major histocompatibility complex, class I, A

Gene Context Sentence

Table 2. Analysis of context sentence of HLA-A gene in 21 abstracts.

PMID Gene Context Sentence
32295479 After predicting and evaluating of the third structure of the protein candidate, the best 3 D predicted model was applied for docking studies with Toll-like receptor 4 (TLR4) and HLA-A11:01. […] In the next step, molecular dynamics (MD) simulation was used to evaluate the stability of the designed fusion protein with TLR4 and HLA-A11:01 receptors. […] MD studies demonstrated that the NOM-TLR4 and NOM-HLA-A*11:01 docked models were stable during simulation time. In silico evaluation showed that the designed chimeric protein could simultaneously elicit humoral and cell-mediated immune responses.
32424945 Here, 82 individuals with COVID-19 were genotyped for HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 loci using next-generation sequencing.
32475052 Among the strong HLA binders (IC50 ≤ 50), we uncovered 16 alleles (the top ones being A02:02, B15:03 and DRB101:02) binding more than 1% of peptides derived from all viruses, 9 (top ones including HLA-A68:01, B15:25, C03:02 and DRB107:01) binding all viruses except HIV-1, and 15 (top ones A02:01 and C*14:02) only binding coronaviruses.
32623831 A bias towards an increased representation of HLA-A26, HLA-DRB115, HLA-DRB110 and DRB111 was also noted but these were either only significant using the UK donor controls, or did not remain significant after correction for multiple tests. […] Likewise, HLA-A02, HLA-B44 and HLA-C*05 may exert a protective effect, but these associations did not remain significant after correction for multiple tests.
32699345 We also found that the frequency of several HLA alleles, including HLA-A*11:01, were significantly associated with the fatality rates, although these factors were associated with number of infected cases and not an independent factor to affect fatality rate in each country.
32717807 Among all the alleles, HLA-A25, B08, B44, B15:01, B51, C01, and C03 showed a positive log-linear correlation with COVID-19 incidence rate fixed on 9 April 2020 in proximity of the national outbreak peak (Pearson’s coefficients between 0.50 and 0.70, p-value < 0.0001), whereas HLA-B14, B18, and B49 showed an inverse log-linear correlation (Pearson’s coefficients between -0.47 and -0.59, p-value < 0.0001).
32759312 We identified 24 immunogenic epitopes in the SARS-CoV-2 protein S that could interact with 17 different MHC-I alleles (namely, HLA-A01:01; HLA-A02:01; HLA-A11:01; HLA-A24:02; HLA-A68:01; HLA-A23:01; HLA-A26:01; HLA-A30:02; HLA-A31:01; HLA-B07:02; HLA-B51:01; HLA-B35:01; HLA-B44:02; HLA-B35:03; HLA-C05:01; HLA-C07:01 and HLA-C*15:02) in the Brazilian population.
32913053 Experience with influenza shows that infection primes CD8+ T cell memory to peptides presented by common HLA types like HLA-A2, which enhances recovery and diminishes clinical severity upon reinfection. […] We identified two HLA-A02:01-restricted SARS-CoV-2-specfic CD8+ T cell epitopes, A2/S269-277 and A2/Orf1ab3183-3191 Using peptide-HLA tetramer enrichment, direct ex vivo assessment of A2/S269+CD8+ and A2/Orf1ab3183+CD8+ populations indicated that A2/S269+CD8+ T cells were detected at comparable frequencies (∼1.3 × 10-5) in acute and convalescent HLA-A02:01+ patients. […] These frequencies were higher than those found in uninfected HLA-A*02:01+ donors (∼2.5 × 10-6), but low when compared to frequencies for influenza-specific (A2/M158) and Epstein-Barr virus (EBV)-specific (A2/BMLF1280) (∼1.38 × 10-4) populations.
32933522 In this study we analysed the regional frequencies for the most common Italian haplotypes from the Italian Bone Marrow Donor Registry (HLA-A, -B, -C and -DRB1 at four-digit level). […] In this study we found that the two most frequent HLA haplotypes in the Italian population, HLA-A:01:01g-B08:01 g-C07:01g-DRB103:01g and HLA-A02.01g-B18.01g-C07.01g-DRB111.04g, had a regional distribution overlapping that of Covid-19 and showed respectively a positive (suggestive of susceptibility) and negative (suggestive of protection) significant correlation with both Covid-19 incidence and mortality.
32988645 We found a trend to a higher rate of the alleles HLA-A32 (p=0.004) in healthy controls than in COVID-19 patients, and of the alleles HLA-B39 (p=0.02) and HLA-C16 (p=0.02) in COVID-19 patients than in healthy controls; however, all these p-values were not significant after correction for multiple comparisons. […] Logistic regression analysis showed that the presence of certain alleles was associated with higher mortality, such as the allele HLA-A11 after controlling for SOFA (OR=7.693; 95% CI=1.063-55.650; p=0.04) or APACHE-II (OR=11.858; 95% CI=1.524-92.273; p=0.02), the allele HLA-C01 after controlling for SOFA (OR=11.182; 95% CI=1.053-118.700; p=0.04) or APACHE-II (OR=17.604; 95% CI=1.629-190.211; p=0.02), and the allele HLA-DQB104 after controlling for SOFA (OR=9.963; 95% CI=1.235-80.358; p=0.03).
33024578 Finally, HLA-A*03 restricted 8-mer peptides are found to be shared broadly by human and coronaviridae helicases in functional hotspots, with potential implications for nucleic acid unwinding upon initial infection.
33047883 We found that a possible association between HLA-A02:01 and an increased risk for COVID-19. […] HLA-A02:01 had a relatively lower capacity to present SARS-CoV-2 antigens compared with other frequent HLA class I molecules, HLA-A11:01 or HLA-A24:02. […] This study suggests that individuals with HLA-A11:01 or HLA-A24:02 genotypes may generate efficiently T-cell-mediated antiviral responses to SARS-CoV-2 compared with HLA-A*02:01.
33085221 We characterized medication orders, focusing on medications with actionable PGx guidance related to 14 commonly assayed genes (CYP2C19, CYP2C9, CYP2D6, CYP3A5, DPYD, G6PD, HLA-A, HLA-B, IFNL3, NUDT15, SLCO1B1, TPMT, UGT1A1, and VKORC1).
33268522 For the development of vaccines based on SARS-CoV-2-specific cytotoxic T lymphocytes (CTLs), we attempted to identify HLA-A02:01-restricted CTL epitopes derived from the non-structural polyprotein 1a of SARS-CoV-2. […] Out of 82 peptides predicted on bioinformatics, 54 peptides showed good binding affinities to HLA-A02:01. […] Using HLA-A*02:01 transgenic mice, 18 in 54 peptides were found to be CTL epitopes in the intracellular cytokine staining assay.
33298875 We identified that the HLA-A11:01, B51:01, and C*14:02 alleles significantly predispose the worst outcome of the patients.
33301503 We found diverse capacities of S protein specific epitope presentation by different HLA alleles with very limited number of predicted epitopes for HLA-B2705, HLA-B4402 and HLA-B4403 and as high as 132 epitopes for HLA-A6601.
33325143 Besides, docking analysis showed that the predicted peptide ‘KIADYNYKL’ was closely bound to the HLA-A0201. […] The results of molecular dynamics simulation through GROMACS software showed that ’HLA-A0201~peptide’ complex was very stable.
33343579 The extended haplotype HLA-A02:05, B58:01, C07:01, DRB103:01 [OR 0.1 (95% CI 0-0.6), Pc = 0.015] was absent in all 182 patients, while the HLA-C04:01 allele and the three-loci haplotype HLA-A30:02, B14:02, C08:02 [OR 3.8 (95% CI 1.8-8.1), Pc = 0.025] were more frequently represented in patients than controls. […] The data emerging from our study suggest that the extended haplotype HLA-A02:05, B58:01, C07:01, DRB103:01 has a protective effect against SARS-CoV-2 infection in the Sardinian population.
33361777 To help achieve these aims, we profiled the entire SARS-CoV-2 proteome across the most frequent 100 HLA-A, HLA-B and HLA-DR alleles in the human population, using host-infected cell surface antigen presentation and immunogenicity predictors from the NEC Immune Profiler suite of tools, and generated comprehensive epitope maps.
33403186 Methods To clarify the relationship between HLA class I and the severity rate, the binding repertoires of each HLA class I allele to SARS-CoV-2 peptides and the allele frequencies of HLA-A, -B, and -A/B haplotypes in each country were quoted. […] Results HLA-A1 and the number of deaths per million population (severity rate) in each country had an exponential approximation correlation with correlation coefficient R=0.4879. […] Weak HLA-A alleles with a repertoire of under 300 also had an exponential approximation correlation with the severity rate (R=0.5972), whereas there was a linear approximation with the infection rate (R=0.6808). […] The weak HLA-A/B haplotype has a stronger effect on the severity rate than the weak HLA-A alone. […] The weak HLA-A is a major factor of severity rate, whereas the weak -B alone has no correlation. […] However, the weak HLA-A/B haplotype has a stronger effect on the severity rate than the weak -A alone.
33586620 Secondly, the 3D model of selected epitopes and HLA-A29:02 were built and Molecular Docking simulation was performed. […] Upon Molecular Docking, interactions between selected epitopes and HLA-A29:02 were further validated by 50 ns Molecular Dynamics (MD) simulation.