RT Journal Article
SR Electronic
T1 Aligning single-cell developmental and reprogramming trajectories identifies molecular determinants of reprogramming outcome
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 122531
DO 10.1101/122531
A1 Davide Cacchiarelli
A1 Xiaojie Qiu
A1 Sanjay Srivatsan
A1 Michael Ziller
A1 Eliah Overbey
A1 Jonna Grimsby
A1 Prapti Pokharel
A1 Ken Livak
A1 Shuqiang Li
A1 Alex Meissner
A1 Tarjei Mikkelsen
A1 John Rinn
A1 Cole Trapnell
YR 2017
UL http://biorxiv.org/content/early/2017/03/30/122531.abstract
AB Cellular reprogramming through manipulation of defined factors holds great promise for large-scale production of cell types needed for use in therapy, as well as for expanding our understanding of the general principles of gene regulation. MYOD-mediated myogenic reprogramming, which converts many cell types into contractile myotubes, remains one of the best characterized model system for direct conversion by defined factors. However, why MYOD can efficiently convert some cell types into myotubes but not others remains poorly understood. Here, we analyze MYOD-mediated reprogramming of human fibroblasts at pseudotemporal resolution using single-cell RNA-Seq. Successfully reprogrammed cells navigate a trajectory with two branches that correspond to two barriers to reprogramming, with cells that select incorrect branches terminating at aberrant or incomplete reprogramming outcomes. Differential analysis of the major branch points alongside alignment of the successful reprogramming path to a primary myoblast trajectory revealed Insulin and BMP signaling as crucial molecular determinants of an individual cell’s reprogramming outcome, that when appropriately modulated, increased efficiency more than five-fold. Our single-cell analysis reveals that MYOD is sufficient to reprogram cells only when the extracellular milieu is favorable, supporting MYOD with upstream signaling pathways that drive normal myogenesis in development.