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Article

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

by
Christoph Metzendorf
1,†,
Katharina Wineberger
1,
Jenny Rausch
1,
Antonio Cigliano
1,‡,
Kristin Peters
1,
Baodong Sun
2,
Daniela Mennerich
3,4,
Thomas Kietzmann
3,4,
Diego F. Calvisi
1,‡,
Frank Dombrowski
1 and
Silvia Ribback
1,*
1
Institut fuer Pathologie, Universitaetsmedizin Greifswald, Friedrich-Loeffler-Str. 23e, 17475 Greifswald, Germany
2
Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA
3
Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90570 Oulu, Finland
4
Biocenter Oulu, University of Oulu, 90570 Oulu, Finland
*
Author to whom correspondence should be addressed.
†
Current affiliation: Department of Immunology, Genetics and Pathology, BMC, Uppsala University, Husargatan 3, 751 24 Uppsala, Sweden.
‡
Current affiliation: Institut fuer Pathologie, Regensburg Universitaetsklinikum, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany.
Molecules 2020, 25(18), 4141; https://doi.org/10.3390/molecules25184141
Submission received: 10 August 2020 / Revised: 6 September 2020 / Accepted: 7 September 2020 / Published: 10 September 2020
(This article belongs to the Special Issue Proteomics Progress in Cancer Research)
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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.
Keywords: clear cell foci; liver; hepatocellular carcinoma; pre-neoplastic lesions clear cell foci; liver; hepatocellular carcinoma; pre-neoplastic lesions

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MDPI and ACS Style

Metzendorf, C.; Wineberger, K.; Rausch, J.; Cigliano, A.; Peters, K.; Sun, B.; Mennerich, D.; Kietzmann, T.; Calvisi, D.F.; Dombrowski, F.; et al. 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. Molecules 2020, 25, 4141. https://doi.org/10.3390/molecules25184141

AMA Style

Metzendorf C, Wineberger K, Rausch J, Cigliano A, Peters K, Sun B, Mennerich D, Kietzmann T, Calvisi DF, Dombrowski F, et al. 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. Molecules. 2020; 25(18):4141. https://doi.org/10.3390/molecules25184141

Chicago/Turabian Style

Metzendorf, Christoph, Katharina Wineberger, Jenny Rausch, Antonio Cigliano, Kristin Peters, Baodong Sun, Daniela Mennerich, Thomas Kietzmann, Diego F. Calvisi, Frank Dombrowski, and et al. 2020. "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" Molecules 25, no. 18: 4141. https://doi.org/10.3390/molecules25184141

APA Style

Metzendorf, C., Wineberger, K., Rausch, J., Cigliano, A., Peters, K., Sun, B., Mennerich, D., Kietzmann, T., Calvisi, D. F., Dombrowski, F., & Ribback, S. (2020). 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. Molecules, 25(18), 4141. https://doi.org/10.3390/molecules25184141

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