Deciphering Single-Cell Genomics Data to Understand Tissue-Resident Immune Function and Development

Tissue immunity strikes a balance between protecting and tolerating the host so that the body can counteract threats while executing critical physiological functions, like nutrient absorption in the gut. This trade-off is facilitated through intricate crosstalk between specialized, tissue-specific immune and non-immune cells. Here, we study tissue-resident immunity in three biological systems by closely coupling my computational perspective with the expertise of classical experimental immunologists. My collaborators and I jointly directed projects integrating targeted functional experiments with design of computational analyses of single-cell RNA-sequencing (scRNA-seq) data, which profiles the transcriptomes of large numbers of cells. First, we use RNA velocity analysis of transcriptional dynamics, coupled with adoptive bone marrow transfers in mice, to investigate the developmental divergence of circulatory natural killer (NK) cells from closely related tissue-resident type 1 innate lymphoid cells (ILC1s). Our results include identification of the first NK-specific progenitor. Next, we focus on human γδ intestinal intraepithelial lymphocytes (γδ IELs), about which much less is known than conventional αβ T cells. By analyzing paired scRNA-seq and single-cell γδ TCR-sequencing data of γδ IELs, in combination with molecular and cellular reactivity experiments, we discover complex roles of several elements of the Vγ4 γδ TCR in conferring cellular reactivity to the ligand butyrophilin-like 3 and 8 (BTNL3/8), which is expressed in healthy gut epithelial cells but lost in some diseases. We show that while all tested Vγ4 TCRs bind BTNL3, many fail to induce full cellular activation linked to the expression of a natural killer (NK)-like gene program  induced by chronic BTNL3/8 exposure. Last, we investigate the role of signaling through IL-17, a key immune cytokine, in the hypothalamus region of the mouse brain. We find that in response to IL-17 signaling, highly specialized glial cells, called tanycytes, induce sex-specific alterations in several brain-resident cell types.  Moreover, we find that IL-17 signaling in tancycytes plays a protective role, specifically in females, against experimental autoimmune encephalomyelitis (EAE). Taken together, the results in this dissertation advance a systems-level understanding of tissue-resident immunity and development, highlighting multifaceted ways that the tissue and immune system are shaped in concert to protect from disease.