Cellular identity loss occurring during both iPS cells generation and malignant transformation can be followed using the somatic markers Thy1 and Bcl11b (ATAC-seq)

Coordinated changes of cellular plasticity and cellular identity are critical for pluripotent reprogramming and oncogenic transformation. However, the sequences of cellular/molecular events that orchestrate these intermingled modifications have never been comparatively dissected. Here, we deconvoluted the cellular trajectories of reprogramming (via Oct4/Sox2/Klf4/c-Myc) and transformation (via Ras/c-Myc) at the single-cell resolution and revealed how the two processes intersect prior to bifurcate. This approach also led to identify the transcription factor (TF) Bcl11b as a broad-range regulator of cell fate changes, as well as a pertinent marker to capture early cellular intermediates that emerge simultaneously during reprogramming and transformation. Multi-omics characterization of these intermediates led to unveil a c-Myc/Atoh8/Sfrp1 regulatory axis that constrains rodent and human reprogramming but also cancer cell plasticity and neuron transdifferentiation. Mechanistically, we found that the TF Atoh8 restrains cellular plasticity, independently of cellular identity, by binding a specific enhancer network. This study provides insights into the partitioned control of cellular plasticity and identity for both regenerative and cancer biology. R-BLTL and T-BLTL intermediates being more prone to reprogram / transform, we FACS-sorted R-BLTL/T-BLTL and R-BHTH/T-BHTH in their way to pluripotency or malignancy to identify new regulators. ATAC-seq analyses were conducted on untreated MEFs alongside R-BLTL and T-BLTL (both Bcl11blow/thy1low), R-BHTH and T-BHTH (both Bcl11bhigh/thy1high) at 5 days of reprogramming or transformation and in iPS and transformed cells (TC).