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Rodrigues LM, Maistro S, Katayama MLH, Rocha VM, Lopez RVM, Lopes EFDT, Gonçalves FT, Fridman C, Serio PADMP, Barros LRC, Leite LAS, Segatelli V, Estevez-Diz MDP, Guindalini RSC, Ribeiro Junior U, Folgueira MAAK. Prevalence of germline variants in Brazilian pancreatic carcinoma patients. Sci Rep 2024; 14:21083. [PMID: 39256447 DOI: 10.1038/s41598-024-71884-4] [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: 05/06/2024] [Accepted: 09/02/2024] [Indexed: 09/12/2024] Open
Abstract
We evaluated the prevalence of pathogenic/likely pathogenic germline variants (PGV) in Brazilian pancreatic adenocarcinoma (PC) patients, that represent a multiethnic population, in a cross-sectional study. We included 192 PC patients unselected for family history of cancer. We evaluated a panel of 113 cancer genes, through genomic DNA sequencing and 46 ancestry-informative markers, through multiplex PCR. The median age was 61 years; 63.5% of the patients presented disease clinical stages III or IV; 8.3% reported personal history of cancer; 4.7% and 16.1% reported first-degree relatives with PC or breast and/or prostate cancer, respectively. Although the main ancestry was European, there was considerable genetic composition admixture. Twelve patients (6.25%) were PGV carriers in PC predisposition genes (ATM, BRCA1, BRCA2, CDKN2A, MSH2, PALB2) and another 25 (13.0%) were PGV carriers in genes with a limited association or not previously associated with PC (ACD, BLM, BRIP1, CHEK2, ERCC4, FANCA, FANCE, FANCM, GALNT12, MITF, MRE11, MUTYH, POLE, RAD51B, RAD51C, RECQL4, SDHA, TERF2IP). The most frequently affected genes were CHEK2, ATM and FANC. In tumor samples from PGV carriers in ACD, BRIP1, MRE11, POLE, SDHA, TERF2IP, which were examined through exome sequencing, the main single base substitutions (SBS) mutational signature was SBS1+5+18, probably associated with age, tobacco smoking and reactive oxygen species. SBS3 associated with homologous repair deficiency was also represented, but on a lower scale. There was no difference in the frequency of PGV carriers between: (a) patients with or without first-degree relatives with cancer; and (b) patients with admixed ancestry versus those with predominantly European ancestry. Furthermore, there was no difference in overall survival between PGV carriers and non-carriers. Therefore, genetic testing should be offered to all Brazilian pancreatic cancer patients, regardless of their ancestry. Genes with limited or previously unrecognized associations with pancreatic cancer should be further investigated to clarify their role in cancer risk.
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Affiliation(s)
- Lívia Munhoz Rodrigues
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Simone Maistro
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Maria Lucia Hirata Katayama
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Vinícius Marques Rocha
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Rossana Veronica Mendoza Lopez
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Edia Filomena di Tullio Lopes
- Registro Hospitalar de Cancer, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, São Paulo, SP, Brazil
| | - Fernanda Toledo Gonçalves
- Departamento de Medicina Legal, Bioetica, Medicina do Trabalho e Medicina Física e Reabilitação, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | - Cintia Fridman
- Departamento de Medicina Legal, Bioetica, Medicina do Trabalho e Medicina Física e Reabilitação, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | | | - Luciana Rodrigues Carvalho Barros
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil
| | - Luiz Antonio Senna Leite
- Departamento de Radiologia e Oncologia, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | - Vanderlei Segatelli
- Departamento de Patologia Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | - Maria Del Pilar Estevez-Diz
- Departamento de Radiologia e Oncologia, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Sao Paulo, SP, Brazil
| | | | - Ulysses Ribeiro Junior
- Division of Digestive Surgery, Department of Gastroenterology, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo FMUSP, Sao Paulo, SP, Brazil
| | - Maria Aparecida Azevedo Koike Folgueira
- Departamento de Radiologia e Oncologia, Comprehensive Center for Precision Oncology - C2PO, Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, FMUSP, Av. Dr. Arnaldo 251, 8º. Andar, sala 69, Sao Paulo, SP, 01246-000, Brazil.
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2
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Calabrese A, von Arx C, Tafuti AA, Pensabene M, De Laurentiis M. Prevention, diagnosis and clinical management of hereditary breast cancer beyond BRCA1/2 genes. Cancer Treat Rev 2024; 129:102785. [PMID: 38870570 DOI: 10.1016/j.ctrv.2024.102785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/18/2024] [Accepted: 06/09/2024] [Indexed: 06/15/2024]
Abstract
The detection of germline pathogenic variants (gPVs) in BRCA1/2 and other breast cancer (BC) genes is rising exponentially thanks to the advent of multi-gene panel testing. This promising technology, coupled with the availability of specific therapies for BC BRCA-related, has increased the number of patients eligible for genetic testing. Implementing multi-gene panel testing for hereditary BC screening holds promise to maximise benefits for patients at hereditary risk of BC. These benefits range from prevention programs to antineoplastic-targeted therapies. However, the clinical management of these patients is complex and requires guidelines based on recent evidence. Furthermore, applying multi-gene panel testing into clinical practice increases the detection of variants of uncertain significance (VUSs). This augments the complexity of patients' clinical management, becoming an unmet need for medical oncologists. This review aims to collect updated evidence on the most common BC-related genes besides BRCA1/2, from their biological role in BC development to their potential impact in tailoring prevention and treatment strategies.
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Affiliation(s)
- A Calabrese
- Department Breast and Thoracic Oncology, Istituto Nazionale Tumori - IRCCS, 'Fondazione G. Pascale', Via Mariano Semmola, 53, 80131 Napoli, NA, Italy
| | - C von Arx
- Department Breast and Thoracic Oncology, Istituto Nazionale Tumori - IRCCS, 'Fondazione G. Pascale', Via Mariano Semmola, 53, 80131 Napoli, NA, Italy.
| | - A A Tafuti
- Department Breast and Thoracic Oncology, Istituto Nazionale Tumori - IRCCS, 'Fondazione G. Pascale', Via Mariano Semmola, 53, 80131 Napoli, NA, Italy
| | - M Pensabene
- Department Breast and Thoracic Oncology, Istituto Nazionale Tumori - IRCCS, 'Fondazione G. Pascale', Via Mariano Semmola, 53, 80131 Napoli, NA, Italy
| | - M De Laurentiis
- Department Breast and Thoracic Oncology, Istituto Nazionale Tumori - IRCCS, 'Fondazione G. Pascale', Via Mariano Semmola, 53, 80131 Napoli, NA, Italy
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3
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Kwong A, Ho CYS, Au CH, Tey SK, Ma ESK. Germline RAD51C and RAD51D Mutations in High-Risk Chinese Breast and/or Ovarian Cancer Patients and Families. J Pers Med 2024; 14:866. [PMID: 39202057 PMCID: PMC11355318 DOI: 10.3390/jpm14080866] [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: 07/09/2024] [Revised: 08/05/2024] [Accepted: 08/14/2024] [Indexed: 09/03/2024] Open
Abstract
BACKGROUND RAD51C and RAD51D are crucial in homologous recombination (HR) DNA repair. The prevalence of the RAD51C and RAD51D mutations in breast cancer varies across ethnic groups. Associations of RAD51C and RAD51D germline pathogenic variants (GPVs) with breast and ovarian cancer predisposition have been recently reported and are of interest. METHODS We performed multi-gene panel sequencing to study the prevalence of RAD51C and RAD51D germline mutations among 3728 patients with hereditary breast and/or ovarian cancer (HBOC). RESULTS We identified 18 pathogenic RAD51C and RAD51D mutation carriers, with a mutation frequency of 0.13% (5/3728) and 0.35% (13/3728), respectively. The most common recurrent mutation was RAD51D c.270_271dupTA; p.(Lys91Ilefs*13), with a mutation frequency of 0.30% (11/3728), which was also commonly identified in Asians. Only four out of six cases (66.7%) of this common mutation tested positive for homologous recombination deficiency (HRD). CONCLUSIONS Taking the family studies in our registry and tumor molecular pathology together, we concluded that this relatively common RAD51D variant showed incomplete penetrance in our local Chinese community. Personalized genetic counseling emphasizing family history for families with this variant, as suggested at the UK Cancer Genetics Group (UKCGG) Consensus meeting, would also be appropriate in Chinese families.
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Affiliation(s)
- Ava Kwong
- Division of Breast Surgery, Department of Surgery, The University of Hong Kong, Hong Kong SAR, China
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong SAR, China
- Cancer Genetics Centre, Breast Surgery Centre, Surgery Centre, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Cecilia Yuen Sze Ho
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Chun Hang Au
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Sze Keong Tey
- Division of Breast Surgery, Department of Surgery, The University of Hong Kong, Hong Kong SAR, China
| | - Edmond Shiu Kwan Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong SAR, China
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
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Fernández-Castillejo S, Roig B, Melé M, Serrano S, Salvat M, Querol M, Brunet J, Pineda M, Cisneros A, Parada D, Badia J, Borràs J, Rodríguez-Balada M, Gumà J. Opportunistic genetic screening increases the diagnostic yield and is medically valuable for care of patients and their relatives with hereditary cancer. J Med Genet 2023; 61:69-77. [PMID: 37591735 PMCID: PMC10803988 DOI: 10.1136/jmg-2023-109389] [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: 05/10/2023] [Accepted: 07/23/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Multigene panel testing by next-generation sequencing (MGP-NGS) enables the detection of germline pathogenic or likely pathogenic variants (PVs/LPVs) in genes beyond those associated with a certain cancer phenotype. Opportunistic genetic screening based on MGP-NGS in patients with suspicion of hereditary cancer reveals these incidental findings (IFs). METHODS MGP-NGS was performed in patients who fulfilled the clinical criteria to undergo genetic testing according to the Catalan Health Service guidelines. Variants were classified following the American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines and the Cancer Variant Interpretation Group UK guidelines. RESULTS IFs were identified in 10 (1.22%) of the 817 patients who underwent MGP-NGS. The mean age at cancer diagnosis was 49.4±9.5 years. Three IFs (30.0%) were detected in PMS2, two (20.0%) in ATM and TP53 and one (10.0%) in MSH6, NTHL1 and VHL. Seven (70.0%) IFs were single-nucleotide substitutions, two (20.0%) were deletions and one (10.0%) was a duplication. Three (30.0) IFs were located in intronic regions, three (30.3%) were nonsense, two (20.0%) were frameshift and two (20.0%) were missense variations. Six (60.0%) IFs were classified as PVs and four (40.0%) as LPVs. CONCLUSIONS Opportunistic genetic screening increased the diagnostic yield by 1.22% in our cohort. Most of the identified IFs were present in clinically actionable genes (n=7; 70.0%), providing these families with an opportunity to join cancer early detection programmes, as well as secondary cancer prevention. IFs might facilitate the diagnosis of asymptomatic individuals and the early management of cancer once it develops.
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Affiliation(s)
- Sara Fernández-Castillejo
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Bàrbara Roig
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Mireia Melé
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Sara Serrano
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Mònica Salvat
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Montserrat Querol
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and Biomedical Research Centre Network for Oncology (CIBERONC), L'Hospitalet de Llobregat, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBGI, Girona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and Biomedical Research Centre Network for Oncology (CIBERONC), L'Hospitalet de Llobregat, Spain
| | - Adela Cisneros
- Hematology Department, ICO and Hospital Germans Trias i Pujol, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - David Parada
- Pathology Molecular Unit, Department of Pathology, Hospital Universitari Sant Joan de Reus (HUSJR), Spain. Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Joan Badia
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Joan Borràs
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Marta Rodríguez-Balada
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Josep Gumà
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
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Lee NY, Hum M, Zihara S, Wang L, Myint MK, Lim DWT, Toh CK, Skanderup A, Samol J, Tan MH, Ang P, Lee SC, Tan EH, Lai GGY, Tan DSW, Yap YS, Lee ASG. Landscape of germline pathogenic variants in patients with dual primary breast and lung cancer. Hum Genomics 2023; 17:66. [PMID: 37461096 PMCID: PMC10353088 DOI: 10.1186/s40246-023-00510-7] [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: 05/10/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Cancer predisposition is most often studied in the context of single cancers. However, inherited cancer predispositions can also give rise to multiple primary cancers. Yet, there is a paucity of studies on genetic predisposition in multiple primary cancers, especially those outside of well-defined cancer predisposition syndromes. This study aimed to identify germline variants associated with dual primary cancers of the breast and lung. METHODS Exome sequencing was performed on germline DNA from 55 Singapore patients (52 [95%] never-smokers) with dual primaries in the breast and lung, confirmed by histopathology. Using two large control cohorts: the local SG10K_Health (n = 9770) and gnomAD non-cancer East Asians (n = 9626); and two additional local case cohorts of early-onset or familial breast cancer (n = 290), and lung cancer (n = 209), variants were assessed for pathogenicity in accordance with ACMG/AMP guidelines. In particular, comparisons were made with known pathogenic or likely pathogenic variants in the ClinVar database, pathogenicity predictions were obtained from in silico prediction software, and case-control association analyses were performed. RESULTS Altogether, we identified 19 pathogenic or likely pathogenic variants from 16 genes, detected in 17 of 55 (31%) patients. Six of the 19 variants were identified using ClinVar, while 13 variants were classified pathogenic or likely pathogenic using ACMG/AMP guidelines. The 16 genes include well-known cancer predisposition genes such as BRCA2, TP53, and RAD51D; but also lesser known cancer genes EXT2, WWOX, GATA2, and GPC3. Most of these genes are involved in DNA damage repair, reaffirming the role of impaired DNA repair mechanisms in the development of multiple malignancies. These variants warrant further investigations in additional populations. CONCLUSIONS We have identified both known and novel variants significantly enriched in patients with primary breast and lung malignancies, expanding the body of known cancer predisposition variants for both breast and lung cancer. These variants are mostly from genes involved in DNA repair, affirming the role of impaired DNA repair in the predisposition and development of multiple cancers.
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Affiliation(s)
- Ning-Yuan Lee
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Melissa Hum
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Sabna Zihara
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Lanying Wang
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Matthew K Myint
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Darren Wan-Teck Lim
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
- SingHealth Duke-NUS Oncology Academic Clinical Programme (ONCO ACP), Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Chee-Keong Toh
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Anders Skanderup
- Genome Institute of Singapore, 60 Biopolis St, Singapore, 138672, Singapore
| | - Jens Samol
- Medical Oncology Department, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore
- Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Min-Han Tan
- Lucence Diagnostics Pte Ltd, 211 Henderson Road, Singapore, 159552, Singapore
| | - Peter Ang
- Oncocare Cancer Centre, Gleneagles Medical Centre, 6 Napier Road, Singapore, 258499, Singapore
| | - Soo-Chin Lee
- Department of Hematology-Oncology, National University Cancer Institute, Singapore (NCIS), National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
- Cancer Science Institute, Singapore (CSI), National University of Singapore, 14 Medical Dr, Singapore, 117599, Singapore
| | - Eng-Huat Tan
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
- Clinical Trials and Epidemiological Sciences, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Gillianne G Y Lai
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
- SingHealth Duke-NUS Oncology Academic Clinical Programme (ONCO ACP), Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Daniel S W Tan
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
- SingHealth Duke-NUS Oncology Academic Clinical Programme (ONCO ACP), Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Genome Institute of Singapore, 60 Biopolis St, Singapore, 138672, Singapore
- Clinical Trials and Epidemiological Sciences, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Yoon-Sim Yap
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
- SingHealth Duke-NUS Oncology Academic Clinical Programme (ONCO ACP), Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Ann S G Lee
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore.
- SingHealth Duke-NUS Oncology Academic Clinical Programme (ONCO ACP), Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore, 117593, Singapore.
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6
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Bucalo A, Conti G, Valentini V, Capalbo C, Bruselles A, Tartaglia M, Bonanni B, Calistri D, Coppa A, Cortesi L, Giannini G, Gismondi V, Manoukian S, Manzella L, Montagna M, Peterlongo P, Radice P, Russo A, Tibiletti MG, Turchetti D, Viel A, Zanna I, Palli D, Silvestri V, Ottini L. Male breast cancer risk associated with pathogenic variants in genes other than BRCA1/2: an Italian case-control study. Eur J Cancer 2023; 188:183-191. [PMID: 37262986 DOI: 10.1016/j.ejca.2023.04.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Germline pathogenic variants (PVs) in BRCA1/2 genes are associated with breast cancer (BC) risk in both women and men. Multigene panel testing is being increasingly used for BC risk assessment, allowing the identification of PVs in genes other than BRCA1/2. While data on actionable PVs in other cancer susceptibility genes are now available in female BC, reliable data are still lacking in male BC (MBC). This study aimed to provide the patterns, prevalence and risk estimates associated with PVs in non-BRCA1/2 genes for MBC in order to improve BC prevention for male patients. METHODS We performed a large case-control study in the Italian population, including 767 BRCA1/2-negative MBCs and 1349 male controls, all screened using a custom 50 cancer gene panel. RESULTS PVs in genes other than BRCA1/2 were significantly more frequent in MBCs compared with controls (4.8% vs 1.8%, respectively) and associated with a threefold increased MBC risk (OR: 3.48, 95% CI: 1.88-6.44; p < 0.0001). PV carriers were more likely to have personal (p = 0.03) and family (p = 0.02) history of cancers, not limited to BC. PALB2 PVs were associated with a sevenfold increased MBC risk (OR: 7.28, 95% CI: 1.17-45.52; p = 0.034), and ATM PVs with a fivefold increased MBC risk (OR: 4.79, 95% CI: 1.12-20.56; p = 0.035). CONCLUSIONS This study highlights the role of PALB2 and ATM PVs in MBC susceptibility and provides risk estimates at population level. These data may help in the implementation of multigene panel testing in MBC patients and inform gender-specific BC risk management and decision making for patients and their families.
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Affiliation(s)
- Agostino Bucalo
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Giulia Conti
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Virginia Valentini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Carlo Capalbo
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics Research Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Daniele Calistri
- Istituto Romagnolo per lo Studio dei Tumori "Dino Amadori"-IRST IRCCS, Meldola, Italy
| | - Anna Coppa
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Laura Cortesi
- Department of Oncology and Haematology, University of Modena and Reggio Emilia, Modena, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy; Istituto Pasteur-Fondazione Cenci Bolognetti, Rome, Italy
| | - Viviana Gismondi
- Hereditary Cancer Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Siranoush Manoukian
- Unità di Genetica Medica, Dipartimento di Oncologia Medica ed Ematologia, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Livia Manzella
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori (INT), Milan, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical and Oncological Sciences, University of Palermo, Palermo, Italy
| | - Maria Grazia Tibiletti
- Dipartimento di Patologia, ASST Settelaghi and Centro di Ricerca per lo studio dei tumori eredo-familiari, Università dell'Insubria, Varese, Italy
| | - Daniela Turchetti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Alessandra Viel
- Unità di Oncogenetica e Oncogenomica Funzionale, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Ines Zanna
- Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence, Italy
| | - Domenico Palli
- Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence, Italy
| | | | - Laura Ottini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy.
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7
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Intronic OTOF mutation causes an atypical splicing defect resulting in auditory neuropathy spectrum disorder. J Genet 2023. [DOI: 10.1007/s12041-023-01420-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
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8
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Alenezi WM, Fierheller CT, Serruya C, Revil T, Oros KK, Subramanian DN, Bruce J, Spiegelman D, Pugh T, Campbell IG, Mes-Masson AM, Provencher D, Foulkes WD, Haffaf ZE, Rouleau G, Bouchard L, Greenwood CMT, Ragoussis J, Tonin PN. Genetic analyses of DNA repair pathway associated genes implicate new candidate cancer predisposing genes in ancestrally defined ovarian cancer cases. Front Oncol 2023; 13:1111191. [PMID: 36969007 PMCID: PMC10030840 DOI: 10.3389/fonc.2023.1111191] [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: 11/29/2022] [Accepted: 02/06/2023] [Indexed: 03/29/2023] Open
Abstract
Not all familial ovarian cancer (OC) cases are explained by pathogenic germline variants in known risk genes. A candidate gene approach involving DNA repair pathway genes was applied to identify rare recurring pathogenic variants in familial OC cases not associated with known OC risk genes from a population exhibiting genetic drift. Whole exome sequencing (WES) data of 15 OC cases from 13 families tested negative for pathogenic variants in known OC risk genes were investigated for candidate variants in 468 DNA repair pathway genes. Filtering and prioritization criteria were applied to WES data to select top candidates for further analyses. Candidates were genotyped in ancestry defined study groups of 214 familial and 998 sporadic OC or breast cancer (BC) cases and 1025 population-matched controls and screened for additional carriers in 605 population-matched OC cases. The candidate genes were also analyzed in WES data from 937 familial or sporadic OC cases of diverse ancestries. Top candidate variants in ERCC5, EXO1, FANCC, NEIL1 and NTHL1 were identified in 5/13 (39%) OC families. Collectively, candidate variants were identified in 7/435 (1.6%) sporadic OC cases and 1/566 (0.2%) sporadic BC cases versus 1/1025 (0.1%) controls. Additional carriers were identified in 6/605 (0.9%) OC cases. Tumour DNA from ERCC5, NEIL1 and NTHL1 variant carriers exhibited loss of the wild-type allele. Carriers of various candidate variants in these genes were identified in 31/937 (3.3%) OC cases of diverse ancestries versus 0-0.004% in cancer-free controls. The strategy of applying a candidate gene approach in a population exhibiting genetic drift identified new candidate OC predisposition variants in DNA repair pathway genes.
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Affiliation(s)
- Wejdan M. Alenezi
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Department of Medical Laboratory Technology, Taibah University, Medina, Saudi Arabia
| | - Caitlin T. Fierheller
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Corinne Serruya
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill Genome Centre, McGill University, Montreal, QC, Canada
| | - Kathleen K. Oros
- Lady Davis Institute for Medical Research of the Jewish General Hospital, Montreal, QC, Canada
| | - Deepak N. Subramanian
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Jeffrey Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Dan Spiegelman
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Trevor Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Ian G. Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l’Université de Montréal and Institut du cancer de Montréal, Montreal, QC, Canada
- Departement of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Diane Provencher
- Centre de recherche du Centre hospitalier de l’Université de Montréal and Institut du cancer de Montréal, Montreal, QC, Canada
- Division of Gynecologic Oncology, Université de Montréal, Montreal, QC, Canada
| | - William D. Foulkes
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Lady Davis Institute for Medical Research of the Jewish General Hospital, Montreal, QC, Canada
- Department of Medical Genetics, McGill University Health Centre, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| | - Zaki El Haffaf
- Centre de recherche du Centre hospitalier de l’Université de Montréal and Institut du cancer de Montréal, Montreal, QC, Canada
- Service de Médecine Génique, Centre Hospitalier de l’Université de Montréal, Montreal, QC, Canada
| | - Guy Rouleau
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of Medical Biology, Centres intégrés universitaires de santé et de services sociaux du Saguenay-Lac-Saint-Jean hôpital Universitaire de Chicoutimi, Saguenay, QC, Canada
- Centre de Recherche du Centre hospitalier l’Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Celia M. T. Greenwood
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Lady Davis Institute for Medical Research of the Jewish General Hospital, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill Genome Centre, McGill University, Montreal, QC, Canada
| | - Patricia N. Tonin
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
- *Correspondence: Patricia N. Tonin,
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9
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Rashid MU, Muhammad N, Shehzad U, Khan FA, Loya A, Hamann U. Prevalence of FANCM germline variants in BRCA1/2 negative breast and/or ovarian cancer patients from Pakistan. Fam Cancer 2023; 22:31-41. [PMID: 35802266 DOI: 10.1007/s10689-022-00304-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/18/2022] [Indexed: 01/12/2023]
Abstract
The Fanconi anemia complementation group M (FANCM) gene is a potential candidate for breast/ovarian cancer susceptibility in European populations. Here, we examined the contribution of FANCM germline variants to hereditary breast and/or ovarian cancer in Pakistan. Comprehensive FANCM variant screening was performed in 201 BRCA1 and BRCA2 (BRCA1/2) negative Pakistani patients with and without triple-negative breast cancer (TNBC) and/or ovarian cancer, using denaturing high-performance liquid chromatography analysis (DHPLC) followed by DNA sequencing. Novel variants were tested for their potential effect on protein function using in silico tools. Reverse transcription (RT)-PCR analysis of RNA extracted from one deletion/insertion (delins) variant (p.K1780delinsNGIT) carrier and three non-carriers was performed to evaluate the impact of this variant on splicing. Furthermore, potentially functional variants were evaluated in 200 healthy female controls. A missense variant (p.V1857M) was identified in a 50-year-old TNBC patient with a family history of breast cancer. It was also identified in the index patient´s daughter, who was diagnosed with osteosarcoma at 15 years of age. Further, one delins variant (p.K1780delinsNGIT) was identified in a 45-year-old non-TNBC patient, but not detected in her brother, who was diagnosed with Hodgkin's lymphoma at 38 years of age. Based on in silico and RNA analyses, p.V1857M and p.K1780delinsNGIT were predicted as variants of uncertain significance (VUS), respectively. Both variants were absent in 200 healthy controls. Our findings suggest a marginal contribution of FANCM variants to hereditary breast/ovarian cancer in Pakistan, which need to be confirmed in larger studies.
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Affiliation(s)
- Muhammad Usman Rashid
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), 7A, Block R3, Johar Town, Lahore, 54000, Punjab, Pakistan.
| | - Noor Muhammad
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), 7A, Block R3, Johar Town, Lahore, 54000, Punjab, Pakistan
| | - Umara Shehzad
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), 7A, Block R3, Johar Town, Lahore, 54000, Punjab, Pakistan
| | - Faiz Ali Khan
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), 7A, Block R3, Johar Town, Lahore, 54000, Punjab, Pakistan
| | - Asif Loya
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
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10
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Clinical Impact of Next-Generation Sequencing Multi-Gene Panel Highlighting the Landscape of Germline Alterations in Ovarian Cancer Patients. Int J Mol Sci 2022; 23:ijms232415789. [PMID: 36555431 PMCID: PMC9779064 DOI: 10.3390/ijms232415789] [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: 10/18/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
BRCA1 and BRCA2 are the most frequently mutated genes in ovarian cancer (OC) crucial both for the identification of cancer predisposition and therapeutic choices. However, germline variants in other genes could be involved in OC susceptibility. We characterized OC patients to detect mutations in genes other than BRCA1/2 that could be associated with a high risk of developing OC and permit patients to enter the most appropriate treatment and surveillance program. Next-generation sequencing analysis with a 94-gene panel was performed on germline DNA of 219 OC patients. We identified 34 pathogenic/likely pathogenic variants in BRCA1/2 and 38 in other 21 genes. The patients with pathogenic/likely pathogenic variants in the non-BRCA1/2 genes mainly developed OC alone compared to the other groups that also developed breast cancer or other tumors (p = 0.001). Clinical correlation analysis showed that the low-risk patients were significantly associated with platinum sensitivity (p < 0.001). Regarding PARP inhibitors (PARPi) response, the patients with pathogenic mutations in the non-BRCA1/2 genes had worse PFS and OS. Moreover, a statistically significantly worse PFS was found for every increase of one thousand platelets before PARPi treatment. To conclude, knowledge about molecular alterations in genes beyond BRCA1/2 in OC could allow for more personalized diagnostic, predictive, prognostic, and therapeutic strategies for OC patients.
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11
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Ye J, Lin Y, Gao X, Lu L, Huang X, Huang S, Bai T, Wu G, Luo X, Li Y, Liang R. Prognosis-Related Molecular Subtypes and Immune Features Associated with Hepatocellular Carcinoma. Cancers (Basel) 2022; 14:cancers14225721. [PMID: 36428813 PMCID: PMC9688639 DOI: 10.3390/cancers14225721] [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: 08/09/2022] [Revised: 10/29/2022] [Accepted: 11/01/2022] [Indexed: 11/23/2022] Open
Abstract
Bioinformatics tools were used to identify prognosis-related molecular subtypes and biomarkers of hepatocellular carcinoma (HCC). Differential expression analysis of four datasets identified 3330 overlapping differentially expressed genes (DEGs) in the same direction in all four datasets. Those genes were involved in the cell cycle, FOXO signaling pathway, as well as complement and coagulation cascades. Based on non-negative matrix decomposition, two molecular subtypes of HCC with different prognoses were identified, with subtype C2 showing better overall survival than subtype C1. Cox regression and Kaplan-Meier analysis showed that 217 of the overlapping DEGs were closely associated with HCC prognosis. The subset of those genes showing an area under the curve >0.80 was used to construct random survival forest and least absolute shrinkage and selection operator models, which identified seven feature genes (SORBS2, DHRS1, SLC16A2, RCL1, IGFALS, GNA14, and FANCI) that may be involved in HCC occurrence and prognosis. Based on the feature genes, risk score and recurrence models were constructed, while a univariate Cox model identified FANCI as a key gene involved mainly in the cell cycle, DNA replication, and mismatch repair. Further analysis showed that FANCI had two mutation sites and that its gene may undergo methylation. Single-sample gene set enrichment analysis showed that Th2 and T helper cells are significantly upregulated in HCC patients compared to controls. Our results identify FANCI as a potential prognostic biomarker for HCC.
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Affiliation(s)
- Jiazhou Ye
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, China
| | - Yan Lin
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, China
| | - Xing Gao
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, China
| | - Lu Lu
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, China
| | - Xi Huang
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, China
| | - Shilin Huang
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, China
| | - Tao Bai
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, China
| | - Guobin Wu
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, China
| | - Xiaoling Luo
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning 530021, China
| | - Yongqiang Li
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, China
- Correspondence: (Y.L.); (R.L.); Tel./Fax: +86-771-5335155 (Y.L. & R.L.)
| | - Rong Liang
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning 530021, China
- Correspondence: (Y.L.); (R.L.); Tel./Fax: +86-771-5335155 (Y.L. & R.L.)
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12
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Marchena-Perea EM, Salazar-Hidalgo ME, Gómez-Sanz A, Arranz-Ledo M, Barroso A, Fernández V, Tejera-Pérez H, Pita G, Núñez-Torres R, Pombo L, Morales-Chamorro R, Cano-Cano JM, Soriano MDC, Garre P, Durán M, Currás-Freixes M, de la Hoya M, Osorio A. A Large Case-Control Study Performed in Spanish Population Suggests That RECQL5 Is the Only RECQ Helicase Involved in Breast Cancer Susceptibility. Cancers (Basel) 2022; 14:cancers14194738. [PMID: 36230663 PMCID: PMC9563930 DOI: 10.3390/cancers14194738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Around 50% of the familial breast cancer (BC) cases are estimated to be caused by variants in low-, moderate-, and high-risk susceptibility genes; however, the other half is of unknown origin. The finding of new susceptibility genes is key to improve diagnosis, take preventive measures, and identify new therapies. In this context, previous studies have discussed whether the genes encoding for the RECQ helicase family could play a role in BC susceptibility, without very conclusive results. To clarify this, in this study, we sequenced the whole coding sequence of the RECQL1, BLM, WRN, RECQL4, and RECQL5 genes in 1993 Spanish BC familial cases and compared it with controls from gnomAD. No association was found for RECQL1, BLM, WRN, and RECQL4; however, we did find an association between RECQL5 and breast cancer as a moderate-risk gene, making it a perfect candidate for further studies. Abstract Around 50% of the familial breast cancer (BC) cases are estimated to be caused by germline variants in known low-, moderate-, and high-risk susceptibility genes, while the other half is of unknown genetic origin. In the present study, we wanted to evaluate the role of the RECQ helicases, some of which have been studied in the past as candidates, with unclear results about their role in the disease. Using next-generation sequencing (NGS) technology, we analyzed the whole coding sequence of BLM, RECQL1, RECQL4, RECQL5, and WRN in almost 2000 index cases from BC Spanish families that had previously tested negative for the known BC susceptibility genes (BRCAX) and compared the results with the controls extracted from gnomAD. Our results suggest that BLM, RECQL1, RECQL4, and WRN do not play a major role in BC susceptibility. However, in the combined analysis, joining the present results with those previously reported in a series of 1334 BC Spanish patients and controls, we found a statistically significant association between Loss of Function (LoF) variants in RECQL5 and BC risk, with an OR of 2.56 (p = 0.009; 95% CI, 1.18–4.98). Our findings support our previous work and places the RECQL5 gene as a new moderate-risk BC gene.
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Affiliation(s)
- Erik Michel Marchena-Perea
- Human Cancer Genetics Programme, Familial Cancer Clinical Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Milton Eduardo Salazar-Hidalgo
- Human Cancer Genetics Programme, Familial Cancer Clinical Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Alicia Gómez-Sanz
- Molecular Oncology Laboratory (CIBERONC), Hospital Clínico San Carlos, IdISSC, 28040 Madrid, Spain
| | - Mónica Arranz-Ledo
- Cancer Genetics Group, Unidad de Excelencia Instituto de Biología y Genética Molecular, Universidad de Valladolid-Consejo Superior de Investigaciones Científicas (IBGM, UVa-CSIC), 47003 Valladolid, Spain
| | - Alicia Barroso
- Human Cancer Genetics Programme, Familial Cancer Clinical Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Victoria Fernández
- Human Cancer Genetics Programme, Familial Cancer Clinical Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Hugo Tejera-Pérez
- Human Cancer Genetics Programme, Human Genotyping Unit (CEGEN), Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Guillermo Pita
- Human Cancer Genetics Programme, Human Genotyping Unit (CEGEN), Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Rocío Núñez-Torres
- Human Cancer Genetics Programme, Human Genotyping Unit (CEGEN), Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Luz Pombo
- Medical Oncology Section, Universitary Hospital Complex of Albacete, 02006 Albacete, Spain
| | - Rafael Morales-Chamorro
- Medical Oncology Section, Hospitalary Compex La Mancha Centro, 13600 Alcázar de San Juan, Spain
| | - Juana María Cano-Cano
- Medical Oncology Service, Universitary General Hospital of Ciudad Real, 13005 Ciudad Real, Spain
| | | | - Pilar Garre
- Molecular Oncology Laboratory (CIBERONC), Hospital Clínico San Carlos, IdISSC, 28040 Madrid, Spain
| | - Mercedes Durán
- Cancer Genetics Group, Unidad de Excelencia Instituto de Biología y Genética Molecular, Universidad de Valladolid-Consejo Superior de Investigaciones Científicas (IBGM, UVa-CSIC), 47003 Valladolid, Spain
| | - María Currás-Freixes
- Human Cancer Genetics Programme, Familial Cancer Clinical Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory (CIBERONC), Hospital Clínico San Carlos, IdISSC, 28040 Madrid, Spain
| | - Ana Osorio
- Human Cancer Genetics Programme, Familial Cancer Clinical Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
- Spanish Network on Rare Diseases (CIBERER), 28029 Madrid, Spain
- Genetics Service, Fundación Jiménez Díaz, 28043 Madrid, Spain
- Correspondence: ; Tel.: +34-917-328-002
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Dettwyler SA, Koeppe ES, Jacobs MF, Stoffel EM. Outcomes of retesting in patients with previously uninformative cancer genetics evaluations. Fam Cancer 2022; 21:375-385. [PMID: 34545504 PMCID: PMC8934750 DOI: 10.1007/s10689-021-00276-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/12/2021] [Indexed: 11/24/2022]
Abstract
Advances in cancer genetics have increased germline pathogenic/likely pathogenic variant (PV/LPV) detection rates. More data is needed to inform which patients with previously uninformative results could benefit most from retesting, especially beyond breast/ovarian cancer populations. Here, we describe retesting outcomes and predictors of PV/LPVs in a cohort of patients unselected by cancer diagnosis. Retrospective chart reviews were conducted for patients at a cancer genetics clinic between 1998 and 2019 who underwent genetic testing (GT) on ≥ 2 dates with ≥ 1 year between tests, with no PV/LPVs on first-line GT. Demographics, retesting indications, and GT details were reviewed to evaluate predictive factors of PV/LPV identification. 139 patients underwent retesting, of whom 24 (17.3%) had a PV/LPV, encompassing 15 genes. 14 PV/LPV carriers (58.3%) only returned for retesting after personal or familial history changes (typically new cancer diagnoses), while 10 (41.7%) retested due to updated GT availability. No specific GT method was most likely to identify PV/LPVs and no specific clinical factors were predictive of a PV/LPV. The identified PV/LPVs were consistent with patients' personal or family histories, but were discordant with the initial referral indication for GT. For 16 (66.7%) PV/LPV carriers, the genetic diagnosis changed clinical management. This study adds to the limited body of literature on retesting outcomes beyond first-line BRCA analysis alone and confirms the utility of multigene panel testing. Retesting certain affected individuals when updated GT is available could result in earlier PV/LPV identification, significantly impacting screening recommendations and potentially reducing cancer-related morbidity and mortality.
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Affiliation(s)
| | - Erika S Koeppe
- Michigan Medicine Cancer Genetics Clinic, Ann Arbor, MI, USA
| | | | - Elena M Stoffel
- Michigan Medicine Cancer Genetics Clinic, Ann Arbor, MI, USA
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14
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Mekonnen N, Yang H, Shin YK. Homologous Recombination Deficiency in Ovarian, Breast, Colorectal, Pancreatic, Non-Small Cell Lung and Prostate Cancers, and the Mechanisms of Resistance to PARP Inhibitors. Front Oncol 2022; 12:880643. [PMID: 35785170 PMCID: PMC9247200 DOI: 10.3389/fonc.2022.880643] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022] Open
Abstract
Homologous recombination (HR) is a highly conserved DNA repair mechanism that protects cells from exogenous and endogenous DNA damage. Breast cancer 1 (BRCA1) and breast cancer 2 (BRCA2) play an important role in the HR repair pathway by interacting with other DNA repair proteins such as Fanconi anemia (FA) proteins, ATM, RAD51, PALB2, MRE11A, RAD50, and NBN. These pathways are frequently aberrant in cancer, leading to the accumulation of DNA damage and genomic instability known as homologous recombination deficiency (HRD). HRD can be caused by chromosomal and subchromosomal aberrations, as well as by epigenetic inactivation of tumor suppressor gene promoters. Deficiency in one or more HR genes increases the risk of many malignancies. Another conserved mechanism involved in the repair of DNA single-strand breaks (SSBs) is base excision repair, in which poly (ADP-ribose) polymerase (PARP) enzymes play an important role. PARP inhibitors (PARPIs) convert SSBs to more cytotoxic double-strand breaks, which are repaired in HR-proficient cells, but remain unrepaired in HRD. The blockade of both HR and base excision repair pathways is the basis of PARPI therapy. The use of PARPIs can be expanded to sporadic cancers displaying the “BRCAness” phenotype. Although PARPIs are effective in many cancers, their efficacy is limited by the development of resistance. In this review, we summarize the prevalence of HRD due to mutation, loss of heterozygosity, and promoter hypermethylation of 35 DNA repair genes in ovarian, breast, colorectal, pancreatic, non-small cell lung cancer, and prostate cancer. The underlying mechanisms and strategies to overcome PARPI resistance are also discussed.
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Affiliation(s)
- Negesse Mekonnen
- Department of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University College of Pharmacy, Seoul, South Korea
- Department of Veterinary Science, School of Animal Science and Veterinary Medicine, Bahir Dar University, Bahir Dar, Ethiopia
| | - Hobin Yang
- Department of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University College of Pharmacy, Seoul, South Korea
| | - Young Kee Shin
- Department of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University College of Pharmacy, Seoul, South Korea
- Bio-MAX/N-Bio, Seoul National University, Seoul, South Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University Graduate School of Convergence Science and Technology, Seoul, South Korea
- LOGONE Bio Convergence Research Foundation, Center for Companion Diagnostics, Seoul, South Korea
- *Correspondence: Young Kee Shin,
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15
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Ruether C, Wuensch C, Randau G, Michgehl U, Trautmann M, Hartmann W, Sandmann S, Dugas M, Khanam T, Burkhardt B. Design of a targeted next-generation DNA sequencing panel for pediatric T-cell lymphoblastic lymphoma to unravel biology and optimize treatment. Genes Chromosomes Cancer 2022; 61:459-470. [PMID: 35278000 DOI: 10.1002/gcc.23037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/26/2022] [Accepted: 03/06/2022] [Indexed: 11/09/2022] Open
Abstract
Low incidence and molecular heterogeneity of pediatric T-cell lymphoblastic lymphoma (T-LBL) require an international, large-scale effort to identify novel clinical biomarkers. The ongoing international clinical trial LBL2018 (NCT04043494) represents an ideal opportunity to implement a common analytic approach. Targeted next-generation sequencing is well-suited for this purpose; however, selection of relevant target genes for T-LBL remains subject of ongoing debates. Our group has recently designed and evaluated a first target panel of 80 candidate genes for T-LBL. The present study aimed at developing a novel optimized gene panel for large-scale application and to promote an international agreement on a common core panel. Small sequence variants obtained from our former study were systematically analyzed and classified with regards to pathogenic relevance, to prioritize candidate genes. Additional genes were curated from literature and online databases for a more comprehensive analysis of relevant functions and signaling pathways. The new target panel TGP-T-LBL entails 84 candidate genes which are key actors in NOTCH, PI3K-AKT, JAK-STAT, RAS signaling, epigenetic regulation, transcription, DNA repair, cell cycle regulation and ribosomal function. From our former gene panel, 35 out of 80 candidate genes were selected for the novel panel. Forty-six out of 84 genes are currently being analyzed in the ongoing international trial LBL2018. Exploratory analysis of prognostic relevance on mutation-level suggested a potential association of PIK3CA variants c.1624G > A(p.Glu542Lys) and c.1633G > A(p.Glu545Lys) to occurrence of relapse, emphasizing particular relevance of mutation analysis in PI3K-AKT signaling. Our approach promotes comprehensive and clinically relevant mutational profiling of pediatric T-LBL. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Charlotte Ruether
- Paediatric Hematology and Oncology, University Hospital Muenster, Germany
| | | | - Gerrit Randau
- Paediatric Hematology and Oncology, University Hospital Muenster, Germany
| | - Ulf Michgehl
- Paediatric Hematology and Oncology, University Hospital Muenster, Germany
| | - Marcel Trautmann
- Division of Translational Pathology, Gerhard-Domagk-Institute of Pathology, University Hospital Muenster, Germany
| | - Wolfgang Hartmann
- Division of Translational Pathology, Gerhard-Domagk-Institute of Pathology, University Hospital Muenster, Germany
| | - Sarah Sandmann
- Institute of Medical Informatics, Muenster University, Germany
| | - Martin Dugas
- Institute of Medical Informatics, Muenster University, Germany
| | - Tasneem Khanam
- Paediatric Hematology and Oncology, University Hospital Muenster, Germany
| | - Birgit Burkhardt
- Paediatric Hematology and Oncology, University Hospital Muenster, Germany
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Next step in molecular genetics of hereditary breast/ovarian cancer: Multigene panel testing in clinical actionably genes and prioritization algorithms in the study of variants of uncertain significance. Eur J Med Genet 2022; 65:104468. [PMID: 35245693 DOI: 10.1016/j.ejmg.2022.104468] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 01/15/2022] [Accepted: 02/25/2022] [Indexed: 02/06/2023]
Abstract
INTRODUCTION BRCA1 and BRCA2 are the two main genes causing hereditary breast and ovarian cancer (HBOC). However, thanks to the development of Next Generation Sequencing (NGS), other genes linked to this syndrome (CHEK2, BRIP1, ATM and PALB2 among others) can be analysed. MATERIAL AND METHODS an analysis by multigene panel testing was performed in 138 index cases (ICs) from HBOC Spanish families with a previous non-informative result for BRCA1/2. The BRCA Hereditary Cancer Master™ Plus kit, including 26 actionable and candidate genes related to HBOC was employed. Once classified, an algorithm was employed to prioritized those variants of unknown significance with a higher risk of having a deleterious effect. Moreover, a mRNA splicing assay was performed for the prioritized VUS c.3402+3A > C in ATM, located at intron 23. RESULTS A total of 82 variants were found: 70 VUS and 12 pathogenic or probably pathogenic variants. The diagnostic yield in actionable genes non-BRCA was 7.97% of the total tested ICs. Overall, 19 VUS were prioritized, which meant 27% of the 70 total VUS. RNA analysis of the variant 3402+3A > C confirmed a deleterious impact on splicing. DISCUSSION The implementation of a multigene panel in HBOC studied families improved the diagnostic yield, concordant with results obtained in previous publications. Due to the important number of VUS obtained in NGS, the application of a prioritization algorithm is needed in order to select those variants in which it is necessary to conduct further studies.
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Fierheller CT, Guitton-Sert L, Alenezi WM, Revil T, Oros KK, Gao Y, Bedard K, Arcand SL, Serruya C, Behl S, Meunier L, Fleury H, Fewings E, Subramanian DN, Nadaf J, Bruce JP, Bell R, Provencher D, Foulkes WD, El Haffaf Z, Mes-Masson AM, Majewski J, Pugh TJ, Tischkowitz M, James PA, Campbell IG, Greenwood CMT, Ragoussis J, Masson JY, Tonin PN. A functionally impaired missense variant identified in French Canadian families implicates FANCI as a candidate ovarian cancer-predisposing gene. Genome Med 2021; 13:186. [PMID: 34861889 PMCID: PMC8642877 DOI: 10.1186/s13073-021-00998-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/27/2021] [Indexed: 12/14/2022] Open
Abstract
Background Familial ovarian cancer (OC) cases not harbouring pathogenic variants in either of the BRCA1 and BRCA2 OC-predisposing genes, which function in homologous recombination (HR) of DNA, could involve pathogenic variants in other DNA repair pathway genes. Methods Whole exome sequencing was used to identify rare variants in HR genes in a BRCA1 and BRCA2 pathogenic variant negative OC family of French Canadian (FC) ancestry, a population exhibiting genetic drift. OC cases and cancer-free individuals from FC and non-FC populations were investigated for carrier frequency of FANCI c.1813C>T; p.L605F, the top-ranking candidate. Gene and protein expression were investigated in cancer cell lines and tissue microarrays, respectively. Results In FC subjects, c.1813C>T was more common in familial (7.1%, 3/42) than sporadic (1.6%, 7/439) OC cases (P = 0.048). Carriers were detected in 2.5% (74/2950) of cancer-free females though female/male carriers were more likely to have a first-degree relative with OC (121/5249, 2.3%; Spearman correlation = 0.037; P = 0.011), suggesting a role in risk. Many of the cancer-free females had host factors known to reduce risk to OC which could influence cancer risk in this population. There was an increased carrier frequency of FANCI c.1813C>T in BRCA1 and BRCA2 pathogenic variant negative OC families, when including the discovery family, compared to cancer-free females (3/23, 13%; OR = 5.8; 95%CI = 1.7–19; P = 0.005). In non-FC subjects, 10 candidate FANCI variants were identified in 4.1% (21/516) of Australian OC cases negative for pathogenic variants in BRCA1 and BRCA2, including 10 carriers of FANCI c.1813C>T. Candidate variants were significantly more common in familial OC than in sporadic OC (P = 0.04). Localization of FANCD2, part of the FANCI-FANCD2 (ID2) binding complex in the Fanconi anaemia (FA) pathway, to sites of induced DNA damage was severely impeded in cells expressing the p.L605F isoform. This isoform was expressed at a reduced level, destabilized by DNA damaging agent treatment in both HeLa and OC cell lines, and exhibited sensitivity to cisplatin but not to a poly (ADP-ribose) polymerase inhibitor. By tissue microarray analyses, FANCI protein was consistently expressed in fallopian tube epithelial cells and only expressed at low-to-moderate levels in 88% (83/94) of OC samples. Conclusions This is the first study to describe candidate OC variants in FANCI, a member of the ID2 complex of the FA DNA repair pathway. Our data suggest that pathogenic FANCI variants may modify OC risk in cancer families. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00998-5.
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Affiliation(s)
- Caitlin T Fierheller
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada
| | - Laure Guitton-Sert
- Genome Stability Laboratory, CHU de Québec-Université Laval Research Center, Oncology Division, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Wejdan M Alenezi
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada.,Department of Medical Laboratory Technology, Taibah University, Medina, Saudi Arabia
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Kathleen K Oros
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Yuandi Gao
- Genome Stability Laboratory, CHU de Québec-Université Laval Research Center, Oncology Division, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Karine Bedard
- Laboratoire de Diagnostic Moléculaire, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Quebec, Canada.,Département de pathologie et biologie cellulaire, Université de Montréal, Montreal, Quebec, Canada
| | - Suzanna L Arcand
- Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada
| | - Corinne Serruya
- Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada
| | - Supriya Behl
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Liliane Meunier
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada
| | - Hubert Fleury
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada
| | - Eleanor Fewings
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Deepak N Subramanian
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Javad Nadaf
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Jeffrey P Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rachel Bell
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Diane Provencher
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada.,Division of Gynecologic Oncology, Université de Montréal, Montreal, Quebec, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Zaki El Haffaf
- Centre de recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada.,Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Paul A James
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,The Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Celia M T Greenwood
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.,Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec-Université Laval Research Center, Oncology Division, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Patricia N Tonin
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada. .,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada. .,Department of Medicine, McGill University, Montreal, Quebec, Canada.
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Xu P, Sun D, Gao Y, Jiang Y, Zhong M, Zhao G, Chen J, Wang Z, Liu Q, Hong J, Chen H, Chen YX, Fang JY. Germline mutations in a DNA repair pathway are associated with familial colorectal cancer. JCI Insight 2021; 6:148931. [PMID: 34549727 PMCID: PMC8492347 DOI: 10.1172/jci.insight.148931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/30/2021] [Indexed: 12/18/2022] Open
Abstract
Aiming to identify rare high-penetrance mutations in new genes for the underlying predisposition in familial colorectal cancer (CRC), we performed whole-exome sequencing in 24 familial CRCs. Mutations in genes that regulate DNA repair (RMI1, PALB2, FANCI) were identified that were related to the Fanconi anemia DNA repair pathway. In one pedigree, we found a nonsense mutation in CHEK2. CHEK2 played an essential role in cell cycle and DNA damage repair. Somatic mutation analysis in CHEK2 variant carriers showed mutations in TP53, APC, and FBXW7. Loss of heterozygosity was found in carcinoma of CHEK2 variant carrier, and IHC showed loss of Chk2 expression in cancer tissue. We identified a second variant in CHEK2 in 126 sporadic CRCs. A KO cellular model for CHEK2 (CHEK2KO) was generated by CRISPR/Cas9. Functional experiments demonstrated that CHEK2KO cells showed defective cell cycle arrest and apoptosis, as well as reduced p53 phosphorylation, upon DNA damage. We associated germline mutations in genes that regulate the DNA repair pathway with the development of CRC. We identified CHEK2 as a regulator of DNA damage response and perhaps as a gene involved in CRC germline predisposition. These findings link CRC predisposition to the DNA repair pathway, supporting the connection between genome integrity and cancer risk.
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Affiliation(s)
- Pingping Xu
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease
| | - Danfeng Sun
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease
| | - Yaqi Gao
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease
| | - Yi Jiang
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease
| | | | | | | | | | - Qiang Liu
- Department of Pathology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Hong
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease
| | - Haoyan Chen
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease
| | - Ying-Xuan Chen
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease
| | - Jing-Yuan Fang
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease
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Gianni P, Matenoglou E, Geropoulos G, Agrawal N, Adnani H, Zafeiropoulos S, Miyara SJ, Guevara S, Mumford JM, Molmenti EP, Giannis D. The Fanconi anemia pathway and Breast Cancer: A comprehensive review of clinical data. Clin Breast Cancer 2021; 22:10-25. [PMID: 34489172 DOI: 10.1016/j.clbc.2021.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/17/2021] [Accepted: 08/05/2021] [Indexed: 02/08/2023]
Abstract
The development of breast cancer depends on several risk factors, including environmental, lifestyle and genetic factors. Despite the evolution of DNA sequencing techniques and biomarker detection, the epidemiology and mechanisms of various breast cancer susceptibility genes have not been elucidated yet. Dysregulation of the DNA damage response causes genomic instability and increases the rate of mutagenesis and the risk of carcinogenesis. The Fanconi Anemia (FA) pathway is an important component of the DNA damage response and plays a critical role in the repair of DNA interstrand crosslinks and genomic stability. The FA pathway involves 22 recognized genes and specific mutations have been identified as the underlying defect in the majority of FA patients. A thorough understanding of the function and epidemiology of these genes in breast cancer is critical for the development and implementation of individualized therapies that target unique tumor profiles. Targeted therapies (PARP inhibitors) exploiting the FA pathway gene defects have been developed and have shown promising results. This narrative review summarizes the current literature on the involvement of FA genes in sporadic and familial breast cancer with a focus on clinical data derived from large cohorts.
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Affiliation(s)
- Panagiota Gianni
- Department of Internal Medicine III, Hematology, Oncology, Palliative Medicine, Rheumatology and Infectious Diseases, University Hospital Ulm, Germany
| | - Evangelia Matenoglou
- Medical School, Aristotle University of Thessaloniki, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios Geropoulos
- Thoracic Surgery Department, University College London Hospitals NHS Foundation Trust, London
| | - Nirav Agrawal
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY
| | - Harsha Adnani
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY
| | - Stefanos Zafeiropoulos
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY; Elmezzi Graduate School of Molecular Medicine, Northwell Health, Manhasset, New York, NY
| | - Santiago J Miyara
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY; Elmezzi Graduate School of Molecular Medicine, Northwell Health, Manhasset, New York, NY
| | - Sara Guevara
- Department of Surgery, North Shore University Hospital, Manhasset, New York, NY
| | - James M Mumford
- Department of Family Medicine, Glen Cove Hospital, Glen Cove, New York, NY; Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, NY
| | - Ernesto P Molmenti
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY; Department of Surgery, North Shore University Hospital, Manhasset, New York, NY; Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, NY
| | - Dimitrios Giannis
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY.
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20
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Moles-Fernández A, Domènech-Vivó J, Tenés A, Balmaña J, Diez O, Gutiérrez-Enríquez S. Role of Splicing Regulatory Elements and In Silico Tools Usage in the Identification of Deep Intronic Splicing Variants in Hereditary Breast/Ovarian Cancer Genes. Cancers (Basel) 2021; 13:cancers13133341. [PMID: 34283047 PMCID: PMC8268271 DOI: 10.3390/cancers13133341] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary There is a significant percentage of hereditary breast and ovarian cancer (HBOC) cases that remain undiagnosed, because no pathogenic variant is detected through massively parallel sequencing of coding exons and exon-intron boundaries of high-moderate susceptibility risk genes. Deep intronic regions may contain variants affecting RNA splicing, leading ultimately to disease, and hence they may explain several cases where the genetic cause of HBOC is unknown. This study aims to characterize intronic regions to identify a landscape of “exonizable” zones and test the efficiency of two in silico tools to detect deep intronic variants affecting the mRNA splicing process. Abstract The contribution of deep intronic splice-altering variants to hereditary breast and ovarian cancer (HBOC) is unknown. Current computational in silico tools to predict spliceogenic variants leading to pseudoexons have limited efficiency. We assessed the performance of the SpliceAI tool combined with ESRseq scores to identify spliceogenic deep intronic variants by affecting cryptic sites or splicing regulatory elements (SREs) using literature and experimental datasets. Our results with 233 published deep intronic variants showed that SpliceAI, with a 0.05 threshold, predicts spliceogenic deep intronic variants affecting cryptic splice sites, but is less effective in detecting those affecting SREs. Next, we characterized the SRE profiles using ESRseq, showing that pseudoexons are significantly enriched in SRE-enhancers compared to adjacent intronic regions. Although the combination of SpliceAI with ESRseq scores (considering ∆ESRseq and SRE landscape) showed higher sensitivity, the global performance did not improve because of the higher number of false positives. The combination of both tools was tested in a tumor RNA dataset with 207 intronic variants disrupting splicing, showing a sensitivity of 86%. Following the pipeline, five spliceogenic deep intronic variants were experimentally identified from 33 variants in HBOC genes. Overall, our results provide a framework to detect deep intronic variants disrupting splicing.
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Affiliation(s)
- Alejandro Moles-Fernández
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (A.M.-F.); (J.D.-V.); (J.B.)
| | - Joanna Domènech-Vivó
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (A.M.-F.); (J.D.-V.); (J.B.)
| | - Anna Tenés
- Area of Clinical and Molecular Genetics, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain;
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (A.M.-F.); (J.D.-V.); (J.B.)
- Medical Oncology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Orland Diez
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (A.M.-F.); (J.D.-V.); (J.B.)
- Area of Clinical and Molecular Genetics, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain;
- Correspondence: (O.D.); (S.G.-E.)
| | - Sara Gutiérrez-Enríquez
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (A.M.-F.); (J.D.-V.); (J.B.)
- Correspondence: (O.D.); (S.G.-E.)
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21
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Fonfria M, de Juan Jiménez I, Tena I, Chirivella I, Richart-Aznar P, Segura A, Sánchez-Heras AB, Martinez-Dueñas E. Prevalence and Clinicopathological Characteristics of Moderate and High-Penetrance Genes in Non-BRCA1/2 Breast Cancer High-Risk Spanish Families. J Pers Med 2021; 11:548. [PMID: 34204722 PMCID: PMC8231620 DOI: 10.3390/jpm11060548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 01/10/2023] Open
Abstract
(1) Background: Over the last decade, genetic counseling clinics have moved from single-gene sequencing to multigene panel sequencing. Multiple genes related to a moderate risk of breast cancer (BC) have emerged, although many questions remain regarding the risks and clinical features associated with these genes. (2) Methods: Ninety-six BC index cases (ICs) with high-risk features for hereditary breast and ovarian cancer (HBOC) and with a previous uninformative result for BRCA1/2 were tested with a panel of 41 genes associated with BC risk. The frequency of pathogenic variants (PVs) was related to the clinical characteristics of BC. (3) Results: We detected a PV rate of 13.5% (excluding two cases each of BRCA1 and MUTYH). Among the 95 assessed cases, 17 PVs were identified in 16 ICs, as follows: BRCA1 (n = 2), CHEK2 (n = 3), ATM (n = 5), MUTYH (n = 2), TP53 (n = 2), BRIP1 (n = 1), CASP8 (n = 1), and MSH2 (n = 1). We also identified a novel loss-of-function variant in CASP8, a candidate gene for increased BC risk. There was no evidence that the clinical characteristics of BC might be related to a higher chance of identifying a PV. (4) Conclusions: In our cohort, which was enriched with families with a high number of BC cases, a high proportion of mutations in ATM and CHEK2 were identified. The clinical characteristics of BC associated with moderate-risk genes were different from those related to BRCA1/2 genes.
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Affiliation(s)
- Maria Fonfria
- Cancer Genetic Counseling Unit, Medical Oncology Department, Castellon Provincial Hospital, 12002 Castellon, Spain; (M.F.); (I.T.); (E.M.-D.)
| | | | - Isabel Tena
- Cancer Genetic Counseling Unit, Medical Oncology Department, Castellon Provincial Hospital, 12002 Castellon, Spain; (M.F.); (I.T.); (E.M.-D.)
| | - Isabel Chirivella
- Medical Oncology Department, INCLIVA Biomedical Research Institute, University of Valencia, 46001 Valencia, Spain;
| | - Paula Richart-Aznar
- Cancer Genetic Counseling Unit, Medical Oncology Department, La Fe University Hospital, 46026 Valencia, Spain; (P.R.-A.); (A.S.)
| | - Angel Segura
- Cancer Genetic Counseling Unit, Medical Oncology Department, La Fe University Hospital, 46026 Valencia, Spain; (P.R.-A.); (A.S.)
| | - Ana Beatriz Sánchez-Heras
- Cancer Genetic Counseling Unit, Medical Oncology Department, Elche University Hospital, 03203 Elche, Spain;
| | - Eduardo Martinez-Dueñas
- Cancer Genetic Counseling Unit, Medical Oncology Department, Castellon Provincial Hospital, 12002 Castellon, Spain; (M.F.); (I.T.); (E.M.-D.)
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Reznick Levi G, Larom G, Ofen Glassner V, Ekhilevitch N, Sharon Swartzman N, Paperna T, Baris-Feldman H, Weiss K. A recurrent pathogenic BRCA2 exon 5-11 duplication in the Christian Arab population in Israel. Fam Cancer 2021; 21:289-294. [PMID: 33999380 DOI: 10.1007/s10689-021-00262-0] [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: 11/20/2020] [Accepted: 05/07/2021] [Indexed: 11/28/2022]
Abstract
Germline pathogenic variants (PVs) in BRCA1/BRCA2 are well-established risk factors for breast cancer (BC) and/or ovarian cancer (OC). Founder PVs have been described in BRCA1/ BRCA2 in several genetic isolates. The Christian Arab population in the Middle East is a relatively isolated ethnic group, yet founder, or recurrent BRCA1/BRCA2 PVs have not been reported in this population. In this study we describe PVs detected in cancer susceptibility genes among a cohort of Christian Arabs from Israel. We reviewed patient records from the Oncogenetic clinic at Rambam Health Care Campus during the years 2013- mid 2020. Thirty-five unrelated Christian Arab patients, with personal or family history of BC and/or OC underwent BRCA1/BRCA2 (14/35) testing or cancer gene panel testing (21/35) as part of their diagnostic workup. Three clinically significant variants in BRCA2, CHEK2 and RAD51C were found in 7/35 patients (20%). A recurrent duplication of the BRCA2 genomic region, encompassing exons 5-10 and the 5' portion of exon 11, was found in 5/33 (15.2%) patients for whom copy number variants (CNVs) analysis was performed. We identified a recurrent pathogenic BRCA2 duplication in Christian Arab patients with a personal/ family history of BC and/or OC. Our findings emphasize the importance of inclusion of CNVs analysis in BRCA1/BRCA2 genetic testing, and specifically for Christian Arab patients suspected of hereditary BC and/or OC.
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Affiliation(s)
| | - Gal Larom
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | | | - Nina Ekhilevitch
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | | | - Tamar Paperna
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - Hagit Baris-Feldman
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Karin Weiss
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel.,The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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23
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Grindedal EM, Jørgensen K, Olsson P, Gravdehaug B, Lurås H, Schlichting E, Vamre T, Wangensteen T, Heramb C, Mæhle L. Mainstreamed genetic testing of breast cancer patients in two hospitals in South Eastern Norway. Fam Cancer 2021; 19:133-142. [PMID: 32002722 PMCID: PMC7101297 DOI: 10.1007/s10689-020-00160-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Studies have shown that a significant number of eligible breast cancer patients are not offered genetic testing or referral to genetic counseling. To increase access to genetic testing in South Eastern Norway, testing has since 2014 been offered directly to breast cancer patients by surgeons and oncologists. This practice is termed “mainstreamed genetic testing”. The aim of this study was to investigate to what extent patients in South Eastern Norway are offered testing. Three hundred and sixty one patients diagnosed in 2016 and 2017 at one regional and one university hospital in South Eastern Norway were included. Data on whether the patients fulfilled the criteria, whether they had been offered testing and if they were tested were collected. In total, 26.6% (96/361) fulfilled the criteria for testing. Seventy five percent (69/92) of these were offered testing, and 71.7% (66/92) were tested. At the university hospital, 90.2% (37/41) of eligible patients were offered testing, and at the regional hospital 62.7% (32/51). Fifty two percent (12/23) of eligible patient not offered testing were younger than 50 years at time of diagnosis. As many as 95.4% (125/131) of all patients who were offered testing, wanted to be tested. The majority of patients who fulfilled the criteria were offered testing, supporting the practice of mainstreamed genetic testing. There were nevertheless differences in rates of testing between the hospitals that affected all groups of patients, indicating that genetic testing may not be equally accessible to all patients. We suggest that efforts should be made to increase awareness and improve routines for genetic testing of breast cancer patients in Norway.
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Affiliation(s)
| | - Kjersti Jørgensen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Pernilla Olsson
- Department of Surgery, Section of Breast and Endocrine Surgery, Innlandet Hospital, Hamar, Norway
| | - Berit Gravdehaug
- Department of Breast and Endocrine Surgery, Akershus University Hospital, Lørenskog, Norway
| | - Hilde Lurås
- Health Services Research Unit, Akershus University Hospital, Lørenskog, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ellen Schlichting
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Oncology, Section of Breast- and Endocrine Surgery, Oslo University Hospital, Oslo, Norway
| | - Tone Vamre
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | | | - Cecilie Heramb
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Lovise Mæhle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
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24
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Sandoval RL, Leite ACR, Barbalho DM, Assad DX, Barroso R, Polidorio N, dos Anjos CH, de Miranda AD, Ferreira ACSDM, Fernandes GDS, Achatz MI. Germline molecular data in hereditary breast cancer in Brazil: Lessons from a large single-center analysis. PLoS One 2021; 16:e0247363. [PMID: 33606809 PMCID: PMC7895369 DOI: 10.1371/journal.pone.0247363] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/05/2021] [Indexed: 11/18/2022] Open
Abstract
Brazil is the largest country in South America and the most genetically heterogeneous. The aim of the present study was to determine the prevalence of germline pathogenic variants (PVs) in Brazilian patients with breast cancer (BC) who underwent genetic counseling and genetic testing at a tertiary Oncology Center. We performed a retrospective analysis of the medical records of Brazilian patients with BC referred to genetic counseling and genetic testing between August 2017 and August 2019. A total of 224 unrelated patients were included in this study. Premenopausal women represented 68.7% of the cohort. The median age at BC diagnosis was 45 years. Multigene panel testing was performed in 219 patients, five patients performed single gene analysis or family variant testing. Forty-eight germline PVs distributed among 13 genes were detected in 20.5% of the patients (46/224). Eighty-five percent of the patients (91/224) fulfilled NCCN hereditary BC testing criteria. Among these patients, 23.5% harbored PVs (45/191). In the group of patients that did not meet NCCN criteria, PV detection rate was 3% (1/33). A total of 61% of the patients (28/46) harbored a PV in a high-penetrance BC gene: 19 (8.5%) BRCA1/2, 8 (3.5%) TP53, 1 (0.5%) PALB2. Moderate penetrance genes (ATM, CHEK2) represented 15.2% (7/46) of the positive results. PVs detection was statistically associated (p<0.05) with BC diagnosis before age 45, high-grade tumors, bilateral BC, history of multiple primary cancers, and family history of pancreatic cancer. According to the current hereditary cancer guidelines, 17.4% (39/224) of the patients had actionable variants. Nine percent of the patients (20/224) had actionable variants in non-BRCA genes, it represented 43.5% of the positive results and 51.2% of the actionable variants. Considering the observed prevalence of PVs in actionable genes beyond BRCA1/2 (9%, 20/224), multigene panel testing may offer an effective first-tier diagnostic approach in this population.
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Affiliation(s)
| | | | | | - Daniele Xavier Assad
- Department of Oncology, Hospital Sírio-Libanês, Brasília, Distrito Federal, Brazil
| | - Romualdo Barroso
- Department of Oncology, Hospital Sírio-Libanês, Brasília, Distrito Federal, Brazil
| | - Natalia Polidorio
- Department of Oncology, Hospital Sírio-Libanês, Brasília, Distrito Federal, Brazil
| | | | | | | | | | - Maria Isabel Achatz
- Department of Oncology, Hospital Sírio-Libanês, São Paulo, São Paulo, Brazil
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25
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Lin B, Li H, Zhang T, Ye X, Yang H, Shen Y. Comprehensive analysis of macrophage-related multigene signature in the tumor microenvironment of head and neck squamous cancer. Aging (Albany NY) 2021; 13:5718-5747. [PMID: 33592580 PMCID: PMC7950226 DOI: 10.18632/aging.202499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 12/16/2020] [Indexed: 04/13/2023]
Abstract
Macrophages are among the most abundant cells of the tumor microenvironment in head and neck squamous cancer (HNSC). Although the marker gene sets of macrophages have been found, the mechanism by which they affect macrophages and whether they further predict the clinical outcome is unclear. In this study, a univariate COX analysis and a random forest algorithm were used to construct a prognostic model. Differential expression of the key gene, methylation status, function, and signaling pathways were further analyzed. We cross-analyzed multiple databases to detect the relationship between the most critical gene and the infiltration of multiple immune cells, as well as its impact on the prognosis of pan-cancer. FANCE is recognized as hub gene by different algorithms. It was overexpressed in HNSC, and high expression was predictive of better prognosis. It might promote apoptosis through the Wnt/β-catenin pathway. The expression of FANCE is inversely proportional to the infiltration of CD4 + T cells and their subsets, tumor-associated macrophages (TAMs), M2 macrophages, but positively co-expressed with M1 macrophages. In summary, FANCE was identified as the hub gene from the macrophage marker gene set, and it may improve the prognosis of HNSC patients by inhibiting lymphocytes and tumor-associated macrophages infiltration.
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Affiliation(s)
- Bo Lin
- Stomatological Center, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
- Guangdong Provincial High-level Clinical Key Specialty, Shenzhen, Guangdong, China
- Guangdong Province Engineering Research Center of Oral Disease Diagnosis and Treatment, Shenzhen, Guangdong, China
| | - Hao Li
- Department of Pathology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Tianwen Zhang
- Stomatological Center, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
- Guangdong Provincial High-level Clinical Key Specialty, Shenzhen, Guangdong, China
| | - Xin Ye
- Guangdong Provincial High-level Clinical Key Specialty, Shenzhen, Guangdong, China
| | - Hongyu Yang
- Stomatological Center, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
- Guangdong Provincial High-level Clinical Key Specialty, Shenzhen, Guangdong, China
- Guangdong Province Engineering Research Center of Oral Disease Diagnosis and Treatment, Shenzhen, Guangdong, China
| | - Yuehong Shen
- Stomatological Center, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
- Guangdong Provincial High-level Clinical Key Specialty, Shenzhen, Guangdong, China
- Guangdong Province Engineering Research Center of Oral Disease Diagnosis and Treatment, Shenzhen, Guangdong, China
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26
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Zarrizi R, Higgs MR, Voßgröne K, Rossing M, Bertelsen B, Bose M, Kousholt AN, Rösner H, Network TC, Ejlertsen B, Stewart GS, Nielsen FC, Sørensen CS. Germline RBBP8 variants associated with early-onset breast cancer compromise replication fork stability. J Clin Invest 2021; 130:4069-4080. [PMID: 32379725 DOI: 10.1172/jci127521] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
Haploinsufficiency of factors governing genome stability underlies hereditary breast and ovarian cancer. One significant pathway that is disabled as a result is homologous recombination repair (HRR). With the aim of identifying new candidate genes, we examined early-onset breast cancer patients negative for BRCA1 and BRCA2 pathogenic variants. Here, we focused on CtIP (RBBP8 gene), which mediates HRR through the end resection of DNA double-strand breaks (DSBs). Notably, these patients exhibited a number of rare germline RBBP8 variants. Functional analysis revealed that these variants did not affect DNA DSB end resection efficiency. However, expression of a subset of variants led to deleterious nucleolytic degradation of stalled DNA replication forks in a manner similar to that of cells lacking BRCA1 or BRCA2. In contrast to BRCA1 and BRCA2, CtIP deficiency promoted the helicase-driven destabilization of RAD51 nucleofilaments at damaged DNA replication forks. Taken together, our work identifies CtIP as a critical regulator of DNA replication fork integrity, which, when compromised, may predispose to the development of early-onset breast cancer.
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Affiliation(s)
- Reihaneh Zarrizi
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Karolin Voßgröne
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Maria Rossing
- Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Birgitte Bertelsen
- Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Muthiah Bose
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - Heike Rösner
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - Bent Ejlertsen
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Finn Cilius Nielsen
- Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Claus S Sørensen
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
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27
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Rofes P, Del Valle J, Torres-Esquius S, Feliubadaló L, Stradella A, Moreno-Cabrera JM, López-Doriga A, Munté E, De Cid R, Campos O, Cuesta R, Teulé Á, Grau È, Sanz J, Capellá G, Díez O, Brunet J, Balmaña J, Lázaro C. BARD1 Pathogenic Variants are Associated with Triple-Negative Breast Cancer in a Spanish Hereditary Breast and Ovarian Cancer Cohort. Genes (Basel) 2021; 12:genes12020150. [PMID: 33498765 PMCID: PMC7911518 DOI: 10.3390/genes12020150] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 12/16/2022] Open
Abstract
Only a small fraction of hereditary breast and/or ovarian cancer (HBOC) cases are caused by germline variants in the high-penetrance breast cancer 1 and 2 genes (BRCA1 and BRCA2). BRCA1-associated ring domain 1 (BARD1), nuclear partner of BRCA1, has been suggested as a potential HBOC risk gene, although its prevalence and penetrance are variable according to populations and type of tumor. We aimed to investigate the prevalence of BARD1 truncating variants in a cohort of patients with clinical suspicion of HBOC. A comprehensive BARD1 screening by multigene panel analysis was performed in 4015 unrelated patients according to our regional guidelines for genetic testing in hereditary cancer. In addition, 51,202 Genome Aggregation Database (gnomAD) non-Finnish, non-cancer European individuals were used as a control population. In our patient cohort, we identified 19 patients with heterozygous BARD1 truncating variants (0.47%), whereas the frequency observed in the gnomAD controls was 0.12%. We found a statistically significant association of truncating BARD1 variants with overall risk (odds ratio (OR) = 3.78; CI = 2.10–6.48; p = 1.16 × 10−5). This association remained significant in the hereditary breast cancer (HBC) group (OR = 4.18; CI = 2.10–7.70; p = 5.45 × 10−5). Furthermore, deleterious BARD1 variants were enriched among triple-negative BC patients (OR = 5.40; CI = 1.77–18.15; p = 0.001) compared to other BC subtypes. Our results support the role of BARD1 as a moderate penetrance BC predisposing gene and highlight a stronger association with triple-negative tumors.
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Affiliation(s)
- Paula Rofes
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 L’Hospitalet de Llobregat, Spain; (P.R.); (J.D.V.); (L.F.); (A.S.); (J.M.M.-C.); (E.M.); (O.C.); (R.C.); (Á.T.); (G.C.)
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, 08908 L’Hospitalet de Llobregat, Spain;
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28929 Madrid, Spain
| | - Jesús Del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 L’Hospitalet de Llobregat, Spain; (P.R.); (J.D.V.); (L.F.); (A.S.); (J.M.M.-C.); (E.M.); (O.C.); (R.C.); (Á.T.); (G.C.)
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, 08908 L’Hospitalet de Llobregat, Spain;
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28929 Madrid, Spain
| | - Sara Torres-Esquius
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), Medical Oncology Department, University Hospital Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (S.T.-E.); (J.B.)
| | - Lídia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 L’Hospitalet de Llobregat, Spain; (P.R.); (J.D.V.); (L.F.); (A.S.); (J.M.M.-C.); (E.M.); (O.C.); (R.C.); (Á.T.); (G.C.)
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, 08908 L’Hospitalet de Llobregat, Spain;
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28929 Madrid, Spain
| | - Agostina Stradella
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 L’Hospitalet de Llobregat, Spain; (P.R.); (J.D.V.); (L.F.); (A.S.); (J.M.M.-C.); (E.M.); (O.C.); (R.C.); (Á.T.); (G.C.)
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, 08908 L’Hospitalet de Llobregat, Spain;
- Medical Oncology Department, Catalan Institute of Oncology, IDIBELL, 08908 L’Hospitalet de Llobregat, Spain;
| | - José Marcos Moreno-Cabrera
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 L’Hospitalet de Llobregat, Spain; (P.R.); (J.D.V.); (L.F.); (A.S.); (J.M.M.-C.); (E.M.); (O.C.); (R.C.); (Á.T.); (G.C.)
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, 08908 L’Hospitalet de Llobregat, Spain;
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28929 Madrid, Spain
| | - Adriana López-Doriga
- Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology, 08908 L’Hospitalet de Llobregat, Spain;
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Elisabet Munté
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 L’Hospitalet de Llobregat, Spain; (P.R.); (J.D.V.); (L.F.); (A.S.); (J.M.M.-C.); (E.M.); (O.C.); (R.C.); (Á.T.); (G.C.)
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, 08908 L’Hospitalet de Llobregat, Spain;
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28929 Madrid, Spain
| | - Rafael De Cid
- Genomes for Life-GCAT Lab Group, IGTP, Institut Germans Trias i Pujol (IGTP), 08916 Badalona, Spain;
| | - Olga Campos
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 L’Hospitalet de Llobregat, Spain; (P.R.); (J.D.V.); (L.F.); (A.S.); (J.M.M.-C.); (E.M.); (O.C.); (R.C.); (Á.T.); (G.C.)
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, 08908 L’Hospitalet de Llobregat, Spain;
| | - Raquel Cuesta
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 L’Hospitalet de Llobregat, Spain; (P.R.); (J.D.V.); (L.F.); (A.S.); (J.M.M.-C.); (E.M.); (O.C.); (R.C.); (Á.T.); (G.C.)
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, 08908 L’Hospitalet de Llobregat, Spain;
| | - Álex Teulé
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 L’Hospitalet de Llobregat, Spain; (P.R.); (J.D.V.); (L.F.); (A.S.); (J.M.M.-C.); (E.M.); (O.C.); (R.C.); (Á.T.); (G.C.)
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, 08908 L’Hospitalet de Llobregat, Spain;
| | - Èlia Grau
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, 08908 L’Hospitalet de Llobregat, Spain;
- Hereditary Cancer Program, Catalan Institute of Oncology, IGTP, 08916 Badalona, Spain
| | - Judit Sanz
- Genetic Counselling Unit, Medical Oncology Department, Althaia Xarxa Assistencial Universitària de Manresa, 08243 Manresa, Spain;
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 L’Hospitalet de Llobregat, Spain; (P.R.); (J.D.V.); (L.F.); (A.S.); (J.M.M.-C.); (E.M.); (O.C.); (R.C.); (Á.T.); (G.C.)
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, 08908 L’Hospitalet de Llobregat, Spain;
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28929 Madrid, Spain
| | - Orland Díez
- Catalan Health Institute, Vall d’Hebron Hospital Universitari, 08035 Barcelona, Spain;
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Joan Brunet
- Medical Oncology Department, Catalan Institute of Oncology, IDIBELL, 08908 L’Hospitalet de Llobregat, Spain;
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBGI, 17007 Girona, Spain
- Medical Sciences Department, School of Medicine, University of Girona, 17007 Girona, Spain
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), Medical Oncology Department, University Hospital Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (S.T.-E.); (J.B.)
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, 08908 L’Hospitalet de Llobregat, Spain; (P.R.); (J.D.V.); (L.F.); (A.S.); (J.M.M.-C.); (E.M.); (O.C.); (R.C.); (Á.T.); (G.C.)
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, 08908 L’Hospitalet de Llobregat, Spain;
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28929 Madrid, Spain
- Correspondence: ; Tel.: +34-93-2607145
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28
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Berliner JL, Cummings SA, Boldt Burnett B, Ricker CN. Risk assessment and genetic counseling for hereditary breast and ovarian cancer syndromes-Practice resource of the National Society of Genetic Counselors. J Genet Couns 2021; 30:342-360. [PMID: 33410258 DOI: 10.1002/jgc4.1374] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 12/20/2022]
Abstract
Cancer risk assessment and genetic counseling for hereditary breast and ovarian cancer (HBOC) are a communication process to inform and prepare patients for genetic test results and the related medical management. An increasing number of healthcare providers are active in the delivery of cancer risk assessment and testing, which can have enormous benefits for enhanced patient care. However, genetics professionals remain key in the multidisciplinary care of at-risk patients and their families, given their training in facilitating patients' understanding of the role of genetics in cancer development, the potential psychological, social, and medical implications associated with cancer risk assessment and genetic testing. A collaborative partnership of non-genetics and genetics experts is the ideal approach to address the growing number of patients at risk for hereditary breast and ovarian cancer. The goal of this practice resource is to provide allied health professionals an understanding of the key components of risk assessment for HBOC as well as the use of risk models and published guidelines for medical management. We also highlight what patient types are appropriate for genetic testing, what are the most appropriate test(s) to consider, and when to refer individuals to a genetics professional. This practice resource is intended to serve as a resource for allied health professionals in determining their approach to delivering comprehensive care for families and individuals facing HBOC. The cancer risk and prevalence figures in this document are based on cisgender women and men; the risks for transgender or non-binary individuals have not been studied and therefore remain poorly understood.
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Affiliation(s)
- Janice L Berliner
- Genetic Counseling Department, Bay Path University, East Longmeadow, MA, USA
| | | | | | - Charité N Ricker
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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29
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ERCC3, a new ovarian cancer susceptibility gene? Eur J Cancer 2020; 141:1-8. [DOI: 10.1016/j.ejca.2020.09.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/22/2020] [Accepted: 09/25/2020] [Indexed: 02/07/2023]
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30
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Prevalence of germline variants in consensus moderate-to-high-risk predisposition genes to hereditary breast and ovarian cancer in BRCA1/2-negative Brazilian patients. Breast Cancer Res Treat 2020; 185:851-861. [PMID: 33128190 DOI: 10.1007/s10549-020-05985-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/15/2020] [Indexed: 12/23/2022]
Abstract
PURPOSE This study aimed to identify and classify genetic variants in consensus moderate-to-high-risk predisposition genes associated with Hereditary Breast and Ovarian Cancer Syndrome (HBOC), in BRCA1/2-negative patients from Brazil. METHODS The study comprised 126 index patients who met NCCN clinical criteria and tested negative for all coding exons and intronic flanking regions of BRCA1/2 genes. Multiplex PCR-based assays were designed to cover the complete coding regions and flanking splicing sites of six genes implicated in HBOC. Sequencing was performed on HiSeq2500 Genome Analyzer. RESULTS Overall, we identified 488 unique variants. We identified five patients (3.97%) that harbored pathogenic or likely pathogenic variants in four genes: ATM (1), CHEK2 (2), PALB2 (1), and TP53 (1). One hundred and thirty variants were classified as variants of uncertain significance (VUS), 10 of which were predicted to disrupt mRNA splicing (seven non-coding variants and three coding variants), while other six missense VUS were classified as probably damaging by prediction algorithms. CONCLUSION A detailed mutational profile of non-BRCA genes is still being described in Brazil. In this study, we contributed to filling this gap, by providing important data on the diversity of genetic variants in a Brazilian high-risk patient cohort. ATM, CHEK2, PALB2 and TP53 are well established as HBOC predisposition genes, and the identification of deleterious variants in such actionable genes contributes to clinical management of probands and relatives.
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Mozaffari NL, Pagliarulo F, Sartori AA. Human CtIP: A 'double agent' in DNA repair and tumorigenesis. Semin Cell Dev Biol 2020; 113:47-56. [PMID: 32950401 DOI: 10.1016/j.semcdb.2020.09.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/20/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022]
Abstract
Human CtIP was originally identified as an interactor of the retinoblastoma protein and BRCA1, two bona fide tumour suppressors frequently mutated in cancer. CtIP is renowned for its role in the resection of DNA double-strand breaks (DSBs) during homologous recombination, a largely error-free DNA repair pathway crucial in maintaining genome integrity. However, CtIP-dependent DNA end resection is equally accountable for alternative end-joining, a mutagenic DSB repair mechanism implicated in oncogenic chromosomal translocations. In addition, CtIP contributes to transcriptional regulation of G1/S transition, DNA damage checkpoint signalling, and replication fork protection pathways. In this review, we present a perspective on the current state of knowledge regarding the tumour-suppressive and oncogenic properties of CtIP and provide an overview of their relevance for cancer development, progression, and therapy.
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Affiliation(s)
- Nour L Mozaffari
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Fabio Pagliarulo
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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Alenezi WM, Fierheller CT, Recio N, Tonin PN. Literature Review of BARD1 as a Cancer Predisposing Gene with a Focus on Breast and Ovarian Cancers. Genes (Basel) 2020; 11:E856. [PMID: 32726901 PMCID: PMC7464855 DOI: 10.3390/genes11080856] [Citation(s) in RCA: 26] [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: 06/30/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/19/2022] Open
Abstract
Soon after the discovery of BRCA1 and BRCA2 over 20 years ago, it became apparent that not all hereditary breast and/or ovarian cancer syndrome families were explained by germline variants in these cancer predisposing genes, suggesting that other such genes have yet to be discovered. BRCA1-associated ring domain (BARD1), a direct interacting partner of BRCA1, was one of the earliest candidates investigated. Sequencing analyses revealed that potentially pathogenic BARD1 variants likely conferred a low-moderate risk to hereditary breast cancer, but this association is inconsistent. Here, we review studies of BARD1 as a cancer predisposing gene and illustrate the challenge of discovering additional cancer risk genes for hereditary breast and/or ovarian cancer. We selected peer reviewed research articles that focused on three themes: (i) sequence analyses of BARD1 to identify potentially pathogenic germline variants in adult hereditary cancer syndromes; (ii) biological assays of BARD1 variants to assess their effect on protein function; and (iii) association studies of BARD1 variants in family-based and case-control study groups to assess cancer risk. In conclusion, BARD1 is likely to be a low-moderate penetrance breast cancer risk gene.
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Affiliation(s)
- Wejdan M. Alenezi
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada; (W.M.A.); (C.T.F.); (N.R.)
- Cancer Research Program, The Research Institute of the 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 0G4, Canada; (W.M.A.); (C.T.F.); (N.R.)
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Neil Recio
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada; (W.M.A.); (C.T.F.); (N.R.)
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Patricia N. Tonin
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada; (W.M.A.); (C.T.F.); (N.R.)
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Department of Medicine, McGill University, Montreal, QC H3A 0G4, Canada
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Suszynska M, Kozlowski P. Summary of BARD1 Mutations and Precise Estimation of Breast and Ovarian Cancer Risks Associated with the Mutations. Genes (Basel) 2020; 11:genes11070798. [PMID: 32679805 PMCID: PMC7397132 DOI: 10.3390/genes11070798] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 12/12/2022] Open
Abstract
Over the last two decades, numerous BARD1 mutations/pathogenic variants (PVs) have been found in patients with breast cancer (BC) and ovarian cancer (OC). However, their role in BC and OC susceptibility remains controversial, and strong evidence-based guidelines for carriers are not yet available. Herein, we present a comprehensive catalog of BARD1 PVs identified in large cumulative cohorts of ~48,700 BC and ~20,800 OC cases (retrieved from 123 studies examining the whole coding sequence of BARD1). Using these resources, we compared the frequency of BARD1 PVs in the cases and ~134,100 controls from the gnomAD database and estimated the effect of the BARD1 PVs on BC and OC risks. The analysis revealed that BARD1 is a BC moderate-risk gene (odds ratio (OR) = 2.90, 95% CIs:2.25–3.75, p < 0.0001) but not an OC risk gene (OR = 1.36, 95% CIs:0.87–2.11, p = 0.1733). In addition, the BARD1 mutational spectrum outlined in this study allowed us to determine recurrent PVs and evaluate the variant-specific risk for the most frequent PVs. In conclusion, these precise estimates improve the understanding of the role of BARD1 PVs in BC and OC predisposition and support the need for BARD1 diagnostic testing in BC patients.
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Affiliation(s)
| | - Piotr Kozlowski
- Correspondence: ; Tel.: +48-618-528-503 (ext. 261); Fax: +48-618-520-532
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Suszynska M, Ratajska M, Kozlowski P. BRIP1, RAD51C, and RAD51D mutations are associated with high susceptibility to ovarian cancer: mutation prevalence and precise risk estimates based on a pooled analysis of ~30,000 cases. J Ovarian Res 2020; 13:50. [PMID: 32359370 PMCID: PMC7196220 DOI: 10.1186/s13048-020-00654-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/24/2020] [Indexed: 12/24/2022] Open
Abstract
Background It is estimated that more than 20% of ovarian cancer cases are associated with a genetic predisposition that is only partially explained by germline mutations in the BRCA1 and BRCA2 genes. Recently, several pieces of evidence showed that mutations in three genes involved in the homologous recombination DNA repair pathway, i.e., BRIP1, RAD51C, and RAD51D, are associated with a high risk of ovarian cancer. To more precisely estimate the ovarian cancer risk attributed to BRIP1, RAD51C, and RAD51D mutations, we performed a meta-analysis based on a comparison of a total of ~ 29,400 ovarian cancer patients from 63 studies and a total of ~ 116,000 controls from the gnomAD database. Results The analysis allowed precise estimation of ovarian cancer risks attributed to mutations in BRIP1, RAD51C, and RAD51D, confirming that all three genes are ovarian cancer high-risk genes (odds ratio (OR) = 4.94, 95%CIs:4.07–6.00, p < 0.0001; OR = 5.59, 95%CIs:4.42–7.07, p < 0.0001; and OR = 6.94, 95%CIs:5.10–9.44, p < 0.0001, respectively). In the present report, we show, for the first time, a mutation-specific risk analysis associated with distinct, recurrent, mutations in the genes. Conclusions The meta-analysis provides evidence supporting the pathogenicity of BRIP1, RAD51C, and RAD51D mutations in relation to ovarian cancer. The level of ovarian cancer risk conferred by these mutations is relatively high, indicating that after BRCA1 and BRCA2, the BRIP1, RAD51C, and RAD51D genes are the most important ovarian cancer risk genes, cumulatively contributing to ~ 2% of ovarian cancer cases. The inclusion of the genes into routine diagnostic tests may influence both the prevention and the potential treatment of ovarian cancer.
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Affiliation(s)
- Malwina Suszynska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Street, 61-704, Poznan, Poland
| | - Magdalena Ratajska
- Department of Pathology, Dunedin School of Medicine, University of Otago, 60 Hanover Street, Dunedin, 9016, New Zealand.,Department of Biology and Medical Genetics, Medical University of Gdansk, Debinki 1 St., 80-210, Gdansk, Poland
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Street, 61-704, Poznan, Poland.
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Deng W, Li J, Dorrah K, Jimenez-Tapia D, Arriaga B, Hao Q, Cao W, Gao Z, Vadgama J, Wu Y. The role of PPM1D in cancer and advances in studies of its inhibitors. Biomed Pharmacother 2020; 125:109956. [PMID: 32006900 PMCID: PMC7080581 DOI: 10.1016/j.biopha.2020.109956] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/08/2020] [Accepted: 01/23/2020] [Indexed: 12/16/2022] Open
Abstract
A greater understanding of factors causing cancer initiation, progression and evolution is of paramount importance. Among them, the serine/threonine phosphatase PPM1D, also referred to as wild-type p53-induced phosphatase 1 (Wip1) or protein phosphatase 2C delta (PP2Cδ), is emerging as an important oncoprotein due to its negative regulation on a number of crucial cancer suppressor pathways. Initially identified as a p53-regulated gene, PPM1D has been afterwards found amplified and more recently mutated in many human cancers such as breast cancer. The latest progress in this field further reveals that selective inhibition of PPM1D to delay tumor onset or reduce tumor burden represents a promising anti-cancer strategy. Here, we review the advances in the studies of the PPM1D activity and its relevance to various cancers, and recent progress in development of PPM1D inhibitors and discuss their potential application in cancer therapy. Consecutive research on PPM1D and its relationship with cancer is essential, as it ultimately contributes to the etiology and treatment of cancer.
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Affiliation(s)
- Wenhong Deng
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China; Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Jieqing Li
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Kimberly Dorrah
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Denise Jimenez-Tapia
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Brando Arriaga
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Qiongyu Hao
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Wei Cao
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Zhaoxia Gao
- Department of General Surgery, 5th Hospital of Wuhan, Wuhan, 430050, China; Department of Surgery, Johns Hopkins Hospital Bayview Campus, Baltimore, MD, USA
| | - Jay Vadgama
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA.
| | - Yong Wu
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA.
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Lhotova K, Stolarova L, Zemankova P, Vocka M, Janatova M, Borecka M, Cerna M, Jelinkova S, Kral J, Volkova Z, Urbanova M, Kleiblova P, Machackova E, Foretova L, Hazova J, Vasickova P, Lhota F, Koudova M, Cerna L, Tavandzis S, Indrakova J, Hruskova L, Kosarova M, Vrtel R, Stranecky V, Kmoch S, Zikan M, Macurek L, Kleibl Z, Soukupova J. Multigene Panel Germline Testing of 1333 Czech Patients with Ovarian Cancer. Cancers (Basel) 2020; 12:E956. [PMID: 32295079 PMCID: PMC7226062 DOI: 10.3390/cancers12040956] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/07/2020] [Accepted: 04/10/2020] [Indexed: 12/18/2022] Open
Abstract
Ovarian cancer (OC) is the deadliest gynecologic malignancy with a substantial proportion of hereditary cases and a frequent association with breast cancer (BC). Genetic testing facilitates treatment and preventive strategies reducing OC mortality in mutation carriers. However, the prevalence of germline mutations varies among populations and many rarely mutated OC predisposition genes remain to be identified. We aimed to analyze 219 genes in 1333 Czech OC patients and 2278 population-matched controls using next-generation sequencing. We revealed germline mutations in 18 OC/BC predisposition genes in 32.0% of patients and in 2.5% of controls. Mutations in BRCA1/BRCA2, RAD51C/RAD51D, BARD1, and mismatch repair genes conferred high OC risk (OR > 5). Mutations in BRIP1 and NBN were associated with moderate risk (both OR = 3.5). BRCA1/2 mutations dominated in almost all clinicopathological subgroups including sporadic borderline tumors of ovary (BTO). Analysis of remaining 201 genes revealed somatic mosaics in PPM1D and germline mutations in SHPRH and NAT1 associating with a high/moderate OC risk significantly; however, further studies are warranted to delineate their contribution to OC development in other populations. Our findings demonstrate the high proportion of patients with hereditary OC in Slavic population justifying genetic testing in all patients with OC, including BTO.
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Affiliation(s)
- Klara Lhotova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (M.U.); (P.K.)
| | - Lenka Stolarova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
| | - Petra Zemankova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (M.U.); (P.K.)
| | - Michal Vocka
- Department of Oncology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 08 Prague, Czech Republic;
| | - Marketa Janatova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (M.U.); (P.K.)
| | - Marianna Borecka
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (M.U.); (P.K.)
| | - Marta Cerna
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
| | - Sandra Jelinkova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
| | - Jan Kral
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
| | - Zuzana Volkova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
| | - Marketa Urbanova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (M.U.); (P.K.)
| | - Petra Kleiblova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (M.U.); (P.K.)
| | - Eva Machackova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic; (E.M.); (L.F.); (J.H.); (P.V.)
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic; (E.M.); (L.F.); (J.H.); (P.V.)
| | - Jana Hazova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic; (E.M.); (L.F.); (J.H.); (P.V.)
| | - Petra Vasickova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic; (E.M.); (L.F.); (J.H.); (P.V.)
| | - Filip Lhota
- Department of Medical Genetics, Centre for Medical Genetics and Reproductive Medicine, Gennet, 170 00 Prague, Czech Republic; (F.L.); (M.K.); (L.C.)
| | - Monika Koudova
- Department of Medical Genetics, Centre for Medical Genetics and Reproductive Medicine, Gennet, 170 00 Prague, Czech Republic; (F.L.); (M.K.); (L.C.)
| | - Leona Cerna
- Department of Medical Genetics, Centre for Medical Genetics and Reproductive Medicine, Gennet, 170 00 Prague, Czech Republic; (F.L.); (M.K.); (L.C.)
| | - Spiros Tavandzis
- Department of Medical Genetics, AGEL Laboratories, AGEL Research and Training Institute, 741 01 Novy Jicin, Czech Republic; (S.T.); (J.I.)
| | - Jana Indrakova
- Department of Medical Genetics, AGEL Laboratories, AGEL Research and Training Institute, 741 01 Novy Jicin, Czech Republic; (S.T.); (J.I.)
| | - Lucie Hruskova
- Department of Medical Genetics, GHC Genetics, 110 00 Prague, Czech Republic;
| | - Marcela Kosarova
- Department of Medical Genetics, Pronatal, 147 00 Prague, Czech Republic;
| | - Radek Vrtel
- Department of Medical Genetics, University Hospital Olomouc, Faculty of Medicine and Dentistry, Palacky University Olomouc, 779 00 Olomouc, Czech Republic;
| | - Viktor Stranecky
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12808 Prague, Czech Republic; (V.S.); (S.K.)
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12808 Prague, Czech Republic; (V.S.); (S.K.)
| | - Michal Zikan
- Department of Gynecology and Obstetrics, Hospital Na Bulovce and First Faculty of Medicine, Charles University, 180 81 Prague, Czech Republic;
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, Czech Republic;
| | - Zdenek Kleibl
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
| | - Jana Soukupova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (M.U.); (P.K.)
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da Costa E Silva Carvalho S, Cury NM, Brotto DB, de Araujo LF, Rosa RCA, Texeira LA, Plaça JR, Marques AA, Peronni KC, Ruy PDC, Molfetta GA, Moriguti JC, Carraro DM, Palmero EI, Ashton-Prolla P, de Faria Ferraz VE, Silva WA. Germline variants in DNA repair genes associated with hereditary breast and ovarian cancer syndrome: analysis of a 21 gene panel in the Brazilian population. BMC Med Genomics 2020; 13:21. [PMID: 32039725 PMCID: PMC7011249 DOI: 10.1186/s12920-019-0652-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/23/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The Hereditary Breast and Ovarian Cancer Syndrome (HBOC) occurs in families with a history of breast/ovarian cancer, presenting an autosomal dominant inheritance pattern. BRCA1 and BRCA2 are high penetrance genes associated with an increased risk of up to 20-fold for breast and ovarian cancer. However, only 20-30% of HBOC cases present pathogenic variants in those genes, and other DNA repair genes have emerged as increasing the risk for HBOC. In Brazil, variants in ATM, ATR, CHEK2, MLH1, MSH2, MSH6, POLQ, PTEN, and TP53 genes have been reported in up to 7.35% of the studied cases. Here we screened and characterized variants in 21 DNA repair genes in HBOC patients. METHODS We systematically analyzed 708 amplicons encompassing the coding and flanking regions of 21 genes related to DNA repair pathways (ABRAXAS1, ATM, ATR, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MLH1, MRE11, MSH2, MSH6, NBN, PALB2, PMS2, PTEN, RAD50, RAD51, TP53 and UIMC1). A total of 95 individuals with HBOC syndrome clinical suspicion in Southeast Brazil were sequenced, and 25 samples were evaluated for insertions/deletions in BRCA1/BRCA2 genes. Identified variants were assessed in terms of population allele frequency and their functional effects were predicted through in silico algorithms. RESULTS We identified 80 variants in 19 genes. About 23.4% of the patients presented pathogenic variants in BRCA1, BRCA2 and TP53, a frequency higher than that identified among previous studies in Brazil. We identified a novel variant in ATR, which was predicted as pathogenic by in silico tools. The association analysis revealed 13 missense variants in ABRAXAS1, BARD1, BRCA2, CHEK2, CDH1, MLH1, PALB2, and PMS2 genes, as significantly associated with increased risk to HBOC, and the patients carrying those variants did not present large insertions or deletions in BRCA1/BRCA2 genes. CONCLUSIONS This study embodies the third report of a multi-gene analysis in the Brazilian population, and addresses the first report of many germline variants associated with HBOC in Brazil. Although further functional analyses are necessary to better characterize the contribution of those variants to the phenotype, these findings would improve the risk estimation and clinical follow-up of patients with HBOC clinical suspicion.
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Affiliation(s)
- Simone da Costa E Silva Carvalho
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
- Regional Blood Center at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Nathalia Moreno Cury
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Regional Blood Center at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Danielle Barbosa Brotto
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Regional Blood Center at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Luiza Ferreira de Araujo
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Regional Blood Center at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Reginaldo Cruz Alves Rosa
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Lorena Alves Texeira
- Division of Internal Medicine and Geriatrics, Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Jessica Rodrigues Plaça
- Regional Blood Center at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Adriana Aparecida Marques
- Regional Blood Center at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Kamila Chagas Peronni
- Regional Blood Center at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Patricia de Cássia Ruy
- Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Greice Andreotti Molfetta
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Julio Cesar Moriguti
- Division of Internal Medicine and Geriatrics, Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Dirce Maria Carraro
- International Research, Center/CIPE, AC Camargo Cancer Center, Sao Paulo, SP, Brazil
| | - Edenir Inêz Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | - Patricia Ashton-Prolla
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Victor Evangelista de Faria Ferraz
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil
- Department of Medical Genetics, University Hospital of the Ribeirão Preto Medical School, Ribeirão Preto, Brazil
| | - Wilson Araujo Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
- Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil.
- Regional Blood Center at University Hospital of the Ribeirão Preto Medical School of University of São Paulo, Ribeirão Preto, SP, Brazil.
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Oliver J, Quezada Urban R, Franco Cortés CA, Díaz Velásquez CE, Montealegre Paez AL, Pacheco-Orozco RA, Castro Rojas C, García-Robles R, López Rivera JJ, Gaitán Chaparro S, Gómez AM, Suarez Obando F, Giraldo G, Maya MI, Hurtado-Villa P, Sanchez AI, Serrano N, Orduz Galvis AI, Aruachan S, Nuñez Castillo J, Frecha C, Riggi C, Jauk F, Gómez García EM, Carranza CL, Zamora V, Torres Mejía G, Romieu I, Castañeda CA, Castillo M, Gitler R, Antoniano A, Rojas Jiménez E, Romero Cruz LE, Vallejo Lecuona F, Delgado Enciso I, Martínez Rizo AB, Flores Carranza A, Benites Godinez V, Méndez Catalá CF, Herrera LA, Chirino YI, Terrazas LI, Perdomo S, Vaca Paniagua F. Latin American Study of Hereditary Breast and Ovarian Cancer LACAM: A Genomic Epidemiology Approach. Front Oncol 2019; 9:1429. [PMID: 31921681 PMCID: PMC6933010 DOI: 10.3389/fonc.2019.01429] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/02/2019] [Indexed: 12/29/2022] Open
Abstract
Purpose: Hereditary Breast and Ovarian Cancer (HBOC) syndrome is responsible for ~5-10% of all diagnosed breast and ovarian cancers. Breast cancer is the most common malignancy and the leading cause of cancer-related mortality among women in Latin America (LA). The main objective of this study was to develop a comprehensive understanding of the genomic epidemiology of HBOC throughout the establishment of The Latin American consortium for HBOC-LACAM, consisting of specialists from 5 countries in LA and the description of the genomic results from the first phase of the study. Methods: We have recruited 403 individuals that fulfilled the criteria for HBOC from 11 health institutions of Argentina, Colombia, Guatemala, Mexico and Peru. A pilot cohort of 222 individuals was analyzed by NGS gene panels. One hundred forty-three genes were selected on the basis of their putative role in susceptibility to different hereditary cancers. Libraries were sequenced in MiSeq (Illumina, Inc.) and PGM (Ion Torrent-Thermo Fisher Scientific) platforms. Results: The overall prevalence of pathogenic variants was 17% (38/222); the distribution spanned 14 genes and varied by country. The highest relative prevalence of pathogenic variants was found in patients from Argentina (25%, 14/57), followed by Mexico (18%, 12/68), Guatemala (16%, 3/19), and Colombia (13%, 10/78). Pathogenic variants were found in BRCA1 (20%) and BRCA2 (29%) genes. Pathogenic variants were found in other 12 genes, including high and moderate risk genes such as MSH2, MSH6, MUTYH, and PALB2. Additional pathogenic variants were found in HBOC unrelated genes such as DCLRE1C, WRN, PDE11A, and PDGFB. Conclusion: In this first phase of the project, we recruited 403 individuals and evaluated the germline genetic alterations in an initial cohort of 222 patients among 4 countries. Our data show for the first time in LA the distribution of pathogenic variants in a broad set of cancer susceptibility genes in HBOC. Even though we used extended gene panels, there was still a high proportion of patients without any detectable pathogenic variant, which emphasizes the larger, unexplored genetic nature of the disease in these populations.
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Affiliation(s)
- Javier Oliver
- Medical Oncology Service, Hospitales Universitarios Regional y Virgen de la Victoria, Institute of Biomedical Research in Malaga, CIMES, University of Málaga, Málaga, Spain
- Laboratorio de Secuenciación, Instituto de Medicina Traslacional e Ingeniería Biomédica, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Mexico
| | - Rosalía Quezada Urban
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla de Baz, Mexico
| | - Claudia Alejandra Franco Cortés
- Laboratorio de Secuenciación, Instituto de Medicina Traslacional e Ingeniería Biomédica, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Clara Estela Díaz Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Mexico
| | - Ana Lorena Montealegre Paez
- Instituto de Nutrición, Genética y Metabolismo, Facultad de Medicina, Universidad El Bosque, Bogota, Colombia
| | | | - Carlos Castro Rojas
- Instituto de Nutrición, Genética y Metabolismo, Facultad de Medicina, Universidad El Bosque, Bogota, Colombia
| | - Reggie García-Robles
- Instituto de Nutrición, Genética y Metabolismo, Facultad de Medicina, Universidad El Bosque, Bogota, Colombia
| | - Juan Javier López Rivera
- Grupo INPAC, Organización Keralty, Departamento de Genética, Clínica Universitaria Colombia, Bogotá, Colombia
| | - Sandra Gaitán Chaparro
- Grupo INPAC, Organización Keralty, Facultad de Medicina, Fundación Universitaria Sanitas, Bogotá, Colombia
| | - Ana Milena Gómez
- Servicio de Genética, Hospital Universitario San Ignacio, Bogotá, Colombia
| | - Fernando Suarez Obando
- Servicio de Genética, Hospital Universitario San Ignacio, Bogotá, Colombia
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Gustavo Giraldo
- Clínica Universitaria Bolivariana, Pontificia Universidad Bolivariana, Medellín, Colombia
| | - Maria Isabel Maya
- Clínica Universitaria Bolivariana, Pontificia Universidad Bolivariana, Medellín, Colombia
| | - Paula Hurtado-Villa
- Departamento Ciencias Básicas de Salud, Facultad de Ciencias de la Salud, Pontificia Universidad Javeriana Cali, Cali, Colombia
- Centro Médico Imbanaco, Cali, Colombia
| | - Ana Isabel Sanchez
- Centro Médico Imbanaco, Cali, Colombia
- Departamento Materno Infantil, Facultad de Ciencias de la Salud, Pontificia Universidad Javeriana Cali, Cali, Colombia
| | - Norma Serrano
- Fundación Cardiovascular de Colombia, Centro de Investigaciones, Floridablanca, Colombia
| | | | - Sandra Aruachan
- Departamento de Investigación y Estudios Clínicos, IMAT - Oncomédica S.A., Montería, Colombia
| | - Johanna Nuñez Castillo
- Departamento de Investigación y Estudios Clínicos, IMAT - Oncomédica S.A., Montería, Colombia
| | - Cecilia Frecha
- Instituto de Medicina Traslacional e Ingeniería Biomédica, CONICET-Instituto Universitario del Hospital Italiano-Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Cecilia Riggi
- Servicio de Ginecología, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Federico Jauk
- Laboratorio de Secuenciación, Instituto de Medicina Traslacional e Ingeniería Biomédica, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | | | | | | | | | - Isabelle Romieu
- Instituto Nacional de Salud Pública, Cuernavaca, Mexico
- Hubert Department of Global Health, Emory University, Atlanta, GA, United States
| | - Carlos Arturo Castañeda
- Departamento de Oncología Médica, Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - Miluska Castillo
- Departamento de Investigación, Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | | | | | - Ernesto Rojas Jiménez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla de Baz, Mexico
| | - Luis Enrique Romero Cruz
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla de Baz, Mexico
| | - Fernando Vallejo Lecuona
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla de Baz, Mexico
| | | | | | | | | | - Claudia Fabiola Méndez Catalá
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Mexico
| | - Luis Alonso Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas-Instituto Nacional de Cancerología, Ciudad de México, Mexico
| | - Yolanda Irasema Chirino
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla de Baz, Mexico
| | - Luis Ignacio Terrazas
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla de Baz, Mexico
| | - Sandra Perdomo
- Instituto de Nutrición, Genética y Metabolismo, Facultad de Medicina, Universidad El Bosque, Bogota, Colombia
- Departamento de Patología, Hospital Universitario Fundación Santa Fe de Bogotá, Bogota, Colombia
| | - Felipe Vaca Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla de Baz, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla de Baz, Mexico
- Instituto Nacional de Cancerología, Ciudad de México, Mexico
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Pfeffer TJ, Schlothauer S, Pietzsch S, Schaufelberger M, Auber B, Ricke-Hoch M, List M, Berliner D, Abou Moulig V, König T, Arany Z, Sliwa K, Bauersachs J, Hilfiker-Kleiner D. Increased Cancer Prevalence in Peripartum Cardiomyopathy. JACC: CARDIOONCOLOGY 2019; 1:196-205. [PMID: 34396183 PMCID: PMC8352111 DOI: 10.1016/j.jaccao.2019.09.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/23/2019] [Accepted: 09/09/2019] [Indexed: 12/11/2022]
Abstract
Objectives This study was designed to analyze the prevalence and potential genetic basis of cancer and heart failure in peripartum cardiomyopathy (PPCM). Background PPCM manifests as heart failure late in pregnancy or postpartum in women without previous heart disease. Methods Clinical history and cancer prevalence were evaluated in a cohort of 236 PPCM patients from Germany and Sweden. Exome sequencing assessed variants in 133 genes associated with cancer predisposition syndromes (CPS) and in 115 genes associated with dilated/hypertrophic cardiomyopathy (DCM/HCM) in 14 PPCM patients with a history of cancer, and in 6 PPCM patients without a history of cancer. Results The prevalence of cancer was 16-fold higher (8.9%, 21 of 236 patients) in PPCM patients compared to age-matched women (German cancer registry, Robert-Koch-Institute: 0.59%; p < 0.001). Cancer before PPCM occurred in 12 of 21 patients of whom 11 obtained cardiotoxic cancer therapies. Of those, 17% fully recovered cardiac function by 7 ± 2 months of follow-up compared to 55% of PPCM patients without cancer (p = 0.015). Cancer occurred after PPCM in 10 of 21 patients; 80% had left ventricular ejection fraction of ≥50% after cancer therapy. Whole-exome sequencing in 14 PPCM patients with cancer revealed that 43% (6 of 14 patients) carried likely pathogenic (Class IV) or pathogenic (Class V) gene variants associated with DCM/HCM in CPT2, DSP, MYH7, TTN, and/or with CPS in ATM, ERCC5, NBN, RECQL4, and SLX4. All CPS variants affected DNA damage response genes. Conclusions Cardiotoxic cancer therapy before PPCM is associated with delayed full recovery. The high cancer prevalence in PPCM is linked to likely pathogenic/pathogenic gene variants associated with DCM/HCM and/or CPS/DNA damage response-related cancer risk. This may warrant genetic testing and screening for heart failure in pregnant women with a cancer history and screening for cancer in PPCM patients.
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Key Words
- ATM, ataxia telangiectasia mutated
- BMBF, Bundesministerium für Bildung und Forschung
- BRCA1, breast cancer 1
- CPS, cancer predisposition syndrome
- DCM, dilated cardiomyopathy
- DDR, DNA damage response
- DFG, Deutsche Forschungsgesellschaft
- ERCC5, excision repair cross-complementing rodent repair deficiency
- FANCA, Fanconi anemia, complementation group
- FKRP, fukutin-related protein
- HCM, hypertrophic cardiomyopathy
- HTX, heart transplantation
- LVAD, left ventricular assist device
- LVEF, left ventricular ejection fraction
- PPCM, peripartum cardiomyopathy
- RECQL4, ATP-dependent DNA helicase Q4
- RYR1, ryanodine receptor 1
- SLX4, structure-specific endonuclease subunit SLX4
- TXNRD2, thioredoxin reductase 2
- VUS, variants of unknown significance
- cancer
- cardiotoxicity
- genetics
- peripartum cardiomyopathy
- whole-exome sequencing
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Affiliation(s)
- Tobias J Pfeffer
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Stella Schlothauer
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Stefan Pietzsch
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Maria Schaufelberger
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Bernd Auber
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Melanie Ricke-Hoch
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Manuel List
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Dominik Berliner
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Valeska Abou Moulig
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Tobias König
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Zolt Arany
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Karen Sliwa
- Hatter Institute for Cardiovascular Research in Africa, University of Cape Town, Cape Town, South Africa
| | - Johann Bauersachs
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
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40
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Vysotskaia V, Kaseniit KE, Bucheit L, Ready K, Price K, Johansen Taber K. Clinical utility of hereditary cancer panel testing: Impact of PALB2, ATM, CHEK2, NBN, BRIP1, RAD51C, and RAD51D results on patient management and adherence to provider recommendations. Cancer 2019; 126:549-558. [PMID: 31682005 PMCID: PMC7003834 DOI: 10.1002/cncr.32572] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/06/2019] [Accepted: 09/16/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Although management guidelines exist for several genes associated with a 2-fold to 5-fold increase in the relative risk for certain cancers, the value of testing for them remains controversial. METHODS De-identified personal and family history data for 654 individuals with pathogenic variants (PVs) in PALB2, ATM, CHEK2, NBN, BRIP1, RAD51C, and/or RAD51D were analyzed for pretest and post-test candidacy for guideline-recommended management of cancer risk. These individuals were invited to complete a survey about provider recommendations and their adherence. RESULTS Twenty-four percent of CHEK2, ATM, PALB2, or NBN PV carriers were appropriate for consideration of annual breast magnetic resonance imaging screening before genetic testing, with the remaining 76% appropriate only after testing. No BRIP1, RAD51C, or RAD51D PV carriers were appropriate for consideration of risk-reducing salpingo-oophorectomy before genetic testing; 100% were appropriate only after testing. Seventeen percent of CHEK2 PV carriers were appropriate for earlier and more frequent colonoscopy before genetic testing, with the remaining 83% appropriate only after testing. Provider recommendations for annual breast magnetic resonance imaging, consideration of risk-reducing salpingo-oophorectomy, and earlier and more frequent colonoscopy were reported by 42%, 26%, and 66% of breast, ovarian, and colorectal cancer risk PV carriers, respectively, before genetic testing, versus 82%, 79%, and 81%, respectively, after testing. Nearly all respondents had planned or undertaken provider-recommended management. CONCLUSIONS Testing for PALB2, ATM, CHEK2, NBN, BRIP1, RAD51C, and RAD51D changed management for those carrying PVs. Provider recommendations were aligned with guidelines, and patients adhered to recommendations, both of which are critical for reducing both long-term cancer morbidity and mortality.
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Affiliation(s)
| | | | | | - Kaylene Ready
- Myriad Women's Health, South San Francisco, California
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41
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Maciaszek JL, Oak N, Chen W, Hamilton KV, McGee RB, Nuccio R, Mostafavi R, Hines-Dowell S, Harrison L, Taylor L, Gerhardt EL, Ouma A, Edmonson MN, Patel A, Nakitandwe J, Pappo AS, Azzato EM, Shurtleff SA, Ellison DW, Downing JR, Hudson MM, Robison LL, Santana V, Newman S, Zhang J, Wang Z, Wu G, Nichols KE, Kesserwan CA. Enrichment of heterozygous germline RECQL4 loss-of-function variants in pediatric osteosarcoma. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004218. [PMID: 31604778 PMCID: PMC6824257 DOI: 10.1101/mcs.a004218] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/28/2019] [Indexed: 02/07/2023] Open
Abstract
Patients harboring germline pathogenic biallelic variants in genes involved in the recognition and repair of DNA damage are known to have a substantially increased cancer risk. Emerging evidence suggests that individuals harboring heterozygous variants in these same genes may also be at heightened, albeit lesser, risk for cancer. Herein, we sought to determine whether heterozygous variants in RECQL4, the gene encoding an essential DNA helicase that is defective in children with the autosomal recessive cancer-predisposing condition Rothmund-Thomson syndrome (RTS), are associated with increased risk for childhood cancer. To address this question, we interrogated germline sequence data from 4435 pediatric cancer patients at St. Jude Children's Research Hospital and 1127 from the National Cancer Institute Therapeutically Applicable Research to Generate Effective Treatment (TARGET) database and identified 24 (0.43%) who harbored loss-of-function (LOF) RECQL4 variants, including five of 249 (2.0%) with osteosarcoma (OS). These RECQL4 variants were significantly overrepresented in children with OS, the cancer most frequently observed in patients with RTS, as compared to 134,187 noncancer controls in the Genome Aggregation Database (gnomAD v2.1; P = 0.00087, odds ratio [OR] = 7.1, 95% CI, 2.9-17). Nine of the 24 (38%) individuals possessed the same c.1573delT (p.Cys525Alafs) variant located in the highly conserved DNA helicase domain, suggesting that disruption of this domain is central to oncogenesis. Altogether these data expand our understanding of the genetic factors predisposing to childhood cancer and reveal a novel association between heterozygous RECQL4 LOF variants and development of pediatric OS.
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Affiliation(s)
- Jamie L Maciaszek
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Ninad Oak
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Wenan Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Kayla V Hamilton
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Rose B McGee
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Regina Nuccio
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Roya Mostafavi
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Stacy Hines-Dowell
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Lynn Harrison
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Leslie Taylor
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Elsie L Gerhardt
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Annastasia Ouma
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Michael N Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Aman Patel
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Joy Nakitandwe
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Alberto S Pappo
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Elizabeth M Azzato
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Sheila A Shurtleff
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Melissa M Hudson
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Victor Santana
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Scott Newman
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Chimene A Kesserwan
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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Kluźniak W, Wokołorczyk D, Rusak B, Huzarski T, Gronwald J, Stempa K, Rudnicka H, Kashyap A, Dębniak T, Jakubowska A, Lener M, Szwiec M, Tomiczek-Szwiec J, Jarkiewicz-Tretyn J, Cechowska M, Domagała P, Szymiczek A, Bagherzadeh M, Lubiński J, Narod SA, Akbari MR, Cybulski C. Inherited variants in XRCC2 and the risk of breast cancer. Breast Cancer Res Treat 2019; 178:657-663. [PMID: 31463769 PMCID: PMC6817746 DOI: 10.1007/s10549-019-05415-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/19/2019] [Indexed: 12/19/2022]
Abstract
Background XRCC2 participates in homologous recombination and in DNA repair. XRCC2 has been reported to be a breast cancer susceptibility gene and is now included in several breast cancer susceptibility gene panels. Methods We sequenced XRCC2 in 617 Polish women with familial breast cancer and found a founder mutation. We then genotyped 12,617 women with breast cancer and 4599 controls for the XRCC2 founder mutation. Results We identified a recurrent truncating mutation of XRCC2 (c.96delT, p.Phe32fs) in 3 of 617 patients with familial breast cancer who were sequenced. The c.96delT mutation was then detected in 29 of 12,617 unselected breast cancer cases (0.23%) compared to 11 of 4599 cancer-free women (0.24%) (OR = 0.96; 95% CI 0.48–1.93). The mutation frequency in 1988 women with familial breast cancer was 0.2% (OR = 0.84, 95% CI 0.27–2.65). Breast cancers in XRCC2 mutation carriers and non-carriers were similar with respect to age of diagnosis and clinical characteristics. Loss of the wild-type XRCC2 allele was observed only in one of the eight breast cancers from patients who carried the XRCC2 mutation. No cancer type was more common in first- or second-degree relatives of XRCC2 mutation carriers than in relatives of the non-carriers. Conclusion XRCC2 c.96delT is a protein-truncating founder variant in Poland. There is no evidence that this mutation predisposes to breast cancer (and other cancers). It is premature to consider XRCC2 as a breast cancer-predisposing gene.
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Affiliation(s)
- Wojciech Kluźniak
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Dominika Wokołorczyk
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Bogna Rusak
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Tomasz Huzarski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland.,Department of Clinical Genetics and Pathology, University of Zielona Góra, Zielona Góra, Poland
| | - Jacek Gronwald
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Klaudia Stempa
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Helena Rudnicka
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Aniruddh Kashyap
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Tadeusz Dębniak
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Anna Jakubowska
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland.,Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Marcin Lener
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Marek Szwiec
- Department of Surgery and Oncology, University of Zielona Góra, Zielona Góra, Poland.,Department of Clinical Oncology, University of Zielona Góra, Zielona Góra, Poland
| | - Joanna Tomiczek-Szwiec
- Faculty of Natural Sciences and Technology, University of Opole, Opole, Poland.,Department of Oncological Gynecology, Oncology Center in Opole, Opole, Poland
| | | | - Magdalena Cechowska
- Cancer Genetics Laboratory, Genetic Outpatients Clinic in Toruń, Toruń, Poland
| | - Paweł Domagała
- Department of Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Agata Szymiczek
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, Canada
| | - Maryam Bagherzadeh
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, Canada
| | - Jan Lubiński
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Steven A Narod
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Mohammad R Akbari
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Cezary Cybulski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland.
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Toss A, Molinaro E, Sammarini M, Del Savio MC, Cortesi L, Facchinetti F, Grandi G. Hereditary ovarian cancers: state of the art. Minerva Med 2019; 110:301-319. [DOI: 10.23736/s0026-4806.19.06091-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Montalban G, Bonache S, Moles-Fernández A, Gisbert-Beamud A, Tenés A, Bach V, Carrasco E, López-Fernández A, Stjepanovic N, Balmaña J, Diez O, Gutiérrez-Enríquez S. Screening of BRCA1/2 deep intronic regions by targeted gene sequencing identifies the first germline BRCA1 variant causing pseudoexon activation in a patient with breast/ovarian cancer. J Med Genet 2019; 56:63-74. [PMID: 30472649 DOI: 10.1136/jmedgenet-2018-105606] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/16/2018] [Accepted: 10/28/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND Genetic analysis of BRCA1 and BRCA2 for the diagnosis of hereditary breast and ovarian cancer (HBOC) is commonly restricted to coding regions and exon-intron boundaries. Although germline pathogenic variants in these regions explain about ~20% of HBOC cases, there is still an important fraction that remains undiagnosed. We have screened BRCA1/2 deep intronic regions to identify potential spliceogenic variants that could explain part of the missing HBOC susceptibility. METHODS We analysed BRCA1/2 deep intronic regions by targeted gene sequencing in 192 high-risk HBOC families testing negative for BRCA1/2 during conventional analysis. Rare variants (MAF <0.005) predicted to create/activate splice sites were selected for further characterisation in patient RNA. The splicing outcome was analysed by RT-PCR and Sanger sequencing, and allelic imbalance was also determined when heterozygous exonic loci were present. RESULTS A novel transcript was detected in BRCA1 c.4185+4105C>T variant carrier. This variant promotes the inclusion of a pseudoexon in mature mRNA, generating an aberrant transcript predicted to encode for a non-functional protein. Quantitative and allele-specific assays determined haploinsufficiency in the variant carrier, supporting a pathogenic effect for this variant. Genotyping of 1030 HBOC cases and 327 controls did not identify additional carriers in Spanish population. CONCLUSION Screening of BRCA1/2 intronic regions has identified the first BRCA1 deep intronic variant associated with HBOC by pseudoexon activation. Although the frequency of deleterious variants in these regions appears to be low, our study highlights the importance of studying non-coding regions and performing comprehensive RNA assays to complement genetic diagnosis.
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Affiliation(s)
- Gemma Montalban
- Oncogenetics Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
| | - Sandra Bonache
- Oncogenetics Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
| | | | | | - Anna Tenés
- Area of Clinical and Molecular Genetics, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Vanessa Bach
- Oncogenetics Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
| | - Estela Carrasco
- High Risk and Cancer Prevention Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
| | - Adrià López-Fernández
- High Risk and Cancer Prevention Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
| | - Neda Stjepanovic
- High Risk and Cancer Prevention Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
- Medical Oncology Department, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Judith Balmaña
- High Risk and Cancer Prevention Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
- Medical Oncology Department, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Orland Diez
- Oncogenetics Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
- Area of Clinical and Molecular Genetics, University Hospital of Vall d'Hebron, Barcelona, Spain
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Insight into genetic susceptibility to male breast cancer by multigene panel testing: Results from a multicenter study in Italy. Int J Cancer 2019; 145:390-400. [DOI: 10.1002/ijc.32106] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 11/29/2018] [Accepted: 12/21/2018] [Indexed: 12/26/2022]
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46
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Duran-Lozano L, Montalban G, Bonache S, Moles-Fernández A, Tenés A, Castroviejo-Bermejo M, Carrasco E, López-Fernández A, Torres-Esquius S, Gadea N, Stjepanovic N, Balmaña J, Gutiérrez-Enríquez S, Diez O. Alternative transcript imbalance underlying breast cancer susceptibility in a family carrying PALB2 c.3201+5G>T. Breast Cancer Res Treat 2018; 174:543-550. [DOI: 10.1007/s10549-018-05094-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 12/07/2018] [Indexed: 12/18/2022]
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