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- Title
Evolution of the nonsense-mediated decay pathway is associated with decreased cytolytic immune infiltration.
- Authors
Zhao, Boyang; Pritchard, Justin R.
- Abstract
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. The interactions between cancers and their immune microenvironments drive a co-evolutionary process. This can start with the mutational changes that generate neo-antigenic epitopes, leading to the activation of a cytotoxic T-cell response. Activated and proliferating T cells can search out and destroy tumor cells. Then, increased killing of the tumor can lead to changes such as increased expression of PD-L1 and/or loss of function mutations in MHC Class I proteins that help a tumor evade immune surveillance. Frameshift mutations in particular have been found to generate highly antigenic epitopes. However, they can also activate nonsense mediated decay (NMD), leading to the suppression of such epitopes. This presents a paradox in how frameshift mutations and NMD interact in eliciting/evading immune surveillance during the course of tumor evolution. Here, we identify a new example of conditional selection, whereby tumors can coordinately mutate and/or amplify genes in the NMD pathway. We observed significant co-occurrence of mutations and copy number alterations among the NMD pathway genes. The co-alterations within the NMD pathway increase the global NMD efficiency and are associated with lower cytolytic activity, and in some cases, worse overall survival.
- Subjects
PROGRAMMED cell death 1 receptors; FRAMESHIFT mutation; MISSENSE mutation; ANTIGEN presentation; T cells; BIOLOGICAL evolution
- Publication
PLoS Computational Biology, 2019, Vol 15, Issue 10, p1
- ISSN
1553-734X
- Publication type
Article
- DOI
10.1371/journal.pcbi.1007467