Extended Data Fig. 7: Single-cell TCR sequencing analysis of tumour-associated T cells from patient 7. | Nature

Extended Data Fig. 7: Single-cell TCR sequencing analysis of tumour-associated T cells from patient 7.

From: Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial

Extended Data Fig. 7

a, Single-cell TCR sequencing analyses of tumour-associated T cells, CD4+ neoantigen assay peptide pool-reactive T cells from peripheral blood ex vivo and CD8+ neoantigen-reactive T cell lines (stimulated with ARHGAP35MUT and SLX4MUT) show enrichment of particular clonotypes. b, Sorting strategy for isolating neoantigen pool-reactive CD4+ T cells from peripheral blood ex vivo. Negative control, DMSO. c, Six TCRs identified in both tumour-associated and neoantigen-reactive T cells from peripheral blood were successfully cloned and expressed in the reporter cell line, as verified by stabilized CD3 surface expression; this experiment was repeated twice in independent experiments. The CDR3 sequences of these TCRs can be found in Supplementary Table 9. d, The largest CD8+ clone detected among the neoantigen-reactive T cell lines established from peripheral blood of patient 7 was experimentally confirmed to be specific for EPT12A, the MHC class I predicted epitope of ARHGAP35MUT. Two-sample two-sided t-tests with Welch correction were used for the comparisons; n = 4 biologically independent replicates; data are mean ± s.d. e, CD4+ ARHGAP35-specific H02 and F10 TCRs (as described in Fig. 4) discriminate between the mutant and wild-type form of the peptide. n = 2 biologically independent samples, each with two technical replicates; data are mean ± s.e.m. f, The ARHGAP35 mutation in the tumour of patient 7 is present in both the initial and relapse tumour specimens, as visualized by the IGV30.