Screening of differentially expressed genes for colorectal cancer and prediction of potential traditional Chinese medicine: based on bioinformatics / 中国中药杂志

This study screened and analyzed the differentially expressed genes(DEGs) between colorectal cancer(CRC) tissues and normal tissues with bioinformatics techniques to predict biomarkers and Chinese medicinals for the diagnosis and treatment of CRC. The microarray data sets GSE21815, GSE106582, and GSE41657 were downloaded from the Gene Expression Omnibus(GEO), and the DEGs were screened by GEO2 R, followed by the Gene Ontology(GO) tern enrichment and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analysis of the DEGs based on DAVID. The protein-protein interaction network was constructed by STRING, and MCODE and Cytohubba plug-ins were used to screen the significant modules and hub genes in the network. UCSC, cBioPortal, and Oncomine were employed for hierarchical clustering, survival analysis, Oncomine analysis, and correlation analysis of clinical data. Coremine Medical was applied to predict the Chinese medicinals acting on hub genes. A total of 284 DEGs were screened out, with 146 up-regulated and 138 down-regulated. The up-regulated genes were mainly involved in cell cycle, NLRs pathway, and TNF signaling pathway, and the down-regulated genes were related to mineral absorption, nitrogen metabolism, and bicarbonate reabsorption in proximal tubules. The 15 hub genes were CDK1, CDC20, AURKA, MELK, TOP2 A, PTTG1, BUB1, CDCA5, CDC45, TPX2, NEK2, CEP55, CENPN, TRIP13, and GINS2, among which CDK1 and CDC20 were regarded as core genes. The high expression of CDK1 and CDC20 suggested poor prognosis, and they significantly expressed in many cancers, especially breast cancer, lung cancer, and CRC. The expression of CDK1 and CDC20 was correlated with gender, tumor type, TNM stage, and KRAS gene mutation. The potential effective medicinals against CRC were Scutellariae Radix, Scutellariae Barbatae Herba, Arnebiae Radix, etc. The significant expression of CDK1 and CDC20 can help distinguish tumor tissues from normal tissues, and is related to survival prognosis. Thus, the two can be used as biomarkers for the diagnosis and treatment of CRC. This study provides a reference for related drug development.

Screening of key genes and pathways of ischemic stroke and prediction of traditional Chinese medicines based on bioinformatics / 中国中药杂志

The aim of this paper was to explore the key genes and pathogenesis of ischemic stroke(IS) by bioinformatics, and predict the potential traditional Chinese medicines for IS. Based on the gene-chip raw data set of GSE22255 from National Center of Biotechnology Information(NCBI), the article enrolled in 20 patients with ischemic stroke and 20 sex-and age-matched controls, and differentially expressed genes(DEGs) were screened based on R language software. The DAVID tool and R language software were used to perform gene ontology(GO) biological process enrichment analysis and Kyoto encyclopedia of genes and gnomes(KEGG) pathway enrichment analysis. The DEGs were imported into STRING to construct a protein-protein interaction network, and the Molecular Complexity Module(MCODE) plug-in of Cytoscape software was used to visualize and analyze the key functional modules. Moreover, the core genes and the medical ontology information retrieval platform(Coremine Medical) were mapped to each other to screen the traditional Chinese medicines and construct drug-active ingredient-target network. Compared with healthy controls, 14 DEGs were obtained, of which 12 genes were up-regulated and 2 genes were down-regulated. DEGs were mainly involved in immune response, inflammatory process, signal transduction, and cell proliferation regulation. The interleukin-17(IL-17), nuclear factor kappaB(NF-κB), tumor necrosis factor(TNF), nucleotide binding oligomerization domain(NOD)-like receptor and other signaling pathways were involved in KEGG pathway enrichment analysis. The key modules of the DEGs-encoding protein interaction network mainly focused on 7 genes of TNF, JUN, recombinant immediate early response 3(IER3), recombinant early growth response protein 1(EGR1), prostaglandin-endoperoxide synthase 2(PTGS2), C-X-C motif chemokine ligand 8(CXCL8) and C-X-C motif chemokine ligand 2(CXCL2), which were involved in biological processes widely such as neuroinflammation and immunity. TNF and JUN were the key nodes in this module, which might become potential biological markers for diagnosis and prognosis evaluation of IS. The potential traditional Chinese medicines for the treatment of IS includes Salviae Miltiorrhizae Radix et Rhizoma, Croci Stigma, Scutellariae Radix, and Cannabis Fructus. The occurrence of stroke was the result of multiple factors. Dysregulation of genes and pathways related to immune regulation and inflammation may be the key link for the development of IS. This study provided research direction and theoretical basis for further exploring the mechanism of action of traditional Chinese medicine in the treatment of IS and searching for potential drug targets.