Related Experiment Video
Updated: Jun 28, 2025
Isolation of Nuclei from Flash-Frozen Liver Tissue for Single-Cell Multiomics
Published on: December 9, 2022
Single-cell multiomics guided mechanistic understanding of Fontan-associated liver disease
Po Hu1,2,3,4, Jack Rychik5, Juanjuan Zhao1,2,3
1Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Insights
Researchers mapped the cellular changes in Fontan-associated liver disease (FALD). Central hepatocytes undergo metabolic shifts before fibrosis, suggesting they are early responders and potential therapeutic targets for FALD.
Area of Science:
- Cardiovascular Medicine
- Hepatology
- Genomics
Background:
- The Fontan operation is standard for single-ventricle congenital heart disease.
- Fontan circulation (FC) leads to central venous hypertension and Fontan-associated liver disease (FALD), a serious complication.
- The underlying mechanisms of FALD remain poorly understood.
Purpose of the Study:
- To create a detailed cellular and molecular atlas of human FALD.
- To identify early cellular events and molecular pathways involved in FALD pathogenesis.
- To uncover potential therapeutic targets for FALD.
Main Methods:
- Generated a single-cell resolution transcriptomic and epigenomic atlas of human FALD livers using multiomic snRNA-ATAC-seq.
- Analyzed cell type-specific gene expression and epigenetic modifications.
- Performed in vitro experiments to validate findings on activin signaling.
Main Results:
- Identified significant cell type-specific transcriptomic and epigenomic alterations in FC livers.
- Observed profound metabolic reprogramming in central hepatocytes (cHep) preceding hepatic stellate cell activation and fibrosis.
- Discovered a ligand-receptor network mediating cHep to hepatic stellate cell signaling and validated activins A/B as promoters of fibrotic activation.
Conclusions:
- Central hepatocytes are likely early responders in FALD pathogenesis due to early metabolic changes.
- A novel network of signaling pathways, including activins, contributes to FALD progression.
- This atlas provides mechanistic insights and potential therapeutic targets for FALD.
Abstract:
The Fontan operation is the current standard of care for single-ventricle congenital heart disease. Individuals with a Fontan circulation (FC) exhibit central venous hypertension and face life-threatening complications of hepatic fibrosis, known as Fontan-associated liver disease (FALD). The fundamental biology and mechanisms of FALD are little understood. Here, we generated a transcriptomic and epigenomic atlas of human FALD at single-cell resolution using multiomic snRNA-ATAC-seq. We found profound cell type-specific transcriptomic and epigenomic changes in FC livers. Central hepatocytes (cHep) exhibited the most substantial changes, featuring profound metabolic reprogramming. These cHep changes preceded substantial activation of hepatic stellate cells and liver fibrosis, suggesting cHep as a potential first "responder" in the pathogenesis of FALD. We also identified a network of ligand-receptor pairs that transmit signals from cHep to hepatic stellate cells, which may promote their activation and liver fibrosis. We further experimentally demonstrated that activins A and B promote fibrotic activation in vitro and identified mechanisms of activin A's transcriptional activation in FALD. Together, our single-cell transcriptomic and epigenomic atlas revealed mechanistic insights into the pathogenesis of FALD and may aid identification of potential therapeutic targets.
