Extended Data Fig. 3: Correlation of DNA mutations, glutamic acid substitutions, and motif neoepitopes. | Nature Cancer

Extended Data Fig. 3: Correlation of DNA mutations, glutamic acid substitutions, and motif neoepitopes.

From: Mutational landscape influences immunotherapy outcomes among patients with non-small-cell lung cancer with human leukocyte antigen supertype B44

Extended Data Fig. 3

MEL – melanoma, NSCLC – non-small cell lung cancer, g. – genomic, A – adenine, C – cytosine, G – guanine, T – thymine. Typical scatter plots depicted with line of best fit calculated by least square method, 95% confidence interval shown in gray. a-d: Mutations that can result in radical glutamic acid substitutions (g.A>G, g.T>A, g.G>A, and g.C>A) are pictured. Each point represents a patient (NSCLC N = 38 patients, MEL N = 14 patients). Glutamic acid and mutation proportions calculated as proportion of all radical mutations. e-g: Correlation of glutamic acid substitutions to glutamic acid neoepitopes and B44 motif neoepitopes in NSCLC B44 patients (N=21). Each point represents the number of substitutions/neoepitopes for each B44 patient. All predicted neoepitopes had an IC50 ≤ 500 nM. a, Correlation of the proportion of g.A>G mutations to proportion of radical glutamic acid substitutions, Pearson correlation coefficient 0.03, P=0.85 (that is, correlation not similar between histologies). b, Correlation of the proportion of g.T>A mutations to proportion of radical glutamic acid substitutions, Pearson correlation coefficient -0.20, P=0.16. c, Correlation of the proportion of g.G>A mutations to proportion of radical glutamic acid substitutions, Pearson correlation coefficient 0.60, P<0.001. d, Correlation of the proportion of g.C>A mutations to proportion of radical glutamic acid substitutions, Pearson correlation coefficient -0.61, P<0.001. e, Correlation of the number of glutamic acid radical substitutions with the number of glutamic acid neoepitopes, Pearson correlation coefficient 0.56, P=0.009. f, Correlation of the number of neoepitopes including glutamic acid with the number of motif neoepitopes, Pearson correlation coefficient 0.89, P<0.001 (removing outlier motif neoepitopes=7, R=0.68, P=0.001). g, Correlation of the number of glutamic acid radical substitutions with the number of motif neoepitopes, Pearson correlation coefficient 0.42, P=0.06.

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