Screening for differential genes of the esophageal squamous cell carcinoma after DDX46 knockdown and bioinformatics analysis of their interaction_Chinese Journal of Clinical Thoracic and Cardiovascular Surgery

Authors：

 LI Bin , LI Zheng , YIN Ci , LIN Junping , YANG Jianbao , ZHU Duojie , FENG Haiming , JING Tao

Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou, 730030, P.R.China;

Corresponding author：

LI Bin, Email: dr.leebin@outlook.com

Keywords：

DDX46; esophageal squamous cell carcinoma; gene chip; differential genes; bioinformatics

DOI：

10.7507/1007-4848.201907051

Video：

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Abstract Full text Figures/Tables Video References Cited by

Objective To explore the mechanism of DDX46 regulation of esophageal squamous cell carcinoma.Methods Picture signals of fluorescence in gene array were scanned and differential expression of gene in two groups (a DDX46-shRNA-LV group and a control-LV group) were compared by GCOSvL.4 software. These differential expressed genes were analyzed by bioinformatics methods finally, and validated by quantitative real time polymerase chain reaction (qRT-PCR) analysis.Results According to the screening criteria of fold change ≥2 and P<0.05, 1 006 genes were differentially expressed after DDX46 knockdown, including 362 up-regulated and 644 down-regulated genes. Bioinformatics analysis and gene co-expression network building identified that these differentially expressed genes were mainly involved in cell cycle, proliferation, apoptosis, adhesion, energy metabolism, immune response, etc. Phosphatidylinositol 3-kinase (PI3K) was the key molecule in the network. The results of RT-qPCR were completely consistent with the results of gene microarra.Conclusion Bioinformatics can effectively exploit the microarray data of esophageal squamous cell carcinoma after DDX46 knockdown, which provides a valuable clue for further exploration of DDX46 tumorigenesis mechanism and helps to find potential drug therapy.

Citation： LI Bin, LI Zheng, YIN Ci, LIN Junping, YANG Jianbao, ZHU Duojie, FENG Haiming, JING Tao. Screening for differential genes of the esophageal squamous cell carcinoma after DDX46 knockdown and bioinformatics analysis of their interaction. Chinese Journal of Clinical Thoracic and Cardiovascular Surgery, 2020, 27(1): 61-67. doi: 10.7507/1007-4848.201907051 Copy

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1. 郑荣寿, 孙可欣, 张思维, 等. 2015 年中国恶性肿瘤流行情况分析. 中华肿瘤杂志, 2019, 41(1): 19-28.
2. Allemani C, Matsuda T, Di Carlo V, et al. Global surveillance of trends in cancer survival 2000-14 (CONCORD-3): analysis of individual records for 37?513?025 patients diagnosed with one of 18 cancers from 322 population-based registries in 71 countries. Lancet, 2018, 391(10125): 1023-1075.
3. Smyth EC, Lagergren J, Fitzgerald RC, et al. Oesophageal cancer. Nat Rev Dis Primers, 2017, 3: 17048.
4. Song Y, Li L, Ou Y, et al. Identification of genomic alterations in oesophageal squamous cell cancer. Nature, 2014, 509(7498): 91-95.
5. 李斌, 朱多杰, 何雯婷, 等. 靶向沉默 DDX46 基因对食管鳞癌 TE-1 细胞增殖及凋亡的影响. 中国胸心血管外科临床杂志, 2017, 24(6): 463-468.
6. Zielske SP, Stevenson M. Importin 7 may be dispensable for human immunodeficiency virus type 1 and simian immunodeficiency virus infection of primary macrophages. J Virol, 2005, 79(17): 11541-11546.
7. 李斌. DDX46基因在食管鳞癌中的表达及其与食管鳞癌相关性研究. 兰州大学, 2016.
8. Calvano SE, Xiao W, Richards DR, et al. A network-based analysis of systemic inflammation in humans. Nature, 2005, 437(7061): 1032-1037.
9. Lee AS, Kranzusch PJ, Doudna JA, et al. eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation. Nature, 2016, 536(7614): 96-99.
10. Linder P, Fuller-Pace FV. Looking back on the birth of DEAD-box RNA helicases. Biochim Biophys Acta, 2013, 1829(8): 750-755.
11. Hooper C, Hilliker A. Packing them up and dusting them off: RNA helicases and mRNA storage. Biochim Biophys Acta, 2013, 1829(8): 824-834.
12. Kosowski TR, Keys HR, Quan TK, et al. DExD/H-box Prp5 protein is in the spliceosome during most of the splicing cycle. RNA, 2009, 15(7): 1345-1362.
13. Liang WW, Cheng SC. A novel mechanism for Prp5 function in prespliceosome formation and proofreading the branch site sequence. Genes Dev, 2015, 29(1): 81-93.
14. Abdelhaleem M, Maltais L, Wain H. The human DDX and DHX gene families of putative RNA helicases. Genomics, 2003, 81(6): 618-622.
15. De Franceschi N, Hamidi H, Alanko J, et al. Integrin traffic-the update. J Cell Sci, 2015, 128(5): 839-852.
16. Moreno-Layseca P, Icha J, Hamidi H, et al. Integrin trafficking in cells and tissues. Nat Cell Biol, 2019, 21(2): 122-132.
17. Wu C, Keightley SY, Leung-Hagesteijn C, et al. Integrin-linked protein kinase regulates fibronectin matrix assembly, E-cadherin expression, and tumorigenicity. J Biol Chem, 1998, 273(1): 528-536.
18. Paul NR, Jacquemet G, Caswell PT. Endocytic trafficking of integrins in cell migration. Curr Biol, 2015, 25(22): R1092-R1105.
19. Hannigan G, Troussard AA, Dedhar S. Integrin-linked kinase: a cancer therapeutic target unique among its ILK. Nat Rev Cancer, 2005, 5(1): 51-63.
20. Janku F, Yap TA, Meric-Bernstam F. Targeting the PI3K pathway in cancer: are we making headway? Nat Rev Clin Oncol, 2018, 15(5): 273-291.
21. Testa JR, Bellacosa A. AKT plays a central role in tumorigenesis. Proc Natl Acad Sci USA, 2001, 98(20): 10983-10985.
22. Gilmore TD. Introduction to NF-κB: players, pathways, perspectives. Oncogene, 2006, 25(51): 6680-6684.
23. Ma CD, Zuo WS, Wang XW, et al. Lapatinib inhibits the activation of NF-κB through reducing phosphorylation of IκB-α in breast cancer cells. Oncol Rep, 2013, 29(2): 812-818.
24. Rabanal-Ruiz Y, Otten EG, Korolchuk VI. mTORC1 as the main gateway to autophagy. Essays Biochem, 2017, 61(6): 565-584.
25. Khan KH, Yap TA, Yan L, et al. Targeting the PI3K-AKT-mTOR signaling network in cancer. Chin J Cancer, 2013, 32(5): 253-265.
26. Lim HJ, Crowe P, Yang JL. Current clinical regulation of PI3K/PTEN/Akt/mTOR signalling in treatment of human cancer. J Cancer Res Clin Oncol, 2015, 141(4): 671-689.
27. Harding MA, Theodorescu D. RhoGDI2: a new metastasis suppressor gene: discovery and clinical translation. Urol Oncol, 2007, 25(5): 401-406.
28. 牛慧彦, 李慧, 王佳贺, 等. RhoGDI2 与 PI3K/Akt/mTOR 信号通路在肺癌细胞中的相关性研究. 中国组织化学与细胞化学杂志, 2011, 20(2): 107-111.

Chinese Journal of Clinical Thoracic and Cardiovascular Surgery

Screening for differential genes of the esophageal squamous cell carcinoma after DDX46 knockdown and bioinformatics analysis of their interaction

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