Single-Cell RNA Sequencing Reveals mRNA Splice Isoform Switching during Kidney Development

Wineberg, Yishay; Bar-Lev, Tali Hana; Futorian, Anna; Ben-Haim, Nissim; Armon, Leah; Ickowicz, Debby; Oriel, Sarit; Bucris, Efrat; Yehuda, Y.; Pode‐Shakked, Naomi; Gilad, Shlomit; Schwessinger, Benjamin; Hohenstein, Peter; Dekel, Benjamin; Urbach, Achia; Kalisky, Tomer

doi:10.1681/asn.2019080770

Cited by 18 publications

(11 citation statements)

References 69 publications

(146 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Ideally, the best way to characterize alternative splicing throughout the different developmental stages is by applying full transcript length single-cell RNA sequencing 44 – 47 . We have recently performed full transcript length single-cell RNA sequencing in the developing mouse fetal kidney 48 and identified a set of transcripts—similar to those found here—that undergo alternative mRNA splicing during the transition between mesenchymal and epithelial cellular states that takes place in the course of mouse fetal kidney development. Likewise, RNA binding motif enrichment analysis suggested that Esrp1/2 and Rbfox1/2 are splicing regulators of the Mesenchymal to Epithelial Transition (MET) that occurs during mouse kidney development, also similar to what we found here.…”

Section: Discussionsupporting

confidence: 57%

Characterization of alternative mRNA splicing in cultured cell populations representing progressive stages of human fetal kidney development

Wineberg

Kanter

Ben-Haim

et al. 2022

Sci Rep

Self Cite

View full text Add to dashboard Cite

Nephrons are the functional units of the kidney. During kidney development, cells from the cap mesenchyme—a transient kidney-specific progenitor state—undergo a mesenchymal to epithelial transition (MET) and subsequently differentiate into the various epithelial cell types that create the tubular structures of the nephron. Faults in this transition can lead to a pediatric malignancy of the kidney called Wilms’ tumor that mimics normal kidney development. While human kidney development has been characterized at the gene expression level, a comprehensive characterization of alternative splicing is lacking. Therefore, in this study, we performed RNA sequencing on cell populations representing early, intermediate, and late developmental stages of the human fetal kidney, as well as three blastemal-predominant Wilms’ tumor patient-derived xenografts. Using this newly generated RNAseq data, we identified a set of transcripts that are alternatively spliced between the different developmental stages. Moreover, we found that cells from the earliest developmental stage have a mesenchymal splice-isoform profile that is similar to that of blastemal-predominant Wilms’ tumor xenografts. RNA binding motif enrichment analysis suggests that the mRNA binding proteins ESRP1, ESRP2, RBFOX2, and QKI regulate alternative mRNA splicing during human kidney development. These findings illuminate new molecular mechanisms involved in human kidney development and pediatric kidney cancer.

show abstract

Section: Discussionsupporting

confidence: 57%

Characterization of alternative mRNA splicing in cultured cell populations representing progressive stages of human fetal kidney development

Wineberg

Kanter

Ben-Haim

et al. 2022

Sci Rep

Self Cite

View full text Add to dashboard Cite

show abstract

“…Studies on renal ASEs have been reported, for instance, by Jing et al, regarding the involvement of alternative splicing of circular RNAs (circRNAs) in the regulation of renal cancer specificity [ 16 ]. Wineberg et al studied the regulatory role of mRNA AS at the single-cell level in kidney development and differentiation [ 17 ]. However, few ASEs have been reported in studies on urinary stones, which characterize a major kidney disease.…”

Section: Discussionmentioning

confidence: 99%

Effects of alternative splicing events and transcriptome changes on kidney stone formation

et al. 2022

View full text Add to dashboard Cite

During the development of urinary stone disease, the formation of tiny crystals that adhere to the renal tubular epithelium induces epithelial cell damage. This damage and repair of the epithelium is associated with the establishment of more crystal adhesion sites, which in turn stimulates further crystal adhesion and, eventually, stone formation. Deposited crystals typically cause changes in epithelial cell gene expression, such as transcriptome changes and alternative splicing events. Although considered important for regulating gene expression, alternative splicing has not been reported in studies related to kidney stones. To date, whether alternative splicing events are involved in the regulation of stone formation and whether crystallographic cell interactions are regulated by alternative splicing at the transcriptional level have remained unknown. Therefore, we conducted RNA sequencing and alternative splicing-related bioassays by modeling the in vitro stone environment. Many alternative splicing events were associated with crystallographic cell interactions. Moreover, these events regulated transcription and significantly affected the capacity of crystals to adhere to renal tubular epithelial cells and regulate apoptosis.

show abstract

“…In this study we used the Cell Population Mapping (CPM) R package [14]. For the single-cell reference matrix we used the transcriptomes of 544 individual cells previously collected from a mouse fetal kidney [20]. tSNE was done using MATLAB with default parameters.…”

Section: Methodsmentioning

confidence: 99%

“…We next used cellular deconvolution [14] to infer a more detailed cellular composition of each tumor. Since cells in Wilms' tumors closely resemble those of the fetal kidney, we used a previously published single-cell gene expression dataset from a fetal mouse developing kidney [20] as reference. The cellular deconvolution algorithm provided a prediction of the proportions of ten cell types from the developing kidney within each of the tumors and archetypes (Figure 4 and Figure S28).…”

Section: S24-s25 and Supplementary Data)mentioning

confidence: 99%

Characterization of the continuous transcriptional heterogeneity in Wilms’ tumors using unsupervised machine learning

Trink

Urbach

Dekel

et al. 2022

Preprint

View full text Add to dashboard Cite

Wilms’ tumors are pediatric malignancies that are thought to arise from faulty kidney development. To date, the course of treatment depends on manual histopathological classification which is difficult since the tumors differ between patients in a continuous manner. Here, we used three computational approaches to characterize the continuous heterogeneity of Wilms’ tumors. We first chose a published dataset of microarray gene expression measurements from high-risk blastemal-type Wilms’ tumors. Then, we used Pareto Task Inference to show that the tumors form a triangle-shaped continuum in latent space that is bounded by three tumor archetypes with “stromal”, “epithelial”, and “blastemal” characteristics, that resemble the un-induced mesenchyme, the Cap mesenchyme, and early epithelial structures of the fetal kidney. We confirmed this by fitting a generative probabilistic “grade of membership” model whereby each tumor is represented as a unique mixture of three hidden “topics” with blastemal, stromal, and epithelial characteristics. Finally, we used cellular deconvolution to show that each tumor is composed of a unique mixture of cell populations resembling the un-induced mesenchyme, the cap mesenchyme, and the early epithelial structures of the fetal kidney. We anticipate that these methodologies will pave the way for more quantitative strategies for tumor stratification and classification.

show abstract

Single-Cell RNA Sequencing Reveals mRNA Splice Isoform Switching during Kidney Development

Cited by 18 publications

References 69 publications

Characterization of alternative mRNA splicing in cultured cell populations representing progressive stages of human fetal kidney development

Characterization of alternative mRNA splicing in cultured cell populations representing progressive stages of human fetal kidney development

Effects of alternative splicing events and transcriptome changes on kidney stone formation

Characterization of the continuous transcriptional heterogeneity in Wilms’ tumors using unsupervised machine learning

Contact Info

Product

Resources

About