Abstract: Pluripotent cells, under the correct conditions, can differentiate into any cell type in the human body. By inducing the expression of the Yamanaka Factors - OCT4, SOX2, c-MYC, and KLF4 in any differentiated cell, one can generate induced pluripotent stem cells (iPSCs). However, cell reprogramming has a low efficiency with only a small fraction of the starting population successfully becoming iPSCs. This led us to question whether certain cell states and trajectories that have a greater propensity to reprogram exist; and if they do, when does this advantage arise during the reprogramming timeline. We barcoded human fibroblasts and reprogrammed them while performing single cell RNA-sequencing at different time points. This allowed simultaneous lineage tracing while observing cell fate changes. We identified an intermediate elite cluster enriched with barcodes that could be traced to the final iPSC population. We then characterized the properties of this cluster and identified a molecular profile enriched for cell-survival, proliferation, and a myriad of developmental programs. Using candidate markers we successfully isolated the intermediate population with fluorescence-activated cell sorting (FACS). The sorted elite intermediate cells formed OCT4-, SOX2-, and NANOG-positive PSCs, while the non-elite cells did not. This study provides fresh insights into cell fate trajectories that lead to pluripotency and contribute to our broader understanding of cellular plasticity and cell fate change.
