Effector memory-type regulatory T cells display phenotypic and functional instability

Regulatory T cells (T cells) hold promise for sustainable therapy of immune disorders. Recent advancements in chimeric antigen receptor development and genome editing aim to enhance the specificity and function of T cells. However, impurities and functional instability pose challenges for the development of safe gene-edited T cell products. Here, we examined different T cell subsets regarding their fate, epigenomic stability, transcriptomes, T cell receptor repertoires, and function ex vivo and after manufacturing. Each T cell subset displayed distinct features, including lineage stability, epigenomics, surface markers, T cell receptor diversity, and transcriptomics. Earlier-differentiated memory T cell populations, including a hitherto unidentified naïve-like memory T cell subset, outperformed late-differentiated effector memory-like T cells in regulatory function, proliferative capacity, and epigenomic stability. High yields of stable, functional T cell products could be achieved by depleting the small effector memory-like T cell subset before manufacturing. Considering T cell subset composition appears critical to maintain lineage stability in the final cell product.