1
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Vince RA, Sun H, Singhal U, Schumacher FR, Trapl E, Rose J, Cullen J, Zaorsky N, Shoag J, Hartman H, Jia AY, Spratt DE, Fritsche LG, Morgan TM. Assessing the Clinical Utility of Published Prostate Cancer Polygenic Risk Scores in a Large Biobank Data Set. Eur Urol Oncol 2024:S2588-9311(24)00111-1. [PMID: 38734542 DOI: 10.1016/j.euo.2024.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/26/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND AND OBJECTIVE Polygenic risk scores (PRSs) have been developed to identify men with the highest risk of prostate cancer. Our aim was to compare the performance of 16 PRSs in identifying men at risk of developing prostate cancer and then to evaluate the performance of the top-performing PRSs in differentiating individuals at risk of aggressive prostate cancer. METHODS For this case-control study we downloaded 16 published PRSs from the Polygenic Score Catalog on May 28, 2021 and applied them to Michigan Genomics Initiative (MGI) patients. Cases were matched to the Michigan Urological Surgery Improvement Collaborative (MUSIC) registry to obtain granular clinical and pathological data. MGI prospectively enrolls patients undergoing surgery at the University of Michigan, and MUSIC is a multi-institutional registry that prospectively tracks demographic, treatment, and clinical variables. The predictive performance of each PRS was evaluated using the area under the covariate-adjusted receiver operating characteristic curve (aAUC), and the association between PRS and disease aggressiveness according to prostate biopsy data was measured using logistic regression. KEY FINDINGS AND LIMITATIONS We included 18 050 patients in the analysis, of whom 15 310 were control subjects and 2740 were prostate cancer cases. The median age was 66.1 yr (interquartile range 59.9-71.6) for cases and 56.6 yr (interquartile range 42.6-66.7) for control subjects. The PRS performance in predicting the risk of developing prostate cancer according to aAUC ranged from 0.51 (95% confidence interval 0.51-0.53) to 0.67 (95% confidence interval 0.66-0.68). By contrast, there was no association between PRS and disease aggressiveness. CONCLUSIONS AND CLINICAL IMPLICATIONS Prostate cancer PRSs have modest real-world performance in identifying patients at higher risk of developing prostate cancer; however, they are limited in distinguishing patients with indolent versus aggressive disease. PATIENT SUMMARY Risk scores using data for multiple genes (called polygenic risk scores) can identify men at higher risk of developing prostate cancer. However, these scores need to be refined to be able to identify men with the highest risk for clinically significant prostate cancer.
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Affiliation(s)
- Randy A Vince
- Department of Urology, University Hospitals Seidman Cancer Center, Case Western Reserve University, Cleveland, OH, USA.
| | - Helen Sun
- Department of Urology, University Hospitals Seidman Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Udit Singhal
- Department of Urology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Erika Trapl
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Johnie Rose
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Jennifer Cullen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Nicholas Zaorsky
- Department of Radiation Oncology, University Hospitals Seidman Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Johnathan Shoag
- Department of Urology, University Hospitals Seidman Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Holly Hartman
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Angela Y Jia
- Department of Radiation Oncology, University Hospitals Seidman Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University Hospitals Seidman Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Lars G Fritsche
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Todd M Morgan
- Department of Urology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
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2
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Wei GH, Dong D, Zhang P, Liu M, Wei Y, Wang Z, Xu W, Zhang Q, Zhu Y, Zhang Q, Yang X, Zhu J, Wang L. Combined SNPs sequencing and allele specific proteomics capture reveal functional causality underpinning the 2p25 prostate cancer susceptibility locus. RESEARCH SQUARE 2024:rs.3.rs-3943095. [PMID: 38645058 PMCID: PMC11030545 DOI: 10.21203/rs.3.rs-3943095/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Genome wide association studies (GWASs) have identified numerous risk loci associated with prostate cancer, yet unraveling their functional significance remains elusive. Leveraging our high-throughput SNPs-seq method, we pinpointed rs4519489 within the multi-ancestry GWAS-discovered 2p25 locus as a potential functional SNP due to its significant allelic differences in protein binding. Here, we conduct a comprehensive analysis of rs4519489 and its associated gene, NOL10, employing diverse cohort data and experimental models. Clinical findings reveal a synergistic effect between rs4519489 genotype and NOL10 expression on prostate cancer prognosis and severity. Through unbiased proteomics screening, we reveal that the risk allele A of rs4519489 exhibits enhanced binding to USF1, a novel oncogenic transcription factor (TF) implicated in prostate cancer progression and prognosis, resulting in elevated NOL10 expression. Furthermore, we elucidate that NOL10 regulates cell cycle pathways, fostering prostate cancer progression. The concurrent expression of NOL10 and USF1 correlates with aggressive prostate cancer characteristics and poorer prognosis. Collectively, our study offers a robust strategy for functional SNP screening and TF identification through high-throughput SNPs-seq and unbiased proteomics, highlighting the rs4519489-USF1-NOL10 regulatory axis as a promising biomarker or therapeutic target for clinical diagnosis and treatment of prostate cancer.
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Affiliation(s)
- Gong-Hong Wei
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School Basic Medical Sciences, Shanghai Medi
| | - Dandan Dong
- Shanghai Medical College of Fudan University
| | - Peng Zhang
- Shanghai Medical College of Fudan University
| | - Mengqi Liu
- Shanghai Medical College of Fudan University
| | - Yu Wei
- Fudan Unversity Shanghai Cancer Center
| | - Zixian Wang
- Shanghai Medical College of Fudan University
| | - Wenjie Xu
- Shanghai Medical College of Fudan University
| | | | - Yao Zhu
- Fudan University Shanghai Cancer Center
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3
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Chen H, Wang Z, Gong L, Wang Q, Chen W, Wang J, Ma X, Ding R, Li X, Zou X, Plass M, Lian C, Ni T, Wei GH, Li W, Deng L, Li L. A distinct class of pan-cancer susceptibility genes revealed by an alternative polyadenylation transcriptome-wide association study. Nat Commun 2024; 15:1729. [PMID: 38409266 PMCID: PMC10897204 DOI: 10.1038/s41467-024-46064-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 02/12/2024] [Indexed: 02/28/2024] Open
Abstract
Alternative polyadenylation plays an important role in cancer initiation and progression; however, current transcriptome-wide association studies mostly ignore alternative polyadenylation when identifying putative cancer susceptibility genes. Here, we perform a pan-cancer 3' untranslated region alternative polyadenylation transcriptome-wide association analysis by integrating 55 well-powered (n > 50,000) genome-wide association studies datasets across 22 major cancer types with alternative polyadenylation quantification from 23,955 RNA sequencing samples across 7,574 individuals. We find that genetic variants associated with alternative polyadenylation are co-localized with 28.57% of cancer loci and contribute a significant portion of cancer heritability. We further identify 642 significant cancer susceptibility genes predicted to modulate cancer risk via alternative polyadenylation, 62.46% of which have been overlooked by traditional expression- and splicing- studies. As proof of principle validation, we show that alternative alleles facilitate 3' untranslated region lengthening of CRLS1 gene leading to increased protein abundance and promoted proliferation of breast cancer cells. Together, our study highlights the significant role of alternative polyadenylation in discovering new cancer susceptibility genes and provides a strong foundational framework for enhancing our understanding of the etiology underlying human cancers.
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Affiliation(s)
- Hui Chen
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Zeyang Wang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Lihai Gong
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Qixuan Wang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Wenyan Chen
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Jia Wang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Xuelian Ma
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Ruofan Ding
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Xing Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Xudong Zou
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Mireya Plass
- Gene Regulation of Cell Identity Group, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Program for Advancing Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain
| | - Cheng Lian
- Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438, China
| | - Gong-Hong Wei
- Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, 90410, Finland
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, The University of California, Irvine, CA, 92697, USA.
| | - Lin Deng
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, 518055, China.
| | - Lei Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China.
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4
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Paller CJ, Barata PC, Lorentz J, Appleman LJ, Armstrong AJ, DeMarco TA, Dreicer R, Elrod JAB, Fleming M, George C, Heath EI, Hussain MHA, Mao S, McKay RR, Morgans AK, Orton M, Pili R, Riedel E, Saraiya B, Sigmond J, Sokolova A, Stadler WM, Tran C, Macario N, Vinson J, Green R, Cheng HH. PROMISE Registry: A prostate cancer registry of outcomes and germline mutations for improved survival and treatment effectiveness. Prostate 2024; 84:292-302. [PMID: 37964482 DOI: 10.1002/pros.24650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND Recently approved treatments and updates to genetic testing recommendations for prostate cancer have created a need for correlated analyses of patient outcomes data via germline genetic mutation status. Genetic registries address these gaps by identifying candidates for recently approved targeted treatments, expanding clinical trial data examining specific gene mutations, and understanding effects of targeted treatments in the real-world setting. METHODS The PROMISE Registry is a 20-year (5-year recruitment, 15-year follow-up), US-wide, prospective genetic registry for prostate cancer patients. Five thousand patients will be screened through an online at-home germline testing to identify and enroll 500 patients with germline mutations, including: pathogenic or likely pathogenic variants and variants of uncertain significance in genes of interest. Patients will be followed for 15 years and clinical data with real time patient reported outcomes will be collected. Eligible patients will enter long-term follow-up (6-month PRO surveys and medical record retrieval). As a virtual study with patient self-enrollment, the PROMISE Registry may fill gaps in genetics services in underserved areas and for patients within sufficient insurance coverage. RESULTS The PROMISE Registry opened in May 2021. 2114 patients have enrolled to date across 48 US states and 23 recruiting sites. 202 patients have met criteria for long-term follow-up. PROMISE is on target with the study's goal of 5000 patients screened and 500 patients eligible for long-term follow-up by 2026. CONCLUSIONS The PROMISE Registry is a novel, prospective, germline registry that will collect long-term patient outcomes data to address current gaps in understanding resulting from recently FDA-approved treatments and updates to genetic testing recommendations for prostate cancer. Through inclusion of a broad nationwide sample, including underserved patients and those unaffiliated with major academic centers, the PROMISE Registry aims to provide access to germline genetic testing and to collect data to understand disease characteristics and treatment responses across the disease spectrum for prostate cancer with rare germline genetic variants.
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Affiliation(s)
- Channing J Paller
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Pedro C Barata
- University Hospitals Seidman Cancer Center, Cleveland, Ohio, USA
| | - Justin Lorentz
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Leonard J Appleman
- University of Pittsburgh Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Andrew J Armstrong
- Duke Cancer Institute Center for Prostate & Urologic Cancers, Durham, North Carolina, USA
| | | | - Robert Dreicer
- University of Virginia Comprehensive Cancer Center, Charlottesville, Virginia, USA
| | - Jo Ann B Elrod
- Fred Hutchinson Cancer Center, Clinical Research Division, Seattle, Washington, USA
| | - Mark Fleming
- Virginia Oncology Associates, Norfolk, Virginia, USA
| | - Christopher George
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Elisabeth I Heath
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Maha H A Hussain
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Shifeng Mao
- Allegheny Health Network Cancer Institute, Pittsburgh, Pennsylvania, USA
| | - Rana R McKay
- Department of Oncology, University of California San Diego Moores Cancer Center, La Jolla, California, USA
| | - Alicia K Morgans
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Matthew Orton
- Indiana University Health Arnett Cancer Center, Lafayette, Indiana, USA
| | - Roberto Pili
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Elyn Riedel
- Prostate Cancer Clinical Trials Consortium, New York, New York, USA
| | - Biren Saraiya
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | | | - Alexandra Sokolova
- Oregon Health & Science University Knight Cancer Institute, Portland, Oregon, USA
| | - Walter M Stadler
- Department of Medicine, The University of Chicago Comprehensive Cancer Center, The University of Chicago Medicine, Chicago, Illinois, USA
| | - Christina Tran
- Prostate Cancer Clinical Trials Consortium, New York, New York, USA
| | - Natalie Macario
- Prostate Cancer Clinical Trials Consortium, New York, New York, USA
| | - Jacob Vinson
- Prostate Cancer Clinical Trials Consortium, New York, New York, USA
| | - Rebecca Green
- Prostate Cancer Clinical Trials Consortium, New York, New York, USA
| | - Heather H Cheng
- Fred Hutchinson Cancer Center, Clinical Research Division, Seattle, Washington, USA
- University of Washington, Department of Medicine, Seattle, Washington, USA
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5
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Taing L, Dandawate A, L’Yi S, Gehlenborg N, Brown M, Meyer C. Cistrome Data Browser: integrated search, analysis and visualization of chromatin data. Nucleic Acids Res 2024; 52:D61-D66. [PMID: 37971305 PMCID: PMC10767960 DOI: 10.1093/nar/gkad1069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/14/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
The Cistrome Data Browser is a resource of ChIP-seq, ATAC-seq and DNase-seq data from humans and mice. It provides maps of the genome-wide locations of transcription factors, cofactors, chromatin remodelers, histone post-translational modifications and regions of chromatin accessible to endonuclease activity. Cistrome DB v3.0 contains approximately 45 000 human and 44 000 mouse samples with about 32 000 newly collected datasets compared to the previous release. The Cistrome DB v3.0 user interface is implemented as a single page application that unifies menu driven and data driven search functions and provides an embedded genome browser, which allows users to find and visualize data more effectively. Users can find informative chromatin profiles through keyword, menu, and data-driven search tools. Browser search functions can predict the regulators of query genes as well as the cell type and factor dependent functionality of potential cis-regulatory elements. Cistrome DB v3.0 expands the display of quality control statistics, incorporates sequence logos into motif enrichment displays and includes more expansive sample metadata. Cistrome DB v3.0 is available at http://db3.cistrome.org/browser.
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Affiliation(s)
- Len Taing
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ariaki Dandawate
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sehi L’Yi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Clifford A Meyer
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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6
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Dai X, Shi X, Luo M, Li P, Gao Y. Integrative analysis of transcriptomic and metabolomic profiles reveals enhanced arginine metabolism in androgen-independent prostate cancer cells. BMC Cancer 2023; 23:1241. [PMID: 38104097 PMCID: PMC10724921 DOI: 10.1186/s12885-023-11707-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/02/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Prostate cancer is a common solid tumor that affects a significant number of men worldwide. Conventional androgen deprivation therapy (ADT) increases the risk of developing castration-resistant prostate cancer (CRPC). Effective clinical management of patients with CRPC is challenging due to the limited understanding. METHODS In this study, transcriptomic and metabolomic profiles of androgen-dependent prostate cancer cell line LNCaP and the androgen-independent cells developed from LNCaP cells (LNCaP-ADR) were investigated using RNA-sequencing and LC-MS/MS, respectively. The differentially expressed genes and metabolites were analyzed, and integrative analysis of transcriptomic and metabolomic data was further conducted to obtain a comprehensive understanding of the metabolic characteristics in LNCaP-ADR cells. Quantitative real-time PCR (QPCR) was employed to ascertain the mRNA expression levels of the selected differentially expressed genes. RESULTS The arginine and proline metabolism pathway was identified as a commonly altered pathway at both the transcriptional and metabolic levels. In the LNCaP-ADR cells, significant upregulation was observed for metabolites including 5-Aminopentanoic acid, L-Arginine, L-Glutamic acid, N-Acetyl-L-alanine, and Pyrrole-2-carboxylic acid at the metabolic level. At the transcriptional level, MAOA, ALDH3A2, ALDH2, ARG1, CKMT2, and CNDP1 were found to be significantly upregulated in the LNCaP-ADR cells. Gene set enrichment analysis (GSEA) identified various enriched gene sets in the LNCaP-ADR cells, encompassing inflammatory response, 9plus2 motile cilium, motile cilium, ciliary plasm, cilium or flagellum-dependent cell motility, cilium movement, cilium, response to endoplasmic reticulum stress, PTEN DN.V1 DN, SRC UP.V1 UP, IL15 UP.V1 DN, RB DN.V1 DN, AKT UP MTOR DN.V1 UP, VEGF A UP.V1 UP, and KRAS.LUNG.BREAST UP.V1 UP. CONCLUSIONS These findings highlight the substantial association between the arginine and proline metabolism pathway and CRPC, emphasizing the need to prioritize strategies that target dysregulated metabolites and differentially expressed genes as essential interventions in the clinical management of CRPC.
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Affiliation(s)
- Xingchen Dai
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
- Department of Nephrology, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xinyi Shi
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
- Ankang Central Hospital, Ankang, China
| | - Mingxiu Luo
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
| | - Pu Li
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yujing Gao
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China.
- National Health Commission Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University, Yinchuan, China.
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7
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Wang A, Shen J, Rodriguez AA, Saunders EJ, Chen F, Janivara R, Darst BF, Sheng X, Xu Y, Chou AJ, Benlloch S, Dadaev T, Brook MN, Plym A, Sahimi A, Hoffman TJ, Takahashi A, Matsuda K, Momozawa Y, Fujita M, Laisk T, Figuerêdo J, Muir K, Ito S, Liu X, Uchio Y, Kubo M, Kamatani Y, Lophatananon A, Wan P, Andrews C, Lori A, Choudhury PP, Schleutker J, Tammela TL, Sipeky C, Auvinen A, Giles GG, Southey MC, MacInnis RJ, Cybulski C, Wokolorczyk D, Lubinski J, Rentsch CT, Cho K, Mcmahon BH, Neal DE, Donovan JL, Hamdy FC, Martin RM, Nordestgaard BG, Nielsen SF, Weischer M, Bojesen SE, Røder A, Stroomberg HV, Batra J, Chambers S, Horvath L, Clements JA, Tilly W, Risbridger GP, Gronberg H, Aly M, Szulkin R, Eklund M, Nordstrom T, Pashayan N, Dunning AM, Ghoussaini M, Travis RC, Key TJ, Riboli E, Park JY, Sellers TA, Lin HY, Albanes D, Weinstein S, Cook MB, Mucci LA, Giovannucci E, Lindstrom S, Kraft P, Hunter DJ, Penney KL, Turman C, Tangen CM, Goodman PJ, Thompson IM, Hamilton RJ, Fleshner NE, Finelli A, Parent MÉ, Stanford JL, Ostrander EA, Koutros S, Beane Freeman LE, Stampfer M, Wolk A, Håkansson N, Andriole GL, Hoover RN, Machiela MJ, Sørensen KD, Borre M, Blot WJ, Zheng W, Yeboah ED, Mensah JE, Lu YJ, Zhang HW, Feng N, Mao X, Wu Y, Zhao SC, Sun Z, Thibodeau SN, McDonnell SK, Schaid DJ, West CM, Barnett G, Maier C, Schnoeller T, Luedeke M, Kibel AS, Drake BF, Cussenot O, Cancel-Tassin G, Menegaux F, Truong T, Koudou YA, John EM, Grindedal EM, Maehle L, Khaw KT, Ingles SA, Stern MC, Vega A, Gómez-Caamaño A, Fachal L, Rosenstein BS, Kerns SL, Ostrer H, Teixeira MR, Paulo P, Brandão A, Watya S, Lubwama A, Bensen JT, Butler EN, Mohler JL, Taylor JA, Kogevinas M, Dierssen-Sotos T, Castaño-Vinyals G, Cannon-Albright L, Teerlink CC, Huff CD, Pilie P, Yu Y, Bohlender RJ, Gu J, Strom SS, Multigner L, Blanchet P, Brureau L, Kaneva R, Slavov C, Mitev V, Leach RJ, Brenner H, Chen X, Holleczek B, Schöttker B, Klein EA, Hsing AW, Kittles RA, Murphy AB, Logothetis CJ, Kim J, Neuhausen SL, Steele L, Ding YC, Isaacs WB, Nemesure B, Hennis AJ, Carpten J, Pandha H, Michael A, Ruyck KD, Meerleer GD, Ost P, Xu J, Razack A, Lim J, Teo SH, Newcomb LF, Lin DW, Fowke JH, Neslund-Dudas CM, Rybicki BA, Gamulin M, Lessel D, Kulis T, Usmani N, Abraham A, Singhal S, Parliament M, Claessens F, Joniau S, den Broeck TV, Gago-Dominguez M, Castelao JE, Martinez ME, Larkin S, Townsend PA, Aukim-Hastie C, Bush WS, Aldrich MC, Crawford DC, Srivastava S, Cullen J, Petrovics G, Casey G, Wang Y, Tettey Y, Lachance J, Tang W, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Yamoah K, Govindasami K, Chokkalingam AP, Keaton JM, Hellwege JN, Clark PE, Jalloh M, Gueye SM, Niang L, Ogunbiyi O, Shittu O, Amodu O, Adebiyi AO, Aisuodionoe-Shadrach OI, Ajibola HO, Jamda MA, Oluwole OP, Nwegbu M, Adusei B, Mante S, Darkwa-Abrahams A, Diop H, Gundell SM, Roobol MJ, Jenster G, van Schaik RH, Hu JJ, Sanderson M, Kachuri L, Varma R, McKean-Cowdin R, Torres M, Preuss MH, Loos RJ, Zawistowski M, Zöllner S, Lu Z, Van Den Eeden SK, Easton DF, Ambs S, Edwards TL, Mägi R, Rebbeck TR, Fritsche L, Chanock SJ, Berndt SI, Wiklund F, Nakagawa H, Witte JS, Gaziano JM, Justice AC, Mancuso N, Terao C, Eeles RA, Kote-Jarai Z, Madduri RK, Conti DV, Haiman CA. Characterizing prostate cancer risk through multi-ancestry genome-wide discovery of 187 novel risk variants. Nat Genet 2023; 55:2065-2074. [PMID: 37945903 PMCID: PMC10841479 DOI: 10.1038/s41588-023-01534-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 09/15/2023] [Indexed: 11/12/2023]
Abstract
The transferability and clinical value of genetic risk scores (GRSs) across populations remain limited due to an imbalance in genetic studies across ancestrally diverse populations. Here we conducted a multi-ancestry genome-wide association study of 156,319 prostate cancer cases and 788,443 controls of European, African, Asian and Hispanic men, reflecting a 57% increase in the number of non-European cases over previous prostate cancer genome-wide association studies. We identified 187 novel risk variants for prostate cancer, increasing the total number of risk variants to 451. An externally replicated multi-ancestry GRS was associated with risk that ranged from 1.8 (per standard deviation) in African ancestry men to 2.2 in European ancestry men. The GRS was associated with a greater risk of aggressive versus non-aggressive disease in men of African ancestry (P = 0.03). Our study presents novel prostate cancer susceptibility loci and a GRS with effective risk stratification across ancestry groups.
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Affiliation(s)
- Anqi Wang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jiayi Shen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Fei Chen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rohini Janivara
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Burcu F. Darst
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Xin Sheng
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yili Xu
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alisha J. Chou
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sara Benlloch
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology,University of Cambridge, Cambridge, UK
| | | | | | - Anna Plym
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Urology Division, Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Ali Sahimi
- Department of Population and Public Health Sciences, Keck School of Medicine,University of Southern California, Los Angeles, CA, USA
| | - Thomas J. Hoffman
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Atushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Genomic Medicine, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Koichi Matsuda
- Department of Computational Biology and Medical Sciences, Laboratory of Clinical Genome Sequencing,Graduate school of Frontier Sciences,The University of Tokyo, Tokyo, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Jéssica Figuerêdo
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Shuji Ito
- Department of Orthopaedics, Shimane University, Izumo, Shimane, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - The Biobank Japan Project
- Corresponding Author: Christopher A. Haiman, Harlyne J. Norris Cancer Research Tower, USC Norris Comprehensive Cancer Center, 1450 Biggy Street, Rm 1504, Los Angeles, CA 90033 or
| | - Yuji Uchio
- Department of Orthopaedics, Shimane University, Izumo, Shimane, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, Manchester, UK
| | - Peggy Wan
- Department of Population and Public Health Sciences, Keck School of Medicine,University of Southern California, Los Angeles, CA, USA
| | - Caroline Andrews
- Harvard TH Chan School of Public Health and Division of Population Sciences,Dana Farber Cancer Institute, Boston, MA, USA
| | - Adriana Lori
- Department of Population Science, American Cancer Society, Kennesaw, GA, USA
| | | | - Johanna Schleutker
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Medical Genetics, Genomics, Laboratory Division, Turku University Hospital, Turku, Finland
| | | | - Csilla Sipeky
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Anssi Auvinen
- Unit of Health Sciences, Faculty of Social Sciences, Tampere University, Tampere, Finland
| | - Graham G. Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health,The University of Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Melissa C. Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Robert J. MacInnis
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health,The University of Melbourne, Victoria, Australia
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Dominika Wokolorczyk
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Christopher T. Rentsch
- Yale School of Medicine, New Haven, CT, USA
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Kelly Cho
- Division of Aging, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | | | - David E. Neal
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK
- University of Cambridge, Department of Oncology, Addenbrooke’s Hospital, Cambridge, UK
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Jenny L. Donovan
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Freddie C. Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Faculty of Medical Science, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Richard M. Martin
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre at University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Borge G. Nordestgaard
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
| | - Sune F. Nielsen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
| | - Maren Weischer
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
| | - Stig E. Bojesen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
| | - Andreas Røder
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Hein V. Stroomberg
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | | | - Lisa Horvath
- Chris O’Brien Lifehouse (COBLH), Camperdown, Sydney, NSW, Australia, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
| | - Judith A. Clements
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | - Wayne Tilly
- Dame Roma Mitchell Cancer Research Laboratories, University of Adelaide, Adelaide, Australia
| | - Gail P. Risbridger
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Prostate Cancer Translational Research Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Markus Aly
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, and Department of Urology, Karolinska University Hospital, Solna, Stockholm, Sweden
- Department of Urology, Karolinska University Hospital, Stockholm, Sweden
| | - Robert Szulkin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- SDS Life Sciences, Stockholm, Sweden
| | - Martin Eklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Tobias Nordstrom
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Sciences at Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Nora Pashayan
- University College London, Department of Applied Health Research, London, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Cambridge, UK
- Department of Applied Health Research, University College London, London, UK
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Cambridge, UK
| | - Maya Ghoussaini
- Open Targets, Wellcome Sanger Institute, Hinxton, Saffron Walden, Hinxton, UK
| | - Ruth C. Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Tim J. Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Jong Y. Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Thomas A. Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Hui-Yi Lin
- School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael B. Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH,, Bethesda, MD, USA
| | - Lorelei A. Mucci
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sara Lindstrom
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - David J. Hunter
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Kathryn L. Penney
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital/Harvard Medical School, Boston, MA, USA
| | - Constance Turman
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Catherine M. Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Phyllis J. Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ian M. Thompson
- CHRISTUS Santa Rosa Hospital – Medical Center, San Antonio, TX, USA
| | - Robert J. Hamilton
- Dept. of Surgical Oncology, Princess Margaret Cancer Centre, Toronto, Canada
- Dept. of Surgery (Urology), University of Toronto, Toronto, Canada
| | - Neil E. Fleshner
- Dept. of Surgical Oncology, Princess Margaret Cancer Centre, Toronto, Canada
| | - Antonio Finelli
- Division of Urology, Princess Margaret Cancer Centre, Toronto, Canada
| | - Marie-Élise Parent
- Epidemiology and Biostatistics Unit, Centre Armand-Frappier Santé Biotechnologie, Laval, QC, Canada
| | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elaine A. Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Laura E. Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Meir Stampfer
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital/Harvard Medical School, Boston, MA, USA
| | - Alicja Wolk
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Niclas Håkansson
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Gerald L. Andriole
- Brady Urological Institute in National Capital Region, Johns Hopkins University, Baltimore, MD, USA
| | - Robert N. Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Mitchell J. Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Karina Dalsgaard Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Michael Borre
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - William J. Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- International Epidemiology Institute, Rockville, MD, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - James E. Mensah
- University of Ghana Medical School, Accra, Ghana
- Korle Bu Teaching Hospital, Accra, Ghana
| | - Yong-Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | | | - Ninghan Feng
- Wuxi Second Hospital, Nanjing Medical University, Wuxi, Jiangzhu Province, China
| | - Xueying Mao
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Yudong Wu
- Department of Urology, First Affiliated Hospital, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Shan-Chao Zhao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zan Sun
- The People’s Hospital of Liaoning Proviouce, The People’s Hospital of China Medical University, Shenyang, China, Shenyang, China
| | - Stephen N. Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Daniel J. Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Catharine M.L. West
- Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Radiotherapy Related Research, The Christie Hospital NHS Foundation Trust, Manchester, UK
| | - Gill Barnett
- University of Cambridge Department of Oncology, Oncology Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | | | - Adam S. Kibel
- Division of Urologic Surgery, Brigham and Womens Hospital, Boston, MA, USA
| | | | - Olivier Cussenot
- GRC 5 Predictive Onco-Urology, Sorbonne Université, Paris, France
- CeRePP, Paris, France
| | | | - Florence Menegaux
- Exposome and Heredity, CESP (UMR 1018), Paris-Saclay Medical School, Paris-Saclay University, Inserm, Gustave Roussy, Villejuif, France
| | - Thérèse Truong
- Exposome and Heredity, CESP (UMR 1018), Paris-Saclay Medical School, Paris-Saclay University, Inserm, Gustave Roussy, Villejuif, France
| | - Yves Akoli Koudou
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Villejuif Cédex, France
| | - Esther M. John
- Department of Medicine, Stanford Cancer Institute,Stanford University School of Medicine, Stanford, CA, USA
| | | | - Lovise Maehle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge, UK
| | - Sue A. Ingles
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Mariana C Stern
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Ana Vega
- Fundación Pública Galega Medicina Xenómica, Santiago De Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago De Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Spain
| | - Antonio Gómez-Caamaño
- Department of Radiation Oncology, Complexo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - Laura Fachal
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago De Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Spain
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
- Fundación Pública Galega Medicina Xenómica, Santiago de Compostela, Spain
| | - Barry S. Rosenstein
- Department of Radiation Oncology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah L. Kerns
- Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Harry Ostrer
- Professor of Pathology and Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Manuel R. Teixeira
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Paula Paulo
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Andreia Brandão
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | | | | | - Jeannette T. Bensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ebonee N. Butler
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - James L. Mohler
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Urology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jack A. Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Manolis Kogevinas
- ISGlobal, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Trinidad Dierssen-Sotos
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- University of Cantabria-IDIVAL, Santander, Spain
| | - Gemma Castaño-Vinyals
- ISGlobal, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Lisa Cannon-Albright
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - Craig C. Teerlink
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - Chad D. Huff
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Patrick Pilie
- Department of Genitourinary Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Yao Yu
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Ryan J. Bohlender
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Jian Gu
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Sara S. Strom
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Luc Multigner
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Rennes, France
| | - Pascal Blanchet
- CHU de Pointe-à-Pitre, Univ Antilles, Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Pointe-à-Pitre, France
| | - Laurent Brureau
- CHU de Pointe-à-Pitre, Univ Antilles, Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Pointe-à-Pitre, France
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia, Bulgaria
| | - Chavdar Slavov
- Department of Urology and Alexandrovska University Hospital, Medical University of Sofia, Sofia, Bulgaria
| | - Vanio Mitev
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia, Bulgaria
| | - Robin J. Leach
- Department of Cell Systems and Anatomy and Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Xuechen Chen
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eric A. Klein
- Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
- Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ann W. Hsing
- Department of Medicine and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Adam B. Murphy
- Department of Urology, Northwestern University, Chicago, IL, USA
| | - Christopher J. Logothetis
- The University of Texas M. D. Anderson Cancer Center, Department of Genitourinary Medical Oncology, Houston, TX, USA
| | - Jeri Kim
- The University of Texas M. D. Anderson Cancer Center, Department of Genitourinary Medical Oncology, Houston, TX, USA
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Linda Steele
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - William B. Isaacs
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Anselm J.M. Hennis
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
- Chronic Disease Research Centre and Faculty of Medical Sciences, University of the West Indies, Bridgetown, Barbados
| | - John Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Kim De Ruyck
- Ghent University, Faculty of Medicine and Health Sciences, Basic Medical Sciences, Ghent, Belgium
| | - Gert De Meerleer
- Ghent University Hospital, Department of Radiotherapy, Ghent, Belgium
| | - Piet Ost
- Ghent University Hospital, Department of Radiotherapy, Ghent, Belgium
| | - Jianfeng Xu
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Azad Razack
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jasmine Lim
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Soo-Hwang Teo
- Cancer Research Malaysia (CRM), Outpatient Centre, Subang Jaya Medical Centre, Subang Jaya, Selangor, Malaysia
| | - Lisa F. Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Daniel W. Lin
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Jay H. Fowke
- Department of Preventive Medicine, Division of Epidemiology,The University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - Benjamin A. Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, Detroit, MI, USA
| | - Marija Gamulin
- Division of Medical Oncology, Urogenital Unit, Department of Oncology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tomislav Kulis
- Department of Urology, University Hospital Center Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Nawaid Usmani
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Aswin Abraham
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Sandeep Singhal
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Matthew Parliament
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Steven Joniau
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - Thomas Van den Broeck
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, Servicio Galego de Saúde, SERGAS, Santiago de Compostela, Spain
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | - Jose Esteban Castelao
- Genetic Oncology Unit, CHUVI Hospital, Complexo Hospitalario Universitario de Vigo, Instituto de Investigación Biomédica Galicia Sur (IISGS), Vigo (Pontevedra), Spain
| | - Maria Elena Martinez
- University of California San Diego, Moores Cancer Center, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Samantha Larkin
- Scientific Education Support, Thames Ditton, Surrey, Formerly Cancer Sciences, University of Southampton, Southampton, UK
| | - Paul A. Townsend
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Surrey, UK
| | | | - William S. Bush
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Melinda C. Aldrich
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dana C. Crawford
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Shiv Srivastava
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Jennifer Cullen
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
- Department of Surgery, Center for Prostate Disease Research,Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Gyorgy Petrovics
- Department of Surgery, Center for Prostate Disease Research,Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Graham Casey
- Department of Public Health Science, Center for Public Health Genomics,University of Virginia, Charlottesville, VA, USA
| | - Ying Wang
- Department of Population Science, American Cancer Society, Kennesaw, GA, USA
| | - Yao Tettey
- Korle Bu Teaching Hospital, Accra, Ghana
- Department of Pathology, University of Ghana, Accra, Ghana
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Andrew A. Adjei
- Department of Pathology, University of Ghana Medical School, Accra, Ghana
| | - Evelyn Tay
- Korle Bu Teaching Hospital, Accra, Ghana
| | | | | | - Kosj Yamoah
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | | | | | - Jacob M. Keaton
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jacklyn N. Hellwege
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Nashville, TN, USA
| | - Peter E. Clark
- Atrium Health/Levine Cancer Institute, Charlotte, NC, USA
| | | | | | | | - Olufemi Ogunbiyi
- Department of Pathology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olayiwola Shittu
- Department of Surgery, College of Medicine, University of Ibadan and Univerity College Hospital, Ibadan, Nigeria
| | - Olukemi Amodu
- Institute of Child Health, College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Akindele O. Adebiyi
- Clinical Epidemiology Unit, Department of Community Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oseremen I. Aisuodionoe-Shadrach
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Hafees O. Ajibola
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Mustapha A. Jamda
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Olabode P. Oluwole
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Maxwell Nwegbu
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | | | | | | | - Halimatou Diop
- Laboratoires Bacteriologie et Virologie, Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Susan M. Gundell
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Monique J. Roobol
- Department of Urology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Ron H.N. van Schaik
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jennifer J. Hu
- The University of Miami School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Maureen Sanderson
- Department of Family and Community Medicine, Meharry Medical College, Nashville, TN, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford Cancer Institute, Stanford, CA, USA
| | - Rohit Varma
- Southern California Eye Institute, CHA Hollywood Presbyterian Medical Center, Los Angeles, CA, USA
| | - Roberta McKean-Cowdin
- Department of Population and Public Health Sciences, Keck School of Medicine,University of Southern California, Los Angeles, CA, USA
| | - Mina Torres
- Southern California Eye Institute, CHA Hollywood Presbyterian Medical Center, Los Angeles, CA, USA
| | - Michael H. Preuss
- The Charles Bronfman Institute for Personalized Medicine,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew Zawistowski
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Sebastian Zöllner
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Zeyun Lu
- Department of Population and Public Health Sciences, Keck School of Medicine,University of Southern California, Los Angeles, CA, USA
| | | | - Douglas F. Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology,, Cambridge, UK
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Todd L. Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Timothy R. Rebbeck
- Harvard TH Chan School of Public Health and Division of Population Sciences, Dana Farber Cancer Institute, Boston, MA, USA
| | - Lars Fritsche
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - John S. Witte
- Department of Epidemiology and Population Health, Stanford Cancer Institute, Stanford, CA, USA
- Departments of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - J. Michael Gaziano
- Division of Aging, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | | | - Nick Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, School of Pharmaceutical Sciences, Shizuoka, Japan
| | - Rosalind A. Eeles
- The Institute of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | | | | | - David V. Conti
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher A. Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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8
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Zhong H, Zhu J, Liu S, Ghoneim DH, Surendran P, Liu T, Fahle S, Butterworth A, Ashad Alam M, Deng HW, Yu H, Wu C, Wu L. Identification of blood protein biomarkers associated with prostate cancer risk using genetic prediction models: analysis of over 140,000 subjects. Hum Mol Genet 2023; 32:3181-3193. [PMID: 37622920 PMCID: PMC10630250 DOI: 10.1093/hmg/ddad139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/01/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023] Open
Abstract
Prostate cancer (PCa) brings huge public health burden in men. A growing number of conventional observational studies report associations of multiple circulating proteins with PCa risk. However, the existing findings may be subject to incoherent biases of conventional epidemiologic studies. To better characterize their associations, herein, we evaluated associations of genetically predicted concentrations of plasma proteins with PCa risk. We developed comprehensive genetic prediction models for protein levels in plasma. After testing 1308 proteins in 79 194 cases and 61 112 controls of European ancestry included in the consortia of BPC3, CAPS, CRUK, PEGASUS, and PRACTICAL, 24 proteins showed significant associations with PCa risk, including 16 previously reported proteins and eight novel proteins. Of them, 14 proteins showed negative associations and 10 showed positive associations with PCa risk. For 18 of the identified proteins, potential functional somatic changes of encoding genes were detected in PCa patients in The Cancer Genome Atlas (TCGA). Genes encoding these proteins were significantly involved in cancer-related pathways. We further identified drugs targeting the identified proteins, which may serve as candidates for drug repurposing for treating PCa. In conclusion, this study identifies novel protein biomarker candidates for PCa risk, which may provide new perspectives on the etiology of PCa and improve its therapeutic strategies.
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Affiliation(s)
- Hua Zhong
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, 701 Ilalo Street, Honolulu, HI 96813, United States
| | - Jingjing Zhu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, 701 Ilalo Street, Honolulu, HI 96813, United States
| | - Shuai Liu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, 701 Ilalo Street, Honolulu, HI 96813, United States
| | - Dalia H Ghoneim
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, 701 Ilalo Street, Honolulu, HI 96813, United States
| | - Praveen Surendran
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Papworth Road, Cambridge Biomedical Campus, Cambridge, CB2 0BB, United Kingdom
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Sarah Fahle
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Papworth Road, Cambridge Biomedical Campus, Cambridge, CB2 0BB, United Kingdom
| | - Adam Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Papworth Road, Cambridge Biomedical Campus, Cambridge, CB2 0BB, United Kingdom
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Papworth Road, Cambridge Biomedical Campus, Cambridge, CB2 0BB, United Kingdom
| | - Md Ashad Alam
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University, 1440 Canal Street, New Orleans, LA 70112, United States
- Center for Outcomes Research, Ochsner Clinic Foundation, New Orleans, LA 70121, United States
| | - Hong-Wen Deng
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University, 1440 Canal Street, New Orleans, LA 70112, United States
| | - Herbert Yu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, 701 Ilalo Street, Honolulu, HI 96813, United States
| | - Chong Wu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 1400 Pressler Street, Houston, TX 77030, United States
| | - Lang Wu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, 701 Ilalo Street, Honolulu, HI 96813, United States
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9
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Roach M, Coleman PW, Kittles R. Prostate Cancer, Race, and Health Disparity: What We Know. Cancer J 2023; 29:328-337. [PMID: 37963367 DOI: 10.1097/ppo.0000000000000688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
ABSTRACT Prostate cancer (PCa) in African American men is one of the most common cancers with a great disparity in outcomes. The higher incidence and tendency to present with more advanced disease have prompted investigators to postulate that this is a problem of innate biology. However, unequal access to health care and poorer quality of care raise questions about the relative importance of genetics versus social/health injustice. Although race is inconsistent with global human genetic diversity, we need to understand the sociocultural reality that race and racism impact biology. Genetic studies reveal enrichment of PCa risk alleles in populations of West African descent and population-level differences in tumor immunology. Structural racism may explain some of the differences previously reported in PCa clinical outcomes; fortunately, there is high-level evidence that when care is comparable, outcomes are comparable.
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Affiliation(s)
- Mack Roach
- From the Particle Therapy Research Program & Outreach, Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Pamela W Coleman
- Department of Surgery/Obstetrics-Gynecology, Howard University College of Medicine, Washington, DC
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10
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Shannon ML, Muhammad A, James NT, Williams ML, Breeyear J, Edwards T, Mosley JD, Choi L, Kannankeril P, Van Driest S. Variant-based heritability assessment of dexmedetomidine and fentanyl clearance in pediatric patients. Clin Transl Sci 2023; 16:1628-1638. [PMID: 37353859 PMCID: PMC10499425 DOI: 10.1111/cts.13574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/12/2023] [Accepted: 06/01/2023] [Indexed: 06/25/2023] Open
Abstract
Despite complex pathways of drug disposition, clinical pharmacogenetic predictors currently rely on only a few high effect variants. Quantification of the polygenic contribution to variability in drug disposition is necessary to prioritize target drugs for pharmacogenomic approaches and guide analytic methods. Dexmedetomidine and fentanyl, often used in postoperative care of pediatric patients, have high rates of inter-individual variability in dosing requirements. Analyzing previously generated population pharmacokinetic parameters, we used Bayesian hierarchical mixed modeling to measure narrow-sense (additive) heritability (h SNP 2 ) of dexmedetomidine and fentanyl clearance in children and identify relative contributions of small, moderate, and large effect-size variants toh SNP 2 . We used genome-wide association studies (GWAS) to identify variants contributing to variation in dexmedetomidine and fentanyl clearance, followed by functional analyses to identify associated pathways. For dexmedetomidine, median clearance was 33.0 L/h (interquartile range [IQR] 23.8-47.9 L/h) andh SNP 2 was estimated to be 0.35 (90% credible interval 0.00-0.90), with 45% ofh SNP 2 attributed to large-, 32% to moderate-, and 23% to small-effect variants. The fentanyl cohort had median clearance of 8.2 L/h (IQR 4.7-16.7 L/h), with estimatedh SNP 2 of 0.30 (90% credible interval 0.00-0.84). Large-effect variants accounted for 30% ofh SNP 2 , whereas moderate- and small-effect variants accounted for 37% and 33%, respectively. As expected, given small sample sizes, no individual variants or pathways were significantly associated with dexmedetomidine or fentanyl clearance by GWAS. We conclude that clearance of both drugs is highly polygenic, motivating the future use of polygenic risk scores to guide appropriate dosing of dexmedetomidine and fentanyl.
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Affiliation(s)
| | - Ayesha Muhammad
- School of MedicineVanderbilt UniversityNashvilleTennesseeUSA
| | - Nathan T. James
- Department of BiostatisticsVanderbilt University Medical CenterNashvilleTennesseeUSA
- Present address:
Berry Consultants, LLCAustinTexasUSA
| | - Michael L. Williams
- Department of BiostatisticsVanderbilt University Medical CenterNashvilleTennesseeUSA
- Present address:
Department of Clinical Pharmacology and Quantitative PharmacologyAstraZenecaGothenburgSweden
| | - Joseph Breeyear
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Todd Edwards
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Jonathan D. Mosley
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Leena Choi
- Department of BiostatisticsVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Prince Kannankeril
- Center for Pediatric Precision Medicine, Department of PediatricsVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Sara Van Driest
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
- Center for Pediatric Precision Medicine, Department of PediatricsVanderbilt University Medical CenterNashvilleTennesseeUSA
- Present address:
All of Us Research ProgramNational Institutes of HealthWashingtonDCUSA
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11
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Spisak S, Tisza V, Nuzzo PV, Seo JH, Pataki B, Ribli D, Sztupinszki Z, Bell C, Rohanizadegan M, Stillman DR, Alaiwi SA, Bartels AH, Papp M, Shetty A, Abbasi F, Lin X, Lawrenson K, Gayther SA, Pomerantz M, Baca S, Solymosi N, Csabai I, Szallasi Z, Gusev A, Freedman ML. A biallelic multiple nucleotide length polymorphism explains functional causality at 5p15.33 prostate cancer risk locus. Nat Commun 2023; 14:5118. [PMID: 37612286 PMCID: PMC10447552 DOI: 10.1038/s41467-023-40616-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/03/2023] [Indexed: 08/25/2023] Open
Abstract
To date, single-nucleotide polymorphisms (SNPs) have been the most intensively investigated class of polymorphisms in genome wide associations studies (GWAS), however, other classes such as insertion-deletion or multiple nucleotide length polymorphism (MNLPs) may also confer disease risk. Multiple reports have shown that the 5p15.33 prostate cancer risk region is a particularly strong expression quantitative trait locus (eQTL) for Iroquois Homeobox 4 (IRX4) transcripts. Here, we demonstrate using epigenome and genome editing that a biallelic (21 and 47 base pairs (bp)) MNLP is the causal variant regulating IRX4 transcript levels. In LNCaP prostate cancer cells (homozygous for the 21 bp short allele), a single copy knock-in of the 47 bp long allele potently alters the chromatin state, enabling de novo functional binding of the androgen receptor (AR) associated with increased chromatin accessibility, Histone 3 lysine 27 acetylation (H3K27ac), and ~3-fold upregulation of IRX4 expression. We further show that an MNLP is amongst the strongest candidate susceptibility variants at two additional prostate cancer risk loci. We estimated that at least 5% of prostate cancer risk loci could be explained by functional non-SNP causal variants, which may have broader implications for other cancers GWAS. More generally, our results underscore the importance of investigating other classes of inherited variation as causal mediators of human traits.
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Affiliation(s)
- Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Viktoria Tisza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Computational Health Informatics Program (CHIP) Boston Children's Hospital Harvard Medical School, Boston, MA, 02215, USA
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary
| | - Pier Vitale Nuzzo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Internal Medicine, School of Medicine, University of Genoa, Genoa, Lgo R. Benzi 10, 16132, Italy
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Balint Pataki
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Dezso Ribli
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Zsofia Sztupinszki
- Computational Health Informatics Program (CHIP) Boston Children's Hospital Harvard Medical School, Boston, MA, 02215, USA
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Mersedeh Rohanizadegan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David R Stillman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sarah Abou Alaiwi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Alan H Bartels
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Marton Papp
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary
- Centre for Bioinformatics, University of Veterinary Medicine, Istvan str. 2, Budapest, 1078, Hungary
| | - Anamay Shetty
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Division of Genetics, Brigham & Women's Hospital, Boston, MA, USA
| | - Forough Abbasi
- Women's Cancer Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Xianzhi Lin
- Women's Cancer Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Kate Lawrenson
- Women's Cancer Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Simon A Gayther
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Mark Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sylvan Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - Norbert Solymosi
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Istvan Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Zoltan Szallasi
- Computational Health Informatics Program (CHIP) Boston Children's Hospital Harvard Medical School, Boston, MA, 02215, USA
- Department of Bioinformatics, Forensic and Insurance Medicine Semmelweis University, Budapest, Hungary
- Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
- National Korányi Institute of Pulmonology, Budapest, 1112, Hungary
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Division of Genetics, Brigham & Women's Hospital, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA.
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12
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Ito S, Liu X, Ishikawa Y, Conti DD, Otomo N, Kote-Jarai Z, Suetsugu H, Eeles RA, Koike Y, Hikino K, Yoshino S, Tomizuka K, Horikoshi M, Ito K, Uchio Y, Momozawa Y, Kubo M, Kamatani Y, Matsuda K, Haiman CA, Ikegawa S, Nakagawa H, Terao C. Androgen receptor binding sites enabling genetic prediction of mortality due to prostate cancer in cancer-free subjects. Nat Commun 2023; 14:4863. [PMID: 37612283 PMCID: PMC10447511 DOI: 10.1038/s41467-023-39858-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 06/27/2023] [Indexed: 08/25/2023] Open
Abstract
Prostate cancer (PrCa) is the second most common cancer worldwide in males. While strongly warranted, the prediction of mortality risk due to PrCa, especially before its development, is challenging. Here, we address this issue by maximizing the statistical power of genetic data with multi-ancestry meta-analysis and focusing on binding sites of the androgen receptor (AR), which has a critical role in PrCa. Taking advantage of large Japanese samples ever, a multi-ancestry meta-analysis comprising more than 300,000 subjects in total identifies 9 unreported loci including ZFHX3, a tumor suppressor gene, and successfully narrows down the statistically finemapped variants compared to European-only studies, and these variants strongly enrich in AR binding sites. A polygenic risk scores (PRS) analysis restricting to statistically finemapped variants in AR binding sites shows among cancer-free subjects, individuals with a PRS in the top 10% have a strongly higher risk of the future death of PrCa (HR: 5.57, P = 4.2 × 10-10). Our findings demonstrate the potential utility of leveraging large-scale genetic data and advanced analytical methods in predicting the mortality of PrCa.
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Affiliation(s)
- Shuji Ito
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Bone and Joint Diseases, Yokohama, Japan
- Department of Orthopedic Surgery, Shimane University, Izumo, Japan
| | - Xiaoxi Liu
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Yuki Ishikawa
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - David D Conti
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Nao Otomo
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
- Department of Orthopedic Surgery, School of Medicine, Keio University, Tokyo, Japan
| | | | - Hiroyuki Suetsugu
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
- Department of Orthopedic Surgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | - Yoshinao Koike
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
- Department of Orthopedic Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Keiko Hikino
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Pharmacogenomics, Yokohama, Japan
| | - Soichiro Yoshino
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
- Department of Orthopedic Surgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kohei Tomizuka
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Momoko Horikoshi
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Genomics of Diabetes and Metabolism, Yokohama, Japan
| | - Kaoru Ito
- RIKEN Center for Integrative Medical Sciences, The Cardiovascular Genomics and Informatics, Yokohama, Japan
| | - Yuji Uchio
- Department of Orthopedic Surgery, Shimane University, Izumo, Japan
| | - Yukihide Momozawa
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Genotyping Development, Yokohama, Japan
| | | | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Koichi Matsuda
- Institute of Medical Science, The University of Tokyo, Laboratory of Genome Technology, Human Genome Center, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Tokyo, Japan
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shiro Ikegawa
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Bone and Joint Diseases, Yokohama, Japan
| | - Hidewaki Nakagawa
- RIKEN Center for Integrative Medical Sciences, Laboratory for Cancer Genomics, Yokohama, Japan
| | - Chikashi Terao
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan.
- Shizuoka General Hospital, The Clinical Research Center, Shizuoka, Japan.
- School of Pharmaceutical Sciences, University of Shizuoka, The Department of Applied Genetics, Shizuoka, Japan.
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13
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Kurup JT, Kim S, Kidder BL. Identifying Cancer Type-Specific Transcriptional Programs through Network Analysis. Cancers (Basel) 2023; 15:4167. [PMID: 37627195 PMCID: PMC10453000 DOI: 10.3390/cancers15164167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Identifying cancer type-specific genes that define cell states is important to develop effective therapies for patients and methods for detection, early diagnosis, and prevention. While molecular mechanisms that drive malignancy have been identified for various cancers, the identification of cell-type defining transcription factors (TFs) that distinguish normal cells from cancer cells has not been fully elucidated. Here, we utilized a network biology framework, which assesses the fidelity of cell fate conversions, to identify cancer type-specific gene regulatory networks (GRN) for 17 types of cancer. Through an integrative analysis of a compendium of expression data, we elucidated core TFs and GRNs for multiple cancer types. Moreover, by comparing normal tissues and cells to cancer type-specific GRNs, we found that the expression of key network-influencing TFs can be utilized as a survival prognostic indicator for a diverse cohort of cancer patients. These findings offer a valuable resource for exploring cancer type-specific networks across a broad range of cancer types.
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Affiliation(s)
- Jiji T. Kurup
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (J.T.K.); (S.K.)
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Seongho Kim
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (J.T.K.); (S.K.)
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Benjamin L. Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (J.T.K.); (S.K.)
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
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14
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Sanchez A, Lhuillier J, Grosjean G, Ayadi L, Maenner S. The Long Non-Coding RNA ANRIL in Cancers. Cancers (Basel) 2023; 15:4160. [PMID: 37627188 PMCID: PMC10453084 DOI: 10.3390/cancers15164160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
ANRIL (Antisense Noncoding RNA in the INK4 Locus), a long non-coding RNA encoded in the human chromosome 9p21 region, is a critical factor for regulating gene expression by interacting with multiple proteins and miRNAs. It has been found to play important roles in various cellular processes, including cell cycle control and proliferation. Dysregulation of ANRIL has been associated with several diseases like cancers and cardiovascular diseases, for instance. Understanding the oncogenic role of ANRIL and its potential as a diagnostic and prognostic biomarker in cancer is crucial. This review provides insights into the regulatory mechanisms and oncogenic significance of the 9p21 locus and ANRIL in cancer.
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Affiliation(s)
| | | | | | - Lilia Ayadi
- CNRS, Université de Lorraine, IMoPA, F-54000 Nancy, France
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15
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Yang X, Zhang Q, Li S, Devarajan R, Luo B, Tan Z, Wang Z, Giannareas N, Wenta T, Ma W, Li Y, Yang Y, Manninen A, Wu S, Wei GH. GATA2 co-opts TGFβ1/SMAD4 oncogenic signaling and inherited variants at 6q22 to modulate prostate cancer progression. J Exp Clin Cancer Res 2023; 42:198. [PMID: 37550764 PMCID: PMC10408074 DOI: 10.1186/s13046-023-02745-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 06/30/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Aberrant somatic genomic alteration including copy number amplification is a hallmark of cancer genomes. We previously profiled genomic landscapes of prostate cancer (PCa), yet the underlying causal genes with prognostic potential has not been defined. It remains unclear how a somatic genomic event cooperates with inherited germline variants contribute to cancer predisposition and progression. METHODS We applied integrated genomic and clinical data, experimental models and bioinformatic analysis to identify GATA2 as a highly prevalent metastasis-associated genomic amplification in PCa. Biological roles of GATA2 in PCa metastasis was determined in vitro and in vivo. Global chromatin co-occupancy and co-regulation of GATA2 and SMAD4 was investigated by coimmunoprecipitation, ChIP-seq and RNA-seq assays. Tumor cellular assays, qRT-PCR, western blot, ChIP, luciferase assays and CRISPR-Cas9 editing methods were performed to mechanistically understand the cooperation of GATA2 with SMAD4 in promoting TGFβ1 and AR signaling and mediating inherited PCa risk and progression. RESULTS In this study, by integrated genomics and experimental analysis, we identified GATA2 as a prevalent metastasis-associated genomic amplification to transcriptionally augment its own expression in PCa. Functional experiments demonstrated that GATA2 physically interacted and cooperated with SMAD4 for genome-wide chromatin co-occupancy and co-regulation of PCa genes and metastasis pathways like TGFβ signaling. Mechanistically, GATA2 was cooperative with SMAD4 to enhance TGFβ and AR signaling pathways, and activated the expression of TGFβ1 via directly binding to a distal enhancer of TGFβ1. Strinkingly, GATA2 and SMAD4 globally mediated inherited PCa risk and formed a transcriptional complex with HOXB13 at the PCa risk-associated rs339331/6q22 enhancer, leading to increased expression of the PCa susceptibility gene RFX6. CONCLUSIONS Our study prioritizes causal genomic amplification genes with prognostic values in PCa and reveals the pivotal roles of GATA2 in transcriptionally activating the expression of its own and TGFβ1, thereby co-opting to TGFβ1/SMAD4 signaling and RFX6 at 6q22 to modulate PCa predisposition and progression.
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Affiliation(s)
- Xiayun Yang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Qin Zhang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Shuxuan Li
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Raman Devarajan
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Binjie Luo
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Zenglai Tan
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Zixian Wang
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Nikolaos Giannareas
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Tomasz Wenta
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Wenlong Ma
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Yuqing Li
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Yuehong Yang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Aki Manninen
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Song Wu
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China.
- Institute of Urology, South China Hospital of Shenzhen University, Shenzhen, China.
| | - Gong-Hong Wei
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China.
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16
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Kazmi N, Valeeva EV, Khasanova GR, Lewis SJ, Plotnikov D. Blood pressure, calcium channel blockers, and the risk of prostate cancer: a Mendelian randomization study. Cancer Causes Control 2023; 34:725-734. [PMID: 37178364 DOI: 10.1007/s10552-023-01712-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/04/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND Observational studies have found some evidence of an association between elevated blood pressure and prostate cancer risk; however, the results are inconclusive. We tested whether systolic blood pressure (SBP) influences prostate cancer risk and evaluated the effect of calcium channel blockers (CCB) on the disease using Mendelian randomization (MR) approach. METHODS We used 278 genetic variants associated with SBP and 16 genetic variants in CCB genes as instrumental variables. Effect estimates were obtained from the UK Biobank sample of 142,995 males and from PRACTICAL consortium (79,148 cases and 61,106 controls). RESULTS For each 10 mm Hg increase in SBP the estimated effect was OR 0.96 (0.90-1.01) for overall prostate cancer; and OR 0.92 (0.85-0.99) for aggressive prostate cancer. The MR-estimated effect of a 10 mm Hg- SBP lowering through CCB genetic variants was OR 1.22 (1.06-1.42) for all prostate cancers and OR 1.49 (1.18-1.89) for aggressive prostate cancer. CONCLUSION The results of our study did not support a causal relationship between SBP and prostate cancer; however, we found weak evidence of a protective effect of high SBP on aggressive prostate cancer and we found that blocking calcium channel receptors may increase prostate cancer risk.
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Affiliation(s)
- Nabila Kazmi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Bristol, UK
| | - Elena V Valeeva
- Central Research Laboratory, Kazan State Medical University, Butlerov Str., 49, Tatarstan, Kazan, Russia, 420012
| | - Gulshat R Khasanova
- Epidemiology and Evidence-Based Medicine Department, Kazan State Medical University, Kazan, Russia
| | - Sarah J Lewis
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Bristol, UK
| | - Denis Plotnikov
- Central Research Laboratory, Kazan State Medical University, Butlerov Str., 49, Tatarstan, Kazan, Russia, 420012.
- School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK.
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17
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Al-Rashidi RR, Noraldeen SAM, Kareem AK, Mahmoud AK, Kadhum WR, Ramírez-Coronel AA, Iswanto AH, Obaid RF, Jalil AT, Mustafa YF, Nabavi N, Wang Y, Wang L. Malignant function of nuclear factor-kappaB axis in prostate cancer: Molecular interactions and regulation by non-coding RNAs. Pharmacol Res 2023; 194:106775. [PMID: 37075872 DOI: 10.1016/j.phrs.2023.106775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/09/2023] [Accepted: 04/16/2023] [Indexed: 04/21/2023]
Abstract
Prostate carcinoma is a malignant situation that arises from genomic alterations in the prostate, leading to changes in tumorigenesis. The NF-κB pathway modulates various biological mechanisms, including inflammation and immune responses. Dysregulation of NF-κB promotes carcinogenesis, including increased proliferation, invasion, and therapy resistance. As an incurable disease globally, prostate cancer is a significant health concern, and research into genetic mutations and NF-κB function has the efficacy to facilitate the introduction of novel therapies. NF-κB upregulation is observed during prostate cancer progression, resulting in increased cell cycle progression and proliferation rates. Additionally, NF-κB endorses resistance to cell death and enhances the capacity for metastasis, particularly bone metastasis. Overexpression of NF-κB triggers chemoresistance and radio-resistance, and inhibition of NF-κB by anti-tumor compounds can reduce cancer progression. Interestingly, non-coding RNA transcripts can regulate NF-κB level and its nuclear transfer, offering a potential avenue for modulating prostate cancer progression.
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Affiliation(s)
| | | | - Ali Kamil Kareem
- Biomedical Engineering Department, Al-Mustaqbal University College, 51001, Hillah, Iraq
| | | | - Wesam R Kadhum
- Department of Pharmacy, Kut University College, Kut 52001, Wasit, Iraq
| | - Andrés Alexis Ramírez-Coronel
- Azogues Campus Nursing Career, Health and Behavior Research Group (HBR), Psychometry and Ethology Laboratory, Catholic University of Cuenca, Ecuador; University of Palermo, Buenos Aires, Argentina; Epidemiology and Biostatistics Research Group, CES University, Colombia
| | - Acim Heri Iswanto
- Department of Public Health, Faculty of Health Science, University of Pembangunan Nasional Veteran Jakarta, Jakarta, Indonesia
| | - Rasha Fadhel Obaid
- Department of Biomedical Engineering, Al-Mustaqbal University College, Babylon, Iraq
| | - Abduladheem Turki Jalil
- Medical Laboratory Technology Department, College of Medical Technology, The Islamic University, Najaf, Iraq
| | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul 41001, Iraq
| | - Noushin Nabavi
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, V6H3Z6 Vancouver, BC, Canada.
| | - Yuzhuo Wang
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, V6H3Z6 Vancouver, BC, Canada; Department of Experimental Therapeutics, BC Cancer Research Institute, V5Z1L3 Vancouver, BC, Canada.
| | - Lin Wang
- Department of Geriatrics, Xijing Hospital, The Air Force Military Medical University, Xi'an 710032, China.
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18
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Boldrini L, Bardi M. WSB1 Involvement in Prostate Cancer Progression. Genes (Basel) 2023; 14:1558. [PMID: 37628609 PMCID: PMC10454498 DOI: 10.3390/genes14081558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Prostate cancer (PC) is polygenic disease involving many genes, and more importantly a host of gene-gene interactions, including transcriptional factors. The WSB1 gene is a transcriptional target of numerous oncoproteins, and its dysregulation can contribute to tumor progression by abnormal activation of targeted oncogenes. Using data from the Cancer Genome Atlas, we tested the possible involvement of WSB1 in PC progression. A multi-dimensional scaling (MDS) model was applied to clarify the association of WSB1 expression with other key genes, such as c-myc, ERG, Enhancer of Zeste 1 and 2 (EHZ1 and EZH2), WNT10a, and WNT 10b. An increased WSB1 expression was associated with higher PC grades and with a worse prognosis. It was also positively related to EZH1, EZH2, WNT10a, and WNT10b. Moreover, MDS showed the central role of WSB1 in influencing the other target genes by its central location on the map. Our study is the first to show a link between WSB1 expression and other genes involved in PC progression, suggesting a novel role for WSB1 in PC progression. This network between WSB1 and EZH2 through WNT/β-catenin may have an important role in PC progression, as suggested by the association between high WSB1 expression and unfavorable prognosis in our analysis.
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Affiliation(s)
- Laura Boldrini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, 56126 Pisa, Italy
| | - Massimo Bardi
- Department of Psychology & Behavioral Neuroscience, Randolph-Macon College, Ashland, VA 23005, USA
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19
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Chen F, Madduri RK, Rodriguez AA, Darst BF, Chou A, Sheng X, Wang A, Shen J, Saunders EJ, Rhie SK, Bensen JT, Ingles SA, Kittles RA, Strom SS, Rybicki BA, Nemesure B, Isaacs WB, Stanford JL, Zheng W, Sanderson M, John EM, Park JY, Xu J, Wang Y, Berndt SI, Huff CD, Yeboah ED, Tettey Y, Lachance J, Tang W, Rentsch CT, Cho K, Mcmahon BH, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Sellers TA, Yamoah K, Murphy AB, Crawford DC, Patel AV, Bush WS, Aldrich MC, Cussenot O, Petrovics G, Cullen J, Neslund-Dudas CM, Stern MC, Kote-Jarai Z, Govindasami K, Cook MB, Chokkalingam AP, Hsing AW, Goodman PJ, Hoffmann TJ, Drake BF, Hu JJ, Keaton JM, Hellwege JN, Clark PE, Jalloh M, Gueye SM, Niang L, Ogunbiyi O, Idowu MO, Popoola O, Adebiyi AO, Aisuodionoe-Shadrach OI, Ajibola HO, Jamda MA, Oluwole OP, Nwegbu M, Adusei B, Mante S, Darkwa-Abrahams A, Mensah JE, Diop H, Van Den Eeden SK, Blanchet P, Fowke JH, Casey G, Hennis AJ, Lubwama A, Thompson IM, Leach R, Easton DF, Preuss MH, Loos RJ, Gundell SM, Wan P, Mohler JL, Fontham ET, Smith GJ, Taylor JA, Srivastava S, Eeles RA, Carpten JD, Kibel AS, Multigner L, Parent MÉ, Menegaux F, Cancel-Tassin G, Klein EA, Andrews C, Rebbeck TR, Brureau L, Ambs S, Edwards TL, Watya S, Chanock SJ, Witte JS, Blot WJ, Michael Gaziano J, Justice AC, Conti DV, Haiman CA. Evidence of Novel Susceptibility Variants for Prostate Cancer and a Multiancestry Polygenic Risk Score Associated with Aggressive Disease in Men of African Ancestry. Eur Urol 2023; 84:13-21. [PMID: 36872133 PMCID: PMC10424812 DOI: 10.1016/j.eururo.2023.01.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/14/2022] [Accepted: 01/24/2023] [Indexed: 03/06/2023]
Abstract
BACKGROUND Genetic factors play an important role in prostate cancer (PCa) susceptibility. OBJECTIVE To discover common genetic variants contributing to the risk of PCa in men of African ancestry. DESIGN, SETTING, AND PARTICIPANTS We conducted a meta-analysis of ten genome-wide association studies consisting of 19378 cases and 61620 controls of African ancestry. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Common genotyped and imputed variants were tested for their association with PCa risk. Novel susceptibility loci were identified and incorporated into a multiancestry polygenic risk score (PRS). The PRS was evaluated for associations with PCa risk and disease aggressiveness. RESULTS AND LIMITATIONS Nine novel susceptibility loci for PCa were identified, of which seven were only found or substantially more common in men of African ancestry, including an African-specific stop-gain variant in the prostate-specific gene anoctamin 7 (ANO7). A multiancestry PRS of 278 risk variants conferred strong associations with PCa risk in African ancestry studies (odds ratios [ORs] >3 and >5 for men in the top PRS decile and percentile, respectively). More importantly, compared with men in the 40-60% PRS category, men in the top PRS decile had a significantly higher risk of aggressive PCa (OR = 1.23, 95% confidence interval = 1.10-1.38, p = 4.4 × 10-4). CONCLUSIONS This study demonstrates the importance of large-scale genetic studies in men of African ancestry for a better understanding of PCa susceptibility in this high-risk population and suggests a potential clinical utility of PRS in differentiating between the risks of developing aggressive and nonaggressive disease in men of African ancestry. PATIENT SUMMARY In this large genetic study in men of African ancestry, we discovered nine novel prostate cancer (PCa) risk variants. We also showed that a multiancestry polygenic risk score was effective in stratifying PCa risk, and was able to differentiate risk of aggressive and nonaggressive disease.
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Affiliation(s)
- Fei Chen
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Burcu F Darst
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alisha Chou
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xin Sheng
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Anqi Wang
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jiayi Shen
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jeannette T Bensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sue A Ingles
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rick A Kittles
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Sara S Strom
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - William B Isaacs
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Maureen Sanderson
- Department of Family and Community Medicine, Meharry Medical College, Nashville, TN, USA
| | - Esther M John
- Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Ying Wang
- Department of Population Science, American Cancer Society, Kennesaw, GA, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | | | - Yao Tettey
- Department of Pathology, University of Ghana, Accra, Ghana; Korle Bu Teaching Hospital, Accra, Ghana
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Christopher T Rentsch
- Yale School of Medicine, New Haven, CT, USA; VA Connecticut Healthcare System, West Haven, CT, USA; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Kelly Cho
- Division of Aging, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Jamaica Plain, MA, USA
| | - Benjamin H Mcmahon
- Theoretical Biology Division, Los Alamos National Lab, Los Alamos, NM, USA
| | | | - Andrew A Adjei
- Department of Pathology, University of Ghana Medical School, Accra, Ghana
| | - Evelyn Tay
- Korle Bu Teaching Hospital, Accra, Ghana
| | | | | | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Kosj Yamoah
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA; Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Adam B Murphy
- Department of Urology, Northwestern University, Chicago, IL, USA
| | - Dana C Crawford
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Alpa V Patel
- Department of Population Science, American Cancer Society, Kennesaw, GA, USA
| | - William S Bush
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Melinda C Aldrich
- Division of Epidemiology, Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Olivier Cussenot
- Department of Urology and Predictive Onco-Urology Group, Sorbonne Université, GRC 5 Predictive Onco-Urology, APHP-Sorbonne Université, Paris, France; CeRePP, Tenon Hospital, Paris, France
| | - Gyorgy Petrovics
- Department of Surgery, Center for Prostate Disease Research, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jennifer Cullen
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA; Department of Surgery, Center for Prostate Disease Research, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | - Mariana C Stern
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Michael B Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Ann W Hsing
- Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Bettina F Drake
- Division of Public Health Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Jennifer J Hu
- The University of Miami School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Jacob M Keaton
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jacklyn N Hellwege
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Nashville, TN, USA
| | - Peter E Clark
- Atrium Health/Levine Cancer Institute, Charlotte, NC, USA
| | | | | | | | - Olufemi Ogunbiyi
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Michael O Idowu
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Olufemi Popoola
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Akindele O Adebiyi
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Oseremen I Aisuodionoe-Shadrach
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Hafees O Ajibola
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Mustapha A Jamda
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Olabode P Oluwole
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Maxwell Nwegbu
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | | | | | | | | | - Halimatou Diop
- Laboratoires Bacteriologie et Virologie, Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Stephen K Van Den Eeden
- Division of Research, Kaiser Permanente, Northern California, Oakland, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Pascal Blanchet
- CHU de Pointe-à-Pitre, Univ Antilles, Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Pointe-à-Pitre, Guadeloupe, France
| | - Jay H Fowke
- Department of Preventive Medicine, Division of Epidemiology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Graham Casey
- Department of Public Health Science, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Anselm J Hennis
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | | | - Ian M Thompson
- CHRISTUS Santa Rosa Medical Center Hospital, San Antonio, TX, USA
| | - Robin Leach
- Department of Urology, Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Susan M Gundell
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Peggy Wan
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - James L Mohler
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Elizabeth T Fontham
- School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Gary J Smith
- Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA; Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Shiv Srivastava
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Rosaline A Eeles
- The Institute of Cancer Research, London, UK; Royal Marsden NHS Foundation Trust, London, UK
| | - John D Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Adam S Kibel
- Department of Urology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Luc Multigner
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Rennes, France
| | - Marie-Élise Parent
- Epidemiology and Biostatistics Unit, Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC, Canada
| | - Florence Menegaux
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Villejuif Cédex, France; Paris-Sud University, Villejuif Cédex, France
| | - Geraldine Cancel-Tassin
- Department of Urology and Predictive Onco-Urology Group, Sorbonne Université, GRC 5 Predictive Onco-Urology, APHP-Sorbonne Université, Paris, France; CeRePP, Tenon Hospital, Paris, France
| | - Eric A Klein
- Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Caroline Andrews
- Harvard TH Chan School of Public Health and Division of Population Sciences, Dana Farber Cancer Institute, Boston, MA, USA; Glickman Urological & Kidney Institute, Cleveland, OH, USA
| | - Timothy R Rebbeck
- Harvard TH Chan School of Public Health and Division of Population Sciences, Dana Farber Cancer Institute, Boston, MA, USA
| | - Laurent Brureau
- CHU de Pointe-à-Pitre, Univ Antilles, Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Pointe-à-Pitre, Guadeloupe, France
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Todd L Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; International Epidemiology Institute, Rockville, MD, USA
| | - J Michael Gaziano
- Division of Aging, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA
| | - Amy C Justice
- Yale School of Medicine, New Haven, CT, USA; VA Connecticut Healthcare System, West Haven, CT, USA
| | - David V Conti
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher A Haiman
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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20
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Pagadala M, Sears TJ, Wu VH, Pérez-Guijarro E, Kim H, Castro A, Talwar JV, Gonzalez-Colin C, Cao S, Schmiedel BJ, Goudarzi S, Kirani D, Au J, Zhang T, Landi T, Salem RM, Morris GP, Harismendy O, Patel SP, Alexandrov LB, Mesirov JP, Zanetti M, Day CP, Fan CC, Thompson WK, Merlino G, Gutkind JS, Vijayanand P, Carter H. Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response. Nat Commun 2023; 14:2744. [PMID: 37173324 PMCID: PMC10182072 DOI: 10.1038/s41467-023-38271-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
With the continued promise of immunotherapy for treating cancer, understanding how host genetics contributes to the tumor immune microenvironment (TIME) is essential to tailoring cancer screening and treatment strategies. Here, we study 1084 eQTLs affecting the TIME found through analysis of The Cancer Genome Atlas and literature curation. These TIME eQTLs are enriched in areas of active transcription, and associate with gene expression in specific immune cell subsets, such as macrophages and dendritic cells. Polygenic score models built with TIME eQTLs reproducibly stratify cancer risk, survival and immune checkpoint blockade (ICB) response across independent cohorts. To assess whether an eQTL-informed approach could reveal potential cancer immunotherapy targets, we inhibit CTSS, a gene implicated by cancer risk and ICB response-associated polygenic models; CTSS inhibition results in slowed tumor growth and extended survival in vivo. These results validate the potential of integrating germline variation and TIME characteristics for uncovering potential targets for immunotherapy.
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Affiliation(s)
- Meghana Pagadala
- Biomedical Sciences Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Timothy J Sears
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Victoria H Wu
- Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, CA, 92093, USA
| | - Eva Pérez-Guijarro
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Hyo Kim
- Undergraduate Bioengineering Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andrea Castro
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - James V Talwar
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Steven Cao
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | | | | | - Divya Kirani
- Undergraduate Biology and Bioinformatics Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jessica Au
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Rany M Salem
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Olivier Harismendy
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Sandip Pravin Patel
- Center for Personalized Cancer Therapy, Division of Hematology and Oncology, UC San Diego Moores Cancer Center, San Diego, CA, 92037, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jill P Mesirov
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Maurizio Zanetti
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
- The Laboratory of Immunology and Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Chun Chieh Fan
- Center for Population Neuroscience and Genetics, Laureate Institute for Brain Research, Tulsa, OK, 74136, USA
- Department of Radiology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Wesley K Thompson
- Division of Biostatistics, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | - Glenn Merlino
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - J Silvio Gutkind
- Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, CA, 92093, USA
| | | | - Hannah Carter
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA.
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21
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Erzurumlu Y, Catakli D, Dogan HK. Potent carotenoid astaxanthin expands the anti-cancer activity of cisplatin in human prostate cancer cells. J Nat Med 2023; 77:572-583. [PMID: 37130999 DOI: 10.1007/s11418-023-01701-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/12/2023] [Indexed: 05/04/2023]
Abstract
Prostate cancer (PCa) is the second most common type of cancer and the sixth cause of death in men worldwide. Radiotherapy and immunotherapy are commonly used in treating PCa, but understanding the crosstalk mechanisms of carcinogenesis and new therapeutic approaches is essential for supporting poor diagnosis and existing therapies. Astaxanthin (ASX) is a member of the xanthophyll family that is an oxygenated derivative of carotenoids whose synthesis is in plant extracts from lycopene. ASX has protective effects on various diseases, such as Parkinson's disease and cancer by showing potent antioxidant and anti-inflammatory properties. However, there is an ongoing need for a detailed investigation of the molecular mechanism of action to expand its therapeutic use. In the present study, we showed the new regulatory role of ASX in PCa cells by affecting the unfolded protein response (UPR) signaling, autophagic activity, epithelial-mesenchymal transition (EMT) and regulating the expression level of angiogenesis-related protein vascular endothelial growth factor A (VEGF-A), proto-oncogene c-Myc and prostate-specific antigen (PSA). Additionally, we determined that it exhibited synergistic action with cisplatin and significantly enhanced apoptotic cell death in PCa cells. Present findings suggest that ASX may be a potent adjuvant therapeutic option in PCa treatment when used alone or combined with chemotherapeutics. Schematic illustration of the biochemical activity of astaxanthin and its combination with cisplatin.
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Affiliation(s)
- Yalcin Erzurumlu
- Department of Biochemistry, Faculty of Pharmacy, Suleyman Demirel University, 32260, Isparta, Turkey.
| | - Deniz Catakli
- Department of Pharmacology, Faculty of Medicine, Suleyman Demirel University, 32260, Isparta, Turkey
| | - Hatice Kubra Dogan
- Department of Bioengineering, Institute of Science, Suleyman Demirel University, 32260, Isparta, Turkey
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22
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Kanesvaran R, Chia PL, Chiong E, Chua MLK, Ngo NT, Ow S, Sim HG, Tan MH, Tay KH, Wong ASC, Wong SW, Tan PH. An approach to genetic testing in patients with metastatic castration-resistant prostate cancer in Singapore. ANNALS OF THE ACADEMY OF MEDICINE, SINGAPORE 2023; 52:135-148. [PMID: 38904491 DOI: 10.47102/annals-acadmedsg.2022372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Introduction There has been a rapid evolution in the treatment strategies for metastatic castration-resistant prostate cancer (mCRPC) following the identification of targetable mutations, making genetic testing essential for patient selection. Although several international guidelines recommend genetic testing for patients with mCRPC, there is a lack of locally endorsed clinical practice guidelines in Singapore. Method A multidisciplinary specialist panel with representation from medical and radiation oncology, urology, pathology, interventional radiology, and medical genetics discussed the challenges associated with patient selection, genetic counselling and sample processing in mCRPC. Results A clinical model for incorporating genetic testing into routine clinical practice in Singapore was formulated. Tumour testing with an assay that is able to detect both somatic and germline mutations should be utilised. The panel also recommended the "mainstreaming" approach for genetic counselling in which pre-test counselling is conducted by the managing clinician and post-test discussion with a genetic counsellor, to alleviate the bottlenecks at genetic counselling stage in Singapore. The need for training of clinicians to provide pre-test genetic counselling and educating the laboratory personnel for appropriate sample processing that facilitates downstream genetic testing was recognised. Molecular tumour boards and multidisciplinary discussions are recommended to guide therapeutic decisions in mCRPC. The panel also highlighted the issue of reimbursement for genetic testing to reduce patient-borne costs and increase the reach of genetic testing among this patient population. Conclusion This article aims to provide strategic and implementable recommendations to overcome the challenges in genetic testing for patients with mCRPC in Singapore.
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Affiliation(s)
| | - Puey Ling Chia
- Department of Medical Oncology, Tan Tock Seng Hospital, Singapore
| | - Edmund Chiong
- Department of Urology, National University Hospital, Singapore
- Department of Surgery, National University of Singapore, Singapore
| | | | - Nye Thane Ngo
- Division of Pathology, Singapore General Hospital, Singapore
| | - Samuel Ow
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
| | - Hong Gee Sim
- Ravenna Urology Clinic, Gleneagles Medical Centre, Singapore
| | | | - Kiang Hiong Tay
- Department of Vascular and Interventional Radiation, Singapore General Hospital, Singapore
| | | | | | - Puay Hoon Tan
- Division of Pathology, Singapore General Hospital, Singapore
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23
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Srinivasan S, Kryza T, Bock N, Tse BWC, Sokolowski KA, Panchadsaram J, Moya L, Stephens C, Dong Y, Röhl J, Alinezhad S, Vela I, Perry-Keene JL, Buzacott K, Gago-Dominguez M, Schleutker J, Maier C, Muir K, Tangen CM, Gronberg H, Pashayan N, Albanes D, Wolk A, Stanford JL, Berndt SI, Mucci LA, Koutros S, Cussenot O, Sorensen KD, Grindedal EM, Key TJ, Haiman CA, Giles GG, Vega A, Wiklund F, Neal DE, Kogevinas M, Stampfer MJ, Nordestgaard BG, Brenner H, Gamulin M, Claessens F, Melander O, Dahlin A, Stattin P, Hallmans G, Häggström C, Johansson R, Thysell E, Rönn AC, Li W, Brown N, Dimeski G, Shepherd B, Dadaev T, Brook MN, Spurdle AB, Stenman UH, Koistinen H, Kote-Jarai Z, Klein RJ, Lilja H, Ecker RC, Eeles R, Clements J, Batra J. Biochemical activity induced by a germline variation in KLK3 (PSA) associates with cellular function and clinical outcome in prostate cancer. RESEARCH SQUARE 2023:rs.3.rs-2650312. [PMID: 37034758 PMCID: PMC10081352 DOI: 10.21203/rs.3.rs-2650312/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Genetic variation at the 19q13.3 KLK locus is linked with prostate cancer susceptibility. The non-synonymous KLK3 SNP, rs17632542 (c.536T>C; Ile163Thr-substitution in PSA) is associated with reduced prostate cancer risk, however, the functional relevance is unknown. Here, we identify that the SNP variant-induced change in PSA biochemical activity as a previously undescribed function mediating prostate cancer pathogenesis. The 'Thr' PSA variant led to small subcutaneous tumours, supporting reduced prostate cancer risk. However, 'Thr' PSA also displayed higher metastatic potential with pronounced osteolytic activity in an experimental metastasis in-vivo model. Biochemical characterization of this PSA variant demonstrated markedly reduced proteolytic activity that correlated with differences in in-vivo tumour burden. The SNP is associated with increased risk for aggressive disease and prostate cancer-specific mortality in three independent cohorts, highlighting its critical function in mediating metastasis. Carriers of this SNP allele had reduced serum total PSA and a higher free/total PSA ratio that could contribute to late biopsy decisions and delay in diagnosis. Our results provide a molecular explanation for the prominent 19q13.3 KLK locus, rs17632542 SNP, association with a spectrum of prostate cancer clinical outcomes.
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Affiliation(s)
- Srilakshmi Srinivasan
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Thomas Kryza
- Mater Research Institute - The University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Nathalie Bock
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Brian WC Tse
- Preclinical Imaging Facility, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Kamil A. Sokolowski
- Preclinical Imaging Facility, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Janaththani Panchadsaram
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Leire Moya
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Carson Stephens
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Ying Dong
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
| | - Joan Röhl
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
| | - Saeid Alinezhad
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Ian Vela
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Department of Urology, Princess Alexandra Hospital, Brisbane, Woolloongabba, Brisbane, QLD, Australia
| | - Joanna L. Perry-Keene
- Pathology Queensland, Sunshine Coast University Hospital Laboratory, Birtinya, Sunshine Coast, QLD, Australia
| | - Katie Buzacott
- Pathology Queensland, Sunshine Coast University Hospital Laboratory, Birtinya, Sunshine Coast, QLD, Australia
| | - The IMPACT Study
- The Institute of Cancer Research, London, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, IDIS, Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - The PROFILE Study Steering Committee
- The Institute of Cancer Research, London, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, UK
- Ronald and Rita McAulay Foundation, London, UK
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- University of Oxford, Oxford, UK
- Queen Mary University of London, London, UK
| | - Johanna Schleutker
- Institute of Biomedicine, Kiinamyllynkatu 10, FI-20014 University of Turku, Finland
- Department of Medical Genetics, Genomics, Laboratory Division, Turku University Hospital, PO Box 52, 20521 Turku, Finland
| | - Christiane Maier
- Humangenetik Tuebingen, Paul-Ehrlich-Str 23, D-72076 Tuebingen, Germany
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, University of Manchester, Manchester, M13 9PL, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Catherine M. Tangen
- SWOG Statistical Center, Division of Public Health Sciences
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Nora Pashayan
- Department of Applied Health Research, University College London, London, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge, CB1 8RN, UK
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, USA
| | - Alicja Wolk
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109-1024, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, USA
| | - Lorelei A. Mucci
- Department of Epidemiology,Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, USA
| | - Olivier Cussenot
- CeRePP and Sorbonne Universite, GRC N°5 AP-HP, Tenon Hospital, Paris, France
| | - Karina Dalsgaard Sorensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University & Department of Molecular Medicine (MOMA), Aarhus University Hospital, DK-8200 Aarhus N., Denmark
| | | | - Timothy J. Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Christopher A. Haiman
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, USA
| | - Graham G. Giles
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain
- Biomedical Network on Rare Diseases (CIBERER), Santiago de Compostela, Spain
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - David E. Neal
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, England
- Department of Oncology, Addenbrooke’s Hospital, University of Cambridge, England
| | - Manolis Kogevinas
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Research Institute), Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Meir J. Stampfer
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts; Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Børge G. Nordestgaard
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
- The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marija Gamulin
- Division of Medical Oncology, Urogenital Unit, Department of Oncology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Belgium
| | - Olle Melander
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Anders Dahlin
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Pär Stattin
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Göran Hallmans
- Department of Public Health and Clinical Medicine, Nutritional Research, Umeå University, Umeå, Sweden
| | - Christel Häggström
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Department of Biobank Research, Umeå University, Umeå, Sweden
| | | | - Elin Thysell
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Ann-Charlotte Rönn
- Clinical Research Center, Karolinska University Hospital, Huddinge, Sweden
| | - Weiqiang Li
- Icahn Institute for Data Science and Genome Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nigel Brown
- Department of Chemical Pathology, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane, QLD, Australia
| | - Goce Dimeski
- Department of Chemical Pathology, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane, QLD, Australia
| | - Benjamin Shepherd
- Department of Anatomical Pathology, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane, QLD, Australia
| | - Tokhir Dadaev
- The Institute of Cancer Research, London, SM2 5NG, UK
| | - Mark N. Brook
- The Institute of Cancer Research, London, SM2 5NG, UK
| | - Amanda B. Spurdle
- Molecular Cancer Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD, Australia
| | - Ulf-Håkan Stenman
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Hannu Koistinen
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Zsofia Kote-Jarai
- The Institute of Cancer Research, London, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | - Robert J. Klein
- Icahn Institute for Data Science and Genome Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hans Lilja
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, England
- Departments of Laboratory Medicine, Surgery (Urology Service) and Medicine (Genitourinary Oncology), Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Rupert C. Ecker
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
- TissueGnostics GmbH, Vienna, Austria
| | - Rosalind Eeles
- The Institute of Cancer Research, London, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | | | - The Australian Prostate Cancer BioResource
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Judith Clements
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT)
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Brisbane, Queensland (QLD), Australia
- Centre for Genomic and Personalised Health, Queensland University of Technology, Brisbane, QLD
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24
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Parlato LA, Welch R, Ong IM, Long J, Cai Q, Steinwandel MD, Blot WJ, Zheng W, Warren Andersen S. Genome-wide association study (GWAS) of circulating vitamin D outcomes among individuals of African ancestry. Am J Clin Nutr 2023; 117:308-316. [PMID: 36811574 PMCID: PMC10196601 DOI: 10.1016/j.ajcnut.2022.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 12/01/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Vitamin D deficiency is more common among African-ancestry individuals and may be associated with adverse health outcomes. Vitamin D binding protein (VDBP) regulates concentrations of biologically active vitamin D. OBJECTIVE We conducted genome-wide association study (GWAS) of VDBP and 25-hydroxyvitamin D among African-ancestry individuals. METHODS Data were collected from 2,602 African American adults from the Southern Community Cohort Study (SCCS) and 6,934 African- or Caribbean-ancestry adults from the UK Biobank. Serum VDBP concentrations were available only in the SCCS and were measured by using the Polyclonal Human VDBP ELISA kit. Serum 25-hydroxyvitamin D concentrations for both study samples were measured by using Diasorin Liason, a chemiluminescent immunoassay. Participants were genotyped for single nucleotide polymorphisms (SNPs) with genome-wide coverage by using Illumina or Affymetrix platforms. Fine-mapping analysis was performed by using forward stepwise linear regression models including all variants with P value < 5 × 10-8 and within 250 kbps of a lead SNP. RESULTS We identified 4 loci notably associated with VDBP concentrations in the SCCS population: rs7041 (per allele β = 0.61 μg/mL, SE = 0.05, P = 1.4 × 10-48) and rs842998 (per allele β = 0.39 μg/mL, SE = 0.03, P = 4.0 × 10-31) in GC, rs8427873 (per allele β = 0.31 μg/mL, SE = 0.04, P = 3.0 × 10-14) near GC and rs11731496 (per allele β = 0.21 μg/mL, SE = 0.03, P = 3.6 × 10-11) in between GC and NPFFR2. In conditional analyses, which included the above-mentioned SNPs, only rs7041 remained notable (P = 4.1 × 10-21). SNP rs4588 in GC was the only GWAS-identified SNP associated with 25-hydroxyvitamin D concentration. Among UK Biobank participants: per allele β = -0.11 μg/mL, SE = 0.01, P = 1.5 × 10-13; in the SCCS: per allele β = -0.12 μg/mL, SE = 0.06, P = 2.8 × 10-02). rs7041 and rs4588 are functional SNPs that influence the binding affinity of VDBP to 25-hydroxyvitamin D. CONCLUSIONS Our results were in line with previous studies conducted in European-ancestry populations, showing that GC, the gene that directly encodes for VDBP, would be important for VDBP and 25-hydroxyvitamin D concentrations. The current study extends our knowledge of the genetics of vitamin D in diverse populations.
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Affiliation(s)
- Lisa A Parlato
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Rene Welch
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA; University of Wisconsin Carbone Cancer Center, Madison, WI, USA; Department of Obstetrics and Gynecology, UW-Health Hospital, University of Wisconsin-Madison, Madison, WI, USA
| | - Irene M Ong
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA; University of Wisconsin Carbone Cancer Center, Madison, WI, USA; Department of Obstetrics and Gynecology, UW-Health Hospital, University of Wisconsin-Madison, Madison, WI, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Mark D Steinwandel
- International Epidemiology Field Station, Vanderbilt Institute for Clinical and Translational Research, Nashville, TN, USA
| | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA; International Epidemiology Field Station, Vanderbilt Institute for Clinical and Translational Research, Nashville, TN, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shaneda Warren Andersen
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA; University of Wisconsin Carbone Cancer Center, Madison, WI, USA; Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
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25
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Zeković M, Bumbaširević U, Živković M, Pejčić T. Alteration of Lipid Metabolism in Prostate Cancer: Multifaceted Oncologic Implications. Int J Mol Sci 2023; 24:ijms24021391. [PMID: 36674910 PMCID: PMC9863986 DOI: 10.3390/ijms24021391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Cancer is increasingly recognized as an extraordinarily heterogeneous disease featuring an intricate mutational landscape and vast intra- and intertumor variability on both genetic and phenotypic levels. Prostate cancer (PCa) is the second most prevalent malignant disease among men worldwide. A single metabolic program cannot epitomize the perplexing reprogramming of tumor metabolism needed to sustain the stemness of neoplastic cells and their prominent energy-consuming functional properties, such as intensive proliferation, uncontrolled growth, migration, and invasion. In cancerous tissue, lipids provide the structural integrity of biological membranes, supply energy, influence the regulation of redox homeostasis, contribute to plasticity, angiogenesis and microenvironment reshaping, mediate the modulation of the inflammatory response, and operate as signaling messengers, i.e., lipid mediators affecting myriad processes relevant for the development of the neoplasia. Comprehensive elucidation of the lipid metabolism alterations in PCa, the underlying regulatory mechanisms, and their implications in tumorigenesis and the progression of the disease are gaining growing research interest in the contemporary urologic oncology. Delineation of the unique metabolic signature of the PCa featuring major aberrant pathways including de novo lipogenesis, lipid uptake, storage and compositional reprogramming may provide novel, exciting, and promising avenues for improving diagnosis, risk stratification, and clinical management of such a complex and heterogeneous pathology.
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Affiliation(s)
- Milica Zeković
- Centre of Research Excellence in Nutrition and Metabolism, Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia
| | - Uros Bumbaširević
- Clinic of Urology, University Clinical Center of Serbia, 11000 Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Marko Živković
- Clinic of Urology, University Clinical Center of Serbia, 11000 Belgrade, Serbia
| | - Tomislav Pejčić
- Clinic of Urology, University Clinical Center of Serbia, 11000 Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Correspondence:
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26
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Jin X, Tanaka H, Jin M, Fujita K, Homma H, Inotsume M, Yong H, Umeda K, Kodera N, Ando T, Okazawa H. PQBP5/NOL10 maintains and anchors the nucleolus under physiological and osmotic stress conditions. Nat Commun 2023; 14:9. [PMID: 36599853 PMCID: PMC9813255 DOI: 10.1038/s41467-022-35602-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Polyglutamine binding protein 5 (PQBP5), also called nucleolar protein 10 (NOL10), binds to polyglutamine tract sequences and is expressed in the nucleolus. Using dynamic imaging of high-speed atomic force microscopy, we show that PQBP5/NOL10 is an intrinsically disordered protein. Super-resolution microscopy and correlative light and electron microscopy method show that PQBP5/NOL10 makes up the skeletal structure of the nucleolus, constituting the granule meshwork in the granular component area, which is distinct from other nucleolar substructures, such as the fibrillar center and dense fibrillar component. In contrast to other nucleolar proteins, which disperse to the nucleoplasm under osmotic stress conditions, PQBP5/NOL10 remains in the nucleolus and functions as an anchor for reassembly of other nucleolar proteins. Droplet and thermal shift assays show that the biophysical features of PQBP5/NOL10 remain stable under stress conditions, explaining the spatial role of this protein. PQBP5/NOL10 can be functionally depleted by sequestration with polyglutamine disease proteins in vitro and in vivo, leading to the pathological deformity or disappearance of the nucleolus. Taken together, these findings indicate that PQBP5/NOL10 is an essential protein needed to maintain the structure of the nucleolus.
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Affiliation(s)
- Xiaocen Jin
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Hikari Tanaka
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Meihua Jin
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kyota Fujita
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Hidenori Homma
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Maiko Inotsume
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Huang Yong
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kenichi Umeda
- Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Noriyuki Kodera
- Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Toshio Ando
- Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Hitoshi Okazawa
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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27
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Gholami M, Zoughi M, Hasanzad M, Larijani B, Amoli MM. Haplotypic variants of COVID-19 related genes are associated with blood pressure and metabolites levels. J Med Virol 2023; 95:e28355. [PMID: 36443248 PMCID: PMC9877746 DOI: 10.1002/jmv.28355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 07/27/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022]
Abstract
The genetic association of coronavirus disease 2019 (COVID-19) with its complications has not been fully understood. This study aimed to identify variants and haplotypes of candidate genes implicated in COVID-19 related traits by combining the literature review and pathway analysis. To explore such genes, the protein-protein interactions and relevant pathways of COVID-19-associated genes were assessed. A number of variants on candidate genes were identified from Genome-wide association studies (GWASs) which were associated with COVID-19 related traits (p ˂ 10-6 ). Haplotypic blocks were assessed using haplotypic structures among the 1000 Genomes Project (r2 ≥ 0.8, D' ≥ 0.8). Further functional analyses were performed on the selected variants. The results demonstrated that a group of variants in ACE and AGT genes were significantly correlated with COVID-19 related traits. Three haplotypes were identified to be involved in the blood metabolites levels and the development of blood pressure. Functional analyses revealed that most GWAS index variants were expression quantitative trait loci and had transcription factor binding sites, exonic splicing enhancers or silencer activities. Furthermore, the proxy haplotype variants, rs4316, rs4353, rs4359, and three variants, namely rs2493133, rs2478543, and rs5051, were associated with blood metabolite and systolic blood pressure, respectively. These variants exerted more regulatory effects compared with other GWAS variants. The present study indicates that the genetic variants and candidate haplotypes of COVID-19 related genes are associated with blood pressure and blood metabolites. However, further observational studies are warranted to confirm these results.
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Affiliation(s)
- Morteza Gholami
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular‐Cellular Sciences InstituteTehran University of Medical SciencesTehranIran,Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences InstituteTehran University of Medical SciencesTehranIran
| | - Marziyeh Zoughi
- Metabolomics and genomics research center endocrinology and metabolism molecular‐cellular sciences instituteTehran University of medical sciencesTehranIran
| | - Mandana Hasanzad
- Personalized Medicine Research Center, Endocrinology and Metabolism Clinical Sciences InstituteTehran University of Medical SciencesTehranIran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences InstituteTehran University of Medical SciencesTehranIran
| | - Mahsa M. Amoli
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular‐Cellular Sciences InstituteTehran University of Medical SciencesTehranIran
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28
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Che B, Zhang W, Li W, Tang K, Yin J, Liu M, Xu S, Huang T, Yu Y, Huang K, Peng Z, Zha C. Bacterial lipopolysaccharide-related genes are involved in the invasion and recurrence of prostate cancer and are related to immune escape based on bioinformatics analysis. Front Oncol 2023; 13:1141191. [PMID: 37188204 PMCID: PMC10175693 DOI: 10.3389/fonc.2023.1141191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/13/2023] [Indexed: 05/17/2023] Open
Abstract
Background The composition of the tumor microbial microenvironment participates in the whole process of tumor disease. However, due to the limitations of the current technical level, the depth and breadth of the impact of microorganisms on tumors have not been fully recognized, especially in prostate cancer (PCa). Therefore, the purpose of this study is to explore the role and mechanism of the prostate microbiome in PCa based on bacterial lipopolysaccharide (LPS)-related genes by means of bioinformatics. Methods The Comparative Toxicogenomics Database (CTD) was used to find bacterial LPS- related genes. PCa expression profile data and clinical data were acquired from TCGA, GTEx, and GEO. The differentially expressed LPS-related hub genes (LRHG) were obtained by Venn diagram, and gene set enrichment analysis (GSEA) was used to investigate the putative molecular mechanism of LRHG. The immune infiltration score of malignancies was investigated using single-sample gene set enrichment analysis (ssGSEA). Using univariate and multivariate Cox regression analysis, a prognostic risk score model and nomogram were developed. Results 6 LRHG were screened. LRHG were involved in functional phenotypes such as tumor invasion, fat metabolism, sex hormone response, DNA repair, apoptosis, and immunoregulation. And it can regulate the immune microenvironment in the tumor by influencing the antigen presentation of immune cells in the tumor. And a prognostic risk score and the nomogram, which were based on LRHG, showed that the low-risk score has a protective effect on patients. Conclusion Microorganisms in the PCa microenvironment may use complex mechanism and networks to regulate the occurrence and development of PCa. Bacterial lipopolysaccharide-related genes can help build a reliable prognostic model and predict progression-free survival in patients with prostate cancer.
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Affiliation(s)
- Bangwei Che
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Wenjun Zhang
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Wei Li
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Kaifa Tang
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
- Department of Urology, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
- *Correspondence: Kaifa Tang,
| | - Jingju Yin
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Miao Liu
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Shenghan Xu
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Tao Huang
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Ying Yu
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Kunyuan Huang
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Zheng Peng
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Cheng Zha
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
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29
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Morova T, Ding Y, Huang CCF, Sar F, Schwarz T, Giambartolomei C, Baca S, Grishin D, Hach F, Gusev A, Freedman M, Pasaniuc B, Lack N. Optimized high-throughput screening of non-coding variants identified from genome-wide association studies. Nucleic Acids Res 2022; 51:e18. [PMID: 36546757 PMCID: PMC9943666 DOI: 10.1093/nar/gkac1198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/19/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
The vast majority of disease-associated single nucleotide polymorphisms (SNP) identified from genome-wide association studies (GWAS) are localized in non-coding regions. A significant fraction of these variants impact transcription factors binding to enhancer elements and alter gene expression. To functionally interrogate the activity of such variants we developed snpSTARRseq, a high-throughput experimental method that can interrogate the functional impact of hundreds to thousands of non-coding variants on enhancer activity. snpSTARRseq dramatically improves signal-to-noise by utilizing a novel sequencing and bioinformatic approach that increases both insert size and the number of variants tested per loci. Using this strategy, we interrogated known prostate cancer (PCa) risk-associated loci and demonstrated that 35% of them harbor SNPs that significantly altered enhancer activity. Combining these results with chromosomal looping data we could identify interacting genes and provide a mechanism of action for 20 PCa GWAS risk regions. When benchmarked to orthogonal methods, snpSTARRseq showed a strong correlation with in vivo experimental allelic-imbalance studies whereas there was no correlation with predictive in silico approaches. Overall, snpSTARRseq provides an integrated experimental and computational framework to functionally test non-coding genetic variants.
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Affiliation(s)
- Tunc Morova
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Yi Ding
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | - Funda Sar
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Tommer Schwarz
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Claudia Giambartolomei
- Central RNA Lab, Istituto Italiano di Tecnologia, Genova 16163, Italy,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sylvan C Baca
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Dennis Grishin
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Faraz Hach
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada,Department of Urologic Science, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Alexander Gusev
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Matthew L Freedman
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA,The Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA,Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nathan A Lack
- To whom correspondence should be addressed. Tel: +1 604 875 4411;
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30
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Seviiri M, Law MH, Ong JS, Gharahkhani P, Fontanillas P, Olsen CM, Whiteman DC, MacGregor S. A multi-phenotype analysis reveals 19 susceptibility loci for basal cell carcinoma and 15 for squamous cell carcinoma. Nat Commun 2022; 13:7650. [PMID: 36496446 PMCID: PMC9741635 DOI: 10.1038/s41467-022-35345-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
Basal cell carcinoma and squamous cell carcinoma are the most common skin cancers, and have genetic overlap with melanoma, pigmentation traits, autoimmune diseases, and blood biochemistry biomarkers. In this multi-trait genetic analysis of over 300,000 participants from Europe, Australia and the United States, we reveal 78 risk loci for basal cell carcinoma (19 previously unknown and replicated) and 69 for squamous cell carcinoma (15 previously unknown and replicated). The previously unknown risk loci are implicated in cancer development and progression (e.g. CDKL1), pigmentation (e.g. TPCN2), cardiometabolic (e.g. FADS2), and immune-regulatory pathways for innate immunity (e.g. IFIH1), and HIV-1 viral load modulation (e.g. CCR5). We also report an optimised polygenic risk score for effective risk stratification for keratinocyte cancer in the Canadian Longitudinal Study of Aging (794 cases and 18139 controls), which could facilitate skin cancer surveillance e.g. in high risk subpopulations such as transplantees.
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Affiliation(s)
- Mathias Seviiri
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia.
- Center for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia.
| | - Matthew H Law
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jue-Sheng Ong
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Puya Gharahkhani
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Catherine M Olsen
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - David C Whiteman
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Stuart MacGregor
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
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31
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Yuan J, Houlahan KE, Ramanand SG, Lee S, Baek G, Yang Y, Chen Y, Strand DW, Zhang MQ, Boutros PC, Mani RS. Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture. Cancer Discov 2022; 12:2838-2855. [PMID: 36108240 PMCID: PMC9722594 DOI: 10.1158/2159-8290.cd-22-0027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 07/18/2022] [Accepted: 09/15/2022] [Indexed: 01/12/2023]
Abstract
Prostate cancer is one of the most heritable human cancers. Genome-wide association studies have identified at least 185 prostate cancer germline risk alleles, most noncoding. We used integrative three-dimensional (3D) spatial genomics to identify the chromatin interaction targets of 45 prostate cancer risk alleles, 31 of which were associated with the transcriptional regulation of target genes in 565 localized prostate tumors. To supplement these 31, we verified transcriptional targets for 56 additional risk alleles using linear proximity and linkage disequilibrium analysis in localized prostate tumors. Some individual risk alleles influenced multiple target genes; others specifically influenced only distal genes while leaving proximal ones unaffected. Several risk alleles exhibited widespread germline-somatic interactions in transcriptional regulation, having different effects in tumors with loss of PTEN or RB1 relative to those without. These data clarify functional prostate cancer risk alleles in large linkage blocks and outline a strategy to model multidimensional transcriptional regulation. SIGNIFICANCE Many prostate cancer germline risk alleles are enriched in the noncoding regions of the genome and are hypothesized to regulate transcription. We present a 3D genomics framework to unravel risk SNP function and describe the widespread germline-somatic interplay in transcription control. This article is highlighted in the In This Issue feature, p. 2711.
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Affiliation(s)
- Jiapei Yuan
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas,State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College., Tianjin, China
| | - Kathleen E Houlahan
- Department of Human Genetics, University of California, Los Angeles, California,Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, California,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada,Vector Institute, Toronto, ON M5G 1M1, Canada,Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | | | - Sora Lee
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - GuemHee Baek
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Yang Yang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammation Biology, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Yong Chen
- Department of Molecular and Cellular Biosciences, Rowan University, Glassboro, New Jersey
| | - Douglas W. Strand
- Department of Urology, UT Southwestern Medical Center, Dallas, Texas
| | - Michael Q. Zhang
- Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, Texas,MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department Automation, Tsinghua University, Beijing 100084, China
| | - Paul C. Boutros
- Department of Human Genetics, University of California, Los Angeles, California,Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, California,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada,Vector Institute, Toronto, ON M5G 1M1, Canada,Department of Urology, University of California, Los Angeles, California,Institute for Precision Health, University of California, Los Angeles, California
| | - Ram S. Mani
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas,Department of Urology, UT Southwestern Medical Center, Dallas, Texas,Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
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32
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Tiong KL, Sintupisut N, Lin MC, Cheng CH, Woolston A, Lin CH, Ho M, Lin YW, Padakanti S, Yeang CH. An integrated analysis of the cancer genome atlas data discovers a hierarchical association structure across thirty three cancer types. PLOS DIGITAL HEALTH 2022; 1:e0000151. [PMID: 36812605 PMCID: PMC9931374 DOI: 10.1371/journal.pdig.0000151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/31/2022] [Indexed: 06/18/2023]
Abstract
Cancer cells harbor molecular alterations at all levels of information processing. Genomic/epigenomic and transcriptomic alterations are inter-related between genes, within and across cancer types and may affect clinical phenotypes. Despite the abundant prior studies of integrating cancer multi-omics data, none of them organizes these associations in a hierarchical structure and validates the discoveries in extensive external data. We infer this Integrated Hierarchical Association Structure (IHAS) from the complete data of The Cancer Genome Atlas (TCGA) and compile a compendium of cancer multi-omics associations. Intriguingly, diverse alterations on genomes/epigenomes from multiple cancer types impact transcriptions of 18 Gene Groups. Half of them are further reduced to three Meta Gene Groups enriched with (1) immune and inflammatory responses, (2) embryonic development and neurogenesis, (3) cell cycle process and DNA repair. Over 80% of the clinical/molecular phenotypes reported in TCGA are aligned with the combinatorial expressions of Meta Gene Groups, Gene Groups, and other IHAS subunits. Furthermore, IHAS derived from TCGA is validated in more than 300 external datasets including multi-omics measurements and cellular responses upon drug treatments and gene perturbations in tumors, cancer cell lines, and normal tissues. To sum up, IHAS stratifies patients in terms of molecular signatures of its subunits, selects targeted genes or drugs for precision cancer therapy, and demonstrates that associations between survival times and transcriptional biomarkers may vary with cancer types. These rich information is critical for diagnosis and treatments of cancers.
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Affiliation(s)
- Khong-Loon Tiong
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
| | - Nardnisa Sintupisut
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
| | - Min-Chin Lin
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
- Psomagen, Rockville, Maryland, United States of America
| | - Chih-Hung Cheng
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
| | - Andrew Woolston
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
- Translational Cancer Immunotherapy & Genomics Lab, Barts Cancer Institute, Charterhouse Square, London, United Kingdom
| | - Chih-Hsu Lin
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
- C3.ai, Redwood City, California, United States of America
| | - Mirrian Ho
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
| | - Yu-Wei Lin
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
- AiLife Diagnostics, Pearland, Texas, United States of America
| | - Sridevi Padakanti
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
| | - Chen-Hsiang Yeang
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
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33
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French AFU Cancer Committee Guidelines - Update 2022-2024: prostate cancer - Diagnosis and management of localised disease. Prog Urol 2022; 32:1275-1372. [DOI: 10.1016/j.purol.2022.07.148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 07/11/2022] [Indexed: 11/17/2022]
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Fu Q, Hong R, Zhou H, Li Y, Liu X, Gong J, Wang X, Chen J, Ran H, Wang L, Li F, Yuan J. Proteomics reveals MRPL4 as a high-risk factor and a potential diagnostic biomarker for prostate cancer. Proteomics 2022; 22:e2200081. [PMID: 36059095 DOI: 10.1002/pmic.202200081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 12/29/2022]
Abstract
Through digital rectal examinations (DRE) and routine prostate-specific antigen (PSA) screening, early prostate cancer (PC) treatment has become possible. However, PC is a complex and heterogeneous disease. In vivo, cancer cells can invade adjacent tissues and metastasize to other tissues resulting in hard cures. Therefore, the key to improving PC patients' survival time is preventing cancer cells' metastasis. We used mass spectrometry to profile primary PC in patients with versus without metastatic PC. We named these two groups of PC patients as high-risk primary PC (n = 11) and low-risk primary PC (n = 7), respectively. At the same time, patients with benign prostatic hyperplasia (BPH, n = 6) were used as controls to explore the possible factors driving PC metastasis. Based on comprehensive mass spectrometry analysis and biological validation, we found significant upregulation of MRPL4 expression in high-risk primary PC relative to low-risk primary PC and BPH. Further, through research of the extensive clinical cohort data in the database, we discovered that MRPL4 could be a high-risk factor for PC and serve as a potential diagnostic biomarker. The MRPL4 might be used as an auxiliary indicator for clinical status/stage of primary PC to predict patient survival time.
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Affiliation(s)
- Qihuan Fu
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Ruixia Hong
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Hang Zhou
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Ying Li
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Xiu Liu
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Jiaqi Gong
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Xiaoyang Wang
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Jiajia Chen
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Haiying Ran
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Liting Wang
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Fang Li
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Jiangbei Yuan
- Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Guangdong province, China
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35
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Pidsley R, Lam D, Qu W, Peters TJ, Luu P, Korbie D, Stirzaker C, Daly RJ, Stricker P, Kench JG, Horvath LG, Clark SJ. Comprehensive methylome sequencing reveals prognostic epigenetic biomarkers for prostate cancer mortality. Clin Transl Med 2022; 12:e1030. [PMID: 36178085 PMCID: PMC9523674 DOI: 10.1002/ctm2.1030] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/02/2022] [Accepted: 08/08/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Prostate cancer is a clinically heterogeneous disease with a subset of patients rapidly progressing to lethal-metastatic prostate cancer. Current clinicopathological measures are imperfect predictors of disease progression. Epigenetic changes are amongst the earliest molecular changes in tumourigenesis. To find new prognostic biomarkers to enable earlier intervention and improved outcomes, we performed methylome sequencing of DNA from patients with localised prostate cancer and long-term clinical follow-up. METHODS We used whole-genome bisulphite sequencing (WGBS) to comprehensively map and compare DNA methylation of radical prostatectomy tissue between patients with lethal disease (n = 7) and non-lethal (n = 8) disease (median follow-up 19.5 years). Validation of differentially methylated regions (DMRs) was performed in an independent cohort (n = 185, median follow-up 15 years) using targeted multiplex bisulphite sequencing of candidate regions. Survival was assessed via univariable and multivariable analyses including clinicopathological measures (log-rank and Cox regression models). RESULTS WGBS data analysis identified cancer-specific methylation patterns including CpG island hypermethylation, and hypomethylation of repetitive elements, with increasing disease risk. We identified 1420 DMRs associated with prostate cancer-specific mortality (PCSM), which showed enrichment for gene sets downregulated in prostate cancer and de novo methylated in cancer. Through comparison with public prostate cancer datasets, we refined the DMRs to develop an 18-gene prognostic panel. Applying this panel to an independent cohort, we found significant associations between PCSM and hypermethylation at EPHB3, PARP6, TBX1, MARCH6 and a regulatory element within CACNA2D4. Strikingly in a multivariable model, inclusion of CACNA2D4 methylation was a better predictor of PCSM versus grade alone (Harrell's C-index: 0.779 vs. 0.684). CONCLUSIONS Our study provides detailed methylome maps of non-lethal and lethal prostate cancer and identifies novel genic regions that distinguish these patient groups. Inclusion of our DNA methylation biomarkers with existing clinicopathological measures improves prognostic models of prostate cancer mortality, and holds promise for clinical application.
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Affiliation(s)
- Ruth Pidsley
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia,School of Clinical MedicineSt Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW SydneySydneyNew South WalesAustralia
| | - Dilys Lam
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia,Present address:
School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia,Present address:
Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Wenjia Qu
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Timothy J. Peters
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia,School of Clinical MedicineSt Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW SydneySydneyNew South WalesAustralia
| | - Phuc‐Loi Luu
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia,School of Clinical MedicineSt Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW SydneySydneyNew South WalesAustralia
| | - Darren Korbie
- Centre for Personalised NanomedicineAustralian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Clare Stirzaker
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia,School of Clinical MedicineSt Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW SydneySydneyNew South WalesAustralia
| | - Roger J. Daly
- Cancer Research Program and Department of Biochemistry and Molecular BiologyBiomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Phillip Stricker
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia,School of Clinical MedicineSt Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW SydneySydneyNew South WalesAustralia,Department of UrologySt. Vincent's Prostate Cancer CentreSydneyNew South WalesAustralia
| | - James G. Kench
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia,Department of Tissue PathologyNSW Health PathologyRoyal Prince Alfred HospitalCamperdownSydneyNew South WalesAustralia
| | - Lisa G. Horvath
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia,School of Clinical MedicineSt Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW SydneySydneyNew South WalesAustralia,Chris O'Brien Lifehouse, CamperdownSydneyNew South WalesAustralia,University of SydneySydneyNew South WalesAustralia
| | - Susan J. Clark
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia,School of Clinical MedicineSt Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW SydneySydneyNew South WalesAustralia
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36
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Chen J, Meng J, Liu Y, Bian Z, Niu Q, Chen J, Zhou J, Zhang L, Zhang M, Liang C. Establishment of a five-enzalutamide-resistance-related-gene-based classifier for recurrence-free survival predicting of prostate cancer. J Cell Mol Med 2022; 26:5379-5390. [PMID: 36168930 PMCID: PMC9639034 DOI: 10.1111/jcmm.17554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 07/15/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022] Open
Abstract
To identify prostate cancer (PCa) patients with a high risk of recurrence is critical before delivering adjuvant treatment. We developed a classifier based on the Enzalutamide treatment resistance‐related genes to assist the currently available staging system in predicting the recurrence‐free survival (RFS) prognosis of PCa patients. We overlapped the DEGs from two datasets to obtain a more convincing Enzalutamide‐resistance‐related‐gene (ERRG) cluster. The five‐ERRG‐based classifier obtained good predictive values in both the training and validation cohorts. The classifier precisely predicted RFS of patients in four cohorts, independent of patient age, pathological tumour stage, Gleason score and PSA levels. The classifier and the clinicopathological factors were combined to construct a nomogram, which had an increased predictive accuracy than that of each variable alone. Besides, we also compared the differences between high‐ and low‐risk subgroups and found their differences were enriched in cancer progression‐related pathways. The five‐ERRG‐based classifier is a practical and reliable predictor, which adds value to the existing staging system for predicting the RFS prognosis of PCa after radical prostatectomy, enabling physicians to make more informed treatment decisions concerning adjuvant therapy.
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Affiliation(s)
- Jing Chen
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology and Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Jialin Meng
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology and Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Yi Liu
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology and Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Zichen Bian
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology and Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Qingsong Niu
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology and Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Junyi Chen
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology and Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Jun Zhou
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology and Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Li Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology and Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
| | - Meng Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology and Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China.,Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, China
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology and Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui, China
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37
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Wu J, Tan X. The role of MTNR1B polymorphism on circadian rhythm-related cancer: A UK Biobank cohort study. Int J Cancer 2022; 151:888-896. [PMID: 35467761 PMCID: PMC9545001 DOI: 10.1002/ijc.34047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/30/2022] [Accepted: 04/19/2022] [Indexed: 11/25/2022]
Abstract
A common G risk allele in the melatonin receptor 1B (MTNR1B, rs10830963) gene has been associated with altered melatonin signaling and secretion. Given that melatonin possesses anticancerogenic properties, we hypothesized that breast and prostate cancer risks vary by rs10830963 genotype. A total of 216 702 participants from the UK Biobank without cancer at baseline (aged 56.4 ± 8.0 years, 50.79% female) were included. Multivariable Cox regression adjusting for known risk factors for breast or prostate cancer was used to estimate the independent effects of the rs10830963 SNP and chronotype on cancer risk. Over a median follow-up of 8 years, 2367 (2.15% of women) incidences of breast cancer and 2866 (2.69% of men) incidences of prostate cancer were documented in females and males, respectively. rs10830963 genotype is not associated with cancer risk independently (female Ptrend = .103, male Ptrend = .281). A late chronotype is associated with breast cancer risk in females (Ptrend = .014), but not prostate cancer risk in males (Ptrend = .915). Further stratification analysis revealed that the rs10830963 genotype is associated with a breast cancer risk in females with moderate evening chronotype (Ptrend = .001) and late chronotype is associated with breast cancer risk in females who carry rs10830963 G risk allele (Ptrend = .015). Our study suggests that having a late chronotype might increase the risk of breast cancer among females, while the effect of MTNR1B rs10830963 genotype on breast cancer risk is mediated by chronotype.
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Affiliation(s)
- Jiafei Wu
- Department of Surgical Sciences (Sleep Science Lab), Uppsala University, Uppsala, Sweden
| | - Xiao Tan
- Department of Surgical Sciences (Sleep Science Lab), Uppsala University, Uppsala, Sweden.,Department of Clinical Neuroscience, Karolinska Institutet, Solna, Sweden
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38
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Kim MS, Naidoo D, Hazra U, Quiver MH, Chen WC, Simonti CN, Kachambwa P, Harlemon M, Agalliu I, Baichoo S, Fernandez P, Hsing AW, Jalloh M, Gueye SM, Niang L, Diop H, Ndoye M, Snyper NY, Adusei B, Mensah JE, Abrahams AOD, Biritwum R, Adjei AA, Adebiyi AO, Shittu O, Ogunbiyi O, Adebayo S, Aisuodionoe-Shadrach OI, Nwegbu MM, Ajibola HO, Oluwole OP, Jamda MA, Singh E, Pentz A, Joffe M, Darst BF, Conti DV, Haiman CA, Spies PV, van der Merwe A, Rohan TE, Jacobson J, Neugut AI, McBride J, Andrews C, Petersen LN, Rebbeck TR, Lachance J. Testing the generalizability of ancestry-specific polygenic risk scores to predict prostate cancer in sub-Saharan Africa. Genome Biol 2022; 23:194. [PMID: 36100952 PMCID: PMC9472407 DOI: 10.1186/s13059-022-02766-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 09/05/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Genome-wide association studies do not always replicate well across populations, limiting the generalizability of polygenic risk scores (PRS). Despite higher incidence and mortality rates of prostate cancer in men of African descent, much of what is known about cancer genetics comes from populations of European descent. To understand how well genetic predictions perform in different populations, we evaluated test characteristics of PRS from three previous studies using data from the UK Biobank and a novel dataset of 1298 prostate cancer cases and 1333 controls from Ghana, Nigeria, Senegal, and South Africa. RESULTS Allele frequency differences cause predicted risks of prostate cancer to vary across populations. However, natural selection is not the primary driver of these differences. Comparing continental datasets, we find that polygenic predictions of case vs. control status are more effective for European individuals (AUC 0.608-0.707, OR 2.37-5.71) than for African individuals (AUC 0.502-0.585, OR 0.95-2.01). Furthermore, PRS that leverage information from African Americans yield modest AUC and odds ratio improvements for sub-Saharan African individuals. These improvements were larger for West Africans than for South Africans. Finally, we find that existing PRS are largely unable to predict whether African individuals develop aggressive forms of prostate cancer, as specified by higher tumor stages or Gleason scores. CONCLUSIONS Genetic predictions of prostate cancer perform poorly if the study sample does not match the ancestry of the original GWAS. PRS built from European GWAS may be inadequate for application in non-European populations and perpetuate existing health disparities.
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Affiliation(s)
- Michelle S Kim
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr, Atlanta, GA, 30332, USA
| | - Daphne Naidoo
- Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | - Ujani Hazra
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr, Atlanta, GA, 30332, USA
| | - Melanie H Quiver
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr, Atlanta, GA, 30332, USA
| | - Wenlong C Chen
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,National Cancer Registry, National Health Laboratory Service, Johannesburg, South Africa
| | - Corinne N Simonti
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr, Atlanta, GA, 30332, USA
| | | | - Maxine Harlemon
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr, Atlanta, GA, 30332, USA
| | - Ilir Agalliu
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Pedro Fernandez
- Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Ann W Hsing
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | | | | | - Lamine Niang
- Universite Cheikh Anta Diop de Dakar, Dakar, Senegal
| | | | - Medina Ndoye
- Universite Cheikh Anta Diop de Dakar, Dakar, Senegal
| | | | | | - James E Mensah
- Korle-Bu Teaching Hospital and University of Ghana Medical School, Accra, Ghana
| | - Afua O D Abrahams
- Korle-Bu Teaching Hospital and University of Ghana Medical School, Accra, Ghana
| | - Richard Biritwum
- Korle-Bu Teaching Hospital and University of Ghana Medical School, Accra, Ghana
| | - Andrew A Adjei
- Department of Pathology, University of Ghana Medical School, Accra, Ghana
| | | | | | | | - Sikiru Adebayo
- College of Medicine, University of Ibadan, Ibadan, Nigeria
| | | | - Maxwell M Nwegbu
- College of Health Sciences, University of Abuja and University of Abuja Teaching Hospital, Abuja, Nigeria
| | - Hafees O Ajibola
- College of Health Sciences, University of Abuja and University of Abuja Teaching Hospital, Abuja, Nigeria
| | - Olabode P Oluwole
- College of Health Sciences, University of Abuja and University of Abuja Teaching Hospital, Abuja, Nigeria
| | - Mustapha A Jamda
- College of Health Sciences, University of Abuja and University of Abuja Teaching Hospital, Abuja, Nigeria
| | - Elvira Singh
- National Cancer Registry, National Health Laboratory Service, Johannesburg, South Africa
| | - Audrey Pentz
- Non-Communicable Diseases Research Division, Wits Health Consortium (PTY) Ltd, Johannesburg, South Africa
| | - Maureen Joffe
- Non-Communicable Diseases Research Division, Wits Health Consortium (PTY) Ltd, Johannesburg, South Africa.,MRC Developmental Pathways to Health Research Unit, Department of Pediatrics, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Burcu F Darst
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David V Conti
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher A Haiman
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Petrus V Spies
- Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - André van der Merwe
- Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Thomas E Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Judith Jacobson
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Alfred I Neugut
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Jo McBride
- Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | | | | | - Timothy R Rebbeck
- Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr, Atlanta, GA, 30332, USA.
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Siltari A, Lönnerbro R, Pang K, Shiranov K, Asiimwe A, Evans-Axelsson S, Franks B, Kiran A, Murtola TJ, Schalken J, Steinbeisser C, Bjartell A, Auvinen A, Smith E, N'Dow J, Plass K, Ribal M, Mottet N, Moris L, Lardas M, Van den Broeck T, Willemse PP, Gandaglia G, Campi R, Greco I, Gacci M, Serni S, Briganti A, Crosti D, Meoni M, Garzonio R, Bangma R, Roobol M, Remmers S, Tilki D, Visakorpi T, Talala K, Tammela T, van Hemelrijck M, Bayer K, Lejeune S, Taxiarchopoulou G, van Diggelen F, Senthilkumar K, Schutte S, Byrne S, Fialho L, Cardone A, Gono P, De Vetter M, Ceke K, De Meulder B, Auffray C, Balaur IA, Taibi N, Power S, Kermani NZ, van Bochove K, Cavelaars M, Moinat M, Voss E, Bernini C, Horgan D, Fullwood L, Holtorf M, Lancet D, Bernstein G, Omar I, MacLennan S, Maclennan S, Healey J, Huber J, Wirth M, Froehner M, Brenner B, Borkowetz A, Thomas C, Horn F, Reiche K, Kreux M, Josefsson A, Tandefekt DG, Hugosson J, Huisman H, Hofmacher T, Lindgren P, Andersson E, Fridhammar A, Vizcaya D, Verholen F, Zong J, Butler-Ransohoff JE, Williamson T, Chandrawansa K, Dlamini D, waldeck R, Molnar M, Bruno A, Herrera R, Jiang S, Nevedomskaya E, Fatoba S, Constantinovici N, Maass M, Torremante P, Voss M, Devecseri Z, Cuperus G, Abott T, Dau C, Papineni K, Wang-Silvanto J, Hass S, Snijder R, Doye V, Wang X, Garnham A, Lambrecht M, Wolfinger R, Rogiers S, Servan A, Lefresne F, Caseriego J, Samir M, Lawson J, Pacoe K, Robinson P, Jaton B, Bakkard D, Turunen H, Kilkku O, Pohjanjousi P, Voima O, Nevalaita L, Reich C, Araujo S, Longden-Chapman E, Burke D, Agapow P, Derkits S, Licour M, McCrea C, Payne S, Yong A, Thompson L, Lujan F, Bussmann M, Köhler I. How well do polygenic risk scores identify men at high risk for prostate cancer? Systematic review and meta-analysis. Clin Genitourin Cancer 2022; 21:316.e1-316.e11. [PMID: 36243664 DOI: 10.1016/j.clgc.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 11/27/2022]
Abstract
OBJECTIVES Genome-wide association studies have revealed over 200 genetic susceptibility loci for prostate cancer (PCa). By combining them, polygenic risk scores (PRS) can be generated to predict risk of PCa. We summarize the published evidence and conduct meta-analyses of PRS as a predictor of PCa risk in Caucasian men. PATIENTS AND METHODS Data were extracted from 59 studies, with 16 studies including 17 separate analyses used in the main meta-analysis with a total of 20,786 cases and 69,106 controls identified through a systematic search of ten databases. Random effects meta-analysis was used to obtain pooled estimates of area under the receiver-operating characteristic curve (AUC). Meta-regression was used to assess the impact of number of single-nucleotide polymorphisms (SNPs) incorporated in PRS on AUC. Heterogeneity is expressed as I2 scores. Publication bias was evaluated using funnel plots and Egger tests. RESULTS The ability of PRS to identify men with PCa was modest (pooled AUC 0.63, 95% CI 0.62-0.64) with moderate consistency (I2 64%). Combining PRS with clinical variables increased the pooled AUC to 0.74 (0.68-0.81). Meta-regression showed only negligible increase in AUC for adding incremental SNPs. Despite moderate heterogeneity, publication bias was not evident. CONCLUSION Typically, PRS accuracy is comparable to PSA or family history with a pooled AUC value 0.63 indicating mediocre performance for PRS alone.
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40
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Inherited risk assessment and its clinical utility for predicting prostate cancer from diagnostic prostate biopsies. Prostate Cancer Prostatic Dis 2022; 25:422-430. [PMID: 35347252 DOI: 10.1038/s41391-021-00458-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/25/2021] [Accepted: 09/10/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Many studies on prostate cancer (PCa) germline variants have been published in the last 15 years. This review critically assesses their clinical validity and explores their utility in prediction of PCa detection rates from prostate biopsy. METHODS An integrative review was performed to (1) critically synthesize findings on PCa germline studies from published papers since 2016, including risk-associated single nucleotide polymorphisms (SNPs), polygenic risk score methods such as genetic risk score (GRS), and rare pathogenic mutations (RPMs); (2) exemplify the findings in a large population-based cohort from the UK Biobank (UKB); (3) identify gaps for implementing inherited risk assessment in clinic based on experience from a healthcare system; (4) evaluate available GRS data on their clinical utility in predicting PCa detection rates from prostate biopsies; and (5) describe a prospective germline-based biopsy trial to address existing gaps. RESULTS SNP-based GRS and RPMs in four genes (HOXB13, BRCA2, ATM, and CHEK2) were significantly and consistently associated with PCa risk in large well-designed studies. In the UKB, positive family history, RPMs in the four implicated genes, and a high GRS (>1.5) identified 8.12%, 1.61%, and 17.38% of men to be at elevated PCa risk, respectively, with hazard ratios of 1.84, 2.74, and 2.39, respectively. Additionally, the performance of GRS for predicting PCa detection rate on prostate biopsy was consistently supported in several retrospective analyses of transrectal ultrasound (TRUS)-biopsy cohorts. Prospective studies evaluating the performance of all three inherited measures in predicting PCa detection rate from contemporary multiparametric MRI (mpMRI)-based biopsy are lacking. A multicenter germline-based biopsy trial to address these gaps is warranted. CONCLUSIONS The complementary performance of three inherited risk measures in PCa risk stratification is consistently supported. Their clinical utility in predicting PCa detection rate, if confirmed in prospective clinical trials, may improve current decision-making for prostate biopsy.
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Zhang N, Huang D, Jiang G, Chen S, Ruan X, Chen H, Huang J, Liu A, Zhang W, Lin X, Wu Y, Zhang Q, Li J, Tsu JH, Wei G, Na R. Genome-Wide 3'-UTR Single Nucleotide Polymorphism Association Study Identifies Significant Prostate Cancer Risk-Associated Functional Loci at 8p21.2 in Chinese Population. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201420. [PMID: 35968571 PMCID: PMC9376745 DOI: 10.1002/advs.202201420] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/24/2022] [Indexed: 05/27/2023]
Abstract
MicroRNAs (miRNAs) are involved in the regulation of gene expression via incomplete base pairing to sequence motifs at the three prime untranslated regions (3'-UTRs) of mRNAs and play critical roles in the etiology of cancers. Single nucleotide polymorphisms (SNPs) in the 3'-UTR miRNA-binding regions may influence the miRNA affinity. However, this biological mechanism in prostate cancer (PCa) remains unclear. Here, a three-stage genome-wide association study of 3'-UTR SNPs (n=33 117) is performed in 5515 Chinese men. Three genome-wide significant variants are discovered at 8p21.2 (rs1567669, rs4872176, and rs4872177), which are all located in a linkage disequilibrium region of the NKX3-1 gene. Phenome-wide association analysis using the FinnGen data reveals a specific association of rs1567669 with PCa over 2,264 disease endpoints. Expression quantitative trait locus analyses based on both Chinese PCa cohort and the GTEx database show that risk alleles of these SNPs are significantly associated with low expression of NKX3-1. Based on the MirSNP database, dual-luciferase reporter assays show that risk alleles of these SNPs downregulate the expression of NKX3-1 via increased miRNA binding. These results indicate that the SNPs at the 3'-UTR of NKX3-1 significantly downregulate NKX3-1 expression by influencing the affinity of miRNA and increase the PCa risk.
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Affiliation(s)
- Ning Zhang
- Department of Urology, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Da Huang
- Department of Urology, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Guangliang Jiang
- Department of Urology, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Siteng Chen
- Department of Urology, Renji HospitalShanghai Jiao Tong University School of MedicineShanghai200080China
| | - Xiaohao Ruan
- Department of Urology, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Haitao Chen
- School of Public Health ShenzhenSun Yat‐sen UniversityGuangzhou510006China
| | - Jingyi Huang
- Department of Urology, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Ao Liu
- Department of Urology, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Wenhui Zhang
- Department of Urology, Changhai HospitalSecond Military Medical UniversityShanghai200433China
| | - Xiaoling Lin
- Department of Urology, Huashan HospitalFudan UniversityShanghai200040China
| | - Yishuo Wu
- Department of Urology, Huashan HospitalFudan UniversityShanghai200040China
| | - Qin Zhang
- Biocenter Oulu, Faculty of Biochemistry and Molecular MedicineUniversity of OuluOulu90014Finland
| | - Jing Li
- Department of Bioinformatics, Center for Translational MedicineSecond Military Medical UniversityShanghai200433China
| | - James Hok‐Leung Tsu
- Division of Urology, Department of Surgery, Queen Mary HospitalThe University of Hong KongHong KongChina
| | - Gong‐Hong Wei
- Biocenter Oulu, Faculty of Biochemistry and Molecular MedicineUniversity of OuluOulu90014Finland
- MOE Key Laboratory of Metabolism and Molecular Medicine & Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Fudan University Shanghai Cancer CenterShanghai Medical College of Fudan UniversityShanghai200032China
| | - Rong Na
- Division of Urology, Department of Surgery, Queen Mary HospitalThe University of Hong KongHong KongChina
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Liao J, Ye Y, Xu X. Comprehensive analysis of tumor mutation burden and immune microenvironment in prostate cancer. Clin Transl Oncol 2022; 24:1986-1997. [PMID: 35732871 DOI: 10.1007/s12094-022-02857-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022]
Abstract
PURPOSE Prostate adenocarcinoma (PRAD) is a high incidence of malignant tumor of the urinary system and the second most common male cancer in the world. Immune checkpoint inhibitor (ICIS) therapy is becoming a new hope for cancer treatment. METHODS To realize the possibility of PRAD patients benefiting from ICIS treatment, we analyzed the mutation spectrum of all PRAD patients, calculated the TMB of each PRAD patient, and divided the patients into high TMB group and low TMB group. Differentially expressed genes (DEGs) between the two groups were identified and path analysis was carried out. The immune cell infiltration of each PRAD patient was evaluated and survival analysis was performed to explore the effect of immune cell infiltration on the prognosis. RESULTS We found that high TMB was associated with better survival outcomes, with higher TMB scores in young patients, T2 and N0 patients. 28 hub genes were screened by the overlap between 229 DEGs and immune-related genes. T cells CD8 and CD4 memory activated in the high TMB group were higher than those in the low TMB group, while Mast cells resting in the low TMB group were higher than that in the high TMB group. High neutrophil infiltration is associated with poor prognosis in patients with PRAD. Finally, from the immune genes used to construct the prognostic risk model of TMB, it is found that CHP2 and NRG1 are independent prognostic factors of PRAD. CONCLUSIONS This study provides new insights into the immune microenvironment and potential immunotherapy of PRAD.
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Affiliation(s)
- Junqun Liao
- Medical Laboratory Science, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400042, China
| | - Yuan Ye
- Clinical Laboratory, Chongqing Nanchuan Maternity and Child Healthcare Hospital, Chongqing, 408400, China
| | - Xuren Xu
- Clinical Laboratory, The People's Hospital of Nanchuan, Chongqing, No.16, Nandajie Road, Nanchuan District, Chongqing, 408400, China.
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43
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Zou X, Wang R, Yang Z, Wang Q, Fu W, Huo Z, Ge F, Zhong R, Jiang Y, Li J, Xiong S, Hong W, Liang W. Family Socioeconomic Position and Lung Cancer Risk: A Meta-Analysis and a Mendelian Randomization Study. Front Public Health 2022; 10:780538. [PMID: 35734761 PMCID: PMC9207765 DOI: 10.3389/fpubh.2022.780538] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundFamily socioeconomic position (SEP) in childhood is an important factor to predict some chronic diseases. However, the association between family SEP in childhood and the risk of lung cancer is not clear.MethodsA systematic search was performed to explore their relationship. We selected education level, socioeconomic positions of parents and childhood housing conditions to represent an individual family SEP. Hazard ratios (HRs) of lung cancer specific-mortality were synthesized using a random effects model. Two-sample Mendelian randomization (MR) was carried out with summary data from published genome-wide association studies of SEP to assess the possible causal relationship of SEP and risk of lung cancer.ResultsThrough meta-analysis of 13 studies, we observed that to compared with the better SEP, the poorer SEP in the childhood was associated with the increased lung cancer risk in the adulthood (HR: 1.25, 95% CI: 1.10 to 1.43). In addition, the dose-response analysis revealed a positive correlation between the poorer SEP and increased lung cancer risk. Same conclusion was reached in MR [(education level) OR 0.50, 95% CI: 0.39 to 0.63; P < 0.001].ConclusionThis study indicates that poor family socioeconomic position in childhood is causally correlated with lung cancer risk in adulthood.Systematic Review Registrationidentifier: 159082.
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Affiliation(s)
- Xusen Zou
- South China University of Technology, School of Public Administration, Guangzhou, China
| | - Runchen Wang
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Nanshan School, Guangzhou Medical University, Guangzhou, China
| | - Zhao Yang
- Peking University First Hospital, Beijing, China
| | - Qixia Wang
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Nanshan School, Guangzhou Medical University, Guangzhou, China
| | - Wenhai Fu
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- First Clinical School, Guangzhou Medical University, Guangzhou, China
| | - Zhenyu Huo
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Nanshan School, Guangzhou Medical University, Guangzhou, China
| | - Fan Ge
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- First Clinical School, Guangzhou Medical University, Guangzhou, China
| | - Ran Zhong
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yu Jiang
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Nanshan School, Guangzhou Medical University, Guangzhou, China
| | - Jiangfu Li
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shan Xiong
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wen Hong
- South China University of Technology, School of Public Administration, Guangzhou, China
- Wen Hong
| | - Wenhua Liang
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Wenhua Liang
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Wade KH, Yarmolinsky J, Giovannucci E, Lewis SJ, Millwood IY, Munafò MR, Meddens F, Burrows K, Bell JA, Davies NM, Mariosa D, Kanerva N, Vincent EE, Smith-Byrne K, Guida F, Gunter MJ, Sanderson E, Dudbridge F, Burgess S, Cornelis MC, Richardson TG, Borges MC, Bowden J, Hemani G, Cho Y, Spiller W, Richmond RC, Carter AR, Langdon R, Lawlor DA, Walters RG, Vimaleswaran KS, Anderson A, Sandu MR, Tilling K, Davey Smith G, Martin RM, Relton CL. Applying Mendelian randomization to appraise causality in relationships between nutrition and cancer. Cancer Causes Control 2022; 33:631-652. [PMID: 35274198 PMCID: PMC9010389 DOI: 10.1007/s10552-022-01562-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 02/10/2022] [Indexed: 02/08/2023]
Abstract
Dietary factors are assumed to play an important role in cancer risk, apparent in consensus recommendations for cancer prevention that promote nutritional changes. However, the evidence in this field has been generated predominantly through observational studies, which may result in biased effect estimates because of confounding, exposure misclassification, and reverse causality. With major geographical differences and rapid changes in cancer incidence over time, it is crucial to establish which of the observational associations reflect causality and to identify novel risk factors as these may be modified to prevent the onset of cancer and reduce its progression. Mendelian randomization (MR) uses the special properties of germline genetic variation to strengthen causal inference regarding potentially modifiable exposures and disease risk. MR can be implemented through instrumental variable (IV) analysis and, when robustly performed, is generally less prone to confounding, reverse causation and measurement error than conventional observational methods and has different sources of bias (discussed in detail below). It is increasingly used to facilitate causal inference in epidemiology and provides an opportunity to explore the effects of nutritional exposures on cancer incidence and progression in a cost-effective and timely manner. Here, we introduce the concept of MR and discuss its current application in understanding the impact of nutritional factors (e.g., any measure of diet and nutritional intake, circulating biomarkers, patterns, preference or behaviour) on cancer aetiology and, thus, opportunities for MR to contribute to the development of nutritional recommendations and policies for cancer prevention. We provide applied examples of MR studies examining the role of nutritional factors in cancer to illustrate how this method can be used to help prioritise or deprioritise the evaluation of specific nutritional factors as intervention targets in randomised controlled trials. We describe possible biases when using MR, and methodological developments aimed at investigating and potentially overcoming these biases when present. Lastly, we consider the use of MR in identifying causally relevant nutritional risk factors for various cancers in different regions across the world, given notable geographical differences in some cancers. We also discuss how MR results could be translated into further research and policy. We conclude that findings from MR studies, which corroborate those from other well-conducted studies with different and orthogonal biases, are poised to substantially improve our understanding of nutritional influences on cancer. For such corroboration, there is a requirement for an interdisciplinary and collaborative approach to investigate risk factors for cancer incidence and progression.
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Affiliation(s)
- Kaitlin H Wade
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK.
| | - James Yarmolinsky
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
| | - Edward Giovannucci
- Departments of Nutrition and Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Sarah J Lewis
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
- Bristol National Institute for Health Research (NIHR) Biomedical Research Centre, Bristol, UK
| | - Iona Y Millwood
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU) and the Medical Research Council Population Health Research Unit (MRC PHRU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Marcus R Munafò
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
- Bristol National Institute for Health Research (NIHR) Biomedical Research Centre, Bristol, UK
- School of Psychological Science, University of Bristol, Bristol, UK
| | - Fleur Meddens
- Department of Economics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Applied Economics, Erasmus School of Economics, Erasmus University Rotterdam, Rotterdam, The Netherlands
| | - Kimberley Burrows
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
| | - Joshua A Bell
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
| | - Neil M Davies
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Daniela Mariosa
- International Agency for Research On Cancer (IARC), Lyon, France
| | | | - Emma E Vincent
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
- Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Karl Smith-Byrne
- International Agency for Research On Cancer (IARC), Lyon, France
| | - Florence Guida
- International Agency for Research On Cancer (IARC), Lyon, France
| | - Marc J Gunter
- International Agency for Research On Cancer (IARC), Lyon, France
| | - Eleanor Sanderson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
| | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Tom G Richardson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
| | - Maria Carolina Borges
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
| | - Jack Bowden
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
- Research Innovation Learning and Development (RILD) Building, University of Exeter Medical School, Exeter, UK
| | - Gibran Hemani
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
| | - Yoonsu Cho
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
| | - Wes Spiller
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
| | - Rebecca C Richmond
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
| | - Alice R Carter
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
| | - Ryan Langdon
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
| | - Deborah A Lawlor
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
- Bristol National Institute for Health Research (NIHR) Biomedical Research Centre, Bristol, UK
| | - Robin G Walters
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU) and the Medical Research Council Population Health Research Unit (MRC PHRU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | - Annie Anderson
- Population Health and Genomics, School of Medicine, University of Dundee, Dundee, Scotland, UK
| | - Meda R Sandu
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
- NIHR Biomedical Research Centre, Bristol, UK
| | - Kate Tilling
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
- Bristol National Institute for Health Research (NIHR) Biomedical Research Centre, Bristol, UK
| | - George Davey Smith
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
- Bristol National Institute for Health Research (NIHR) Biomedical Research Centre, Bristol, UK
| | - Richard M Martin
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
| | - Caroline L Relton
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
- Bristol National Institute for Health Research (NIHR) Biomedical Research Centre, Bristol, UK
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Genome-Wide Association Study of Fluorescent Oxidation Products Accounting for Tobacco Smoking Status in Adults from the French EGEA Study. Antioxidants (Basel) 2022; 11:antiox11050802. [PMID: 35624665 PMCID: PMC9137810 DOI: 10.3390/antiox11050802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 12/14/2022] Open
Abstract
Oxidative stress (OS) is the main pathophysiological mechanism involved in several chronic diseases, including asthma. Fluorescent oxidation products (FlOPs), a global biomarker of damage due to OS, is of growing interest in epidemiological studies. We conducted a genome-wide association study (GWAS) of the FlOPs level in 1216 adults from the case-control and family-based EGEA study (mean age 43 years old, 51% women, and 23% current smokers) to identify genetic variants associated with FlOPs. The GWAS was first conducted in the whole sample and then stratified according to smoking status, the main exogenous source of reactive oxygen species. Among the top genetic variants identified by the three GWAS, those located in BMP6 (p = 3 × 10−6), near BMPER (p = 9 × 10−6), in GABRG3 (p = 4 × 10−7), and near ATG5 (p = 2 × 10−9) are the most relevant because of both their link to biological pathways related to OS and their association with several chronic diseases for which the role of OS in their pathophysiology has been pointed out. BMP6 and BMPER are of particular interest due to their involvement in the same biological pathways related to OS and their functional interaction. To conclude, this study, which is the first GWAS of FlOPs, provides new insights into the pathophysiology of chronic OS-related diseases.
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Larson NB, McDonnell SK, Fogarty Z, Liu Y, French AJ, Tillmans LS, Cheville JC, Wang L, Schaid DJ, Thibodeau SN. A microRNA Transcriptome-wide Association Study of Prostate Cancer Risk. Front Genet 2022; 13:836841. [PMID: 35432445 PMCID: PMC9006872 DOI: 10.3389/fgene.2022.836841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Large genome-wide association studies have identified hundreds of single-nucleotide polymorphisms associated with increased risk of prostate cancer (PrCa), and many of these risk loci is presumed to confer regulatory effects on gene expression. While eQTL studies of long RNAs has yielded many potential risk genes, the relationship between PrCa risk genetics and microRNA expression dysregulation is understudied. We performed an microRNA transcriptome-wide association study of PrCa risk using small RNA sequencing and genome-wide genotyping data from N = 441 normal prostate epithelium tissue samples along with N = 411 prostate adenocarcinoma tumor samples from the Cancer Genome Atlas (TCGA). Genetically regulated expression prediction models were trained for all expressed microRNAs using the FUSION TWAS software. TWAS for PrCa risk was performed with both sets of models using single-SNP summary statistics from the recent PRACTICAL consortium PrCa case-control OncoArray GWAS meta-analysis. A total of 613 and 571 distinct expressed microRNAs were identified in the normal and tumor tissue datasets, respectively (overlap: 480). Among these, 79 (13%) normal tissue microRNAs demonstrated significant cis-heritability (median cis-h2 = 0.15, range: 0.03–0.79) for model training. Similar results were obtained from TCGA tumor samples, with 48 (9%) microRNA expression models successfully trained (median cis-h2 = 0.14, range: 0.06–0.60). Using normal tissue models, we identified two significant TWAS microRNA associations with PrCa risk: over-expression of mir-941 family microRNAs (PTWAS = 2.9E-04) and reduced expression of miR-3617-5p (PTWAS = 1.0E-03). The TCGA tumor TWAS also identified a significant association with miR-941 overexpression (PTWAS = 9.7E-04). Subsequent finemapping of the TWAS results using a multi-tissue database indicated limited evidence of causal status for each microRNA with PrCa risk (posterior inclusion probabilities <0.05). Future work will examine downstream regulatory effects of microRNA dysregulation as well as microRNA-mediated risk mechanisms via competing endogenous RNA relationships.
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Affiliation(s)
- Nicholas B. Larson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
- *Correspondence: Nicholas B. Larson,
| | - Shannon K. McDonnell
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Zachary Fogarty
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Yuanhang Liu
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Amy J. French
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Lori S. Tillmans
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - John C. Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center, Tampa, FL, United States
| | - Daniel J. Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Stephen N. Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
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Prostate Cancer Susceptibility Loci Identified in GATA2 and ZMIZ1 in Chinese Population. Int J Genomics 2022; 2022:8553530. [PMID: 35372566 PMCID: PMC8970932 DOI: 10.1155/2022/8553530] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/04/2021] [Accepted: 12/01/2021] [Indexed: 12/26/2022] Open
Abstract
Background Common genetic risk variants for prostate cancer (PCa) have been identified at approximately 170 loci using genome-wide association studies (GWAS), most of which were identified in European populations. Recently, GWAS were applied to a large Japanese cohort and identified 12 novel susceptibility loci associated with PCa risk. In this study, we aim to investigate PCa susceptibility loci in the Chinese population. The study data will be used to promote PCa risk control in China. Methods A total of 235 PCa patients and 252 control subjects (all unrelated) were enrolled in this case-control PCa study. Nine single nucleotide polymorphisms (SNPs) were genotyped in GATA2 (rs73862213, rs2335052, and rs10934857), ZMIZ1 (rs704017, rs77911174, and rs3740259), and SUN2 (rs78397383, rs5750680, and rs138705) genes. The associations between the candidate SNPs and PCa were analyzed using multiple-factor logistic regression and haplotype analysis. Results The allele frequency distributions of rs73862213 and rs2335052 in the GATA2 gene and rs704017 and rs77911174 in the ZMIZ1 gene were found to be significantly different between PCa cases and controls. Haplotype analysis revealed that the G-C-A haplotype of the GATA2 gene (order of SNPs: rs73862213-rs2335052-rs10934857) and the G-G-G haplotype of the ZMIZ1 gene (order of SNPs: rs704017-rs77911174-rs3740259) were associated with increased PCa risk. None of the SUN2 haplotypes were associated with PCa. Conclusions Our study data indicates that the minor alleles of rs73862213 and rs2335052 in the GATA2 gene and rs704017 and rs77911174 in the ZMIZ1 gene were associated with increased PCa risk. These findings greatly extended our knowledge of the etiology of PCa.
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Pavel AG, Stambouli D, Gener I, Preda A, Anton G, Baston C. Genetic variant located on chromosome 17p12 contributes to prostate cancer onset and biochemical recurrence. Sci Rep 2022; 12:4546. [PMID: 35296725 PMCID: PMC8927158 DOI: 10.1038/s41598-022-08472-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 03/07/2022] [Indexed: 12/24/2022] Open
Abstract
The genetic contribution to prostate cancer (PC) onset and clinical heterogeneity has an important impact on the disease stratification accuracy. Despite the fact that radical prostatectomy (RP) is an effective treatment for localized PC, a considerable number of individuals develop biochemical recurrence (BCR) following surgery. In the present study, we decided to investigate the significance of genetic variability in a homogeneous group of Romanian men and to determine if genotyping could provide information regarding the possible implications of rs4054823 susceptibility loci in PC progression and outcome. A total of 78 samples from both PC and benign prostatic hyperplasia (BPH) patients were genotyped. The genotype frequencies were examined to see if there was a link between the 17p12 SNP and PC disease. When compared to the BPH group, the PC group had a significantly higher frequency of the T risk variant (P = 0.0056) and TT genotype (P = 0.0164). Subsequent analysis revealed that the TT genotype had a significantly higher frequency among younger PC patients based on their age at diagnosis and that it was related with a greater probability of BCR (P = 0.02). According to our findings, the TT genotype appears to be a risk factor for early-onset PC and a potential predictor for BCR after RP.
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Affiliation(s)
- Anca Gabriela Pavel
- Molecular Genetics Department, Cytogenomic Medical Laboratory, Bucharest, Romania. .,The Romania Academy, "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania.
| | - Danae Stambouli
- Molecular Genetics Department, Cytogenomic Medical Laboratory, Bucharest, Romania
| | - Ismail Gener
- Department of Nephrology, Urology, Immunology and Immunology of Transplant, Dermatology, Allergology, Faculty of Medicine, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania.,Department of Nephrology, Fundeni Clinical Institute, Bucharest, Romania
| | - Adrian Preda
- Center of Urological Surgery, Dialysis and Renal Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Gabriela Anton
- The Romania Academy, "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - Catalin Baston
- Department of Nephrology, Urology, Immunology and Immunology of Transplant, Dermatology, Allergology, Faculty of Medicine, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania.,Center of Urological Surgery, Dialysis and Renal Transplantation, Fundeni Clinical Institute, Bucharest, Romania
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PITX1 Is a Regulator of TERT Expression in Prostate Cancer with Prognostic Power. Cancers (Basel) 2022; 14:cancers14051267. [PMID: 35267575 PMCID: PMC8909694 DOI: 10.3390/cancers14051267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Most prostate cancer is of an indolent form and is curable. However, some prostate cancer belongs to rather aggressive subtypes leading to metastasis and death, and immediate therapy is mandatory. However, for these, the therapeutic options are highly invasive, such as radical prostatectomy, radiation or brachytherapy. Hence, a precise diagnosis of these tumor subtypes is needed, and the thus far applied diagnostic means are insufficient for this. Besides this, for their endless cell divisions, prostate cancer cells need the enzyme telomerase to elongate their telomeres (chromatin endings). In this study, we developed a gene regulatory model based on large data from transcription profiles from prostate cancer and chromatin-immuno-precipitation studies. We identified the developmental regulator PITX1 regulating telomerase. Besides observing experimental evidence of PITX1′s functional role in telomerase regulation, we also found PITX1 serving as a prognostic marker, as concluded from an analysis of more than 15,000 prostate cancer samples. Abstract The current risk stratification in prostate cancer (PCa) is frequently insufficient to adequately predict disease development and outcome. One hallmark of cancer is telomere maintenance. For telomere maintenance, PCa cells exclusively employ telomerase, making it essential for this cancer entity. However, TERT, the catalytic protein component of the reverse transcriptase telomerase, itself does not suit as a prognostic marker for prostate cancer as it is rather low expressed. We investigated if, instead of TERT, transcription factors regulating TERT may suit as prognostic markers. To identify transcription factors regulating TERT, we developed and applied a new gene regulatory modeling strategy to a comprehensive transcriptome dataset of 445 primary PCa. Six transcription factors were predicted as TERT regulators, and most prominently, the developmental morphogenic factor PITX1. PITX1 expression positively correlated with telomere staining intensity in PCa tumor samples. Functional assays and chromatin immune-precipitation showed that PITX1 activates TERT expression in PCa cells. Clinically, we observed that PITX1 is an excellent prognostic marker, as concluded from an analysis of more than 15,000 PCa samples. PITX1 expression in tumor samples associated with (i) increased Ki67 expression indicating increased tumor growth, (ii) a worse prognosis, and (iii) correlated with telomere length.
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Salachan PV, Rasmussen M, Fredsøe J, Ulhøi B, Borre M, Sørensen KD. Microbiota of the prostate tumor environment investigated by whole-transcriptome profiling. Genome Med 2022; 14:9. [PMID: 35078527 PMCID: PMC8787950 DOI: 10.1186/s13073-022-01011-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 01/05/2022] [Indexed: 02/08/2023] Open
Abstract
Background With over 350,000 estimated deaths worldwide in 2018, prostate cancer (PCa) continues to be a major health concern and a significant cause of cancer-associated mortality among men. While cancer in general is considered a disease of the human genome, there is a growing body of evidence suggesting that changes to the healthy microbiota could play a vital role in cancer development, progression, and/or treatment outcome. Methods Using a metatranscriptomic approach, we annotated the microbial reads obtained from total RNA sequencing of 106 prostate tissue samples from 94 PCa patients (discovery cohort). We investigated microbial dysbiosis associated with PCa by systematically comparing the microbiomes between benign and malignant tissue samples, between less vs. more-aggressive PCa, and between patients who had biochemical recurrence as opposed to those who did not. We further performed differential gene expression and cell type enrichment analysis to explore the host transcriptomic and cellular responses to selected microbial genera. A public dataset (GSE115414) of total RNA sequencing reads from 24 prostate tissue samples (8 benign and 16 malignant) served as the validation cohort. Results We observed decreased species diversity and significant under-representation of Staphylococcus saprophyticus and Vibrio parahaemolyticus, as well as significant over-abundance of Shewanella in malignant as compared to benign prostate tissue samples in both the discovery (p < 0.01) and validation (p < 0.05) cohorts. In addition, we identified Microbacterium species (p < 0.01) to be significantly over-abundant in pathologically advanced T3 tumors compared to T2 in the discovery cohort. Malignant samples having high vs. low Shewanella counts were associated with downregulated Toll-like receptor signaling pathways and decreased enrichment of dendritic cells. Malignant samples having low vs. high V. parahaemolyticus counts were enriched for olfactory transduction and drug metabolism pathways. Finally, malignant samples were enriched for M1 and M2 macrophages as compared to benign tissue samples. Conclusions The results from this exploratory study support the existence of an important biological link between the prostate microbiota and PCa development/progression. Our results highlight Shewanella, V. parahaemolyticus, and Microbacterium sp. as interesting candidates for further investigation of their association with PCa. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01011-3.
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