Fate Erasure Logic of Gene Networks Underlying Direct Neuronal Conversion of Somatic Cells by MicroRNAs II

Neurogenic microRNAs 9/9* and 124 (miR-9/9*-124) drive the direct reprogramming of human fibroblasts into neurons with the initiation of the fate erasure of fibroblasts. However, whether the miR-9/9*-124 fate erasure logic extends to neuronal conversion of other somatic cell types remains unknown. Here, we uncover that miR-9/9*-124 induce neuronal conversion of multiple cell types: dura fibroblasts, astrocytes, smooth muscle cells, and pericytes. We reveal the cell type-specific and pan-somatic gene network erasure induced by miR-9/9*-124, including cell cycle, morphology, and proteostasis gene networks. Leveraging these pan-somatic gene networks, we predict upstream regulators that may antagonize somatic fate erasure. Among the predicted regulators, we identify TP53 (p53) whose inhibition is sufficient to enhance neuronal conversion even in post-mitotic cells. This study extends miR-9/9*-124 reprogramming to alternate somatic cells, reveals the pan-somatic gene network fate erasure logic of miR-9/9*-124, and shows a neurogenic role for p53-inhibition in the miR-9/9*-124-signaling cascade. RNA-sequencing from a panel of human dermal fibroblasts, including the following lines: AG13369 (NIA Aging Cell Culture Repository at the Coriell Institute for Medical Research), AG08379 (NIA Aging Cell Culture Repository at the Coriell Institute for Medical Research), AG06858 (NIA Aging Cell Culture Repository at the Coriell Institute for Medical Research), GM23974 (NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research), GM23966 (NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research), and F09-110 (deidentified fibroblast contributed by Pat Blanner). RNA was collected from each line expressing pT-miR-9/9*-124 for 20 days (Day 20) as compared to starting fibroblasts (Day 0).