Global changes in unproductive splicing and the NMD system efficiency in tumors

The Nonsense-Mediated Decay (NMD) pathway is a mRNA quality control mechanism, which not only degrades deleterious transcripts but also orchestrates a large number of post-transcriptional regulatory programs through unproductive splicing. Here, we developed a robust metric derived from the quantification of splicing in the RNA-seq data to measure NMD efficiency at a sample level. We demonstrate that NMD efficiency varies substantially both between and within tissues, with the magnitude of variation comparable to that observed upon knockdown of the core NMD factor UPF1. By analyzing TCGA cancer cohorts, we further show that, in many tumors, unproductive splicing events exhibit coordinated changes towards either collective suppression or collective activation of NMD isoforms, which is indicative of a global deregulation of the NMD pathway activity. Consistently, we observed a striking divergence of NMD efficiency in cancers from the tissue-specific baseline level suggesting that tumors partially erase the NMD signature of their tissue of origin. The application of the developed metric to RNA-binding protein knockdowns allowed identification of several novel potential regulators of NMD efficiency. In sum, this study provides a solid framework for NMD efficiency quantification, describes its biological and clinical relevance, and opens new avenues for dissecting mechanisms of post-transcriptional gene expression regulation by the NMD pathway.