A hierarchical approach employing metabolic and gene expression profiles to identify the pathways that confer cytotoxicity in HepG2 cells.
BACKGROUND
Free fatty acids (FFA) and tumor necrosis factor alpha (TNF-alpha) 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-alpha, saturated fatty acid was found to be cytotoxic and its toxicity was exacerbated by TNF-alpha. In order to identify the processes associated with the toxicity of saturated FFA and TNF-alpha, 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.


RESULTS
A hierarchical framework consisting of three stages was developed to identify the processes and genes that regulate the toxicity. First, discriminant analysis identified that fatty acid oxidation and intracellular triglyceride accumulation were the most relevant in differentiating the cytotoxic phenotype. Second, gene set enrichment analysis (GSEA) was applied to the cDNA microarray data to identify the transcriptionally altered pathways and processes. Finally, the genes and gene sets that regulate the metabolic responses identified in step 1 were identified by integrating the expression of the enriched gene sets and the metabolic profiles with a multi-block partial least squares (MBPLS) regression model.


CONCLUSIONS
The hierarchical approach suggested potential mechanisms involved in mediating the cytotoxic and cytoprotective pathways, as well as identified novel targets, such as NADH dehydrogenases, aldehyde dehydrogenases 1A1 (ALDH1A1) and endothelial membrane protein 3 (EMP3) as modulator of the toxic phenotypes. These predictions, as well as, some specific targets that were suggested by the analysis were experimentally validated.
Li
Zheng
Z
Department of Chemical Engineering and Material Science, Michigan State University, East Lansing, MI 48824, USA. lizheng1@gmail.com
Srivastava
Shireesh
S
Yang
Xuerui
X
Mittal
Sheenu
S
Norton
Paul
P
Resau
James
J
Haab
Brian
B
Chan
Christina
C
D000444:Aldehyde Dehydrogenase / Q000235:genetics; D000080924:Aldehyde Dehydrogenase 1 Family; D045744:Cell Line, Tumor; D003198:Computer Simulation; D005230:Fatty Acids, Nonesterified / Q000494:pharmacology*; D015870:Gene Expression / Q000187:drug effects; D020869:Gene Expression Profiling; D018197:Hepatoblastoma / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics / Q000378:metabolism*; D053858:Metabolic Networks and Pathways / Q000187:drug effects / Q000235:genetics*; D008954:Models, Biological; D009245:NADH Dehydrogenase / Q000235:genetics; D050697:Retinal Dehydrogenase; D014409:Tumor Necrosis Factor-alpha / Q000494:pharmacology*
D005230:Fatty Acids, Nonesterified; D014409:Tumor Necrosis Factor-alpha; D000080924:Aldehyde Dehydrogenase 1 Family; D000444:Aldehyde Dehydrogenase; C510223:ALDH1A1 protein, human; D050697:Retinal Dehydrogenase; D009245:NADH Dehydrogenase