Molecular Diagnostics

Long non-coding RNA dysregulation is a frequent event in non-small cell lung carcinoma pathogenesis



Long non-coding RNAs compose an important level of epigenetic regulation in normal physiology and disease. Despite the plethora of publications of lncRNAs in human cancer, the landscape is still unclear.


Microarray analysis in 44 NSCLC paired specimens was followed by qPCR-based validation in 29 (technical) and 38 (independent) tissue pairs. Cross-validation of the selected targets was achieved in 850 NSCLC tumours from TCGA datasets.


Twelve targets were successfully validated by qPCR (upregulated: FEZF1-AS1, LINC01214, LINC00673, PCAT6, NUTM2A-AS1, LINC01929; downregulated: PCAT19, FENDRR, SVIL-AS1, LANCL1-AS1, ADAMTS9-AS2 and LINC00968). All of them were successfully cross validated in the TCGA datasets. Abnormal DNA methylation was observed in the promoters of FENDRR, FEZF1-AS1 and SVIL-AS1. FEZF1-AS1 and LINC01929 were associated with survival in the TCGA set.


Our study provides through multiple levels of internal and external validation, a comprehensive list of dysregulated lncRNAs in NSCLC. We therefore envisage this dataset to serve as an important source for the lung cancer research community assisting future investigations on the involvement of lncRNAs in the pathogenesis of the disease and providing novel biomarkers for diagnosis, prognosis and therapeutic stratification.

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Fig. 1: Overexpressed lncRNAs in NSCLC.
Fig. 2: Downregulated lncRNAs in NSCLC.
Fig. 3: Bar chart diagrams showing the expression levels of the validated lncRNAs in NSCLC cell lines and a normal lung fibroblast cell line (IMR90), which was used as a calibrator (RQ = 1) for the analysis, with the exception of FEZF1-AS1 and LINC01929, which are not expressed in IMR90.
Fig. 4: DNA methylation of lncRNA promoters in NSCLC.


  1. 1.

    Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H. et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775–1789 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. 2.

    Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223–227 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. 3.

    Frankish, A., Diekhans, M., Ferreira, A. M., Johnson, R., Jungreis, I., Loveland, J. et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 47, D766–D773 (2019).

    CAS  PubMed  Google Scholar 

  4. 4.

    Yang, G., Lu, X. & Yuan, L. LncRNA: a link between RNA and cancer. Biochim. Biophys. Acta 1839, 1097–1109 (2014).

    CAS  PubMed  Google Scholar 

  5. 5.

    Ulitsky, I. & Bartel, D. P. lincRNAs: genomics, evolution, and mechanisms. Cell 154, 26–46 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. 6.

    Cabili, M. N., Trapnell, C., Goff, L., Koziol, M., Tazon-Vega, B., Regev, A. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915–1927 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. 7.

    Clark, M. B., Johnston, R. L., Inostroza-Ponta, M., Fox, A. H., Fortini, E., Moscato, P. et al. Genome-wide analysis of long noncoding RNA stability. Genome Res. 22, 885–898 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Iyer, M. K., Niknafs, Y. S., Malik, R., Singhal, U., Sahu, A., Hosono, Y. et al. The landscape of long noncoding RNAs in the human transcriptome. Nat. Genet 47, 199–208 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. 9.

    Yan, X., Hu, Z., Feng, Y., Hu, X., Yuan, J., Zhao, S. D. et al. Comprehensive genomic characterization of long non-coding RNAs across human cancers. Cancer Cell 28, 529–540 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. 10.

    Ashouri, A., Sayin, V. I., Van den Eynden, J., Singh, S. X., Papagiannakopoulos, T. & Larsson, E. Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events. Nat. Commun. 7, 13197 (2016).

    CAS  PubMed  Google Scholar 

  11. 11.

    Herbst, R. S., Morgensztern, D. & Boshoff, C. The biology and management of non-small cell lung cancer. Nature 553, 446–454 (2018).

    CAS  PubMed  Google Scholar 

  12. 12.

    Field, J. K., Duffy, S. W., Devaraj, A. & Baldwin, D. R. Implementation planning for lung cancer screening: five major challenges. Lancet Respir. Med. 4, 685–687 (2016).

    PubMed  Google Scholar 

  13. 13.

    White, N. M., Cabanski, C. R., Silva-Fisher, J. M., Dang, H. X., Govindan, R. & Maher, C. A. Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer. Genome Biol. 15, 429 (2014).

    PubMed  PubMed Central  Google Scholar 

  14. 14.

    Yang, J., Lin, J., Liu, T., Chen, T., Pan, S., Huang, W. et al. Analysis of lncRNA expression profiles in non-small cell lung cancers (NSCLC) and their clinical subtypes. Lung Cancer 85, 110–115 (2014).

    PubMed  Google Scholar 

  15. 15.

    Zhao, W., Luo, J. & Jiao, S. Comprehensive characterization of cancer subtype associated long non-coding RNAs and their clinical implications. Sci. Rep. 4, 6591 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. 16.

    Zhou, M., Guo, M., He, D., Wang, X., Cui, Y., Yang, H. et al. A potential signature of eight long non-coding RNAs predicts survival in patients with non-small cell lung cancer. J. Transl. Med. 13, 231 (2015).

    PubMed  PubMed Central  Google Scholar 

  17. 17.

    Yu, H., Xu, Q., Liu, F., Ye, X., Wang, J. & Meng, X. Identification and validation of long noncoding RNA biomarkers in human non-small-cell lung carcinomas. J. Thorac. Oncol. 10, 645–654 (2015).

    CAS  PubMed  Google Scholar 

  18. 18.

    Feng, N., Ching, T., Wang, Y., Liu, B., Lin, H., Shi, O. et al. Analysis of microarray data on gene expression and methylation to identify long non-coding RNAs in non-small cell lung cancer. Sci. Rep. 6, 37233 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. 19.

    Cheng, Z., Bai, Y., Wang, P., Wu, Z., Zhou, L., Zhong, M. et al. Identification of long noncoding RNAs for the detection of early stage lung squamous cell carcinoma by microarray analysis. Oncotarget 8, 13329–13337 (2017).

    PubMed  PubMed Central  Google Scholar 

  20. 20.

    Nikolaidis, G., Raji, O. Y., Markopoulou, S., Gosney, J. R., Bryan, J., Warburton, C. et al. DNA methylation biomarkers offer improved diagnostic efficiency in lung cancer. Cancer Res. 72, 5692–5701 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. 21.

    Bediaga, N. G., Davies, M. P., Acha-Sagredo, A., Hyde, R., Raji, O. Y., Page, R. et al. A microRNA-based prediction algorithm for diagnosis of non-small lung cell carcinoma in minimal biopsy material. Br. J. Cancer 109, 2404–2411 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. 22.

    Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).

    PubMed  PubMed Central  Google Scholar 

  23. 23.

    Phipson, B., Lee, S., Majewski, I. J., Alexander, W. S. & Smyth, G. K. Robust Hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression. Ann. Appl. Stat. 10, 946–963 (2016).

    PubMed  PubMed Central  Google Scholar 

  24. 24.

    Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004).

    PubMed  PubMed Central  Google Scholar 

  25. 25.

    Shaw, R. J., Liloglou, T., Rogers, S. N., Brown, J. S., Vaughan, E. D., Lowe, D. et al. Promoter methylation of P16, RARbeta, E-cadherin, cyclin A1 and cytoglobin in oral cancer: quantitative evaluation using pyrosequencing. Br. J. Cancer 94, 561–568 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. 26.

    Wan, L., Zhang, L., Fan, K. & Wang, J. J. Diagnostic significance of circulating long noncoding RNA PCAT6 in patients with non-small cell lung cancer. Onco Targets Ther. 10, 5695–5702 (2017).

    PubMed  PubMed Central  Google Scholar 

  27. 27.

    Nie, W., Ge, H. J., Yang, X. Q., Sun, X., Huang, H., Tao, X. et al. LncRNA-UCA1 exerts oncogenic functions in non-small cell lung cancer by targeting miR-193a-3p. Cancer Lett. 371, 99–106 (2016).

    CAS  PubMed  Google Scholar 

  28. 28.

    Shi, X., Sun, M., Liu, H., Yao, Y., Kong, R., Chen, F. et al. A critical role for the long non-coding RNA GAS5 in proliferation and apoptosis in non-small-cell lung cancer. Mol. Carcinog. 54(Suppl. 1), E1–E12 (2015).

    CAS  PubMed  Google Scholar 

  29. 29.

    Sun, M., Liu, X. H., Wang, K. M., Nie, F. Q., Kong, R., Yang, J. S. et al. Downregulation of BRAF activated non-coding RNA is associated with poor prognosis for non-small cell lung cancer and promotes metastasis by affecting epithelial-mesenchymal transition. Mol. Cancer 13, 68 (2014).

    PubMed  PubMed Central  Google Scholar 

  30. 30.

    Han, L., Zhang, E. B., Yin, D. D., Kong, R., Xu, T. P., Chen, W. M. et al. Low expression of long noncoding RNA PANDAR predicts a poor prognosis of non-small cell lung cancer and affects cell apoptosis by regulating Bcl-2. Cell Death Dis. 6, e1665 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Nie, F. Q., Sun, M., Yang, J. S., Xie, M., Xu, T. P., Xia, R. et al. Long noncoding RNA ANRIL promotes non-small cell lung cancer cell proliferation and inhibits apoptosis by silencing KLF2 and P21 expression. Mol. Cancer Ther. 14, 268–277 (2015).

    CAS  PubMed  Google Scholar 

  32. 32.

    Cao, B., Liu, C. & Yang, G. Down-regulation of lncRNA ADAMTS9-AS2 contributes to gastric cancer development via activation of PI3K/Akt pathway. Biomed. Pharmacother. 107, 185–193 (2018).

    CAS  PubMed  Google Scholar 

  33. 33.

    Liu, C., Yang, Z., Deng, Z., Zhou, Y., Gong, Q., Zhao, R. et al. Upregulated lncRNA ADAMTS9-AS2 suppresses progression of lung cancer through inhibition of miR-223-3p and promotion of TGFBR3. IUBMB Life 70, 536–546 (2018).

    CAS  PubMed  Google Scholar 

  34. 34.

    Wang, A., Jin, C., Li, H., Qin, Q. & Li, L. LncRNA ADAMTS9-AS2 regulates ovarian cancer progression by targeting miR-182-5p/FOXF2 signaling pathway. Int J. Biol. Macromol. 120, 1705–1713 (2018).

    CAS  PubMed  Google Scholar 

  35. 35.

    Xu, T. P., Huang, M. D., Xia, R., Liu, X. X., Sun, M., Yin, L. et al. Decreased expression of the long non-coding RNA FENDRR is associated with poor prognosis in gastric cancer and FENDRR regulates gastric cancer cell metastasis by affecting fibronectin1 expression. J. Hematol. Oncol. 7, 63 (2014).

    PubMed  PubMed Central  Google Scholar 

  36. 36.

    Kun-Peng, Z., Chun-Lin, Z. & Xiao-Long, M. Antisense lncRNA FOXF1-AS1 Promotes Migration and Invasion of Osteosarcoma Cells Through the FOXF1/MMP-2/-9 Pathway. Int J. Biol. Sci. 13, 1180–1191 (2017).

    PubMed  PubMed Central  Google Scholar 

  37. 37.

    Miao, L., Huang, Z., Zengli, Z., Li, H., Chen, Q., Yao, C. et al. Loss of long noncoding RNA FOXF1-AS1 regulates epithelial-mesenchymal transition, stemness and metastasis of non-small cell lung cancer cells. Oncotarget 7, 68339–68349 (2016).

    PubMed  PubMed Central  Google Scholar 

  38. 38.

    Najgebauer, H., Liloglou, T., Jithesh, P. V., Giger, O. T., Varro, A. & Sanderson, C. M. Integrated omics profiling reveals novel patterns of epigenetic programming in cancer-associated myofibroblasts. Carcinogenesis 40, 500–512 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. 39.

    He, R., Zhang, F. H. & Shen, N. LncRNA FEZF1-AS1 enhances epithelial-mesenchymal transition (EMT) through suppressing E-cadherin and regulating WNT pathway in non-small cell lung cancer (NSCLC). Biomed. Pharmacother. 95, 331–338 (2017).

    CAS  PubMed  Google Scholar 

  40. 40.

    Jin, S., Chen, S., Ma, Y., Yang, B. & Liu, Y. LincRNA FEZF1-AS1 contributes to the proliferation of LAD cells by silencing p57 expression. Oncotarget 8, 103004–103013 (2017).

    PubMed  PubMed Central  Google Scholar 

  41. 41.

    Zhang, Z., Sun, L., Zhang, Y., Lu, G., Li, Y. & Wei, Z. Long non-coding RNA FEZF1-AS1 promotes breast cancer stemness and tumorigenesis via targeting miR-30a/Nanog axis. J. Cell Physiol. 233, 8630–8638 (2018).

    CAS  PubMed  Google Scholar 

  42. 42.

    Shi, X., Ma, C., Zhu, Q., Yuan, D., Sun, M., Gu, X. et al. Upregulation of long intergenic noncoding RNA 00673 promotes tumor proliferation via LSD1 interaction and repression of NCALD in non-small-cell lung cancer. Oncotarget 7, 25558–25575 (2016).

    PubMed  PubMed Central  Google Scholar 

  43. 43.

    Lu, W., Zhang, H., Niu, Y., Wu, Y., Sun, W., Li, H. et al. Long non-coding RNA linc00673 regulated non-small cell lung cancer proliferation, migration, invasion and epithelial mesenchymal transition by sponging miR-150-5p. Mol. Cancer 16, 118 (2017).

    PubMed  PubMed Central  Google Scholar 

  44. 44.

    Roth, A., Boulay, K., Gross, M., Polycarpou-Schwarz, M., Mallette, F. A., Regnier, M. et al. Targeting LINC00673 expression triggers cellular senescence in lung cancer. RNA Biol. 15, 1499–1511 (2018).

    PubMed  PubMed Central  Google Scholar 

  45. 45.

    Huang, M., Hou, J., Wang, Y., Xie, M., Wei, C., Nie, F. et al. Long noncoding RNA LINC00673 is activated by SP1 and exerts oncogenic properties by interacting with LSD1 and EZH2 in gastric cancer. Mol. Ther. 25, 1014–1026 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. 46.

    Ba, M. C., Long, H., Cui, S. Z., Gong, Y. F., Yan, Z. F., Wu, Y. B. et al. Long noncoding RNA LINC00673 epigenetically suppresses KLF4 by interacting with EZH2 and DNMT1 in gastric cancer. Oncotarget 8, 95542–95553 (2017).

    PubMed  PubMed Central  Google Scholar 

  47. 47.

    Ma, C., Wu, G., Zhu, Q., Liu, H., Yao, Y., Yuan, D. et al. Long intergenic noncoding RNA 00673 promotes non-small-cell lung cancer metastasis by binding with EZH2 and causing epigenetic silencing of HOXA5. Oncotarget 8, 32696–32705 (2017).

    PubMed  PubMed Central  Google Scholar 

  48. 48.

    Shi, X., Liu, Z., Liu, Z., Feng, X., Hua, F., Hu, X. et al. Long noncoding RNA PCAT6 functions as an oncogene by binding to EZH2 and suppressing LATS2 in non-small-cell lung cancer. EBioMedicine 37, 177–187 (2018).

    PubMed  PubMed Central  Google Scholar 

  49. 49.

    Huang, W., Su, G., Huang, X., Zou, A., Wu, J., Yang, Y. et al. Long noncoding RNA PCAT6 inhibits colon cancer cell apoptosis by regulating anti-apoptotic protein ARC expression via EZH2. Cell Cycle 18, 69–83 (2019).

    CAS  PubMed  Google Scholar 

  50. 50.

    Wang, Y., Zhou, J., Xu, Y. J. & Hu, H. B. Long non-coding RNA LINC00968 acts as oncogene in NSCLC by activating the Wnt signaling pathway. J. Cell Physiol. 233, 3397–3406 (2018).

    CAS  PubMed  Google Scholar 

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We would like to thank Dr. Gordon K. Smyth and Dr Ramyar Molania from the Walter & Eliza Hall Institute of Medical Research, Melbourne, Australia for their invaluable assistance in the bioinformatics analysis. We would also want to acknowledge the voluntary contribution of patients with their specimens and information as well as the nursing staff that recruited them in the study.

Author information




The study was conceived and designed by T.L. and A.A.S. Methodology was developed by A.A.S., P.P. and T.L. Data acquisition was carried out by A.A.S., B.U., P.P., C.M., L.R., M.P.A.D., J.K.F. Analysis and interpretation of the data was undertaken by A.A.S., N.G.B., M.W.M., T.L. Writing, review, and/or revision of the manuscript was done by A.A.S., N.G.B., B.U., M.P.A.D., J.K.F. and T.L. This research was supervised by T.L.

Corresponding author

Correspondence to Triantafillos Liloglou.

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Ethics approval and consent to participate

Ethical approval was obtained from the Liverpool Central Research Ethics Committee (ref 97/141). All patients were recruited following voluntary informed consent, and the study was performed in accordance with the Declaration of Helsinki.

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Not applicable.

Data availability

Microarray data have been deposited in the Gene Expression Omnibus (GEO) database (GSE130740).

Competing interests

The authors declare no competing interests.

Funding information

This research was supported by the Roy Castle Lung Cancer Foundation, UK (Grant no 2014/05/Liloglou) and a Roy Castle Lung Cancer Senior Fellowship (MPAD).

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Acha-Sagredo, A., Uko, B., Pantazi, P. et al. Long non-coding RNA dysregulation is a frequent event in non-small cell lung carcinoma pathogenesis. Br J Cancer 122, 1050–1058 (2020).

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