Background
Liver disease due to viral hepatitis is a leading cause of mortality in PWH. Elucidating host genes that affect HBV transcription may accelerate hepatitis B virus (HBV) cure discovery. We hypothesized that host genes modulate HBV transcription during nucleos(t)ide analogue (NUC) therapy.
Methods
We used mRNA-capture slides (10X Genomics) on liver biopsies from 14 people with HIV and CHB (PWHHB) to sequence 100-250 million read-pairs per sample (Illumina NovaSeq 6000). Reads were mapped to a custom human+HBV reference. After quality control, we applied robust cell-type decomposition within gene expression spots to identify hepatocytes where HBV replicates and immune cell populations. We applied linear mixed-effects regression (LMER) using HBV RNA as a covariate to identify host genes associated with HBV transcription. Pathway analysis was performed.
Results
Among 7 HBeAg-positive (EP) PWHHB, median values were: HBV DNA (Log10 IU/ml) 4.1, HIV RNA <20 cp/ml, duration of NUCs 7 years (0.1 – 12.5); 1 participant was treatment-naïve and 1 underwent rapid HBeAg seroconversion (HBeSC) post-biopsy. Among 7 HBeAg-negative (EN) PWHHB, all but one had undetectable HBV DNA, all had HIV RNA <20 cp/ml, and NUC duration was 8.1 years (7.0 – 9.1). We analyzed 54,250 genes across 25,109 cell spots. LMER on HBV+ hepatocytes (spots) among EP identified 727 upregulated and 76 downregulated host genes (mean fixed effect + 6SD, adjusted p-value < 0.05). The expression pattern of the top 50 significant genes varied with NUC duration, showing higher expression in hepatocytes from EP with long-term NUC. These genes comprised several enriched pathways crucial to liver function, such as the lipid metabolic process (adjusted p-value = 1.6e-05, fold enrichment = 10.64). Furthermore, immune response pathways to viral infection were enriched, highlighted by 15 upregulated genes (e.g., C3, APOA1). Enriched lymphocyte markers surrounding HBV-transcribing hepatocytes were identified in EP with the longest antiviral treatment and in most EN compared to those EP with short-term treatment. Notably, the post-biopsy HBeSC EP with short-term NUC exhibited pronounced expression of these markers around HBV+ hepatocytes.
Conclusions
Spatial transcriptomics of liver from PWHHB reveals that HBV transcription was closely associated with host metabolic processes and immune responses. These findings underscore intricate dynamics between HBV and host cellular machinery, yielding putative genes and pathways affecting HBV transcription.
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