Nonsense-mediated RNA decay and its bipolar function in cancer

Abstract

Nonsense-mediated decay (NMD) was first described as a quality-control mechanism that targets and rapidly degrades aberrant mRNAs carrying premature termination codons (PTCs). However, it was found that NMD also degrades a significant number of normal transcripts, thus arising as a mechanism of gene expression regulation. Based on these important functions, NMD regulates several biological processes and is involved in the pathophysiology of a plethora of human genetic diseases, including cancer. The present review aims to discuss the paradoxical, pro- and anti-tumorigenic roles of NMD, and how cancer cells have exploited both functions to potentiate the disease. Considering recent genetic and bioinformatic studies, we also provide a comprehensive overview of the present knowledge of the advantages and disadvantages of different NMD modulation-based approaches in cancer therapy, reflecting on the challenges imposed by the complexity of this disease. Furthermore, we discuss significant advances in the recent years providing new perspectives on the implications of aberrant NMD-escaping frameshifted transcripts in personalized immunotherapy design and predictive biomarker optimization. A better understanding of how NMD differentially impacts tumor cells according to their own genetic identity will certainly allow for the application of novel and more effective personalized treatments in the near future.

Keywords: Biomarker; Cancer therapy; Environmental stress; Immunotherapy; Neoantigen; Nonsense-mediated RNA decay (NMD); Oncogene; Tumor microenvironment; Tumor suppressor gene.

Fig. 1

Simplified representation of the nonsense-mediated mRNA decay (NMD) model in mammalian cells. a When the ribosome stops at a premature termination codon (PTC), the interaction of UPF1 and eRF3 induces premature translation termination. b After this interaction, the SURF complex is formed by eRF1, eRF3, SMG1 associated with SMG8 and SMG9, DHX34 and UPF1. c Then, UPF1 interacts with UPF2-UPF3B, either bound to the EJC downstream of the PTC (EJC-dependent NMD model) or diffused in the cytoplasm (EJC-independent NMD model), to form the DECID complex and induces the SMG1-mediated phosphorylation of UPF1. At this point, translation has terminated with the dissociation of the ribosomal subunits, the release factors and the nascent peptide. d Phosphorylated UPF1 triggers the decay phase by recruiting factors that lead to mRNA degradation, such as SMG6, which produces an endonucleolytic cleavage, SMG5-SMG7 dimer, which recruits the CCR4-NOT deadenylase complex, and/or PNRC2, which recruits the decapping complex (DCPC)

Fig. 2

Schematic representation of alternative splicing (AS) patterns inducing nonsense-mediated mRNA decay (NMD)-sensitive mRNA isoforms. The first mRNA isoform represents a productive transcript that encodes a functional protein. The following isoforms represent NMD-sensitive transcripts promoted by different AS patterns. Poison cassette inclusion leads to the retention of a premature translation-termination codon (PTC)-containing exon, while exon skipping can induce a frameshift in the mRNA sequence, introducing a downstream PTC. On the other hand, intron retention and alternative 5′/3′ splice sites may promote an NMD-target by including an in-frame PTC. Inclusion of two exons that usually are spliced separately may result in a frameshift, creating a PTC-positive isoform. The last isoform represents an AS pattern that leads to skipping in the 3′ untranslated region (3’UTR), which results in the presence of an exon junction complex downstream of the normal termination codon, favoring a premature context. AUG: start codon; NTC: normal termination codon

Fig. 3

Roles of nonsense-mediated mRNA decay (NMD) in cancer. a Disabling mutations or changes in the gene expression level of the key NMD factors (UPF1 as an example) occur in different cancer types [for example, lung inflammatory myofibroblastic tumor (IMT), pancreatic adenosquamous carcinoma (ASC), lung adenocarcinoma (ADC), and hepatocellular carcinoma (HCC)]. The case on the left represents mutated (Mut) UPF1, which leads to a decreased NMD activity resulting in the upregulation of an NMD target encoding the mitogen activated protein kinase kinase kinase 14 (MAP 3 K14) and stimulating NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) activity, thus inducing chemokine production and immune infiltrations. The example in the middle illustrates lower NMD activity due to the downregulation of UPF1, which causes the upregulation of several factors of the transforming growth factor beta (TGF-β) pathway. This favors the epithelial-mesenchymal transition (EMT) and consequently, the number of metastatic events. The example on the right shows the interaction between three oncoproteins, STAT3, GLI1 and tGL1, to induce higher protein levels of UPF3A, which inhibits NMD activity, increasing malignant progression of the tumor. b Tumor suppressor genes can completely loss their function by PTC acquisition and subsequent NMD degradation, combined with either deletion of the wild-type allele, or haploinsufficiency of the remaining allele. On the other hand, a tumor suppressor gene can experience an NMD-resistant mutation, leading to a dominant-negative protein that hampers the wild-type function. c The tumor microenvironment modulates NMD in order to overcome different types of cellular stresses associated with the unconstrained growth of the tumor. Stresses such as hypoxia, production of reactive oxygen species (ROS), or nutrient deprivation promote, eIF2α phosphorylation, which inhibits NMD and therefore, several mRNAs encoding stress-responsive factors are stabilized, allowing tumor progression and adaptation. WT: wild type; PTC: premature termination codon; aa: amino acid

Fig. 4

Summary of nonsense-mediated mRNA decay (NMD) inhibition/escaping and activation strategies for cancer treatment. a NMD activation in cancer therapy. The search of small molecules boosting NMD activity is still under research, but supposes a potential treatment for those cancer types where tumor-suppressive functions of NMD are beneficial. A more developed and gene-specific approach is the use of oligonucleotides designed to promote NMD over cancer- and/or stress-related transcripts. b Global and gene-specific NMD inhibition in cancer therapy. Nonsense suppressor compounds inducing read-through of premature termination codons (PTCs) by the ribosome allow the synthesis of full-length tumor suppressor proteins. This approach can be combined with global NMD inhibition to increase steady-state PTC-containing transcript levels by the use of translational inhibitors, small inhibiting molecules, calcium release modulators or cytoskeleton disrupting agents. In order to avoid non-desired off-targets affected by the general NMD inhibition, antisense oligonucleotides (ASOs) blocking the deposition of an EJC downstream of a PTC allows gene-specific targeting. EJC: exon junction complex. c Global NMD inhibition in cancer immunotherapy. Immune checkpoint inhibitors against negative regulators of T cell activation like CTLA-4 or PD-1 are commonly used in cancer immunotherapy to boost the anti-tumor immune response. NMD inhibition is a potential adjuvant therapy given the propensity of the tumor to produce neoantigens that trigger the immune response. Cancer cells experience numerous frameshift mutations resulting in PTC-containing transcripts that upon NMD inhibition can give rise to neoantigenic peptides detected by the immune system. Moreover, the tumor cellular landscape of NMD-escaping frameshifted transcripts can be used as a biomarker of value for personalized immunotherapy design and prediction of its response