Retention of epigenetic and transcriptional memory among reprogrammed T cells (T-iPSCs) imparts selective advantage for T cell re-differentiation.

Abstract

Abstract Various somatic cell types reprogramed into induced pluripotent stem cells (iPSCs) can be differentiated into T cells. It remains unclear what impact the input cells reprogramed into iPSCs have on T cell differentiation. We hypothesized that preservation of T cell genetic and/or epigenetic memory would bias iPSC clones toward T cell differentiation. CD8 naïve T cells (TN), CD8 stem memory T cells (TSM), and fibroblasts (FB) were reprogramed into iPSCs using nonintegrating Sendai virus to deliver Yamanaka factors. Input cells and iPSC clones were subjected to RNA-seq and ATAC-seq to assess whether epigenetic and transcriptomic memory are retained after reprogramming. Pluripotent associated genes (NANOG, LIN28A/B, SOX2) had increased expression in both T cell− and FB-iPSCs compared to their cells of origin. Of interest, gene enrichment analysis of fibroblasts and FB-iPSCs identified fibroblast related annotations, including migration and growth factors, in reprogramed iPSCs. Among CD8 TN− and TSM-iPSCs as a group, expression of only 41 genes and 6 genomic regions were retained, but these included known mature T cell genes, CD3ɛ, ZBTB7B, and CD95 as well as a region crucial for T cell signaling. Therefore, although much of the transcriptome and accessible genome is overridden in TN/TSM-iPSCs, there exists maintenance of both the transcriptome and chromatin accessibility after reprogramming. CD8 T-iPSCs were superior to FB-iPSCs in producing T progenitors in vitro. Highlighted here is the importance of starting populations for reprogramming and differentiation into T lineage cells. Leveraging the benefits of epigenetic and transcriptomic memory of input T cells could provide a more robust source of T cells for adoptive cell therapy. Supported in part by funds from NIH P01 CA065493 and R37 AI34495 from the National Cancer Institute and National Institute of Allergy and Infectious disease, respectively, the Childrens' Cancer Research Fund, and Chan-Zuckerberg Biohub.