Fig. 6: Structural modeling demonstrates that pre-treatment T^Prolif_Tox clonotypes are predicted to bind patient-matched HLA-specific tumor neo-antigen but the T^Prolif_Tox signature and the clones that express it are lost after radiotherapy.

a Whole exome and RNA sequencing mutational analyses were performed pre-treatment and at 6 weeks post-radiation for the primary tumor of HyPR Patient 02, demonstrating substantial overlap in transcribed coding mutations, which translation into candidate neo-antigens. b Predicted binding between TCRs and neo-antigen-HLA complexes for HyPR-HN Patient 02. Binding scores were zero-shifted and normalized. Binding prediction for each neo-peptide-HLA complex was compared between T^Prolif_Tox TCRs and patient-matched irrelevant naïve TCRs. Within each pHLA complex, we performed 10,000 bootstrap replicates by sampling with replacement from the control group and, for each replicate, recording the lowest PAE_SD scores. This bootstrap procedure generated an empirical null distribution of extreme binding scores. The 95% confidence interval for the minimum PAE_SD was calculated using the T distribution. The empirical p-value was then calculated using this same T distribution. For each neo-peptide-HLA complex, a T^Prolif_Tox clonotype demonstrates the greatest predicted binding affinity. Among all HyPR-HN patients, (c) the T^Prolif_Tox expression profile and (d) the associated clonotypes that express it are lost after radiation and do not return to the tumor. Pre-ex Pre-exhausted T cells, Reg Regulatory T cells, TRM Tissue-resident memory T cells, Prolif Proliferative T cells, Ex^CD8 Exhausted CD8 T cells, Ex^CD4 Exhausted CD4 T cells, IFN Type I interferon-responsive T cells. The box plot represents the 25th to 75th percentile, and the whiskers represent 1.5x the interquartile range.