Decoding Hepatocellular Carcinoma in Fontan-Associated Liver Disease: Genomic and Transcriptomic Insights

Highlight

• FALD-associated HCCs show distinct genomic mutation profiles, including DNA double-strand break repair deficiency signatures and increased structural variants.
• Postoperative stress from congenital heart surgery contributes to genomic alterations shared by FALD and non-Fontan CHS HCCs.
• FALD HCCs have elevated copy number alterations and structural variants compared to benign FALD liver nodules, implicating these genomic changes as hepatocarcinogenesis triggers.
• Transcriptomic profiling places FALD HCC within established poor-prognosis HCC subclasses characterized by progenitor-like phenotypes.

Study Background

Fontan-associated liver disease (FALD) is a chronic hepatic complication arising in patients who have undergone the Fontan procedure, a palliative surgery for single-ventricle congenital heart defects. Due to chronic venous congestion and hypoxia caused by altered hemodynamics, FALD can progress to cirrhosis and significantly increase the risk of hepatocellular carcinoma (HCC). The prognosis for FALD patients who develop HCC is notably poor, underscoring a critical need for a deeper understanding of the molecular mechanisms underlying hepatocarcinogenesis in this unique clinical context. Given that the pathophysiology of FALD differs from more common etiologies of liver disease, targeted genomic and transcriptomic analyses could elucidate distinctive carcinogenic pathways and identify prognostic biomarkers or therapeutic targets.

Study Design

This study enrolled 10 patients with FALD-related HCC, 2 patients with non-Fontan congenital heart surgery (CHS)-associated HCC, and 1 patient with FALD focal nodular hyperplasia (FNH) as a benign liver lesion comparator. Comprehensive genomic analyses were performed, including whole-genome sequencing (WGS) and RNA transcriptome sequencing, to characterize mutation burdens, structural variants, and gene expression profiles. The genomic landscapes of these cases were compared against large-scale HCC datasets available in established databases to contextualize findings relative to HCCs of other etiologies.

Key Findings

Tumor Mutation Burden and Mutation Signatures: FALD HCCs exhibited mutation burdens comparable to those of conventional HCC cases sourced from public databases. Notably, mutation signature analysis revealed prominent DNA double-strand break (DSB) repair deficiency patterns, implicating compromised genomic maintenance pathways in FALD hepatocarcinogenesis. Interestingly, similar mutation signatures were observed in non-Fontan CHS HCCs and even in benign FALD FNH lesions, suggesting that postoperative physiological stress may initiate or propagate mutational processes.

Structural Variants and Copy Number Alterations: FALD and non-Fontan CHS HCCs demonstrated significantly higher numbers of copy number alterations (CNAs) and structural variants—including short deletions and chromosomal translocations—compared to benign FALD FNH. The burden of these structural genomic changes frequently affected genes known to be recurrently altered in HCC, indicating these alterations could act as oncogenic triggers in this specialized patient population. The rarity of such variants in benign lesions highlights their likely role in malignant transformation.

Transcriptome Profiling and HCC Subclassification: RNA sequencing-based expression analysis revealed that individual FALD and non-Fontan CHS HCCs clustered into recognized HCC molecular subclasses characterized by progenitor-like or stemness phenotypes. These subclasses are associated with less differentiated tumor cells and correlate clinically with poorer prognosis. Importantly, FALD HCCs did not cluster into any uncommon molecular subclasses, suggesting that despite unique etiological origins, their transcriptomic landscape aligns with aggressive conventional HCC subtypes.

Expert Commentary

This pioneering molecular characterization of FALD-associated HCC sheds light on how chronic hemodynamic stress and surgery-related factors may influence tumor development through genomic instability and structural genomic alterations. The observation of DNA repair deficiency signatures parallels findings in other cancer types where defective homologous recombination promotes carcinogenesis. Clinically, recognizing that FALD HCCs reside within poor-prognosis transcriptional subclasses highlights the urgency for vigilant surveillance and potentially aggressive management strategies.

Limitations include the relatively small sample size and the lack of longitudinal data correlating mutation dynamics with clinical outcomes. Moreover, the shared mutation signatures between benign and malignant lesions indicate complexity in attributing causality solely to genetic events, emphasizing the likely contribution of epigenetic and microenvironmental factors. Future studies integrating multi-omics data and larger cohorts are needed to validate these findings and unveil therapeutic vulnerabilities.

Conclusion

FALD-associated HCC exhibits distinct genomic and transcriptomic profiles that differentiate it from HCCs of other causes. Genomic instability evidenced by DNA double-strand break repair deficiency and increased copy number alterations likely plays a critical role in the pathogenesis of these tumors. Transcriptomic classification places these cancers in aggressive progenitor-like HCC subclasses, accounting for their poor clinical prognosis. This integrated molecular insight not only advances understanding of Fontan-associated hepatocarcinogenesis but also sets the foundation for developing tailored surveillance protocols and targeted therapeutic strategies.

Funding and Clinical Trials

The study was supported by grants from relevant cardiovascular and oncology research foundations aligned with institutional policies. No registered clinical trials were reported.

References

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