Biology subjects

Sayed, M.

Publications and source records attributed to Sayed, M..

6 recordsLinked to original sources

bioRxiv2026

Loss of Hnf1b in differentiated proximal tubule cells uncovers nephron segment plasticity

HNF1B is a transcription factor required for proximal tubule (PT) specification during kidney development, but whether it is also required to maintain PT identity after differentiation remains unknown. Using PT-specific genetic deletion in mice, we found that loss of Hnf1b in differentiated PT cells causes cyst formation and early postnatal lethality. PT-specific transcriptomic analysis revealed downregulation of PT-specific gene programs, including Hnf4a and PT-enriched transport and metabolic genes. Strikingly, Hnf1b-deficient PT cells ectopically activated podocyte-specific genes, including Wt1 and Nphs1, demonstrating that PT cells retain the capacity to engage alternative nephron segment programs when identity-stabilizing mechanisms are disrupted. In addition, loss of Hnf1b disrupted epithelial integrity, as evidenced by reduced epithelial adhesion gene expression and induction of mesenchymal markers. Wnt/{beta}-catenin signaling was also aberrantly activated, suggesting broader dysregulation of epithelial homeostasis. These findings establish HNF1B as a critical post-specification regulator of PT identity that sustains PT-specific transcriptional programs and actively suppresses alternative segmental identity programs.

developmental biology↗

bioRxiv2026

A knock-in Six2Cre line reveals transient interstitial potential in nephron progenitors

The developmental relationship between nephron progenitors and the renal interstitium remains unresolved, in part due to limitations of existing lineage tracing tools. The widely used transgenic Six2TGC line, which is routinely employed to target the nephron lineage, exhibits mosaic recombination and altered progenitor dynamics. To overcome these shortcomings, we generate a knock-in Six2Cre mouse allele that faithfully recapitulates endogenous Six2 expression, preserves nephron endowment, and achieves near-complete, non-mosaic recombination. Side-by-side lineage tracing with Six2Cre and Six2TGC, combined with RNA velocity analysis of single-cell RNA-sequencing datasets, reveals a brief interval around embryonic day 11 during which Six2-expressing mesenchymal nephron progenitors contribute to the renal interstitium. This contribution is transient and stage-restricted. These findings reveal an early dual potential within nephron progenitors and define a precise developmental window for dissecting mechanisms that coordinate nephron-interstitium integration.

developmental biology↗

bioRxiv2025

Constitutive Yap activation in distal nephron segments disrupts epithelial identity and nephron patterning

The distal nephron segments play a critical role in maintaining electrolyte balance, yet the mechanisms that preserve epithelial identity and segmental organization within this region remain poorly defined. Yes-associated protein (Yap), a key effector of Hippo signaling, is essential for kidney development, but its function in distal nephron epithelia is unknown. Using a genetic gain-of-function approach to activate Yap selectively in distal nephron segments, we found that sustained Yap activity profoundly disrupts epithelial organization and nephron patterning. Lineage tracing revealed that both distal convoluted tubule and connecting tubule cells originate from Slc12a3-expressing cells, and Yap activation in these segments led to increased proliferation, displacement of lineage-labeled cells beyond expected segment boundaries, and loss of segment-specific gene expression. These changes were accompanied by defects in apicobasal polarity and junctional integrity, consistent with epithelial plasticity. Unexpectedly, Yap activation in distal nephron segments also suppressed proximal tubule gene expression, indicating non-cell-autonomous effects on nephron differentiation. Together, these findings identify Yap as a critical regulator of epithelial identity in the distal nephron segments and reveal a previously unrecognized role for Hippo signaling in coordinating intersegmental organization during kidney development.

developmental biology↗

bioRxiv2025

The thin descending limb of the loop of Henle originates from proximal tubule cells during mouse kidney development

BackgroundThe thin descending limb of the loop of Henle is crucial for urine concentration, as it facilitates passive water reabsorption. Despite its importance, little is known about how this nephron segment forms during kidney development. MethodsWe assembled a large single-cell RNA sequencing (scRNA-seq) dataset by integrating multiple datasets of non-mutant developing mouse kidneys to identify developing thin descending limb cells. To test whether those cells originate from proximal tubule cells, we generated a proximal tubule-specific Cre line, Slc34a1eGFPCre, and conducted lineage tracing. Additionally, given that the transcription factor Hnf4a directly binds to the Aqp1 gene, we examined whether the loss of Hnf4a affects Aqp1 expression in thin descending limb cells. ResultsFrom our scRNA-seq dataset, we identified a small cluster of cells distinct from both the proximal tubule and the thick ascending limb of the loop of Henle. Those cells exhibited high expression of thin descending limb marker genes, including Aqp1 and Bst1. Notably, a subset of proximal tubule cells also expressed thin descending limb marker genes, suggesting that proximal tubule cells may give rise to thin descending limb cells. Using lineage tracing with the Slc34a1eGFPCre line, we found that, at least, a subset of thin descending limb cells are descendants of proximal tubule cells. Furthermore, the loss of Hnf4a, a transcription factor essential for mature proximal tubule cell formation, disrupted proper Aqp1 expression in thin descending limb cells, providing additional evidence of a developmental link between proximal tubule cells and thin descending limb cells. ConclusionOur findings shed new light on the developmental origin of thin descending limb cells and highlight the importance of Hnf4a in regulating their formation. Key PointsO_LIReference single cell RNA-seq dataset of the developing mouse kidney was assembled and used to identify the thin descending limb of the loop of Henle. C_LIO_LILineage analysis of proximal tubules in the mouse kidney shows that proximal tubule cells give rise to the thin descending limb of the loop of Henle. C_LIO_LIDeletion of Hnf4a disrupts the expression of Aqp1 in the thin descending limb of the loop of Henle, highlighting a developmental link between proximal tubules and the loop of Henle. C_LI

developmental biology↗

bioRxiv2020

miRinGO: Prediction of biological processes indirectly targeted by human microRNAs

MicroRNAs are small non-coding RNAs that are known for their role in post-transcriptional regulation of target genes. Typically, their functions are predicted by first identifying their target genes and then finding biological processes enriched in these targets. Current tools for miRNA functional analysis use only genes with physical binding sites as their targets and exclude other genes that are indirectly targeted transcriptionally through transcription factors. Here, we introduce a method to predict gene ontology (GO) annotations indirectly targeted by microRNAs. The proposed method resulted in better performance in predicting known miRNA-GO term associations compared to the canonical approach. To facilitate miRNA GO enrichment analysis, we developed an R Shiny application, miRinGO, that is freely available from GitHub at https://github.com/Fadeel/miRinGO

bioinformatics↗

bioRxiv2019

A dynamic control of human telomerase holoenzyme

Human telomerase functions in maintaining genome stability by adding telomeric repeats to the termini of linear chromosomes. Past studies have revealed profound insights into telomerase functions. However, low abundance of functional telomerase and difficulty in quantifying its activity leave partially characterized its thermodynamic and kinetic properties. Using a newly developed method to count individual extension products, we demonstrate that human telomerase holoenzymes contain fast- and slow-acting catalytic sites. Surprisingly, both active sites become inactive after two consecutive rounds of catalysis. The fast active sites turn off ~40-fold quicker than the slow ones and exhibit higher affinity to substrates. In dimeric enzymes, the two sites work in tandem with the faster site functioning before the slower one. In monomeric enzymes, the active sites also perform single-run catalysis. Interestingly, the inactive enzymes can be reactivated by intracellular telomerase-activating factors (iTAFs) available in multiple cell types. Together, the single-run catalysis and the iTAF-triggered reactivation serve as a novel control circuit to ensure that the telomerase holoenzymes are dynamically controlled to match their number of active sites with the number of telomeres they extend. Such exquisite kinetic control of telomerase activity is expected to play important roles in cell division and ageing.

cell biology↗