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BackgroundFollowing the launch of the global COVID-19 vaccination campaign, there have been increased reports of autoimmune diseases developing de novo following vaccination. These cases include rheumatoid arthritis, autoimmune hepatitis, immune thrombotic thrombocytopenia, and connective tissue diseases. Nevertheless, COVID-19 vaccines are considered safe for patients with autoimmune diseases and are strongly recommended.ObjectivesThe aim of this in silico analysis is to investigate the presence of protein epitopes encoded by the BNT-162b2 mRNA vaccine, one of the most commonly administered COVID-19 vaccines, that could elicit an aberrant adaptive immune response in predisposed individuals.MethodsThe FASTA sequence of the protein encoded by the BNT-162b2 vaccine was retrieved from http://genome.ucsc.edu and used as a key input to the Immune Epitope Database and Analysis Resource (www.iedb.org). Linear peptides with 90% BLAST homology were selected, and T-cell, B-cell, and MHC ligand assays without MHC restriction were searched and evaluated. HLA-disease associations were screened on the HLA-SPREAD platform (https://hla-spread.igib.res.in) by selecting only positive markers.ResultsA total of 183 epitopes were found, corresponding to 178 SARS-CoV-2 and 5 SARS-CoV spike epitopes, respectively. Results were obtained from 22 T-cell assays, 398 B-cell assays, and 2 MHC ligand assays. Complementary receptors included 1080 T-cell receptors and 0 B-cell receptors.Specifically, the IEDB_epitope:1329790 (NATNVVIKVCEFQFCNDPFLGVYY) was shown to bind to HLA-DRB1*15:02 and HLA-DRB1*15:03 alleles, whereas the IEDB_epitope:1392457 (TKCTLKSFTVEKGIYQTSNFRVQPT) was reported to bind to HLA-DRB1*07:01, HLA-DRB1*03:01, HLA-DRB3*01:01, and HLA-DRB4*01:01 alleles. The HLA alleles detected were found to be positively associated with various immunological disorders (Table 1).Table 1.MHC-restricted epitopes of the BNT-162b2 vaccine and potentially associated immunological conditionsEpitopeAssayMHC moleculeAssociated disease (population)NATNVVIKVCEFQFCNDPFLGVYY + OX(C10)cellular MHC/mass spectrometry ligand presentationHLA-DRB1*15:02Takayasu arteritis (Japanese) Arthritis (Taiwanese) Scleroderma (Japanese) Colitis (Japanese)HLA-DRB1*15:03Systemic lupus erythematosus (Mexican American)TKCTLKSFTVEKGIYQTSNFRVQPT + SCM(K2)as aboveHLA-DRB1*07:01Allergy, hypersensitivity (Caucasian)HLA-DRB1*03:01Type 1 diabetes (African) Sarcoidosis, good prognosis (Finnish)HLA-DRB3*01:01Graves' disease (Caucasian) Thymoma (Caucasian) Sarcoidosis (Scandinavian) Autoimmune hepatitis (Caucasian)HLA-DRB4*01:01Vitiligo (Saudi Arabian)ConclusionSimilar to the SARS-CoV-2 spike protein, the protein product of the BNT-162b2 mRNA vaccine contains immunogenic epitopes that may trigger autoimmune phenomena in predisposed individuals. Genotyping for HLA alleles may help identify at-risk individuals. However, further research is needed to elucidate the underlying mechanisms and potential clinical implications.References[1]Vita R, Mahajan S, Overton JA et al. The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res. 2019 Jan 8;47(D1):D339-D343. doi: 10.1093/nar/gky1006.[2]Dholakia D, Kalra A, Misir BR et al. HLA-SPREAD: a natural language processing based resource for curating HLA association from PubMed s. BMC Genomics 23, 10 (2022). https://doi.org/10.1186/s12864-021-08239-0[3]Parker R, Partridge T, Wormald C et al. Mapping the SARS-CoV-2 spike glycoprotein-derived peptidome presented by HLA class II on dendritic cells. Cell Rep. 2021 May 25;35(8):109179. doi: 10.1016/j.celrep.2021.109179.[4]Knierman MD, Lannan MB, Spindler LJ et al. The Human Leukocyte Antigen Class II Immunopeptidome of the SARS-CoV-2 Spike Glycoprotein. Cell Rep. 2020 Dec 1;33(9):108454. doi: 10.1016/j.celrep.2020.108454.Acknowledgements:NIL.Disclosure of InterestsNone Declared.
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Objectives: The COVID-19 pandemic has led to significant morbidity and mortality in lung transplant recipients (LTR). Respiratory viral infections may be associated with de-novo HLA donor-specific antibody (DSA) production and impact lung transplant outcome. Since one of the immunomodulation strategies post-SARS-CoV-2 infection in LTR include decreasing or holding anti-metabolites, concerns have been raised for higher incidence of de-novo DSA production in LTR. Method(s): We performed a retrospective chart review of 80 consecutive LTR diagnosed with COVID-19 to investigate this concern. COVID-19 disease severity was divided into 3 groups: mild, moderate, and severe. Mild disease was defined as patients with COVID-19 diagnosis who were stable enough to be treated as out-patients. Moderate disease was defined as patients who required admission to the hospital and were on less than 10 liters of oxygen at rest. Severe disease was identified as patients who required hospitalization and were on more than 10 liters of oxygen with or without mechanical ventilation or extra corporal membrane oxygenation (ECMO). Groups were compared using the Kruskal-Wallis test. Result(s): A total of 23, 47, and 10 LTR were diagnosed with mild, moderate, and severe COVID-19 respectively. De-novo HLA DSAwere detected in 0/23 (0%), 3/47 (6.3%), and 4/10 (40%) LTR with mild, moderate, and severe COVID-19 respectively (p = 0.0007) within 6 months post-COVID-19 diagnosis. Conclusion(s): Severe COVID-19 may be associated with increased risk of de novo HLA DSA production resulting in allograft dysfunction.Copyright © 2023 Elsevier Inc.
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Background & Aim: Immunological characteristics of COVID-19 show pathological hyperinflammation associated with lymphopenia and dysfunctional T cell responses. These features provide a rationale for restoring functional T cell immunity in COVID-19 patients by adoptive transfer of SARS-CoV-2 specific T cells. Methods, Results & Conclusion(s): To generate SARS-CoV-2 specific T cells, we isolated peripheral blood mononuclear cells from 7 COVID-19 recovered and 13 unexposed donors. Consequently, we stimulated cells with SARS-CoV-2 peptide mixtures covering spike, membrane and nucleocapsid proteins. Then, we culture expanded cells with IL-2 for 21 days. We assessed immunophenotypes, cytokine profiles, antigen specificity of the final cell products. Our results show that SARSCoV- 2 specific T cells could be expanded in both COVID-19 recovered and unexposed groups. Immunophenotypes were similar in both groups showing CD4+ T cell dominance, but CD8+ and CD3+CD56+ T cells were also present. Antigen specificity was determined by ELISPOT, intracellular cytokine assay, and cytotoxicity assays. One out of 14 individuals who were previously unexposed to SARS-CoV-2 failed to show antigen specificity. Moreover, ex-vivo expanded SARS-CoV-2 specific T cells mainly consisted of central and effector memory subsets with reduced alloreactivity against HLA-unmatched cells suggesting the possibility for the development of third-party partial HLA-matching products. In conclusion, our findings show that SARSCoV- 2 specific T cell can be readily expanded from both COVID-19 and unexposed individuals and can therefore be manufactured as a biopharmaceutical product to treat severe COVID-19 patients.Copyright © 2023 International Society for Cell & Gene Therapy
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The human leukocyte antigen (HLA) is a critical component of antigen presentation and plays crucial role in conferring differential susceptibility and severity of diseases caused by viruses such as COVID-19. The immunogenetic profile of populations, BCG vaccination status, and a host of lifestyle factors might contribute to the observed variations in mortality rates due to COVID-19. These genetic, epigenetic, and environmental factors could widely influence infection dynamics and immune responses against COVID-19. The aim of this review is to provide an update on HLA association with SARS-CoV-2 infection in global populations and to highlight the possible neurological involvements. We also set out to explore the HLA immunogenetic markers related to COVID‐19 infections that can be used in screening high‐risk individuals for personalized therapies and in community-based vaccine development. © 2023 Elsevier Inc. All rights reserved.
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BACKGROUND This review is devoted to the analysis of the features of the immune response in COVID-19. The review indicates the clinical manifestations of COVID-19, modern data on the immunopathogenesis of the disease and its complications are considered. AIM OF STUDY To clarify some pathogenetic mechanisms of the immune response in COVID-19, which can help in creating an algorithm for examining patients for early prognosis and prevention of severe course and complications of the disease. MATERIAL AND METHODS To achieve this goal, the results of domestic and foreign scientific studies on the pathogenesis, diagnosis and treatment of COVID-19 were analyzed. The literature search was carried out in electronic search engines Scopus and PubMed. For the analysis, scientific articles published in the period from 2019 to 2021 were selected;88% of analyzed works are not older than 5 years. CONCLUSION The late production of type I IFN, an increase in the level of pro-inflammatory monocytes, a decrease in the expression of HLA-DR on monocytes, violation of the presentation of the virus and the formation of specific lymphocytes, the death of T-lymphocytes and profound immunosuppression are of greatest importance for the development of a severe form of COVID-19. © 2023 Sklifosovsky Research Institute for Emergency Medicine. All rights reserved.
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Objectives Human leukocyte antigens (HLA) are highly diverse transmembrane proteins that present viral peptides to T cells and launch pathogen-specific immune responses. We aim to investigate the correlation between HLA evolutionary divergence (HED), a surrogate for the capacity to present different peptides, and the outcomes of SARS-CoV-2 infection in a cohort from the St. Louis Metropolitan area. Methods We enrolled adult patients with SARS-CoV-2 infection confirmed by RT-PCR who were hospitalized at two tertiary hospitals in St. Louis between March and July 2020. Genomic DNA was extracted from peripheral blood and genotyped by next-generation sequencing (NGS). HLA alleles were assigned based on key-exon sequences (G group) and limited to the 2-field resolution. HED was calculated by Grantham distance, which considers the difference in composition, polarity, and molecular volume between each pair of amino acids from maternal and paternal HLA. The HED score was obtained for HLA class I (HLA-A, -B, and -C) genotypes using the HLAdivR package in R. Clinical data were collected retrospectively from electronic medical records. A poor outcome was defined as an admission to the intensive care unit (ICU), a need for mechanical ventilation, or death. A favorable outcome was defined as the absence of the above poor outcomes. Results A total of 234 patients were enrolled in this study, 96 being females (41%). The median age and BMI were 66 years old and 28.30 kg/m2, respectively. African Americans comprised 71.4% of the cohort. Only 19 patients (8.1%) presented with no comorbidity;the rest had one or more comorbidities, with cardiovascular diseases being the most common. A total of 137 (58.5%) patients had poor outcomes from SARS-CoV-2 infection, while 97 (41.5%) patients had a favorable outcome. We detected a significant association between higher HLA-B HED and favorable outcomes, with each 1-point increase in HLA-B HED associated with 8% increased probability for the composite endpoint (OR 1.08, 95% CI=1.01-1.16, P = 0.04). The HED scores calculated for HLA-A or HLA-C were not significantly different between patients with favorable or poor outcomes. In a multivariate logistic regression analysis, increased HLA-B HED score, younger age, and no comorbidity were independently associated with favorable outcomes (P = 0.02, P = 0.01, and P = 0.05, respectively). Conclusion Our study shows a significant correlation between lower HLA-B HED scores and poor outcomes after SARS-CoV-2 infection. This finding suggests that maximizing the presentation of diverse SARS-CoV-2 peptides by HLA-B alleles may improve the clearance of SARS-CoV-2. Further studies are warranted to understand the functional and mechanistic implications of this finding.
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Background/Objectives: Validated association between COVID-19 and the most obvious candidate genes, e.g. HLA, is still missing. A weak association with class I HLA-C*04:01 was found for infection in Sardinians and for severity in another mixed population. Auto-antibodies to interferon type I have been implicated in the severity of COVID-19 in two studies. Method(s): The binding affinity between HLA molecules and SARS-CoV-2 spike protein and IFNalpha subunits was evaluated in silico. The presence of antibodies against one or more of the 12 IFNalpha subunits was evaluated in 160 hospitalized COVID-19 patients. The 10 most frequent haplotypes in the Italian population were tested in 1.997 SARS-CoV-2 infected patients (hospitalized versus not hospitalized). Result(s): The presence of auto-antibodies against at least one IFNalpha subunit was detected in 26% of patients. The haplotype A*24:02-B*35:02-C*04:01-DRB1*11:04-DQB1*03:01 was found to predispose to severity (p = 0.0018;p = 0.07 after Bonferroni correction) in patients <50 years. The haplotype includes alleles able to bind spike with low affinity (i.e. C*04:01 and DRB1*11:04) and IFNalpha with high affinity (i.e. DRB1*11:04). Conclusion(s): One of the 10 most frequent ancestral haplotype of the Italian population predisposes to severity likely reducing both innate immunity through IFNalpha auto-antibodies induction and adaptive immunity through weaker spike protein presentation.
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The effectiveness of the antiviral immune response largely depends on the activation of cytotoxic T cells. The heterogeneous group of functionally active T cells expressing the CD56 molecule (NKT-like cells), that combines the properties of T lymphocytes and NK cells, is poorly studied in COVID-19. This work aimed to analyze the activation and differentiation of both circulating NKT-like cells and CD56- T cells during COVID-19 among intensive care unit (ICU) patients, moderate severity (MS) patients, and convalescents. A decreased proportion of CD56+ T cells was found in ICU patients with fatal outcome. Severe COVID-19 was accompanied by a decrease in the proportion of CD8+ T cells, mainly due to the CD56- cell death, and a redistribution of the NKT-like cell subset composition with a predominance of more differentiated cytotoxic CD8+ T cells. The differentiation process was accompanied by an increase in the proportions of KIR2DL2/3+ and NKp30+ cells in the CD56+ T cell subset of COVID-19 patients and convalescents. Decreased percentages of NKG2D+ and NKG2A+ cells and increased PD-1 and HLA-DR expression levels were found in both CD56- and CD56+ T cells, and can be considered as indicators of COVID-19 progression. In the CD56- T cell fraction, increased CD16 levels were observed in MS patients and in ICU patients with lethal outcome, suggesting a negative role for CD56-CD16+ T cells in COVID-19. Overall, our findings suggest an antiviral role of CD56+ T cells in COVID-19.
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CD8-Positive T-Lymphocytes , COVID-19 , Humans , COVID-19/metabolism , T-Lymphocyte Subsets , Killer Cells, Natural , Cell DifferentiationABSTRACT
The direct causes of dermatomyositis, a common autoimmune disease, have not yet been accurately identified, but several studies have linked this condition to various patient-associated and environmental factors, such as viral infections and area of residence. In the present report, we describe our experience with a patient presenting with anti-melanoma differentiation-associated gene 5 (MDA5) antibody-positive dermatomyositis, which developed after vaccination against coronavirus disease 2019 (COVID-19). This patient was simultaneously diagnosed with anti-glutamic acid decarboxylase (GAD) antibody-positive slowly progressive insulin-dependent diabetes (SPIDDM); her human leukocyte antigen (HLA) test revealed that she expressed the DRB1*04:05 allele. This is important as this genotype is known to increase susceptibility to both anti-MDA5 antibody-positive dermatomyositis and type I diabetes. To the best of our knowledge, this is the first case of dermatomyositis complicated by SPIDDM identified after COVID-19 vaccination against COVID-19 and presenting with an underlying susceptible genotype. The patient's genetic predisposition may also be important for the development of autoimmune disease after COVID-19 vaccination.
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The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) accountable for the coronavirus disease 2019 (Covid-19) prompted a catastrophic pandemic striking millions of people with diverse presentations, from asymptomatic to severe, potentially lethal disease requiring unprecedented levels of specialized care and extraordinary resources that have overwhelmed healthcare systems around the world. In this detailed communication we postulating a novel hypothesis, based on the viral replication and transplantation immunology. This based on reviewing published journal articles and text book chapters to account for variable mortality and degrees of morbidity among various race and origins. Homo sapiens evolution over millions of years, for that the matter the origin of any biologic form of life form initiated by microorganisms. The entire body of a human has several millions of bacterial and viral genomes incorporated over millions of years. Perhaps the answer or a clue lies how compatible a foreign genomic sequence fits into three billion copies of human genome.
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COVID-19 , Humans , SARS-CoV-2 , Virus ReplicationABSTRACT
Assessment of viral load levels in various biological samples taken from the respiratory tract can be an indicator of an ongoing process of active viral replication and may be used to monitor severe respiratory viral infections. The study of the relationship between SARS-CoV-2 viral load and immunological laboratory parameters is an important step in the search for clinical markers of COVID-19. The aim of this research was to quantify viral load in patients with COVID-19 and to identify the relationship between viral load and changes in the parameters of the cellular component of the immune system. A laboratory examination was carried out on 74 patients diagnosed with COVID-19, they were divided into 3 groups based on the severity of the disease: mild, moderate, severe. Total viral load in clinical samples was determined by the number of SARS-CoV-2 RNA copies per 100 copies of the reference RNaseP gene. A comprehensive assessment of the cellular component of the immune system was performed using flow cytometry and direct monoclonal antibodies, and the IL-6, and C-reactive protein concentrations were determined. We revealed a relationship between the development of serious clinical conditions in the patients with COVID-19, and the levels of viral load. High levels of viral RNA in biological samples correlate with main indicators of the T cell component of the immune system associated with disease severity. In a subgroup of patients with an extremely high viral load, strong positive correlations were found between the relative numbers of cytotoxic lymphocytes (CD3+CD8+), activated T lymphocytes (CD3+HLA-DR+), as well as absolute and relative numbers of activated B lymphocytes and NK cells (CD3-CD25+). Laboratory monitoring of the cellular component of the immune system, along with the assessment of viral loads, should improve early assessment of clinical condition in the patients with COVID-19. Changes in expression levels of activation markers on immune cells can be potentially viewed as indicators of recovery during COVID-19.Copyright © Nikitin Yu.V. et al., 2023 The article can be used under the Creative Commons Attribution 4.0 License.
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Introduction: Matched unrelated donors (MUD) for hematopoietic progenitor cell (HPC) transplantation are facilitated through the National Marrow Donor Program. Most peripheral blood collections (HPC-A) are obtained in a single day apheresis collection. Extensive planning is required to coordinate the mobilization, collection, and shipment of the product with the conditioning and infusing at the transplant center. Typically, these products are infused fresh, although the COVID pandemic has necessitated cryopreservation in many instances. It was perceived that the number of two-day MUD collections was increasing at our institution. This study was performed to determine if this was true and to evaluate potential causes. Method(s): The project was considered a laboratory quality improvement project;IRB approval was not required per institutional guideline. Data was collected retrospectively for 120 HPC(A) MUD from August 2017-November 2020 including donor's age, weight, and sex, along with recipient to donor weight ratio. Each factor was analyzed against CD34 yield per day of collection. Result(s): Of the 120 donors, 5.6% collected over 2 days in 2017(n=1), 3.7 % (n=1, 2018), 3.6 % (n=1, 2019) with highest observation 17% (n=8) in 2020 (Image). Donor age, donor weight, donor sex, and recipient to donor weight ratio were compared to absolute CD34 yield. There was not a correlation seen between CD34 yield and donor age nor weight. However, donor sex along with recipient/donor weight ratio each showed a correlation in the number of collections required. Of those requiring a second day of collection, 73% were female while 27% were male. Two-day collections could be predicted with 83% accuracy in female with >1.09 recipient/donor weight ratio and male with > 1.49 recipient/donor weight ratio.(Figure Presented) Conclusion(s): The observed trend of increased 2-day NMDP collections coincided with an increase in frequency of female donors. Not surprisingly, higher recipient/donor weight was associated with a higher likelihood of 2-day collections. The size and scope of this study do not allow us to determine a definitive cause. However, it was noted these findings coincided with new donor selection guidelines prioritizing HLA-DP match potentially leading to an increase in female donors being selected. Unexpected two-day collection can have significant effects on transplantation. Developing a predictive algorithm with 83% accuracy allows for patient and staff preparation to anticipate the likelihood for additional collections. Having the product collected and received in advance, prior to patient conditioning improves logistics and removes some variability from scheduling. Larger, multicenter studies are required to determine if increased numbers of two-day collection of MUD are occurring at other centers and to the potential causesCopyright © 2023 American Society for Transplantation and Cellular Therapy
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Introduction: Allogeneic hematopoietic stem cell transplantation (alloHSCT) is a potentially curative option for patients with hematologic diseases. When considered candidates, patients face barriers to receive a transplant. Therefore, we aimed to analyze factors that limit or favor access to an alloHSCT in a population that has been HLA typed and therefore with a potential intent-to-transplant. Method(s): We retrospectively reviewed records from 2015 until the start of the COVID19 pandemic in two Mexican government- funded transplant centers and one private that have in-house HLA typing;in two of them, an outpatient transplant strategy is followed for most patients. HLA-typed patients who were potentially eligible for transplantation were included and their outcomes were assessed in an intent-to-transplant basis. We compared the outcomes of patients who underwent transplantation to those who did not and evaluated contributing barriers to access alloHSCT with multivariate logistic regression. Result(s): A total of n=374 patients were analyzed. The median age at HLA-typing was 35 years (IQR 23-47);59.3% had acute(Table Presented) leukemia, 17.4% bone marrow failure or myelodysplastic neoplasms, 13.1% lymphoma, 8% myeloproliferative neoplasms, 1.1% chronic lymphocytic leukemia and 1.1% multiple myeloma. Most patients (55.9%) had government insurance coverage. Median time from diagnosis to HLA-typing was 8 months (IQR 3-19). The majority had a potential donor (94.4%): 56.4% haploidentical, 37.4% a matched sibling donor and 0.5% an unrelated donor. Almost half of them received a transplant (n=185, 49.5%), the median time from HLA-typing to alloHSCT was 2 months (IQR 1-5.5). Disease activity or progression was the biggest barrier for transplantation;Table 1. Donor availability limited transplant access for 12.1% of patients. Access to transplantation was favored by private/out-of-pocket payment (OR 2.1 95% CI 1.3-3.4), and receiving care in the outpatient center (OR 6.4 95% CI 4-10.0), while HLA matching was not (OR 1.2 95% CI 0.8-1.8). Non-relapse mortality in alloHSCT was 21%. Median overall survival (OS) from the intent-to-transplant cohort was 16 months (CI 95% 12.4-19.6). An OS landmark analysis for patients alive at or beyond 2 months (the median time from HLA-typing to alloHSCT) showed prolonged survival in alloHSCT (30 vs 12 months, p <.001), Figure 1. By the time of the analysis 159 patients (42.5%) were still alive and 115 (30.7%) were event-free.(Figure Presented)Conclusion: The most frequent barrier to transplantation was the disease itself, followed by the transplant waitlist and comorbidities. Access to resources and an outpatient strategy or "center effect" favored alloHSCT. In the era of haploidentical transplantation, donor availability was a smaller issue. Efforts to improve timely referrals and access to effective pre-transplant therapies should be undertaken.Copyright © 2023 American Society for Transplantation and Cellular Therapy
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Background: Severe COVID-19 outcomes have been reported in people living with HIV (PLWH). High SARS-CoV-2 RNAemia has emerged as a hallmark of severe COVID-19, yet its pathogenic role in the context of COVID-19 in PLWH is currently unknown. We hereby measured SARS-CoV-2 RNAemia and explored its association with T-cell/humoral responses and clinical severity in PLWH. Method(s): Unvaccinated PLWH and age/sex-matched people living without HIV (PLWOH) hospitalized for radiologically-confirmed COVID-19 pneumonia were consecutively enrolled (March 2020-January 2021). We measured: SARS-CoV-2 RNAemia (RT-qPCR);T-cell activation (HLA-DR+CD-38+), cytotoxic T-cells [granzyme-B(GRZB)+perforin(PRF)+], GRZB/PRF production (MFI) by cytotoxic T-cells (flow cytometry);SARS-CoV-2-specific cytokines (IFN-gamma/ TNF-alpha/IL-2/IL-4/IL-17A)-producing T-cells, after SARS-CoV-2 spike peptides challenge (flow cytometry);anti-RBD antibodies (ELISA), Spike-ACE2 binding inhibition (receptor binding inhibition assay). Statistics: Mann-Whitney test and Spearman's correlation. Result(s): 18 PLWH (16 on cART;median CD4 361.5/mL;HIV-RNA< 50 cp/ mL in 15/18) and 18 PLWOH were included at a median of 10 days from symptoms onset (Fig.1A). PLWH had lower PaO2/FiO2 [140 (122-151.5) vs. 207 (156.3-309.3);P=0.0005] and higher SARS-CoV-2 RNAemia (Fig.1B). While humoral responses were comparable between groups ( Fig.1C-D), as was T-cell activation, PLWH showed skewed T-cell responses: higher perforin production by cytotoxic T-cells (Fig.1E);fewer SARS-CoV-2-specific IFN-gamma+ and IL-4+ CD4 T-cells (Fig.1F);lower Th1 tri-functional (IFN-gamma+TNF-alpha+IL-2+) and bi-functional (IFN-gamma+TNF-alpha+) CD4 T-cells (Fig.1G);reduced TNF-alpha+ CD8 T-cells (Fig.1H). Interestingly, SARS-CoV-2 RNAemia correlated negatively with PaO2/FiO2 nadir and SARS-CoV-2-specific T-cells, yet positively with perforin production by cytotoxic T-cells (Fig.1I-M). No correlations between RNAemia and humoral responses were found. Conclusion(s): As compared to HIV-uninfected patients, PLWH hospitalized for COVID-19 pneumonia feature high SARS-CoV-2 RNAemia which is linked to respiratory failure and skewed T-cell responses, with higher perforin production by cytotoxic T-cells, and yet fewer polyfunctional SARS-CoV-2-specific T-cells. Our data suggest a link between HIV-related T-cell dysfunction and poor control over circulating SARS-CoV-2 that may in turn influence COVID-19 severity in PLWH. (Figure Presented).
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BACKGROUND: The high prevalence and mortality rate of coronavirus disease 2019 (COVID-19) is a major global concern. Bioinformatics approaches have helped to develop new strategies to combat infectious agents, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Indeed, the structural proteins of microorganisms provide suitable epitopes for the development of vaccines to prevent infectious diseases. OBJECTIVES: The present study aimed to use bioinformatics tools to find peptides from the membrane (M) and nucleocapsid (N) proteins with effective cellular and humoral immunogenicity. MATERIAL AND METHODS: Sequences of the M and N proteins were sourced from the National Center for Biotechnology Information (NCBI). The conserved regions of the proteins with the highest immunogenicity were identified and assessed using different servers, and the physicochemical and biochemical properties of the epitopes were evaluated. Finally, allergenicity, antigenicity and docking to human leukocyte antigen (HLA) were investigated. RESULTS: The data indicated that the best epitopes were LVIGFLFLT and LFLTWICLL (as membrane epitopes), and KLDDKDPNFKDQ (as a nucleocapsid epitope), with significant immunogenicity and no evidence of allergenicity. The 3 epitopes are stable peptides that can interact with HLA to induce strong immune responses. CONCLUSIONS: The findings indicate that 3 common epitopes could effectively elicit an immune response against the disease. Hence, in vitro and in vivo studies are recommended to confirm the theoretical information.
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Autoimmune diseases are a group of different inflammatory disorders characterized by systemic or localized inflammation, affecting approximately 0.1–1% of the general population. Several studies suggest that genetic risk loci are shared between different autoimmune diseases and pathogenic mechanisms may also be shared. The strategy of performing differential gene expression profiles in autoimmune disorders has unveiled new transcripts that may be shared among these disorders. Microarray technology and bioinformatics offer the most comprehensive molecular evaluations and it is widely used to understand the changes in gene expression in specific organs or in peripheral blood cells. The major goal of transcriptome studies is the identification of specific biomarkers for different diseases. It is believed that such knowledge will contribute to the development of new drugs, new strategies for early diagnosis, avoiding tissue autoimmune destruction, or even preventing the development of autoimmune disease. In this review, we primarily focused on the transcription profiles of three typical autoimmune disorders, including type 1 diabetes mellitus (destruction of pancreatic islet beta cells), systemic lupus erythematosus (immune complex systemic disorder affecting several organs and tissues), and multiple sclerosis (inflammatory and demyelinating disease of the nervous system). © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2014, 2022.
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Background: COVID-19 is a viral disease affecting mostly respiratory system with variable severity of the clinical course. Several clinical and laboratory parameters are associated with poor outcome. Progression of the clinical stage is associated with the exaggerated immune response and the cytokine storm. Method(s): We focused on the search of potential prognostic markers of fatal outcome among immune parameters. To this end, we examined the immune profile in 823 COVID-19 patients hospitalized in University Teaching Hospital in Martin (Slovakia) on admission and its changes over time during the first week of hospitalization. The examined immune profile consisted of the differential blood cell counts, serum concentration of immunoglobulins and basic complement compounds C4 and C3, flow cytometric lymphocyte subsets phenotyping and the measurement of selected activation and inhibition markers. Result(s): Although none of examined parameters alone had sufficient AUC value to be considered as a marker of (un)favourable outcome, we found several significant differences among different severity groups of patients, as well as between survivors and non-survivors. Severity of COVID-19 correlated with the severity of neutrophilia, thrombocytopenia, depletion of leukocyte (except for neutrophils) and lymphocyte subsets. In comparison to the fatal outcome, survival was associated with higher concentration of C3 and IgM, lower proportion of CD8+CD38+ cells, higher proportion of CD8+NKG2A+ and NK NKG2A+ cells on admission and with the significant increase in the expression on HLA-DR on both CD3+ and CD8+ cells over the first week. Conclusion(s): Our results point out to the dysregulated functional status of depleted CD8+ cells with their over-activation and possibly insufficient compensatory inhibition in COVID-19 non-survivors. Based on our results, the increase in HLA-DR expression on CD3+ and CD8+ cells is necessary for recovery.
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We found a higher incidence of myocarditis in young males who had received Pfizer-BioNTech BNT162b2 vaccinations as compared with historical controls and unvaccinated individuals. The analyses focused on risk following the first and second vaccine in adults and adolescents, as well as risk in adults following the third (booster) vaccine. Males, mainly aged 12-30 years, were found to be at higher risk. However, the question remains what causes lead one specific young male, but not another, to develop post-vaccination myocarditis. The HLA molecule is known to play an important role in infectious and auto-inflammatory diseases. We hypothesized that differences in HLA alleles could lead to either protection or susceptibility to vaccination-induced myocarditis. On this basis, HLA typing was performed using next-generation sequencing technology for the HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1 loci, in 21 wellcharacterized patients who developed myocarditis after the second Pfizer BNT162b2 vaccination. The HLA genotypes were compared with high-resolution HLA data of 272 healthy controls from the Hadassah Bone Marrow registry samples, who are representative of HLA frequencies in the Israeli population. Our findings demonstrated that in HLA class II, DRB1*14:01 (19.04% vs. 5.3%, Pcorr = 0.028, OR = 4.17), HLA-DQB1*05:03 (19.04% vs. 6.06%, Pcorr = 0.034, OR = 3.64) and DRB1*15:03 (7.14% vs. 0.0%, Pcorr = 0.003, OR = 41.76) were significantly associated with disease susceptibility. We further discovered susceptibility motifs in the HLA-DR peptidebinding grooves: His60 (Pcorr0.01, OR = 3.52) and Arg70 (Pcorr = 0.0047, OR = 3.43). Our findings suggest that immunogenetic fingerprints in HLA peptide-binding grooves may have changed the binding affinity of different peptides derived from the Pfizer-BioNTech BNT162b2 vaccination, and induced myocarditis.
ABSTRACT
HLA molecules play a key role in transplant medicine and disease pathogenesis, being a useful tool in predicting disease progression and identifying potential solid organ donors (SOD). The Coronavirus disease 2019 (SARS-CoV-2) pandemic had a huge worldwide impact, which strongly affected the activity of different transplant programs. So far, it has been shown that HLA type may be a crucial differentiator between individuals who have varying occurrence, morbidity, and mortality response to SARS-CoV-2. In this work, we investigated if differences in the frequency of SOD HLA alleles, were impacted during SARS-CoV-2 pandemic. We performed a retrospective file audit of all HLA-typings done in 2 subsets of SOD pre-pandemic period (ppp) (n = 379) and pandemic period (pp) (n = 351), collected in equivalent timeframes. We discuss data for the major HLA-A, HLA-B, HLA-C, and HLA-DRB1 allele groups at serological phenotyping level. Overall, there was a 7% SOD decrease in the pp. Considering both periods, the most common allele groups were HLA-A2, HLA-B35, HLA-Cw7, HLA-DR7 and HLA-DQ2. For the ppp group, the most common alleles were HLA-A2, HLA-B35, HLA-Cw7, HLADR13 and HLA-DQ2, while in the pp group the most common alleles were HLA-A2, HLA-B44, HLA-Cw7, HLA-DR4 and HLA-DQ2. When comparing both populations at the serological phenotyping level an increased in relative frequency was found for 10, 12, 8, 8 and 2, and a decreased was found for 10, 24, 8, 6 and 5 for HLA-A, -B, -C, -DR and -DQ, respectively. The significant variation within the HLA frequencies between the different pre-pandemic and pandemic groups highlights the value of population-specific HLA-typing. Furthermore, the identification of different frequencies among both populations will impact in patients HLA compatibility with SOD thus impacting their transplantability.