Innate lymphoid cell heterogeneity and etiology-specific reprogramming in hepatocellular carcinoma

Hepatocellular carcinoma (HCC), the third leading cause of cancer-related deaths worldwide, arises from diverse etiologies that shape the tumor immune landscape, including the composition and function of innate lymphoid cells (ILCs). In this study, we integrated scRNA-seq, bulk RNA-seq, and CyTOF to profile ILCs from tumor and adjacent non-tumor liver tissues of 50 HCC patients with different etiologies (hepatitis B viral, HBV and non-viral, NV). ScRNA-seq revealed heterogenous ILC and NK clusters in non-tumor and tumor tissues. Notably, ILC1 could be subdivided into proliferative (ILC1p) and cytotoxic (ILC1c) phenotypes. ILC2 displayed classic type-2 immune traits with phenotypic heterogeneity, while ILC3 expressed key transcription factors and IL18. ILC subsets diverged significantly by disease etiology. In NV-HCC, ILC2s exhibited a pro-fibrotic and tumor-promoting signature with elevated IL13, TGFB1, and AREG expression. ILC1s in NV-HCC showed activated and cytotoxic phenotypes, whereas in HBV-HCC, they showed signs of exhaustion with increased CD96 and TIGIT. ILC1 from NV-HCC also displayed enhanced IL-2/IL-15 signaling and interactions with CD8 + T cells via HLA-E, suggestive of potential antitumor crosstalk. While our single-cell cohort size was limited, necessitating validation in larger datasets, our study reveals etiology-associated differences in ILC phenotypes in HCC and provides insight into their potential roles in modulating immune responses within the tumor microenvironment.