Extensive Phenotypic Analysis, Transcription Factor Profiling, and Effector Cytokine Production of Human MAIT Cells by Flow Cytometry

The mucosa-associated invariant T (MAIT) cells are a large and relatively recently described innate-like antimicrobial T cell subset in humans. The study of human MAIT cells is still in its infancy, and many aspects of MAIT cell immunobiology in health and disease remain unexplored. Here, we describe methodological approaches and protocols to investigate the expression of a broad spectrum of surface receptors on human MAIT cells, and to examine their unique transcription factor profile, as well as their antimicrobial effector function using multicolor flow cytometry-based techniques. We provide specific guidance on protocols and describe potential pitfalls for each of the presented methodologies. Finally, we discuss future prospects and current limitations of multicolor flow cytometry-based approaches to the study of human MAIT cells.