Recent single-cell transcriptomic data has implicated foetal immune cells in the pathogenesis of biliary atresia (BA) but why there are immature B-cells present in the postnatal liver is unknown. To understand the mechanisms behind this, we performed a meta-analysis of RNA sequencing data from infants with BA at the time of Kasai and age-matched controls. Previous analyses had been limited by small numbers of controls; however, here, we have increased power to detect associations.

We obtained transcriptomic data from n=177 children with BA and n=78 controls from Gene Expression Omnibus. After filtering and quality control, we performed differential gene expression analysis comparing BA versus control (using DESeq2), with p-value adjustment for multiple testing.

We identified 1,815 significantly differentially expressed genes (figure 1A). Many were involved in extracellular matrix remodelling/fibrosis (e.g. CAPG, TGFBI) and phagocytic activity (e.g. CHIT1, CYBA). We observed increased expression of TREM2 (figure 1B), which is implicated in profibrogenic scar-associated macrophages in adults and has not previously been described in children.

Patients with BA had increased expression of multiple markers of haematopoiesis, including erythroid lineage (e.g. GYPA, HBA1) and early B-cell (e.g. RAG2) (figure 1C). We identified up-regulation of insulin-like growth factor 2 (IGF2, log2 fold change 2.5, pFDR = 2.8x10^-40, figure 1D). IGF2 is a growth factor for haematopoietic stem cells in the foetal liver. IGF2 is secreted by hepatocyte progenitors and we observed upregulation of markers of these progenitors (e.g. DLK1, figure 1E).

Postnatal liver haematopoiesis is active in children with BA but not controls. Ongoing haematopoiesis may be driven by IGF2 secreted by hepatocyte progenitors. In contrast to other causes of neonatal hepatitis, specific interactions between haematopoiesis and other immune cells may play a role in exacerbating intra-hepatic injury in BA.