An integrated reverse functional genomic and metabolic approach to understanding orotic acid-induced fatty liver

Abstract

. An integrated reverse functional genomic and metabolic approach to understanding orotic acid-induced fatty liver. Physiol Genomics 17: 140-149, 2004. First published January 27, 2004 10.1152/physiolgenomics.00158.2003.-In functional genomics, DNA microarrays for gene expression profiling are increasingly being used to provide insights into biological function or pathology. To better understand the significance of the multiple transcriptional changes across a time period, the temporal changes in phenotype must be described. Orotic acid-induced fatty liver disease was investigated at the transcriptional and metabolic levels using microarrays and metabolic profiling in two strains of rats. Highresolution 1 H-NMR spectroscopic analysis of liver tissue indicated that Kyoto rats compared with Wistar rats are predisposed to the insult. Metabolite analysis and gene expression profiling following orotic acid treatment identified perturbed metabolic pathways, including those involved in fatty acid, triglyceride, and phospholipid synthesis, ␤-oxidation, altered nucleotide, methyl donor, and carbohydrate metabolism, and stress responses. Multivariate analysis and statistical bootstrapping were used to investigate co-responses with transcripts involved in metabolism and stress responses. This reverse functional genomic strategy highlighted the relationship between changes in the transcription of stearoyl-CoA desaturase 1 and those of other lipid-related transcripts with changes in NMR-derived lipid profiles. The results suggest that the integration of 1 H-NMR and gene expression data sets represents a robust method for identifying a focused line of research in a complex system. transcriptomics; metabolomics/metabonomics; DNA microarray; system biology; bioinformatics DNA MICROARRAYS are increasingly being used in functional genomic strategies for understanding gene function and pathology (5,26,27). To fully use the information generated by this technology, it is necessary to have a description of the changing phenotype so that gene expression can be understood in a biological context. To achieve this, there is recognition that the large-scale analysis of metabolites, as by proton nuclear magnetic resonance spectroscopy ( 1 H-NMR) or mass spectrometry, provides a final conduit to link differential mRNA responses with specific metabolic pathways by defining a metabolic phenotype (10,12,24). The analysis of multivariate data sets that are generated within these different tiers of biological organization may potentially yield critical information about the mechanisms involved in biological transitions. However, enhanced understanding of complex biological systems requires the development of strategies for integration of the different tiers, which link information derived at each level in a systematic way (24, 34). In particular in complex biological systems where large data sets will be the routine, there is a need to integrate the different functional genomic approaches, taking into consideration the scaling and correlation ...

Metabonomics Techniques and Applications to Pharmaceutical Research & Development

“…It has also been found that evaluation of both transcriptomic and metabolic changes following administration of the toxin bromobenzene provides a more sensitive approach for detecting the effects of the toxin (67). In a similar fashion, changes in gene expression detected in microarray experiments can lead to the identification of changed enzyme activity, and this can also be achieved by analysis of metabolic perturbations (68).…”

Role of the AMPK/SREBP-1 pathway in the development of orotic acid-induced fatty liver

“…Depletion of PRPP by an OA dose is followed by a reduction in purine biosynthesis, including ATP, and defects in lipid transport from the liver ( 21 ). Recent studies have suggested an alternative mechanism of OA toxicity in which altered transcription of genes involved in fatty acid metabolism contribute to fatty liver; however, the exact mechanism of the gene expression changes remains to be elucidated ( 22 ). To understand the molecular mechanism of OA-induced fatty liver, we tested the effects of OA on the AMPK/SREBP-1 pathway in human hepatoma cell lines and rat or mouse hepatocytes as well as in rats and mice in vivo.…”

Fenofibrate prevents orotic acid—Induced hepatic steatosis in rats

“…In addition to the effect of orotic acid supplementation on hepatic VLDL secretion, it has been reported that this component is capable of altering the transcription of genes involved in fatty acid synthesis (Buang et al, 2005;Griffin et al, 2004), growth and inflammation control (Griffin et al, 2004). Other studies have reported that orotic acid administration produces alterations on metabolism of tryptophan to niacin (Fukuwatari et al, 2002) and improves cardiac function (Ferdinandy et al, 1998).…”