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Open Access Research article

Zonation related function and ubiquitination regulation in human hepatocellular carcinoma cells in dynamic vs. static culture conditions

Shu Cheng1, Jean-Matthieu Prot2, Eric Leclerc2 and Frédéric Y Bois13*

Author Affiliations

1 Chaire de Modélisation Mathématique pour la Toxicologie Systémique, Université de Technologie de Compiègne, BP 20529, 60205 Compiègne Cedex, France

2 CNRS UMR 6600, Laboratoire de Biomécanique et Bioingénierie, Université de Technologie de Compiègne, BP 20529, 60205 Compiègne Cedex, France

3 INERIS, DRC/VIVA/METO, Parc ALATA, BP 2, 60550 Verneuil en Halatte, France

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BMC Genomics 2012, 13:54  doi:10.1186/1471-2164-13-54

Published: 1 February 2012

Abstract

Background

Understanding hepatic zonation is important both for liver physiology and pathology. There is currently no effective systemic chemotherapy for human hepatocellular carcinoma (HCC) and its pathogenesis is of special interest. Genomic and proteomic data of HCC cells in different culture models, coupled to pathway-based analysis, can help identify HCC-related gene and pathway dysfunctions.

Results

We identified zonation-related expression profiles contributing to selective phenotypes of HCC, by integrating relevant experimental observations through gene set enrichment analysis (GSEA). Analysis was based on gene and protein expression data measured on a human HCC cell line (HepG2/C3A) in two culture conditions: dynamic microfluidic biochips and static Petri dishes. Metabolic activity (HCC-related cytochromes P450) and genetic information processing were dominant in the dynamic cultures, in contrast to kinase signaling and cancer-specific profiles in static cultures. That, together with analysis of the published literature, leads us to propose that biochips culture conditions induce a periportal-like hepatocyte phenotype while standard plates cultures are more representative of a perivenous-like phenotype. Both proteomic data and GSEA results further reveal distinct ubiquitin-mediated protein regulation in the two culture conditions.

Conclusions

Pathways analysis, using gene and protein expression data from two cell culture models, confirmed specific human HCC phenotypes with regard to CYPs and kinases, and revealed a zonation-related pattern of expression. Ubiquitin-mediated regulation mechanism gives plausible explanations of our findings. Altogether, our results suggest that strategies aimed at inhibiting activated kinases and signaling pathways may lead to enhanced metabolism-mediated drug resistance of treated tumors. If that were the case, mitigating inhibition or targeting inactive forms of kinases would be an alternative.

Keywords:
hepatocellular carcinoma; hepatic zonation; ubiquitination system; gene sets analysis; Petri plates; PDMS microfluidic biochips