Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver

Tallulah S. Andrews, Diana Nakib, Catia T. Perciani, Xue Zhong Ma, Lewis Liu, Erin Winter, Damra Camat, Sai W. Chung, Patricia Lumanto, Justin Manuel, Shantel Mangroo, Bettina Hansen, Bal Arpinder, Cornelia Thoeni, Blayne Sayed, Jordan Feld, Adam Gehring, Aliya Gulamhusein, Gideon M. Hirschfield, Amanda Ricciuto, Gary D. Bader, Ian D. McGilvray, Sonya MacParland

Abstract

Background & Aims: Primary sclerosing cholangitis (PSC) is an immune-mediated cholestatic liver disease for which there is an unmet need to understand the cellular composition of the affected liver and how it underlies disease pathogenesis. We aimed to generate a comprehensive atlas of the PSC liver using multi-omic modalities and protein-based functional validation. Methods: We employed single-cell and single-nucleus RNA sequencing (47,156 cells and 23,000 nuclei) and spatial transcriptomics (one sample by 10x Visium and five samples with Nanostring GeoMx DSP) to profile the cellular ecosystem in 10 PSC livers. Transcriptomic profiles were compared to 24 neurologically deceased donor livers (107,542 cells) and spatial transcriptomics controls, as well as 18,240 cells and 20,202 nuclei from three PBC livers. Flow cytometry was performed to validate PSC-specific differences in immune cell phenotype and function. Results: PSC explants with parenchymal cirrhosis and prominent periductal fibrosis contained a population of cholangiocyte-like hepatocytes that were surrounded by diverse immune cell populations. PSC-associated biliary, mesenchymal, and endothelial populations expressed chemokine and cytokine transcripts involved in immune cell recruitment. Additionally, expanded CD4+ T cells and recruited myeloid populations in the PSC liver expressed the corresponding receptors to these chemokines and cytokines, suggesting potential recruitment. Tissue-resident macrophages, by contrast, were reduced in number and exhibited a dysfunctional and downregulated inflammatory response to lipopolysaccharide and interferon-γ stimulation. Conclusions: We present a comprehensive atlas of the PSC liver and demonstrate an exhaustion-like phenotype of myeloid cells and markers of chronic cytokine expression in late-stage PSC lesions. This atlas expands our understanding of the cellular complexity of PSC and has potential to guide the development of novel treatments. Impact and Implications: Primary sclerosing cholangitis (PSC) is a rare liver disease characterized by chronic inflammation and irreparable damage to the bile ducts, which eventually results in liver failure. Due to a limited understanding of the underlying pathogenesis of disease, treatment options are limited. To address this, we sequenced healthy and diseased livers to compare the activity, interactions, and localization of immune and non-immune cells. This revealed that hepatocytes lining PSC scar regions co-express cholangiocyte markers, whereas immune cells infiltrate the scar lesions. Of these cells, macrophages, which typically contribute to tissue repair, were enriched in immunoregulatory genes and demonstrated a lack of responsiveness to stimulation. These cells may be involved in maintaining hepatic inflammation and could be a target for novel therapies.

Datasets

1. All cells types from snRNA-seq of human primary sclerosing cholangitis patients and healthy controls
Metadata
mapped_reference_assembly
mapped_reference_annotation
alignment_software
donor_id
donor_age
self_reported_ethnicity_ontology_term_id
donor_cause_of_death
donor_living_at_sample_collection
organism_ontology_term_id
sample_uuid
sample_preservation_method
tissue_ontology_term_id
development_stage_ontology_term_id
sample_derivation_process
tissue_type
suspension_derivation_process
suspension_dissociation_reagent
suspension_uuid
suspension_type
tissue_handling_interval
library_uuid
assay_ontology_term_id
cell_type_ontology_term_id
author_cell_type
disease_ontology_term_id
reported_diseases
sex_ontology_term_id
clusters_res_0.5
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
GRCh38105780 cells
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Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver
2. All cells types from scRNA-seq of human primary sclerosing cholangitis patients and healthy controls
Metadata
mapped_reference_assembly
mapped_reference_annotation
alignment_software
donor_id
donor_age
self_reported_ethnicity_ontology_term_id
donor_cause_of_death
donor_living_at_sample_collection
organism_ontology_term_id
sample_uuid
sample_preservation_method
tissue_ontology_term_id
development_stage_ontology_term_id
sample_derivation_process
tissue_type
suspension_derivation_process
suspension_dissociation_reagent
suspension_dissociation_time
suspension_uuid
suspension_type
tissue_handling_interval
library_uuid
assay_ontology_term_id
sequencing_platform
cell_type_ontology_term_id
author_cell_type
disease_ontology_term_id
reported_diseases
sex_ontology_term_id
clusters_res_0.5
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
GRCh3889637 cells
Preview
Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver

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Source data

https://cellxgene.cziscience.com/collections/0c8a364b-97b5-4cc8-a593-23c38c6f0ac5

Alias names

Single-cell and spatial transcriptomics characterisation of the immunological landscape in the healthy and PSC human liver, Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations, GSE115469, GSE243977, GSE247128, PMID38199298

Cite this study

Andrews, T.S., Nakib, D., Perciani, C.T., Ma, X.Z., Liu, L., Winter, E., Camat, D., Chung, S.W., Lumanto, P., Manuel, J. and Mangroo, S., 2024. Single-cell and spatial transcriptomics characterisation of the immunological landscape in the healthy and PSC human liver. Journal of Hepatology. https://doi.org/10.1016/j.jhep.2023.12.023