ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer
Fig 6
Splicing epitopes and response to immune therapy.
(A) Proportion of splicing-affected self-epitopes (self-epitopes) over the total of epitopes, i.e., splicing-derived neoepitopes (splicing-neoepitopes) plus self-epitopes, (y axis) for patients treated with anti-CTLA4, separated by type of splicing alteration (x axis) and by patient response: responder (green) or non-responder (red). (B) As in (A) but for a different cohort of melanoma patients treated with anti-PD1. (C) Cumulative plots of the binding affinities (x axis) of splicing-neoepitopes in melanoma tumors from exonization events separated in responders (green) and non-responders (red) to anti-PD1 therapy. Kolmogorov-Smirnov test p-value (KS) = 0.0465 (D) As in (C), for splicing-derived neoepitopes from neoskipping events, KS = 0.0274. (E) Cumulative plots of the affinities of splicing-neoepitopes in melanoma tumors from intron retention events separated in responders (green) and non-responders (red) to anti-CTLA4 therapy, KS = 0.0016. (F) Frequency of splicing-neoepitopes represented according to the total number of patients in which are predicted (x axis, total_patients_expressed) and to the absolute count-difference in responders and non-responders to anti-PD1 therapy (y axis, Difference number patients each class). Epitopes are indicated in green if they are more frequent in responders, and in red otherwise. The size of the point indicates the number of cases. (G) The same as in (F) but for responders and non-responders to anti-CTLA4 therapy.