1
|
Innella G, Fortuno C, Caleca L, Feng BJ, Carroll C, Parsons MT, Miccoli S, Montagna M, Calistri D, Cortesi L, Pasini B, Manoukian S, Giachino D, Matricardi L, Foti MC, Zampiga V, Piombino C, Barbieri E, Lutati FV, Azzolini J, Danesi R, Arcangeli V, Caputo SM, Boutry-Kryza N, Goussot V, Hiraki S, Richardson M, Ferrari S, Radice P, Spurdle AB, Turchetti D. Atypical cancer risk profile in carriers of Italian founder BRCA1 variant p.His1673del: Implications for classification and clinical management. Cancer Med 2024; 13:e70114. [PMID: 39194334 DOI: 10.1002/cam4.70114] [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: 02/23/2024] [Revised: 07/29/2024] [Accepted: 08/06/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND BRCA1:c.5017_5019del (p.His1673del) is a founder variant relatively frequent in Northern Italy. Despite previous suggestion of pathogenicity, variant classification in public databases is still conflicting, needing additional evidence. METHODS Maximum likelihood penetrance of breast/ovarian and other cancer types was estimated using full pedigree data from 53 informative Italian families. The effect of the variant on BRCA1-ABRAXAS1 interaction was assessed using a GFP-fragment reassembly-based PPI assay. Results were combined with additional data from multiple sources to classify the variant according to ACMG/AMP classification rules specified for BRCA1/2. RESULTS Variant-carriers displayed increased risk for ovarian cancer (HR = 33.0, 95% CI = 7.0-155.0; cumulative risk at age 70 = 27.6%, 95% CI = 12.6-40.0%) but not for breast cancer (HR = 0.7, 95% CI = 0.2-2.2). An increased risk of uterine cancer (HR = 8.0, 95% CI = 1.03-61.6) emerged, warranting further evaluation. Likelihood-ratio in favor of pathogenicity was 98898642.82 under assumption of standard BRCA1 breast and ovarian penetrance, and 104240832.84 after excluding breast cancer diagnoses (based on penetrance results). Functional analysis demonstrated that the variant abrogates the BRCA1-ABRAXAS1 binding, supporting the PS3 code assignment within the ACMG/AMP rule-based model. Collectively, these findings allowed to classify the variant as pathogenic. CONCLUSION Pathogenicity of BRCA1:c.5017_5019del(p.His1673del) has been confirmed; however, breast cancer risk in Italian families is not increased, unlike in families from other countries and in carriers of most BRCA1 pathogenic variants. The knowledge of atypical risk profiles for this and other variants will pave the way for personalized management based on specific genotype.
Collapse
Affiliation(s)
- Giovanni Innella
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Medical Genetics Unit, Bologna, Italy
| | - Cristina Fortuno
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Laura Caleca
- Unit of Predictive Medicine: Molecular Bases of Genetic Risk, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | | | - Michael T Parsons
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Daniele Calistri
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Laura Cortesi
- Division of Medical Oncology, Department of Oncology and Hematology, University Hospital of Modena, Modena, Italy
| | - Barbara Pasini
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Daniela Giachino
- Medical Genetic Unit, San Luigi Gonzaga University Hospital, Torino, Italy
- Department of Clinical and Biological Sciences, University of Turin, Torino, Italy
| | - Laura Matricardi
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Maria Cristina Foti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Valentina Zampiga
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Claudia Piombino
- Division of Medical Oncology, Department of Oncology and Hematology, University Hospital of Modena, Modena, Italy
| | - Elena Barbieri
- Division of Medical Oncology, Department of Oncology and Hematology, University Hospital of Modena, Modena, Italy
| | | | - Jacopo Azzolini
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Rita Danesi
- Romagna Cancer Registry, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Valentina Arcangeli
- Romagna Cancer Registry, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Sandrine M Caputo
- Department of Genetics, Institut Curie, Paris, France and Paris Sciences Lettres Research University, Paris, France
| | | | - Vincent Goussot
- Département de Biologie et Pathologie des Tumeurs, Centre de Lutte Contre le Cancer Georges François Leclerc, Dijon, France
| | | | | | | | - Paolo Radice
- Unit of Predictive Medicine: Molecular Bases of Genetic Risk, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Amanda B Spurdle
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Daniela Turchetti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Medical Genetics Unit, Bologna, Italy
| |
Collapse
|
2
|
Block I, Mateu-Regué À, Do TTN, Miceikaite I, Sdogati D, Larsen MJ, Hao Q, Nielsen HR, Boonen SE, Skytte AB, Jensen UB, Høffding LK, De Nicolo A, Viel A, Tudini E, Parsons MT, Hansen TVO, Rossing M, Kruse TA, Spurdle AB, Thomassen M. Male with an apparently normal phenotype carrying a BRCA1 exon 20 duplication in trans to a BRCA1 frameshift variant. Breast Cancer Res 2024; 26:6. [PMID: 38195559 PMCID: PMC10775606 DOI: 10.1186/s13058-023-01755-9] [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: 06/27/2023] [Accepted: 12/16/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND Reports of dual carriers of pathogenic BRCA1 variants in trans are extremely rare, and so far, most individuals have been associated with a Fanconi Anemia-like phenotype. METHODS We identified two families with a BRCA1 in-frame exon 20 duplication (Ex20dup). In one male individual, the variant was in trans with the BRCA1 frameshift variant c.2475delC p.(Asp825Glufs*21). We performed splicing analysis and used a transcription activation domain (TAD) assay to assess the functional impact of Ex20dup. We collected pedigrees and mapped the breakpoints of the duplication by long- and short-read genome sequencing. In addition, we performed a mitomycin C (MMC) assay from the dual carrier using cultured lymphoblastoid cells. RESULTS Genome sequencing and RNA analysis revealed the BRCA1 exon 20 duplication to be in tandem. The duplication was expressed without skipping any one of the two exon 20 copies, resulting in a lack of wild-type transcripts from this allele. TAD assay indicated that the Ex20dup variant has a functional level similar to the well-known moderate penetrant pathogenic BRCA1 variant c.5096G > A p.(Arg1699Gln). MMC assay of the dual carrier indicated a slightly impaired chromosomal repair ability. CONCLUSIONS This is the first reported case where two BRCA1 variants with demonstrated functional impact are identified in trans in a male patient with an apparently normal clinical phenotype and no BRCA1-associated cancer. The results pinpoint a minimum necessary BRCA1 protein activity to avoid a Fanconi Anemia-like phenotype in compound heterozygous status and yet still predispose carriers to hormone-related cancers. These findings urge caution when counseling families regarding potential Fanconi Anemia risk. Furthermore, prudence should be taken when classifying individual variants as benign based on co-occurrence in trans with well-established pathogenic variants.
Collapse
Affiliation(s)
- Ines Block
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Institute of Pharmacology and Clinical Pharmacy, University of Marburg, Marburg, Germany
| | - Àngels Mateu-Regué
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Thi Tuyet Nhu Do
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Ieva Miceikaite
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Daniel Sdogati
- Lundbeckfonden Center of Excellence NanoCAN, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
- Molecular Oncology, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Qin Hao
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | | | - Susanne E Boonen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Anne-Bine Skytte
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Louise K Høffding
- Center for Clinical Genetics and Genomic Diagnostics, Zealand University Hospital, Roskilde, Denmark
| | - Arcangela De Nicolo
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandra Viel
- Unit of Functional Oncogenetics and Genomics, Centro Di Riferimento Oncologico Di Aviano (CRO) IRCCS, Aviano, (PN), Italy
| | - Emma Tudini
- Population Health Program, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
| | - Michael T Parsons
- Population Health Program, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
| | - Thomas V O Hansen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maria Rossing
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.
- Clinical Genome Center, Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
| |
Collapse
|
3
|
Hughes T, Rose AM. The emergence of Fanconi anaemia type S: a phenotypic spectrum of biallelic BRCA1 mutations. Front Oncol 2023; 13:1278004. [PMID: 38146508 PMCID: PMC10749362 DOI: 10.3389/fonc.2023.1278004] [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: 08/15/2023] [Accepted: 10/23/2023] [Indexed: 12/27/2023] Open
Abstract
BRCA1 is involved in the Fanconi anaemia (FA) pathway, which coordinates repair of DNA interstrand cross-links. FA is a rare genetic disorder characterised by bone marrow failure, cancer predisposition and congenital abnormalities, caused by biallelic mutations affecting proteins in the FA pathway. Germline monoallelic pathogenic BRCA1 mutations are known to be associated with hereditary breast/ovarian cancer, however biallelic mutations of BRCA1 were long predicted to be incompatible with embryonic viability, hence BRCA1 was not considered to be a canonical FA gene. Despite this, several patients with biallelic pathogenic BRCA1 mutations and FA-like phenotypes have been identified - defining a new FA type (FA-S) and designating BRCA1 as an FA gene. This report presents a scoping review of the cases of biallelic BRCA1 mutations identified to date, discusses the functional effects of the mutations identified, and proposes a phenotypic spectrum of BRCA1 mutations based upon available clinical and genetic data. We report that this FA-S cohort phenotype includes short stature, microcephaly, facial dysmorphisms, hypo/hyperpigmented lesions, intellectual disability, chromosomal sensitivity to crosslinking agents and predisposition to breast/ovarian cancer and/or childhood cancers, with some patients exhibiting sensitivity to chemotherapy. Unlike most other types of FA, FA-S patients lack bone marrow failure.
Collapse
Affiliation(s)
- Tirion Hughes
- University of Oxford Medical School, Oxford, United Kingdom
| | - Anna M. Rose
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| |
Collapse
|