The chromatin state in WT and HPK1KO tumor specific T cells

We then investigated how HPK1 induces new changes by comparing the open chromatin regions (OCRs) with WT control and founded that the ATAC-seq tracks were aligned with the previously reported OCRs of exhausted . HPK1 knockout induced loss of peaks in loci enriched in exhausted T (Tex) cells (e.g., PD-1, TIM-3, LAG-3, and TOX locus), indicating that HPK1 knockout could overcome some negative effects caused by TME, ameliorate T cell exhaustion and thus extend their effector function (Figure S2F). Moreover, we also found that more accessible regions in HPK1-knockout CD8+TILs showed significant enrichment for pathways associated with cell cycle, antigen processing and presentation, T cell receptor signaling, Glyoxylate and dicarboxylate metabolism, AMPK pathway, and C-type lectin receptor signaling pathway (Figure S2G). It has been demonstrated that many peak changes were unique to either the early dysfunctional or functional state and included TCR signaling and cytokine production pathway genes. Pauken and the colleagues identified two metagenes in anti-PD-L1–treated exhausted T cell (TEX) compared to control TEX; one corresponding to leukocyte activation and one to cell cycle. The anti-PD-L1–treated TEX metagenes displayed some overlap with effector T cells (TEFF), largely driven by cell cycle pathways, but minimal overlap with Memory T cell (TMEM). Thus, we concluded that HPK1-/- TILs are prone to be effort T cells defined according to the chromatin states. Overall design: Assay for Transposase-Accessible Chromatin using sequencing to analyze the chromatin state in WT and HPK1KO tumor specific T cells.