Identification of Hub Genes in Tongue Squamous Cell Carcinoma Based on Weighted Gene Co-expression Network Analysis

doi:10.13701/j.cnki.kqyxyj.2020.05.006

Abstract

Abstract: Objective: To excavate hub genes closely related to tongue squamous cell carcinoma (TSCC). Methods: GSE34105 dataset was downloaded from Gene Expression Omnibus Database (GEO). Key modules were screened by weighted gene co-expression network analysis (WGCNA). Hub genes were screened by topological parameters of nodes in module networks, and survival analysis was used for external verification of hub genes. GO and KEGG enriched analysis and GSEA analysis were performed to obtain the biological processes involved in hub genes. Results: The turquoise module (Cor=0.88, P<0.05) which was most closely related to TSCC was obtained. Two hub genes, CAP1 and TMBIM6, were obtained based on Cytoscape, which were adverse prognostic factors. Their high expression was significantly associated with shortening the survival time of patients (P<0.05). GSEA analysis of their high expression group was mainly involved in cysteine and methionine metabolism, Vibrio cholerae infection, oxidative phosphorylation, DNA replication, basal excision repair, cell meiosis, protein production, fructose and mannose metabolism, Helicobacter pylori Epithelial signal transduction in infection. Conclusion: This study screened two hub genes by constructing a gene co-expression network, which may become a potential biomarker of TSCC gene, affecting the occurrence and prognosis of TSCC.

Key words: WGCNA, tongue squamous cell carcinoma, pathogenesis, hub genes

LI Tianke, ZHANG Ying, ZHANG Suxin, CHEN Zhong, BAO Yang, ZHANG Guanhua. Identification of Hub Genes in Tongue Squamous Cell Carcinoma Based on Weighted Gene Co-expression Network Analysis[J]. Journal of Oral Science Research, 2020, 36(5): 423-427.

References

[1] 孙国文,张笑佛,李田,等.Hedgehog信号通路效应蛋白在舌癌组织中的表达及意义[J],口腔医学研究,2015,31(4): 393-396.
[2] 代梦莹, 张洋, 张照楠, 等. 长链非编码RNAHOTAIR对舌鳞状细胞癌增殖及迁移侵袭能力的影响[J], 口腔医学研究,2018, 34(6): 627-631.
[3] Xie N, Wang C, Liu X, et al. Tumor budding correlates with occult cervical lymph node metastasis and poor prognosis in clinical early-stage tongue squamous cell carcinoma[J]. J Oral Pathol Med, 2015, 44(4): 266-272.
[4] Yang Y, Zhou J, Wu H, et al. Diagnostic value of sentinel lymph node biopsy for cT1/T2N0 tongue squamous cell carcinoma: a meta-analysis[J]. Eur Arch Otorhinolaryngol, 2017, 274(11): 3843-3852.
[5] Näsman A, Bersani C, Lindquist D, et al. Human papillomavirus and potentially relevant biomarkers in tonsillar and base of tongue squamous cell carcinoma[J].Anticancer Res, 2017, 37(10): 5319-5328.
[6] Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis[J]. BMC Bioinformatics, 2008, 9: 559.
[7] Botía JA, Vandrovcova J, Forabosco P, et al. An additional k-means clustering step improves the biological features of WGCNA gene co-expression networks[J]. BMC Syst Biol, 2017, 11(1):47.
[8] Yamamoto T, Kobayashiooka Y, Zhou GL, et al. Identification and characterization of Csh3 as an SH3 protein that interacts with fission yeast Cap1[J]. FEMS Yeast Res, 2015, 15(8):fov097.
[9] Kim HK, Yadav RK, Bhattarai KR, et al. Transmembrane BAX Inhibitor Motif-6 (TMBIM6) protects against cisplatin-induced testicular toxicity[J]. Hum Reprod, 2018, 33(3):378-389.
[10] Zhang H, Zhou G. CAP1 (cyclase-associated protein 1) exerts distinct functions in the proliferation and metastatic potential of breast cancer cells mediated by ERK[J]. Sci Rep, 2016, 6:25933.
[11] Zhang M, Yan L, Wang GJ, et al. Resistin effects on pancreatic cancer progression and chemoresistance are mediated through its receptors CAP1 and TLR4[J]. J Cell Physiol, 2019, 234(6):9457-9466.
[12] Xie S, Liu Y, Li X, et al. Phosphorylation of the cytoskeletal protein CAP1 regulates non-small cell lung cancer survival and proliferation by GSK3β[J]. J Cancer, 2018, 9(16):2825-2833.
[13] Fjeldbo CS, Aarnes EK, Malinen E, et al. Identification and validation of reference genes for RT-qPCR studies of hypoxia in squamous cervical cancer patients[J]. PLoS One, 2016, 11(5): e0156259.
[14] Qi H, Chen G. P2.02-050 weighted genes co-expression network analysis of lung cancers concerning patients overall survival and cancer stage[J]. J Thorac Oncol, 2017, 12(11): S2117-S2118.

[1]	ZHOU Qun, QIU Jiaxuan. Plumbagin Induces Tongue Squamous Cell Carcinoma Cells Apoptosis via ROS-mediated JNK Signaling Pathway [J]. Journal of Oral Science Research, 2020, 36(10): 921-924.
[2]	DENG Xuan, YANG Fang, TANG Xiqing. Effect of Down-regulation of Mucin-1 on Growth of Xenografts of Human Tongue Squamous Cell Carcinoma Tca-8113 in Nude Mice [J]. Journal of Oral Science Research, 2019, 35(8): 776-780.
[3]	WANG Rui, LI Li-heng, XU Ai-wen, AN Feng. Lentivirus Mediated Down-regulation of Med19 Expression Enhances Sensitivity of Tongue Squamous Cell Carcinoma to Cisplatin [J]. Journal of Oral Science Research, 2019, 35(6): 559-562.
[4]	CHENG Hui-na, ZHOU Qing. Research Progress of Idiopathic Condylar Resorption. [J]. Journal of Oral Science Research, 2019, 35(5): 427-429.
[5]	ZHANG Xin-yu, WU Shuang-yan, WU Hong, XU Zhu-qing, WANG Yun-ying, XU Xiao-na, LI Xin, ZHENG Jian-jin. Effect of Human Umbilical Cord Mesenchymal Stem Cells on Invasion and Migration of Cal-27 Cells from Tongue Squamous Cell Carcinoma. [J]. Journal of Oral Science Research, 2019, 35(5): 443-447.
[6]	GUO Jianan, HE Wei. Research Progress on Mechanism of Cleft Palate Caused by MicroRNA [J]. Journal of Oral Science Research, 2019, 35(12): 1111-1114.
[7]	CHEN Chang, PENG Yong-jian, CHEN Yan. Effects of eIF4E-siRNA on Adhesion and Movement Ability of Tongue Squamous Cell Carcinoma Cells [J]. Journal of Oral Science Research, 2019, 35(1): 51-55.
[8]	WU Yue-lin, ZHAO Lei, WU Ya-fei.. Research Progress of Papillon-Lefèvre Syndrome. [J]. Journal of Oral Science Research, 2018, 34(9): 928-931.
[9]	SHAO Ming-jing,WANG He, DONG Li, ZHANG Hong-chao, LIU Xu, MENG Pei-song.. Therapeutic Effect of Aloe-emodin Nanometer Liposome-mediated Photodynamic Therapy on Human Tongue Squamous Cell Carcinoma Tca-8113 Cells. [J]. Journal of Oral Science Research, 2018, 34(9): 948-951.
[10]	DAI Meng-ying, ZHANG Yang, ZHANG Zhao-nan, SU Wei-peng, ZHANG Song-an, LIU Pan, ZHAO Hua-rong. Effects of Long Non-coding RNA HOTAIR on Proliferation, Migration, and Invasion of Tongue Squamous Cell Carcinoma [J]. Journal of Oral Science Research, 2018, 34(6): 627-631.
[11]	FENG Tie-jun, WANG Yu-dong, PAN Xuan, CHI Yu-feng. Effect of Transfection of DEK Gene Small Interference RNA on Proliferation and Apoptosis of Tongue Squamous Cell Carcinoma. [J]. Journal of Oral Science Research, 2018, 34(4): 414-418.
[12]	WANG Qian, HOU Da-wei. Research Progress in Pathogenesis of Oral Squamous Cell Carcinoma [J]. Journal of Oral Science Research, 2018, 34(11): 1164-1167.
[13]	HUANG Yu-si, ZHANG Lei, LIU Le-tian, MA Yao, LIU Xin. Effects of DVDMS-PDT on Proliferation and Migration of Human Tongue Squamous Carcinoma Cell Line HSC-4 [J]. Journal of Oral Science Research, 2018, 34(11): 1208-1211.
[14]	ZHOU Yan-meng, LANG Chun-mei, SHEN Hang, HU Fang-yuan, HU Ming, DENG Wen-bo.. Effects of Two-dimensional and Three-dimensional Culture on Biological Characteristics of Human Tongue Squamous Cell Carcinoma TCA8113 Cell Lines. [J]. Journal of Oral Science Research, 2018, 34(10): 1122-1126.
[15]	LIU Yu-lan, MENG Lin, TANG Qi, BU Wen-huan, HUANG Guo-shuai, DAI Yi-bin, LIU Qi-lin, SUN Hong-chen. Ascorbic Acid Carbon Dots Kill Tongue Squamous Cell Carcinoma Cell by Promoting Autophagy [J]. Journal of Oral Science Research, 2018, 34(1): 35-38.