Extended Data Fig. 1: Lower burden and expression of predicted neoantigens in MSS versus MSI-H CRC.
From: Low neoantigen expression and poor T-cell priming underlie early immune escape in colorectal cancer
(a) Total expressed neoantigens by patient including hypermutant MSS cases (in purple). N = 62 MSI-H, 68 MSI-L, and 275 (including 9 hypermutant) MSS patients. All other plots exclude hypermutant MSS cases. (b) Mean expression of all neoantigens, regardless of clonality, by patient. N = 62 MSI-H, 68 MSI-L, and 266 MSS patients. (c-d) Analysis of patients with available ABSOLUTE purity for estimation of clonality (adjVAF). N = 50 MSI-H, 58 MSI-L, and 236 non-hypermutant MSS patients. (c) Empirical cumulative distribution function of mean neoantigen clonality (adjVAF) by patient. Significance was assessed by two-sided Kolmogorov-Smirnov test. (d) Total expressed clonal neoantigens with predicted HLA-I binding IC50 ≤ 500 nM by patient. (e) Mean allele-specific expression of clonal SNV-derived neoantigens by patient, excluding neoantigens with zero gene level expression but including those with zero allele-specific expression. N = 41 MSI-H, 53 MSI-L, and 219 MSS patients. (f-g) Abundance distributions of HLA-I ligandomes by MS in PDOs from MSS CRC patients CRC_01 (f) and CRC_04 (g) with epitope abundance above the median in gray, below the median in light blue, and neoantigens in red. Data from Newey, A, et al., 2019. Significance in (b), (d), and (e) was assessed by two-tailed Wilcoxon Rank Sum test with Holm’s correction for multiple comparisons. Source data for panels (a-e) can be found in Source Data Fig. 1a-e.
