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Development. 2018 Aug 30;145(16). pii: dev164038. doi: 10.1242/dev.164038.

Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney.

Author information

1
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
2
Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI 48109, USA.
3
Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA.
4
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
5
Graduate Program in Quantitative and Computational Biology, Princeton University, Princeton, NJ 08544, USA.
6
Department of Electrical Engineering and Computer Science, Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
7
Flatiron Institute, Simons Foundation, New York, NY 10010, USA.
8
Department of Computer Science, Princeton University, Princeton, NJ.
9
Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA spencejr@umich.edu kretzler@umich.edu cristina.cebrian@cchmc.org.
10
Department of Cell and Developmental Biology, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA.
11
Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI 48109, USA spencejr@umich.edu kretzler@umich.edu cristina.cebrian@cchmc.org.

Abstract

The mammalian kidney develops through reciprocal interactions between the ureteric bud and the metanephric mesenchyme to give rise to the entire collecting system and the nephrons. Most of our knowledge of the developmental regulators driving this process arises from the study of gene expression and functional genetics in mice and other animal models. In order to shed light on human kidney development, we have used single-cell transcriptomics to characterize gene expression in different cell populations, and to study individual cell dynamics and lineage trajectories during development. Single-cell transcriptome analyses of 6414 cells from five individual specimens identified 11 initial clusters of specific renal cell types as defined by their gene expression profile. Further subclustering identifies progenitors, and mature and intermediate stages of differentiation for several renal lineages. Other lineages identified include mesangium, stroma, endothelial and immune cells. Novel markers for these cell types were revealed in the analysis, as were components of key signaling pathways driving renal development in animal models. Altogether, we provide a comprehensive and dynamic gene expression profile of the developing human kidney at the single-cell level.

KEYWORDS:

Branching; Fetal; Human; Kidney; Single cell

PMID:
30166318
PMCID:
PMC6124540
DOI:
10.1242/dev.164038
[Indexed for MEDLINE]
Free PMC Article

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