Abstract 6484: Single-cell transcriptomic analysis of hepatocellular carcinoma: elucidating intratumoral heterogeneity and immune microenvironment crosstalk

Abstract Background: Hepatocellular carcinoma (HCC), the third leading cause of cancer deaths worldwide, exhibits significant cellular and molecular heterogeneity. The advent of single-cell transcriptomic methodologies has significantly disclosed its intra-tumoral cellular diversity to an unprecedented level. Interactions between cells within the tumor microenvironment (TME) are crucial for cancer progression and affect how tumors respond to current therapies. Objective: This study aimed to utilize single-cell data to address two main objectives: (1) to dissect the heterogeneous nature of HCC tumors by identifying tumor subclones and their molecular features, key transcription factors, and implicated pathways; and (2) to explore the intricate communication between tumor cells and immune cells, with a focus on the pathways that significantly influence tumor growth and metastasis. Methods: The tissue samples of HCC were obtained from nine patients undergoing surgery immediately from the operation theater after resection, with informed consent. Dissociated tumor single cells were subjected to scRNA-seq by 10X Genomics platform. Results: Our analysis identified seven distinct tumor subclones, validating the presence of high tumor heterogeneity. Among these, one subclone, designated as SC6, exhibited particularly distinctive molecular characteristics. Further investigation revealed that NFE2L3 exhibited the highest activity score during the TFs analysis, indicating its significant regulatory role in SC6 cluster, and was intricately associated with pathways involved in extracellular matrix organization and immune regulation. Through cellular communication analysis, we discovered that tumor-associated macrophages (TAMs) and dendritic cells (DCs) exhibited the highest communication intensity with SC6 cluster when acting as the source of ligands. Further investigation revealed critical ligand-receptor pairs, including some integrin family genes functioning as receptors. This interaction suggests that these integrins may engage with ligands secreted by TAMs or DCs within the TME, potentially promoting tumor cell proliferation and migration. Conclusions: Through comprehensive analysis of scRNA-seq data, we elucidated the intricate heterogeneity within HCC, identifying distinct characteristics of various tumor subclones. Our investigation revealed key transcription factors that predominate in specific subclones. Additionally, we uncovered robust intercellular communication between tumor cells and myeloid cells. Citation Format: Qingyang Zhang, Yu-Man Tsui, Vanilla Xin Zhang, Daniel Wai-Hung Ho, Irene Oi-Lin Ng. Single-cell transcriptomic analysis of hepatocellular carcinoma: elucidating intratumoral heterogeneity and immune microenvironment crosstalk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6484.