1
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Richardson ME, Holdren M, Brannan T, de la Hoya M, Spurdle AB, Tavtigian SV, Young CC, Zec L, Hiraki S, Anderson MJ, Walker LC, McNulty S, Turnbull C, Tischkowitz M, Schon K, Slavin T, Foulkes WD, Cline M, Monteiro AN, Pesaran T, Couch FJ. Specifications of the ACMG/AMP variant curation guidelines for the analysis of germline ATM sequence variants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.28.24307502. [PMID: 38854136 PMCID: PMC11160822 DOI: 10.1101/2024.05.28.24307502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer (HBOP) Variant Curation Expert Panel (VCEP) is composed of internationally recognized experts in clinical genetics, molecular biology and variant interpretation. This VCEP made specifications for ACMG/AMP guidelines for the ataxia telangiectasia mutated (ATM) gene according to the Food and Drug Administration (FDA)-approved ClinGen protocol. These gene-specific rules for ATM were modified from the American College of Medical Genetics and Association for Molecular Pathology (ACMG/AMP) guidelines and were tested against 33 ATM variants of various types and classifications in a pilot curation phase. The pilot revealed a majority agreement between the HBOP VCEP classifications and the ClinVar-deposited classifications. Six pilot variants had conflicting interpretations in ClinVar and reevaluation with the VCEP's ATM-specific rules resulted in four that were classified as benign, one as likely pathogenic and one as a variant of uncertain significance (VUS) by the VCEP, improving the certainty of interpretations in the public domain. Overall, 28 the 33 pilot variants were not VUS leading to an 85% classification rate. The ClinGen-approved, modified rules demonstrated value for improved interpretation of variants in ATM.
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Affiliation(s)
| | - Megan Holdren
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, 28040 Madrid, Spain
| | - Amanda B Spurdle
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Sean V Tavtigian
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | | | | | | | | | - Logan C Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Shannon McNulty
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Clare Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Marc Tischkowitz
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Katherine Schon
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Thomas Slavin
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - William D Foulkes
- Departments of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Melissa Cline
- UC Santa Cruz Genomics Institute, Mail Stop: Genomics, University of California, Santa Cruz, CA, USA
| | - Alvaro N Monteiro
- Department of Cancer Epidemiology, H Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | | | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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2
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Wang Y, Sun Y, Tan M, Lin X, Tai P, Huang X, Jin Q, Yuan D, Xu T, He B. Association Between Polymorphisms in DNA Damage Repair Pathway Genes and Female Breast Cancer Risk. DNA Cell Biol 2024; 43:219-231. [PMID: 38634815 DOI: 10.1089/dna.2023.0331] [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] [Indexed: 04/19/2024] Open
Abstract
Breast cancer risk have been discussed to be associated with polymorphisms in genes as well as abnormal DNA damage repair function. This study aims to assess the relationship between genes single nucleotide polymorphisms (SNPs) related to DNA damage repair and female breast cancer risk in Chinese population. A case-control study containing 400 patients and 400 healthy controls was conducted. Genotype was identified using the sequence MassARRAY method and expression of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor-2 (HER-2) in tumor tissues was analyzed by immunohistochemistry assay. The results revealed that ATR rs13091637 decreased breast cancer risk influenced by ER, PR (CT/TT vs. CC: adjusted odds ratio [OR] = 1.54, 95% confidence interval [CI]: 1.04-2.27, p = 0.032; CT/TT vs. CC: adjusted OR = 1.63, 95%CI: 1.14-2.35, p = 0.008) expression. Stratified analysis revealed that PALB2 rs16940342 increased breast cancer risk in response to menstrual status (AG/GG vs. AA: adjusted OR = 1.72, 95%CI: 1.13-2.62, p = 0.011) and age of menarche (AG/GG vs. AA: adjusted OR = 1.54, 95%CI: 1.03-2.31, p = 0.037), whereas ATM rs611646 and Ku70 rs132793 were associated with reduced breast cancer risk influenced by menarche (GA/AA vs. GG: adjusted OR = 0.50, 95%CI: 0.30-0.95, p = 0.033). In a summary, PALB2 rs16940342, ATR rs13091637, ATM rs611646, and Ku70 rs132793 were associated with breast cancer risk.
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Affiliation(s)
- Ying Wang
- School of Basic-Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yalan Sun
- School of Basic-Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Mingjuan Tan
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xin Lin
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Ping Tai
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xiaoqin Huang
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Qing Jin
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Dan Yuan
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Tao Xu
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Bangshun He
- School of Basic-Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Deparment of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
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3
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Beck JJ, Slunecka JL, Johnson BN, Van Asselt AJ, Finnicum CT, Ageton C, Krie A, Nickles H, Cowan K, Maxwell J, Boomsma DI, de Geus E, Ehli EA, Hottenga JJ. Breast Cancer Polygenic Risk Score Validation and Effects of Variable Imputation. Cancers (Basel) 2024; 16:1578. [PMID: 38672660 PMCID: PMC11048743 DOI: 10.3390/cancers16081578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/30/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Breast cancer (BC) is a complex disease affecting one in eight women in the USA. Advances in population genomics have led to the development of polygenic risk scores (PRSs) with the potential to augment current risk models, but replication is often limited. We evaluated 2 robust PRSs with 313 and 3820 SNPs and the effects of multiple genotype imputation replications in BC cases and control populations. Biological samples from BC cases and cancer-free controls were drawn from three European ancestry cohorts. Genotyping on the Illumina Global Screening Array was followed by stringent quality control measures and 20 genotype imputation replications. A total of 468 unrelated cases and 4337 controls were scored, revealing significant differences in mean PRS percentiles between cases and controls (p < 0.001) for both SNP sets (313-SNP PRS: 52.81 and 48.07; 3820-SNP PRS: 55.45 and 49.81), with receiver operating characteristic curve analysis showing area under the curve values of 0.596 and 0.603 for the 313-SNP and 3820-SNP PRS, respectively. PRS fluctuations (from ~2-3% up to 9%) emerged across imputation iterations. Our study robustly reaffirms the predictive capacity of PRSs for BC by replicating their performance in an independent BC population and showcases the need to average imputed scores for reliable outcomes.
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Affiliation(s)
- Jeffrey J. Beck
- Avera Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD 57105, USA (E.A.E.)
| | - John L. Slunecka
- Avera Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD 57105, USA (E.A.E.)
| | - Brandon N. Johnson
- Avera Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD 57105, USA (E.A.E.)
| | - Austin J. Van Asselt
- Avera Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD 57105, USA (E.A.E.)
| | - Casey T. Finnicum
- Avera Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD 57105, USA (E.A.E.)
| | | | - Amy Krie
- Avera Cancer Institute, Sioux Falls, SD 57105, USA
| | | | - Kenneth Cowan
- Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer at University of Nebraska Medical Center, Omaha, NE 68105, USA
| | - Jessica Maxwell
- Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer at University of Nebraska Medical Center, Omaha, NE 68105, USA
| | - Dorret I. Boomsma
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (J.-J.H.)
| | - Eco de Geus
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (J.-J.H.)
| | - Erik A. Ehli
- Avera Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD 57105, USA (E.A.E.)
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (J.-J.H.)
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Ruberu TLM, Braun D, Parmigiani G, Biswas S. Bayesian meta-analysis of penetrance for cancer risk. Biometrics 2024; 80:ujae038. [PMID: 38819308 PMCID: PMC11140851 DOI: 10.1093/biomtc/ujae038] [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: 09/05/2022] [Revised: 07/12/2023] [Accepted: 05/01/2024] [Indexed: 06/01/2024]
Abstract
Multi-gene panel testing allows many cancer susceptibility genes to be tested quickly at a lower cost making such testing accessible to a broader population. Thus, more patients carrying pathogenic germline mutations in various cancer-susceptibility genes are being identified. This creates a great opportunity, as well as an urgent need, to counsel these patients about appropriate risk-reducing management strategies. Counseling hinges on accurate estimates of age-specific risks of developing various cancers associated with mutations in a specific gene, ie, penetrance estimation. We propose a meta-analysis approach based on a Bayesian hierarchical random-effects model to obtain penetrance estimates by integrating studies reporting different types of risk measures (eg, penetrance, relative risk, odds ratio) while accounting for the associated uncertainties. After estimating posterior distributions of the parameters via a Markov chain Monte Carlo algorithm, we estimate penetrance and credible intervals. We investigate the proposed method and compare with an existing approach via simulations based on studies reporting risks for two moderate-risk breast cancer susceptibility genes, ATM and PALB2. Our proposed method is far superior in terms of coverage probability of credible intervals and mean square error of estimates. Finally, we apply our method to estimate the penetrance of breast cancer among carriers of pathogenic mutations in the ATM gene.
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Affiliation(s)
| | - Danielle Braun
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, United States
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA 02215, United States
| | - Giovanni Parmigiani
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, United States
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA 02215, United States
| | - Swati Biswas
- Department of Mathematical Sciences, University of Texas at Dallas, Richardson, TX 75080, United States
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5
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Rosenblum LS, Auger SM, Zhu H, Zhou Z, Xin W, Reiner J, Wolf Z, Leach NT. Prenatal Testing for Variants in Genes Associated with Hereditary Cancer Risk: Laboratory Experience and Considerations. J Mol Diagn 2024; 26:202-212. [PMID: 38171482 DOI: 10.1016/j.jmoldx.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 10/29/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Prenatal molecular genetic testing for familial variants that cause inherited disorders has been performed for decades and is accepted as standard of care. However, the spectrum of genes considered for prenatal testing is expanding because of genetic testing for hereditary cancer risk (HCR) and inclusion of conditions with associated cancer risk in carrier screening panels. A few of these disorders, such as ataxia telangiectasia and Bloom syndrome, include increased cancer risk as part of the phenotype, already meet professional guidelines for prenatal testing, and may be associated with increased cancer risk in heterozygous carriers. In addition, recent studies implicate heterozygosity for variants in lysosomal storage disease genes in HCR etiology. Currently, there is no specific professional guidance regarding prenatal testing for HCR. To determine the prevalence of such testing, we reviewed 1345 consecutive prenatal specimens received in our laboratory for familial variant-specific testing and identified 65 (4.8%) with a known or likely HCR component, plus 210 (15.6%) for lysosomal storage disease. These specimens were classified into five distinct categories for clarity and to enable evaluation. Our experience assessing prenatal specimens for variants associated with HCR, with or without a constitutional phenotype, provides metrics for and contributes to the points to consider in prenatal testing for HCR.
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Affiliation(s)
- Lynne S Rosenblum
- Molecular Diagnostics Laboratory, Labcorp, Westborough, Massachusetts.
| | - Stephanie M Auger
- Molecular Diagnostics Laboratory, Labcorp, Westborough, Massachusetts
| | - Hui Zhu
- Molecular Diagnostics Laboratory, Labcorp, Westborough, Massachusetts
| | - Zhaoqing Zhou
- Molecular Diagnostics Laboratory, Labcorp, Westborough, Massachusetts
| | - Winnie Xin
- Molecular Diagnostics Laboratory, Labcorp, Westborough, Massachusetts
| | - Jennifer Reiner
- Molecular Diagnostics Laboratory, Labcorp, Westborough, Massachusetts
| | - Zena Wolf
- Molecular Diagnostics Laboratory, Labcorp, Westborough, Massachusetts
| | - Natalia T Leach
- Molecular Diagnostics Laboratory, Labcorp, Westborough, Massachusetts
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6
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Kansuttiviwat C, Lertwilaiwittaya P, Roothumnong E, Nakthong P, Dungort P, Meesamarnpong C, Tansa-Nga W, Pongsuktavorn K, Wiboonthanasarn S, Tititumjariya W, Phuphuripan N, Lertbussarakam C, Wattanarangsan J, Sritun J, Punuch K, Kammarabutr J, Mutirangura P, Thongnoppakhun W, Limwongse C, Pithukpakorn M. Germline mutations of 4567 patients with hereditary breast-ovarian cancer spectrum in Thailand. NPJ Genom Med 2024; 9:9. [PMID: 38355628 PMCID: PMC10866978 DOI: 10.1038/s41525-024-00400-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
Multi-gene panel testing has led to the detection of pathogenic/likely pathogenic (P/LP) variants in many cancer susceptibility genes in patients with breast-ovarian cancer spectrum. However, the clinical and genomic data of Asian populations, including Thai cancer patients, was underrepresented, and the clinical significance of multi-gene panel testing in Thailand remains undetermined. In this study, we collected the clinical and genetic data from 4567 Thai patients with cancer in the hereditary breast-ovarian cancer (HBOC) spectrum who underwent multi-gene panel testing. Six hundred and ten individuals (13.4%) had germline P/LP variants. Detection rates of germline P/LP variants in breast, ovarian, pancreatic, and prostate cancer were 11.8%, 19.8%, 14.0%, and 7.1%, respectively. Non-BRCA gene mutations accounted for 35% of patients with germline P/LP variants. ATM was the most common non-BRCA gene mutation. Four hundred and thirty-two breast cancer patients with germline P/LP variants (80.4%) met the current NCCN genetic testing criteria. The most common indication was early-onset breast cancer. Ten patients harbored double pathogenic variants in this cohort. Our result showed that a significant proportion of non-BRCA P/LP variants were identified in patients with HBOC-related cancers. These findings support the benefit of multi-gene panel testing for inherited cancer susceptibility among Thai HBOC patients. Some modifications of the testing policy may be appropriate for implementation in diverse populations.
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Affiliation(s)
- Chalermkiat Kansuttiviwat
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pongtawat Lertwilaiwittaya
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ekkapong Roothumnong
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Panee Nakthong
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Peerawat Dungort
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chutima Meesamarnpong
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Warisara Tansa-Nga
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Khontawan Pongsuktavorn
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Supakit Wiboonthanasarn
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Warunya Tititumjariya
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nannipa Phuphuripan
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Jantanee Wattanarangsan
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jiraporn Sritun
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kittiporn Punuch
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jirayu Kammarabutr
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pornthira Mutirangura
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Wanna Thongnoppakhun
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chanin Limwongse
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Manop Pithukpakorn
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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7
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Peters MLB, Eckel A, Seguin CL, Davidi B, Howard DH, Knudsen AB, Pandharipande PV. Cost-Effectiveness Analysis of Screening for Pancreatic Cancer Among High-Risk Populations. JCO Oncol Pract 2024; 20:278-290. [PMID: 38086003 PMCID: PMC10911581 DOI: 10.1200/op.23.00495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/05/2023] [Accepted: 10/30/2023] [Indexed: 12/19/2023] Open
Abstract
PURPOSE We evaluated the potential cost-effectiveness of combined magnetic resonance imaging (MRI) and endoscopic ultrasound (EUS) screening for pancreatic ductal adenocarcinoma (PDAC) among populations at high risk for the disease. METHODS We used a microsimulation model of the natural history of PDAC to estimate the lifetime health benefits, costs, and cost-effectiveness of PDAC screening among populations with specific genetic risk factors for PDAC, including BRCA1 and BRCA2, PALB2, ATM, Lynch syndrome, TP53, CDKN2A, and STK11. For each high-risk population, we simulated 29 screening strategies, defined by starting age and frequency. Screening included MRI with follow-up EUS in a subset of patients. Costs of tests were based on Medicare reimbursement for MRI, EUS, fine-needle aspiration biopsy, and pancreatectomy. Cancer-related cost by stage of disease and phase of treatment was based on the literature. For each high-risk population, we performed an incremental cost-effectiveness analysis, assuming a willingness-to-pay (WTP) threshold of $100,000 US dollars (USD) per quality-adjusted life year (QALY) gained. RESULTS For men with relative risk (RR) 12.33 (CDKN2A) and RR 28 (STK11), annual screening was cost-effective, starting at age 55 and 40 years, respectively. For women, screening was only cost-effective for those with RR 28 (STK11), with annual screening starting at age 45 years. CONCLUSION Combined MRI/EUS screening may be a cost-effective approach for the highest-risk populations (among mutations considered, those with RR >12). However, for those with moderate risk (RR, 5-12), screening would only be cost-effective at higher WTP thresholds (eg, $200K USD/QALY) or with once-only screening.
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Affiliation(s)
- Mary Linton B. Peters
- Division of Medical Oncology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA
- Institute for Technology Assessment, Massachusetts General Hospital, Boston, MA
| | - Andrew Eckel
- Institute for Technology Assessment, Massachusetts General Hospital, Boston, MA
| | - Claudia L. Seguin
- Department of Radiology, The Ohio State University College of Medicine, Columbus, OH
| | - Barak Davidi
- Institute for Technology Assessment, Massachusetts General Hospital, Boston, MA
| | - David H. Howard
- Department of Health Policy and Management, Rollins School of Public Health, Emory University, Atlanta, GA
| | - Amy B. Knudsen
- Institute for Technology Assessment, Massachusetts General Hospital, Boston, MA
- Department of Radiology, Massachusetts General Hospital, Boston, MA
| | - Pari V. Pandharipande
- Department of Radiology, The Ohio State University College of Medicine, Columbus, OH
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8
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Tam LT, Cole B, Stasi SM, Paulson VA, Wright JN, Hoeppner C, Holtzclaw S, Crotty EE, Ellenbogen RG, Lee A, Ermoian RP, Lockwood CM, Leary SES, Ronsley R. Somatic Versus Germline: A Case Series of Three Children With ATM-Mutated Medulloblastoma. JCO Precis Oncol 2024; 8:e2300333. [PMID: 38207225 DOI: 10.1200/po.23.00333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/03/2023] [Accepted: 11/07/2023] [Indexed: 01/13/2024] Open
Abstract
Somatic versus Germline-A Case Series of Three Children with ATM- mutated Medulloblastoma.
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Affiliation(s)
- Lydia T Tam
- Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - Bonnie Cole
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA
| | - Shannon M Stasi
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA
- Division of Hematology, Oncology, Bone Marrow Transplant & Cellular Therapy, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - Vera A Paulson
- Genetics Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Jason N Wright
- Department of Radiology, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - Corrine Hoeppner
- Division of Hematology, Oncology, Bone Marrow Transplant & Cellular Therapy, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - Susan Holtzclaw
- Division of Hematology, Oncology, Bone Marrow Transplant & Cellular Therapy, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - Erin E Crotty
- Division of Hematology, Oncology, Bone Marrow Transplant & Cellular Therapy, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA
- Department of Neurological Surgery, Seattle Children's Hospital, University of Washington, Seattle, WA
- Department of Radiation Oncology, University of Washington, Seattle, WA
| | - Richard G Ellenbogen
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA
| | - Amy Lee
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA
| | | | - Christina M Lockwood
- Genetics Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Sarah E S Leary
- Division of Hematology, Oncology, Bone Marrow Transplant & Cellular Therapy, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA
- Department of Neurological Surgery, Seattle Children's Hospital, University of Washington, Seattle, WA
- Department of Radiation Oncology, University of Washington, Seattle, WA
| | - Rebecca Ronsley
- Division of Hematology, Oncology, Bone Marrow Transplant & Cellular Therapy, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA
- Department of Neurological Surgery, Seattle Children's Hospital, University of Washington, Seattle, WA
- Department of Radiation Oncology, University of Washington, Seattle, WA
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9
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Behl T, Kumar A, Vishakha, Sehgal A, Singh S, Sharma N, Yadav S, Rashid S, Ali N, Ahmed AS, Vargas-De-La-Cruz C, Bungau SG, Khan H. Understanding the mechanistic pathways and clinical aspects associated with protein and gene based biomarkers in breast cancer. Int J Biol Macromol 2023; 253:126595. [PMID: 37648139 DOI: 10.1016/j.ijbiomac.2023.126595] [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: 05/02/2023] [Revised: 08/22/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023]
Abstract
Cancer is one of the most widespread and severe diseases with a huge mortality rate. In recent years, the second-leading mortality rate of any cancer globally has been breast cancer, which is one of the most common and deadly cancers found in women. Detecting breast cancer in its initial stages simplifies treatment, decreases death risk, and recovers survival rates for patients. The death rate for breast cancer has risen to 0.024 % in some regions. Sensitive and accurate technologies are required for the preclinical detection of BC at an initial stage. Biomarkers play a very crucial role in the early identification as well as diagnosis of women with breast cancer. Currently, a wide variety of cancer biomarkers have been discovered for the diagnosis of cancer. For the identification of these biomarkers from serum or other body fluids at physiological amounts, many detection methods have been developed. In the case of breast cancer, biomarkers are especially helpful in discovering those who are more likely to develop the disease, determining prognosis at the time of initial diagnosis and choosing the best systemic therapy. In this study we have compiled various clinical aspects and signaling pathways associated with protein-based biomarkers and gene-based biomarkers.
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Affiliation(s)
- Tapan Behl
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Dehradun 248007, Uttarakhand, India
| | - Ankush Kumar
- Institute of Pharmaceutical Sciences, IET Bhaddal Technical Campus, Ropar 140108, Punjab, India
| | - Vishakha
- Institute of Pharmaceutical Sciences, IET Bhaddal Technical Campus, Ropar 140108, Punjab, India
| | - Aayush Sehgal
- GHG Khalsa College of Pharmacy, Gurusar Sadhar, 141104 Ludhiana, Punjab, India
| | - Sukhbir Singh
- Department of Pharmaceutics, MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana Ambala 133203, Haryana, India
| | - Neelam Sharma
- Department of Pharmaceutics, MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana Ambala 133203, Haryana, India
| | - Shivam Yadav
- School of Pharmacy, Babu Banarasi Das University, Lucknow 226028, Uttar Pradesh, India
| | - Summya Rashid
- Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia.
| | - Nemat Ali
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadah 11451, Saudi Arabia
| | - Amira Saber Ahmed
- Hormones Department, Medical Research and Clinical Studies Institute, National Research Centre, Giza 12622, Egypt
| | - Celia Vargas-De-La-Cruz
- Department of Pharmacology, Bromatology and Toxicology, Faculty of Pharmacy and Biochemistry, Universidad Nacional Mayor de San Marcos, Lima 150001, Peru; E-Health Research Center, Universidad de Ciencias y Humanidades, Lima 15001, Peru
| | - Simona Gabriela Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, Oradea 410087, Romania; Doctoral School of Biomedical Sciences, University of Oradea, Oradea 410087, Romania
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University, Mardan 23200, Pakistan.
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10
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Pantaleo A, Forte G, Fasano C, Lepore Signorile M, Sanese P, De Marco K, Di Nicola E, Latrofa M, Grossi V, Disciglio V, Simone C. Understanding the Genetic Landscape of Pancreatic Ductal Adenocarcinoma to Support Personalized Medicine: A Systematic Review. Cancers (Basel) 2023; 16:56. [PMID: 38201484 PMCID: PMC10778202 DOI: 10.3390/cancers16010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most fatal malignancies worldwide. While population-wide screening recommendations for PDAC in asymptomatic individuals are not achievable due to its relatively low incidence, pancreatic cancer surveillance programs are recommended for patients with germline causative variants in PDAC susceptibility genes or a strong family history. In this study, we sought to determine the prevalence and significance of germline alterations in major genes (ATM, BRCA1, BRCA2, CDKN2A, EPCAM, MLH1, MSH2, MSH6, PALB2, PMS2, STK11, TP53) involved in PDAC susceptibility. We performed a systematic review of PubMed publications reporting germline variants identified in these genes in PDAC patients. Overall, the retrieved articles included 1493 PDAC patients. A high proportion of these patients (n = 1225/1493, 82%) were found to harbor alterations in genes (ATM, BRCA1, BRCA2, PALB2) involved in the homologous recombination repair (HRR) pathway. Specifically, the remaining PDAC patients were reported to carry alterations in genes playing a role in other cancer pathways (CDKN2A, STK11, TP53; n = 181/1493, 12.1%) or in the mismatch repair (MMR) pathway (MLH1, MSH2, MSH6, PMS2; n = 87/1493, 5.8%). Our findings highlight the importance of germline genetic characterization in PDAC patients for better personalized targeted therapies, clinical management, and surveillance.
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Affiliation(s)
- Antonino Pantaleo
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Giovanna Forte
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Candida Fasano
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Martina Lepore Signorile
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Paola Sanese
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Katia De Marco
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Elisabetta Di Nicola
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Marialaura Latrofa
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Valentina Grossi
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Vittoria Disciglio
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Cristiano Simone
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
- Medical Genetics, Department of Precision and Regenerative Medicine and Jonic Area (DiMePRe-J), University of Bari Aldo Moro, 70124 Bari, Italy
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11
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Bu R, Siraj AK, Al-Rasheed M, Iqbal K, Azam S, Qadri Z, Haqawi W, Tulbah A, Al-Dayel F, Almalik O, Al-Kuraya KS. Identification and characterization of ATM founder mutation in BRCA-negative breast cancer patients of Arab ethnicity. Sci Rep 2023; 13:20924. [PMID: 38017116 PMCID: PMC10684510 DOI: 10.1038/s41598-023-48231-0] [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: 09/04/2023] [Accepted: 11/23/2023] [Indexed: 11/30/2023] Open
Abstract
Breast cancer (BC) is the most prevalent malignancy among women worldwide with germline pathogenic variants/likely pathogenic variants (PVs/LPVs) in BRCA1/2 accounting for a large portion of hereditary cases. Recently, heterozygous PVs/LPVs in the ATM serine/threonine kinase or Ataxia-telangiectasia mutated gene (ATM) has been identified as a moderate susceptibility factor for BC in diverse ethnicities. However, the prevalence of ATM PVs/LPVs in BC susceptibility in Arab populations remains largely unexplored. This study investigated the prevalence of ATM PVs/LPVs among BC patients from Saudi Arabia, employing capture-sequencing technology for ATM PVs/LPVs screening in a cohort of 715 unselected BC patients without BRCA1/2 PVs/LPVs. In addition, founder mutation analysis was conducted using the PHASE program. In our entire cohort, four unique PVs/LPVs in the ATM gene were identified in six cases (0.8%). Notably, one recurrent LPV, c.6115G > A:p.Glu2039Lys was identified in three cases, for which haplotype analysis confirmed as a novel putative founder mutation traced back to 13 generations on average. This founder mutation accounted for half of all identified mutant cases and 0.4% of total screened cases. This study further reveals a significant correlation between the presence of ATM mutation and family history of BC (p = 0.0127). These findings underscore an approximate 0.8% prevalence of ATM germline PVs/LPVs in Arab BC patients without BRCA1/2 PVs/LPVs and suggest a founder effect of specific recurrent ATM mutation. These insights can help in the design of a genetic testing strategy tailored to the local population in Saudi Arabia, thereby, enabling more accurate clinical management and risk prediction.
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Affiliation(s)
- Rong Bu
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Abdul K Siraj
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Maha Al-Rasheed
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Kaleem Iqbal
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Saud Azam
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Zeeshan Qadri
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Wael Haqawi
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Asma Tulbah
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Fouad Al-Dayel
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Osama Almalik
- Department of Surgery, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Khawla S Al-Kuraya
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia.
- Research Centre at KFNCCC, Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, 11211, Riyadh, Saudi Arabia.
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12
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Fasullo M, Simeone D, Everett J, Agarunov E, Khanna L, Gonda T. A Blueprint for a Comprehensive, Multidisciplinary Pancreatic Cancer Screening Program. Am J Gastroenterol 2023:00000434-990000000-00890. [PMID: 37782292 DOI: 10.14309/ajg.0000000000002534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/06/2023] [Indexed: 10/03/2023]
Affiliation(s)
- Matthew Fasullo
- Division of Gastroenterology, New York University, New York, New York, USA
| | - Diane Simeone
- Department of Surgery, Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Jessica Everett
- Department of Medicine, Perlmutter Cancer Center, New York University, New York, New York, USA
| | - Emil Agarunov
- Division of Gastroenterology, New York University, New York, New York, USA
| | - Lauren Khanna
- Division of Gastroenterology, New York University, New York, New York, USA
| | - Tamas Gonda
- Division of Gastroenterology, New York University, New York, New York, USA
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13
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Ünsal O, Güvercin B, Özet A, Ergün MA. Analysis of Turkish Breast Cancer Patients With ATM-Heterozygous Germline Mutation According to Clinicopathological Features. Cureus 2023; 15:e47324. [PMID: 38021491 PMCID: PMC10657162 DOI: 10.7759/cureus.47324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
OBJECTIVE The ATM gene is one of the most common breast cancer (BC) susceptibility genes after BRCA1/2 and has been shown to be a moderate BC susceptibility gene. The association between ATM germline mutation and clinical features of BC is now unknown. In this article, clinicopathological features of BC patients with ATM germline heterozygous mutation were investigated. MATERIALS AND METHODS Patients admitted to the Medical Genetics department of a tertiary hospital between January 2020 and December 2022 were examined. Only invasive BC patients with pathogenic mutation, likely pathogenic mutation, or variants of uncertain significance (VUS) were included in the study. RESULTS In all, 121 patients were included in the study. The median age at the first cancer diagnosis of the patients was 44 years. Of the total number of patients, 75.2% (91) had the histological subtype of infiltrating ductal carcinoma, and 43% (52) had Luminal B molecular subtype features. At a median follow-up of 16 months, 5.8% (7) of patients developed cancer in the contralateral breast. In addition, 7.4% (9) of the patients developed a second primary cancer during follow-up. When the patients were compared according to ATM variant classification, the localization, histologic types, and molecular subtypes of the BC were not different between all groups (respectively; p=0.68, p=0.65, p=0.32). CONCLUSIONS To the best of our knowledge, this is the first publication that evaluates the clinical and pathological characteristics of BC patients with germline heterozygous ATM mutations in the Turkish population. When patients were compared according to variant classifications of ATM mutation, patients' histological and molecular subtypes were similar.
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Affiliation(s)
- Oktay Ünsal
- Department of Medical Oncology, Gazi University Faculty of Medicine, Ankara, TUR
| | - Büşra Güvercin
- Department of Internal Medicine, Gazi University Faculty of Medicine, Ankara, TUR
| | - Ahmet Özet
- Department of Medical Oncology, Gazi University Faculty of Medicine, Ankara, TUR
| | - Mehmet Ali Ergün
- Department of Medical Genetics, Gazi University Faculty of Medicine, Ankara, TUR
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14
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Ahuja S, Aneja H, Yadav AK, Ranga S, Chintamani, Paul J. Evaluation of Ataxia-Telangiectasia Mutated IVS10 Mutation in Breast Cancer Along with Clinicopathological Parameters. J Midlife Health 2023; 14:272-279. [PMID: 38504739 PMCID: PMC10946688 DOI: 10.4103/jmh.jmh_71_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/17/2023] [Indexed: 03/21/2024] Open
Abstract
Background Breast cancer is the most common cancer in women worldwide, with an estimated 2.26 million new cases diagnosed in 2020. The important genes associated include BRCA1, BRCA2, CHEK2, PTEN, TP53, and ataxia-telangiectasia mutated (ATM). ATM is responsible for repairing double-strand breaks in DNA making it a significant candidate in breast cancer predisposition. ATM variant, c.1066-6T>G, has been associated with an increased risk of breast cancer in some but not all studies. The Indian studies on the allele IVS10-6T>G are very limited. The present study was undertaken to evaluate the associations between c.1066-6T>G ATM gene variant and breast cancer incidence in Indian women and its correlation with histological grade, stage, and surrogate molecular classification. Materials and Methods Routine histopathological processing was done after adequate fixation of the specimen followed by staining with hematoxylin and eosin and immunohistochemistry for ER, PR, Her2neu, and Ki67. Single-nucleotide polymorphism for ATM allele IVS10-6T>G was studied after DNA extraction, polymerase chain reaction amplification, and restriction enzyme digestion. Results All cases were found to be negative for ATM allele IVS10-6T>G mutation. Maximum number of patients (19 cases; 52.78%) had pT2 stage tumor followed by 11 patients (30.56%) with pT3. Majority of cases were luminal B (11; 30.56%) followed by triple negative (10; 27.78%). Conclusion Although the results obtained by mutational analysis in the present study are not in agreement with the previous study on Indian women it agrees with the numerous previous studies and meta-analyses done on women with breast carcinoma in the Western world.
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Affiliation(s)
- Sana Ahuja
- Department of Pathology, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Himani Aneja
- Department of Pathology, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Amit Kumar Yadav
- Department of Pathology, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Sunil Ranga
- Department of Pathology, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Chintamani
- Department of Surgery, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Jaishree Paul
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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15
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Guadagnolo D, Mastromoro G, Marchionni E, Germani A, Libi F, Sadeghi S, Savio C, Petrucci S, De Marchis L, Piane M, Pizzuti A. Heterozygous Pathogenic Nonsense Variant in the ATM Gene in a Family with Unusually High Gastric Cancer Susceptibility. Biomedicines 2023; 11:2062. [PMID: 37509701 PMCID: PMC10377208 DOI: 10.3390/biomedicines11072062] [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: 06/29/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Germline pathogenic variants (PVs) in the Ataxia Telangiectasia mutated (ATM) gene (MIM* 607585) increase the risk for breast, pancreatic, gastric, and prostatic cancer and, to a reduced extent, ovarian and colon cancer and melanoma, with moderate penetrance and variable expressivity. We describe a family presenting early-onset gastric cancer and harboring a heterozygous pathogenic ATM variant. The proband had gastric cancer (age 45) and reported a sister deceased due to diffuse gastric cancer (age 30) and another sister who developed diffuse gastric cancer (age 52) and ovarian serous cancer. Next generation sequencing for cancer susceptibility genes (APC, ATM, BRD1, BRIP1, CDH1, CDK4, CDKN2A, CHEK2, EPCAM, MLH1, MRE11, MSH2, MSH6, MUTYH, NBN, PALB2, PMS2, PTEN, RAD50, RAD51C, RAD51D, RECQL1, SMAD4, STK11, and TP53) was performed. Molecular analysis identified the truncating c.5944C>T, p.(Gln1982*) variant in the ATM (NM_000051.3; NP_000042.3) in the proband. The variant had segregated in the living affected sister and in the unaffected daughter of the deceased affected sister. Familial early-onset gastric cancer is an unusual presentation for ATM-related malignancies. Individual variants may result in different specific risks. Genotype-phenotype correlations are challenging given the low penetrance and variable expressivity. Careful family history assessments are pivotal for prevention planning and are strengthened by the availability of molecular diagnoses.
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Affiliation(s)
- Daniele Guadagnolo
- Department of Experimental Medicine, School of Medicine and Dentistry, Sapienza University of Rome, 00185 Rome, Italy
| | - Gioia Mastromoro
- Department of Experimental Medicine, School of Medicine and Dentistry, Sapienza University of Rome, 00185 Rome, Italy
| | - Enrica Marchionni
- Department of Experimental Medicine, School of Medicine and Dentistry, Sapienza University of Rome, 00185 Rome, Italy
| | - Aldo Germani
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
- Medical Genetics Unit, Department of Diagnostic Sciences, Sant'Andrea University Hospital, 00189 Rome, Italy
| | - Fabio Libi
- Medical Genetics Unit, Department of Diagnostic Sciences, Sant'Andrea University Hospital, 00189 Rome, Italy
| | - Soha Sadeghi
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
- Medical Genetics Unit, Department of Diagnostic Sciences, Sant'Andrea University Hospital, 00189 Rome, Italy
| | - Camilla Savio
- Medical Genetics Unit, Department of Diagnostic Sciences, Sant'Andrea University Hospital, 00189 Rome, Italy
| | - Simona Petrucci
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
- Medical Genetics Unit, Department of Diagnostic Sciences, Sant'Andrea University Hospital, 00189 Rome, Italy
| | - Laura De Marchis
- Department of Radiological, Oncological and Anatomopathological Science, Sapienza University of Rome, 00185 Rome, Italy
- Oncology B Unit, Department of Hematology, Dermatology and Oncology, Policlinico Umberto I Univeristy Hospital, 00161 Rome, Italy
| | - Maria Piane
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
- Medical Genetics Unit, Department of Diagnostic Sciences, Sant'Andrea University Hospital, 00189 Rome, Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, School of Medicine and Dentistry, Sapienza University of Rome, 00185 Rome, Italy
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16
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Obata H, Ogawa M, Zalutsky MR. DNA Repair Inhibitors: Potential Targets and Partners for Targeted Radionuclide Therapy. Pharmaceutics 2023; 15:1926. [PMID: 37514113 PMCID: PMC10384049 DOI: 10.3390/pharmaceutics15071926] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
The present review aims to explore the potential targets/partners for future targeted radionuclide therapy (TRT) strategies, wherein cancer cells often are not killed effectively, despite receiving a high average tumor radiation dose. Here, we shall discuss the key factors in the cancer genome, especially those related to DNA damage response/repair and maintenance systems for escaping cell death in cancer cells. To overcome the current limitations of TRT effectiveness due to radiation/drug-tolerant cells and tumor heterogeneity, and to make TRT more effective, we propose that a promising strategy would be to target the DNA maintenance factors that are crucial for cancer survival. Considering their cancer-specific DNA damage response/repair ability and dysregulated transcription/epigenetic system, key factors such as PARP, ATM/ATR, amplified/overexpressed transcription factors, and DNA methyltransferases have the potential to be molecular targets for Auger electron therapy; moreover, their inhibition by non-radioactive molecules could be a partnering component for enhancing the therapeutic response of TRT.
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Affiliation(s)
- Honoka Obata
- Department of Advanced Nuclear Medicine Sciences, National Institutes for Quantum Science and Technology (QST), 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
- Department of Molecular Imaging and Theranostics, National Institutes for Quantum Science and Technology (QST), 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
- Departments of Radiology and Radiation Oncology, Duke University Medical Center, Durham, NC 27710, USA
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo 060-0812, Japan
| | - Mikako Ogawa
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo 060-0812, Japan
| | - Michael R Zalutsky
- Departments of Radiology and Radiation Oncology, Duke University Medical Center, Durham, NC 27710, USA
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17
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Lukashchuk N, Barnicle A, Adelman CA, Armenia J, Kang J, Barrett JC, Harrington EA. Impact of DNA damage repair alterations on prostate cancer progression and metastasis. Front Oncol 2023; 13:1162644. [PMID: 37434977 PMCID: PMC10331135 DOI: 10.3389/fonc.2023.1162644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/01/2023] [Indexed: 07/13/2023] Open
Abstract
Prostate cancer is among the most common diseases worldwide. Despite recent progress with treatments, patients with advanced prostate cancer have poor outcomes and there is a high unmet need in this population. Understanding molecular determinants underlying prostate cancer and the aggressive phenotype of disease can help with design of better clinical trials and improve treatments for these patients. One of the pathways often altered in advanced prostate cancer is DNA damage response (DDR), including alterations in BRCA1/2 and other homologous recombination repair (HRR) genes. Alterations in the DDR pathway are particularly prevalent in metastatic prostate cancer. In this review, we summarise the prevalence of DDR alterations in primary and advanced prostate cancer and discuss the impact of alterations in the DDR pathway on aggressive disease phenotype, prognosis and the association of germline pathogenic alterations in DDR genes with risk of developing prostate cancer.
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Affiliation(s)
- Natalia Lukashchuk
- Translational Medicine, Oncology Research and Development (R&D), AstraZeneca, Cambridge, United Kingdom
| | - Alan Barnicle
- Translational Medicine, Oncology Research and Development (R&D), AstraZeneca, Cambridge, United Kingdom
| | - Carrie A. Adelman
- Translational Medicine, Oncology Research and Development (R&D), AstraZeneca, Cambridge, United Kingdom
| | - Joshua Armenia
- Oncology Data Science, Oncology Research and Development (R&D), AstraZeneca, Cambridge, United Kingdom
| | - Jinyu Kang
- Global Medicines Development, Oncology Research and Development (R&D), AstraZeneca, Gaithersburg, MD, United States
| | - J. Carl Barrett
- Translational Medicine, Oncology Research and Development (R&D), AstraZeneca, Waltham, MA, United States
| | - Elizabeth A. Harrington
- Translational Medicine, Oncology Research and Development (R&D), AstraZeneca, Cambridge, United Kingdom
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18
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Hernandez-Martinez JM, Rosell R, Arrieta O. Somatic and germline ATM variants in non-small-cell lung cancer: Therapeutic implications. Crit Rev Oncol Hematol 2023:104058. [PMID: 37343657 DOI: 10.1016/j.critrevonc.2023.104058] [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: 05/15/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023] Open
Abstract
ATM is an apical kinase of the DNA damage response involved in the repair of DNA double-strand breaks. Germline ATM variants (gATM) have been associated with an increased risk of developing lung adenocarcinoma (LUAD), and approximately 9% of LUAD tumors harbor somatic ATM mutations (sATM). Biallelic carriers of pathogenic gATM exhibit a plethora of immunological abnormalities, but few studies have evaluated the contribution of immune dysfunction to lung cancer susceptibility. Indeed, little is known about the clinicopathological characteristics of lung cancer patients with sATM or gATM alterations. The introduction of targeted therapies and immunotherapies, and the increasing number of clinical trials evaluating treatment combinations, warrants a careful reexamination of the benefits and harms that different therapeutic approaches have had in lung cancer patients with sATM or gATM. This review will discuss the role of ATM in the pathogenesis of lung cancer, highlighting potential therapeutic approaches to manage ATM-deficient lung cancers.
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Affiliation(s)
- Juan-Manuel Hernandez-Martinez
- Thoracic Oncology Unit and Experimental Oncology Laboratory, Instituto Nacional de Cancerología de México (INCan); CONACYT-Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Rafael Rosell
- Institut d'Investigació en Ciències Germans Trias i Pujol, Badalona, Spain; (4)Institut Català d'Oncologia, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Oscar Arrieta
- Thoracic Oncology Unit and Experimental Oncology Laboratory, Instituto Nacional de Cancerología de México (INCan).
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Parvin S, Akter J, Takenobu H, Katai Y, Satoh S, Okada R, Haruta M, Mukae K, Wada T, Ohira M, Ando K, Kamijo T. ATM depletion induces proteasomal degradation of FANCD2 and sensitizes neuroblastoma cells to PARP inhibitors. BMC Cancer 2023; 23:313. [PMID: 37020276 PMCID: PMC10077671 DOI: 10.1186/s12885-023-10772-y] [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: 05/16/2022] [Accepted: 03/26/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND Genomic alterations, including loss of function in chromosome band 11q22-23, are frequently observed in neuroblastoma, which is the most common extracranial childhood tumour. In neuroblastoma, ATM, a DNA damage response-associated gene located on 11q22-23, has been linked to tumorigenicity. Genetic changes in ATM are heterozygous in most tumours. However, it is unclear how ATM is associated with tumorigenesis and cancer aggressiveness. METHODS To elucidate its molecular mechanism of action, we established ATM-inactivated NGP and CHP-134 neuroblastoma cell lines using CRISPR/Cas9 genome editing. The knock out cells were rigorously characterized by analyzing proliferation, colony forming abilities and responses to PARP inhibitor (Olaparib). Western blot analyses were performed to detect different protein expression related to DNA repair pathway. ShRNA lentiviral vectors were used to knockdown ATM expression in SK-N-AS and SK-N-SH neuroblastoma cell lines. ATM knock out cells were stably transfected with FANCD2 expression plasmid to over-expressed the FANCD2. Moreover, knock out cells were treated with proteasome inhibitor MG132 to determine the protein stability of FANCD2. FANCD2, RAD51 and γH2AX protein expressions were determined by Immunofluorescence microscopy. RESULTS Haploinsufficient ATM resulted in increased proliferation (p < 0.01) and cell survival following PARP inhibitor (olaparib) treatment. However, complete ATM knockout decreased proliferation (p < 0.01) and promoted cell susceptibility to olaparib (p < 0.01). Complete loss of ATM suppressed the expression of DNA repair-associated molecules FANCD2 and RAD51 and induced DNA damage in neuroblastoma cells. A marked downregulation of FANCD2 expression was also observed in shRNA-mediated ATM-knockdown neuroblastoma cells. Inhibitor experiments demonstrated that the degradation of FANCD2 was regulated at the protein level through the ubiquitin-proteasome pathway. Reintroduction of FANCD2 expression is sufficient to reverse decreased proliferation mediated by ATM depletion. CONCLUSIONS Our study revealed the molecular mechanism underlying ATM heterozygosity in neuroblastomas and elucidated that ATM inactivation enhances the susceptibility of neuroblastoma cells to olaparib treatment. These findings might be useful in the treatment of high-risk NB patients showing ATM zygosity and aggressive cancer progression in future.
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Affiliation(s)
- Sultana Parvin
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
- Laboratory of Tumor Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, 338-8570, Japan
| | - Jesmin Akter
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
| | - Hisanori Takenobu
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
| | - Yutaka Katai
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
| | - Shunpei Satoh
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
| | - Ryu Okada
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
- Laboratory of Tumor Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, 338-8570, Japan
| | - Masayuki Haruta
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
| | - Kyosuke Mukae
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
| | - Tomoko Wada
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
| | - Miki Ohira
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
| | - Kiyohiro Ando
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan
| | - Takehiko Kamijo
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama, 362-0806, Japan.
- Laboratory of Tumor Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, 338-8570, Japan.
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20
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Hall JC, Chang SD, Gephart MH, Pollom E, Butler S. Stereotactic Radiosurgery for Brain Metastases in Patients With a Heterozygous Germline Ataxia Telangiectasia Mutated Gene. Cureus 2023; 15:e37712. [PMID: 37206490 PMCID: PMC10191388 DOI: 10.7759/cureus.37712] [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] [Accepted: 04/17/2023] [Indexed: 05/21/2023] Open
Abstract
Germline mutations in the ataxia telangiectasia mutated (ATM) gene are associated with increased radiation sensitivity. Present literature lacks consensus on whether patients with heterozygous germline ATM mutations may be at greater risk of radiation-associated toxicities when treated with radiation therapy (RT), and there is little data considering more modern and conformal RT techniques such as stereotactic radiosurgery (SRS). Our report presents two cases of patients with heterozygous germline ATM mutations treated with SRS for brain metastases. One patient developed grade 3 radiation necrosis (RN) of an irradiated 16.3 cm3 resection cavity, but did not develop RN at other sites of punctate brain metastases treated with SRS. Similarly, the second report describes a patient who did not develop RN at any of the 31 irradiated sites of sub-centimeter (all ≤5 mm) brain metastases. The described cases demonstrate that some patients with germline ATM variants can safely undergo SRS for smaller brain metastases; however, clinical caution should be considered for patients with larger targets or a history of prior radiation toxicity. Given these findings and the lingering uncertainty surrounding the degree of radiosensitivity across ATM variants, future research is needed to determine whether more conservative dose-volume limits would potentially mitigate the risk of RN when treating larger brain metastases in this radiosensitive population.
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Affiliation(s)
- Jennifer C Hall
- Radiation Oncology, Stanford University School of Medicine, Stanford, USA
| | - Steven D Chang
- Neurosurgery, Stanford University School of Medicine, Stanford, USA
| | | | - Erqi Pollom
- Radiation Oncology, Stanford University School of Medicine, Stanford, USA
| | - Santino Butler
- Radiation Oncology, Stanford University School of Medicine, Stanford, USA
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21
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Hosseini S, Acar A, Sen M, Meeder K, Singh P, Yin K, Sutton JM, Hughes K. Penetrance of Gastric Adenocarcinoma Susceptibility Genes: A Systematic Review. Ann Surg Oncol 2023; 30:1795-1807. [PMID: 36528743 DOI: 10.1245/s10434-022-12829-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/01/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Gastric adenocarcinoma (GAC) is the fifth most common cancer in the world, and the presence of germline pathogenic variants has been linked with approximately 5% of gastric cancer diagnoses. Multiple GAC susceptibility genes have been identified, but information regarding the risk associated with pathogenic variants in these genes remains obscure. We conducted a systematic review of existing studies reporting the penetrance of GAC susceptibility genes. METHODS A structured search query was devised to identify GAC-related papers indexed in MEDLINE/PubMed. A semi-automated natural language processing algorithm was applied to identify penetrance papers for inclusion. Original studies reporting the penetrance of GAC were included and the full-text articles were independently reviewed. Summary statistics, effect estimates, and precision parameters from these studies were compiled into a table using a predetermined format to ensure consistency. RESULTS Forty-five studies were identified reporting the penetrance of GAC among patients harboring mutations in 13 different genes: APC, ATM, BRCA1, BRCA2, CDH1, CHEK2, MLH1, MSH2, MSH6, PMS2, MUTYH-Monoallelic, NBN, and STK11. CONCLUSION Our systematic review highlights the importance of testing for germline pathogenic variants in patients before the development of GAC. Management of patients who harbor a pathogenic mutation is multifactorial, and clinicians should consider cancer risk for each applicable gene-cancer association throughout the screening and management process. The scarcity of studies we found investigating the risk of GAC among patients with pathogenic variants in GAC susceptibility genes highlights the need for more investigations that focus on producing robust risk estimates for gene-cancer associations.
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Affiliation(s)
- Sahar Hosseini
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ahmet Acar
- Department of Emergency, Avrupa Hospital, Istanbul, Turkey
| | - Meghdeep Sen
- College of Medicine, American University of Antigua, Coolidge, Antigua, Antigua and Barbuda
| | - Kiersten Meeder
- Division of Oncologic and Endocrine Surgery, Department of Surgery, Medical University of South Carolina, Charleston, SC, USA
| | - Preeti Singh
- Department of Surgery, Montefiore Medical Center, Bronx, NY, USA
| | - Kanhua Yin
- Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Jeffrey M Sutton
- Division of Oncologic and Endocrine Surgery, Department of Surgery, Medical University of South Carolina, Charleston, SC, USA
| | - Kevin Hughes
- Division of Oncologic and Endocrine Surgery, Department of Surgery, Medical University of South Carolina, Charleston, SC, USA.
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22
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Genetic Considerations in the Locoregional Management of Breast Cancer: a Review of Current Evidence. CURRENT BREAST CANCER REPORTS 2023. [DOI: 10.1007/s12609-023-00478-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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23
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Fencer MG, Krupa KA, Bleich GC, Grumet S, Eladoumikdachi FG, Kumar S, Kowzun MJ, Potdevin LB. Diagnosis, Management, and Surveillance for Patients With PALB2, CHEK2, and ATM Gene Mutations. Clin Breast Cancer 2023; 23:e194-e199. [PMID: 36966080 DOI: 10.1016/j.clbc.2023.02.004] [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: 10/22/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/18/2023]
Abstract
BACKGROUND This study aims to capture clinical and surgical practice patterns of patients with deleterious mutations in partner and localizer of BRCA2 (PALB2), checkpoint kinase 2 (CHEK2) and ataxia telangiesctasia mutated (ATM) genes. MATERIALS AND METHODS This study is a retrospective chart review of patients with PALB2, CHEK2 or ATM mutations. Patient demographics, testing indications, management decisions, and surveillance strategies were recorded. RESULTS Sixty-two patients were found to have deleterious mutations: 14 (23%) with a PALB2 mutation, 30 (48%) with a CHEK2 mutation, and 18 (29%) patients with an ATM mutation. Thirty-one (50%) patients have a history of breast cancer. Twenty-three patients were diagnosed and treated prior to genetic testing while 8 patients learned of their mutation status and breast cancer diagnosis simultaneously. Of these 8 patients, 4 sought treatment at our institution, 3 underwent bilateral mastectomy, and 1 patient opted for lumpectomy and surveillance. Thirty-one patients had no history of breast cancer. After genetic diagnosis, 3 of the 9 patients who continued clinical follow-up proceeded with bilateral prophylactic mastectomy within 2 years. Clinical surveillance continued for 23 months on average. CONCLUSION Most patients who learned of their genetic and breast cancer diagnoses simultaneously underwent bilateral mastectomy, whereas only a third of patients without cancer opted for bilateral prophylactic mastectomy.
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Affiliation(s)
- Maria G Fencer
- Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, USA; Rutgers-New Jersey Medical School, Newark, NJ, USA.
| | - Kelly A Krupa
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | | | - Sherry Grumet
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | | | - Shicha Kumar
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Maria J Kowzun
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
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24
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Borja NA, Silva-Smith R, Huang M, Parekh DJ, Sussman D, Tekin M. Atypical ATMs: Broadening the phenotypic spectrum of ATM-associated hereditary cancer. Front Oncol 2023; 13:1068110. [PMID: 36865800 PMCID: PMC9971806 DOI: 10.3389/fonc.2023.1068110] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/03/2023] [Indexed: 02/16/2023] Open
Abstract
Heterozygous, loss-of-function germline variants in ATM have been associated with an increased lifetime risk of breast, pancreas, prostate, stomach, ovarian, colorectal, and melanoma cancers. We conducted a retrospective review of thirty-one unrelated patients found to be heterozygous for a germline pathogenic variant in ATM and identified a significant proportion of patients in this cohort with cancers not currently associated with the ATM hereditary cancer syndrome, including carcinomas of the gallbladder, uterus, duodenum, kidney, and lung as well as a vascular sarcoma. A comprehensive review of the literature found 25 relevant studies where 171 individuals with a germline deleterious ATM variant have been diagnosed with the same or similar cancers. The combined data from these studies were then used to estimate the prevalence of germline ATM pathogenic variants in these cancers, which ranged between 0.45% and 2.2%. Analysis of tumor sequencing performed in large cohorts demonstrated that the frequency of deleterious somatic ATM alterations in these atypical cancers equaled or exceeded the alteration frequency in breast cancer and occurred at a significantly higher rate than in other DNA-damage response tumor suppressors, namely BRCA1 and CHEK2. Furthermore, multi-gene analysis of somatic alterations in these atypical cancers demonstrated significant co-occurrence of pathogenic alterations in ATM with BRCA1 and CHEK2, while there was significant mutual exclusivity between pathogenic alterations in ATM and TP53. This indicates that germline ATM pathogenic variants may play a role in cancer initiation and progression in these atypical ATM malignancies, potentially influencing these cancers to be driven toward DNA-damage repair deficiency and away from loss of TP53. As such, these findings provide evidence for broadening of the ATM-cancer susceptibility syndrome phenotype to improve the recognition of affected patients and provide more efficacious, germline-directed therapies.
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Affiliation(s)
- Nicholas A. Borja
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Rachel Silva-Smith
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Marilyn Huang
- Division of Gynecologic Oncology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, United States
| | - Dipen J. Parekh
- Desai Sethi Urology Institute, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Daniel Sussman
- Division of Digestive Health and Liver Diseases, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Mustafa Tekin
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States,John P. Hussmann Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, United States,*Correspondence: Mustafa Tekin,
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25
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Chevarin M, Alcantara D, Albuisson J, Collonge-Rame MA, Populaire C, Selmani Z, Baurand A, Sawka C, Bertolone G, Callier P, Duffourd Y, Jonveaux P, Bignon YJ, Coupier I, Cornelis F, Cordier C, Mozelle-Nivoix M, Rivière JB, Kuentz P, Thauvin C, Boidot R, Ghiringhelli F, O'Driscoll M, Faivre L, Nambot S. The "extreme phenotype approach" applied to male breast cancer allows the identification of rare variants of ATR as potential breast cancer susceptibility alleles. Oncotarget 2023; 14:111-125. [PMID: 36749285 PMCID: PMC9904323 DOI: 10.18632/oncotarget.28358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/23/2023] [Indexed: 02/08/2023] Open
Abstract
In oncogenetics, some patients could be considered as "extreme phenotypes", such as those with very early onset presentation or multiple primary malignancies, unusually high numbers of cancers of the same spectrum or rare cancer types in the same parental branch. For these cases, a genetic predisposition is very likely, but classical candidate gene panel analyses often and frustratingly remains negative. In the framework of the EX2TRICAN project, exploring unresolved extreme cancer phenotypes, we applied exome sequencing on rare familial cases with male breast cancer, identifying a novel pathogenic variant of ATR (p.Leu1808*). ATR has already been suspected as being a predisposing gene to breast cancer in women. We next identified 3 additional ATR variants in a cohort of both male and female with early onset and familial breast cancers (c.7762-2A>C; c.2078+1G>A; c.1A>G). Further molecular and cellular investigations showed impacts on transcripts for variants affecting splicing sites and reduction of ATR expression and phosphorylation of the ATR substrate CHEK1. This work further demonstrates the interest of an extended genetic analysis such as exome sequencing to identify very rare variants that can play a role in cancer predisposition in extreme phenotype cancer cases unexplained by classical cancer gene panels testing.
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Affiliation(s)
- Martin Chevarin
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Unité Fonctionnelle Innovation diagnostique dans les maladies rares, laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon Bourgogne, Dijon, France
| | - Diana Alcantara
- Human DNA Damage Response Disorders Group, University of Sussex, Genome Damage and Stability Centre, Brighton, United Kingdom
| | - Juliette Albuisson
- Service d’Oncogénétique, Centre Georges François Leclerc, Dijon, France
- Département de biologie et pathologie des tumeurs, Centre Georges François Leclerc, Dijon, France
| | | | - Céline Populaire
- Oncobiologie Génétique Bioinformatique, PCBio, CHU Besançon, Besançon, France
| | - Zohair Selmani
- Oncobiologie Génétique Bioinformatique, PCBio, CHU Besançon, Besançon, France
| | - Amandine Baurand
- Service d’Oncogénétique, Centre Georges François Leclerc, Dijon, France
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Caroline Sawka
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Geoffrey Bertolone
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Patrick Callier
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Unité Fonctionnelle Innovation diagnostique dans les maladies rares, laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon Bourgogne, Dijon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | - Yannis Duffourd
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | - Philippe Jonveaux
- Laboratoire de Génétique Médicale, INSERM U954, Hôpitaux de Brabois, Vandoeuvre les Nancy, France
| | - Yves-Jean Bignon
- Laboratoire d’Oncologie Moléculaire, Centre Jean Perrin, Clermont-Ferrand, France
| | | | - François Cornelis
- Université Bordeaux, IMB, UMR 5251, Talence, France
- Service d’imagerie diagnostique et interventionnelle de l’adulte, Hôpital Pellegrin, CHU de Bordeaux, France
| | | | | | - Jean-Baptiste Rivière
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | - Paul Kuentz
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Oncobiologie Génétique Bioinformatique, PCBio, CHU Besançon, Besançon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | - Christel Thauvin
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Romain Boidot
- Département de biologie et pathologie des tumeurs, Centre Georges François Leclerc, Dijon, France
| | - François Ghiringhelli
- Département d’oncologie médicale, INSERM LNC U1231, Centre Georges François Leclerc, Dijon, France
| | - Marc O'Driscoll
- Human DNA Damage Response Disorders Group, University of Sussex, Genome Damage and Stability Centre, Brighton, United Kingdom
| | - Laurence Faivre
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Service d’Oncogénétique, Centre Georges François Leclerc, Dijon, France
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | - Sophie Nambot
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Service d’Oncogénétique, Centre Georges François Leclerc, Dijon, France
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
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26
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ATM suppresses c-Myc overexpression in the mammary epithelium in response to estrogen. Cell Rep 2023; 42:111909. [PMID: 36640339 PMCID: PMC10023214 DOI: 10.1016/j.celrep.2022.111909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/27/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
ATM gene mutation carriers are predisposed to estrogen-receptor-positive breast cancer (BC). ATM prevents BC oncogenesis by activating p53 in every cell; however, much remains unknown about tissue-specific oncogenesis after ATM loss. Here, we report that ATM controls the early transcriptional response to estrogens. This response depends on topoisomerase II (TOP2), which generates TOP2-DNA double-strand break (DSB) complexes and rejoins the breaks. When TOP2-mediated ligation fails, ATM facilitates DSB repair. After estrogen exposure, TOP2-dependent DSBs arise at the c-MYC enhancer in human BC cells, and their defective repair changes the activation profile of enhancers and induces the overexpression of many genes, including the c-MYC oncogene. CRISPR/Cas9 cleavage at the enhancer also causes c-MYC overexpression, indicating that this DSB causes c-MYC overexpression. Estrogen treatment induced c-Myc protein overexpression in mammary epithelial cells of ATM-deficient mice. In conclusion, ATM suppresses the c-Myc-driven proliferative effects of estrogens, possibly explaining such tissue-specific oncogenesis.
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27
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Nierenberg JL, Adamson AW, Hu D, Huntsman S, Patrick C, Li M, Steele L, Tong B, Shieh Y, Fejerman L, Gruber SB, Haiman CA, John EM, Kushi LH, Torres-Mejía G, Ricker C, Weitzel JN, Ziv E, Neuhausen SL. Whole exome sequencing and replication for breast cancer among Hispanic/Latino women identifies FANCM as a susceptibility gene for estrogen-receptor-negative breast cancer. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.25.23284924. [PMID: 36747679 PMCID: PMC9901069 DOI: 10.1101/2023.01.25.23284924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Introduction Breast cancer (BC) is one of the most common cancers globally. Genetic testing can facilitate screening and risk-reducing recommendations, and inform use of targeted treatments. However, genes included in testing panels are from studies of European-ancestry participants. We sequenced Hispanic/Latina (H/L) women to identify BC susceptibility genes. Methods We conducted a pooled BC case-control analysis in H/L women from the San Francisco Bay area, Los Angeles County, and Mexico (4,178 cases and 4,344 controls). Whole exome sequencing was conducted on 1,043 cases and 1,188 controls and a targeted 857-gene panel on the remaining samples. Using ancestry-adjusted SKAT-O analyses, we tested the association of loss of function (LoF) variants with overall, estrogen receptor (ER)-positive, and ER-negative BC risk. We calculated odds ratios (OR) for BC using ancestry-adjusted logistic regression models. We also tested the association of single variants with BC risk. Results We saw a strong association of LoF variants in FANCM with ER-negative BC (p=4.1×10-7, OR [CI]: 6.7 [2.9-15.6]) and a nominal association with overall BC risk. Among known susceptibility genes, BRCA1 (p=2.3×10-10, OR [CI]: 24.9 [6.1-102.5]), BRCA2 (p=8.4×10-10, OR [CI]: 7.0 [3.5-14.0]), and PALB2 (p=1.8×10-8, OR [CI]: 6.5 [3.2-13.1]) were strongly associated with BC. There were nominally significant associations with CHEK2, RAD51D, and TP53. Conclusion In H/L women, LoF variants in FANCM were strongly associated with ER-negative breast cancer risk. It previously was proposed as a possible susceptibility gene for ER-negative BC, but is not routinely tested in clinical practice. Our results demonstrate that FANCM should be added to BC gene panels.
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Affiliation(s)
- Jovia L Nierenberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Aaron W Adamson
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Carmina Patrick
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Min Li
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Linda Steele
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Barry Tong
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yiwey Shieh
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Laura Fejerman
- Department of Public Health Service, University of California, Davis, Davis, CA, USA
- UC Davis Comprehensive Cancer Center, University of California, Davis, Davis, CA, USA
| | - Stephen B Gruber
- Department of Medical Oncology and Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Esther M John
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | | | - Charité Ricker
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Elad Ziv
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
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28
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Genetic Predisposition to Colorectal Cancer: How Many and Which Genes to Test? Int J Mol Sci 2023; 24:ijms24032137. [PMID: 36768460 PMCID: PMC9916931 DOI: 10.3390/ijms24032137] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/25/2023] Open
Abstract
Colorectal cancer is one of the most common tumors, and genetic predisposition is one of the key risk factors in the development of this malignancy. Lynch syndrome and familial adenomatous polyposis are the best-known genetic diseases associated with hereditary colorectal cancer. However, some other genetic disorders confer an increased risk of colorectal cancer, such as Li-Fraumeni syndrome (TP53 gene), MUTYH-associated polyposis (MUTYH gene), Peutz-Jeghers syndrome (STK11 gene), Cowden syndrome (PTEN gene), and juvenile polyposis syndrome (BMPR1A and SMAD4 genes). Moreover, the recent advances in molecular techniques, in particular Next-Generation Sequencing, have led to the identification of many new genes involved in the predisposition to colorectal cancers, such as RPS20, POLE, POLD1, AXIN2, NTHL1, MSH3, RNF43 and GREM1. In this review, we summarized the past and more recent findings in the field of cancer predisposition genes, with insights into the role of the encoded proteins and into the associated genetic disorders. Furthermore, we discussed the possible clinical utility of genetic testing in terms of prevention protocols and therapeutic approaches.
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Miyazaki A, Itoi-Ochi S, Hayashi M, Ota A, Nagai K, Inoue S, Tomita N, Eguchi H, Okazaki Y, Ishida H, Hashimoto T. A Case of Lamina Lucida-Type Linear IgA Disease Complicated by Colon Polyposis and Rectal Adenocarcinoma. Case Rep Dermatol 2023; 15:126-132. [PMID: 37899945 PMCID: PMC10601694 DOI: 10.1159/000532104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/19/2023] [Indexed: 10/31/2023] Open
Abstract
Linear IgA disease (LAD) is a rare autoimmune bullous disease characterized by IgA deposition in the basement membrane zone (BMZ). A 66-year-old male was treated for myelodysplastic syndrome at our hospital for 5 years, during which his condition remained stable. He visited our department because of erythema with itching, which appeared 1 year ago and gradually exacerbated with the development of blisters and erosions. During the first visit, multiple erythemas with erosions and crusts on their periphery were observed on the trunk and lower limbs. Histopathological examination revealed subepidermal blisters with inflammatory cell infiltration, mainly constituting of neutrophils, eosinophils, and lymphocytes. Direct and indirect immunofluorescence showed linear IgA deposits in the BMZ and IgA anti-BMZ antibodies, respectively, while immunoblotting using a concentrated culture supernatant of HaCaT cells detected IgA antibodies reactive to 120-kDa LAD-1. Accordingly, the patient was diagnosed with lamina lucida-type LAD. Subsequent colonoscopy revealed multiple colorectal polyps and rectal adenocarcinoma (Tis, N0, and M0). Multigene panel test showed an ATM variant of unknown significance but did not detect any pathogenic variants associated with intestinal polyposis syndrome. The skin lesions quickly resolved with oral diaphenylsulfone 50 mg/day and resection of the colorectal polyps and adenocarcinoma. To our knowledge, this is the first reported case of LAD associated with multiple colorectal polyps and rectal adenocarcinoma. Additionally, we also analyzed reported cases of LAD associated with malignancy from the literature.
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Affiliation(s)
- Akiko Miyazaki
- Department of Dermatology, Suita Municipal Hospital, Osaka, Japan
| | - Saori Itoi-Ochi
- Department of Dermatology, Suita Municipal Hospital, Osaka, Japan
| | - Mami Hayashi
- Department of Dermatology, Suita Municipal Hospital, Osaka, Japan
| | - Asako Ota
- Department of Dermatology, Suita Municipal Hospital, Osaka, Japan
| | - Kengo Nagai
- Department of Gastroenterology, Suita Municipal Hospital, Osaka, Japan
| | - Shinya Inoue
- Department of Hematology, Suita Municipal Hospital, Osaka, Japan
| | - Naohiro Tomita
- Cancer Treatment Center, Toyonaka Municipal Hospital, Osaka, Japan
| | - Hidetaka Eguchi
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Hideyuki Ishida
- Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Saitama, Japan
| | - Takashi Hashimoto
- Department of Dermatology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
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El Nachef L, Berthel E, Ferlazzo ML, Le Reun E, Al-Choboq J, Restier-Verlet J, Granzotto A, Sonzogni L, Bourguignon M, Foray N. Cancer and Radiosensitivity Syndromes: Is Impaired Nuclear ATM Kinase Activity the Primum Movens? Cancers (Basel) 2022; 14:cancers14246141. [PMID: 36551628 PMCID: PMC9776478 DOI: 10.3390/cancers14246141] [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: 10/28/2022] [Revised: 12/01/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
There are a number of genetic syndromes associated with both high cancer risk and clinical radiosensitivity. However, the link between these two notions remains unknown. Particularly, some cancer syndromes are caused by mutations in genes involved in DNA damage signaling and repair. How are the DNA sequence errors propagated and amplified to cause cell transformation? Conversely, some cancer syndromes are caused by mutations in genes involved in cell cycle checkpoint control. How is misrepaired DNA damage produced? Lastly, certain genes, considered as tumor suppressors, are not involved in DNA damage signaling and repair or in cell cycle checkpoint control. The mechanistic model based on radiation-induced nucleoshuttling of the ATM kinase (RIANS), a major actor of the response to ionizing radiation, may help in providing a unified explanation of the link between cancer proneness and radiosensitivity. In the frame of this model, a given protein may ensure its own specific function but may also play additional biological role(s) as an ATM phosphorylation substrate in cytoplasm. It appears that the mutated proteins that cause the major cancer and radiosensitivity syndromes are all ATM phosphorylation substrates, and they generally localize in the cytoplasm when mutated. The relevance of the RIANS model is discussed by considering different categories of the cancer syndromes.
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Affiliation(s)
- Laura El Nachef
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Elise Berthel
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Mélanie L. Ferlazzo
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Eymeric Le Reun
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Joelle Al-Choboq
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Juliette Restier-Verlet
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Adeline Granzotto
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Laurène Sonzogni
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Michel Bourguignon
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
- Department of Biophysics and Nuclear Medicine, Université Paris Saclay (UVSQ), 78035 Versailles, France
| | - Nicolas Foray
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
- Correspondence: ; Tel.: +33-04-7878-2828
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31
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McCarthy-Leo C, Darwiche F, Tainsky MA. DNA Repair Mechanisms, Protein Interactions and Therapeutic Targeting of the MRN Complex. Cancers (Basel) 2022; 14:5278. [PMID: 36358700 PMCID: PMC9656488 DOI: 10.3390/cancers14215278] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 08/27/2023] Open
Abstract
Repair of a DNA double-strand break relies upon a pathway of proteins to identify damage, regulate cell cycle checkpoints, and repair the damage. This process is initiated by a sensor protein complex, the MRN complex, comprised of three proteins-MRE11, RAD50, and NBS1. After a double-stranded break, the MRN complex recruits and activates ATM, in-turn activating other proteins such as BRCA1/2, ATR, CHEK1/2, PALB2 and RAD51. These proteins have been the focus of many studies for their individual roles in hereditary cancer syndromes and are included on several genetic testing panels. These panels have enabled us to acquire large amounts of genetic data, much of which remains a challenge to interpret due to the presence of variants of uncertain significance (VUS). While the primary aim of clinical testing is to accurately and confidently classify variants in order to inform medical management, the presence of VUSs has led to ambiguity in genetic counseling. Pathogenic variants within MRN complex genes have been implicated in breast, ovarian, prostate, colon cancers and gliomas; however, the hundreds of VUSs within MRE11, RAD50, and NBS1 precludes the application of these data in genetic guidance of carriers. In this review, we discuss the MRN complex's role in DNA double-strand break repair, its interactions with other cancer predisposing genes, the variants that can be found within the three MRN complex genes, and the MRN complex's potential as an anti-cancer therapeutic target.
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Affiliation(s)
- Claire McCarthy-Leo
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Fatima Darwiche
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Michael A. Tainsky
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Molecular Therapeutics Program, Karmanos Cancer Institute at Wayne State University School of Medicine, Detroit, MI 48201, USA
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32
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Li S, MacInnis RJ, Lee A, Nguyen-Dumont T, Dorling L, Carvalho S, Dite GS, Shah M, Luccarini C, Wang Q, Milne RL, Jenkins MA, Giles GG, Dunning AM, Pharoah PDP, Southey MC, Easton DF, Hopper JL, Antoniou AC. Segregation analysis of 17,425 population-based breast cancer families: Evidence for genetic susceptibility and risk prediction. Am J Hum Genet 2022; 109:1777-1788. [PMID: 36206742 PMCID: PMC9606477 DOI: 10.1016/j.ajhg.2022.09.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/12/2022] [Indexed: 01/25/2023] Open
Abstract
Rare pathogenic variants in known breast cancer-susceptibility genes and known common susceptibility variants do not fully explain the familial aggregation of breast cancer. To investigate plausible genetic models for the residual familial aggregation, we studied 17,425 families ascertained through population-based probands, 86% of whom were screened for pathogenic variants in BRCA1, BRCA2, PALB2, CHEK2, ATM, and TP53 via gene-panel sequencing. We conducted complex segregation analyses and fitted genetic models in which breast cancer incidence depended on the effects of known susceptibility genes and other unidentified major genes and a normally distributed polygenic component. The proportion of familial variance explained by the six genes was 46% at age 20-29 years and decreased steadily with age thereafter. After allowing for these genes, the best fitting model for the residual familial variance included a recessive risk component with a combined genotype frequency of 1.7% (95% CI: 0.3%-5.4%) and a penetrance to age 80 years of 69% (95% CI: 38%-95%) for homozygotes, which may reflect the combined effects of multiple variants acting in a recessive manner, and a polygenic variance of 1.27 (95% CI: 0.94%-1.65), which did not vary with age. The proportion of the residual familial variance explained by the recessive risk component was 40% at age 20-29 years and decreased with age thereafter. The model predicted age-specific familial relative risks consistent with those observed by large epidemiological studies. The findings have implications for strategies to identify new breast cancer-susceptibility genes and improve disease-risk prediction, especially at a young age.
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Affiliation(s)
- Shuai Li
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, 207 Bouverie Street, Carlton, VIC 3053, Australia; Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3051, Australia.
| | - Robert J MacInnis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, 207 Bouverie Street, Carlton, VIC 3053, Australia; Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC 3004, Australia
| | - Andrew Lee
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Tu Nguyen-Dumont
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3051, Australia
| | - Leila Dorling
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Gillian S Dite
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, 207 Bouverie Street, Carlton, VIC 3053, Australia; Genetic Technologies Ltd., Fitzroy, VIC 3065, Australia
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, 207 Bouverie Street, Carlton, VIC 3053, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia; Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC 3004, Australia
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, 207 Bouverie Street, Carlton, VIC 3053, Australia
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, 207 Bouverie Street, Carlton, VIC 3053, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia; Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC 3004, Australia
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia; Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3051, Australia
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, 207 Bouverie Street, Carlton, VIC 3053, Australia
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
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Loveday C, Garrett A, Law P, Hanks S, Poyastro-Pearson E, Adlard JW, Barwell J, Berg J, Brady AF, Brewer C, Chapman C, Cook J, Davidson R, Donaldson A, Douglas F, Greenhalgh L, Henderson A, Izatt L, Kumar A, Lalloo F, Miedzybrodzka Z, Morrison PJ, Paterson J, Porteous M, Rogers MT, Walker L, Eccles D, Evans DG, Snape K, Hanson H, Houlston RS, Turnbull C. Analysis of rare disruptive germline mutations in 2,135 enriched BRCA-negative breast cancers excludes additional high-impact susceptibility genes. Ann Oncol 2022; 33:1318-1327. [PMID: 36122798 DOI: 10.1016/j.annonc.2022.09.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 08/15/2022] [Accepted: 09/01/2022] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND Breast cancer has a significant heritable basis, of which approximately 60% remains unexplained. Testing for BRCA1/BRCA2 offers useful discrimination of breast cancer risk within families, and identification of additional breast cancer susceptibility genes could offer clinical utility. PATIENTS AND METHODS We included 2,135 invasive breast cancer cases recruited via the BOCS study, a retrospective UK study of familial breast cancer. ELIGIBILITY CRITERIA female, BRCA-negative, white European ethnicity, and one of: i) breast cancer family history, ii) bilateral disease, iii) young age of onset (<30 years), iv) concomitant ovarian cancer. We undertook exome sequencing of cases and performed gene-level burden testing of rare damaging variants against those from 51,377 ethnicity-matched population controls from gnomAD. RESULTS 159/2135 (7.4%) cases had a qualifying variant in an established breast cancer susceptibility gene, with minimal evidence of signal in other cancer susceptibility genes. Known breast cancer susceptibility genes PALB2, CHEK2 and ATM were the only genes to retain statistical significance after correcting for multiple testing. Due to the enrichment of hereditary cases in the series, we had good power (>80%) to detect a gene of BRCA1-like risk (odds ratio = 10.6) down to a population minor allele frequency of 4.6 x 10-5 (1 in 10,799, less than one tenth that of BRCA1)and of PALB2-like risk (odds ratio = 5.0) down to a population minor allele frequency of 2.8 x 10-4 (1 in 1,779, less than half that of PALB2). Power was lower for identification of novel moderate penetrance genes (odds ratio = 2-3) like CHEK2 and ATM. CONCLUSIONS This is the largest case-control whole-exome analysis of enriched breast cancer published to date. Whilst additional breast cancer susceptibility genes likely exist, those of high penetrance are likely to be of very low mutational frequency. Contention exists regarding the clinical utility of such genes.
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Affiliation(s)
- C Loveday
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - A Garrett
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - P Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - S Hanks
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - E Poyastro-Pearson
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - J W Adlard
- Yorkshire Regional Genetics Service, St James's University Hospital, Leeds, UK
| | - J Barwell
- Leicestershire Genetics Centre, University Hospitals of Leicester National Health Service (NHS) Trust, Leicester, UK
| | - J Berg
- Division of Medical Sciences, Human Genetics, University of Dundee, Dundee, UK
| | - A F Brady
- North West Thames Regional Genetics Service, Kennedy Galton Centre, London, UK
| | - C Brewer
- Peninsula Regional Genetics Service, Royal Devon & Exeter Hospital, Exeter, UK
| | - C Chapman
- West Midlands Regional Genetics Service, Birmingham Women's Hospital, Birmingham, UK
| | - J Cook
- Sheffield Regional Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - R Davidson
- West of Scotland Regional Genetics Service, Ferguson Smith Centre for Clinical Genetics, Glasgow, UK
| | - A Donaldson
- South Western Regional Genetics Service, University Hospitals of Bristol NHS Foundation Trust, Bristol, UK
| | - F Douglas
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - L Greenhalgh
- Cheshire and Merseyside Clinical Genetics Service, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - A Henderson
- Northern Genetics Service (Cumbria), Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK
| | - L Izatt
- South East Thames Regional Genetics Service, Guy's and St. Thomas NHS Foundation Trust, London, UK
| | - A Kumar
- North East Thames Regional Genetics Service, Great Ormond St. Hospital, London, UK
| | - F Lalloo
- University Department of Medical Genetics & Regional Genetics Service, St. Mary's Hospital, Manchester, UK
| | - Z Miedzybrodzka
- University of Aberdeen and North of Scotland Clinical Genetics Service, Aberdeen Royal Infirmary, Aberdeen, UK
| | - P J Morrison
- Belfast Health and Social Care (HSC) Trust & Department of Medical Genetics, Northern Ireland Regional Genetics Service, Queen's University Belfast, Belfast, UK
| | - J Paterson
- East Anglian Regional Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - M Porteous
- South East of Scotland Clinical Genetics Service, Western General Hospital, Edinburgh, UK
| | - M T Rogers
- All Wales Medical Genetics Service, University Hospital of Wales, Cardiff, UK
| | - L Walker
- Oxford Regional Genetics Service, Oxford Radcliffe Hospitals NHS Trust, Oxford, UK
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- Individual collaborators and their affiliations are listed in the Appendix
| | - D Eccles
- Faculty of Medicine, University of Southampton, Southampton University Hospitals NHS Trust, Southampton, UK
| | - D G Evans
- University Department of Medical Genetics & Regional Genetics Service, St. Mary's Hospital, Manchester, UK
| | - K Snape
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.; South West Thames Regional Genetics Service, St. George's Hospital, London, UK
| | - H Hanson
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.; South West Thames Regional Genetics Service, St. George's Hospital, London, UK
| | - R S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - C Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.; Royal Marsden NHS Foundation Hospital, London, UK.
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Laitman Y, Nielsen SM, Bernstein-Molho R, Heald B, Hatchell KE, Esplin ED, Friedman E. Cancer risks associated with heterozygous ATM loss of function and missense pathogenic variants based on multigene panel analysis. Breast Cancer Res Treat 2022; 196:355-361. [PMID: 36094610 DOI: 10.1007/s10549-022-06723-z] [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: 06/13/2022] [Accepted: 08/19/2022] [Indexed: 11/02/2022]
Abstract
PURPOSE Cancer risks conferred by germline, heterozygous, ATM pathogenic/likely pathogenic variants (PSVs) are yet to be consistently determined. The current study assessed these risks by analysis of a large dataset of ATM heterozygote loss of function (LOF) and missense PSV carriers tested with a multigene panel (MGP). METHODS De-identified data of all individuals who underwent ATM sequencing as part of MGP between October 2015 and February 2020 were reviewed. In cancer cases, rates for the six most prevalent variants and for all LOF and missense PSV combined were compared with rates of the same PSV in ethnically matched, healthy population controls. Statistical analysis included Chi-square tests and odds ratios calculations. RESULTS For female breast cancer cases, LOF )1794/219,269) and missense (301/219,269) ATM PSVs were seen at higher rates compared to gnomAD non-cancer controls (n = 157/56,001 and n = 27/61,208; p < 0.00001, respectively). Notably, the rate of the c.103C > T variant was higher in controls than in breast cancer cases [p = 0.001; OR 0.31 (95% CI 0.1-0.6)]. For all cancer cases combined, compared with non-cancer population controls, LOF (n = 143) and missense (n = 15) PSVs reported in both datasets were significantly more prevalent in cancer cases [ORLOF 1.7 (95% 1.5-1.9) ORmissense 3.0 (95% CI 2.3-4); p = 0.0001]. CONCLUSION Both LOF and missense heterozygous ATM PSVs are more frequently detected in cases of several cancer types (breast, ovarian, prostate, lung, pancreatic) compared with healthy population controls. However, not all ATM PSVs confer an increased cancer risk (e.g., breast).
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Affiliation(s)
- Yael Laitman
- The Oncogenetics Unit, Institute of Human Genetics, The Sheba Medical Center, Tel-Hashomer, Israel
| | | | - Rinat Bernstein-Molho
- The Oncogenetics Unit, Institute of Human Genetics, The Sheba Medical Center, Tel-Hashomer, Israel.,The Breast Cancer Unit, Oncology Institute, The Sheba Medical Center, Tel-Hashomer, Israel.,The Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | | | | | | | - Eitan Friedman
- The Oncogenetics Unit, Institute of Human Genetics, The Sheba Medical Center, Tel-Hashomer, Israel. .,The Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel. .,Meirav High-Risk Clinic, Sheba Medical Center, 52621, Tel-Hashomer, Israel.
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35
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Peters MLB, Eckel A, Lietz A, Seguin C, Mueller P, Hur C, Pandharipande PV. Genetic testing to guide screening for pancreatic ductal adenocarcinoma: Results of a microsimulation model. Pancreatology 2022; 22:760-769. [PMID: 35752568 PMCID: PMC9474673 DOI: 10.1016/j.pan.2022.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND First-degree relatives (FDRs) of patients with pancreatic ductal adenocarcinoma (PDAC) have elevated PDAC risk, partially due to germline genetic variants. We evaluated the potential effectiveness of genetic testing to target MRI-based screening among FDRs. METHODS We used a microsimulation model of PDAC, calibrated to Surveillance, Epidemiology, and End Results (SEER) data, to estimate the potential life expectancy (LE) gain of screening for each of the following groups of FDRs: individuals who test positive for each of eight variants associated with elevated PDAC risk (e.g., BRCA2, CDKN2A); individuals who test negative; and individuals who do not test. Screening was assumed to take place if LE gains were achievable. We simulated multiple screening approaches, defined by starting age and frequency. Sensitivity analysis evaluated changes in results given varying model assumptions. RESULTS For women, 92% of mutation carriers had projected LE gains from screening for PDAC, if screening strategies (start age, frequency) were optimized. Among carriers, LE gains ranged from 0.1 days (ATM+ women screened once at age 70) to 510 days (STK11+ women screened annually from age 40). For men, LE gains were projected for all mutation carriers, ranging from 0.2 days (BRCA1+ men screened once at age 70) to 620 days (STK11+ men screened annually from age 40). For men and women who did not undergo genetic testing, or for whom testing showed no variant, screening yielded small LE benefit (0-2.1 days). CONCLUSIONS Genetic testing of FDRs can inform targeted PDAC screening by identifying which FDRs may benefit.
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Affiliation(s)
- Mary Linton B Peters
- Division of Medical Oncology, Department of Medicine, Beth Israel Deaconess Medical Center, USA.
| | - Andrew Eckel
- Institute for Technology Assessment, Massachusetts General Hospital, USA
| | - Anna Lietz
- Institute for Technology Assessment, Massachusetts General Hospital, USA
| | - Claudia Seguin
- Institute for Technology Assessment, Massachusetts General Hospital, USA
| | - Peter Mueller
- Institute for Technology Assessment, Massachusetts General Hospital, USA
| | - Chin Hur
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Current Affiliation: Division of Gastroenterology, Columbia University College of Physicians and Surgeons, USA
| | - Pari V Pandharipande
- Institute for Technology Assessment and Department of Radiology, Massachusetts General Hospital, USA
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Frequency of germline genetic variants in women with a personal or family history of breast cancer from Brazil. Mol Biol Rep 2022; 49:9509-9520. [PMID: 35980532 DOI: 10.1007/s11033-022-07840-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/03/2022] [Indexed: 01/10/2023]
Abstract
BACKGROUND About 5-10% of breast cancer cases are related to genetic and hereditary factors. The application of Next Generation Sequencing (NGS) in oncology has allowed the identification of genetic variants present in several genes related to the increased risk of breast cancer. This study aimed to determine the frequency of germline genetic variants in patients with a family and/or personal history of breast cancer. METHODS An analysis of positive reports from NGS panels was carried out in female individuals with a personal and/or family history of breast cancer, present in the database of a private laboratory in Brazil. RESULTS From about 2000 reports, 183 individuals presented 219 different germline genetic variants. The genes with the highest number of variants were BRCA2 (16.0%), ATM (15.0%) and BRCA1 (12.8%). Among the variants found, 78 were either pathogenic or probably pathogenic, accounting for 35% of all variants discovered. The gene with the highest proportion of pathogenic/probably pathogenic variants was TP53 (80%) and the most frequent pathogenic variant was also reported in this gene (c.1010G > A p.(Arg337His)). Furthermore, the study obtained a high proportion of variants of uncertain significance (VUS) (65%) and approximately 32% of the variants found were in genes of moderate penetrance. CONCLUSIONS Our results could improve the risk estimation and clinical follow-up of Brazilian patients with a history of breast cancer.
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A Genome-First Approach to Estimate Prevalence of Germline Pathogenic Variants and Risk of Pancreatic Cancer in Select Cancer Susceptibility Genes. Cancers (Basel) 2022; 14:cancers14133257. [PMID: 35805029 PMCID: PMC9265005 DOI: 10.3390/cancers14133257] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/28/2022] [Accepted: 07/01/2022] [Indexed: 12/20/2022] Open
Abstract
Patients with germline pathogenic variants (GPV) in cancer predisposition genes are at increased risk of pancreatic ductal adenocarcinoma (PDAC), the most common type of pancreatic cancer. The genes most frequently found to harbor GPV in unselected PDAC cases are ATM, BRCA1, BRCA2, CDKN2A, CHEK2, and PALB2. However, GPV prevalence and gene-specific associations have not been extensively studied in the general population. To further explore these associations, we analyzed genomic and phenotypic data obtained from the UK Biobank (UKB) and Geisinger MyCode Community Health Initiative (GHS) cohorts comprising 200,600 and 175,449 participants, respectively. We estimated the frequency and calculated relative risks (RRs) of heterozygotes in both cohorts and a subset of individuals with PDAC. The combined frequency of heterozygous carriers of GPV in the general population ranged from 1.22% for CHEK2 to 0.05% for CDKN2A. The frequency of GPV in PDAC cases varied from 2.38% (ATM) to 0.19% (BRCA1 and CDKN2A). The RRs of PDAC were elevated for all genes except for BRCA1 and varied widely by gene from high (ATM) to low (CHEK2, BRCA2). This work expands our understanding of the frequencies of GPV heterozygous carriers and associations between PDAC and GPV in several important PDAC susceptibility genes.
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Aguiar T, Teixeira A, Scliar MO, Sobral de Barros J, Lemes RB, Souza S, Tolezano G, Santos F, Tojal I, Cypriano M, Caminada de Toledo SR, Valadares E, Borges Pinto R, Pinto Artigalas OA, Caetano de Aguirre Neto J, Novak E, Cristofani LM, Miura Sugayama SM, Odone V, Cunha IW, Lima da Costa CM, Rosenberg C, Krepischi A. Unraveling the Genetic Architecture of Hepatoblastoma Risk: Birth Defects and Increased Burden of Germline Damaging Variants in Gastrointestinal/Renal Cancer Predisposition and DNA Repair Genes. Front Genet 2022; 13:858396. [PMID: 35495172 PMCID: PMC9039399 DOI: 10.3389/fgene.2022.858396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/08/2022] [Indexed: 12/21/2022] Open
Abstract
The ultrarare hepatoblastoma (HB) is the most common pediatric liver cancer. HB risk is related to a few rare syndromes, and the molecular bases remain elusive for most cases. We investigated the burden of rare damaging germline variants in 30 Brazilian patients with HB and the presence of additional clinical signs. A high frequency of prematurity (20%) and birth defects (37%), especially craniofacial (17%, including craniosynostosis) and kidney (7%) anomalies, was observed. Putative pathogenic or likely pathogenic monoallelic germline variants mapped to 10 cancer predisposition genes (CPGs: APC, CHEK2, DROSHA, ERCC5, FAH, MSH2, MUTYH, RPS19, TGFBR2 and VHL) were detected in 33% of the patients, only 40% of them with a family history of cancer. These findings showed a predominance of CPGs with a known link to gastrointestinal/colorectal and renal cancer risk. A remarkable feature was an enrichment of rare damaging variants affecting different classes of DNA repair genes, particularly those known as Fanconi anemia genes. Moreover, several potentially deleterious variants mapped to genes impacting liver functions were disclosed. To our knowledge, this is the largest assessment of rare germline variants in HB patients to date, contributing to elucidate the genetic architecture of HB risk.
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Affiliation(s)
- Talita Aguiar
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Columbia University Irving Medical Center, New York, NY, United States
| | - Anne Teixeira
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Marília O. Scliar
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Juliana Sobral de Barros
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Renan B. Lemes
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Silvia Souza
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Giovanna Tolezano
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Fernanda Santos
- Department of Pediatric Oncology, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Israel Tojal
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Monica Cypriano
- GRAACC—Grupo de Apoio Ao Adolescente e Criança Com Câncer, Federal University of São Paulo, São Paulo, Brazil
| | | | - Eugênia Valadares
- Benjamim Guimarães Foundation - Department of Pediatrics Hospital da Baleia, Belo Horizonte, Brazil
| | - Raquel Borges Pinto
- Department of Genetics, Hospital da Criança Conceição, Hospitalar Conceição Group, Porto Alegre, Brazil
| | | | | | - Estela Novak
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
- Molecular Genetics—Foundation Pro Sangue Blood Center of São Paulo, São Paulo, Brazil
| | - Lilian Maria Cristofani
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Sofia M. Miura Sugayama
- Department of Pediatric, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil
| | - Vicente Odone
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | | | | | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ana Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- *Correspondence: Ana Krepischi,
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Lesueur F, Easton DF, Renault AL, Tavtigian SV, Bernstein JL, Kote-Jarai Z, Eeles RA, Plaseska-Karanfia D, Feliubadaló L, Arun B, Herold N, Versmold B, Schmutzler RK, Nguyen-Dumont T, Southey MC, Dorling L, Dunning AM, Ghiorzo P, Dalmasso BS, Cavaciuti E, Le Gal D, Roberts NJ, Dominguez-Valentin M, Rookus M, Taylor AMR, Goldstein AM, Goldgar DE, Stoppa-Lyonnet D, Andrieu N. First international workshop of the ATM and cancer risk group (4-5 December 2019). Fam Cancer 2022; 21:211-227. [PMID: 34125377 PMCID: PMC9969796 DOI: 10.1007/s10689-021-00248-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 03/17/2021] [Indexed: 12/17/2022]
Abstract
The first International Workshop of the ATM and Cancer Risk group focusing on the role of Ataxia-Telangiectasia Mutated (ATM) gene in cancer was held on December 4 and 5, 2019 at Institut Curie in Paris, France. It was motivated by the fact that germline ATM pathogenic variants have been found to be associated with different cancer types. However, due to the lack of precise age-, sex-, and site-specific risk estimates, no consensus on management guidelines for variant carriers exists, and the clinical utility of ATM variant testing is uncertain. The meeting brought together epidemiologists, geneticists, biologists and clinicians to review current knowledge and on-going challenges related to ATM and cancer risk. This report summarizes the meeting sessions content that covered the latest results in family-based and population-based studies, the importance of accurate variant classification, the effect of radiation exposures for ATM variant carriers, and the characteristics of ATM-deficient tumors. The report concludes that ATM variant carriers outside of the context of Ataxia-Telangiectasia may benefit from effective cancer risk management and therapeutic strategies and that efforts to set up large-scale studies in the international framework to achieve this goal are necessary.
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Affiliation(s)
- Fabienne Lesueur
- Genetic Epidemiology of Cancer Team, INSERM U900, Institut Curie, 26 rue d'Ulm, 75005, Paris, France
- Institut Curie, Paris, France
- Mines ParisTech, Fontainebleau, France
- PSL Research University, Paris, France
| | - Douglas F Easton
- Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Cambridge, UK
- Department of Oncology, Strangeways Research Laboratory, University of Cambridge, Cambridge, UK
| | - Anne-Laure Renault
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | | | | | | | | | - Dijana Plaseska-Karanfia
- Research Centre for Genetic Engineering and Biotechnology « Georgi D. Efremov », MASA, Skopje, UK
| | - Lidia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Banu Arun
- University of Texas MD Anderson Cancer Center, Houston, USA
| | - Natalie Herold
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Beatrix Versmold
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Rita Katharina Schmutzler
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Tú Nguyen-Dumont
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Victoria, 3004, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Victoria, 3004, Australia
| | - Leila Dorling
- Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Department of Oncology, Strangeways Research Laboratory, University of Cambridge, Cambridge, UK
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Bruna Samia Dalmasso
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Eve Cavaciuti
- Genetic Epidemiology of Cancer Team, INSERM U900, Institut Curie, 26 rue d'Ulm, 75005, Paris, France
- Institut Curie, Paris, France
- Mines ParisTech, Fontainebleau, France
- PSL Research University, Paris, France
| | - Dorothée Le Gal
- Genetic Epidemiology of Cancer Team, INSERM U900, Institut Curie, 26 rue d'Ulm, 75005, Paris, France
- Institut Curie, Paris, France
- Mines ParisTech, Fontainebleau, France
- PSL Research University, Paris, France
| | - Nicholas J Roberts
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University, Baltimore, USA
| | - Mev Dominguez-Valentin
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Matti Rookus
- Netherlands Cancer Institute NKI, Amsterdam, The Netherlands
| | - Alexander M R Taylor
- Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, UK
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, USA
| | | | - Dominique Stoppa-Lyonnet
- Université Paris Descartes, Paris, France
- Service de Génétique, Institut Curie, Paris, France
- INSERM U830, Paris, France
| | - Nadine Andrieu
- Genetic Epidemiology of Cancer Team, INSERM U900, Institut Curie, 26 rue d'Ulm, 75005, Paris, France.
- Institut Curie, Paris, France.
- Mines ParisTech, Fontainebleau, France.
- PSL Research University, Paris, France.
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Ramamurthy C, Nassar AH, Abou Alaiwi S, Adib E, Akl EW, Yang S, Esplin ED, Liss MA, Tomlinson GE, Sonpavde GP. Prevalence of pathogenic germline cancer risk variants in testicular cancer patients: Identifying high risk groups. Urol Oncol 2022; 40:113.e9-113.e15. [PMID: 35022142 DOI: 10.1016/j.urolonc.2021.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/14/2021] [Accepted: 12/15/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Germline studies in testicular cancer have focused on unselected populations but so far have not led to recommendations for testicular cancer screening. OBJECTIVE Herein, we hypothesized that men with testicular cancer and an additional risk factor for hereditary cancer predisposition carry a higher rate of pathogenic variants than men with testicular cancer without another risk factor. METHODS AND RESULTS 187 patients with a personal history of testicular cancer underwent germline testing via Invitae. Patients were divided into low-risk and high-risk patients. Low-risk patients (n=83) had testicular cancer as their only primary malignancy without a family history of testicular cancer. High-risk patients (n=104) had additional primary malignancies and/or a family history of testicular cancer. 23.1% of patients harbored pathogenic germline variants with 19.6% carrying actionable variants. Among low-risk patients, 13.5% carried pathogenic variants versus 29.9% in the high-risk cohort. Of patients with a family history of non-testicular cancers and a personal history of additional primary malignancies, 32% harbored pathogenic variants. CONCLUSION High-risk patients are twice as likely to harbor pathogenic variants compared to low-risk patients. Importantly, patients with a family history of cancer and other primary malignancies represent a subset of patients that may benefit from genetic evaluation.
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Affiliation(s)
| | - Amin H Nassar
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Sarah Abou Alaiwi
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Elio Adib
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Elie W Akl
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Shan Yang
- Invitae Corporation, San Francisco, CL
| | | | - Michael A Liss
- Department of Medical Oncology, UT Health San Antonio, San Antonio, TX
| | - Gail E Tomlinson
- Department of Pediatrics, Division of Hematology and Oncology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Guru P Sonpavde
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA
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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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Shen L, Zhang S, Wang K, Wang X. Familial Breast Cancer: Disease Related Gene Mutations and Screening Strategies for Chinese Population. Front Oncol 2021; 11:740227. [PMID: 34926254 PMCID: PMC8671637 DOI: 10.3389/fonc.2021.740227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/12/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND About 5%-10% of the breast cancer cases have a hereditary background, and this subset is referred to as familial breast cancer (FBC). In this review, we summarize the susceptibility genes and genetic syndromes associated with FBC and discuss the FBC screening and high-risk patient consulting strategies for the Chinese population. METHODS We searched the PubMed database for articles published between January 2000 and August 2021. Finally, 380 pieces of literature addressing the genes and genetic syndromes related to FBC were included and reviewed. RESULTS We identified 16 FBC-related genes and divided them into three types (high-, medium-, and low-penetrance) of genes according to their relative risk ratios. In addition, six genetic syndromes were found to be associated with FBC. We then summarized the currently available screening strategies for FBC and discussed those available for high-risk Chinese populations. CONCLUSION Multiple gene mutations and genetic disorders are closely related to FBC. The National Comprehensive Cancer Network (NCCN) guidelines recommend corresponding screening strategies for these genetic diseases. However, such guidelines for the Chinese population are still lacking. For screening high-risk groups in the Chinese population, genetic testing is recommended after genetic counseling.
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Affiliation(s)
| | | | | | - Xiaochen Wang
- Department of Breast Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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A Review of Breast Cancer Risk Factors in Adolescents and Young Adults. Cancers (Basel) 2021; 13:cancers13215552. [PMID: 34771713 PMCID: PMC8583289 DOI: 10.3390/cancers13215552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary Cancer diagnosed in patients between the ages of 15 and 39 deserves special consideration. Diagnoses within this cohort of adolescents and young adults include childhood cancers which present at an older age than expected, or an early presentation of cancers that are typically observed in older adults, such as breast cancer. Cancers within this age group are associated with worse disease-free and overall survival rates, and the incidence of these cases are rising. Knowing an individual’s susceptibility to disease can change their clinical management and allow for the risk-testing of relatives. This review discusses the risk factors that contribute to breast cancer in this unique cohort of patients, including inherited genetic risk factors, as well as environmental and lifestyle factors. We also describe risk models that allow clinicians to quantify a patient’s lifetime risk of developing disease. Abstract Cancer in adolescents and young adults (AYAs) deserves special consideration for several reasons. AYA cancers encompass paediatric malignancies that present at an older age than expected, or early-onset of cancers that are typically observed in adults. However, disease diagnosed in the AYA population is distinct to those same cancers which are diagnosed in a paediatric or older adult setting. Worse disease-free and overall survival outcomes are observed in the AYA setting, and the incidence of AYA cancers is increasing. Knowledge of an individual’s underlying cancer predisposition can influence their clinical care and may facilitate early tumour surveillance strategies and cascade testing of at-risk relatives. This information can further influence reproductive decision making. In this review we discuss the risk factors contributing to AYA breast cancer, such as heritable predisposition, environmental, and lifestyle factors. We also describe a number of risk models which incorporate genetic factors that aid clinicians in quantifying an individual’s lifetime risk of disease.
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Duzkale Teker N, Eyerci N. Double Heterozygous Mutations in the BRCA2 and ATM Genes: A Case Report and Review of the Literature. Breast Care (Basel) 2021; 16:412-417. [PMID: 34602949 DOI: 10.1159/000511430] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 09/08/2020] [Indexed: 11/19/2022] Open
Abstract
Introduction Germline mutations of the BRCA1 and BRCA2 genes are responsible for about a quarter of hereditary breast cancers (BCs). In this study, we aimed to determine the importance of rare double heterozygous (DH) pathogenic variant carriership in BRCA2and ATM genes in a patient diagnosed with BC and pancreas cancer (PC). Case Report A 54-year-old female patient was diagnosed with BC at the age of 34 years and with PC at the age of 48 years. The multigene panel and next-generation sequencing technique were used to evaluate the status of the patient's cancer susceptibility genes. Pathogenic variants c.537dup (p.Ile180Tyrfs*3) in the BRCA2 gene and c.5065C>T (p.Gln1689Ter) in the ATM gene were detected as DH in the patient. Co-segregation analysis was performed on the relatives of the patient using Sanger sequencing. Discussion/Conclusion Multiple primary malignant neoplasms can be encountered more frequently in DH pathogenic variant carriers, and the diagnosis of malignancies can be made at an earlier age through surveillance guided by genetic testing. In this rare case, more patient studies are needed to determine the contribution of DH in BRCA2 and ATM genes to the phenotype.
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Affiliation(s)
- Neslihan Duzkale Teker
- Department of Medical Genetics, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara, Turkey
| | - Nilnur Eyerci
- Department of Medical Biology, Faculty of Medicine, Kafkas University, Kars, Turkey
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Zhang F, Wang J, Ma M, Xu Y, Lu X, Wei S. Genomic alteration profiles of lung cancer and their relationship to clinical features and prognosis value using individualized genetic testing. J Thorac Dis 2021; 13:5007-5015. [PMID: 34527339 PMCID: PMC8411145 DOI: 10.21037/jtd-21-1031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/23/2021] [Indexed: 11/22/2022]
Abstract
Background This study aimed to use a panel targeting 197 genes and 38 fusions to observe the features of gene variations in lung cancer patients, as well as their prognostic values. Methods Patients admitted to our hospital between 2016 and 2017 were enrolled. All patients received OseqTM-Drug genetic testing using peripheral venous blood, followed by 1–2 years of observation. Results For all included patients, 32 genes were observed with mutations. EGFR exhibited the highest mutation rate (46.5%), followed by TP53. The majority of patients carried only one mutant gene. Interestingly, 18 (41.8%) patients showed no mutations, and some cases carried mutations in six genes simultaneously. There was no statistical relationship between mutations and demographic influence. Pathological subtypes were associated with mutations including FLI1, IGF1R, and NOTCH1. A significant correlation was observed between mutant genes and stage at diagnosis, however this requires further confirmation as there was only one case in these mutations: AKT2, AR, STK11, VEGFA, HDAC6, and ASPSCR. For the 33 patients with lymph node metastases at the time of diagnosis, no correlation with any gene mutant was found. Finally, no associations between the survival or prognosis indices (1-year survival, 1-year progression, progression free survival (PFS), and overall survival (OS)) were observed with gene mutations. Conclusions Together, individualized genetic testing is a feasible and minimally invasive approach in cancer genetic analysis. However, gene mutation detection has a limited efficacy in the prediction of prognosis.
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Affiliation(s)
- Fan Zhang
- Department of Oncology, The 4th Hospital of Hebei Medical University, Shijiazhuang, China
| | - Junyan Wang
- Department of Oncology, The 4th Hospital of Hebei Medical University, Shijiazhuang, China
| | - Minting Ma
- Department of Oncology, The 4th Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yu Xu
- Department of Oncology, The 4th Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xiangjun Lu
- Department of Oncology, The 4th Hospital of Hebei Medical University, Shijiazhuang, China
| | - Suju Wei
- Department of Oncology, The 4th Hospital of Hebei Medical University, Shijiazhuang, China
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Hsu FC, Roberts NJ, Childs E, Porter N, Rabe KG, Borgida A, Ukaegbu C, Goggins MG, Hruban RH, Zogopoulos G, Syngal S, Gallinger S, Petersen GM, Klein AP. Risk of Pancreatic Cancer Among Individuals With Pathogenic Variants in the ATM Gene. JAMA Oncol 2021; 7:1664-1668. [PMID: 34529012 DOI: 10.1001/jamaoncol.2021.3701] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Importance Pathogenic germline variants in the ATM gene have been associated with pancreatic cancer risk. Although genetic testing identifies these variants in approximately 1% to 3% of unselected patients with pancreatic cancer, the lifetime risk of pancreatic cancer among individuals with pathogenic ATM variants has not been well estimated. Objective To estimate age-specific penetrance of pancreatic cancer in individuals with a pathogenic variant in the ATM gene. Design, Setting, and Participants This was a multicenter cohort study of pancreatic cancer family registries in the US and Canada using pedigree data from 130 pancreatic cancer kindreds with a pathogenic germline ATM variant. Data analyses were performed from January 2020 to February 2021. Main Outcomes and Measures Observational age-specific risk of pancreatic cancer. Penetrance was estimated using modified segregation analysis. Results The study population of 130 families (123 [95%] White families) comprised 2227 family members (mean age [SD], 58 [22] years; 1096 [49%] women) with complete records (ie, including familial relationships, pancreatic cancer diagnosis, ATM status, proband status, and age), of which 155 individuals had positive results for an ATM pathogenic variant, 16 had a negative result, and the remainder did not have a test result. In these 130 families, 217 individuals had pancreatic cancer: 78 families had 1 such member; 34 families had 2 such members; and 18 families had 3 or more members with pancreatic cancer. The average (range) age at diagnosis was 64 (31-98) years. The cumulative risk of pancreatic cancer among individuals with a germline pathogenic ATM variant was estimated to be 1.1% (95% CI, 0.8%-1.3%) by age 50 years; 6.3% (95% CI, 3.9%-8.7%) by age 70 years; and 9.5% (95% CI, 5.0%-14.0%) by age 80 years. Overall, the relative risk of pancreatic cancer was 6.5 (95% CI, 4.5-9.5) in ATM variant carriers compared with noncarriers. Conclusions and Relevance This multicenter cohort study found that individuals with a germline pathogenic ATM variant were at an increased lifetime risk of pancreatic cancer. These risk estimates can help guide decision-making when evaluating the risks and benefits of enhanced early detection surveillance.
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Affiliation(s)
- Fang-Chi Hsu
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Nicholas J Roberts
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland.,Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, Maryland
| | - Erica Childs
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Nancy Porter
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Kari G Rabe
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Ayelet Borgida
- Divison of General Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Chinedu Ukaegbu
- Division of Gastroenterology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Michael G Goggins
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland.,Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, Maryland.,Division of Gastroenterology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Ralph H Hruban
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland.,Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, Maryland
| | - George Zogopoulos
- The Research Institute of the McGill University Health Centre and the Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
| | - Sapna Syngal
- Population Sciences Division, Dana-Farber Cancer Institute, Boston, Massachusetts.,Gastroenterology Division, Brigham and Women's Hospital, Boston, Massachusetts
| | - Steven Gallinger
- Divison of General Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Gloria M Petersen
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, Maryland
| | - Alison P Klein
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland.,Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, Maryland.,Division of Gastroenterology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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Gene Signatures Induced by Ionizing Radiation as Prognostic Tools in an In Vitro Experimental Breast Cancer Model. Cancers (Basel) 2021; 13:cancers13184571. [PMID: 34572798 PMCID: PMC8465284 DOI: 10.3390/cancers13184571] [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: 07/22/2021] [Revised: 09/02/2021] [Accepted: 09/07/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The present work analyzed the expression of genes involved in radiation, using an in vitro experimental breast cancer model developed by the combined treatment of low doses of high linear energy transfer (LET) radiation α particle radiation and estrogen yielding different stages in a malignantly transformed breast cancer cell model called Alpha model. Results showed important findings of genes involved in cancers of the breast, lung, and nervous system, and others. Most of those genes analyzed in these studies such as ATM, selenoproteins, GABA receptor, interleukins, epsin, and cathepsin inhibitors like stefins, and metallothioneins can be used for new prognostic tools and future therapies since they affect cancer progression and metastasis. In conclusion, gene signature demonstrated to be specific to cell line types, hence cell-dependency must be considered in future radiotherapy treatment planning since molecular and clinical features affect such results. Thus, using gene technology and molecular information is possible to improve therapies and reduction of side effects. Abstract This study aimed to analyze the expression of genes involved in radiation, using an Affymetrix system with an in vitro experimental breast cancer model developed by the combined treatment of low doses of high linear energy transfer (LET) radiation α particle radiation and estrogen yielding different stages in a malignantly transformed breast cancer cell model called Alpha model. Altered expression of different molecules was detected in the non-tumorigenic Alpha3, a malignant cell line transformed only by radiation and originally derived from the parental MCF-10F human cell line; that was compared with the Alpha 5 cell line, another cell line exposed to radiation and subsequently grown in the presence 17β-estradiol. This Alpha5, a tumorigenic cell line, originated the Tumor2 cell line. It can be summarized that the Alpha 3 cell line was characterized by greater gene expression of ATM and IL7R than control, Alpha5, and Tumor2 cell lines, it presented higher selenoprotein gene expression than control and Tumor2; epsin 3 gene expression was higher than control; stefin A gene expression was higher than Alpha5; and metallothionein was higher than control and Tumor2 cell line. Therefore, radiation, independently of estrogen, induced increased ATM, IL7R, selenoprotein, GABA receptor, epsin, stefin, and metallothioneins gene expression in comparison with the control. Results showed important findings of genes involved in cancers of the breast, lung, nervous system, and others. Most genes analyzed in these studies can be used for new prognostic tools and future therapies since they affect cancer progression and metastasis. Most of all, it was revealed that in the Alpha model, a breast cancer model developed by the authors, the cell line transformed only by radiation, independently of estrogen, was characterized by greater gene expression than other cell lines. Understanding the effect of radiotherapy in different cells will help us improve the clinical outcome of radiotherapies. Thus, gene signature has been demonstrated to be specific to tumor types, hence cell-dependency must be considered in future treatment planning. Molecular and clinical features affect the results of radiotherapy. Thus, using gene technology and molecular information is possible to improve therapies and reduction of side effects while providing new insights into breast cancer-related fields.
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Abstract
Pancreatic cancer is associated with both family and hereditary cancer syndromes. Multigene panel testing for pancreatic cancer detected the germline variants BRCA1/2, PALB2, ATM, TP53, MLH1, STK11/LKB1, APC, CDKN2A, and SPINK1/PRSS1 as high-risk genes. A latest genome-wide association study revealed the common, but low-risk germline variants in pancreatic cancer patients. Active pancreatic surveillance using magnetic resonance imaging and endoscopic ultrasound is recommended for high-risk individuals who have a family history of pancreatic cancer or harbor these germline pathogenic variants to improve the detection rate and prognosis of pancreatic cancer. Since poly-ADP-ribose polymerase (PARP) inhibitor has been shown to be effective in improving the prognosis of BRCA-positive pancreatic cancer as well as hereditary breast and ovarian cancer syndrome, PARP inhibitor therapy is currently being applied as precision medicine to pancreatic cancer patients harboring the BRCA1/2 germline variant. This review highlights the importance of surveillance for germline pathogenic variants in pancreatic cancer and is expected to lead to improvements in the diagnosis and prevention of pancreatic cancer as well as facilitate the development of effective therapeutic strategies and precision medicine.
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Abstract
Clonal haematopoiesis (CH) is a common, age-related expansion of blood cells with somatic mutations that is associated with an increased risk of haematological malignancies, cardiovascular disease and all-cause mortality. CH may be caused by point mutations in genes associated with myeloid neoplasms, chromosomal copy number changes and loss of heterozygosity events. How inherited and environmental factors shape the incidence of CH is incompletely understood. Even though the several varieties of CH may have distinct phenotypic consequences, recent research points to an underlying genetic architecture that is highly overlapping. Moreover, there are numerous commonalities between the inherited variation associated with CH and that which has been linked to age-associated biomarkers and diseases. In this Review, we synthesize what is currently known about how inherited variation shapes the risk of CH and how this genetic architecture intersects with the biology of diseases that occur with ageing.
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Affiliation(s)
- Alexander J Silver
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alexander G Bick
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Michael R Savona
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA.
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Bhai P, Levy MA, Rooney K, Carere DA, Reilly J, Kerkhof J, Volodarsky M, Stuart A, Kadour M, Panabaker K, Schenkel LC, Lin H, Ainsworth P, Sadikovic B. Analysis of Sequence and Copy Number Variants in Canadian Patient Cohort With Familial Cancer Syndromes Using a Unique Next Generation Sequencing Based Approach. Front Genet 2021; 12:698595. [PMID: 34326862 PMCID: PMC8314385 DOI: 10.3389/fgene.2021.698595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
Background Hereditary cancer predisposition syndromes account for approximately 10% of cancer cases. Next generation sequencing (NGS) based multi-gene targeted panels is now a frontline approach to identify pathogenic mutations in cancer predisposition genes in high-risk families. Recent evolvement of NGS technologies have allowed simultaneous detection of sequence and copy number variants (CNVs) using a single platform. In this study, we have analyzed frequency and nature of sequence variants and CNVs, in a Canadian cohort of patients, suspected with hereditary cancer syndrome, referred for genetic testing following specific genetic testing guidelines based on patient's personal and/or family history of cancer. Methods A 2870 patients were subjected to a single NGS based multi-gene targeted hereditary cancer panel testing algorithm to identify sequence variants and CNVs in cancer predisposition genes at our reference laboratory in Southwestern Ontario. CNVs identified by NGS were confirmed by alternative techniques like Multiplex ligation-dependent probe amplification (MLPA). Results A 15% (431/2870) patients had a pathogenic variant and 36% (1032/2870) had a variant of unknown significance (VUS), in a cancer susceptibility gene. A total of 287 unique pathogenic variant were identified, out of which 23 (8%) were novel. CNVs identified by NGS based approach accounted for 9.5% (27/287) of pathogenic variants, confirmed by alternate techniques with high accuracy. Conclusion This study emphasizes the utility of NGS based targeted testing approach to identify both sequence and CNVs in patients suspected with hereditary cancer syndromes in clinical setting and expands the mutational spectrum of high and moderate penetrance cancer predisposition genes.
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Affiliation(s)
- Pratibha Bhai
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Kathleen Rooney
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Deanna Alexis Carere
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Michael Volodarsky
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Mike Kadour
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Department of Pathology and Laboratory Medicine, London Health Sciences Centre, London, ON, Canada
| | - Karen Panabaker
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Laila C Schenkel
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Hanxin Lin
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Peter Ainsworth
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Department of Pathology and Laboratory Medicine, London Health Sciences Centre, London, ON, Canada
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
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