Single-cell profiling of tissue-associated T cell phenotypes in human autoimmune diseases

Abstract

T cells are a major component of the body’s adaptive immune system and indispensable to the immune response against pathogens, tumors, and allergens. T cells are also implicated in mediating responses against self, which can lead to autoimmune diseases that display heterogenous manifestations and exact damage to a wide range of organs and tissues. For most autoimmune diseases, current therapeutics aim to address active symptom manifestations and are often ineffective in leading to sustained disease remission. Thus, identification of therapeutic targets for achieving long-lasting remission and mitigating organ damage are critical, but reliant on a deeper understanding of the cells and cell networks present at sites of active disease. Motivated by this, the present dissertation aims to further the field’s knowledge of the phenotypic compositions, developmental relationships, and clonal attributes of T cells within and across multiple autoimmune disease-affected organs. First, interrogation of lesional and non-lesional skin biopsies of patients with cutaneous lupus using single-cell RNA sequencing revealed heterogeneous T cell states present in the skin, unified by a potent interferon response not found in skin T cells from other autoimmune conditions. A cross-tissue examination of T cells in cutaneous lupus and lupus nephritis suggested that while T cells infiltrating kidney drive tissue pathology through cytotoxicity, T cells in the skin are unlikely to be directly cytotoxic. The results here yield a key new insight that it is not the case that T cells in lupus perform the same functions across different target tissues. Next, the application of paired single-cell RNA and TCR sequencing to synovial tissue and blood samples of patients with RA yielded insights into the phenotypes of T cells in the inflamed tissue. Among others, we identified T peripheral helper (Tph) CD4+ cells and GZMK-expressing CD8+ cells as being strongly enriched in synovial tissue compared to blood. The application of T cell receptor information further identified novel characteristics about these cell states, including altered expression profiles of clonally-expanded Tph cells and a limited clonal relationship between GZMK+ cells and cytotoxic CD8+ cells. The specific identification of pathologic T cells and their associated TCRs in tissue is highly important for understanding both disease mechanisms and putative avenues to target. Here, we develop a framework to detect and track alloreactive T cells in a patient experiencing kidney rejection following immune checkpoint inhibitor therapy. Through a combination of in vitro assays and TCR tracking, we identify and study a population of alloreactive CD8+ T cells present in the rejected kidney that expands in blood after the initiation of therapy. This framework, applied using assays to highlight autoreactive cells, can work to track and understand the dynamics of these cells across time and location. Combined, the work in this dissertation furthers the field’s understanding of the heterogenous contributions of T cells across organs affected by autoimmunity.