Mechanisms Of Age-related Changes in Transcriptional Regulation, TCR Repertoire, and Cytokine Expression

转录调控、TCR 库和细胞因子表达与年龄相关的变化机制

• 批准号: 9348193
• 负责人: Nan-ping Peter Weng
• 金额: $ 52.38万
• 依托单位: NATIONAL INSTITUTE ON AGING
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/9348193
• 关键词: Affinity; Age; Aging; Amino Acids; Antigens; Binding; Biochemical; CD4 Positive T Lymphocytes; CD8B1 gene; Cell physiology; Cells; ChIP-seq; Chromatin; Complex; Consensus; Cytomegalovirus; Development; Disease; Dissociation; Ensure; Epitopes; Exhibits; Future; Gene Expression; Genes; Genetic; Genetic Transcription; Goals; HLA-A2 Antigen; High-Throughput Nucleotide Sequencing; Human; Immune; Immune response; Immune system; Immunity; Individual; Influenza A virus; Length; Machine Learning; Memory; Methods; MicroRNAs; Portraits; Post-Transcriptional Regulation; Role; Structure; Study Subject; T cell response; T memory cell; T-Cell Receptor; T-Lymphocyte; Time; Tissue-Specific Gene Expression; Transcriptional Regulation; Variant; Viral; Viral Antigens; Virus Diseases; age related; base; comparative; cytokine; differential expression; histone modification; interest; microbial; next generation sequencing; pathogen; personalized medicine; preference

A diverse T cell receptor (TCR) repertoire is essential for controlling viral infections. However, information on human TCR repertoires in general and to defined viral antigens is limited. We performed a comprehensive analysis of TCR repertoires of CD4+ and CD8+, and CD8+ TCR repertoires specific for two dominant viral epitopes: pp65495503 (NLV) of cytomegalovirus and M15866 (GIL) of influenza A virus using the high-throughput sequencing (HTS) and single-cell paired TCR analysis. We provided a comparative analysis of the TCR repertoires of CD4+ and CD8+ T cells. TCR diversity of CD4+ T cells ranges from 1.8-8.2 x105 and is 3-4 times greater on average than that of CD8+ T cells in each study subject. Furthermore, there was little overlap in TCR sequences between CD4+ (0.3%) and CD8+ (1.3%) T cells. Further analysis showed that CD4+ and CD8+ T cells exhibited distinct preferences for certain amino acids in the CDR3, and this was further confirmed by a support vector machine classifier, suggesting there are distinct and discernible differences between TCR CDR3 in CD4+ and CD8+ T cells. Finally, we identified 6-12% of the unique TCRs that share an identical CDR3 with different V genes. Together, our findings reveal the distinct features of the TCR repertoire between CD4+ and CD8+ T cells and could potentially be used to evaluate the competency of T cell immunity. For antigen-specific CD8+ TCR repertoires, we identified thousands of new NLV- and GIL-specific TCR and TCR sequences, as well as dozens of distinct CDR3 and CDR3 consensus motifs. This diversity is substantially greater than previously described for T cell responses to single viral epitopes, both for private and public TCR clonotypes, and exhibited a high degree of individual variations (12028,000 clonotypes per subject). However, diversity is effectively restricted by preferential V-J combinations, CDR3 lengths, and CDR3/CDR3 pairings. We further found that GIL-specific, but not NLV-specific, TCRs exhibited a surprisingly wide range of binding affinities, with dissociation constants (KDs) from 2 to 200 M. Finally, we determined the crystal structures of two unrelated GIL-specific TCRs in complex with GILHLA-A2 and two TCR-NLV- HLA-A2 complexes. These structures provide an explanation of the lower diversity of GIL-specific than NLV-specific repertoires. Remarkably, these two anti-viral TCR repertoires occupied 0.220% of the total CD8+ TCR repertoire, ensuring broad and robust T cell responses to single epitopes. Our comprehensive genetic, biochemical, and structural portrait of two different anti-viral T cell responses may contribute to the future development of predictors of immunity or disease at the personal level.

不同的T细胞受体（TCR）库对于控制病毒感染是必不可少的。然而，关于人TCR库的一般信息和关于定义的病毒抗原的信息是有限的。我们使用高通量测序（HTS）和单细胞配对TCR分析，对CD4+和CD8 + TCR库以及对两种主要病毒表位（巨细胞病毒的pp65495503（NLV）和甲型流感病毒的M15866（GIL））具有特异性的CD8 + TCR库进行了全面分析。我们提供了CD4+和CD8 + T细胞TCR库的比较分析。在每个研究对象中，CD4 + T细胞的TCR多样性范围为1.8 - 8.2 × 105，平均比CD8 + T细胞的TCR多样性大3 - 4倍。此外，在CD4+（0.3%）和CD8+（1.3%）T细胞之间TCR序列几乎没有重叠。 进一步的分析显示，CD4+和CD8 + T细胞对CDR 3中的某些氨基酸表现出不同的偏好，并且这通过支持向量机分类器进一步证实，表明CD4+和CD8 + T细胞中的TCR CDR 3之间存在明显且可辨别的差异。最后，我们鉴定了6 - 12%的独特TCR，其与不同的V基因共享相同的CDR 3。总之，我们的研究结果揭示了CD4+和CD8 + T细胞之间TCR库的不同特征，并可能用于评估T细胞免疫的能力。 对于抗原特异性CD 8 + TCR谱系，我们鉴定了数千种新的NLV和GIL特异性TCR和TCR序列，以及数十种不同的CDR 3和CDR 3共有基序。这种多样性基本上大于先前描述的针对单个病毒表位的T细胞应答，对于私有和公共TCR克隆型，并且表现出高度的个体变异（每个受试者12028，000个克隆型）。然而，多样性受到优先V-J组合、CDR 3长度和CDR 3/CDR 3配对的有效限制。我们进一步发现，GIL特异性而非NLV特异性的TCR表现出令人惊讶的宽范围的结合亲和力，解离常数（KD）为2至200 M。最后，我们确定了与GILHLA-A2复合的两种不相关的GIL特异性TCR和两种TCR-NLV-HLA-A2复合物的晶体结构。这些结构提供了一个较低的多样性GIL特异性比NLV特异性库的解释。值得注意的是，这两种抗病毒TCR库占总CD8 + TCR库的0.220%，确保了对单个表位的广泛和稳健的T细胞应答。我们对两种不同抗病毒T细胞反应的全面遗传、生物化学和结构描述可能有助于未来在个人水平上开发免疫或疾病的预测因子。