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

Abstract

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 (v-akt murine thymoma viral oncogene homolog)/mTOR (mammalian target of rapamycin)-signaling. Here, we report the transcriptome and proteome of CCF extracted from human liver biopsies by laser capture microdissection. We found 14 genes and 22 proteins differentially expressed in CCF and the majority of these were expressed at lower levels in CCF. Using immunohistochemistry, the reduced expressions of STBD1 (starch-binding domain-containing protein 1), USP28 (ubiquitin-specific peptidase 28), monad/WDR92 (WD repeat domain 92), CYB5B (Cytochrome b5 type B), and HSPE1 (10 kDa heat shock protein, mitochondrial) were validated in CCF in independent specimens. Knockout of Stbd1, the gene coding for Starch-binding domain-containing protein 1, in mice did not have a significant effect on liver glycogen levels, indicating that additional factors are required for glycogen overload in CCF. Usp28 knockout mice did not show changes in glycogen storage in diethylnitrosamine-induced liver carcinoma, demonstrating that CCF are distinct from this type of cancer model, despite the decreased USP28 expression. Moreover, our data indicates that decreased USP28 expression is a novel factor contributing to the pre-neoplastic character of CCF. In summary, our work identifies several novel and unexpected candidates that are differentially expressed in CCF and that have functions in glycogen metabolism and tumorigenesis.

Lipid Droplet-Associated Proteins Perilipin 1 and 2: Molecular Markers of Steatosis and Microvesicular Steatotic Foci in Chronic Hepatitis C

“…Altered metabolism with accumulations of lipids and/or glycogen have previously been shown in preneoplastic and early neoplastic foci in mice giving rise to HCC [ 78 ]. Ribback and coauthors were able to identify glycogenotic clear cell foci in human tissue that resembled foci in rat hepatocarcinogenesis and they presented evidence that glycogenotic foci are in fact very early preneoplastic lesions [ 63 , 79 ]. Cano and coauthors detected higher numbers of clear cell foci and viral infection in patients with non-cirrhotic, non-fibrolamellar HCC in young patients [ 80 ].…”

Hepatic ChREBP orchestrates intrahepatic carbohydrate metabolism to limit hepatic glucose 6-phosphate and glycogen accumulation in a mouse model for acute Glycogen Storage Disease type Ib

“…These findings indicate that the transcriptional regulation of Stbd1 by ChREBP warrants in-depth molecular investigation. Previous work showed unaltered [ 36 ] or lower [ 37 ] hepatic glycogen content in Stbd1 knockout mice. Additionally, Stbd1 / Gaa double-knockout livers show reduced glycogen content as compared to Gaa (single-) knockout mice [ 33 ].…”