Vogl, M. | bioRxiv Science

bioRxiv2026

Endogenous PROM1 activation redistributes liver cancer cells along a preexisting differentiation axis

CD133 is widely used as a marker of stem-like cells in hepatocellular carcinoma, yet its functional contribution remains incompletely defined. In PLC/PRF/5 cells, acute CRISPR activation of endogenous PROM1 suppresses hepatic programs, whereas PROM1 knockdown elicits an opposing hepatocyte-identity response, together defining a PROM1-responsive transcriptional axis. Single-cell profiling shows that this axis is preexisting and tracks endogenous PROM1 heterogeneity, separating a hepatocyte-like, PROM1-low compartment from a PROM1-enriched, less hepatocyte-like compartment. Sustained PROM1 activation reduces the hepatocyte-like compartment and shifts the population toward intermediate positions along this axis. Related transcriptional patterns are detectable in an independent HuH-7 dataset and a human HCC case. Endogenous ALFA tagging identifies candidate CD133-associated proteins. Together, these findings support CD133 as an active contributor to tumor-cell state redistribution, extending its role beyond a mere marker of stem-like populations.

cancer biology↗

bioRxiv2022

Oncogenic YAP mediates changes in chromatin accessibility and activity that drive cell cycle gene expression and cell migration

YAP, the key protein effector of the Hippo pathway, is a transcriptional co-activator that controls the expression of cell cycle genes, promotes cell growth and proliferation and regulates organ size. YAP modulates gene transcription by binding to distal enhancers, but the mechanisms of gene regulation by YAP-bound enhancers remain poorly understood. Here we show that constitute active YAP5SA leads to widespread changes in chromatin accessibility in untransformed MCF10A cells. Newly accessible regions include YAP-bound enhancers that mediate activation of cycle genes regulated by the Myb-MuvB (MMB) complex. By CRISPR-interference we identify a role for YAP-bound enhancers in phosphorylation of Pol II at Ser5 at MMB-regulated promoters, extending previously published studies that suggested YAP primarily regulates the pause-release step and transcriptional elongation. YAP5SA also leads to less accessible "closed" chromatin regions, which are not directly YAP-bound but which contain binding motifs for the p53 family of transcription factors. Diminished accessibility at these regions is, at least in part, a consequence of reduced expression and chromatin-binding of the p53 family member {Delta}Np63 resulting in downregulation of {Delta}Np63-target genes and promoting YAP-mediated cell migration. In summary, our studies uncover changes in chromatin accessibility and activity that contribute to the oncogenic activities of YAP.

molecular biology↗