Abstract
BackgroundBy studying genome-wide expression patterns in healthy and diseased tissues across a wide range of pathophysiological conditions, DNA microarrays have revealed unique insights into complex diseases. However, the high-dimensionality of microarray data makes interpretation of heterogeneous gene expression studies inherently difficult.ResultsUsing a large-scale analysis of more than 40 microarray studies encompassing ~2400 mammalian tissue samples, we identified a common theme across heterogeneous microarray studies evident by a robust genome-wide inverse regulation of metabolic and cell signaling pathways: We found that upregulation of cell signaling pathways was invariably accompanied by downregulation of cell metabolic transcriptional activity (and vice versa). Several findings suggest that this characteristic gene expression pattern represents a new principle of mammalian transcriptional regulation. First, this coordinated transcriptional pattern occurred in a wide variety of physiological and pathophysiological conditions and was identified across all 20 human and animal tissue types examined. Second, the differences in metabolic gene expression predicted the magnitude of differences for signaling and all other pathways, i.e. tissue samples with similar expression levels of metabolic transcripts did not show any differences in gene expression for all other pathways. Third, this transcriptional pattern predicted a profound effect on the proteome, evident by differences in structure, stability and post-translational modifications of proteins belonging to signaling and metabolic pathways, respectively.ConclusionsOur data suggest that in a wide range of physiological and pathophysiological conditions, gene expression changes exhibit a recurring pattern along a transcriptional axis, characterized by an inverse regulation of major metabolic and cell signaling pathways. Given its widespread occurrence and its predicted effects on protein structure, protein stability and post-translational modifications, we propose a new principle for transcriptional regulation in mammalian biology.
Highlights
By studying genome-wide expression patterns in healthy and diseased tissues across a wide range of pathophysiological conditions, DNA microarrays have revealed unique insights into complex diseases
We examined gene expression patterns across 20 large microarray datasets of different human tissues by comparing, in each tissue type, the 10 samples with the highest vs. the lowest gene expression of transcripts belonging to the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway of oxidative phosphorylation (OXPHOS) using Significance Analysis of Microarrays [3]
A highly coordinated transcriptional response pattern became apparent, as all major metabolic pathways were positively correlated to OXPHOS expression, while cell signaling pathways were inversely correlated to OXPHOS (Figures 1A, B, and Additional Files 1A-1C; detailed study and sample characteristics are listed in Additional Files 2 and 3)
Summary
By studying genome-wide expression patterns in healthy and diseased tissues across a wide range of pathophysiological conditions, DNA microarrays have revealed unique insights into complex diseases. By applying transcriptional profiling technology to healthy and diseased tissues across a wide range of pathophysiological conditions, DNA microarrays have revealed unique insights into complex disease patterns. In a previous study examining failing and non-diseased dog hearts, we observed an intriguing reciprocal transcriptional regulation of selected cell signaling and metabolic processes [1] To extend this initial observation beyond myocardial tissue and selected pathways, we used a systems biology approach based on KEGG pathways (Kyoto Encyclopedia of Genes and Genomes [2]) in a large collection of ~2400 mammalian tissue samples derived from more than 20 diseased and non-diseased tissues. We identified a robust genome-wide reciprocal regulation of metabolic and cell signaling pathways which was present across all 20 different tissues examined
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