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Emami NC, Cavazos TB, Rashkin SR, Cario CL, Graff RE, Tai CG, Mefford JA, Kachuri L, Wan E, Wong S, Aaronson D, Presti J, Habel LA, Shan J, Ranatunga DK, Chao CR, Ghai NR, Jorgenson E, Sakoda LC, Kvale MN, Kwok PY, Schaefer C, Risch N, Hoffmann TJ, Van Den Eeden SK, Witte JS. A Large-Scale Association Study Detects Novel Rare Variants, Risk Genes, Functional Elements, and Polygenic Architecture of Prostate Cancer Susceptibility. Cancer Res 2021; 81:1695-1703. [PMID: 33293427 PMCID: PMC8137514 DOI: 10.1158/0008-5472.can-20-2635] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/27/2020] [Accepted: 12/02/2020] [Indexed: 11/16/2022]
Abstract
To identify rare variants associated with prostate cancer susceptibility and better characterize the mechanisms and cumulative disease risk associated with common risk variants, we conducted an integrated study of prostate cancer genetic etiology in two cohorts using custom genotyping microarrays, large imputation reference panels, and functional annotation approaches. Specifically, 11,984 men (6,196 prostate cancer cases and 5,788 controls) of European ancestry from Northern California Kaiser Permanente were genotyped and meta-analyzed with 196,269 men of European ancestry (7,917 prostate cancer cases and 188,352 controls) from the UK Biobank. Three novel loci, including two rare variants (European ancestry minor allele frequency < 0.01, at 3p21.31 and 8p12), were significant genome wide in a meta-analysis. Gene-based rare variant tests implicated a known prostate cancer gene (HOXB13), as well as a novel candidate gene (ILDR1), which encodes a receptor highly expressed in prostate tissue and is related to the B7/CD28 family of T-cell immune checkpoint markers. Haplotypic patterns of long-range linkage disequilibrium were observed for rare genetic variants at HOXB13 and other loci, reflecting their evolutionary history. In addition, a polygenic risk score (PRS) of 188 prostate cancer variants was strongly associated with risk (90th vs. 40th-60th percentile OR = 2.62, P = 2.55 × 10-191). Many of the 188 variants exhibited functional signatures of gene expression regulation or transcription factor binding, including a 6-fold difference in log-probability of androgen receptor binding at the variant rs2680708 (17q22). Rare variant and PRS associations, with concomitant functional interpretation of risk mechanisms, can help clarify the full genetic architecture of prostate cancer and other complex traits. SIGNIFICANCE: This study maps the biological relationships between diverse risk factors for prostate cancer, integrating different functional datasets to interpret and model genome-wide data from over 200,000 men with and without prostate cancer.See related commentary by Lachance, p. 1637.
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Affiliation(s)
- Nima C Emami
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Taylor B Cavazos
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
| | - Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Clinton L Cario
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Caroline G Tai
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Joel A Mefford
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, California
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Eunice Wan
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Simon Wong
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - David Aaronson
- Department of Urology, Kaiser Oakland Medical Center, Oakland, California
| | - Joseph Presti
- Department of Urology, Kaiser Oakland Medical Center, Oakland, California
| | - Laurel A Habel
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Jun Shan
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Dilrini K Ranatunga
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Chun R Chao
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California
| | - Nirupa R Ghai
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Mark N Kvale
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Pui-Yan Kwok
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Catherine Schaefer
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Neil Risch
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
- Division of Research, Kaiser Permanente Northern California, Oakland, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Thomas J Hoffmann
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Stephen K Van Den Eeden
- Division of Research, Kaiser Permanente Northern California, Oakland, California
- Department of Urology, University of California San Francisco, San Francisco, California
| | - John S Witte
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California.
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
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Association of imputed prostate cancer transcriptome with disease risk reveals novel mechanisms. Nat Commun 2019; 10:3107. [PMID: 31308362 PMCID: PMC6629701 DOI: 10.1038/s41467-019-10808-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/04/2019] [Indexed: 12/16/2022] Open
Abstract
Here we train cis-regulatory models of prostate tissue gene expression and impute expression transcriptome-wide for 233,955 European ancestry men (14,616 prostate cancer (PrCa) cases, 219,339 controls) from two large cohorts. Among 12,014 genes evaluated in the UK Biobank, we identify 38 associated with PrCa, many replicating in the Kaiser Permanente RPGEH. We report the association of elevated TMPRSS2 expression with increased PrCa risk (independent of a previously-reported risk variant) and with increased tumoral expression of the TMPRSS2:ERG fusion-oncogene in The Cancer Genome Atlas, suggesting a novel germline-somatic interaction mechanism. Three novel genes, HOXA4, KLK1, and TIMM23, additionally replicate in the RPGEH cohort. Furthermore, 4 genes, MSMB, NCOA4, PCAT1, and PPP1R14A, are associated with PrCa in a trans-ethnic meta-analysis (N = 9117). Many genes exhibit evidence for allele-specific transcriptional activation by PrCa master-regulators (including androgen receptor) in Position Weight Matrix, Chip-Seq, and Hi-C experimental data, suggesting common regulatory mechanisms for the associated genes.
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Dorn J, Bayani J, Yousef GM, Yang F, Magdolen V, Kiechle M, Diamandis EP, Schmitt M. Clinical utility of kallikrein-related peptidases (KLK) in urogenital malignancies. Thromb Haemost 2017; 110:408-22. [DOI: 10.1160/th13-03-0206] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 05/25/2013] [Indexed: 12/19/2022]
Abstract
SummaryKallikrein-related peptidases (KLK), which represent a major tissue-associated proteolytic system, stand for a rich source of biomarkers that may allow molecular classification, early diagnosis and prognosis of human malignancies as well as prediction of response or failure to cancer-directed drugs. International research points to an important role of certain KLKs in female and male urogenital tract malignancies, in addition to cancers of the lung, brain, skin, head and neck, and the gastrointestinal tract. Regarding the female/male urogenital tract, remarkably, all of the KLKs are expressed in the normal prostate, testis, and kidney whereas the uterus, the ovary, and the urinary bladder are expressing a limited number of KLKs only. Most of the information regarding KLK expression in tumour-affected organs is available for ovarian cancer; all of the 12 KLKs tested so far were found to be elevated in the malignant state, depicting them as valuable biomarkers to distinguish between the normal and the cancerous phenotype. In contrast, for kidney cancer, a series of KLKs was found to be downregulated, while other KLKs were not expressed. Evidently, depending on the type of cancer or cancer stage, individual KLKs may show characteristics of a Janus-faced behaviour, by either expanding or inhibiting cancer progression and metastasis.
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Assis J, Pereira C, Nogueira A, Pereira D, Carreira R, Medeiros R. Genetic variants as ovarian cancer first-line treatment hallmarks: A systematic review and meta-analysis. Cancer Treat Rev 2017; 61:35-52. [PMID: 29100168 DOI: 10.1016/j.ctrv.2017.10.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 10/02/2017] [Accepted: 10/07/2017] [Indexed: 01/13/2023]
Abstract
BACKGROUND The potential predictive value of genetic polymorphisms in ovarian cancer first-line treatment is inconsistently reported. We aimed to review ovarian cancer pharmacogenetic studies to update and summarize the available data and to provide directions for further research. METHODS A systematic review followed by a meta-analysis was conducted on cohort studies assessing the involvement of genetic polymorphisms in ovarian cancer first-line treatment response retrieved through a MEDLINE database search by November 2016. Studies were pooled and summary estimates and 95% confidence intervals (CI) were calculated using random or fixed-effects models as appropriate. RESULTS One hundred and forty-two studies gathering 106871 patients were included. Combined data suggested that GSTM1-null genotype patients have a lower risk of death compared to GSTM1-wt carriers, specifically in advanced stages (hazard ratio (HR), 0.68; 95% CI, 0.48-0.97) and when submitted to platinum-based chemotherapy (aHR, 0.61; 95% CI, 0.39-0.94). ERCC1 rs11615 and rs3212886 might have also a significant impact in treatment outcome (aHR, 0.67; 95% CI, 0.51-0.89; aHR, 1.28; 95% CI, 1.01-1.63, respectively). Moreover, ERCC2 rs13181 and rs1799793 showed a distinct ethnic behavior (Asians: aHR, 1.41; 95% CI, 0.80-2.49; aHR, 1.07; 95% CI, 0.62-1.86; Caucasians: aHR, 0.10; 95% CI, 0.01-0.96; aHR, 0.18; 95% CI, 0.05-0.68, respectively). CONCLUSION(S) The definition of integrative predictive models should encompass genetic information, especially regarding GSTM1 homozygous deletion. Justifying additional pharmacogenetic investigation are variants in ERCC1 and ERCC2, which highlight the DNA Repair ability to ovarian cancer prognosis. Further knowledge could aid to understand platinum-treatment failure and to tailor chemotherapy strategies.
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Affiliation(s)
- Joana Assis
- Molecular Oncology and Viral Pathology Group - Research Center, Portuguese Institute of Oncology, Porto, Portugal; FMUP, Faculty of Medicine of Porto University, Porto, Portugal
| | - Carina Pereira
- Molecular Oncology and Viral Pathology Group - Research Center, Portuguese Institute of Oncology, Porto, Portugal; CINTESIS, Center for Health Technology and Services Research, FMUP, Porto, Portugal
| | - Augusto Nogueira
- Molecular Oncology and Viral Pathology Group - Research Center, Portuguese Institute of Oncology, Porto, Portugal; FMUP, Faculty of Medicine of Porto University, Porto, Portugal
| | - Deolinda Pereira
- Oncology Department, Portuguese Institute of Oncology, Porto, Portugal
| | - Rafael Carreira
- Centre of Biological Engineering, University of Minho, Braga, Portugal; SilicoLife, Lda, Braga, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group - Research Center, Portuguese Institute of Oncology, Porto, Portugal; Research Department, Portuguese League Against Cancer (NRNorte), Porto, Portugal; CEBIMED, Faculty of Health Sciences of Fernando Pessoa University, Porto, Portugal.
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Fonseca-Sanchéz MA, Pérez-Plasencia C, Fernández-Retana J, Arechaga-Ocampo E, Marchat LA, Rodríguez-Cuevas S, Bautista-Piña V, Arellano-Anaya ZE, Flores-Pérez A, Diaz-Chávez J, López-Camarillo C. microRNA-18b is upregulated in breast cancer and modulates genes involved in cell migration. Oncol Rep 2013; 30:2399-410. [PMID: 23970382 DOI: 10.3892/or.2013.2691] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 08/02/2013] [Indexed: 11/06/2022] Open
Abstract
microRNAs are small non-coding RNAs of ~22 nucleotides that function at post-transcriptional level as negative regulators of gene expression. Aberrant expression of microRNAs could promote uncontrolled proliferation, migration and invasion of human cancer cells. In this study, we analyzed the expression of microRNA-18b (miR-18b) in breast cancer cell lines and in a set of clinical specimens. Our results showed that miR-18b was upregulated in four out of five breast cancer cell lines and also in breast tumors. In order to identify potential gene targets, we carried out transcriptional profiling of MDA-MB-231 breast cancer cells that ectopically expressed miR-18b. Our results showed that 263 genes were significantly modulated in miR-18b-deficient cells (fold change >1.5; P≤0.05). We found that knock-down of miR-18b induced the upregulation of 55 olfactory receptor (OR) genes and nine genes (NLRP7, KLK3, OLFM3, POSTN, MAGED4B, KIR3DL3, CRX, SEMG1 and CEACAM5) with key roles in cell migration and metastasis. Consistently, we found that ectopic inhibition of miR-18b suppressed the migration of two breast cancer cell models in vitro. In conclusion, we have uncovered genes directly or indirectly modulated by miR-18b which may represent potential therapeutic targets in breast cancer. Our data also pointed out a role of miR-18b in migration of breast cancer cells.
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Affiliation(s)
- Miguel A Fonseca-Sanchéz
- Oncogenomics and Cancer Proteomics Laboratory, Genomics Sciences Program, Autonomous University of Mexico City, Mexico City, Mexico
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