Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency [SCRB-Seq]

Induced pluripotency is a promising avenue for disease modeling and therapy, but the molecular principles underlying this process, particularly in human cells, remain poorly understood due to donor-to-donor variability and intercellular heterogeneity. Here we constructed and characterized a clonal, inducible human reprogramming system that provides a reliable source of cells at any stage of the process. This system enabled integrative transcriptional and epigenomic analysis across the human reprogramming timeline at high resolution. We observed distinct waves of gene network activation, including the ordered re-activation of broad developmental regulators followed by early embryonic patterning genes and culminating in the emergence of a signature reminiscent of pre-implantation stages. Moreover, complementary functional analyses allowed us to identify and validate novel regulators of the reprogramming process. Altogether, this study sheds light on the molecular underpinnings of induced pluripotency in human cells and provides a robust cell platform for further studies. Overall design: hiF-T cells are secondary reprogrammable cells derived from hiF cells obtained thorough the directed differentiation of a dox-inducible OKMS hIPSC line obtained from reprogramming BJ fibroblasts. After directed differentiation, hiF cells were infected with a lentivirus expressing the human telomerase and after clonal expansion individual hiF-T clones were obtained. The multiplexed data is available at: https://refinery.stemcellcommons.org/data_sets/GSE69351_DGE/