Barnholtz‐Sloan, Jill S.

Combining DNA methylation markers with a swallowable device for sampling the distal esophagus effectively detects Barrett’s neoplasias.

Abstract BACKGROUND: Incidence of glioma varies significantly by sex, and most glioma histologies occur with greater incidence in males. Previous analyses have examined the impact of estrogen exposure as a risk factor for these tumors, but have found results of varying significance and low effect size. There may be differences in effect of previously discovered risk alleles that contribute to sex differences. METHODS: Using data collected for three previous glioma GWAS in European-ancestry populations (MD Anderson Cancer Center, the San Francisco Adult Glioma Study, and the Glioma International Case Control Study) we assessed sex-specific effects for 14 previously identified and 13 newly identified glioma risk SNPs (27 total) overall and for glioblastoma (GBM) and non-GBM tumors separately. There were 3,892 male cases (59% GBM), 4,522 male controls, 2,500 female cases (52% GBM) and 4,940 female controls. Sex-specific odds ratios (ORM and ORF), 95% confidence intervals (95% CI) and p values (pM and pF) were generated using stratified logistic regression models. Data from each study were analyzed separately and combined using inverse variance weighted meta-analysis. Results were considered statistically significant at p<6.2x10-4. RESULTS: In GBM, rs11979158 (7p11.2, pM=1.01x10-10, ORM=1.43 [95% CI: 1.28-1.59]; pF=3.43x10-3, ORF=1.22 [95% CI: 1.07-1.39]) and rs2562152 (16p13.3, pM=5.59x10-4, ORM=1.23 [95% CI: 1.09-1.39]; pF=1.22x10-1, ORF=1.12 [95% CI: 0.97-1.29]) had significant effect in males only. In non-GBM gliomas, rs12076373 (1q44, pM=3.56x10-7, ORM=1.41, 95% CI: 1.23-1.61; pF=1.76x10-2, ORF=1.20, 95% CI: 1.03-1.38), rs11979158 (7p11.2, pM=1.77x10-5, ORM=1.32 [95% CI: 1.16-1.49]; pF=2.73x10-1, ORF=1.08 [95% CI: 0.94-1.24]), and rs3751667 (16p13.3, pM=9.44x10-7, ORM=1.30 [95% CI: 1.17-1.44]; pF=5.18x10-2, ORF=1.13 [95% CI: 1.00-1.28]) had significant effect in males only. Effect size for rs55705857 (8q24.21) varied significantly by sex, with ORM=2.63 (95% CI: 2.24-3.09, pM=4.42x10-32), as compared to ORF=3.95 (95% CI: 3.28-4.76, pF=1.82x10-47). A sensitivity analysis was performed due to allele frequency heterogeneity by study and results did not change. CONCLUSIONS: Sex differences and other demographic differences in cancer susceptibility can provide important clues to etiology, and these differences can be leveraged for discovery in genetic association studies. Significant differences in effect size may suggest variation in genetic effect of risk alleles or in unidentified risk factors that vary in prevalence or effect by sex. There may also be differences in the distribution of molecular subtypes within each histology by sex. Further investigation using an agnostic approach may further elucidate the relationship between effect of risk alleles and sex. Citation Format: Quinn T. Ostrom, Ben Kinnersley, Margaret Wrensch, Jeanette E. Eckel-Passow, Georgina Armstrong, Terri Rice, Yanwen Chen, John Wiencke, Lucie McCoy, Helen Hansen, Christopher Amos, Jonine L. Bernstein, Elizabeth B. Claus, Dora Il'yasova, Christoffer Johansen, Daniel Lachance, Rose Lai, Ching C. Lau, Ryan T. Merrell, Sara H. Olson, Siegal Sadetzki, Joellen Schildkraut, Sanjay Shete, Richard S. Houlston, Robert B. Jenkins, Beatrice Melin, Melissa Bondy, Jill S. Barnholtz-Sloan. Estimating sex-specific effects of genetic loci associated with glioma risk [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 1315. doi:10.1158/1538-7445.AM2017-1315

Abstract Epithelial ovarian cancer (EOC) is a rare but deadly disease for which there is notably poorer survival in women of African Ancestry (AA) compared to women of European Ancestry (EA). Previous EA-based genome-wide association studies (GWAS) have identified 30 common, low penetrant EOC susceptibility alleles. Using the custom-designed 533,631 SNP Illumina OncoArray and imputation to ~12 million genetic variants in the 1000 Genomes Phase 3, we conducted a GWAS in 755 AA EOC cases, including 537 high-grade serous ovarian cancer (HGSOC) cases, and 1,235 AA controls from the Ovarian Cancer Association Consortium (OCAC). We identified novel susceptibility loci with suggestive evidence of association with EOC, based on a threshold of P<1x10-6, at three distinct loci including 10p15.1 (lead SNP rs4525119, intronic to AKR1C3, P=4.9 x 10-7, minor allele frequency [MAF]=0.33), 3p25.3 (lead SNP rs7643459, intronic to LOC101927394, P=8.4 x 10-7, MAF=0.36), and 4q13.3 (lead SNP rs4286604, 15 kb 3’ of UGT2A1, P=8.5x10-7, MAF=0.27). In analysis of HGSOC, we identified suggestive evidence of association at six distinct loci including 5q11.2 (lead SNP rs37792, 132 kb 5’ of FST, P=6.0x10-8, MAF=0.34), Xq27.2 (lead SNP rs57403204, 81 kb 3' of MAGEC1, P=1.7x10-7, MAF=0.06), 10p15.1 (lead SNP rs79079890, LOC105376360 intronic, P=3.0x10-7, MAF=0.03), 17p25.1 (lead SNP rs66459581, 5 kb 5’ of PRPSAP1, P=5.1x10-7, MAF=0.23), 15p12 (lead SNP rs116046250, GABRG3 intronic, P=8.7x10-7, MAF=0.05), and 4q21.21 (lead SNP rs192876988, 30 kb 3’ of GK2, P=9.2x10-7, MAF=0.05). These SNPs showed no evidence of association with risk in the OCAC EA GWAS including up to 23,543 EOC cases and 29,444 controls. Of the SNPs identified with suggestive evidence of association in our GWAS, two are located near genes known to regulate hormones and previously reported in relation to diseases of the ovary (AKR1C3 and FST), two have been linked to cancer (AKR1C3 and MAGEC1) and one represents testis-specific expression (GK2). Of the 30 SNPs identified previously in a EA EOC GWAS, we observed nominally significant associations (P<0.05) with consistent direction of effect for eight SNPs in AA women. Our investigation presents evidence of (1) variants for EOC shared among EA and AA women and (2) novel EOC risk loci of importance for AA women. Citation Format: Ani Manichaikul, Lauren C. Peres, Xin-Qun Wang, Kate Lawrenson, Sarah Abbott, Ann G. Schwartz, Anna H. Wu, Edward Peters, Patricia G. Moorman, Michele L. Cote, Melissa Bondy, Linda Kelemen, Ellen L. Goode, Jill Barnholtz-Sloan, Simon A. Gather, Andrew Berchuck, Jennifer A. Doherty, Paul Pharoah, Joellen Schildkraut. Identification of novel epithelial ovarian cancer loci in women of African ancestry from the Ovarian Cancer Association Consortium [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 1307. doi:10.1158/1538-7445.AM2017-1307

Abstract BACKGROUND: Glioma accounts for ~27% of all primary brain tumors and is responsible for ~13,000 cancer-related deaths in the US each year. Glioma tumors can be broadly classified into glioblastoma (GBM) and lower-grade non-GBM. Typically gliomas have a poor prognosis irrespective of medical care, with the most common form, GBM, having a five-year survival rate of only 5%. While genome-wide association studies (GWAS) have transformed our understanding of glioma susceptibility, individual studies have had limited power to identify risk loci. METHODS: We performed the largest glioma GWAS to date, comprising a meta-analysis of six existing GWAS (6,405 cases, 14,100 controls) as well as new GWAS from the Glioma International Case Control Consortium (GICC; 4,572 cases and 3,286 controls) and University of California, San Francisco (UCSF)-Mayo (1,519 cases, 804 controls), totaling 12,496 cases (6,191 classified as GBM, 5,819 as non-GBM) and 18,190 controls. RESULTS: We identified five new risk loci for GBM at 1p31.3 (rs12752552; near JAK1, P=2.04×10-9, odds ratio (OR)=1.22), 11q14.1 (rs11233250; P=9.95×10-10, OR=1.24), 16p13.3 (rs2562152; near MPG, P=1.93x10-8, OR=1.21), 16q12.1 (rs10852606; HEATR3, P=1.29×10-11, OR=1.18), 22q13.1 (rs2235573; P=1.76×10-10, OR=1.15) and eight for non-GBM at 1q32.1 (rs4252707; MDM4, P=3.34×10-9, OR=1.19), 1q44 (rs12076373; AKT3, P=2.63×10-10, OR=1.23), 2q33.3 (rs7572263; near IDH1, P=2.18×10-10, OR=1.20), 3p14.1 (rs11706832; LRIG1, P=7.66×10-9, OR=1.15), 10q24.33 (rs11598018; OBFC1, P=3.39×10-8, OR=1.14), 11q21 (rs7107785; P=3.87×10-10, OR=1.16), 14q12 (rs10131032; P=5.07x10-11, OR=1.33) and 16p13.3 (rs3751667; P=2.61×10-9, OR=1.18). Case-only analyses confirmed the specificity of 11q14.1, 16p13.3 and 22q13.1 associations for GBM and 1q44, 2q33.3, 3p14.1, 11q21 and 14q12 for non-GBM tumors. In the combined meta-analysis, among previously published glioma risk SNPs, those for all glioma at 17p13.1 (TP53), GBM at 5p15.33 (TERT), 7p11.2 (EGFR), 9p21.3 (CDKN2B-AS1) and 20q13.33 (RTEL1) and for non-GBM at 8q24.21 (CCDC26), 11q23.2, 11q23.3 (PHLDB1) and 15q24.2 (ETFA) showed even greater evidence for association. SNPs at 10q25.2 and 12q12.1 for non-GBM tumors retained genome-wide significance (i.e. P<5.0x10-8). Associations at the previously reported loci for GBM at 3q26.2 (near TERC) and 12q23.33 (POLR3B) did not retain statistical significance. CONCLUSIONS: Our findings substantiate genetic susceptibility to GBM and non-GBM glioma being highly distinct, consistent with their distinctive molecular profiles presumably resulting from different etiological pathways. Functional analyses should lead to further insights into the biological basis of the different glioma histologies. Such information can inform gene discovery initiatives and therefore have a measurable impact on the successful development of new therapeutic agents. Citation Format: Ben Kinnersley, Beatrice S. Melin, Jill S. Barnholtz-Sloan, Margaret R. Wrensch, Christoffer Johansen, Dora Il’yasova, Quinn Ostrom, and members of GICC, Karim Labreche, Jeanette E. Eckel-Passow, Paul A. Decker, Marianne Labussière, Ahmed Idbaih, Khe Hoang-Xuan, Anna-Luisa Di Stefano, Karima Mokhtari, Jean-Yves Delattre, Pilar Galan, Konstantinos Gousias, Johannes Schramm, Minouk J. Schoemaker, Sarah J. Fleming, Stefan Herms, Stefanie Heilmann, Marcus M. Nöthen, Heinz-Erich Wichmann, Stefan Schreiber, Anthony Swerdlow, Mark Lathrop, Matthias Simon, Marc Sanson, Preetha Rajaraman, Stephen Chanock, Martha Linet, Zhaoming Wang, Meredith Yeager, Rose K. Lai, Elizabeth B. Claus, Sara H. Olson, Robert B. Jenkins, Richard S. Houlston, Melissa L. Bondy. Genome-wide association study of glioma reveals specific differences in genetic susceptibility to glioblastoma and non-glioblastoma [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 1302. doi:10.1158/1538-7445.AM2017-1302

Abstract Esophageal adenocarcinoma is a deadly cancer with increasing incidence in the United States, but mechanisms underlying pathogenesis are still mostly elusive. In addressing this question, we assessed gene fusion landscapes by comprehensive RNA sequencing (RNAseq) of 55 pretreatment esophageal adenocarcinoma and 49 nonmalignant biopsy tissues from patients undergoing endoscopy for Barrett's esophagus. In this cohort, we identified 21 novel candidate esophageal adenocarcinoma–associated fusions occurring in 3.33% to 11.67% of esophageal adenocarcinomas. Two candidate fusions were selected for validation by PCR and Sanger sequencing in an independent set of pretreatment esophageal adenocarcinoma (N = 115) and nonmalignant (N = 183) biopsy tissues. In particular, we observed RPS6KB1–VMP1 gene fusion as a recurrent event occurring in approximately 10% of esophageal adenocarcinoma cases. Notably, esophageal adenocarcinoma cases harboring RPS6KB1–VMP1 fusions exhibited significantly poorer overall survival as compared with fusion-negative cases. Mechanistic investigations established that the RPS6KB1–VMP1 transcript coded for a fusion protein, which significantly enhanced the growth rate of nondysplastic Barrett's esophagus cells. Compared with the wild-type VMP1 protein, which mediates normal cellular autophagy, RPS6KB1–VMP1 fusion exhibited aberrant subcellular localization and was relatively ineffective in triggering autophagy. Overall, our findings identified RPS6KB1–VMP1 as a genetic fusion that promotes esophageal adenocarcinoma by modulating autophagy-related processes, offering new insights into the molecular pathogenesis of esophageal adenocarcinomas. Cancer Res; 76(19); 5628–33. ©2016 AACR.

Abstract Background: Numerous epidemiologic studies have examined the association between aspirin (ASA), non-steroid anti-inflammatory drugs (NSAIDs) and the development of glioma, but the results have been inconsistent. The goal of this study was to evaluate the relationship between the intake of these drugs and glioma risk in a large, international case-control study. Methods: Between 2010 and 2015, the Glioma International Case-Control Study (GICC) recruited newly diagnosed glioma cases and matched controls in 14 different sites across five countries. Each subject was interviewed using a standardized questionnaire to obtain NSAIDs and ASA use. We examined the associations between ever use (at least > 6 months), duration of drug use and glioma histology. Ever use data on 4533 glioma cases and 4171 controls was combined using maximum likelihood estimation/restricted maximum likelihood meta-analysis methods. Furthermore, based on a priori hypotheses, we performed subgroup analyses based on gender and glioma histological grades. Results: Use of ASA for > 6 months was associated with a 33% lower glioma risk compared to those who never took it (adjusted Meta-OR 0.67, 95% CI 0.54-0.83). Duration of intake showed a significant trend test (p < 0.0001), with ORs became lower for increasing number of years of ASA use. In subgroup analyses, intake of ASA was significantly associated with glioma risk in both men and women (adjusted Meta-OR = 0.65, 95% CI 0.51-0.84 for men; adjusted Meta-OR = 0.74, 95% CI 0.58-0.93 for women). ASA intake was protective for grade IV glioma (glioblastoma) and grade II/III glioma (adjusted meta-OR 0.63, 95% CI 0.5-0.8 for glioblastoma; adjusted meta-OR 0.67, 95% CI 0.50 - 0.89 for grade II/III glioma). For NSAIDs intake, ever use > 6 months was not associated with glioma risk (adjusted meta-OR 0.87, 95% CI 0.71-1.07). However, NSAIDs use was protective for women (adjusted meta-OR 0.72, 95% CI 0.55-0.93) in subgroup analyses but not for men (adjusted meta-OR 1.03; 95% CI 0.86-1.23). The interaction between gender, NSAIDs and glioma risk was significant (p-value 0.0076).. Sensitivity analyses excluding those who took ASA or NSAIDs within the past 12 months for headache, and the removal of proxy respondents did not change our results. Conclusion: ASA was associated with a significant protective effect for glioma, but NSAIDs were only associated with reduced glioma risk in women. Given the possibility of recall bias in case-control studies of brain tumors, we may verify dosage and duration of drug intake in those countries with electronic pharmacy records within the GICC. Citation Format: Rose K. Lai, Renke Zhou, E. Susan Amirian, Christoffer Johansen, Michael E. Scheurer, Georgina N. Armstrong, Ching C. Lau, Elizabeth B. Claus, Jill S. Barnholtz-Sloan, Dora Il’yasova, Joellen Schildkraut, Francis Ali-Osman, Siegal Sadetzki, Richard Houlston, Robert B. Jenkins, Daniel Lachance, Sara H. Olson, Jonine L. Bernstein, Ryan T. Merrell, Margaret R. Wrensch, Faith G. Davis, Sanjay Shete, Christopher I. Amos, Beatrice S. Melin, Melissa Bondy. Aspirin, non-steroidal anti-inflammatory drugs (NSAIDs) and the risk of glioma: Results from the Glioma International Case Control Study. [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 3446.

AbstractBackgroundFamilial aggregation and segregation analysis studies have provided evidence of a genetic basis for esophageal adenocarcinoma (EAC) and its premalignant precursor, Barrett's esophagus (BE). We aim to demonstrate the utility of linkage analysis to identify the genomic regions that might contain the genetic variants that predispose individuals to this complex trait (BE and EAC).MethodsWe genotyped 144 individuals in 42 multiplex pedigrees chosen from 1000 singly ascertained BE/EAC pedigrees, and performed both model‐based and model‐free linkage analyses, using S.A.G.E. and other software. Segregation models were fitted, from the data on both the 42 pedigrees and the 1000 pedigrees, to determine parameters for performing model‐based linkage analysis. Model‐based and model‐free linkage analyses were conducted in two sets of pedigrees: the 42 pedigrees and a subset of 18 pedigrees with female affected members that are expected to be more genetically homogeneous. Genome‐wide associations were also tested in these families.ResultsLinkage analyses on the 42 pedigrees identified several regions consistently suggestive of linkage by different linkage analysis methods on chromosomes 2q31, 12q23, and 4p14. A linkage on 15q26 is the only consistent linkage region identified in the 18 female‐affected pedigrees, in which the linkage signal is higher than in the 42 pedigrees. Other tentative linkage signals are also reported.ConclusionOur linkage study of BE/EAC pedigrees identified linkage regions on chromosomes 2, 4, 12, and 15, with some reported associations located within our linkage peaks. Our linkage results can help prioritize association tests to delineate the genetic determinants underlying susceptibility to BE and EAC.

AbstractVaricella zoster virus (VZV) is a neurotropic α‐herpesvirus that causes chickenpox and establishes life‐long latency in the cranial nerve and dorsal root ganglia of the host. To date, VZV is the only virus consistently reported to have an inverse association with glioma. The Glioma International Case‐Control Study (GICC) is a large, multisite consortium with data on 4533 cases and 4171 controls collected across five countries. Here, we utilized the GICC data to confirm the previously reported associations between history of chickenpox and glioma risk in one of the largest studies to date on this topic. Using two‐stage random‐effects restricted maximum likelihood modeling, we found that a positive history of chickenpox was associated with a 21% lower glioma risk, adjusting for age and sex (95% confidence intervals (CI): 0.65–0.96). Furthermore, the protective effect of chickenpox was stronger for high‐grade gliomas. Our study provides additional evidence that the observed protective effect of chickenpox against glioma is unlikely to be coincidental. Future studies, including meta‐analyses of the literature and investigations of the potential biological mechanism, are warranted.