Natural antisense transcript deregulation in non-small cell lung cancer

Abstract

Lung cancer represents an enormous health burden, representing the most common cause of cancer death worldwide. The poor therapeutic outcome is largely due to a complex molecular background as well as late stage diagnosis, with most patients presenting unresectable local tumors, or metastatic disease. While mutations of driver genes is a well-known mechanism, approximately half of all non-small cell lung cancer (NSCLC) tumors harbor no known clinically relevant oncogenic drivers, emphasizing the need to explore alternative mechanisms such as non-coding RNAs (ncRNAs). ncRNAs are RNA molecules that do not encode for protein, but have the ability to regulate DNA, proteins, as well as other RNA species. These genes exhibit tissue specific regulation and have emerged as important players in several tumor types including lung cancer. Natural antisense transcripts (NATS) are ncRNAs that are transcribed from the opposite strand of protein coding genes. These NATs overlap with, and are often involved in the regulation of, their sense counterparts. NATs can recruit regulatory complexes to their transcriptional locus, leading to silencing of overlapping sense partner gene transcription, and have recently been described in cancer to silence tumor suppressor genes such as CDKN2A/B. NATs are quite prevalent as it is estimated that 25-40% of genes display overlapping transcriptional partners, emphasizing their potential in gene regulation. However, only a few NATs have been characterized in cancer. Here we take an unbiased approach to study NAT deregulation as a mechanism for altered sense partner expression in NSCLC. We performed RNA-sequencing on a set of 65 NSCLC tumors including 36 adenocarcinomas and 29 squamous cell carcinomas as well as matched nonmalignant lung tissues. A sign-rank test was used to identify NATs and partner genes with significantly altered expression between tumor and matched normal tissues. These findings were validated in an external dataset of lung tumors from TCGA. Survival analysis was performed using a Cox Proportional hazard model, as well as the log-rank method. We have identified a NAT of OIP5, a lung cancer oncogene required for chromatin segregation, to be significantly underexpressed in NSCLC. In the same tumors we find the overlapping partner gene, OIP5 mRNA, to be significantly overexpressed, suggesting that OIP5-AS1 may negatively regulate its sense counterpart. In addition, we find that expression of both OIP5 and OIP5-AS1 are significantly associated with 5-year survival. These findings suggest that deregulation of OIP5 through its antisense RNA may represent a novel mechanism regulating tumor phenotypes in NSCLC.