Integrated Single-Cell and Bulk Transcriptomic Analysis Reveals an Endothelial Gene Signature Shaping EndMT and Prognosis in Hepatocellular Carcinoma

<h4>Background</h4>Hepatocellular carcinoma (HCC) is one of the most prevalent malignant tumors of the liver, with increasing incidence and mortality rates globally. This study investigates the role of endothelial cells (ECs) in the progression of HCC, particularly focusing on the process of endothelial-to-mesenchymal transition (EndMT) and its underlying molecular mechanisms.<h4>Methods</h4>We utilized single-cell RNA sequencing (scRNA-seq) and multiomics analyses to explore the involvement of ECs in HCC and their transformation mechanisms. The study emphasized the potential application of EC-related genes (ECRGs) in prognostic evaluation for HCC patients. Furthermore, HCC organoids were utilized to validate the functional relevance of selected ECRGs.<h4>Results</h4>ECs play a critical role in the progression of HCC, particularly through mechanisms related to EndMT and its influence on patient prognosis. We identified 19 key ECRGs that are pivotal to the initiation and development of HCC and constructed a robust prognostic model using LASSO regression analysis. Notably, this gene signature effectively stratifies HCC subtypes and reveals significant differences in immune cell infiltration and immune checkpoint gene expression among EC-related prognostic groups, underscoring its potential relevance in guiding immunotherapy, sorafenib therapy, and transarterial chemoembolization (TACE) outcomes. Furthermore, the coculture system of HCC and vascular organoids successfully mimicked the EndMT process, revealing spatial colocalization of three ECRGs-MPZL2, KITLG, and PCDH1-with established EndMT markers, suggesting their potential as therapeutic targets in tumor-associated endothelial plasticity.<h4>Conclusions</h4>This study emphasizes ECs' role in HCC progression and how EndMT affects prognosis. HCC organoids revealed ECRGs linked to EndMT, like MPZL2, KITLG, and PCDH1, as potential therapeutic targets.