Related Experiment Video
Updated: Aug 6, 2026
Generation and Single-Cell Transcriptomic Analysis of Hepatocellular Carcinoma Organoids following Drug Treatment
Published on: May 26, 2026
Dissecting liver cancer stem cell heterogeneity via single-cell RNA sequencing and developing a stemness-based
Jinhan Zhao1, Jiaqi Feng1, Pengpeng Zhang1
1Department of Lung Cancer, Tianjin Lung Cancer Center, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, P.R. China.
Liver cancer stem cells drive hepatocellular carcinoma (HCC) progression. This study identifies distinct stemness-enriched subpopulations (Cluster 3 and Cluster 4) and develops a prognostic signature (C3C4-SPS) for HCC patient risk stratification.
Area of Science:
- Oncology
- Genomics
- Metabolomics
Background:
- Liver cancer stem cells (CSCs) are key drivers of hepatocellular carcinoma (HCC) initiation, progression, and recurrence.
- Understanding the molecular and metabolic heterogeneity of CSC subpopulations is critical for targeted therapy development.
Purpose of the Study:
- To characterize the molecular and metabolic heterogeneity of liver CSC subpopulations in HCC.
- To identify stemness-enriched CSC subpopulations and their role in tumor progression.
- To develop a prognostic signature for HCC based on CSC features.
Main Methods:
- Integrated single-cell RNA sequencing data from two HCC cohorts (GSE149614, GSE156625).
- Applied clustering, annotation, mitochondrial scoring, CytoTRACE, and pseudotime analyses to identify and characterize CSC subpopulations.
- Developed and validated the Cluster 3 and Cluster 4 Stemness-based Prognostic Signature (C3C4-SPS) using survival analysis.
Main Results:
- Identified eight malignant cell subpopulations in HCC, revealing significant intratumoral heterogeneity.
- Discovered two stemness-enriched subpopulations (Cluster 3 and Cluster 4) with high metabolic activity and distinct functional pathways (oxidative phosphorylation vs. fatty acid oxidation).
- Demonstrated that high expression of signature genes from these clusters is associated with unfavorable HCC prognosis, and the C3C4-SPS model effectively stratified patient risk.
Conclusions:
- Systematically characterized molecular and metabolic heterogeneity of liver CSC subpopulations in HCC.
- Elucidated the critical roles of stemness-enriched CSCs in HCC tumor progression and patient prognosis.
- The C3C4-SPS model offers a novel tool for prognostic assessment and potential individualized therapy targeting stemness in HCC.
