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Updated: Mar 6, 2026
A Three-Dimensional Spheroid Model to Investigate the Tumor-Stromal Interaction in Hepatocellular Carcinoma
Published on: September 30, 2021
Circumventing intratumoral heterogeneity to identify potential therapeutic targets in hepatocellular carcinoma
Ao Huang1, Xin Zhao2, Xin-Rong Yang1
1Liver Surgery Department, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, China.
Background & Aims:
Identifying target genetic mutations in hepatocellular carcinoma (HCC) for therapy is made challenging by intratumoral heterogeneity. Circulating cell-free DNAs (cfDNA) may contain a more complete mutational spectrum compared to a single tumor sample. This study aimed to identify the most efficient strategy to identify all the mutations within heterogeneous HCCs.
Methods:
Whole exome sequencing (WES) and targeted deep sequencing (TDS) were carried out in 32 multi-regional tumor samples from five patients. Matched preoperative cfDNAs were sequenced accordingly. Intratumoral heterogeneity was measured using the average percentage of non-ubiquitous mutations (present in parts of tumor regions). Profiling efficiencies of single tumor specimen and cfDNA were compared. The strategy with the highest performance was used to screen for actionable mutations.
Results:
Variable levels of heterogeneity with branched and parallel evolution patterns were observed. The heterogeneity decreased at higher sequencing depth of TDS compared to measurements by WES (28.1% vs. 34.9%, p<0.01) but remained unchanged when additional samples were analyzed. TDS of single tumor specimen identified an average of 70% of the total mutations from multi-regional tissues. Although genome profiling efficiency of cfDNA increased with sequencing depth, an average of 47.2% total mutations were identified using TDS, suggesting that tissue samples outperformed it. TDS of single tumor specimen in 66 patients and cfDNAs in four unresectable HCCs showed that 38.6% (26/66 and 1/4) of patients carried mutations that were potential therapeutic targets.
Conclusions:
TDS of single tumor specimen could identify actionable mutations targets for therapy in HCC. cfDNA may serve as secondary alternative in profiling HCC genome.
Lay Summary:
Targeted deep sequencing of single tumor specimen is a more efficient method to identify mutations in hepatocellular carcinoma made from mixed subtypes compared to circulating cell-free DNA in blood. cfDNA may serve as secondary alternative in profiling HCC genome. Identifying mutations may help clinicians choose targeted therapy for better individual treatments.
Insights
Targeted deep sequencing of single tumor tissue is more effective than circulating cell-free DNA for identifying mutations in hepatocellular carcinoma (HCC). This approach helps pinpoint therapeutic targets for personalized cancer treatment.
Area of Science:
- Oncology
- Genetics
- Molecular Biology
Background:
- Hepatocellular carcinoma (HCC) presents intratumoral heterogeneity, complicating targeted therapy identification.
- Circulating cell-free DNA (cfDNA) offers a potential alternative for comprehensive mutational profiling.
- Accurate identification of genetic mutations is crucial for effective HCC treatment strategies.
Purpose of the Study:
- To determine the most efficient strategy for identifying all mutations in heterogeneous HCC.
- To compare the efficacy of targeted deep sequencing (TDS) and cfDNA analysis for mutation detection.
- To screen for actionable mutations using the optimal profiling method.
Main Methods:
- Whole exome sequencing (WES) and TDS were performed on 32 multi-regional tumor samples from five HCC patients.
- Matched preoperative cfDNAs were sequenced.
- Intratumoral heterogeneity was quantified, and profiling efficiencies of single tumor specimens versus cfDNA were compared.
Main Results:
- TDS of a single tumor specimen identified an average of 70% of total mutations, outperforming cfDNA (47.2%).
- Higher sequencing depth in TDS reduced heterogeneity measurements compared to WES.
- 38.6% of patients analyzed had actionable mutations identified via TDS of single tumor specimens.
Conclusions:
- Targeted deep sequencing of single tumor specimens is a highly efficient method for identifying actionable mutations in HCC.
- cfDNA serves as a secondary option for profiling HCC genomes.
- Identifying specific mutations enables personalized therapeutic strategies for HCC patients.
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