Investigating how sequence variation in T cell receptors and human leukocyte antigens shapes T cell development

Abstract

T cells are critical agents of the adaptive immune system that orchestrate killing of infected and cancerous cells. Some T cells erroneously target healthy cells, leading to autoimmune disease. Whether a T cell becomes activated depends on the immunological synapse it forms with an antigen presenting cell (APC). At the core of the immunological synapse are two key proteins: (1) the T cell receptor (TCR) and (2) the major histocompatibility complex (MHC) presenting a peptide from a candidate pathogen. This dissertation examines genetic variation on both sides of this immunological synapse. Genetic variation in the MHC confers extreme risk for autoimmune disease and largely consists of germline polymorphisms, which are consistent across an individual’s cells. In contrast, genetic variation on the T cell side of the immunological synapse is largely somatic. Each developing T cell stochastically rearranges and edits the genes encoding its TCR, creating a repertoire of TCR sequences within each individual. Analysis of TCR sequence data traditionally proceeds by considering each TCR as a “molecular barcode” and identifying T cells that match exactly on this molecular barcode. However, the vast majority TCR sequences are observed only once, in one individual. A major theme throughout this dissertation is an alternate approach to TCR sequence analysis: (a) decomposing each TCR amino acid sequence to a collection of physicochemical features such as hydrophobicity and electrostatic charge, and (b) testing how these sequence features relate to T cell development outcomes, such as thymic selection and transcriptional fate. This approach enables two general discoveries: (1) TCR sequence features regulate T cell transcriptional fates, and (2) MHC genetic variants which confer risk for autoimmune disease influence which TCR sequences pass thymic selection. Specifically, we find that hydrophobicity throughout the CDR3 region of the TCR sequence promotes regulatory T cell fate. Most surprisingly, we observe a constellation of TCR sequence features that are consistently enriched in memory T cells compared to naïve T cells. We develop a TCR scoring function “TCR-mem,” which quantifies the extent of these features in each TCR, and show through TCR transduction experiments that increased TCR-mem increases T cell activation even among T cells that recognize the same peptide-MHC complex. Each of these projects provide new scoring functions that allow researchers to score and rank TCR sequences for functional follow up, regardless of whether the TCR sequences have been observed previously. Altogether, this dissertation provides new approaches to study sequence variation in MHC and TCR molecules, and sheds light on how this variation may alter critical T cell functionality.