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Validating Single-cell Genomics for the Study of Renal Development

Overview
Journal Kidney Int
Publisher Elsevier
Specialty Nephrology
Date 2014 Apr 25
PMID 24759149
Citations 2
Authors
Affiliations
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Abstract

Single-cell genomics will enable studies of the earliest events in kidney development, although it is unclear if existing technologies are mature enough to generate accurate and reproducible data on kidney progenitors. Here we designed a pilot study to validate a high-throughput assay to measure the expression levels of key regulators of kidney development in single cells isolated from embryonic mice. Our experiment produced 4608 expression measurements of 22 genes, made in small cell pools, and 28 single cells purified from the RET-positive ureteric bud. There were remarkable levels of concordance with expression data generated by traditional microarray analysis on bulk ureteric bud tissue with the correlation between our average single-cell measurements and GUDMAP measurements for each gene of 0.82-0.85. Nonetheless, a major motivation for single-cell technology is to uncover dynamic biology hidden in population means. There was evidence for extensive and surprising variation in expression of Wnt11 and Etv5, both downstream targets of activated RET. The variation for all genes in the study was strongly consistent with burst-like promoter kinetics. Thus, our results can inform the design of future single-cell experiments, which are poised to provide important insights into kidney development and disease.

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References
1.
White M, Myers C, Corbo J, Cohen B . Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks. Proc Natl Acad Sci U S A. 2013; 110(29):11952-7. PMC: 3718143. DOI: 10.1073/pnas.1307449110. View

2.
Jain S, Naughton C, Yang M, Strickland A, Vij K, Encinas M . Mice expressing a dominant-negative Ret mutation phenocopy human Hirschsprung disease and delineate a direct role of Ret in spermatogenesis. Development. 2004; 131(21):5503-13. DOI: 10.1242/dev.01421. View

3.
Gerstein M, Kundaje A, Hariharan M, Landt S, Yan K, Cheng C . Architecture of the human regulatory network derived from ENCODE data. Nature. 2012; 489(7414):91-100. PMC: 4154057. DOI: 10.1038/nature11245. View

4.
Spurgeon S, Jones R, Ramakrishnan R . High throughput gene expression measurement with real time PCR in a microfluidic dynamic array. PLoS One. 2008; 3(2):e1662. PMC: 2244704. DOI: 10.1371/journal.pone.0001662. View

5.
Golding I, Paulsson J, Zawilski S, Cox E . Real-time kinetics of gene activity in individual bacteria. Cell. 2005; 123(6):1025-36. DOI: 10.1016/j.cell.2005.09.031. View