Abstract
Transcriptome sequencing has led to the widespread identification of long non-coding RNAs (lncRNAs). Subsequently, these genes have been shown to hold functional importance in human cellular biology, which can be exploited by tumors to drive the hallmarks of cancer. Due to the complex tertiary structure and unknown binding motifs of lncRNAs, there is a growing disparity between the number of lncRNAs identified and those that have been functionally characterized. As such, lncRNAs deregulated in cancer may represent critical components of cancer pathways that could serve as novel therapeutic intervention points. Pseudogenes are non-coding DNA sequences that are defunct relatives of their protein-coding parent genes but retain high sequence similarity. Interestingly, certain lncRNAs expressed from pseudogene loci have been shown to regulate the protein-coding parent genes of these pseudogenes in trans particularly because of this sequence complementarity. We hypothesize that this phenomenon occurs more broadly than previously realized, and that aberrant expression of lncRNAs overlapping pseudogene loci provides an alternative mechanism of cancer gene deregulation. Using RNA-sequencing data from two cohorts of lung adenocarcinoma, each paired with patient-matched non-malignant lung samples, we discovered 104 deregulated pseudogene-derived lncRNAs. Remarkably, many of these deregulated lncRNAs (i) were expressed from the loci of pseudogenes related to known cancer genes, (ii) had expression that significantly correlated with protein-coding parent gene expression, and (iii) had lncRNA protein-coding parent gene expression that was significantly associated with survival. Here, we uncover evidence to suggest the lncRNA-pseudogene-protein-coding gene axis as a prominent mechanism of cancer gene regulation in lung adenocarcinoma, and highlights the clinical utility of exploring the non-coding regions of the cancer transcriptome.
Highlights
Lung cancer is an enormous health burden, representing the most common cause of cancer death worldwide
We found 104 long non-coding RNAs (lncRNAs) expressed from 102 pseudogene loci to be significantly deregulated in lung adenocarcinoma (LUAD) (Supplementary Table S2)
Pseudogene-derived lncRNAs have been shown to be involved in cancer and regulate the expression of their parent genes
Summary
Lung cancer is an enormous health burden, representing the most common cause of cancer death worldwide. LncRNAs have been observed to function through a wide variety of regulatory mechanisms, targeting DNA, proteins, and other RNA species; with defined roles in RNA degradation or stabilization, protein translocation and complex formation, and recruitment of complexes to transcriptional loci (Lee et al, 1999; Wang et al, 2011; Kung et al, 2013; Simon et al, 2013) This broad functional repertoire has been shown to be exploited by many cancer types, including LUAD, to drive various hallmarks of cancer (Bhan et al, 2017; Peng et al, 2017).
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