title: Identification of differentially expressed genes associated with the enhancement of X-ray susceptibility by RITA in a hypopharyngeal squamous cell carcinoma cell line (FaDu).
abstract: BACKGROUND
  Next generation sequencing and bio-informatic analyses were conducted to investigate the mechanism of reactivation of p53 and induction of tumor cell apoptosis (RITA)-enhancing X-ray susceptibility in FaDu cells.
  
  
  METHODS
  The cDNA was isolated from FaDu cells treated with 0 X-ray, 8 Gy X-ray, or 8 Gy X-ray + RITA. Then, cDNA libraries were created and sequenced using next generation sequencing, and each assay was repeated twice. Subsequently, differentially expressed genes (DEGs) were identified using Cuffdiff in Cufflinks and their functions were predicted by pathway enrichment analyses. Genes that were constantly up- or down-regulated in 8 Gy X-ray-treated FaDu cells and 8 Gy X-ray + RITA-treated FaDu cells were obtained as RITA genes. Afterward, the protein-protein interaction (PPI) relationships were obtained from the STRING database and a PPI network was constructed using Cytoscape. Furthermore, ClueGO was used for pathway enrichment analysis of genes in the PPI network.
  
  
  RESULTS
  Total 2,040 and 297 DEGs were identified in FaDu cells treated with 8 Gy X-ray or 8 Gy X-ray + RITA, respectively. PARP3 and NEIL1 were enriched in base excision repair, and CDK1 was enriched in p53 signaling pathway. RFC2 and EZH2 were identified as RITA genes. In the PPI network, many interaction relationships were identified (e.g., RFC2-CDK1, EZH2-CDK1 and PARP3-EZH2). ClueGO analysis showed that RFC2 and EZH2 were related to cell cycle.
  
  
  CONCLUSIONS
  RFC2, EZH2, CDK1, PARP3 and NEIL1 may be associated, and together enhance the susceptibility of FaDu cells treated with RITA to the deleterious effects of X-ray.
authors.affiliation: Department of Radiation Oncology, The Third Affiliated Hospital of Harbin Medical University, Harbin, China.
authors.forename: Jinwei
authors.initials: J
authors.lastname: Luan
authors.affiliation: Department of Radiation Oncology, The Third Affiliated Hospital of Harbin Medical University, Harbin, China.
authors.forename: Xianglan
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Radiation Oncology, The Third Affiliated Hospital of Harbin Medical University, Harbin, China.
authors.forename: Rutao
authors.initials: R
authors.lastname: Guo
authors.affiliation: Department of Radiation Oncology, The Third Affiliated Hospital of Harbin Medical University, Harbin, China.
authors.forename: Shanshan
authors.initials: S
authors.lastname: Liu
authors.affiliation: Department of Radiation Oncology, The Third Affiliated Hospital of Harbin Medical University, Harbin, China.
authors.forename: Hongyu
authors.initials: H
authors.lastname: Luo
authors.affiliation: Department of Radiation Oncology, The Third Affiliated Hospital of Harbin Medical University, Harbin, China.
authors.forename: Qingshan
authors.initials: Q
authors.lastname: You
keywords: RITA; X-ray; hypopharyngeal squamous cell carcinoma; next generation sequencing