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

细胞分化，即一个细胞变成具有特殊功能的不同细胞的过程，这是生物学的基础。T细胞命运和功能的多样性对健康的免疫系统至关重要。我们对T细胞如何分化的大部分理解是基于对具有不同功能的T细胞组的研究。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，需要分析单个细胞在分化过程中的情况。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决定细胞命运和分子异质性的驱动因素。为了诱导T细胞的激活和分化，免疫抗原提呈细胞识别外源物质并将其递送给T细胞上的受体(称为同源多肽相互作用)。与转录网络一起，基因转录的表观遗传调控和不对称分裂可以通过同源多肽相互作用在T细胞激活后早期确定不同的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见解，了解单个小鼠T细胞如何在T细胞激活后早期分化为不同的分化途径。这项研究的长期目标是在单细胞水平上表征调控细胞命运决定和细胞分化过程的分子机制。短期目标是描述单个T细胞在不同同源多肽相互作用激活后发生分化后的早期转录和染色质可及性模式。将使用包括单细胞转录学和表观基因组学、细胞生物学、T细胞分化的免疫学模型和计算分析在内的多学科方法来表征T细胞分化的早期分子机制。在这个5年周期中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实习生)和四名本科生提供单细胞基因组和免疫学研究的培训机会，并将形成未来细胞分化研究项目和正在进行的研究培训机会的基础。这项研究对于解决细胞分化中的一个缺口：染色质可及区的细胞到细胞的异质性仍然未知，该研究将反映细胞命运指定的早期阶段单个细胞之间的表观遗传状态的分化。这项研究将为细胞分化和T细胞生物学中调控基因表达和细胞命运指定的基本分子机制提供新的见解。这项研究的发现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.