Excavating novel diagnostic and prognostic long non-coding RNAs (lncRNAs) for head and neck squamous cell carcinoma: an integrated bioinformatics analysis of competing endogenous RNAs (ceRNAs) and gene co-expression networks

References

• Mehanna H, Paleri V, West CM, et al. Head and neck cancer–Part 1: epidemiology, presentation, and prevention. BMJ. 2010;341:c4684.
   PubMed Web of Science ®Google Scholar
• Mandal R, Şenbabaoğlu Y, Desrichard A, et al. The head and neck cancer immune landscape and its immunotherapeutic implications. JCI Insight. 2016;1(17). DOI:10.1172/jci.insight.89829
   PubMed Web of Science ®Google Scholar
• Lee NY, Ferris RL, Psyrri A, et al. Avelumab plus standard-of-care chemoradiotherapy versus chemoradiotherapy alone in patients with locally advanced squamous cell carcinoma of the head and neck: a randomised, double-blind, placebo-controlled, multicentre, phase 3 trial. Lancet Oncol. 2021;22(4):450–462.
   PubMed Web of Science ®Google Scholar
• Braakhuis BJ, Brakenhoff RH, Leemans CR. Treatment choice for locally advanced head and neck cancers on the basis of risk factors: biological risk factors. Ann Oncol. 2012;23(Suppl 10):x173–177.
   PubMedGoogle Scholar
• Chow LQM. Head and neck cancer. N Engl J Med. 2020;382:60–72.
   PubMed Web of Science ®Google Scholar
• Ang KK. Multidisciplinary management of locally advanced SCCHN: optimizing treatment outcomes. The Oncologist. 2008;13(8):899–910.
   PubMed Web of Science ®Google Scholar
• Huarte M. The emerging role of lncRNAs in cancer. Nat Med. 2015;21(11):1253–1261.
   PubMed Web of Science ®Google Scholar
• Matsui M, Corey DR. Non-coding RNAs as drug targets. Nat Rev Drug Discov. 2016;16(3):167–179.
   PubMed Web of Science ®Google Scholar
• Hu Q, Ye Y, Chan L-C, et al. Oncogenic lncRNA downregulates cancer cell antigen presentation and intrinsic tumor suppression. Nature Immunology. 2019;20(7):835–851.
   PubMed Web of Science ®Google Scholar
• Xu Y, Wu J, Peng X, et al. LncRNA LINC00341 mediates PM(2.5)-induced cell cycle arrest in human bronchial epithelial cells. Toxicol Lett. 2017;276:1–10.
   PubMed Web of Science ®Google Scholar
• Li T, Chen Y, Zhang J, et al. TUG1 promotes cells proliferation and inhibits cells apoptosis through regulating AURKA in epithelial ovarian cancer cells. Medicine (Baltimore). 2018;97(e12131). DOI:10.1097/md.0000000000012131
   Google Scholar
• Xu H, Jiang Y, Xu X, et al. Inducible degradation of lncRNA Sros1 promotes IFN-γ-mediated activation of innate immune responses by stabilizing Stat1 mRNA. Nature Immunology. 2019;20(12):1621–1630.
   PubMed Web of Science ®Google Scholar
• Luo H, et al. HOTTIP lncRNA promotes hematopoietic stem cell self-renewal leading to AML-like disease in mice. undefined, undefined (2019).
   Google Scholar
• Salmena L, Poliseno L, Tay Y, et al. A ceRNA hypothesis: the Rosetta stone of a hidden RNA language? Cell. 2011;146(3):353–358.
   PubMed Web of Science ®Google Scholar
• Qi X, Zhang D-H, Wu N, et al. ceRNA in cancer: possible functions and clinical implications. J Med Genet. 2015;52(10):710–718.
   PubMed Web of Science ®Google Scholar
• Ninomiya K, Adachi S, Natsume T, et al. LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation. EMBO J. 2019;39(3):e102729.
   PubMed Web of Science ®Google Scholar
• Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9(1):559.
   PubMed Web of Science ®Google Scholar
• van Dam S, Võsa U, van der Graaf A, et al. Gene co-expression analysis for functional classification and gene-disease predictions. Brief Bioinform. 2018;19(4):575–592.
   PubMed Web of Science ®Google Scholar
• Blum A, Wang P, Zenklusen JC. SnapShot: TCGA-analyzed tumors. Cell. 2018;173(2):530.
   PubMed Web of Science ®Google Scholar
• Tomczak K, Czerwińska P, Wiznerowicz M. The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge. Contemp Oncol (Pozn). 2015;19(1A):A68–77.
   PubMedGoogle Scholar
• Li R, Qu H, Wang S, et al. GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC. Bioinformatics. 2018;34(14):2515–2517.
   PubMed Web of Science ®Google Scholar
• Law CW, Alhamdoosh M, Su S, et al. RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR. F1000Res. 2016;5:1408.
   PubMedGoogle Scholar
• Tang Z, Li C, Kang B, et al. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 2017;45(W1):W98–w102.
   PubMed Web of Science ®Google Scholar
• Ardlie KG, Deluca DS, Segrè AV, Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science. 2015;348(6235):648–660.
   PubMed Web of Science ®Google Scholar
• Mi H, Muruganujan A, Ebert D, et al. PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic Acids Res. 2019;47(D1):D419–d426.
   PubMed Web of Science ®Google Scholar
• Li JH, Liu S, Zhou H, et al. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014;42(D1):D92–97.
   PubMed Web of Science ®Google Scholar
• Chen Y, Wang X. miRDB: an online database for prediction of functional microRNA targets. Nucleic Acids Research. 2020;48(D1):D127–D131.
   PubMed Web of Science ®Google Scholar
• Shannon P, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504.
   PubMed Web of Science ®Google Scholar
• Chin CH, Chen S-H, Wu -H-H, et al. cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol. 2014;8(Suppl 4):S11.
   PubMed Web of Science ®Google Scholar
• Yao Y, Zhang T, Qi L, et al. Integrated analysis of co-expression and ceRNA network identifies five lncRNAs as prognostic markers for breast cancer. J Cell Mol Med. 2019;23(12):8410–8419.
   PubMed Web of Science ®Google Scholar
• Langfelder P, Zhang B, Horvath S. Defining clusters from a hierarchical cluster tree: the dynamic tree cut package for R. Bioinformatics. 2008;24(5):719–720.
   PubMed Web of Science ®Google Scholar
• Zhang T, Jiang M, Chen L, et al. Prediction of gene phenotypes based on GO and KEGG pathway enrichment scores. BioMed Research International. 2013;2013:870795.
   PubMed Web of Science ®Google Scholar
• Yu G, Wang LG, Han Y, et al. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287.
   PubMed Web of Science ®Google Scholar
• Luo W, Brouwer C. Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics. 2013;29(14):1830–1831.
   PubMed Web of Science ®Google Scholar
• Rich JT, Neely JG, Paniello RC, et al. A practical guide to understanding Kaplan-Meier curves. Otolaryngol Head Neck Surg. 2010;143(3):331–336.
   PubMed Web of Science ®Google Scholar
• Schmitt AM, Chang HY. Long noncoding RNAs in cancer pathways. Cancer Cell. 2016;29(4):452–463.
   PubMed Web of Science ®Google Scholar
• Jiang MC, Ni JJ, Cui WY, et al. Emerging roles of lncRNA in cancer and therapeutic opportunities. Am J Cancer Res. 2019;9(7):1354–1366.
   PubMed Web of Science ®Google Scholar
• Brisotto G, Guerrieri Roberto, Colizzi Francesca, et al. Long noncoding RNAs as innovative urinary diagnostic biomarkers. Methods Mol Biol. 2021;2292:73–94.
   PubMedGoogle Scholar
• Shi T, Gao G, Cao Y. Long noncoding RNAs as novel biomarkers have a promising future in cancer diagnostics. Dis Markers. 2016;2016:9085195.
   PubMed Web of Science ®Google Scholar
• Walker C, Mojares E, Del Río Hernández A. Role of extracellular matrix in development and cancer progression. Int J Mol Sci. 2018;19(10):3028.
   Web of Science ®Google Scholar
• Winkler J, Abisoye-Ogunniyan A, Metcalf KJ, et al. Concepts of extracellular matrix remodelling in tumour progression and metastasis. Nat Commun. 2020;11:5120.
   PubMed Web of Science ®Google Scholar
• Rabinovitch RC, Samborska B, Faubert B, et al. AMPK maintains cellular metabolic homeostasis through regulation of mitochondrial reactive oxygen species. Cell Rep. 2017;21(1):1–9.
   PubMed Web of Science ®Google Scholar
• Garcia D, Shaw RJ. AMPK: mechanisms of cellular energy sensing and restoration of metabolic balance. Mol Cell. 2017;66(6):789–800.
   PubMed Web of Science ®Google Scholar
• Lin B, White JT, Ferguson C, et al. PART-1: a novel human prostate-specific, androgen-regulated gene that maps to chromosome 5q12. Cancer Res. 2000;60(4):858–863.
   PubMed Web of Science ®Google Scholar
• Kang M, Ren M, Li Y, et al. Exosome-mediated transfer of lncRNA PART1 induces gefitinib resistance in esophageal squamous cell carcinoma via functioning as a competing endogenous RNA. J Exp Clin Cancer Res. 2018;37(1):171.
   PubMed Web of Science ®Google Scholar
• Lou T, Ke K, Zhang L, et al. PART1 facilitates the malignant progression of colorectal cancer via miR-150-5p/LRG1 axis. J Cell Biochem. 2020;121(10):4271–4281.
   PubMed Web of Science ®Google Scholar
• Chen Y, Zhou X, Huang C, et al. LncRNA PART1 promotes cell proliferation and progression in non-small-cell lung cancer cells via sponging miR-17-5p. J Cell Biochem. 2021;122(3–4):315–325.
   PubMed Web of Science ®Google Scholar
• Zhao X, Hong Y, Cheng Q, et al. PART1 exerts tumor-suppressive functions in tongue squamous cell carcinoma via miR-503-5p. Onco Targets Ther. 2020;13:9977–9989.
   PubMedGoogle Scholar
• Song Y, Pan Y, Liu J. Functional analysis of lncRNAs based on competitive endogenous RNA in tongue squamous cell carcinoma. PeerJ. 2019;7:e6991.
   PubMed Web of Science ®Google Scholar
• Zhu K, Miao C, Tian Y, et al. lncRNA MIR4435-2HG promoted clear cell renal cell carcinoma malignant progression via miR-513a-5p/KLF6 axis. J Cell Mol Med. 2020;24(17):10013–10026.
   PubMed Web of Science ®Google Scholar
• Wang H, Wu M, Lu Y, et al. LncRNA MIR4435-2HG targets desmoplakin and promotes growth and metastasis of gastric cancer by activating Wnt/β-catenin signaling. Aging (Albany NY). 2019;11(17):6657–6673.
   PubMedGoogle Scholar
• Dong X, Yang Z, Yang H, et al. Long non-coding RNA MIR4435-2HG promotes colorectal cancer proliferation and metastasis through miR-206/YAP1 axis. Front Oncol. 2020;10:160.
   PubMed Web of Science ®Google Scholar
• Xu H, Zhang B, Yang Y, et al. LncRNA MIR4435-2HG potentiates the proliferation and invasion of glioblastoma cells via modulating miR-1224-5p/TGFBR2 axis. J Cell Mol Med. 2020;24(11):6362–6372.
   PubMed Web of Science ®Google Scholar
• Zhu L, Wang A, Gao M, et al. LncRNA MIR4435-2HG triggers ovarian cancer progression by regulating miR-128-3p/CKD14 axis. Cancer Cell Int. 2020;20(1):145.
   PubMed Web of Science ®Google Scholar
• Qian H, Chen L, Huang J, et al. The lncRNA MIR4435-2HG promotes lung cancer progression by activating β-catenin signalling. Journal of Molecular Medicine (Berlin, Germany). 2018;96(8):753–764.
   PubMed Web of Science ®Google Scholar
• Bai Y, Lin H, Chen J, et al. Identification of prognostic glycolysis-related lncRNA signature in tumor immune microenvironment of hepatocellular carcinoma. Front Mol Biosci. 2021;8:645084.
   PubMed Web of Science ®Google Scholar
• Wang S, Chen X, Qiao T. Long noncoding RNA MIR44352HG promotes the progression of head and neck squamous cell carcinoma by regulating the miR3835p/RBM3 axis. Oncol Rep. 2021;45(6). DOI:10.3892/or.2021.8050
   Web of Science ®Google Scholar
• Hanahan D, Weinberg R. A. Hallmarks of cancer: the next generation. Cell. 2011;144(5):646–674.
   PubMed Web of Science ®Google Scholar
• Liang X, Wu Z, Shen S, et al. LINC01980 facilitates esophageal squamous cell carcinoma progression via regulation of miR-190a-5p/MYO5A pathway. Arch Biochem Biophys. 2020;686:108371.
   PubMed Web of Science ®Google Scholar
• Zhang S, Liang Y, Wu Y, et al. Upregulation of a novel lncRNA LINC01980 promotes tumor growth of esophageal squamous cell carcinoma. Biochem Biophys Res Commun. 2019;513(1):73–80.
   PubMed Web of Science ®Google Scholar
• Zang Y, Yi Q, Pan J, et al. LINC01980 stimulates the progression of hepatocellular carcinoma via downregulating caspase 9. Journal of B.U.ON.: official journal of the Balkan Union of Oncology. 2020;25(3): 1395–1403.
   PubMed Web of Science ®Google Scholar