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Mukhtar TK, Wilcox N, Dennis J, Yang X, Naven M, Mavaddat N, Perry JRB, Gardner E, Easton DF. Protein-truncating and rare missense variants in ATM and CHEK2 and associations with cancer in UK Biobank whole-exome sequence data. J Med Genet 2024:jmg-2024-110127. [PMID: 39209703 DOI: 10.1136/jmg-2024-110127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 08/18/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Deleterious germline variants in ATM and CHEK2 have been associated with a moderately increased risk of breast cancer. Risks for other cancers remain unclear. METHODS Cancer associations for coding variants in ATM and CHEK2 were evaluated using whole-exome sequence data from UK Biobank linked to cancer registration data (348 488 participants), and analysed both as a retrospective case-control and a prospective cohort study. Odds ratios, hazard ratios, and combined relative risks (RRs) were estimated by cancer type and gene. Separate analyses were performed for protein-truncating variants (PTVs) and rare missense variants (rMSVs; allele frequency <0.1%). RESULTS PTVs in ATM were associated with increased risks of nine cancers at p<0.001 (pancreas, oesophagus, lung, melanoma, breast, ovary, prostate, bladder, lymphoid leukaemia (LL)), and three at p<0.05 (colon, diffuse non-Hodgkin's lymphoma (DNHL), rectosigmoid junction). Carriers of rMSVs had increased risks of four cancers (p<0.05: stomach, pancreas, prostate, Hodgkin's disease (HD)). RRs were highest for breast, prostate, and any cancer where rMSVs lay in the FAT or PIK domains, and had a Combined Annotation Dependent Depletion score in the highest quintile.PTVs in CHEK2 were associated with three cancers at p<0.001 (breast, prostate, HD) and six at p<0.05 (oesophagus, melanoma, ovary, kidney, DNHL, myeloid leukaemia). Carriers of rMSVs had increased risks of five cancers (p<0.001: breast, prostate, LL; p<0.05: melanoma, multiple myeloma). CONCLUSION PTVs in ATM and CHEK2 are associated with a wide range of cancers, with the highest RR for pancreatic cancer in ATM PTV carriers. These findings can inform genetic counselling of carriers.
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Affiliation(s)
- Toqir K Mukhtar
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Primary Care and Public Health, Imperial College London, London, UK
| | - Naomi Wilcox
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Xin Yang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Marc Naven
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Nasim Mavaddat
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - John R B Perry
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Eugene Gardner
- Metabolic Research Laboratory, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
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2
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McCarthy-Leo C, Baughan S, Dlugas H, Abraham P, Gibbons J, Baldwin C, Chung S, Feldman GL, Dyson G, Finley RL, Tainsky MA. Germline variant profiling of CHEK2 sequencing variants in breast cancer patients. Cancer Genet 2024; 288-289:10-19. [PMID: 39208550 DOI: 10.1016/j.cancergen.2024.08.081] [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: 05/06/2024] [Revised: 07/17/2024] [Accepted: 08/18/2024] [Indexed: 09/04/2024]
Abstract
The cell cycle checkpoint kinase 2 (CHEK2) is a tumor suppressor gene coding for a protein kinase with a role in the cell cycle and DNA repair pathways. Variants within CHEK2 are associated with an increased risk of developing breast, colorectal, prostate and several other types of cancer. Comprehensive genetic risk assessment leads to early detection of hereditary cancer and provides an opportunity for better survival. Multigene panel screening can identify the presence of pathogenic variants in hereditary cancer predisposition genes (HCPG), including CHEK2. Multigene panels, however, also result in large quantities of genetic data some of which cannot be interpreted and are classified as variants of uncertain significance (VUS). A VUS provides no information for use in medical management and leads to ambiguity in genetic counseling. In the absence of variant segregation data, in vitro functional analyses can be used to clarify variant annotations, aiding in accurate clinical management of patient risk and treatment plans. In this study, we performed whole exome sequencing (WES) to investigate the prevalence of germline variants in 210 breast cancer (BC) patients and conspicuously among the many variants in HCPGs that we found, we identified 16 individuals with non-synonymous or frameshift CHEK2 variants, sometimes along with additional variants within other BC susceptibility genes. Using this data, we investigated the prevalence of these CHEK2 variants in African American (AA) and Caucasian (CA) populations identifying the presence of two novel frameshift variants, c.1350delA (p.Val451Serfs*18) and c.1528delC (p.Gln510Argfs*3) and a novel missense variant, c262C>T (p.Pro88Ser). Along with the current clinical classifications, we assembled available experimental data and computational predictions of function for these CHEK2 variants, as well as explored the role these variants may play in polygenic risk assessment.
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Affiliation(s)
- Claire McCarthy-Leo
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Scott Baughan
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Hunter Dlugas
- Biostatistics and Bioinformatics Core, Karmanos Cancer Institute, Detroit, MI, United States
| | - Prisca Abraham
- Wayne State University School of Medicine, Detroit, MI, United States
| | - Janice Gibbons
- Wayne State University School of Medicine, Detroit, MI, United States
| | - Carolyn Baldwin
- Wayne State University School of Medicine, Detroit, MI, United States
| | - Sarah Chung
- Wayne State University School of Medicine, Detroit, MI, United States
| | - Gerald L Feldman
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Gregory Dyson
- Biostatistics and Bioinformatics Core, Karmanos Cancer Institute, Detroit, MI, United States; Department of Oncology, Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States
| | - Russell L Finley
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Michael A Tainsky
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, United States; Department of Oncology, Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States.
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3
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Pilenzi L, Anaclerio F, Dell'Elice A, Minelli M, Giansante R, Cicirelli M, Tinari N, Grassadonia A, Pantalone A, Grossi S, Canale N, Bruno A, Calabrese G, Ballerini P, Stuppia L, Antonucci I. The Crucial Role of Hereditary Cancer Panel Testing in Unaffected Individuals with a Strong Family History of Cancer: A Retrospective Study of a Cohort of 103 Healthy Subjects. Cancers (Basel) 2024; 16:2327. [PMID: 39001389 PMCID: PMC11240828 DOI: 10.3390/cancers16132327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/16/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024] Open
Abstract
Hereditary cancer syndromes caused by germline mutations account for 5-10% of all cancers. The finding of a genetic mutation could have far-reaching consequences for pharmaceutical therapy, personalized prevention strategies, and cascade testing. According to the National Comprehensive Cancer Network's (NCCN) and the Italian Association of Medical Oncology (AIOM) guidelines, unaffected family members should be tested only if the affected one is unavailable. This article explores whether germline genetic testing may be offered to high-risk families for hereditary cancer even if a living affected relative is missing. A retrospective study was carried out on 103 healthy subjects tested from 2017 to 2023. We enrolled all subjects with at least two first- or second-degree relatives affected by breast, ovarian, pancreatic, gastric, prostate, or colorectal cancer. All subjects were tested by Next Generation Sequencing (NGS) multi-gene panel of 27 cancer-associated genes. In the study population, 5 (about 5%) pathogenic/likely pathogenic variants (PVs/LPVs) were found, while 40 (42%) had a Variant of Uncertain Significance (VUS). This study highlights the importance of genetic testing for individuals with a strong family history of hereditary malignancies. This approach would allow women who tested positive to receive tailored treatment and prevention strategies based on their personal mutation status.
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Affiliation(s)
- Lucrezia Pilenzi
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Federico Anaclerio
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Anastasia Dell'Elice
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Maria Minelli
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Department of Medical Genetics, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Roberta Giansante
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Department of Medical Genetics, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Michela Cicirelli
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Department of Medical Genetics, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Nicola Tinari
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Antonino Grassadonia
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Department of Innovative Technologies in Medicine and Dentistry, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Andrea Pantalone
- Orthopaedic and Traumatology Department, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Simona Grossi
- U.O.C. Chirurgia Generale ad Indirizzo Senologico, Eusoma Breast Center ASL2 Abruzzo, 66026 Ortona, Italy
| | - Nicole Canale
- U.O.C. Chirurgia Generale ad Indirizzo Senologico, Eusoma Breast Center ASL2 Abruzzo, 66026 Ortona, Italy
| | - Annalisa Bruno
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Department of Innovative Technologies in Medicine and Dentistry, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | | | - Patrizia Ballerini
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Department of Innovative Technologies in Medicine and Dentistry, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Liborio Stuppia
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Department of Psychological, Health and Territorial Sciences, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Ivana Antonucci
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Department of Psychological, Health and Territorial Sciences, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
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4
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Zemankova P, Cerna M, Horackova K, Ernst C, Soukupova J, Borecka M, Blümcke B, Cerna L, Cerna M, Curtisova V, Dolezalova T, Duskova P, Dvorakova L, Foretova L, Havranek O, Hauke J, Hahnen E, Hodulova M, Hovhannisyan M, Hruskova L, Janatova M, Janikova M, Jelinkova S, Just P, Kosarova M, Koudova M, Krutilkova V, Machackova E, Matejkova K, Michalovska R, Misove A, Nehasil P, Nemcova B, Novotny J, Panczak A, Pesek P, Scheinost O, Springer D, Stastna B, Stranecky V, Subrt I, Tavandzis S, Tureckova E, Vesela K, Vlckova Z, Vocka M, Wappenschmidt B, Zima T, Kleibl Z, Kleiblova P. A deep intronic recurrent CHEK2 variant c.1009-118_1009-87delinsC affects pre-mRNA splicing and contributes to hereditary breast cancer predisposition. Breast 2024; 75:103721. [PMID: 38554551 PMCID: PMC10998186 DOI: 10.1016/j.breast.2024.103721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 04/01/2024] Open
Abstract
Germline CHEK2 pathogenic variants confer an increased risk of female breast cancer (FBC). Here we describe a recurrent germline intronic variant c.1009-118_1009-87delinsC, which showed a splice acceptor shift in RNA analysis, introducing a premature stop codon (p.Tyr337PhefsTer37). The variant was found in 21/10,204 (0.21%) Czech FBC patients compared to 1/3250 (0.03%) controls (p = 0.04) and in 4/3639 (0.11%) FBC patients from an independent German dataset. In addition, we found this variant in 5/2966 (0.17%) Czech (but none of the 443 German) ovarian cancer patients, three of whom developed early-onset tumors. Based on these observations, we classified this variant as likely pathogenic.
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Affiliation(s)
- Petra Zemankova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic; Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marta Cerna
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Klara Horackova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Corinna Ernst
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Jana Soukupova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Marianna Borecka
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Britta Blümcke
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University of Cologne and University Hospital Cologne, Cologne, Germany
| | | | - Monika Cerna
- Institute of Medical Genetics, University Hospital Pilsen, Pilsen, Czech Republic
| | - Vaclava Curtisova
- Department of Medical Genetics, University Hospital Olomouc, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Tatana Dolezalova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Petra Duskova
- Hospital Ceske Budejovice, Ceske Budejovice, Czech Republic
| | - Lenka Dvorakova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ondrej Havranek
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic; BIOCEV, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan Hauke
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University of Cologne and University Hospital Cologne, Cologne, Germany
| | | | - Milena Hovhannisyan
- 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
| | - Maria Janikova
- Department of Medical Genetics, University Hospital Olomouc, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Sandra Jelinkova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Pavel Just
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | | | | | - Vera Krutilkova
- Department of Medical Genetics, AGEL Laboratories, AGEL Research and Training Institute, Novy Jicin, Czech Republic
| | - Eva Machackova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Katerina Matejkova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | | | - Adela Misove
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Petr Nehasil
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic; Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic; Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Barbora Nemcova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Jan Novotny
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Ales Panczak
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Pavel Pesek
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | | | - Drahomira Springer
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 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; Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Viktor Stranecky
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Ivan Subrt
- Institute of Medical Genetics, University Hospital Pilsen, Pilsen, Czech Republic
| | - Spiros Tavandzis
- Department of Medical Genetics, AGEL Laboratories, AGEL Research and Training Institute, Novy Jicin, Czech Republic
| | - Eva Tureckova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Kamila Vesela
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | | | - Michal Vocka
- Department of Oncology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Barbara Wappenschmidt
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Tomas Zima
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 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; Institute of Pathological Physiology, First Faculty of Medicine, Charles University, 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.
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5
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Sanoguera-Miralles L, Llinares-Burguet I, Bueno-Martínez E, Ramadane-Morchadi L, Stuani C, Valenzuela-Palomo A, García-Álvarez A, Pérez-Segura P, Buratti E, de la Hoya M, Velasco-Sampedro EA. Comprehensive splicing analysis of the alternatively spliced CHEK2 exons 8 and 10 reveals three enhancer/silencer-rich regions and 38 spliceogenic variants. J Pathol 2024; 262:395-409. [PMID: 38332730 DOI: 10.1002/path.6243] [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: 08/30/2023] [Revised: 10/26/2023] [Accepted: 11/28/2023] [Indexed: 02/10/2024]
Abstract
Splicing is controlled by a large set of regulatory elements (SREs) including splicing enhancers and silencers, which are involved in exon recognition. Variants at these motifs may dysregulate splicing and trigger loss-of-function transcripts associated with disease. Our goal here was to study the alternatively spliced exons 8 and 10 of the breast cancer susceptibility gene CHEK2. For this purpose, we used a previously published minigene with exons 6-10 that produced the expected minigene full-length transcript and replicated the naturally occurring events of exon 8 [Δ(E8)] and exon 10 [Δ(E10)] skipping. We then introduced 12 internal microdeletions of exons 8 and 10 by mutagenesis in order to map SRE-rich intervals by splicing assays in MCF-7 cells. We identified three minimal (10-, 11-, 15-nt) regions essential for exon recognition: c.863_877del [ex8, Δ(E8): 75%] and c.1073_1083del and c.1083_1092del [ex10, Δ(E10): 97% and 62%, respectively]. Then 87 variants found within these intervals were introduced into the wild-type minigene and tested functionally. Thirty-eight of them (44%) impaired splicing, four of which (c.883G>A, c.883G>T, c.884A>T, and c.1080G>T) induced negligible amounts (<5%) of the minigene full-length transcript. Another six variants (c.886G>A, c.886G>T, c.1075G>A, c.1075G>T, c.1076A>T, and c.1078G>T) showed significantly strong impacts (20-50% of the minigene full-length transcript). Thirty-three of the 38 spliceogenic variants were annotated as missense, three as nonsense, and two as synonymous, underlying the fact that any exonic change is capable of disrupting splicing. Moreover, c.883G>A, c.883G>T, and c.884A>T were classified as pathogenic/likely pathogenic variants according to ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based criteria. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Científicas - Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Inés Llinares-Burguet
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Científicas - Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Elena Bueno-Martínez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Científicas - Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Lobna Ramadane-Morchadi
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Cristiana Stuani
- Molecular Pathology Lab. International Centre of Genetic Engineering and Biotechnology, Trieste, Italy
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Científicas - Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Alicia García-Álvarez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Científicas - Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Emanuele Buratti
- Molecular Pathology Lab. International Centre of Genetic Engineering and Biotechnology, Trieste, Italy
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Eladio A Velasco-Sampedro
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Científicas - Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
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6
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Chrysafi P, Jani CT, Lotz M, Al Omari O, Singh H, Stafford K, Agarwal L, Rupal A, Dar AQ, Dangelo A, Lam P. Prevalence of Variants of Uncertain Significance in Patients Undergoing Genetic Testing for Hereditary Breast and Ovarian Cancer and Lynch Syndrome. Cancers (Basel) 2023; 15:5762. [PMID: 38136308 PMCID: PMC10742236 DOI: 10.3390/cancers15245762] [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: 11/03/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Hereditary Breast and Ovarian Cancer (HBOC) and Lynch Syndrome (LS) are the most common inherited cancer syndromes identified with genetic testing. Testing, though, commonly reveals variants of uncertain significance (VUSs). This is a retrospective observational study designed to determine the prevalence of pathogenic mutations and VUSs in patients tested for HBOC and/or LS and to explore the characteristics of the VUS population. Patients 18-80 years old that met NCCN criteria for HBOC and/or LS genetic screening were tested between 2006 and 2020 at Mount Auburn Hospital in Cambridge, Massachusetts. A total of 663 patients were included in the study, with a mean age of 50 years old and 90% being females. Pathogenic mutations were identified in 12.5% and VUSs in 28.3%. VUS prevalence was associated with race (p-value = 0.019), being particularly higher in Asian populations. Patients with a personal history of breast cancer or family history of breast or ovarian cancer were more likely to have a VUS (personal breast: OR: 1.55; CI: 1.08-2.25; family breast: OR: 1.68; CI: 1.08-2.60, family ovarian OR: 2.29; CI: 1.04-5.45). In conclusion, VUSs appear to be detected in almost one third patients tested for cancer genetic syndromes, and thus future work is warranted to determine their significance in cancer development.
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Affiliation(s)
- Pavlina Chrysafi
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA; (P.C.); (M.L.); (K.S.); (A.D.); (P.L.)
- Department of Medicine, Harvard Medical School, Boston, MA 02129, USA
| | - Chinmay T. Jani
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA; (P.C.); (M.L.); (K.S.); (A.D.); (P.L.)
- Department of Medicine, Harvard Medical School, Boston, MA 02129, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146, USA
| | - Margaret Lotz
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA; (P.C.); (M.L.); (K.S.); (A.D.); (P.L.)
- Division of Hematology and Oncology, Mount Auburn Hospital, Cambridge, MA 02138, USA
| | - Omar Al Omari
- Department of Pulmonary and Critical Care, Temple University, Philadelphia, PA 19122, USA;
| | - Harpreet Singh
- Department of Pulmonary and Critical Care, Medical College of Wisconsin, Milwaukee, WI 53226, USA;
| | - Katherine Stafford
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA; (P.C.); (M.L.); (K.S.); (A.D.); (P.L.)
- Department of Medicine, Harvard Medical School, Boston, MA 02129, USA
| | - Lipisha Agarwal
- Department of Pulmonary and Critical Care, University of Vermont, Burlington, VT 05405, USA;
| | - Arashdeep Rupal
- Department of Pulmonary and Critical Care, University of South Florida, Tampa, FL 33620, USA;
| | - Abdul Qadir Dar
- Department of Medicine, Lahey Medical Center, Burlington, MA 01805, USA;
| | - Abby Dangelo
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA; (P.C.); (M.L.); (K.S.); (A.D.); (P.L.)
- Division of Hematology and Oncology, Mount Auburn Hospital, Cambridge, MA 02138, USA
| | - Prudence Lam
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA; (P.C.); (M.L.); (K.S.); (A.D.); (P.L.)
- Department of Medicine, Harvard Medical School, Boston, MA 02129, USA
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