants in 278 EMT‐related genes that were nominally (P < 0.05) associated with invasive EOC. These SNPs were then genotyped in a larger study of 14,525 invasive‐cancer patients and 23,447 controls. A P‐value <0.05 and a false discovery rate (FDR) <0.2 were considered statistically significant. In the larger dataset, GPC6/GPC5 rs17702471 was associated with the endometrioid subtype among Caucasians (odds ratio (OR) = 1.16, 95% CI = 1.07–1.25, P = 0.0003, FDR = 0.19), whereas F8 rs7053448 (OR = 1.69, 95% CI = 1.27–2.24, P = 0.0003, FDR = 0.12), F8 rs7058826 (OR = 1.69, 95% CI = 1.27–2.24, P = 0.0003, FDR = 0.12), and CAPN13 rs1983383 (OR = 0.79, 95% CI = 0.69–0.90, P = 0.0005, FDR = 0.12) were associated with combined invasive EOC among Asians. In silico functional analyses revealed that GPC6/GPC5 rs17702471 coincided with DNA regulatory elements. These results suggest that EMT gene variants do not appear to play a significant role in the susceptibility to EOC.

Abstract The known genetic variance for epithelial ovarian cancer (EOC) accounts for less than half the familial risks of the disease. BRCA1 and BRCA2 are the major high-penetrance EOC susceptibility genes. More recently genes that interact with BRCA1 and BRCA2 in the same biological pathways, but conferring more moderate penetrance (e.g. RAD51C, RAD51D) have also been identified. Mutations in these genes result in defects in homologous recombination and double strand break repair (HR/DSB). We hypothesized that other genes operating in these and other DNA repair pathways may also confer EOC susceptibility. Whole exome sequencing data, available from more than 400 high-grade serous ovarian cancers, were used to identify 24 candidate genes harboring germline truncating mutations in at least 2 cases, followed by replication analysis using targeted resequencing in ~3,000 cases and 3,000 controls. Subjects were also sequenced for the known susceptibility genes listed above. The data confirmed the previously reported contributions of BRCA1, BRCA2, RAD51C and RAD51D to EOC. In addition, we identified BRIP1, and FANCM as candidate EOC susceptibility genes. Surprisingly, for several genes we found truncating mutations were equally prevalent in cases as they were in controls. These mutations may still represent rare low-penetrance susceptibility alleles for EOC, which we are too limited in sample size and power to confirm; or more likely, it indicates that cells can tolerate heterozygous loss-of-function mutations in apparently critical DNA repair genes without any impact on neoplastic development. These findings may have implications for risk prediction and prevention strategies for EOC and possibly for the identification of novel therapeutic targets. Citation Format: Susan J. Ramus, Honglin Song, Ed Dicks, Maria Intermaggio, Jane Hayward, Jonathan P. Tyrer, Jacek Gronwald, Susanne Krüger Kjær, Alice Wittemore, Beth Karlan, Kunle Odunsi, Usha Menon, David D. Bowtell, Ellen L. Goode, Paul D.P. Pharoah, Simon A. Gayther. Whole exome and targeted resequencing, of population based ovarian cancer cases and controls, identifies susceptibility genes for ovarian cancer [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr POSTER-CTRL-1213.