Immunogenetics最新文献_第8页

Comparison between qPCR and RNA-seq reveals challenges of quantifying HLA expression. qPCR与RNA-seq的比较揭示了HLA表达定量的挑战。

IF 3.2 4区医学

Immunogenetics Pub Date : 2023-06-01 DOI: 10.1007/s00251-023-01296-7

Vitor R C Aguiar, Erick C Castelli, Richard M Single, Arman Bashirova, Veron Ramsuran, Smita Kulkarni, Danillo G Augusto, Maureen P Martin, Maria Gutierrez-Arcelus, Mary Carrington, Diogo Meyer

{"title":"Comparison between qPCR and RNA-seq reveals challenges of quantifying HLA expression.","authors":"Vitor R C Aguiar, Erick C Castelli, Richard M Single, Arman Bashirova, Veron Ramsuran, Smita Kulkarni, Danillo G Augusto, Maureen P Martin, Maria Gutierrez-Arcelus, Mary Carrington, Diogo Meyer","doi":"10.1007/s00251-023-01296-7","DOIUrl":"https://doi.org/10.1007/s00251-023-01296-7","url":null,"abstract":"Human leukocyte antigen (HLA) class I and II loci are essential elements of innate and acquired immunity. Their functions include antigen presentation to T cells leading to cellular and humoral immune responses, and modulation of NK cells. Their exceptional influence on disease outcome has now been made clear by genome-wide association studies. The exons encoding the peptide-binding groove have been the main focus for determining HLA effects on disease susceptibility/pathogenesis. However, HLA expression levels have also been implicated in disease outcome, adding another dimension to the extreme diversity of HLA that impacts variability in immune responses across individuals. To estimate HLA expression, immunogenetic studies traditionally rely on quantitative PCR (qPCR). Adoption of alternative high-throughput technologies such as RNA-seq has been hampered by technical issues due to the extreme polymorphism at HLA genes. Recently, however, multiple bioinformatic methods have been developed to accurately estimate HLA expression from RNA-seq data. This opens an exciting opportunity to quantify HLA expression in large datasets but also brings questions on whether RNA-seq results are comparable to those by qPCR. In this study, we analyze three classes of expression data for HLA class I genes for a matched set of individuals: (a) RNA-seq, (b) qPCR, and (c) cell surface HLA-C expression. We observed a moderate correlation between expression estimates from qPCR and RNA-seq for HLA-A, -B, and -C (0.2 ≤ rho ≤ 0.53). We discuss technical and biological factors which need to be accounted for when comparing quantifications for different molecular phenotypes or using different techniques.","PeriodicalId":13446,"journal":{"name":"Immunogenetics","volume":"75 3","pages":"249-262"},"PeriodicalIF":3.2,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9883133/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9595180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Innate receptors modulating adaptive T cell responses: KIR-HLA interactions and T cell-mediated control of chronic viral infections. 调节适应性 T 细胞反应的先天受体：KIR-HLA 相互作用和 T 细胞介导的慢性病毒感染控制。

IF 3.2 4区医学

Immunogenetics Pub Date : 2023-06-01 Epub Date: 2023-01-31 DOI: 10.1007/s00251-023-01293-w

Laura Mora-Bitria, Becca Asquith

引用次数: 0

Genetic variation of glycophorins and infectious disease. 糖蛋白遗传变异与传染病。

IF 3.2 4区医学

Immunogenetics Pub Date : 2023-06-01 DOI: 10.1007/s00251-022-01280-7

Edward J Hollox, Sandra Louzada

{"title":"Genetic variation of glycophorins and infectious disease.","authors":"Edward J Hollox, Sandra Louzada","doi":"10.1007/s00251-022-01280-7","DOIUrl":"https://doi.org/10.1007/s00251-022-01280-7","url":null,"abstract":"Glycophorins are transmembrane proteins of red blood cells (RBCs), heavily glycosylated on their external-facing surface. In humans, there are four glycophorin proteins, glycophorins A, B, C and D. Glycophorins A and B are encoded by two similar genes GYPA and GYPB, and glycophorin C and glycophorin D are encoded by a single gene, GYPC. The exact function of glycophorins remains unclear. However, given their abundance on the surface of RBCs, it is likely that they serve as a substrate for glycosylation, giving the RBC a negatively charged, complex glycan \"coat\". GYPB and GYPE (a closely related pseudogene) were generated from GYPA by two duplication events involving a 120-kb genomic segment between 10 and 15 million years ago. Non-allelic homologous recombination between these 120-kb repeats generates a variety of duplication alleles and deletion alleles, which have been systematically catalogued from genomic sequence data. One allele, called DUP4, encodes the Dantu NE blood type and is strongly protective against malaria as it alters the surface tension of the RBC membrane. Glycophorins interact with other infectious pathogens, including viruses, as well as the malarial parasite Plasmodium falciparum, but the role of glycophorin variation in mediating the effects of these pathogens remains underexplored.","PeriodicalId":13446,"journal":{"name":"Immunogenetics","volume":"75 3","pages":"201-206"},"PeriodicalIF":3.2,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10205821/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9511628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Distinct frequency patterns of LILRB3 and LILRA6 allelic variants in Europeans. 欧洲人LILRB3和LILRA6等位基因变异的不同频率模式

IF 3.2 4区医学

Immunogenetics Pub Date : 2023-06-01 DOI: 10.1007/s00251-022-01286-1

Arman A Bashirova, Wojciech Kasprzak, Colm O'hUigin, Mary Carrington

{"title":"Distinct frequency patterns of LILRB3 and LILRA6 allelic variants in Europeans.","authors":"Arman A Bashirova, Wojciech Kasprzak, Colm O'hUigin, Mary Carrington","doi":"10.1007/s00251-022-01286-1","DOIUrl":"https://doi.org/10.1007/s00251-022-01286-1","url":null,"abstract":"The leukocyte immunoglobulin-like receptor (LILR)B3 and LILRA6 genes encode homologous myeloid inhibitory and activating orphan receptors, respectively. Both genes exhibit a strikingly high level of polymorphism at the amino acid level and LILRA6 (but not LILRB3) displays copy number variation (CNV). Although multiple alleles have been reported for both genes, limited data is available on frequencies of these alleles among humans. We have sequenced LILRB3/A6 exons encoding signal peptides and ectodomains in 91 healthy blood donors of European descent who carry one or two copies of LILRA6 per diploid genome. Analysis of haplotypes among individuals with two LILRA6 copies, representing the majority in this cohort (N = 86), shows that common LILRB3 and LILRA6 alleles encode some distinct amino acid sequences in homologous regions of the receptors, which could potentially impact their respective functions differentially. Comparison of sequences in individuals with one vs. two copies of LILRA6 supports non-allelic homologous recombination between LILRB3 and LILRA6 as a mechanism for generating LILRA6 CNV and LILRB3 diversity. These data characterize LILRB3/LILRA6 genetic variation in more detail than previously described and underscore the need to determine their ligands.","PeriodicalId":13446,"journal":{"name":"Immunogenetics","volume":"75 3","pages":"263-267"},"PeriodicalIF":3.2,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10205885/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9521047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Evolution of SARS-CoV-2-specific CD4⁺ T cell epitopes. sars - cov -2特异性CD4+ T细胞表位的进化

IF 3.2 4区医学

Immunogenetics Pub Date : 2023-06-01 DOI: 10.1007/s00251-023-01295-8

Marina Brand, Can Keşmir

{"title":"Evolution of SARS-CoV-2-specific CD4+ T cell epitopes.","authors":"Marina Brand, Can Keşmir","doi":"10.1007/s00251-023-01295-8","DOIUrl":"https://doi.org/10.1007/s00251-023-01295-8","url":null,"abstract":"Vaccination clearly decreases coronavirus disease 2019 (COVID-19) mortality; however, they also impose selection pressure on the virus, which promotes the evolution of immune escape variants. For example, despite the high vaccination level in especially Western countries, the Omicron variant caused millions of breakthrough infections, suggesting that the highly mutated spike protein in the Omicron variant can escape antibody immunity much more efficiently than the other variants of concern (VOCs). In this study, we investigated the resistance/susceptibility of T helper cell responses that are necessary for generating efficient long-lasting antibody immunity, in several VOCs. By predicting T helper cell epitopes on the spike protein for most common HLA-DRB1 alleles worldwide, we found that although most of high frequency HLA-DRB1 alleles have several potential T helper cell epitopes, few alleles like HLA-DRB1 13:01 and 11:01 are not predicted to have any significant T helper cell responses after vaccination. Using these predictions, a population based on realistic human leukocyte antigen-II (HLA-II) frequencies were simulated to visualize the T helper cell immunity on the population level. While a small fraction of this population had alarmingly little predicted CD4 T cell epitopes, the majority had several epitopes that should be enough to generate efficient B cell responses. Moreover, we show that VOC spike mutations hardly affect T helper epitopes and mainly occur in other residues of the spike protein. These results suggest that lack of long-lasting antibody responses is not likely due to loss of T helper cell epitopes in new VOCs.","PeriodicalId":13446,"journal":{"name":"Immunogenetics","volume":"75 3","pages":"283-293"},"PeriodicalIF":3.2,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9887569/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10322368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Correction to: The immunogenetics of COVID-19. 更正为:COVID-19的免疫遗传学。

IF 3.2 4区医学

Immunogenetics Pub Date : 2023-06-01 DOI: 10.1007/s00251-023-01300-0

Anshika Srivastava, Jill A Hollenbach

引用次数: 0

Immunogenetics special issue 2023: Immunogenetics of infectious disease. 免疫遗传学特刊2023:传染病的免疫遗传学。

IF 3.2 4区医学

Immunogenetics Pub Date : 2023-06-01 DOI: 10.1007/s00251-023-01301-z

Paul J Norman

引用次数: 0

The immunogenetics of COVID-19. COVID-19的免疫遗传学。

IF 3.2 4区医学

Immunogenetics Pub Date : 2023-06-01 DOI: 10.1007/s00251-022-01284-3

Anshika Srivastava, Jill A Hollenbach

{"title":"The immunogenetics of COVID-19.","authors":"Anshika Srivastava, Jill A Hollenbach","doi":"10.1007/s00251-022-01284-3","DOIUrl":"https://doi.org/10.1007/s00251-022-01284-3","url":null,"abstract":"The worldwide coronavirus disease 2019 pandemic was sparked by the severe acute respiratory syndrome caused by coronavirus 2 (SARS-CoV-2) that first surfaced in December 2019 (COVID-19). The effects of COVID-19 differ substantially not just between patients individually but also between populations with different ancestries. In humans, the human leukocyte antigen (HLA) system coordinates immune regulation. Since HLA molecules are a major component of antigen-presenting pathway, they play an important role in determining susceptibility to infectious disease. It is likely that differential susceptibility to SARS-CoV-2 infection and/or disease course in COVID-19 in different individuals could be influenced by the variations in the HLA genes which are associated with various immune responses to SARS-CoV-2. A growing number of studies have identified a connection between HLA variation and diverse COVID-19 outcomes. Here, we review research investigating the impact of HLA on individual responses to SARS-CoV-2 infection and/or progression, also discussing the significance of MHC-related immunological patterns and its use in vaccine design.","PeriodicalId":13446,"journal":{"name":"Immunogenetics","volume":"75 3","pages":"309-320"},"PeriodicalIF":3.2,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9762652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9518355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Role of T cells in severe COVID-19 disease, protection, and long term immunity. T细胞在重症COVID-19疾病、保护和长期免疫中的作用。

IF 3.2 4区医学

Immunogenetics Pub Date : 2023-06-01 DOI: 10.1007/s00251-023-01294-9

Julia Maret Hermens, Can Kesmir

{"title":"Role of T cells in severe COVID-19 disease, protection, and long term immunity.","authors":"Julia Maret Hermens, Can Kesmir","doi":"10.1007/s00251-023-01294-9","DOIUrl":"https://doi.org/10.1007/s00251-023-01294-9","url":null,"abstract":"Infection with SARS-CoV-2 causes wide range of disease severities from asymptomatic to life-threatening disease. Understanding the contribution of immunological traits in immunity against SARS-CoV-2 and in protection against severe COVID-19 could result in effective measures to prevent development of severe disease. While the role of cytokines and antibodies has been thoroughly studied, this is not the case for T cells. In this review, the association between T cells and COVID-19 disease severity and protection upon reexposure is discussed. While infiltration of overactivated cytotoxic T cells might be harmful in the infected tissue, fast responding T cells are important in the protection against severe COVID-19. This protection could even be viable in the long term as long-living memory T cells seem to be stabilized and mutations do not appear to have a large impact on T cell responses. Thus, after vaccination and infections, memory T cells should be able to help prevent onset of severe disease for most cases. Considering this, it would be useful to add N or M proteins in vaccinations, alongside the S protein which is currently used, as this results in a broader T cell response.","PeriodicalId":13446,"journal":{"name":"Immunogenetics","volume":"75 3","pages":"295-307"},"PeriodicalIF":3.2,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9905767/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9521546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

Impact of high human genetic diversity in Africa on immunogenicity and efficacy of RTS,S/AS01 vaccine. 非洲高度的人类基因多样性对 RTS,S/AS01 疫苗免疫原性和有效性的影响。

IF 2.9 4区医学

Immunogenetics Pub Date : 2023-06-01 Epub Date: 2023-04-21 DOI: 10.1007/s00251-023-01306-8

Stephen Tukwasibwe, Gerald Mboowa, Ivan Sserwadda, Joaniter I Nankabirwa, Emmanuel Arinaitwe, Isaac Ssewanyana, Yoweri Taremwa, Gerald Tumusiime, Moses R Kamya, Prasanna Jagannathan, Annettee Nakimuli

引用次数: 0