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The transcriptional landscape of a hepatoma cell line grown on scaffolds of extracellular matrix proteins

Ghosh, Souvik and Börsch, Anastasiya and Ghosh, Shreemoyee and Zavolan, Mihaela. (2021) The transcriptional landscape of a hepatoma cell line grown on scaffolds of extracellular matrix proteins. BMC Genomics, 22 (1). p. 238.

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Official URL: https://edoc.unibas.ch/82967/

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Abstract

The behavior of cells in vivo is complex and highly dynamic, as it results from an interplay between intercellular matrix proteins with surface receptors and other microenvironmental cues. Although the effects of the cellular niche have been investigated for a number of cell types using different molecular approaches, comprehensive assessments of how the global transcriptome responds to 3D scaffolds composed of various extracellular matrix (ECM) constituents at different concentrations are still lacking.; In this study, we explored the effects of two diverse extracellular matrix (ECM) components, Collagen I and Matrigel, on the transcriptional profile of cells in a cell culture system. Culturing Huh-7 cells on traditional cell culture plates (Control) or on the ECM components at different concentrations to modulate microenvironment properties, we have generated transcriptomics data that may be further explored to understand the differentiation and growth potential of this cell type for the development of 3D cultures. Our analysis infers transcription factors that are most responsible for the transcriptome response to the extracellular cues.; Our data indicates that the Collagen I substrate induces a robust transcriptional response in the Huh-7 cells, distinct from that induced by Matrigel. Enhanced hepatocyte markers (ALB and miR-122) reveal a potentially robust remodelling towards primary hepatocytes. Our results aid in defining the appropriate culture and transcription pathways while using hepatoma cell lines. As systems mimicking the in vivo structure and function of liver cells are still being developed, our study could potentially circumvent bottlenecks of limited availability of primary hepatocytes for preclinical studies of drug targets.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (Zavolan)
UniBasel Contributors:Zavolan, Mihaela and Ghosh, Souvik and Ghosh, Shreemoyee and Börsch, Anastasiya
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:BioMed Central
e-ISSN:1471-2164
Note:Publication type according to Uni Basel Research Database: Journal article
Identification Number:
Last Modified:31 Aug 2021 12:36
Deposited On:31 Aug 2021 12:36

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