Bioinformatics Analysis of lncRNA-mRNA Interaction Network in Different Clinical Stages of Esophageal Squamous Cell Carcinoma

Document Type : Research Articles

Authors

• Seyed Navid Goftari ¹
• Ahmad Reza Bahrami ^{1, 2}
• Maryam M. Matin ^{1, 3}

¹ Department of Biology, Faculty of science, Ferdowsi University of Mashhad, Mashhad, Iran

² Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran

³ Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran

https://doi.org/10.22067/jcmr.2023.84078.1079

Abstract

Esophageal cancer is one of the most aggressive gastrointestinal malignancies, and esophageal squamous cell carcinoma (ESCC) is the most prevalent esophagus neoplastic disease with high mortality rates in some Asian countries. Nonetheless, the etiology of ESCC continues to be vaguely comprehended, and the role of long noncoding RNAs in different clinical stages of this type of malignancy remains to be clarified. Here, we aimed to investigate the crucial genes corresponding to various clinical stages of ESCC, determine the hub lncRNAs in these stages, and predict patients’ overall survival time. In the current study, the cancer genome atlas (TCGA) RNA-seq public data was analyzed in order to discover novel biomarkers or therapeutic targets implicated in the progression of ESCC. Stage-related genes were analyzed, the protein-protein interaction network for any stage was constructed and the top 5 genes with the most Maximal Clique Centrality score in each network were selected as the hub mRNAs. LncRNAs interacting with each stage hub mRNA were also determined as stage-related hub lncRNAs. Gene set enrichment analysis on stage-associated modules was also carried out. Finally, Cox regression analysis was performed to assess the prognostic significance of identified hub lncRNAs in the survival of patients with ESCC. Finally, hub mRNAs and hub lncRNAs associated with ESCC progression were identified, which may have implications as biomarkers and targets for therapeutic interventions. Six lncRNAs, including AC013391.2, AC104088.1, AC026341.3, AL139023.1, AL583808.1, and LINC01707 were also identified to be significantly correlated with ESCC patients’ overall survival time, which could be potential predictors for the survival rate of patients, however, more research is required in order to confirm the results experimentally.

Keywords

• ESCC clinical stages
• TCGA
• WGCNA
• hub mRNA
• hub lncRNA
• prognostic factor

References

Aravalli, R. N., Cressman, E. N. & Steer, C. J. (2013). Cellular and molecular mechanisms of hepatocellular carcinoma: an update. Archives of Toxicology 87: 227-247.

Blighe, K., Rana, S. & Lewis, M. (2019). EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling. R package version 1.2. 0. R package version 1.16.

Bray, F., Ferlay, J., Soerjomataram, I., Siegel, R. L., Torre, L. A. & Jemal, A. (2018). Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: A Cancer Journal for Clinicians 68: 394-424.

Chen, J., Song, Y., Li, M., Zhang, Y., Lin, T., Sun, J., Wang, D., Liu, Y., Guo, J. & Yu, W. (2021). Comprehensive analysis of ceRNA networks reveals prognostic lncRNAs related to immune infiltration in colorectal cancer. BMC Cancer 21: 1-17.

Chen, N., Zhang, G., Fu, J. & Wu, Q. (2020). Identification of key modules and hub genes involved in esophageal squamous cell carcinoma tumorigenesis using WCGNA. Cancer Control 27: 1073274820978817.

Cherubini, C., Filippi, S. & Loppini, A. (2018). Systems Biology Modeling of Nonlinear Cancer Dynamics. Systems Biology: 203-213.

Chin, C. H., Chen, S. H., Wu, H.H., Ho, C.W., Ko, M.T. & Lin, C.Y. (2014). cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Systems Biology 8: 1-7.

Cui, H., Zhang, Y., Zhang, Q., Chen, W., Zhao, H. & Liang, J. (2017). A comprehensive genome‐wide analysis of long noncoding RNA expression profile in hepatocellular carcinoma. Cancer Medicine 6: 2932-2941.

DiSiena, M., Perelman, A., Birk, J. & Rezaizadeh, H. (2021). Esophageal cancer: An updated review. Southern Medical Journal 114: 161-168.

Feng, J.L., Zheng, W.J., Xu, L., Zhou, Q.Y. & Chen, J. (2023). Identification of potential LncRNAs as papillary thyroid carcinoma biomarkers based on integrated bioinformatics analysis using TCGA and RNA sequencing data. Scientific Reports 13: 4350.

Feng, Q., Zhang, H., Yao, D., Chen, W.D. & Wang, Y.D. (2019). Emerging role of non-coding RNAs in esophageal squamous cell carcinoma. International Journal of Molecular Sciences 21: 258.

Fukunaga, T. & Hamada, M. (2017). RIblast: an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach. Bioinformatics 33: 2666-2674.

Gao, G.D., Liu, X.Y., Lin, Y., Liu, H.F. & Zhang, G.J. (2018). LncRNA CASC9 promotes tumorigenesis by affecting EMT and predicts poor prognosis in esophageal squamous cell cancer. European Review for Medical & Pharmacological Sciences 22:422-429.

Geng, W., Lv, Z., Fan, J., Xu, J., Mao, K., Yin, Z., Qing, W. & Jin, Y. (2021). Identification of the prognostic significance of somatic mutation-derived LncRNA signatures of genomic instability in lung adenocarcinoma. Frontiers in Cell and Developmental Biology 9: 657667.

Hu, D. & Messadi, D. V. (2023). Immune-Related Long Non-Coding RNA Signatures for Tongue Squamous Cell Carcinoma. Current Oncology 30: 4817-4832.

Huang, D. W., Sherman, B. T., Tan, Q., Collins, J. R., Alvord, W. G., Roayaei, J., Stephens, R., Baseler, M. W., Lane, H. C. & Lempicki, R. A. (2007). The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biology 8: 1-16.

Jia, J., Li, H., Chu, J., Sheng, J., Wang, C., Jia, Z., Meng, W., Yin, H., Wan, J. & He, F. (2021). LncRNA FAM83A-AS1 promotes ESCC progression by regulating miR-214/CDC25B axis. Journal of Cancer 12:1200-1211.

Kadian, L., Arora, M., Prasad, C., Pramanik, R. & Chauhan, S. (2022). Signaling pathways and their potential therapeutic utility in esophageal squamous cell carcinoma. Clinical and Translational Oncology 24: 1014-1032.

Lánczky, A. & Győrffy, B. (2021). Web-based survival analysis tool tailored for medical research (KMplot): development and implementation. Journal of Medical Internet Research 23: 27633.

Langfelder, P. & Horvath, S. (2008). WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9: 1-13.

Li, G., Luo, J., Liang, C., Xiao, Q., Ding, P. & Zhang, Y. (2019). Prediction of LncRNA-disease associations based on network consistency projection. Ieee Access 7:58849-58856.

Li, X., Jin, F. & Li, Y. (2021). A novel autophagy‐related lncRNA prognostic risk model for breast cancer. Journal of Cellular and Molecular Medicine 25: 4-14.

Li, X., Xiao, X., Chang, R. & Zhang, C. (2020). Comprehensive bioinformatics analysis identifies lncRNA HCG22 as a migration inhibitor in esophageal squamous cell carcinoma. Journal of Cellular Biochemistry 121: 468-481.

Liau, X. L., Salvamani, S., Gunasekaran, B., Chellappan, D. K., Rhodes, A., Ulaganathan, V. & Tiong, Y. L. (2023). CCAT 1-A Pivotal Oncogenic Long Non-Coding RNA in Colorectal Cancer. British Journal of Biomedical Science 80: 11103.

Lin, C., Wang, Y., Zhang, S., Yu, L., Guo, C. & Xu, H. (2017). Transcriptional and posttranscriptional regulation of HOXA13 by lncRNA HOTTIP facilitates tumorigenesis and metastasis in esophageal squamous carcinoma cells. Oncogene 36:5392-5406.

Liu, J.Q., Deng, M., Xue, N.N., Li, T.X., Guo, Y.X., Gao, L., Zhao, D. & Fan, R.-T. (2020). lncRNA KLF3-AS1 suppresses cell migration and invasion in ESCC by impairing miR-185-5p-targeted KLF3 inhibition. Molecular Therapy-Nucleic Acids 20: 231-241.

Love, M. I., Huber, W. & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15:1-21.

Luo, X.J., He, M.M., Liu, J., Zheng, J.B., Wu, Q.N., Chen, Y.X., Meng, Q., Luo, K.J., Chen, D.L. & Xu, R.H. (2022). LncRNA TMPO-AS1 promotes esophageal squamous cell carcinoma progression by forming biomolecular condensates with FUS and p300 to regulate TMPO transcription. Experimental & Molecular Medicine 54: 834-847.

Mambetsariev, I., Fricke, J., Gruber, S. B., Tan, T., Babikian, R., Kim, P., Vishnubhotla, P., Chen, J., Kulkarni, P. & Salgia, R. (2023). Clinical Network Systems Biology: Traversing the Cancer Multiverse. Journal of Clinical Medicine 12: 4535.

McCabe, E. M. & Rasmussen, T. P. (2021).lncRNA involvement in cancer stem cell function and epithelial-mesenchymal transitions. Seminars in Cancer Biology, Vol. 75, 38-48: Elsevier.

Pinu, F. R., Beale, D. J., Paten, A. M., Kouremenos, K., Swarup, S., Schirra, H. J. & Wishart, D. (2019). Systems biology and multi-omics integration: viewpoints from the metabolomics research community. Metabolites 9:76.

Ren, L., Fang, X., Shrestha, S. M., Ji, Q., Ye, H., Liang, Y., Liu, Y., Feng, Y., Dong, J. & Shi, R. (2022). LncRNA SNHG16 promotes development of oesophageal squamous cell carcinoma by interacting with EIF4A3 and modulating RhoU mRNA stability. Cellular & Molecular Biology Letters 27: 89.

Ren, P., Zhang, H., Chang, L., Hong, X.D. & Xing, L. (2020). LncRNA NR2F1-AS1 promotes proliferation and metastasis of ESCC cells via regulating EMT. European Review for Medical & Pharmacological Sciences 24:3686-3693.

Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B. & Ideker, T. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 13: 2498-2504.

Sheikh, M., Roshandel, G., McCormack, V. & Malekzadeh, R. (2023). Current status and future prospects for esophageal cancer. Cancers 15:765.

Shi, X., Sun, M., Liu, H., Yao, Y. & Song, Y. (2013). Long non-coding RNAs: a new frontier in the study of human diseases. Cancer Letters 339:159-166.

Shin, J. W. & Chung, Y.-H. (2013). Molecular targeted therapy for hepatocellular carcinoma: current and future. World Journal of Gastroenterology: WJG 19: 6144.

Siegel, R. L., Miller, K. D., Wagle, N. S. & Jemal, A. (2023). Cancer statistics, 2023. Ca Cancer J Clin 73:17-48.

Song, J., Zhang, S., Sun, Y., Gu, J., Ye, Z., Sun, X. & Tang, Q. (2021). A radioresponse-related lncRNA biomarker signature for risk classification and prognosis prediction in non-small-cell lung cancer. Journal of Oncology 2021:4338838.

Sun, M. & Kraus, W. L. (2015). From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease. Endocrine Reviews 36:25-64.

Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A. & Tsafou, K. P. (2015). STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic Acids Research 43: 447-452.

Tan, Y. T., Lin, J. F., Li, T., Li, J. J., Xu, R. H. & Ju, H. Q. (2021). LncRNA‐mediated posttranslational modifications and reprogramming of energy metabolism in cancer. Cancer Communications 41: 109-120.

Tang, J., Xu, H., Liu, Q., Zheng, J., Pan, C., Li, Z., Wen, W., Wang, J., Zhu, Q. & Wang, Z. (2021). LncRNA LOC146880 promotes esophageal squamous cell carcinoma progression via miR-328-5p/FSCN1/MAPK axis. Aging (Albany NY) 13:14198.

Wang, B.r., Chu, D.x., Cheng, M.y., Jin, Y., Luo, H.g. & Li, N. (2022). Progress of HOTAIR-microRNA in hepatocellular carcinoma. Hereditary Cancer in Clinical Practice 20: 4.

Wang, C., Song, C., Liu, Q., Zhang, R., Fu, R., Wang, H., Yin, D., Song, W., Zhang, H. & Dou, K. (2021a). Gene expression analysis suggests immunological changes of peripheral blood monocytes in the progression of patients with coronary artery disease. Frontiers in Genetics 12: 641117.

Wang, P., Chen, Y., Zheng, Y., Fu, Y. & Ding, Z. (2021b). Identification of epithelial-mesenchymal transition-(EMT-) related LncRNA for prognostic prediction and risk stratification in esophageal squamous cell carcinoma. Disease Markers 2021: 1-18.

Wickham, H., Chang, W. & Wickham, M. H. (2016). Package ‘ggplot2’. Create Elegant Data Visualisations Using the Grammar of Graphics. Version 2:1-189.

Wu, Q., Zhang, H., Yang, D., Min, Q., Wang, Y., Zhang, W. & Zhan, Q. (2022). The m6A-induced lncRNA CASC8 promotes proliferation and chemoresistance via upregulation of hnRNPL in esophageal squamous cell carcinoma. International Journal of Biological Sciences 18: 4824-4836.

Yang, M., Lu, H., Liu, J., Wu, S., Kim, P. & Zhou, X. (2022). lncRNAfunc: a knowledgebase of lncRNA function in human cancer. Nucleic Acids Research 50: 1295-1306.

Yu, J., Wu, X., Huang, K., Zhu, M., Zhang, X., Zhang, Y., Chen, S., Xu, X. & Zhang, Q. (2019). Bioinformatics identification of lncRNA biomarkers associated with the progression of esophageal squamous cell carcinoma. Molecular Medicine Reports 19: 5309-5320.

Yu, S. J. (2016). A concise review of updated guidelines regarding the management of hepatocellular carcinoma around the world: 2010-2016. Clinical and Molecular Hepatology 22: 7.

Yuan, D., Guo, T., Zhu, D., Ge, H., Zhao, Y., Huang, A., Wang, X., Cao, X., He, C. & Qian, H. (2022). Exosomal lncRNA ATB derived from ovarian cancer cells promotes angiogenesis via regulating miR-204-3p/TGFβR2 axis. Cancer Management and Research: 327-337.

Zhang, H., Pan, E., Zhang, Y., Zhao, C., Liu, Q., Pu, Y. & Yin, L. (2022a). LncRNA RPL34-AS1 suppresses the proliferation, migration and invasion of esophageal squamous cell carcinoma via targeting miR-575/ACAA2 axis. BMC Cancer 22: 1017.

Zhang, J., Ling, X., Fang, C. & Ma, J. (2022b). Identification and validation of an eight-lncRNA signature that predicts prognosis in patients with esophageal squamous cell carcinoma. Cellular & Molecular Biology Letters 27: 1-18.

Zhang, L., Li, P., Liu, E., Xing, C., Zhu, D., Zhang, J., Wang, W. & Jiang, G. (2020). Prognostic value of a five-lncRNA signature in esophageal squamous cell carcinoma. Cancer Cell International 20: 1-10.

Zhao, F., Dong, Z., Li, Y., Liu, S., Guo, P., Zhang, D. & Li, S. (2022). Comprehensive analysis of molecular clusters and prognostic signature based on m7G-related LncRNAs in esophageal squamous cell carcinoma. Frontiers in Oncology 12:893186.

Zheng, Z.J., Li, Y.S., Zhu, J.D., Zou, H.Y., Fang, W.K., Cui, Y.Y. & Xie, J.J. (2022). Construction of the Six-lncRNA prognosis signature as a novel biomarker in esophageal squamous cell carcinoma. Frontiers in Genetics 13:839589.