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Naidoo L, Arumugam T, Ramsuran V. HLA-B and C Expression Contributes to COVID-19 Disease Severity within a South African Cohort. Genes (Basel) 2024; 15:522. [PMID: 38674456 PMCID: PMC11050528 DOI: 10.3390/genes15040522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Globally, SARS-CoV-2 has negatively impacted many lives and industries due to its rapid spread, severe outcomes, and the need for the implementation of lockdown strategies across the world. SARS-CoV-2 disease severity varies among different populations. Host genetics have been associated with various diseases, and their ability to alter disease susceptibility and severity. In addition, Human Leukocyte Antigen (HLA) expression levels and alleles vary significantly among ethnic groups, which might impact the host's response to SARS-CoV-2. Our previous study highlighted that HLA-A might have an effect on COVID-19 disease severity across ethnicities. Therefore, in this study, we aim to examine the effect of HLA-B and C expression levels on COVID-19 disease severity. To achieve this, we used real-time PCR to measure the HLA mRNA expression levels of SARS-CoV-2-infected individuals from a South African cohort and compared them across ethnic groups, disease outcomes, gender, comorbidities, and age. Our results show (1) that the effect of HLA-B mRNA expression levels was associated with differences in disease severity when we compare symptomatic vs. asymptomatic (p < 0.0001). While HLA-C mRNA expression levels were not associated with COVID-19 disease severity. (2) In addition, we observed that HLA-B and HLA-C mRNA expression levels were significantly different between South African Black individuals and South African Indian individuals (p < 0.0001, p < 0.0001). HLA-B mRNA expression levels among symptomatic South African Black individuals were significantly higher than symptomatic South African Indian individuals (p < 0.0001). In addition, the HLA-B mRNA expression levels of symptomatic South African Black individuals were significantly higher than asymptomatic South African Black individuals (p > 0.0001). HLA-C mRNA expression levels among symptomatic South African Black individuals were significantly higher than among symptomatic South African Indian individuals (p = 0.0217). (3) HLA-C expression levels were significantly different between males and females (p = 0.0052). In addition, the HLA-C expression levels of asymptomatic males are higher than asymptomatic females (p = 0.0375). (4) HLA-B expression levels were significantly different between individuals with and without comorbidities (p = 0.0009). In addition, we observed a significant difference between individuals with no comorbidities and non-communicable diseases (p = 0.0034), in particular, hypertension (p = 0.0487). (5) HLA-B expression levels were significantly different between individuals between 26-35 and 56-65 years (p = 0.0380). Our work is expected to strengthen the understanding of the relationship between HLA and COVID-19 by providing insights into HLA-B and C expression levels across ethnic populations in South Africa among COVID-19-symptomatic and asymptomatic individuals. Our results highlight that HLA-B mRNA expression levels contribute to COVID-19 severity as well as variation in ethnicities associated with COVID-19. Further studies are needed to examine the effect of HLA expression levels across various ethnic groups with contributing factors.
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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), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4041, South Africa
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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.
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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
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Wang S, Zhao N, Luo T, Kou S, Sun M, Chen K. Causality between COVID-19 and multiple myeloma: a two-sample Mendelian randomization study and Bayesian co-localization. Clin Exp Med 2024; 24:42. [PMID: 38400850 PMCID: PMC10894079 DOI: 10.1007/s10238-024-01299-y] [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: 08/24/2023] [Accepted: 01/18/2024] [Indexed: 02/26/2024]
Abstract
Infection is the leading cause of morbidity and mortality in patients with multiple myeloma (MM). Studying the relationship between different traits of Coronavirus 2019 (COVID-19) and MM is critical for the management and treatment of MM patients with COVID-19. But all the studies on the relationship so far were observational and the results were also contradictory. Using the latest publicly available COVID-19 genome-wide association studies (GWAS) data, we performed a bidirectional Mendelian randomization (MR) analysis of the causality between MM and different traits of COVID-19 (SARS-CoV-2 infection, COVID-19 hospitalization, and severe COVID-19) and use multi-trait analysis of GWAS(MTAG) to identify new associated SNPs in MM. We performed co-localization analysis to reveal potential causal pathways between diseases and over-representation enrichment analysis to find involved biological pathways. IVW results showed SARS-CoV-2 infection and COVID-19 hospitalization increased risk of MM. In the reverse analysis, the causal relationship was not found between MM for each of the different symptoms of COVID-19. Co-localization analysis identified LZTFL1, MUC4, OAS1, HLA-C, SLC22A31, FDX2, and MAPT as genes involved in COVID-19-mediated causation of MM. These genes were mainly related to immune function, glycosylation modifications and virus defense. Three novel MM-related SNPs were found through MTAG, which may regulate the expression of B3GNT6. This is the first study to use MR to explore the causality between different traits of COVID-19 and MM. The results of our two-way MR analysis found that SARS-CoV-2 infection and COVID-19 hospitalization increased the susceptibility of MM.
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Affiliation(s)
- Shuaiyuan Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, 450052, Henan, China
- Henan Key Laboratory of Tumor Pathology, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Na Zhao
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Ting Luo
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Songzi Kou
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Miaomiao Sun
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Kuisheng Chen
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Academy of Medical Science, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Henan Key Laboratory of Tumor Pathology, Zhengzhou University, Zhengzhou, 450052, Henan, China.
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Kumwichar P, Chongsuvivatwong V, Vasoppakarn S, Atthakul N, Nakhonsri V, Ngamphiw C, Khunkham P, Janpoung W, Tongsima S. Incidence rates of myocarditis and pericarditis within 30 days following homologous and heterologous BNT162b2 vaccinations in individuals 5-40 years of age. Vaccine 2024; 42:844-852. [PMID: 38246843 DOI: 10.1016/j.vaccine.2024.01.026] [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: 08/23/2023] [Revised: 12/14/2023] [Accepted: 01/08/2024] [Indexed: 01/23/2024]
Abstract
INTRODUCTION Due to the data scarcity in low- and middle-income countries, we aimed to examine the incidence rate of myocarditis and pericarditis within 30 days after each dose of homologous (3 × BNT162b2) and heterologous prime-boost (2 × BBIBP-CorV/BNT162b2) vaccine regimen among individuals younger than 40 years. METHODS We conducted a historical control cohort using routinely recorded data from Thai national vaccine and insurance claims databases. Sex-specific incidence rate ratios (IRRs) for myocarditis and pericarditis were calculated for each vaccination strategy and contrasted with incidence rates among the non-immunised population in the pre-COVID-19 period. From August 2021 to September 2022, we tracked the incidence of myocarditis and pericarditis within 30 days after vaccinations using < 40-year-old national population databases. Our reference was the average monthly incidence of these conditions in the non-immunised population from August to October 2019. The exposure of interest was immunisation against the SARS-CoV-2 virus, incorporating the following vaccination strategies: three-dose 3 × BNT162b2 regimen, three-dose 2 × BBIBP-CorV/BNT162b2 regimen, and non-immunisation. RESULTS For myocarditis, a total of 215 cases were identified among 7,594,965 individuals in the 3 × BNT162b2 cohort, 5 cases among 2,914,643 individuals in the 2 × BBIBP-CorV/BNT162b2 cohort, and 115 cases among 32,424,780 non-immunised individuals. The sex-specific IRRs (95 % confidence intervals) of myocarditis and pericarditis after the homologous vaccination were 3.09 (1.61, 5.93) and 1.84 (0.72, 4.73) for females and 7.43 (3.11, 17.73) and 10.48 (3.90, 28.15) for males, respectively. Conversely, the IRRs of myocarditis after the heterologous vaccination were not significant (females: 2.24 (0.70, 7.17); males: 1.99 (0.48, 8.21)). IRRs could not be obtained for pericarditis after the heterologous vaccination because of the small number of observed events. CONCLUSIONS The study observed a significantly increased risk of myocarditis and pericarditis following homologous 3 × BNT162b2 vaccination but had insufficient power to confirm an increased risk for myocarditis following the heterologous prime-boost 2 × BBIBP-CorV/BNT162b2 vaccination. The incidence of pericarditis following the heterologous vaccination was too rare to evaluate.
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Affiliation(s)
- Ponlagrit Kumwichar
- Department of Epidemiology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
| | - Virasakdi Chongsuvivatwong
- Department of Epidemiology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Sanya Vasoppakarn
- Bureau of Service Quality Development, National Health Security Office, Lak Si, Bangkok, Thailand
| | - Narumol Atthakul
- Bureau of Service Quality Development, National Health Security Office, Lak Si, Bangkok, Thailand
| | - Vorthunju Nakhonsri
- National Biobank of Thailand, National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand
| | - Chumpol Ngamphiw
- National Biobank of Thailand, National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand
| | - Peerapat Khunkham
- National Biobank of Thailand, National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand
| | - Watcharapot Janpoung
- National Biobank of Thailand, National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sissades Tongsima
- National Biobank of Thailand, National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand
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Bouchlarhem A, Boulouiz S, Bazid Z, Ismaili N, El Ouafi N. Is There a Causal Link Between Acute Myocarditis and COVID-19 Vaccination: An Umbrella Review of Published Systematic Reviews and Meta-Analyses. CLINICAL MEDICINE INSIGHTS-CARDIOLOGY 2024; 18:11795468231221406. [PMID: 38249317 PMCID: PMC10798131 DOI: 10.1177/11795468231221406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/25/2023] [Indexed: 01/23/2024]
Abstract
Introduction A few months after the beginning of the coronavirus disease of 2019 (COVID-19) vaccination, several reports of myocarditis secondary to the vaccines were published, sometimes with fulminant cases, but until today there is no proven causal link between these 2 events, but with many hypotheses proposed. Methods A systematic review of current evidence regarding myocarditis after COVID-19 vaccination was performed by searching several databases including PubMed/Medline and Web of Science. The quality of Meta-analysis was assessed using the AMSTAR-2 tool as well as other qualitative criteria. Results Our umbrella review appraised 4 Meta-analysis of retrospective studies (range: 5-12), The number of vaccine doses included ranged from 12 to 179 million, with the number of myocarditis cases observed ranging from 343 to 1489. All types of vaccines were evaluated, with no exclusions. The overall incidence ranged from 0.89 to 2.36 cases of myocarditis per 100 000 doses of vaccine received. Heterogeny was assessed in 3 of the Meta-analysis, and was highly significant (>75%) in all included studies, and with a significant P-value (P < .05). Regarding publication bias, 3 of the Meta-analysis conducted the egger and begg regression, with a significant result in only 1. Regarding the assessment of the methodology by the AMSTAR-2 scale indicating that the quality was very critical in 1, low in 2, and moderate in 1 Meta-analysis. Conclusion The quality of current non-randomized evidence on real causality and incidence of myocarditis after COVID-19 vaccine is still low.
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Affiliation(s)
- Amine Bouchlarhem
- Faculty of Medicine and Pharmacy, Mohammed First University, Oujda, Morocco
- Department of Cardiology, Mohammed VI University Hospital, Mohammed First University, Oujda, Morocco
| | - Soumia Boulouiz
- Faculty of Medicine and Pharmacy, Mohammed First University, Oujda, Morocco
- Department of Cardiology, Mohammed VI University Hospital, Mohammed First University, Oujda, Morocco
| | - Zakaria Bazid
- Faculty of Medicine and Pharmacy, Mohammed First University, Oujda, Morocco
- Department of Cardiology, Mohammed VI University Hospital, Mohammed First University, Oujda, Morocco
| | - Nabila Ismaili
- Faculty of Medicine and Pharmacy, Mohammed First University, Oujda, Morocco
- Department of Cardiology, Mohammed VI University Hospital, Mohammed First University, Oujda, Morocco
- Faculty of Medicine and Pharmacy, Mohammed First University, LAMCESM, Oujda, Morocco
| | - Noha El Ouafi
- Faculty of Medicine and Pharmacy, Mohammed First University, Oujda, Morocco
- Department of Cardiology, Mohammed VI University Hospital, Mohammed First University, Oujda, Morocco
- Faculty of Medicine and Pharmacy, Mohammed First University, LAMCESM, Oujda, Morocco
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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
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Hoseinnezhad T, Soltani N, Ziarati S, Behboudi E, Mousavi MJ. The role of HLA genetic variants in COVID-19 susceptibility, severity, and mortality: A global review. J Clin Lab Anal 2024; 38:e25005. [PMID: 38251811 PMCID: PMC10829690 DOI: 10.1002/jcla.25005] [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: 10/06/2023] [Revised: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic has had a profound global impact, with variations in susceptibility, severity, and mortality rates across different regions. While many factors can contribute to the spread and impact of the disease, specifically human leukocyte antigen (HLA) genetic variants have emerged as potential contributors to COVID-19 outcomes. METHODS In this comprehensive narrative review, we conducted a thorough literature search to identify relevant studies investigating the association between HLA genetic variants and COVID-19 outcomes. Additionally, we analyzed allelic frequency data from diverse populations to assess differences in COVID-19 incidence and severity. RESULTS Our review provides insights into the immunological mechanisms involving HLA-mediated responses to COVID-19 and highlights potential research directions and therapeutic interventions. We found evidence suggesting that certain HLA alleles, such as HLA-A02, may confer a lower risk of COVID-19, while others, like HLA-C04, may increase the risk of severe symptoms and mortality. Furthermore, our analysis of allele frequency distributions revealed significant variations among different populations. CONCLUSION Considering host genetic variations, particularly HLA genetic variants, is crucial for understanding COVID-19 susceptibility and severity. These findings have implications for personalized treatment and interventions based on an individual's genetic profile. However, further research is needed to unravel the precise mechanisms underlying the observed associations and explore the potential for targeted therapies or preventive measures based on HLA genetic variants.
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Affiliation(s)
- Taraneh Hoseinnezhad
- Student Research CommitteeBushehr University of Medical SciencesBushehrIran
- Department of Hematology, School of Para‐MedicineBushehr University of Medical SciencesBushehrIran
| | - Nasrin Soltani
- Student Research CommitteeBushehr University of Medical SciencesBushehrIran
- Department of Hematology, School of Para‐MedicineBushehr University of Medical SciencesBushehrIran
| | - Sarina Ziarati
- Student Research CommitteeBushehr University of Medical SciencesBushehrIran
| | - Emad Behboudi
- Department of Basic Medical SciencesKhoy University of Medical SciencesKhoyIran
| | - Mohammad Javad Mousavi
- Department of Hematology, School of Para‐MedicineBushehr University of Medical SciencesBushehrIran
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Poller W, Sahoo S, Hajjar R, Landmesser U, Krichevsky AM. Exploration of the Noncoding Genome for Human-Specific Therapeutic Targets-Recent Insights at Molecular and Cellular Level. Cells 2023; 12:2660. [PMID: 37998395 PMCID: PMC10670380 DOI: 10.3390/cells12222660] [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: 10/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
While it is well known that 98-99% of the human genome does not encode proteins, but are nevertheless transcriptionally active and give rise to a broad spectrum of noncoding RNAs [ncRNAs] with complex regulatory and structural functions, specific functions have so far been assigned to only a tiny fraction of all known transcripts. On the other hand, the striking observation of an overwhelmingly growing fraction of ncRNAs, in contrast to an only modest increase in the number of protein-coding genes, during evolution from simple organisms to humans, strongly suggests critical but so far essentially unexplored roles of the noncoding genome for human health and disease pathogenesis. Research into the vast realm of the noncoding genome during the past decades thus lead to a profoundly enhanced appreciation of the multi-level complexity of the human genome. Here, we address a few of the many huge remaining knowledge gaps and consider some newly emerging questions and concepts of research. We attempt to provide an up-to-date assessment of recent insights obtained by molecular and cell biological methods, and by the application of systems biology approaches. Specifically, we discuss current data regarding two topics of high current interest: (1) By which mechanisms could evolutionary recent ncRNAs with critical regulatory functions in a broad spectrum of cell types (neural, immune, cardiovascular) constitute novel therapeutic targets in human diseases? (2) Since noncoding genome evolution is causally linked to brain evolution, and given the profound interactions between brain and immune system, could human-specific brain-expressed ncRNAs play a direct or indirect (immune-mediated) role in human diseases? Synergistic with remarkable recent progress regarding delivery, efficacy, and safety of nucleic acid-based therapies, the ongoing large-scale exploration of the noncoding genome for human-specific therapeutic targets is encouraging to proceed with the development and clinical evaluation of novel therapeutic pathways suggested by these research fields.
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Affiliation(s)
- Wolfgang Poller
- Department for Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum Charité (DHZC), Charité-Universitätsmedizin Berlin, 12200 Berlin, Germany;
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 10785 Berlin, Germany
| | - Susmita Sahoo
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1030, New York, NY 10029, USA;
| | - Roger Hajjar
- Gene & Cell Therapy Institute, Mass General Brigham, 65 Landsdowne St, Suite 143, Cambridge, MA 02139, USA;
| | - Ulf Landmesser
- Department for Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum Charité (DHZC), Charité-Universitätsmedizin Berlin, 12200 Berlin, Germany;
- German Center for Cardiovascular Research (DZHK), Site Berlin, 10785 Berlin, Germany
- Berlin Institute of Health, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Anna M. Krichevsky
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
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Lopes-Ribeiro Á, Oliveira PDM, Retes H, Barbosa-Stancioli EF, da Fonseca FG, Tsuji M, Coelho-dos-Reis JGA. Surveillance of SARS-CoV-2 immunogenicity: loss of immunodominant HLA-A*02-restricted epitopes that activate CD8 + T cells. Front Immunol 2023; 14:1229712. [PMID: 38022506 PMCID: PMC10656734 DOI: 10.3389/fimmu.2023.1229712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction and methods In this present work, coronavirus subfamilies and SARS-CoV-2 Variants of Concern (VOCs) were investigated for the presence of MHC-I immunodominant viral peptides using in silico and in vitro tools. Results In our results, HLA-A*02 haplotype showed the highest number of immunodominant epitopes but with the lowest combined prediction score. Furthermore, a decrease in combined prediction score was observed for HLA-A*02-restricted epitopes when the original strain was compared to the VOCs, indicating that the mutations on the VOCs are promoting escape from HLA-A2-mediated antigen presentation, which characterizes a immune evasion process. Additionally, epitope signature analysis revealed major immunogenic peptide loss for structural (S) and non-structural (ORF8) proteins of VOCs in comparison to the Wuhan sequence. Discussion These results may indicate that the antiviral CD8+ T-cell responses generated by original strains could not be sufficient for clearance of variants in either newly or reinfection with SARS-CoV-2. In contrast, N epitopes remain the most conserved and reactive peptides across SARS-CoV-2 VOCs. Overall, our data could contribute to the rational design and development of new vaccinal platforms to induce a broad cellular CD8+ T cell antiviral response, aiming at controlling viral transmission of future SARS-CoV-2 variants.
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Affiliation(s)
- Ágata Lopes-Ribeiro
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Patrícia de Melo Oliveira
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Henrique Morais Retes
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Edel Figueiredo Barbosa-Stancioli
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Flávio Guimarães da Fonseca
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Centro de Tecnologia (CT) Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Moriya Tsuji
- Aaron Diamond AIDS Research Center, Irving Medical School, Columbia University, New York, NY, United States
| | - Jordana Grazziela Alves Coelho-dos-Reis
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Rao V, Banerjee U, Sambaturu N, Chunchanur S, Ambica R, Chandra N. Pressured cytotoxic T cell epitope strength among SARS-CoV-2 variants correlates with COVID-19 severity. HLA 2023; 102:464-476. [PMID: 37134008 DOI: 10.1111/tan.15071] [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: 09/15/2022] [Revised: 02/13/2023] [Accepted: 04/11/2023] [Indexed: 05/04/2023]
Abstract
Heterogeneity in susceptibility among individuals to COVID-19 has been evident through the pandemic worldwide. Cytotoxic T lymphocyte (CTL) responses generated against pathogens in certain individuals are known to impose selection pressure on the pathogen, thus driving emergence of new variants. In this study, we probe the role played by host genetic heterogeneity in terms of HLA-genotypes in determining differential COVID-19 severity in patients. We use bioinformatic tools for CTL epitope prediction to identify epitopes under immune pressure. Using HLA-genotype data of COVID-19 patients from a local cohort, we observe that the recognition of pressured epitopes from the parent strain Wuhan-Hu-1 correlates with COVID-19 severity. We also identify and rank list HLA-alleles and epitopes that offer protectivity against severe disease in infected individuals. Finally, we shortlist a set of 6 pressured and protective epitopes that represent regions in the viral proteome that are under high immune pressure across SARS-CoV-2 variants. Identification of such epitopes, defined by the distribution of HLA-genotypes among members of a population, could potentially aid in prediction of indigenous variants of SARS-CoV-2 and other pathogens.
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Affiliation(s)
- Vishal Rao
- Department of Biochemistry, Indian Institute of Science (IISc), Bangalore, India
| | - Ushashi Banerjee
- Department of Biochemistry, Indian Institute of Science (IISc), Bangalore, India
| | - Narmada Sambaturu
- Department of Biochemistry, Indian Institute of Science (IISc), Bangalore, India
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Sneha Chunchanur
- Department of Microbiology, Bangalore Medical College and Research Institute (BMCRI), Bangalore, India
| | - R Ambica
- Department of Microbiology, Bangalore Medical College and Research Institute (BMCRI), Bangalore, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science (IISc), Bangalore, India
- Center for BioSystems Science and Engineering (BSSE), Indian Institute of Science (IISc), Bangalore, India
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11
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Balnis J, Lauria EJM, Yucel R, Singer HA, Alisch RS, Jaitovich A. Peripheral Blood Omics and Other Multiplex-based Systems in Pulmonary and Critical Care Medicine. Am J Respir Cell Mol Biol 2023; 69:383-390. [PMID: 37379507 PMCID: PMC10557924 DOI: 10.1165/rcmb.2023-0153ps] [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: 04/27/2023] [Accepted: 06/28/2023] [Indexed: 06/30/2023] Open
Abstract
Over the last years, the use of peripheral blood-derived big datasets in combination with machine learning technology has accelerated the understanding, prediction, and management of pulmonary and critical care conditions. The goal of this article is to provide readers with an introduction to the methods and applications of blood omics and other multiplex-based technologies in the pulmonary and critical care medicine setting to better appreciate the current literature in the field. To accomplish that, we provide essential concepts needed to rationalize this approach and introduce readers to the types of molecules that can be obtained from the circulating blood to generate big datasets; elaborate on the differences between bulk, sorted, and single-cell approaches; and the basic analytical pipelines required for clinical interpretation. Examples of peripheral blood-derived big datasets used in recent literature are presented, and limitations of that technology are highlighted to qualify both the current and future value of these methodologies.
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Affiliation(s)
- Joseph Balnis
- Division of Pulmonary and Critical Care Medicine and
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Eitel J. M. Lauria
- School of Computer Science and Mathematics, Marist College, Poughkeepsie, New York
| | - Recai Yucel
- Department of Epidemiology and Biostatistics, Temple University, Philadelphia, Pennsylvania; and
| | - Harold A. Singer
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Reid S. Alisch
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Ariel Jaitovich
- Division of Pulmonary and Critical Care Medicine and
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
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Rahman MA, Amin MA, Yeasmin MN, Islam MZ. Molecular Biomarker Identification Using a Network-Based Bioinformatics Approach That Links COVID-19 With Smoking. Bioinform Biol Insights 2023; 17:11779322231186481. [PMID: 37461741 PMCID: PMC10350588 DOI: 10.1177/11779322231186481] [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: 12/18/2022] [Accepted: 06/21/2023] [Indexed: 07/20/2023] Open
Abstract
The COVID-19 coronavirus, which primarily affects the lungs, is the source of the disease known as SARS-CoV-2. According to "Smoking and COVID-19: a scoping review," about 32% of smokers had a severe case of COVID-19 pneumonia at their admission time and 15% of non-smokers had this case of COVID-19 pneumonia. We were able to determine which genes were expressed differently in each group by comparing the expression of gene transcriptomic datasets of COVID-19 patients, smokers, and healthy controls. In all, 37 dysregulated genes are common in COVID-19 patients and smokers, according to our analysis. We have applied all important methods namely protein-protein interaction, hub-protein interaction, drug-protein interaction, tf-gene interaction, and gene-MiRNA interaction of bioinformatics to analyze to understand deeply the connection between both smoking and COVID-19 severity. We have also analyzed Pathways and Gene Ontology where 5 significant signaling pathways were validated with previous literature. Also, we verified 7 hub-proteins, and finally, we validated a total of 7 drugs with the previous study.
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Affiliation(s)
| | - Md Al Amin
- Department of Computer Science & Engineering, Prime University, Dhaka, Bangladesh
| | - Most Nilufa Yeasmin
- Department of Information & Communication Technology, Islamic University, Kushtia, Bangladesh
| | - Md Zahidul Islam
- Department of Information & Communication Technology, Islamic University, Kushtia, Bangladesh
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13
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Velastegui E, Vera E, Vanden Berghe W, Muñoz MS, Orellana-Manzano A. "HLA-C: evolution, epigenetics, and pathological implications in the major histocompatibility complex". Front Genet 2023; 14:1206034. [PMID: 37465164 PMCID: PMC10350511 DOI: 10.3389/fgene.2023.1206034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023] Open
Abstract
HLA-C, a gene located within the major histocompatibility complex, has emerged as a prominent target in biomedical research due to its involvement in various diseases, including cancer and autoimmune disorders; even though its recent addition to the MHC, the interaction between HLA-C and KIR is crucial for immune responses, particularly in viral infections. This review provides an overview of the structure, origin, function, and pathological implications of HLA-C in the major histocompatibility complex. In the last decade, we systematically reviewed original publications from Pubmed, ScienceDirect, Scopus, and Google Scholar. Our findings reveal that genetic variations in HLA-C can determine susceptibility or resistance to certain diseases. However, the first four exons of HLA-C are particularly susceptible to epigenetic modifications, which can lead to gene silencing and alterations in immune function. These alterations can manifest in diseases such as alopecia areata and psoriasis and can also impact susceptibility to cancer and the effectiveness of cancer treatments. By comprehending the intricate interplay between genetic and epigenetic factors that regulate HLA-C expression, researchers may develop novel strategies for preventing and treating diseases associated with HLA-C dysregulation.
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Affiliation(s)
- Erick Velastegui
- Escuela Politécnica Nacional, Departamento de Ciencias de los Alimentos y Biotecnología, Facultad de Ingeniería Química y Agroindustria, Quito, Ecuador
| | - Edwin Vera
- Escuela Politécnica Nacional, Departamento de Ciencias de los Alimentos y Biotecnología, Facultad de Ingeniería Química y Agroindustria, Quito, Ecuador
| | - Wim Vanden Berghe
- Epigenetic Signaling Lab, Faculty Biomedical Sciences, PPES, University of Antwerp, Antwerp, Belgium
| | - Mindy S. Muñoz
- Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Andrea Orellana-Manzano
- Escuela Superior Politécnica del Litoral, Laboratorio para investigaciones biomédicas, Facultad de Ciencias de la Vida (FCV), Guayaquil, Ecuador
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Bnina AB, El Bahri Y, Cheybi A, Lazrek NB, Chouchane S, Omezzine A, Naija W, Bouatay A. Association between Human Leukocyte Antigen (HLA) DQB1*06 and HLA DQB1*03 and adverse outcomes in a group of critically ill patients with COVID-19 in Tunisia: a cross-sectional study. Pan Afr Med J 2023; 45:109. [PMID: 37719057 PMCID: PMC10504440 DOI: 10.11604/pamj.2023.45.109.39956] [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: 04/05/2023] [Accepted: 06/08/2023] [Indexed: 09/19/2023] Open
Abstract
Introduction Human Leukocyte Antigen (HLA) system is a highly polymorphic genetic system associated with the prognosis of several infectious diseases. The aim of this study is to investigate the association of HLA polymorphism with the outcome of coronavirus disease 2019 (COVID-19) in Tunisian critically ill patients. Methods this retrospective cross-sectional study included 42 consecutive patients hospitalized in intensive care unit (ICU) for COVID-19 in March 2021. Genotyping of HLA loci was performed by LABType™ sequence-specific oligonucleotide (SSO) typing kits (One lambda Inc, USA). Statistical analyses were performed using Statistical Package for Social Sciences (SPSS®) version 23.0. A p-value <0.05 was considered significant. Multivariable regression analysis was performed for the association between HLA polymorphism with adverse outcomes with adjustment for potential confounders such as age, sex, co-morbidities and blood type. Results patients included in our study had a mean age of 64.5 ± 11.5 (34-83) years and were mainly men (64.3%; (n=27)). The most common cardiovascular risk factors were obesity (61.9%; (n=26)) and hypertension (26.2%; (n=11)). Thirty-two patients died (76.2%). Eleven patients (26.2%) required intubation during hospitalization. We found that HLA DQB1*06 allele was significantly associated with protection against mortality aOR: 0.066, 95% CI 0.005-0.821; p = 0.035. HLA DQB1*03 allele was significantly associated with protection against intubation aOR: 0.151, 95% CI 0.023-0.976; p = 0.047. Conclusion it was found that there are 2 protective HLA alleles against COVID-19 severity and mortality in critically ill patients. This could allow focusing on people genetically predisposed to develop severe forms of COVID-19.
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Affiliation(s)
- Amène Ben Bnina
- Hematology Laboratory, Sahloul Teaching Hospital, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Yasmine El Bahri
- Hematology Laboratory, Sahloul Teaching Hospital, Sousse, Tunisia
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
| | - Amény Cheybi
- Hematology Laboratory, Sahloul Teaching Hospital, Sousse, Tunisia
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
| | - Nada Ben Lazrek
- Hematology Laboratory, Sahloul Teaching Hospital, Sousse, Tunisia
| | - Syrine Chouchane
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
- Department of Anesthesia and Intensive Care, Sahloul Teaching Hospital, Sousse, Tunisia
| | - Asma Omezzine
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- Biochemistry Laboratory, Sahloul Teaching Hospital, Sousse, Tunisia
| | - Walid Naija
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
- Department of Anesthesia and Intensive Care, Sahloul Teaching Hospital, Sousse, Tunisia
| | - Amina Bouatay
- Hematology Laboratory, Sahloul Teaching Hospital, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
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15
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Mashayekhi P, Omrani MD, Yassin Z, Dehghanifard A, Ashouri L, Aghabozorg Afjeh SS, Shabanzadeh Z. Influence of HLA-A, -B, -DR Polymorphisms on the Severity of COVID-19: A Case-Control Study in the Iranian Population. ARCHIVES OF IRANIAN MEDICINE 2023; 26:261-266. [PMID: 38301089 PMCID: PMC10685865 DOI: 10.34172/aim.2023.40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 03/12/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND As an emerging pandemic disease, COVID-19 encompasses a spectrum of clinical diagnoses, from the common cold to severe respiratory syndrome. Considering the shreds of evidence demonstrating the relationship between human leukocyte antigen (HLA) allele diversity and infectious disease susceptibility, this study was conducted to determine the association of HLA alleles with COVID-19 severity in Iranian subjects. METHODS In this case-control study, a total of 200 unrelated individuals (consisting of 100 people with severe COVID-19 and an average age of 55.54 as the case group, and 100 patients with mild COVID-19 with an average age of 48.97 as the control group) were recruited, and HLA typing (Locus A, B, and DR) was performed using the Olerup sequence-specific oligonucleotide (SSO) HLA-typing kit. RESULTS Our results showed that HLA-A*11 and HLA-DRB1*14 alleles were more frequently observed in severe COVID-19 cases, while HLA-B*52 was more common in mild cases, which was in agreement with some previous studies. CONCLUSION Our results confirmed the evidence for the association of HLA alleles with COVID-19 outcomes. We found that HLA-A*11 and HLA-DRB1*14 alleles may be susceptibility factors for severe COVID-19, while HLA-B*52 may be a protective factor. These findings provide new insight into the pathogenesis of COVID-19 and help patient management.
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Affiliation(s)
- Parisa Mashayekhi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mir Davood Omrani
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zeynab Yassin
- Antimicrobial resistance Research Center, Institute Of Immunology And Infectious Disease, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Dehghanifard
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Leila Ashouri
- Antimicrobial resistance Research Center, Institute Of Immunology And Infectious Disease, Iran University of Medical Sciences, Tehran, Iran
| | | | - Zahra Shabanzadeh
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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16
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Scaramuzzo G, Nucera F, Asmundo A, Messina R, Mari M, Montanaro F, Johansen MD, Monaco F, Fadda G, Tuccari G, Hansbro NG, Hansbro PM, Hansel TT, Adcock IM, David A, Kirkham P, Caramori G, Volta CA, Spadaro S. Cellular and molecular features of COVID-19 associated ARDS: therapeutic relevance. J Inflamm (Lond) 2023; 20:11. [PMID: 36941580 PMCID: PMC10027286 DOI: 10.1186/s12950-023-00333-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/08/2023] [Indexed: 03/23/2023] Open
Abstract
The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection can be asymptomatic or cause a disease (COVID-19) characterized by different levels of severity. The main cause of severe COVID-19 and death is represented by acute (or acute on chronic) respiratory failure and acute respiratory distress syndrome (ARDS), often requiring hospital admission and ventilator support.The molecular pathogenesis of COVID-19-related ARDS (by now termed c-ARDS) is still poorly understood. In this review we will discuss the genetic susceptibility to COVID-19, the pathogenesis and the local and systemic biomarkers correlated with c-ARDS and the therapeutic options that target the cell signalling pathways of c-ARDS.
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Affiliation(s)
- Gaetano Scaramuzzo
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Department of Emergency, Section of Intensive Care and Anesthesia, Azienda Ospedaliera-Universitaria Sant'Anna, Ferrara, Italy
| | - Francesco Nucera
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Alessio Asmundo
- Medicina Legale, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Roberto Messina
- Intensive Care Unit, Dipartimento di Patologia Umana e dell'Età Evolutiva Gaetano Barresi, Università di Messina, Messina, Italy
| | - Matilde Mari
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Department of Emergency, Section of Intensive Care and Anesthesia, Azienda Ospedaliera-Universitaria Sant'Anna, Ferrara, Italy
| | - Federica Montanaro
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Department of Emergency, Section of Intensive Care and Anesthesia, Azienda Ospedaliera-Universitaria Sant'Anna, Ferrara, Italy
| | - Matt D Johansen
- Centre for Inflammation, School of Life Sciences, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia
| | - Francesco Monaco
- Chirurgia Toracica, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Guido Fadda
- Section of Pathological Anatomy, Department of Human Pathology of Adult and Developmental Age "Gaetano Barresi", University of Messina, Messina, Italy
| | - Giovanni Tuccari
- Section of Pathological Anatomy, Department of Human Pathology of Adult and Developmental Age "Gaetano Barresi", University of Messina, Messina, Italy
| | - Nicole G Hansbro
- Centre for Inflammation, School of Life Sciences, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia
| | - Philip M Hansbro
- Centre for Inflammation, School of Life Sciences, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia
| | - Trevor T Hansel
- Medical Research Council and Asthma, UK Centre in Allergic Mechanisms of Asthma, London, UK
| | - Ian M Adcock
- Airway Disease Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Antonio David
- Intensive Care Unit, Dipartimento di Patologia Umana e dell'Età Evolutiva Gaetano Barresi, Università di Messina, Messina, Italy
| | - Paul Kirkham
- Department of Biomedical Sciences, Faculty of Sciences and Engineering, University of Wolverhampton, West Midlands, Wolverhampton, UK
| | - Gaetano Caramori
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy.
| | - Carlo Alberto Volta
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Department of Emergency, Section of Intensive Care and Anesthesia, Azienda Ospedaliera-Universitaria Sant'Anna, Ferrara, Italy
| | - Savino Spadaro
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Department of Emergency, Section of Intensive Care and Anesthesia, Azienda Ospedaliera-Universitaria Sant'Anna, Ferrara, Italy
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17
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Yiang GT, Wu CC, Lu CL, Hu WC, Tsai YJ, Huang YM, Su WL, Lu KC. Endoplasmic Reticulum Stress in Elderly Patients with COVID-19: Potential of Melatonin Treatment. Viruses 2023; 15:156. [PMID: 36680196 PMCID: PMC9863214 DOI: 10.3390/v15010156] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
Aging processes, including immunosenescence, inflammation, inflammasome formation, genomic instability, telomeric attrition, and altered autophagy, are involved in viral infections and they may contribute to increased pathophysiological responses to the SARS-CoV-2 infection in the elderly; this poses additional risks of accelerated aging, which could be found even after recovery. Aging is associated with oxidative damage. Moreover, SARS-CoV-2 infections may increase the production of reactive oxygen species and such infections will disturb the Ca++ balance via an endoplasmic reticulum (ER) stress-mediated unfolded protein response. Although vaccine development and anti-inflammation therapy lower the severity of COVID-19, the prevalence and mortality rates are still alarming in some countries worldwide. In this review, we describe the involvement of viral proteins in activating ER stress transducers and their downstream signals and in inducing inflammation and inflammasome formation. Furthermore, we propose the potential of melatonin as an ER stress modulator, owing to its antioxidant, anti-inflammatory, and immunoregulatory effects in viral infections. Considering its strong safety profile, we suggest that additive melatonin supplementation in the elderly could be beneficial in treating COVID-19.
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Affiliation(s)
- Giou-Teng Yiang
- Department of Emergency Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei 231, Taiwan
- School of Medicine, Tzu Chi University, Hualien 970, Taiwan
| | - Chia-Chao Wu
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei 114, Taiwan
| | - Chien-Lin Lu
- Division of Nephrology, Department of Medicine, Fu Jen Catholic University Hospital, School of Medicine, Fu Jen Catholic University, New Taipei 24352, Taiwan
| | - Wan-Chung Hu
- Department of Clinical Pathology, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei 231, Taiwan
| | - Yi-Ju Tsai
- Graduate Institute of Biomedical and Pharmaceutical Science, College of Medicine, Fu Jen Catholic University, New Taipei 243, Taiwan
| | - Yiao-Mien Huang
- Department of Dentistry, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei 231, Taiwan
| | - Wen-Lin Su
- School of Medicine, Tzu Chi University, Hualien 970, Taiwan
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei 231, Taiwan
| | - Kuo-Cheng Lu
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
- Division of Nephrology, Department of Medicine, Fu Jen Catholic University Hospital, School of Medicine, Fu Jen Catholic University, New Taipei 24352, Taiwan
- Division of Nephrology, Department of Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei 231, Taiwan
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18
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Margaroli C, Benson P, Gastanadui MG, Song C, Viera L, Xing D, Wells JM, Patel R, Gaggar A, Payne GA. Spatial transcriptomic profiling of coronary endothelial cells in SARS-CoV-2 myocarditis. Front Med (Lausanne) 2023; 10:1118024. [PMID: 36968839 PMCID: PMC10034160 DOI: 10.3389/fmed.2023.1118024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
Objectives Our objective was to examine coronary endothelial and myocardial programming in patients with severe COVID-19 utilizing digital spatial transcriptomics. Background Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has well-established links to thrombotic and cardiovascular events. Endothelial cell infection was initially proposed to initiate vascular events; however, this paradigm has sparked growing controversy. The significance of myocardial infection also remains unclear. Methods Autopsy-derived cardiac tissue from control (n = 4) and COVID-19 (n = 8) patients underwent spatial transcriptomic profiling to assess differential expression patterns in myocardial and coronary vascular tissue. Our approach enabled transcriptional profiling in situ with preserved anatomy and unaltered local SARS-CoV-2 expression. In so doing, we examined the paracrine effect of SARS-CoV-2 infection in cardiac tissue. Results We observed heterogeneous myocardial infection that tended to colocalize with CD31 positive cells within coronary capillaries. Despite these differences, COVID-19 patients displayed a uniform and unique myocardial transcriptional profile independent of local viral burden. Segmentation of tissues directly infected with SARS-CoV-2 showed unique, pro-inflammatory expression profiles including upregulated mediators of viral antigen presentation and immune regulation. Infected cell types appeared to primarily be capillary endothelial cells as differentially expressed genes included endothelial cell markers. However, there was limited differential expression within the endothelium of larger coronary vessels. Conclusion Our results highlight altered myocardial programming during severe COVID-19 that may in part be associated with capillary endothelial cells. However, similar patterns were not observed in larger vessels, diminishing endotheliitis, and endothelial activation as key drivers of cardiovascular events during COVID-19.
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Affiliation(s)
- Camilla Margaroli
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Paul Benson
- Department of Pathology, Division of Anatomic Pathology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Maria G. Gastanadui
- Cardiopulmonary Research Program, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Medicine, Division of Cardiovascular Disease, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Chunyan Song
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- Cardiopulmonary Research Program, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Medicine, Division of Cardiovascular Disease, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Liliana Viera
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- Lung Health Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Dongqi Xing
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- Cardiopulmonary Research Program, University of Alabama at Birmingham, Birmingham, AL, United States
- Lung Health Center, University of Alabama at Birmingham, Birmingham, AL, United States
- Vascular Biology and Hypertension Program, University of Alabama at Birmingham, Birmingham, AL, United States
| | - J. Michael Wells
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- Cardiopulmonary Research Program, University of Alabama at Birmingham, Birmingham, AL, United States
- Lung Health Center, University of Alabama at Birmingham, Birmingham, AL, United States
- Vascular Biology and Hypertension Program, University of Alabama at Birmingham, Birmingham, AL, United States
- Medical Service at Birmingham VA Medical Center, Birmingham, AL, United States
| | - Rakesh Patel
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, United States
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Amit Gaggar
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- Cardiopulmonary Research Program, University of Alabama at Birmingham, Birmingham, AL, United States
- Lung Health Center, University of Alabama at Birmingham, Birmingham, AL, United States
- Vascular Biology and Hypertension Program, University of Alabama at Birmingham, Birmingham, AL, United States
- Medical Service at Birmingham VA Medical Center, Birmingham, AL, United States
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Gregory A. Payne
- Program in Protease/Matrix Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- Cardiopulmonary Research Program, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Medicine, Division of Cardiovascular Disease, University of Alabama at Birmingham, Birmingham, AL, United States
- Vascular Biology and Hypertension Program, University of Alabama at Birmingham, Birmingham, AL, United States
- Medical Service at Birmingham VA Medical Center, Birmingham, AL, United States
- Comprehensive Cardiovascular Center, University of Alabama at Birmingham, Birmingham, AL, United States
- *Correspondence: Gregory A. Payne,
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Innate Immunity in Cardiovascular Diseases-Identification of Novel Molecular Players and Targets. J Clin Med 2023; 12:jcm12010335. [PMID: 36615135 PMCID: PMC9821340 DOI: 10.3390/jcm12010335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/20/2022] [Accepted: 12/25/2022] [Indexed: 01/03/2023] Open
Abstract
During the past few years, unexpected developments have driven studies in the field of clinical immunology. One driver of immense impact was the outbreak of a pandemic caused by the novel virus SARS-CoV-2. Excellent recent reviews address diverse aspects of immunological re-search into cardiovascular diseases. Here, we specifically focus on selected studies taking advantage of advanced state-of-the-art molecular genetic methods ranging from genome-wide epi/transcriptome mapping and variant scanning to optogenetics and chemogenetics. First, we discuss the emerging clinical relevance of advanced diagnostics for cardiovascular diseases, including those associated with COVID-19-with a focus on the role of inflammation in cardiomyopathies and arrhythmias. Second, we consider newly identified immunological interactions at organ and system levels which affect cardiovascular pathogenesis. Thus, studies into immune influences arising from the intestinal system are moving towards therapeutic exploitation. Further, powerful new research tools have enabled novel insight into brain-immune system interactions at unprecedented resolution. This latter line of investigation emphasizes the strength of influence of emotional stress-acting through defined brain regions-upon viral and cardiovascular disorders. Several challenges need to be overcome before the full impact of these far-reaching new findings will hit the clinical arena.
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Arab F, Mollazadeh S, Ghayourbabaei F, Moghbeli M, Saburi E. The role of HLA genotypes in understanding the pathogenesis of severe COVID-19. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2023; 24:14. [PMID: 36718139 PMCID: PMC9878497 DOI: 10.1186/s43042-023-00392-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has caused human tragedy through the global spread of the viral pathogen SARS-CoV-2. Although the underlying factors for the severity of COVID-19 in different people are still unknown, several gene variants can be used as predictors of disease severity, particularly variations in viral receptor genes such as angiotensin-converting enzyme 2 (ACE2) or major histocompatibility complex (MHC) genes. The reaction of the immune system, as the most important defense strategy in the case of viruses, plays a decisive role. The innate immune system is important both as a primary line of defense and as a trigger of the acquired immune response. The HLA-mediated acquired immune response is linked to the acquired immune system. In various diseases, it has been shown that genetic alterations in components of the immune system can play a crucial role in how the body responds to pathogens, especially viruses. One of the most important host genetic factors is the human leukocyte antigen (HLA) profile, which includes HLA classes I and II and may be symbolic of the diversity of immune response and genetic predisposition in disease progression. COVID-19 will have direct contact with the acquired immune system as an intracellular pathogen after exposure to the proteasome and its components through class I HLA. Therefore, it is assumed that in different genotypes of the HLA-I class, an undesirable supply causes an insufficient activation of the immune system. Insufficient binding of antigen delivered by class I HLA to host lymphocytes results in uncertain identification and insufficient activation of the acquired immune system. The absence of secretion of immune cytokines such as interferons, which play an important role in controlling viral infection in the early stages, is a complication of this event. Understanding the allelic diversity of HLA in people infected with coronavirus compared with uninfected people of one race not only allows identification of people with HLA susceptible to COVID-19 but also provides better insight into the behavior of the virus, which helps to take effective preventive and curative measures earlier.
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Affiliation(s)
- Fatemeh Arab
- grid.411583.a0000 0001 2198 6209Medical Genetics and Molecular Medicine Department, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Samaneh Mollazadeh
- grid.464653.60000 0004 0459 3173Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Farnaz Ghayourbabaei
- grid.411301.60000 0001 0666 1211Department of Biology, Faculty of Sciences, University of Ferdowsi, Mashhad, Iran
| | - Meysam Moghbeli
- grid.411583.a0000 0001 2198 6209Medical Genetics and Molecular Medicine Department, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Saburi
- grid.411583.a0000 0001 2198 6209Medical Genetics and Molecular Medicine Department, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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21
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Fakhkhari M, Caidi H, Sadki K. HLA alleles associated with COVID-19 susceptibility and severity in different populations: a systematic review. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2023; 24:10. [PMID: 36710951 PMCID: PMC9867832 DOI: 10.1186/s43042-023-00390-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/15/2023] [Indexed: 01/23/2023] Open
Abstract
Background COVID-19 is a respiratory disease caused by a novel coronavirus called as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Detected for the first time in December 2019 in Wuhan and it has quickly spread all over the world in a couple of months and becoming a world pandemic. Symptoms of the disease and clinical outcomes are very different in infected people. These differences highlight the paramount need to study and understand the human genetic variation that occurring viral infections. Human leukocyte antigen (HLA) is an important component of the viral antigen presentation pathway, and it plays an essential role in conferring differential viral susceptibility and severity of diseases. HLA alleles have been involved in the immune response to viral diseases such as SARS-CoV-2. Main body of the abstract Herein, we sought to evaluate this hypothesis by summarizing the association between HLA class I and class II alleles with COVID-19 susceptibility and/or severity reported in previous studies among different populations (Chinese, Italian, Iranian, Japanese, Spanish, etc.). The findings of all selected articles showed that several alleles have been found associated with COVID-19 susceptibility and severity. Even results across articles have been inconsistent and, in some cases, conflicting, highlighting that the association between the HLA system and the COVID-19 outcome might be ethnic-dependent, there were some alleles in common between some populations such as HLA-DRB1*15 and HLA-A*30:02. Conclusion These contradictory findings warrant further large, and reproducible studies to decipher any possible genetic predisposition underlying susceptibility to SARS-COV-2 and disease progression and host immune response.
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Affiliation(s)
- Meryem Fakhkhari
- grid.31143.340000 0001 2168 4024Research Laboratory in Oral Biology and Biotechnology, Faculty of Dental Medicine, Mohammed V University in Rabat, Rabat, Morocco
| | - Hayat Caidi
- grid.416738.f0000 0001 2163 0069NARST Surveillance Unit, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Khalid Sadki
- grid.31143.340000 0001 2168 4024Research Laboratory in Oral Biology and Biotechnology, Faculty of Dental Medicine, Mohammed V University in Rabat, Rabat, Morocco
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22
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Chen LC, Nersisyan S, Wu CJ, Chang CM, Tonevitsky A, Guo CL, Chang WC. On the peptide binding affinity changes in population-specific HLA repertoires to the SARS-CoV-2 variants Delta and Omicron. J Autoimmun 2022; 133:102952. [PMID: 36427410 PMCID: PMC9650568 DOI: 10.1016/j.jaut.2022.102952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/05/2022] [Accepted: 11/06/2022] [Indexed: 11/13/2022]
Abstract
OBJECTIVE To investigate the changes of Spike protein-HLA binding affinity profiles between the Wuhan strain and two dominant variants, the Delta and the Omicron strains, among the Taiwanese, the British and the Russian populations. METHODS The HLA frequencies and the HLA-peptide binding affinity profiles in the T-CoV database were combined to conduct the study. We focused on the public alleles in the three populations (HLA-A, HLA-B, HLA-C, HLA-DRB1, and/or HLA-DPA1/DPB1 alleles) and the altered peptides of the spike protein (compared to the Wuhan strain) in the Delta G/478K·V1 (B.1.617.2 + AY.1 + AY.2) and the Omicron (BA.1) strains. RESULTS For the Delta strain, tight bindings of the altered peptides to the HLA alleles decrease in all three populations and almost vanish in the Taiwanese population. For the Omicron strain, tight bindings are mostly preserved for both HLA classes and in the Taiwanese and the British populations, with a slight reduction in HLA class II in the Taiwanese (1.4%), while the Russian population preserves a relatively high fraction of tight bindings for both HLA classes. CONCLUSION We comprehensively reported the changes in the HLA-associated SARS-CoV-2 Spike protein peptide binding profiles among the Taiwanese, the British, and the Russian populations. Further studies are needed to understand the immunological mechanisms and the clinical value of our findings.
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Affiliation(s)
- Lu-Chun Chen
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Institute of Molecular Biology, The National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia,Armenian Bioinformatics Institute (ABI), Yerevan, Armenia
| | - Chang-Jiun Wu
- Department of Genomic Medicine, University of Texas, MD Anderson Cancer Center. Houston Texas, USA
| | - Che-Mai Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Chin-Lin Guo
- Institute of Physics, Academia Sinica, Taipei, Taiwan,Corresponding author. Institute of Physics, Academia Sinica, No. 128, Sec. 2, Academia Rd., Nangang Dist., Taipei City 115201, Taiwan. Tel.: (886) 988545414
| | - Wei-Chiao Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan,Department of Medical Education and Research, Integrative Research Center for Critical Care, Wan fang Hospital, Taipei Medical University, Taipei, Taiwan,Master Program in Clinical Genomics and Proteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan,Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan,Corresponding author. Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, No. 250 Wuxing St., Xinyi Dist., Taipei City 110, Taiwan. Tel.: (886) 928121979
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23
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Heidecker B, Dagan N, Balicer R, Eriksson U, Rosano G, Coats A, Tschöpe C, Kelle S, Poland GA, Frustaci A, Klingel K, Martin P, Hare JM, Cooper LT, Pantazis A, Imazio M, Prasad S, Lüscher TF. Myocarditis following COVID-19 vaccine: incidence, presentation, diagnosis, pathophysiology, therapy, and outcomes put into perspective. A clinical consensus document supported by the Heart Failure Association of the European Society of Cardiology (ESC) and the ESC Working Group on Myocardial and Pericardial Diseases. Eur J Heart Fail 2022; 24:2000-2018. [PMID: 36065751 PMCID: PMC9538893 DOI: 10.1002/ejhf.2669] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 08/12/2022] [Accepted: 08/25/2022] [Indexed: 01/18/2023] Open
Abstract
Over 10 million doses of COVID-19 vaccines based on RNA technology, viral vectors, recombinant protein, and inactivated virus have been administered worldwide. Although generally very safe, post-vaccine myocarditis can result from adaptive humoral and cellular, cardiac-specific inflammation within days and weeks of vaccination. Rates of vaccine-associated myocarditis vary by age and sex with the highest rates in males between 12 and 39 years. The clinical course is generally mild with rare cases of left ventricular dysfunction, heart failure and arrhythmias. Mild cases are likely underdiagnosed as cardiac magnetic resonance imaging (CMR) is not commonly performed even in suspected cases and not at all in asymptomatic and mildly symptomatic patients. Hospitalization of symptomatic patients with electrocardiographic changes and increased plasma troponin levels is considered necessary in the acute phase to monitor for arrhythmias and potential decline in left ventricular function. In addition to evaluation for symptoms, electrocardiographic changes and elevated troponin levels, CMR is the best non-invasive diagnostic tool with endomyocardial biopsy being restricted to severe cases with heart failure and/or arrhythmias. The management beyond guideline-directed treatment of heart failure and arrhythmias includes non-specific measures to control pain. Anti-inflammatory drugs such as non-steroidal anti-inflammatory drugs, and corticosteroids have been used in more severe cases, with only anecdotal evidence for their effectiveness. In all age groups studied, the overall risks of SARS-CoV-2 infection-related hospitalization and death are hugely greater than the risks from post-vaccine myocarditis. This consensus statement serves as a practical resource for physicians in their clinical practice, to understand, diagnose, and manage affected patients. Furthermore, it is intended to stimulate research in this area.
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Affiliation(s)
- Bettina Heidecker
- Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin und Humboldt, Universität zu Berlin, Berlin, Germany
| | - Noa Dagan
- Clalit Health Services, Clalit Research Institute, Ramat Gan, Israel
| | - Ran Balicer
- Clalit Health Services, Clalit Research Institute, Ramat Gan, Israel
| | - Urs Eriksson
- Department of Internal Medicine, Division of Cardiology, GZO - Zurich Regional Health Center, Wetzikon & University of Zurich, Zurich, Switzerland
| | | | - Andrew Coats
- Monash University, Melbourne, Victoria, Australia.,University of Warwick, Warwick, UK
| | - Carsten Tschöpe
- Cardiology, German Heart Center, Charité - University Medicine, Berlin, Germany
| | - Sebastian Kelle
- Cardiology, German Heart Center, Charité - University Medicine, Berlin, Germany
| | | | - Andrea Frustaci
- Department of Cardiovascular, Respiratory, Nephrologic, Anesthesiologic and Geriatric Sciences, La Sapienza University, Rome, Italy.,IRCCS L. Spallanzani, Rome, Italy
| | - Karin Klingel
- Cardiopathology, Institute for Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Pilar Martin
- Cientro Nacional de Investigationes Cardiovasculares, Madrid, Spain
| | - Joshua M Hare
- Interdisciplinary Stem Cell Institute, University of Miami, Miami, FL, USA
| | - Leslie T Cooper
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN, USA, and Cardiology, Mayo Clinic Jacksonville, Jacksonville, FL, USA
| | - Antonis Pantazis
- Royal Brompton and Harefield Hospitals and Imperial College London, London, UK
| | - Massimo Imazio
- Cardiothoracic Department, Cardiology, Udine University Health Integrated Agency, Udine, Italy
| | - Sanjay Prasad
- Royal Brompton and Harefield Hospitals and Imperial College London, London, UK
| | - Thomas F Lüscher
- Royal Brompton and Harefield Hospitals and Imperial College London, London, UK.,Center for Molecular Cardiology, University of Zurich, Zurich, Switzerland
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24
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Shared 6mer Peptides of Human and Omicron (21K and 21L) at SARS-CoV-2 Mutation Sites. Antibodies (Basel) 2022; 11:antib11040068. [PMID: 36412834 PMCID: PMC9680445 DOI: 10.3390/antib11040068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/18/2022] [Accepted: 10/21/2022] [Indexed: 12/14/2022] Open
Abstract
We investigated the short sequences involving Omicron 21K and Omicron 21L variants to reveal any possible molecular mimicry-associated autoimmunity risks and changes in those. We first identified common 6mers of the viral and human protein sequences present for both the mutant (Omicron) and nonmutant (SARS-CoV-2) versions of the same viral sequence and then predicted the binding affinities of those sequences to the HLA supertype representatives. We evaluated change in the potential autoimmunity risk, through comparative assessment of the nonmutant and mutant viral sequences and their similar human peptides with common 6mers and affinities to the same HLA allele. This change is the lost and the new, or de novo, autoimmunity risk, associated with the mutations in the Omicron 21K and Omicron 21L variants. Accordingly, e.g., the affinity of virus-similar sequences of the Ig heavy chain junction regions shifted from the HLA-B*15:01 to the HLA-A*01:01 allele at the mutant sequences. Additionally, peptides of different human proteins sharing 6mers with SARS-CoV-2 proteins at the mutation sites of interest and with affinities to the HLA-B*07:02 allele, such as the respective SARS-CoV-2 sequences, were lost. Among all, any possible molecular mimicry-associated novel risk appeared to be prominent in HLA-A*24:02 and HLA-B*27:05 serotypes upon infection with Omicron 21L. Associated disease, pathway, and tissue expression data supported possible new risks for the HLA-B*27:05 and HLA-A*01:01 serotypes, while the risks for the HLA-B*07:02 serotypes could have been lost or diminished, and those for the HLA-A*03:01 serotypes could have been retained, for the individuals infected with Omicron variants under study. These are likely to affect the complications related to cross-reactions influencing the relevant HLA serotypes upon infection with Omicron 21K and Omicron 21L.
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25
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Rao V, Chandra N. In-silico study of influence of HLA heterogeneity on CTL responses across ethnicities to SARS-CoV-2. Hum Immunol 2022; 83:797-802. [PMID: 36229378 PMCID: PMC9550298 DOI: 10.1016/j.humimm.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/12/2022] [Accepted: 09/29/2022] [Indexed: 11/04/2022]
Abstract
Differences in outcome to COVID-19 infection in different individuals is largely attributed to genetic heterogeneity leading to differential immune responses across individuals and populations. HLA is one such genetic factor that varies across individuals leading to differences in how T-cell responses are triggered against SARS-CoV-2, directly influencing disease susceptibility. HLA alleles that influence COVID-19 outcome, by virtue of epitope binding and presentation, have been identified in cohorts worldwide. However, the heterogeneity in HLA distribution across ethnic groups limits the generality of such association. In this study, we address this limitation by comparing the recognition of CTL epitopes across HLA genotypes and ethnic groups. Using HLA allele frequency data for ethnic groups from Allele Frequency Net Database (AFND), we construct synthetic populations for each ethnic group and show that CTL epitope strength varies across HLA genotypes and populations. We also observe that HLA genotypes, in certain cases, can have high CTL epitope strengths in the absence of top-responsive HLA alleles. Finally, we show that the theoretical estimate of responsiveness and hence protection offered by a HLA allele is bound to vary across ethnic groups, due to the influence of other HLA alleles within the HLA genotype on CTL epitope recognition. This emphasizes the need for studying HLA-disease associations at the genotype level rather than at a single allele level.
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Affiliation(s)
- Vishal Rao
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, India; Center for BioSystems Science and Engineering (BSSE), Indian Institute of Science, Bangalore, India.
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26
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Margaroli C, Benson P, Gastanadui MG, Song C, Viera L, Xing D, Wells JM, Patel R, Gaggar A, Payne GA. Spatial transcriptomic profiling of coronary endothelial cells in SARS-CoV-2 myocarditis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.25.509426. [PMID: 36203548 PMCID: PMC9536040 DOI: 10.1101/2022.09.25.509426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
OBJECTIVES Our objective was to examine coronary endothelial and myocardial programming in patients with severe COVID-19 utilizing digital spatial transcriptomics. BACKGROUND Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has well-established links to thrombotic and cardiovascular events. Endothelial cell infection was initially proposed to initiate vascular events; however, this paradigm has sparked growing controversy. The significance of myocardial infection also remains unclear. METHODS Autopsy-derived cardiac tissue from control (n = 4) and COVID-19 (n = 8) patients underwent spatial transcriptomic profiling to assess differential expression patterns in myocardial and coronary vascular tissue. Our approach enabled transcriptional profiling in situ with preserved anatomy and unaltered local SARS-CoV-2 expression. In so doing, we examined the paracrine effect of SARS-CoV-2 infection in cardiac tissue. RESULTS We observed heterogeneous myocardial infection that tended to colocalize with CD31 positive cells within coronary capillaries. Despite these differences, COVID-19 patients displayed a uniform and unique myocardial transcriptional profile independent of local viral burden. Segmentation of tissues directly infected with SARS-CoV-2 showed unique, pro-inflammatory expression profiles including upregulated mediators of viral antigen presentation and immune regulation. Infected cell types appeared to primarily be capillary endothelial cells as differentially expressed genes included endothelial cell markers. However, there was limited differential expression within the endothelium of larger coronary vessels. CONCLUSIONS Our results highlight altered myocardial programming during severe COVID-19 that may in part be associated with capillary endothelial cells. However, similar patterns were not observed in larger vessels, diminishing endotheliitis and endothelial activation as key drivers of cardiovascular events during COVID-19. CONDENSED ABSTRACT SARS-CoV-2 is linked to thrombotic and cardiovascular events; however, the mechanism remains uncertain. Our objective was to examine coronary endothelial and myocardial programming in patients with severe COVID-19 utilizing digital spatial transcriptomics. Autopsy-derived coronary arterial and cardiac tissues from control and COVID-19 patients underwent spatial transcriptomic profiling. Our approach enabled transcriptional profiling in situ with preserved anatomy and unaltered local SARS-CoV-2 expression. We observed unique, pro-inflammatory expression profiles among all COVID-19 patients. While heterogeneous viral expression was noted within the tissue, SARS-CoV-2 tended to colocalize with CD31 positive cells within coronary capillaries and was associated with unique expression profiles. Similar patterns were not observed in larger coronary vessels. Our results highlight altered myocardial programming during severe COVID-19 that may in part be associated with capillary endothelial cells. Such results diminish coronary arterial endotheliitis and endothelial activation as key drivers of cardiovascular events during COVID-19 infection. LIST OF HIGHLIGHTS SARS-CoV-2 has variable expression patterns within the myocardium of COVID-19 patientsSARS-CoV-2 infection induces a unique myocardial transcriptional programming independent of local viral burdenSARS-CoV-2 myocarditis is predominantly associated with capillaritis, and tissues directly infected with SARS-CoV-2 have unique, pro-inflammatory expression profilesDiffuse endothelial activation of larger coronary vessels was absent, diminishing large artery endotheliitis as a significant contributor to cardiovascular events during COVID-19 infection.
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27
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Noninvasive nasopharyngeal proteomics of COVID-19 patient identify abnormalities related to complement and coagulation cascade and mucosal immune system. PLoS One 2022; 17:e0274228. [PMID: 36094909 PMCID: PMC9467311 DOI: 10.1371/journal.pone.0274228] [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: 06/20/2022] [Accepted: 08/23/2022] [Indexed: 11/25/2022] Open
Abstract
Serum or plasma have been the primary focus of proteomics studies for COVID-19 to identity biomarkers and potential drug targets. The nasal mucosal environment which consists of lipids, mucosal immune cells, and nasal proteome, has been largely neglected but later revealed to have critical role combating SARS-CoV-2 infection. We present a bottom-up proteomics investigation of the host response to SARS-CoV-2 infection in the nasopharyngeal environment, featuring a noninvasive approach using proteins in nasopharyngeal swabs collected from groups of 76 SARS-CoV-2 positive and 76 negative patients. Results showed that 31 significantly down-regulated and 6 up-regulated proteins were identified (p < 0.05, log2 FC > 1.3) in SARS-CoV-2 positive patient samples as compared to the negatives; these proteins carry potential value as markers for the early detection of COVID-19, disease monitoring, as well as be drug targets. The down-regulation of coagulation factor 5 indicates a thrombotic abnormality in COVID-19 patients and the decreased IgG4 suggests an abnormal immune response at the point of entry in human nasopharyngeal environment, which is in consistent with KEGG and GO pathway analysis. Our study also demonstrated that mass spectrometry proteomics analysis of nasopharyngeal swabs can be used as a powerful early approach to evaluate host response to SARS-CoV-2 viral infection.
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28
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David S, Dorado G, Duarte EL, David-Bosne S, Trigueiro-Louro J, Rebelo-de-Andrade H. COVID-19: impact on Public Health and hypothesis-driven investigations on genetic susceptibility and severity. Immunogenetics 2022; 74:381-407. [PMID: 35348847 PMCID: PMC8961091 DOI: 10.1007/s00251-022-01261-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/14/2022] [Indexed: 12/12/2022]
Abstract
COVID-19 is a new complex multisystem disease caused by the novel coronavirus SARS-CoV-2. In slightly over 2 years, it infected nearly 500 million and killed 6 million human beings worldwide, causing an unprecedented coronavirus pandemic. Currently, the international scientific community is engaged in elucidating the molecular mechanisms of the pathophysiology of SARS-CoV-2 infection as a basis of scientific developments for the future control of COVID-19. Global exome and genome analysis efforts work to define the human genetics of protective immunity to SARS-CoV-2 infection. Here, we review the current knowledge regarding the SARS-CoV-2 infection, the implications of COVID-19 to Public Health and discuss genotype to phenotype association approaches that could be exploited through the selection of candidate genes to identify the genetic determinants of severe COVID-19.
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Affiliation(s)
- Susana David
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA,IP), Lisboa, Portugal.
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal.
| | - Guillermo Dorado
- Atlántida Centro de Investigación y Desarrollo de Estudios Profesionales (CIDEP), Granada, Spain
| | - Elsa L Duarte
- MED-Instituto Mediterrâneo para a Agricultura, Ambiente e Desenvolvimento, Escola de Ciências e Tecnologia, Universidade de Évora, Évora, Portugal
| | | | - João Trigueiro-Louro
- Departamento de Doenças Infeciosas, INSA, IP, Lisboa, Portugal
- Host-Pathogen Interaction Unit, Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- Hospital Egas Moniz, Centro Hospitalar Lisboa Ocidental, Lisboa, Portugal
| | - Helena Rebelo-de-Andrade
- Departamento de Doenças Infeciosas, INSA, IP, Lisboa, Portugal
- Host-Pathogen Interaction Unit, Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
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29
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Sharif-zak M, Abbasi-Jorjandi M, Asadikaram G, Ghoreshi ZAS, Rezazadeh-Jabalbarzi M, Rashidinejad H. Influence of Disease Severity and Gender on HLA-C Methylation in COVID-19 Patients. IRANIAN JOURNAL OF SCIENCE AND TECHNOLOGY, TRANSACTIONS A: SCIENCE 2022; 46:1309-1316. [PMID: 35912367 PMCID: PMC9325662 DOI: 10.1007/s40995-022-01334-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 07/01/2022] [Indexed: 12/03/2022]
Abstract
In the pathophysiology of COVID-19, immunomodulatory factors play a vital role. Viruses have epigenetic effects on various genes, particularly methylation. Explaining the changes in immunological factor methylation levels during viral infections requires substantial consideration. HLA-C is a crucial determinant of immune function and NK cell activity and is primarily implicated in viral infections. This research focused on studying HLA-C methylation in COVID-19 patients with different severity. Peripheral blood samples were collected from 470 patients (235 men and 235 women) with RT-qPCR-confirmed COVID-19 test and classified into moderate, severe, and critical groups based on WHO criteria. Also, one hundred (50 men and 50 women) healthy subjects were selected as the control group. Peripheral blood mononuclear cells were used for DNA extraction, and the methylation-specific PCR (MSP) method and gel electrophoresis were used to determine the methylation status of the HLA-C. Significant statistical differences in HLA-C methylation were observed among cases and controls and various stages of the disease. HLA-C methylation in men and women has decreased in all stages (p < 0.05). In comparison with control, HLA-C methylation in both genders were as follows: moderate (women: 41.0%, men: 52.33%), severe (women: 43.42%, men: 64.86%), critical (women: 42.33%, men: 60.07%), and total patients (women: 45.52%, men: 56.97%). Furthermore, the methylation levels in men were higher than in women in all groups (p < 0.05). Significantly, among all groups, the severe group of men participants showed the highest methylation percentage (p < 0.05). No significant differences were detected for different disease severity in the women group (p > 0.1). This study found that HLA-C methylation was significantly lower in COVID-19 patients with different disease severity. There were also significant differences in HLA-C methylation between men and women patients with different severity. Therefore, during managing viral infections, particularly COVID-19, it is critical to consider patient gender and disease severity.
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Dobrijević Z, Gligorijević N, Šunderić M, Penezić A, Miljuš G, Tomić S, Nedić O. The association of human leucocyte antigen (HLA) alleles with COVID-19 severity: A systematic review and meta-analysis. Rev Med Virol 2022; 33:e2378. [PMID: 35818892 PMCID: PMC9349710 DOI: 10.1002/rmv.2378] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/10/2022] [Accepted: 07/04/2022] [Indexed: 01/28/2023]
Abstract
Due to their pivotal role in orchestrating the immune response, HLA loci were recognized as candidates for genetic association studies related to the severity of COVID-19. Since the findings on the effects of HLA alleles on the outcome of SARS-CoV-2 infection remain inconclusive, we aimed to elucidate the potential involvement of genetic variability within HLA loci in the molecular genetics of COVID-19 by classifying the articles according to different disease severity/outcomes and by conducting a systematic review with meta-analysis. Potentially eligible studies were identified by searching PubMed, Scopus and Web of Science literature databases. A total of 28 studies with 13,073 participants were included in qualitative synthesis, while the results of 19 studies with 10,551 SARS-CoV-2-positive participants were pooled in the meta-analysis. According to the results of quantitative data synthesis, association with COVID-19 severity or with the lethal outcome was determined for the following alleles and allele families: HLA-A*01, HLA-A*03, HLA-A*11, HLA-A*23, HLA-A*31, HLA-A*68, HLA-A*68:02, HLA-B*07:02, HLA-B*14, HLA-B*15, HLA-B*40:02, HLA-B*51:01, HLA-B*53, HLA-B*54, HLA-B*54:01, HLA-C*04, HLA-C*04:01, HLA-C*06, HLA-C*07:02, HLA-DRB1*11, HLA-DRB1*15, HLA-DQB1*03 and HLA-DQB1*06 (assuming either allelic or dominant genetic model). We conclude that alleles of HLA-A, -B, -C, -DRB1 and -DQB1 loci may represent potential biomarkers of COVID-19 severity and/or mortality, which needs to be confirmed in a larger set of studies.
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Affiliation(s)
- Zorana Dobrijević
- Department for MetabolismUniversity of Belgrade—Institute for the Application of Nuclear EnergyBelgradeSerbia
| | - Nikola Gligorijević
- Department for MetabolismUniversity of Belgrade—Institute for the Application of Nuclear EnergyBelgradeSerbia
| | - Miloš Šunderić
- Department for MetabolismUniversity of Belgrade—Institute for the Application of Nuclear EnergyBelgradeSerbia
| | - Ana Penezić
- Department for MetabolismUniversity of Belgrade—Institute for the Application of Nuclear EnergyBelgradeSerbia
| | - Goran Miljuš
- Department for MetabolismUniversity of Belgrade—Institute for the Application of Nuclear EnergyBelgradeSerbia
| | - Sergej Tomić
- Department for Immunology and ImmunoparasitologyUniversity of Belgrade—Institute for the Application of Nuclear EnergyBelgradeSerbia
| | - Olgica Nedić
- Department for MetabolismUniversity of Belgrade—Institute for the Application of Nuclear EnergyBelgradeSerbia
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31
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Basir HRG, Majzoobi MM, Ebrahimi S, Noroozbeygi M, Hashemi SH, Keramat F, Mamani M, Eini P, Alizadeh S, Solgi G, Di D. Susceptibility and Severity of COVID-19 Are Both Associated With Lower Overall Viral–Peptide Binding Repertoire of HLA Class I Molecules, Especially in Younger People. Front Immunol 2022; 13:891816. [PMID: 35911710 PMCID: PMC9331187 DOI: 10.3389/fimmu.2022.891816] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/10/2022] [Indexed: 12/24/2022] Open
Abstract
An important number of studies have been conducted on the potential association between human leukocyte antigen (HLA) genes and COVID-19 susceptibility and severity since the beginning of the pandemic. However, case–control and peptide-binding prediction methods tended to provide inconsistent conclusions on risk and protective HLA alleles, whereas some researchers suggested the importance of considering the overall capacity of an individual’s HLA Class I molecules to present SARS-CoV-2-derived peptides. To close the gap between these approaches, we explored the distributions of HLA-A, -B, -C, and -DRB1 1st-field alleles in 142 Iranian patients with COVID-19 and 143 ethnically matched healthy controls, and applied in silico predictions of bound viral peptides for each individual’s HLA molecules. Frequency comparison revealed the possible predisposing roles of HLA-A*03, B*35, and DRB1*16 alleles and the protective effect of HLA-A*32, B*58, B*55, and DRB1*14 alleles in the viral infection. None of these results remained significant after multiple testing corrections, except HLA-A*03, and no allele was associated with severity, either. Compared to peptide repertoires of individual HLA molecules that are more likely population-specific, the overall coverage of virus-derived peptides by one’s HLA Class I molecules seemed to be a more prominent factor associated with both COVID-19 susceptibility and severity, which was independent of affinity index and threshold chosen, especially for people under 60 years old. Our results highlight the effect of the binding capacity of different HLA Class I molecules as a whole, and the more essential role of HLA-A compared to HLA-B and -C genes in immune responses against SARS-CoV-2 infection.
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Affiliation(s)
- Hamid Reza Ghasemi Basir
- Department of Pathology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | | | - Samaneh Ebrahimi
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mina Noroozbeygi
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Seyed Hamid Hashemi
- Brucellosis Research Centre, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Fariba Keramat
- Brucellosis Research Centre, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mojgan Mamani
- Brucellosis Research Centre, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Peyman Eini
- Brucellosis Research Centre, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Saeed Alizadeh
- Department of Radiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ghasem Solgi
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
- *Correspondence: Ghasem Solgi, ; Da Di,
| | - Da Di
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- *Correspondence: Ghasem Solgi, ; Da Di,
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32
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Suslova TA, Vavilov MN, Belyaeva SV, Evdokimov AV, Stashkevich DS, Galkin A, Kofiadi IA. Distribution of HLA-A, -B, -C, -DRB1, -DQB1, -DPB1 allele frequencies in patients with COVID-19 bilateral pneumonia in Russians, living in the Chelyabinsk region (Russia). Hum Immunol 2022; 83:547-550. [PMID: 35525710 PMCID: PMC9046060 DOI: 10.1016/j.humimm.2022.04.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/06/2022] [Accepted: 04/23/2022] [Indexed: 12/14/2022]
Abstract
In this population-based case-control study conducted in the Chelyabinsk region of Russia, we examined the distribution of HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1, in a group of 100 patients with confirmed COVID-19 bilateral pneumonia. Typing was performed by NGS and statistical calculations were carried out with the Arlequin program. HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1 alleles were compared between patients with COVID-19 and 99 healthy controls. We identified that COVID-19 susceptibility is associated with alleles and genotypes rs9277534A (disequilibrium with HLA-DPB1*02:01, -02:02, -04:01, -04:02, -17:01 alleles) with low expression of protein products HLA-DPB1 (pc < 0.028) and homozygosity at HLA-C*04 (p = 0.024, pc = 0.312). Allele HLA-A*01:01 was decreased in a group of patients with severe forms of bilateral pneumonia, and therefore it may be considered as a protective factor for the development of severe symptoms of COVID-19 (p = 0.009, pc = 0.225). Our studies provide further evidence for the functional association between HLA genes and COVID-19.
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Affiliation(s)
| | | | | | | | | | - Alexander Galkin
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 East 61st Street, New York, NY 10065, United States
| | - Ilya A Kofiadi
- Pirogov Russian National Reseach Medical University, Moscow, Russia
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Richard D, Phillip S, Hosseinali A, Gracie DZ, Hai L, January W, Holtgrewe M, Charlotte T, Melina M, Xiaomin W, Zehra K, Jacopo S, Jan-Moritz D, Ralf-Harto H, Bernd H, Anja B, Sandra S, Dilduz T, Norbert S, Martin W, Stefan H, Carsten S, Wolfgang P, Leif E S, Dieter B, Florian K, Toumy G, Ulf L, Jan B, Khai L, Rubelt F, Bettina H. Highly multiplexed immune repertoire sequencing links multiple lymphocyte classes with severity of response to COVID-19. EClinicalMedicine 2022; 48:101438. [PMID: 35600330 PMCID: PMC9106482 DOI: 10.1016/j.eclinm.2022.101438] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Disease progression of subjects with coronavirus disease 2019 (COVID-19) varies dramatically. Understanding the various types of immune response to SARS-CoV-2 is critical for better clinical management of coronavirus outbreaks and to potentially improve future therapies. Disease dynamics can be characterized by deciphering the adaptive immune response. METHODS In this cross-sectional study we analyzed 117 peripheral blood immune repertoires from healthy controls and subjects with mild to severe COVID-19 disease to elucidate the interplay between B and T cells. We used an immune repertoire Primer Extension Target Enrichment method (immunoPETE) to sequence simultaneously human leukocyte antigen (HLA) restricted T cell receptor beta chain (TRB) and unrestricted T cell receptor delta chain (TRD) and immunoglobulin heavy chain (IgH) immune receptor repertoires. The distribution was analyzed of TRB, TRD and IgH clones between healthy and COVID-19 infected subjects. Using McFadden's Adjusted R2 variables were examined for a predictive model. The aim of this study is to analyze the influence of the adaptive immune repertoire on the severity of the disease (value on the World Health Organization Clinical Progression Scale) in COVID-19. FINDINGS Combining clinical metadata with clonotypes of three immune receptor heavy chains (TRB, TRD, and IgH), we found significant associations between COVID-19 disease severity groups and immune receptor sequences of B and T cell compartments. Logistic regression showed an increase in shared IgH clonal types and decrease of TRD in subjects with severe COVID-19. The probability of finding shared clones of TRD clonal types was highest in healthy subjects (controls). Some specific TRB clones seems to be present in severe COVID-19 (Figure S7b). The most informative models (McFadden´s Adjusted R2=0.141) linked disease severity with immune repertoire measures across all three cell types, as well as receptor-specific cell counts, highlighting the importance of multiple lymphocyte classes in disease progression. INTERPRETATION Adaptive immune receptor peripheral blood repertoire measures are associated with COVID-19 disease severity. FUNDING The study was funded with grants from the Berlin Institute of Health (BIH).
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Affiliation(s)
| | - Suwalski Phillip
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
| | | | | | - Lin Hai
- Roche Sequencing Solutions Pleasanton, CA 94588, United States
| | - Weiner January
- Core Unit Bioinformatics Berlin, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, DE 10178, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics Berlin, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, DE 10178, Germany
| | - Thibeault Charlotte
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Müller Melina
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
| | - Wang Xiaomin
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
| | - Karadeniz Zehra
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
| | - Saccomanno Jacopo
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Doehn Jan-Moritz
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Hübner Ralf-Harto
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | | | - Blüher Anja
- Signature Diagnostics GmbH, DE 14473, Germany
| | | | - Telman Dilduz
- Roche Sequencing Solutions Pleasanton, CA 94588, United States
| | - Suttorp Norbert
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Witzenrath Martin
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Hippenstiel Stefan
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Skurk Carsten
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
| | - Poller Wolfgang
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
| | - Sander Leif E
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Beule Dieter
- Core Unit Bioinformatics Berlin, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, DE 10178, Germany
| | - Kurth Florian
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | | | - Landmesser Ulf
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Germany
| | - Berka Jan
- Roche Sequencing Solutions Pleasanton, CA 94588, United States
| | - Luong Khai
- Roche Sequencing Solutions Pleasanton, CA 94588, United States
| | | | - Florian Rubelt
- Roche Sequencing Solutions Pleasanton, CA 94588, United States
| | - Heidecker Bettina
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
- Corresponding authors.
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Biancolella M, Colona VL, Mehrian-Shai R, Watt JL, Luzzatto L, Novelli G, Reichardt JKV. COVID-19 2022 update: transition of the pandemic to the endemic phase. Hum Genomics 2022; 16:19. [PMID: 35650595 PMCID: PMC9156835 DOI: 10.1186/s40246-022-00392-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/26/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19, which is caused by the SARS-CoV-2, has ravaged the world for the past 2 years. Here, we review the current state of research into the disease with focus on its history, human genetics and genomics and the transition from the pandemic to the endemic phase. We are particularly concerned by the lack of solid information from the initial phases of the pandemic that highlighted the necessity for better preparation to face similar future threats. On the other hand, we are gratified by the progress into human genetic susceptibility investigations and we believe now is the time to explore the transition from the pandemic to the endemic phase. The latter will require worldwide vigilance and cooperation, especially in emerging countries. In the transition to the endemic phase, vaccination rates have lagged and developed countries should assist, as warranted, in bolstering vaccination rates worldwide. We also discuss the current status of vaccines and the outlook for COVID-19.
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Affiliation(s)
| | - Vito Luigi Colona
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133, Rome, Italy
| | - Ruty Mehrian-Shai
- Sheba Medical Center, Pediatric Hemato-Oncology, Edmond and Lilly Safra Children's Hospital, Tel Hashomer 2 Sheba Road, 52621, Ramat Gan, Israel
| | - Jessica Lee Watt
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Smithfield, QLD, 4878, Australia
| | - Lucio Luzzatto
- Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.,University of Florence, Florence, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133, Rome, Italy. .,IRCCS Neuromed, Pozzilli, Isernia, Italy. .,Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV, USA. .,Department of Biomedicine and Prevention, School of Medicine and Surgery, Via Montpellier 1, 00133, Rome, Italy.
| | - Juergen K V Reichardt
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, QLD, 4878, Australia
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35
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Augusto DG, Hollenbach JA. HLA variation and antigen presentation in COVID-19 and SARS-CoV-2 infection. Curr Opin Immunol 2022; 76:102178. [PMID: 35462277 PMCID: PMC8947957 DOI: 10.1016/j.coi.2022.102178] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/26/2022] [Accepted: 03/16/2022] [Indexed: 01/09/2023]
Abstract
The extraordinary variation of the human leukocyte antigen (HLA) molecules is critical for diversifying antigen presentation to T cells. Coupled with the rise of novel strains and rapidly evolving immune evasion by SARS-CoV-2 proteins, HLA-mediated immunity in COVID-19 is critically important but far from being fully understood. A growing number of studies have found the association of HLA variants with different COVID-19 outcomes and that HLA genotypes associate with differential immune responses against SARS-CoV-2. Prediction studies have shown that mutations in multiple viral strains, most concentrated in the Spike protein, affect the affinity between these mutant peptides and HLA molecules. Understanding the impact of this variation on T-cell responses is critical for comprehending the immunogenic mechanisms in both natural immunity and vaccine development.
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Affiliation(s)
- Danillo G Augusto
- Department of Neurology, University of California, San Francisco,
CA, USA,Programa de Pós-Graduação em Genética, Universidade Federal do
Paraná, Curitiba, Brazil
| | - Jill A Hollenbach
- Department of Neurology, University of California, San Francisco,
CA, USA,Department of Epidemiology and Biostatistics, University of
California, San Francisco, CA, USA
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36
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Liu F, Cocker ATH, Pugh JL, Djaoud Z, Parham P, Guethlein LA. Natural LILRB1 D1-D2 variants show frequency differences in populations and bind to HLA class I with various avidities. Immunogenetics 2022; 74:513-525. [PMID: 35562487 PMCID: PMC9103611 DOI: 10.1007/s00251-022-01264-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/02/2022] [Indexed: 11/27/2022]
Abstract
Leukocyte immunoglobulin-like receptor B1 (LILRB1) is widely expressed on various immune cells and the engagement of LILRB1 to HLA class I and pathogen-derived proteins can modulate the immune response. In the current study, 108 LILRB1 alleles were identified by screening the LILRB1 locus from the 1000 Genomes Phase 3 database. Forty-six alleles that occurred in three or more individuals encode 28 LILRB1 allotypes, and the inferred LILRB1 allotypes were then grouped into 9 LILRB1 D1-D2 variants for further analysis. We found that variants 1, 2, and 3 represent the three most frequent LILRB1 D1-D2 variants and the nine variants show frequency differences in populations. The binding assay demonstrated that variant 1 bound to HLA class I with the highest avidity, and all tested LILRB1 D1-D2 variants bound to HLA-C with lower avidity than to HLA-A and -B. Locus-specific polymorphisms at positions 183, 189, and 268 in HLA class I and dimorphisms in HLA-A (positions 207 and 253) and in HLA-B (position 194) affect their binding to LILRB1. Notably, the electrostatic interaction plays a critical role in the binding of LILRB1 to HLA class I as revealed by electrostatic analysis and by comparison of different binding avidities caused by polymorphisms at positions 72 and 103 of LILRB1. In this paper, we present a comprehensive study of the population genetics and binding abilities of LILRB1. The data will help us better understand the LILRB1-related diversity of the immune system and lay a foundation for functional studies.
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Affiliation(s)
- Fuguo Liu
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, 94305, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA
| | - Alexander T H Cocker
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, 94305, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA
| | - Jason L Pugh
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, 94305, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA
| | - Zakia Djaoud
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, 94305, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA
| | - Peter Parham
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, 94305, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA
| | - Lisbeth A Guethlein
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, 94305, USA.
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA.
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37
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Liu H, Hu B, Huang J, Wang Q, Wang F, Pan F, Chen L. Endoplasmic Reticulum Aminopeptidase 1 Is Involved in Anti-viral Immune Response of Hepatitis B Virus by Trimming Hepatitis B Core Antigen to Generate 9-Mers Peptides. Front Microbiol 2022; 13:829241. [PMID: 35602060 PMCID: PMC9115554 DOI: 10.3389/fmicb.2022.829241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 03/17/2022] [Indexed: 02/05/2023] Open
Abstract
Endoplasmic reticulum aminopeptidase 1 (ERAP1) is a processing enzyme of antigenic peptides presented to major histocompatibility complex (MHC) class I molecules. ERAP1-dependent trimming of epitope repertoire determines an efficacy of adoptive CD8+ T-cell responses in several viral diseases; however, its role in hepatitis B virus (HBV) infection remains unknown. Here, we show that the serum level of ERAP1 in patients with chronic hepatitis B (CHB) (n = 128) was significantly higher than that of healthy controls (n = 44) (8.78 ± 1.82 vs. 3.52 ± 1.61, p < 0.001). Furthermore, peripheral ERAP1 level is moderately correlated with HBV DNA level in patients with CHB (r = 0.731, p < 0.001). HBV-transfected HepG2.2.15 cells had substantially increased ERAP1 expression and secretion than the germline HepG2 cells (p < 0.001). The co-culture of ERAP1-specific inhibitor ERAP1-IN-1 pretreated HepG2.2.15 cells or ERAP1 knockdown HepG2.2.15 cells with CD8+ T cells led to 14-24% inhibition of the proliferation of CD8+ T cells. Finally, liquid chromatography tandem mass spectrometry (LC-MS/MS) test demonstrated that ERAP1-IN-1 blocks completely the production of a 9-mers peptide (30-38, LLDTASALY) derived from Hepatitis B core antigen (HBcAg). The predictive analysis by NetMHCpan-4.1 server showed that human leukocyte antigen (HLA)-C*04:01 is a strong binder for the 9-mers peptide in HepG2.2.15 cells. Taken together, our results demonstrated that ERAP1 trims HBcAg to produce 9-mers LLDTASALY peptides for binding onto HLA-C*04:01 in HepG2.2.15 cells, facilitating the potential activation of CD8+ T cells.
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Affiliation(s)
- Huanhuan Liu
- Department of Laboratory Medicine, Second Hospital of Anhui Medical University, Hefei, China
| | - Bingqi Hu
- Department of Laboratory Medicine, Second Hospital of Anhui Medical University, Hefei, China
| | - Junfeng Huang
- Department of Laboratory Medicine, Second Hospital of Anhui Medical University, Hefei, China
| | - Qin Wang
- Department of Laboratory Medicine, Second Hospital of Anhui Medical University, Hefei, China
| | - Feier Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Faming Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Liwen Chen
- Department of Laboratory Medicine, Second Hospital of Anhui Medical University, Hefei, China
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38
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Autoantibodies against interleukin-1 receptor antagonist in multisystem inflammatory syndrome in children: a multicentre, retrospective, cohort study. THE LANCET RHEUMATOLOGY 2022; 4:e329-e337. [PMID: 35368387 PMCID: PMC8963770 DOI: 10.1016/s2665-9913(22)00064-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background Multisystem inflammatory syndrome in children (MIS-C) is a rare but serious complication of infection with SARS-CoV-2. A possible involvement of pathogenetically relevant autoantibodies has been discussed. Recently, neutralising autoantibodies against inflammatory receptor antagonists progranulin and interleukin-1 receptor antagonist (IL-1Ra) were found in adult patients with critical COVID-19. The aim of this study was to investigate the role of such autoantibodies in MIS-C. Methods In this multicentre, retrospective, cohort study, plasma and serum samples were collected from patients (0–18 years) with MIS-C (as per WHO criteria) treated at five clinical centres in Germany and Spain. As controls, we included plasma or serum samples from children with Kawasaki disease, children with inactive systemic juvenile idiopathic arthritis, and children with suspected growth retardation (non-inflammatory control) across four clinical centres in Germany and Spain (all aged ≤18 years). Serum samples from the CoKiBa trial were used as two further control groups, from healthy children (negative for SARS-CoV-2 antibodies) and children with previous mild or asymptomatic COVID-19 (aged ≤17 years). MIS-C and control samples were analysed for autoantibodies against IL-1Ra and progranulin, and for IL-1Ra concentrations, by ELISA. Biochemical analysis of plasma IL-1Ra was performed with native Western blots and isoelectric focusing. Functional activity of the autoantibodies was examined by an in vitro IL-1β-signalling reporter assay. Findings Serum and plasma samples were collected between March 6, 2011, and June 2, 2021. Autoantibodies against IL-1Ra could be detected in 13 (62%) of 21 patients with MIS-C (11 girls and ten boys), but not in children with Kawasaki disease (n=24; nine girls and 15 boys), asymptomatic or mild COVID-19 (n=146; 72 girls and 74 boys), inactive systemic juvenile idiopathic arthritis (n=10; five girls and five boys), suspected growth retardation (n=33; 13 girls and 20 boys), or in healthy controls (n=462; 230 girls and 232 boys). Anti-IL-1Ra antibodies in patients with MIS-C belonged exclusively to the IgG1 subclass, except in one patient who had additional IL-1Ra-specific IgM antibodies. Autoantibodies against progranulin were only detected in one (5%) patient with MIS-C. In patients with MIS-C who were positive for anti-IL-1Ra antibodies, free plasma IL-1Ra concentrations were reduced, and immune-complexes of IL-1Ra were detected. Notably, an additional, hyperphosphorylated, transiently occurring atypical isoform of IL-1Ra was observed in all patients with MIS-C who were positive for anti-IL-1Ra antibodies. Anti-IL-1Ra antibodies impaired IL-1Ra function in reporter cell assays, resulting in amplified IL-1β signalling. Interpretation Anti-IL-1Ra autoantibodies were observed in a high proportion of patients with MIS-C and were specific to these patients. Generation of these autoantibodies might be triggered by an atypical, hyperphosphorylated isoform of IL-1Ra. These autoantibodies impair IL-1Ra bioactivity and might thus contribute to increased IL-1β-signalling in MIS-C. Funding NanoBioMed fund of the University of Saarland, José Carreras Center for Immuno and Gene Therapy, Dr Rolf M Schwiete Stiftung, Staatskanzlei Saarland, German Heart Foundation, Charity of the Blue Sisters, Bavarian Ministry of Health, the Center for Interdisciplinary Clinical Research at University Hospital Münster, EU Horizon 2020.
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Nersisyan S, Zhiyanov A, Zakharova M, Ishina I, Kurbatskaia I, Mamedov A, Galatenko A, Shkurnikov M, Gabibov A, Tonevitsky A. Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules. PeerJ 2022; 10:e13354. [PMID: 35502206 PMCID: PMC9055995 DOI: 10.7717/peerj.13354] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/08/2022] [Indexed: 01/15/2023] Open
Abstract
The T-cell immune response is a major determinant of effective SARS-CoV-2 clearance. Here, using the recently developed T-CoV bioinformatics pipeline (https://t-cov.hse.ru) we analyzed the peculiarities of the viral peptide presentation for the Omicron, Delta and Wuhan variants of SARS-CoV-2. First, we showed the absence of significant differences in the presentation of SARS-CoV-2-derived peptides by the most frequent HLA class I/II alleles and the corresponding HLA haplotypes. Then, the analysis was limited to the set of peptides originating from the Spike proteins of the considered SARS-CoV-2 variants. The major finding was the destructive effect of the Omicron mutations on PINLVRDLPQGFSAL peptide, which was the only tight binder from the Spike protein for HLA-DRB1*03:01 allele and some associated haplotypes. Specifically, we predicted a dramatical decline in binding affinity of HLA-DRB1*03:01 and this peptide both because of the Omicron BA.1 mutations (N211 deletion, L212I substitution and EPE 212-214 insertion) and the Omicron BA.2 mutations (V213G substitution). The computational prediction was experimentally validated by ELISA with the use of corresponding thioredoxin-fused peptides and recombinant HLA-DR molecules. Another finding was the significant reduction in the number of tightly binding Spike peptides for HLA-B*07:02 HLA class I allele (both for Omicron and Delta variants). Overall, the majority of HLA alleles and haplotypes was not significantly affected by the mutations, suggesting the maintenance of effective T-cell immunity against the Omicron and Delta variants. Finally, we introduced the Omicron variant to T-CoV portal and added the functionality of haplotype-level analysis to it.
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Affiliation(s)
- Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,Institute of Molecular Biology, The National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia,Armenian Bioinformatics Institute (ABI), Yerevan, Armenia
| | - Anton Zhiyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maria Zakharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Irina Ishina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Inna Kurbatskaia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Azad Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexei Galatenko
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia
| | - Maxim Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Alexander Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,Art Photonics GmbH, Berlin, Germany
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Smatti MK, Alkhatib HA, Al Thani AA, Yassine HM. Will Host Genetics Affect the Response to SARS-CoV-2 Vaccines? Historical Precedents. Front Med (Lausanne) 2022; 9:802312. [PMID: 35360730 PMCID: PMC8962369 DOI: 10.3389/fmed.2022.802312] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/10/2022] [Indexed: 11/25/2022] Open
Abstract
Recent progress in genomics and bioinformatics technologies have allowed for the emergence of immunogenomics field. This intersection of immunology and genetics has broadened our understanding of how the immune system responds to infection and vaccination. While the immunogenetic basis of the huge clinical variability in response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is currently being extensively studied, the host genetic determinants of SARS-CoV-2 vaccines remain largely unknown. Previous reports evidenced that vaccines may not protect all populations or individuals equally, due to multiple host- and vaccine-specific factors. Several studies on vaccine response to measles, rubella, hepatitis B, smallpox, and influenza highlighted the contribution of genetic mutations or polymorphisms in modulating the innate and adaptive immunity following vaccination. Specifically, genetic variants in genes encoding virus receptors, antigen presentation, cytokine production, or related to immune cells activation and differentiation could influence how an individual responds to vaccination. Although such knowledge could be utilized to generate personalized vaccine strategies to optimize the vaccine response, studies in this filed are still scarce. Here, we briefly summarize the scientific literature related to the immunogenetic determinants of vaccine-induced immunity, highlighting the possible role of host genetics in response to SARS-CoV-2 vaccines as well.
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Affiliation(s)
- Maria K. Smatti
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Biomedical Research Center, Qatar University, Doha, Qatar
| | | | | | - Hadi M. Yassine
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Biomedical Research Center, Qatar University, Doha, Qatar
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Hovhannisyan A, Madelian V, Avagyan S, Nazaretyan M, Hyussyan A, Sirunyan A, Arakelyan R, Manukyan Z, Yepiskoposyan L, Mayilyan KR, Jordan F. HLA-C*04:01 Affects HLA Class I Heterozygosity and Predicted Affinity to SARS-CoV-2 Peptides, and in Combination With Age and Sex of Armenian Patients Contributes to COVID-19 Severity. Front Immunol 2022; 13:769900. [PMID: 35185875 PMCID: PMC8850920 DOI: 10.3389/fimmu.2022.769900] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/13/2022] [Indexed: 12/14/2022] Open
Abstract
The novel SARS-CoV-2 coronavirus infection has become a global health concern, causing the COVID-19 pandemic. The disease symptoms and outcomes depend on the host immunity, in which the human leukocyte antigen (HLA) molecules play a distinct role. The HLA alleles have an inter-population variability, and understanding their link to the COVID-19 in an ethnically distinct population may contribute to personalized medicine. The present study aimed at detecting associations between common HLA alleles and COVID-19 susceptibility and severity in Armenians. In 299 COVID-19 patients (75 asymptomatic, 102 mild/moderate, 122 severe), the association between disease severity and classic HLA-I and II loci was examined. We found that the advanced age, male sex of patients, and sex and age interaction significantly contributed to the severity of the disease. We observed that an age-dependent effect of HLA-B*51:01 carriage [odds ratio (OR)=0.48 (0.28-0.80), Pbonf <0.036] is protective against severe COVID-19. Contrary, the HLA-C*04:01 allele, in a dose-dependent manner, was associated with a significant increase in the disease severity [OR (95% CI) =1.73 (1.20-2.49), Pbonf <0.021] and an advancing age (P<0.013). The link between HLA-C*04:01 and age was secondary to a stronger association between HLA-C*04:01 and disease severity. However, HLA-C*04:01 exerted a sex-dependent differential distribution between clinical subgroups [females: P<0.0012; males: P=0.48]. The comparison of HLA-C*04:01 frequency between subgroups and 2,781 Armenian controls revealed a significant incidence of HLA-C*04:01 deficiency in asymptomatic COVID-19. HLA-C*04:01 homozygous genotype in patients blueprinted a decrease in heterozygosity of HLA-B and HLA class-I loci. In HLA-C*04:01 carriers, these changes translated to the SARS-CoV-2 peptide presentation predicted inefficacy by HLA-C and HLA class-I molecules, simultaneously enhancing the appropriate HLA-B potency. In patients with clinical manifestation, due to the high prevalence of HLA-C*04:01, these effects provided a decrease of the HLA class-I heterozygosity and an ability to recognize SARS-CoV-2 peptides. Based on our observations, we developed a prediction model involving demographic variables and HLA-C*04:01 allele for the identification of potential cases with the risk of hospitalization (the area under the curve (AUC) = 86.2%) or severe COVID-19 (AUC =71%).
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Affiliation(s)
- Anahit Hovhannisyan
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
- Russian-Armenian University, Yerevan, Armenia
| | - Vergine Madelian
- Armenian Bone Marrow Donor Registry Charitable Trust, Yerevan, Armenia
| | - Sevak Avagyan
- Armenian Bone Marrow Donor Registry Charitable Trust, Yerevan, Armenia
| | - Mihran Nazaretyan
- Armenian Bone Marrow Donor Registry Charitable Trust, Yerevan, Armenia
| | - Armine Hyussyan
- Armenian Bone Marrow Donor Registry Charitable Trust, Yerevan, Armenia
| | - Alina Sirunyan
- Armenian Bone Marrow Donor Registry Charitable Trust, Yerevan, Armenia
| | | | | | | | - Karine R. Mayilyan
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Frieda Jordan
- Armenian Bone Marrow Donor Registry Charitable Trust, Yerevan, Armenia
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Deb P, Zannat K, Talukder S, Bhuiyan AH, Jilani MSA, Saif‐Ur‐Rahman KM. Association of
HLA
gene polymorphism with susceptibility, severity, and mortality of
COVID
‐19: A systematic review. HLA 2022; 99:281-312. [DOI: 10.1111/tan.14560] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/22/2021] [Accepted: 01/20/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Paroma Deb
- Department of Virology Dhaka Medical College Dhaka Bangladesh
| | | | - Shiny Talukder
- Rangamati General Hospital PCR Laboratory Rangamati Bangladesh
| | | | - Md. Shariful Alam Jilani
- Department of Microbiology Ibrahim Medical College Dhaka Bangladesh
- Department of Microbiology BIRDEM General Hospital Dhaka Bangladesh
| | - K. M. Saif‐Ur‐Rahman
- Health Systems and Population Studies Division, icddr,b Dhaka Bangladesh
- Department of Public Health and Health Systems Nagoya University Graduate School of Medicine Nagoya Japan
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