Bile acid dysregulation, microbiome dysbiosis and epigenetic modifications in hepatocellular carcinoma: Biomarker for earlier detection

Liew, R., Sekar, K., Chong, S. L., Bonney, G., Bunchaliew, C., Chang, J. P. E., Chia, P. Y., Chiow, A., Chong, Q. F., Choo, J., De Roza, M., Shelat, V. G., Goh, B., de Villa, V. H., Ithnin, S., Kam, J. H., Lee, G. H., Lim, J., Ong, K. K., … Chow, P. K. H. (2025, September 19–20).

Bile acid dysregulation, microbiome dysbiosis and epigenetic modifications in hepatocellular carcinoma: Biomarker for earlier detection. SingHealth Duke-NUS Scientific Congress 2025, Academia, SGH Campus, Singapore.

An urgent need for better early detection.

• Rising prevelance of metabolic-associated HCC.
• Curable only if detected early, but early detection fails (AFP/US: 63% sensitivity)
• Bile acid dysregulation was found in multiple HCC cohort studies (PLANet/ ELEGANCE/ SCHS), but the mechanism remains unknown.

METHOD

• Multi-omics profiling: Stool metagenomics (shotgun) and BA qualification (LC-MS/MS) in 50 ELEGANCE subjects (16 controls/ 9 pre-HCC), validated in 196 high-risk patients (27 developed HCC).
• Tissue Transcriptomics: Bulk RNA-seq of paired tumour/ adjacent normal tissues from 115 PLANet HCC cases.
• Epigenetic Exploration: Nano-ChIP-seq (n=10) for H3K27ac in tumour/adjacent tissues (PLANet cohort).

RESULTS

Differential microbial species in HCC patients, patients without HCC, and patients who progressed to HCC. Expanded PLSDA plot showing bacterial species and abundance in each sample, clustered by distinct subgroups, suggesting pre-diagnostic signatures relating to cancer development and the gut-liver axis.

Depletion in beneficial microbes is more significant in NBNC-HCC vs HBV-HCC. Significant depletion of critical butyrate producers in HCC patients. Depletion is more extensive in NBNC-HCC than HBV-HCC, suggesting a more extensive
metabolic disruption in NBNC HCC’s gut-liver axis.

Significant Serum Bile Acid Elevation Found At Least 6 Months Before Clinical Detection of HCC (via US + AFP). Elevated 12α-hydroxylated bile acids from the classical pathway and a declining non-12α-hydroxylated /12α-hydroxylated ratio emerges ≥6 months before HCC is clinically diagnosed.

This pathogenic shift precedes visible tumour formation, offering novel preclinical biomarkers for early HCC risk stratification and closer surveillance in high-risk populations.

Divergent Bile Acid Dysregulation between Aetiologies: CYP7A1-Driven in Non-Viral vs. NTCP Failure in HBV.

Novel H3k27ac Enhancement found at CYP7A1 promoter region in HCC Tumour vs Paired-normal. Novel discovery of H3K27ac enhancement at the CYP7A1 promoter in 100% of NBNCHCC tumours, directly linking enhancer dysregulation to pathogenic CYP7A1gene upregulation (log2FC=1.68). Subset of HBV-HCC exhibits this phenomenon.

CONCLUSION

Elevated bile acid emerges ≥6 months before HCC diagnosis serving as
potential early biomarker for high-risk surveillance. Specifics of bile acid
dysregulation unique to aetiologies. First-reported H3K27ac enhancement of
CYP7A1 in HCC.