Li Zheng, Srivastava Shireesh, Yang Xuerui, Mittal Sheenu, Norton Paul, Resau James, Haab Brian, Chan Christina
Department of Chemical Engineering and Material Science, Michigan State University, East Lansing, MI 48824, USA.
BMC Syst Biol. 2007 May 11;1:21. doi: 10.1186/1752-0509-1-21.
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.
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.
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.
游离脂肪酸（FFA）和肿瘤坏死因子α（TNF-α）与许多肥胖相关代谢紊乱的发病机制有关。当人肝癌细胞（HepG2）暴露于不同类型的FFA和TNF-α时，发现饱和脂肪酸具有细胞毒性，并且TNF-α会加剧其毒性。为了确定与饱和FFA和TNF-α毒性相关的过程，测量了代谢和基因表达谱以表征细胞状态。开发了一个计算模型来整合这些不同的数据，以揭示饱和脂肪酸毒性所涉及的潜在途径和机制。
开发了一个由三个阶段组成的分层框架，以识别调节毒性的过程和基因。首先，判别分析确定脂肪酸氧化和细胞内甘油三酯积累在区分细胞毒性表型方面最为相关。其次，将基因集富集分析（GSEA）应用于cDNA微阵列数据，以识别转录改变的途径和过程。最后，通过将富集基因集的表达和代谢谱与多块偏最小二乘（MBPLS）回归模型相结合，确定调节步骤1中鉴定的代谢反应的基因和基因集。
分层方法揭示了介导细胞毒性和细胞保护途径的潜在机制，并确定了新的靶点，如NADH脱氢酶、醛脱氢酶1A1（ALDH1A1）和内皮膜蛋白3（EMP3）作为毒性表型的调节因子。这些预测以及分析中提出的一些特定靶点经过了实验验证。
