Spatial transcriptomics reveal impaired metabolic liver zonation in acute-on-chronic liver failure

Extrahepatic organ failures are key determinants of acute-on-chronic liver failure (ACLF). While the role of systemic inflammation and mitochondrial dysfunction in the pathogenesis of ACLF is well known, the contribution of the liver itself is less understood. We therefore performed transcriptome and functional analyses of the liver in order to identify hepatic drivers of ACLF.

Bulk-RNA sequencing and spatial transcriptomics were performed in liver specimens from patients with compensated cirrhosis, decompensated cirrhosis or ACLF. In addition, detailed analyses of genes involved in energy metabolism, as well as a metabolome analysis and functional analyses were performed.

In total, 39 patients were included (9 compensated cirrhosis, 15 decompensated cirrhosis, 15 ACLF). ACLF was associated with changes in the hepatic transcriptome, clearly distinct from compensated and decompensated cirrhosis. Most strongly downregulated in ACLF were pathways involved in substrate metabolism and mitochondrial function, including downregulation of multiple genes of glucose and amino acid metabolism. In line, spatial transcriptomics revealed a breakdown of the functional liver zonation in ACLF, with decreasing proportions of hepatocytes specialized in gluconeogenesis/β-oxidation (compensated cirrhosis 68%, decompensated cirrhosis 52%, ACLF 12%; P<0.03). Branched chain ketoacid dehydrogenase kinase (BCKDK), a key regulator of branched-chain amino acid catabolism, was strongly downregulated in ACLF (0,33- fold expression vs. compensated cirrhosis, P<0.05) and may link dysregulation of branched-chain amino acid and glucose metabolism.

ACLF is characterized by distinct changes in the hepatic transcriptome, which affect key pathways in substrate metabolism and mitochondrial function and are associated with loss of functional liver zonation. Downregulation of BCKDK in ACLF might be of particular interest, as it links altered branched-chained amino acid metabolism to impaired glucose production.

Extrahepatic organ failures are well known features of acute-on-chronic liver failure (ACLF), but the contribution of the liver itself to their pathogenesis is not well understood. By RNA sequencing and spatial transcriptomics of liver specimens, we could identify profoundly impaired metabolic and mitochondrial hepatic programs, suggesting that the liver might play a key role in the development of extrahepatic organ failures by compromising the body's energy supply. These findings are important since they provide a rationale for further studying molecular targets in the liver as therapeutic strategies for ACLF.