GEN3VA: aggregation and analysis of gene expression signatures from related studies.

BACKGROUND: Genome-wide gene expression profiling of mammalian cells is becoming a staple of many published biomedical and biological research studies. Such data is deposited into data repositories such as the Gene Expression Omnibus (GEO) for potential reuse. However, these repositories currently do not provide simple interfaces to systematically analyze collections of related studies. RESULTS: Here we present GENE Expression and Enrichment Vector Analyzer (GEN3VA), a web-based system that enables the integrative analysis of aggregated collections of tagged gene expression signatures identified and extracted from GEO. Each tagged collection of signatures is presented in a report that consists of heatmaps of the differentially expressed genes; principal component analysis of all signatures; enrichment analysis with several gene set libraries across all signatures, which we term enrichment vector analysis; and global mapping of small molecules that are predicted to reverse or mimic each signature in the aggregate. We demonstrate how GEN3VA can be used to identify common molecular mechanisms of aging by analyzing tagged signatures from 244 studies that compared young vs. old tissues in mammalian systems. In a second case study, we collected 86 signatures from treatment of human cells with dexamethasone, a glucocorticoid receptor (GR) agonist. Our analysis confirms consensus GR target genes and predicts potential drug mimickers. CONCLUSIONS: GEN3VA can be used to identify, aggregate, and analyze themed collections of gene expression signatures from diverse but related studies. Such integrative analyses can be used to address concerns about data reproducibility, confirm results across labs, and discover new collective knowledge by data reuse. GEN3VA is an open-source web-based system that is freely available at: http://amp.pharm.mssm.edu/gen3va .

Photoinduced unfolding of beta-lactoglobulin mediated by a water-soluble porphyrin.

We investigated the effects that the irradiation of a tetra-anionic porphyrin (mesotetrakis(sulfonatophenyl)porphyrin) noncovalently bound to beta-lactoglobulin (BLG) produces on the conformation of the protein. Although BLG is not a potential target for the biomedical applications of porphyrins, it is a useful model for investigating the effects of photoactive ligands on small globular proteins. We show in this paper that irradiation causes a large unfolding of the protein and that the conformational change is not mediated by the formation of reactive oxygen species. Instead, our data are consistent with an electron-transfer mechanism that is capable of triggering structural changes in the protein and causes the Trp19 residue to undergo chemical modifications to form a derivative of kynurenine. This demonstrates that protein unfolding is prompted by a type-III photosensitizing mechanisms. Type-III mechanisms have been suggested previously, but they have been largely neglected as useful mediators of biomolecular damage. Our study demonstrates that porphyrins can be used as mediators of localized protein conformational changes and that the biomedical applications as well as the mechanistic details of electron transfer between exogenous ligands and proteins merit further investigation.

Irradiation of the porphyrin causes unfolding of the protein in the protoporphyrin IX/beta-lactoglobulin noncovalent complex.

Porphyrins such as protoporphyrin IX (PPIX) are known to occasionally cause conformational changes in proteins for which they are specific ligands. It has also been established that irradiation of porphyrins noncovalently intercalated between bases or bound to one of the grooves can cause conformational effects on DNA. Conversely, there is no evidence reported in the literature of conformational changes caused by noncovalently bound PPIX to globular proteins for which the porphyrin is not a specific ligand. This study shows that the irradiation of the porphyrin in the PPIX/lactoglobulin noncovalent complex indeed causes a local and limited (approximately 7%) unfolding of the protein near the location of Trp19. This event causes the intrinsic fluorescence spectrum of the protein to shift to the red by 2 nm and the average decay lifetime to lengthen by approximately 0.5 ns. The unfolding of lactoglobulin occurs only at pH >7 because of the increased instability of the protein at alkaline pH. The photoinduced unfolding does not depend on the presence of O2 in solution; therefore, it is not mediated by formation of singlet oxygen and is likely the result of electron transfer between the porphyrin and amino acid residues.