Calvisi, D. F. | Search bioRxiv

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↗

bioRxiv2020

Transcriptomic and Proteomic analysis of clear cell foci (CCF) in the human non-cirrhotic liver identifies several differentially expressed genes and proteins with functions in cancer cell biology and glycogen metabolism.

Clear cell foci (CCF) of the liver are considered to be pre-neoplastic lesions of hepatocellular adenomas and carcinomas. They are hallmarked by glycogen-overload and activation of AKT/mTOR-signaling. Here we report the transcriptome and proteome of CCF extracted from human liver biopsies by laser capture microdissection. We mainly found genes and proteins with lower expression in CCF compared to control samples. Of 14 differentially expressed transcripts only 3 were overexpressed and belong to previously uncharacterized long non-coding RNAs. At the protein level, 3 proteins were at least 1.5-fold higher expressed in CCF than in control samples, while 22 proteins were at least 1.5-fold less abundant. Using immunohistochemistry, the reduced expressions of STBD1, USP28, monad/WDR92, CYB5B and HSPE1 were validated in CCF. Knockout of STBD1, the gene coding for Starch-binding domain-containing protein 1, in mice did not have an effect on liver glycogen levels. Similiarly, Usp28 knockout in mice did not affect glycogen storage in diethylnitrosamine-induced liver carcinoma. Thus, these data indicate that reduced expression of STBD1 or USP28 in CCF is unlikely to explain glycogen overload. Our study revealed several novel proteins and RNAs that are differentially expressed in CCF and have functions relevant for carcinogenesis or the glycogen metabolism.

cancer biology↗