单细胞多组学分析揭示肝细胞癌免疫治疗耐药背后的细胞类型特异性遗传调控程序

Although outcomes for patients with advanced hepatocellular carcinoma (HCC) have improved with the advent of immune-checkpoint inhibitor (ICI)-based therapies, only approximately 30% of patients achieve an objective response. With the rapid development of single-cell technologies, increasing attention has been paid to immunosuppressive cell types in the tumor microenvironment (TME) from a transcriptomic perspective; however, the contribution of genetic variation to immunotherapy resistance remains largely unexplored. Here, we employed single-cell multiomics of 14 treatment-naïve and ICI-resistant HCC patients to investigate cell type-specific genetic regulation underlying chromatin accessibility and gene expression within the HCC TME. High-quality single-cell ATAC-seq data were generated for 155,700 cells and annotated into 11 major cell types, including B cells, CAFs, CD4⁺ T cells, CD8⁺ T cells, dendritic cells, endothelial cells, macrophages, monocytes, NK cells, Tregs, and tumor cells. Leveraging genotype information inferred from single-cell ATAC-seq, RASQUAL systematically mapped 23,329 chromatin accessibility-associated quantitative trait loci (caQTLs) across all cell types. We found a wide range of cell number-normalized caQTLs in different cell types (0.01 to 0.22). Notably, tumor cells exhibited the highest frequency of caQTLs, suggesting greater genetic susceptibility within their regulatory landscape. Colocalization with liver cancer-related GWAS signals, combined with peak-to-gene association analyses, identified enhancer-like regulatory elements that may modulate genes involved in tumor progression and immunotherapy resistance. In summary, our study delineates the cell type-specific genetic control and regulatory architecture of HCC TME and provides mechanistic insights into the molecular basis of immunotherapy resistance. Acknowledgement: This study is supported by Li Ka Shing Foundation and CUHK Strategic Seed Funding for Collaborative Research Scheme.