Evidence for selective silencing of MHC-binding neoepitopes to avoid immune surveillance.

Abstract

2591 Background: Overall response rates to immune checkpoint inhibition (ICI) are < 50% even in TMB-high patients (e.g. Checkmate-227), suggesting other mechanisms of immune escape exist beyond expressing checkpoints. At least 18% of somatic-specific exonic DNA variants are not expressed into mRNA (Rabizadeh, 2018), yet the selection criteria for which variants to silence remains unclear. We sought to determine if immunogenicity of variants factors into their suppression. Methods: Somatic-specific single nucleotide variants (SNVs) were identified from paired tumor/normal whole-exome sequencing (WES), and annotated as expressed if observed in > = 2 RNAseq reads. MHC1 binding affinity for 9-mer neoepitope peptides resulting from said SNVs were predicted using NetMHC within presented HLA-types. Cases with > 200 non-synonymous exonic mutations were designated as TMB-high in accordance with Rizvi et al, 2015. Tumor immune activity was inferred by RNAseq expression of 6 checkpoint/TME markers, as well as by estimating immune infiltration using RNAseq deconvolution of immune genesets (Bindea et al 2013). Significant associations between TMB, neoantigen-load, expressed neoepitope binding affinities, and immune activity were analyzed. Results: Within a clinical database of 1,363 cases with T/N/R sequencing, a total of 147,015 potential neoepitopes were identified. A small but significant enrichment was observed for silencing neoepitopes that are predicted to bind MHC1 (OR = 1.22, p = 2.4e-78 one-sided Fishers test). The silencing rate was similar between the 17% of patients with high TMB vs others, but was increased in 35% of all patients with high inferred immune infiltration (N = 490, OR = 1.30, p = 1.8e-31). A further silencing enrichment was observed in 19% of all patients displaying high immune activity but low PDL1 expression (N = 263, OR = 1.44, p = 4.0e-45). Conclusions: We observe significant preferential silencing of MHC binding neoepitopes. Specifically, when tumor infiltrating immune cells are activated, silencing neoepitopes may be an alternative to checkpoint expression for avoiding an immune cascade. Patients with TILs and silenced neoepitopes may benefit from epigenetic priming therapy prior to ICI therapy.