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Ning Y, Zhang Y, Tian T, Chen Y, Wang J, Lei K, Cui Z. Reclassifying BRCA1 c.4358-2A > G and BRCA2 c.475 + 5G > C variants from "Uncertain Significance" to "Pathogenic" based on minigene assays and clinical evidence. J Cancer Res Clin Oncol 2024; 150:62. [PMID: 38300310 PMCID: PMC10834553 DOI: 10.1007/s00432-023-05597-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/25/2023] [Indexed: 02/02/2024]
Abstract
BACKGROUND Pathogenic variants in BRCA genes play a crucial role in the pathogenesis of ovarian cancer. Intronic variants of uncertain significance (VUS) may contribute to pathogenicity by affecting splicing. Currently, the significance of many intronic variants in BRCA has not been clarified, impacting patient treatment strategies and the management of familial cases. METHOD A retrospective study was conducted to analyze BRCA intronic VUS in a cohort of 707 unrelated ovarian cancer patients at a single institution from 2018 to 2023. Three splicing predictors were employed to analyze detected intronic VUS. Variants predicted to have splicing alterations were selected for further validation through minigene assays. Patient and familial investigations were conducted to comprehend cancer incidence within pedigrees and the application of poly (ADP-ribose) polymerase inhibitors (PARPi) by the patients. In accordance with the guidelines of the American College of Medical Genetics and Genomics (ACMG), the intronic VUS were reclassified based on minigene assay results and clinical evidence. RESULT Approximately 9.8% (69/707) of patients were identified as carriers of 67 different VUS in BRCA1/2, with four intronic variants accounting for 6% (4/67) of all VUS. Splicing predictors indicated potential splicing alterations in splicing for BRCA1 c.4358-2A>G and BRCA2 c.475+5G>C variants. Minigene assays utilizing the pSPL3 exon trapping vector revealed that these variants induced changes in splicing sites and frameshift, resulting in premature termination of translation (p. Ala1453Glyfs and p. Pro143Glyfs). According to ACMG guidelines, BRCA1 c.4358-2A>G and BRCA2 c.475+5G>C were reclassified as pathogenic variants. Pedigree investigations were conducted on patients with BRCA1 c.4358-2A>G variant, and the detailed utilization of PARPi provided valuable insights into research on PARPi resistance. CONCLUSION Two intronic VUS were reclassified as pathogenic variants. A precise classification of variants is crucial for the effective treatment and management of both patients and healthy carriers.
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Affiliation(s)
- Ying Ning
- Department of Clinical Medicine, Qingdao University, Qingdao, 266003, China
| | - Yu Zhang
- Department of Clinical Medicine, Qingdao University, Qingdao, 266003, China
| | - Tian Tian
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Laoshan District, Qingdao, 266000, China
| | - Yu Chen
- Department of Clinical Medicine, Qingdao University, Qingdao, 266003, China
| | - Jia Wang
- Center of Tumor Immunology and Cytotherapy, Medical Research Center, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Laoshan District, Qingdao, 266000, China
| | - Ke Lei
- Center of Tumor Immunology and Cytotherapy, Medical Research Center, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Laoshan District, Qingdao, 266000, China.
| | - Zhumei Cui
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Laoshan District, Qingdao, 266000, China.
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Dragoš VŠ, Strojnik K, Klančar G, Škerl P, Stegel V, Blatnik A, Banjac M, Krajc M, Novaković S. Identification of Spliceogenic Variants beyond Canonical GT-AG Splice Sites in Hereditary Cancer Genes. Int J Mol Sci 2022; 23:7446. [PMID: 35806449 PMCID: PMC9267136 DOI: 10.3390/ijms23137446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 02/01/2023] Open
Abstract
Pathogenic/likely pathogenic variants in susceptibility genes that interrupt RNA splicing are a well-documented mechanism of hereditary cancer syndromes development. However, if RNA studies are not performed, most of the variants beyond the canonical GT-AG splice site are characterized as variants of uncertain significance (VUS). To decrease the VUS burden, we have bioinformatically evaluated all novel VUS detected in 732 consecutive patients tested in the routine genetic counseling process. Twelve VUS that were predicted to cause splicing defects were selected for mRNA analysis. Here, we report a functional characterization of 12 variants located beyond the first two intronic nucleotides using RNAseq in APC, ATM, FH, LZTR1, MSH6, PALB2, RAD51C, and TP53 genes. Based on the analysis of mRNA, we have successfully reclassified 50% of investigated variants. 25% of variants were downgraded to likely benign, whereas 25% were upgraded to likely pathogenic leading to improved clinical management of the patient and the family members.
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Alenezi WM, Fierheller CT, Revil T, Serruya C, Mes-Masson AM, Foulkes WD, Provencher D, El Haffaf Z, Ragoussis J, Tonin PN. Case Review: Whole-Exome Sequencing Analyses Identify Carriers of a Known Likely Pathogenic Intronic BRCA1 Variant in Ovarian Cancer Cases Clinically Negative for Pathogenic BRCA1 and BRCA2 Variants. Genes (Basel) 2022; 13:genes13040697. [PMID: 35456503 PMCID: PMC9032308 DOI: 10.3390/genes13040697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/01/2022] [Accepted: 04/14/2022] [Indexed: 12/04/2022] Open
Abstract
Background: Detecting pathogenic intronic variants resulting in aberrant splicing remains a challenge in routine genetic testing. We describe germline whole-exome sequencing (WES) analyses and apply in silico predictive tools of familial ovarian cancer (OC) cases reported clinically negative for pathogenic BRCA1 and BRCA2 variants. Methods: WES data from 27 familial OC cases reported clinically negative for pathogenic BRCA1 and BRCA2 variants and 53 sporadic early-onset OC cases were analyzed for pathogenic variants in BRCA1 or BRCA2. WES data from carriers of pathogenic BRCA1 or BRCA2 variants were analyzed for pathogenic variants in 10 other OC predisposing genes. Loss of heterozygosity analysis was performed on tumor DNA from variant carriers. Results: BRCA1 c.5407-25T>A intronic variant, identified in two affected sisters and one sporadic OC case, is predicted to create a new splice effecting transcription of BRCA1. WES data from BRCA1 c.5407-25T>A carriers showed no evidence of pathogenic variants in other OC predisposing genes. Sequencing the tumor DNA from the variant carrier showed complete loss of the wild-type allele. Conclusions: The findings support BRCA1 c.5407-25T>A as a likely pathogenic variant and highlight the importance of investigating intronic sequences as causal variants in OC families where the involvement of BRCA1 is highly suggestive.
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Affiliation(s)
- Wejdan M. Alenezi
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; (W.M.A.); (C.T.F.); (T.R.); (W.D.F.); (J.R.)
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada;
- Department of Medical Laboratory Technology, Taibah University, Medina 42353, Saudi Arabia
| | - Caitlin T. Fierheller
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; (W.M.A.); (C.T.F.); (T.R.); (W.D.F.); (J.R.)
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada;
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; (W.M.A.); (C.T.F.); (T.R.); (W.D.F.); (J.R.)
- McGill Genome Centre, McGill University, Montreal, QC H3A 0G1, Canada
| | - Corinne Serruya
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada;
| | - Anne-Marie Mes-Masson
- Département de Médecine, Université de Montréal, Montreal, QC H3T 1J4, Canada;
- Institut du Cancer de Montréal, Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, QC H2X 0A9, Canada; (D.P.); (Z.E.H.)
| | - William D. Foulkes
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; (W.M.A.); (C.T.F.); (T.R.); (W.D.F.); (J.R.)
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada;
- Lady Davis Institute for Medical Research of the Jewish General Hospital, Montreal, QC H3T 1E2, Canada
- Department of Medical Genetics, McGill University Health Centre, Montreal, QC H3H 1P3, Canada
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 1G5, Canada
| | - Diane Provencher
- Institut du Cancer de Montréal, Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, QC H2X 0A9, Canada; (D.P.); (Z.E.H.)
- Division of Gynecologic Oncology, Université de Montréal, Montreal, QC H4A 3J1, Canada
| | - Zaki El Haffaf
- Institut du Cancer de Montréal, Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, QC H2X 0A9, Canada; (D.P.); (Z.E.H.)
- Service de Médecine Génique, Centre Hospitalier de l’Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; (W.M.A.); (C.T.F.); (T.R.); (W.D.F.); (J.R.)
- McGill Genome Centre, McGill University, Montreal, QC H3A 0G1, Canada
| | - Patricia N. Tonin
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; (W.M.A.); (C.T.F.); (T.R.); (W.D.F.); (J.R.)
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada;
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Correspondence: ; Tel.: +1-(514)-934-1934 (ext. 44069)
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Gameiro A, Almeida F, Nascimento C, Correia J, Ferreira F. Tyrosine Kinase Inhibitors Are Promising Therapeutic Tools for Cats with HER2-Positive Mammary Carcinoma. Pharmaceutics 2021; 13:pharmaceutics13030346. [PMID: 33800900 PMCID: PMC8002158 DOI: 10.3390/pharmaceutics13030346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 12/21/2022] Open
Abstract
Feline mammary carcinoma (FMC) is a common neoplasia in cat, being HER2-positive the most prevalent subtype. In woman’s breast cancer, tyrosine kinase inhibitors (TKi) are used as a therapeutic option, by blocking the phosphorylation of the HER2 tyrosine kinase domain. Moreover, clinical trials demonstrated that TKi produce synergistic antiproliferative effects in combination with mTOR inhibitors, overcoming resistance to therapy. Thus, to uncover new chemotherapeutic strategies for cats, the antiproliferative effects of two TKi (lapatinib and neratinib), and their combination with a mTOR inhibitor (rapamycin), were evaluated in FMC cell lines (CAT-M, FMCp and FMCm) and compared with a human breast cancer cell line (SkBR-3). Results revealed that both TKi induced antiproliferative effects in all feline cell lines, by blocking the phosphorylation of EGFR members and its downstream effectors. Furthermore, combined treatments with rapamycin presented synergetic antiproliferative effects. Additionally, the DNA sequence of the her2 TK domain (exons 18 to 20) was determined in 40 FMC tissue samples, and despite several mutations were found none of them were described as inducing resistance to therapy. Altogether, our results demonstrated that TKi and combined protocols may be useful in the treatment of cats with mammary carcinomas, and that TKi-resistant FMC are rare.
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Affiliation(s)
- Andreia Gameiro
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal; (A.G.); (F.A.); (C.N.); (J.C.)
| | - Filipe Almeida
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal; (A.G.); (F.A.); (C.N.); (J.C.)
- Antiviral Resistance Laboratory, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016 Lisbon, Portugal
| | - Catarina Nascimento
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal; (A.G.); (F.A.); (C.N.); (J.C.)
| | - Jorge Correia
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal; (A.G.); (F.A.); (C.N.); (J.C.)
| | - Fernando Ferreira
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal; (A.G.); (F.A.); (C.N.); (J.C.)
- Correspondence: ; Tel.: +351-21-365-2800 (ext. 431234)
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De Paolis E, Pietragalla A, De Bonis M, Fagotti A, Urbani A, Scambia G, Minucci A. The BRCA1 c.788G > T (NM_007294.4) variant in a high grade serous ovarian cancer (HGSOC) patient: foods for thought. Mol Biol Rep 2021; 48:2985-92. [PMID: 33656647 DOI: 10.1007/s11033-021-06243-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/18/2021] [Indexed: 12/20/2022]
Abstract
In this report we described the case of a BRCA1/2 (BRCA) molecular testing performed on tumor sample in a High Grade Serous Ovarian Cancer (HGSOC) patient with two different Next Generation Tumor Sequencing (NGTS) pipelines. The two clinical reports leaded to apparently different BRCA status, providing important foods for thought. After NGTS, the gene sequencing information (i.e., reads) are aligned to the reference gene sequences obtained from public databases, in order to provide an uniform nomenclature for unambiguous variant designation. However, the criteria adopted for variant reporting in tissue test are not always univocal. Particularly, this is the case of rare and unclassified BRCA variants for which the molecular evaluation may be a relevant challenge. Here we described a BRCA1 unclassified variant that may be re-evaluated in the context of alternative BRCA1 transcripts due to its different biological effect. We underlined that an in-depth knowledge of BRCA testing is mandatory for its appropriate use.
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