Karyadi, Danielle M.

Abstract African American Hereditary Prostate Cancer Study (AAHPC) was developed as a national collaboration to explore the role of genetics in the causation of hereditary prostate cancer (HPC) in African American (AA) men. AAHPC is in partnership with the International Consortium for Prostate Cancer Genetics (ICPCG), which conducts collaborative studies of HPC genetics in multiplex families. As part of an ICPCG sequencing study of 539 affected individuals from 366 HPC pedigrees, we performed whole exome sequencing in 21 ICPCG AA families, of which there were 14 AAHPC affected men from 11 pedigrees. The combined ICPCG AA cohort consisted of N=26 affected members. Post-variant calling quality control (QC) was implemented using Golden Helix SVS 8 software with filters set for removal of variants with Read Depth < 10, Quality Score < 20, Quality Score: Read Depth Ratio < 0.5, Call Rate < 0.75. Variants were additionally filtered by MAF based on the NHLBI ESP650051-V2 exomes variant frequencies for the AA population using a MAF threshold of 5%. Following QC, 176/299 SNVs and 20/39 INDELs remained for further analysis. In these analyses, we focused on 13 known cancer genes (MSR1, AR, BRCA1, BRCA2, BTNL2, EPHB2, CDH1, RNASEL, ELAC2, HOXB13, CHEK2, TP53 and NBN). Three sequenced families had > 1 affected members sequenced (2 or 3 per family) and the remaining 18 families had one member sequenced. Under the dominant model, our preliminary results show that no rare variants in the 13 candidate genes were found in 3/3 affecteds in two families. Rare SNVs in seven candidate genes (AR, CDH1, ELAC2, HOXB13, RNASEL, BRCA2 and EPHB2) were found in 2/3 affecteds for two families and 2/2 affecteds in one family. Several of the remaining 18 affected men (1 sequenced per pedigree) shared the same rare SNV in these candidate genes. For INDELs, rare variants in three candidate genes were found in pedigrees with ≥ 2 affecteds. Several of the remaining 18 affected men (one sequenced per pedigree) shared the same rare INDEL. Additional QC is underway to validate these variants and bioinformatic analyses are being used to predict effects of the variants in an effort to unravel the complex genetic heterogeneity of HPC in AA. Citation Format: Cheryl D. Cropp, Shannon K. McDonnell, Sumit Middha, Melissa DeRycke, Danielle M. Karyadi, Daniel Schaid, Stephen N. Thibodeau, William B. Isaacs, Elaine A. Ostrander, Janet Stanford, Kathleen A. Cooney, Joan E. Bailey-Wilson, John D. Carpten. Rare variant discovery in known cancer genes from whole-exome sequencingof African American hereditary prostate cancer families. [abstract]. In: Proceedings of the Eighth AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 13-16, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2016;25(3 Suppl):Abstract nr B40.

Abstract Prostate cancer (PCa) will impact one in six American men and many low-risk men endure therapy, while other men die of PCa. Optimal treatment selection depends on distinguishing indolent tumors from those that will cause prostate cancer specific mortality (PCSM). To date, sequencing of prostate tumor DNA has highlighted the fact that prostate tumors develop differently than other cancers. Instead of recurrent protein-altering mutations, many prostate tumors harbor “closed chain” structural rearrangements that may mediate tumor evolution. However, we do not yet understand which somatic mutations are involved in aggressive disease and PCSM. To address this crucial question, we are using whole genome sequencing to pinpoint somatic genetic features in tumor/normal paired samples from four PCSM and six non-PCSM patients with treatment-naïve, Gleason 8+ tumors. Tumor and normal DNA were sequenced to a mean coverage of 95.3X and 48.3X, respectively. Tumor DNA purity ranged from 49%-79% and tumor ploidy ranged from 1.96 to 2.22. To define the genomic landscape of aggressive PCa, we will compare our findings with published studies and genotype high-priority candidates in at least 50 additional low- and high-grade tumors. We will also compare somatic mutations in PCSM versus non-PCSM cases and use network analysis to identify pathways that may be involved in progression and metastasis. Finally, we will characterize the clonal evolution of PCa tumors using deep digital sequencing to distinguish mutations that were present in the original tumor clone from subclonal mutations that arose after oncogenesis. In this way, we aim to identify potential oncogenic drivers and candidate mediators of progression and metastasis. Ultimately, we aim to 1) Uncover somatic mutations that are specific to aggressive tumors 2) Determine whether PCSM tumors have unique genetic features, and 3) Understand the role of clonal evolution in oncogenesis and progression. As more tumors are sequenced, this approach may yield valuable markers for diagnosis, prognosis and treatment selection. Note: This abstract was not presented at the meeting. Citation Format: Brennan J. Decker, Danielle M. Karyadi, Eric Karlins, Brian W. Davis, Lori S. Tillmans, Stephen N. Thibodeau, Elaine A. Ostrander. Whole genome sequencing of high-grade treatment-naïve prostate tumors. [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 1536. doi:10.1158/1538-7445.AM2014-1536

Abstract A recent genome-wide association study found that genetic variants on chromosomes 3, 6, 7, 10, 11, 19 and X were associated with prostate cancer risk. We evaluated the most significant single-nucleotide polymorphisms (SNP) in these loci using a worldwide consortium of 13 groups (PRACTICAL). Blood DNA from 7,370 prostate cancer cases and 5,742 male controls was analyzed by genotyping assays. Odds ratios (OR) associated with each genotype were estimated using unconditional logistic regression. Six of the seven SNPs showed clear evidence of association with prostate cancer (P = 0.0007-P = 10−17). For each of these six SNPs, the estimated per-allele OR was similar to those previously reported and ranged from 1.12 to 1.29. One SNP on 3p12 (rs2660753) showed a weaker association than previously reported [per-allele OR, 1.08 (95% confidence interval, 1.00-1.16; P = 0.06) versus 1.18 (95% confidence interval, 1.06-1.31)]. The combined risks associated with each pair of SNPs were consistent with a multiplicative risk model. Under this model, and in combination with previously reported SNPs on 8q and 17q, these loci explain 16% of the familial risk of the disease, and men in the top 10% of the risk distribution have a 2.1-fold increased risk relative to general population rates. This study provides strong confirmation of these susceptibility loci in multiple populations and shows that they make an important contribution to prostate cancer risk prediction. (Cancer Epidemiol Biomarkers Prev 2008;17(8):2052–61)

Abstract Prostate cancer is a leading and increasingly prevalent cause of cancer death in men. Whereas family history of disease is one of the strongest prostate cancer risk factors and suggests a hereditary component, the predisposing genetic factors remain unknown. We first showed that KLF6 is a tumor suppressor somatically inactivated in prostate cancer and since then, its functional loss has been further established in prostate cancer cell lines and other human cancers. Wild-type KLF6, but not patient-derived mutants, suppresses cell growth through p53-independent transactivation of p21. Here we show that a germline KLF6 single nucleotide polymorphism, confirmed in a tri-institutional study of 3,411 men, is significantly associated with an increased relative risk of prostate cancer in men, regardless of family history of disease. This prostate cancer–associated allele generates a novel functional SRp40 DNA binding site and increases transcription of three alternatively spliced KLF6 isoforms. The KLF6 variant proteins KLF6-SV1 and KLF6-SV2 are mislocalized to the cytoplasm, antagonize wtKLF6 function, leading to decreased p21 expression and increased cell growth, and are up-regulated in tumor versus normal prostatic tissue. Thus, these results are the first to identify a novel mechanism of self-encoded tumor suppressor gene inactivation and link a relatively common single nucleotide polymorphism to both regulation of alternative splicing and an increased risk in a major human cancer.