Determining the gene-regulatory impact of microbial exposure on central immune training

Cornell University, Ithaca NY

Investigators

Abstract

PROJECT SUMMARY/ABSTRACT Epidemiological studies highlight the ability of early-in-life microbial exposure to induce environmentally adaptive, long-term shifts in the immune response. The immune system’s adaptive potential may be explained in part by central immune training, the process by which hematopoietic stem and progenitor cells (HSPCs) undergo lasting epigenetic reprogramming after receiving inflammatory signals. Importantly, the epigenetic inheritance of immune training from HSPCs into mature immune cells results in their enhanced responsiveness to pathogens they have never been exposed to previously; however, the mechanisms underlying the maintenance and transfer of immune training remain to be comprehensively investigated. Here, I will focus on the training of CD8+ T cells, thus describing immune training in an adaptive immune cell type for the first time. By leveraging a mouse model system of immune training, I will complete an interdisciplinary project determining the gene-regulatory impact of microbial exposure on central immune training. Specific Aim 1 entails the joint profiling of gene expression and chromatin accessibility at single-cell resolution to uncover the genes, enhancers, and transcription factors that are responsive to microbial exposure in HSPCs. The results of Aim 1 will provide insight into how, and where, microbial exposure initiates epigenetic reprogramming. Specific Aim 2 employs CRISPR-mediated transcription factor knockouts, ATAC-seq, and functional CD8+ T cell assays within an Artificial Thymic Organoid (ATO) system to examine the requirement of the transcription factors FOSB and KLF6, which preliminary data implicate as mediating central immune training. The results of Aim 2 will determine the requirement of specific TFs in maintaining and transferring immune training from HSPCs to CD8+ T cells. Specific Aim 3 utilizes enzymatic methylation sequencing and chromatin conformation capture approaches to investigate the epigenetic mechanism by which immune training is transferred from HSPCs to CD8+ T cells. The results of Aim 3 will determine the role of DNA methylation in transferring immune training from HSPCs to CD8+ T cells and the role of chromatin architecture in facilitating differential gene expression in trained CD8+ T cells. I will utilize the expertise obtained from my previous research experiences, along with expert-led training, to perform the proposed experiments. Further, by enhancing my skills as a communicator, mentor, and teacher of science, I will become a well-rounded researcher, allowing me to seamlessly transition into a postdoctoral position after completing my thesis work. The Grimson and Rudd labs, my mentoring committee, and collaborators within the Genomics Innovation Hub at Cornell University, will provide invaluable mentorship, support, and training, ensuring my mastery of all research techniques required for the completion of this proposal. Ultimately, this proposal will advance the understanding of the gene-regulatory underpinnings of central immune training and will facilitate significant development in my path to becoming an independent researcher.