Biology subjects

Stewart, B. J.

Publications and source records attributed to Stewart, B. J..

4 recordsLinked to original sources

bioRxiv2024

A unique subset of pericystic endothelium associates with aberrant microvascular remodelling and impaired blood perfusion early in polycystic kidney disease

Hallmarks of autosomal dominant polycystic kidney disease (ADPKD), the most common hereditary kidney anomaly, include expanding fluid-filled epithelial cysts, inflammation, and fibrosis. Despite previous work showing the potential of vascular-based therapies, renal microvascular alterations in ADPKD, and their timing, are poorly understood. Using single-cell transcriptomics of human kidney microvasculature, we identify a population of endothelial cells adjacent to cysts in ADPKD. This pericystic endothelium, distinguishable by its expression of osteopontin (SPP1), has a distinct molecular profile compared to the common endothelial cell injury signature in other kidney diseases. SPP1+ pericystic endothelium was also present in an orthologous mouse model of ADPKD before overt kidney functional decline. By interrogating geometric, topological and fractal properties from three-dimensional imaging of early ADPKD mouse kidneys, we show that pericystic endothelium associates with disorganisation and non-uniformity of the renal cortical microvasculature. Concurrently, we detected region-specific reductions in cortical blood flow within ADPKD murine kidneys using arterial spin labelling. We conclude that ADPKD kidneys contain a unique subset of endothelium manifesting with aberrant remodelling and impaired blood perfusion. Its detection, prior to renal functional decline, advocates the vasculature as a therapeutic target to modulate or preserve renal function in early ADPKD.

pathology↗

bioRxiv2023

Temporal profiling of human lymphoid tissues reveals coordinated defence to viral challenge

Adaptive immunity is generated in lymphoid organs, but how these structures defend themselves during infection in humans is unknown. The nasal epithelium is a major site of viral entry, with adenoid nasal-associated lymphoid tissue (NALT) generating early adaptive responses. Here, using a nasopharyngeal biopsy, we examined longitudinal immune responses in NALT following viral challenge, using SARS-CoV-2 infection as a natural experimental model. In acute infection, infiltrating monocytes formed a subepithelial and peri-follicular shield, recruiting NET-forming neutrophils, whilst tissue macrophages expressed pro-repair molecules during convalescence to promote the restoration of tissue integrity. Germinal centre B cells expressed anti-viral transcripts that inversely correlated with fate-defining transcription factors. Among T cells, tissue-resident memory CD8 T cells alone showed clonal expansion and maintained cytotoxic transcriptional programmes into convalescence. Together our study provides a unique insight into how human nasal adaptive immune responses are generated and sustained in the face of viral challenge.

immunology↗

bioRxiv2023

PAX8 and transient Wnt signalling are critical for induction and completion of human renal mesenchymal-to-epithelial transition

During kidney development, nephron epithelia arise de novo from fate-committed mesenchymal progenitors through a mesenchymal-to-epithelial transition (MET). Downstream of fate specification, transcriptional mechanisms that drive establishment of epithelial morphology through MET are poorly understood. We used human renal organoids derived from induced pluripotent stem cells, which recapitulate nephrogenesis, to investigate mechanisms controlling the renal MET programme. Multi-ome profiling of organoids revealed dynamic changes in gene expression and chromatin accessibility driven by transcriptional activators and repressors throughout renal MET. CRISPR-interference-based gene perturbation revealed that PAX8 is essential for initiation of MET in human renal organoids, contrary to mouse, by activating a cell adhesion programme. Furthermore, while Wnt/{beta}-Catenin signalling specifies nephron fate, we find that it must be attenuated to allow HNF1B and TEAD transcription factors to drive completion of MET. These results reveal how the developing kidney balances fate-commitment and morphogenesis with implications for understanding both developmental kidney diseases and aberrant epithelial plasticity following adult renal tubular injury.

developmental biology↗

bioRxiv2020

Predicting the impact of sequence motifs on gene regulation using single-cell data

BackgroundBinding of transcription factors (TFs) at proximal promoters and distal enhancers is central to gene regulation. Yet, identification of TF binding sites, also known as regulatory motifs, and quantification of their impact on gene expression remains challenging. ResultsHere we infer putative regulatory motifs along with their cell type-specific importance using a convolutional neural network trained on single-cell data. Comparison of the importance score to expression levels across cells allows us to identify the TFs most likely to be binding at a given motif. Using multiple mouse tissues we obtain a model with cell type resolution which explains 29% of the variance in gene expression. Finally, by applying scover to distal enhancers identified using scATAC-seq from the mouse cerebral cortex we characterize changes in distal regulatory motifs during development. ConclusionsIt is possible to identify regulatory motifs as well as their importance from single-cell data using a neural network model where all of the parameters and outputs are easily interpretable to the user.

bioinformatics↗