Gene expression profiles of liver cancer cell lines reveal two hepatocyte-like and fibroblast-like clusters

Abstract

Cancer cell lines are widely used in basic research to study cancer development, growth, invasion, or metastasis. They are also used for the development and screening of anticancer drugs. However, there are no clear criteria for choosing the most suitable cell lines among the wide variety of cancer cell lines commercially available for research, and the choice is often based on previously published reports. Here, we investigated the characteristics of liver cancer cell lines by analyzing the gene expression data available in the Cancer Cell Line Encyclopedia. Unsupervised clustering analysis of 28 liver cancer cell lines yielded two main clusters. One cluster showed a gene expression pattern similar to that of hepatocytes, and the other showed a pattern similar to that of fibroblasts. Analysis of hepatocellular carcinoma gene expression profiles available in The Cancer Genome Atlas showed that the gene expression patterns in most hepatoma tissues were similar to those in the hepatocyte-like cluster. With respect to liver cancer research, our findings may be useful for selecting an appropriate cell line for a specific study objective. Furthermore, our approach of utilizing a public database for comparing the properties of cell lines could be an attractive cell line selection strategy that can be applied to other fields of research.

VEGF‑mediated tumour growth and EMT in 2D and 3D cell culture models of hepatocellular carcinoma

“…HepG2 cell lines have not been previously used, to the best of our knowledge, in 3D cultures, but only in several 2D culture-related studies. Fukuyama et al ( 42 ) stated in their study that three liver cancer cell lines (Huh7, HepG2 and Hep3B) fell in the same hierarchical cluster and shared a common origin. These cell lines and primary hepatocytes appeared next to each other in cluster and demonstrated similar gene expression patterns.…”

Gene Expression of Liver Tissue and Primary and Secondary Liver Cancer with a Particular Focus on Hepatocellular Carcinoma: A Mini-review on Basic Biomedical Assessment

“…According to an analysis of HCC gene expression profiles from The Cancer Genome Atlas, most hepatoma tissues reveal gene expression patterns that are comparable to those in the hepatocyte-like cluster. 30 This aids in the differential diagnosis of cases with a challenging histology.…”

Experimental Models of Hepatocellular Carcinoma—A Preclinical Perspective

“…Thus far, HCC 2D systems are limited to around 30 publicly available cell lines [47]. A very recent study investigated the gene expression profile of 28 liver carcinoma cell lines, as a relevant criterion for selecting a suitable cell line for HCC studies [48].…”