Abstract A04: Altered expression of lncRNAs overlapping pseudogene loci as an alternative mechanism of cancer gene regulation
Authors: Stewart Greg L. , Enfield Katey S.S. , Martinez Victor D. , Marshall Erin A. , Lam Stephen , Lam Wan L. 
Published: February 2019

Abstract
The advent of next-generation sequencing has begun to reveal the functional importance of long noncoding RNAs (lncRNAs) in human cell biology, which can be exploited by tumors to drive the hallmarks of cancer. Due to their complex tertiary structure and unknown binding motifs, there is a growing disparity between number of lncRNAs identified and those that have been functionally characterized. As such, lncRNAs deregulated in cancer may represent critical members of cancer pathways that could hold therapeutic applicability. Pseudogenes are noncoding DNA sequences that are defunct relatives of their protein-coding parent genes but retain high sequence homology. Interestingly, several lncRNAs expressed from pseudogene loci have been shown to regulate the protein-coding parent genes of these pseudogenes in trans due to 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.
Illumina HiSeq reads were processed and aligned to the ENSEMBL annotation. Two datasets were selected due to their paired nature, complete with both lung adenocarcinoma (LUAD) and nonmalignant lung profiles (TCGA n=108, BCCA n=72). LncRNAs were filtered based on positional overlap within pseudogene loci. Differential expression was identified by Wilcoxon sign-rank test (FDR p&lt;0.05). To identify lncRNAs that likely regulate protein-coding parent gene expression in trans, tumors were ranked by lncRNA expression, and protein-coding parent gene expression of top and bottom ranked tertiles was compared by Mann Whitney U-test (p&lt;0.05). Survival analysis was performed using a Cox proportional hazard model.
Our analysis identified 129 lncRNAs expressed from pseudogene loci that were significantly deregulated in LUAD in both datasets, many of which were correlated with clinical features such as smoking status and patient survival. 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) protein-coding parent gene expression was significantly associated with survival. For example, AC008132.13 is a lncRNA expressed from a pseudogene to the B cell receptor (BCR), a previously described cancer gene involved in driving B-cell malignancies. AC008132.13 was overexpressed in LUAD and significantly positively correlated with BCR expression. In addition, BCR was significantly associated with patient survival (p=4.3e-04).
This work uncovers evidence to suggest that the lncRNA-pseudogene-protein-coding gene axis is a prominent mechanism of gene deregulation exploited by lung tumors. Further characterization of this understudied gene-regulatory mechanism could reveal novel means of silencing oncogenes or reactivating tumor-suppressor genes.
Citation Format: Greg L. Stewart, Katey S.S. Enfield, Victor D. Martinez, Erin A. Marshall, Stephen Lam, Wan L. Lam. Altered expression of lncRNAs overlapping pseudogene loci as an alternative mechanism of cancer gene regulation [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr A04.