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Sun Z, Bai C, Su M, Tang H, Wu X, Wang Y, Bao H, Liu X, Wu X, Shao Y, Xu B. Comprehensive profiling of pathogenic germline large genomic rearrangements in a pan-cancer analysis. Mol Oncol 2023; 17:1917-1929. [PMID: 37013911 PMCID: PMC10483597 DOI: 10.1002/1878-0261.13430] [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: 12/21/2022] [Revised: 03/07/2023] [Accepted: 04/03/2023] [Indexed: 04/05/2023] Open
Abstract
The presence of large genomic rearrangements (LGRs) has been heavily investigated in breast and ovarian cancer. However, correlations between LGRs and cancer types beyond these two have not been extensively profiled, likely due to the highly inefficient methods of detecting these types of alterations. This study utilized next-generation sequencing (NGS) to analyze and classify the germline LGR profile in 17 025 cancer patients across 22 cancer types. We characterized newly identified LGRs based on predicted pathogenicity and took a closer look at genes that acquire both germline and somatic mutations within our samples. The detection method for LGRs was validated using droplet digital polymerase chain reaction (ddPCR) assay of commonly investigated LGR genes. In total, 15 659 samples from across 22 cancer types were retained for analysis after filtering. We observed that, in our cohort, the cancer types with the highest proportion of germline LGRs were ovarian cancer (4.7%), renal cell carcinoma (2.5%), breast cancer (2%), glioma (1.8%) and thyroid carcinoma (1.8%). Annotation of detected germline variants revealed several genes-MSH2, FANCA and PMS2-that contain novel LGRs. We observed co-occurrences between germline LGRs in MSH2 and somatic single nucleotide variants/insertion and deletions (SNVs/InDels) in BRCA2, KTM2B, KDM5A, CHD8, and HNF1A. Furthermore, our analysis showed that samples with pathogenic and likely pathogenic germline LGRs tended to also have higher mutational burden, chromosomal instability, and microsatellite instability ratio compared to samples with pathogenic germline SNVs/InDels. In this study, we demonstrated the prevalence of pathogenic germline LGRs beyond breast and ovarian cancer. The profiles of these pathogenic or likely pathogenic alterations will fuel further investigations and highlight new understanding of LGRs across multiple cancer types.
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Affiliation(s)
- Zhe Sun
- The First Clinical Medical CollegeGuangzhou University of Chinese MedicineGuangdongChina
| | - Chujie Bai
- Department of Bone and Soft Tissue Tumor, Key Laboratory of Carcinogenesis and Translational ResearchPeking University Cancer Hospital and InstituteBeijingChina
| | - Miaoyi Su
- Department of Radiation OncologyGuangqian HospitalQuanzhouChina
| | - Haimeng Tang
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Xiaoying Wu
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Yue Wang
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Hua Bao
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Xunbiao Liu
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Xue Wu
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Yang Shao
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
- School of Public HealthNanjing Medical UniversityChina
| | - Bei Xu
- Department of Medical OncologyZhongshan HospitalShanghaiChina
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2
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Guevara-Hoyer K, Fuentes-Antrás J, de la Fuente-Muñoz E, Fernández-Arquero M, Solano F, Pérez-Segura P, Neves E, Ocaña A, Pérez de Diego R, Sánchez-Ramón S. Genomic crossroads between non-Hodgkin’s lymphoma and common variable immunodeficiency. Front Immunol 2022; 13:937872. [PMID: 35990641 PMCID: PMC9390007 DOI: 10.3389/fimmu.2022.937872] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/07/2022] [Indexed: 12/03/2022] Open
Abstract
Common variable immunodeficiency (CVID) represents the largest group of primary immunodeficiencies that may manifest with infections, inflammation, autoimmunity, and cancer, mainly B-cell non-Hodgkin’s lymphoma (NHL). Indeed, NHL may result from chronic or recurrent infections and has, therefore, been recognized as a clinical phenotype of CVID, although rare. The more one delves into the mechanisms involved in CVID and cancer, the stronger the idea that both pathologies can be a reflection of the same primer events observed from different angles. The potential effects of germline variants on specific somatic modifications in malignancies suggest that it might be possible to anticipate critical events during tumor development. In the same way, a somatic alteration in NHL could be conditioning a similar response at the transcriptional level in the shared signaling pathways with genetic germline alterations in CVID. We aimed to explore the genomic substrate shared between these entities to better characterize the CVID phenotype immunodeficiency in NHL. By means of an in-silico approach, we interrogated the large, publicly available datasets contained in cBioPortal for the presence of genes associated with genetic pathogenic variants in a panel of 50 genes recurrently altered in CVID and previously described as causative or disease-modifying. We found that 323 (25%) of the 1,309 NHL samples available for analysis harbored variants of the CVID spectrum, with the most recurrent alteration presented in NHL occurring in PIK3CD (6%) and STAT3 (4%). Pathway analysis of common gene alterations showed enrichment in inflammatory, immune surveillance, and defective DNA repair mechanisms similar to those affected in CVID, with PIK3R1 appearing as a central node in the protein interaction network. The co-occurrence of gene alterations was a frequent phenomenon. This study represents an attempt to identify common genomic grounds between CVID and NHL. Further prospective studies are required to better know the role of genetic variants associated with CVID and their reflection on the somatic pathogenic variants responsible for cancer, as well as to characterize the CVID-like phenotype in NHL, with the potential to influence early CVID detection and therapeutic management.
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Affiliation(s)
- Kissy Guevara-Hoyer
- Cancer Immunomonitoring and Immuno-Mediated Pathologies Support Unit, IdSSC, Department of Clinical Immunology, San Carlos Clinical Hospital, Madrid, Spain
- Department of Clinical Immunology, IML and IdSSC, San Carlos Clinical Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain
- *Correspondence: Kissy Guevara-Hoyer,
| | - Jesús Fuentes-Antrás
- Oncology Department, San Carlos Clinical Hospital, Madrid, Spain
- Experimental Therapeutics and Translational Oncology Unit, Medical Oncology Department, San Carlos University Hospital, Madrid, Spain
| | - Eduardo de la Fuente-Muñoz
- Cancer Immunomonitoring and Immuno-Mediated Pathologies Support Unit, IdSSC, Department of Clinical Immunology, San Carlos Clinical Hospital, Madrid, Spain
- Department of Clinical Immunology, IML and IdSSC, San Carlos Clinical Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain
| | - Miguel Fernández-Arquero
- Cancer Immunomonitoring and Immuno-Mediated Pathologies Support Unit, IdSSC, Department of Clinical Immunology, San Carlos Clinical Hospital, Madrid, Spain
- Department of Clinical Immunology, IML and IdSSC, San Carlos Clinical Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain
| | - Fernando Solano
- Department of Hematology, General University Hospital Nuestra Señora del Prado, Talavera de la Reina, Spain
| | | | - Esmeralda Neves
- Department of Immunology, Centro Hospitalar e Universitário do Porto, Porto, Portugal
- Unit for Multidisciplinary Research in Biomedicine (UMIB), Hospital and University Center of Porto, Porto, Portugal
| | - Alberto Ocaña
- Oncology Department, San Carlos Clinical Hospital, Madrid, Spain
- Experimental Therapeutics and Translational Oncology Unit, Medical Oncology Department, San Carlos University Hospital, Madrid, Spain
| | - Rebeca Pérez de Diego
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, Madrid, Spain
| | - Silvia Sánchez-Ramón
- Cancer Immunomonitoring and Immuno-Mediated Pathologies Support Unit, IdSSC, Department of Clinical Immunology, San Carlos Clinical Hospital, Madrid, Spain
- Department of Clinical Immunology, IML and IdSSC, San Carlos Clinical Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain
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3
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Zografos E, Andrikopoulou A, Papatheodoridi AM, Kaparelou M, Bletsa G, Liontos M, Dimopoulos MA, Zagouri F. Multi-Gene Mutation Profiling by Targeted Next-Generation Sequencing in Premenopausal Breast Cancer. Genes (Basel) 2022; 13:genes13081362. [PMID: 36011273 PMCID: PMC9407588 DOI: 10.3390/genes13081362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
Breast cancer has distinct etiology, prognoses, and clinical outcomes at premenopausal ages. Determination of the frequency of germline and somatic mutations will refine our understanding of the genetic contribution to premenopausal breast cancer susceptibility. We applied a comprehensive next generation sequencing-based approach to analyze blood and/or tissue samples of 54 premenopausal breast cancer patients treated in our clinic. Genetic testing results were descriptively analyzed in correlation with clinicopathological data. In the present study, 42.5% of premenopausal breast cancer patients tested carried pathogenic mutations in cancer predisposition genes (CHEK2, BRCA1, TP53, and MUTYH). Germline variants of unknown/uncertain significance (VUSs) in eight different cancer susceptibility genes, namely BRCA1, BRCA2, CHEK2, RAD51C, RAD51D, ATM, BRIP1, and PMS2, were also identified in 14 premenopausal patients (35%). Of the breast tumors tested, 61.8% harbored pathogenic somatic variants in tumor suppressor genes (TP53, NF1, RB), genes involved in DNA repair (BRCA1, BRCA2, ATM, RAD50), cell proliferation (PTEN, PIK3C FGFR3, AKT1, ROS1, ERBB2, NOTCH1), and cell adhesion (CTNNB1). This descriptive study employs the powerful NGS technology to highlight the high frequency of premenopausal cases attributable to genetic predisposition. Mutation identification in a larger cohort may further ensure that these patients receive tailored treatment according to their menopausal status.
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Affiliation(s)
- Eleni Zografos
- Department of Clinical Therapeutics, Alexandra Hospital, School of Medicine, National and Kapodistrian University of Athens, 80 Vasilissis Sofias Avenue, 11528 Athens, Greece; (E.Z.); (A.A.); (A.M.P.); (M.K.); (M.L.); (M.-A.D.)
| | - Angeliki Andrikopoulou
- Department of Clinical Therapeutics, Alexandra Hospital, School of Medicine, National and Kapodistrian University of Athens, 80 Vasilissis Sofias Avenue, 11528 Athens, Greece; (E.Z.); (A.A.); (A.M.P.); (M.K.); (M.L.); (M.-A.D.)
| | - Alkistis Maria Papatheodoridi
- Department of Clinical Therapeutics, Alexandra Hospital, School of Medicine, National and Kapodistrian University of Athens, 80 Vasilissis Sofias Avenue, 11528 Athens, Greece; (E.Z.); (A.A.); (A.M.P.); (M.K.); (M.L.); (M.-A.D.)
| | - Maria Kaparelou
- Department of Clinical Therapeutics, Alexandra Hospital, School of Medicine, National and Kapodistrian University of Athens, 80 Vasilissis Sofias Avenue, 11528 Athens, Greece; (E.Z.); (A.A.); (A.M.P.); (M.K.); (M.L.); (M.-A.D.)
| | | | - Michalis Liontos
- Department of Clinical Therapeutics, Alexandra Hospital, School of Medicine, National and Kapodistrian University of Athens, 80 Vasilissis Sofias Avenue, 11528 Athens, Greece; (E.Z.); (A.A.); (A.M.P.); (M.K.); (M.L.); (M.-A.D.)
| | - Meletios-Athanasios Dimopoulos
- Department of Clinical Therapeutics, Alexandra Hospital, School of Medicine, National and Kapodistrian University of Athens, 80 Vasilissis Sofias Avenue, 11528 Athens, Greece; (E.Z.); (A.A.); (A.M.P.); (M.K.); (M.L.); (M.-A.D.)
| | - Flora Zagouri
- Department of Clinical Therapeutics, Alexandra Hospital, School of Medicine, National and Kapodistrian University of Athens, 80 Vasilissis Sofias Avenue, 11528 Athens, Greece; (E.Z.); (A.A.); (A.M.P.); (M.K.); (M.L.); (M.-A.D.)
- Correspondence:
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4
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Qing T, Mohsen H, Cannataro VL, Marczyk M, Rozenblit M, Foldi J, Murray M, Townsend JP, Kluger Y, Gerstein M, Pusztai L. Cancer Relevance of Human Genes. J Natl Cancer Inst 2022; 114:988-995. [PMID: 35417011 PMCID: PMC9275765 DOI: 10.1093/jnci/djac068] [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: 09/03/2021] [Revised: 01/03/2022] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND We hypothesize that genes that directly or indirectly interact with core cancer genes (CCGs) in a comprehensive gene-gene interaction network may have functional importance in cancer. METHODS We categorized 12 767 human genes into CCGs (n = 468), 1 (n = 5467), 2 (n = 5573), 3 (n = 915), and more than 3 steps (n = 416) removed from the nearest CCG in the Search Tool for the Retrieval of Interacting Genes/Proteins network. We estimated cancer-relevant functional importance in these neighborhood categories using 1) gene dependency score, which reflects the effect of a gene on cell viability after knockdown; 2) somatic mutation frequency in The Cancer Genome Atlas; 3) effect size that estimates to what extent a mutation in a gene enhances cell survival; and 4) negative selection pressure of germline protein-truncating variants in healthy populations. RESULTS Cancer biology-related functional importance of genes decreases as their distance from the CCGs increases. Genes closer to cancer genes show greater connectedness in the network, have greater importance in maintaining cancer cell viability, are under greater negative germline selection pressure, and have higher somatic mutation frequency in cancer. Based on these 4 metrics, we provide cancer relevance annotation to known human genes. CONCLUSIONS A large number of human genes are connected to CCGs and could influence cancer biology to various extent when dysregulated; any given mutation may be functionally important in one but not in another individual depending on genomic context.
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Affiliation(s)
- Tao Qing
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Hussein Mohsen
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | | | - Michal Marczyk
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Mariya Rozenblit
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Julia Foldi
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Michael Murray
- Department of Genetics, Yale Center for Genomic Health, New Haven, CT, USA
| | - Jeffrey P Townsend
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Yuval Kluger
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Pathology, School of Medicine, Yale University, New Haven, CT, USA
- Applied Mathematics Program, Yale University, New Haven, CT, USA
| | - Mark Gerstein
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
- Department of Statistics & Data Science, Yale University, New Haven, CT, USA
| | - Lajos Pusztai
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
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5
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Santonja Á, Moya-García AA, Ribelles N, Jiménez-Rodríguez B, Pajares B, Fernández-De Sousa CE, Pérez-Ruiz E, Del Monte-Millán M, Ruiz-Borrego M, de la Haba J, Sánchez-Rovira P, Romero A, González-Neira A, Lluch A, Alba E. Role of germline variants in the metastasis of breast carcinomas. Oncotarget 2022; 13:843-862. [PMID: 35782051 PMCID: PMC9245581 DOI: 10.18632/oncotarget.28250] [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: 03/04/2022] [Accepted: 06/20/2022] [Indexed: 11/25/2022] Open
Abstract
Most cancer-related deaths in breast cancer patients are associated with metastasis, a multistep, intricate process that requires the cooperation of tumour cells, tumour microenvironment and metastasis target tissues. It is accepted that metastasis does not depend on the tumour characteristics but the host’s genetic makeup. However, there has been limited success in determining the germline genetic variants that influence metastasis development, mainly because of the limitations of traditional genome-wide association studies to detect the relevant genetic polymorphisms underlying complex phenotypes. In this work, we leveraged the extreme discordant phenotypes approach and the epistasis networks to analyse the genotypes of 97 breast cancer patients. We found that the host’s genetic makeup facilitates metastases by the dysregulation of gene expression that can promote the dispersion of metastatic seeds and help establish the metastatic niche—providing a congenial soil for the metastatic seeds.
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Affiliation(s)
- Ángela Santonja
- Instituto de Investigación Biomédica de Málaga (IBIMA), Hospitales Universitarios Regional y Virgen de la Victoria de Málaga, Spain.,Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, Málaga, Spain.,These authors contributed equally to this work
| | - Aurelio A Moya-García
- Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, Málaga, Spain.,Departmento de Biología Molecular y Bioquímica, Universidad de Málaga, Málaga, Spain.,These authors contributed equally to this work
| | - Nuria Ribelles
- Unidad de Gestión Clínica Intercentro de Oncología, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospitales Universitarios Regional y Virgen de la Victoria de Málaga, Málaga, Spain.,Centro de Investigación Biomédica en Red de Oncología, CIBERONC-ISCIII, Madrid, Spain
| | - Begoña Jiménez-Rodríguez
- Unidad de Gestión Clínica Intercentro de Oncología, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospitales Universitarios Regional y Virgen de la Victoria de Málaga, Málaga, Spain
| | - Bella Pajares
- Unidad de Gestión Clínica Intercentro de Oncología, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospitales Universitarios Regional y Virgen de la Victoria de Málaga, Málaga, Spain
| | - Cristina E Fernández-De Sousa
- Instituto de Investigación Biomédica de Málaga (IBIMA), Hospitales Universitarios Regional y Virgen de la Victoria de Málaga, Spain.,Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, Málaga, Spain
| | | | - María Del Monte-Millán
- Centro de Investigación Biomédica en Red de Oncología, CIBERONC-ISCIII, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, Madrid, Spain
| | | | - Juan de la Haba
- Centro de Investigación Biomédica en Red de Oncología, CIBERONC-ISCIII, Madrid, Spain.,Biomedical Research Institute, Complejo Hospitalario Reina Sofía, Córdoba, Spain
| | | | - Atocha Romero
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Madrid, Spain
| | - Anna González-Neira
- Human Genotyping-CEGEN Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ana Lluch
- Centro de Investigación Biomédica en Red de Oncología, CIBERONC-ISCIII, Madrid, Spain.,Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain.,INCLIVA Biomedical Research Institute, Universidad de Valencia, Valencia, Spain
| | - Emilio Alba
- Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, Málaga, Spain.,Unidad de Gestión Clínica Intercentro de Oncología, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospitales Universitarios Regional y Virgen de la Victoria de Málaga, Málaga, Spain.,Centro de Investigación Biomédica en Red de Oncología, CIBERONC-ISCIII, Madrid, Spain
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6
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El Hadi C, Ayoub G, Bachir Y, Haykal M, Jalkh N, Kourie HR. Polygenic and Network-Based Studies in Risk Identification and Demystification of cancer. Expert Rev Mol Diagn 2022; 22:427-438. [PMID: 35400274 DOI: 10.1080/14737159.2022.2065195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Diseases were initially thought to be the consequence of a single gene mutation. Advances in DNA sequencing tools and our understanding of gene behavior have revealed that complex diseases, such as cancer, are the product of genes cooperating with each other and with their environment in orchestrated communication networks. Seeing that the function of individual genes is still used to analyze cancer, the shift to using functionally interacting groups of genes as a new unit of study holds promise for demystifying cancer. AREAS COVERED The literature search focused on three types of cancer, namely breast, lung, and prostate, but arguments from other cancers were also included. The aim was to prove that multigene analyses can accurately predict and prognosticate cancer risk, subtype cancer for more personalized and effective treatments, and discover anti-cancer therapies. Computational intelligence is being harnessed to analyze this type of data and is proving indispensable to scientific progress. EXPERT OPINION In the future, comprehensive profiling of all kinds of patient data (e.g., serum molecules, environmental exposures) can be used to build universal networks that should help us elucidate the molecular mechanisms underlying diseases and provide appropriate preventive measures, ensuring lifelong health and longevity.
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Affiliation(s)
| | - George Ayoub
- Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Yara Bachir
- Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Michèle Haykal
- Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Nadine Jalkh
- Medical Genetics Unit, Technology and Health division, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Hampig Raphael Kourie
- Department of Hematology-Oncology, Hotel Dieu de France University Hospital, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
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7
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Fasching PA, Yadav S, Hu C, Wunderle M, Häberle L, Hart SN, Rübner M, Polley EC, Lee KY, Gnanaolivu RD, Hadji P, Hübner H, Tesch H, Ettl J, Overkamp F, Lux MP, Ekici AB, Volz B, Uhrig S, Lüftner D, Wallwiener M, Müller V, Belleville E, Untch M, Kolberg HC, Beckmann MW, Reis A, Hartmann A, Janni W, Wimberger P, Taran FA, Fehm TN, Wallwiener D, Brucker SY, Schneeweiss A, Hartkopf AD, Couch FJ. Mutations in BRCA1/2 and Other Panel Genes in Patients With Metastatic Breast Cancer -Association With Patient and Disease Characteristics and Effect on Prognosis. J Clin Oncol 2021; 39:1619-1630. [PMID: 33780288 PMCID: PMC8274805 DOI: 10.1200/jco.20.01200] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 12/25/2020] [Accepted: 02/04/2021] [Indexed: 12/17/2022] Open
Abstract
PURPOSE Among patients with metastatic breast cancer (mBC), the frequency of germline mutations in cancer susceptibility genes and the clinical relevance of these mutations are unclear. In this study, a prospective cohort of patients with mBC was used to determine mutation rates for breast cancer (BC) predisposition genes, to evaluate the clinical characteristics of patients with mutations, and to assess the influence of mutations on patient outcome. PATIENTS AND METHODS Germline DNA from 2,595 patients with mBC enrolled in the prospective PRAEGNANT registry was evaluated for mutations in cancer predisposition genes. The frequencies of mutations in known BC predisposition genes were compared with results from a prospective registry of patients with nonmetastatic BC sequenced using the same QIAseq method and with public reference controls. Associations between mutation status and tumor characteristics, progression-free survival, and overall survival were assessed. RESULTS Germline mutations in 12 established BC predisposition genes (including BRCA1 and BRCA2) were detected in 271 (10.4%) patients. A mutation in BRCA1 or BRCA2 was seen in 129 patients (5.0%). BRCA1 mutation carriers had a higher proportion of brain metastasis (27.1%) compared with nonmutation carriers (12.8%). Mutations were significantly enriched in PRAEGNANT patients with mBC compared with patients with nonmetastatic BC (10.4% v 6.6%, P < .01). Mutations did not significantly modify progression-free survival or overall survival for patients with mBC. CONCLUSION Multigene panel testing may be considered in all patients with mBC because of the high frequency of germline mutations in BRCA1/2 and other BC predisposition genes. Although the prognosis of mutation carriers and nonmutation carriers with mBC was similar, differences observed in tumor characteristics have implications for treatment and for future studies of targeted therapies.
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Affiliation(s)
- Peter A. Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | | | - Chunling Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Marius Wunderle
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Lothar Häberle
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
- Biostatistics Unit, Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Steven N. Hart
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Matthias Rübner
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Eric C. Polley
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Kun Y. Lee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Peyman Hadji
- Frankfurt Center of Bone Health, Frankfurt, Germany
| | - Hanna Hübner
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Hans Tesch
- Oncology Practice at Bethanien Hospital Frankfurt, Frankfurt, Germany
| | - Johannes Ettl
- Department of Obstetrics and Gynecology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | | | - Michael P. Lux
- Klinik für Gynäkologie und Geburtshilfe Frauenklinik St Louise, Paderborn, St Josefs-Krankenhaus, Salzkotten, Germany
- Kooperatives Brustzentrum Paderborn, Paderborn, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Bernhard Volz
- Ansbach University of Applied Sciences, Ansbach, Germany
| | - Sabrina Uhrig
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Diana Lüftner
- Department of Hematology, Oncology and Tumour Immunology, Charité University Hospital, Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Markus Wallwiener
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Volkmar Müller
- Department of Gynecology, Hamburg-Eppendorf University Medical Center, Hamburg, Germany
| | | | - Michael Untch
- Department of Gynecology and Obstetrics, Helios Clinics Berlin Buch, Berlin, Germany
| | | | - Matthias W. Beckmann
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Wolfgang Janni
- Department of Gynecology and Obstetrics, Ulm University Hospital, Ulm, Germany
| | - Pauline Wimberger
- Department of Gynecology and Obstetrics, Carl Gustav Carus Faculty of Medicine and University Hospital, Technical University of Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Carl Gustav Carus Faculty of Medicine and University Hospital, Technical University of Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Florin-Andrei Taran
- Department of Obstetrics and Gynecology, University Hospital Freiburg, Freiburg, Germany
| | - Tanja N. Fehm
- Department of Gynecology and Obstetrics, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Diethelm Wallwiener
- Department of Obstetrics and Gynecology, University of Tuebingen, Tuebingen, Germany
| | - Sara Y. Brucker
- Department of Obstetrics and Gynecology, University of Tuebingen, Tuebingen, Germany
| | - Andreas Schneeweiss
- National Center for Tumor Diseases, Heidelberg University Hospital, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas D. Hartkopf
- Department of Obstetrics and Gynecology, University of Tuebingen, Tuebingen, Germany
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
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8
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Porta‐Pardo E, Valencia A, Godzik A. Understanding oncogenicity of cancer driver genes and mutations in the cancer genomics era. FEBS Lett 2020; 594:4233-4246. [PMID: 32239503 PMCID: PMC7529711 DOI: 10.1002/1873-3468.13781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 01/23/2020] [Accepted: 02/09/2020] [Indexed: 12/12/2022]
Abstract
One of the key challenges of cancer biology is to catalogue and understand the somatic genomic alterations leading to cancer. Although alternative definitions and search methods have been developed to identify cancer driver genes and mutations, analyses of thousands of cancer genomes return a remarkably similar catalogue of around 300 genes that are mutated in at least one cancer type. Yet, many features of these genes and their role in cancer remain unclear, first and foremost when a somatic mutation is truly oncogenic. In this review, we first summarize some of the recent efforts in completing the catalogue of cancer driver genes. Then, we give an overview of different aspects that influence the oncogenicity of somatic mutations in the core cancer driver genes, including their interactions with the germline genome, other cancer driver mutations, the immune system, or their potential role in healthy tissues. In the coming years, this research holds promise to illuminate how, when, and why cancer driver genes and mutations are really drivers, and thereby move personalized cancer medicine and targeted therapies forward.
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Affiliation(s)
- Eduard Porta‐Pardo
- Barcelona Supercomputing Center (BSC)BarcelonaSpain
- Josep Carreras Leukaemia Research Institute (IJC)BadalonaSpain
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC)BarcelonaSpain
- Institucio Catalana de Recerca I Estudis Avançats (ICREA)BarcelonaSpain
| | - Adam Godzik
- Division of Biomedical SciencesUniversity of California Riverside School of MedicineRiversideCAUSA
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9
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Youssef O, Almangush A, Zidi YHS, Loukola A, Carpén O. Nonmalignant Formalin-Fixed Paraffin-Embedded Tissues as a Source to Study Germline Variants and Cancer Predisposition: A Systematic Review. Biopreserv Biobank 2020; 18:337-345. [PMID: 32551987 DOI: 10.1089/bio.2020.0021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: Archived formalin-fixed paraffin-embedded (FFPE) specimens from nonmalignant tissues derived from cancer patients are a vast and potentially valuable resource for high-quality genotyping analyses and could have a role in establishing inherited cancer risk. Methods: We systematically searched PubMed, Ovid MEDLINE, and Scopus databases for all articles that compared genotyping performance of DNA from nonmalignant FFPE tissue with blood DNA derived from cancer patients irrespective of tumor type. Two independent researchers screened the retrieved studies, removed duplicates, excluded irrelevant studies, and extracted genotyping data from the eligible studies. These studies included, but were not limited to, genotyping technique, reported call rate, and concordance. Results: Thirteen studies were reviewed, in which DNA from nonmalignant FFPE tissues derived from cancer patients was successfully purified and genotyped. All these studies used different approaches for genotyping of DNA from nonmalignant FFPE tissues to amplify single nucleotide polymorphisms (SNPs) and to estimate of loss of heterozygosity. The concordance between genotypes from nonmalignant FFPE tissues and blood derived from cancer patients was observed to be high, whereas the call rate of the tested SNPs was not reported in all included studies. Conclusion: This review illustrates that DNA from nonmalignant FFPE tissues derived from cancer patients can serve as an alternative and reliable source for assessment of germline DNA for various purposes, including assessment of cancer predisposition.
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Affiliation(s)
- Omar Youssef
- Department of Pathology, University of Helsinki, Helsinki, Finland.,Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Alhadi Almangush
- Department of Pathology, University of Helsinki, Helsinki, Finland.,Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Pathology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Yossra H S Zidi
- Department of Pathology, University of Helsinki, Helsinki, Finland.,Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anu Loukola
- Department of Pathology, University of Helsinki, Helsinki, Finland.,Helsinki Biobank, HUS Helsinki University Hospital, Helsinki, Finland
| | - Olli Carpén
- Department of Pathology, University of Helsinki, Helsinki, Finland.,Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Helsinki Biobank, HUS Helsinki University Hospital, Helsinki, Finland
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10
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Qing T, Mohsen H, Marczyk M, Ye Y, O'Meara T, Zhao H, Townsend JP, Gerstein M, Hatzis C, Kluger Y, Pusztai L. Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden. Nat Commun 2020; 11:2438. [PMID: 32415133 PMCID: PMC7228928 DOI: 10.1038/s41467-020-16293-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/21/2020] [Indexed: 11/24/2022] Open
Abstract
Cancers harbor many somatic mutations and germline variants, we hypothesized that the combined effect of germline variants that alter the structure, expression, or function of protein-coding regions of cancer-biology related genes (gHFI) determines which and how many somatic mutations (sM) must occur for malignant transformation. We show that gHFI and sM affect overlapping genes and the average number of gHFI in cancer hallmark genes is higher in patients who develop cancer at a younger age (r = -0.77, P = 0.0051), while the average number of sM increases in increasing age groups (r = 0.92, P = 0.000073). A strong negative correlation exists between average gHFI and average sM burden in increasing age groups (r = -0.70, P = 0.017). In early-onset cancers, the larger gHFI burden in cancer genes suggests a greater contribution of germline alterations to the transformation process while late-onset cancers are more driven by somatic mutations.
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Affiliation(s)
- Tao Qing
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Hussein Mohsen
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Michal Marczyk
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
- Data Mining Division, Silesian University of Technology, Gliwice, Poland
| | - Yixuan Ye
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Tess O'Meara
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Hongyu Zhao
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, USA
| | - Jeffrey P Townsend
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, USA
| | - Mark Gerstein
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
- Department of Statistics & Data Science, Yale University, New Haven, CT, USA
| | - Christos Hatzis
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
- Bristol-Myers Squibb, New York, NY, USA
| | - Yuval Kluger
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Pathology, School of Medicine, Yale University, New Haven, CT, USA
- Program of Applied Mathematics, Yale University, New Haven, CT, USA
| | - Lajos Pusztai
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA.
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11
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Buckingham L, Mitchell R, Maienschein-Cline M, Green S, Hu VH, Cobleigh M, Rotmensch J, Burgess K, Usha L. Somatic variants of potential clinical significance in the tumors of BRCA phenocopies. Hered Cancer Clin Pract 2019; 17:21. [PMID: 31346352 PMCID: PMC6636136 DOI: 10.1186/s13053-019-0117-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 06/27/2019] [Indexed: 11/10/2022] Open
Abstract
Background BRCA phenocopies are individuals with the same phenotype (i.e. cancer consistent with Hereditary Breast and Ovarian Cancer syndrome = HBOC) as their affected relatives, but not the same genotype as assessed by blood germline testing (i.e. they do not carry a germline BRCA1 or BRCA2 mutation). There is some evidence of increased risk for HBOC-related cancers in relatives of germline variant carriers even though they themselves test negative for the familial variant (BRCA non-carriers). At this time, BRCA phenocopies are recommended to undergo the same cancer surveillance as individuals in the general population. This raises the question of whether the increased cancer risk in BRCA non-carriers is due to alterations (germline, somatic or epigenetic) in other cancer-associated genes which were not analyzed during BRCA analysis. Methods To assess the nature and potential clinical significance of somatic variants in BRCA phenocopy tumors, DNA from BRCA non-carrier tumor tissue was analyzed using next generation sequencing of 572 cancer genes. Tumor diagnoses of the 11 subjects included breast, ovarian, endometrial and primary peritoneal carcinoma. Variants were called using FreeBayes genetic variant detector. Variants were annotated for effect on protein sequence, predicted function, and frequency in different populations from the 1000 genomes project, and presence in variant databases COSMIC and ClinVar using Annovar. Results None of the familial BRCA1/2 mutations were found in the tumor samples tested. The most frequently occurring somatic gene variants were ROS1(6/11 cases) and NUP98 (5/11 cases). BRCA2 somatic variants were found in 2/6 BRCA1 phenocopies, but 0/5 BRCA2 phenocopies. Variants of uncertain significance were found in other DNA repair genes (ERCC1, ERCC3, ERCC4, FANCD2, PALB2), one mismatch repair gene (PMS2), a DNA demethylation enzyme (TET2), and two histone modifiers (EZH2, SUZ12). Conclusions Although limited by a small sample size, these results support a role of selected somatic variants and epigenetic mechanisms in the development of tumors in BRCA phenocopies.
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Affiliation(s)
- Lela Buckingham
- 1Department of Pathology, Rush University Medical Center, Chicago, IL USA
| | | | | | - Stefan Green
- 4University of Illinois at Chicago Research Resources Center, Chicago, IL USA
| | - Vincent Hong Hu
- 4University of Illinois at Chicago Research Resources Center, Chicago, IL USA
| | - Melody Cobleigh
- 2Rush Cancer Institute, Rush University Medical Center, Chicago, IL USA
| | - Jacob Rotmensch
- 2Rush Cancer Institute, Rush University Medical Center, Chicago, IL USA
| | - Kelly Burgess
- 2Rush Cancer Institute, Rush University Medical Center, Chicago, IL USA
| | - Lydia Usha
- 2Rush Cancer Institute, Rush University Medical Center, Chicago, IL USA
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12
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Farashi S, Kryza T, Clements J, Batra J. Post-GWAS in prostate cancer: from genetic association to biological contribution. Nat Rev Cancer 2019; 19:46-59. [PMID: 30538273 DOI: 10.1038/s41568-018-0087-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genome-wide association studies (GWAS) have been successful in deciphering the genetic component of predisposition to many human complex diseases including prostate cancer. Germline variants identified by GWAS progressively unravelled the substantial knowledge gap concerning prostate cancer heritability. With the beginning of the post-GWAS era, more and more studies reveal that, in addition to their value as risk markers, germline variants can exert active roles in prostate oncogenesis. Consequently, current research efforts focus on exploring the biological mechanisms underlying specific susceptibility loci known as causal variants by applying novel and precise analytical methods to available GWAS data. Results obtained from these post-GWAS analyses have highlighted the potential of exploiting prostate cancer risk-associated germline variants to identify new gene networks and signalling pathways involved in prostate tumorigenesis. In this Review, we describe the molecular basis of several important prostate cancer-causal variants with an emphasis on using post-GWAS analysis to gain insight into cancer aetiology. In addition to discussing the current status of post-GWAS studies, we also summarize the main molecular mechanisms of potential causal variants at prostate cancer risk loci and explore the major challenges in moving from association to functional studies and their implication in clinical translation.
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Affiliation(s)
- Samaneh Farashi
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Thomas Kryza
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Judith Clements
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Jyotsna Batra
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia.
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia.
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