Deconvoluting the spatial immune landscape in the Hepatitis B Virus infected human liver at single-cell resolution

Chronic hepatitis B virus (cHBV) infection remains a major global health problem due to risk of progression to cirrhosis and hepatocellular carcinoma. However, the interactions of immune cells and virally infected parenchymal cells, in particular that mediate immune escape, remain poorly understood. We thus set out to generate a spatially resolved cell atlas of the cHBV-infected liver.

To this end, we applied multiplexed ion beam imaging by time-of-flight (MIBI-TOF) to profile the expression of 38 proteins at sub-cellular resolution in liver tissue from a first cohort of 4 patients diagnosed with cHBV infection.

Our panel enabled the simultaneous detection of liver parenchymal cells, immune cells, stromal cells, and HBV antigens within the liver microenvironment. Cells were organized into distinct microenvironmental niches, each associated with specific functions. Niches compositions varied across liver zonation. HBV-infected hepatocytes were concentrated in Zone 3. Proximity analysis identified CD103+tissue-resident memory T cells (TRM), macrophages, and NK cells as the closest immune cells to HBV-infected hepatocytes, suggesting these cells as key mediators for HBV clearance. Patients were stratified into two groups based on liver enzyme levels: mid immune-active and high immune-active. High immune-active patients exhibited an increased density of PD-1-CD103+TRM cells, while PD-1+CD103+TRM cells were higher in the mid immune-active group. The different expression pattern of additional exhaustion markers between these two TRM subsets revealed they may have distinct functional roles in the immune response to HBV.

These findings suggest that spatial profiling can reveal immune interactions contributing to disease progression during cHBV infection.

Publication History

Article published online:
20 January 2025