Impending hepatocellular carcinoma diagnosis in cirrhotic patients after HCV cure features a natural killer cell signature

Introduction: The risk of developing hepatocellular carcinoma (HCC) in chronically infected hepatitis C virus (HCV) patients with liver cirrhosis is significantly elevated. This risk remains high even after a sustained virological response (SVR) with direct acting antivirals (DAA). To date, disease-associated signatures of natural killer (NK) cells indicating HCC development are unclear. This study investigated NK cell signatures and functions in eight cohorts covering the time span of HCC development, diagnosis, and onset. In-depth analysis of NK cell profiles from cirrhotic patients that developed HCC (HCV-HCC) post SVR compared to those who remained tumor-free (HCV-noHCC) revealed increasingly dissimilar NK cell signatures over time. We identified expression patterns with persistently high frequencies of TIM-3 and CD38 on NK cells that was largely absent in healthy controls and was associated with a high probability of HCC development. Functional assays revealed that the NK cells had potent cytotoxic features. In contrast to HCV-HCC, the signature of HCV-noHCC converged with the signature found in healthy controls over time. Regarding tissue-distribution, single-cell-sequencing showed high frequencies of these cells in liver tissue and the invasive margin, but markedly lower frequencies in tumors. Conclusion: We show that HCV-related HCC development has profound effects on the imprint of NK cells. Persistent co-expression of TIM-3 hi and CD38 + on NK cells is an early indicator for HCV-related HCC development. We propose profiling of NK cells may be a rapid and valuable tool to assess the risk of HCC development in a timely manner in cirrhotic patients after HCV cure.