3
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Lerner LK, Nguyen TV, Castro LP, Vilar JB, Munford V, Le Guillou M, Mohammad MM, Vergé V, Rosselli F, Menck CFM, Sarasin A, Aoufouchi S. Large deletions in immunoglobulin genes are associated with a sustained absence of DNA Polymerase η. Sci Rep 2020; 10:1311. [PMID: 31992747 PMCID: PMC6987143 DOI: 10.1038/s41598-020-58180-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 01/08/2020] [Indexed: 01/27/2023] Open
Abstract
Somatic hypermutation of immunoglobulin genes is a highly mutagenic process that is B cell-specific and occurs during antigen-driven responses leading to antigen specificity and antibody affinity maturation. Mutations at the Ig locus are initiated by Activation-Induced cytidine Deaminase and are equally distributed at G/C and A/T bases. This requires the establishment of error-prone repair pathways involving the activity of several low fidelity DNA polymerases. In the physiological context, the G/C base pair mutations involve multiple error-prone DNA polymerases, while the generation of mutations at A/T base pairs depends exclusively on the activity of DNA polymerase η. Using two large cohorts of individuals with xeroderma pigmentosum variant (XP-V), we report that the pattern of mutations at Ig genes becomes highly enriched with large deletions. This observation is more striking for patients older than 50 years. We propose that the absence of Pol η allows the recruitment of other DNA polymerases that profoundly affect the Ig genomic landscape.
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Affiliation(s)
- Leticia K Lerner
- Centre National de la Recherche Scientifique UMR8200, Gustave Roussy, 94805, Villejuif, France
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Thuy V Nguyen
- Centre National de la Recherche Scientifique UMR8200, Gustave Roussy, 94805, Villejuif, France
- Department of Genetics, Faculty of Biology, University of Science, Ho Chi Minh City, Vietnam
| | - Ligia P Castro
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Juliana B Vilar
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Veridiana Munford
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Morwenna Le Guillou
- Centre National de la Recherche Scientifique UMR8200, Gustave Roussy, 94805, Villejuif, France
- Université Paris-Saclay, 91400, Orsay, France
| | - Mahwish Mian Mohammad
- Centre National de la Recherche Scientifique UMR8200, Gustave Roussy, 94805, Villejuif, France
- Sorbonne Université, Paris, 75006, France
| | - Véronique Vergé
- Haematology Unit, Gustave Roussy, 94805, Villejuif, France
- Université Paris-Saclay, 91400, Orsay, France
| | - Filippo Rosselli
- Centre National de la Recherche Scientifique UMR8200, Gustave Roussy, 94805, Villejuif, France
- Université Paris-Saclay, 91400, Orsay, France
| | - Carlos F M Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alain Sarasin
- Centre National de la Recherche Scientifique UMR8200, Gustave Roussy, 94805, Villejuif, France
- Université Paris-Saclay, 91400, Orsay, France
| | - Said Aoufouchi
- Centre National de la Recherche Scientifique UMR8200, Gustave Roussy, 94805, Villejuif, France.
- Université Paris-Saclay, 91400, Orsay, France.
- Sorbonne Université, Paris, 75006, France.
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5
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Girard E, Eon-Marchais S, Olaso R, Renault AL, Damiola F, Dondon MG, Barjhoux L, Goidin D, Meyer V, Le Gal D, Beauvallet J, Mebirouk N, Lonjou C, Coignard J, Marcou M, Cavaciuti E, Baulard C, Bihoreau MT, Cohen-Haguenauer O, Leroux D, Penet C, Fert-Ferrer S, Colas C, Frebourg T, Eisinger F, Adenis C, Fajac A, Gladieff L, Tinat J, Floquet A, Chiesa J, Giraud S, Mortemousque I, Soubrier F, Audebert-Bellanger S, Limacher JM, Lasset C, Lejeune-Dumoulin S, Dreyfus H, Bignon YJ, Longy M, Pujol P, Venat-Bouvet L, Bonadona V, Berthet P, Luporsi E, Maugard CM, Noguès C, Delnatte C, Fricker JP, Gesta P, Faivre L, Lortholary A, Buecher B, Caron O, Gauthier-Villars M, Coupier I, Servant N, Boland A, Mazoyer S, Deleuze JF, Stoppa-Lyonnet D, Andrieu N, Lesueur F. Familial breast cancer and DNA repair genes: Insights into known and novel susceptibility genes from the GENESIS study, and implications for multigene panel testing. Int J Cancer 2018; 144:1962-1974. [PMID: 30303537 PMCID: PMC6587727 DOI: 10.1002/ijc.31921] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 09/11/2018] [Accepted: 09/25/2018] [Indexed: 12/16/2022]
Abstract
Pathogenic variants in BRCA1 and BRCA2 only explain the underlying genetic cause of about 10% of hereditary breast and ovarian cancer families. Because of cost‐effectiveness, multigene panel testing is often performed even if the clinical utility of testing most of the genes remains questionable. The purpose of our study was to assess the contribution of rare, deleterious‐predicted variants in DNA repair genes in familial breast cancer (BC) in a well‐characterized and homogeneous population. We analyzed 113 DNA repair genes selected from either an exome sequencing or a candidate gene approach in the GENESIS study, which includes familial BC cases with no BRCA1 or BRCA2 mutation and having a sister with BC (N = 1,207), and general population controls (N = 1,199). Sequencing data were filtered for rare loss‐of‐function variants (LoF) and likely deleterious missense variants (MV). We confirmed associations between LoF and MV in PALB2, ATM and CHEK2 and BC occurrence. We also identified for the first time associations between FANCI, MAST1, POLH and RTEL1 and BC susceptibility. Unlike other associated genes, carriers of an ATM LoF had a significantly higher risk of developing BC than carriers of an ATM MV (ORLoF = 17.4 vs. ORMV = 1.6; pHet = 0.002). Hence, our approach allowed us to specify BC relative risks associated with deleterious‐predicted variants in PALB2, ATM and CHEK2 and to add MAST1, POLH, RTEL1 and FANCI to the list of DNA repair genes possibly involved in BC susceptibility. We also highlight that different types of variants within the same gene can lead to different risk estimates. What's new? Pathogenic variants in BRCA1 and BRCA2 only explain the genetic cause of about 10% of hereditary breast and ovarian cancer families, and the clinical usefulness of testing other genes following the recent introduction of cost‐effective multigene panel sequencing in diagnostics laboratories remains questionable. This large case‐control study describes genetic variation in 113 DNA repair genes and specifies breast cancer relative risks associated with rare deleterious‐predicted variants in PALB2, ATM, and CHEK2. Importantly, different types of variants within the same gene can lead to different risk estimates. The results may help improve risk prediction models and define gene‐specific consensus management guidelines.
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Affiliation(s)
- Elodie Girard
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Séverine Eon-Marchais
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Anne-Laure Renault
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | | | - Marie-Gabrielle Dondon
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Laure Barjhoux
- Département de Biopathologie, Centre Léon Bérard, Lyon, France
| | - Didier Goidin
- Life Sciences and Diagnostics Group, Agilent Technologies France, Les Ulis, France
| | - Vincent Meyer
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Dorothée Le Gal
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Juana Beauvallet
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Noura Mebirouk
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Christine Lonjou
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Juliette Coignard
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France.,Université Paris Sud, Paris, France
| | - Morgane Marcou
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Eve Cavaciuti
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Céline Baulard
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Marie-Thérèse Bihoreau
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | | | - Dominique Leroux
- Département de Génétique, CHU de Grenoble, Hôpital Couple-Enfant, Grenoble, France
| | - Clotilde Penet
- Consultation d'Oncogénétique, Institut Jean-Godinot & ICC Courlancy, Reims, France
| | | | - Chrystelle Colas
- Département de Génétique Groupe Hospitalier Pitié-Salpêtrière, APHP, Paris, France.,Service de Génétique, Institut Curie, Paris, France
| | - Thierry Frebourg
- Département de Génétique, Hôpital Universitaire de Rouen, Rouen, France
| | - François Eisinger
- Institut Paoli Calmette, Département d'Anticipation et de Suivi des Cancers, Oncogénétique Clinique, Institut Paoli-Calmettes & Aix Marseille Université, Inserm, IRD, SESSTIM, Marseille, France
| | - Claude Adenis
- Service de Génétique, Centre Oscar-Lambret, Lille, France
| | - Anne Fajac
- Service d'Oncogénétique, Hôpital Tenon, Paris, France
| | - Laurence Gladieff
- Service d'Oncologie Médicale, Institut Claudius Regaud - IUCT-Oncopole, Toulouse, France
| | - Julie Tinat
- Département de Génétique, Hôpital Universitaire de Rouen, Rouen, France
| | | | | | - Sophie Giraud
- Service de Génétique, Hospices Civils de Lyon, Groupement Hospitalier EST, Bron, France
| | | | | | | | | | - Christine Lasset
- Université Claude Bernard Lyon 1, Villeurbanne; CNRS UMR 5558, Unité de Prévention et Epidémiologie Génétique, Lyon, Centre, Léon Bérard, France
| | | | - Hélène Dreyfus
- Clinique Sainte Catherine, Avignon & CHU de Grenoble, Département de Génétique, Hôpital Couple-Enfant, Grenoble, France
| | - Yves-Jean Bignon
- Université Clermont Auvergne; Inserm, U1240, Centre Jean Perrin, Clermont-Ferrand, France
| | | | - Pascal Pujol
- Service de Génétique Médicale et Oncogénétique, Hôpital Arnaud de Villeneuve, CHU Montpellier & INSERM 896, CRCM Val d'Aurelle, Montpellier, France
| | | | - Valérie Bonadona
- Université Claude Bernard Lyon 1, Villeurbanne; CNRS UMR 5558, Unité de Prévention et Epidémiologie Génétique, Lyon, Centre, Léon Bérard, France
| | - Pascaline Berthet
- Unité de Pathologie Gynécologique, Centre François Baclesse, Caen, France
| | - Elisabeth Luporsi
- Service de Génétique UF4128 CHR Metz-Thionville, Hôpital de Mercy, Metz, France
| | - Christine M Maugard
- Hôpitaux Universitaires de Strasbourg, UF1422 Oncogénétique moléculaire, Laboratoire d'Oncobiologie & UF6948 Oncogénétique Evaluation familiale et suivi, Strasbourg, France
| | - Catherine Noguès
- Institut Paoli Calmette, Département d'Anticipation et de Suivi des Cancers, Oncogénétique Clinique, Institut Paoli-Calmettes & Aix Marseille Université, Inserm, IRD, SESSTIM, Marseille, France
| | - Capucine Delnatte
- Unité d'Oncogénétique, Centre René Gauducheau, Nantes, Saint Herblain, France
| | | | - Paul Gesta
- Service d'Oncogénétique Régional Poitou-Charentes, Niort, France
| | - Laurence Faivre
- Institut GIMI, CHU de Dijon, Hôpital d'Enfants, Oncogénétique & Centre de Lutte contre le Cancer Georges François Leclerc, Dijon, France
| | - Alain Lortholary
- Service d'Oncologie Médicale, Centre Catherine de Sienne, Nantes, France
| | | | - Olivier Caron
- Gustave Roussy, Université Paris-Saclay, Département de Médecine Oncologique, Villejuif, France
| | | | - Isabelle Coupier
- Service de Génétique Médicale et Oncogénétique, Hôpital Arnaud de Villeneuve, CHU Montpellier & INSERM 896, CRCM Val d'Aurelle, Montpellier, France
| | - Nicolas Servant
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Sylvie Mazoyer
- Inserm, U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Dominique Stoppa-Lyonnet
- Service de Génétique, Institut Curie, Paris, France.,Inserm, U830, Institut Curie, Paris, France.,Université Paris Descartes, Paris, France
| | - Nadine Andrieu
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Fabienne Lesueur
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
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