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Parsons BL, Beal MA, Dearfield KL, Douglas GR, Gi M, Gollapudi BB, Heflich RH, Horibata K, Kenyon M, Long AS, Lovell DP, Lynch AM, Myers MB, Pfuhler S, Vespa A, Zeller A, Johnson GE, White PA. Severity of effect considerations regarding the use of mutation as a toxicological endpoint for risk assessment: A report from the 8th International Workshop on Genotoxicity Testing (IWGT). ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024. [PMID: 38828778 DOI: 10.1002/em.22599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/13/2024] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
Exposure levels without appreciable human health risk may be determined by dividing a point of departure on a dose-response curve (e.g., benchmark dose) by a composite adjustment factor (AF). An "effect severity" AF (ESAF) is employed in some regulatory contexts. An ESAF of 10 may be incorporated in the derivation of a health-based guidance value (HBGV) when a "severe" toxicological endpoint, such as teratogenicity, irreversible reproductive effects, neurotoxicity, or cancer was observed in the reference study. Although mutation data have been used historically for hazard identification, this endpoint is suitable for quantitative dose-response modeling and risk assessment. As part of the 8th International Workshops on Genotoxicity Testing, a sub-group of the Quantitative Analysis Work Group (WG) explored how the concept of effect severity could be applied to mutation. To approach this question, the WG reviewed the prevailing regulatory guidance on how an ESAF is incorporated into risk assessments, evaluated current knowledge of associations between germline or somatic mutation and severe disease risk, and mined available data on the fraction of human germline mutations expected to cause severe disease. Based on this review and given that mutations are irreversible and some cause severe human disease, in regulatory settings where an ESAF is used, a majority of the WG recommends applying an ESAF value between 2 and 10 when deriving a HBGV from mutation data. This recommendation may need to be revisited in the future if direct measurement of disease-causing mutations by error-corrected next generation sequencing clarifies selection of ESAF values.
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Affiliation(s)
- Barbara L Parsons
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Marc A Beal
- Bureau of Chemical Safety, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Kerry L Dearfield
- U.S. Environmental Protection Agency and U.S. Department of Agriculture, Washington, DC, USA
| | - George R Douglas
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Min Gi
- Department of Environmental Risk Assessment, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | | | - Robert H Heflich
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Michelle Kenyon
- Portfolio and Regulatory Strategy, Drug Safety Research and Development, Pfizer, Groton, Connecticut, USA
| | - Alexandra S Long
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - David P Lovell
- Population Health Research Institute, St George's Medical School, University of London, London, UK
| | | | - Meagan B Myers
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Alisa Vespa
- Pharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Andreas Zeller
- Pharmaceutical Sciences, pRED Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - George E Johnson
- Swansea University Medical School, Swansea University, Swansea, Wales, UK
| | - Paul A White
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
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2
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Houlahan KE, Khan A, Greenwald NF, Vivas CS, West RB, Angelo M, Curtis C. Germline-mediated immunoediting sculpts breast cancer subtypes and metastatic proclivity. Science 2024; 384:eadh8697. [PMID: 38815010 DOI: 10.1126/science.adh8697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 04/05/2024] [Indexed: 06/01/2024]
Abstract
Tumors with the same diagnosis can have different molecular profiles and response to treatment. It remains unclear when and why these differences arise. Somatic genomic aberrations occur within the context of a highly variable germline genome. Interrogating 5870 breast cancer lesions, we demonstrated that germline-derived epitopes in recurrently amplified genes influence somatic evolution by mediating immunoediting. Individuals with a high germline-epitope burden in human epidermal growth factor receptor 2 (HER2/ERBB2) are less likely to develop HER2-positive breast cancer compared with other subtypes. The same holds true for recurrent amplicons defining three aggressive estrogen receptor (ER)-positive subgroups. Tumors that overcome such immune-mediated negative selection are more aggressive and demonstrate an "immune cold" phenotype. These data show that the germline genome plays a role in dictating somatic evolution.
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Affiliation(s)
- Kathleen E Houlahan
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Aziz Khan
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Noah F Greenwald
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Robert B West
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Christina Curtis
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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3
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Dinh KN, Vázquez-García I, Chan A, Malhotra R, Weiner A, McPherson AW, Tavaré S. CINner: modeling and simulation of chromosomal instability in cancer at single-cell resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.587939. [PMID: 38617259 PMCID: PMC11014621 DOI: 10.1101/2024.04.03.587939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Cancer development is characterized by chromosomal instability, manifesting in frequent occurrences of different genomic alteration mechanisms ranging in extent and impact. Mathematical modeling can help evaluate the role of each mutational process during tumor progression, however existing frameworks can only capture certain aspects of chromosomal instability (CIN). We present CINner, a mathematical framework for modeling genomic diversity and selection during tumor evolution. The main advantage of CINner is its flexibility to incorporate many genomic events that directly impact cellular fitness, from driver gene mutations to copy number alterations (CNAs), including focal amplifications and deletions, missegregations and whole-genome duplication (WGD). We apply CINner to find chromosome-arm selection parameters that drive tumorigenesis in the absence of WGD in chromosomally stable cancer types. We found that the selection parameters predict WGD prevalence among different chromosomally unstable tumors, hinting that the selective advantage of WGD cells hinges on their tolerance for aneuploidy and escape from nullisomy. Direct application of CINner to model the WGD proportion and fraction of genome altered (FGA) further uncovers the increase in CNA probabilities associated with WGD in each cancer type. CINner can also be utilized to study chromosomally stable cancer types, by applying a selection model based on driver gene mutations and focal amplifications or deletions. Finally, we used CINner to analyze the impact of CNA probabilities, chromosome selection parameters, tumor growth dynamics and population size on cancer fitness and heterogeneity. We expect that CINner will provide a powerful modeling tool for the oncology community to quantify the impact of newly uncovered genomic alteration mechanisms on shaping tumor progression and adaptation.
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Affiliation(s)
- Khanh N. Dinh
- Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA
- Department of Statistics, Columbia University, New York, NY, USA
| | - Ignacio Vázquez-García
- Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew Chan
- Case Western Reserve University, Cleveland, OH, USA
| | - Rhea Malhotra
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Stanford University, Palo Alto, CA, USA
| | - Adam Weiner
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andrew W. McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simon Tavaré
- Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA
- Department of Statistics, Columbia University, New York, NY, USA
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4
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Hu Z, Wu Z, Liu W, Ning Y, Liu J, Ding W, Fan J, Cai S, Li Q, Li W, Yang X, Dou Y, Wang W, Peng W, Lu F, Zhuang X, Qin T, Kang X, Feng C, Xu Z, Lv Q, Wang Q, Wang C, Wang X, Wang Z, Wang J, Jiang J, Wang B, Mills GB, Ma D, Gao Q, Li K, Chen G, Chen X, Sun C. Proteogenomic insights into early-onset endometrioid endometrial carcinoma: predictors for fertility-sparing therapy response. Nat Genet 2024; 56:637-651. [PMID: 38565644 DOI: 10.1038/s41588-024-01703-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024]
Abstract
Endometrial carcinoma remains a public health concern with a growing incidence, particularly in younger women. Preserving fertility is a crucial consideration in the management of early-onset endometrioid endometrial carcinoma (EEEC), particularly in patients under 40 who maintain both reproductive desire and capacity. To illuminate the molecular characteristics of EEEC, we undertook a large-scale multi-omics study of 215 patients with endometrial carcinoma, including 81 with EEEC. We reveal an unexpected association between exposome-related mutational signature and EEEC, characterized by specific CTNNB1 and SIGLEC10 hotspot mutations and disruption of downstream pathways. Interestingly, SIGLEC10Q144K mutation in EEECs resulted in aberrant SIGLEC-10 protein expression and promoted progestin resistance by interacting with estrogen receptor alpha. We also identified potential protein biomarkers for progestin response in fertility-sparing treatment for EEEC. Collectively, our study establishes a proteogenomic resource of EEECs, uncovering the interactions between exposome and genomic susceptibilities that contribute to the development of primary prevention and early detection strategies for EEECs.
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Affiliation(s)
- Zhe Hu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Zimeng Wu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Wei Liu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Yan Ning
- Department of Pathology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Jingbo Liu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Wencheng Ding
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Junpeng Fan
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Shuyan Cai
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Qinlan Li
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Wenting Li
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Xiaohang Yang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Yingyu Dou
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Wei Wang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Wenju Peng
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Funian Lu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Xucui Zhuang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Tianyu Qin
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Xiaoyan Kang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Chenzhao Feng
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Zhiying Xu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Qiaoying Lv
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Qian Wang
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Chao Wang
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Xinyu Wang
- The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, P. R. China
| | - Zhiqi Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital; Peking University People's Hospital, Xicheng District, Beijing, P. R. China
| | - Jianliu Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital; Peking University People's Hospital, Xicheng District, Beijing, P. R. China
| | - Jie Jiang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, P. R. China
| | - Beibei Wang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | | | - Ding Ma
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Qinglei Gao
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
| | - Kezhen Li
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
| | - Gang Chen
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
| | - Xiaojun Chen
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China.
| | - Chaoyang Sun
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
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5
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Torres-Esquius S, Llop-Guevara A, Gutiérrez-Enríquez S, Romey M, Teulé À, Llort G, Herrero A, Sánchez-Henarejos P, Vallmajó A, González-Santiago S, Chirivella I, Cano JM, Graña B, Simonetti S, Díaz de Corcuera I, Ramon y Cajal T, Sanz J, Serrano S, Otero A, Churruca C, Sánchez-Heras AB, Servitja S, Guillén-Ponce C, Brunet J, Denkert C, Serra V, Balmaña J. Prevalence of Homologous Recombination Deficiency Among Patients With Germline RAD51C/D Breast or Ovarian Cancer. JAMA Netw Open 2024; 7:e247811. [PMID: 38648056 PMCID: PMC11036141 DOI: 10.1001/jamanetworkopen.2024.7811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/21/2024] [Indexed: 04/25/2024] Open
Abstract
Importance RAD51C and RAD51D are involved in DNA repair by homologous recombination. Germline pathogenic variants (PVs) in these genes are associated with an increased risk of ovarian and breast cancer. Understanding the homologous recombination deficiency (HRD) status of tumors from patients with germline PVs in RAD51C/D could guide therapeutic decision-making and improve survival. Objective To characterize the clinical and tumor characteristics of germline RAD51C/D PV carriers, including the evaluation of HRD status. Design, Setting, and Participants This retrospective cohort study included 91 index patients plus 90 relatives carrying germline RAD51C/D PV (n = 181) in Spanish hospitals from January 1, 2014, to December 31, 2021. Genomic and functional HRD biomarkers were assessed in untreated breast and ovarian tumor samples (n = 45) from June 2022 to February 2023. Main Outcomes and Measures Clinical and pathologic characteristics were assessed using descriptive statistics. Genomic HRD by genomic instability scores, functional HRD by RAD51, and gene-specific loss of heterozygosity were analyzed. Associations between HRD status and tumor subtype, age at diagnosis, and gene-specific loss of heterozygosity in RAD51C/D were investigated using logistic regression or the t test. Results A total of 9507 index patients were reviewed, and 91 patients (1.0%) were found to carry a PV in RAD51C/D; 90 family members with a germline PV in RAD51C/D were also included. A total of 157 of carriers (86.7%) were women and 181 (55.8%) had received a diagnosis of cancer, mainly breast cancer or ovarian cancer. The most prevalent PVs were c.1026+5_1026+7del (11 of 56 [19.6%]) and c.709C>T (9 of 56 [16.1%]) in RAD51C and c.694C>T (20 of 35 [57.1%]) in RAD51D. In untreated breast cancer and ovarian cancer, the prevalence of functional and genomic HRD was 55.2% (16 of 29) and 61.1% (11 of 18) for RAD51C, respectively, and 66.7% (6 of 9) and 90.0% (9 of 10) for RAD51D. The concordance between HRD biomarkers was 91%. Tumors with the same PV displayed contrasting HRD status, and age at diagnosis did not correlate with the occurrence of HRD. All breast cancers retaining the wild-type allele were estrogen receptor positive and lacked HRD. Conclusions and Relevance In this cohort study of germline RAD51C/D breast cancer and ovarian cancer, less than 70% of tumors displayed functional HRD, and half of those that did not display HRD were explained by retention of the wild-type allele, which was more frequent among estrogen receptor-positive breast cancers. Understanding which tumors are associated with RAD51C/D and HRD is key to identify patients who can benefit from targeted therapies, such as PARP (poly [adenosine diphosphate-ribose] polymerase) inhibitors.
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Affiliation(s)
- Sara Torres-Esquius
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
| | - Alba Llop-Guevara
- Experimental Therapeutics Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
- Translational Medicine, DNA Damage Response Department, AstraZeneca, Barcelona, Spain
| | | | - Marcel Romey
- Institute of Pathology, Universitätsklinikum Marburg, Marburg, Germany
| | - Àlex Teulé
- Hereditary Cancer Program, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Gemma Llort
- Department of Medical Oncology, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Ana Herrero
- Department of Medical Oncology, Hospital Miguel Servet de Zaragoza, Zaragoza, Spain
| | | | - Anna Vallmajó
- Genetic Counseling Unit, Arnau de Vilanova University Hospital, Lleida, Spain
| | | | - Isabel Chirivella
- Cancer Genetic Counseling, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Juana Maria Cano
- Department of Medical Oncology, Hospital General Universitario de Ciudad Real, Ciudad Real, Spain
| | - Begoña Graña
- Department of Medical Oncology, Xerencia de Xestión Integrada de A Coruña, Coruña, Spain
| | - Sara Simonetti
- Molecular Oncology Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
| | | | - Teresa Ramon y Cajal
- Department of Medical Oncology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Judit Sanz
- Unidad de Cáncer Familiar y Hereditario, Althaia Xarxa Assistencial Universitària de Manresa, Manresa, Spain
| | - Sara Serrano
- Department of Medical Oncology, Institute of Oncology of Southern Catalonia (IOCS), Hospital Universitari Sant Joan de Reus, Reus, Spain
| | - Andrea Otero
- Institute of Oncology and Molecular Medicine of Asturias (IMOMA) S. A., Oviedo, Spain
| | - Cristina Churruca
- Department of Medical Oncology, Hospital Universitario Donostia, San Sebastián, Gipuzkoa, Spain
| | - Ana Beatriz Sánchez-Heras
- Cancer Genetic Counselling Unit, Medical Oncology Department, Hospital General Universitario de Elche, Elche, Spain
| | - Sonia Servitja
- Department of Medical Oncology, Hospital del Mar-CIBERONC, Barcelona, Spain
| | - Carmen Guillén-Ponce
- Department of Medical Oncology, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, Girona, Spain
- Precision Oncology Group (OncoGIR-Pro), Institut d’Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Carsten Denkert
- Institute of Pathology, Universitätsklinikum Marburg, Marburg, Germany
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
- Medical Oncology Department, Hospital Universitari Vall d’Hebron, Barcelona, Spain
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6
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Kuhlen M, Hofmann TG, Golas MM. Puzzling phenomenon: adult-onset cancer predisposition and pediatric cancer. Trends Cancer 2024:S2405-8033(24)00049-9. [PMID: 38503638 DOI: 10.1016/j.trecan.2024.02.011] [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: 12/21/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/21/2024]
Abstract
Pathogenic variants (PVs) in DNA repair-linked adult-onset cancer predisposition genes, including double heterozygosity, are increasingly identified in pediatric patients with cancer. Their role in childhood cancer, however, remains poorly understood. Integrating comprehensive tumor analysis is integral for understanding the contribution of such PVs in cancer development and personalized cancer care.
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Affiliation(s)
- Michaela Kuhlen
- Pediatrics and Adolescent Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany.
| | - Thomas G Hofmann
- Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Monika M Golas
- Human Genetics, Faculty of Medicine, University of Augsburg, Augsburg, Germany
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7
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Hurst ZA, Liyanarachchi S, Brock P, He H, Nabhan F, Veloski C, Toland AE, Ringel MD, Jhiang SM. Presumed Pathogenic Germ Line and Somatic Variants in African American Thyroid Cancer. Thyroid 2024; 34:378-387. [PMID: 38062767 PMCID: PMC10951570 DOI: 10.1089/thy.2023.0487] [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] [Indexed: 01/24/2024]
Abstract
Background: African American (AA) thyroid cancer patients have worse prognoses than European Americans (EA), which has been attributed to both health care disparities and possible genetic differences. We investigated the impact of both germ line and somatic variants on clinical outcome in a cohort of AA nonmedullary thyroid cancer (NMTC) patients who had received therapeutic intervention from cancer centers. Methods: Whole-exome sequencing was performed on DNA from available blood/normal tissues (N = 37) and paired tumor samples (N = 32) collected from 37 and 29 AA NMTC patients, respectively. Variants with Combined Annotation Depletion Dependent (CADD) score of ≥20 and VarSome Clinical classification of likely pathogenic or pathogenic were classified as presumed pathogenic germ line or somatic variants (PPGVs/PPSVs). PPGVs/PPSVs in cancer-related genes and PPGVs in cardiovascular risk genes were further investigated, and PPGVs/PPSVs associated with African (AFR) ancestry were identified. Results: Among 17 PPGVs identified in 16 cancer predisposition or known cancer-related genes, only WRN was previously known to associate with NMTC predisposition. Among PPSVs, BRAFV600E was most the prevalent and detected in 12 of the 29 (41%) tumors. Examining PPGVs/PPSVs among three patients who died from NMTC, one patient who died from papillary thyroid carcinoma/anaplastic thyroid carcinoma (PTC/ATC) led us to speculate that the PPGV ERCC4R799W may have increased the risk of PPSV TP53R273H acquisition. Among PPGVs identified in 18 cardiovascular risk genes, PPGVs in SC5NA, GYG1, CBS, CFTR, and SI are known to have causal and pathogenic implications in cardiovascular disease. Conclusion: In this cohort, most AA-NMTC patients exhibit favorable outcomes after therapeutic intervention given at cancer centers, suggesting that health care disparity is the major contributor for worse prognoses among AA-NMTC patients. Nevertheless, the clinical impact of PPGVs that might facilitate the acquisition of TP53 tumor mutations, and/or PPGVs that predispose individuals to adverse cardiovascular events, which could be exacerbated by therapy-induced cardiotoxicity, needs to be further explored. Integrated analysis of PPGV/PPSV profiles among NMTC patients with different stages of disease may help to identify NMTC patients who require close monitoring or proactive intervention.
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Affiliation(s)
- Zachary A. Hurst
- Division of Gastroenterology, Hepatology and Nutrition, Department of Internal Medicine, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, Ohio, USA
- Department of Physiology and Cell Biology, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Sandya Liyanarachchi
- Department of Molecular Medicine and Therapeutics, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Pamela Brock
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Huiling He
- Department of Molecular Medicine and Therapeutics, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Fadi Nabhan
- Division of Endocrinology, Diabetes, and Metabolism, Department of Internal Medicine, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Colleen Veloski
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Amanda E. Toland
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, Ohio, USA
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Matthew D. Ringel
- Department of Molecular Medicine and Therapeutics, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, Ohio, USA
- Division of Endocrinology, Diabetes, and Metabolism, Department of Internal Medicine, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Sissy M. Jhiang
- Department of Physiology and Cell Biology, The Ohio State University College of Medicine, Columbus, Ohio, USA
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8
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Sengodan SK, Hu X, Peddibhotla V, Balamurugan K, Mitrophanov AY, McKennett L, Kharat SS, Sanawar R, Singh VK, Albaugh ME, Burkett SS, Zhao Y, Tran B, Malys T, Sterneck E, De S, Sharan SK. Mismatch repair protein MLH1 suppresses replicative stress in BRCA2-deficient breast tumors. J Clin Invest 2024; 134:e173718. [PMID: 38271119 PMCID: PMC10977984 DOI: 10.1172/jci173718] [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: 07/06/2023] [Accepted: 01/22/2024] [Indexed: 01/27/2024] Open
Abstract
Loss of BRCA2 (breast cancer 2) is lethal for normal cells. Yet it remains poorly understood how, in BRCA2 mutation carriers, cells undergoing loss of heterozygosity overcome the lethality and undergo tissue-specific neoplastic transformation. Here, we identified mismatch repair gene mutL homolog 1 (MLH1) as a genetic interactor of BRCA2 whose overexpression supports the viability of Brca2-null cells. Mechanistically, we showed that MLH1 interacts with Flap endonuclease 1 (FEN1) and competes to process the RNA flaps of Okazaki fragments. Together, they restrained the DNA2 nuclease activity on the reversed forks of lagging strands, leading to replication fork (RF) stability in BRCA2-deficient cells. In these cells, MLH1 also attenuated R-loops, allowing the progression of stable RFs, which suppressed genomic instability and supported cell viability. We demonstrated the significance of their genetic interaction by the lethality of Brca2-mutant mice and inhibition of Brca2-deficient tumor growth in mice by Mlh1 loss. Furthermore, we described estrogen as inducing MLH1 expression through estrogen receptor α (ERα), which might explain why the majority of BRCA2 mutation carriers develop ER-positive breast cancer. Taken together, our findings reveal a role of MLH1 in relieving replicative stress and show how it may contribute to the establishment of BRCA2-deficient breast tumors.
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Affiliation(s)
- Satheesh K. Sengodan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland USA
| | - Xiaoju Hu
- Rutgers Cancer Institute of New Jersey, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Vaishnavi Peddibhotla
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland USA
| | - Kuppusamy Balamurugan
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Alexander Y. Mitrophanov
- Statistical Consulting and Scientific Programming, Frederick National Laboratory for Cancer Research, NIH, Frederick, Maryland, USA
| | - Lois McKennett
- Laboratory Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Suhas S. Kharat
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland USA
| | - Rahul Sanawar
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Vinod Kumar Singh
- Rutgers Cancer Institute of New Jersey, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Mary E. Albaugh
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland USA
- Laboratory Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Sandra S. Burkett
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland USA
| | - Yongmei Zhao
- NCI Advanced Technology Research Facility, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Bao Tran
- NCI Advanced Technology Research Facility, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Tyler Malys
- Statistical Consulting and Scientific Programming, Frederick National Laboratory for Cancer Research, NIH, Frederick, Maryland, USA
| | - Esta Sterneck
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Subhajyoti De
- Rutgers Cancer Institute of New Jersey, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Shyam K. Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland USA
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9
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Song S, Koh Y, Kim S, Lee SM, Kim HU, Ko JM, Lee SH, Yoon SS, Park S. Systematic analysis of Mendelian disease-associated gene variants reveals new classes of cancer-predisposing genes. Genome Med 2023; 15:107. [PMID: 38143269 PMCID: PMC10749499 DOI: 10.1186/s13073-023-01252-w] [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: 07/12/2023] [Accepted: 10/30/2023] [Indexed: 12/26/2023] Open
Abstract
BACKGROUND Despite the acceleration of somatic driver gene discovery facilitated by recent large-scale tumor sequencing data, the contribution of inherited variants remains largely unexplored, primarily focusing on previously known cancer predisposition genes (CPGs) due to the low statistical power associated with detecting rare pathogenic variant-phenotype associations. METHODS Here, we introduce a generalized log-regression model to measure the excess of pathogenic variants within genes in cancer patients compared to control samples. It aims to measure gene-level cancer risk enrichment by collapsing rare pathogenic variants after controlling the population differences across samples. RESULTS In this study, we investigate whether pathogenic variants in Mendelian disease-associated genes (OMIM genes) are enriched in cancer patients compared to controls. Utilizing data from PCAWG and the 1,000 Genomes Project, we identify 103 OMIM genes demonstrating significant enrichment of pathogenic variants in cancer samples (FDR 20%). Through an integrative approach considering three distinct properties, we classify these CPG-like OMIM genes into four clusters, indicating potential diverse mechanisms underlying tumor progression. Further, we explore the function of PAH (a key metabolic enzyme associated with Phenylketonuria), the gene exhibiting the highest prevalence of pathogenic variants in a pan-cancer (1.8%) compared to controls (0.6%). CONCLUSIONS Our findings suggest a possible cancer progression mechanism through metabolic profile alterations. Overall, our data indicates that pathogenic OMIM gene variants contribute to cancer progression and introduces new CPG classifications potentially underpinning diverse tumorigenesis mechanisms.
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Affiliation(s)
- Seulki Song
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Structural Biology Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Calle de Melchor Fernández Almagro, 3, Madrid, 28029, Spain
| | - Youngil Koh
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Biomedical Research Institute and Departments of Internal Medicine, Seoul National University Hospital, Seoul, 03080, Republic of Korea
| | - Seokhyeon Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Sang Mi Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea.
| | - Sung-Soo Yoon
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
- Biomedical Research Institute and Departments of Internal Medicine, Seoul National University Hospital, Seoul, 03080, Republic of Korea.
| | - Solip Park
- Structural Biology Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Calle de Melchor Fernández Almagro, 3, Madrid, 28029, Spain.
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10
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Chen C, Lin CJ, Pei YC, Ma D, Liao L, Li SY, Fan L, Di GH, Wu SY, Liu XY, Wang YJ, Hong Q, Zhang GL, Xu LL, Li BB, Huang W, Shi JX, Jiang YZ, Hu X, Shao ZM. Comprehensive genomic profiling of breast cancers characterizes germline-somatic mutation interactions mediating therapeutic vulnerabilities. Cell Discov 2023; 9:125. [PMID: 38114467 PMCID: PMC10730692 DOI: 10.1038/s41421-023-00614-3] [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: 07/13/2023] [Accepted: 10/08/2023] [Indexed: 12/21/2023] Open
Abstract
Germline-somatic mutation interactions are universal and associated with tumorigenesis, but their role in breast cancer, especially in non-Caucasians, remains poorly characterized. We performed large-scale prospective targeted sequencing of matched tumor-blood samples from 4079 Chinese females, coupled with detailed clinical annotation, to map interactions between germline and somatic alterations. We discovered 368 pathogenic germline variants and identified 5 breast cancer DNA repair-associated genes (BCDGs; BRCA1/BRCA2/CHEK2/PALB2/TP53). BCDG mutation carriers, especially those with two-hit inactivation, demonstrated younger onset, higher tumor mutation burden, and greater clinical benefits from platinum drugs, PARP inhibitors, and immune checkpoint inhibitors. Furthermore, we leveraged a multiomics cohort to reveal that clinical benefits derived from two-hit events are associated with increased genome instability and an immune-activated tumor microenvironment. We also established an ethnicity-specific tool to predict BCDG mutation and two-hit status for genetic evaluation and therapeutic decisions. Overall, this study leveraged the large sequencing cohort of Chinese breast cancers, optimizing genomics-guided selection of DNA damaging-targeted therapy and immunotherapy within a broader population.
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Affiliation(s)
- Chao Chen
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cai-Jin Lin
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu-Chen Pei
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ding Ma
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Li Liao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Si-Yuan Li
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lei Fan
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Gen-Hong Di
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Song-Yang Wu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xi-Yu Liu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yun-Jin Wang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Qi Hong
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Guo-Liang Zhang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Lin-Lin Xu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Bei-Bei Li
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wei Huang
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Jin-Xiu Shi
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Xin Hu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China.
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11
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Hanson H, Astiazaran-Symonds E, Amendola LM, Balmaña J, Foulkes WD, James P, Klugman S, Ngeow J, Schmutzler R, Voian N, Wick MJ, Pal T, Tischkowitz M, Stewart DR. Management of individuals with germline pathogenic/likely pathogenic variants in CHEK2: A clinical practice resource of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100870. [PMID: 37490054 PMCID: PMC10623578 DOI: 10.1016/j.gim.2023.100870] [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: 02/14/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 07/26/2023] Open
Abstract
PURPOSE Although the role of CHEK2 germline pathogenic variants in cancer predisposition is well known, resources for managing CHEK2 heterozygotes in clinical practice are limited. METHODS An international workgroup developed guidance on clinical management of CHEK2 heterozygotes informed by peer-reviewed publications from PubMed. RESULTS Although CHEK2 is considered a moderate penetrance gene, cancer risks may be considered as a continuous variable, which are influenced by family history and other modifiers. Consequently, early cancer detection and prevention for CHEK2 heterozygotes should be guided by personalized risk estimates. Such estimates may result in both downgrading lifetime breast cancer risks to those similar to the general population or upgrading lifetime risk to a level at which CHEK2 heterozygotes are offered high-risk breast surveillance according to country-specific guidelines. Risk-reducing mastectomy should be guided by personalized risk estimates and shared decision making. Colorectal and prostate cancer surveillance should be considered based on assessment of family history. For CHEK2 heterozygotes who develop cancer, no specific targeted medical treatment is recommended at this time. CONCLUSION Systematic prospective data collection is needed to establish the spectrum of CHEK2-associated cancer risks and to determine yet-unanswered questions, such as the outcomes of surveillance, response to cancer treatment, and survival after cancer diagnosis.
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Affiliation(s)
- Helen Hanson
- Southwest Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Esteban Astiazaran-Symonds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD; Department of Medicine, College of Medicine-Tucson, University of Arizona, Tucson, AZ
| | | | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain; Medical Oncology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Hospital Campus, Barcelona, Spain
| | - William D Foulkes
- Departments of Human Genetics, Oncology and Medicine, McGill University, Montréal, QC, Canada
| | - Paul James
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia; Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Susan Klugman
- Division of Reproductive & Medical Genetics, Department of Obstetrics & Gynecology and Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Joanne Ngeow
- Genomic Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Rita Schmutzler
- Center of Integrated Oncology (CIO), University of Cologne, Cologne, Germany; Center for Hereditary Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| | - Nicoleta Voian
- Providence Genetic Risk Clinic, Providence Cancer Institute, Portland, OR
| | - Myra J Wick
- Departments of Obstetrics and Gynecology and Clinical Genomics, Mayo Clinic, Rochester, MN
| | - Tuya Pal
- Department of Medicine, Vanderbilt University Medical Center/Vanderbilt-Ingram Cancer Center, Nashville, TN
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
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12
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Sia TY, Maio A, Kemel YM, Arora KS, Gordhandas SB, Kahn RM, Salo-Mullen EE, Sheehan MA, Tejada PR, Bandlamudi C, Zhou Q, Iasonos A, Grisham RN, O'Cearbhaill RE, Tew WP, Roche KL, Zivanovic O, Sonoda Y, Gardner GJ, Chi DS, Latham AJ, Carlo MI, Murciano-Goroff YR, Will M, Walsh MF, Robson ME, Mandelker DL, Berger MF, Abu-Rustum NR, Brown CL, Offit K, Hamilton JG, Aghajanian C, Weigelt B, Stadler ZK, Liu YL. Germline Pathogenic Variants and Genetic Counseling by Ancestry in Patients With Epithelial Ovarian Cancer. JCO Precis Oncol 2023; 7:e2300137. [PMID: 37738546 PMCID: PMC10861001 DOI: 10.1200/po.23.00137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/11/2023] [Accepted: 07/17/2023] [Indexed: 09/24/2023] Open
Abstract
PURPOSE To evaluate rates of germline pathogenic/likely pathogenic variants (PVs) and genetic counseling by ancestry in patients with epithelial ovarian cancer (EOC). METHODS Patients with pathologically confirmed EOC who underwent clinical tumor-normal sequencing from January 1, 2015, to December 31, 2020, inclusive of germline analysis of ≥76 genes were included. Patients with newly identified PVs were referred for Clinical Genetics Service (CGS) counseling. Ancestry groups were defined using self-reported race/ethnicity and Ashkenazi Jewish (AJ) heritage. Genetic ancestry was inferred computationally using validated algorithms. Logistic regression models were built. RESULTS Of 1,266 patients, self-reported ancestry (AJ, 17%; Asian, 10%; Black/African American, 5.4%; Hispanic, 6.2%; non-Hispanic White, 57%; other, 0.16%; unknown, 4.0%) correlated with genetic ancestry (AJ ancestry, 18%; admixed, 10%; African, 4%; East Asian [EAS], 6%; European, 56%; Native American, 0.2%; South Asian [SAS], 4%; unknown, 2%). Germline PVs were observed in 313 (25%) patients, including 195 (15%) with PVs in EOC-associated genes. Those with PVs were younger at diagnosis (59 v 62 years; P < .001) and more likely to have high-grade serous ovarian cancer (83% v 72%; P = .009). PV prevalence varied between ancestry groups (P < .001), with highest rates in the AJ (39.9%) and Asian (26.5%) groups and similar rates (>10%) across other ancestry groups. Use of genetic ancestry demonstrated similar findings and further characterized high rates of PV in EAS/SAS groups. Younger age, high-grade serous histology, and self-reported AJ or Asian ancestry were associated with PV in an EOC-associated gene. Rates of CGS counseling for newly identified PVs were high (80%) across ancestry groups. CONCLUSION Rates of PV, particularly in EOC-associated genes, were high regardless of ancestry, with similar rates of counseling between groups, emphasizing the importance of universal genetic testing in all patients with EOC.
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Affiliation(s)
- Tiffany Y. Sia
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anna Maio
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yelena M. Kemel
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kanika S. Arora
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sushmita B. Gordhandas
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan M. Kahn
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Erin E. Salo-Mullen
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Margaret A. Sheehan
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Prince Rainier Tejada
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chaitanya Bandlamudi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Qin Zhou
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alexia Iasonos
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rachel N. Grisham
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Roisin E. O'Cearbhaill
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - William P. Tew
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Kara Long Roche
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY
| | - Oliver Zivanovic
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY
| | - Yukio Sonoda
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY
| | - Ginger J. Gardner
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY
| | - Dennis S. Chi
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY
| | - Alicia J. Latham
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Maria I. Carlo
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Yonina R. Murciano-Goroff
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Marie Will
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Michael F. Walsh
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Mark E. Robson
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Diana L. Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F. Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nadeem R. Abu-Rustum
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY
| | - Carol L. Brown
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Jada G. Hamilton
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Psychiatry, Weill Cornell Medical College, New York, NY
- Department of Psychiatry and Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Carol Aghajanian
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zsofia K. Stadler
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Ying L. Liu
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
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13
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Hao S, Zhao X, Fan Y, Liu Z, Zhang X, Li W, Yuan H, Zhang J, Zhang Y, Ma T, Tao H. Prevalence and spectrum of cancer predisposition germline mutations in young patients with the common late-onset cancers. Cancer Med 2023; 12:18394-18404. [PMID: 37610374 PMCID: PMC10524041 DOI: 10.1002/cam4.6445] [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: 02/12/2023] [Revised: 06/30/2023] [Accepted: 08/03/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Pathogenic germline variants (PGVs) can play a vital role in the oncogenesis process in carriers. Previous studies have recognized that PGVs contribute to early onset of tumorigenesis in certain cancer types, for example, colorectal cancer and breast cancer. However, the reported prevalence data of cancer-associated PGVs were highly inconsistent due to nonuniform patient cohorts, sequencing methods, and prominent difficulties in pathogenicity interpretation of variants. In addition to the above difficulties, due to the rarity of cases, the prevalence of cancer PGV carriers in young cancer patients affected by late-onset cancer types has not been comprehensively evaluated to date. METHODS A total of 131 young cancer patients (1-29 years old at diagnosis) were enrolled in this study. The patients were affected by six common late-onset cancer types, namely, lung cancer, liver cancer, colorectal cancer, gastric cancer, renal cancer, and head-neck cancer. Cancer PGVs were identified and analyzed. based on NGS-based targeted sequencing followed by bioinformatic screening and strict further evaluations of variant pathogenicity. RESULTS Twenty-three cancer PGVs in 21 patients were identified, resulting in an overall PGV prevalence of 16.0% across the six included cancer types, which was approximately double the prevalence reported in a previous pancancer study. Nine of the 23 PGVs are novel, thus expanding the cancer PGV spectrum. Seven of the 23 (30.4%) PGVs are potential therapeutic targets of olaparib, with potential implications for clinical manipulation. Additionally, a small prevalence of somatic mutations of some classic cancer hallmark genes in young patients, in contrast to all-age patients, was revealed. CONCLUSION This study demonstrates the high prevalence of PGVs in young cancer patients with the common late-onset cancers and the potentially significant clinical implications of cancer PGVs, the findings highlight the value of PGV screening in young patients across lung cancer, liver cancer, colorectal cancer, gastric cancer, renal cancer, or head-neck cancer.
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Affiliation(s)
- Shaoyu Hao
- Thoracic Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical SciencesJinanChina
| | - Ximeng Zhao
- Jichenjunchuang Clinical LaboratoryHangzhouChina
| | - Yue Fan
- Department of Integrated Traditional Chinese Medicine and Western MedicineZhong Shan Hospital, Fudan UniversityShanghaiChina
| | - Zhengchuang Liu
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Xiang Zhang
- Jichenjunchuang Clinical LaboratoryHangzhouChina
| | - Wei Li
- Jichenjunchuang Clinical LaboratoryHangzhouChina
| | | | - Jie Zhang
- Jichenjunchuang Clinical LaboratoryHangzhouChina
| | | | - Tonghui Ma
- Jichenjunchuang Clinical LaboratoryHangzhouChina
| | - Houquan Tao
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical CollegeHangzhouChina
- Department of GastroenterologyZhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical CollegeHangzhouChina
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14
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Franch-Expósito S, Mehine M, Ptashkin RN, Bolton KL, Bandlamudi C, Srinivasan P, Zhang L, Goodell MA, Gedvilaite E, Menghrajani K, Sánchez-Vela P, Mandelker D, Comen E, Norton L, Benayed R, Gao T, Papaemmanuil E, Taylor B, Levine R, Offit K, Stadler Z, Berger MF, Zehir A. Associations Between Cancer Predisposition Mutations and Clonal Hematopoiesis in Patients With Solid Tumors. JCO Precis Oncol 2023; 7:e2300070. [PMID: 37561983 PMCID: PMC10581611 DOI: 10.1200/po.23.00070] [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: 02/10/2023] [Revised: 05/31/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023] Open
Abstract
PURPOSE Clonal hematopoiesis (CH), the expansion of clones in the hematopoietic system, has been linked to different internal and external features such as aging, genetic ancestry, smoking, and oncologic treatment. However, the interplay between mutations in known cancer predisposition genes and CH has not been thoroughly examined in patients with solid tumors. METHODS We used prospective tumor-blood paired sequencing data from 46,906 patients who underwent Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) testing to interrogate the associations between CH and rare pathogenic or likely pathogenic (P/LP) germline variants. RESULTS We observed an enrichment of CH-positive patients among those carrying P/LP germline mutations and identified a significant association between P/LP germline variants in ATM and CH. Germline and CH comutation patterns in ATM, TP53, and CHEK2 suggested biallelic inactivation as a potential mediator of clonal expansion. Moreover, we observed that CH-PPM1D mutations, similar to somatic tumor-associated PPM1D mutations, were depleted in patients with P/LP germline mutations in the DNA damage response (DDR) genes ATM, CHEK2, and TP53. Patients with solid tumors and harboring P/LP germline mutations, CH mutations, and mosaicism chromosomal alterations might be at an increased risk of developing secondary leukemia while germline variants in TP53 were identified as an independent risk factor (hazard ratio, 36; P < .001) for secondary leukemias. CONCLUSION Our results suggest a close relationship between inherited variants and CH mutations within the DDR genes in patients with solid tumors. Associations identified in this study might translate into enhanced clinical surveillance for CH and associated comorbidities in patients with cancer harboring these germline mutations.
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Affiliation(s)
- Sebastià Franch-Expósito
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Miika Mehine
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan N. Ptashkin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- C2i Genomics, New York, NY
| | - Kelly L. Bolton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chaitanya Bandlamudi
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Preethi Srinivasan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Natera Inc, San Carlos, CA
| | - Linda Zhang
- Department of Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX
| | - Margaret A. Goodell
- Department of Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX
| | - Erika Gedvilaite
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kamal Menghrajani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pablo Sánchez-Vela
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth Comen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryma Benayed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Precision Medicine and Biosamples, AstraZeneca, New York, NY
| | - Teng Gao
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Elli Papaemmanuil
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Barry Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ross Levine
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zsofia Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F. Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Precision Medicine and Biosamples, AstraZeneca, New York, NY
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15
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Brewer T, Yehia L, Bazeley P, Eng C. Integrating somatic CNV and gene expression in breast cancers from women with PTEN hamartoma tumor syndrome. NPJ Genom Med 2023; 8:14. [PMID: 37407629 DOI: 10.1038/s41525-023-00361-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023] Open
Abstract
Women with germline PTEN variants (PTEN hamartoma tumor syndrome, PHTS) have up to 85% lifetime risk of female breast cancer (BC). We previously showed that PHTS-derived BCs are distinct from sporadic BCs both at the clinical and genomic levels. In this study, we examined somatic copy number variations (CNV) and transcriptome data to further characterize the somatic landscape of PHTS-derived BCs. We analyzed exome sequencing data from 44 BCs from women with PHTS for CNV. The control group comprised of 558 women with sporadic BCs from The Cancer Genome Atlas (TCGA) dataset. Here, we found that PHTS-derived BCs have several distinct CNV peaks compared to TCGA. Furthermore, RNA sequencing data revealed that PHTS-derived BCs have a distinct immunologic cell type signature, which points toward cancer immune evasion. Transcriptomic data also revealed PHTS-derived BCs with pathogenic germline PTEN variants appear to have vitamin E degradation as a key pathway associated with tumorigenesis. In conclusion, our study revealed distinct CNV x transcript features in PHTS-derived BCs, which further facilitate understanding of BC biology arising in the setting of germline PTEN mutations.
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Affiliation(s)
- Takae Brewer
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
| | - Lamis Yehia
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Peter Bazeley
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA.
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
- Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
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16
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Wen H, Xu Q, Sheng X, Li H, Wang X, Wu X. Prevalence and Landscape of Pathogenic or Likely Pathogenic Germline Variants and Their Association With Somatic Phenotype in Unselected Chinese Patients With Gynecologic Cancers. JAMA Netw Open 2023; 6:e2326437. [PMID: 37523182 PMCID: PMC10391307 DOI: 10.1001/jamanetworkopen.2023.26437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/01/2023] Open
Abstract
Importance Understanding germline and somatic status in patients with gynecologic cancers could improve risk assessment and guide therapeutic decision-making. Objective To evaluate the prevalence and landscape of germline pathogenic or likely pathogenic (P/LP) variants and explore whether these variants are associated with somatic phenotypes and cancer risk in unselected patients with gynecologic cancers. Design, Setting, and Participants This cross-sectional study retrospectively enrolled unselected patients in China with a gynecologic cancer, including ovarian, cervical, and endometrial, who underwent tumor-normal sequencing using a 520-gene panel from October 1, 2017, through May 31, 2021. Exposure Germline variants in gynecologic cancers. Main Outcomes and Measures The P/LP germline variant rates in 62 cancer predisposition genes were assessed using descriptive statistics. The associations of P/LP variant status with age, somatic profiles, and cancer risk were also investigated using the Fisher exact test or Student t test. Results A total of 1610 women (median [IQR] age, 54 [47-62] years; 1201 [74.6%] with stage III-IV disease) were included (945 with ovarian cancer, 307 with endometrial cancer, and 358 with cervical cancer). The prevalence of patients with P/LP variants was 20.5% (194 of 945) for ovarian cancer, 13.4% (41 of 307) for endometrial cancer, and 6.4% (23 of 358) for cervical cancer; 95.1% of the germline findings (n = 252) were potentially actionable, mainly in homologous recombination repair (HRR) and mismatch repair genes. Chinese patients with endometrial cancer had a higher rate of P/LP variants than a White population from The Cancer Genome Atlas (42 of 307 [13.7%] vs 24 of 367 [6.5%]; P = .003). In endometrial and cervical cancers, the prevalence of P/LP variants was 12.7% (30 of 237) and 4.8% (13 of 270), respectively, in patients diagnosed at age 45 years or older and increased to 25.0% (9 of 36; P = .09) and 12.0% (10 of 83; P = .04), respectively, for those with an onset age of less than 45 years. Mismatch repair P/LP variants were associated with a younger age at onset for ovarian cancer (46 vs 54 years; P = .02) and endometrial cancer (48 vs 57 years; P < .001), while HRR P/LP variants were associated with a younger age at onset for cervical cancer (46 vs 52 years; P = .04). Carriers of HRR P/LP variants had more prevalent somatic TP53 variants and less common somatic variants in oncogenic driver genes vs noncarriers. BRCA1/2 P/LP variants were also associated with moderate risks for endometrial and cervical cancer. Conclusions and Relevance This study delineates the landscape of germline P/LP variants in Chinese women with gynecologic cancers. The findings highlight the hereditary factor in cervical cancer that has long been neglected and suggest the importance of next-generation sequencing-based genetic testing with a large gene panel for gynecologic cancers.
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Affiliation(s)
- Hao Wen
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qin Xu
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Xiujie Sheng
- Department of Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huawen Li
- Department of Gynecology, Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China
| | - Xipeng Wang
- Department of Obstetrics and Gynecology, Xinhua Hospital Affiliated to Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Xiaohua Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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17
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Sia TY, Gordhandas SB, Birsoy O, Kemel Y, Maio A, Salo-Mullen E, Sheehan M, Hensley ML, Rubinstein M, Makker V, Grisham RN, O'Cearbhaill RE, Roche KL, Mueller JJ, Leitao MM, Sonoda Y, Chi DS, Abu-Rustum NR, Berger MF, Ellenson LH, Latham A, Stadler Z, Offit K, Aghajanian C, Weigelt B, Mandelker D, Liu YL. Germline drivers of gynecologic carcinosarcomas. Gynecol Oncol 2023; 174:34-41. [PMID: 37149903 PMCID: PMC10330315 DOI: 10.1016/j.ygyno.2023.04.024] [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: 01/27/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/09/2023]
Abstract
OBJECTIVES To describe the prevalence of germline pathogenic variants (gPVs) in endometrial and ovarian carcinosarcomas and determine if gPVs are drivers of carcinosarcoma. METHODS Patients with endometrial or ovarian carcinosarcomas who underwent clinical tumor-normal sequencing from 1/1/2015 to 6/1/2021 and consented to germline assessment of ≥76 cancer predisposition genes were included. In patients with gPVs, biallelic inactivation was identified through analysis of loss of heterozygosity and somatic pathogenic alterations. RESULTS Of 216 patients identified, 167 (77%) were diagnosed with endometrial carcinosarcoma and 49 (23%) with ovarian carcinosarcoma. Overall, 33 gPVs were observed in 29 patients (13%); 20 gPVs (61%) had biallelic loss in tumors. The rate of high-penetrance gPVs overall was 7% (16 of 216); 88% of high-penetrance gPVs had biallelic loss. In the endometrial carcinosarcoma cohort, 22 gPVs were found in 19 (11%) of 167 patients; 12 gPVs (55%) had biallelic loss in tumors, including 8 (89%) of 9 in high-penetrance gPVs. Among the ovarian carcinosarcoma cohort, 11 gPVs were found in 10 (20%) of 49 patients; 8 gPVs (73%) had biallelic loss in tumors, and all evaluable high-penetrance gPVs (n = 6) had biallelic loss. All gPVs in homologous recombination (BRCA1, BRCA2, RAD51C) and Lynch syndrome (MSH2, MSH6) genes had biallelic loss in tumors (n = 15). CONCLUSIONS gPVs in genes affecting homologous recombination- or Lynch-associated mismatch repair exhibited biallelic inactivation within tumors, suggesting likely drivers of gynecologic carcinosarcoma. Our data support germline testing for patients with gynecologic carcinosarcomas, given implications for treatment and risk-reduction in patients and at-risk family members.
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Affiliation(s)
- Tiffany Y Sia
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sushmita B Gordhandas
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ozge Birsoy
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yelena Kemel
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna Maio
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Erin Salo-Mullen
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Margaret Sheehan
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martee L Hensley
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Maria Rubinstein
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Vicky Makker
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Rachel N Grisham
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Roisin E O'Cearbhaill
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Kara Long Roche
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY, USA
| | - Jennifer J Mueller
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY, USA
| | - Mario M Leitao
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY, USA
| | - Yukio Sonoda
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY, USA
| | - Dennis S Chi
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY, USA
| | - Nadeem R Abu-Rustum
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY, USA
| | - Michael F Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lora H Ellenson
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alicia Latham
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Zsofia Stadler
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Carol Aghajanian
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying L Liu
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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18
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Yap TA, Stadler ZK, Stout LA, Schneider BP. Aligning Germline Cancer Predisposition With Tumor-Based Next-Generation Sequencing for Modern Oncology Diagnosis, Interception, and Therapeutic Development. Am Soc Clin Oncol Educ Book 2023; 43:e390738. [PMID: 37390373 DOI: 10.1200/edbk_390738] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
In the era of precision medicine, genomic interrogation for identification of both germline and somatic genetic alterations has become increasingly important. While such germline testing was usually undertaken via a phenotype-driven single-gene approach, with the advent of next-generation sequencing (NGS) technologies, the widespread utilization of multigene panels, often agnostic of cancer phenotype, has become a commonplace in many different cancer types. At the same time, somatic tumor testing in oncology performed for the purpose of guiding therapeutic decisions for targeted therapies has also rapidly expanded, recently starting to incorporate not just patients with recurrent or metastatic cancer but even patients with early-stage disease. An integrated approach may be the best approach for the optimal management of patients with different cancers. The lack of complete congruence between germline and somatic NGS tests does not minimize the power or importance of either, but highlights the need to understand their limitations so as not to overlook an important finding or omission. NGS tests built to more uniformly and comprehensively evaluate both the germline and tumor simultaneously are urgently required and are in development. In this article, we discuss approaches to somatic and germline analyses in patients with cancer and the knowledge gained from integration of tumor-normal sequencing. We also detail strategies for the incorporation of genomic analysis into oncology care delivery models and the important emergence of poly(ADP-ribose) polymerase and other DNA Damage Response inhibitors in the clinic for patients with cancer with germline and somatic BRCA1 and BRCA2 mutations.
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Affiliation(s)
- Timothy A Yap
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Leigh Anne Stout
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN
| | - Bryan P Schneider
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN
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19
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Torrezan GT. Untangling the mechanisms of cancer predisposition. Nat Rev Cancer 2023:10.1038/s41568-023-00577-3. [PMID: 37130968 DOI: 10.1038/s41568-023-00577-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- Giovana Tardin Torrezan
- Clinical and Functional Genomics Group, International Research Center/CIPE, A.C. Camargo Cancer Center, Sao Paulo, Brazil.
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20
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Glodzik D, Selenica P, Rogge RA, Silverman IM, Mandelker D, Harris S, Zhao J, Zinda M, Veloso A, Malani N, Riaz N, Koehler M, Daber RD, Johnson V, Rimkunas V, Reis-Filho JS. Detection of Biallelic Loss of DNA Repair Genes in Formalin-Fixed, Paraffin-Embedded Tumor Samples Using a Novel Tumor-Only Sequencing Panel. J Mol Diagn 2023; 25:295-310. [PMID: 36944408 PMCID: PMC10340082 DOI: 10.1016/j.jmoldx.2023.02.004] [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: 09/01/2022] [Revised: 11/21/2022] [Accepted: 02/09/2023] [Indexed: 03/23/2023] Open
Abstract
Patient selection for synthetic lethal-based cancer therapy may be improved by assessment of gene-specific loss of heterozygosity (LOH) and biallelic loss of function (LOF). This report describes SyNthetic lethal Interactions for Precision Diagnostics (SNiPDx), a targeted next-generation sequencing (NGS) panel for detection of LOH and biallelic LOF alterations in 26 target genes focused on DNA damage response pathways, in tumor-only formalin-fixed, paraffin-embedded (FFPE) samples. NGS was performed across all exons of these 26 genes and encompassed a total of 7632 genome-wide single-nucleotide polymorphisms on genomic DNA from 80 FFPE solid tumor samples. The Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing algorithm was optimized to assess tumor purity and copy number based on heterozygous single-nucleotide polymorphisms. SNiPDx demonstrated high sensitivity (95%) and specificity (91%) for LOH detection compared with whole genome sequencing. Positive agreement with local NGS-based testing in the detection of genetic alterations was 95%. SNiPDx detected 93% of biallelic ATM LOF mutations, 100% of ATM single-nucleotide variants and small insertions/deletions, and 100% of all ATM LOH status events identified by orthogonal NGS-based testing. SNiPDx is a novel, clinically feasible test for analysis of allelic status in FFPE tumor samples, which demonstrated high accuracy when compared with other NGS-based approaches in clinical use.
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Affiliation(s)
| | - Pier Selenica
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | | | | | | | | | | | - Nadeem Riaz
- Memorial Sloan Kettering Cancer Center, New York, New York
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21
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Liu Y, Gusev A, Kraft P. Germline Cancer Gene Expression Quantitative Trait Loci Are Associated with Local and Global Tumor Mutations. Cancer Res 2023; 83:1191-1202. [PMID: 36745477 PMCID: PMC10106413 DOI: 10.1158/0008-5472.can-22-2624] [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: 08/19/2022] [Revised: 12/13/2022] [Accepted: 02/01/2023] [Indexed: 02/07/2023]
Abstract
Somatic mutations drive cancer development and are relevant to patient responses to treatment. Emerging evidence shows that variations in the somatic genome can be influenced by the germline genetic background. However, the mechanisms underlying these germline-somatic associations remain largely obscure. We hypothesized that germline variants can influence somatic mutations in a nearby cancer gene ("local impact") or a set of recurrently mutated cancer genes across the genome ("global impact") through their regulatory effect on gene expression. To test this hypothesis, tumor targeted sequencing data from 12,413 patients across 11 cancer types in the Dana-Farber Profile cohort were integrated with germline cancer gene expression quantitative trait loci (eQTL) from the Genotype-Tissue Expression Project. Variants that upregulate ATM expression were associated with a decreased risk of somatic ATM mutations across 8 cancer types. GLI2, WRN, and CBFB eQTL were associated with global tumor mutational burden of cancer genes in ovarian cancer, glioma, and esophagogastric carcinoma, respectively. An EPHA5 eQTL was associated with mutations in cancer genes specific to colorectal cancer, and eQTL related to expression of APC, WRN, GLI1, FANCA, and TP53 were associated with mutations in genes specific to endometrial cancer. These findings provide evidence that germline-somatic associations are mediated through expression of specific cancer genes, opening new avenues for research on the underlying biological processes. SIGNIFICANCE Analysis of associations between the germline genetic background and somatic mutations in patients with cancer suggests that germline variants can influence local and global tumor mutations by altering expression of cancer-related genes. See related commentary by Kar, p. 1165.
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Affiliation(s)
- Yuxi Liu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
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22
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Houlahan KE, Khan A, Greenwald NF, West RB, Angelo M, Curtis C. Germline-mediated immunoediting sculpts breast cancer subtypes and metastatic proclivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532870. [PMID: 36993286 PMCID: PMC10055121 DOI: 10.1101/2023.03.15.532870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cancer represents a broad spectrum of molecularly and morphologically diverse diseases. Individuals with the same clinical diagnosis can have tumors with drastically different molecular profiles and clinical response to treatment. It remains unclear when these differences arise during disease course and why some tumors are addicted to one oncogenic pathway over another. Somatic genomic aberrations occur within the context of an individual's germline genome, which can vary across millions of polymorphic sites. An open question is whether germline differences influence somatic tumor evolution. Interrogating 3,855 breast cancer lesions, spanning pre-invasive to metastatic disease, we demonstrate that germline variants in highly expressed and amplified genes influence somatic evolution by modulating immunoediting at early stages of tumor development. Specifically, we show that the burden of germline-derived epitopes in recurrently amplified genes selects against somatic gene amplification in breast cancer. For example, individuals with a high burden of germline-derived epitopes in ERBB2, encoding human epidermal growth factor receptor 2 (HER2), are significantly less likely to develop HER2-positive breast cancer compared to other subtypes. The same holds true for recurrent amplicons that define four subgroups of ER-positive breast cancers at high risk of distant relapse. High epitope burden in these recurrently amplified regions is associated with decreased likelihood of developing high risk ER-positive cancer. Tumors that overcome such immune-mediated negative selection are more aggressive and demonstrate an "immune cold" phenotype. These data show the germline genome plays a previously unappreciated role in dictating somatic evolution. Exploiting germline-mediated immunoediting may inform the development of biomarkers that refine risk stratification within breast cancer subtypes.
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Affiliation(s)
- Kathleen E. Houlahan
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Aziz Khan
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Noah F Greenwald
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert B. West
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christina Curtis
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine (Oncology), Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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23
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Belcaid L, Bertelsen B, Wadt K, Tuxen I, Spanggaard I, Højgaard M, Benn Sørensen J, Ravn J, Lassen U, Cilius Nielsen F, Rohrberg K, Westmose Yde C. New pathogenic germline variants identified in mesothelioma. Lung Cancer 2023; 179:107172. [PMID: 36944283 DOI: 10.1016/j.lungcan.2023.03.008] [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: 11/15/2022] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
Abstract
BACKGROUND Mesothelioma (MM) is associated with asbestos exposure, tumor heterogeneity and aggressive clinical behavior. Identification of germline pathogenic variants (PVs) in mesothelioma is relevant for identifying potential actionable targets and genetic counseling. METHODS 44 patients underwent whole exome sequencing (WES) or whole genome sequencing (WGS). Germline variants were selected according to association with inherited cancer using a 168-gene in silico panel, and variants classified according to ACMG/AMP classification as pathogenic (class 5) or likely pathogenic (class 4). RESULTS In total, 16 patients (36%) were found to carry pathogenic or likely pathogenic variants in 13 cancer associated genes (ATM, BAP1, BRCA2, CDKN2A, FANCA, FANCC, FANCD2, FANCM, MUTYH, NBN, RAD51B, SDHA and XPC). The germline PVs occurred in DNA repair pathways, including homologous recombination repair (HRR) (75%), nucleotide excision repair (6%), cell cycle regulatory (7%), base excision repair (6%), and hypoxic pathway (6%). Five (31%) patients with a germline PV had a first or second degree relative with mesothelioma compared to none for patients without a germline PV. Previously undiagnosed BRCA2 germline PVs were identified in two patients. Potential actionable targets based on the germline PVs were found in four patients (9%). CONCLUSION This study revealed a high frequency of germline PVs in patients with mesothelioma. Furthermore, we identified germline PVs in two genes (NBN & RAD51B) not previously associated with mesothelioma. The data support germline testing in mesothelioma and provide a rationale for additional investigation of the HRR pathway as a potential actionable target.
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Affiliation(s)
- Laila Belcaid
- Dept. of Oncology, Copenhagen University Hospital, Rigshospitalet, Denmark.
| | - Birgitte Bertelsen
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Karin Wadt
- Dept. of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Ida Tuxen
- Dept. of Oncology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Iben Spanggaard
- Dept. of Oncology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Martin Højgaard
- Dept. of Oncology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Jens Benn Sørensen
- Dept. of Oncology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Jesper Ravn
- Dept. of Thoracic Surgery, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Ulrik Lassen
- Dept. of Oncology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Finn Cilius Nielsen
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Denmark
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24
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Kuzbari Z, Bandlamudi C, Loveday C, Garrett A, Mehine M, George A, Hanson H, Snape K, Kulkarni A, Allen S, Jezdic S, Ferrandino R, Westphalen CB, Castro E, Rodon J, Mateo J, Burghel GJ, Berger MF, Mandelker D, Turnbull C. Germline-focused analysis of tumour-detected variants in 49,264 cancer patients: ESMO Precision Medicine Working Group recommendations. Ann Oncol 2023; 34:215-227. [PMID: 36529447 DOI: 10.1016/j.annonc.2022.12.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/01/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The European Society for Medical Oncology Precision Medicine Working Group (ESMO PMWG) was reconvened to update its 2018/19 recommendations on follow-up of putative germline variants detected on tumour-only sequencing, which were based on an analysis of 17 152 cancers. METHODS We analysed an expanded dataset including 49 264 paired tumour-normal samples. We applied filters to tumour-detected variants based on variant allele frequency, predicted pathogenicity and population variant frequency. For 58 cancer-susceptibility genes, we then examined the proportion of filtered tumour-detected variants of true germline origin [germline conversion rate (GCR)]. We conducted subanalyses based on the age of cancer diagnosis, specific tumour types and 'on-tumour' status (established tumour-gene association). RESULTS Analysis of 45 472 nonhypermutated solid malignancy tumour samples yielded 21 351 filtered tumour-detected variants of which 3515 were of true germline origin. 3.1% of true germline pathogenic variants were absent from the filtered tumour-detected variants. For genes such as BRCA1, BRCA2 and PALB2, the GCR in filtered tumour-detected variants was >80%; conversely for TP53, APC and STK11 this GCR was <2%. CONCLUSION Strategic germline-focused analysis can prioritise a subset of tumour-detected variants for which germline follow-up will produce the highest yield of most actionable true germline variants. We present updated recommendations around germline follow-up of tumour-only sequencing including (i) revision to 5% for the minimum per-gene GCR, (ii) inclusion of actionable intermediate penetrance genes ATM and CHEK2, (iii) definition of a set of seven 'most actionable' cancer-susceptibility genes (BRCA1, BRCA2, PALB2, MLH1, MSH2, MSH6 and RET) in which germline follow-up is recommended regardless of tumour type.
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Affiliation(s)
- Z Kuzbari
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - C Bandlamudi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - C Loveday
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK. https://twitter.com/LovedayChey
| | - A Garrett
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK. https://twitter.com/DrAliceGarrett
| | - M Mehine
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - A George
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, London, UK
| | - H Hanson
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK; South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - K Snape
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK. https://twitter.com/genetikos
| | - A Kulkarni
- South East Thames Regional Genetics Service, Guy's and St Thomas' NHS Foundation Trust, London, UK. https://twitter.com/Anju__Kulkarni
| | - S Allen
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - S Jezdic
- Scientific and Medical Division, European Society for Medical Oncology, Lugano, Switzerland
| | - R Ferrandino
- Scientific and Medical Division, European Society for Medical Oncology, Lugano, Switzerland
| | - C B Westphalen
- Department of Medicine III and Comprehensive Cancer Center (CCC Munich LMU) University Hospital, LMU Munich, Munich, Germany
| | - E Castro
- Genitourinary Cancers Translational Research Group, Institute of Biomedical Research in Málaga (IBIMA), Málaga, Spain. https://twitter.com/Ecastromarcos
| | - J Rodon
- Investigational Cancer Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Mateo
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona; Vall d'Hebron University Hospital, Barcelona, Spain
| | - G J Burghel
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK. https://twitter.com/BurghelG
| | - M F Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - D Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - C Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, London, UK.
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25
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Belhadj S, Khurram A, Bandlamudi C, Palou-Márquez G, Ravichandran V, Steinsnyder Z, Wildman T, Catchings A, Kemel Y, Mukherjee S, Fesko B, Arora K, Mehine M, Dandiker S, Izhar A, Petrini J, Domchek S, Nathanson KL, Brower J, Couch F, Stadler Z, Robson M, Walsh M, Vijai J, Berger M, Supek F, Karam R, Topka S, Offit K. NBN Pathogenic Germline Variants are Associated with Pan-Cancer Susceptibility and In Vitro DNA Damage Response Defects. Clin Cancer Res 2023; 29:422-431. [PMID: 36346689 PMCID: PMC9843434 DOI: 10.1158/1078-0432.ccr-22-1703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/26/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
PURPOSE To explore the role of NBN as a pan-cancer susceptibility gene. EXPERIMENTAL DESIGN Matched germline and somatic DNA samples from 34,046 patients were sequenced using Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets and presumed pathogenic germline variants (PGV) identified. Allele-specific and gene-centered analysis of enrichment was conducted and a validation cohort of 26,407 pan-cancer patients was analyzed. Functional studies utilized cellular models with analysis of protein expression, MRN complex formation/localization, and viability assessment following treatment with γ-irradiation. RESULTS We identified 83 carriers of 32 NBN PGVs (0.25% of the studied series), 40% of which (33/83) carried the Slavic founder p.K219fs. The frequency of PGVs varied across cancer types. Patients harboring NBN PGVs demonstrated increased loss of the wild-type allele in their tumors [OR = 2.7; confidence interval (CI): 1.4-5.5; P = 0.0024; pan-cancer], including lung and pancreatic tumors compared with breast and colorectal cancers. p.K219fs was enriched across all tumor types (OR = 2.22; CI: 1.3-3.6; P = 0.0018). Gene-centered analysis revealed enrichment of PGVs in cases compared with controls in the European population (OR = 1.9; CI: 1.3-2.7; P = 0.0004), a finding confirmed in the replication cohort (OR = 1.8; CI: 1.2-2.6; P = 0.003). Two novel truncating variants, p.L19* and p.N71fs, produced a 45 kDa fragment generated by alternative translation initiation that maintained binding to MRE11. Cells expressing these fragments showed higher sensitivity to γ-irradiation and lower levels of radiation-induced KAP1 phosphorylation. CONCLUSIONS Burden analyses, biallelic inactivation, and functional evidence support the role of NBN as contributing to a broad cancer spectrum. Further studies in large pan-cancer series and the assessment of epistatic and environmental interactions are warranted to further define these associations.
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Affiliation(s)
- Sami Belhadj
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
- Ambry Genetics, Aliso Viejo, California
| | - Aliya Khurram
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
| | - Chaitanya Bandlamudi
- Department of Pathology, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Guillermo Palou-Márquez
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), Barcelona institute for Science and Technology, Barcelona, Spain
| | - Vignesh Ravichandran
- Department of Pathology, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zoe Steinsnyder
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
| | - Temima Wildman
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
| | - Amanda Catchings
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
| | - Yelena Kemel
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
| | - Semanti Mukherjee
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
| | - Benjamin Fesko
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
| | - Kanika Arora
- Department of Pathology, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Miika Mehine
- Department of Pathology, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sita Dandiker
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
| | - Aalin Izhar
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
| | - John Petrini
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
| | - Susan Domchek
- Basser Center for BRCA and Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Katherine L. Nathanson
- Basser Center for BRCA and Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jamie Brower
- Basser Center for BRCA and Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Fergus Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Zsofia Stadler
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
| | - Mark Robson
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
- Breast Medicine Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael Walsh
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joseph Vijai
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Michael Berger
- Department of Pathology, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fran Supek
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), Barcelona institute for Science and Technology, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | | | - Sabine Topka
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
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26
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Alenezi WM, Fierheller CT, Serruya C, Revil T, Oros KK, Subramanian DN, Bruce J, Spiegelman D, Pugh T, Campbell IG, Mes-Masson AM, Provencher D, Foulkes WD, Haffaf ZE, Rouleau G, Bouchard L, Greenwood CMT, Ragoussis J, Tonin PN. Genetic analyses of DNA repair pathway associated genes implicate new candidate cancer predisposing genes in ancestrally defined ovarian cancer cases. Front Oncol 2023; 13:1111191. [PMID: 36969007 PMCID: PMC10030840 DOI: 10.3389/fonc.2023.1111191] [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: 11/29/2022] [Accepted: 02/06/2023] [Indexed: 03/29/2023] Open
Abstract
Not all familial ovarian cancer (OC) cases are explained by pathogenic germline variants in known risk genes. A candidate gene approach involving DNA repair pathway genes was applied to identify rare recurring pathogenic variants in familial OC cases not associated with known OC risk genes from a population exhibiting genetic drift. Whole exome sequencing (WES) data of 15 OC cases from 13 families tested negative for pathogenic variants in known OC risk genes were investigated for candidate variants in 468 DNA repair pathway genes. Filtering and prioritization criteria were applied to WES data to select top candidates for further analyses. Candidates were genotyped in ancestry defined study groups of 214 familial and 998 sporadic OC or breast cancer (BC) cases and 1025 population-matched controls and screened for additional carriers in 605 population-matched OC cases. The candidate genes were also analyzed in WES data from 937 familial or sporadic OC cases of diverse ancestries. Top candidate variants in ERCC5, EXO1, FANCC, NEIL1 and NTHL1 were identified in 5/13 (39%) OC families. Collectively, candidate variants were identified in 7/435 (1.6%) sporadic OC cases and 1/566 (0.2%) sporadic BC cases versus 1/1025 (0.1%) controls. Additional carriers were identified in 6/605 (0.9%) OC cases. Tumour DNA from ERCC5, NEIL1 and NTHL1 variant carriers exhibited loss of the wild-type allele. Carriers of various candidate variants in these genes were identified in 31/937 (3.3%) OC cases of diverse ancestries versus 0-0.004% in cancer-free controls. The strategy of applying a candidate gene approach in a population exhibiting genetic drift identified new candidate OC predisposition variants in DNA repair pathway genes.
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Affiliation(s)
- Wejdan M. Alenezi
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Department of Medical Laboratory Technology, Taibah University, Medina, Saudi Arabia
| | - Caitlin T. Fierheller
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Corinne Serruya
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill Genome Centre, McGill University, Montreal, QC, Canada
| | - Kathleen K. Oros
- Lady Davis Institute for Medical Research of the Jewish General Hospital, Montreal, QC, Canada
| | - Deepak N. Subramanian
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Jeffrey Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Dan Spiegelman
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Trevor Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Ian G. Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l’Université de Montréal and Institut du cancer de Montréal, Montreal, QC, Canada
- Departement of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Diane Provencher
- Centre de recherche du Centre hospitalier de l’Université de Montréal and Institut du cancer de Montréal, Montreal, QC, Canada
- Division of Gynecologic Oncology, Université de Montréal, Montreal, QC, Canada
| | - William D. Foulkes
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Lady Davis Institute for Medical Research of the Jewish General Hospital, Montreal, QC, Canada
- Department of Medical Genetics, McGill University Health Centre, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| | - Zaki El Haffaf
- Centre de recherche du Centre hospitalier de l’Université de Montréal and Institut du cancer de Montréal, Montreal, QC, Canada
- Service de Médecine Génique, Centre Hospitalier de l’Université de Montréal, Montreal, QC, Canada
| | - Guy Rouleau
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of Medical Biology, Centres intégrés universitaires de santé et de services sociaux du Saguenay-Lac-Saint-Jean hôpital Universitaire de Chicoutimi, Saguenay, QC, Canada
- Centre de Recherche du Centre hospitalier l’Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Celia M. T. Greenwood
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Lady Davis Institute for Medical Research of the Jewish General Hospital, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill Genome Centre, McGill University, Montreal, QC, Canada
| | - Patricia N. Tonin
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
- *Correspondence: Patricia N. Tonin,
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Murciano-Goroff YR, Schram AM, Rosen EY, Won H, Gong Y, Noronha AM, Janjigian YY, Stadler ZK, Chang JC, Yang SR, Mandelker D, Offit K, Berger MF, Donoghue MTA, Bandlamudi C, Drilon A. Reversion mutations in germline BRCA1/2-mutant tumors reveal a BRCA-mediated phenotype in non-canonical histologies. Nat Commun 2022; 13:7182. [PMID: 36418296 PMCID: PMC9684575 DOI: 10.1038/s41467-022-34109-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/12/2022] [Indexed: 11/25/2022] Open
Abstract
The association between loss of BRCA1/2 and a homologous recombination deficiency phenotype is lineage dependent. In BRCA-associated cancers such as breast, ovarian, pancreas and prostate, this phenotype confers sensitivity to PARP inhibitors and platinum-therapies. Somatic reversion mutations restoring BRCA1/2 function mediate resistance, and have exclusively been reported in BRCA-associated tumors. In this study, we analyze matched tumor and normal sequencing from 31,927 patients and identify 846 (2.7%) patients with germline BRCA1/2 variants across 43 different cancer types, including 11 with somatic reversion mutations. While nine are in BRCA-associated tumors, we find two reversion mutations in non-BRCA-associated histologies, namely lung and esophagogastric adenocarcinomas. Both were detected following platinum therapy. Whole exome sequencing confirms the homologous recombination deficiency phenotype of these tumors. While reversion mutations arise in all BRCA-associated cancer types, here we show that reversion mutations arising post-platinum in non-BRCA associated histologies, while rare, may indicate BRCA1/2 mediated tumorigenesis.
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Affiliation(s)
| | - Alison M Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Ezra Y Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Helen Won
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- LOXO Oncology at Lilly, Stamford, CT, USA
| | - Yixiao Gong
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anne Marie Noronha
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Jason C Chang
- Weill Cornell Medical College, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Soo-Ryum Yang
- Weill Cornell Medical College, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Michael F Berger
- Weill Cornell Medical College, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark T A Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chaitanya Bandlamudi
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medical College, New York, NY, USA.
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28
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Detecting mismatch repair deficiency in solid neoplasms: immunohistochemistry, microsatellite instability, or both? Mod Pathol 2022; 35:1515-1528. [PMID: 35668150 DOI: 10.1038/s41379-022-01109-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 12/25/2022]
Abstract
In managing patients with solid tumors, the value of detecting the status of tumor DNA mismatch repair function is widely recognized. Mismatch repair protein immunohistochemistry and molecular microsatellite instability testing constitute the two major test modalities currently in use, yet each is associated with caveats and limitations that can be consequential. Most notably, the traditional approach of defining mismatch repair protein immunohistochemistry abnormality by complete loss of staining in all tumor cells is evolving. Partial or clonal loss is becoming recognized as a manifestation of gene abnormality; in some cases, such clonal loss is associated with germline pathogenic variants. The current criteria and cutoff values for defining microsatellite instability-high are developed primarily according to colorectal tumors. Non-colorectal cases, and occasionally even colorectal tumors, that are mismatch repair-deficient by immunohistochemistry but not microsatellite instability-high by current standards are being recognized. Emerging data suggest that these immunohistochemistry abnormal / non-microsatellite instability-high cases warrant further genetic workup for Lynch syndrome detection. Whether these tumors respond to immunotherapy is a question still to be addressed. It is imperative that pathologists as well as clinicians and investigators be aware of such intricacies regarding routine immunohistochemistry and microsatellite instability testing and the results they generate. This review summarizes our current understanding of the advantages and limitations of these tests and offer our view on what constitutes the most optimal strategy in test selection and how best to utilize case context to enhance the interpretation of the test results.
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Liu YL, Maio A, Kemel Y, Salo-Mullen EE, Sheehan M, Tejada PR, Trottier M, Arnold AG, Fleischut MH, Latham A, Carlo MI, Murciano-Goroff YR, Walsh MF, Mandelker D, Mehta N, Bandlamudi C, Arora K, Zehir A, Berger MF, Solit DB, Aghajanian C, Diaz LA, Robson ME, Brown CL, Offit K, Hamilton JG, Stadler ZK. Disparities in cancer genetics care by race/ethnicity among pan-cancer patients with pathogenic germline variants. Cancer 2022; 128:3870-3879. [PMID: 36041233 PMCID: PMC10335605 DOI: 10.1002/cncr.34434] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Germline risk assessment is increasing as part of cancer care; however, disparities in subsequent genetic counseling are unknown. METHODS Pan-cancer patients were prospectively consented to tumor-normal sequencing via custom next generation sequencing panel (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets) inclusive of germline analysis of ≥76 genes from January 2015 through December 2019 (97.5% research nonbillable) with protocol for genetics referral. Rates of pathogenic/likely pathogenic germline variants (PVs) and downstream counseling were compared across ancestry groups (mutually exclusive groups based on self-reported race/ethnicity and Ashkenazi Jewish [AJ] heritage) using nonparametric tests and multivariable logistic regression models. RESULTS Among 15,775 patients (59.6%, non-Hispanic [NH]-White; 15.7%, AJ; 20.5%, non-White [6.9%, Asian; 6.8%, Black/African American (AA); 6.7%, Hispanic; 0.1%, Other], and 4.2%, unknown), 2663 (17%) had a PV. Non-White patients had a lower PV rate (n = 433, 13.4%) compared to NH-Whites (n = 1451, 15.4%) and AJ patients (n = 683, 27.6%), p < .01, with differences in mostly moderate and low/recessive/uncertain penetrance variants. Among 2239 patients with new PV, 1652 (73.8%) completed recommended genetic counseling. Non-White patients had lower rates of genetic counseling (67.7%) than NH-White (73.7%) and AJ patients (78.8%), p < .01, with lower rates occurring in Black/AA (63%) compared to NH-White patients, even after adjustment for confounders (odds ratio, 0.60; 95% confidence interval, 0.37-0.97; p = .036). Non-White, particularly Black/AA and Asian, probands had a trend toward lower rates and numbers of at-risk family members being seen for counseling/genetic testing. CONCLUSIONS Despite minimizing barriers to genetic testing, non-White patients were less likely to receive recommended cancer genetics follow-up, with potential implications for oncologic care, cancer risk reduction, and at-risk family members. LAY SUMMARY Genetic testing is becoming an important part of cancer care, and we wanted to see if genetics care was different between individuals of different backgrounds. We studied 15,775 diverse patients with cancer who had genetic testing using a test called MSK-IMPACT that was covered by research funding. Clinically important genetic findings were high in all groups. However, Black patients were less likely to get recommended counseling compared to White patients. Even after removing many roadblocks, non-White and especially Black patients were less likely to get recommended genetics care, which may affect their cancer treatments and families.
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Affiliation(s)
- Ying L Liu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Anna Maio
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yelena Kemel
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Erin E Salo-Mullen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Margaret Sheehan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Prince Ray Tejada
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Magan Trottier
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Angela G Arnold
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Alicia Latham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Maria I Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Yonina R Murciano-Goroff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Michael F Walsh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nikita Mehta
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Chaitanya Bandlamudi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kanika Arora
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ahmet Zehir
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- AstraZeneca, New York, New York, USA
| | - Michael F Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Carol Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Luis A Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Carol L Brown
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, New York, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Jada G Hamilton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Psychiatry and Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Psychiatry, Weill Cornell Medical College, New York, New York, USA
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
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30
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Queen A, Bhutto HN, Yousuf M, Syed MA, Hassan MI. Carbonic anhydrase IX: A tumor acidification switch in heterogeneity and chemokine regulation. Semin Cancer Biol 2022; 86:899-913. [PMID: 34998944 DOI: 10.1016/j.semcancer.2022.01.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/30/2021] [Accepted: 01/03/2022] [Indexed: 02/07/2023]
Abstract
The primary physiological process of respiration produces carbon dioxide (CO2) that reacts with water molecules which subsequently liberates bicarbonate (HCO-3) and protons. Carbonic anhydrases (CAs) are the primary catalyst involved in this conversion. More than 16 isoforms of human CAs show organ or subcellular specific activity. Dysregulation of each CA is associated with multiple pathologies. Out of these members, the overexpression of membrane-bound carbonic anhydrase IX (CAIX) is associated explicitly with hypoxic tumors or various solid cancers. CAIX helps tumors deal with higher CO2 by sequestering it with bicarbonate ions and helping cancer cells to grow in a comparatively hypoxic or acidic environment, thus acting as a pH adaptation switch. CAIX-mediated adaptations in cancer cells include angiogenesis, metabolic alterations, tumor heterogeneity, drug resistance, and regulation of cancer-specific chemokines. This review comprehensively collects and describe the cancer-specific expression mechanism and role of CAIX in cancer growth, progression, heterogeneity, and its structural insight to develop future combinatorial targeted cancer therapies.
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Affiliation(s)
- Aarfa Queen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Humaira Naaz Bhutto
- Department of Biotechnology, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mohd Yousuf
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mansoor Ali Syed
- Department of Biotechnology, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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Kammula AV, Schäffer AA, Rajagopal PS. Characterization of Oncology Clinical Trials Using Germline Genetic Data. JAMA Netw Open 2022; 5:e2242370. [PMID: 36383380 PMCID: PMC9669814 DOI: 10.1001/jamanetworkopen.2022.42370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
IMPORTANCE The recent successes of poly-ADP ribose polymerase (PARP) inhibitors and belzutifan support germline genetic data as an exciting, accessible source for biomarkers in cancer treatment. This study hypothesizes, however, that most oncology clinical trials using germline data largely prioritize BRCA1/2 as biomarkers and PARP inhibitors as therapy. OBJECTIVE To characterize past and ongoing oncology trials that use germline data. DESIGN, SETTING, AND PARTICIPANTS This retrospective cross-sectional study of oncology trials used the Informa Trialtrove database to evaluate trial attributes. Trials using germline information (including the terms germline, hereditary, or inherited in the title, treatment plan, interventions, end points, objectives, results, or notes) and conducted globally between December 1, 1990, and April 4, 2022 (data freeze date), were included. MAIN OUTCOMES AND MEASURES Trials by cancer type, phase, participants, sponsor type, end points, outcomes, and locations were described. Associated biomarkers and mechanisms of action for studied therapeutic interventions were counted. How germline data in trial inclusion and exclusion criteria are associated with end points, outcomes, and enrollment were also examined. RESULTS A total of 887 of 84 297 (1.1%) oncology clinical trials in the Trialtrove database that use germline data were identified. Most trials were conducted in cancer types where PARP inhibitors are already approved. A total of 74.8% (672) of trials were performed in the phase 2 setting or above. Trials were primarily sponsored by industry (523 trials [59.0%]), academia (382 trials [43.1%]), and the government (274 trials [30.9%]), where trials may have multiple sponsor types. Among 343 trials using germline data with outcomes in Trialtrove, 180 (52.5%) reported meeting primary end points. Although BRCA1/2 are the most frequent biomarkers seen (BRCA1, 224 trials [25.3%]; BRCA2, 228 trials [25.7%]), trials also examine pharmacogenomic variants and germline mediators of somatic biomarkers. PARP inhibitors or immunotherapy were tested in 69.9% of trials; PARP inhibition was the most frequently studied mechanism (367 trials [41.4%]). An overwhelming number of trials using germline data were conducted in the US, Canada, and Europe vs other countries, mirroring disparities in cancer genetics data. Germline data in inclusion and exclusion criteria are associated with altered end point, outcomes, and enrollment compared with oncology trials with no germline data use. Examples of inclusion and exclusion criteria regarding germline data that may unintentionally exclude patients were identified. CONCLUSIONS AND RELEVANCE These findings suggest that for germline biomarkers to gain clinical relevance, trials must expand biomarkers, therapies, and populations under study.
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Affiliation(s)
- Ashwin V Kammula
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
- University of Maryland, College Park
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Padma Sheila Rajagopal
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
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Nassar AH, Adib E, Abou Alaiwi S, El Zarif T, Groha S, Akl EW, Nuzzo PV, Mouhieddine TH, Perea-Chamblee T, Taraszka K, El-Khoury H, Labban M, Fong C, Arora KS, Labaki C, Xu W, Sonpavde G, Haddad RI, Mouw KW, Giannakis M, Hodi FS, Zaitlen N, Schoenfeld AJ, Schultz N, Berger MF, MacConaill LE, Ananda G, Kwiatkowski DJ, Choueiri TK, Schrag D, Carrot-Zhang J, Gusev A. Ancestry-driven recalibration of tumor mutational burden and disparate clinical outcomes in response to immune checkpoint inhibitors. Cancer Cell 2022; 40:1161-1172.e5. [PMID: 36179682 PMCID: PMC9559771 DOI: 10.1016/j.ccell.2022.08.022] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 07/01/2022] [Accepted: 08/18/2022] [Indexed: 01/28/2023]
Abstract
The immune checkpoint inhibitor (ICI) pembrolizumab is US FDA approved for treatment of solid tumors with high tumor mutational burden (TMB-high; ≥10 variants/Mb). However, the extent to which TMB-high generalizes as an accurate biomarker in diverse patient populations is largely unknown. Using two clinical cohorts, we investigated the interplay between genetic ancestry, TMB, and tumor-only versus tumor-normal paired sequencing in solid tumors. TMB estimates from tumor-only panels substantially overclassified individuals into the clinically important TMB-high group due to germline contamination, and this bias was particularly pronounced in patients with Asian/African ancestry. Among patients with non-small cell lung cancer treated with ICIs, those misclassified as TMB-high from tumor-only panels did not associate with improved outcomes. TMB-high was significantly associated with improved outcomes only in European ancestries and merits validation in non-European ancestry populations. Ancestry-aware tumor-only TMB calibration and ancestry-diverse biomarker studies are critical to ensure that existing disparities are not exacerbated in precision medicine.
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Affiliation(s)
- Amin H Nassar
- Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT 06510, USA; Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Elio Adib
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sarah Abou Alaiwi
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Talal El Zarif
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Stefan Groha
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Population Sciences, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Elie W Akl
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Pier Vitale Nuzzo
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tarek H Mouhieddine
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Tomin Perea-Chamblee
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kodi Taraszka
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Habib El-Khoury
- Center for Prevention of Progression of Blood Cancers, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Muhieddine Labban
- Department of Urologic Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Christopher Fong
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kanika S Arora
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chris Labaki
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Wenxin Xu
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Guru Sonpavde
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Robert I Haddad
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - F Stephen Hodi
- Melanoma Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Noah Zaitlen
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Adam J Schoenfeld
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, 1275 York Avenue, New York, NY 10065, USA
| | - Nikolaus Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael F Berger
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Laura E MacConaill
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA; Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Guruprasad Ananda
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Toni K Choueiri
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Deborah Schrag
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jian Carrot-Zhang
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alexander Gusev
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Population Sciences, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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Pietzak EJ, Whiting K, Srinivasan P, Bandlamudi C, Khurram A, Joseph V, Walasek A, Bochner E, Clinton T, Almassi N, Truong H, de Jesus Escano MR, Wiseman M, Mandelker D, Kemel Y, Zhang L, Walsh MF, Cadoo KA, Coleman JA, Al-Ahmadie H, Rosenberg JE, Iyer GV, Solit DB, Ostrovnaya I, Offit K, Robson ME, Stadler ZK, Berger MF, Bajorin DF, Carlo M, Bochner BH. Inherited Germline Cancer Susceptibility Gene Variants in Individuals with Non-Muscle-Invasive Bladder Cancer. Clin Cancer Res 2022; 28:4267-4277. [PMID: 35833951 PMCID: PMC9527498 DOI: 10.1158/1078-0432.ccr-22-1006] [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: 03/30/2022] [Revised: 06/07/2022] [Accepted: 07/12/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE Identification of inherited germline variants can guide personalized cancer screening, prevention, and treatment. Pathogenic and likely pathogenic (P/LP) germline variants in cancer predisposition genes are frequent among patients with locally advanced or metastatic urothelial carcinoma, but their prevalence and significance in patients with non-muscle-invasive bladder cancer (NMIBC), the most common form of urothelial carcinoma, is understudied. EXPERIMENTAL DESIGN Germline analysis was conducted on paired tumor/normal sequencing results from two distinct cohorts of patients initially diagnosed with NMIBC. Associations between clinicopathologic features and clinical outcomes with the presence of P/LP germline variants in ≥76 hereditary cancer predisposition genes were analyzed. RESULTS A similar frequency of P/LP germline variants were seen in our two NMIBC cohorts [12% (12/99) vs. 8.7% (10/115), P = 0.4]. In the combined analysis, P/LP germline variants were found only in patients with high-grade NMIBC (22/163), but none of the 46 patients with low-grade NMIBC (13.5% vs. 0%, P = 0.005). Fifteen (9.2%) patients with high-grade NMIBC had P/LP variants in DNA damage response genes, most within the nucleotide excision repair (ERCC2/3) and homologous recombination repair (BRCA1, NBN, RAD50) pathways. Contrary to prior reports in patients with NMIBC not receiving Bacillus Calmette-Guerin (BCG), P/LP germline variants were not associated with worse recurrence-free or progression-free survival in patients treated with BCG or with risk of developing upper tract urothelial carcinoma. CONCLUSIONS Our results support offering germline counseling and testing for all patients with high-grade bladder cancer, regardless of initial tumor stage. Therapeutic strategies that target impaired DNA repair may benefit patients with high-grade NMIBC.
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Affiliation(s)
- Eugene J. Pietzak
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Corresponding Author: Eugene J. Pietzak, Urology Service, Department of Surgery, Kimmel Center for Prostate and Urologic Cancers, Memorial Sloan Kettering Cancer Center, 353 East 68th Street, New York, NY 10065. Phone: 646-422-4781; Fax: 212-988-0759. E-mail:
| | - Karissa Whiting
- Biostatistics Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Preethi Srinivasan
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chaitanya Bandlamudi
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aliya Khurram
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vijai Joseph
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aleksandra Walasek
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily Bochner
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Timothy Clinton
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nima Almassi
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hong Truong
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Manuel R. de Jesus Escano
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michal Wiseman
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Diana Mandelker
- Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yelena Kemel
- Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Liying Zhang
- Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F. Walsh
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Karen A. Cadoo
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,St. James's Hospital Dublin, Trinity College Dublin, Trinity St. James's Cancer Institute, Dublin, Ireland
| | - Jonathan A. Coleman
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hikmat Al-Ahmadie
- Genitourinary Pathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jonathan E. Rosenberg
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gopakumar V. Iyer
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B. Solit
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Irina Ostrovnaya
- Biostatistics Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark E. Robson
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zsofia K. Stadler
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F. Berger
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dean F. Bajorin
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria Carlo
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bernard H. Bochner
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
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Pallikonda HA, Turajlic S. Predicting cancer evolution for patient benefit: Renal cell carcinoma paradigm. Biochim Biophys Acta Rev Cancer 2022; 1877:188759. [PMID: 35835341 DOI: 10.1016/j.bbcan.2022.188759] [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: 03/18/2022] [Revised: 06/20/2022] [Accepted: 07/06/2022] [Indexed: 10/17/2022]
Abstract
Evolutionary features of cancer have important clinical implications, but their evaluation in the clinic is currently limited. Here, we review current approaches to reconstruct tumour subclonal structure and discuss tumour sampling method and experimental design influence. We describe clear-cell renal cell carcinoma (ccRCC) as an exemplar for understanding and predicting cancer evolutionary dynamics. Finally, we discuss how understanding cancer evolution can benefit patients.
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Affiliation(s)
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, United Kingdom; Melanoma and Kidney Cancer Team, Institute of Cancer Research, London, United Kingdom.
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35
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Schwartz A, Manning DK, Koeller DR, Chittenden A, Isidro RA, Hayes CP, Abraamyan F, Manam MD, Dwan M, Barletta JA, Sholl LM, Yurgelun MB, Rana HQ, Garber JE, Ghazani AA. An integrated somatic and germline approach to aid interpretation of germline variants of uncertain significance in cancer susceptibility genes. Front Oncol 2022; 12:942741. [PMID: 36091175 PMCID: PMC9453486 DOI: 10.3389/fonc.2022.942741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic profiles of tumors are often unique and represent characteristic mutational signatures defined by DNA damage or DNA repair response processes. The tumor-derived somatic information has been widely used in therapeutic applications, but it is grossly underutilized in the assessment of germline genetic variants. Here, we present a comprehensive approach for evaluating the pathogenicity of germline variants in cancer using an integrated interpretation of somatic and germline genomic data. We have previously demonstrated the utility of this integrated approach in the reassessment of pathogenic germline variants in selected cancer patients with unexpected or non-syndromic phenotypes. The application of this approach is presented in the assessment of rare variants of uncertain significance (VUS) in Lynch-related colon cancer, hereditary paraganglioma-pheochromocytoma syndrome, and Li-Fraumeni syndrome. Using this integrated method, germline VUS in PMS2, MSH6, SDHC, SHDA, and TP53 were assessed in 16 cancer patients after genetic evaluation. Comprehensive clinical criteria, somatic signature profiles, and tumor immunohistochemistry were used to re-classify VUS by upgrading or downgrading the variants to likely or unlikely actionable categories, respectively. Going forward, collation of such germline variants and creation of cross-institutional knowledgebase datasets that include integrated somatic and germline data will be crucial for the assessment of these variants in a larger cancer cohort.
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Affiliation(s)
- Alison Schwartz
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Danielle K. Manning
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Diane R. Koeller
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Anu Chittenden
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Raymond A. Isidro
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Connor P. Hayes
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Feruza Abraamyan
- Harvard Medical School, Boston, MA, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Monica Devi Manam
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Meaghan Dwan
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Justine A. Barletta
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Matthew B. Yurgelun
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Huma Q. Rana
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Judy E. Garber
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Arezou A. Ghazani
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- *Correspondence: Arezou A. Ghazani,
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Brewer T, Yehia L, Bazeley P, Eng C. Exome sequencing reveals a distinct somatic genomic landscape in breast cancer from women with germline PTEN variants. Am J Hum Genet 2022; 109:1520-1533. [PMID: 35931053 PMCID: PMC9388380 DOI: 10.1016/j.ajhg.2022.07.005] [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: 03/25/2022] [Accepted: 07/01/2022] [Indexed: 02/06/2023] Open
Abstract
Germline PTEN variants (PTEN hamartoma tumor syndrome [PHTS]) confer up to 85% lifetime risk of female breast cancer (BC). BCs arising in PHTS are clinically distinct from sporadic BCs, including younger age of onset, multifocality, and an increased risk of second primary BCs. Yet, there is no previous investigation into the underlying genomic landscape of this entity. We sought to address the hypothesis that BCs arising in PHTS have a distinct genomic landscape compared to sporadic counterparts. We performed and analyzed exome sequencing data from 44 women with germline PTEN variants who developed BCs. The control cohort comprised of 497 women with sporadic BCs from The Cancer Genome Atlas (TCGA) dataset. We demonstrate that PHTS-derived BCs have a distinct somatic mutational landscape compared to the sporadic counterparts, namely second somatic hits in PTEN, distinct mutational signatures, and increased genomic instability. The PHTS group had a significantly higher frequency of somatic PTEN variants compared to TCGA (22.7% versus 5.6%; odds ratio [OR] 4.93; 95% confidence interval [CI] 2.21 to 10.98; p < 0.001) and a lower mutational frequency in PIK3CA (22.7% versus 33.4%; OR 0.59; 95% CI 0.28 to 1.22; p = 0.15). Somatic variants in PTEN and PIK3CA were mutually exclusive in PHTS (p = 0.01) but not in TCGA. Our findings have important implications for the personalized management of PTEN-related BCs, especially in the context of more accessible genetic testing.
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Affiliation(s)
- Takae Brewer
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Lamis Yehia
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Peter Bazeley
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA,Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA,Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA,Corresponding author
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TP53-dependent toxicity of CRISPR/Cas9 cuts is differential across genomic loci and can confound genetic screening. Nat Commun 2022; 13:4520. [PMID: 35927263 PMCID: PMC9352712 DOI: 10.1038/s41467-022-32285-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/26/2022] [Indexed: 12/14/2022] Open
Abstract
CRISPR/Cas9 gene editing can inactivate genes in a precise manner. This process involves DNA double-strand breaks (DSB), which may incur a loss of cell fitness. We hypothesize that DSB toxicity may be variable depending on the chromatin environment in the targeted locus. Here, by analyzing isogenic cell line pair CRISPR experiments jointly with previous screening data from across ~900 cell lines, we show that TP53-associated break toxicity is higher in genomic regions that harbor active chromatin, such as gene regulatory elements or transcription elongation histone marks. DSB repair pathway choice and DNA sequence context also associate with toxicity. We also show that, due to noise introduced by differential toxicity of sgRNA-targeted sites, the power of genetic screens to detect conditional essentiality is reduced in TP53 wild-type cells. Understanding the determinants of Cas9 cut toxicity will help improve design of CRISPR reagents to avoid incidental selection of TP53-deficient and/or DNA repair deficient cells. Toxicity of CRISPR/Cas9 induced DNA breaks depends on their repair mechanism, and on the chromatin environment at the cut site. Here the authors show that edits in active genes or regulatory elements can incur a higher toxicity via a TP53-dependent mechanism.
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38
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Diagnostics of BAP1-Tumor Predisposition Syndrome by a Multitesting Approach: A Ten-Year-Long Experience. Diagnostics (Basel) 2022; 12:diagnostics12071710. [PMID: 35885614 PMCID: PMC9317020 DOI: 10.3390/diagnostics12071710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/17/2022] Open
Abstract
Germline mutations in the tumor suppressor gene BRCA1-associated protein-1 (BAP1) lead to BAP1 tumor predisposition syndrome (BAP1-TPDS), characterized by high susceptibility to several tumor types, chiefly melanoma, mesothelioma, renal cell carcinoma, and basal cell carcinoma. Here, we present the results of our ten-year experience in the molecular diagnosis of BAP1-TPDS, along with a clinical update and cascade genetic testing of previously reported BAP1-TPDS patients and their relatives. Specifically, we sequenced germline DNA samples from 101 individuals with suspected BAP1-TPDS and validated pathogenic variants (PVs) by assessing BAP1 somatic loss in matching tumor specimens. Overall, we identified seven patients (7/101, 6.9%) carrying six different germline BAP1 PVs, including one novel variant. Consistently, cascade testing revealed a total of seven BAP1 PV carriers. In addition, we explored the mutational burden of BAP1-TPDS tumors by targeted next-generation sequencing. Lastly, we found that certain tumors present in PV carriers retain a wild-type BAP1 allele, suggesting a sporadic origin of these tumors or a functional role of heterozygous BAP1 in neoplastic development. Altogether, our findings have important clinical implications for therapeutic response of BAP1-TPDS patients.
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Koeller DR, Manning DK, Schwartz A, Chittenden A, Hayes CP, Abraamyan F, Rana HQ, Lindeman NI, Garber JE, Ghazani AA. An optimized protocol for evaluating pathogenicity of VHL germline variants in patients suspected with von Hippel-Lindau syndrome: Using somatic genome to inform the role of germline variants. MethodsX 2022; 9:101761. [PMID: 35774415 PMCID: PMC9237939 DOI: 10.1016/j.mex.2022.101761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/13/2022] [Indexed: 12/17/2022] Open
Abstract
The interpretation of hereditary genetic sequencing variants is often limited due to the absence of functional data and other key evidence to assess the role of variants in disease. Cancer genetics is unique, as two sets of genomic information are often available from a cancer patient: somatic and germline. Despite the progress made in the integrated analysis of somatic and germline findings, the assessment of pathogenicity of germline variants in high penetrance genes remains grossly underutilized. Indeed, standard ACMG/AMP guidelines for interpreting germline sequence variants do not address the evidence derived from tumor data in cancer. Previously, we have demonstrated the utility of somatic tumor data as supporting evidence to elucidate the role of germline variants in patients suspected with VHL syndrome and other cancers. We have leveraged the key elements of cancer genetics in these cases: genes with expected high disease penetrance and those with a known biallelic mechanism of tumorigenicity. Here we provide our optimized protocol for evaluating the pathogenicity of germline VHL variants using informative somatic profiling data. This protocol provides details of case selection, assessment of personal and family evidence, somatic tumor profiles, and loss of heterozygosity (LOH) as supporting evidence for the re-evaluation of germline variants.
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Affiliation(s)
- Diane R Koeller
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Danielle K Manning
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Alison Schwartz
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Anu Chittenden
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Connor P Hayes
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Feruza Abraamyan
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Huma Q Rana
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Division of Population Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Judy E Garber
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Division of Population Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Arezou A Ghazani
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
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Mukherjee S, Bandlamudi C, Hellmann MD, Kemel Y, Drill E, Rizvi H, Tkachuk K, Khurram A, Walsh MF, Zauderer MG, Mandelker D, Topka S, Zehir A, Srinivasan P, Selvan ME, Carlo MI, Cadoo KA, Latham A, Hamilton JG, Liu YL, Lipkin SM, Belhadj S, Bond GL, Gümüş ZH, Klein RJ, Ladanyi M, Solit DB, Robson ME, Jones DR, Kris MG, Vijai J, Stadler ZK, Amos CI, Taylor BS, Berger MF, Rudin CM, Offit K. Germline Pathogenic Variants Impact Clinicopathology of Advanced Lung Cancer. Cancer Epidemiol Biomarkers Prev 2022; 31:1450-1459. [PMID: 35477182 PMCID: PMC9250622 DOI: 10.1158/1055-9965.epi-21-1287] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/31/2022] [Accepted: 04/25/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The genetic factors that modulate risk for developing lung cancer have not been fully defined. Here, we sought to determine the prevalence and clinical significance of germline pathogenic/likely pathogenic variants (PV) in patients with advanced lung cancer. METHODS We studied clinical and tumor characteristics of germline PV in 5,118 patients who underwent prospective genomic profiling using paired tumor-normal tissue samples in 468 cancer genes. RESULTS Germline PV in high/moderate-penetrance genes were observed in 222 (4.3%) patients; of these, 193 patients had PV in DNA damage repair (DDR) pathway genes including BRCA2 (n = 54), CHEK2 (n = 30), and ATM (n = 26) that showed high rate of biallelic inactivation in tumors. BRCA2 heterozygotes with lung adenocarcinoma were more likely to be never smokers and had improved survival compared with noncarriers. Fourteen patients with germline PV in lung cancer predisposing genes (TP53, EGFR, BAP1, and MEN1) were diagnosed at younger age compared with noncarriers, and of tumor suppressors, 75% demonstrated biallelic inactivation in tumors. A significantly higher proportion of germline PV in high/moderate-penetrance genes were detected in high-risk patients who had either a family history of any cancer, multiple primary tumors, or early age at diagnosis compared with unselected patients (10.5% vs. 4.1%; P = 1.7e-04). CONCLUSIONS These data underscore the biological and clinical importance of germline mutations in highly penetrant DDR genes as a risk factor for lung cancer. IMPACT The family members of lung cancer patients harboring PV in cancer predisposing genes should be referred for genetic counseling and may benefit from proactive surveillance.
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Affiliation(s)
| | | | | | - Yelena Kemel
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Esther Drill
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Hira Rizvi
- Memorial Sloan Kettering Cancer Center, United States
| | - Kaitlyn Tkachuk
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Aliya Khurram
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Michael F Walsh
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Diana Mandelker
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Sabine Topka
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | | | - Maria I Carlo
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Karen A Cadoo
- St. James’s Hospital, Trinity College Dublin, Trinity St. James’s Cancer Institute, Dublin 8, Ireland
| | - Alicia Latham
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, United States
| | - Jada G Hamilton
- Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Ying L Liu
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Sami Belhadj
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Gareth L Bond
- University of Birmingham, Birmingham, United Kingdom
| | - Zeynep H Gümüş
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Robert J Klein
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - David B Solit
- Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Mark E Robson
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - David R Jones
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Mark G Kris
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Joseph Vijai
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Zsofia K Stadler
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, United States
| | | | - Barry S Taylor
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Michael F Berger
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Charles M Rudin
- Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
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41
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Vali-Pour M, Park S, Espinosa-Carrasco J, Ortiz-Martínez D, Lehner B, Supek F. The impact of rare germline variants on human somatic mutation processes. Nat Commun 2022; 13:3724. [PMID: 35764656 PMCID: PMC9240060 DOI: 10.1038/s41467-022-31483-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 06/17/2022] [Indexed: 02/07/2023] Open
Abstract
Somatic mutations are an inevitable component of ageing and the most important cause of cancer. The rates and types of somatic mutation vary across individuals, but relatively few inherited influences on mutation processes are known. We perform a gene-based rare variant association study with diverse mutational processes, using human cancer genomes from over 11,000 individuals of European ancestry. By combining burden and variance tests, we identify 207 associations involving 15 somatic mutational phenotypes and 42 genes that replicated in an independent data set at a false discovery rate of 1%. We associate rare inherited deleterious variants in genes such as MSH3, EXO1, SETD2, and MTOR with two phenotypically different forms of DNA mismatch repair deficiency, and variants in genes such as EXO1, PAXIP1, RIF1, and WRN with deficiency in homologous recombination repair. In addition, we identify associations with other mutational processes, such as APEX1 with APOBEC-signature mutagenesis. Many of the genes interact with each other and with known mutator genes within cellular sub-networks. Considered collectively, damaging variants in the identified genes are prevalent in the population. We suggest that rare germline variation in diverse genes commonly impacts mutational processes in somatic cells.
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Affiliation(s)
- Mischan Vali-Pour
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Solip Park
- Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Jose Espinosa-Carrasco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Daniel Ortiz-Martínez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ben Lehner
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
| | - Fran Supek
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
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Pich O, Bailey C, Watkins TBK, Zaccaria S, Jamal-Hanjani M, Swanton C. The translational challenges of precision oncology. Cancer Cell 2022; 40:458-478. [PMID: 35487215 DOI: 10.1016/j.ccell.2022.04.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/16/2022] [Accepted: 04/05/2022] [Indexed: 12/11/2022]
Abstract
The translational challenges in the field of precision oncology are in part related to the biological complexity and diversity of this disease. Technological advances in genomics have facilitated large sequencing efforts and discoveries that have further supported this notion. In this review, we reflect on the impact of these discoveries on our understanding of several concepts: cancer initiation, cancer prevention, early detection, adjuvant therapy and minimal residual disease monitoring, cancer drug resistance, and cancer evolution in metastasis. We discuss key areas of focus for improving cancer outcomes, from biological insights to clinical application, and suggest where the development of these technologies will lead us. Finally, we discuss practical challenges to the wider adoption of molecular profiling in the clinic and the need for robust translational infrastructure.
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Affiliation(s)
- Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Chris Bailey
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK; Department of Medical Oncology, University College London Hospitals, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
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de Bruijn I, Li X, Sumer SO, Gross B, Sheridan R, Ochoa A, Wilson M, Wang A, Zhang H, Lisman A, Abeshouse A, Zhang E, Thum A, Sadagopan A, Heins Z, Kandoth C, Rodenburg S, Tan S, Lukasse P, van Hagen S, Fijneman RJA, Meijer GA, Schultz N, Gao J. Genome Nexus: A Comprehensive Resource for the Annotation and Interpretation of Genomic Variants in Cancer. JCO Clin Cancer Inform 2022; 6:e2100144. [PMID: 35148171 PMCID: PMC8846305 DOI: 10.1200/cci.21.00144] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
PURPOSE Interpretation of genomic variants in tumor samples still presents a challenge in research and the clinical setting. A major issue is that information for variant interpretation is fragmented across disparate databases, and aggregation of information from these requires building extensive infrastructure. To this end, we have developed Genome Nexus, a one-stop shop for variant annotation with a user-friendly interface for cancer researchers and clinicians. METHODS Genome Nexus (1) aggregates variant information from sources that are relevant to cancer research and clinical applications, (2) allows high-performance programmatic access to the aggregated data via a unified application programming interface, (3) provides a reference page for individual cancer variants, (4) provides user-friendly tools for annotating variants in patients, and (5) is freely available under an open source license and can be installed in a private cloud or local environment and integrated with local institutional resources. RESULTS Genome Nexus is available at https://www.genomenexus.org. It displays annotations from more than a dozen resources including those that provide variant effect information (variant effect predictor), protein sequence annotation (Uniprot, Pfam, and dbPTM), functional consequence prediction (Polyphen-2, Mutation Assessor, and SIFT), population prevalences (gnomAD, dbSNP, and ExAC), cancer population prevalences (Cancer hotspots and SignalDB), and clinical actionability (OncoKB, CIViC, and ClinVar). We describe several use cases that demonstrate the utility of Genome Nexus to clinicians, researchers, and bioinformaticians. We cover single-variant annotation, cohort analysis, and programmatic use of the application programming interface. Genome Nexus is unique in providing a user-friendly interface specific to cancer that allows high-performance annotation of any variant including unknown ones. CONCLUSION Interpretation of cancer genomic variants is improved tremendously by having an integrated resource for annotations. Genome Nexus is freely available under an open source license.
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Affiliation(s)
- Ino de Bruijn
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY,Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Xiang Li
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Selcuk Onur Sumer
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Benjamin Gross
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Robert Sheridan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Angelica Ochoa
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Manda Wilson
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Avery Wang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Aaron Lisman
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Adam Abeshouse
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Emily Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY,Cornell University, Ithaca, NY
| | - Alice Thum
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY,MongoDB, New York, NY
| | | | - Zachary Heins
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY,Boston University, Boston, MA
| | - Cyriac Kandoth
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY,Department of Pathology and Lab Medicine, University of California, Los Angeles, CA
| | | | - Sander Tan
- The Hyve, Utrecht, the Netherlands,Directie Informatie Technologie, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | | | - Gerrit A. Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY,Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY,Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY,Jianjiong Gao, PhD, Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065; e-mail:
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Sculco M, La Vecchia M, Aspesi A, Pinton G, Clavenna MG, Casalone E, Allione A, Grosso F, Libener R, Muzio A, Rena O, Baietto G, Parini S, Boldorini R, Giachino D, Papotti M, Scagliotti GV, Migliore E, Mirabelli D, Moro L, Magnani C, Ferrante D, Matullo G, Dianzani I. Malignant pleural mesothelioma: Germline variants in DNA repair genes may steer tailored treatment. Eur J Cancer 2022; 163:44-54. [PMID: 35032816 DOI: 10.1016/j.ejca.2021.12.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 11/25/2021] [Accepted: 12/19/2021] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Malignant pleural mesothelioma (MPM) is a tumour associated with asbestos exposure. Approximately, 10% of patients with MPM carry a germline pathogenic variant (PV), mostly in DNA repair genes, suggesting the occurrence of inherited predispositions. AIM This article aimed to 1) search for new predisposing genes and assess the prevalence of PVs in DNA repair genes, by next-generation sequencing (NGS) analysis of germline DNA from 113 unselected patients with MPM and 2) evaluate whether these patients could be sensitive to tailored treatments. METHODS NGS was performed using a custom panel of 107 cancer-predisposing genes. To investigate the response to selected drugs in conditions of DNA repair insufficiency, we created a three-dimensional-MPM cell model that had a defect in ataxia telangiectasia mutated (ATM), the master regulator of DNA repair. RESULTS We identified PVs in approximately 7% of patients with MPM (8/113) and a new PV in BAP1 in a further patient with familial MPM. Most of these PVs were in genes involved or supposedly involved in DNA repair (BRCA1, BRIP1, CHEK2, SLX4, FLCN and BAP1). In vitro studies showed apoptosis induction in ATM-silenced/inhibited MPM spheroids treated with an enhancer of zeste homologue 2 inhibitor (tazemetostat). CONCLUSIONS Overall these data suggest that patients with MPM and DNA repair insufficiency may benefit from this treatment, which induces synthetic lethality.
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Affiliation(s)
- Marika Sculco
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Marta La Vecchia
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Anna Aspesi
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Giulia Pinton
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Michela G Clavenna
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | | | | | - Federica Grosso
- Mesothelioma Unit, AO SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Roberta Libener
- Department of Integrated Activities Research and Innovation, AO SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Alberto Muzio
- Division of Medical Oncology, Ospedale Santo Spirito, Casale Monferrato (Alessandria), Italy
| | - Ottavio Rena
- Thoracic Surgery Unit, AOU Maggiore della Carità, Novara, Italy
| | - Guido Baietto
- Thoracic Surgery Unit, AOU Maggiore della Carità, Novara, Italy
| | - Sara Parini
- Thoracic Surgery Unit, AOU Maggiore della Carità, Novara, Italy
| | - Renzo Boldorini
- Department of Health Sciences, Section of Pathological Anatomy, Università del Piemonte Orientale, Novara, Italy
| | - Daniela Giachino
- Medical Genetics Unit, Department of Clinical and Biological Sciences, Università di Torino, AOU S. Luigi Gonzaga, Orbassano, (Torino), Italy
| | | | - Giorgio V Scagliotti
- Department of Oncology, Università di Torino, AOU S. Luigi Gonzaga, Orbassano, Torino, Italy
| | - Enrica Migliore
- Unit of Cancer Epidemiology, CPO-Piemonte and Università di Torino, Italy
| | - Dario Mirabelli
- Unit of Cancer Epidemiology, CPO-Piemonte and Università di Torino, Italy; Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates "G. Scansetti", Università di Torino, Italy
| | - Laura Moro
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Corrado Magnani
- Department of Translational Medicine, Unit of Medical Statistics, Università del Piemonte Orientale and Cancer Epidemiology, CPO Piemonte, Novara, Italy
| | - Daniela Ferrante
- Department of Translational Medicine, Unit of Medical Statistics, Università del Piemonte Orientale and Cancer Epidemiology, CPO Piemonte, Novara, Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, Università di Torino, Italy; Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates "G. Scansetti", Università di Torino, Italy; Medical Genetics Unit, AOU Città Della Salute e della Scienza di Torino, Italy.
| | - Irma Dianzani
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy; Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates "G. Scansetti", Università di Torino, Italy.
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