T cell exhaustion and residency dynamics inform clinical outcomes in hepatocellular carcinoma

Background and aims: Despite recent translation of immunotherapies into clinical practice, the immunobiology of hepatocellular carcinoma, in particular the role and clinical relevance of exhausted and liver-resident T cells remain unclear. We therefore dissected the landscape of exhausted and resident T cell responses in the peripheral blood and tumor microenvironment of HCC patients. Methods: Lymphocytes were isolated from blood, tumor and tumor-surrounding liver tissue from HCC patients (n=40, n=10 treated with anti-PD-1 therapy). Phenotype, function and response to anti-PD-1 were analyzed by mass and flow cytometry ex vivo and in vitro, tissue residence was further assessed by immunohistochemistry and imaging mass cytometry. Gene signatures were assessed in silico. Results: We identified significant enrichment of heterogeneous populations of exhausted CD8+ T cells (TEX) in the tumor microenvironment. Strong enrichment of severely exhausted CD8 T cells expressing multiple immune checkpoints in addition to PD-1 was linked to poor progression-free and overall survival. In contrast, PD-1 was also expressed on a subset of more functional and metabolically active CD103+ tissue-resident memory T cells (TRM) that expressed few additional immune checkpoints and were associated with better survival. TEX enrichment was independent from BCLC stage, AFP levels or age as a variable for progression-free survival in our cohort. These findings were in line with in silico gene signature analysis of TCGA-HCC tumor transcriptomes. A higher baseline TEX/TRM ratio was associated with disease control in anti-PD-1 treated patients. Conclusion: Our data inform about a role of peripheral and intratumoral TEX - TRM dynamics in determining the outcomes of HCC patients. The dynamics between exhausted and liver-resident T cells have implications for immune-based diagnostics, rational patient selection and monitoring during HCC immunotherapies. Lay summary: The role of the immune response in hepatocellular carcinoma (HCC) remains unclear. T cells, particularly effector or tissue-resident T cells can mediate protection against tumor cells, but are frequently dysfunctional and exhausted in cancer. To understand if these immune populations play significant roles in HCC, we investigated blood and tumor-derived T cells from HCC patients for different T cell types using advanced immune profiling technology able to characterize these populations in detail. We found that patients with a dominance of exhausted CD8+ T cells (TEX) had poor survival, in contrast to patients with a dominance of tissue-resident memory cells (TRM) and longer survival. This correlated with the molecular profile, metabolic and functional status of these cell populations. The enrichment of TEX was independently associated with prognosis in addition to disease stage, age and tumor markers. A high TRM proportion was also associated with better outcome to checkpoint therapy. Thus, these T cell populations are novel biomarkers relevant for HCC patients.