Intron retention is a source of neoepitopes in cancer

Abstract

We present an in silico approach to identifying neoepitopes derived from intron retention events in tumor transcriptomes. Using mass spectrometry immunopeptidome analysis, we show that retained intron neoepitopes are processed and presented on MHC I on the surface of cancer cell lines. RNA-derived neoepitopes should be considered for prospective personalized cancer vaccine development.

Figure 1.

A, In silico pipeline detects intron retention events from transcriptome sequencing, determines open reading frames extending into introns, and identifies putative HLA-specific neoepitopes. B, Distribution of total RI load, neoepitope-yielding RI load, and RI neoepitope load in patient cohorts (n = 27 Hugo samples, n = 21 Snyder samples). Boxplots show the median, first, and third quartiles, whiskers extend to 1.5 x the interquartile range, and outlying points are plotted individually. C, Somatic and RI neoepitope load by patient. Within each cohort, patients are sorted by total neoepitope load. Neoepitope counts (y-axis values) are represented in natural log format.

Figure 2.

A, Two RI neoepitopes identified in the MeWo cell line originating from gene KCNAB2 were both predicted in silico and found by mass spectrometry in the MeWo immunopeptidome. Integrative Genomics Viewer (IGV) sashimi plot indicating RNA-Seq read depth (RI expression in TPM=5.13, percent-spliced-in [PSI] value=1.07%) and mass spectra. Experiments were repeated five times with independent measurements for cell line MeWo. Neoepitopes shown had one peptide-to-spectrum match (PSM) and were identified in one replicate within 1% false discovery rate (FDR). B, Predicted RI neoepitopes were found to have mass spectrometric evidence supporting their presentation in complex with MHC I using the same methodology in additional tumor cell lines: SK-MEL-5, CA46, DOHH-2, HL-60, and THP-1.