A hierarchical approach employing metabolic and gene expression profiles to identify the pathways that confer cytotoxicity in HepG2 cells

Abstract

Background: Free fatty acids (FFA) and tumor necrosis factor alpha (TNF-α) have been implicated in the pathogenesis of many obesity-related metabolic disorders. When human hepatoblastoma cells (HepG2) were exposed to different types of FFA and TNF-α, saturated fatty acid was found to be cytotoxic and its toxicity was exacerbated by TNF-α. In order to identify the processes associated with the toxicity of saturated FFA and TNF-α, the metabolic and gene expression profiles were measured to characterize the cellular states. A computational model was developed to integrate these disparate data to reveal the underlying pathways and mechanisms involved in saturated fatty acid toxicity.

Distinct gene expression profiles characterize cellular responses to palmitate and oleate

“…These experiments were similar in palmitate concentration and duration to the adaptive experiments performed in the present study, and in our hands, these concentrations did not induce markers of ER stress in HepG2 cells. In contrast, Li et al ( 30) and Srivastava et al . (31 ) tested in HepG2 cells a 24 h exposure of 700 µM palmitate, oleate, and linoleate, a level that would induce ER stress and cytotoxicity with palmitate.…”

A Comparative Study of Genome-Wide Transcriptional Profiles of Primary Hepatocytes in Collagen Sandwich and Monolayer Cultures

“…7 However, neither did this study investigate longer time points nor did it compare monolayers to other, more stable culture conditions. DNA microarray measurements have also been used to study specific pathways through which toxicity was conferred in human hepatoblastoma cells 8 and to understand the effects of nonparenchymal cells in 2D cocultures of hepatocytes with fibroblasts or sinusoidal endothelial cells. 9,10 We hypothesized that the enhanced in vivo liver-like phenotypes in CS cultures were a result of the underlying differences in the transcriptional program between hepatocytes cultured in CS and HMs.…”

“…13 Further, GSEA has been used to identify pathways involved in liver toxicity in human hepatoblastoma cells. 8 GSEA is designed to identify predefined gene sets that are differentially expressed in a treatment and a control. All the genes expressed on each gene chip are ranked based upon their differential expression in CS and HM cultures.…”

Polar lipid remodeling and increased sulfatide expression are associated with the glioma therapeutic candidates, wild type p53 elevation and the topoisomerase-1 inhibitor, Irinotecan

“…Because the single-gene analyses revealed only modest changes and did not illuminate globally affected pathways, a GSEA was performed. GSEA has been applied widely as a tool for such gene-set analyses [31][32][33][34]. Altogether, 3 such regulated pathways emerged in the analysis according to the criteria (NOM p-value < 0.01 and False Discovery Rate q < 0.25) recommended by Subramanian et al [33].…”