Single-cell analysis of the molecular regulation of T cell differentiation

细胞分化，即细胞变成具有专门功能的不同细胞的过程，是生物学的基础。健康的免疫系统所必需的是T细胞命运和功能的多样性。我们对T细胞如何分化的大部分理解都是基于对具有不同功能的T细胞群的研究。然而，为了更好地了解不同的T细胞命运和功能是如何形成的，需要在分化过程中分析单个细胞。单细胞基因组学技术的进步已经开始使单细胞及其分化谱系的直接分子分析成为可能，揭示了单细胞水平上细胞命运决定和分子异质性的驱动因素。 为了诱导T细胞活化和分化，免疫抗原呈递细胞识别外源因子并将其呈递给T细胞上的受体（称为同源肽相互作用）。与转录网络一起，基因转录和不对称分裂的表观遗传调控可以有助于在T细胞活化后早期通过同源肽相互作用指定不同的T细胞命运。在以前的工作中，使用单细胞基因表达分析，我们提供了新的转录和表观遗传学的见解，单个小鼠T细胞如何分化成不同的分化路径T细胞活化后早期。 这项研究的长期目标是在单细胞水平上表征调节细胞命运决定和细胞分化过程的分子机制。短期的目标是表征早期转录和染色质的可及性模式在单个T细胞经历不同同源肽相互作用激活后的分化。一个多学科的方法，包括单细胞转录组学和表观基因组学，细胞生物学，T细胞分化的免疫学模型和计算分析，将被用来表征T细胞分化的早期分子机制。在这5年周期内提出的研究将为至少四名研究生（两名理学硕士和两名哲学博士）和四名本科生提供单细胞基因组学和免疫学研究的培训机会，并将为未来的细胞分化研究项目和正在进行的研究培训机会奠定基础。 这项研究对于解决细胞分化中的一个缺口具有重要意义：染色质可及性区域中的细胞间异质性仍然未知，这将反映细胞命运规范早期阶段单细胞中表观遗传状态的分化。这项研究将为细胞分化和T细胞生物学过程中调控基因表达和细胞命运规范的基本分子机制提供新的见解。这项研究的结果将广泛适用于研究其他细胞分化系统是如何调节的。

Cell differentiation, i.e. the process of a cell becoming different cells with specialized functions, is fundamental to biology. Essential to a healthy immune system is the diversity in T cell fate and function. Much of our understanding of how T cells differentiate is based on studies on groups of T cells that have different functions. However, to better understand how different T cell fates and functions are formed requires analyzing single cells during differentiation. Advances in single-cell genomics technologies have begun to enable the direct molecular analysis of single cells and their differentiation lineages, revealing drivers of cell fate decisions and molecular heterogeneity at the single cell level. To induce T cell activation and differentiation, immune antigen presenting cells recognize foreign agents and present them to receptors on T cells (called cognate-peptide interactions). Together with transcriptional networks, epigenetic regulation of gene transcription and asymmetric division can contribute to specifying different T cell fates early after T cell activation by cognate-peptide interactions. In previous works, using single-cell gene expression analyses, we provided novel transcriptional and epigenetic insights into how single mouse T cells diverge into different paths of differentiation early after T cell activation. The long-term aim of this research is to characterize the molecular mechanisms that regulate cell fate decisions and cell differentiation processes at the single-cell level. The short-term aims are to characterize the early transcription and chromatin accessibility patterns in single T cells undergoing differentiation after activation by different cognate-peptide interactions. A multidisciplinary approach, including single-cell transcriptomics and epigenomics, cell biology, immunology models of T cell differentiation, and computational analyses, will be used to characterize early molecular mechanisms underlying T cell differentiation. The research proposed over this 5 year cycle will provide training opportunities in single cell genomics and immunology research for at least four graduate students (two Master of Science and two Doctor of Philosophy trainees) and four undergraduate students, and will form the basis for future research projects on cell differentiation and ongoing research training opportunities. This research is significant to address a gap in cell differentiation: cell-to-cell heterogeneity in chromatin accessibility regions, which would reflect the differentiation of epigenetic states among single cells at early phases of cell fate specification, remains unknown. This research will provide novel insights into the fundamental molecular mechanisms regulating gene expression and cell fate specification during cell differentiation and T cell biology. The findings from this research will be broadly applicable to the study of how other cellular systems of differentiation are regulated.