Machine learning-based classification of binary dynamic fluorescence signals reveals muscle stem cell fate transitions in response to pro-regenerative niche factors

The proper regulation of muscle stem cell (MuSC) fate by cues from the niche is essential for regeneration of skeletal muscle. How pro-regenerative niche factors control the dynamics of MuSC fate decisions remains unknown due to limitations of population-level endpoint assays. To address this knowledge gap, we developed a novel binary dynamic fluorescence time lapse imaging analysis (BDFA) approach that leverages machine learning classification strategies to track single cell fate decisions with high temporal resolution. Using two fluorescent reporters that read out maintenance of stemness and myogenic commitment, we constructed detailed lineage trees for individual MuSCs and their progeny, classifying each division event as symmetric self-renewing, asymmetric, or symmetric committed. Our analysis reveals that treatment with the lipid metabolite, prostaglandin E2 (PGE2), accelerates the rate of MuSC proliferation over time, while biasing division events toward symmetric self-renewal. In contrast, the IL6 family member, Oncostatin M (OSM) decreases the proliferation rate after the first generation, while blocking myogenic commitment. These insights into the dynamics of MuSC regulation by niche cues were uniquely enabled by our BDFA approach. We anticipate that similar binary live cell readouts derived from BDFA will markedly expand our understanding of how niche factors control tissue regeneration in real time. ### Competing Interest Statement The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: A.T.V.H. and H.M.B. are named inventors on patent applications held by Stanford University regarding PGE2 and muscle regeneration licensed to Myoforte Therapeutics. H.M.B. is a cofounder of Myoforte Therapeutics, and receives consulting fees and has equity and stock options from Myoforte Therapeutics. H.M.B. is a cofounder of Rejuvenation Technologies, Inc., and has equity and stock options in the company. M.T., C.M.M., C.A.H., Y.X.W., K.E.G.M., A.K., and A.C. declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.