title: Caspase-related apoptosis genes in gliomas by RNA-seq and bioinformatics analysis.
abstract: Gliomas are the most common malignant tumors of the brain. The aim of this study is to identify caspase-dependent apoptotic genes and uncover their potential regulatory mechanism in glioma progression. Human glioma cell line U251 was used. Three experiment groups were set as control group, H2O2group (treated with H2O2) and caspase inhibitor group (treated with caspase inhibitor). For samples in each group, RNA-sequencing was performed on Illumina platform and differentially expressed genes (DEGs) between any two of the three groups were selected using NOISeq package. By overlapping analysis, the caspase inhibitor-related DEGs were further screened out, followed by enrichment analyses. Drugs associating with these genes were selected by WebGestalt. Protein-protein interaction (PPI) network analysis was conducted based on SRINIG database. A set of 105 caspase inhibitor-related DEGs were identified, which were significantly enriched in cellular components related functions (for example, TUBB2A, RPSA and RPL5); and metabolism related pathways (for example, PSMC3, KHSRP, RPL5 and RPSA). In addition, KHSRP and TUBB2A were significantly associated with several drugs such as cefotaxime, cefacetrile and netilmicin. Besides, PSMC3 and RPL5 were identified as crucial nodes in the PPI network. Several crucial genes in gliomas cells such as TUBB2A, RPSA, RPL5, PSMC3 and KHSRP were identified, which might play significant roles in apoptosis in a caspase-dependent manner. These genes might also involve in the regulation of metabolism related functions and pathways. KHSRP and TUBB2A might be novel targets of three drugs, cefotaxime, cefacetrile and netilmicin.
authors.affiliation: Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun, Jilin Province, China.
authors.forename: Rui
authors.initials: R
authors.lastname: Wang
authors.affiliation: Department of Neurosurgery, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, Jilin Province 130033, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Wei
authors.affiliation: Department of Science and Education Section, China-Japan Union Hospital of Jilin University, Changchun, Jilin Province, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wei
authors.affiliation: Department of Neurosurgery, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, Jilin Province 130033, China.
authors.forename: Zhaohui
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Neurosurgery, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, Jilin Province 130033, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Tian
authors.affiliation: Department of Neurosurgery, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, Jilin Province 130033, China. Electronic address: chaodu303@sina.com.
authors.forename: Chao
authors.initials: C
authors.lastname: Du
mesh_terms: D017209:Apoptosis / Q000235:genetics*; D001932:Brain Neoplasms / Q000235:genetics*; D061945:Caspase Inhibitors / Q000494:pharmacology; D020169:Caspases / Q000235:genetics*; D045744:Cell Line, Tumor; D019295:Computational Biology; D030562:Databases, Protein; D015870:Gene Expression / Q000187:drug effects; D020869:Gene Expression Profiling; D005910:Glioma / Q000235:genetics* / Q000473:pathology; D006801:Humans; D060066:Protein Interaction Maps / Q000235:genetics; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000235:genetics
chemical_list: D061945:Caspase Inhibitors; D020169:Caspases
keywords: Apoptosis; Caspase inhibitor; Differentially expressed gene; Enrichment analysis; Gliomas; Protein-protein interaction