Lisa Chu

Two susceptibility loci identified for prostate cancer aggressiveness

Most men diagnosed with prostate cancer will experience indolent disease; hence discovering genetic variants that distinguish aggressive from non-aggressive prostate cancer is of critical clinical importance for disease prevention and treatment. In a multistage, case-only genome-wide association study of 12,518 prostate cancer cases, we identify two loci associated with Gleason score, a pathological measure of disease aggressiveness: rs35148638 at 5q14.3 (RASA1, P=6.49×10-9) and rs78943174 at 3q26.31 (NAALADL2, P=4.18×10-8). In a stratified case-control analysis, the SNP at 5q14.3 appears specific for aggressive prostate cancer (P=8.85×10-5) with no association for non-aggressive prostate cancer compared to controls (P=0.57). The proximity of these loci to genes involved in vascular disease suggests potential biological mechanisms worthy of further investigation.

Integration of multiethnic fine-mapping and genomic annotation to prioritize candidate functional SNPs at prostate cancer susceptibility regions

Interpretation of biological mechanisms underlying genetic risk associations for prostate cancer is complicated by the relatively large number of risk variants (n = 100) and the thousands of surrogate SNPs in linkage disequilibrium. Here, we combined three distinct approaches: multiethnic fine-mapping, putative functional annotation (based upon epigenetic data and genome-encoded features), and expression quantitative trait loci (eQTL) analyses, in an attempt to reduce this complexity. We examined 67 risk regions using genotyping and imputation-based fine-mapping in populations of European (cases/controls: 8600/6946), African (cases/controls: 5327/5136), Japanese (cases/controls: 2563/4391) and Latino (cases/controls: 1034/1046) ancestry. Markers at 55 regions passed a region-specific significance threshold (P-value cutoff range: 3.9 × 10(-4)-5.6 × 10(-3)) and in 30 regions we identified markers that were more significantly associated with risk than the previously reported variants in the multiethnic sample. Novel secondary signals (P < 5.0 × 10(-6)) were also detected in two regions (rs13062436/3q21 and rs17181170/3p12). Among 666 variants in the 55 regions with P-values within one order of magnitude of the most-associated marker, 193 variants (29%) in 48 regions overlapped with epigenetic or other putative functional marks. In 11 of the 55 regions, cis-eQTLs were detected with nearby genes. For 12 of the 55 regions (22%), the most significant region-specific, prostate-cancer associated variant represented the strongest candidate functional variant based on our annotations; the number of regions increased to 20 (36%) and 27 (49%) when examining the 2 and 3 most significantly associated variants in each region, respectively. These results have prioritized subsets of candidate variants for downstream functional evaluation.

Prostate cancer susceptibility in men of African ancestry at 8q24

The 8q24 region harbors multiple risk variants for distinct cancers, including >8 for prostate cancer. In this study, we conducted fine mapping of the 8q24 risk region (127.8-128.8Mb) in search of novel associations with common and rare variation in 4853 prostate cancer case patients and 4678 control subjects of African ancestry. All statistical tests were two-sided. We identified three independent associations at P values of less than 5.00×10(-8), all of which were replicated in studies from Ghana and Uganda (combined sample = 5869 case patients, 5615 control subjects; rs114798100: risk allele frequency [RAF] = 0.04, per-allele odds ratio [OR] = 2.31, 95% confidence interval [CI] = 2.04 to 2.61, P = 2.38×10(-40); rs72725879: RAF = 0.33, OR = 1.37, 95% CI = 1.30 to 1.45, P = 3.04×10(-27); and rs111906932: RAF = 0.03, OR = 1.79, 95% CI = 1.53 to 2.08, P = 1.39×10(-13)). Risk variants rs114798100 and rs111906923 are only found in men of African ancestry, with rs111906923 representing a novel association signal. The three variants are located within or near a number of prostate cancer-associated long noncoding RNAs (lncRNAs), including PRNCR1, PCAT1, and PCAT2. These findings highlight ancestry-specific risk variation and implicate prostate-specific lncRNAs at the 8q24 prostate cancer susceptibility region.

Sex steroid hormone metabolism in relation to risk of aggressive prostate cancer.

Background: The combined action of androgens and estrogens—specifically their balance—may play a role in prostate carcinogenesis, but existing evidence is sparse and inconsistent. We investigated associations between serum sex steroid hormones, including estrogen metabolites, and risk of aggressive prostate cancer. Methods: In a case–control study nested within the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial cohort, we measured serum estrone, estradiol, and 13 estrogen metabolites, in the 2-, 4-, or 16-hydroxylation pathways, using an LC/MS-MS assay. Cases (n = 195) were non-Hispanic white men ages 55 to 70 years when diagnosed with aggressive prostate cancer (stage III or IV and/or Gleason ≥7). Controls (n = 195) were non-Hispanic white men without prostate cancer who were frequency matched to cases by age and year at blood draw, and time since baseline screen. Only men with serum testosterone and sex hormone-binding globulin measured previously were eligible. Logistic regression models were used to estimate ORs and 95% confidence intervals (95% CI). Results: Risk of aggressive prostate cancer was strongly inversely associated with estradiol:testosterone ratio (OR4th quartile vs. 1st = 0.27; 95% CI, 0.12–0.59, Ptrend = 0.003) and positively associated with 2:16α-hydroxyestrone ratio (OR4th quartile vs. 1st = 2.44; 95% CI, 1.34–4.45, Ptrend = 0.001). Individual estrogen metabolites were unrelated to risk. Conclusions: Our findings suggest that sex steroid hormones, specifically the estrogen-androgen balance, may be important in the development of aggressive prostate cancer. Impact: Improved understanding of the hormonal etiology of prostate cancer is critical for prevention and therapeutic interventions. Cancer Epidemiol Biomarkers Prev; 23(11); 2374–82. ©2014 AACR.

Finasteride concentrations and prostate cancer risk: results from the Prostate Cancer Prevention Trial.

Objective In the Prostate Cancer Prevention Trial (PCPT), finasteride reduced the risk of prostate cancer by 25%, even though high-grade prostate cancer was more common in the finasteride group. However, it remains to be determined whether finasteride concentrations may affect prostate cancer risk. In this study, we examined the association between serum finasteride concentrations and the risk of prostate cancer in the treatment arm of the PCPT and determined factors involved in modifying drug concentrations. Methods Data for this nested case-control study are from the PCPT. Cases were drawn from men with biopsy-proven prostate cancer and matched controls. Finasteride concentrations were measured using a liquid chromatography-mass spectrometry validated assay. The association of serum finasteride concentrations with prostate cancer risk was determined by logistic regression. We also examine whether polymorphisms in the enzyme target and metabolism genes of finasteride are related to drug concentrations using linear regression. Results and Conclusions Among men with detectable finasteride concentrations, there was no association between finasteride concentrations and prostate cancer risk, low-grade or high-grade, when finasteride concentration was analyzed as a continuous variable or categorized by cutoff points. Since there was no concentration-dependent effect on prostate cancer, any exposure to finasteride intake may reduce prostate cancer risk. Of the twenty-seven SNPs assessed in the enzyme target and metabolism pathway, five SNPs in two genes, CYP3A4 (rs2242480; rs4646437; rs4986910), and CYP3A5 (rs15524; rs776746) were significantly associated with modifying finasteride concentrations. These results suggest that finasteride exposure may reduce prostate cancer risk and finasteride concentrations are affected by genetic variations in genes responsible for altering its metabolism pathway. Trial Registration ClinicalTrials.gov NCT00288106

Whole-exome sequencing of over 4100 men of African ancestry and prostate cancer risk

Prostate cancer is the most common non-skin cancer in males, with a ∼1.5-2-fold higher incidence in African American men when compared with whites. Epidemiologic evidence supports a large heritable contribution to prostate cancer, with over 100 susceptibility loci identified to date that can explain ∼33% of the familial risk. To explore the contribution of both rare and common variation in coding regions to prostate cancer risk, we sequenced the exomes of 2165 prostate cancer cases and 2034 controls of African ancestry at a mean coverage of 10.1×. We identified 395 220 coding variants down to 0.05% frequency [57% non-synonymous (NS), 42% synonymous and 1% gain or loss of stop codon or splice site variant] in 16 751 genes with the strongest associations observed in SPARCL1 on 4q22.1 (rs13051, Ala49Asp, OR = 0.78, P = 1.8 × 10(-6)) and PTPRR on 12q15 (rs73341069, Val239Ile, OR = 1.62, P = 2.5 × 10(-5)). In gene-level testing, the two most significant genes were C1orf100 (P = 2.2 × 10(-4)) and GORAB (P = 2.3 × 10(-4)). We did not observe exome-wide significant associations (after correcting for multiple hypothesis testing) in single variant or gene-level testing in the overall case-control or case-case analyses of disease aggressiveness. In this first whole-exome sequencing study of prostate cancer, our findings do not provide strong support for the hypothesis that NS coding variants down to 0.5-1.0% frequency have large effects on prostate cancer risk in men of African ancestry. Higher-coverage sequencing efforts in larger samples will be needed to study rarer variants with smaller effect sizes associated with prostate cancer risk.

Methodological Considerations in Estimation of Phenotype Heritability Using Genome- Wide SNP Data, Illustrated by an Analysis of the Heritability of Height in a Large Sample of African Ancestry Adults

Height has an extremely polygenic pattern of inheritance. Genome-wide association studies (GWAS) have revealed hundreds of common variants that are associated with human height at genome-wide levels of significance. However, only a small fraction of phenotypic variation can be explained by the aggregate of these common variants. In a large study of African-American men and women (n = 14,419), we genotyped and analyzed 966,578 autosomal SNPs across the entire genome using a linear mixed model variance components approach implemented in the program GCTA (Yang et al Nat Genet 2010), and estimated an additive heritability of 44.7% (se: 3.7%) for this phenotype in a sample of evidently unrelated individuals. While this estimated value is similar to that given by Yang et al in their analyses, we remain concerned about two related issues: (1) whether in the complete absence of hidden relatedness, variance components methods have adequate power to estimate heritability when a very large number of SNPs are used in the analysis; and (2) whether estimation of heritability may be biased, in real studies, by low levels of residual hidden relatedness. We addressed the first question in a semi-analytic fashion by directly simulating the distribution of the score statistic for a test of zero heritability with and without low levels of relatedness. The second question was addressed by a very careful comparison of the behavior of estimated heritability for both observed (self-reported) height and simulated phenotypes compared to imputation R2 as a function of the number of SNPs used in the analysis. These simulations help to address the important question about whether todays GWAS SNPs will remain useful for imputing causal variants that are discovered using very large sample sizes in future studies of height, or whether the causal variants themselves will need to be genotyped de novo in order to build a prediction model that ultimately captures a large fraction of the variability of height, and by implication other complex phenotypes. Our overall conclusions are that when study sizes are quite large (5,000 or so) the additive heritability estimate for height is not apparently biased upwards using the linear mixed model; however there is evidence in our simulation that a very large number of causal variants (many thousands) each with very small effect on phenotypic variance will need to be discovered to fill the gap between the heritability explained by known versus unknown causal variants. We conclude that todays GWAS data will remain useful in the future for causal variant prediction, but that finding the causal variants that need to be predicted may be extremely laborious.

Abstract 5066: Generalizability of established prostate cancer risk variants in men of African ancestry

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CAnnBackground: Genome-wide association studies have identified more than eighty risk variants for prostate cancer, mainly in European or Asian populations. The generalizability of these variants in other racial/ethnic populations needs to be understood before the loci can be utilized widely in risk modeling.nnMethods: We examined 82 previously reported risk variants in 5,096 prostate cancer cases and 4,972 controls of African ancestry. Association testing was performed using logistic regression adjusted for age, study and global ancestry. Cumulative effects were assessed through a multi-SNP genetic risk score.nnResults: Among the 82 known risk alleles, 68 (83%) were positively associated with prostate cancer risk in men of African ancestry and 30 (37%) were minimally replicated at p<0.05, with the most statistically significant variants being rs6983561 (p=1.1×10-16) and rs13254738 (p=1.8×10-15) at 8q24, as well as rs10896449 at 11q13 (p=5.5×10-7). With ≥80% statistical power, 27 variants failed to replicate at p<0.05. An aggregate score comprised of 79 unlinked alleles was strongly and equally associated with overall prostate cancer risk (per-allele odds ratio (OR)=1.06; p=1.2×10-47) and aggressive prostate cancer risk (OR=1.06; p=1.2×10-22).nnConclusions: The consistent directions of effect for the vast majority of variants in men of African ancestry indicate common functional alleles that are shared across populations. Some variants that failed to replicate may not be the best markers of prostate cancer risk for men of African ancestry, and thus further exploration of these loci through sequencing and fine-mapping is needed.nnCitation Format: Ying Han, Lisa B. Signorello, Sara S. Strom, Rick A. Kittles, Benjamin A. Rybicki, Janet L. Stanford, Phyllis J. Goodman, Sonja I. Berndt, John Carpten, Graham Casey, Lisa Chu, David V. Conti, Kristin A. Rand, Ryan Diver, Anselm JM Hennis, Esther M. John, Adam S. Kibel, Eric A. Klein, Suzanne Kolb, Loic Le Marchand, M Cristina Leske, Adam B. Murphy, Christine Neslund-Dudas, Jong Y. Park, Curtis A. Pettaway, Timothy R. Rebbeck, Susan M. Gapstur, Siqun Lilly Zheng, Suh-Yuh Wu, John S. Witte, Jianfeng Xu, William B. Isaacs, Sue A. Ingles, Ann W. Hsing, The PRACTICAL Consortium, The ELLIPSE GAME-ON Consortium, Douglas F. Easton, Rosalind A. Eeles, Fredrick R. Schumacher, Stephen J. Chanock, Barbara Nemesure, William J. Blot, Daniel O. Stram, Brian E. Henderson, Christopher A. Haiman. Generalizability of established prostate cancer risk variants in men of African ancestry. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5066. doi:10.1158/1538-7445.AM2014-5066

Abstract 2552: A genome-wide association study of prostate cancer in West African men.

Age-adjusted mortality rates for prostate cancer are higher for Africa compared with North America or Western Europe. In addition, African American men are noted to have higher age-adjusted incidence rates of this malignancy than European American men. Coupled with the fact that West Africa is the principal ancestral region of African-American men has led to the hypothesis that there may exist distinct ancestral genetic profiles which mediate prostate cancer risk. In addition, advantages of conducting a genome-wide association study (GWAS) of prostate cancer in African men include a more discrete linkage disequilibrium (LD) structure, a higher number of private single nucleotide polymorphisms (SNPs), the predominance of symptomatic disease, and assessment of unique exposures. The Ghana Prostate Study was conducted collaboratively involving the US National Cancer Institute (NCI) and the University of Ghana during 2006-2012. The NCI Cancer Genomics Research Laboratory genotyped 494 prostate cancer cases and 498 population controls using the Illumina HumanOmni5-Quad BeadChip. Associations were assessed using multivariate logistic regression adjusted for age and genetic ancestry. We sought to validate the 30 most promising SNP associations with prostate cancer through the African American Prostate Cancer GWAS Consortium. A novel locus at 10p14 for prostate cancer risk was the strongest signal detected, and the 8 SNPs at this locus were in LD. This locus is located 360 kb 5’ of GATA3 and the 8 SNPs reside within an intron of LincRNA gene RP11-543F8.2. Analysis of African 1000 Genomes Project data did not indicate LD between 10p14 SNPs and splice or exonic SNPs of this gene, while HaploReg found no significant enrichment of enhancer elements. None of the most promising 30 SNPs replicated in the African American Prostate Cancer GWAS Consortium. This may be due to chance or differences in population genetics, environment, and/or proportion of symptomatic disease. Further genetic studies of prostate cancer in African men are needed to validate the 10p14 susceptibility locus. Citation Format: Michael B. Cook, Zhaoming Wang, Edward D. Yeboah, Andrew A. Adjei, Yao Tettey, Richard B. Biritwum, Evelyn Tay, Ann Truelove, Shelley Niwa, Lisa Chu, Meredith Yeager, Amy Hutchinson, Kai Yu, Christopher A. Haiman, African American Prostate Cancer GWAS Consortium, Robert N. Hoover, Ann Hsing, Stephen J. Chanock. A genome-wide association study of prostate cancer in West African men. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2552. doi:10.1158/1538-7445.AM2013-2552