In Silico Methods for Studying T Cell Biology

Abstract

T cell function is dictated by a delicate balance of stimuli that shapes T-cell phenotype, the latter characterizable using a number of immunogenic assays. Thanks to advancements in next-generation sequencing technology, and the intersection between genetics, engineering, computer science, biostatistics, and immunology, it is now possible to profile immune cells residing in any organ or disease site at single cell resolution. Herein we review the most common approaches available to describe T cell activation, T cell molecular heterogeneity, and T cell function. We present informatic tools useful to both seasoned bioinformaticians and novices alike, providing a comprehensive overview of the in silico methods used to study T cell biology. With the goal of making this manuscript useful to a broad range of readers, we focus only on freely available tools and algorithms, and we describe the concepts using simple and direct language. We hope this work will serve to assist and inspire researchers interested in T cell biology.

Keywords: Adoptive T cell transfer (ACT); Complementarity-determining region 3 (CDR3); Cytometry by time of flight (CyTOF); Human leukocyte antigen (HLA); Major histocompatibility complex (MHC); Next-generation sequencing (NGS); T cell receptor (TCR); Tumor infiltrating lymphocytes (TILs); t-distributed stochastic neighbor embedding (tSNE) algorithm.