Single-Cell Multiomics Analysis Reveals Heterogeneous Cell States Linked to Metastatic Potential in Liver Cancer Cell Lines

Abstract

Liver cancer is a malignant neoplasm with a high mortality and recurrence rate. The most common liver cancer is hepatocellular carcinoma (HCC). One of the major obstacles to successful treatment of HCC is a high rate of metastasis. However, the molecular mechanisms that drive high metastasis rates remain unclear. Single-cell multi-omics methods provide deep and comprehensive insight into cell states, and may elucidate mechanisms underlying disease processes, including metastasis. We combined single-cell transcriptomic, proteomic and chromatin accessibility data to investigate how heterogeneous phenotypes contribute to metastatic potential in five HCC cell lines. We confirmed that the prevalence of a mesenchymal state is linked to the metastatic potential. Levels of cell proliferation were also linked to metastatic capacity, though this correlate was not absolute across cell lines. In addition, we identified a rare hypoxic subtype that has a higher capacity for glycolysis and exhibits dormant, invasive, and malignant characteristics. This subtype has increased metastatic potential. We further identified a robust 14-gene panel representing this hypoxia signature and verified its presence in clinical samples. Our data suggest that the presence of this hypoxia signature could serve as a prognostic index. We investigated phenotypes in HCC cell lines that include EMT capacity, cell proliferation, and hypoxia status and linked these to their metastatic potential. Our data provide a valuable data resource, facilitate a deeper understanding of metastatic mechanism, and may help diagnosis of metastatic potential in individual patients, thus supporting personalized medicine.