Escape from nonsense-mediated decay associates with anti-tumor immunogenicity.
Date
2020-07-30Author
Litchfield, K
Reading, JL
Lim, EL
Xu, H
Liu, P
Al-Bakir, M
Wong, YNS
Rowan, A
Funt, SA
Merghoub, T
Perkins, D
Lauss, M
Svane, IM
Jönsson, G
Herrero, J
Larkin, J
Quezada, SA
Hellmann, MD
Turajlic, S
Swanton, C
Type
Journal Article
Metadata
Show full item recordAbstract
Frameshift insertion/deletions (fs-indels) are an infrequent but highly immunogenic mutation subtype. Although fs-indels are degraded through the nonsense-mediated decay (NMD) pathway, we hypothesise that some fs-indels escape degradation and elicit anti-tumor immune responses. Using allele-specific expression analysis, expressed fs-indels are enriched in genomic positions predicted to escape NMD, and associated with higher protein expression, consistent with degradation escape (NMD-escape). Across four independent melanoma cohorts, NMD-escape mutations are significantly associated with clinical-benefit to checkpoint inhibitor (CPI) therapy (Pmeta = 0.0039). NMD-escape mutations are additionally found to associate with clinical-benefit in the low-TMB setting. Furthermore, in an adoptive cell therapy treated melanoma cohort, NMD-escape mutation count is the most significant biomarker associated with clinical-benefit. Analysis of functional T cell reactivity screens from personalized vaccine studies shows direct evidence of fs-indel derived neoantigens eliciting immune response, particularly those with highly elongated neo open reading frames. NMD-escape fs-indels represent an attractive target for biomarker optimisation and immunotherapy design.
Collections
Subject
Adoptive Transfer
Antigens, Neoplasm
Biomarkers, Tumor
Frameshift Mutation
Humans
INDEL Mutation
Immunotherapy, Adoptive
Melanoma
Nonsense Mediated mRNA Decay
T-Lymphocytes
Tumor Escape
Whole Exome Sequencing
Language
eng
Date accepted
2020-06-30
License start date
2020-07-30
Citation
Nature Communications, 2020, 11 (1), pp. 3800 -
Publisher
NATURE PUBLISHING GROUP