Goode, Ellen L.

Background The rarity of mutations in PALB2, CHEK2 and ATM make it difficult to estimate precisely associated cancer risks. Population-based family studies have provided evidence that at least some of these mutations are associated with breast cancer risk as high as those associated with rare BRCA2 mutations. We aimed to estimate the relative risks associated with specific rare variants in PALB2, CHEK2 and ATM via a multicentre case-control study. Methods We genotyped 10 rare mutations using the custom iCOGS array: PALB2 c.1592delT, c.2816T>G and c.3113G>A, CHEK2 c.349A>G, c.538C>T, c.715G>A, c.1036C>T, c.1312G>T, and c.1343T>G and ATM c.7271T>G. We assessed associations with breast cancer risk (42 671 cases and 42 164 controls), as well as prostate (22 301 cases and 22 320 controls) and ovarian (14 542 cases and 23 491 controls) cancer risk, for each variant. Results For European women, strong evidence of association with breast cancer risk was observed for PALB2 c.1592delT OR 3.44 (95% CI 1.39 to 8.52, p=7.1×10−5), PALB2 c.3113G>A OR 4.21 (95% CI 1.84 to 9.60, p=6.9×10−8) and ATM c.7271T>G OR 11.0 (95% CI 1.42 to 85.7, p=0.0012). We also found evidence of association with breast cancer risk for three variants in CHEK2, c.349A>G OR 2.26 (95% CI 1.29 to 3.95), c.1036C>T OR 5.06 (95% CI 1.09 to 23.5) and c.538C>T OR 1.33 (95% CI 1.05 to 1.67) (p≤0.017). Evidence for prostate cancer risk was observed for CHEK2 c.1343T>G OR 3.03 (95% CI 1.53 to 6.03, p=0.0006) for African men and CHEK2 c.1312G>T OR 2.21 (95% CI 1.06 to 4.63, p=0.030) for European men. No evidence of association with ovarian cancer was found for any of these variants. Conclusions This report adds to accumulating evidence that at least some variants in these genes are associated with an increased risk of breast cancer that is clinically important.

Abstract Background: The strongest known risk factor for endometrial cancer is obesity. To determine whether SNPs associated with increased body mass index (BMI) or waist–hip ratio (WHR) are associated with endometrial cancer risk, independent of measured BMI, we investigated relationships between 77 BMI and 47 WHR SNPs and endometrial cancer in 6,609 cases and 37,926 country-matched controls. Methods: Logistic regression analysis and fixed effects meta-analysis were used to test for associations between endometrial cancer risk and (i) individual BMI or WHR SNPs, (ii) a combined weighted genetic risk score (wGRS) for BMI or WHR. Causality of BMI for endometrial cancer was assessed using Mendelian randomization, with BMIwGRS as instrumental variable. Results: The BMIwGRS was significantly associated with endometrial cancer risk (P = 3.4 × 10−17). Scaling the effect of the BMIwGRS on endometrial cancer risk by its effect on BMI, the endometrial cancer OR per 5 kg/m2 of genetically predicted BMI was 2.06 [95% confidence interval (CI), 1.89–2.21], larger than the observed effect of BMI on endometrial cancer risk (OR = 1.55; 95% CI, 1.44–1.68, per 5 kg/m2). The association attenuated but remained significant after adjusting for BMI (OR = 1.22; 95% CI, 1.10–1.39; P = 5.3 × 10−4). There was evidence of directional pleiotropy (P = 1.5 × 10−4). BMI SNP rs2075650 was associated with endometrial cancer at study-wide significance (P < 4.0 × 10−4), independent of BMI. Endometrial cancer was not significantly associated with individual WHR SNPs or the WHRwGRS. Conclusions: BMI, but not WHR, is causally associated with endometrial cancer risk, with evidence that some BMI-associated SNPs alter endometrial cancer risk via mechanisms other than measurable BMI. Impact: The causal association between BMI SNPs and endometrial cancer has possible implications for endometrial cancer risk modeling. Cancer Epidemiol Biomarkers Prev; 25(11); 1503–10. ©2016 AACR.

Telomeres cap chromosome ends, protecting them from degradation, double‐strand breaks, and end‐to‐end fusions. Telomeres are maintained by telomerase, a reverse transcriptase encoded by TERT, and an RNA template encoded by TERC. Loci in the TERT and adjoining CLPTM1L region are associated with risk of multiple cancers. We therefore investigated associations between variants in 22 telomere structure and maintenance gene regions and colorectal, breast, prostate, ovarian, and lung cancer risk. We performed subset‐based meta‐analyses of 204,993 directly‐measured and imputed SNPs among 61,851 cancer cases and 74,457 controls of European descent. Independent associations for SNP minor alleles were identified using sequential conditional analysis (with gene‐level p value cutoffs ≤3.08 × 10−5). Of the thirteen independent SNPs observed to be associated with cancer risk, novel findings were observed for seven loci. Across the DCLRE1B region, rs974494 and rs12144215 were inversely associated with prostate and lung cancers, and colorectal, breast, and prostate cancers, respectively. Across the TERC region, rs75316749 was positively associated with colorectal, breast, ovarian, and lung cancers. Across the DCLRE1B region, rs974404 and rs12144215 were inversely associated with prostate and lung cancers, and colorectal, breast, and prostate cancers, respectively. Near POT1, rs116895242 was inversely associated with colorectal, ovarian, and lung cancers, and RTEL1 rs34978822 was inversely associated with prostate and lung cancers. The complex association patterns in telomere‐related genes across cancer types may provide insight into mechanisms through which telomere dysfunction in different tissues influences cancer risk.

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 Purpose: Ovarian cancer (OC) patients received maximum benefits when complete dissection with no macroscopic disease is achieved. It has been suggested that surgical outcome is associated with tumor biology and therefore can be predicted from tumor molecular characteristics such as gene expression levels. Noticeably, several debulking-associated genes have been independently reported based on meta-data analysis and further validations in individual center's cohorts. Furthermore, a recent OC study of the cancer genome atlas (TCGA) project revealed the presence of four expression subtypes in high-grade serous ovarian cancer (HGSOC). We have independently confirmed this association with prognosis in our OC cohort. With the awareness that surgical practices and rates of complete resection vary among institutions, we sought to evaluate whether expression changes of previously reported debulking-associated genes are associated with complete dissection in a HGSOC cohort in a center with an aggressive surgical approach. Further, we also tested if the HGSOC four expression subtypes are associated with complete dissection. Experimental Design: We constructed a cohort of 262 stage III/IV HGSOC patient cases diagnosed in Mayo Clinic between 1993 and 2011. Cases were categorized into two groups based upon debulking outcome: 84 complete resection cases with no gross visible residual disease (RD0), 178 cases with residual disease greater than 0 cm (RD1). Tumor mRNA expression was previously measured using Agilent 4x44k platforms. Eight previously published debulking-associated genes were evaluated for their expression differences between RD0 and RD1 patient groups using t-test: FABP4, ADH1B, POSTN, CXCL14, FAP, NUAK1, PTCH1 and TGFBR2. For testing subtype-debulking associations, we first quantified molecular subtype activation scores of individual tumors using single-sample gene set enrichment analysis (ssGSEA), and computed standardized scores after permutation-based scaling adjustments to account for gene set size difference. Then, standardized subtype scores are associated with complete dissection (RD0) vs. other surgical outcome (RD1) using logistic regression. The independent subtype-associations were further evaluated by adjusting known debulking outcome factors, including age, ascites, tumor grade and stage. Results: For eight previously reported debulking-associated genes, only one demonstrated a significant expression difference between RD0 and RD1 groups: CXCL14, t-test p-value = 9.2x10-3. When comparing debulking vs. HGSOC subtypes, we observed a significantly reduced probability of complete resection for the mesenchymal subtype (p-value = 1.1x10-2, OR = 0.56, 95% CI [0.35, 0.87]). Consistent with this observation, we have previously described the mesenchymal subtype as a poor prognosis group. On the other hand, the immunoreactive subtype was associated with a higher likelihood of complete resection (p-value = 9.4 x 10-3, OR=2.19, 95% CI = [1.22, 4.01]). The significant associations between these two subtype activities and complete resection in advanced stage disease remained after adjusting for age, ascites, tumor grade and sub-stage: mesenchymal (p-value = 1.5 x 10-2 ,OR = 0.48, 95% CI = [0.26, 0.85]); immunoreactive subtype (p-value = 4.8 x 10-2 , OR = 2.11, 95% CI = [1.04, 4.53]). Conclusion: This single center HGSOC analysis demonstrates the important of validation of debulking signatures in centers with diverse rates of complete resection. We were only able to validate an association with complete resection for one of eight previously reported debulking-associated genes. We also showed that HGSOC subtypes have significant associations with likelihood of complete dissection. Further studies are warranted for confirming subtype associations in other institutional HGSOC cohorts. Citation Format: Chen Wang, Jamie Bakkum-Gamez, Andrea Mariani, William Cliby, Ellen Goode. Tumor expression subtypes of high-grade serous ovarian cancer demonstrate associations with likelihood of complete resection: a single-center study. [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 B80.

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.