Elevated exhausted effector tissue resident CD8+ T-cells in Chronic Graft versus Host Disease patient Oral mucosa unveiled by spatial transcriptomics and scRNA seq analysis

Abstract

Abstract Chronic graft-versus-host disease (cGVHD), an autoimmune-like disease following allogeneic hematopoietic stem cell transplantation where T cells can attack host tissue. Oral mucosa (OM) is a most common cGVHD effector site in the oral cavity. We studied T cell populations and tissue-specific signals that regulate their differentiation and functionality. Patient OM biopsies from ongoing clinical trials (NCT03602599, NCT00331968) were taken at 6 months post-transplant. We found enrichment of immune cells in the OM mainly in the CD8 T-cell cluster and identified two unique populations in the OM of cGVHD patients: one characterized by expression of proliferative markers and the other more prominent, characterized by exhaustion makers (TIM3, LAG3, TIGIT). The latter had low expression of CD69 but expressed markers of tissue residency; CD103, BLIMP1, PD1, FABP5. Interestingly, this population showed high expression of BATF, IRF4, and RUNX3, transcription factors that induce sustained effector CD8 T-cell programming. These exhausted cells displayed higher expression of effector molecules IFNG, GZMB, PRF1 inducing sustained CD8 T-cell effector function. Ligand-receptor analysis revealed strong interactions between CXCL9-CXCR3 in CD8 T-cells and myeloid cells. Spatial transcriptomic analysis confirmed the CD8 T-cell infiltration in the submucosal region of OM in cGVHD colocalizing with the elevated markers of exhaustion, surrounded by myeloid cells, thus confirming the striking interaction of CXCL9 and CXCR3. These exhausted CD8 T-cells may play an important role in cGVHD pathogenesis causing by driving sustained tissue damage and could serve as a might be used as a novel target for cGVHD therapy. This work was supported by the intramural programs of the NIDCR and NCI.