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Boussamet L, Montassier E, Mathé C, Garcia A, Morille J, Shah S, Dugast E, Wiertlewski S, Gourdel M, Bang C, Stürner KH, Masson D, Nicot AB, Vince N, Laplaud DA, Feinstein DL, Berthelot L. Investigating the metabolite signature of an altered oral microbiota as a discriminant factor for multiple sclerosis: a pilot study. Sci Rep 2024; 14:7786. [PMID: 38565581 PMCID: PMC10987558 DOI: 10.1038/s41598-024-57949-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/23/2024] [Indexed: 04/04/2024] Open
Abstract
In multiple sclerosis (MS), alterations of the gut microbiota lead to inflammation. However, the role of other microbiomes in the body in MS has not been fully elucidated. In a pilot case-controlled study, we carried out simultaneous characterization of faecal and oral microbiota and conducted an in-depth analysis of bacterial alterations associated with MS. Using 16S rRNA sequencing and metabolic inference tools, we compared the oral/faecal microbiota and bacterial metabolism pathways in French MS patients (n = 14) and healthy volunteers (HV, n = 21). A classification model based on metabolite flux balance was established and validated in an independent German cohort (MS n = 12, HV n = 38). Our analysis revealed decreases in diversity indices and oral/faecal compartmentalization, the depletion of commensal bacteria (Aggregatibacter and Streptococcus in saliva and Coprobacter and Roseburia in faeces) and enrichment of inflammation-associated bacteria in MS patients (Leptotrichia and Fusobacterium in saliva and Enterobacteriaceae and Actinomyces in faeces). Several microbial pathways were also altered (the polyamine pathway and remodelling of bacterial surface antigens and energetic metabolism) while flux balance analysis revealed associated alterations in metabolite production in MS (nitrogen and nucleoside). Based on this analysis, we identified a specific oral metabolite signature in MS patients, that could discriminate MS patients from HV and rheumatoid arthritis patients. This signature allowed us to create and validate a discrimination model on an independent cohort, which reached a specificity of 92%. Overall, the oral and faecal microbiomes were altered in MS patients. This pilot study highlights the need to study the oral microbiota and oral health implications in patients with autoimmune diseases on a larger scale and suggests that knowledge of the salivary microbiome could help guide the identification of new pathogenic mechanisms associated with the microbiota in MS patients.
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Affiliation(s)
- Léo Boussamet
- Nantes Université, Inserm, CHU de Nantes, CR2TI (Center for Research On Transplantation and Translational Immunology), 30 Bd Jean Monnet, 44000, Nantes, France
| | - Emmanuel Montassier
- Nantes Université, Inserm, CHU de Nantes, CR2TI (Center for Research On Transplantation and Translational Immunology), 30 Bd Jean Monnet, 44000, Nantes, France
- Emergency Department, Nantes Hospital, Nantes, France
| | - Camille Mathé
- Nantes Université, Inserm, CHU de Nantes, CR2TI (Center for Research On Transplantation and Translational Immunology), 30 Bd Jean Monnet, 44000, Nantes, France
| | - Alexandra Garcia
- Nantes Université, Inserm, CHU de Nantes, CR2TI (Center for Research On Transplantation and Translational Immunology), 30 Bd Jean Monnet, 44000, Nantes, France
| | - Jérémy Morille
- Nantes Université, Inserm, CHU de Nantes, CR2TI (Center for Research On Transplantation and Translational Immunology), 30 Bd Jean Monnet, 44000, Nantes, France
| | - Sita Shah
- Nantes Université, Inserm, CHU de Nantes, CR2TI (Center for Research On Transplantation and Translational Immunology), 30 Bd Jean Monnet, 44000, Nantes, France
| | - Emilie Dugast
- Nantes Université, Inserm, CHU de Nantes, CR2TI (Center for Research On Transplantation and Translational Immunology), 30 Bd Jean Monnet, 44000, Nantes, France
| | - Sandrine Wiertlewski
- Nantes Université, Inserm, CHU de Nantes, CR2TI (Center for Research On Transplantation and Translational Immunology), 30 Bd Jean Monnet, 44000, Nantes, France
- Neurology Department, Nantes Hospital, Nantes, France
| | | | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Klarissa H Stürner
- Department of Neurology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Damien Masson
- Clinical Biochemistry Department, Nantes Hospital, Nantes, France
| | - Arnaud B Nicot
- Nantes Université, Inserm, CHU de Nantes, CR2TI (Center for Research On Transplantation and Translational Immunology), 30 Bd Jean Monnet, 44000, Nantes, France
| | - Nicolas Vince
- Nantes Université, Inserm, CHU de Nantes, CR2TI (Center for Research On Transplantation and Translational Immunology), 30 Bd Jean Monnet, 44000, Nantes, France
| | - David-Axel Laplaud
- Nantes Université, Inserm, CHU de Nantes, CR2TI (Center for Research On Transplantation and Translational Immunology), 30 Bd Jean Monnet, 44000, Nantes, France
- Neurology Department, Nantes Hospital, Nantes, France
| | - Douglas L Feinstein
- Jesse Brown VA Medical Center, 835 South Wolcott Ave, MC513, E720, Chicago, IL, 60612, USA.
- Department of Anesthesiology, University of Illinois, Chicago, IL, USA.
| | - Laureline Berthelot
- Nantes Université, Inserm, CHU de Nantes, CR2TI (Center for Research On Transplantation and Translational Immunology), 30 Bd Jean Monnet, 44000, Nantes, France.
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Douillard V, Dos Santos Brito Silva N, Bourguiba-Hachemi S, Naslavsky MS, Scliar MO, Duarte YAO, Zatz M, Passos-Bueno MR, Limou S, Gourraud PA, Launay É, Castelli EC, Vince N. Optimal population-specific HLA imputation with dimension reduction. HLA 2024; 103:e15282. [PMID: 37950640 DOI: 10.1111/tan.15282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/29/2023] [Accepted: 10/14/2023] [Indexed: 11/13/2023]
Abstract
Human genomics has quickly evolved, powering genome-wide association studies (GWASs). SNP-based GWASs cannot capture the intense polymorphism of HLA genes, highly associated with disease susceptibility. There are methods to statistically impute HLA genotypes from SNP-genotypes data, but lack of diversity in reference panels hinders their performance. We evaluated the accuracy of the 1000 Genomes data as a reference panel for imputing HLA from admixed individuals of African and European ancestries, focusing on (a) the full dataset, (b) 10 replications from 6 populations, and (c) 19 conditions for the custom reference panels. The full dataset outperformed smaller models, with a good F1-score of 0.66 for HLA-B. However, custom models outperformed the multiethnic or population models of similar size (F1-scores up to 0.53, against up to 0.42). We demonstrated the importance of using genetically specific models for imputing populations, which are currently underrepresented in public datasets, opening the door to HLA imputation for every genetic population.
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Affiliation(s)
- Venceslas Douillard
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Nayane Dos Santos Brito Silva
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
- São Paulo State University, Molecular Genetics and Bioinformatics Laboratory, School of Medicine, Botucatu, Brazil
| | - Sonia Bourguiba-Hachemi
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Michel S Naslavsky
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Marilia O Scliar
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Yeda A O Duarte
- Medical-Surgical Nursing Department, School of Nursing, University of São Paulo, São Paulo, Brazil
- Epidemiology Department, Public Health School, University of São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Sophie Limou
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Pierre-Antoine Gourraud
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Élise Launay
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
- Department of Pediatrics and Pediatric Emergency, Hôpital Femme Enfant Adolescent, CHU de Nantes, Nantes, France
| | - Erick C Castelli
- São Paulo State University, Molecular Genetics and Bioinformatics Laboratory, School of Medicine, Botucatu, Brazil
| | - Nicolas Vince
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
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Silva NSB, Bourguiba-Hachemi S, Douillard V, Koskela S, Degenhardt F, Clancy J, Limou S, Meyer D, Masotti C, Knorst S, Naslavsky MS, Franke A, Castelli EC, Gourraud PA, Vince N. 18th International HLA and Immunogenetics Workshop: Report on the SNP-HLA Reference Consortium (SHLARC) component. HLA 2024; 103:e15293. [PMID: 37947386 DOI: 10.1111/tan.15293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023]
Abstract
The SNP-HLA Reference Consortium (SHLARC), a component of the 18th International HLA and Immunogenetics Workshop, is aimed at collecting diverse and extensive human leukocyte antigen (HLA) data to create custom reference panels and enhance HLA imputation techniques. Genome-wide association studies (GWAS) have significantly contributed to identifying genetic associations with various diseases. The HLA genomic region has emerged as the top locus in GWAS, particularly in immune-related disorders. However, the limited information provided by single nucleotide polymorphisms (SNPs), the hallmark of GWAS, poses challenges, especially in the HLA region, where strong linkage disequilibrium (LD) spans several megabases. HLA imputation techniques have been developed using statistical inference in response to these challenges. These techniques enable the prediction of HLA alleles from genotyped GWAS SNPs. Here we present the SHLARC activities, a collaborative effort to create extensive, and multi-ethnic reference panels to enhance HLA imputation accuracy.
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Affiliation(s)
- Nayane S B Silva
- Center for Research in Transplantation and Translational Immunology, Nantes Université, INSERM, Ecole Centrale Nantes, Nantes, France
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, Brazil
| | - Sonia Bourguiba-Hachemi
- Center for Research in Transplantation and Translational Immunology, Nantes Université, INSERM, Ecole Centrale Nantes, Nantes, France
| | - Venceslas Douillard
- Center for Research in Transplantation and Translational Immunology, Nantes Université, INSERM, Ecole Centrale Nantes, Nantes, France
| | - Satu Koskela
- Finnish Red Cross Blood Service Biobank, Helsinki, Finland
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, University Hospital Schleswig Holstein - Campus Kiel, Kiel, Germany
| | - Jonna Clancy
- Finnish Red Cross Blood Service Biobank, Helsinki, Finland
| | - Sophie Limou
- Center for Research in Transplantation and Translational Immunology, Nantes Université, INSERM, Ecole Centrale Nantes, Nantes, France
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Cibele Masotti
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Stefan Knorst
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Michel Satya Naslavsky
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, University Hospital Schleswig Holstein - Campus Kiel, Kiel, Germany
| | - Erick C Castelli
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, Brazil
| | - Pierre-Antoine Gourraud
- Center for Research in Transplantation and Translational Immunology, Nantes Université, INSERM, Ecole Centrale Nantes, Nantes, France
| | - Nicolas Vince
- Center for Research in Transplantation and Translational Immunology, Nantes Université, INSERM, Ecole Centrale Nantes, Nantes, France
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Ba R, Durand A, Mauduit V, Chauveau C, Le Bas-Bernardet S, Salle S, Guérif P, Morin M, Petit C, Douillard V, Rousseau O, Blancho G, Kerleau C, Vince N, Giral M, Gourraud PA, Limou S. KiT-GENIE, the French genetic biobank of kidney transplantation. Eur J Hum Genet 2023; 31:1291-1299. [PMID: 36737541 PMCID: PMC10620190 DOI: 10.1038/s41431-023-01294-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/16/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
KiT-GENIE is a monocentric DNA biobank set up to consolidate the very rich and homogeneous DIVAT French cohort of kidney donors and recipients (D/R) in order to explore the molecular factors involved in kidney transplantation outcomes. We collected DNA samples for kidney transplantations performed in Nantes, and we leveraged GWAS genotyping data for securing high-quality genetic data with deep SNP and HLA annotations through imputations and for inferring D/R genetic ancestry. Overall, the biobank included 4217 individuals (n = 1945 D + 2,272 R, including 1969 D/R pairs), 7.4 M SNPs and over 200 clinical variables. KiT-GENIE represents an accurate snapshot of kidney transplantation clinical practice in Nantes between 2002 and 2018, with an enrichment in living kidney donors (17%) and recipients with focal segmental glomerulosclerosis (4%). Recipients were predominantly male (63%), of European ancestry (93%), with a mean age of 51yo and 86% experienced their first graft over the study period. D/R pairs were 93% from European ancestry, and 95% pairs exhibited at least one HLA allelic mismatch. The mean follow-up time was 6.7 years with a hindsight up to 25 years. Recipients experienced biopsy-proven rejection and graft loss for 16.6% and 21.3%, respectively. KiT-GENIE constitutes one of the largest kidney transplantation genetic cohorts worldwide to date. It includes homogeneous high-quality clinical and genetic data for donors and recipients, hence offering a unique opportunity to investigate immunogenetic and genetic factors, as well as donor-recipient interactions and mismatches involved in rejection, graft survival, primary disease recurrence and other comorbidities.
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Affiliation(s)
- Rokhaya Ba
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Axelle Durand
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Vincent Mauduit
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Christine Chauveau
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Stéphanie Le Bas-Bernardet
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Sonia Salle
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Pierrick Guérif
- CHU Nantes, Nantes Université, Service de Néphrologie-Immunologie Clinique, ITUN, F-44000, Nantes, France
| | - Martin Morin
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Clémence Petit
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
- CHU Nantes, Nantes Université, Service de Néphrologie-Immunologie Clinique, ITUN, F-44000, Nantes, France
| | - Venceslas Douillard
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Olivia Rousseau
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Gilles Blancho
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
- CHU Nantes, Nantes Université, Service de Néphrologie-Immunologie Clinique, ITUN, F-44000, Nantes, France
| | - Clarisse Kerleau
- CHU Nantes, Nantes Université, Service de Néphrologie-Immunologie Clinique, ITUN, F-44000, Nantes, France
| | - Nicolas Vince
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Magali Giral
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
- CHU Nantes, Nantes Université, Service de Néphrologie-Immunologie Clinique, ITUN, F-44000, Nantes, France
| | - Pierre-Antoine Gourraud
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France
| | - Sophie Limou
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche Translationnelle en Transplantation et Immunologie, UMR 1064, F-44000, Nantes, France.
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Goodin DS, Khankhanian P, Gourraud PA, Vince N. Multiple sclerosis: Exploring the limits and implications of genetic and environmental susceptibility. PLoS One 2023; 18:e0285599. [PMID: 37379505 DOI: 10.1371/journal.pone.0285599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/27/2023] [Indexed: 06/30/2023] Open
Abstract
OBJECTIVE To explore and describe the basis and implications of genetic and environmental susceptibility to multiple sclerosis (MS) using the Canadian population-based data. BACKGROUND Certain parameters of MS-epidemiology are directly observable (e.g., the recurrence-risk of MS in siblings and twins, the proportion of women among MS patients, the population-prevalence of MS, and the time-dependent changes in the sex-ratio). By contrast, other parameters can only be inferred from the observed parameters (e.g., the proportion of the population that is "genetically susceptible", the proportion of women among susceptible individuals, the probability that a susceptible individual will experience an environment "sufficient" to cause MS, and if they do, the probability that they will develop the disease). DESIGN/METHODS The "genetically susceptible" subset (G) of the population (Z) is defined to include everyone with any non-zero life-time chance of developing MS under some environmental conditions. The value for each observed and non-observed epidemiological parameter is assigned a "plausible" range. Using both a Cross-sectional Model and a Longitudinal Model, together with established parameter relationships, we explore, iteratively, trillions of potential parameter combinations and determine those combinations (i.e., solutions) that fall within the acceptable range for both the observed and non-observed parameters. RESULTS Both Models and all analyses intersect and converge to demonstrate that probability of genetic-susceptibitly, P(G), is limited to only a fraction of the population {i.e., P(G) ≤ 0.52)} and an even smaller fraction of women {i.e., P(G│F) < 0.32)}. Consequently, most individuals (particularly women) have no chance whatsoever of developing MS, regardless of their environmental exposure. However, for any susceptible individual to develop MS, requires that they also experience a "sufficient" environment. We use the Canadian data to derive, separately, the exponential response-curves for men and women that relate the increasing likelihood of developing MS to an increasing probability that a susceptible individual experiences an environment "sufficient" to cause MS. As the probability of a "sufficient" exposure increases, we define, separately, the limiting probability of developing MS in men (c) and women (d). These Canadian data strongly suggest that: (c < d ≤ 1). If so, this observation establishes both that there must be a "truly" random factor involved in MS pathogenesis and that it is this difference, rather than any difference in genetic or environmental factors, which primarily accounts for the penetrance difference between women and men. CONCLUSIONS The development of MS (in an individual) requires both that they have an appropriate genotype (which is uncommon in the population) and that they have an environmental exposure "sufficient" to cause MS given their genotype. Nevertheless, the two principal findings of this study are that: P(G) ≤ 0.52)} and: (c < d ≤ 1). Threfore, even when the necessary genetic and environmental factors, "sufficient" for MS pathogenesis, co-occur for an individual, they still may or may not develop MS. Consequently, disease pathogenesis, even in this circumstance, seems to involve an important element of chance. Moreover, the conclusion that the macroscopic process of disease development for MS includes a "truly" random element, if replicated (either for MS or for other complex diseases), provides empiric evidence that our universe is non-deterministic.
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Affiliation(s)
- Douglas S Goodin
- Department of Neurology, San Francisco & the San Francisco VA Medical Center, University of California, San Francisco, San Francisco, California, United States of Ameirca
| | - Pouya Khankhanian
- Kaiser Permanente, Walnut Creek Medical Center, Dublin, California, United States of Ameirca
| | - Pierre-Antoine Gourraud
- Center for Neuro-Engineering and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of Ameirca
| | - Nicolas Vince
- INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes Université, Nantes, France
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Silva NDSB, Souza ADS, Andrade HDS, Pereira RN, Castro CFB, Vince N, Limou S, Naslavsky MS, Zatz M, Duarte YADO, Mendes-Junior CT, Castelli EDC. Immunogenetics of HLA-B: SNP, allele, and haplotype diversity in populations from different continents and ancestry backgrounds. HLA 2023; 101:634-646. [PMID: 37005006 DOI: 10.1111/tan.15043] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 04/04/2023]
Abstract
HLA-B is among the most variable gene in the human genome. This gene encodes a key molecule for antigen presentation to CD8+ T lymphocytes and NK cell modulation. Despite the myriad of studies evaluating its coding region (with an emphasis on exons 2 and 3), few studies evaluated introns and regulatory sequences in real population samples. Thus, HLA-B variability is probably underestimated. We applied a bioinformatics pipeline tailored for HLA genes on 5347 samples from 80 different populations, which includes more than 1000 admixed Brazilians, to evaluate the HLA-B variability (SNPs, indels, MNPs, alleles, and haplotypes) in exons, introns, and regulatory regions. We observed 610 variable sites throughout HLA-B; the most frequent variants are shared worldwide. However, the haplotype distribution is geographically structured. We detected 920 full-length haplotypes (exons, introns, and untranslated regions) encoding 239 different protein sequences. HLA-B gene diversity is higher in admixed populations and Europeans while lower in African ancestry individuals. Each HLA-B allele group is associated with specific promoter sequences. This HLA-B variation resource may improve HLA imputation accuracy and disease-association studies and provide evolutionary insights regarding HLA-B genetic diversity in human populations.
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Affiliation(s)
- Nayane Dos Santos Brito Silva
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, São Paulo, Brazil
- INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes Université, UMR 1064, F-44000, Nantes, France
| | - Andreia da Silva Souza
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, São Paulo, Brazil
| | - Heloisa de Souza Andrade
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, São Paulo, Brazil
| | - Raphaela Neto Pereira
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, São Paulo, Brazil
| | - Camila Ferreira Bannwart Castro
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, São Paulo, Brazil
- UniFSP, Centro Universitário Sudoeste Paulista, Itapetininga, São Paulo, Brazil
| | - Nicolas Vince
- INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes Université, UMR 1064, F-44000, Nantes, France
| | - Sophie Limou
- INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes Université, UMR 1064, F-44000, Nantes, France
| | - Michel Satya Naslavsky
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
- Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - Celso Teixeira Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Erick da Cruz Castelli
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, São Paulo, Brazil
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Durand A, Winkler CA, Vince N, Douillard V, Geffard E, Binns-Roemer E, Ng DK, Gourraud PA, Reidy K, Warady B, Furth S, Kopp JB, Kaskel FJ, Limou S. Identification of Novel Genetic Risk Factors for Focal Segmental Glomerulosclerosis in Children: Results From the Chronic Kidney Disease in Children (CKiD) Cohort. Am J Kidney Dis 2023; 81:635-646.e1. [PMID: 36623684 DOI: 10.1053/j.ajkd.2022.11.003] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 11/02/2022] [Indexed: 01/09/2023]
Abstract
RATIONALE & OBJECTIVE Focal segmental glomerulosclerosis (FSGS) is a major cause of pediatric nephrotic syndrome, and African Americans exhibit an increased risk for developing FSGS compared with other populations. Predisposing genetic factors have previously been described in adults. Here we performed genomic screening of primary FSGS in a pediatric African American population. STUDY DESIGN Prospective cohort with case-control genetic association study design. SETTING & PARTICIPANTS 140 African American children with chronic kidney disease from the Chronic Kidney Disease in Children (CKiD) cohort, including 32 cases with FSGS. PREDICTORS Over 680,000 common single-nucleotide polymorphisms (SNPs) were tested for association. We also ran a pathway enrichment analysis and a human leucocyte antigen (HLA)-focused association study. OUTCOME Primary biopsy-proven pediatric FSGS. ANALYTICAL APPROACH Multivariate logistic regression models. RESULTS The genome-wide association study revealed 169 SNPs from 14 independent loci significantly associated with FSGS (false discovery rate [FDR]<5%). We observed notable signals for genetic variants within the APOL1 (P=8.6×10-7; OR, 25.8 [95% CI, 7.1-94.0]), ALMS1 (P=1.3×10-7; 13.0% in FSGS cases vs 0% in controls), and FGFR4 (P=4.3×10-6; OR, 24.8 [95% CI, 6.3-97.7]) genes, all of which had previously been associated with adult FSGS, kidney function, or chronic kidney disease. We also highlighted novel, functionally relevant genes, including GRB2 (which encodes a slit diaphragm protein promoting podocyte structure through actin polymerization) and ITGB1 (which is linked to renal injuries). Our results suggest a major role for immune responses and antigen presentation in pediatric FSGS through (1) associations with SNPs in PTPRJ (or CD148, P=3.5×10-7), which plays a role in T-cell receptor signaling, (2) HLA-DRB1∗11:01 association (P=6.1×10-3; OR, 4.5 [95% CI, 1.5-13.0]), and (3) signaling pathway enrichment (P=1.3×10-6). LIMITATIONS Sample size and no independent replication cohort with genomic data readily available. CONCLUSIONS Our genetic study has identified functionally relevant risk factors and the importance of immune regulation for pediatric primary FSGS, which contributes to a better description of its molecular pathophysiological mechanisms.
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Affiliation(s)
- Axelle Durand
- Center for Research in Transplantation and Translational Immunology (UMR 1064), Nantes Université, Ecole Centrale Nantes, CHU Nantes, INSERM, F-44000 Nantes, France
| | - Cheryl A Winkler
- Basic Research Laboratory, Center for Cancer Research, Frederick National Laboratory, National Cancer Institute, Frederick, Maryland
| | - Nicolas Vince
- Center for Research in Transplantation and Translational Immunology (UMR 1064), Nantes Université, Ecole Centrale Nantes, CHU Nantes, INSERM, F-44000 Nantes, France
| | - Venceslas Douillard
- Center for Research in Transplantation and Translational Immunology (UMR 1064), Nantes Université, Ecole Centrale Nantes, CHU Nantes, INSERM, F-44000 Nantes, France
| | - Estelle Geffard
- Center for Research in Transplantation and Translational Immunology (UMR 1064), Nantes Université, Ecole Centrale Nantes, CHU Nantes, INSERM, F-44000 Nantes, France
| | - Elizabeth Binns-Roemer
- Basic Research Laboratory, Center for Cancer Research, Frederick National Laboratory, National Cancer Institute, Frederick, Maryland
| | - Derek K Ng
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Pierre-Antoine Gourraud
- Center for Research in Transplantation and Translational Immunology (UMR 1064), Nantes Université, Ecole Centrale Nantes, CHU Nantes, INSERM, F-44000 Nantes, France
| | - Kimberley Reidy
- Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, New York
| | | | - Susan Furth
- Children's Hospital of Pennsylvania, Philadelphia, Pennsylvania
| | - Jeffrey B Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Frederick J Kaskel
- Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, New York
| | - Sophie Limou
- Center for Research in Transplantation and Translational Immunology (UMR 1064), Nantes Université, Ecole Centrale Nantes, CHU Nantes, INSERM, F-44000 Nantes, France.
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8
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Ed‐driouch C, Chéneau F, Simon F, Pasquier G, Combès B, Kerbrat A, Le Page E, Limou S, Vince N, Laplaud D, Mars F, Dumas C, Edan G, Gourraud P. Multiple sclerosis clinical decision support system based on projection to reference datasets. Ann Clin Transl Neurol 2022; 9:1863-1873. [PMID: 36412095 PMCID: PMC9735373 DOI: 10.1002/acn3.51649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/07/2022] [Revised: 07/08/2022] [Accepted: 07/27/2022] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE Multiple sclerosis (MS) is a multifactorial disease with increasingly complicated management. Our objective is to use on-demand computational power to address the challenges of dynamically managing MS. METHODS A phase 3 clinical trial data (NCT00906399) were used to contextualize the medication efficacy of peg-interferon beta-1a vs placebo on patients with relapsing-remitting MS (RRMS). Using a set of reference patients (PORs), selected based on adequate features similar to those of an individual patient, we visualize disease activity by measuring the percentage of relapses, accumulation of new T2 lesions on MRI, and worsening EDSS during the clinical trial. RESULTS We developed MS Vista, a functional prototype of clinical decision support system (CDSS), with a user-centered design and distributed infrastructure. MS Vista shows the medication efficacy of peginterferon beta-1a versus placebo for each individual patient with RRMS. In addition, MS Vista initiated the integration of a longitudinal magnetic resonance imaging (MRI) viewer and interactive dual physician-patient data display to facilitate communication. INTERPRETATION The pioneer use of PORs for each individual patient enables personalized analytics sustaining the dialog between neurologists, patients and caregivers with quantified evidence.
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Affiliation(s)
- Chadia Ed‐driouch
- Nantes Université, INSERM, CR2TI ‐ Center for Research in Transplantation and Translational ImmunologyF‐44000NantesFrance,Département Automatique, Productique et Informatique, IMT AtlantiqueCNRS, LS2N, UMR CNRS6004NantesFrance
| | - Florent Chéneau
- Département Automatique, Productique et Informatique, IMT AtlantiqueCNRS, LS2N, UMR CNRS6004NantesFrance
| | - Françoise Simon
- Nantes Université, INSERM, CR2TI ‐ Center for Research in Transplantation and Translational ImmunologyF‐44000NantesFrance,Mount Sinai School of Medicine and Columbia UniversityNew YorkNYUSA
| | | | - Benoit Combès
- Université de Rennes, Inria, CNRS, Inserm IRISA UMR 6074, Empenn ERL U 1228F‐35000RennesFrance
| | - Anne Kerbrat
- Université de Rennes, Inria, CNRS, Inserm IRISA UMR 6074, Empenn ERL U 1228F‐35000RennesFrance,CRC‐SEP, CICP 1414 INSERM, CHU Pontchaillou RennesRennesFrance
| | | | - Sophie Limou
- Nantes Université, INSERM, CR2TI ‐ Center for Research in Transplantation and Translational ImmunologyF‐44000NantesFrance,Ecole Centrale Nantes, Department of MathematicsComputer Sciences and BiologyF-44000NantesFrance
| | - Nicolas Vince
- Nantes Université, INSERM, CR2TI ‐ Center for Research in Transplantation and Translational ImmunologyF‐44000NantesFrance
| | - David‐Axel Laplaud
- Nantes Université, CRC‐SEP, CHU Nantes, CIC 1413, Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERMNantesFrance
| | - Franck Mars
- Nantes Université, Centrale NantesCNRS, LS2N, UMR 6004F‐44000NantesFrance
| | - Cédric Dumas
- Département Automatique, Productique et Informatique, IMT AtlantiqueCNRS, LS2N, UMR CNRS6004NantesFrance
| | - Gilles Edan
- Université de Rennes, Inria, CNRS, Inserm IRISA UMR 6074, Empenn ERL U 1228F‐35000RennesFrance,CRC‐SEP, CICP 1414 INSERM, CHU Pontchaillou RennesRennesFrance
| | - Pierre‐Antoine Gourraud
- Nantes Université, CHU Nantes, Pôle Hospitalo‐Universitaire 11: Santé Publique, Clinique des données, INSERM CIC 1413F‐44000NantesFrance
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9
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Domenighetti C, Douillard V, Sugier PE, Sreelatha AAK, Schulte C, Grover S, May P, Bobbili DR, Radivojkov-Blagojevic M, Lichtner P, Singleton AB, Hernandez DG, Edsall C, Gourraud PA, Mellick GD, Zimprich A, Pirker W, Rogaeva E, Lang AE, Koks S, Taba P, Lesage S, Brice A, Corvol JC, Chartier-Harlin MC, Mutez E, Brockmann K, Deutschländer AB, Hadjigeorgiou GM, Dardiotis E, Stefanis L, Simitsi AM, Valente EM, Petrucci S, Duga S, Straniero L, Zecchinelli A, Pezzoli G, Brighina L, Ferrarese C, Annesi G, Quattrone A, Gagliardi M, Matsuo H, Nakayama A, Hattori N, Nishioka K, Chung SJ, Kim YJ, Kolber P, van de Warrenburg BPC, Bloem BR, Aasly J, Toft M, Pihlstrøm L, Guedes LC, Ferreira JJ, Bardien S, Carr J, Tolosa E, Ezquerra M, Pastor P, Diez-Fairen M, Wirdefeldt K, Pedersen NL, Ran C, Belin AC, Puschmann A, Rödström EY, Clarke CE, Morrison KE, Tan M, Krainc D, Burbulla LF, Farrer MJ, Krüger R, Gasser T, Sharma M, Vince N, Elbaz A. The Interaction between HLA-DRB1 and Smoking in Parkinson's Disease Revisited. Mov Disord 2022; 37:1929-1937. [PMID: 35810454 PMCID: PMC9597672 DOI: 10.1002/mds.29133] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/09/2022] [Accepted: 06/06/2022] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Two studies that examined the interaction between HLA-DRB1 and smoking in Parkinson's disease (PD) yielded findings in opposite directions. OBJECTIVE To perform a large-scale independent replication of the HLA-DRB1 × smoking interaction. METHODS We genotyped 182 single nucleotide polymorphism (SNPs) associated with smoking initiation in 12 424 cases and 9480 controls to perform a Mendelian randomization (MR) analysis in strata defined by HLA-DRB1. RESULTS At the amino acid level, a valine at position 11 (V11) in HLA-DRB1 displayed the strongest association with PD. MR showed an inverse association between genetically predicted smoking initiation and PD only in absence of V11 (odds ratio, 0.74, 95% confidence interval, 0.59-0.93, PInteraction = 0.028). In silico predictions of the influence of V11 and smoking-induced modifications of α-synuclein on binding affinity showed findings consistent with this interaction pattern. CONCLUSIONS Despite being one of the most robust findings in PD research, the mechanisms underlying the inverse association between smoking and PD remain unknown. Our findings may help better understand this association. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Cloé Domenighetti
- Université Paris-Saclay, UVSQ, Univ. Paris-Sud, Inserm, Team “Exposome, heredity, cancer and health”, CESP, 94807, Villejuif, France
| | - Venceslas Douillard
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-4400 Nantes, France
| | - Pierre-Emmanuel Sugier
- Université Paris-Saclay, UVSQ, Univ. Paris-Sud, Inserm, Team “Exposome, heredity, cancer and health”, CESP, 94807, Villejuif, France
| | - Ashwin Ashok Kumar Sreelatha
- Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tubingen, Germany
| | - Claudia Schulte
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tubingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tubingen, Germany
| | - Sandeep Grover
- Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tubingen, Germany
| | - Patrick May
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-Belval, Luxembourg
| | - Dheeraj R. Bobbili
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-Belval, Luxembourg
| | | | - Peter Lichtner
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Andrew B. Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD 20892, USA
- Center For Alzheimer’s and Related Dementias, NIA, NIH, Bethesda, MD 20892, USA
| | - Dena G. Hernandez
- Molecular Genetics Section, Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD 20892, USA
| | - Connor Edsall
- Molecular Genetics Section, Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD 20892, USA
| | - Pierre-Antoine Gourraud
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-4400 Nantes, France
| | - George D. Mellick
- Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Queensland, Australia
| | | | - Walter Pirker
- Department of Neurology, Klinik Ottakring, Vienna, Austria
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
| | - Anthony E. Lang
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
- Edmond J. Safra Program in Parkinson’s Disease, Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, UHN, Toronto, Ontario, Canada
- Division of Neurology, University of Toronto, Toronto, Ontario, Canada
- Krembil Brain Institute, Toronto, Ontario, Canada
| | - Sulev Koks
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, Australia
- Perron Institute for Neurological and Translational Science, Nedlands, Western Australia, Australia
| | - Pille Taba
- Department of Neurology and Neurosurgery, University of Tartu, Estonia
- Neurology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Suzanne Lesage
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Department of Neurologie, Paris, France
| | - Alexis Brice
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Department of Neurologie, Paris, France
| | - Jean-Christophe Corvol
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Department of Neurologie, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Paris, France
| | - Marie-Christine Chartier-Harlin
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog- Centre de Recherche Lille Neurosciences & Cognition, F-59000 Lille, France
| | - Eugénie Mutez
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog- Centre de Recherche Lille Neurosciences & Cognition, F-59000 Lille, France
| | - Kathrin Brockmann
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tubingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tubingen, Germany
| | - Angela B. Deutschländer
- Department of Neurology, Ludwig Maximilians University of Munich, Germany
- Department of Neurology, Max Planck Institute of Psychiatry, Munich, Germany
- Department of Neurology and Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Georges M. Hadjigeorgiou
- Department of Neurology, Laboratory of Neurogenetics, University of Thessaly, University Hospital of Larissa, Larissa, Greece
- Department of Neurology, Medical School, University of Cyprus, Nicosia, Cyprus
| | - Efthimos Dardiotis
- Department of Neurology, Laboratory of Neurogenetics, University of Thessaly, University Hospital of Larissa, Larissa, Greece
| | - Leonidas Stefanis
- 1st Department of Neurology, Eginition Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Athina Maria Simitsi
- 1st Department of Neurology, Eginition Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Enza Maria Valente
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| | - Simona Petrucci
- UOC Medical Genetics and Advanced Cell Diagnostics, S. Andrea University Hospital, Rome, Italy
- Department of Clinical and Molecular Medicine, University of Rome, Rome, Italy
| | - Stefano Duga
- Department of Biomedical Sciences - Humanitas University, Milan, Italy
- Humanitas Clinical and Research Center, IRCCS, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Letizia Straniero
- Department of Biomedical Sciences - Humanitas University, Milan, Italy
| | - Anna Zecchinelli
- Parkinson Institute, Azienda Socio Sanitaria Territoriale (ASST) Gaetano Pini/CTO, Milano
| | - Gianni Pezzoli
- Parkinson Institute, Fontazione Grigioni - Via Zuretti, 35, Milan 20125 Italy
| | - Laura Brighina
- Department of Neurology, San Gerardo Hospital, Monza, Italy
- Department of Medicine and Surgery and Milan Center for Neuroscience, University of Milano Bicocca, Milano, Italy
| | - Carlo Ferrarese
- Department of Neurology, San Gerardo Hospital, Monza, Italy
- Department of Medicine and Surgery and Milan Center for Neuroscience, University of Milano Bicocca, Milano, Italy
| | - Grazia Annesi
- Institute for Biomedical Research and Innovation, National Research Council, Cosenza, Italy
| | - Andrea Quattrone
- Institute of Neurology, Magna Graecia University, Catanzaro, Italy
| | - Monica Gagliardi
- Institute of Molecular Bioimaging and Physiology National Research Council, Catanzaro, Italy
| | - Hirotaka Matsuo
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Saitama 359-8513, Japan
| | - Akiyoshi Nakayama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Saitama 359-8513, Japan
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Kenya Nishioka
- Department of Neurology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Sun Ju Chung
- Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Yun Joong Kim
- Department of Neurology, Yonsei University College of Medicine, Seoul, South Korea
| | - Pierre Kolber
- Neurology, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
| | - Bart PC van de Warrenburg
- Radboud University Medical Centre, Donders Institute for Brain, Cognition and Behaviour, Department of Neurology, Nijmegen, The Netherlands
| | - Bastiaan R. Bloem
- Radboud University Medical Centre, Donders Institute for Brain, Cognition and Behaviour, Department of Neurology, Nijmegen, The Netherlands
| | - Jan Aasly
- Department of Neurology, St Olav’s Hospital and Norwegian University of Science and Technology, Trondheim
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Leonor Correia Guedes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Department of Neurosciences and Mental Health, Neurology, Hospital de Santa Maria, Centro Hospitalar Universitario Lisboa Norte (CHULN), Lisbon, Portugal
| | - Joaquim J. Ferreira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Laboratory of Clinical Pharmacology and Therapeutics, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Jonathan Carr
- Division of Neurology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Eduardo Tolosa
- Parkinson’s disease & Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED: CB06/05/0018-ISCIII) Barcelona, Spain
| | - Mario Ezquerra
- Lab of Parkinson Disease and Other Neurodegenerative Movement Disorders, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, ES-08036 Barcelona, Catalonia
| | - Pau Pastor
- Fundació per la Recerca Biomèdica i Social Mútua Terrassa, Terrassa, Barcelona, Spain
- Movement Disorders Unit, Department of Neurology, Hospital Universitari Mutua de Terrassa, Terrassa, Barcelona, Spain
| | - Monica Diez-Fairen
- Fundació per la Recerca Biomèdica i Social Mútua Terrassa, Terrassa, Barcelona, Spain
- Movement Disorders Unit, Department of Neurology, Hospital Universitari Mutua de Terrassa, Terrassa, Barcelona, Spain
| | - Karin Wirdefeldt
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Nancy L. Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Caroline Ran
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Andrea C. Belin
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Andreas Puschmann
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Neurology, Getingevägen 4, 221 85, Lund, Sweden
| | - Emil Ygland Rödström
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Neurology, Getingevägen 4, 221 85, Lund, Sweden
| | - Carl E. Clarke
- University of Birmingham and Sandwell and West Birmingham Hospitals NHS Trust, United Kingdom
| | - Karen E. Morrison
- Faculty of Medicine, Health and Life Sciences, Queens University, Belfast, United Kingdom
| | - Manuela Tan
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Dimitri Krainc
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Lena F. Burbulla
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Metabolic Biochemistry, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Matt J. Farrer
- Department of Neurology, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Rejko Krüger
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-Belval, Luxembourg
- Neurology, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
- Parkinson’s Research Clinic, Centre Hospitalier de Luxembourg, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Thomas Gasser
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tubingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tubingen, Germany
| | - Manu Sharma
- Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tubingen, Germany
| | - Nicolas Vince
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-4400 Nantes, France
| | - Alexis Elbaz
- Université Paris-Saclay, UVSQ, Univ. Paris-Sud, Inserm, Team “Exposome, heredity, cancer and health”, CESP, 94807, Villejuif, France
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10
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Valencia A, Vergara C, Thio CL, Vince N, Douillard V, Grifoni A, Cox AL, Johnson EO, Kral AH, Goedert JJ, Mangia A, Piazzolla V, Mehta SH, Kirk GD, Kim AY, Lauer GM, Chung RT, Price JC, Khakoo SI, Alric L, Cramp ME, Donfield SM, Edlin BR, Busch MP, Alexander G, Rosen HR, Murphy EL, Wojcik GL, Carrington M, Gourraud PA, Sette A, Thomas DL, Duggal P. Trans-ancestral fine-mapping of MHC reveals key amino acids associated with spontaneous clearance of hepatitis C in HLA-DQβ1. Am J Hum Genet 2022; 109:299-310. [PMID: 35090584 DOI: 10.1016/j.ajhg.2022.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/14/2021] [Indexed: 12/27/2022] Open
Abstract
Spontaneous clearance of acute hepatitis C virus (HCV) infection is associated with single nucleotide polymorphisms (SNPs) on the MHC class II. We fine-mapped the MHC region in European (n = 1,600; 594 HCV clearance/1,006 HCV persistence) and African (n = 1,869; 340 HCV clearance/1,529 HCV persistence) ancestry individuals and evaluated HCV peptide binding affinity of classical alleles. In both populations, HLA-DQβ1Leu26 (p valueMeta = 1.24 × 10-14) located in pocket 4 was negatively associated with HCV spontaneous clearance and HLA-DQβ1Pro55 (p valueMeta = 8.23 × 10-11) located in the peptide binding region was positively associated, independently of HLA-DQβ1Leu26. These two amino acids are not in linkage disequilibrium (r2 < 0.1) and explain the SNPs and classical allele associations represented by rs2647011, rs9274711, HLA-DQB1∗03:01, and HLA-DRB1∗01:01. Additionally, HCV persistence classical alleles tagged by HLA-DQβ1Leu26 had fewer HCV binding epitopes and lower predicted binding affinities compared to clearance alleles (geometric mean of combined IC50 nM of persistence versus clearance; 2,321 nM versus 761.7 nM, p value = 1.35 × 10-38). In summary, MHC class II fine-mapping revealed key amino acids in HLA-DQβ1 explaining allelic and SNP associations with HCV outcomes. This mechanistic advance in understanding of natural recovery and immunogenetics of HCV might set the stage for much needed enhancement and design of vaccine to promote spontaneous clearance of HCV infection.
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Affiliation(s)
- Ana Valencia
- Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Universidad Pontificia Bolivariana, Medellín, Antioquia 050031, Colombia
| | - Candelaria Vergara
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Chloe L Thio
- Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Nicolas Vince
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes 44000, France
| | - Venceslas Douillard
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes 44000, France
| | - Alba Grifoni
- Center for infectious Diseases and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Andrea L Cox
- Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC 27709, USA
| | - Alex H Kral
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC 27709, USA
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alessandra Mangia
- Liver Unit, Medical Sciences Department, Fondazione "Casa Sollievo della Sofferenza" IRCCS, 71013 San Giovanni Rotondo, Italy
| | - Valeria Piazzolla
- Liver Unit, Medical Sciences Department, Fondazione "Casa Sollievo della Sofferenza" IRCCS, 71013 San Giovanni Rotondo, Italy
| | - Shruti H Mehta
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Gregory D Kirk
- Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Arthur Y Kim
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Georg M Lauer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Raymond T Chung
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jennifer C Price
- Division of Gastroenterology, Department of Medicine, School of Medicine, University of California, San Francisco, CA 94143, USA
| | - Salim I Khakoo
- University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK
| | - Laurent Alric
- Internal Medicine-Department of Digestive Diseases, Rangueil Hospital, Toulouse University, 1, 31400 Toulouse, France
| | | | | | - Brian R Edlin
- SUNY Downstate College of Medicine, Brooklyn, NY 11203, USA
| | - Michael P Busch
- University of California San Francisco and Vitalant Research Institute, San Francisco, CA 94118, USA
| | - Graeme Alexander
- UCL Institute for Liver and Digestive Health, The Royal Free Hospital, Pond St, Hampstead, London NW3 2QG, UK
| | | | - Edward L Murphy
- University of California San Francisco and Vitalant Research Institute, San Francisco, CA 94118, USA
| | - Genevieve L Wojcik
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Pierre-Antoine Gourraud
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes 44000, France
| | - Alessandro Sette
- Center for infectious Diseases and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - David L Thomas
- Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Priya Duggal
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD 21205, USA.
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11
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Ba R, Geffard E, Douillard V, Simon F, Mesnard L, Vince N, Gourraud PA, Limou S. Surfing the Big Data Wave: Omics Data Challenges in Transplantation. Transplantation 2022; 106:e114-e125. [PMID: 34889882 DOI: 10.1097/tp.0000000000003992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/26/2022]
Abstract
In both research and care, patients, caregivers, and researchers are facing a leap forward in the quantity of data that are available for analysis and interpretation, marking the daunting "big data era." In the biomedical field, this quantitative shift refers mostly to the -omics that permit measuring and analyzing biological features of the same type as a whole. Omics studies have greatly impacted transplantation research and highlighted their potential to better understand transplant outcomes. Some studies have emphasized the contribution of omics in developing personalized therapies to avoid graft loss. However, integrating omics data remains challenging in terms of analytical processes. These data come from multiple sources. Consequently, they may contain biases and systematic errors that can be mistaken for relevant biological information. Normalization methods and batch effects have been developed to tackle issues related to data quality and homogeneity. In addition, imputation methods handle data missingness. Importantly, the transplantation field represents a unique analytical context as the biological statistical unit is the donor-recipient pair, which brings additional complexity to the omics analyses. Strategies such as combined risk scores between 2 genomes taking into account genetic ancestry are emerging to better understand graft mechanisms and refine biological interpretations. The future omics will be based on integrative biology, considering the analysis of the system as a whole and no longer the study of a single characteristic. In this review, we summarize omics studies advances in transplantation and address the most challenging analytical issues regarding these approaches.
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Affiliation(s)
- Rokhaya Ba
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
- Département Informatique et Mathématiques, Ecole Centrale de Nantes, Nantes, France
| | - Estelle Geffard
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
| | - Venceslas Douillard
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
| | - Françoise Simon
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
- Mount Sinai School of Medicine, New York, NY
| | - Laurent Mesnard
- Urgences Néphrologiques et Transplantation Rénale, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
- Sorbonne Université, Paris, France
| | - Nicolas Vince
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
| | - Pierre-Antoine Gourraud
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
| | - Sophie Limou
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Institute of Health and Medical Research, Centre de Recherche en Transplantation et Immunologie, UMR 1064, Institut de Transplantation Urologie-Néphrologie, Nantes, France
- Département Informatique et Mathématiques, Ecole Centrale de Nantes, Nantes, France
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12
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Geffard E, Boussamet L, Walencik A, Delbos F, Limou S, Gourraud PA, Vince N. HLA-EPI: A new EPIsode in exploring donor/recipient epitopic compatibilities. HLA 2021; 99:79-92. [PMID: 34862850 PMCID: PMC9545700 DOI: 10.1111/tan.14505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/16/2021] [Accepted: 12/02/2021] [Indexed: 11/30/2022]
Abstract
The HLA system plays a pivotal role both in transplantation and immunology. While classical HLA genotypes matching is made at the allelic level, recent progresses were developed to explore antibody–antigen recognition by studying epitopes. Donor to recipient matching at the epitopic level is becoming a trending topic in the transplantation research field because anti‐HLA antibodies are epitope‐specific rather than allele‐specific. Indeed, different HLA alleles often share common epitopes. We present the HLA‐Epi tool (hla.univ-nantes.fr) to study an HLA genotype at the epitope level. Using the international HLA epitope registry (Epregistry.com.br) as a reference, we developed HLA‐Epi to easily determine epitopic and allelic compatibility levels between several HLA genotypes. The epitope database covers the most common HLA alleles (N = 2976 HLA alleles), representing more than 99% of the total observed frequency of HLA alleles. The freely accessible web tool HLA‐Epi calculates an epitopic mismatch load between different sets of potential recipient‐donor pairs at different resolution levels. We have characterized the epitopic mismatches distribution in a cohort of more than 10,000 kidney transplanted pairs from European ancestry, which showed low number of epitopic mismatches: 56.9 incompatibilities on average. HLA‐Epi allows the exploration of epitope pairing matching to better understand epitopes contribution to immune responses regulation, particularly during transplantation. This free and ready‐to‐use bioinformatics tool not only addresses limitations of other related tools, but also offers a cost‐efficient and reproducible strategy to analyze HLA epitopes as an alternative to HLA allele compatibility. In the future, this could improve sensitization prevention for allograft allocation decisions and reduce the risk of alloreactivity.
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Affiliation(s)
- Estelle Geffard
- Centre de Recherche en Transplantation et Immunologie, Université de Nantes, CHU Nantes, Inserm, Nantes, France
| | - Léo Boussamet
- Centre de Recherche en Transplantation et Immunologie, Université de Nantes, CHU Nantes, Inserm, Nantes, France
| | - Alexandre Walencik
- Centre de Recherche en Transplantation et Immunologie, Université de Nantes, CHU Nantes, Inserm, Nantes, France.,Laboratoire d'Histocompatibilité et d'Immunogénétique, EFS Centre - Pays de la Loire, Nantes, France
| | - Florent Delbos
- Laboratoire d'Histocompatibilité et d'Immunogénétique, EFS Centre - Pays de la Loire, Nantes, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie, Université de Nantes, CHU Nantes, Inserm, Nantes, France.,Département Informatique et Mathématiques, Ecole Centrale de Nantes, Nantes, France
| | - Pierre-Antoine Gourraud
- Centre de Recherche en Transplantation et Immunologie, Université de Nantes, CHU Nantes, Inserm, Nantes, France
| | - Nicolas Vince
- Centre de Recherche en Transplantation et Immunologie, Université de Nantes, CHU Nantes, Inserm, Nantes, France
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13
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Douillard V, Castelli EC, Mack SJ, Hollenbach JA, Gourraud PA, Vince N, Limou S. Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research. Front Genet 2021; 12:774916. [PMID: 34925459 PMCID: PMC8677840 DOI: 10.3389/fgene.2021.774916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/08/2021] [Indexed: 01/11/2023] Open
Abstract
The current SARS-CoV-2 pandemic era launched an immediate and broad response of the research community with studies both about the virus and host genetics. Research in genetics investigated HLA association with COVID-19 based on in silico, population, and individual data. However, they were conducted with variable scale and success; convincing results were mostly obtained with broader whole-genome association studies. Here, we propose a technical review of HLA analysis, including basic HLA knowledge as well as available tools and advice. We notably describe recent algorithms to infer and call HLA genotypes from GWAS SNPs and NGS data, respectively, which opens the possibility to investigate HLA from large datasets without a specific initial focus on this region. We thus hope this overview will empower geneticists who were unfamiliar with HLA to run MHC-focused analyses following the footsteps of the Covid-19|HLA & Immunogenetics Consortium.
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Affiliation(s)
- Venceslas Douillard
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | | | - Steven J. Mack
- Division of Allergy, Immunology and Bone Marrow Transplantation, Department of Pediatrics, School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Jill A. Hollenbach
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Pierre-Antoine Gourraud
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | - Nicolas Vince
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
- Ecole Centrale de Nantes, Department of Computer Sciences and Mathematics in Biology, Nantes, France
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14
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Bashirova AA, Zheng W, Akdag M, Augusto DG, Vince N, Dong KL, O'hUigin C, Carrington M. Population-specific diversity of the immunoglobulin constant heavy G chain (IGHG) genes. Genes Immun 2021; 22:327-334. [PMID: 34864821 PMCID: PMC8674132 DOI: 10.1038/s41435-021-00156-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/11/2021] [Accepted: 11/22/2021] [Indexed: 12/27/2022]
Abstract
Human immunoglobulin G (IgG) molecules, IgG1, IgG2 and IgG3, exhibit substantial inter-individual variation in their constant heavy chain regions, as discovered by serological methods. This polymorphism is encoded by the IGHG1, IGHG2, and IGHG3 genes and may influence antibody function. We sequenced the coding fragments of these genes in 95 European Americans, 94 African Americans, and 94 Black South Africans. Striking differences were observed between the population groups, including extremely low amino acid sequence variation in IGHG1 among South Africans, and higher IGHG2 and IGHG3 diversity in individuals of African descent compared to individuals of European descent. Molecular definition of the loci illustrates a greater level of allelic polymorphism than previously described, including the presence of common IGHG2 and IGHG3 variants that were indistinguishable serologically. Comparison of our data with the 1000 Genome Project sequences indicates overall agreement between the datasets, although some inaccuracies in the 1000 Genomes Project are likely. These data represent the most comprehensive analysis of IGHG polymorphisms across major populations, which can now be applied to deciphering their functional impact.
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Affiliation(s)
- Arman A Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA
| | - Wanjing Zheng
- The Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA
| | - Marjan Akdag
- Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA
| | - Danillo G Augusto
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Nicolas Vince
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000, Nantes, France
| | - Krista L Dong
- Females Rising through Education, Support, and Health, Durban, KwaZulu-Natal, South Africa
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Colm O'hUigin
- Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
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15
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Douillard V, Castelli EC, Mack SJ, Hollenbach JA, Gourraud PA, Vince N, Limou S. Current HLA Investigations on SARS-CoV-2 and Perspectives. Front Genet 2021; 12:774922. [PMID: 34912378 PMCID: PMC8667766 DOI: 10.3389/fgene.2021.774922] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/08/2021] [Indexed: 01/11/2023] Open
Abstract
The rapid, global spread of the SARS-CoV-2 virus during the current pandemic has triggered numerous efforts in clinical and research settings to better understand the host genetics' interactions and the severity of COVID-19. Due to the established major role played by MHC/HLA polymorphism in infectious disease course and susceptibility, immunologists and geneticists have teamed up to investigate its contribution to the SARS-CoV-2 infection and COVID-19 progression. A major goal of the Covid-19|HLA & Immunogenetics Consortium is to support and unify these efforts. Here, we present a review of HLA immunogenomics studies in the SARS-CoV-2 pandemic and reflect on the role of various HLA data, their limitation and future perspectives.
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Affiliation(s)
- Venceslas Douillard
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | | | - Steven J. Mack
- Division of Allergy, Immunology and Bone Marrow Transplantation, Department of Pediatrics, School of Medicine, University of California, San Francisco, CA, United States
| | - Jill A. Hollenbach
- Department of Neurology, University of California, San Francisco and Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, United States
| | - Pierre-Antoine Gourraud
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Nicolas Vince
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Sophie Limou
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
- Ecole Centrale de Nantes, Department of Computer Sciences and Mathematics in Biology, Nantes, France
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16
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Goodin DS, Khankhanian P, Gourraud PA, Vince N. The nature of genetic and environmental susceptibility to multiple sclerosis. PLoS One 2021; 16:e0246157. [PMID: 33750973 PMCID: PMC7984655 DOI: 10.1371/journal.pone.0246157] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 01/15/2021] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVE To understand the nature of genetic and environmental susceptibility to multiple sclerosis (MS) and, by extension, susceptibility to other complex genetic diseases. BACKGROUND Certain basic epidemiological parameters of MS (e.g., population-prevalence of MS, recurrence-risks for MS in siblings and twins, proportion of women among MS patients, and the time-dependent changes in the sex-ratio) are well-established. In addition, more than 233 genetic-loci have now been identified as being unequivocally MS-associated, including 32 loci within the major histocompatibility complex (MHC), and one locus on the X chromosome. Despite this recent explosion in genetic associations, however, the association of MS with the HLA-DRB1*15:01~HLA-DQB1*06:02~a1 (H+) haplotype has been known for decades. DESIGN/METHODS We define the "genetically-susceptible" subset (G) to include everyone with any non-zero life-time chance of developing MS. Individuals who have no chance of developing MS, regardless of their environmental experiences, belong to the mutually exclusive "non-susceptible" subset (G-). Using these well-established epidemiological parameters, we analyze, mathematically, the implications that these observations have regarding the genetic-susceptibility to MS. In addition, we use the sex-ratio change (observed over a 35-year interval in Canada), to derive the relationship between MS-probability and an increasing likelihood of a sufficient environmental exposure. RESULTS We demonstrate that genetic-susceptibitly is confined to less than 7.3% of populations throughout Europe and North America. Consequently, more than 92.7% of individuals in these populations have no chance whatsoever of developing MS, regardless of their environmental experiences. Even among carriers of the HLA-DRB1*15:01~HLA-DQB1*06:02~a1 haplotype, far fewer than 32% can possibly be members the (G) subset. Also, despite the current preponderance of women among MS patients, women are less likely to be in the susceptible (G) subset and have a higher environmental threshold for developing MS compared to men. Nevertheless, the penetrance of MS in susceptible women is considerably greater than it is in men. Moreover, the response-curves for MS-probability in susceptible individuals increases with an increasing likelihood of a sufficient environmental exposure, especially among women. However, these environmental response-curves plateau at under 50% for women and at a significantly lower level for men. CONCLUSIONS The pathogenesis of MS requires both a genetic predisposition and a suitable environmental exposure. Nevertheless, genetic-susceptibility is rare in the population (< 7.3%) and requires specific combinations of non-additive genetic risk-factors. For example, only a minority of carriers of the HLA-DRB1*15:01~HLA-DQB1*06:02~a1 haplotype are even in the (G) subset and, thus, genetic-susceptibility to MS in these carriers must result from the combined effect this haplotype together with the effects of certain other (as yet, unidentified) genetic factors. By itself, this haplotype poses no MS-risk. By contrast, a sufficient environmental exposure (however many events are involved, whenever these events need to act, and whatever these events might be) is common, currently occurring in, at least, 76% of susceptible individuals. In addition, the fact that environmental response-curves plateau well below 50% (especially in men), indicates that disease pathogenesis is partly stochastic. By extension, other diseases, for which monozygotic-twin recurrence-risks greatly exceed the disease-prevalence (e.g., rheumatoid arthritis, diabetes, and celiac disease), must have a similar genetic basis.
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Affiliation(s)
- Douglas S. Goodin
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States of America
| | - Pouya Khankhanian
- Center for Neuro-Engineering and Therapeutics, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Pierre-Antoine Gourraud
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States of America
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France
- Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
| | - Nicolas Vince
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France
- Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
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17
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Gauttier V, Pengam S, Durand J, Biteau K, Mary C, Morello A, Néel M, Porto G, Teppaz G, Thepenier V, Danger R, Vince N, Wilhelm E, Girault I, Abes R, Ruiz C, Trilleaud C, Ralph K, Trombetta ES, Garcia A, Vignard V, Martinet B, Glémain A, Bruneau S, Haspot F, Dehmani S, Duplouye P, Miyasaka M, Labarrière N, Laplaud D, Le Bas-Bernardet S, Blanquart C, Catros V, Gouraud PA, Archambeaud I, Aublé H, Metairie S, Mosnier JF, Costantini D, Blancho G, Conchon S, Vanhove B, Poirier N. Selective SIRPα blockade reverses tumor T cell exclusion and overcomes cancer immunotherapy resistance. J Clin Invest 2021; 130:6109-6123. [PMID: 33074246 DOI: 10.1172/jci135528] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [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: 12/06/2019] [Accepted: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
T cell exclusion causes resistance to cancer immunotherapies via immune checkpoint blockade (ICB). Myeloid cells contribute to resistance by expressing signal regulatory protein-α (SIRPα), an inhibitory membrane receptor that interacts with ubiquitous receptor CD47 to control macrophage phagocytosis in the tumor microenvironment. Although CD47/SIRPα-targeting drugs have been assessed in preclinical models, the therapeutic benefit of selectively blocking SIRPα, and not SIRPγ/CD47, in humans remains unknown. We report a potent synergy between selective SIRPα blockade and ICB in increasing memory T cell responses and reverting exclusion in syngeneic and orthotopic tumor models. Selective SIRPα blockade stimulated tumor nest T cell recruitment by restoring murine and human macrophage chemokine secretion and increased anti-tumor T cell responses by promoting tumor-antigen crosspresentation by dendritic cells. However, nonselective SIRPα/SIRPγ blockade targeting CD47 impaired human T cell activation, proliferation, and endothelial transmigration. Selective SIRPα inhibition opens an attractive avenue to overcoming ICB resistance in patients with elevated myeloid cell infiltration in solid tumors.
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Affiliation(s)
| | | | | | | | | | | | - Mélanie Néel
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064.,Institut de Transplantation Urologie Néphrologie (ITUN), F-44000 Nantes, France.,CHU Nantes, Nantes, France
| | - Georgia Porto
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064.,Institut de Transplantation Urologie Néphrologie (ITUN), F-44000 Nantes, France
| | | | | | - Richard Danger
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064.,Institut de Transplantation Urologie Néphrologie (ITUN), F-44000 Nantes, France.,CHU Nantes, Nantes, France
| | - Nicolas Vince
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064.,Institut de Transplantation Urologie Néphrologie (ITUN), F-44000 Nantes, France
| | | | | | - Riad Abes
- OSE Immunotherapeutics, Nantes, France
| | | | - Charlène Trilleaud
- OSE Immunotherapeutics, Nantes, France.,Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064.,Institut de Transplantation Urologie Néphrologie (ITUN), F-44000 Nantes, France
| | - Kerry Ralph
- Cancer Immunology & Immune Modulation, Boehringer Ingelheim, Ridgefield, Connecticut, USA
| | - E Sergio Trombetta
- Cancer Immunology & Immune Modulation, Boehringer Ingelheim, Ridgefield, Connecticut, USA
| | - Alexandra Garcia
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064.,Institut de Transplantation Urologie Néphrologie (ITUN), F-44000 Nantes, France.,CHU Nantes, Nantes, France
| | - Virginie Vignard
- CHU Nantes, Nantes, France.,Université de Nantes, CNRS, INSERM, Center for Research in Cancerology and Immunology Nantes-Angers (CRCINA), F-44000 Nantes, France
| | - Bernard Martinet
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064.,Institut de Transplantation Urologie Néphrologie (ITUN), F-44000 Nantes, France
| | - Alexandre Glémain
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064.,Institut de Transplantation Urologie Néphrologie (ITUN), F-44000 Nantes, France
| | - Sarah Bruneau
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064.,Institut de Transplantation Urologie Néphrologie (ITUN), F-44000 Nantes, France
| | - Fabienne Haspot
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064.,Institut de Transplantation Urologie Néphrologie (ITUN), F-44000 Nantes, France
| | - Safa Dehmani
- OSE Immunotherapeutics, Nantes, France.,Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064.,Institut de Transplantation Urologie Néphrologie (ITUN), F-44000 Nantes, France
| | - Pierre Duplouye
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064.,Institut de Transplantation Urologie Néphrologie (ITUN), F-44000 Nantes, France
| | - Masayuki Miyasaka
- Immunology Frontier Research Center, Osaka University, Yamada-oka, Suita, Japan
| | - Nathalie Labarrière
- Université de Nantes, CNRS, INSERM, Center for Research in Cancerology and Immunology Nantes-Angers (CRCINA), F-44000 Nantes, France
| | - David Laplaud
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064.,Institut de Transplantation Urologie Néphrologie (ITUN), F-44000 Nantes, France.,CHU Nantes, Nantes, France
| | - Stéphanie Le Bas-Bernardet
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064.,Institut de Transplantation Urologie Néphrologie (ITUN), F-44000 Nantes, France
| | - Christophe Blanquart
- Université de Nantes, CNRS, INSERM, Center for Research in Cancerology and Immunology Nantes-Angers (CRCINA), F-44000 Nantes, France
| | - Véronique Catros
- Université de Rennes, INSERM, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), UMR_S 1241, CRB Santé Rennes, Rennes, France
| | - Pierre-Antoine Gouraud
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064.,Institut de Transplantation Urologie Néphrologie (ITUN), F-44000 Nantes, France
| | - Isabelle Archambeaud
- CHU Nantes, Nantes, France.,Institut des Maladies de l'Appareil Digestif (IMAD), Service d'Hépato-Gastro-Entérologie et Chirurgie Digestive
| | - Hélène Aublé
- CHU Nantes, Nantes, France.,Institut des Maladies de l'Appareil Digestif (IMAD), Service d'Hépato-Gastro-Entérologie et Chirurgie Digestive.,Centre d'investigation Clinique and
| | - Sylvie Metairie
- CHU Nantes, Nantes, France.,Institut des Maladies de l'Appareil Digestif (IMAD), Service d'Hépato-Gastro-Entérologie et Chirurgie Digestive
| | - Jean-François Mosnier
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064.,Institut de Transplantation Urologie Néphrologie (ITUN), F-44000 Nantes, France.,Service d'Anatomie et Cytologie Pathologiques, CHU Nantes, Nantes, France
| | | | - Gilles Blancho
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064.,Institut de Transplantation Urologie Néphrologie (ITUN), F-44000 Nantes, France.,CHU Nantes, Nantes, France
| | - Sophie Conchon
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064.,Institut de Transplantation Urologie Néphrologie (ITUN), F-44000 Nantes, France
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18
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Geffard E, Limou S, Walencik A, Daya M, Watson H, Torgerson D, Barnes KC, Cesbron Gautier A, Gourraud PA, Vince N. Easy-HLA: a validated web application suite to reveal the full details of HLA typing. Bioinformatics 2020; 36:2157-2164. [PMID: 31750874 PMCID: PMC8248894 DOI: 10.1093/bioinformatics/btz875] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 12/06/2018] [Revised: 09/19/2019] [Accepted: 11/20/2019] [Indexed: 01/10/2023] Open
Abstract
Motivation The HLA system plays a pivotal role in both clinical applications and immunology
research. Typing HLA genes in patient and donor is indeed required in hematopoietic stem
cell and solid-organ transplantation, and the histocompatibility complex region exhibits
countless genetic associations with immune-related pathologies. Since the discovery of
HLA antigens, the HLA system nomenclature and typing methods have constantly evolved,
which leads to difficulties in using data generated with older methodologies. Results Here, we present Easy-HLA, a web-based software suite designed to facilitate analysis
and gain knowledge from HLA typing, regardless of nomenclature or typing method.
Easy-HLA implements a computational and statistical method of HLA haplotypes inference
based on published reference populations containing over 600 000 haplotypes to upgrade
missing or partial HLA information: ‘HLA-Upgrade’ tool infers high-resolution HLA typing
and ‘HLA-2-Haplo’ imputes haplotype pairs and provides additional functional annotations
(e.g. amino acids and KIR ligands). We validated both tools using two independent
cohorts (total n = 2500). For HLA-Upgrade, we reached a prediction
accuracy of 92% from low- to high-resolution of European genotypes. We observed a 96%
call rate and 76% accuracy with HLA-2-Haplo European haplotype pairs prediction. In
conclusion, Easy-HLA tools facilitate large-scale immunogenetic analysis and promotes
the multi-faceted HLA expertise beyond allelic associations by providing new functional
immunogenomics parameters. Availability and implementation Easy-HLA is a web application freely available (free account) at: https://hla.univ-nantes.fr. Supplementary information Supplementary data are
available at Bioinformatics online.
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Affiliation(s)
- Estelle Geffard
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes F-44000, France
| | - Sophie Limou
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes F-44000, France
| | - Alexandre Walencik
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes F-44000, France.,Laboratoire d'Histocompatibilité et d'Immunogénétique, EFS Centre-Pays de la Loire, Nantes F-44000, France
| | - Michelle Daya
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Harold Watson
- Faculty of Medical Sciences Cave Hill Campus, The University of the West Indies, Bridgetown BB11000, Barbados
| | - Dara Torgerson
- McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 0G1, Canada
| | | | | | - Anne Cesbron Gautier
- Laboratoire d'Histocompatibilité et d'Immunogénétique, EFS Centre-Pays de la Loire, Nantes F-44000, France
| | - Pierre-Antoine Gourraud
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes F-44000, France
| | - Nicolas Vince
- Nantes Université, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes F-44000, France
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19
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Vince N, Douillard V, Geffard E, Meyer D, Castelli EC, Mack SJ, Limou S, Gourraud P. Cover Image. Genet Epidemiol 2020. [DOI: 10.1002/gepi.22237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nicolas Vince
- Centre de Recherche en Transplantation et Immunologie, ITUN, UMR 1064 Université de Nantes, CHU Nantes, Inserm Nantes France
| | - Venceslas Douillard
- Centre de Recherche en Transplantation et Immunologie, ITUN, UMR 1064 Université de Nantes, CHU Nantes, Inserm Nantes France
| | - Estelle Geffard
- Centre de Recherche en Transplantation et Immunologie, ITUN, UMR 1064 Université de Nantes, CHU Nantes, Inserm Nantes France
| | | | | | - Steven J. Mack
- Department of Pediatrics, University of California, San Francisco UCSF Benioff Children's Hospital Oakland Oakland California
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie, ITUN, UMR 1064 Université de Nantes, CHU Nantes, Inserm Nantes France
- Ecole Centrale de Nantes Nantes France
| | - Pierre‐Antoine Gourraud
- Centre de Recherche en Transplantation et Immunologie, ITUN, UMR 1064 Université de Nantes, CHU Nantes, Inserm Nantes France
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20
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Vince N, Douillard V, Geffard E, Meyer D, Castelli EC, Mack SJ, Limou S, Gourraud PA. SNP-HLA Reference Consortium (SHLARC): HLA and SNP data sharing for promoting MHC-centric analyses in genomics. Genet Epidemiol 2020; 44:733-740. [PMID: 32681667 PMCID: PMC7540691 DOI: 10.1002/gepi.22334] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 06/19/2020] [Accepted: 07/03/2020] [Indexed: 12/19/2022]
Abstract
Genome‐wide associations studies have repeatedly identified the major histocompatibility complex genomic region (6p21.3) as key in immune pathologies. Researchers have also aimed to extend the biological interpretation of associations by focusing directly on human leukocyte antigen (HLA) polymorphisms and their combination as haplotypes. To circumvent the effort and high costs of HLA typing, statistical solutions have been developed to infer HLA alleles from single‐nucleotide polymorphism (SNP) genotyping data. Though HLA imputation methods have been developed, no unified effort has yet been undertaken to share large and diverse imputation models, or to improve methods. By training the HIBAG software on SNP + HLA data generated by the Consortium on Asthma among African‐ancestry Populations in the Americas (CAAPA) to create reference panels, we highlighted the importance of (a) the number of individuals in reference panels, with a twofold increase in accuracy (from 10 to 100 individuals) and (b) the number of SNPs, with a 1.5‐fold increase in accuracy (from 500 to 24,504 SNPs). Results showed improved accuracy with CAAPA compared to the African American models available in HIBAG, highlighting the need for precise population‐matching. The SNP‐HLA Reference Consortium is an international endeavor to gather data, enhance HLA imputation and broaden access to highly accurate imputation models for the immunogenomics community.
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Affiliation(s)
- Nicolas Vince
- Centre de Recherche en Transplantation et Immunologie, ITUN, UMR 1064, Université de Nantes, CHU Nantes, Inserm, Nantes, France
| | - Venceslas Douillard
- Centre de Recherche en Transplantation et Immunologie, ITUN, UMR 1064, Université de Nantes, CHU Nantes, Inserm, Nantes, France
| | - Estelle Geffard
- Centre de Recherche en Transplantation et Immunologie, ITUN, UMR 1064, Université de Nantes, CHU Nantes, Inserm, Nantes, France
| | | | - Erick C Castelli
- UNESP-Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Steven J Mack
- Department of Pediatrics, University of California, San Francisco, UCSF Benioff Children's Hospital Oakland, Oakland, California
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie, ITUN, UMR 1064, Université de Nantes, CHU Nantes, Inserm, Nantes, France.,Ecole Centrale de Nantes, Nantes, France
| | - Pierre-Antoine Gourraud
- Centre de Recherche en Transplantation et Immunologie, ITUN, UMR 1064, Université de Nantes, CHU Nantes, Inserm, Nantes, France
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21
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Savage SA, Viard M, O'hUigin C, Zhou W, Yeager M, Li SA, Wang T, Ramsuran V, Vince N, Vogt A, Hicks B, Burdett L, Chung C, Dean M, de Andrade KC, Freedman ND, Berndt SI, Rothman N, Lan Q, Cerhan JR, Slager SL, Zhang Y, Teras LR, Haagenson M, Chanock SJ, Spellman SR, Wang Y, Willis A, Askar M, Lee SJ, Carrington M, Gadalla SM. Genome-wide Association Study Identifies HLA-DPB1 as a Significant Risk Factor for Severe Aplastic Anemia. Am J Hum Genet 2020; 106:264-271. [PMID: 32004448 PMCID: PMC7010969 DOI: 10.1016/j.ajhg.2020.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 01/07/2020] [Indexed: 12/20/2022] Open
Abstract
Severe aplastic anemia (SAA) is a rare disorder characterized by hypoplastic bone marrow and progressive pancytopenia. The etiology of acquired SAA is not understood but is likely related to abnormal immune responses and environmental exposures. We conducted a genome-wide association study of individuals with SAA genetically matched to healthy controls in discovery (359 cases, 1,396 controls) and validation sets (175 cases, 1,059 controls). Combined analyses identified linked SNPs in distinct blocks within the major histocompatibility complex on 6p21. The top SNP encodes p.Met76Val in the P4 binding pocket of the HLA class II gene HLA-DPB1 (rs1042151A>G, odds ratio [OR] 1.75, 95% confidence interval [CI] 1.50-2.03, p = 1.94 × 10-13) and was associated with HLA-DP cell surface expression in healthy individuals (p = 2.04 × 10-6). Phylogenetic analyses indicate that Val76 is not monophyletic and likely occurs in conjunction with different HLA-DP binding groove conformations. Imputation of HLA-DPB1 alleles revealed increased risk of SAA associated with Val76-encoding alleles DPB1∗03:01, (OR 1.66, p = 1.52 × 10-7), DPB1∗10:01 (OR 2.12, p = 0.0003), and DPB1∗01:01 (OR 1.60, p = 0.0008). A second SNP near HLA-B, rs28367832G>A, reached genome-wide significance (OR 1.49, 95% CI 1.22-1.78, p = 7.27 × 10-9) in combined analyses; the association remained significant after excluding cases with clonal copy-neutral loss-of-heterozygosity affecting class I HLA genes (8.6% of cases and 0% of controls). SNPs in the HLA class II gene HLA-DPB1 and possibly class I (HLA-B) are associated with SAA. The replacement of Met76 to Val76 in certain HLA-DPB1 alleles might influence risk of SAA through mechanisms involving DP peptide binding specificity, expression, and/or other factors affecting DP function.
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Affiliation(s)
- Sharon A Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Colm O'hUigin
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Weiyin Zhou
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Meredith Yeager
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Shengchao Alfred Li
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Veron Ramsuran
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nicolas Vince
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Aurelie Vogt
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Belynda Hicks
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Laurie Burdett
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Charles Chung
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Kelvin C de Andrade
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55902, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55902, USA
| | - Yawei Zhang
- Section of Surgical Outcomes and Epidemiology, Department of Surgery, Yale Medical School, New Haven, CT 06520, USA
| | - Lauren R Teras
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, 30303, USA
| | - Michael Haagenson
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Youjin Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Amanda Willis
- Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, TX 76798, USA
| | - Medhat Askar
- Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, TX 76798, USA
| | - Stephanie J Lee
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Shahinaz M Gadalla
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
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22
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Montassier E, Al-Ghalith GA, Mathé C, Le Bastard Q, Douillard V, Garnier A, Guimon R, Raimondeau B, Touchefeu Y, Duchalais E, Vince N, Limou S, Gourraud PA, Laplaud DA, Nicot AB, Soulillou JP, Berthelot L. Distribution of Bacterial α1,3-Galactosyltransferase Genes in the Human Gut Microbiome. Front Immunol 2020; 10:3000. [PMID: 31998300 PMCID: PMC6970434 DOI: 10.3389/fimmu.2019.03000] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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: 06/25/2019] [Accepted: 12/06/2019] [Indexed: 12/20/2022] Open
Abstract
Because of a loss-of-function mutation in the GGTA1 gene, humans are unable to synthetize α1,3-Galactose (Gal) decorated glycans and develop high levels of circulating anti-α1,3-Galactose antibodies (anti-Gal Abs). Anti-Gal Abs have been identified as a major obstacle of organ xenotransplantation and play a role in several host-pathogen relationships including potential susceptibility to infection. Anti-Gal Abs are supposed to stem from immunization against the gut microbiota, an assumption derived from the observation that some pathogens display α1,3-Gal and that antibiotic treatment decreases the level of anti-Gal. However, there is little information to date concerning the microorganisms producing α1,3-Gal in the human gut microbiome. Here, available α1,3-Galactosyltransferase (GT) gene sequences from gut bacteria were selectively quantified for the first time in the gut microbiome shotgun sequences of 163 adult individuals from three published population-based metagenomics analyses. We showed that most of the gut microbiome of adult individuals contained a small set of bacteria bearing α1,3-GT genes. These bacteria belong mainly to the Enterobacteriaceae family, including Escherichia coli, but also to Pasteurellaceae genera, Haemophilus influenza and Lactobacillus species. α1,3-Gal antigens and α1,3-GT activity were detected in healthy stools of individuals exhibiting α1,3-GT bacterial gene sequences in their shotgun data.
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Affiliation(s)
- Emmanuel Montassier
- Microbiota Hosts Antibiotics and bacterial Resistances (MiHAR), Université de Nantes, Nantes, France.,Laboratoire EA3826 Thérapeutiques cliniques et expérimentales des infections IRS2 Nantes Biotech, Université de Nantes, Nantes, France.,Department of Emergency Medicine, CHU de Nantes, Nantes, France
| | - Gabriel A Al-Ghalith
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN, United States
| | - Camille Mathé
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU de Nantes, Nantes, France
| | - Quentin Le Bastard
- Microbiota Hosts Antibiotics and bacterial Resistances (MiHAR), Université de Nantes, Nantes, France.,Department of Emergency Medicine, CHU de Nantes, Nantes, France
| | - Venceslas Douillard
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU de Nantes, Nantes, France.,CHU de Nantes, CIC 1413, Pôle Hospitalo-Universitaire 11 Santé Publique, Clinique des données, Nantes, France
| | - Abel Garnier
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU de Nantes, Nantes, France.,CHU de Nantes, CIC 1413, Pôle Hospitalo-Universitaire 11 Santé Publique, Clinique des données, Nantes, France
| | - Rémi Guimon
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU de Nantes, Nantes, France.,CHU de Nantes, CIC 1413, Pôle Hospitalo-Universitaire 11 Santé Publique, Clinique des données, Nantes, France
| | - Bastien Raimondeau
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU de Nantes, Nantes, France
| | - Yann Touchefeu
- Institut des Maladies de l'Appareil Digestif, CHU Nantes, Nantes, France.,INSERM U1235, Nantes, France
| | - Emilie Duchalais
- Institut des Maladies de l'Appareil Digestif, CHU Nantes, Nantes, France.,INSERM U1235, Nantes, France
| | - Nicolas Vince
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU de Nantes, Nantes, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU de Nantes, Nantes, France
| | - Pierre-Antoine Gourraud
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU de Nantes, Nantes, France.,CHU de Nantes, CIC 1413, Pôle Hospitalo-Universitaire 11 Santé Publique, Clinique des données, Nantes, France
| | - David A Laplaud
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France.,Neurology department, CIC Neurology, CHU de Nantes, Nantes, France
| | - Arnaud B Nicot
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU de Nantes, Nantes, France
| | - Jean-Paul Soulillou
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU de Nantes, Nantes, France
| | - Laureline Berthelot
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU de Nantes, Nantes, France
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23
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Daya M, Rafaels N, Brunetti TM, Chavan S, Levin AM, Shetty A, Gignoux CR, Boorgula MP, Wojcik G, Campbell M, Vergara C, Torgerson DG, Ortega VE, Doumatey A, Johnston HR, Acevedo N, Araujo MI, Avila PC, Belbin G, Bleecker E, Bustamante C, Caraballo L, Cruz A, Dunston GM, Eng C, Faruque MU, Ferguson TS, Figueiredo C, Ford JG, Gan W, Gourraud PA, Hansel NN, Hernandez RD, Herrera-Paz EF, Jiménez S, Kenny EE, Knight-Madden J, Kumar R, Lange LA, Lange EM, Lizee A, Maul P, Maul T, Mayorga A, Meyers D, Nicolae DL, O'Connor TD, Oliveira RR, Olopade CO, Olopade O, Qin ZS, Rotimi C, Vince N, Watson H, Wilks RJ, Wilson JG, Salzberg S, Ober C, Burchard EG, Williams LK, Beaty TH, Taub MA, Ruczinski I, Mathias RA, Barnes KC. Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations. Nat Commun 2019; 10:4082. [PMID: 31484942 PMCID: PMC6726619 DOI: 10.1038/s41467-019-12158-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Michelle Daya
- Department of Medicine, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Nicholas Rafaels
- Department of Medicine, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Tonya M Brunetti
- Department of Medicine, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Sameer Chavan
- Department of Medicine, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Aniket Shetty
- Department of Medicine, University of Colorado Denver, Aurora, CO, 80045, USA
| | | | | | - Genevieve Wojcik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Monica Campbell
- Department of Medicine, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Candelaria Vergara
- Department of Medicine, Johns Hopkins University, Baltimore, MD, 21224, USA
| | - Dara G Torgerson
- Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Victor E Ortega
- Center for Human Genomics and Personalized Medicine, Wake Forest School of Medicine, Winston-Salem, 27157, USA
| | - Ayo Doumatey
- Center for Research on Genomics & Global Health, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Nathalie Acevedo
- Institute for Immunological Research, Universidad de Cartagena, Cartagena, 130000, Colombia
| | - Maria Ilma Araujo
- Immunology Service, Universidade Federal da Bahia, Salvador, 401110170, Brazil
| | - Pedro C Avila
- Department of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Gillian Belbin
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eugene Bleecker
- Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, 85724, USA
| | - Carlos Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Luis Caraballo
- Institute for Immunological Research, Universidad de Cartagena, Cartagena, 130000, Colombia
| | - Alvaro Cruz
- Universidade Federal da Bahia, Salvador, 401110170, Brazil
| | - Georgia M Dunston
- Department of Microbiology, Howard University College of Medicine, Washington, DC, 20059, USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Mezbah U Faruque
- National Human Genome Center, Howard University College of Medicine, Washington, DC, 20059, USA
| | - Trevor S Ferguson
- Caribbean Institute for Health Research, The University of the West Indies, Kingston, 00007, Jamaica
| | - Camila Figueiredo
- Departamento de Biorregulacao, Universidade Federal da Bahia, Salvador, 401110170, Brazil
| | - Jean G Ford
- Department of Medicine, Einstein Medical Center, Philadelphia, PA, 19141, USA
| | - Weiniu Gan
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Pierre-Antoine Gourraud
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR, 1064, ATIP-Avenir, Equipe 5, Nantes, France
| | - Nadia N Hansel
- Department of Medicine, Johns Hopkins University, Baltimore, MD, 21224, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Edwin Francisco Herrera-Paz
- Facultad de Medicina, Universidad Católica de Honduras, San Pedro Sula, 21102, Honduras.,Universidad Tecnológica Centroamericana (UNITEC), Facultad de Ciencias Médicas, Tegucigalpa, Honduras
| | - Silvia Jiménez
- Institute for Immunological Research, Universidad de Cartagena, Cartagena, 130000, Colombia
| | - Eimear E Kenny
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jennifer Knight-Madden
- Caribbean Institute for Health Research, The University of the West Indies, Kingston, 00007, Jamaica
| | - Rajesh Kumar
- Department of Pediatrics, Northwestern University, Chicago, IL, 60611, USA
| | - Leslie A Lange
- Department of Medicine, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Ethan M Lange
- Department of Medicine, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Antoine Lizee
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR, 1064, ATIP-Avenir, Equipe 5, Nantes, France
| | - Pissamai Maul
- Genetics and Epidemiology of Asthma in Barbados, The University of the West Indies, Chronic Disease Research Centre, Jemmots Lane, St. Michael, BB11115, Barbados
| | - Trevor Maul
- Genetics and Epidemiology of Asthma in Barbados, The University of the West Indies, Chronic Disease Research Centre, Jemmots Lane, St. Michael, BB11115, Barbados
| | - Alvaro Mayorga
- Centro de Neumologia y Alergias, San Pedro Sula, 21102, Honduras
| | - Deborah Meyers
- Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, 85724, USA
| | - Dan L Nicolae
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Ricardo Riccio Oliveira
- Laboratório de Patologia Experimental, Centro de Pesquisas Gonçalo Moniz, Salvador, 40296-710, Brazil
| | - Christopher O Olopade
- Department of Medicine and Center for Global Health, University of Chicago, Chicago, IL, 60637, USA
| | | | - Zhaohui S Qin
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, 30322, USA
| | - Charles Rotimi
- Center for Research on Genomics & Global Health, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nicolas Vince
- Université de Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR, 1064, ATIP-Avenir, Equipe 5, Nantes, France
| | - Harold Watson
- Faculty of Medical Sciences, The University of the West Indies, Queen Elizabeth Hospital, Bridgetown, St. Michael, BB11000, Barbados
| | - Rainford J Wilks
- Caribbean Institute for Health Research, The University of the West Indies, Kingston, 00007, Jamaica
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Steven Salzberg
- Departments of Biomedical Engineering and Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Esteban G Burchard
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Terri H Beaty
- Department of Epidemiology, Bloomberg School of Public Health, JHU, Baltimore, MD, 21205, USA
| | - Margaret A Taub
- Department of Biostatistics, Bloomberg School of Public Health, JHU, Baltimore, MD, 21205, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, JHU, Baltimore, MD, 21205, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University, Baltimore, MD, 21224, USA
| | - Kathleen C Barnes
- Department of Medicine, University of Colorado Denver, Aurora, CO, 80045, USA.
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24
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Renand A, Habes S, Mosnier JF, Aublé H, Judor JP, Vince N, Hulin P, Nedellec S, Métairie S, Archambeaud I, Brouard S, Gournay J, Conchon S. Immune Alterations in Patients With Type 1 Autoimmune Hepatitis Persist Upon Standard Immunosuppressive Treatment. Hepatol Commun 2018; 2:968-981. [PMID: 30094407 PMCID: PMC6078209 DOI: 10.1002/hep4.1202] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/08/2018] [Indexed: 12/11/2022] Open
Abstract
Autoimmune hepatitis (AIH) is a rare disease characterized by an immune attack of the liver. This study consists of a comprehensive analysis of immune alterations related to AIH at diagnosis, and during remission phase under treatment. A total of 37 major lymphocyte populations were analyzed from the peripheral blood of new‐onset AIH patients (AIHn; n = 14), AIH patients with controlled disease (n = 11), and healthy subjects (n = 14). Liver biopsy analyses were performed to complete the blood phenotypic analysis. Four blood lymphocyte populations were significantly altered in AIHn patients at diagnosis compared with healthy subjects. Levels of mucosal‐associated invariant T cells (MAIT), Type 1/Type 17 helper (Th1/ Th17) cells, clusters of differentiation (CD4) T cells, and invariant natural killer T cells were decreased, whereas MAIT granzyme B+ (GrB) cells were increased. A trend toward an increase of CD8+CD161+GrB+ cells was also observed. These alterations were not restored with standard immunosuppressive treatments. In the liver of AIHn patients, CD4, forkhead box P3 (Foxp3), and MAIT cell markers were enriched in the portal tract, and CD8, CD161, and GrB markers were enriched in the hepatic lobule. During remission, the hepatic lobule was clear of infiltrating T cells, but residual CD4 and MAIT cells were found in the portal tract, where Foxp3 was decreased, as previously described. In vitro, MAIT cells were functionally altered in AIH patients. Ex vivo MAIT cell activity (GrB) was linked to severe fibrosis. Conclusion: Our work proposes a global view of the lymphocyte alterations from diagnosis to remission phase in AIH patients. The absence of blood immune homeostasis restoration and the persistence of a CD4 infiltrate in the liver under standard immunosuppression could form the basis of the high risk of relapse observed in AIH. (Hepatology Communications 2018; 00:000‐000)
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Affiliation(s)
- Amédée Renand
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM Université de Nantes Nantes France.,Institut de Transplantation Urologie Néphrologie CHU de Nantes Nantes France
| | - Sarah Habes
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM Université de Nantes Nantes France.,Institut de Transplantation Urologie Néphrologie CHU de Nantes Nantes France.,Service Hépato-Gastro-entérologie et Assistance Nutritionnelle CHU Nantes Nantes France
| | - Jean-François Mosnier
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM Université de Nantes Nantes France.,Service Anatomie et Cytologie Pathologiques CHU Nantes Nantes France
| | - Hélène Aublé
- Centre d'Investigation Clinique gastro-nutrition CHU Nantes Nantes France
| | - Jean-Paul Judor
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM Université de Nantes Nantes France.,Institut de Transplantation Urologie Néphrologie CHU de Nantes Nantes France
| | - Nicolas Vince
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM Université de Nantes Nantes France.,Institut de Transplantation Urologie Néphrologie CHU de Nantes Nantes France
| | - Philippe Hulin
- MicroPICell Imaging Core Facility, SFR Santé F. Bonamy UMS016, INSERM, CNRS Université de Nantes Nantes France
| | - Steven Nedellec
- MicroPICell Imaging Core Facility, SFR Santé F. Bonamy UMS016, INSERM, CNRS Université de Nantes Nantes France
| | - Sylvie Métairie
- Service Chirurgie Digestive et Endocrinienne CHU Nantes Nantes France
| | - Isabelle Archambeaud
- Service Hépato-Gastro-entérologie et Assistance Nutritionnelle CHU Nantes Nantes France.,Institut des Maladies de l'Appareil Digestif, IMAD CHU Nantes Nantes France
| | - Sophie Brouard
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM Université de Nantes Nantes France.,Institut de Transplantation Urologie Néphrologie CHU de Nantes Nantes France
| | - Jérôme Gournay
- Service Hépato-Gastro-entérologie et Assistance Nutritionnelle CHU Nantes Nantes France.,Institut des Maladies de l'Appareil Digestif, IMAD CHU Nantes Nantes France
| | - Sophie Conchon
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM Université de Nantes Nantes France.,Institut de Transplantation Urologie Néphrologie CHU de Nantes Nantes France
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25
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Vince N, Mouillot G, Malphettes M, Limou S, Boutboul D, Guignet A, Bertrand V, Pellet P, Gourraud PA, Debré P, Oksenhendler E, Théodorou I, Fieschi C. Genetic screening of male patients with primary hypogammaglobulinemia can guide diagnosis and clinical management. Hum Immunol 2018; 79:571-577. [PMID: 29709555 DOI: 10.1016/j.humimm.2018.04.014] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 10/17/2022]
Abstract
The precise diagnosis of an immunodeficiency is sometimes difficult to assess, especially due to the large spectrum of phenotypic variation reported among patients. Common variable immunodeficiency disorders (CVID) do not have, for a large part, an identified genetic cause. The identification of a causal genetic mutation is important to confirm, or in some cases correct, the diagnosis. We screened >150 male patients with hypogammaglobulinemia for mutations in three genes involved in pediatric X-linked primary immunoglobulin deficiency: CD40LG, SH2D1A and BTK. The SH2D1A screening allowed to reclassify two individuals with an initial CVID presentation as XLP after mutations identification. All these mutations were associated with a lack of protein expression. In addition, 4 patients with a primary diagnosis of CVID and one with a primary IgG subclass deficiency were requalified as XLA after identifying BTK mutations. Interestingly, two out of these 5 patients carried a damaging coding BTK mutation associated with a lower, but detectable, BTK expression in monocytes, suggesting that a dysfunctional protein explains the disease phenotype in these patients. In conclusion, our results advocate to include SH2D1A and BTK in newly developed targeted NGS genetic testing, to contribute to providing the most appropriate medical treatment and genetic counselling.
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Affiliation(s)
- Nicolas Vince
- EA3963, Université Paris 7 Denis Diderot, Centre Hayem, Hôpital Saint-Louis, 1 Avenue Claude Vellefaux, 75010 Paris, France; Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France; Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.
| | - Gaël Mouillot
- Laboratoire Central d'Immunologie Cellulaire et Tissulaire, Hôpital Pitié Salpêtrière et INSERM UMR-S945, Bâtiment CERVI, Paris, France
| | - Marion Malphettes
- EA3963, Université Paris 7 Denis Diderot, Centre Hayem, Hôpital Saint-Louis, 1 Avenue Claude Vellefaux, 75010 Paris, France; Département d'Immunologie Clinique, Hôpital Saint-Louis, AP-HP, 1 Avenue Claude Vellefaux, 75010 Paris, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France; Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France; Ecole Centrale de Nantes, Nantes, France
| | - David Boutboul
- EA3963, Université Paris 7 Denis Diderot, Centre Hayem, Hôpital Saint-Louis, 1 Avenue Claude Vellefaux, 75010 Paris, France
| | - Angélique Guignet
- EA3963, Université Paris 7 Denis Diderot, Centre Hayem, Hôpital Saint-Louis, 1 Avenue Claude Vellefaux, 75010 Paris, France
| | - Véronique Bertrand
- Laboratoire Central d'Immunologie Cellulaire et Tissulaire, Hôpital Pitié Salpêtrière et INSERM UMR-S945, Bâtiment CERVI, Paris, France
| | - Philippe Pellet
- Laboratoire Central d'Immunologie Cellulaire et Tissulaire, Hôpital Pitié Salpêtrière et INSERM UMR-S945, Bâtiment CERVI, Paris, France
| | - Pierre-Antoine Gourraud
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France; Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
| | - Patrice Debré
- Laboratoire Central d'Immunologie Cellulaire et Tissulaire, Hôpital Pitié Salpêtrière et INSERM UMR-S945, Bâtiment CERVI, Paris, France
| | - Eric Oksenhendler
- Département d'Immunologie Clinique, Hôpital Saint-Louis, AP-HP, 1 Avenue Claude Vellefaux, 75010 Paris, France
| | - Ioannis Théodorou
- Laboratoire Central d'Immunologie Cellulaire et Tissulaire, Hôpital Pitié Salpêtrière et INSERM UMR-S945, Bâtiment CERVI, Paris, France
| | - Claire Fieschi
- EA3963, Université Paris 7 Denis Diderot, Centre Hayem, Hôpital Saint-Louis, 1 Avenue Claude Vellefaux, 75010 Paris, France; Département d'Immunologie Clinique, Hôpital Saint-Louis, AP-HP, 1 Avenue Claude Vellefaux, 75010 Paris, France
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26
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Martin MP, Naranbhai V, Shea PR, Qi Y, Ramsuran V, Vince N, Gao X, Thomas R, Brumme ZL, Carlson JM, Wolinsky SM, Goedert JJ, Walker BD, Segal FP, Deeks SG, Haas DW, Migueles SA, Connors M, Michael N, Fellay J, Gostick E, Llewellyn-Lacey S, Price DA, Lafont BA, Pymm P, Saunders PM, Widjaja J, Wong SC, Vivian JP, Rossjohn J, Brooks AG, Carrington M. Killer cell immunoglobulin-like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1. J Clin Invest 2018; 128:1903-1912. [PMID: 29461980 DOI: 10.1172/jci98463] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [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: 11/06/2017] [Accepted: 02/13/2018] [Indexed: 01/11/2023] Open
Abstract
HLA-B*57 control of HIV involves enhanced CD8+ T cell responses against infected cells, but extensive heterogeneity exists in the level of HIV control among B*57+ individuals. Using whole-genome sequencing of untreated B*57+ HIV-1-infected controllers and noncontrollers, we identified a single variant (rs643347A/G) encoding an isoleucine-to-valine substitution at position 47 (I47V) of the inhibitory killer cell immunoglobulin-like receptor KIR3DL1 as the only significant modifier of B*57 protection. The association was replicated in an independent cohort and across multiple outcomes. The modifying effect of I47V was confined to B*57:01 and was not observed for the closely related B*57:03. Positions 2, 47, and 54 tracked one another nearly perfectly, and 2 KIR3DL1 allotypes differing only at these 3 positions showed significant differences in binding B*57:01 tetramers, whereas the protective allotype showed lower binding. Thus, variation in an immune NK cell receptor that binds B*57:01 modifies its protection. These data highlight the exquisite specificity of KIR-HLA interactions in human health and disease.
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Affiliation(s)
- Maureen P Martin
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Vivek Naranbhai
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Patrick R Shea
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Ying Qi
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Veron Ramsuran
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.,KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nicolas Vince
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.,ATIP-Avenir, Centre de Recherche en Transplantation et Immunologie, UMR 1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), Centre Hospitalier Universitaire (CHU) de Nantes, Nantes, France
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | | | - Steven M Wolinsky
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - James J Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| | | | - Steven G Deeks
- San Francisco General Hospital Medical Center, San Francisco, California, USA
| | - David W Haas
- Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Stephen A Migueles
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Nelson Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Jacques Fellay
- School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland
| | - Emma Gostick
- Cardiff University School of Medicine, Heath Park, University Hospital of Wales, Cardiff, United Kingdom.,Non-Human Primate Immunogenetics and Cellular Immunology Unit, NIAID, NIH, Bethesda, Maryland, USA
| | - Sian Llewellyn-Lacey
- Cardiff University School of Medicine, Heath Park, University Hospital of Wales, Cardiff, United Kingdom.,Non-Human Primate Immunogenetics and Cellular Immunology Unit, NIAID, NIH, Bethesda, Maryland, USA
| | - David A Price
- Cardiff University School of Medicine, Heath Park, University Hospital of Wales, Cardiff, United Kingdom.,Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Bernard A Lafont
- Viral Immunology Section, Office of the Scientific Director, NIAID, NIH, Bethesda, Maryland, USA
| | - Phillip Pymm
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Philippa M Saunders
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Jacqueline Widjaja
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Shu Cheng Wong
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Julian P Vivian
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- Cardiff University School of Medicine, Heath Park, University Hospital of Wales, Cardiff, United Kingdom.,Non-Human Primate Immunogenetics and Cellular Immunology Unit, NIAID, NIH, Bethesda, Maryland, USA.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Andrew G Brooks
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.,Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
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27
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Goodin DS, Khankhanian P, Gourraud PA, Vince N. Highly conserved extended haplotypes of the major histocompatibility complex and their relationship to multiple sclerosis susceptibility. PLoS One 2018; 13:e0190043. [PMID: 29438392 PMCID: PMC5810982 DOI: 10.1371/journal.pone.0190043] [Citation(s) in RCA: 17] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 12/07/2017] [Indexed: 12/03/2022] Open
Abstract
Objective To determine the relationship between highly-conserved extended-haplotypes (CEHs) in the major histocompatibility complex (MHC) and MS-susceptibility. Background Among the ~200 MS-susceptibility regions, which are known from genome-wide analyses of single nucleotide polymorphisms (SNPs), the MHC accounts for roughly a third of the currently explained variance and the strongest MS-associations are for certain Class II alleles (e.g., HLA-DRB1*15:01; HLA-DRB1*03:01; and HLA-DRB1*13:03), which frequently reside on CEHs within the MHC. Design/Methods Autosomal SNPs (441,547) from 11,376 MS cases and 18,872 controls in the WTCCC dataset were phased. The most significant MS associated SNP haplotype was composed of 11 SNPs in the MHC Class II region surrounding the HLA-DRB1 gene. We also phased alleles at the HLA-A, HLA-C, HLA-B, HLA-DRB1, and HLA-DQB1 loci. This data was used to probe the relationship between CEHs and MS susceptibility. Results We phased a total of 59,884 extended haplotypes (HLA-A, HLA-C, HLA-B, HLA-DRB1, HLA-DQB1 and SNP haplotypes) from 29,942 individuals. Of these, 10,078 unique extended haplotypes were identified. The 10 most common CEHs accounted for 22% (13,302) of the total. By contrast, the 8,446 least common extended haplotypes also accounted for approximately 20% (12,298) of the total. This extreme frequency-disparity among extended haplotypes necessarily complicates interpretation of reported disease-associations with specific HLA alleles. In particular, the HLA motif HLA-DRB1*15:01~HLA-DQB1*06:02 is strongly associated with MS risk. Nevertheless, although this motif is almost always found on the a1 SNP haplotype, it can rarely be found on others (e.g., a27 and a36), and, in these cases, it seems to have no apparent disease-association (OR = 0.7; CI = 0.3–1.3 and OR = 0.7; CI = 0.2–2.2, respectively). Furthermore, single copy carriers of the a1 SNP-haplotype without this HLA motif still have an increased disease risk (OR = 2.2; CI = 1.2–3.8). In addition, even among the set of CEHs, which carry the Class II motif of HLA-DRB1*15:01~HLA-DQB1*06:02~a1, different CEHs have differing strengths in their MS-associations. Conclusions The MHC in diverse human populations consists, primarily, of a very small collection of very highly-selected CEHs. Our findings suggest that the MS-association with the HLA-DRB1*15:01~HLA-DQB1*06:02 haplotype may be due primarily to the combined attributes of the CEHs on which this particular HLA-motif often resides.
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Affiliation(s)
- Douglas S. Goodin
- Department of Neurology, University of California, San Francisco, CA, United States of America
- * E-mail:
| | - Pouya Khankhanian
- Center for Neuro-engineering and Therapeutics, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Pierre-Antoine Gourraud
- Department of Neurology, University of California, San Francisco, CA, United States of America
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France
- Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
| | - Nicolas Vince
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France
- Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
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28
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Abstract
Over the past decade, genetic association studies have uncovered numerous determinants of kidney function in the general, diabetic, hypertensive, CKD, ESRD, and GN-based study populations (e.g., IgA nephropathy, membranous nephropathy, FSGS). These studies have led to numerous novel and unanticipated findings, which are helping improve our understanding of factors and pathways affecting both normal and pathologic kidney function. In this review, we report on major discoveries and advances resulting from this rapidly progressing research domain. We also predict some of the next steps the nephrology community should embrace to accelerate the identification of genetic and molecular processes leading to kidney dysfunction, pathophysiologically based disease subgroups, and specific therapeutic targets, as we attempt to transition toward a more precision-based medicine approach.
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Affiliation(s)
- Sophie Limou
- Centre de Recherche en Transplantation et Immunologie Unité Mixte de Recherche 1064, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Nantes, Nantes, France
- Institut de Transplantation Urologie et Néphrologie, Centre Hospitalier Universitaire Nantes, Nantes, France
- Ecole Centrale de Nantes, Nantes, France
- Basic Science Program, Basic Research Laboratory, National Cancer Institute/National Institutes of Health, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, Maryland
| | - Nicolas Vince
- Centre de Recherche en Transplantation et Immunologie Unité Mixte de Recherche 1064, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Nantes, Nantes, France
- Institut de Transplantation Urologie et Néphrologie, Centre Hospitalier Universitaire Nantes, Nantes, France
| | - Afshin Parsa
- Division of Nephrology, University of Maryland School of Medicine, Baltimore, Maryland; and
- Department of Medicine, Baltimore VA Medical Center, Baltimore, Maryland
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Herve C, Vince N, Brouard S, Giral M, Blancho G, Gourraud PA. P218 The kidney transplantation application (KITAPP): A visualization and contextualization tool in a kidney graft patients’ cohort. Hum Immunol 2017. [DOI: 10.1016/j.humimm.2017.06.278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Vince N, Walencik A, Geffard E, Limou S, Gautier AC, Gourraud PA. P103 SNP-HLA reference consortium: HLA and SNP data sharing for promoting HLA centric analyses in genomics. Hum Immunol 2017. [DOI: 10.1016/j.humimm.2017.06.163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Vince N, Daya M, Hollenbach J, Lizee A, Barnes K, Torgerson D, Gourraud PA. P039 HLA component of the consortium on asthma among African-ancestry populations in the Americas (CAAPA). Hum Immunol 2017. [DOI: 10.1016/j.humimm.2017.06.099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Vince N, Li H, Ramsuran V, Naranbhai V, Duh FM, Fairfax BP, Saleh B, Knight JC, Anderson SK, Carrington M. HLA-C Level Is Regulated by a Polymorphic Oct1 Binding Site in the HLA-C Promoter Region. Am J Hum Genet 2016; 99:1353-1358. [PMID: 27817866 DOI: 10.1016/j.ajhg.2016.09.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [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] [Received: 07/15/2016] [Accepted: 09/29/2016] [Indexed: 01/08/2023] Open
Abstract
Differential HLA-C levels influence several human diseases, but the mechanisms responsible are incompletely characterized. Using a validated prediction algorithm, we imputed HLA-C cell surface levels in 228 individuals from the 1000 Genomes dataset. We tested 68,726 SNPs within the MHC for association with HLA-C level. The HLA-C promoter region variant, rs2395471, 800 bp upstream of the transcription start site, gave the most significant association with HLA-C levels (p = 4.2 × 10-66). This imputed expression quantitative trait locus, termed impeQTL, was also shown to associate with HLA-C expression in a genome-wide association study of 273 donors in which HLA-C mRNA expression levels were determined by quantitative PCR (qPCR) (p = 1.8 × 10-20) and in two cohorts where HLA-C cell surface levels were determined directly by flow cytometry (n = 369 combined, p < 10-15). rs2395471 is located in an Oct1 transcription factor consensus binding site motif where the A allele is predicted to have higher affinity for Oct1 than the G allele. Mobility shift electrophoresis demonstrated that Oct1 binds to both alleles in vitro, but decreased HLA-C promoter activity was observed in a luciferase reporter assay for rs2395471_G relative to rs2395471_A on a fixed promoter background. The rs2395471 variant accounts for up to 36% of the explained variation of HLA-C level. These data strengthen our understanding of HLA-C transcriptional regulation and provide a basis for understanding the potential consequences of manipulating HLA-C levels therapeutically.
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Affiliation(s)
- Nicolas Vince
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Hongchuan Li
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Veron Ramsuran
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Vivek Naranbhai
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Center for the AIDS Programme of Research in South Africa, University of KwaZuluNatal, Durban 4091, South Africa
| | - Fuh-Mei Duh
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Benjamin P Fairfax
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Bahara Saleh
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Stephen K Anderson
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
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Le Gall C, Laurent J, Vince N, Lizee A, Agrawal A, Walencik A, Rettman P, Gagne K, Retiere C, Hollenbach J, Cesbron A, Limou S, Gourraud PA. Multidimensional reduction of multicentric cohort heterogeneity: An alternative method to increase statistical power and robustness. Hum Immunol 2016; 77:1024-1029. [PMID: 27262455 DOI: 10.1016/j.humimm.2016.05.013] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/13/2016] [Accepted: 05/18/2016] [Indexed: 11/25/2022]
Abstract
Modern clinical research takes advantage of multicentric cohorts to increase sample size and gain in statistical power. However, combining individuals from different recruitment centers provides heterogeneity in the dataset that needs to be accounted for to obtain robust results. Sophisticated statistical multivariate models adjusting for center effect can be implemented, but they can become unstable and can be complex to interpret with the increasing number of covariates to consider. Here, we present a multidimensional reduction technique to identify heterogeneity in a French multicentric cohort of hematopoietic stem cell transplantations and characterize a homogeneous subgroup prior to performing simple statistical univariate analyses. The exclusion of outliers allowed the identification of two genetic factors associated with post-transplantation overall survival. We therefore provide proof-of-concept that a sample size reduction method can efficiently account for heterogeneity and center effect in multicentric cohorts while increasing statistical power and robustness for discovery of new association signals.
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Affiliation(s)
| | | | - Nicolas Vince
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Antoine Lizee
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Alisha Agrawal
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Alexandre Walencik
- Etablissement français du Sang, Nantes, France; Inserm Unit 1064, Hospital and University of Nantes, Nantes, France
| | | | - Katia Gagne
- Etablissement français du Sang, Nantes, France
| | | | - Jill Hollenbach
- Department of Neurology, University of California, San Francisco, CA, USA
| | | | - Sophie Limou
- Molecular Genetic Epidemiology Section, Basic Research Laboratory, Basic Science Program, NCI/NIH, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD, USA
| | - Pierre-Antoine Gourraud
- Methodomics, Toulouse, France; Department of Neurology, University of California, San Francisco, CA, USA; Etablissement français du Sang, Nantes, France.
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Ebbo M, Gérard L, Carpentier S, Vély F, Cypowyj S, Farnarier C, Vince N, Malphettes M, Fieschi C, Oksenhendler E, Schleinitz N, Vivier E. Low Circulating Natural Killer Cell Counts are Associated With Severe Disease in Patients With Common Variable Immunodeficiency. EBioMedicine 2016; 6:222-230. [PMID: 27211564 PMCID: PMC4856746 DOI: 10.1016/j.ebiom.2016.02.025] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [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: 12/22/2015] [Revised: 02/12/2016] [Accepted: 02/15/2016] [Indexed: 02/08/2023] Open
Abstract
Natural Killer (NK) cells have been shown to exert antiviral and antitumoural activities. Nevertheless most available data are derived from mouse models and functions of these cells in human remain unclear. To evaluate the impact of low circulating NK cell counts and to provide some clues to the role of NK cells in natural conditions, we studied a large cohort of patients with common variable immunodeficiency (CVID) included in a multicenter cohort of patients with primary hypogammaglobulinaemia. Patients were classified into three groups on the basis of their NK cell counts: severe and mild NK cell lymphopenia (< 50 and 50–99 × 106/L respectively), and normal NK cell counts (> 100 × 106/L). Clinical events were analyzed and compared between these three groups of patients. During study period, 457 CVID patients were included: 99 (21.7%) with severe NK cell lymphopenia, 118 (25.8%) with mild NK cell lymphopenia and 240 (52.5%) with normal NK cell counts. Non-infectious complications (57% vs. 36% and 35%), and, particularly, granulomatous complications (25.3% vs. 13.6% and 8.8%), were more frequent in patients with severe NK cell lymphopenia than in other groups. Invasive infections (68.7% vs. 60.2% and 48.8%), including bacteraemia (22.2% vs. 5.9% and 8.3%) and infectious pneumonia (63.6% vs. 59.3% and 44.2%), were also more frequent in this population. However, no difference was observed for viral infections and neoplasms. Low circulating NK cell counts are associated with more severe phenotypes of CVID, which may indicate a protective role of these immune cells against severe bacterial infections and other complications and non-redundant immune functions when the adaptive immune response is not optimal. CVID patients with low NK cell counts present increased rates of severe bacterial infections and granuloma. Mortality appears to be especially high in CVID patients with both severe CD4+ T cell and NK cell deficiency. NK cells could have non-redundant immune functions in patients with non-optimal adaptive immune response.
Forty years after their discovery, the functions of Natural Killer (NK) cells in natura remain poorly understood. Association studies linking clinical symptoms and defects in NK cell numbers or function are exceptional and poorly described in large cohorts of human patients. Our study analyzes the correlation between NK cell lymphopenia and clinical events in a large cohort of immunocompromised patients. We report the unexpected findings that severe invasive bacterial infections, especially bacteremia episodes, and non-infectious complications, especially granulomatous complications, are more frequent in common variable immunodeficiency patients with severe NK cell deficiency. These findings in natura highlights that NK cells may play a pivotal role in immunity in immunocompromised individuals, when the adaptive immune system is not optimal.
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Affiliation(s)
- Mikael Ebbo
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University UM2, 13288 Marseille, France; Inserm U1104, 13288 Marseille, France; CNRS UMR7280, 13288 Marseille, France; Médecine Interne, Hôpital de la Timone, Assistance Publique - Hôpitaux de Marseille, Aix-Marseille University, 13005 Marseille, France
| | - Laurence Gérard
- Immunopathologie Clinique, Hôpital Saint-Louis, Assistance Publique - Hôpitaux de Paris, 75010 Paris, France; EA3518, University Paris 7 Denis Diderot, Paris, France
| | - Sabrina Carpentier
- MI-mAbs Consortium (Aix Marseille University), CIML, 13288 Marseille, France
| | - Frédéric Vély
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University UM2, 13288 Marseille, France; Inserm U1104, 13288 Marseille, France; CNRS UMR7280, 13288 Marseille, France; Immunologie, Hôpital de la Conception, Assistance Publique -Hôpitaux de Marseille, 13385 Marseille, France
| | - Sophie Cypowyj
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University UM2, 13288 Marseille, France; Inserm U1104, 13288 Marseille, France; CNRS UMR7280, 13288 Marseille, France
| | - Catherine Farnarier
- Immunologie, Hôpital de la Conception, Assistance Publique -Hôpitaux de Marseille, 13385 Marseille, France
| | - Nicolas Vince
- Inserm U1126, University Paris 7 Denis Diderot, Paris, France
| | - Marion Malphettes
- Immunopathologie Clinique, Hôpital Saint-Louis, Assistance Publique - Hôpitaux de Paris, 75010 Paris, France; Inserm U1126, University Paris 7 Denis Diderot, Paris, France
| | - Claire Fieschi
- Immunopathologie Clinique, Hôpital Saint-Louis, Assistance Publique - Hôpitaux de Paris, 75010 Paris, France; Inserm U1126, University Paris 7 Denis Diderot, Paris, France
| | - Eric Oksenhendler
- Immunopathologie Clinique, Hôpital Saint-Louis, Assistance Publique - Hôpitaux de Paris, 75010 Paris, France
| | - Nicolas Schleinitz
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University UM2, 13288 Marseille, France; Inserm U1104, 13288 Marseille, France; CNRS UMR7280, 13288 Marseille, France; Médecine Interne, Hôpital de la Timone, Assistance Publique - Hôpitaux de Marseille, Aix-Marseille University, 13005 Marseille, France
| | - Eric Vivier
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University UM2, 13288 Marseille, France; Inserm U1104, 13288 Marseille, France; CNRS UMR7280, 13288 Marseille, France; MI-mAbs Consortium (Aix Marseille University), CIML, 13288 Marseille, France.
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Boutboul D, Vince N, Mahevas M, Bories JC, Fieschi C. TNFA, ANXA11 and BTNL2 Polymorphisms in CVID Patients with Granulomatous Disease. J Clin Immunol 2016; 36:110-2. [PMID: 26783045 DOI: 10.1007/s10875-016-0234-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 01/07/2016] [Indexed: 10/22/2022]
Affiliation(s)
- David Boutboul
- INSERM U1126, Institut Universitaire d'Hématologie, Centre Hayem, Hôpital Saint Louis, Université Paris Diderot, 1 avenue Claude Vellefaux, Paris, France.,Clinical Immunology Department, Hôpital Saint Louis, Assistance Publique Hôpitaux de Paris, Université Paris Diderot, 1 avenue Claude Vellefaux, Paris, France
| | - Nicolas Vince
- INSERM U1126, Institut Universitaire d'Hématologie, Centre Hayem, Hôpital Saint Louis, Université Paris Diderot, 1 avenue Claude Vellefaux, Paris, France
| | - Matthieu Mahevas
- Service de Médecine Interne, Hôpital Henri Mondor, Assistance Publique Hôpitaux de Paris, Université Paris Est Créteil, Créteil, France
| | - Jean-Christophe Bories
- INSERM U1126, Institut Universitaire d'Hématologie, Centre Hayem, Hôpital Saint Louis, Université Paris Diderot, 1 avenue Claude Vellefaux, Paris, France
| | - Claire Fieschi
- INSERM U1126, Institut Universitaire d'Hématologie, Centre Hayem, Hôpital Saint Louis, Université Paris Diderot, 1 avenue Claude Vellefaux, Paris, France. .,Clinical Immunology Department, Hôpital Saint Louis, Assistance Publique Hôpitaux de Paris, Université Paris Diderot, 1 avenue Claude Vellefaux, Paris, France.
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Ericsen AJ, Starrett GJ, Greene JM, Lauck M, Raveendran M, Deiros DR, Mohns MS, Vince N, Cain BT, Pham NH, Weinfurter JT, Bailey AL, Budde ML, Wiseman RW, Gibbs R, Muzny D, Friedrich TC, Rogers J, O'Connor DH. Whole genome sequencing of SIV-infected macaques identifies candidate loci that may contribute to host control of virus replication. Genome Biol 2014; 15:478. [PMID: 25418588 PMCID: PMC4223156 DOI: 10.1186/s13059-014-0478-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 09/17/2014] [Indexed: 12/22/2022] Open
Abstract
Background A small percentage of human immunodeficiency virus (HIV)-infected people and simian immunodeficiency virus (SIV)-infected macaques control virus replication without antiretroviral treatment. The major determinant of this control is host expression of certain major histocompatibility complex alleles. However, this association is incompletely penetrant, suggesting that additional loci modify the major histocompatibility complex’s protective effect. Here, to identify candidate control-modifying loci, we sequence the genomes of 12 SIV-infected Mauritian cynomolgus macaques that experienced divergent viral load set points despite sharing the protective M1 major histocompatibility complex haplotype. Results Our genome-wide analysis of haplotype-level variation identifies seven candidate control-modifying loci on chromosomes 2, 3, 7, 8, 9, 10, and 14. The highest variant density marks the candidate on chromosome 7, which is the only control-modifying locus to comprise genes with known immunological function. Upon closer inspection, we found an allele for one of these genes, granzyme B, to be enriched in M1(+) controllers. Given its established role as a cytotoxic effector molecule that participates in CD8-mediated killing of virus-infected cells, we test the role of variation within gzmb in modifying SIV control by prospectively challenging M1(+) granzyme B-defined macaques. Conclusions Our study establishes a framework for using whole genome sequencing to identify haplotypes that may contribute to complex clinical phenotypes. Further investigation into the immunogenetics underlying spontaneous HIV control may contribute to the rational design of a vaccine that prevents acquired immune deficiency syndrome. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0478-z) contains supplementary material, which is available to authorized users.
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Vince N, Bashirova AA, Lied A, Gao X, Dorrell L, McLaren PJ, Fellay J, Carrington M. HLA class I and KIR genes do not protect against HIV type 1 infection in highly exposed uninfected individuals with hemophilia A. J Infect Dis 2014; 210:1047-51. [PMID: 24719475 DOI: 10.1093/infdis/jiu214] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A recent genome-wide association study (GWAS) involving patients with hemophilia A who were exposed to but uninfected with human immunodeficiency virus type 1 (HIV-1) did not reveal genetic variants associated with resistance to HIV-1 infection, beyond homozygosity for CCR5-Δ32. Since variation in HLA class I and KIR genes is not well interrogated by standard GWAS techniques, we tested whether these 2 loci were involved in protection from HIV-1 infection in the same hemophilia cohort, using controls from the general population. Our data indicate that HLA class I alleles, presence or absence of KIR genes, and functionally relevant combinations of the HLA/KIR genotypes are not involved in resistance to parenterally transmitted HIV-1 infection.
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Affiliation(s)
- Nicolas Vince
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Maryland Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts
| | - Arman A Bashirova
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Maryland Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts
| | - Alexandra Lied
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Maryland
| | - Lucy Dorrell
- Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Paul J McLaren
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Maryland Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts
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Bashirova AA, Apps R, Vince N, Mochalova Y, Yu XG, Carrington M. Diversity of the human LILRB3/A6 locus encoding a myeloid inhibitory and activating receptor pair. Immunogenetics 2013; 66:1-8. [PMID: 24096970 DOI: 10.1007/s00251-013-0730-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 08/10/2013] [Indexed: 12/24/2022]
Abstract
Leukocyte immunoglobulin-like receptor (LILR)B3 and LILRA6 represent a pair of inhibitory/activating receptors with identical extracellular domains and unknown ligands. LILRB3 can mediate inhibitory signaling via immunoreceptor tyrosine-based inhibition motifs in its cytoplasmic tail whereas LILRA6 can signal through association with an activating adaptor molecule, FcRγ, which bears a cytoplasmic tail with an immunoreceptor tyrosine-based activation motif. The receptors are encoded by two highly polymorphic neighboring genes within the leukocyte receptor complex on human chromosome 19. Here, we report that the two genes display similar levels of single nucleotide polymorphisms with the majority of polymorphic sites being identical. In addition, the LILRA6 gene exhibits copy number variation (CNV) whereas LILRB3 does not. A screen of healthy Caucasians indicated that 32 % of the subjects possessed more than two copies of LILRA6, whereas 4 % have only one copy of the gene per diploid genome. Analysis of mRNA expression in the major fractions of PBMCs showed that LILRA6 is primarily expressed in monocytes, similarly to LILRB3, and its expression level correlates with copy number of the gene. We suggest that the LILRA6 CNV may influence the level of the activating receptor on the cell surface, potentially affecting signaling upon LILRB3/A6 ligation.
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Affiliation(s)
- Arman A Bashirova
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
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Bashirova A, Apps R, Vince N, Yu X, Carringotn M. Genetic polymorphism in the human LILRB3/LILRA6 locus (118.13). The Journal of Immunology 2012. [DOI: 10.4049/jimmunol.188.supp.118.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
LILRB3 is an orphan receptor expressed on the surface of myeloid cells. It is structurally distinct from HLA class I binding LILRs and extremely polymorphic in the extracellular domain. LILRB3 can mediate negative signaling through its ITIM-bearing cytoplasmic tail. LILRA6 is identical to LILRB3 in the extracellular part but is potentially an activating receptor. The molecules are encoded by two neighboring genes on human chromosome 19. We have analyzed polymorphism in the LILRB3/A6 locus and found that LILRA6 exhibits a level of polymorphism comparable to LILRB3 with similar polymorphic sites. Moreover, we identified copy number variation (CNV) in the LILRA6 locus with 33% of healthy individuals possessing duplication of LILRA6 and 4% bearing deletion of the gene. Duplications and deletions of LILRA6 and a constant number of LILRB3 seem to be a consequence of unequal crossing-over between the two genes resulting in exchange of the extracellular domains between the receptors. Such exchange explains the maintenance of structural similarity of the two receptors and identity of polymorphic sites. Analysis of mRNA expression in the major PBMC fractions shows that LILRA6 is primarily expressed on monocytes, similarly to LILRB3, and its expression level correlates with the CNV. We suggest that the LILRA6 CNV may influence the ratio of inhibitory vs activating versions of this receptor on the cell surface, potentially affecting the biological consequence of LILRB3/A6 ligation.
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Affiliation(s)
- Arman Bashirova
- 1NCI/SAIC-Frederick, Frederick, MD
- 2Ragon Institute of MGH, MIT and Harvard, Charlestown, MD
| | | | - Nicolas Vince
- 1NCI/SAIC-Frederick, Frederick, MD
- 2Ragon Institute of MGH, MIT and Harvard, Charlestown, MD
| | - Xu Yu
- 2Ragon Institute of MGH, MIT and Harvard, Charlestown, MD
| | - Mary Carringotn
- 1NCI/SAIC-Frederick, Frederick, MD
- 2Ragon Institute of MGH, MIT and Harvard, Charlestown, MD
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Vince N, Boutboul D, Mouillot G, Just N, Peralta M, Casanova JL, Conley ME, Bories JC, Oksenhendler E, Malphettes M, Fieschi C. Defects in the CD19 complex predispose to glomerulonephritis, as well as IgG1 subclass deficiency. J Allergy Clin Immunol 2010; 127:538-541.e1-5. [PMID: 21159371 DOI: 10.1016/j.jaci.2010.10.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 10/11/2010] [Accepted: 10/13/2010] [Indexed: 12/01/2022]
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Mouillot G, Carmagnat M, Gérard L, Garnier JL, Fieschi C, Vince N, Karlin L, Viallard JF, Jaussaud R, Boileau J, Donadieu J, Gardembas M, Schleinitz N, Suarez F, Hachulla E, Delavigne K, Morisset M, Jacquot S, Just N, Galicier L, Charron D, Debré P, Oksenhendler E, Rabian C. B-cell and T-cell phenotypes in CVID patients correlate with the clinical phenotype of the disease. J Clin Immunol 2010; 30:746-55. [PMID: 20437084 DOI: 10.1007/s10875-010-9424-3] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 04/13/2010] [Indexed: 12/28/2022]
Abstract
BACKGROUND Common variable immunodeficiency (CVID) is a heterogeneous disorder characterized by recurrent infections and defective immunoglobulin production. METHODS The DEFI French national prospective study investigated peripheral T-cell and B-cell compartments in 313 CVID patients grouped according to their clinical phenotype, using flow cytometry. RESULTS In patients developing infection only (IO), the main B-cell or T-cell abnormalities were a defect in switched memory B cells and a decrease in naive CD4(+) T cells associated with an increase in CD4(+)CD95(+) cells. These abnormalities were more pronounced in patients developing lymphoproliferation (LP), autoimmune cytopenia (AC), or chronic enteropathy (CE). Moreover, LP and AC patients presented an increase in CD21(low) B cells and CD4(+)HLA-DR(+) T cells and a decrease in regulatory T cells. CONCLUSION In these large series of CVID patients, the major abnormalities of the B-cell and T-cell compartments, although a hallmark of CVID, were only observed in half of the IO patients and were more frequent and severe in patients with additional lymphoproliferative, autoimmune, and digestive complications.
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Affiliation(s)
- Gaël Mouillot
- Immunology Laboratory, INSERM UMR-S945, CIB Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France.
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Malphettes M, Gérard L, Carmagnat M, Mouillot G, Vince N, Boutboul D, Bérezné A, Nove-Josserand R, Lemoing V, Tetu L, Viallard JF, Bonnotte B, Pavic M, Haroche J, Larroche C, Brouet JC, Fermand JP, Rabian C, Fieschi C, Oksenhendler E. Late-onset combined immune deficiency: a subset of common variable immunodeficiency with severe T cell defect. Clin Infect Dis 2009; 49:1329-38. [PMID: 19807277 DOI: 10.1086/606059] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Common variable immunodeficiency (CVID) is a primary immune deficiency defined by defective antibody production. In most series, a small proportion of patients present with opportunistic infections (OIs). METHODS The French DEFI study has enrolled patients with primary hypogammaglobulinemia and allows a detailed clinical and immunologic description of patients with previous OIs and/or at risk for OIs. RESULTS Among 313 patients with CVID, 28 patients (8.9%) presented with late-onset combined immune deficiency (LOCID), defined by the occurrence of an OI and/or a CD4(+) T cell count <200 x 10(6) cells/L, and were compared with the remaining 285 patients with CVID. The patients with LOCID more frequently belonged to consanguineous families (29% vs 8%; P = .004). They differed from patients with CVID with a higher prevalence of splenomegaly (64% vs 31%), granuloma (43% vs 10%), gastrointestinal disease (75% vs 42%), and lymphoma (29% vs 4%). Even on immunoglobulin substitution, they required more frequent antibiotics administration and hospitalization. Lymphocyte counts were lower, with a marked decrease in CD4(+) T cell counts (158 x 10(6) vs 604 x 10(6) cells/L; P < .001) and a severe defect in naive CD45RA(+)CCR7(+)CD4(+) T cell counts (<20% of total CD4(+) T cells in 71% of patients with LOCID vs 37% of patients with CVID; P = .001). The CD19(+) B cell compartment was also significantly decreased (20 x 10(6) vs 102 x 10(6) cells/L; P < .001). CONCLUSIONS LOCID differs from classic CVID in its clinical and immunologic characteristics. Systematic T cell phenotype may help to discriminate such patients from those with CVID. Identification of this phenotype should result in a more fitted diagnostic and therapeutic approach of infections and could provide insights for genetic diagnosis.
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Affiliation(s)
- Marion Malphettes
- Département d'Immunologie, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris, Paris, France.
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