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Al-kaabi M, Deshpande P, Firth M, Pavlos R, Chopra A, Basiri H, Currenti J, Alves E, Kalams S, Fellay J, Phillips E, Mallal S, John M, Gaudieri S. Epistatic interaction between ERAP2 and HLA modulates HIV-1 adaptation and disease outcome in an Australian population. PLoS Pathog 2024; 20:e1012359. [PMID: 38980912 PMCID: PMC11259285 DOI: 10.1371/journal.ppat.1012359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 07/19/2024] [Accepted: 06/19/2024] [Indexed: 07/11/2024] Open
Abstract
A strong genetic predictor of outcome following untreated HIV-1 infection is the carriage of specific alleles of human leukocyte antigens (HLAs) that present viral epitopes to T cells. Residual variation in outcome measures may be attributed, in part, to viral adaptation to HLA-restricted T cell responses. Variants of the endoplasmic reticulum aminopeptidases (ERAPs) influence the repertoire of T cell epitopes presented by HLA alleles as they trim pathogen-derived peptide precursors to optimal lengths for antigen presentation, along with other functions unrelated to antigen presentation. We investigated whether ERAP variants influence HLA-associated HIV-1 adaptation with demonstrable effects on overall HIV-1 disease outcome. Utilizing host and viral data of 249 West Australian individuals with HIV-1 subtype B infection, we identified a novel association between two linked ERAP2 single nucleotide polymorphisms (SNPs; rs2248374 and rs2549782) with plasma HIV RNA concentration (viral load) (P adjusted = 0.0024 for both SNPs). Greater HLA-associated HIV-1 adaptation in the HIV-1 Gag gene correlated significantly with higher viral load, lower CD4+ T cell count and proportion; P = 0.0103, P = 0.0061, P = 0.0061, respectively). When considered together, there was a significant interaction between the two ERAP2 SNPs and HLA-associated HIV-1 adaptation on viral load (P = 0.0111). In a comprehensive multivariate model, addition of ERAP2 haplotypes and HLA associated adaptation as an interaction term to known HLA and CCR5 determinants and demographic factors, increased the explanatory variance of population viral load from 17.67% to 45.1% in this dataset. These effects were not replicated in publicly available datasets with comparably sized cohorts, suggesting that any true global epistasis may be dependent on specific HLA-ERAP allelic combinations. Our data raises the possibility that ERAP2 variants may shape peptide repertoires presented to HLA class I-restricted T cells to modulate the degree of viral adaptation within individuals, in turn contributing to disease variability at the population level. Analyses of other populations and experimental studies, ideally with locally derived ERAP genotyping and HLA-specific viral adaptations are needed to elucidate this further.
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Affiliation(s)
- Marwah Al-kaabi
- School of Human Sciences, University of Western Australia, Crawley, Australia
| | - Pooja Deshpande
- School of Human Sciences, University of Western Australia, Crawley, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Martin Firth
- School of Physics, Mathematics and Computing, Department of Mathematics and Statistics, University of Western Australia, Crawley, Australia
| | - Rebecca Pavlos
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Hamed Basiri
- School of Human Sciences, University of Western Australia, Crawley, Australia
| | - Jennifer Currenti
- School of Human Sciences, University of Western Australia, Crawley, Australia
| | - Eric Alves
- School of Human Sciences, University of Western Australia, Crawley, Australia
| | - Spyros Kalams
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss HIV Cohort Study, Zurich, Switzerland
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Mina John
- School of Human Sciences, University of Western Australia, Crawley, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Australia
| | - Silvana Gaudieri
- School of Human Sciences, University of Western Australia, Crawley, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
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Lu HF, Chou CH, Lin YJ, Uchiyama S, Terao C, Wang YW, Yang JS, Liu TY, Wong HSC, Chen SCC, Tsai FJ. The genome-wide association study of serum IgE levels demonstrated a shared genetic background in allergic diseases. Clin Immunol 2024; 260:109897. [PMID: 38199299 DOI: 10.1016/j.clim.2024.109897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/12/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024]
Abstract
Immunoglobulin E (IgE) synthessis is highly related to a variety of atopic diseases, and several genome-wide association studies (GWASs) have demonstrated the association between genes and IgE level. In this study, we conducted the largest genome-wide association study of IgE involving a Taiwanese Han population. Eight independent variants exhibited genome-wide significance. Among them, an intronic SNP of CD28, rs1181388, and an intergenic SNP, rs1002957030, on 11q23.2 were identified as novel signals for IgE. Seven of the loci were replicated successfully in a meta-analysis using data on Japanese population. Among all the human leukocyte antigen (HLA) regions, HLA-DQA1*03:02 - HLA-DQB1*03:03 was the most significant haplotype (OR = 1.25, SE = 0.02, FDR = 1.6 × 10-14), corresponding to HLA-DQA1 Asp160 and HLA-DQB1 Leu87 amino acid residues. The genetic correlation showed significance between IgE and allergic diseases including asthma, atopic dermatitis, and pollinosis. IgE PRS was significantly correlated with total IgE levels. Furthermore, the top decile IgE polygenic risk score (PRS) group had the highest risk of asthma for the Taiwan Biobank and Biobank Japan cohorts. IgE PRS may be used to aid in predicting the occurrence of allergic reactions before symptoms occur and biomarkers are detectable. Our study provided a more comprehensive understanding of the impact of genomic variants, including complex HLA alleles, on serum IgE levels.
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Affiliation(s)
- Hsing-Fang Lu
- Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan; Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chen-Hsing Chou
- PhD Program for Health Science and Industry, College of Health Care, China Medical University, Taichung, Taiwan; Department of Health Services Administration, China Medical University, Taichung, Taiwan
| | - Ying-Ju Lin
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan; School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Shunsuke Uchiyama
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan; The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yu-Wen Wang
- Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan
| | - Jai-Sing Yang
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, 404327, Taiwan
| | - Ting-Yuan Liu
- Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan
| | - Henry Sung-Ching Wong
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Sean Chun-Chang Chen
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Fuu-Jen Tsai
- Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan; School of Chinese Medicine, China Medical University, Taichung, Taiwan; Department of Biotechnology and Bioinformatics, Asia University, Taichung, Taiwan.
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3
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Slater N, Sooda A, McLeish E, Beer K, Brusch A, Shakya R, Bundell C, James I, Chopra A, Mastaglia FL, Needham M, Coudert JD. High-resolution HLA genotyping in inclusion body myositis refines 8.1 ancestral haplotype association to DRB1*03:01:01 and highlights pathogenic role of arginine-74 of DRβ1 chain. J Autoimmun 2024; 142:103150. [PMID: 38043487 DOI: 10.1016/j.jaut.2023.103150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/01/2023] [Accepted: 11/15/2023] [Indexed: 12/05/2023]
Abstract
OBJECTIVES Inclusion body myositis (IBM) is a progressive inflammatory-degenerative muscle disease of older individuals, with some patients producing anti-cytosolic 5'-nucleotidase 1A (NT5C1A, aka cN1A) antibodies. Human Leukocyte Antigens (HLA) is the highest genetic risk factor for developing IBM. In this study, we aimed to further define the contribution of HLA alleles to IBM and the production of anti-cN1A antibodies. METHODS We HLA haplotyped a Western Australian cohort of 113 Caucasian IBM patients and 112 ethnically matched controls using Illumina next-generation sequencing. Allele frequency analysis and amino acid alignments were performed using the Genentech/MiDAS bioinformatics package. Allele frequencies were compared using Fisher's exact test. Age at onset analysis was performed using the ggstatsplot package. All analysis was carried out in RStudio version 1.4.1717. RESULTS Our findings validated the independent association of HLA-DRB1*03:01:01 with IBM and attributed the risk to an arginine residue in position 74 within the DRβ1 protein. Conversely, DRB4*01:01:01 and DQA1*01:02:01 were found to have protective effects; the carriers of DRB1*03:01:01 that did not possess these alleles had a fourteenfold increased risk of developing IBM over the general Caucasian population. Furthermore, patients with the abovementioned genotype developed symptoms on average five years earlier than patients without. We did not find any HLA associations with anti-cN1A antibody production. CONCLUSIONS High-resolution HLA sequencing more precisely characterised the alleles associated with IBM and defined a haplotype linked to earlier disease onset. Identification of the critical amino acid residue by advanced biostatistical analysis of immunogenetics data offers mechanistic insights and future directions into uncovering IBM aetiopathogenesis.
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Affiliation(s)
- Nataliya Slater
- Murdoch University, Centre for Molecular Medicine and Innovative Therapeutics, Murdoch, WA, Australia
| | - Anuradha Sooda
- Murdoch University, Centre for Molecular Medicine and Innovative Therapeutics, Murdoch, WA, Australia
| | - Emily McLeish
- Murdoch University, Centre for Molecular Medicine and Innovative Therapeutics, Murdoch, WA, Australia
| | - Kelly Beer
- Murdoch University, Centre for Molecular Medicine and Innovative Therapeutics, Murdoch, WA, Australia; Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
| | - Anna Brusch
- PathWest Laboratory Medicine, Dept of Clinical Immunology, QEII Medical Centre, Nedlands, WA, Australia
| | - Rakesh Shakya
- PathWest Laboratory Medicine, Dept of Clinical Immunology, QEII Medical Centre, Nedlands, WA, Australia
| | - Christine Bundell
- PathWest Laboratory Medicine, Dept of Clinical Immunology, QEII Medical Centre, Nedlands, WA, Australia
| | - Ian James
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia; Murdoch University, Institute for Immunology and Infection Diseases, Murdoch, WA, Australia
| | - Abha Chopra
- Murdoch University, Institute for Immunology and Infection Diseases, Murdoch, WA, Australia
| | - Frank L Mastaglia
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia; University of Western Australia, Centre for Neuromuscular & Neurological Disorders, Crawley, WA, Australia
| | - Merrilee Needham
- Murdoch University, Centre for Molecular Medicine and Innovative Therapeutics, Murdoch, WA, Australia; Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia; University of Notre Dame Australia, School of Medicine, Fremantle, WA, Australia; Fiona Stanley Hospital, Department of Neurology, Murdoch, WA, Australia
| | - Jerome D Coudert
- Murdoch University, Centre for Molecular Medicine and Innovative Therapeutics, Murdoch, WA, Australia; Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia; University of Notre Dame Australia, School of Medicine, Fremantle, WA, Australia.
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4
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Guillen-Guio B, Paynton ML, Allen RJ, Chin DP, Donoghue LJ, Stockwell A, Leavy OC, Hernandez-Beeftink T, Reynolds C, Cullinan P, Martinez F, Booth HL, Fahy WA, Hall IP, Hart SP, Hill MR, Hirani N, Hubbard RB, McAnulty RJ, Millar AB, Navaratnam V, Oballa E, Parfrey H, Saini G, Sayers I, Tobin MD, Whyte MK, Adegunsoye A, Kaminski N, Ma SF, Strek ME, Zhang Y, Fingerlin TE, Molina-Molina M, Neighbors M, Sheng XR, Oldham JM, Maher TM, Molyneaux PL, Flores C, Noth I, Schwartz DA, Yaspan BL, Jenkins RG, Wain LV, Hollox EJ. Association study of human leukocyte antigen variants and idiopathic pulmonary fibrosis. ERJ Open Res 2024; 10:00553-2023. [PMID: 38375425 PMCID: PMC10875457 DOI: 10.1183/23120541.00553-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/05/2023] [Indexed: 02/21/2024] Open
Abstract
Introduction Idiopathic pulmonary fibrosis (IPF) is a chronic interstitial pneumonia marked by progressive lung fibrosis and a poor prognosis. Recent studies have highlighted the potential role of infection in the pathogenesis of IPF, and a prior association of the HLA-DQB1 gene with idiopathic fibrotic interstitial pneumonia (including IPF) has been reported. Owing to the important role that the human leukocyte antigen (HLA) region plays in the immune response, here we evaluated if HLA genetic variation was associated specifically with IPF risk. Methods We performed a meta-analysis of associations of the HLA region with IPF risk in individuals of European ancestry from seven independent case-control studies of IPF (comprising 5159 cases and 27 459 controls, including a prior study of fibrotic interstitial pneumonia). Single nucleotide polymorphisms, classical HLA alleles and amino acids were analysed and signals meeting a region-wide association threshold of p<4.5×10-4 and a posterior probability of replication >90% were considered significant. We sought to replicate the previously reported HLA-DQB1 association in the subset of studies independent of the original report. Results The meta-analysis of all seven studies identified four significant independent single nucleotide polymorphisms associated with IPF risk. However, none met the posterior probability for replication criterion. The HLA-DQB1 association was not replicated in the independent IPF studies. Conclusion Variation in the HLA region was not consistently associated with risk in studies of IPF. However, this does not preclude the possibility that other genomic regions linked to the immune response may be involved in the aetiology of IPF.
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Affiliation(s)
- Beatriz Guillen-Guio
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
- Joint first authors
| | - Megan L. Paynton
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Joint first authors
| | - Richard J. Allen
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Daniel P.W. Chin
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | - Olivia C. Leavy
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Tamara Hernandez-Beeftink
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Carl Reynolds
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Paul Cullinan
- National Heart & Lung Institute, Imperial College London, London, UK
| | | | - Helen L. Booth
- University College Hospital, University College London, London, UK
| | | | - Ian P. Hall
- School of Medicine, University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | - Simon P. Hart
- Hull York Medical School, University of Hull, Hull, UK
| | - Mike R. Hill
- MRC Population Health Unit, University of Oxford, Oxford, UK
| | - Nik Hirani
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Richard B. Hubbard
- School of Medicine, University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | | | - Ann B. Millar
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Vidya Navaratnam
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
- Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, QLD, Australia
| | | | - Helen Parfrey
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - Gauri Saini
- School of Medicine, University of Nottingham, Nottingham, UK
| | - Ian Sayers
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Martin D. Tobin
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Moira K.B. Whyte
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | | | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Shwu-Fan Ma
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Mary E. Strek
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tasha E. Fingerlin
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA
| | - Maria Molina-Molina
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Barcelona, Spain
- Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | | | | | - Justin M. Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Toby M. Maher
- National Heart and Lung Institute, Imperial College London, London, UK
- Division of Pulmonary and Critical Care Medicine, University of Southern California, Los Angeles, USA
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas’ NHS Foundation Trust, London, UK
| | - Carlos Flores
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Genomics Division, Instituto Tecnologico y de Energias Renovables, Santa Cruz de Tenerife, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Imre Noth
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | | | | | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Louise V. Wain
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
- Joint senior authors
| | - Edward J. Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Joint senior authors
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Castro-Santos P, Rojas-Martinez A, Riancho JA, Lapunzina P, Flores C, Carracedo Á, Díaz-Peña R. HLA-A*11:01 and HLA-C*04:01 are associated with severe COVID-19. HLA 2023; 102:731-739. [PMID: 37528566 DOI: 10.1111/tan.15160] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/04/2023] [Accepted: 07/09/2023] [Indexed: 08/03/2023]
Abstract
We analyzed the association between HLA polymorphisms and susceptibility to SARS-CoV-2 infection and disease severity. Genotyping data from a total of 9373 COVID-19-positive cases from the Spanish Coalition to Unlock Research on Host Genetics on COVID-19 (SCOURGE) consortium and 5943 population controls were included in the study. We found an association of the alleles HLA-B*14:02 and HLA-C*08:02 with a lower risk to COVID-19 infection (p = 0.006, OR = 0.84, 95% CI = [0.75-0.95], p = 0.024, OR = 0.86, 95% CI = [0.78-0.95], respectively). We also found the alleles HLA-A*11:01 and HLA-C*04:01 associated with disease severity (p = 0.033, OR = 1.16, 95% CI = [1.04-1.31], p = 0.045, OR = 1.14, 95% CI = [1.05-1.25], respectively). These results suggest that an effective presentation of viral peptides by HLA class I alleles involve a faster infection clearance, decreasing the susceptibility and severity of COVID-19.
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Affiliation(s)
- Patricia Castro-Santos
- Fundación Pública Galega de Medicina Xenómica (SERGAS), Centro Nacional de Genotipado, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Faculty of Health Sciences, Universidad Autónoma de Chile, Talca, Chile
| | | | - José A Riancho
- IDIVAL, Cantabria, Spain
- Universidad de Cantabria, Cantabria, Spain
- Hospital U M Valdecilla, Cantabria, Spain
| | - Pablo Lapunzina
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IDIPAZ, Madrid, Spain
- ERN-ITHACA-European Reference Network, Paris, France
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Ángel Carracedo
- Fundación Pública Galega de Medicina Xenómica (SERGAS), Centro Nacional de Genotipado, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Grupo de Medicina Xenómica-CIMUS-Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Roberto Díaz-Peña
- Fundación Pública Galega de Medicina Xenómica (SERGAS), Centro Nacional de Genotipado, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Faculty of Health Sciences, Universidad Autónoma de Chile, Talca, Chile
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6
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Zhang X, Li Y, Han X, Xu Y, Wang H, Wang T, Zhang T. Role of the Killer Immunoglobulin-like Receptor and Human Leukocyte Antigen I Complex Polymorphisms in Kaposi Sarcoma-Associated Herpesvirus Infection. Open Forum Infect Dis 2023; 10:ofad435. [PMID: 37636520 PMCID: PMC10456215 DOI: 10.1093/ofid/ofad435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/15/2023] [Indexed: 08/29/2023] Open
Abstract
Background Kaposi sarcoma, caused by the pathogen Kaposi sarcoma-associated herpesvirus (KSHV), is the most common neoplasm for patients with AIDS. Susceptibility to KSHV has been associated with several different genetic risk variants. The purpose of this study was to test whether variants of killer cell immunoglobulin-like receptors (KIRs) and their human leukocyte antigen (HLA-I) ligands influence the risk of KSHV infection. Methods A case-control study was performed in Xinjiang, a KSHV-endemic region of China. We recruited 299 individuals with HIV, including 123 KSHV-seropositive persons and 176 KSHV-seronegative controls. We used logistic regression and the MiDAS package to evaluate the association between KIR/HLA-I polymorphisms and KSHV infection. Results HLA-A*31:01, HLA-C*03:04, and HLA-C*12:03 were found to be associated with KSHV infection, with A*31:01 showing a protective effect under 3 different models (dominant: 0.30 [95% confidence interval {CI}, .08-.82], P = .031; additive: 0.30 [95% CI, .09-.80], P = .030; overdominant: 0.31 [95% CI, .09-.88], P = .042). The effect of A*31:01 might cause the variants of amino acid at HLA-A position 56, with individuals carrying an arginine having a lower KSHV infection risk. The increased homozygous KIR2DL3 was associated with a relatively high KSHV viral load (16.30% vs 41.94%, P = .010). Conclusions This study provides further insight into the link between HLA-I alleles and KIR genes and KSHV infection, highlighting KSHV-susceptible variants of HLA-I and KSHV replication caused by specific KIR genotype, and revealing a potential role of KIR-mediated natural killer cell activation in anti-KSHV infection.
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Affiliation(s)
- Xin Zhang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Fudan University, Ministry of Education, Shanghai, China
| | - Yi Li
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Fudan University, Ministry of Education, Shanghai, China
| | - Xinyu Han
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Fudan University, Ministry of Education, Shanghai, China
| | - Yiyun Xu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Fudan University, Ministry of Education, Shanghai, China
| | - Haili Wang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Fudan University, Ministry of Education, Shanghai, China
| | - Tianye Wang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Fudan University, Ministry of Education, Shanghai, China
| | - Tiejun Zhang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Fudan University, Ministry of Education, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
- Yiwu Research Institute, Fudan University, Yiwu, China
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7
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Guillen-Guio B, Paynton ML, Allen RJ, Chin DP, Donoghue LJ, Stockwell A, Leavy OC, Hernandez-Beeftink T, Reynolds C, Cullinan P, Martinez F, Booth HL, Fahy WA, Hall IP, Hart SP, Hill MR, Hirani N, Hubbard RB, McAnulty RJ, Millar AB, Navaratnam V, Oballa E, Parfrey H, Saini G, Sayers I, Tobin MD, Whyte MKB, Adegunsoye A, Kaminski N, Shwu-Fan M, Strek ME, Zhang Y, Fingerlin TE, Molina-Molina M, Neighbors M, Sheng XR, Oldham JM, Maher TM, Molyneaux PL, Flores C, Noth I, Schwartz DA, Yaspan BL, Jenkins RG, Wain LV, Hollox EJ. Association study of human leukocyte antigen (HLA) variants and idiopathic pulmonary fibrosis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.20.23292940. [PMID: 37546732 PMCID: PMC10402235 DOI: 10.1101/2023.07.20.23292940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Introduction Idiopathic pulmonary fibrosis (IPF) is a chronic interstitial pneumonia marked by progressive lung fibrosis and a poor prognosis. Recent studies have highlighted the potential role of infection in the pathogenesis of IPF and a prior association of the HLA-DQB1 gene with idiopathic fibrotic interstitial pneumonia (including IPF) has been reported. Due to the important role that the Human Leukocyte Antigen (HLA) region plays in the immune response, here we evaluated if HLA genetic variation was associated specifically with IPF risk. Methods We performed a meta-analysis of associations of the HLA region with IPF risk in individuals of European ancestry from seven independent case-control studies of IPF (comprising a total of 5,159 cases and 27,459 controls, including the prior study of fibrotic interstitial pneumonia). Single nucleotide polymorphisms, classical HLA alleles and amino acids were analysed and signals meeting a region-wide association threshold p<4.5×10-4 and a posterior probability of replication >90% were considered significant. We sought to replicate the previously reported HLA-DQB1 association in the subset of studies independent of the original report. Results The meta-analysis of all seven studies identified four significant independent single nucleotide polymorphisms associated with IPF risk. However, none met the posterior probability for replication criterion. The HLA-DQB1 association was not replicated in the independent IPF studies. Conclusion Variation in the HLA region was not consistently associated with risk in studies of IPF. However, this does not preclude the possibility that other genomic regions linked to the immune response may be involved in the aetiology of IPF.
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Affiliation(s)
- Beatriz Guillen-Guio
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Megan L. Paynton
- Department of Population Health Sciences, University of Leicester, UK
| | - Richard J. Allen
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Daniel P.W. Chin
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | - Olivia C. Leavy
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Tamara Hernandez-Beeftink
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | | | | | | | | | - Ian P. Hall
- University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | | | | | | | - Richard B. Hubbard
- University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | | | | | - Vidya Navaratnam
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
- Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, QLD, Australia
| | | | - Helen Parfrey
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | | | - Ian Sayers
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Martin D. Tobin
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | | | | | | | | | | | - Maria Molina-Molina
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Barcelona, Spain
- Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigacion Biomedica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | | | | | | | - Toby M. Maher
- National Heart and Lung Institute, Imperial College London, London, UK
- Division of Pulmonary and Critical Care Medicine, University of Southern California, Los Angeles, USA
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St Thomas’ NHS Foundation Trust, London, UK
| | - Carlos Flores
- Centro de Investigacion Biomedica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Genomics Division, Instituto Tecnologico y de Energias Renovables, Santa Cruz de Tenerife, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Imre Noth
- University of Virginia, Virginia, USA
| | | | | | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Louise V. Wain
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Edward J. Hollox
- Department of Genetics and Genome Biology, University of Leicester, UK
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Wang YA, Ranti D, Bieber C, Galsky M, Bhardwaj N, Sfakianos JP, Horowitz A. NK Cell-Targeted Immunotherapies in Bladder Cancer: Beyond Checkpoint Inhibitors. Bladder Cancer 2023; 9:125-139. [PMID: 38993289 PMCID: PMC11181717 DOI: 10.3233/blc-220109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 05/15/2023] [Indexed: 07/13/2024]
Abstract
BACKGROUND For decades, immunotherapies have been integral for the treatment and management of bladder cancer, with immune checkpoint inhibitors (ICIs) transforming patient care in recent years. However, response rates are poor to T cell-targeted ICIs such as programmed cell death protein 1 (PD-1) and programmed cell death-ligand 1 (PD-L1) blocking antibodies, framing a critical need for complementary immunotherapies. Promising strategies involve harnessing the activation potential of natural killer (NK) cells. They quickly exert their antitumor activity via signaling through germline-encoded activating receptors and are rapidly sensitized to new tissue microenvironments via their regulation by polymorphic HLA class I, KIR and NKG2A receptors. OBJECTIVE In this review, we examined the roles of currently available NK-targeted antitumor treatment strategies such as engineered viral vectors, small-molecule IMiDs, NK agonist antibodies, interleukins, and chimeric antigen receptor (CAR) NK cells, and their potential for improving the efficacy of immunotherapy in the treatment of bladder cancer. METHODS Through review of current literature, we summarized our knowledge of NK cells in solid tumors and hematologic malignancies as their roles pertain to novel immunotherapies already being applied to the treatment of bladder cancer or that offer rationale for considering as potential novel immunotherapeutic strategies. RESULTS NK cells play a critical role in shaping the tumor microenvironment (TME) that can be exploited to improve T cell-targeted immunotherapies. CONCLUSIONS Emerging evidence suggests that NK cells are a prime target for improving antitumor functions in immunotherapies for the treatment of bladder cancer. Further research into profiling NK cells in settings of immunotherapies for bladder cancer could help identify patients who might maximally benefit from NK cell-targeted immunotherapies and the various approaches for exploiting their antitumor properties.
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Affiliation(s)
- Yuanshuo A Wang
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Ranti
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christine Bieber
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew Galsky
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nina Bhardwaj
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John P Sfakianos
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amir Horowitz
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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9
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Chang D, Hammer C, Holweg CTJ, Selvaraj S, Rathore N, McCarthy MI, Yaspan BL, Choy DF. A genome-wide association study of chronic spontaneous urticaria risk and heterogeneity. J Allergy Clin Immunol 2023; 151:1351-1356. [PMID: 36343773 DOI: 10.1016/j.jaci.2022.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/10/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Chronic spontaneous urticaria (CSU) is a dermatologic condition characterized by spontaneous, pruritic hives and/or angioedema that persists for 6 weeks or longer with no identifiable trigger. Antihistamines and second-line therapies such as omalizumab are effective for some CSU patients, but others remain symptomatic, with significant impact on quality of life. This variable response to treatment and autoantibody levels across patients highlight clinically heterogeneous subgroups. OBJECTIVE We aimed to highlight pathways involved in CSU by investigating the genetics of CSU risk and subgroups. METHODS We performed a genome-wide association study (GWAS) of 679 CSU patients and 4446 controls and a GWAS of chronic urticaria (CU)-index, which measures IgG autoantibodies levels, by comparing 447 CU index-low to 183 CU index-high patients. We also tested whether polygenic scores for autoimmune-related disorders were associated with CSU risk and CU index. RESULTS We identified 2 loci significantly associated with disease risk. The strongest association mapped to position 56 of HLA-DQA1 (P = 1.69 × 10-9), where the arginine residue was associated with increased risk (odds ratio = 1.64). The second association signal colocalized with expression-quantitative trait loci for ITPKB in whole blood (Pcolocalization = .997). The arginine residue at position 56 of HLA-DQA1 was also associated with increased risk of CU index-high (P = 6.15 × 10-5, odds ratio = 1.86), while the ITKPB association was not (P = .64). Polygenic scores for 3 autoimmune-related disorders (hypothyroidism, type 1 diabetes, and vitiligo) were associated with CSU risk and CU index (P < 2.34 × 10-3, odds ratio > 1.72). CONCLUSION A GWAS of CSU identified 2 genome-wide significant loci, highlighting the shared genetics between CU index and autoimmune disorders.
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Affiliation(s)
- Diana Chang
- Department of Human Genetics, Genentech Inc, South San Francisco, Calif.
| | - Christian Hammer
- Department of Human Genetics, Genentech Inc, South San Francisco, Calif; Department of Cancer Immunology, Genentech Inc, South San Francisco, Calif
| | | | - Suresh Selvaraj
- Department of Biosample and Repository Management, Genentech Inc, South San Francisco, Calif
| | - Nisha Rathore
- Biomarker Discovery OMNI, Genentech Inc, South San Francisco, Calif
| | - Mark I McCarthy
- Department of Human Genetics, Genentech Inc, South San Francisco, Calif
| | - Brian L Yaspan
- Department of Human Genetics, Genentech Inc, South San Francisco, Calif
| | - David F Choy
- Biomarker Discovery OMNI, Genentech Inc, South San Francisco, Calif
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10
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McLeish E, Sooda A, Slater N, Kachigunda B, Beer K, Paramalingam S, Lamont PJ, Chopra A, Mastaglia FL, Needham M, Coudert JD. Uncovering the significance of expanded CD8+ large granular lymphocytes in inclusion body myositis: Insights into T cell phenotype and functional alterations, and disease severity. Front Immunol 2023; 14:1153789. [PMID: 37063893 PMCID: PMC10098158 DOI: 10.3389/fimmu.2023.1153789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/10/2023] [Indexed: 04/03/2023] Open
Abstract
IntroductionInclusion body myositis (IBM) is a progressive inflammatory myopathy characterised by skeletal muscle infiltration and myofibre invasion by CD8+ T lymphocytes. In some cases, IBM has been reported to be associated with a systemic lymphoproliferative disorder of CD8+ T cells exhibiting a highly differentiated effector phenotype known as T cell Large Granular Lymphocytic Leukemia (T-LGLL). MethodsWe investigated the incidence of a CD8+ T-LGL lymphoproliferative disorder in 85 IBM patients and an aged-matched group of 56 Healthy Controls (HC). Further, we analysed the phenotypical characteristics of the expanded T-LGLs and investigated whether their occurrence was associated with any particular HLA alleles or clinical characteristics. ResultsBlood cell analysis by flow cytometry revealed expansion of T-LGLs in 34 of the 85 (40%) IBM patients. The T cell immunophenotype of T-LGLHIGH patients was characterised by increased expression of surface molecules including CD57 and KLRG1, and to a lesser extent of CD94 and CD56 predominantly in CD8+ T cells, although we also observed modest changes in CD4+ T cells and γδ T cells. Analysis of Ki67 in CD57+ KLRG1+ T cells revealed that only a small proportion of these cells was proliferating. Comparative analysis of CD8+ and CD4+ T cells isolated from matched blood and muscle samples donated by three patients indicated a consistent pattern of more pronounced alterations in muscles, although not significant due to small sample size. In the T-LGLHIGH patient group, we found increased frequencies of perforin-producing CD8+ and CD4+ T cells that were moderately correlated to combined CD57 and KLRG1 expression. Investigation of the HLA haplotypes of 75 IBM patients identified that carriage of the HLA-C*14:02:01 allele was significantly higher in T-LGLHIGH compared to T-LGLLOW individuals. Expansion of T-LGL was not significantly associated with seropositivity patient status for anti-cytosolic 5'-nucleotidase 1A autoantibodies. Clinically, the age at disease onset and disease duration were similar in the T-LGLHIGH and T-LGLLOW patient groups. However, metadata analysis of functional alterations indicated that patients with expanded T-LGL more frequently relied on mobility aids than T-LGLLOW patients indicating greater disease severity. ConclusionAltogether, these results suggest that T-LGL expansion occurring in IBM patients is correlated with exacerbated immune dysregulation and increased disease burden.
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Affiliation(s)
- Emily McLeish
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia
- *Correspondence: Emily McLeish, ; Jerome David Coudert,
| | - Anuradha Sooda
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia
| | - Nataliya Slater
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia
| | - Barbara Kachigunda
- Harry Butler Institute, Centre for Biosecurity and One Health, Murdoch University, Murdoch, WA, Australia
| | - Kelly Beer
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
| | | | - Phillipa J. Lamont
- Neurogenetic Unit, Department of Neurology, Royal Perth Hospital, Perth, WA, Australia
| | - Abha Chopra
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Frank Louis Mastaglia
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
| | - Merrilee Needham
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
- School of Medicine, University of Notre Dame, Fremantle, WA, Australia
- Department of Neurology, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Jerome David Coudert
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
- School of Medicine, University of Notre Dame, Fremantle, WA, Australia
- *Correspondence: Emily McLeish, ; Jerome David Coudert,
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11
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Hammer C, Ruppel J, Kamen L, Hunkapiller J, Mellman I, Quarmby V. Allelic Variation in HLA-DRB1 is Associated with Development ofAnti-Drug Antibodies in Cancer Patients Treated with Atezolizumab that are Neutralizing in Vitro. Clin Transl Sci 2022; 15:1393-1399. [PMID: 35263013 PMCID: PMC9199883 DOI: 10.1111/cts.13264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 02/14/2022] [Accepted: 02/18/2022] [Indexed: 11/29/2022] Open
Abstract
The treatment of diseases with biologic agents can result in the formation of anti-drug antibodies (ADA). Although drivers for ADA formation are unknown, a role for antigen presentation is likely, and variation in human leukocyte antigen (HLA) genes has been shown to be associated with occurrence of ADA for several biologics. Here, we performed an HLA-wide association study in 1,982 patients treated with the anti-PD-L1 antibody atezolizumab across 8 clinical trials. On average, 29.8% of patients were ADA positive (N=591, range of 13.5% - 38.4% per study), and 14.6% of patients were positive for ADA that were neutralizing in vitro (NAb, N=278, range of 6.4% - 21.9% per study). In a meta-analysis of logistic regression coefficients, we found statistically significant associations between HLA class II alleles and ADA status. The top-associated alleles were HLA-DRB1*01:01 in a comparison of ADA-positive versus ADA-negative patients (p=3.4*10-5 , odds ratio=1.96, 95% confidence interval=1.64-2.28), and HLA-DQA1*01:01 when comparing NAb-positive with ADA-negative patients (p=2.8 x 10-7 , OR=2.31, 95% CI=1.98-2.66). Both alleles occur together on a common HLA haplotype, and analyses considering only NAb-negative, ADA-positive patients did no yield significant results, suggesting that the genetic association is mainly driven by NAb status. In conclusion, our study showed that HLA class II genotype is associated with the risk of developing ADA, and specifically NAb, in patients treated with atezolizumab, but the effect estimates suggest that immunogenetic factors are not sufficient as clinically meaningful predictors.
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Affiliation(s)
| | - Jane Ruppel
- Genentech, Inc, South San Francisco, CA, 94080, USA
| | - Lynn Kamen
- Genentech, Inc, South San Francisco, CA, 94080, USA
| | | | - Ira Mellman
- Genentech, Inc, South San Francisco, CA, 94080, USA
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