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Updated: Apr 5, 2026
Mass Cytometry Analysis of Systemic and Local Immune Responses in Hepatocellular Carcinoma
Published on: April 25, 2025
TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways in
Daniel Wai-Hung Ho1, Alan Ka-Lun Kai, Irene Oi-Lin Ng
1Department of Pathology and State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong SAR, China.
Abstract:
This study systematically evaluates the TCGA whole-transcriptome sequencing data of hepatocellular carcinoma (HCC) by comparing the global gene expression profiles between tumors and their corresponding nontumorous liver tissue. Based on the differential gene expression analysis, we identified a number of novel dysregulated genes, in addition to those previously reported. Top-listing upregulated (CENPF and FOXM1) and downregulated (CLEC4G, CRHBP, and CLEC1B) genes were successfully validated using qPCR on our cohort of 65 pairs of human HCCs. Further examination for the mechanistic overview by subjecting significantly upregulated and downregulated genes to gene set enrichment analysis showed that different cellular pathways were involved. This study provides useful information on the transcriptomic landscape and molecular mechanism of hepatocarcinogenesis for development of new biomarkers and further in-depth characterization.
Insights
This study analyzed hepatocellular carcinoma (HCC) gene expression, identifying novel upregulated and downregulated genes. These findings offer insights into HCC development and potential new biomarkers.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- Hepatocellular carcinoma (HCC) remains a significant global health challenge.
- Understanding the molecular underpinnings of HCC is crucial for developing effective treatments.
- Previous studies have identified some genetic alterations in HCC, but a comprehensive transcriptomic analysis is needed.
Purpose of the Study:
- To systematically evaluate whole-transcriptome sequencing data in HCC.
- To identify novel dysregulated genes in HCC compared to nontumorous liver tissue.
- To elucidate the molecular mechanisms and pathways involved in hepatocarcinogenesis.
Main Methods:
- Utilized The Cancer Genome Atlas (TCGA) whole-transcriptome sequencing data for HCC.
- Performed differential gene expression analysis between tumor and nontumorous tissues.
- Validated key upregulated (CENPF, FOXM1) and downregulated (CLEC4G, CRHBP, CLEC1B) genes using quantitative PCR (qPCR).
- Conducted gene set enrichment analysis (GSEA) to explore mechanistic pathways.
Main Results:
- Identified numerous novel differentially expressed genes in HCC.
- Confirmed significant upregulation of CENPF and FOXM1.
- Confirmed significant downregulation of CLEC4G, CRHBP, and CLEC1B.
- Revealed involvement of distinct cellular pathways in hepatocarcinogenesis through GSEA.
Conclusions:
- The study provides a comprehensive transcriptomic landscape of HCC.
- Identified key genes and pathways implicated in HCC development.
- Findings support the development of novel biomarkers and therapeutic strategies for HCC.
