1
|
Bosart K, Petreaca RC, Bouley RA. In silico analysis of several frequent SLX4 mutations appearing in human cancers. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001216. [PMID: 38828439 PMCID: PMC11143449 DOI: 10.17912/micropub.biology.001216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024]
Abstract
SLX4 is an interactor and activator of structure-specific exonuclease that helps resolve tangled recombination intermediates arising at stalled replication forks. It is one of the many factors that assist with homologous recombination, the major mechanism for restarting replication. SLX4 mutations have been reported in many cancers but a pan cancer map of all the mutations has not been undertaken. Here, using data from the Catalogue of Somatic Mutations in Cancers (COSMIC), we show that mutations occur in almost every cancer and many of them truncate the protein which should severely alter the function of the enzyme. We identified a frequent R1779W point mutation that occurs in the SLX4 domain required for heterodimerization with its partner, SLX1. In silico protein structure analysis of this mutation shows that it significantly alters the protein structure and is likely to destabilize the interaction with SLX1. Although this brief communication is limited to only in silico analysis, it identifies certain high frequency SLX4 mutations in human cancers that would warrant further in vivo studies. Additionally, these mutations may be potentially actionable for drug therapies.
Collapse
Affiliation(s)
- Korey Bosart
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States
| | - Ruben C Petreaca
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States
- Molecular Genetics, The Ohio State University at Marion, Marion, Ohio, United States
| | - Renee A Bouley
- Chemistry and Biochemistry, The Ohio State University at Marion, Marion, Ohio, United States
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Taylor SJ, Arends MJ, Langdon SP. Inhibitors of the Fanconi anaemia pathway as potential antitumour agents for ovarian cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2020; 1:26-52. [PMID: 36046263 PMCID: PMC9400734 DOI: 10.37349/etat.2020.00003] [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: 10/24/2019] [Accepted: 12/18/2019] [Indexed: 11/30/2022] Open
Abstract
The Fanconi anaemia (FA) pathway is an important mechanism for cellular DNA damage repair, which functions to remove toxic DNA interstrand crosslinks. This is particularly relevant in the context of ovarian and other cancers which rely extensively on interstrand cross-link generating platinum chemotherapy as standard of care treatment. These cancers often respond well to initial treatment, but reoccur with resistant disease and upregulation of DNA damage repair pathways. The FA pathway is therefore of great interest as a target for therapies that aim to improve the efficacy of platinum chemotherapies, and reverse tumour resistance to these. In this review, we discuss recent advances in understanding the mechanism of interstrand cross-link repair by the FA pathway, and the potential of the component parts as targets for therapeutic agents. We then focus on the current state of play of inhibitor development, covering both the characterisation of broad spectrum inhibitors and high throughput screening approaches to identify novel small molecule inhibitors. We also consider synthetic lethality between the FA pathway and other DNA damage repair pathways as a therapeutic approach.
Collapse
Affiliation(s)
- Sarah J Taylor
- Cancer Research UK Edinburgh Centre and Edinburgh Pathology, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, EH4 2XU Edinburgh, UK
| | - Mark J Arends
- Cancer Research UK Edinburgh Centre and Edinburgh Pathology, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, EH4 2XU Edinburgh, UK
| | - Simon P Langdon
- Cancer Research UK Edinburgh Centre and Edinburgh Pathology, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, EH4 2XU Edinburgh, UK
| |
Collapse
|
4
|
Surowy H, Varga D, Burwinkel B, Marmé F, Sohn C, Luedeke M, Rinckleb A, Maier C, Deissler H, Volcic M, Wiesmüller L, Hasenburg A, Klar M, Hoegel J, Vogel W. A low-frequency haplotype spanning SLX4/FANCP constitutes a new risk locus for early-onset breast cancer (<60 years) and is associated with reduced DNA repair capacity. Int J Cancer 2017; 142:757-768. [PMID: 29044504 DOI: 10.1002/ijc.31105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/31/2017] [Accepted: 09/25/2017] [Indexed: 01/21/2023]
Abstract
Only a fraction of breast cancer (BC) cases can be yet explained by mutations in genes or genomic variants discovered in linkage, genome-wide association and sequencing studies. The known genes entailing medium or high risk for BC are strongly enriched for a function in DNA double strand repair. Thus, aiming at identifying low frequency variants conferring an intermediate risk, we here investigated 17 variants (MAF: 0.01-0.1) in 10 candidate genes involved in DNA repair or cell cycle control. In an exploration cohort of 437 cases and 1189 controls, we show the variant rs3810813 in the SLX4/FANCP gene to be significantly associated with both BC (≤60 years; OR = 2.6(1.6-3.9), p = 1.6E-05) and decreased DNA repair capacity (≤60 years; beta = 37.8(17.9-57.8), p = 5.3E-4). BC association was confirmed in a verification cohort (N = 2441). Both associations were absent from cases diagnosed >60 years and stronger the earlier the diagnosis. By imputation we show that rs3810813 tags a haplotype with 5 additional variants with the same allele frequency (R2 > 0.9), and a pattern of association very similar for both phenotypes (cases <60 years, p < 0.001, the Bonferroni threshold derived from unlinked variants in the region). In young cases (≤60 years) carrying the risk haplotype, micronucleus test results are predictive for BC (AUC > 0.9). Our findings propose a risk variant with high penetrance on the haplotype spanning SLX4/FANCP to be functionally associated to BC predisposition via decreased repair capacity and suggest this variant is carried by a fraction of these haplotypes that is enriched in early onset BC cases.
Collapse
Affiliation(s)
- Harald Surowy
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, Ulm, D-89081, Germany.,Division of Molecular Biology of Breast Cancer, Department of Obstetrics and Gynecology, University of Heidelberg, Im Neuenheimer Feld 440, Heidelberg, D-69120, Germany.,Molecular Epidemiology, C080, German Cancer Research Center, Im Neuenheimer Feld 581, Heidelberg, D-69120, Germany.,Harald Surowy's current address is: Institute of Human Genetics, University of Duesseldorf, Universitaetsstr. 1, Duesseldorf, 40225, Germany
| | - Dominic Varga
- Department of Obstetrics and Gynecology, Ulm University, Prittwitzstr. 43, Ulm, D-89075, Germany.,Dominic Varga's current address is: Department of Gynecology, Donauklinik, Krankenhausstr 11, Neu-Ulm, 89231, Germany
| | - Barbara Burwinkel
- Division of Molecular Biology of Breast Cancer, Department of Obstetrics and Gynecology, University of Heidelberg, Im Neuenheimer Feld 440, Heidelberg, D-69120, Germany.,Molecular Epidemiology, C080, German Cancer Research Center, Im Neuenheimer Feld 581, Heidelberg, D-69120, Germany
| | - Frederik Marmé
- Division of Molecular Biology of Breast Cancer, Department of Obstetrics and Gynecology, University of Heidelberg, Im Neuenheimer Feld 440, Heidelberg, D-69120, Germany.,National Centre for Tumor Diseases, Heidelberg, D-69120, Germany
| | - Christof Sohn
- Division of Molecular Biology of Breast Cancer, Department of Obstetrics and Gynecology, University of Heidelberg, Im Neuenheimer Feld 440, Heidelberg, D-69120, Germany
| | - Manuel Luedeke
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, Ulm, D-89081, Germany
| | - Antje Rinckleb
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, Ulm, D-89081, Germany
| | - Christiane Maier
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, Ulm, D-89081, Germany
| | - Helmut Deissler
- Department of Obstetrics and Gynecology, Ulm University, Prittwitzstr. 43, Ulm, D-89075, Germany.,Helmut Deissler's current address is: HD/U Biomedical Services, Im Wiblinger Hart 62, Ulm, 89079, Germany
| | - Meta Volcic
- Department of Obstetrics and Gynecology, Ulm University, Prittwitzstr. 43, Ulm, D-89075, Germany
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, Prittwitzstr. 43, Ulm, D-89075, Germany
| | - Annette Hasenburg
- Department of Obstetrics and Gynecology, University of Freiburg, Hugstetter Straße 55, Freiburg, D-79106, Germany.,Annete Hasenburg's current address is: Klinik und Poliklinik für Geburtshilfe und Frauengesundheit, University of Mainz, Langenbeckstr. 1, Mainz, 55131, Germany
| | - Maximilian Klar
- Department of Obstetrics and Gynecology, University of Freiburg, Hugstetter Straße 55, Freiburg, D-79106, Germany
| | - Josef Hoegel
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, Ulm, D-89081, Germany
| | - Walther Vogel
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, Ulm, D-89081, Germany
| |
Collapse
|
5
|
Bogliolo M, Surrallés J. Fanconi anemia: a model disease for studies on human genetics and advanced therapeutics. Curr Opin Genet Dev 2015; 33:32-40. [PMID: 26254775 DOI: 10.1016/j.gde.2015.07.002] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 07/19/2015] [Accepted: 07/21/2015] [Indexed: 12/18/2022]
Abstract
Fanconi anemia (FA) is characterized by bone marrow failure, malformations, and chromosome fragility. We review the recent discovery of FA genes and efforts to develop genetic therapies for FA in the last five years. Because current data exclude FANCM as an FA gene, 15 genes remain bona fide FA genes and three (FANCO, FANCR and FANCS) cause an FA like syndrome. Monoallelic mutations in 6 FA associated genes (FANCD1, FANCJ, FANCM, FANCN, FANCO and FANCS) predispose to breast and ovarian cancer. The products of all these genes are involved in the repair of stalled DNA replication forks by unhooking DNA interstrand cross-links and promoting homologous recombination. The genetic characterization of patients with FA is essential for developing therapies, including hematopoietic stem cell transplantation from a savior sibling donor after embryo selection, gene therapy, or genome editing using genetic recombination or engineered nucleases. Newly acquired knowledge about FA promises to provide therapeutic strategies in the near future.
Collapse
Affiliation(s)
- Massimo Bogliolo
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Spain
| | - Jordi Surrallés
- Genome Instability and DNA Repair Group, Department of Genetics and Microbiology, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain; Centre for Biomedical Network Research on Rare Diseases (CIBERER), Spain.
| |
Collapse
|
6
|
Spinella JF, Healy J, Saillour V, Richer C, Cassart P, Ouimet M, Sinnett D. Whole-exome sequencing of a rare case of familial childhood acute lymphoblastic leukemia reveals putative predisposing mutations in Fanconi anemia genes. BMC Cancer 2015. [PMID: 26201965 PMCID: PMC4512039 DOI: 10.1186/s12885-015-1549-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer. While the multi-step model of pediatric leukemogenesis suggests interplay between constitutional and somatic genomes, the role of inherited genetic variability remains largely undescribed. Nonsyndromic familial ALL, although extremely rare, provides the ideal setting to study inherited contributions to ALL. Toward this goal, we sequenced the exomes of a childhood ALL family consisting of mother, father and two non-twinned siblings diagnosed with concordant pre-B hyperdiploid ALL and previously shown to have inherited a rare form of PRDM9, a histone H3 methyltransferase involved in crossing-over at recombination hotspots and Holliday junctions. We postulated that inheritance of additional rare disadvantaging variants in predisposing cancer genes could affect genomic stability and lead to increased risk of hyperdiploid ALL within this family. METHODS Whole exomes were captured using Agilent's SureSelect kit and sequenced on the Life Technologies SOLiD System. We applied a data reduction strategy to identify candidate variants shared by both affected siblings. Under a recessive disease model, we focused on rare non-synonymous or frame-shift variants in leukemia predisposing pathways. RESULTS Though the family was nonsyndromic, we identified a combination of rare variants in Fanconi anemia (FA) genes FANCP/SLX4 (compound heterozygote - rs137976282/rs79842542) and FANCA (rs61753269) and a rare homozygous variant in the Holliday junction resolvase GEN1 (rs16981869). These variants, predicted to affect protein function, were previously identified in familial breast cancer cases. Based on our in-house database of 369 childhood ALL exomes, the sibs were the only patients to carry this particularly rare combination and only a single hyperdiploid patient was heterozygote at both FANCP/SLX4 positions, while no FANCA variant allele carriers were identified. FANCA is the most commonly mutated gene in FA and is essential for resolving DNA interstrand cross-links during replication. FANCP/SLX4 and GEN1 are involved in the cleavage of Holliday junctions and their mutated forms, in combination with the rare allele of PRDM9, could alter Holliday junction resolution leading to nondisjunction of chromosomes and segregation defects. CONCLUSION Taken together, these results suggest that concomitant inheritance of rare variants in FANCA, FANCP/SLX4 and GEN1 on the specific genetic background of this familial case, could lead to increased genomic instability, hematopoietic dysfunction, and higher risk of childhood leukemia.
Collapse
Affiliation(s)
| | - Jasmine Healy
- Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada.
| | - Virginie Saillour
- Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada.
| | - Chantal Richer
- Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada.
| | - Pauline Cassart
- Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada.
| | - Manon Ouimet
- Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada.
| | - Daniel Sinnett
- Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada. .,Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Qc, Canada. .,Division of Hematology-Oncology, Sainte-Justine UHC Research Center, 3175 Côte Ste-Catherine, Montréal (Québec), H3T 1C5, Canada.
| |
Collapse
|
7
|
Sousa FG, Matuo R, Tang SW, Rajapakse VN, Luna A, Sander C, Varma S, Simon PHG, Doroshow JH, Reinhold WC, Pommier Y. Alterations of DNA repair genes in the NCI-60 cell lines and their predictive value for anticancer drug activity. DNA Repair (Amst) 2015; 28:107-15. [PMID: 25758781 DOI: 10.1016/j.dnarep.2015.01.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 01/23/2015] [Indexed: 12/26/2022]
Abstract
Loss of function of DNA repair (DNAR) genes is associated with genomic instability and cancer predisposition; it also makes cancer cells reliant on a reduced set of DNAR pathways to resist DNA-targeted therapy, which remains the core of the anticancer armamentarium. Because the landscape of DNAR defects across numerous types of cancers and its relation with drug activity have not been systematically examined, we took advantage of the unique drug and genomic databases of the US National Cancer Institute cancer cell lines (the NCI-60) to characterize 260 DNAR genes with respect to deleterious mutations and expression down-regulation; 169 genes exhibited a total of 549 function-affecting alterations, with 39 of them scoring as putative knockouts across 31 cell lines. Those mutations were compared to tumor samples from 12 studies of The Cancer Genome Atlas (TCGA) and The Cancer Cell Line Encyclopedia (CCLE). Based on this compendium of alterations, we determined which DNAR genomic alterations predicted drug response for 20,195 compounds present in the NCI-60 drug database. Among 242 DNA damaging agents, 202 showed associations with at least one DNAR genomic signature. In addition to SLFN11, the Fanconi anemia-scaffolding gene SLX4 (FANCP/BTBD12) stood out among the genes most significantly related with DNA synthesis and topoisomerase inhibitors. Depletion and complementation experiments validated the causal relationship between SLX4 defects and sensitivity to raltitrexed and cytarabine in addition to camptothecin. Therefore, we propose new rational uses for existing anticancer drugs based on a comprehensive analysis of DNAR genomic parameters.
Collapse
Affiliation(s)
- Fabricio G Sousa
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Centro de Estudos em Células Tronco, Terapia Celular e Genética Toxicológica, Programa de Pós-Graduação em Farmácia, Universidade Federal de Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
| | - Renata Matuo
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Centro de Estudos em Células Tronco, Terapia Celular e Genética Toxicológica, Programa de Pós-Graduação em Farmácia, Universidade Federal de Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
| | - Sai-Wen Tang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Vinodh N Rajapakse
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Augustin Luna
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Computational Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
| | - Chris Sander
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
| | - Sudhir Varma
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; HiThru Analytics LLC, Laurel, MD 20707, USA
| | - Paul H G Simon
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - James H Doroshow
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - William C Reinhold
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
8
|
Catucci I, Peterlongo P, Ciceri S, Colombo M, Pasquini G, Barile M, Bonanni B, Verderio P, Pizzamiglio S, Foglia C, Falanga A, Marchetti M, Galastri L, Bianchi T, Corna C, Ravagnani F, Bernard L, Fortuzzi S, Sardella D, Scuvera G, Peissel B, Manoukian S, Tondini C, Radice P. PALB2 sequencing in Italian familial breast cancer cases reveals a high-risk mutation recurrent in the province of Bergamo. Genet Med 2014; 16:688-94. [PMID: 24556926 DOI: 10.1038/gim.2014.13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 01/22/2014] [Indexed: 12/17/2022] Open
Abstract
PURPOSE Monoallelic germ-line deleterious mutations of PALB2 (partner and localizer of BRCA2) are associated with breast cancer risk and have been found in several populations, with carrier frequencies of ~1-2%. Initially, these mutations were considered to have moderate penetrance, but accumulating evidence now indicates that they are associated with much higher risk. METHODS In this study, we sequenced the PALB2 coding regions unlinked to BRCA (breast cancer) genes in 575 probands from Italian breast cancer families recruited in Milan. RESULTS We found 12 carriers (2.1%) of deleterious mutations, and none of the mutations was found in 784 controls collected in Milan. One of these mutations, the c.1027C>T (p.Gln343X), was found to be recurrent in the province of Bergamo in northern Italy, being detected in 6/113 (5.3%) familial breast cancer cases and 2/477 (0.4%) controls recruited in this area (Fisher's exact test: P < 0.01). CONCLUSIONS Our data provide confirmatory findings that, in the Italian population also, deleterious mutations of PALB2 are relatively frequent predisposing factors for breast cancer and may be associated with high risk of the disease.
Collapse
Affiliation(s)
- Irene Catucci
- 1] IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy [2] Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Peterlongo
- 1] IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy [2] Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sara Ciceri
- 1] IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy [2] Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Mara Colombo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Graziella Pasquini
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Monica Barile
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan, Italy
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan, Italy
| | - Paolo Verderio
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sara Pizzamiglio
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Claudia Foglia
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Anna Falanga
- Department of Immunohematology and Transfusion Medicine, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
| | - Marina Marchetti
- Department of Immunohematology and Transfusion Medicine, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
| | - Laura Galastri
- Associazione Italiana Volontari Sangue Comunale Milano, Milan, Italy
| | - Tiziana Bianchi
- Associazione Italiana Volontari Sangue Comunale Milano, Milan, Italy
| | - Chiara Corna
- Unit of Medical Oncology, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
| | - Fernando Ravagnani
- Immunohematology and Transfusion Medicine Service, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Loris Bernard
- Department of Experimental Oncology, Istituto Europeo di Oncologia, Cogentech, Milan, Italy
| | - Stefano Fortuzzi
- IFOM Cogentech, Consortium for Genomic Technologies, Milan, Italy
| | | | - Giulietta Scuvera
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Carlo Tondini
- Unit of Medical Oncology, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| |
Collapse
|
9
|
Abstract
Background SLX4 encodes a DNA repair protein that regulates three structure-specific endonucleases and is necessary for resistance to DNA crosslinking agents, topoisomerase I and poly (ADP-ribose) polymerase (PARP) inhibitors. Recent studies have reported mutations in SLX4 in a new subtype of Fanconi anemia (FA), FA-P. Monoallelic defects in several FA genes are known to confer susceptibility to breast and ovarian cancers. Methods and Results To determine if SLX4 is involved in breast cancer susceptibility, we sequenced the entire SLX4 coding region in 738 (270 Jewish and 468 non-Jewish) breast cancer patients with 2 or more family members affected by breast cancer and no known BRCA1 or BRCA2 mutations. We found a novel nonsense (c.2469G>A, p.W823*) mutation in one patient. In addition, we also found 51 missense variants [13 novel, 23 rare (MAF<0.1%), and 15 common (MAF>1%)], of which 22 (5 novel and 17 rare) were predicted to be damaging by Polyphen2 (score = 0.65–1). We performed functional complementation studies using p.W823* and 5 SLX4 variants (4 novel and 1 rare) cDNAs in a human SLX4-null fibroblast cell line, RA3331. While wild type SLX4 and all the other variants fully rescued the sensitivity to mitomycin C (MMC), campthothecin (CPT), and PARP inhibitor (Olaparib) the p.W823* SLX4 mutant failed to do so. Conclusion Loss-of-function mutations in SLX4 may contribute to the development of breast cancer in very rare cases.
Collapse
|
10
|
Low prevalence of SLX4 loss-of-function mutations in non-BRCA1/2 breast and/or ovarian cancer families. Eur J Hum Genet 2012; 21:883-6. [PMID: 23211700 DOI: 10.1038/ejhg.2012.268] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 10/12/2012] [Accepted: 11/02/2012] [Indexed: 11/08/2022] Open
Abstract
Fanconi anemia is a genetically heterogeneous autosomal recessive disorder characterized by development abnormalities, bone marrow failure, and childhood cancers. Compelling evidence indicates a common genetic basis for FA and breast/ovarian cancer susceptibility. Recently, biallelic germ-line mutations in SLX4 have been demonstrated to cause a previously unknown FA subtype (FA-P). We address the role of SLX4/FANCP in breast/ovarian cancer susceptibility by conducting a comprehensive mutation scanning in 486 index cases from non-BRCA1/BRCA2 multiple-case breast and/or ovarian cancer families (non-BRCA1/2 families) from Spain. We detected one unequivocal loss-of-function mutation (p.Glu1517X). In addition, one missense change (p.Arg372Trp) predicted to be pathogenic by in silico analysis co-segregates with disease in one family. Overall, the study indicates that SLX4 mutation screening will have a very low impact (if any) in the genetic counseling of non-BRCA1/2 families.
Collapse
|
11
|
Bakker JL, van Mil SE, Crossan G, Sabbaghian N, De Leeneer K, Poppe B, Adank M, Gille H, Verheul H, Meijers-Heijboer H, de Winter JP, Claes K, Tischkowitz M, Waisfisz Q. Analysis of the novel fanconi anemia gene SLX4/FANCP in familial breast cancer cases. Hum Mutat 2012; 34:70-3. [PMID: 22911665 DOI: 10.1002/humu.22206] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 08/08/2012] [Indexed: 01/05/2023]
Abstract
SLX4/FANCP is a recently discovered novel disease gene for Fanconi anemia (FA), a rare recessive disorder characterized by chromosomal instability and increased cancer susceptibility. Three of the 15 FA genes are breast cancer susceptibility genes in heterozygous mutation carriers--BRCA2, PALB2, and BRIP1. To investigate if defects in SLX4 also predispose to breast cancer, the gene was sequenced in a cohort of 729 BRCA1/BRCA2-negative familial breast cancer cases. We identified a single splice site mutation (c.2013+2T>A), which causes a frameshift by skipping of exon 8. We also identified 39 missense variants, four of which were selected for functional testing in a Mitomycin C-induced growth inhibition assay, and appeared indistinguishable from wild type. Although this is the first study that describes a truncating SLX4 mutation in breast cancer patients, our data indicate that germline mutations in SLX4 are very rare and are unlikely to make a significant contribution to familial breast cancer.
Collapse
Affiliation(s)
- Janine L Bakker
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|