1
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Plowman JN, Matoy EJ, Uppala LV, Draves SB, Watson CJ, Sefranek BA, Stacey ML, Anderson SP, Belshan MA, Blue EE, Huff CD, Fu Y, Stessman HAF. Targeted sequencing for hereditary breast and ovarian cancer in BRCA1/2-negative families reveals complex genetic architecture and phenocopies. HGG ADVANCES 2024; 5:100306. [PMID: 38734904 PMCID: PMC11166883 DOI: 10.1016/j.xhgg.2024.100306] [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: 01/09/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024] Open
Abstract
Approximately 20% of breast cancer cases are attributed to increased family risk, yet variation in BRCA1/2 can only explain 20%-25% of cases. Historically, only single gene or single variant testing were common in at-risk family members, and further sequencing studies were rarely offered after negative results. In this study, we applied an efficient and inexpensive targeted sequencing approach to provide molecular diagnoses in 245 human samples representing 134 BRCA mutation-negative (BRCAX) hereditary breast and ovarian cancer (HBOC) families recruited from 1973 to 2019 by Dr. Henry Lynch. Sequencing identified 391 variants, which were functionally annotated and ranked based on their predicted clinical impact. Known pathogenic CHEK2 breast cancer variants were identified in five BRCAX families in this study. While BRCAX was an inclusion criterion for this study, we still identified a pathogenic BRCA2 variant (p.Met192ValfsTer13) in one family. A portion of BRCAX families could be explained by other hereditary cancer syndromes that increase HBOC risk: Li-Fraumeni syndrome (gene: TP53) and Lynch syndrome (gene: MSH6). Interestingly, many families carried additional variants of undetermined significance (VOUSs) that may further modify phenotypes of syndromic family members. Ten families carried more than one potential VOUS, suggesting the presence of complex multi-variant families. Overall, nine BRCAX HBOC families in our study may be explained by known likely pathogenic/pathogenic variants, and six families carried potential VOUSs, which require further functional testing. To address this, we developed a functional assay where we successfully re-classified one family's PMS2 VOUS as benign.
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Affiliation(s)
- Jocelyn N Plowman
- Department of Pharmacology and Neuroscience, Creighton University, Omaha, NE 68178, USA
| | - Evanjalina J Matoy
- Department of Pharmacology and Neuroscience, Creighton University, Omaha, NE 68178, USA
| | - Lavanya V Uppala
- Department of Pharmacology and Neuroscience, Creighton University, Omaha, NE 68178, USA
| | - Samantha B Draves
- Department of Pharmacology and Neuroscience, Creighton University, Omaha, NE 68178, USA
| | - Cynthia J Watson
- Creighton University Core Facilities, Creighton University, Omaha, NE 68178, USA
| | - Bridget A Sefranek
- Creighton University Core Facilities, Creighton University, Omaha, NE 68178, USA
| | - Mark L Stacey
- Creighton University Core Facilities, Creighton University, Omaha, NE 68178, USA
| | - Samuel P Anderson
- Creighton University Core Facilities, Creighton University, Omaha, NE 68178, USA
| | - Michael A Belshan
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE 68178, USA
| | - Elizabeth E Blue
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA; Institute for Public Health Genetics, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute, Seattle, WA 98195, USA
| | - Chad D Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yusi Fu
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, USA
| | - Holly A F Stessman
- Department of Pharmacology and Neuroscience, Creighton University, Omaha, NE 68178, USA; Creighton University Core Facilities, Creighton University, Omaha, NE 68178, USA.
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2
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Pires C, Marques IJ, Valério M, Saramago A, Santo PE, Santos S, Silva M, Moura MM, Matos J, Pereira T, Cabrera R, Lousa D, Leite V, Bandeiras TM, Vicente JB, Cavaco BM. CHEK2 germline variants identified in familial nonmedullary thyroid cancer lead to impaired protein structure and function. J Biol Chem 2024; 300:105767. [PMID: 38367672 PMCID: PMC10956065 DOI: 10.1016/j.jbc.2024.105767] [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: 07/13/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/19/2024] Open
Abstract
Approximately 5 to 15% of nonmedullary thyroid cancers (NMTC) present in a familial form (familial nonmedullary thyroid cancers [FNMTC]). The genetic basis of FNMTC remains largely unknown, representing a limitation for diagnostic and clinical management. Recently, germline mutations in DNA repair-related genes have been described in cases with thyroid cancer (TC), suggesting a role in FNMTC etiology. Here, two FNMTC families were studied, each with two members affected with TC. Ninety-four hereditary cancer predisposition genes were analyzed through next-generation sequencing, revealing two germline CHEK2 missense variants (c.962A > C, p.E321A and c.470T > C, p.I157T), which segregated with TC in each FNMTC family. p.E321A, located in the CHK2 protein kinase domain, is a rare variant, previously unreported in the literature. Conversely, p.I157T, located in CHK2 forkhead-associated domain, has been extensively described, having conflicting interpretations of pathogenicity. CHK2 proteins (WT and variants) were characterized using biophysical methods, molecular dynamics simulations, and immunohistochemistry. Overall, biophysical characterization of these CHK2 variants showed that they have compromised structural and conformational stability and impaired kinase activity, compared to the WT protein. CHK2 appears to aggregate into amyloid-like fibrils in vitro, which opens future perspectives toward positioning CHK2 in cancer pathophysiology. CHK2 variants exhibited higher propensity for this conformational change, also displaying higher expression in thyroid tumors. The present findings support the utility of complementary biophysical and in silico approaches toward understanding the impact of genetic variants in protein structure and function, improving the current knowledge on CHEK2 variants' role in FNMTC genetic basis, with prospective clinical translation.
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Affiliation(s)
- Carolina Pires
- Unidade de Investigação em Patobiologia Molecular, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal; NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Inês J Marques
- Unidade de Investigação em Patobiologia Molecular, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal; NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Mariana Valério
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ana Saramago
- Unidade de Investigação em Patobiologia Molecular, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
| | - Paulo E Santo
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Sandra Santos
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Margarida Silva
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Margarida M Moura
- Unidade de Investigação em Patobiologia Molecular, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
| | - João Matos
- Serviço de Anatomia Patológica, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
| | - Teresa Pereira
- Serviço de Anatomia Patológica, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
| | - Rafael Cabrera
- Serviço de Anatomia Patológica, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
| | - Diana Lousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Valeriano Leite
- Unidade de Investigação em Patobiologia Molecular, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal; Serviço de Endocrinologia, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
| | | | - João B Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Branca M Cavaco
- Unidade de Investigação em Patobiologia Molecular, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal.
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3
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Infante M, Arranz-Ledo M, Lastra E, Olaverri A, Ferreira R, Orozco M, Hernández L, Martínez N, Durán M. Profiling of the genetic features of patients with breast, ovarian, colorectal and extracolonic cancers: Association to CHEK2 and PALB2 germline mutations. Clin Chim Acta 2024; 552:117695. [PMID: 38061684 DOI: 10.1016/j.cca.2023.117695] [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: 09/13/2023] [Revised: 12/04/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND AND AIMS Cancer predisposition goes beyond BRCA and DNA Mismatch Repair (MMR) genes since multi-gene panel testing has become the routine diagnostic tool for hereditary cancer suspicion (HCS) cases. CHEK2 and PALB2 are some of the foremost-mutated non-BRCA/MMR actionable genes in families with a significant familial aggregation. Therefore, the purpose of this work is to unravel which tumours other than breast, ovary or colorectal display the patients. MATERIALS AND METHODS We have analysed 528 probands that meet the inclusion criteria for Hereditary Breast and Ovarian Cancer and Lynch Syndrome established by our Hereditary Cancer Regional Program with a customized 35 genes-panel by using Ion Torrent™ Technology. RESULTS We have identified pathogenic variants (PVs) in 61 families (1.55%), of which more than half (31 probands) harboured PVs in CHEK2 and PALB2 genes. Ours results reveal that not only were PVs CHEK2 and PALB2 carriers more likely to have family history of cancer not limited to breast, ovarian or colorectal cancers, but also they are prone to other extracolonic cancers, noteworthy endometrial and gastric cancers. CONCLUSIONS Multigene panel testing improves the chance of finding PVs in actionable genes in families with HCS. In addition, the coexistence of variants should be recorded to implement a polygenic risk algorithm that might explain the missing heritability in the aforementioned families.
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Affiliation(s)
- Mar Infante
- Cancer Genetics Group, Unit of Excellence Institute of Biomedicine and Molecular Genetics , University of Valladolid-Spanish National Research Council (IBGM, UVa-CSIC), C/ Sanz y Forés 3, 47003 Valladolid, Spain.
| | - Mónica Arranz-Ledo
- Cancer Genetics Group, Unit of Excellence Institute of Biomedicine and Molecular Genetics , University of Valladolid-Spanish National Research Council (IBGM, UVa-CSIC), C/ Sanz y Forés 3, 47003 Valladolid, Spain
| | - Enrique Lastra
- Unit of Genetic Counseling in Cancer, Burgos University Hospital, Burgos, Spain
| | - Amaya Olaverri
- Unit of Genetic Counseling in Cancer, Rio Hortega University Hospital, Valladolid, Spain
| | - Raquel Ferreira
- Unit of Genetic Counseling in Cancer, Rio Hortega University Hospital, Valladolid, Spain
| | - Marta Orozco
- Unit of Genetic Counseling in Cancer, Rio Hortega University Hospital, Valladolid, Spain
| | - Lara Hernández
- Cancer Genetics Group, Unit of Excellence Institute of Biomedicine and Molecular Genetics , University of Valladolid-Spanish National Research Council (IBGM, UVa-CSIC), C/ Sanz y Forés 3, 47003 Valladolid, Spain
| | - Noemí Martínez
- Cancer Genetics Group, Unit of Excellence Institute of Biomedicine and Molecular Genetics , University of Valladolid-Spanish National Research Council (IBGM, UVa-CSIC), C/ Sanz y Forés 3, 47003 Valladolid, Spain
| | - Mercedes Durán
- Cancer Genetics Group, Unit of Excellence Institute of Biomedicine and Molecular Genetics , University of Valladolid-Spanish National Research Council (IBGM, UVa-CSIC), C/ Sanz y Forés 3, 47003 Valladolid, Spain
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4
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Alonso‐Luna O, Mercado‐Celis GE, Melendez‐Zajgla J, Barquera R, Zapata‐Tarres M, Juárez‐Villegas LE, Mendoza‐Caamal EC, Rey‐Helo E, Borges‐Yañez SA. Germline mutations in pediatric cancer cohort with mixed-ancestry Mexicans. Mol Genet Genomic Med 2024; 12:e2332. [PMID: 38093606 PMCID: PMC10767611 DOI: 10.1002/mgg3.2332] [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: 05/23/2023] [Revised: 08/11/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Childhood cancer is one of the primary causes of disease-related death in 5- to 14-year-old children and currently no prevention strategies exist to reduce the incidence of this disease. Childhood cancer has a larger hereditary component compared with cancer in adults. Few genetic studies have been conducted on children with cancer. Additionally, Latin American populations are underrepresented in genomic studies compared with other populations. Therefore, the aim of this study is to analyze germline mutations in a group of mixed-ancestry Mexican pediatric patients with solid and hematological cancers. METHODS We analyzed genetic variants from 40 Mexican childhood cancer patients and their relatives. DNA from saliva or blood samples was used for whole-exome sequencing. All variants were identified following GATK best practices. RESULTS We found that six patients (15%) were carriers of germline mutations in CDKN2A, CHEK2, DICER1, FANCA, MSH6, MUTYH, NF1, and SBDS cancer predisposition genes, and additional new variants predicted to be deleterious by in silico algorithms. A population genetics analysis detected five components consistent with the demographic models assumed for modern mixed-ancestry Mexicans. CONCLUSIONS This report identifies potential genetic risk factors and provides a better understanding of the underlying mechanisms of childhood cancer in this population.
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Grants
- 365882 Consejo Nacional de Ciencia y Tecnología, CONACyT, Mexico
- 253316 Consejo Nacional de Ciencia y Tecnología, CONACyT, Mexico
- Fundacion Carlos Slim as part of the inaugural phase of Slim Initiative in Genomic Medicine for the Americas, SIGMA
- Broad Institute of MIT and Harvard
- Instituto Nacional de Medicina Genomica (INMEGEN)
- Division de Estudios de Posgrado e Investigacion de la Facultad de Odontologia
- Programa de Maestria y Doctorado en Ciencias Medicas, Odontologicas y de la Salud, UNAM
- "Aqui nadie se rinde, ANSER (I.A.P)
- Max Planck Institute for Evolutionary Anthropology (MPI-EVA)
- Consejo Nacional de Ciencia y Tecnología, CONACyT, Mexico
- Max Planck Institute for Evolutionary Anthropology (MPI‐EVA)
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Affiliation(s)
- Oscar Alonso‐Luna
- Programa de Maestria y Doctorado en Ciencias Medicas, Odontologicas y de la SaludCiudad Universitaria, Universidad Nacional Autonoma de MexicoMexico CityMexico
| | | | - Jorge Melendez‐Zajgla
- Laboratorio de Genomica Funcional del CancerInstituto Nacional de Medicina GenomicaMexico CityMexico
| | - Rodrigo Barquera
- Department of ArchaeogeneticsMax Plank Institute for Evolutionary Anthropology (MPI‐EVA)LeipzigGermany
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5
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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: 4] [Impact Index Per Article: 4.0] [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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6
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Stolarova L, Kleiblova P, Zemankova P, Stastna B, Janatova M, Soukupova J, Achatz MI, Ambrosone C, Apostolou P, Arun BK, Auer P, Barnard M, Bertelsen B, Blok MJ, Boddicker N, Brunet J, Burnside ES, Calvello M, Campbell I, Chan SH, Chen F, Chiang JB, Coppa A, Cortesi L, Crujeiras-González A, De Leeneer K, De Putter R, DePersia A, Devereux L, Domchek S, Efremidis A, Engel C, Ernst C, Evans DGR, Feliubadaló L, Fostira F, Fuentes-Ríos O, Gómez-García EB, González S, Haiman C, Hansen TVO, Hauke J, Hodge J, Hu C, Huang H, Ishak NDB, Iwasaki Y, Konstantopoulou I, Kraft P, Lacey J, Lázaro C, Li N, Lim WK, Lindstrom S, Lori A, Martinez E, Martins A, Matsuda K, Matullo G, McInerny S, Michailidou K, Montagna M, Monteiro AN, Mori L, Nathanson K, Neuhausen SL, Nevanlinna H, Olson JE, Palmer J, Pasini B, Patel A, Piane M, Poppe B, Radice P, Renieri A, Resta N, Richardson ME, Rosseel T, Ruddy KJ, Santamariña M, Dos Santos ES, Teras L, Toland AE, Trentham-Dietz A, Vachon CM, Volk AE, Weber-Lassalle N, Weitzel JN, Wiesmuller L, Winham S, Yadav S, Yannoukakos D, Yao S, Zampiga V, Zethoven M, Zhang ZW, Zima T, Spurdle AB, Vega A, Rossing M, Del Valle J, De Nicolo A, Hahnen E, Claes KB, Ngeow J, Momozawa Y, James PA, Couch FJ, Macurek L, Kleibl Z. ENIGMA CHEK2gether Project: A Comprehensive Study Identifies Functionally Impaired CHEK2 Germline Missense Variants Associated with Increased Breast Cancer Risk. Clin Cancer Res 2023; 29:3037-3050. [PMID: 37449874 PMCID: PMC10425727 DOI: 10.1158/1078-0432.ccr-23-0212] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/06/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
PURPOSE Germline pathogenic variants in CHEK2 confer moderately elevated breast cancer risk (odds ratio, OR ∼ 2.5), qualifying carriers for enhanced breast cancer screening. Besides pathogenic variants, dozens of missense CHEK2 variants of uncertain significance (VUS) have been identified, hampering the clinical utility of germline genetic testing (GGT). EXPERIMENTAL DESIGN We collected 460 CHEK2 missense VUS identified by the ENIGMA consortium in 15 countries. Their functional characterization was performed using CHEK2-complementation assays quantifying KAP1 phosphorylation and CHK2 autophosphorylation in human RPE1-CHEK2-knockout cells. Concordant results in both functional assays were used to categorize CHEK2 VUS from 12 ENIGMA case-control datasets, including 73,048 female patients with breast cancer and 88,658 ethnicity-matched controls. RESULTS A total of 430/460 VUS were successfully analyzed, of which 340 (79.1%) were concordant in both functional assays and categorized as functionally impaired (N = 102), functionally intermediate (N = 12), or functionally wild-type (WT)-like (N = 226). We then examined their association with breast cancer risk in the case-control analysis. The OR and 95% CI (confidence intervals) for carriers of functionally impaired, intermediate, and WT-like variants were 2.83 (95% CI, 2.35-3.41), 1.57 (95% CI, 1.41-1.75), and 1.19 (95% CI, 1.08-1.31), respectively. The meta-analysis of population-specific datasets showed similar results. CONCLUSIONS We determined the functional consequences for the majority of CHEK2 missense VUS found in patients with breast cancer (3,660/4,436; 82.5%). Carriers of functionally impaired missense variants accounted for 0.5% of patients with breast cancer and were associated with a moderate risk similar to that of truncating CHEK2 variants. In contrast, 2.2% of all patients with breast cancer carried functionally wild-type/intermediate missense variants with no clinically relevant breast cancer risk in heterozygous carriers.
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Affiliation(s)
- Lenka Stolarova
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petra Kleiblova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Petra Zemankova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Pathophysiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Barbora Stastna
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Marketa Janatova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Jana Soukupova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Maria Isabel Achatz
- A.C. Camargo Cancer Center and Oncology Center, Hospital Sirio-Libanes, Sao Paulo, Brazil
| | - Christine Ambrosone
- Department of Cancer Prevention & Control, Roswell Park Cancer Center, Buffalo, New York
- WCHS Inc., Baltimore, Maryland
| | - Paraskevi Apostolou
- Human Molecular Genetics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos," Athens, Greece
| | - Banu K. Arun
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paul Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin
- WHI, USA
| | - Mollie Barnard
- Slone Epidemiology Center, Boston University, Boston, Massachusetts
| | - Birgitte Bertelsen
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marinus J. Blok
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Nicholas Boddicker
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
- CARRIERS, USA
| | - Joan Brunet
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Elizabeth S. Burnside
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin
- WWHS, Charlotte, North Carolina
| | - Mariarosaria Calvello
- Division of Cancer Prevention and Genetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Ian Campbell
- Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Sock Hoai Chan
- Cancer Genetics Service, National Cancer Centre, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Fei Chen
- Keck School of Medicine, University of Southern California, Los Angeles, California
- MEC, USA
| | - Jian Bang Chiang
- Cancer Genetics Service, National Cancer Centre, Singapore, Singapore
| | - Anna Coppa
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Laura Cortesi
- Department of Oncology and Haematology, Modena University Hospital, Modena, Italy
| | - Ana Crujeiras-González
- Fundacion Publica Galega de Medicina Xenomica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Robin De Putter
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Allison DePersia
- Center for Medical Genetics, NorthShore University Health System, Evanston, Illinois
| | - Lisa Devereux
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
- Lifepool, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Susan Domchek
- CARRIERS, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anna Efremidis
- Clinical Cancer Genetics and Family Consultants, CLINICAGENE, Athens Medical Center, Athens, Greece
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Corinna Ernst
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - D. Gareth R. Evans
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - Lidia Feliubadaló
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos," Athens, Greece
| | - Olivia Fuentes-Ríos
- Fundacion Publica Galega de Medicina Xenomica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Encarna B. Gómez-García
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Sara González
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Christopher Haiman
- Keck School of Medicine, University of Southern California, Los Angeles, California
- MEC, USA
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
| | - Jan Hauke
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - James Hodge
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
- CPS3, Kennesaw, Georgia
| | - Chunling Hu
- CARRIERS, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Hongyan Huang
- T.H. Chan School of Public Health, Harvard University, Cambridge, Massachusetts
- NHS, Reston, Virginia
| | | | - Yusuke Iwasaki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos," Athens, Greece
| | - Peter Kraft
- T.H. Chan School of Public Health, Harvard University, Cambridge, Massachusetts
- NHS, Reston, Virginia
| | - James Lacey
- Beckman Research Institute, City of Hope Cancer Center, Duarte, California
- CTS, USA
| | - Conxi Lázaro
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Na Li
- Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Sara Lindstrom
- WHI, USA
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Adriana Lori
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
- American Cancer Society, Atlanta, Georgia
| | - Elana Martinez
- Duke-NUS Medical School, Singapore, Singapore
- Department of Family Medicine and Public Health, University of California San Diego, San Diego, California
| | - Alexandra Martins
- Inserm UMR1245, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, Normandie University, Rouen, France
| | - Koichi Matsuda
- Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Simone McInerny
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, and Royal Melbourne Hospital, Melbourne, Australia
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, Padua, Italy
| | - Alvaro N.A. Monteiro
- Cancer Epidemiology Program, Division of Population Sciences, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Luigi Mori
- Endocrine and Metabolic Disease Unit, ASST Spedali Civili of Brescia, Brescia, Italia
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Katherine Nathanson
- CARRIERS, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Janet E. Olson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
- MCBCS, USA
| | - Julie Palmer
- Slone Epidemiology Center, Boston University, Boston, Massachusetts
| | - Barbara Pasini
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Alpa Patel
- Department of Population Science, American Cancer Society, Atlanta, Georgia
- CPS-II, USA
| | - Maria Piane
- Department of Clinical and Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Paolo Radice
- Department of Experimental Oncology, Molecular Bases of Genetic Risk and Genetic Testing Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Nicoletta Resta
- Department of Precision and Regenerative Medicine and Ionian Area, Medical Genetics Unit, University of Bari, Bari, Italy
| | | | - Toon Rosseel
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Kathryn J. Ruddy
- MCBCS, USA
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Marta Santamariña
- Fundacion Publica Galega de Medicina Xenomica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | | | - Lauren Teras
- Department of Population Science, American Cancer Society, Atlanta, Georgia
- CPS-II, USA
| | - Amanda E. Toland
- Department of Cancer Biology & Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Amy Trentham-Dietz
- WWHS, Charlotte, North Carolina
- University of Wisconsin, Madison, Wisconsin
| | | | - Alexander E. Volk
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nana Weber-Lassalle
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | | | - Lisa Wiesmuller
- Department of Obstetrics and Gynecology, Ulm University, Ulm, Germany
| | - Stacey Winham
- MMHS, USA
- Department Quantitative Sciences, Mayo Clinic, Rochester, Minnesota
| | - Siddhartha Yadav
- CARRIERS, USA
- Department of Medical Oncology, Mayo Clinic, Rochester, Minnesota
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos," Athens, Greece
| | - Song Yao
- WCHS Inc., Baltimore, Maryland
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Valentina Zampiga
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori," Meldola, Italy
| | - Magnus Zethoven
- Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Ze Wen Zhang
- Cancer Genetics Service, National Cancer Centre, Singapore, Singapore
| | - Tomas Zima
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Amanda B. Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Ana Vega
- Fundacion Publica Galega de Medicina Xenomica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Maria Rossing
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jesús Del Valle
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Arcangela De Nicolo
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Kathleen B.M. Claes
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Joanne Ngeow
- Cancer Genetics Service, National Cancer Centre, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Paul A. James
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
- Inserm UMR1245, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, Normandie University, Rouen, France
| | - Fergus J. Couch
- CARRIERS, USA
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Zdenek Kleibl
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Pathophysiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
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7
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Kumpula TA, Koivuluoma S, Soikkonen L, Vorimo S, Moilanen J, Winqvist R, Mantere T, Kuismin O, Pylkäs K. Evaluating the role of CHEK2 p.(Asp438Tyr) allele in inherited breast cancer predisposition. Fam Cancer 2023; 22:291-294. [PMID: 36653541 PMCID: PMC10276058 DOI: 10.1007/s10689-023-00327-2] [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: 11/22/2022] [Accepted: 01/15/2023] [Indexed: 01/20/2023]
Abstract
CHEK2 is a well-established breast cancer susceptibility gene. The most frequent pathogenic CHEK2 variant is 1100delC, a loss-of-function mutation conferring 2-fold risk for breast cancer. This gene also harbors other rare variants encountered in the clinical gene panels for hereditary cancer. One of these is CHEK2 c.1312 G > T, p.(Asp438Tyr) in the kinase domain of the protein, but due to its rarity its clinical significance for breast cancer predisposition has remained unclear. Here, we tested the prevalence of CHEK2 p.(Asp438Tyr) allele showing enrichment in the Northern Finnish population, in a total of 2284 breast cancer patients from this geographical region. Genotyping was performed for DNA samples extracted from peripheral blood using high-resolution melt analysis. Fourteen CHEK2 p.(Asp438Tyr) carriers were identified (14/2284, 0.6%, P = 0.67): two in the cohort of breast cancer cases with the indication of inherited disease susceptibility (2/281, 0.7%, P = 1.00) and twelve in the breast cancer cohort unselected for the family history of disease and age at disease onset (12/2003, 0.6%, P = 0.66). This frequency did not differ from the frequency in the general population (10/1299, 0.8%). No CHEK2 p.(Asp438Tyr) homozygotes were identified. Our results indicate that CHEK2 p.(Asp438Tyr) carriers do not have an increased risk for breast cancer and the classification of the CHEK2 p.(Asp438Tyr) variant can be changed from the variant of uncertain significance (VUS) to likely benign for breast cancer.
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Affiliation(s)
- Timo A Kumpula
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, Oulu and NordLab Oulu, FI-90014 University of Oulu, Oulu, P.O. Box 5000, Finland
| | - Susanna Koivuluoma
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, Oulu and NordLab Oulu, FI-90014 University of Oulu, Oulu, P.O. Box 5000, Finland
| | - Leila Soikkonen
- Department of Clinical Genetics, Medical Research Center Oulu and PEDEGO Research Unit, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Sandra Vorimo
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, Oulu and NordLab Oulu, FI-90014 University of Oulu, Oulu, P.O. Box 5000, Finland
| | - Jukka Moilanen
- Department of Clinical Genetics, Medical Research Center Oulu and PEDEGO Research Unit, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, Oulu and NordLab Oulu, FI-90014 University of Oulu, Oulu, P.O. Box 5000, Finland
| | - Tuomo Mantere
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, Oulu and NordLab Oulu, FI-90014 University of Oulu, Oulu, P.O. Box 5000, Finland
| | - Outi Kuismin
- Department of Clinical Genetics, Medical Research Center Oulu and PEDEGO Research Unit, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, Oulu and NordLab Oulu, FI-90014 University of Oulu, Oulu, P.O. Box 5000, Finland.
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8
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Fife JD, Cassa CA. Estimating clinical risk in gene regions from population sequencing cohort data. Am J Hum Genet 2023; 110:940-949. [PMID: 37236177 PMCID: PMC10257006 DOI: 10.1016/j.ajhg.2023.05.003] [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: 01/10/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
While pathogenic variants can significantly increase disease risk, it is still challenging to estimate the clinical impact of rare missense variants more generally. Even in genes such as BRCA2 or PALB2, large cohort studies find no significant association between breast cancer and rare missense variants collectively. Here, we introduce REGatta, a method to estimate clinical risk from variants in smaller segments of individual genes. We first define these regions by using the density of pathogenic diagnostic reports and then calculate the relative risk in each region by using over 200,000 exome sequences in the UK Biobank. We apply this method in 13 genes with established roles across several monogenic disorders. In genes with no significant difference at the gene level, this approach significantly separates disease risk for individuals with rare missense variants at higher or lower risk (BRCA2 regional model OR = 1.46 [1.12, 1.79], p = 0.0036 vs. BRCA2 gene model OR = 0.96 [0.85, 1.07] p = 0.4171). We find high concordance between these regional risk estimates and high-throughput functional assays of variant impact. We compare our method with existing methods and the use of protein domains (Pfam) as regions and find REGatta better identifies individuals at elevated or reduced risk. These regions provide useful priors and are potentially useful for improving risk assessment for genes associated with monogenic diseases.
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Affiliation(s)
- James D Fife
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christopher A Cassa
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
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Bottillo I, Savino E, Majore S, Mulargia C, Valiante M, Ferraris A, Rossi V, Svegliati F, Ciccone MP, Brusco F, Grammatico B, Di Giacomo G, Bargiacchi S, D'Angelantonio D, Grammatico P. Two unrelated cases with biallelic CHEK2 variants:a novel condition with constitutional chromosomal instability? Eur J Hum Genet 2023; 31:474-478. [PMID: 36529819 PMCID: PMC10133322 DOI: 10.1038/s41431-022-01270-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 12/03/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
Constitutional heterozygous mutations in CHEK2 gene have been associated with hereditary cancer risk. To date, only a few homozygous CHEK2 mutations have been reported in families with cancer susceptibility. Here, we report two unrelated individuals with a personal and familial cancer history in whom biallelic CHEK2 alterations were identified. The first case resulted homozygous for the CHEK2 c.793-1 G > A (p.Asp265Thrfs*10) variant, and the second one was found to be compound heterozygous for the c.1100delC (p.Thr367Metfs*15) and the c.1312 G > T (p.Asp438Tyr) variants. Multiple cytogenetic anomalies were demonstrated on peripheral lymphocytes of both patients. A literature revision showed that a single other CHEK2 homozygous variant was previously associated to a constitutional randomly occurring multi-translocation karyotype from peripheral blood in humans. We hypothesize that, at least some biallelic CHEK2 mutations might be associated with a novel disorder, further expanding the group of chromosome instability syndromes. Additional studies on larger cohorts are needed to confirm if chromosomal instability could represent a marker for CHEK2 constitutionally mutated recessive genotypes, and to investigate the cancer risk and the occurrence of other anomalies typically observed in chromosome instability syndromes.
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Affiliation(s)
- Irene Bottillo
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy.
| | - Emanuele Savino
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Silvia Majore
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Claudia Mulargia
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Michele Valiante
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Alessandro Ferraris
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Valentina Rossi
- Breast Oncology Unit, San Camillo-Forlanini Hospital, Rome, Italy
| | | | - Maria Pia Ciccone
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Francesca Brusco
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Barbara Grammatico
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Gianluca Di Giacomo
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Simone Bargiacchi
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Daniela D'Angelantonio
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Paola Grammatico
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
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10
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CHEK2 Alterations in Pediatric Malignancy: A Single-Institution Experience. Cancers (Basel) 2023; 15:cancers15061649. [PMID: 36980535 PMCID: PMC10046043 DOI: 10.3390/cancers15061649] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Background: Approximately 10% of pediatric malignancies are secondary to germline alterations in cancer-predisposing genes. Checkpoint kinase 2 (CHEK2) germline loss-of-function variants have been reported in pediatric cancer patients, but clinical phenotypes and outcomes are poorly described. We present our single-institution experience of pediatric oncology patients with CHEK2 germline alterations, including clinical presentations and outcomes. Methods: Pediatric oncology patients with CHEK2 germline alterations were identified among those assessed by clinical or translational research at the Institute for Genomic Medicine at Nationwide Children’s Hospital. A chart review of disease course was conducted on identified patients. Results: We identified 6 patients with germline CHEK2 variants from a cohort of 300 individuals, including 1 patient with concurrent presentation of Burkitt lymphoma and neuroblastoma, 3 patients with brain tumors, 1 patient with Ewing sarcoma, and 1 patient with myelodysplastic syndrome. Three patients had a family history of malignancies. Four patients were in remission; one was undergoing treatment; one patient had developed treatment-related meningiomas. We review prior data regarding CHEK2 variants in this population, challenges associated with variant interpretation, and genetic counseling for individuals with CHEK2 variants. Conclusions: CHEK2 germline loss-of-function alterations occur in patients with a variety of pediatric tumors. Larger multicenter studies will improve our understanding of the incidence, phenotype, and molecular biology of CHEK2 germline variants in pediatric cancers.
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Cine N, Ugurtas C, Gokbayrak M, Aydin D, Demir G, Kuru S, Sunnetci-Akkoyunlu D, Eren-Keskin S, Simsek T, Cabuk D, Aksu MG, Canturk NZ, Savli H. The role of next-generation sequencing in the examination of signaling genes in Brca1/2-negative breast cancer cases. Ann Hum Genet 2023; 87:28-49. [PMID: 36479692 DOI: 10.1111/ahg.12488] [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: 12/28/2021] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Breast cancer is the most prevalent malignancy in women worldwide. Although pathogenic variants in the BRCA1/2 genes are responsible for the majority of hereditary breast cancer cases, a substantial proportion of patients are negative for pathogenic variations in these genes. In cancers, the signal transduction pathways of the cell are usually affected first. Therefore, this study aimed to detect and classified genetic variations in non-BRCA signaling genes and investigate the underlying genetic causes of susceptibility to breast cancer. METHODS Ninety-six patients without pathogenic variants in the BRCA1/2 genes who met the inclusion criteria were enrolled in the study, and 34 genes were analyzed using next-generation sequencing (NGS) for genetic analysis. RESULTS Based on the ClinVar database or American College of Medical Genetics criteria, a total of 55 variants of 16 genes were detected in 43 (44.8%) of the 96 patients included in the study. The pathogenic variants were found in the TP53, CHEK2, and RET genes, whereas the likely pathogenic variants were found in the FGFR1, FGFR3, EGFR, and NOTCH1 genes. CONCLUSION The examination of signaling genes in patients who met the established criteria for hereditary breast cancer but were negative for BRCA1/2 pathogenic variants provided additional information for approximately 8% of the families. The results of the present study suggest that NGS is a powerful tool for investigating the underlying genetic causes of occurrence and progression of breast cancer.
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Affiliation(s)
- Naci Cine
- Department of Medical Genetics, Kocaeli University Faculty of Medicine, Kocaeli, Turkey.,Department of Medical Genetics and Molecular Biology, Kocaeli University Institute of Health Sciences, Kocaeli, Turkey
| | - Cansu Ugurtas
- Department of Medical Genetics, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Merve Gokbayrak
- Department of Medical Genetics, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Duygu Aydin
- Department of Medical Genetics, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Gulhan Demir
- Department of Medical Genetics, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Seda Kuru
- Department of Medical Genetics, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | | | - Seda Eren-Keskin
- Department of Medical Genetics, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Turgay Simsek
- Department of General Surgery, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Devrim Cabuk
- Department of Medical Oncology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Maksut Gorkem Aksu
- Department of Radiation Oncology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Nuh Zafer Canturk
- Department of General Surgery, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Hakan Savli
- Department of Medical Genetics, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
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12
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Nurmi AK, Suvanto M, Dennis J, Aittomäki K, Blomqvist C, Nevanlinna H. Pathogenic Variant Spectrum in Breast Cancer Risk Genes in Finnish Patients. Cancers (Basel) 2022; 14:cancers14246158. [PMID: 36551643 PMCID: PMC9776204 DOI: 10.3390/cancers14246158] [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: 11/08/2022] [Revised: 12/03/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Recurrent pathogenic variants have been detected in several breast and ovarian cancer (BC/OC) risk genes in the Finnish population. We conducted a gene-panel sequencing and copy number variant (CNV) analysis to define a more comprehensive spectrum of pathogenic variants in BRCA1, BRCA2, PALB2, CHEK2, ATM, BARD1, RAD51C, RAD51D, BRIP1, and FANCM genes in Finnish BC patients. The combined frequency of pathogenic variants in the BRCA1/2 genes was 1.8% in 1356 unselected patients, whereas variants in the other genes were detected altogether in 8.3% of 1356 unselected patients and in 12.9% of 699 familial patients. CNVs were detected in 0.3% of both 1137 unselected and 612 familial patients. A few variants covered most of the pathogenic burden in the studied genes. Of the BRCA1/2 carriers, 70.8% had 1 of 10 recurrent variants. In the other genes combined, 92.1% of the carrier patients had at least 1 of 11 recurrent variants. In particular, PALB2 c.1592delT and CHEK2 c.1100delC accounted for 88.9% and 82.9%, respectively, of the pathogenic variation in each gene. Our results highlight the importance of founder variants in the BC risk genes in the Finnish population and could be used in the designing of population screening for the risk variants.
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Affiliation(s)
- Anna K. Nurmi
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland
| | - Maija Suvanto
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Kristiina Aittomäki
- Department of Clinical Genetics, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland
| | - Carl Blomqvist
- Department of Oncology, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland
- Correspondence:
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13
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Paduano F, Colao E, Fabiani F, Rocca V, Dinatolo F, Dattola A, D’Antona L, Amato R, Trapasso F, Baudi F, Perrotti N, Iuliano R. Germline Testing in a Cohort of Patients at High Risk of Hereditary Cancer Predisposition Syndromes: First Two-Year Results from South Italy. Genes (Basel) 2022; 13:genes13071286. [PMID: 35886069 PMCID: PMC9319682 DOI: 10.3390/genes13071286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 12/04/2022] Open
Abstract
Germline pathogenic variants (PVs) in oncogenes and tumour suppressor genes are responsible for 5 to 10% of all diagnosed cancers, which are commonly known as hereditary cancer predisposition syndromes (HCPS). A total of 104 individuals at high risk of HCPS were selected by genetic counselling for genetic testing in the past 2 years. Most of them were subjects having a personal and family history of breast cancer (BC) selected according to current established criteria. Genes analysis involved in HCPS was assessed by next-generation sequencing (NGS) using a custom cancer panel with high- and moderate-risk susceptibility genes. Germline PVs were identified in 17 of 104 individuals (16.3%) analysed, while variants of uncertain significance (VUS) were identified in 21/104 (20.2%) cases. Concerning the germline PVs distribution among the 13 BC individuals with positive findings, 8/13 (61.5%) were in the BRCA1/2 genes, whereas 5/13 (38.4%) were in other high- or moderate-risk genes including PALB2, TP53, ATM and CHEK2. NGS genetic testing showed that 6/13 (46.1%) of the PVs observed in BC patients were detected in triple-negative BC. Interestingly, the likelihood of carrying the PVs in the moderate-to-high-risk genes calculated by the cancer risk model BOADICEA was significantly higher in pathogenic variant carriers than in negative subjects. Collectively, this study shows that multigene panel testing can offer an effective diagnostic approach for patients at high risk of hereditary cancers.
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Affiliation(s)
- Francesco Paduano
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
- Stem Cells and Medical Genetics Units, Tecnologica Research Institute and Marrelli Health, 88900 Crotone, Italy
- Correspondence: (F.P.); (R.I.)
| | - Emma Colao
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
| | - Fernanda Fabiani
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
| | - Valentina Rocca
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Experimental and Clinical Medicine, Campus S. Venuta, University Magna Graecia of Catanzaro, Viale Europa, Località Germaneto, 88100 Catanzaro, Italy
| | - Francesca Dinatolo
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
| | - Adele Dattola
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
| | - Lucia D’Antona
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Rosario Amato
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Francesco Trapasso
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Experimental and Clinical Medicine, Campus S. Venuta, University Magna Graecia of Catanzaro, Viale Europa, Località Germaneto, 88100 Catanzaro, Italy
| | - Francesco Baudi
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Nicola Perrotti
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Rodolfo Iuliano
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
- Correspondence: (F.P.); (R.I.)
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14
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Boonen RA, Vreeswijk MP, van Attikum H. CHEK2 variants: linking functional impact to cancer risk. Trends Cancer 2022; 8:759-770. [DOI: 10.1016/j.trecan.2022.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/23/2022]
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15
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Na R, Hong J, Gu H, Lee W, Lee JL, Chun S, Min WK. RNA Sequencing Provides Evidence for Pathogenicity of a Novel CHEK2 Splice Variant (C.1009-7T>G). Ann Lab Med 2022; 42:380-383. [PMID: 34907112 PMCID: PMC8677473 DOI: 10.3343/alm.2022.42.3.380] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/22/2021] [Accepted: 11/26/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
- Rae Na
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jinyoung Hong
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyunjung Gu
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Woochang Lee
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jae-Lyun Lee
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sail Chun
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Won-Ki Min
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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16
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Yang F, Long N, Anekpuritanang T, Bottomly D, Savage JC, Lee T, Solis-Ruiz J, Borate U, Wilmot B, Tognon C, Bock AM, Pollyea DA, Radhakrishnan S, Radhakrishnan S, Patel P, Collins RH, Tantravahi S, Deininger MW, Fan G, Druker B, Shinde U, Tyner JW, Press RD, McWeeney S, Agarwal A. Identification and prioritization of myeloid malignancy germline variants in a large cohort of adult patients with AML. Blood 2022; 139:1208-1221. [PMID: 34482403 PMCID: PMC9211447 DOI: 10.1182/blood.2021011354] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/12/2021] [Indexed: 11/20/2022] Open
Abstract
Inherited predisposition to myeloid malignancies is more common than previously appreciated. We analyzed the whole-exome sequencing data of paired leukemia and skin biopsy samples from 391 adult patients from the Beat AML 1.0 consortium. Using the 2015 American College of Medical Genetics and Genomics (ACMG) guidelines for variant interpretation, we curated 1547 unique variants from 228 genes. The pathogenic/likely pathogenic (P/LP) germline variants were identified in 53 acute myeloid leukemia (AML) patients (13.6%) in 34 genes, including 6.39% (25/391) of patients harboring P/LP variants in genes considered clinically actionable (tier 1). 41.5% of the 53 patients with P/LP variants were in genes associated with the DNA damage response. The most frequently mutated genes were CHEK2 (8 patients) and DDX41 (7 patients). Pathogenic germline variants were also found in new candidate genes (DNAH5, DNAH9, DNMT3A, and SUZ12). No strong correlation was found between the germline mutational rate and age of AML onset. Among 49 patients who have a reported history of at least one family member affected with hematological malignancies, 6 patients harbored known P/LP germline variants and the remaining patients had at least one variant of uncertain significance, suggesting a need for further functional validation studies. Using CHEK2 as an example, we show that three-dimensional protein modeling can be one of the effective methodologies to prioritize variants of unknown significance for functional studies. Further, we evaluated an in silico approach that applies ACMG curation in an automated manner using the tool for assessment and (TAPES) prioritization in exome studies, which can minimize manual curation time for variants. Overall, our findings suggest a need to comprehensively understand the predisposition potential of many germline variants in order to enable closer monitoring for disease management and treatment interventions for affected patients and families.
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Affiliation(s)
- Fei Yang
- Department of Pathology and Laboratory Medicine and
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Nicola Long
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Tauangtham Anekpuritanang
- Department of Pathology and Laboratory Medicine and
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Department of Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok
| | - Daniel Bottomly
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Division of Bioinformatics & Computational Biology and
| | - Jonathan C Savage
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR
| | - Tiffany Lee
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Jose Solis-Ruiz
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Uma Borate
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Beth Wilmot
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Division of Bioinformatics & Computational Biology and
| | - Cristina Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Allison M Bock
- Department of Medicine, University of Colorado, Aurora, CO
| | | | | | | | - Prapti Patel
- University of Texas Southwestern Medical Center, Dallas, TX
| | | | | | | | - Guang Fan
- Department of Pathology and Laboratory Medicine and
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Brian Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Ujwal Shinde
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Department of Cell, Developmental & Cancer Biology
| | - Richard D Press
- Department of Pathology and Laboratory Medicine and
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Shannon McWeeney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Division of Bioinformatics & Computational Biology and
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
- Department of Cell, Developmental & Cancer Biology
- Division of Hematology and Oncology, and
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR
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17
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Boonen RA, Wiegant WW, Celosse N, Vroling B, Heijl S, Kote-Jarai Z, Mijuskovic M, Cristea S, Solleveld-Westerink N, van Wezel T, Beerenwinkel N, Eeles R, Devilee P, Vreeswijk MP, Marra G, van Attikum H. Functional Analysis Identifies Damaging CHEK2 Missense Variants Associated with Increased Cancer Risk. Cancer Res 2022; 82:615-631. [PMID: 34903604 PMCID: PMC9359737 DOI: 10.1158/0008-5472.can-21-1845] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/14/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023]
Abstract
Heterozygous carriers of germline loss-of-function variants in the tumor suppressor gene checkpoint kinase 2 (CHEK2) are at an increased risk for developing breast and other cancers. While truncating variants in CHEK2 are known to be pathogenic, the interpretation of missense variants of uncertain significance (VUS) is challenging. Consequently, many VUS remain unclassified both functionally and clinically. Here we describe a mouse embryonic stem (mES) cell-based system to quantitatively determine the functional impact of 50 missense VUS in human CHEK2. By assessing the activity of human CHK2 to phosphorylate one of its main targets, Kap1, in Chek2 knockout mES cells, 31 missense VUS in CHEK2 were found to impair protein function to a similar extent as truncating variants, while 9 CHEK2 missense VUS resulted in intermediate functional defects. Mechanistically, most VUS impaired CHK2 kinase function by causing protein instability or by impairing activation through (auto)phosphorylation. Quantitative results showed that the degree of CHK2 kinase dysfunction correlates with an increased risk for breast cancer. Both damaging CHEK2 variants as a group [OR 2.23; 95% confidence interval (CI), 1.62-3.07; P < 0.0001] and intermediate variants (OR 1.63; 95% CI, 1.21-2.20; P = 0.0014) were associated with an increased breast cancer risk, while functional variants did not show this association (OR 1.13; 95% CI, 0.87-1.46; P = 0.378). Finally, a damaging VUS in CHEK2, c.486A>G/p.D162G, was also identified, which cosegregated with familial prostate cancer. Altogether, these functional assays efficiently and reliably identified VUS in CHEK2 that associate with cancer. SIGNIFICANCE Quantitative assessment of the functional consequences of CHEK2 variants of uncertain significance identifies damaging variants associated with increased cancer risk, which may aid in the clinical management of patients and carriers.
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Affiliation(s)
- Rick A.C.M. Boonen
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Wouter W. Wiegant
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Nandi Celosse
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Bas Vroling
- Bio-Prodict, Nijmegen, the Netherlands
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Center, Nijmegen, the Netherlands
| | | | | | - Martina Mijuskovic
- The Institute of Cancer Research, London, United Kingdom
- Illumina Cambridge Ltd., Cambridge, United Kingdom
| | - Simona Cristea
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Niko Beerenwinkel
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Rosalind Eeles
- The Institute of Cancer Research, London, United Kingdom
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Maaike P.G. Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Giancarlo Marra
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
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18
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Yeast as a Tool to Understand the Significance of Human Disease-Associated Gene Variants. Genes (Basel) 2021; 12:genes12091303. [PMID: 34573285 PMCID: PMC8465565 DOI: 10.3390/genes12091303] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/23/2021] [Accepted: 08/23/2021] [Indexed: 02/05/2023] Open
Abstract
At present, the great challenge in human genetics is to provide significance to the growing amount of human disease-associated gene variants identified by next generation DNA sequencing technologies. Increasing evidences suggest that model organisms are of pivotal importance to addressing this issue. Due to its genetic tractability, the yeast Saccharomyces cerevisiae represents a valuable model organism for understanding human genetic variability. In the present review, we show how S. cerevisiae has been used to study variants of genes involved in different diseases and in different pathways, highlighting the versatility of this model organism.
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19
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Bazinet A, Heath J, Chong AS, Simo-Cheyou ER, Worme S, Rivera Polo B, Foulkes WD, Caplan S, Johnson NA, Orthwein A, Mercier FE. Common clonal origin of chronic myelomonocytic leukemia and B-cell acute lymphoblastic leukemia in a patient with a germline CHEK2 variant. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006090. [PMID: 33986034 PMCID: PMC8208041 DOI: 10.1101/mcs.a006090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/10/2021] [Indexed: 12/17/2022] Open
Abstract
Hematological malignancies are broadly divided into myeloid and lymphoid neoplasms, reflecting the two major cellular lineages of the hematopoietic system. It is generally rare for hematological malignancies to spontaneously progress with a switch from myeloid to lymphoid lineage. We describe the exceptional case of a patient who sequentially developed myelodysplastic syndrome (MDS), chronic myelomonocytic leukemia (CMML), and B-cell acute lymphoblastic leukemia (B-ALL), as well as our investigation into the underlying pathogenesis. Using whole-exome sequencing (WES) performed on sorted CMML and B-ALL cell fractions, we identified both common and unique potential driver mutations, suggesting a branching clonal evolution giving rise to both diseases. Interestingly, we also identified a germline variant in the cancer susceptibility gene CHEK2 We validated that this variant (c.475T > C; p.Y159H), located in the forkhead-associated (FHA) domain, impairs its capacity to bind BRCA1 in cellulo. This unique case provides novel insight into the genetics of complex hematological diseases and highlights the possibility that such patients may carry inherited predispositions.
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Affiliation(s)
- Alexandre Bazinet
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada.,Division of Hematology, Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada.,Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - John Heath
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada.,Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - Anne-Sophie Chong
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada
| | | | - Samantha Worme
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada.,Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - Barbara Rivera Polo
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec H4A 3T2, Canada
| | - William D Foulkes
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec H4A 3T2, Canada
| | - Stephen Caplan
- Division of Hematology, Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - Nathalie A Johnson
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada.,Division of Hematology, Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada.,Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - Alexandre Orthwein
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada.,Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec H4A 3T2, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - François E Mercier
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada.,Division of Hematology, Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada.,Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
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20
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CHEK2 Pathogenic Variants in Greek Breast Cancer Patients: Evidence for Strong Associations with Estrogen Receptor Positivity, Overuse of Risk-Reducing Procedures and Population Founder Effects. Cancers (Basel) 2021; 13:cancers13092106. [PMID: 33925588 PMCID: PMC8123864 DOI: 10.3390/cancers13092106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 01/13/2023] Open
Abstract
Simple Summary CHEK2 germline pathogenic variants are identified at a relatively high frequency among hereditary breast cancer cases and are known to be associated with intermediate breast cancer risk i.e., 2–2.5-fold increase, compared to the general population. Histopathological characteristics and clinical outcomes of breast cancer patients who are CHEK2 carriers have not been thoroughly investigated. We have therefore sought to determine the CHEK2 variant spectrum and identify variants with possible founder effect, while investigating the clinicopathological features and outcomes of Greek patients who were CHEK2 carriers. Three variants have been identified as Greek founders. The vast majority of CHEK2-associated breast tumors were hormone receptor positive, underlying a possible benefit from chemoprophylaxis with tamoxifen. A trend for longer survival was observed in patients that underwent mastectomy and received hormone-therapy. Nearly half of patients underwent a risk-reducing surgery, which was not mandated according to current guidelines or relevant risks associated with CHEK2. Abstract CHEK2 germline pathogenic variants predispose to breast cancer and possibly to other malignancies, with their spectrum and frequency being variable among populations. Τhe majority of CHEK2-associated breast tumors are hormone receptor positive; however, relevant clinical outcomes are not well defined. Herein, we illustrate the histopathological characteristics and clinical outcomes of 52 Greek breast cancer patients who are CHEK2 carriers. Genetic analysis was performed by Sanger/massively parallel sequencing, followed by MLPA. Subsequent haplotype analysis investigated possible founder effects. Blood relatives were offered cascade testing. CHEK2 variant spectrum was characterized by variability, while influenced by founder effects. The majority of carriers, i.e., 60.8%, were diagnosed with breast cancer before the age of 45. Notably, 91.5% of breast tumors were hormone receptor positive. Hormone therapy and mastectomy at diagnosis seem to have a positive trend on overall survival, after a median follow-up of 9.5 years. Remarkably, 41.9% of patients underwent risk-reducing surgery, one third of which involved salpingo-oophorectomy. Nearly half of families responded to cascade testing. Our data highlight the need for guideline-adherent choices, based on the evidence that CHEK2 carriers are at moderate risk for breast cancer and no risk for ovarian cancer, while underscore the possible role of chemoprevention with tamoxifen.
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21
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SEARCH FOR DIAGNOSTIC RELATIONSHIPS IN PATIENTS WITH IRRITABLE BOWEL SYNDROME AND COLORECTAL POLYPS. WORLD OF MEDICINE AND BIOLOGY 2021. [DOI: 10.26724/2079-8334-2021-1-75-74-78] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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22
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Stolarova L, Kleiblova P, Janatova M, Soukupova J, Zemankova P, Macurek L, Kleibl Z. CHEK2 Germline Variants in Cancer Predisposition: Stalemate Rather than Checkmate. Cells 2020; 9:cells9122675. [PMID: 33322746 PMCID: PMC7763663 DOI: 10.3390/cells9122675] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/04/2020] [Accepted: 12/10/2020] [Indexed: 12/15/2022] Open
Abstract
Germline alterations in many genes coding for proteins regulating DNA repair and DNA damage response (DDR) to DNA double-strand breaks (DDSB) have been recognized as pathogenic factors in hereditary cancer predisposition. The ATM-CHEK2-p53 axis has been documented as a backbone for DDR and hypothesized as a barrier against cancer initiation. However, although CHK2 kinase coded by the CHEK2 gene expedites the DDR signal, its function in activation of p53-dependent cell cycle arrest is dispensable. CHEK2 mutations rank among the most frequent germline alterations revealed by germline genetic testing for various hereditary cancer predispositions, but their interpretation is not trivial. From the perspective of interpretation of germline CHEK2 variants, we review the current knowledge related to the structure of the CHEK2 gene, the function of CHK2 kinase, and the clinical significance of CHEK2 germline mutations in patients with hereditary breast, prostate, kidney, thyroid, and colon cancers.
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Affiliation(s)
- Lenka Stolarova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 12800 Prague, Czech Republic; (L.S.); (M.J.); (J.S.); (P.Z.)
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic;
| | - Petra Kleiblova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic;
| | - Marketa Janatova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 12800 Prague, Czech Republic; (L.S.); (M.J.); (J.S.); (P.Z.)
| | - Jana Soukupova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 12800 Prague, Czech Republic; (L.S.); (M.J.); (J.S.); (P.Z.)
| | - Petra Zemankova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 12800 Prague, Czech Republic; (L.S.); (M.J.); (J.S.); (P.Z.)
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic;
| | - Zdenek Kleibl
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 12800 Prague, Czech Republic; (L.S.); (M.J.); (J.S.); (P.Z.)
- Correspondence: ; Tel.: +420-22496-745
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23
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Prevalence of germline variants in consensus moderate-to-high-risk predisposition genes to hereditary breast and ovarian cancer in BRCA1/2-negative Brazilian patients. Breast Cancer Res Treat 2020; 185:851-861. [PMID: 33128190 DOI: 10.1007/s10549-020-05985-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/15/2020] [Indexed: 12/23/2022]
Abstract
PURPOSE This study aimed to identify and classify genetic variants in consensus moderate-to-high-risk predisposition genes associated with Hereditary Breast and Ovarian Cancer Syndrome (HBOC), in BRCA1/2-negative patients from Brazil. METHODS The study comprised 126 index patients who met NCCN clinical criteria and tested negative for all coding exons and intronic flanking regions of BRCA1/2 genes. Multiplex PCR-based assays were designed to cover the complete coding regions and flanking splicing sites of six genes implicated in HBOC. Sequencing was performed on HiSeq2500 Genome Analyzer. RESULTS Overall, we identified 488 unique variants. We identified five patients (3.97%) that harbored pathogenic or likely pathogenic variants in four genes: ATM (1), CHEK2 (2), PALB2 (1), and TP53 (1). One hundred and thirty variants were classified as variants of uncertain significance (VUS), 10 of which were predicted to disrupt mRNA splicing (seven non-coding variants and three coding variants), while other six missense VUS were classified as probably damaging by prediction algorithms. CONCLUSION A detailed mutational profile of non-BRCA genes is still being described in Brazil. In this study, we contributed to filling this gap, by providing important data on the diversity of genetic variants in a Brazilian high-risk patient cohort. ATM, CHEK2, PALB2 and TP53 are well established as HBOC predisposition genes, and the identification of deleterious variants in such actionable genes contributes to clinical management of probands and relatives.
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24
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Hirsch S, Gieldon L, Sutter C, Dikow N, Schaaf CP. Germline testing for homologous recombination repair genes—opportunities and challenges. Genes Chromosomes Cancer 2020; 60:332-343. [DOI: 10.1002/gcc.22900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022] Open
Affiliation(s)
- Steffen Hirsch
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ) Heidelberg Germany
| | - Laura Gieldon
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Christian Sutter
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Nicola Dikow
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Christian P. Schaaf
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas
- Jan and Dan Duncan Neurological Research Institute Texas Children's Hospital Houston Texas
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25
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SoRelle JA, Gemmell AP, Ross TS. Different Interpretations of the Same Genetic Data. Ann Intern Med 2020; 173:239-240. [PMID: 32598223 DOI: 10.7326/l20-0192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Jeffrey A SoRelle
- University of Texas Southwestern Medical Center, Dallas, Texas (J.A.S.)
| | - Amber P Gemmell
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas (A.P.G., T.S.R.)
| | - Theodora S Ross
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas (A.P.G., T.S.R.)
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26
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Fostira F, Konstantopoulou I. Variant Interpretation in Patients With Metastatic Breast Cancer. JAMA Oncol 2020; 6:581-582. [PMID: 31999302 DOI: 10.1001/jamaoncol.2019.6397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Florentia Fostira
- Molecular Diagnostics Laboratory, Institute of Nuclear & Radiological Sciences and Technology, Energy & Safety, National Centre for Scientific Research "Demokritos", Athens, Greece
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, Institute of Nuclear & Radiological Sciences and Technology, Energy & Safety, National Centre for Scientific Research "Demokritos", Athens, Greece
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27
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Computational analysis of high-risk SNPs in human CHK2 gene responsible for hereditary breast cancer: A functional and structural impact. PLoS One 2019; 14:e0220711. [PMID: 31398194 PMCID: PMC6688789 DOI: 10.1371/journal.pone.0220711] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/22/2019] [Indexed: 12/18/2022] Open
Abstract
Nowadays CHK2 mutation is studied frequently in hereditary breast and ovarian cancer patients in addition to BRCA1/BRCA2. CHK2 is a tumor suppressor gene that encodes a serine/threonine kinase, also involved in pathways such as DNA repair, cell cycle regulation and apoptosis in response to DNA damage. CHK2 is a well-studied moderate penetrance gene that correlates with third high risk susceptibility gene with an increased risk for breast cancer. Hence before planning large population study, it is better to scrutinize putative functional SNPs of CHK2 using different computational tools. In this study, we have used various computational approaches to identify nsSNPs which are deleterious to the structure and/or function of CHK2 protein that might be causing this disease. Computational analysis was performed by different in silico tools including SIFT, Align GVGD, SNAP-2, PROVEAN, Poly-Phen-2, PANTHER, PhD-SNP, MUpro, iPTREE-STAB, Consurf, InterPro, NCBI Conserved Domain Search tool, ModPred, SPARKS-X, RAMPAGE, Verify-3D, FT Site, COACH and PyMol. Out of 78 nsSNP of human CHK2 gene, seven nsSNPs were predicted functionally most significant SNPs. Among these seven nsSNP, p.Arg160Gly, p.Gly210Arg and p.Ser415Phe are highly conserved residues with conservation score of 9 and three nsSNP were predicted to be involved in post translational modification. The p.Arg160Gly and p.Gly210Arg may interfere in phosphopeptide binding site on FHA conserved domain. The p.Ser415Phe may interfere in formation of activation loop of protein-kinase domain and might interfere in interactions of CHK2 with ligand. The study concludes that mutation of serine to phenylalanine at position 415 is a major mutation in native CHK2 protein which might contribute to its malfunction, ultimately causing disease. This is the first comprehensive study, where CHK2 gene variants are analyzed using in silico tools hence it will be of great help while considering large scale studies and also in developing precision medicines related to these polymorphisms in the era of personalized medicine.
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28
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Fostira F, Kostantopoulou I, Apostolou P, Papamentzelopoulou MS, Papadimitriou C, Faliakou E, Christodoulou C, Boukovinas I, Razis E, Tryfonopoulos D, Barbounis V, Vagena A, Vlachos IS, Kalfakakou D, Fountzilas G, Yannoukakos D. One in three highly selected Greek patients with breast cancer carries a loss-of-function variant in a cancer susceptibility gene. J Med Genet 2019; 57:53-61. [PMID: 31300551 PMCID: PMC6929701 DOI: 10.1136/jmedgenet-2019-106189] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/05/2019] [Accepted: 06/13/2019] [Indexed: 02/01/2023]
Abstract
BACKGROUND Gene panel testing has become the norm for assessing breast cancer (BC) susceptibility, but actual cancer risks conferred by genes included in panels are not established. Contrarily, deciphering the missing hereditability on BC, through identification of novel candidates, remains a challenge. We aimed to investigate the mutation prevalence and spectra in a highly selected cohort of Greek patients with BC, questioning an extensive number of genes, implicated in cancer predisposition and DNA repair, while calculating gene-specific BC risks that can ultimately lead to important associations. METHODS To further discern BC susceptibility, a comprehensive 94-cancer gene panel was implemented in a cohort of 1382 Greek patients with BC, highly selected for strong family history and/or very young age (<35 years) at diagnosis, followed by BC risk calculation, based on a case-control analysis. RESULTS Herein, 31.5% of patients tested carried pathogenic variants (PVs) in 28 known, suspected or candidate BC predisposition genes. In total, 24.8% of the patients carried BRCA1/2 loss-of-function variants. An additional 6.7% carried PVs in additional genes, the vast majority of which can be offered meaningful clinical changes. Significant association to BC predisposition was observed for ATM, PALB2, TP53, RAD51C and CHEK2 PVs. Primarily, compared with controls, RAD51C PVs and CHEK2 damaging missense variants were associated with high (ORs 6.19 (Exome Aggregation Consortium (ExAC)) and 12.6 (Fabulous Ladies Over Seventy (FLOSSIES)), p<0.01) and moderate BC risk (ORs 3.79 (ExAC) and 5.9 (FLOSSIES), p<0.01), respectively. CONCLUSION Studying a large and unique cohort of highly selected patients with BC, deriving from a population with founder effects, provides important insight on distinct associations, pivotal for patient management.
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Affiliation(s)
- Florentia Fostira
- InRaSTES, Molecular Diagnostics Laboratory, National Centre for Scientific Research NCSR Demokritos, Athens, Greece
| | - Irene Kostantopoulou
- InRaSTES, Molecular Diagnostics Laboratory, National Centre for Scientific Research NCSR Demokritos, Athens, Greece
| | - Paraskevi Apostolou
- InRaSTES, Molecular Diagnostics Laboratory, National Centre for Scientific Research NCSR Demokritos, Athens, Greece
| | - Myrto S Papamentzelopoulou
- InRaSTES, Molecular Diagnostics Laboratory, National Centre for Scientific Research NCSR Demokritos, Athens, Greece
| | - Christos Papadimitriou
- Second Department of Surgery, Oncology Unit, National and Kapodistrian University of Athens, Aretaiio Hospital, Athens, Greece
| | - Eleni Faliakou
- Breast Cancer Unit, Mitera Maternity Hospital, Athens, Greece
| | | | - Ioannis Boukovinas
- Department of Medical Oncology, Bioclinic of Thessaloniki, Thessaloniki, Greece
| | - Evangelia Razis
- Third Department of Medical Oncology, Hygeia Hospital, Athens, Greece
| | | | - Vasileios Barbounis
- Third Medical Oncology Department, Metropolitan Hospital Athens, Athens, Greece
| | - Andromache Vagena
- InRaSTES, Molecular Diagnostics Laboratory, National Centre for Scientific Research NCSR Demokritos, Athens, Greece
| | - Ioannis S Vlachos
- Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA
| | - Despoina Kalfakakou
- InRaSTES, Molecular Diagnostics Laboratory, National Centre for Scientific Research NCSR Demokritos, Athens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Drakoulis Yannoukakos
- InRaSTES, Molecular Diagnostics Laboratory, National Centre for Scientific Research NCSR Demokritos, Athens, Greece
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Kleiblova P, Stolarova L, Krizova K, Lhota F, Hojny J, Zemankova P, Havranek O, Vocka M, Cerna M, Lhotova K, Borecka M, Janatova M, Soukupova J, Sevcik J, Zimovjanova M, Kotlas J, Panczak A, Vesela K, Cervenkova J, Schneiderova M, Burocziova M, Burdova K, Stranecky V, Foretova L, Machackova E, Tavandzis S, Kmoch S, Macurek L, Kleibl Z. Identification of deleterious germline CHEK2 mutations and their association with breast and ovarian cancer. Int J Cancer 2019; 145:1782-1797. [PMID: 31050813 DOI: 10.1002/ijc.32385] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/24/2019] [Indexed: 12/15/2022]
Abstract
Germline mutations in checkpoint kinase 2 (CHEK2), a multiple cancer-predisposing gene, increase breast cancer (BC) risk; however, risk estimates differ substantially in published studies. We analyzed germline CHEK2 variants in 1,928 high-risk Czech breast/ovarian cancer (BC/OC) patients and 3,360 population-matched controls (PMCs). For a functional classification of VUS, we developed a complementation assay in human nontransformed RPE1-CHEK2-knockout cells quantifying CHK2-specific phosphorylation of endogenous protein KAP1. We identified 10 truncations in 46 (2.39%) patients and in 11 (0.33%) PMC (p = 1.1 × 10-14 ). Two types of large intragenic rearrangements (LGR) were found in 20/46 mutation carriers. Truncations significantly increased unilateral BC risk (OR = 7.94; 95%CI 3.90-17.47; p = 1.1 × 10-14 ) and were more frequent in patients with bilateral BC (4/149; 2.68%; p = 0.003), double primary BC/OC (3/79; 3.80%; p = 0.004), male BC (3/48; 6.25%; p = 8.6 × 10-4 ), but not with OC (3/354; 0.85%; p = 0.14). Additionally, we found 26 missense VUS in 88 (4.56%) patients and 131 (3.90%) PMC (p = 0.22). Using our functional assay, 11 variants identified in 15 (0.78%) patients and 6 (0.18%) PMC were scored deleterious (p = 0.002). Frequencies of functionally intermediate and neutral variants did not differ between patients and PMC. Functionally deleterious CHEK2 missense variants significantly increased BC risk (OR = 3.90; 95%CI 1.24-13.35; p = 0.009) and marginally OC risk (OR = 4.77; 95%CI 0.77-22.47; p = 0.047); however, carriers low frequency will require evaluation in larger studies. Our study highlights importance of LGR detection for CHEK2 analysis, careful consideration of ethnicity in both cases and controls for risk estimates, and demonstrates promising potential of newly developed human nontransformed cell line assay for functional CHEK2 VUS classification.
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Affiliation(s)
- Petra Kleiblova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Lenka Stolarova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Katerina Krizova
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the ASCR, Prague, Czech Republic
| | - Filip Lhota
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan Hojny
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Petra Zemankova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ondrej Havranek
- BIOCEV, First Faculty of Medicine, Charles University, Prague, Czech Republic.,Department of Hematology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Michal Vocka
- Department of Oncology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Marta Cerna
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Klara Lhotova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marianna Borecka
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marketa Janatova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jana Soukupova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan Sevcik
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martina Zimovjanova
- Department of Oncology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Jaroslav Kotlas
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Ales Panczak
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Kamila Vesela
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Jana Cervenkova
- Department of Radiology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Michaela Schneiderova
- First Department of Surgery, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Monika Burocziova
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the ASCR, Prague, Czech Republic
| | - Kamila Burdova
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the ASCR, Prague, Czech Republic
| | - Viktor Stranecky
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Eva Machackova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Spiros Tavandzis
- Department of Medical Genetics, AGEL Laboratories, AGEL Research and Training Institute, Novy Jicin, Czech Republic
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the ASCR, Prague, Czech Republic
| | - Zdenek Kleibl
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
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