Evolution of the nonsense-mediated decay pathway is associated with decreased cytolytic immune infiltration

• Published in: PLoS computational biology Vol. 15; no. 10; p. e1007467
• Main Authors: Zhao, Boyang, Pritchard, Justin R
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.10.2019; Public Library of Science (PLoS)
• Subjects: Analysis; Antigen presentation; Antigenic determinants; Antigens; Biological Evolution; Biology and Life Sciences; Biomarkers; Biomedical engineering; Cancer; Cancer therapies; Clinical trials; Coevolution; Computer and Information Sciences; Computer Simulation; Cytolytic activity; Cytosol - metabolism; Cytotoxicity; Cytotoxicity, Immunologic - genetics; Databases, Genetic; Decay; Dependence; Engineering schools; Epitopes; Evolution; Evolution, Molecular; Frameshift mutation; Frameshift Mutation - genetics; Gene expression; Genes; Genetic research; Genomes; Humans; Immune response; Immune response (cell-mediated); Immunotherapy; Inflammation; Ipilimumab; Learning algorithms; Lung cancer; Lymphocytes T; Machine Learning; Medicine and Health Sciences; Melanoma; Metastases; Missense mutation; Mutation; Mutation - genetics; Mutation, Missense - genetics; Neoplasms - genetics; Nivolumab; Nonsense Mediated mRNA Decay - physiology; Patients; Pembrolizumab; Peptides; Regression analysis; Regression models; Respiratory system agents; Response rates; Suppressors; Survival; T cells; Tumors; United States > US; Pennsylvania
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1007467

The somatic co-evolution of tumors and the cellular immune responses that combat them drives the diversity of immune-tumor interactions. This includes tumor mutations that generate neo-antigenic epitopes that elicit cytotoxic T-cell activity and subsequent pressure to select for genetic loss of antigen presentation. Most studies have focused on how tumor missense mutations can drive tumor immunity, but frameshift mutations have the potential to create far greater antigenic diversity. However, expression of this antigenic diversity is potentially regulated by Nonsense Mediated Decay (NMD) and NMD has been shown to be of variable efficiency in cancers. Here we studied how mutational changes influence global NMD and cytolytic immune responses. Using TCGA datasets, we derived novel patient-level metrics of 'NMD burden' and interrogated how different mutation and most importantly NMD burdens influence cytolytic activity using machine learning models and survival outcomes. We find that NMD is a significant and independent predictor of immune cytolytic activity. Different indications exhibited varying dependence on NMD and mutation burden features. We also observed significant co-alteration of genes in the NMD pathway, with a global increase in NMD efficiency in patients with NMD co-alterations. Finally, NMD burden also stratified patient survival in multivariate regression models in subset of cancer types. Our work suggests that beyond selecting for mutations that elicit NMD in tumor suppressors, tumor evolution may react to the selective pressure generated by inflammation to globally enhance NMD through coordinated amplification and/or mutation.