title: Analysis of gene profiles in glioma cells identifies potential genes, miRNAs, and target sites of migratory cells.
abstract: OBJECTIVE
  To explore the potential molecular mechanisms involved in migratory glioma cells.
  
  
  METHODS
  The gene expression profiles of GSE28167, employing human malignant glioma U251MG cells cultured on strictly aligned versus randomly oriented electrospun nanofibers of polycaprolactone, were downloaded from the Gene Expression Omnibus database. Gene differential expression analysis was carried out by the package of Gene Expression Omnibus query and limma in R language. The Gene Set Analysis Toolkit V2 was used for pathway analysis. Gene set enrichment analysis was used to screen for target sites of transcription factors, miRNA and small drug molecules.
  
  
  RESULTS
  Totally 586 differentially expressed genes were identified and the differentially expressed genes were mainly enriched in the pathway of muscle cell TarBase, MAPK cascade, adipogenesis and epithelium TarBase. Thirty-two significant target sites of transcription factors, such as hsa_RTAAACA_V$FREAC2_01, were screened. The top 20 potential miRNAs including MIR-124A, MIR-34A and MIR-34C were screened for a constructing gene-miRNA interaction network. Small molecules that can inhibit the motility of glioma cells such as diclofenamide and valinomycin were mined. By integrating the regulatory relationships among transcription factors, miRNAs and differentially expressed genes, we found that 7 differentially expressed genes, including SOX4, ANKRD28 and CCND1, might play crucial roles in the migration of glioma cells.
  
  
  CONCLUSIONS
  The screened migration-associated genes, significant pathways, and small molecules give us new insight for the mechanism of migratory glioma cells. Interest in such genes as potential target genes in the treatment of glioblastoma justifies functional validation studies.
authors.affiliation: Department of Neurosurgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai - PR China.
authors.forename: Fei
authors.initials: F
authors.lastname: Xue
authors.forename: Rui
authors.initials: R
authors.lastname: Shen
authors.forename: Xianzhen
authors.initials: X
authors.lastname: Chen
mesh_terms: D001932:Brain Neoplasms / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D002465:Cell Movement / Q000235:genetics*; D054703:Cyclic Nucleotide Phosphodiesterases, Type 4 / Q000235:genetics; D019938:Cyclin D1 / Q000235:genetics; D049029:Dystrophin-Associated Proteins / Q000235:genetics; D058851:GPI-Linked Proteins / Q000235:genetics; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D005910:Glioma / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000235:genetics; D035683:MicroRNAs / Q000032:analysis*; D009419:Nerve Tissue Proteins / Q000235:genetics; D009479:Neuropeptides / Q000235:genetics; D020796:Receptor, Platelet-Derived Growth Factor alpha / Q000235:genetics; D055751:SOXC Transcription Factors / Q000235:genetics; D015398:Signal Transduction / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: C514564:ANKRD28 protein, human; C530104:CCND1 protein, human; C490915:DTNA protein, human; D049029:Dystrophin-Associated Proteins; D058851:GPI-Linked Proteins; D047908:Intracellular Signaling Peptides and Proteins; D035683:MicroRNAs; D009419:Nerve Tissue Proteins; D009479:Neuropeptides; C522183:RGMA protein, human; C083431:SOX4 protein, human; D055751:SOXC Transcription Factors; D014157:Transcription Factors; D019938:Cyclin D1; D020796:Receptor, Platelet-Derived Growth Factor alpha; D054703:Cyclic Nucleotide Phosphodiesterases, Type 4; C517376:PDE4D protein, human