Search

Tissue-resident memory CD8 T cells (T RM ) kill infected cells and recruit additional immune cells to limit pathogen invasion at barrier sites. Small intestinal (SI) T RM cells consist of distinct subpopulations with higher expression of effector molecules or greater memory potential. We hypothesized that occupancy of diverse anatomical niches imprints these distinct T RM transcriptional programs. We leveraged human samples and a murine model of acute systemic viral infection to profile the location and transcriptome of pathogen-specific T RM cell differentiation at single-transcript resolution. We developed computational approaches to capture cellular locations along three anatomical axes of the small intestine and to visualize the spatiotemporal distribution of cell types and gene expression. T RM populations were spatially segregated: with more effector- and memory-like T RM preferentially localized at the villus tip or crypt, respectively. Modeling ligand-receptor activity revealed patterns of key cellular interactions and cytokine signaling pathways that initiate and maintain T RM differentiation and functional diversity, including different TGFβ sources. Alterations in the cellular networks induced by loss of TGFβRII expression revealed a model consistent with TGFβ promoting progressive T RM maturation towards the villus tip. Ultimately, we have developed a framework for the study of immune cell interactions with the spectrum of tissue cell types, revealing that T cell location and functional state are fundamentally intertwined., Competing Interests: M.R-C. is a co-founder, scientific advisor, and board member of TCura Bioscience, Inc. A.F. is a co-founder, CEO, and board member of TCura Bioscience, Inc. B.S.B. receives consulting fees from Bristol Myers Squibb, Pfizer, and research grants from Merck, Gilead. A.W.G. is a co-founder of TCura Bioscience, Inc. and serves on the scientific advisory board of ArsenalBio and Foundery Innovations. The rest of the authors declare that they have no competing interests.