ABSTRACT
Objective: To explore the key genes and potential therapeutic drugs for osteoarthritis (OA) by bioinformatics.Method: The microarray data GSE55235 was downloaded from the data platform of gene expression omnibus (GEO) and the differentially expressed genes were screened by R language software (3.5.0).Then,the differentially expressed genes were subjected to gene ontology (GO) enrichment analysis and Kyoto encyclopedia of genes and genomes (KEGG) signaling pathway analysis with David online database.The protein-protein interaction was analyzed by String 10.5 online database and visual editing was analyzed by Cytoscape v3.6.1 software.Subnetwork module analysis was utilized by MCODE plugin to screen the core genes in the process of OA.Finally,small molecule drugs with potential treatment for OA were analyzed by connectivity map (CMap) database.Result: A total of 556 differentially expressed genes were screened,among which 252 were up-regulated and 304 were down-regulated.These genes were mainly involved in extracellular matrix (ECM) organization,inflammatory response,cell adhesion,immune response,collagen binding,etc.The analysis of KEGG pathway showed that differential genes were mainly involved in ECM-receptor interaction,phosphatidylinositol 3 kinase-protein kinase B (PI3K/Akt) signaling pathway and osteoclast differentiation.Some genes,such as interleukin-6(IL-6),JUN,vascular endothelial growth factor α(VEGFA),FOS,MYC and early growth response gene-1(EGR-1),activating transcription factor-3(ATF-3),playing critical role in the process of OA were identified by protein-protein interaction.Some potential small molecular drugs for the treatment of OA have also been screened,such as lycorine and anisomycin.Conclusion: The selected key genes may be targets for the diagnosis of OA or potential targets for the treatment of OA,and the selected small molecular drugs can be developed as the key drugs for the treatment of OA.
ABSTRACT
The connectivity map (CMAP) database is established initially to connect biology, chemistry, and clinical conditions, which helps to discover the connection of disease-gene-drug. The CMAP approach has been applied in the field of drug discovery and development, which is widely recognized. In recently years, CMAP analysis has been applied in the research on Chinese materia medica (CMM). The study of CMM is facing a wide range of challenges, such as complicated ingredients, multiple targets, multiple pathways of action and complex functioning mechanism. The idea of employing CMAP in the CMM research has brought a new perspective for researchers and provides a systematic method for elucidating the mechanism of CMM.
ABSTRACT
Retinal prostheses are being developed to restore vision for the blind with retinal diseases such as retinitis pigmentosa (RP) or age-related macular degeneration (AMD). Among the many issues for prosthesis development, stimulation encoding strategy is one of the most essential electrophysiological issues. The more we understand the retinal circuitry how it encodes and processes visual information, the greater it could help decide stimulation encoding strategy for retinal prosthesis. Therefore, we examined how retinal ganglion cells (RGCs) in in-vitro retinal preparation act together to encode a visual scene with multielectrode array (MEA). Simultaneous recording of many RGCs with MEA showed that nearby neurons often fired synchronously, with spike delays mostly within 1 ms range. This synchronized firing - narrow correlation - was blocked by gap junction blocker, heptanol, but not by glutamatergic synapse blocker, kynurenic acid. By tracking down all the RGC pairs which showed narrow correlation, we could harvest 40 functional connectivity maps of RGCs which showed the cell cluster firing together. We suggest that finding functional connectivity map would be useful in stimulation encoding strategy for the retinal prosthesis since stimulating the cluster of RGCs would be more efficient than separately stimulating each individual RGC.