Title:
Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver.
Background:
- Despite PSC’s progression to end-stage liver disease, its pathogenesis remains poorly understood, posing a significant barrier to the development of effective, targeted therapies.
- Prior transcriptomic studies—which analyze the complete set of RNA transcripts to understand gene activity—have primarily relied on bulk tissue expression, limiting cellular resolution and leaving key questions about disease mechanisms unanswered.
- These studies have implicated various immune cells in PSC, but lacked a comprehensive view of liver cell populations.
Objective:
- The primary objective of this research study was to generate a comprehensive atlas of the PSC liver using multi-omic modalities and protein-based functional validation.
- The study aimed to understand the cellular composition of the affected liver and how it contributes to disease pathogenesis by comparing the activity, interactions, and localization of immune and non-immune cells in healthy and diseased livers.
Research Institution/Team: This research was primarily led by teams at the Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, and the University of Toronto (including its Departments of Immunology, Laboratory Medicine and Pathobiology, and The Donnelly Centre). Additional contributions came from the University of Western Ontario and The Hospital for Sick Children.
Study Design:
- Multi-omic profiling integrates different types of molecular data—including single-cell, single-nucleus, and spatial transcriptomics—to provide a comprehensive understanding of cell identities, gene expression patterns, and spatial organization within the liver.
- Functional validation involves applying lab-based methods such as flow cytometry and stimulation assays to demonstrate that the molecular patterns observed, like immune cell exhaustion, correspond to actual cellular behaviors in the tissue.
- The study cohort included 10 livers from patients with primary sclerosing cholangitis (PSC), 3 livers from patients with primary biliary cholangitis (PBC), and 24 neurologically deceased donor (NDD) livers serving as healthy controls, with balanced sex distribution and a wide age range.
- PSC and PBC samples were obtained at the time of liver transplantation from explanted tissue sections or perfusable caudate lobes, representing late-stage disease.
Key Findings:
- Researchers created a detailed cellular and molecular map of the human liver—covering healthy individuals as well as those with PSC and PBC.
- This atlas combines three powerful techniques (single-cell, single-nucleus, and spatial transcriptomics) to map the cellular makeup, gene activity, and spatial arrangement of liver tissue.
- These complementary approaches offer a detailed view of how immune and non-immune cells behave and interact in healthy, PSC, and PBC livers.
- In PSC and PBC livers, they discovered a new type of liver cell—liver cells (hepatocytes) that start to look and behave like bile duct cells (cholangiocytes), which were found mainly in areas of liver scarring and showed signs of losing their usual identity or function.
- Immune cells also played a key role. A specific kind of immune cell (CD206+ macrophages) in PSC livers was found to be less capable of responding to threats, showing what scientists call an “exhaustion-like” state. These cells also expressed genes that may help regulate or suppress immune activity.
- Other immune cells—like CD4+ T cells, neutrophils, B cells, dendritic cells, and some rare natural killer T-like cells—were found clustered in scarred areas of the PSC liver, showing a strong but potentially dysregulated immune response.
- Finally, spatial mapping revealed how all these cells are positioned relative to one another, shedding light on how their location and interaction within scarred regions may drive disease progression.
Impact on PSC Community:
- This research significantly advances the understanding of the complex cellular and immunological changes that occur in the PSC liver, addressing the existing limited knowledge of the disease's pathogenesis.
- By mapping the cellular ecosystem at an unprecedented resolution, this study provides crucial insights into why current treatments are limited and why PSC progresses to liver failure.
- The comprehensive cellular atlas and the identification of dysfunctional macrophage populations and disease-associated cell subtypes offer new potential targets for therapeutic intervention.
- This foundational work supports the creation of innovative precision medicine strategies that could improve outcomes and quality of care for people with PSC.
