Chromatin profiling of renal allograft-infiltrating cells reveals epigenetic regulation of CD8+ T cell exhaustion in chronically rejected human kidney allografts

Abstract

Abstract Purpose Our single cell RNA sequencing (scRNA-seq) analysis found that T cells in chronically rejected kidney allografts and peripheral blood mononuclear cells (PBMCs) of the same kidney transplant recipients (KTR) exhibited a spectrum of dynamic cell states; herein, we investigate how T cell states are regulated at the epigenetic level during chronic rejection. Methods H3K27me3 and H3K27ac CUT&Tag was performed in live T cells isolated from PBMCs and allografts of 3 KTR with failed transplants. All transplants had chronic cellular and antibody mediated rejection on pathology. Results With CD8+ T cell infiltration into allografts, H3K27me3 was deposited at the gene loci associated with T cell quiescence and stemness (TCF7, BACH2, FOXP1, IL7R, etc.), whereas H3K27ac was mostly deposited at the gene loci involved in T cell effector (GZMB, ID2, ZEB2, etc) and exhaustion (TOX, TOX2, TIGIT, PDCD1, HAVCR2, etc) programs. Conclusion Our prior scRNA-seq analysis revealed that most CD8+ T cells in PBMCs maintain TCF7+ stem-like cell phenotypes. However, most CD8+ T cells infiltrated in chronically rejected allografts lose stemness, becoming either TCF7−GZMBhi effector or TCF7−PDCD1hiHAVCR2hi exhausted T cells. Herein our CUT&Tag analysis reveals that chromatin remodeling mediates such dynamic changes of T cell states. Of note, although T-cell exhaustion occurs in chronically rejected allografts, it only represents dynamic changes of T cell states. We propose that TCF7+ allogenic T cells in the periphery maintain stem-like property. Without proper epigenetic silencing of their function, TCF7+ allogenic T cells produce not only exhausted progeny but also effector cell progeny to mediate allograft rejection. Supported by internal