Spatiotemporal single-cell profiling of gastrointestinal GVHD reveals invasive and resident memory T cell states

Biology Biology
Genomics Genomics
Immunology Immunology
Alex K. Shalek Alex K. Shalek
Jim Kaminski Jim Kaminski
José Ordovas-Montañes José Ordovas-Montañes

Tkachev et al.▾ Tkachev, V., Kaminski, J.*, Potter, E.L.*, Furlan, S.N.*, Yu, A., Hunt, D.J., McGuckin, C., Zheng, H., Colonna, L., Gerdemann, U., Carlson, J., Hoffman, M., Olvera, J., English, C., Baldessari, A., Panoskaltsis-Mortari, A., Watkins, B., Qayed, M., Suessmuth, Y., Betz, K., Bratrude, B., Langston, A., Horan, J., Ordovas-Montanes, J., Shalek, A.K., Blazar, B.R., Roederer, M., Kean, L.S.


August, 2020


One of the central challenges in the field of allo-immunity is deciphering the mechanisms driving T cells to infiltrate and subsequently occupy target organs to cause disease. The act of CD8-dominated T cell infiltration is critical to acute graft-versus-host disease (aGVHD), wherein donor T cells become activated, tissue-infiltrating and highly cytotoxic, causing wide-spread tissue damage after allogeneic hematopoietic stem cell transplant (allo-HCT). However, in human and non-human primate studies, deconvolving the transcriptional programs of newly recruited relative to resident memory T cells in the gastrointestinal (GI) tract has remained a challenge. In this study, we combined the novel technique of Serial Intravascular Staining (SIVS) with single-cell RNA-Seq (scRNA-seq) to enable detailed dissection of the tightly connected processes by which T cells first infiltrate tissues and then establish a pathogenic tissue residency program after allo-HCT in non-human primates. Our results have enabled the creation of a spatiotemporal map of the transcriptional drivers of CD8 T cell infiltration into the primary aGVHD target-organ, the GI tract. We identify the large and small intestines as the only two sites demonstrating allo-specific, rather than lymphdepletion-driven T cell infiltration. The donor CD8 T cells that infiltrate the GI tract demonstrate a highly activated, cytotoxic phenotype while simultaneously rapidly developing canonical tissue-resident memory (TRM) protein expression and transcriptional signatures, driven by IL-15/IL-21 signaling. Moreover, by combining SIVS and transcriptomic analysis, we have been able to work backwards from this pathogenic TRM programing, and, for the first time, identify a cluster of genes directly associated with tissue invasiveness, prominently including specific chemokines and adhesion molecules and their receptors, as well as a central cytoskeletal transcriptional node. The clinical relevance of this new tissue invasion signature was validated by its ability to discriminate the CD8 T cell transcriptome of patients with GI aGVHD. These results provide new insights into the mechanisms controlling tissue infiltration and pathogenic CD8 TRM transcriptional programing, uncovering critical transitions in allo-immune tissue invasion and destruction.