Tumour-specific antigens are one of the principal targets in immune checkpoint inhibitor (CPI) treatment and fundamental to the development of personalised immunotherapy. The search for immunogenic neoantigens has primarily focused on mutations in protein-coding regions of genes. In this study, we investigate how novel open-reading frames (neoORFs) in the 5’ and 3’ untranslated region (UTR) of genes (generated by premature start-gain and stop-loss mutations respectively) contribute to the immune landscape of cancer.
We analysed two pan-cancer CPI-treated patient cohorts from the Hartwig Medical Foundation (HMF, n = 384), and Genomics England (GEL, n = 364). The frequency and length of UTR neoORFs for each patient tumour were predicted from whole genome sequencing data using PrimeCUTR, an R-based bioinformatics tool we developed. CPI treatment response was determined based on RECIST 1.1 criteria.
Start-gain neoORFs occurred in 65.4–75.5% (GEL–HMF) of patients, while stop-loss neoORFs were found in 18.6–30.5%. 53.2–65.6% had start-gain neoORFs spanning 20 amino acids or more, with an overall median length of 28 amino acids. Among prevalent cancer groups, lung and head and neck cancer had the longest start-gain neoORFs. CPI response in HMF was associated with longer total length of start-gain (but not frameshift or stop-loss) neoORFs (P = 0.005). This association was also seen subsetting for low tumour mutational burden (TMB) (P = 0.014). In GEL, survival benefit was specifically seen in melanoma (n = 155), where patients with start-gain neoORFs longer than 28 amino acids (n = 60) had greater OS compared to those without (HR 0.59, 95% CI 0.36–0.95, P = 0.03).
UTR neoORFs occur frequently in cancer, yielding a promising source of neoantigens. We designed a computational pipeline for identifying these neoORFs, which will be made available upon peer-review. We show that 5’ UTR start-gain neoORFs were associated with clinical response to CPI, even in the low TMB setting which is typically linked to reduced CPI response. These findings warrant further study to validate UTR neoORFs as a biomarker and target for personalised immunotherapy.
The authors.
National Institute for Health and Care Research.
K.R. Litchfield: Financial Interests, Personal, Invited Speaker: Roche Tissue Diagnostics; Financial Interests, Personal, Other, Consulting work: Monopteros Therapeutics; Financial Interests, Institutional, Research Grant: Ono/LifeArc; Financial Interests, Institutional, Research Grant, Research funding: Genesis Therapeutics; Non-Financial Interests, Institutional, Proprietary Information, Collaboration on data analysis: BMS All other authors have declared no conflicts of interest.