Objectives and Study

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.

Methods

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.

Results

We identified 1,815 significantly differentially expressed genes (Fig. 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 (Fig. 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) (Fig. 1C). We identified up-regulation of insulin-like growth factor 2 (IGF2, log2 fold change 2.5, pFDR = 2.8x10-40, Fig. 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, Fig. 1E).

Conclusions

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.

Objectives and Study

Monogenic liver disease is caused by rare, pathogenic mutations. Exome and genome sequencing frequently identifies variants of unknown significance in these genes. It is not clear whether such non-pathogenic variants confer increased risk of liver injury beyond childhood. Here, we found that these variants increase the severity of liver damage and may act as a ‘second hit’.

Methods

We identified 77 monogenic paediatric liver diseases. For each gene, we searched for evidence of a liver phenotype in individuals not known to have genetic disease using population-based datasets. We identified genome-wide significant associations (p<5x10-8) between variants (e.g. single nucleotide polymorphisms) and liver biochemistry (ALT, bilirubin, GGT, ALP) in n=1,654,950 participants from the Common Metabolic Disease Portal and n=394,841 from UK BioBank using GeneBass.

Results

We found 89 genome-wide associations for biomarkers of liver injury in otherwise apparently healthy individuals across genes from 44/77 (57%) monogenic disorders (Fig 1). For example, common variants in ABCB11 (the cause of PFIC type 2) were associated with GGT (p=2.0x10-33) and ALT (p=8.4x10-39). Similarly, common polymorphisms in JAG1 (that do not cause Alagille’s syndrome) were associated with GGT (p=2.3x10-9) and ALT (p=5.9x10-10).

Significant associations were found most frequently for 5/7 (71%) of cholestatic disorders and 5/7 (71%) bile acid metabolism disorders, compared to 3/8 (38%) of congenital fibrotic disorders.

In addition to affecting liver enzymes, serum lipid profile (e.g. total cholesterol) was affected by genes from 23/44 (52%).

Conclusions

Common variants in genes that cause rare monogenic liver disease also confer a risk of liver injury later in life. Understanding the mechanisms of these genes provides an opportunity for recognition and treatment of common liver diseases.