This is an unedited manuscript that has been accepted for publication. Nature Research are providing this early version of the manuscript as a service to our customers. The manuscript will undergo copyediting, typesetting and a proof review before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers apply.

Resolving the fibrotic niche of human liver cirrhosis at single-cell level

Article metrics

Abstract

Currently there are no effective antifibrotic therapies for liver cirrhosis, a major killer worldwide. To obtain a cellular resolution of directly relevant pathogenesis and to inform therapeutic design, we profile the transcriptomes of over 100,000 human single cells, yielding molecular definitions for non-parenchymal cell types present in healthy and cirrhotic human liver. We uncover a novel scar-associated TREM2+CD9+ macrophage subpopulation, which expands in liver fibrosis, differentiates from circulating monocytes and is pro-fibrogenic. We also define novel ACKR1+ and PLVAP+ endothelial cells that expand in cirrhosis, are topographically scar-restricted and enhance leucocyte transmigration. Multi-lineage ligand-receptor modelling of interactions between the novel scar-associated macrophages, endothelial cells and PDGFRα+ collagen-producing mesenchymal cells reveals intra-scar activity of several pro-fibrogenic pathways including TNFRSF12A, PDGFR and NOTCH signalling. Our work dissects unanticipated aspects of the cellular and molecular basis of human organ fibrosis at a single-cell level, and provides the conceptual framework required to discover rational therapeutic targets in liver cirrhosis.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Author information

Correspondence to P. Ramachandran or N. C. Henderson.

Supplementary information

Supplementary Information

This file contains Supplementary Note 1 (Annotation of hepatic lymphoid cells), Supplementary Note 2 (Annotation of liver mononuclear phagocytes), Supplementary Note 3: Annotation of liver endothelial cells) and Supplementary References.

Reporting Summary

Supplementary Table 1

| Quality metrics for single-cell RNA-seq datasets This table provides a summary of mean±SEM of number of genes (nGene), number of UMIs (nUMI) and mitochondrial gene fraction (fraction.mito) for each human scRNA-seq sample presented in the manuscript (n=5 healthy liver, n=5 cirrhotic liver, n=4 cirrhotic PBMC). Pre-QC (prior to removal of poor quality cells) and Post-QC (after removal of poor quality cells) data are shown. The fraction of cells removed from each dataset as poor quality (nGene<300 or fraction.mito>0.3) are listed.

Supplementary Table 2

| Cell lineage signature genes for supervised clustering This table provides the list of genes used as lineage signatures for signature analysis (Extended Data Figs. 1e, 2b).

Supplementary Table 3

| Marker genes for unsupervised clustering of liver-resident cells This table provides the list of marker genes specific to each of the identified clusters from 66,135 liver-resident cells isolated from 5 healthy and 5 cirrhotic human livers, AUC classifier (Fig. 1e).

Supplementary Table 4

| Marker genes for supervised clustering of liver-resident cell lineages This table provides the list of marker genes specific to each of the identified lineages from 66,135 liver-resident cells isolated from 5 healthy and 5 cirrhotic human livers, AUC classifier (Fig. 1e).

Supplementary Table 5

| Marker genes for unsupervised clustering of T cells and ILCs This table provides the list of marker genes specific to each of the identified clusters from 36,900 T cells and innate lymphoid cells (ILC) isolated from 5 healthy and 5 cirrhotic human livers, AUC classifier (Extended Data Fig. 3d).

Supplementary Table 6

| Marker genes for unsupervised clustering of imputed T cells and ILCs This table provides the list of marker genes specific to each of the identified clusters from 7,380 T cells and innate lymphoid cells (ILC) isolated from 5 healthy and 5 cirrhotic human livers, after scImpute processing, AUC classifier (Extended Data Fig. 3e).

Supplementary Table 7

| Marker genes for unsupervised clustering of B cells and plasma cells This table provides the list of marker genes specific to each of the identified clusters from 2,746 B cells and plasma cells isolated from 5 healthy and 5 cirrhotic human livers, AUC classifier (Extended Data Fig. 3g).

Supplementary Table 8

| Marker genes for unsupervised clustering of mononuclear phagocytes This table provides the list of marker genes specific to each of the identified clusters from 10,737 mononuclear phagocytes isolated from 5 healthy and 5 cirrhotic human livers, AUC classifer (Fig. 2d).

Supplementary Table 9

| Distinguishing metagene signatures and associated ontology terms for MP SOM This table provides the list of genes associated with each SOM metagene signature identified as distinguishing subpopulations within the mononuclear phagocyte lineage dataset, scrat, and their associated gene ontology terms, Fisher’s exact test (Extended Data Fig. 5a, b).

Supplementary Table 10

| Differential gene modules and associated ontology terms expressed over MP pseudotemporal trajectory This table provides the list of genes associated with each module of differentially-expressed genes over the MP pseudotemporal trajectory, monocle::differentialGeneTest, and their associated gene ontology terms, Fisher’s exact test (Fig. 3c, d, Extended Data Fig. 5e, f).

Supplementary Table 11

| Marker genes for unsupervised clustering of mouse MP This table provides the list of marker genes specific to each of the identified clusters from 3,250 mouse mononuclear phagocytes (mMP) isolated from healthy (n=3) and fibrotic (n=3) mouse livers, AUC classifier (Extended Data Fig. 6c).

Supplementary Table 12

| Transcription factor regulons differentially expressed over MP pseudotemporal trajectory and in KC This table provides the list of transcription factor regulons differentially expressed over the MP pseudotime trajectory, monocle::differentialGeneTest, and in KC (Extended Data Fig. 5h, i).

Supplementary Table 13

| Marker genes for unsupervised clustering of endothelial cells This table provides the list of marker genes specific to each of the identified clusters from 8,020 liver endothelial cells isolated from 4 healthy and 3 cirrhotic human livers, AUC classifier (Fig. 4c).

Supplementary Table 14

| Distinguishing metagene signatures and associated ontology terms for endothelia SOM This table provides the list of genes associated with each SOM metagene signature identified as distinguishing subpopulations within the endothelia lineage dataset (8,020 cells), scrat, and their associated gene ontology terms, Fisher’s exact test (Extended Data Figure 8g).

Supplementary Table 15

| Marker transcription factor regulons for unsupervised clustering of endothelial cells This table provides the list of marker regulons specific to each of the identified clusters in the 8,020 endothelia cell dataset, AUC classifier (Extended Data Figure 8h).

Supplementary Table 16

| Marker genes for unsupervised clustering of mesenchymal cells This table provides the list of marker genes specific to each of the identified clusters from 2,318 mesenchymal cells isolated from 4 healthy and 3 cirrhotic human livers, AUC classifier (Fig. 5b).

Supplementary Table 17

| Marker genes for unsupervised sub-clustering of scar-associated mesenchymal cells This table provides the list of marker genes specific to each of the 2 identified clusters from 319 scar-associated mesenchymal cells isolated from 4 healthy and 3 cirrhotic human livers, AUC classifier (Extended Data Figure 9c).

Supplementary Table 18

| Ligand-receptor interactions identified as significant in the fibrotic niche This table provides the list of ligand-receptor interactions identified as significant by CellPhoneDB between pairs of cellular subpopulations within the fibrotic niche of a cirrhotic human liver, permutation test (Fig. 6a, e, Extended Data Figure 10f, i, l).

Supplementary Table 19

| Antibodies used in the study This table provides a list of commercial antibodies and conditions used in this study (Methods).

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.