Single-cell atlas of hepatic T cells reveals expansion of liver-resident naive-like CD4+ T cells in primary sclerosing cholangitis.

BACKGROUND AND AIMS Little is known on the composition of intrahepatic immune cells and their contribution to the pathogenesis of primary sclerosing cholangitis (PSC). We here aimed to create an atlas of intrahepatic T cells and thereby in detail characterize T cells in human inflamed liver. METHODS Different single-cell RNA sequencing methods were combined with in silico analyses on intrahepatic and peripheral T cells from patients with PSC (n=11) and healthy donors (HD, n=4). Multi-parameter flow cytometry and functional in vitro experiments were conducted on patients with PSC (n=24) and controls (HCV, n=5; NASH, n=3; ALD, n=16; LRM, n=10; HD, n=10). RESULTS We here present the landscape of intrahepatic T cells in PSC and reveal a population of intrahepatic naive-like CD4+ T cells, which was present in all liver diseases tested, but particularly expanded in PSC. This population had a transcriptome and T cell receptor repertoire similar to circulating naive T cells but expressed a set of genes associated with tissue residency. Their periductal location supported the concept of tissue-resident naive-like T cells in livers of patients with PSC. Trajectory inference suggested a developmental propensity of these cells to acquire a TH17 polarization-state. Functional and chromatin accessibility experiments revealed a predisposition of circulating naive T cells from patients with PSC to polarize towards TH17 cells. CONCLUSION We report on the first atlas of intrahepatic T cells in PSC, which led to the identification of a previously unrecognized population of tissue-resident naive-like T cells in the inflamed human liver and to the finding that naive CD4+ T cells in PSC harbour the propensity to develop into TH17 cells. LAY SUMMARY The composition of intrahepatic immune cells in primary sclerosing cholangitis (PSC) and their contribution to disease pathogenesis is widely unknown. We here generated a single-cell atlas of intrahepatic T cells in PSC, a type of immune cells that has previously been involved in the pathogenesis of PSC. This atlas provides a valuable data source to the field. Using that atlas, we identified a population of liver-resident naive-like CD4+ T cells which are expanded in livers of patients with PSC compared to healthy liver tissue and other liver diseases. Trajectory inference suggest that these cells have a propensity to acquire TH17-associated effector functions. Since TH17-polarized cells are considered to contribute to the development of PSC, our findings point towards a so far underestimated role of naive T cells in PSC.