Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk

Abstract

to clarify that statements made comparing this and previous studies relate to the published analyses of data within those studies and not the detection of genes within the datasets themselves. The changes made are shown below and both the online full-text and PDF versions have been updated. In the Introduction, the following statement was changed: Original However, existing datasets have apparently not provided the transcriptional depth to identify the signalling pathways that operate within the human fetal kidney, and fail to detect several known ligand and receptor expression patterns in mouse. Corrected The analyses performed on existing datasets have not comprehensively identified the signalling pathway components known to be operating within the mouse fetal kidney. In the Discussion, the following statements were changed: Original For example, although >20,000 cells were profiled at P1 (Adam et al., 2017), several known signalling molecules with functionally validated roles in the nephrogenic niche such as Gdnf, Fgf20, Fgf9, Bmp7, Wnt4 and Fgf8 were not detected in that analysis, precluding further insight into signalling interactions. Corrected Although >20,000 cells were profiled at P1 (Adam et al., 2017), several known signalling molecules with functionally validated roles in the nephrogenic niche were not highlighted in that analysis. Original The improved resolution of gene expression in our study may be due to sequencing depth (∼3000 genes detected per cell), biological replication and differential expression analysis with the edgeR method, which has recently been shown to be a top performer in a comparison of 36 differential expression analysis methods for scRNA-seq data (Soneson and Robinson, 2018). Corrected The improved analysis of signalling interactions provided in this study may be due to sequencing depth (∼3000 genes detected per cell), biological replication and differential expression analysis with the edgeR method, which has recently been shown to be a top performer in a comparison of 36 differential expression analysis methods for scRNA-seq data (Soneson and Robinson, 2018).

Paracrine and autocrine R-spondin signalling is essential for the maintenance and differentiation of renal stem cells

“…Indeed, age-dependent changes of nephron progenitors that affect their proliferation capacity and lifespan have been described, previously 25 . At late stages of embryogenesis, Rspo3 expression becomes almost exclusively restricted to stromal progenitors, which is consistent with recent single sequencing data at E18.5 that highlighted Rspo3 as a marker for the stromal compartment 26 . Stromal expression appears to be important for nephron progenitor maintenance, as Rspo3 deletion in this compartment resulted in progenitor loss at later stages of development.…”

Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

“…Single-cell RNA sequencing (scRNA-seq) is an increasingly powerful technology which enables analysis of gene expression in individual cells. ScRNA-seq has been recently used to study organism development [1][2][3], normal tissues [4][5][6], cancer [7][8][9][10] and other diseases [11,12]. These studies have shed light on tissue heterogeneity and provided previously inaccessible insights into tissue functioning.…”

Age-Dependent Changes in the Progenitor Translatome Coordinated in part byTsc1Increase Perception of Signaling Inputs to End Nephrogenesis

“…Transcriptome analysis at the single cell level is a powerful new tool applied effectively to build detailed maps of cellular constituents and their developmental trajectories in various tissues. While multiple studies have generated single-cell transcriptomic data for mouse (Adam et al, 2017;Brunskill et al, 2014;Combes et al, 2019;Magella et al, 2018) and human (Lindstrom et al, 2018;Wang et al, 2018) kidney development, the overwhelming focus in these early phases has been on enumerating the cell types compromising the kidney, with mechanistic exploration delegated for future investigation.…”