<abstract xmlns="http://www.w3.org/1999/xhtml"><sec id="j_raon-2016-0010_s_001_w2aab3b8c17b1b7b1aab1c15b1Aa"><h3>Background</h3><p>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.</p></sec><sec id="j_raon-2016-0010_s_002_w2aab3b8c17b1b7b1aab1c15b2Aa"><h3>Materials and methods</h3><p>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.</p></sec><sec id="j_raon-2016-0010_s_003_w2aab3b8c17b1b7b1aab1c15b3Aa"><h3>Results</h3><p>Total 2,040 and 297 DEGs were identified in FaDu cells treated with 8 Gy X-ray or 8 Gy X-ray + RITA, respectively. <italic>PARP3</italic> and <italic>NEIL1</italic> were enriched in base excision repair, and <italic>CDK1</italic> was enriched in p53 signaling pathway. <italic>RFC2</italic> and <italic>EZH2</italic> 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 <italic>RFC2</italic> and <italic>EZH2</italic> were related to cell cycle.</p></sec><sec id="j_raon-2016-0010_s_004_w2aab3b8c17b1b7b1aab1c15b4Aa"><h3>Conclusions</h3><p><italic>RFC2</italic>, <italic>EZH2</italic>, <italic>CDK1</italic>, <italic>PARP3</italic> and <italic>NEIL1</italic> may be associated, and together enhance the susceptibility of FaDu cells treated with RITA to the deleterious effects of X-ray.</p></sec></abstract>

BackgroundNext 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.Materials and methodsThe 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.ResultsTotal 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.ConclusionsRFC2, 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.

Identification of differentially expressed genes associated with the enhancement of X-ray susceptibility by RITA in a hypopharyngeal squamous cell carcinoma cell line (FaDu)

Department of Radiation Oncology, The Third Affiliated Hospital of Harbin Medical University, Harbin, China

Radiology and Oncology

This article is distributed under the terms of the Creative Commons Attribution Non-Commercial License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

BackgroundNext generation sequencing and bio-informatic analyses were conducted to investigate the mechanism of reactivation of p53 and induction of tumor cell...

Identification of differentially expressed genes associated with the enhancement of X-ray susceptibility by RITA in a hypopharyngeal squamous cell carcinoma cell line (FaDu)

Article Category: Research Article

Published Online: Feb 22, 2016

Page range: 168 - 174

Received: Apr 22, 2015

Accepted: Jan 03, 2016

DOI: https://doi.org/10.1515/raon-2016-0010

© 2016 Radiol Oncol

This article is distributed under the terms of the Creative Commons Attribution Non-Commercial License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.