Jennifer A. Doherty

Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease

Genetic variants have been associated with myriad molecular phenotypes that provide new insight into the range of mechanisms underlying genetic traits and diseases. Identifying any particular genetic variants cascade of effects, from molecule to individual, requires assaying multiple layers of molecular complexity. We introduce the Enhancing GTEx (eGTEx) project that extends the GTEx project to combine gene expression with additional intermediate molecular measurements on the same tissues to provide a resource for studying how genetic differences cascade through molecular phenotypes to impact human health.

Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer Subtypes

Purpose of ReviewOnly recently has it become clear that epithelial ovarian cancer (EOC) is comprised of such distinct histotypes—with different cells of origin, morphology, molecular features, epidemiologic factors, clinical features, and survival patterns—that they can be thought of as different diseases sharing an anatomical location. Herein, we review opportunities and challenges in studying EOC heterogeneity,Recent FindingsThe 2014 World Health Organization diagnostic guidelines incorporate accumulated evidence that high- and low-grade serous tumors have different underlying pathogenesis, and that, on the basis of shared molecular features, most high-grade tumors, including some previously classified as endometrioid, are now considered to be high-grade serous. At the same time, several studies have reported that high-grade serous EOC, which is the most common histotype, is itself made up of reproducible subtypes discernable by gene expression patterns.SummaryThese major advances in understanding set the stage for a new era of research on EOC risk and clinical outcomes with the potential to reduce morbidity and mortality. We highlight the need for multidisciplinary studies with pathology review using the current guidelines, further molecular characterization of the histotypes and subtypes, inclusion of women of diverse racial/ethnic and socioeconomic backgrounds, and updated epidemiologic and clinical data relevant to current generations of women at risk of EOC.

Ovarian cancer risk, ALDH2 polymorphism and alcohol drinking: Asian data from the Ovarian Cancer Association Consortium

The aldehyde dehydrogenase 2 (ALDH2) polymorphism rs671 (Glu504Lys) causes ALDH2 inactivation and adverse acetaldehyde exposure among Asians, but little is known of the association between alcohol consumption and rs671 and ovarian cancer (OvCa) in Asians. We conducted a pooled analysis of Asian ancestry participants in the Ovarian Cancer Association Consortium. We included seven case‐control studies and one cohort study comprising 460 invasive OvCa cases, 37 borderline mucinous OvCa and 1274 controls of Asian descent with information on recent alcohol consumption. Pooled odds ratios (OR) with 95% confidence intervals (CI) for OvCa risk associated with alcohol consumption, rs671 and their interaction were estimated using logistic regression models adjusted for potential confounders. No significant association was observed for daily alcohol intake with invasive OvCa (OR comparing any consumption to none = 0.83; 95% CI = 0.58‐1.18) or with individual histotypes. A significant decreased risk was seen for carriers of one or both Lys alleles of rs671 for invasive mucinous OvCa (OR = 0.44; 95% CI = 0.20‐0.97) and for invasive and borderline mucinous tumors combined (OR = 0.48; 95% CI = 0.26‐0.89). No significant interaction was observed between alcohol consumption and rs671 genotypes. In conclusion, self‐reported alcohol consumption at the quantities estimated was not associated with OvCa risk among Asians. Because the rs671 Lys allele causes ALDH2 inactivation leading to increased acetaldehyde exposure, the observed inverse genetic association with mucinous ovarian cancer is inferred to mean that alcohol intake may be a risk factor for this histotype. This association will require replication in a larger sample.

Racial/ethnic differences in the epidemiology of ovarian cancer: a pooled analysis of 12 case-control studies

Background Ovarian cancer incidence differs substantially by race/ethnicity, but the reasons for this are not well understood. Data were pooled from the African American Cancer Epidemiology Study (AACES) and 11 case-control studies in the Ovarian Cancer Association Consortium (OCAC) to examine racial/ethnic differences in epidemiological characteristics with suspected involvement in epithelial ovarian cancer (EOC) aetiology. Methods We used multivariable logistic regression to estimate associations for 17 reproductive, hormonal and lifestyle characteristics and EOC risk by race/ethnicity among 10 924 women with invasive EOC (8918 Non-Hispanic Whites, 433 Hispanics, 911 Blacks, 662 Asian/Pacific Islanders) and 16 150 controls (13 619 Non-Hispanic Whites, 533 Hispanics, 1233 Blacks, 765 Asian/Pacific Islanders). Likelihood ratio tests were used to evaluate heterogeneity in the risk factor associations by race/ethnicity. Results We observed statistically significant racial/ethnic heterogeneity for hysterectomy and EOC risk (P = 0.008), where the largest odds ratio (OR) was observed in Black women [OR = 1.64, 95% confidence interval (CI) = 1.34-2.02] compared with other racial/ethnic groups. Although not statistically significant, the associations for parity, first-degree family history of ovarian or breast cancer, and endometriosis varied by race/ethnicity. Asian/Pacific Islanders had the greatest magnitude of association for parity (≥3 births: OR = 0.38, 95% CI = 0.28-0.54), and Black women had the largest ORs for family history (OR = 1.77, 95% CI = 1.42-2.21) and endometriosis (OR = 2.42, 95% CI = 1.65-3.55). Conclusions Although racial/ethnic heterogeneity was observed for hysterectomy, our findings support the validity of EOC risk factors across all racial/ethnic groups, and further suggest that any racial/ethnic population with a higher prevalence of a modifiable risk factor should be targeted to disseminate information about prevention.

Epidemiologic paradigms for progress in ovarian cancer research

tasked the Institute of Medicine (IOM) to “make recommendations for public and private sector efforts that could facilitate progress in reducing the incidence of and the morbidity and mortality from ovarian cancer,” with an emphasis on advancing research on ovarian carcinogenesis across the cancer continuum [4]. Notably, several recommendations in the report are particularly relevant to the implementation of populationbased studies of ovarian cancer risk and survival. These span primary prevention, screening/early detection, and secondary prevention. With respect to primary prevention, a key recommendation was to “identify and evaluate the underlying mechanisms of both new and established risk factors for ovarian cancers...accounting for the various ovarian cancer subtypes [4].” The ultimate goal of such work is to improve upon risk prediction models to identify high-risk women who could benefit from prevention measures. To date, risk models have had low predictive capacity [5–9], in part due to the heterogeneity of risk factor associations across tumor histotypes [10] and the relatively few strong risk factors identified for the most common and deadly histotype, high-grade serous tumors. In addition, the IOM committee recommended that researchers “focus on the development and assessment of early detection strategies that extend beyond current imaging modalities and biomarkers and that reflect the pathobiology of each ovarian cancer subtype [4],” given that CA-125 and transvaginal ultrasound screening protocols have not led to significant reductions in mortality from ovarian cancer [11–14]. Finally, population science can play a role to “develop more effective pharmacologic and nonpharmacologic therapies...that take into account the unique biology and clinical course of ovarian cancer [4].” To achieve these goals, it is critical to consider new approaches in conducting epidemiologic studies of ovarian cancer risk and survival Editorial

The contribution of parent-to-offspring transmission of telomeres to the heritability of telomere length in humans

Leukocyte telomere length (LTL) is a heritable trait with two potential sources of heritability (h2): inherited variation in non-telomeric regions (e.g., SNPs that influence telomere maintenance) and variability in the lengths of telomeres in gametes that produce offspring zygotes (i.e., “direct” inheritance). Prior studies of LTL h2 have not attempted to disentangle these two sources. Here, we use a novel approach for detecting the direct inheritance of telomeres by studying the association between identity-by-descent (IBD) sharing at chromosome ends and phenotypic similarity in LTL. We measured genome-wide SNPs and LTL for a sample of 5,069 Bangladeshi adults with substantial relatedness. For each of the 7,254 relative pairs identified, we used SNPs near the telomeres to estimate the number of chromosome ends shared IBD, a proxy for the number of telomeres shared IBD (Tshared). We then estimated the association between Tshared and the squared pairwise difference in LTL ((ΔLTL)2) within various classes of relatives (siblings, avuncular, cousins, and distant), adjusting for overall genetic relatedness (ϕ). The association between Tshared and (ΔLTL)2 was inverse among all relative pair types. In a meta-analysis including all relative pairs (ϕ >0.05), the association between Tshared and (ΔLTL)2 (P=0.002) was stronger than the association between ϕ and (ΔLTL)2 (P=0.45). Our results provide strong evidence that telomere length (TL) in parental germ cells impacts TL in offspring cells and contributes to LTL h2 despite telomere “reprogramming” during embryonic development. Applying our method to larger studies will enable robust estimation of LTL h2 attributable to direction transmission.

Menstrual pain and risk of epithelial ovarian cancer: results from the Ovarian Cancer Association Consortium

Menstrual pain, a common gynecological condition, has been associated with increased risk of ovarian cancer in some, but not all studies. Furthermore, potential variations in the association between menstrual pain and ovarian cancer by histologic subtype have not been adequately evaluated due to lack of power. We assessed menstrual pain using either direct questions about having experienced menstrual pain, or indirect questions about menstrual pain as indication for use of hormones or medications. We used multivariate logistic regression to calculate the odds ratio (OR) for the association between severe menstrual pain and ovarian cancer, adjusting for potential confounders and multinomial logistic regression to calculate ORs for specific histologic subtypes. We observed no association between ovarian cancer and menstrual pain assessed by indirect questions. Among studies using direct question, severe pain was associated with a small but significant increase in overall risk of ovarian cancer (OR = 1.07, 95% CI: 1.01–1.13), after adjusting for endometriosis and other potential confounders. The association appeared to be more relevant for clear cell (OR = 1.48, 95% CI: 1.10–1.99) and serous borderline (OR = 1.31, 95% CI: 1.05–1.63) subtypes. In this large international pooled analysis of case‐control studies, we observed a small increase in risk of ovarian cancer for women reporting severe menstrual pain. While we observed an increased ovarian cancer risk with severe menstrual pain, the possibility of recall bias and undiagnosed endometriosis cannot be excluded. Future validation in prospective studies with detailed information on endometriosis is needed.

Telomere length and lung cancer mortality among heavy smokers

Background: Accumulating evidence suggests that short telomere length is associated with increased overall mortality, but the relationship with cancer mortality is less clear. We examined whether telomere length (global, and chromosome arm 5p- and 13q-specific) is associated with lung cancer mortality among cases from the β-Carotene and Retinol Efficacy Trial of heavy smokers. Methods: Telomere length was measured on average 6 years before diagnosis for 788 lung cancer cases. Adjusted Cox proportional hazards models of all-cause and lung cancer–specific mortality were assessed for lung cancer overall and by histotype. Results: Short telomere length was associated with increased mortality for small cell lung cancer (SCLC), particularly stage III/IV SCLC [HR and 95% confidence interval for shortest vs. longest telomere length tertile: 3.32 (1.78–6.21)]. Associations were strongest for those randomized to the active intervention and when telomere length was measured ≤5 years before diagnosis. All-cause mortality patterns were similar. Short chromosome 5p telomere length was suggestively associated with lung cancer mortality, but there was no association with chromosome 13q telomere length. Conclusions: Our large prospective study suggests that among heavy smokers who developed lung cancer, short prediagnosis telomere length is associated with increased risk of death from SCLC. Impact: This is the first study to examine telomere length and mortality in lung cancer cases by histotype. If the association between short telomere length and SCLC mortality is replicated, elucidation of mechanisms through which telomere length influences survival for this highly aggressive cancer may inform more effective use of telomere-targeted therapeutics. Cancer Epidemiol Biomarkers Prev; 27(7); 829–37. ©2018 AACR.

Abstract 4958: Prediagnostic peripheral blood DNA methylation and lung cancer survival

Epigenetic regulation plays a critical role in cell and tissue development and differentiation, is a known mechanism of carcinogenesis, and is altered by various exposures including cigarette smoking and age. Peripheral blood methylation represents a combination of these factors as well as blood cell type distributions that reflect underlying immunophenotypes. Hematopoiesis is programmed through epigenetic changes, and blood cell type-specific methylation markers can be leveraged to “fingerprint” cell type distributions. We examined associations between pre-diagnostic methylation markers in peripheral blood with overall lung cancer survival in very heavy smokers from the Beta Carotene and Retinol Efficacy Trial (CARET). CARET was a randomized, double-blinded, placebo-controlled chemoprevention trial of daily β-carotene and retinyl palmitate in smokers with ≥20 pack-years, and smokers who were occupationally exposed to asbestos. Methylation was successfully measured using the Illumina 850K EPIC BeadArray on average 5 years prior to diagnosis for 331 lung cancer cases, of whom 253 died during follow up (median survival 329 days). Cox proportional hazards regression models were used to examine the relationship between CpG-specific methylation and survival. Models were adjusted for age at blood draw, sex, race, enrollment year, placebo/active intervention, asbestos exposure, current/former smoking and time since quit, pack years, average number of cigarettes per day and histologic type, and were fit separately depending on the time between blood draw and lung cancer diagnosis: 0-3 years (n = 107), 3-5 years (n = 77), and 5+ years (n = 147). After adjusting for multiple comparisons by computing the false discovery rate (FDR) q-value, there were 1,028, 296, and 4 CpGs that were statistically significantly associated with survival (q ≤0.010) for samples collected 0-3 years, 3-5 years, and 5+ years before diagnosis, respectively. After controlling for blood cell type distributions, much larger numbers of CpGs were statistically significantly associated with survival: 10,481, 456, and 257, respectively. The top canonical pathways of CpGs identified in samples drawn 0-3 years prior to diagnosis included PTEN signaling (p = 1.1E-5) and PI3K signaling in B lymphoctyes (p = 3.7E-5). We observed that the number of methylated CpGs in peripheral blood that are associated with subsequent survival increases dramatically when measured closer to lung cancer diagnosis. As well, we observed that the number of methylated markers is increased by controlling for immunophenotype. Our study provides evidence that peripheral blood methylation markers measured many years prior to diagnosis may be associated with poor lung cancer survival, and that increasing changes in methylation over time may also be associated. This points to the critical role of the immune system, even prior to diagnosis, in influencing cancer outcomes. Citation Format: Jennifer A. Doherty, Xuan Zhang, Devin C. Koestler, Matt J. Barnett, Mark D. Thornquist, Gary E. Goodman, Carmen J. Marsit. Prediagnostic peripheral blood DNA methylation and lung cancer survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4958. doi:10.1158/1538-7445.AM2017-4958

Polycystic ovary syndrome, oligomenorrhea, and risk of ovarian cancer histotypes: Evidence from the Ovarian Cancer Association Consortium

Background: Polycystic ovary syndrome (PCOS), and one of its distinguishing characteristics, oligomenorrhea, have both been associated with ovarian cancer risk in some but not all studies. However, these associations have been rarely examined by ovarian cancer histotypes, which may explain the lack of clear associations reported in previous studies. Methods: We analyzed data from 14 case–control studies including 16,594 women with invasive ovarian cancer (n = 13,719) or borderline ovarian disease (n = 2,875) and 17,718 controls. Adjusted study-specific ORs were calculated using logistic regression and combined using random-effects meta-analysis. Pooled histotype-specific ORs were calculated using polytomous logistic regression. Results: Women reporting menstrual cycle length >35 days had decreased risk of invasive ovarian cancer compared with women reporting cycle length ≤35 days [OR = 0.70; 95% confidence interval (CI) = 0.58–0.84]. Decreased risk of invasive ovarian cancer was also observed among women who reported irregular menstrual cycles compared with women with regular cycles (OR = 0.83; 95% CI = 0.76–0.89). No significant association was observed between self-reported PCOS and invasive ovarian cancer risk (OR = 0.87; 95% CI = 0.65–1.15). There was a decreased risk of all individual invasive histotypes for women with menstrual cycle length >35 days, but no association with serous borderline tumors (Pheterogeneity = 0.006). Similarly, we observed decreased risks of most invasive histotypes among women with irregular cycles, but an increased risk of borderline serous and mucinous tumors (Pheterogeneity < 0.0001). Conclusions: Our results suggest that menstrual cycle characteristics influence ovarian cancer risk differentially based on histotype. Impact: These results highlight the importance of examining ovarian cancer risk factors associations by histologic subtype. Cancer Epidemiol Biomarkers Prev; 27(2); 174–82. ©2017 AACR.