Fig. 6: Validation of neoantigen-stimulated T cell responses from prostate cancer patients. | Nature Machine Intelligence

Fig. 6: Validation of neoantigen-stimulated T cell responses from prostate cancer patients.

From: Sliding-attention transformer neural architecture for predicting T cell receptor–antigen–human leucocyte antigen binding

Fig. 6

a, Schematic of the validation experiment. Somatic mutations were identified by the WES of surgically resected prostate tissues and matched normal cells (PBMCs), and their expression was confirmed by tumour RNA-seq. Candidate immunogenic peptides were selected and validated based on the statistics of binding prediction by PISTE. b, In vitro detection of T cell responses for PBMCs stimulated with individual neoantigens by IFN-γ ELISA. c, IFN-γ production on CD8+ T cells against selected peptides was detected by flow cytometry for patient PCA03 and patient PCA06. Percentages shown in the density plots are frequencies of reactive IFN-γ+ cells as a proportion of all the CD8+ T cells. P value was determined via one-way analysis of variance with Dunnett’s multiple comparisons test. n = 3 repeated technical measurements; error bars show the standard error of the mean. The dashed line indicates the baseline for the identification of positive reactions (Methods). SSC-H, side scatter height. Panel a created with BioRender.com.

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