Molecular Diagnostics

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

Abstract

Background

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.

Methods

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.

Results

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.

Conclusions

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.

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Acknowledgements

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.

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Authors

Contributions

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). https://doi.org/10.1038/s41416-020-0742-9

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