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

Forced transcription factor expression can transdifferentiate somatic cells into other specialised cell types or reprogram them into induced pluripotent stem cells (iPSCs) with variable efficiency. To better understand the heterogeneity of these processes, we used single-cell RNA sequencing to follow the transdifferentation of murine pre-B cells into macrophages as well as their reprogramming into iPSCs. Even in these highly efficient systems, there was substantial variation in the speed and path of fate conversion. We predicted and validated that these differences are inversely coupled and arise in the starting cell population, with Mychigh large pre-BII cells transdifferentiating slowly but reprogramming efficiently and Myclow small pre-BII cells transdifferentiating rapidly but failing to reprogram. Strikingly, differences in Myc activity predict the efficiency of reprogramming across a wide range of somatic cell types. These results illustrate how single cell expression and computational analyses can identify the origins of heterogeneity in cell fate conversion processes. We would like to thank Ido Amit and Diego Adhemar Jaitin for help with the MARS-Seq technique and the CRG/UPF FACS Unit for help with the cell sorting. Work in the lab of TG was supported by the European Research Council (ERC) Synergy Grant (4D-Genome) and by AGAUR (SGR-1136). Research in the lab of BL was supported by an ERC Consolidator grant (616434), the Spanish Ministry of Economy and Competitiveness (BFU2011-26206), the AXA Research Fund, the Bettencourt Schueller Foundation and AGAUR (SGR-831). We acknowledge support of the Spanish Ministry of Economy and Competitiveness, Centro de Excelencia Severo Ochoa 2013–2017 (SEV-2012–0208) and of the CERCA Programme/Generalitat de Catalunya.