1
|
Gutiérrez-Bautista JF, Sampedro A, Ballesta-Alcaraz L, Aguilera-Franco M, Olivares-Durán MJ, Cobo F, Reguera JA, Rodríguez-Granger J, Torres-Llamas A, Martín-Sánchez J, Aznar-Peralta I, Vilchez JR, López-Nevot MÁ, Sampedro-Martínez A. Analysis of HLA Alleles in Different Cohorts of Patients Infected by L. infantum from Southern Spain. Int J Mol Sci 2024; 25:8205. [PMID: 39125781 PMCID: PMC11311343 DOI: 10.3390/ijms25158205] [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: 06/14/2024] [Revised: 07/15/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
Leishmaniasis is an infectious disease caused by protozoa of the genus Leishmania, which is endemic in certain areas of Europe, such as southern Spain. The disease manifests in various clinical phenotypes, including visceral, cutaneous, mucosal, or asymptomatic leishmaniasis. This diversity in clinical outcomes may be influenced by the host immune response, with human leukocyte antigen (HLA) molecules playing a crucial role in determining susceptibility and progression of the infection. This study explores the association between specific HLA variants and Leishmania infantum infection. We recruited four cohorts: a control group, asymptomatic individuals, patients with symptomatic disease, and cohabitants of infected individuals. HLA typing was performed for all participants, followed by an association analysis with infection status and disease progression. Our findings indicate that the HLA-B*38 and HLA-C*03 alleles are associated with protection against L. infantum infection. These results contribute to a better understanding of the disease's progression, offer potential for new therapeutic approaches such as vaccines, and expand the existing knowledge in the literature.
Collapse
Affiliation(s)
- Juan Francisco Gutiérrez-Bautista
- Departamento de Bioquímica, Biología Molecular e Inmunología III, University of Granada, 18016 Granada, Spain
- Servicio de Análisis Clínicos e Inmunología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (L.B.-A.); (M.J.O.-D.); (J.R.V.)
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain;
| | - Antonio Sampedro
- Centro de Salud Zaidín Sur, Distrito Granada Metropolitano, Servicio Andaluz de Salud, 18007 Granada, Spain;
| | - Lucia Ballesta-Alcaraz
- Servicio de Análisis Clínicos e Inmunología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (L.B.-A.); (M.J.O.-D.); (J.R.V.)
| | - María Aguilera-Franco
- Servicio de Microbiología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (M.A.-F.); (F.C.); (J.A.R.); (J.R.-G.)
| | - María José Olivares-Durán
- Servicio de Análisis Clínicos e Inmunología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (L.B.-A.); (M.J.O.-D.); (J.R.V.)
| | - Fernando Cobo
- Servicio de Microbiología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (M.A.-F.); (F.C.); (J.A.R.); (J.R.-G.)
| | - Juan Antonio Reguera
- Servicio de Microbiología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (M.A.-F.); (F.C.); (J.A.R.); (J.R.-G.)
| | - Javier Rodríguez-Granger
- Servicio de Microbiología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (M.A.-F.); (F.C.); (J.A.R.); (J.R.-G.)
| | - Andrés Torres-Llamas
- Departamento de Parasitología, University of Granada, 18016 Granada, Spain; (A.T.-L.); (J.M.-S.)
| | - Joaquina Martín-Sánchez
- Departamento de Parasitología, University of Granada, 18016 Granada, Spain; (A.T.-L.); (J.M.-S.)
| | - Inés Aznar-Peralta
- GENYO Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian, 18016 Granada, Spain
| | - Jose Ramon Vilchez
- Servicio de Análisis Clínicos e Inmunología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (L.B.-A.); (M.J.O.-D.); (J.R.V.)
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain;
| | - Miguel Ángel López-Nevot
- Departamento de Bioquímica, Biología Molecular e Inmunología III, University of Granada, 18016 Granada, Spain
- Servicio de Análisis Clínicos e Inmunología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (L.B.-A.); (M.J.O.-D.); (J.R.V.)
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain;
| | - Antonio Sampedro-Martínez
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain;
- Servicio de Microbiología, University Hospital Virgen de las Nieves, 18014 Granada, Spain; (M.A.-F.); (F.C.); (J.A.R.); (J.R.-G.)
| |
Collapse
|
2
|
Marchal A, Cirulli ET, Neveux I, Bellos E, Thwaites RS, Schiabor Barrett KM, Zhang Y, Nemes-Bokun I, Kalinova M, Catchpole A, Tangye SG, Spaan AN, Lack JB, Ghosn J, Burdet C, Gorochov G, Tubach F, Hausfater P, Dalgard CL, Zhang SY, Zhang Q, Chiu C, Fellay J, Grzymski JJ, Sancho-Shimizu V, Abel L, Casanova JL, Cobat A, Bolze A. Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection. HGG ADVANCES 2024; 5:100300. [PMID: 38678364 PMCID: PMC11215417 DOI: 10.1016/j.xhgg.2024.100300] [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: 12/04/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 04/29/2024] Open
Abstract
Human genetic studies of critical COVID-19 pneumonia have revealed the essential role of type I interferon-dependent innate immunity to SARS-CoV-2 infection. Conversely, an association between the HLA-B∗15:01 allele and asymptomatic SARS-CoV-2 infection in unvaccinated individuals was recently reported, suggesting a contribution of pre-existing T cell-dependent adaptive immunity. We report a lack of association of classical HLA alleles, including HLA-B∗15:01, with pre-omicron asymptomatic SARS-CoV-2 infection in unvaccinated participants in a prospective population-based study in the United States (191 asymptomatic vs. 945 symptomatic COVID-19 cases). Moreover, we found no such association in the international COVID Human Genetic Effort cohort (206 asymptomatic vs. 574 mild or moderate COVID-19 cases and 1,625 severe or critical COVID-19 cases). Finally, in the Human Challenge Characterisation study, the three HLA-B∗15:01 individuals infected with SARS-CoV-2 developed symptoms. As with other acute primary infections studied, no classical HLA alleles favoring an asymptomatic course of SARS-CoV-2 infection were identified.
Collapse
Affiliation(s)
- Astrid Marchal
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France
| | | | - Iva Neveux
- Department of Internal Medicine, University of Nevada School of Medicine, Reno, NV, USA
| | - Evangelos Bellos
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Ivana Nemes-Bokun
- Department of Infectious Disease, Imperial College London, London, UK
| | | | | | - Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, New South Wales, Australia
| | - András N Spaan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Justin B Lack
- NIAID Collaborative Bioinformatics Resource, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD, USA
| | - Jade Ghosn
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMR1137, University Paris Cité, Paris, France; AP-HP, Bichat-Claude Bernard Hospital, Infectious and Tropical Diseases Department, Paris, France
| | - Charles Burdet
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMR1137, University Paris Cité, Paris, France; AP-HP, Hôpital Bichat, Centre d'Investigation Clinique, INSERM CIC 1425, Paris, France; Département Epidémiologie, Biostatistiques et Recherche Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, 75018 Paris, France
| | - Guy Gorochov
- Sorbonne Université, INSERM Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, Département d'immunologie Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Florence Tubach
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Département de Santé Publique, Unitéde Recherche Clinique PSL-CFX, CIC-1901, Paris, France
| | - Pierre Hausfater
- Emergency Department, Hôpital Pitié-Salpêtrière, APHP-Sorbonne Université, Paris, France; GRC-14 BIOSFAST Sorbonne Université, UMR INSERM 1135, CIMI, Sorbonne Université, Paris, France
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Joseph J Grzymski
- Department of Internal Medicine, University of Nevada School of Medicine, Reno, NV, USA; Renown Health, Reno, NV, USA
| | - Vanessa Sancho-Shimizu
- Department of Infectious Disease, Imperial College London, London, UK; Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Department of Pediatrics, Necker Hospital for Sick Children, Paris, France; Howard Hughes Medical Institute, New York, NY, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
| | | |
Collapse
|
3
|
Tanaka K, Meguro A, Hara Y, Endo L, Izawa A, Muraoka S, Kaneko A, Somekawa K, Hirata M, Otsu Y, Matsumoto H, Nagasawa R, Kubo S, Murohashi K, Aoki A, Fujii H, Watanabe K, Horita N, Kato H, Kobayashi N, Takeuchi I, Nakajima A, Inoko H, Mizuki N, Kaneko T. HLA-DQA1*01:03 and DQB1*06:01 are risk factors for severe COVID-19 pneumonia. HLA 2024; 104:e15609. [PMID: 39041300 DOI: 10.1111/tan.15609] [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: 02/26/2024] [Revised: 06/28/2024] [Accepted: 07/10/2024] [Indexed: 07/24/2024]
Abstract
The clinical spectrum of COVID-19 includes a wide range of manifestations, from mild symptoms to severe pneumonia. HLA system plays a pivotal role in immune responses to infectious diseases. The purpose of our study was to investigate the association between HLA and COVID-19 severity in a Japanese population. The study included 209 Japanese COVID-19 patients aged ≥20 years. Saliva samples were collected and used to determine the HLA genotype by HLA imputation through genome-wide association analyses. The association between HLA genotype and COVID-19 severity was then evaluated. The allele frequency was compared between patients with respiratory failure (severe group: 91 cases) and those without respiratory failure (non-severe group: 118 cases), categorising the data into three time periods: pre-Omicron epidemic period, Omicron epidemic period, and total period of this study (from January 2021 to May 2023). In comparing the severe and non-severe groups, the frequencies of the HLA-DQA1*01:03 (35.1% vs. 10.5%, odds ratio [OR] = 4.57, corrected p [pc] = 0.041) and -DQB1*06:01 (32.4% vs. 7.9%, OR = 5.54, pc = 0.030) alleles were significantly higher in the severe group during the pre-Omicron epidemic period. During the Omicron epidemic period, HLA-DQB1*06 (32.4% vs. 7.9%, OR = 5.54, pc = 0.030) was significantly higher in the severe group. During total period of this study, HLA-DQA1*01:03 (30.2% vs. 14.4%, OR = 2.57, corrected pc = 0.0013) and -DQB1*06:01 (44.5% vs. 26.7%, OR = 2.20, pc = 0.013) alleles were significantly higher in the severe group. HLA-DQB1*06:01 and -DQA1*01:03 were in strong linkage disequilibrium with each other (r2 = 0.91) during total period of this study, indicating that these two alleles form a haplotype. The frequency of the HLA-DQA1*01:03-DQB1*06:01 in the severe group was significantly higher than in the non-severe group during pre-Omicron epidemic period (32.4% vs. 7.9%, OR = 5.59, pc = 0.00072), and total period of this study (28.6% vs. 13.1%, OR = 2.63, pc = 0.0013). During Omicron epidemic period, the haplotype did not demonstrate statistical significance, although the odds ratio indicated a value greater 1. Frequencies of the HLA-DQA1*01:03 and -DQB1*06:01 alleles were significantly higher in severe COVID-19 patients, suggesting that these alleles are risk factors for severe COVID-19 pneumonia in the Japanese population.
Collapse
Affiliation(s)
- Katsushi Tanaka
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Akira Meguro
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yu Hara
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Lisa Endo
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ami Izawa
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Suguru Muraoka
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ayami Kaneko
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kohei Somekawa
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Momo Hirata
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yukiko Otsu
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiromi Matsumoto
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ryo Nagasawa
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Sosuke Kubo
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kota Murohashi
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ayako Aoki
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiroaki Fujii
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Keisuke Watanabe
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Nobuyuki Horita
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hideaki Kato
- Infection Prevention and Control Department, Yokohama City University Hospital, Yokohama, Japan
| | - Nobuaki Kobayashi
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ichiro Takeuchi
- Department of Emergency Medicine, School of Medicine, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Atsushi Nakajima
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Hidetoshi Inoko
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Japan
| | - Nobuhisa Mizuki
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Kaneko
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| |
Collapse
|
4
|
Naidoo L, Arumugam T, Ramsuran V. Narrative Review Explaining the Role of HLA-A, -B, and -C Molecules in COVID-19 Disease in and around Africa. Infect Dis Rep 2024; 16:380-406. [PMID: 38667755 PMCID: PMC11049896 DOI: 10.3390/idr16020029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) has left a devasting effect on various regions globally. Africa has exceptionally high rates of other infectious diseases, such as tuberculosis (TB), human immunodeficiency virus (HIV), and malaria, and was not impacted by COVID-19 to the extent of other continents Globally, COVID-19 has caused approximately 7 million deaths and 700 million infections thus far. COVID-19 disease severity and susceptibility vary among individuals and populations, which could be attributed to various factors, including the viral strain, host genetics, environment, lifespan, and co-existing conditions. Host genetics play a substantial part in COVID-19 disease severity among individuals. Human leukocyte antigen (HLA) was previously been shown to be very important across host immune responses against viruses. HLA has been a widely studied gene region for various disease associations that have been identified. HLA proteins present peptides to the cytotoxic lymphocytes, which causes an immune response to kill infected cells. The HLA molecule serves as the central region for infectious disease association; therefore, we expect HLA disease association with COVID-19. Therefore, in this narrative review, we look at the HLA gene region, particularly, HLA class I, to understand its role in COVID-19 disease.
Collapse
Affiliation(s)
- Lisa Naidoo
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa; (L.N.); (T.A.)
| | - Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa; (L.N.); (T.A.)
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa; (L.N.); (T.A.)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban 4041, South Africa
| |
Collapse
|
5
|
Santos-Rebouças CB, Ferreira CDS, Nogueira JDS, Brustolini OJ, de Almeida LGP, Gerber AL, Guimarães APDC, Piergiorge RM, Struchiner CJ, Porto LC, de Vasconcelos ATR. Immune response stability to the SARS-CoV-2 mRNA vaccine booster is influenced by differential splicing of HLA genes. Sci Rep 2024; 14:8982. [PMID: 38637586 PMCID: PMC11026523 DOI: 10.1038/s41598-024-59259-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
Many molecular mechanisms that lead to the host antibody response to COVID-19 vaccines remain largely unknown. In this study, we used serum antibody detection combined with whole blood RNA-based transcriptome analysis to investigate variability in vaccine response in healthy recipients of a booster (third) dose schedule of the mRNA BNT162b2 vaccine against COVID-19. The cohort was divided into two groups: (1) low-stable individuals, with antibody concentration anti-SARS-CoV IgG S1 below 0.4 percentile at 180 days after boosting vaccination; and (2) high-stable individuals, with antibody values greater than 0.6 percentile of the range in the same period (median 9525 [185-80,000] AU/mL). Differential gene expression, expressed single nucleotide variants and insertions/deletions, differential splicing events, and allelic imbalance were explored to broaden our understanding of the immune response sustenance. Our analysis revealed a differential expression of genes with immunological functions in individuals with low antibody titers, compared to those with higher antibody titers, underscoring the fundamental importance of the innate immune response for boosting immunity. Our findings also provide new insights into the determinants of the immune response variability to the SARS-CoV-2 mRNA vaccine booster, highlighting the significance of differential splicing regulatory mechanisms, mainly concerning HLA alleles, in delineating vaccine immunogenicity.
Collapse
Affiliation(s)
- Cíntia Barros Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Cristina Dos Santos Ferreira
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Jeane de Souza Nogueira
- Histocompatibility and Cryopreservation Laboratory, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Otávio José Brustolini
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Luiz Gonzaga Paula de Almeida
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Alexandra Lehmkuhl Gerber
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Ana Paula de Campos Guimarães
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil
| | - Rafael Mina Piergiorge
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Cláudio José Struchiner
- School of Applied Mathematics, Getúlio Vargas Foundation, Rio de Janeiro, Brazil
- Social Medicine Institute Hesio Cordeiro, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Luís Cristóvão Porto
- Histocompatibility and Cryopreservation Laboratory, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Ana Tereza Ribeiro de Vasconcelos
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Getúlio Vargas, Av., 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651‑075, Brazil.
| |
Collapse
|
6
|
Warren RL, Abraham R, Calingo M, Garant JM, Jones SJM, Birol I. Establishing association between HLA-C*04:01 and severe COVID-19. HLA 2024; 103:e15355. [PMID: 38273454 DOI: 10.1111/tan.15355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 01/27/2024]
Affiliation(s)
- René L Warren
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Rohan Abraham
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Marc Calingo
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Jean-Michel Garant
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| |
Collapse
|
7
|
Marchal A, Cirulli ET, Neveux I, Bellos E, Thwaites RS, Schiabor Barrett KM, Zhang Y, Nemes-Bokun I, Kalinova M, Catchpole A, Tangye SG, Spaan AN, Lack JB, Ghosn J, Burdet C, Gorochov G, Tubach F, Hausfater P, Dalgard CL, Zhang SY, Zhang Q, Chiu C, Fellay J, Grzymski JJ, Sancho-Shimizu V, Abel L, Casanova JL, Cobat A, Bolze A. Lack of association between HLA and asymptomatic SARS-CoV-2 infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.06.23299623. [PMID: 38168184 PMCID: PMC10760282 DOI: 10.1101/2023.12.06.23299623] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Human genetic studies of critical COVID-19 pneumonia have revealed the essential role of type I interferon-dependent innate immunity to SARS-CoV-2 infection. Conversely, an association between the HLA-B*15:01 allele and asymptomatic SARS-CoV-2 infection in unvaccinated individuals was recently reported, suggesting a contribution of pre-existing T cell-dependent adaptive immunity. We report a lack of association of classical HLA alleles, including HLA-B*15:01, with pre-omicron asymptomatic SARS-CoV-2 infection in unvaccinated participants in a prospective population-based study in the US (191 asymptomatic vs. 945 symptomatic COVID-19 cases). Moreover, we found no such association in the international COVID Human Genetic Effort cohort (206 asymptomatic vs. 574 mild or moderate COVID-19 cases and 1,625 severe or critical COVID-19 cases). Finally, in the Human Challenge Characterisation study, the three HLA-B*15:01 individuals infected with SARS-CoV-2 developed symptoms. As with other acute primary infections, no classical HLA alleles favoring an asymptomatic course of SARS-CoV-2 infection were identified. These findings suggest that memory T-cell immunity to seasonal coronaviruses does not strongly influence the outcome of SARS-CoV-2 infection in unvaccinated individuals.
Collapse
Affiliation(s)
- Astrid Marchal
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
| | | | - Iva Neveux
- Department of Internal Medicine, University of Nevada School of Medicine, Reno, NV, USA
| | - Evangelos Bellos
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Ryan S. Thwaites
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | | | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Ivana Nemes-Bokun
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | | | | | - Stuart G. Tangye
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, NSW, Australia
| | - András N. Spaan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands, EU
| | - Justin B. Lack
- NIAID Collaborative Bioinformatics Resource, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA
| | - Jade Ghosn
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMR1137, University of Paris, Paris, France, EU
- AP-HP, Bichat Claude Bernard Hospital, Infectious and Tropical Diseases Department, Paris, France, EU
| | - Charles Burdet
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMR1137, University of Paris, Paris, France, EU
- Epidémiologie clinique du Centre d’Investigation Clinique (CIC-EP), INSERM CIC 1425, Hôpital Bichat, 75018 Paris, France, EU
- Département Epidémiologie, Biostatistiques et Recherche Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, 75018 Paris, France, EU
| | - Guy Gorochov
- Sorbonne Université, INSERM Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Département d’immunologie Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France, EU
| | - Florence Tubach
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié Salpêtrière, Département de Santé Publique, Unité de Recherche Clinique PSL-CFX, CIC-1901, Paris, France, EU
| | - Pierre Hausfater
- Emergency Department, Hôpital Pitié-Salpêtrière, APHP-Sorbonne Université, Paris, France, EU
- GRC-14 BIOFAST Sorbonne Université, UMR INSERM 1135, CIMI, Sorbonne Université, Paris, France, EU
| | | | | | | | | | | | | | | | | | | | - Clifton L. Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Christopher Chiu
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Joseph J. Grzymski
- Department of Internal Medicine, University of Nevada School of Medicine, Reno, NV, USA
- Renown Health, Reno, NV, USA
| | - Vanessa Sancho-Shimizu
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | | |
Collapse
|
8
|
Nogawa S, Kanamori H, Tokuda K, Kawafune K, Chijiiwa M, Saito K, Takahashi S. A web-based genome-wide association study reveals the susceptibility loci of common adverse events following COVID-19 vaccination in the Japanese population. Sci Rep 2023; 13:20820. [PMID: 38012279 PMCID: PMC10682012 DOI: 10.1038/s41598-023-47632-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has spread rapidly worldwide. To prevent its spread, mRNA-based vaccines made by Pfizer/BioNTech (BNT162b1) and Moderna (mRNA-1273) have been widely used, including in Japan. Various adverse events have been reported following the COVID-19 mRNA vaccination, with differences observed among individuals. However, analyses of the genetic background associated with the susceptibility to side effects have been limited. In the present study, we performed genome-wide association studies (GWAS) for self-reported adverse events of the COVID-19 mRNA vaccination in 4545 Japanese individuals and identified 14 associated loci. Among these, 6p21 was associated with 37.5 °C or higher fever, 38 °C or higher fever, and muscle pain. HLA allele association analysis revealed that various HLA alleles were associated with the adverse effects; HLA-DQA1*03:01 and HLA-A*11:01 were more reliably associated with the adverse effects. Our results may enable the preparation and management of adverse effects by identifying the susceptibility to these adverse events. Furthermore, we obtained valuable data that may lead to a better understanding of the mechanisms of action of the COVID-19 mRNA vaccines.
Collapse
Affiliation(s)
- Shun Nogawa
- Genequest Inc., Siba 5-29-11, Minato-ku, Tokyo, 108-0014, Japan
| | - Hajime Kanamori
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
- Division of Infection Control, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
| | - Koichi Tokuda
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
- Division of Infection Control, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
| | - Kaoru Kawafune
- Genequest Inc., Siba 5-29-11, Minato-ku, Tokyo, 108-0014, Japan
| | - Miyuki Chijiiwa
- Genequest Inc., Siba 5-29-11, Minato-ku, Tokyo, 108-0014, Japan
| | - Kenji Saito
- Genequest Inc., Siba 5-29-11, Minato-ku, Tokyo, 108-0014, Japan
| | - Shoko Takahashi
- Genequest Inc., Siba 5-29-11, Minato-ku, Tokyo, 108-0014, Japan.
| |
Collapse
|
9
|
Castro-Santos P, Carracedo Á, Díaz-Peña R. HLA alleles: important pieces to the COVID-19 puzzle. Trends Immunol 2023; 44:754-756. [PMID: 37690961 DOI: 10.1016/j.it.2023.08.011] [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: 08/16/2023] [Accepted: 08/31/2023] [Indexed: 09/12/2023]
Abstract
Research on human leukocyte antigen (HLA) molecules in coronavirus disease 2019 (COVID-19) raised high expectations but has yielded limited results. Augusto et al.'s recent study in Nature unveils a strong association of HLA-B*15:01 with asymptomatic COVID-19, representing an important contribution to genetics in COVID-19.
Collapse
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
| | - 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; Grupo de Medicina Xenómica- CIMUS- Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, 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.
| |
Collapse
|