Transcriptomic profiling of Escherichia coli K-12 in response to a compendium of stressors.

Environmental perturbations impact multiple cellular traits, including gene expression. Bacteria respond to these stressful situations through complex gene interaction networks, thereby inducing stress tolerance and survival of cells. In this paper, we study the response mechanisms of E. coli when exposed to different environmental stressors via differential expression and co-expression analysis. Gene co-expression networks were generated and analyzed via Weighted Gene Co-expression Network Analysis (WGCNA). Based on the gene co-expression networks, genes with similar expression profiles were clustered into modules. The modules were analysed for identification of hub genes, enrichment of biological processes and transcription factors. In addition, we also studied the link between transcription factors and their differentially regulated targets to understand the regulatory mechanisms involved. These networks validate known gene interactions and provide new insights into genes mediating transcriptional regulation in specific stress environments, thus allowing for in silico hypothesis generation.

The effects of size and shape of the ovarian cancer spheroids on the drug resistance and migration.

BACKGROUND: High fatality in ovarian cancer is attributed to metastasis, propagated by the release of multi-cellular aggregates/spheroids into the peritoneal cavity and their subsequent mesothelial invasion of peritoneal organs. Spheroids are therefore a common and clinically relevant in vitro model for ovarian cancer research. Spheroids in patients vary significantly in size and shape and display enhanced resistance to anti-cancer drugs compared to monolayers. However, there is no consensus on how spheroid size and shape affect drug resistance. Moreover, existing data regarding the influence of epithelial-to-mesenchymal transition (EMT) profile on spheroid shape and migration is inconclusive. METHODS: We formed spheroids with OVCAR-3 and OVCAR-8 cells, chosen for their established genetic similarity to the patient tumor samples. We monitored their morphology using confocal microscope with dipping objective and fluorescent microscope. We characterized important EMT biomarkers; E-cadherin, Vimentin and Slug through western blotting in monolayers and spheroids. We treated these spheroids with Taxol and Cisplatin and investigated their migratory profile based on their morphology. RESULTS: We report two distinct multicellular structures: loose aggregates (OVCAR-3) and compact spheroids (OVCAR-8). We attribute these different morphologies to the expression of the EMT biomarkers, and their changes upon spheroid formation. Importantly, we did not observe a difference in resistance to the anti-cancer drugs as a function of spheroid size and shape. However, migration capacity of compact spheroid (OVCAR-8) was 15-fold higher compared to that of loose aggregates (OVCAR-3). CONCLUSIONS: These results highlight the importance of spheroid size and shape on anti-cancer drug resistance and migration profiles. The results of this study can, therefore, help to elucidate general rules for ovarian cancer studies based on 3D samples.