Single-Nucleus RNA Sequencing Identifies New Classes of Proximal Tubular Epithelial Cells in Kidney Fibrosis.
Animals
Aristolochic Acids
Cell Communication
Cell Movement
Cell Nucleus
Chromosome Mapping
Epithelial Cells
/ metabolism
Fibroblasts
/ metabolism
Fibrosis
Kidney Tubules, Proximal
/ pathology
Macrophages
/ metabolism
Male
Mice
Phenotype
RNA
/ genetics
Regeneration
Sequence Analysis, RNA
Transcriptome
cell biology and structure
chronic kidney disease
epithelial
kidney tubule
mRNA
proximal tubule
renal epithelial cell
renal fibrosis
renal tubular epithelial cells
scRNA-seq
Journal
Journal of the American Society of Nephrology : JASN
ISSN: 1533-3450
Titre abrégé: J Am Soc Nephrol
Pays: United States
ID NLM: 9013836
Informations de publication
Date de publication:
10 2021
10 2021
Historique:
received:
08
08
2020
accepted:
19
05
2021
pubmed:
23
6
2021
medline:
15
12
2021
entrez:
22
6
2021
Statut:
ppublish
Résumé
Proximal tubular cells (PTCs) are the most abundant cell type in the kidney. PTCs are central to normal kidney function and to regeneration versus organ fibrosis following injury. This study used single-nucleus RNA sequencing (snRNAseq) to describe the phenotype of PTCs in renal fibrosis. Kidneys were harvested from naïve mice and from mice with renal fibrosis induced by chronic aristolochic acid administration. Nuclei were isolated using Nuclei EZ Lysis buffer. Libraries were prepared on the 10× platform, and snRNAseq was completed using the Illumina NextSeq 550 System. Genome mapping was carried out with high-performance computing. A total of 23,885 nuclei were analyzed. PTCs were found in five abundant clusters, mapping to S1, S1-S2, S2, S2-cortical S3, and medullary S3 segments. Additional cell clusters ("new PTC clusters") were at low abundance in normal kidney and in increased number in kidneys undergoing regeneration/fibrosis following injury. These clusters exhibited clear molecular phenotypes, permitting labeling as proliferating, New-PT1, New-PT2, and (present only following injury) New-PT3. Each cluster exhibited a unique gene expression signature, including multiple genes previously associated with renal injury response and fibrosis progression. Comprehensive pathway analyses revealed metabolic reprogramming, enrichment of cellular communication and cell motility, and various immune activations in new PTC clusters. In ligand-receptor analysis, new PTC clusters promoted fibrotic signaling to fibroblasts and inflammatory activation to macrophages. These data identify unrecognized PTC phenotype heterogeneity and reveal novel PTCs associated with kidney fibrosis.
Sections du résumé
BACKGROUND
Proximal tubular cells (PTCs) are the most abundant cell type in the kidney. PTCs are central to normal kidney function and to regeneration versus organ fibrosis following injury. This study used single-nucleus RNA sequencing (snRNAseq) to describe the phenotype of PTCs in renal fibrosis.
METHODS
Kidneys were harvested from naïve mice and from mice with renal fibrosis induced by chronic aristolochic acid administration. Nuclei were isolated using Nuclei EZ Lysis buffer. Libraries were prepared on the 10× platform, and snRNAseq was completed using the Illumina NextSeq 550 System. Genome mapping was carried out with high-performance computing.
RESULTS
A total of 23,885 nuclei were analyzed. PTCs were found in five abundant clusters, mapping to S1, S1-S2, S2, S2-cortical S3, and medullary S3 segments. Additional cell clusters ("new PTC clusters") were at low abundance in normal kidney and in increased number in kidneys undergoing regeneration/fibrosis following injury. These clusters exhibited clear molecular phenotypes, permitting labeling as proliferating, New-PT1, New-PT2, and (present only following injury) New-PT3. Each cluster exhibited a unique gene expression signature, including multiple genes previously associated with renal injury response and fibrosis progression. Comprehensive pathway analyses revealed metabolic reprogramming, enrichment of cellular communication and cell motility, and various immune activations in new PTC clusters. In ligand-receptor analysis, new PTC clusters promoted fibrotic signaling to fibroblasts and inflammatory activation to macrophages.
CONCLUSIONS
These data identify unrecognized PTC phenotype heterogeneity and reveal novel PTCs associated with kidney fibrosis.
Identifiants
pubmed: 34155061
pii: 00001751-202110000-00018
doi: 10.1681/ASN.2020081143
pmc: PMC8722798
doi:
Substances chimiques
Aristolochic Acids
0
RNA
63231-63-0
aristolochic acid I
94218WFP5T
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2501-2516Subventions
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 107964/Z/15/Z
Pays : United Kingdom
Informations de copyright
Copyright © 2021 by the American Society of Nephrology.
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