Objective:

To investigate the 3D genomic and epigenetic mechanisms driving macrophage dysfunction induced by HBeAg.

Approach:

• Integration of Techniques: Utilized RNA-sequencing (RNA-seq), high-throughput chromosome conformation capture (Hi-C), and chromatin immunoprecipitation-sequencing (ChIP-seq) to analyze control and HBeAg-stimulated macrophages.
• Cross-Validation: Key findings were validated using human HBV-infected datasets.

Key Findings:

• HBeAg activated pro-inflammatory transcriptional programs, particularly the TNF signaling pathway, and upregulated functional genes such as MET and FHOD3.
• Hi-C analysis showed significant global 3D chromatin reorganization, including B-to-A compartment switching and enhancer accumulation, which exposed new regulatory elements affecting gene expression.
• Restructuring of topologically associating domains (TADs) revealed new regulatory elements affecting gene expression, including the upregulation of FLNB and SESN2.
• Specific intrachromosomal loop disruptions led to downregulation of certain genes, including KBTBD11 and BLVRB.

Interpretation:

HBeAg induces a coordinated restructuring of the 3D genome and targeted epigenetic reprogramming, contributing to macrophage dysfunction through mechanisms involving H3K27ac enhancer deposition and alterations in structural boundaries.

Limitations:

• The study primarily used murine macrophage models, which may not fully replicate human responses, limiting the generalizability of the findings.
• Further research is needed to explore the clinical implications of identified structural variants and their relevance in human HBV infection.

Conclusion:

The findings provide novel mechanistic insights into HBV-related liver diseases, highlighting potential therapeutic targets such as MET, FLNB, and BLVRB.