Similar articles

Abstract: Objective: In this study, we aimed to expand current knowledge of head and neck squamous cell carcinoma (HNSCC)-associated long noncoding RNAs (lncRNAs), and to discover potential lncRNA prognostic biomarkers for HNSCC based on next-generation RNA-seq. Methods: RNA-seq data of 546 samples from patients with HNSCC were downloaded from The Cancer Genome Atlas (TCGA), including 43 paired samples of tumor tissue and adjacent normal tissue. An integrated analysis incorporating differential expression, weighted gene co-expression networks, functional enrichment, clinical parameters, and survival analysis was conducted to discover HNSCC-associated lncRNAs. The function of CYTOR was verified by cell-based experiments. To further identify lncRNAs with prognostic significance, a multivariate Cox proportional hazard regression analysis was performed. The identified lncRNAs were validated with an independent cohort using clinical feature relevance analysis and multivariate Cox regression analysis. Results: We identified nine HNSCC-relevant lncRNAs likely to play pivotal roles in HNSCC onset and development. By functional enrichment analysis, we revealed that CYTOR might participate in the multistep pathological processes of cancer, such as ribosome biogenesis and maintenance of genomic stability. CYTOR was identified to be positively correlated with lymph node metastasis, and significantly negatively correlated with overall survival (OS) and disease free survival (DFS) of HNSCC patients. Moreover, CYTOR inhibited cell apoptosis following treatment with the chemotherapeutic drug diamminedichloroplatinum (DDP). HCG22, the most dramatically down-regulated lncRNA in tumor tissue, may function in epidermis differentiation. It was also significantly associated with several clinical features of patients with HNSCC, and positively correlated with patient survival. CYTOR and HCG22 maintained their prognostic values independent of several clinical features in multivariate Cox hazards analysis. Notably, validation either based on an independent HNSCC cohort or by laboratory experiments confirmed these findings. Conclusions: Our transcriptomic analysis suggested that dysregulation of these HNSCC-associated lncRNAs might be involved in HNSCC oncogenesis and progression. Moreover, CYTOR and HCG22 were confirmed as two independent prognostic factors for HNSCC patient survival, providing new insights into the roles of these lncRNAs in HNSCC as well as clinical applications.

头颈部肿瘤转录组分析揭示与核糖体生物合成和表皮分化相关的关键长链非编码RNA

[1]Aken BL, Ayling S, Barrell D, et al., 2016. The Ensembl gene annotation system. Database, 2016:baw093.

[2]Anders S, Pyl PT, Huber W, 2015. HTSeq—a python framework to work with high-throughput sequencing data. Bioinformatics, 31(2):166-169.

[3]Barna M, Pusic A, Zollo O, et al., 2008. Suppression of Myc oncogenic activity by ribosomal protein haploinsufficiency. Nature, 456(7224):971-975.

[4]Bartkova J, Hořejší Z, Koed K, et al., 2005. DNA damage response as a candidate anti-cancer barrier in early human tumorigenesis. Nature, 434(7035):864-870.

[5]Bartonicek N, Maag JLV, Dinger ME, 2016. Long noncoding RNAs in cancer: mechanisms of action and technological advancements. Mol Cancer, 15(1):43.

[6]Benjamini Y, Hochberg Y, 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Statist Soc B, 57(1):289-300.

[7]Bhatt AN, Mathur R, Farooque A, et al., 2010. Cancer biomarkers—current perspectives. Indian J Med Res, 132:129-149.

[8]Cheetham SW, Gruhl F, Mattick JS, et al., 2013. Long noncoding RNAs and the genetics of cancer. Br J Cancer, 108(12):2419-2425.

[9]Chen WM, Huang MD, Sun DP, et al., 2016. Long intergenic non-coding RNA 00152 promotes tumor cell cycle progression by binding to EZH2 and repressing p15 and p21 in gastric cancer. Oncotarget, 7(9):9773-9787.

[10]https://doi.org/10.18632/oncotarget.6949

[11]Chi LM, Lee CW, Chang KP, et al., 2009. Enhanced interferon signaling pathway in oral cancer revealed by quantitative proteome analysis of microdissected specimens using ¹⁶O/¹⁸O labeling and integrated two-dimensional LC-ESI-MALDI tandem MS. Mol Cell Proteomics, 8(7):1453-1474.

[12]de Lena PG, Paz-Gallardo A, Paramio JM, et al., 2017. Clusterization in head and neck squamous carcinomas based on lncRNA expression: molecular and clinical correlates. Clin Epigenetics, 9:36.

[13]Derrien T, Johnson R, Bussotti G, et al., 2012. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res, 22(9):1775-1789.

[14]Eales KL, Hollinshead KER, Tennant DA, 2016. Hypoxia and metabolic adaptation of cancer cells. Oncogenesis, 5(1):e190.

[15]Engreitz JM, Ollikainen N, Guttman M, 2016. Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression. Nat Rev Mol Cell Biol, 17(12):756-770.

[16]Feng L, Houck JR, Lohavanichbutr P, et al., 2017. Transcriptome analysis reveals differentially expressed lncRNAs between oral squamous cell carcinoma and healthy oral mucosa. Oncotarget, 8(19):31521-31531.

[17]https://doi.org/10.18632/oncotarget.16358

[18]Gabay M, Li YL, Felsher DW, 2014. MYC activation is a hallmark of cancer initiation and maintenance. Cold Spring Harb Perspect Med, 4(6):a014241.

[19]Geng YJ, Xie SL, Li Q, et al., 2011. Large intervening non-coding RNA HOTAIR is associated with hepatocellular carcinoma progression. J Int Med Res, 39(6):2119-2128.

[20]Gold KA, Lee HY, Kim ES, 2009. Targeted therapies in squamous cell carcinoma of the head and neck. Cancer, 115(5):922-935.

[21]Hajjari M, Salavaty A, 2015. HOTAIR: an oncogenic long non-coding RNA in different cancers. Cancer Biol Med, 12(1):1-9.

[22]Harrow J, Frankish A, Gonzalez JM, et al., 2012. GENCODE: the reference human genome annotation for the encode project. Genome Res, 22(9):1760-1774.

[23]Holoch D, Moazed D, 2015. RNA-mediated epigenetic regulation of gene expression. Nat Rev Genet, 16(2):71-84.

[24]Huarte M, 2015. The emerging role of lncRNAs in cancer. Nat Med, 21(11):1253-1261.

[25]Kassambara A, Kosinski M, 2017. Survminer: Drawing Survival Curves Using ‘ggplot2’. R Package Version 0.4.0. https://CRAN.R-project.org/package=survminer [Accessed on June 10, 2017].

[26]Kim K, Jutooru I, Chadalapaka G, et al., 2013. HOTAIR is a negative prognostic factor and exhibits pro-oncogenic activity in pancreatic cancer. Oncogene, 32(13):1616-1625.

[27]Kinsella RJ, Kähäri A, Haider S, et al., 2011. Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database, 2011:bar030.

[28]Kohl M, Wiese S, Warscheid B, 2011. Cytoscape: software for visualization and analysis of biological networks. In: Hamacher M, Eisenacher M, Stephan C (Eds.), Data Mining in Proteomics. Humana Press, p.291-303.

[29]Lamouille S, Xu J, Derynck R, 2014. Molecular mechanisms of epithelial-mesenchymal transition. Nat Rev Mol Cell Biol, 15(3):178-196.

[30]Langfelder P, Horvath S, 2008. WGCNA: an R package for weighted correlation network analysis. BMC Bioinform, 9:559.

[31]Law CW, Chen Y, Shi W, et al., 2014. voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol, 15(2):R29.

[32]LeBleu VS, O'Connell JT, Gonzalez Herrera KN, et al., 2014. PGC-1α mediates mitochondrial biogenesis and oxidative phosphorylation in cancer cells to promote metastasis. Nat Cell Biol, 16(10):992-1003.

[33]Leemans CR, Braakhuis BJM, Brakenhoff RH, 2011. The molecular biology of head and neck cancer. Nat Rev Cancer, 11(1):9-22.

[34]Li DD, Feng JP, Wu TY, et al., 2013. Long intergenic noncoding RNA HOTAIR is overexpressed and regulates PTEN methylation in laryngeal squamous cell carcinoma. Am J Pathol, 182(1):64-70.

[35]Li X, Wu Z, Mei Q, et al., 2013. Long non-coding RNA HOTAIR, a driver of malignancy, predicts negative prognosis and exhibits oncogenic activity in oesophageal squamous cell carcinoma. Br J Cancer, 109(8):2266-2278.

[36]Liu BD, Sun LJ, Liu Q, et al., 2015. A cytoplasmic NF-κB interacting long noncoding RNA blocks IκB phosphorylation and suppresses breast cancer metastasis. Cancer Cell, 27(3):370-381.

[37]Liu R, Cheng Y, Yu J, et al., 2015. Identification and validation of gene module associated with lung cancer through coexpression network analysis. Gene, 563(1):56-62.

[38]Mäbert K, Cojoc M, Peitzsch C, et al., 2014. Cancer biomarker discovery: current status and future perspectives. Int J Radiat Biol, 90(8):659-677.

[39]McCarthy DJ, Chen YS, Smyth GK, 2012. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res, 40(10):4288-4297.

[40]Miller DL, Davis JW, Taylor KH, et al., 2015. Identification of a human papillomavirus-associated oncogenic miRNA panel in human oropharyngeal squamous cell carcinoma validated by bioinformatics analysis of the cancer genome atlas. Am J Pathol, 185(3):679-692.

[41]Min SN, Wei T, Wang XT, et al., 2017. Clinicopathological and prognostic significance of homeobox transcript antisense RNA expression in various cancers: a meta-analysis. Medicine (Baltimore), 96(23):e7084.

[42]Nohata N, Abba MC, Gutkind JS, 2016. Unraveling the oral cancer lncRNAome: identification of novel lncRNAs associated with malignant progression and HPV infection. Oral Oncol, 59:58-66.

[43]Nötzold L, Frank L, Gandhi M, et al., 2017. The long non-coding RNA LINC00152 is essential for cell cycle progression through mitosis in HeLa cells. Sci Rep, 7:2265.

[44]Parshall MB, 2013. Unpacking the 2×2 table. Hear Lung J Acute Crit Care, 42(3):221-226.

[45]Peng WX, Koirala P, Mo YY, 2017. LncRNA-mediated regulation of cell signaling in cancer. Oncogene, 36(41):5661-5667.

[46]Posner MR, Hershock DM, Blajman CR, et al., 2007. Cisplatin and fluorouracil alone or with docetaxel in head and neck cancer. New Engl J Med, 357(17):1705-1715.

[47]Pritzker KPH, 2015. Predictive and prognostic cancer biomarkers revisited. Expert Rev Mol Diagn, 15(8):971-974.

[48]Quek XC, Thomson DW, Maag JLV, et al., 2015. LncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res, 43(D1):D168-D173.

[49]R Development Core Team, 2011. R: A Language and Environment for Statistical Computing. R Development Core Team, Vienna, Austria.

[50]Rhodes DR, Yu JJ, Shanker K, et al., 2004. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia, 6(1):1-6.

[51]Rickman DS, Millon R, de Reynies A, et al., 2008. Prediction of future metastasis and molecular characterization of head and neck squamous-cell carcinoma based on transcriptome and genome analysis by microarrays. Oncogene, 27(51):6607-6622.

[52]Robinson MD, McCarthy DJ, Smyth GK, 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1):139-140.

[53]Ruggero D, Pandolfi PP, 2003. Does the ribosome translate cancer? Nat Rev Cancer, 3(3):179-192.

[54]Salazar C, Calvopiña D, Punyadeera C, 2014. miRNAs in human papilloma virus associated oral and oropharyngeal squamous cell carcinomas. Expert Rev Mol Diagn, 14(8):1033-1040.

[55]Salyakina D, Tsinoremas NF, 2016. Non-coding RNAs profiling in head and neck cancers. NPJ Genomic Med, 1:15004.

[56]Schmitt AM, Chang HY, 2016. Long noncoding RNAs in cancer pathways. Cancer Cell, 29(4):452-463.

[57]Schmitt AM, Garcia JT, Hung T, et al., 2016. An inducible long noncoding RNA amplifies DNA damage signaling. Nat Genet, 48(11):1370-1376.

[58]Seiwert TY, Salama JK, Vokes EE, 2007. The chemoradiation paradigm in head and neck cancer. Nat Clin Pract Oncol, 4(3):156-171.

[59]Signal B, Gloss BS, Dinger ME, 2016. Computational approaches for functional prediction and characterisation of long noncoding RNAs. Trends Genet, 32(10):620-637.

[60]Song L, Langfelder P, Horvath S, 2012. Comparison of co-expression measures: mutual information, correlation, and model based indices. BMC Bioinformatics, 13:328.

[61]Subramanian A, Tamayo P, Mootha VK, et al., 2005. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA, 102(43):15545-15550.

[62]Supek F, Bošnjak M, Škunca N, et al., 2011. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE, 6(7):e21800.

[63]Therneau T, 2017. A Package for Survival Analysis in S. R Package Version 2.41-2. https://CRAN.R-project.org/ package=survival [Accessed on Mar. 20, 2017].

[64]Tsai MC, Manor O, Wan Y, et al., 2010. Long noncoding RNA as modular scaffold of histone modification complexes. Science, 329(5992):689-693.

[65]van Riggelen J, Yetil A, Felsher DW, 2010. MYC as a regulator of ribosome biogenesis and protein synthesis. Nat Rev Cancer, 10(4):301-309.

[66]Wade M, Wahl GM, 2006. c-Myc, genome instability, and tumorigenesis: the devil is in the details. Curr Top Microbiol Immunol, 302:169-203.

[67]Wilson WR, Hay MP, 2011. Targeting hypoxia in cancer therapy. Nat Rev Cancer, 11(6):393-410.

[68]Yan L, Zhan C, Wu JH, et al., 2016. Expression profile analysis of head and neck squamous cell carcinomas using data from The Cancer Genome Atlas. Mol Med Rep, 13(5):4259-4265.

[69]Yates A, Akanni W, Amode MR, et al., 2016. Ensembl 2016. Nucleic Acids Res, 44(D1):D710-D716.

[70]Yu GC, Wang LG, Han YY, et al., 2012. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS A J Integr Biol, 16(5):284-287.

[71]Yu JJ, Liu Y, Guo C, et al., 2017. Upregulated long non-coding RNA LINC00152 expression is associated with progression and poor prognosis of tongue squamous cell carcinoma. J Cancer, 8(4):523-530.

[72]Zaidi MR, Davis S, Noonan FP, et al., 2011. Interferon-γ links ultraviolet radiation to melanomagenesis in mice. Nature, 469(7331):548-553.

[73]Zhang B, Horvath S, 2005. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol, 4(1):Article 17.

[74]Zhang SC, Tian LL, Ma PH, et al., 2015. Potential role of differentially expressed lncRNAs in the pathogenesis of oral squamous cell carcinoma. Arch Oral Biol, 60(10):1581-1587.

[75]Zhao J, Liu YC, Zhang WH, et al., 2015. Long non-coding RNA Linc00152 is involved in cell cycle arrest, apoptosis, epithelial to mesenchymal transition, cell migration and invasion in gastric cancer. Cell Cycle, 14(19):3112-3123.

[76]List of electronic supplementary materials

[77]Fig. S1 Determination of parameter β of the adjacency function in the WGCNA algorithm

[78]Fig. S2 Hierarchical clustering of samples based on the gene expression profile

[79]Fig. S3 Overview of the workflow of the study design

[80]Fig. S4 Functional profiling of modules identified by WGCNA

[81]Fig. S5 Co-expression of six hub lncRNAs visualized using Cytoscape software based on the top 50 most connected genes of each given lncRNA

[82]Fig. S6 Kaplan-Meier analysis of disease free survival in HNSCC patients

[83]Fig. S7 Effects of CYTOR knockdown on cell apoptosis, proliferation, and migration in TSCC15 cells

[84]Table S1 Results of differential expression analysis

[85]Table S2 GO term enrichment analysis for WGCNA modules and HNSCC-associated lncRNAs

[86]Table S3 Cancer hallmarks enrichment analysis for HNSCC-associated lncRNAs

[87]Table S4 GO term enrichment analysis for HNSCC-associated lncRNAs

[88]Table S5 KEGG pathway enrichment analysis for HNSCC-associated lncRNAs

[89]Table S6 OR analysis and multivariate Cox regression analysis in HNSCC

[90]Table S7 WGCNA network of six lncRNAs

[91]Table S8 OR and multivariate Cox regression analysis based on Oncomine dataset