{"title":"T cell transcriptional landscapes are shaped by TCR sequence similarity.","authors":"Hao Wang, Zhicheng Ji","doi":"10.1101/2023.11.27.568912","DOIUrl":null,"url":null,"abstract":"<p><p>T cells exhibit high heterogeneity in both their gene expression profiles and antigen specificities, but the precise relationship between these two features remains largely unknown. Utilizing a large-scale single-cell immune-profiling dataset that includes both T cell receptor (TCR) sequences and gene expression profiles of individual cells, we systematically investigated how the transcriptional profiles of T cells are linked to their TCR sequence similarity. We observed that T cells sharing the same clonotype often belong to the same cell type, and that gene expression similarity among T cells correlates with TCR sequence similarity. Furthermore, we identified features such as clonality, VJ gene usage, sequence motifs, and amino acid preferences that are distinctly associated with specific T cell subtypes. These findings suggest that T cell transcriptional landscapes are broadly shared and influenced by TCR sequence similarity.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10705237/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"bioRxiv : the preprint server for biology","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1101/2023.11.27.568912","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
Abstract
T cells exhibit high heterogeneity in both their gene expression profiles and antigen specificities, but the precise relationship between these two features remains largely unknown. Utilizing a large-scale single-cell immune-profiling dataset that includes both T cell receptor (TCR) sequences and gene expression profiles of individual cells, we systematically investigated how the transcriptional profiles of T cells are linked to their TCR sequence similarity. We observed that T cells sharing the same clonotype often belong to the same cell type, and that gene expression similarity among T cells correlates with TCR sequence similarity. Furthermore, we identified features such as clonality, VJ gene usage, sequence motifs, and amino acid preferences that are distinctly associated with specific T cell subtypes. These findings suggest that T cell transcriptional landscapes are broadly shared and influenced by TCR sequence similarity.
T 细胞在基因表达谱和抗原特异性方面都表现出高度的异质性。我们分析了 15 个单细胞免疫分析数据集,系统地研究了 T 细胞受体(TCR)序列与 T 细胞基因表达谱之间的关联。我们的研究结果表明,具有相同或相似 TCR 序列的 T 细胞往往具有高度相似的基因表达谱。此外,我们还建立了一个基础模型,利用 TCR 信息预测 T 细胞的基因表达水平。