Long Non Coding RNAs (lncRNAs) Are Dysregulated in Malignant Pleural Mesothelioma (MPM)

Casey M Wright,Sonja Klebe,Michaela B Kirschner,Kenneth J O'Byrne,Steven G Gray,Glen Reid,Yuen Yee Cheng,Brian Mccaughan,Karin Schelch,Mir Alireza Hoda,Nico Van Zandwijk

doi:10.1371/journal.pone.0070940

Abstract

Malignant Pleural Mesothelioma (MPM) is an aggressive cancer that is often diagnosed at an advanced stage and is characterized by a long latency period (20–40 years between initial exposure and diagnosis) and prior exposure to asbestos. Currently accurate diagnosis of MPM is difficult due to the lack of sensitive biomarkers and despite minor improvements in treatment, median survival rates do not exceed 12 months. Accumulating evidence suggests that aberrant expression of long non-coding RNAs (lncRNAs) play an important functional role in cancer biology. LncRNAs are a class of recently discovered non-protein coding RNAs >200 nucleotides in length with a role in regulating transcription. Here we used NCode long noncoding microarrays to identify differentially expressed lncRNAs potentially involved in MPM pathogenesis. High priority candidate lncRNAs were selected on the basis of statistical (P<0.05) and biological significance (>3-fold difference). Expression levels of 9 candidate lncRNAs were technically validated using RT-qPCR, and biologically validated in three independent test sets: (1) 57 archived MPM tissues obtained from extrapleural pneumonectomy patients, (2) 15 cryopreserved MPM and 3 benign pleura, and (3) an extended panel of 10 MPM cell lines. RT-qPCR analysis demonstrated consistent up-regulation of these lncRNAs in independent datasets. ROC curve analysis showed that two candidates were able to separate benign pleura and MPM with high sensitivity and specificity, and were associated with nodal metastases and survival following induction chemotherapy. These results suggest that lncRNAs have potential to serve as biomarkers in MPM.

Highlights

Malignant Pleural Mesothelioma (MPM) is an aggressive cancer often diagnosed at an advanced stage and characterized by a long latency period [1]
There is still a lack of knowledge surrounding the functional implications of long non-coding RNAs (lncRNAs) dysregulation and the precise role they play in carcinogenesis
We have found that lncRNA expression profiles can distinguish malignant mesothelium and benign pleura, and that some lncRNAs are associated with nodal metastasis and long term survival

Summary

Introduction

Malignant Pleural Mesothelioma (MPM) is an aggressive cancer often diagnosed at an advanced stage and characterized by a long latency period (vis. 20–60 years) [1]. In order to identify biomarkers and novel therapeutic targets for MPM, a better understanding of MPM biology is required. To this end, much work has focused on mRNA expression profiles and DNA copy number changes in MPM, with microRNA profiling a more recent addition. Gutschner et al suggested eight molecular functions of lncRNAs, these being; regulators of gene expression, sponges which sequester microRNAs preventing inhibition of their target transcripts [5], modulators of protein activity and localisation, as endo-siRNAs that target other RNAs for target degradation, as regulators of alternative splicing, scaffolds and as important controllers of chromatin remodelling and histone modifications [6]

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Results

Conclusion