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Saei H, Morinière V, Heidet L, Gribouval O, Lebbah S, Tores F, Mautret-Godefroy M, Knebelmann B, Burtey S, Vuiblet V, Antignac C, Nitschké P, Dorval G. VNtyper enables accurate alignment-free genotyping of MUC1 coding VNTR using short-read sequencing data in autosomal dominant tubulointerstitial kidney disease. iScience 2023; 26:107171. [PMID: 37456840 PMCID: PMC10338300 DOI: 10.1016/j.isci.2023.107171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/06/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
The human genome comprises approximately 3% of tandem repeats with variable length (VNTR), a few of which have been linked to human rare diseases. Autosomal dominant tubulointerstitial kidney disease-MUC1 (ADTKD-MUC1) is caused by specific frameshift variants in the coding VNTR of the MUC1 gene. Calling variants from VNTR using short-read sequencing (SRS) is challenging due to poor read mappability. We developed a computational pipeline, VNtyper, for reliable detection of MUC1 VNTR pathogenic variants and demonstrated its clinical utility in two distinct cohorts: (1) a historical cohort including 108 families with ADTKD and (2) a replication naive cohort comprising 2,910 patients previously tested on a panel of genes involved in monogenic renal diseases. In the historical cohort all cases known to carry pathogenic MUC1 variants were re-identified, and a new 25bp-frameshift insertion in an additional mislaid family was detected. In the replication cohort, we discovered and validated 30 new patients.
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Affiliation(s)
- Hassan Saei
- Laboratoire des Maladies Rénales Héréditaires, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
| | - Vincent Morinière
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
| | - Laurence Heidet
- Laboratoire des Maladies Rénales Héréditaires, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
- Service de Néphrologie Pédiatrique, Centre de Référence MARHEA, Hôpital Necker-Enfants Malades, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
| | - Olivier Gribouval
- Laboratoire des Maladies Rénales Héréditaires, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
| | - Said Lebbah
- Département de Santé Publique, Unité de Recherche Clinique, Hôpital Pitié-Salpêtrière, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
| | - Frederic Tores
- Plateforme Bio-informatique, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
| | - Manon Mautret-Godefroy
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
| | - Bertrand Knebelmann
- Service de Néphrologie, Centre de Référence MARHEA, Hôpital Necker-Enfants Malades, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
| | - Stéphane Burtey
- Inserm, C2VN, INRAE, C2VN, Aix-Marseille Université, Marseille, France
- Centre de Néphrologie et Transplantation Rénale, AP-HM Hôpital de la Conception, Marseille, France
| | - Vincent Vuiblet
- Service de Néphrologie, CHU de Reims, Reims, France
- Service de Pathologie, CHU De Reims, Reims, France
- Institut d'Intelligence Artificielle en Santé, Université de Reims Champagne-Ardenne et CHU de Reims, Reims, France
| | - Corinne Antignac
- Laboratoire des Maladies Rénales Héréditaires, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
| | - Patrick Nitschké
- Plateforme Bio-informatique, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
| | - Guillaume Dorval
- Laboratoire des Maladies Rénales Héréditaires, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
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Sbihi Z, Tanita K, Bachelet C, Bole C, Jabot-Hanin F, Tores F, Le Loch M, Khodr R, Hoshino A, Lenoir C, Oleastro M, Villa M, Spossito L, Prieto E, Danielian S, Brunet E, Picard C, Taga T, Abdrabou SSMA, Isoda T, Yamada M, Palma A, Kanegane H, Latour S. Identification of Germline Non-coding Deletions in XIAP Gene Causing XIAP Deficiency Reveals a Key Promoter Sequence. J Clin Immunol 2022; 42:559-571. [PMID: 35000057 DOI: 10.1007/s10875-021-01188-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/21/2021] [Indexed: 11/24/2022]
Abstract
PURPOSE X-linked inhibitor of apoptosis protein (XIAP) deficiency, also known as the X-linked lymphoproliferative syndrome of type 2 (XLP-2), is a rare immunodeficiency characterized by recurrent hemophagocytic lymphohistiocytosis, splenomegaly, and inflammatory bowel disease. Variants in XIAP including missense, non-sense, frameshift, and deletions of coding exons have been reported to cause XIAP deficiency. We studied three young boys with immunodeficiency displaying XLP-2-like clinical features. No genetic variation in the coding exons of XIAP was identified by whole-exome sequencing (WES), although the patients exhibited a complete loss of XIAP expression. METHODS Targeted next-generation sequencing (NGS) of the entire locus of XIAP was performed on DNA samples from the three patients. Molecular investigations were assessed by gene reporter expression assays in HEK cells and CRISPR-Cas9 genome editing in primary T cells. RESULTS NGS of XIAP identified three distinct non-coding deletions in the patients that were predicted to be driven by repetitive DNA sequences. These deletions share a common region of 839 bp that encompassed the first non-coding exon of XIAP and contained regulatory elements and marks specific of an active promoter. Moreover, we showed that among the 839 bp, the exon was transcriptionally active. Finally, deletion of the exon by CRISPR-Cas9 in primary cells reduced XIAP protein expression. CONCLUSIONS These results identify a key promoter sequence contained in the first non-coding exon of XIAP. Importantly, this study highlights that sequencing of the non-coding exons that are not currently captured by WES should be considered in the genetic diagnosis when no variation is found in coding exons.
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Affiliation(s)
- Zineb Sbihi
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Kay Tanita
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Camille Bachelet
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France.,Université de Paris, Paris, France
| | - Christine Bole
- Genomics Core Facility, Institut Imagine-Structure Fédérative de Recherche Necker, INSERM UMR 1163, INSERM US24/CNRS UMS3633, Université de Paris, Paris, France
| | - Fabienne Jabot-Hanin
- Genomics Core Facility, Institut Imagine-Structure Fédérative de Recherche Necker, INSERM UMR 1163, INSERM US24/CNRS UMS3633, Université de Paris, Paris, France.,Bioinformatic Platform, INSERM UMR 1163, Institut Imagine, Paris, France
| | - Frederic Tores
- Genomics Core Facility, Institut Imagine-Structure Fédérative de Recherche Necker, INSERM UMR 1163, INSERM US24/CNRS UMS3633, Université de Paris, Paris, France.,Bioinformatic Platform, INSERM UMR 1163, Institut Imagine, Paris, France
| | - Marc Le Loch
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, Paris, France
| | - Radi Khodr
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Akihiro Hoshino
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Christelle Lenoir
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Matias Oleastro
- Immunology and Rheumatology Division, Hospital de Pediatria S.A.M.I.C. Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Mariana Villa
- Immunology and Rheumatology Division, Hospital de Pediatria S.A.M.I.C. Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Lucia Spossito
- Immunology and Rheumatology Division, Hospital de Pediatria S.A.M.I.C. Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Emma Prieto
- Immunology and Rheumatology Division, Hospital de Pediatria S.A.M.I.C. Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Silvia Danielian
- Immunology and Rheumatology Division, Hospital de Pediatria S.A.M.I.C. Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Erika Brunet
- Laboratory of Dynamic of Genome and Immune System, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Capucine Picard
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France.,Université de Paris, Paris, France.,Study Center for Primary Immunodeficiencies, Necker-Enfants Malades Hospital, APHP, Paris, France
| | - Takashi Taga
- Department of Pediatrics, Shiga University of Medical Science, Otsu, Japan
| | | | - Takeshi Isoda
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Masafumi Yamada
- Department of Pediatrics, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Alejandro Palma
- Immunology and Rheumatology Division, Hospital de Pediatria S.A.M.I.C. Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Hirokazu Kanegane
- Department of Child Health and Development, Graduate School of Medical and Dental Sciences, TMDU, Tokyo, Japan
| | - Sylvain Latour
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France. .,Université de Paris, Paris, France.
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Moretti C, Blanco M, Ialy-Radio C, Serrentino ME, Gobé C, Friedman R, Battail C, Leduc M, Ward MA, Vaiman D, Tores F, Cocquet J. Battle of the Sex Chromosomes: Competition between X and Y Chromosome-Encoded Proteins for Partner Interaction and Chromatin Occupancy Drives Multicopy Gene Expression and Evolution in Muroid Rodents. Mol Biol Evol 2021; 37:3453-3468. [PMID: 32658962 PMCID: PMC7743899 DOI: 10.1093/molbev/msaa175] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transmission distorters (TDs) are genetic elements that favor their own transmission to the detriments of others. Slx/Slxl1 (Sycp3-like-X-linked and Slx-like1) and Sly (Sycp3-like-Y-linked) are TDs, which have been coamplified on the X and Y chromosomes of Mus species. They are involved in an intragenomic conflict in which each favors its own transmission, resulting in sex ratio distortion of the progeny when Slx/Slxl1 versus Sly copy number is unbalanced. They are specifically expressed in male postmeiotic gametes (spermatids) and have opposite effects on gene expression: Sly knockdown leads to the upregulation of hundreds of spermatid-expressed genes, whereas Slx/Slxl1-deficiency downregulates them. When both Slx/Slxl1 and Sly are knocked down, sex ratio distortion and gene deregulation are corrected. Slx/Slxl1 and Sly are, therefore, in competition but the molecular mechanism remains unknown. By comparing their chromatin-binding profiles and protein partners, we show that SLX/SLXL1 and SLY proteins compete for interaction with H3K4me3-reader SSTY1 (Spermiogenesis-specific-transcript-on-the-Y1) at the promoter of thousands of genes to drive their expression, and that the opposite effect they have on gene expression is mediated by different abilities to recruit SMRT/N-Cor transcriptional complex. Their target genes are predominantly spermatid-specific multicopy genes encoded by the sex chromosomes and the autosomal Speer/Takusan. Many of them have coamplified with not only Slx/Slxl1/Sly but also Ssty during muroid rodent evolution. Overall, we identify Ssty as a key element of the X versus Y intragenomic conflict, which may have influenced gene content and hybrid sterility beyond Mus lineage since Ssty amplification on the Y predated that of Slx/Slxl1/Sly.
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Affiliation(s)
- Charlotte Moretti
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France.,Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Mélina Blanco
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France
| | - Côme Ialy-Radio
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France
| | | | - Clara Gobé
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France
| | | | - Christophe Battail
- Univ. Grenoble Alpes, CEA, INSERM, IRIG, Biology of Cancer and Infection UMR_S 1036, 38000 Grenoble, France
| | - Marjorie Leduc
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France.,Plateforme Protéomique 3P5, Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France
| | - Monika A Ward
- Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Daniel Vaiman
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France
| | - Frederic Tores
- Plateforme de Bio-informatique, Institut Imagine, Université de Paris, Paris, France
| | - Julie Cocquet
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France
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Rosain J, Oleaga-Quintas C, Deswarte C, Verdin H, Marot S, Syridou G, Mansouri M, Mahdaviani SA, Venegas-Montoya E, Tsolia M, Mesdaghi M, Chernyshova L, Stepanovskiy Y, Parvaneh N, Mansouri D, Pedraza-Sánchez S, Bondarenko A, Espinosa-Padilla SE, Yamazaki-Nakashimada MA, Nieto-Patlán A, Kerner G, Lambert N, Jacques C, Corvilain E, Migaud M, Grandin V, Herrera MT, Jabot-Hanin F, Boisson-Dupuis S, Picard C, Nitschke P, Puel A, Tores F, Abel L, Blancas-Galicia L, De Baere E, Bole-Feysot C, Casanova JL, Bustamante J. A Variety of Alu-Mediated Copy Number Variations Can Underlie IL-12Rβ1 Deficiency. J Clin Immunol 2018; 38:617-627. [PMID: 29995221 DOI: 10.1007/s10875-018-0527-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/19/2018] [Indexed: 10/28/2022]
Abstract
PURPOSE Inborn errors of IFN-γ immunity underlie Mendelian susceptibility to mycobacterial disease (MSMD). Autosomal recessive complete IL-12Rβ1 deficiency is the most frequent genetic etiology of MSMD. Only two of the 84 known mutations are copy number variations (CNVs), identified in two of the 213 IL-12Rβ1-deficient patients and two of the 164 kindreds reported. These two CNVs are large deletions found in the heterozygous or homozygous state. We searched for novel families with IL-12Rβ1 deficiency due to CNVs. METHODS We studied six MSMD patients from five unrelated kindreds displaying adverse reactions to BCG vaccination. Three of the patients also presented systemic salmonellosis, two had mucocutaneous candidiasis, and one had disseminated histoplasmosis. We searched for CNVs and other variations by IL12RB1-targeted next-generation sequencing (NGS). RESULTS We identified six new IL-12Rβ1-deficient patients with a complete loss of IL-12Rβ1 expression on phytohemagglutinin-activated T cells and/or EBV-transformed B cells. The cells of these patients did not respond to IL-12 and IL-23. Five different CNVs encompassing IL12RB1 (four deletions and one duplication) were identified in these patients by NGS coverage analysis, either in the homozygous state (n = 1) or in trans (n = 4) with a single-nucleotide variation (n = 3) or a small indel (n = 1). Seven of the nine mutations are novel. Interestingly, four of the five CNVs were predicted to be driven by nearby Alu elements, as well as the two previously reported large deletions. The IL12RB1 locus is actually enriched in Alu elements (44.7%), when compared with the rest of the genome (10.5%). CONCLUSION The IL12RB1 locus is Alu-enriched and therefore prone to rearrangements at various positions. CNVs should be considered in the genetic diagnosis of IL-12Rβ1 deficiency.
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Affiliation(s)
- Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France.,Study Center for Primary Immunodeficiencies, AP-HP, Necker Hospital for Sick Children, Paris, France
| | - Carmen Oleaga-Quintas
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France
| | - Caroline Deswarte
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France
| | - Hannah Verdin
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Stéphane Marot
- Study Center for Primary Immunodeficiencies, AP-HP, Necker Hospital for Sick Children, Paris, France
| | | | - Mahboubeh Mansouri
- Department of Allergy and Clinical Immunology, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - S Alireza Mahdaviani
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Edna Venegas-Montoya
- The Immunodeficiencies Research Unit, National Institute of Pediatrics, Mexico City, Mexico
| | - Maria Tsolia
- Second Department of Pediatrics, P. and A. Kyriakou Children's Hospital, National and Kapodistrian University of Athens (NKUA), Athens, Greece
| | - Mehrnaz Mesdaghi
- Department of Allergy and Clinical Immunology, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Liudmyla Chernyshova
- Department of Pediatric Infectious Diseases and Immunology, Shupyk National Medical Academy for Postgraduate Education, Kiev, Ukraine
| | - Yuriy Stepanovskiy
- Department of Pediatric Infectious Diseases and Immunology, Shupyk National Medical Academy for Postgraduate Education, Kiev, Ukraine
| | - Nima Parvaneh
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Davood Mansouri
- Department of Internal Medicine, Division of Infectious Disease and Clinical Immunology, NRITLD, Masih Daneshvari Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Clinical Tuberculosis and Epidemiology Research Center, NRITLD, Masih Daneshvari Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sigifredo Pedraza-Sánchez
- Unit of Biochemistry, National Institute for Medical Sciences and Nutrition Salvador Zubiran (INCMNSZ), Mexico City, Mexico
| | - Anastasia Bondarenko
- Department of Pediatric Infectious Diseases and Immunology, Shupyk National Medical Academy for Postgraduate Education, Kiev, Ukraine
| | | | | | - Alejandro Nieto-Patlán
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France
| | - Gaspard Kerner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France
| | - Nathalie Lambert
- Study Center for Primary Immunodeficiencies, AP-HP, Necker Hospital for Sick Children, Paris, France
| | - Corinne Jacques
- Study Center for Primary Immunodeficiencies, AP-HP, Necker Hospital for Sick Children, Paris, France
| | - Emilie Corvilain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France.,Free University of Brussels, Brussels, Belgium
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France
| | - Virginie Grandin
- Study Center for Primary Immunodeficiencies, AP-HP, Necker Hospital for Sick Children, Paris, France
| | - María T Herrera
- Department of Microbiology Research, National Institute of Respiratory Diseases (INER), Mexico City, Mexico
| | - Fabienne Jabot-Hanin
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France
| | - Stéphanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Capucine Picard
- Imagine Institute, Paris Descartes University, Paris, France.,Study Center for Primary Immunodeficiencies, AP-HP, Necker Hospital for Sick Children, Paris, France.,Pediatric Hematology-Immunology Unit, AP-HP, Necker Hospital for Sick Children, Paris, France
| | - Patrick Nitschke
- Bioinformatics Core Facility, Imagine Institute, SFR-Necker, INSERM UMR1163 and INSERM US24/CNRS UMS3633, Paris Descartes Sorbonne Paris Cite University, Paris, France
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Frederic Tores
- Bioinformatics Core Facility, Imagine Institute, SFR-Necker, INSERM UMR1163 and INSERM US24/CNRS UMS3633, Paris Descartes Sorbonne Paris Cite University, Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | | | - Elfride De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Christine Bole-Feysot
- Genomic Core Facility, INSERM UMR1163, SFR-Necker, Imagine Institute, Paris, France.,INSERM US24/CNRS UMS3633, Paris Descartes Sorbonne Paris Cite University, Paris, France
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA.,Pediatric Hematology-Immunology Unit, AP-HP, Necker Hospital for Sick Children, Paris, France.,Howard Hughes Medical Institute, New York, NY, USA
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France. .,Imagine Institute, Paris Descartes University, Paris, France. .,Study Center for Primary Immunodeficiencies, AP-HP, Necker Hospital for Sick Children, Paris, France. .,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA.
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5
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Moretti C, Vaiman D, Tores F, Cocquet J. Expression and epigenomic landscape of the sex chromosomes in mouse post-meiotic male germ cells. Epigenetics Chromatin 2016; 9:47. [PMID: 27795737 PMCID: PMC5081929 DOI: 10.1186/s13072-016-0099-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/17/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND During meiosis, the X and Y chromosomes are transcriptionally silenced. The persistence of repressive chromatin marks on the sex chromatin after meiosis initially led to the assumption that XY gene silencing persists to some extent in spermatids. Considering the many reports of XY-linked genes expressed and needed in the post-meiotic phase of mouse spermatogenesis, it is still unclear whether or not the mouse sex chromatin is a repressive or permissive environment, after meiosis. RESULTS To determine the transcriptional and chromatin state of the sex chromosomes after meiosis, we re-analyzed ten ChIP-Seq datasets performed on mouse round spermatids and four RNA-seq datasets from male germ cells purified at different stages of spermatogenesis. For this, we used the last version of the genome (mm10/GRCm38) and included reads that map to several genomic locations in order to properly interpret the high proportion of sex chromosome-encoded multicopy genes. Our study shows that coverage of active epigenetic marks H3K4me3 and Kcr is similar on the sex chromosomes and on autosomes. The post-meiotic sex chromatin nevertheless differs from autosomal chromatin in its enrichment in H3K9me3 and its depletion in H3K27me3 and H4 acetylation. We also identified a posttranslational modification, H3K27ac, which specifically accumulates on the Y chromosome. In parallel, we found that the X and Y chromosomes are enriched in genes expressed post-meiotically and display a higher proportion of spermatid-specific genes compared to autosomes. Finally, we observed that portions of chromosome 14 and of the sex chromosomes share specific features, such as enrichment in H3K9me3 and the presence of multicopy genes that are specifically expressed in round spermatids, suggesting that parts of chromosome 14 are under the same evolutionary constraints than the sex chromosomes. CONCLUSIONS Based on our expression and epigenomic studies, we conclude that, after meiosis, the mouse sex chromosomes are no longer silenced but are nevertheless regulated differently than autosomes and accumulate different chromatin marks. We propose that post-meiotic selective constraints are at the basis of the enrichment of spermatid-specific genes and of the peculiar chromatin composition of the sex chromosomes and of parts of chromosome 14.
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Affiliation(s)
- Charlotte Moretti
- Institut National de la Sante et de la Recherche Medicale (INSERM) U1016, Institut Cochin, Paris, France ; Centre National de la Recherche Scientifique (CNRS), UMR8104, Paris, France ; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Daniel Vaiman
- Institut National de la Sante et de la Recherche Medicale (INSERM) U1016, Institut Cochin, Paris, France ; Centre National de la Recherche Scientifique (CNRS), UMR8104, Paris, France ; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Frederic Tores
- INSERM U1163, Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, 24 Boulevard du Montparnasse, 75015 Paris, France
| | - Julie Cocquet
- Institut National de la Sante et de la Recherche Medicale (INSERM) U1016, Institut Cochin, Paris, France ; Centre National de la Recherche Scientifique (CNRS), UMR8104, Paris, France ; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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Toubiana J, Courtine E, Tores F, Asfar P, Daubin C, Rousseau C, Ouaaz F, Marin N, Cariou A, Chiche JD, Mira JP. Association of REL polymorphisms and outcome of patients with septic shock. Ann Intensive Care 2016; 6:28. [PMID: 27059500 PMCID: PMC4826362 DOI: 10.1186/s13613-016-0130-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 03/21/2016] [Indexed: 01/15/2023] Open
Abstract
Background cRel, a subunit of NF-κB, is implicated in the inflammatory response observed in autoimmune disease. Hence, knocked-out mice for cRel had a significantly higher mortality, providing new and important functions of cRel in the physiopathology of septic shock. Whether genetic variants in the human REL gene are associated with severity of septic shock is unknown. Methods We genotyped a population of 1040 ICU patients with septic shock and 855 ICU controls for two known polymorphisms of REL; REL rs842647 and REL rs13031237. Outcome of patients according to the presence of REL variant alleles was compared. Results The distribution of REL variant alleles was not significantly different between patients and controls. Among the septic shock group, REL rs13031237*T minor allele was not associated with worse outcome. In contrast, REL rs842647*G minor allele was significantly associated with more multi-organ failure and early death [OR 1.4; 95 % CI (1.02–1.8)]. Conclusion In a large ICU population, we report a significant clinical association between a variation in the human REL gene and severity and mortality of septic shock, suggesting for the first time a new insight into the role of cRel in response to infection in humans.
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Affiliation(s)
- Julie Toubiana
- Medical School, Paris Descartes University, Paris, France. .,INSERM U1016, CNRS UMR 8104, Cochin Institute, Paris, France. .,Department of Pediatric and Infectious Diseases, Necker University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France.
| | - Emilie Courtine
- Medical School, Paris Descartes University, Paris, France.,INSERM U1016, CNRS UMR 8104, Cochin Institute, Paris, France
| | - Frederic Tores
- Bioinformatics Platform, Institut Imagine, Paris Descartes University- Sorbonne Paris Cité, 75015, Paris, France
| | - Pierre Asfar
- Medical Intensive Care Unit, Angers University Hospital, Angers, France
| | - Cédric Daubin
- Medical Intensive Care, Caen University Hospital, Caen, France
| | | | - Fatah Ouaaz
- INSERM U1016, CNRS UMR 8104, Cochin Institute, Paris, France
| | - Nathalie Marin
- Intensive Care Unit, Cochin University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Alain Cariou
- Medical School, Paris Descartes University, Paris, France.,Intensive Care Unit, Cochin University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Jean-Daniel Chiche
- Medical School, Paris Descartes University, Paris, France.,INSERM U1016, CNRS UMR 8104, Cochin Institute, Paris, France.,Intensive Care Unit, Cochin University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Jean-Paul Mira
- Medical School, Paris Descartes University, Paris, France.,INSERM U1016, CNRS UMR 8104, Cochin Institute, Paris, France.,Intensive Care Unit, Cochin University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
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Carayol J, Schellenberg GD, Tores F, Hager J, Ziegler A, Dawson G. Assessing the impact of a combined analysis of four common low-risk genetic variants on autism risk. Mol Autism 2010; 1:4. [PMID: 20678243 PMCID: PMC2907567 DOI: 10.1186/2040-2392-1-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Accepted: 02/22/2010] [Indexed: 02/02/2023] Open
Abstract
Background Autism is a complex disorder characterized by deficits involving communication, social interaction, and repetitive and restrictive patterns of behavior. Twin studies have shown that autism is strongly heritable, suggesting a strong genetic component. In other disease states with a complex etiology, such as type 2 diabetes, cancer and cardiovascular disease, combined analysis of multiple genetic variants in a genetic score has helped to identify individuals at high risk of disease. Genetic scores are designed to test for association of genetic markers with disease. Method The accumulation of multiple risk alleles markedly increases the risk of being affected, and compared with studying polymorphisms individually, it improves the identification of subgroups of individuals at greater risk. In the present study, we show that this approach can be applied to autism by specifically looking at a high-risk population of children who have siblings with autism. A two-sample study design and the generation of a genetic score using multiple independent genes were used to assess the risk of autism in a high-risk population. Results In both samples, odds ratios (ORs) increased significantly as a function of the number of risk alleles, with a genetic score of 8 being associated with an OR of 5.54 (95% confidence interval [CI] 2.45 to 12.49). The sensitivities and specificities for each genetic score were similar in both analyses, and the resultant area under the receiver operating characteristic curves were identical (0.59). Conclusions These results suggest that the accumulation of multiple risk alleles in a genetic score is a useful strategy for assessing the risk of autism in siblings of affected individuals, and may be better than studying single polymorphisms for identifying subgroups of individuals with significantly greater risk.
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Spielmann N, Mutch DM, Rousseau F, Tores F, Hager J, Bertrais S, Basdevant A, Tounian P, Dubern B, Galan P, Clément K. Cathepsin S genotypes are associated with Apo-A1 and HDL-cholesterol in lean and obese French populations. Clin Genet 2008; 74:155-63. [DOI: 10.1111/j.1399-0004.2008.01043.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Carayol J, Philippi A, Tores F. Estimating haplotype relative risks in complex disease from unphased SNPs data in families using a likelihood adjusted for ascertainment. Genet Epidemiol 2006; 30:666-76. [PMID: 16917928 DOI: 10.1002/gepi.20178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The understanding of complex diseases and insights to improve their medical management may be achieved through the deduction of how specific haplotypes may play a joint effect to change relative risk information. In this paper we describe an ascertainment adjusted likelihood-based method to estimate haplotype relative risks using pooled family data coming from association and/or linkage studies that were used to identify specific haplotypes. Haplotype-based analysis tends to require a large amount of parameters to capture all the information that leads to efficiency problems. An adaptation of the Stochastic Expectation Maximization algorithm is used for haplotypes inference from genotypic data and to reduce the number of nuisance parameters for risk estimation. Using different simulations, we show that this method provides unbiased relative risk estimates even in case of departure from Hardy-Weinberg equilibrium.
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Philippi A, Roschmann E, Tores F, Lindenbaum P, Benajou A, Germain-Leclerc L, Marcaillou C, Fontaine K, Vanpeene M, Roy S, Maillard S, Decaulne V, Saraiva JP, Brooks P, Rousseau F, Hager J. Haplotypes in the gene encoding protein kinase c-beta (PRKCB1) on chromosome 16 are associated with autism. Mol Psychiatry 2005; 10:950-60. [PMID: 16027742 DOI: 10.1038/sj.mp.4001704] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Autism is a developmental disorder characterized by impairments in social interaction and communication associated with repetitive patterns of interest or behavior. Autism is highly influenced by genetic factors. Genome-wide linkage and candidate gene association approaches have been used to try and identify autism genes. A few loci have repeatedly been reported linked to autism. Several groups reported evidence for linkage to a region on chromosome 16p. We have applied a direct physical identity-by-descent (IBD) mapping approach to perform a high-density (0.85 megabases) genome-wide linkage scan in 116 families from the AGRE collection. Our results confirm linkage to a region on chromosome 16p with autism. High-resolution single-nucleotide polymorphism (SNP) genotyping and analysis of this region show that haplotypes in the protein kinase c-beta gene are strongly associated with autism. An independent replication of the association in a second set of 167 trio families with autism confirmed our initial findings. Overall, our data provide evidence that the PRKCB1 gene on chromosome 16p may be involved in the etiology of autism.
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Abstract
MOTIVATION Giving a meaningful representation of a pedigree is not obvious when it includes consanguinity loops, individuals with multiple mates or several related families. RESULTS We show that finding a perfectly meaningful representation of a pedigree is equivalent to the interval graph sandwich problem and we propose an algorithm for drawing pedigrees.
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Affiliation(s)
- F Tores
- GIS Infobiogen, 7 rue Guy Môquet, BP 8, 94801 Villejuif cedex Généthon, 1 bis rue de l'Internationale, 91000 Evry, France
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Tores F, Uhry Z, Detroyes B, Demenais F, Martinez M. Sib-pair linkage analysis of alcohol dependence taking into account covariates and age-of-onset variability: evaluation of the residual approach. Genet Epidemiol 1999; 17 Suppl 1:S349-54. [PMID: 10597461 DOI: 10.1002/gepi.1370170759] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The construction of residuals allowed us to consider a phenotype related to alcohol dependence (ALDX1) adjusted for age, gender and current smoking status. Using the Haseman and Elston regression test, we compared genome scan results for detection of loci for the unadjusted and adjusted ALDX1 phenotypes in the Collaborative Study on the Genetics of Alcoholism (COGA) data. More markers were significant at the 1% level for the binary than for the residual analyses. Overall, our residual analyses do not show substantial improvement in their ability to detect linkage for alcohol dependence in the COGA data. This may be due to the relatively small sample size of discordant sib pairs.
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Affiliation(s)
- F Tores
- INSERM U358, Hôpital Saint-Louis, Paris, France
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