Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming.

Some somatic cells are plastic, having the capacity to convert into other specialized cells (transdifferentiation) or into induced pluripotent stem cells (iPSCs, reprogramming) in response to transcription factor over-expression. To explore what makes a cell plastic and whether susceptibility to different cell conversion processes is coupled, we exposed bone marrow derived pre-B cells to two different transcription factor protocols that efficiently convert them either into macrophages (iMac) or iPS cells, and monitored the two processes over time using single cell gene expression analysis. We isolated CD19+ B cell precursors from the bone marrow of reprogrammable mice and infected them with a retrovirus encoding a hormone inducible form of C/EBPα (C/EBPα-ER-hCD4). After expansion in culture, we induced them to either trans-differentiate to macrophages or to reprogram into iPSCs. To induce the macrophage fate, we treated the cells with beta-estradiol to activate C/EBPα for up to 114h. To induce an iPSC fate, we treated them with beta-estradiol for 18 hours and, after washing out the hormone, added doxycycline to induce OSKM. We collected samples before induction (0h), at 6h, 18h, 42h, 66h and 114h after C/EBPα induction during transdifferentiation, and at days 2, 4, 6 and 8 after OSKM induction in 18h-pulsed cells. We collected two pools of 192 cells at each time point and sequenced their mRNA using MARS-­Seq.