Screening and Identification of Key Biomarkers in Melanoma: Evidence from Bioinformatic Analyses
JOURNAL OF COMPUTATIONAL BIOLOGY
Authors: Xia, Yijun; Xie, Juan; Zhao, Jun; Lou, Yin; Cao, Dongsheng
Abstract
Melanoma is an extremely malignant and occult tumor. To identify candidate genes related to melanoma carcinogenesis and progression, the microarray data sets GSE83583, GSE130244, and GSE31879 were retrieved from the Gene Expression Omnibus (GEO) database using the GEO2R analytical tool provided by the National Center for Biotechnology Information (NCBI). Gene expression analysis was carried out using the DAVID database for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional enrichment analyses of differentially expressed genes. A protein-protein interaction network was constructed with the STRING database, the interaction data were imported into Cytoscape software, and the network topology was analyzed to identify key genes. Hub gene expression was verified in the Gene Expression Profiling Interactive Analysis and Human Protein Atlas databases. In addition, Kaplan-Meier survival analysis was performed on hub genes. A total of 142 differentially expressed genes were identified in melanoma tissues, including 50 upregulated genes and 92 downregulated genes. Five central genes (CCNA2, EBP, GABBR2, TRIM32, and ADAM10) were found based on the degree of the nodes. These genes are mainly enriched in protein serine/threonine kinase activity and apoptosis pathways. Survival analysis showed CCNA2 to be related to the overall survival (OS) of patients, and increased expression of TRIM32 led to increased OS and disease-free survival risk. Bioinformatics methods can be used to effectively select key genes in melanoma, and CCNA2 and TRIM32 may be new targets for treatment of this disease.
IMP regulates Kuzbanian to control the timing of Notch signalling in Drosophila follicle cells
DEVELOPMENT
Authors: Fic, Weronika; Faria, Celia; St Johnston, Daniel
Abstract
The timing of Drosophila egg chamber development is controlled by a germline Delta signal that activates Notch in the follicle cells to induce them to cease proliferation and differentiate. Here, we report that follicle cells lacking the RNA-binding protein IMP go through one extra division owing to a delay in the Delta-dependent S2 cleavage of Notch. The timing of Notch activation has previously been shown to be controlled by cis-inhibition by Delta in the follicle cells, which is relieved when the miRNA pathway represses Delta expression. imp mutants are epistatic to Delta mutants and give an additive phenotype with belle and Dicer-1 mutants, indicating that IMP functions independently of both cis-inhibition and the miRNA pathway. We find that the imp phenotype is rescued by overexpression of Kuzbanian, the metalloprotease that mediates the Notch S2 cleavage. Furthermore, Kuzbanian is not enriched at the apical membrane in imp mutants, accumulating instead in late endosomes. Thus, IMP regulates Notch signalling by controlling the localisation of Kuzbanian to the apical domain, where Notch cleavage occurs, revealing a novel regulatory step in the Notch pathway.