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

View ORCID ProfileJustin R Pritchard, View ORCID ProfileBoyang Zhao
doi: https://doi.org/10.1101/535773
Justin R Pritchard
The Pennsylvania State University
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  • For correspondence: jrp94@psu.edu
Boyang Zhao
The Pennsylvania State University
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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. 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. 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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 04, 2019.
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Evolution of the nonsense-mediated decay (NMD) pathway is associated with decreased cytolytic immune infiltration
Justin R Pritchard, Boyang Zhao
bioRxiv 535773; doi: https://doi.org/10.1101/535773
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Evolution of the nonsense-mediated decay (NMD) pathway is associated with decreased cytolytic immune infiltration
Justin R Pritchard, Boyang Zhao
bioRxiv 535773; doi: https://doi.org/10.1101/535773

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