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

Jinwei Luan

Jinwei Luan

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Luan, Jinwei
, 
Xianglan Li

Xianglan Li

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Li, Xianglan
, 
Rutao Guo

Rutao Guo

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Guo, Rutao
, 
Shanshan Liu

Shanshan Liu

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Liu, Shanshan
, 
Hongyu Luo

Hongyu Luo

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Luo, Hongyu
 e 
Qingshan You

Qingshan You

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You, Qingshan
  
22 feb 2016
Identification of differentially expressed genes associated with the enhancement of X-ray susceptibility by RITA in a hypopharyngeal squamous cell carcinoma cell line (FaDu)'s Cover Image
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Categoria dell'articolo: Research Article
Pubblicato online: 22 feb 2016
Pagine: 168 - 174
Ricevuto: 22 apr 2015
Accettato: 03 gen 2016
DOI: https://doi.org/10.1515/raon-2016-0010
Parole chiave
© 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.
Venn diagram of DEGs between 0 GY X-ray-treated FaDu cells and 8 GY X-ray-treated FaDu cells, as well as the DEGs between 8 GY X-ray-treated FaDu cells and 8 GY X-ray + RITA-treated FaDu cells.
Venn diagram of DEGs between 0 GY X-ray-treated FaDu cells and 8 GY X-ray-treated FaDu cells, as well as the DEGs between 8 GY X-ray-treated FaDu cells and 8 GY X-ray + RITA-treated FaDu cells.
The PPI network for the RITA genes and their related DEGs. The red hubs represent the up-regulated DEGs; the green hubs represent the down-regulated DEGs; the triangle hubs represent the RITA genes; the lines represent the interactions between the genes.
The PPI network for the RITA genes and their related DEGs. The red hubs represent the up-regulated DEGs; the green hubs represent the down-regulated DEGs; the triangle hubs represent the RITA genes; the lines represent the interactions between the genes.
Functional annotation for RFC2 and EZH2 clusters. Node color represents the functional groups; node size reflects the p-value, with the smaller the node size indicating larger p-values, while the larger node size represents smaller p-values.
Functional annotation for RFC2 and EZH2 clusters. Node color represents the functional groups; node size reflects the p-value, with the smaller the node size indicating larger p-values, while the larger node size represents smaller p-values.

The KEGG pathway enrichment for the DEGs between 0 GY X-ray treated FaDu cells and 8 GY X-ray treated FaDu cells, as well as 8 GY X-ray treated FaDu cells and 8 GY X-ray + RITA treated FaDu cells_

TermCountP valueGene symbols
gy8ctl vs. gy0ctl
hsa03030: DNA replication285.85E-19POLA1, POLA2, RPA3, RPA1, PRIM1, RPA2, POLE4, MCM7, POLE3, FEN1
hsa04110: Cell cycle431.91E-11E2F1, E2F2, DBF4, PRKDC, PKMYT1, CHEK1, CDC45, MCM7, CDKN2B, CDKN2C …
hsa03430: Mismatch repair161.15E-09EXO1, SSBP1, MSH2, LIG1, MLH1, RPA3, RFC5, POLD3, RPA1, RPA2 …
hsa00240: Pyrimidine metabolism322.00E-08POLR2G, DTYMK, POLA1, CAD, POLA2, CMPK2, TK1, PRIM1, TYMS, POLE4 …
hsa03410: Base excision repair162.06E-06HMGB1, UNG, NEIL3, LIG1, POLE, NEIL1, POLD3, POLD4, POLE4, POLE3 …
hsa03440: Homologous recombination143.36E-06RAD51C, XRCC3, NBN, BLM, SSBP1, MRE11A, EME1, RPA3, RAD51, POLD3 …
hsa03420: Nucleotide excision repair152.25E-04LIG1, POLE, RPA3, RFC5, POLD3, RPA1, RPA2, POLD4, RFC3, POLE4 …
hsa00230: Purine metabolism333.73E-04XDH, POLR2G, POLA1, POLA2, PFAS, PRIM1, POLE4, POLE3, PDE4A, ENTPD8 …
hsa05200: Pathways in cancer520.010417112FGF19, E2F1, HSP90AB1, E2F2, PTGS2, PDGFB, PGF, STAT5A, ARNT2, FGF11 …
hsa05219: Bladder cancer110.016627297E2F1, E2F2, TYMP, CDKN1A, PGF, VEGFA, RB1, DAPK2, CDK4, MMP2, DAPK1
hsa04115: p53 signaling pathway150.018499656CDK1, CYCS, CHEK1, ATR, CDK4, CCNG2, GTSE1, CCNB1, CDKN1A, CCNB2 …
hsa04512: ECM-receptor interaction170.024887625HSPG2, SDC4, COL5A1, CHAD, HMMR, VWF, LAMB3, LAMB2, ITGB8, ITGA5 …
hsa03020: RNA polymerase80.03298698POLR3G, POLR2G, POLR3K, POLR1E, POLR1A, POLR1C, POLR1B, POLR3B
hsa00970: Aminoacyl-tRNA biosynthesis100.036943456IARS, NARS2, LARS, FARSB, EPRS, WARS2, DARS2, AARS2, KARS, EARS2
hsa03040: Spliceosome220.044130211NCBP1, MAGOH, TRA2B, LSM6, TRA2A, SNRPD1, HSPA1A, PRPF4, RBMX, HNRNPA1 …
hsa05222: Small cell lung cancer160.048720159E2F1, TRAF1, E2F2, CKS1B, PTGS2, PIK3CD, CYCS, SKP2, RB1, BIRC3 …
gy8rita vs. gy8ctl
hsa03410: Base excision repair40.014381142NEIL1, LIG3, PARP3, SMUG1
hsa05212: Pancreatic cancer50.021107952AKT1, PGF, PIK3CB, ERBB2, RALGDS
hsa05213: Endometrial cancer40.040674333AKT1, PIK3CB, ERBB2, CTNNA1
hsa04150: mTOR signaling pathway40.040674333AKT1, PGF, PIK3CB, EIF4E2

The top ten up- and down-regulated DEGs between 0 GY X-ray treated FaDu cells and 8 GY X-ray treated FaDu cells, as well as 8 GY X-ray treated FaDu cells and 8 GY X-ray + RITA treated FaDu cells_

Gene symbolslog2 fold changeP-valueGene symbolslog2 fold changeP-value
BMF−1.79769e+3081.23E-11BMF−1.79769e+3081.23E-11
SDCBP−1.79769e+3080.00097112SDCBP−1.79769e+3080.00097112
IL32−1.79769e+3080.0110064IL32−1.79769e+3080.0110064
MAD1L1−1.79769e+3089.77E-05MAD1L1−1.79769e+3089.77E-05
SIRT3−1.79769e+3080.00289562SIRT3−1.79769e+3080.00289562
Up-regulatedKAZN−1.79769e+3087.93E-10KAZN−1.79769e+3087.93E-10
TSPAN4−1.79769e+3080.0136997TSPAN4−1.79769e+3080.0136997
PPAN-P2RY11−1.79769e+3084.71E-08PPAN-P2RY11−1.79769e+3084.71E-08
CDC14B−1.79769e+3081.49E-06CDC14B−1.79769e+3081.49E-06
CXCL16−1.79769e+3080.000434357CXCL16−1.79769e+3080.000434357
C3orf14−5.884420.006353KCTD2−3.89011.23E-06
TTC28-AS1−3.105541.30E-09TSPAN4−3.682340.0124825
KRT4−2.863980FGFR3−3.476030.0322468
ALPP−2.687411.30E-13PLEKHM1.1−3.416180.0191408
MND1−2.647520.022297CHFR−3.398240.0369514
Down-regulatedDHRS2−2.389834.17E-11KREMEN2−3.328240.033903
FGF3−2.331562.25E-12SMAP2−3.31990.0215792
TERC−2.2680.027132EPS15L1−3.305180.00562372
UTP20−2.237280MORF4L2−3.07310.0300806
GAL−2.226610PIGQ−2.940790.0327601

SUMMARY statistics of paired-end (PE) RNA-Seq reads in six cell lines

SampleTotal PE readsTotal high quality PE readsTotal mapped PE readsTotal uniquely mapped PE reads
Sample_L141211001104678868650424 (82.3%)6846290 (79.1%)6749179
Sample_L141211002115102109627883 (83.6%)7197526 (74.7%)7097908
Sample_L141211003111194109365349 (84.2%)6910499 (73.7%)6825529
Sample_L141211004112719349510517 (84.3%)6752339 (70.9%)6669811
Sample_L141211005108544149110446 (83.9%)7129465 (78.2%)7043831
Sample_L141211006105322458802840 (83.5%)6752224 (76.7%)6671073
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Medicina, Medicina clinica, Medicina interna, Ematologia, Oncologia, Radiologia
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