Biology subjects

Wilson, S. B.

Publications and source records attributed to Wilson, S. B..

8 recordsLinked to original sources

bioRxiv2026

S3-enriched kidney proximal nephrons from stem cells facilitate tubular injury modelling

Chronic kidney disease (CKD) is a major global health challenge affecting >840 million people, with rising prevalence driven by common conditions including diabetes, hypertension, obesity, and drug toxicity. The proximal tubule (PT) is central to kidney function yet is highly injury-prone, particularly within the S3 segment which plays key roles in drug clearance and CKD pathology. Despite decades of in vitro PT model development, achieving accurate functional and structural segmentation of the PT with distinct PT sub-cell types has remained challenging. Here, we report an enrichment of S3-like cells within PT-enhanced kidney organoids (PT-EKO) that confers segment-specific functionality and injury susceptibility. This advanced platform facilitated physiologically relevant modelling of hyperglycaemia-induced damage, including rapid detection of injury biomarker Kidney Injury Molecule-1 (KIM-1). Integrating with both static and organ-on-chip culture systems, the translational potential of S3-enriched PT-EKO was underscored by its amenability to scale-up via cryopreservation of day 13 progenitors with retained differentiation capacity. PT-EKO applications were further broadened as an expandable high-yield source of isolatable PT cells, retaining PT characteristics across multiple passages and cryopreservation. Together, these findings present a high-fidelity platform for modelling tubular injury and advancing translational applications including CKD drug development, cell-specific nephrotoxicity testing and cellular therapies. SIGNIFICANCE STATEMENTAdvancing stem cell-based proximal nephron models, here we identify proximal tubule-enhanced kidney organoids (PT-EKO) as an enriched source of the nephrons most injury-prone cell type; S3 proximal tubule cells. This advanced platform provides physiologically-relevant modelling of tubular injury and a scalable source of high-quality PT cells, paving the way for more accurate modelling, screening, and cellular therapy applications.

bioengineering↗

bioRxiv2025

In vitro plasticity between ureteric epithelial and distal nephron identity and maturity is controlled by extracellular signals.

Several studies have described human pluripotent stem cell (hPSC)-derived ureteric epithelium, which in the embryo arises from the nephric duct and forms the collecting ducts of the kidney. However, hPSC-derived distal nephron epithelium can also adopt a ureteric phenotype, despite this not occurring during embryogenesis. In this study, RETtdTomato and GATA3mCherry reporter lines were used to further investigate this plasticity. Induction of anterior intermediate mesoderm resulted in the spontaneous formation of an epithelial plexus with a nephric duct-like identity. Subsequent addition of RSPO1 induced patterning of distalized nephrons, including distal convoluted tubule and thick ascending limb of loop of Henle but lacking proximal segments or glomeruli. This epithelium showed a capacity to adopt ureteric epithelial or nephric duct-like states in ex vivo co-culture in response to external cues. The same epithelium seeded as single cells in Matrigel formed epithelial spheroids and adopted a RET+ ureteric tip identity. This in vitro continuum between nephric duct, ureteric epithelium and distal nephron illustrates the role of the microenvironment in cellular identity. Highlights and eTOCO_ST_ABSHighlightsC_ST_ABSO_LIDistal renal epithelium shows substantial plasticity in vitro C_LIO_LIIdentity can be shifted towards distal nephron, including distal convoluted tubule and loop of Henle, in response to prolonged RSPO1 C_LIO_LIDistal epithelial identity can shift in ex vivo culture in response to surrounding signals C_LIO_LICollecting duct is supported by Matrigel culture C_LI eTOC blurbKairath and colleagues investigate the plasticity of induced renal epithelium in response to external signalling cues in vitro and ex vivo. Initial patterning generates a plastic epithelium able to pattern to specific distal nephron. The same epithelium, cultured in Matrigel patterns to ureteric epithelium.

developmental biology↗

bioRxiv2025

Classification of indeterminate and off-target cell types within human kidney organoid differentiation

Human pluripotent stem cell-derived organoids are multicellular models of developing tissues proposed to recapitulate developmental stages of lineage commitment across time. Assessing how accurately protocols recapitulate development is challenged by the lack of accurate reference data sets for early human development, the presence of off-target states and the potential to form cellular states not present in vivo. This study addresses these challenges with respect to differentiation of human pluripotent stem cells to kidney organoids. Based on a factorial single-cell transcriptomic analysis across a 27-day differentiation protocol, including 150,957 cells collected at five time points, we present a comprehensive classification of predicted identity, representing an in vitro temporal transcriptional atlas. For early stages, cellular identity was defined in relation to existing human developmental data across time and organ system. As renal structures arose, this was coupled with the kidney-specific classification methods. In this way we identify predicted cellular states, predictable off-target cell types based on embryology and transitional mesodermal populations with no clear in vivo equivalent. An analysis of all existing single cell data on this same protocol suggests the presence of the same off-target trajectories irrespective of cell line or laboratory. This study provides a valuable resource to better identify and understand how off-target populations arise in vitro, benefiting the advancement of kidney organoid technologies towards therapeutic outcomes.

cell biology↗

bioRxiv2025

Generation of multi-lineage kidney assembloids with integration between nephrons and a single exiting collecting duct

A functional kidney requires a patent connection between all nephrons and the collecting duct network to ensure an exit path for the urinary filtrate. While it is now possible to separately direct the differentiation of pluripotent stem cells to nephron-forming or nephric duct-forming populations, the controlled integration of these two systems has not been demonstrated in human. We report the formation of an integrated kidney assembloid via the co-culture of distinct nephric duct progenitor and nephron-forming cultures in the absence of any requirement for cell enrichment. Nephrons within these kidney assembloids connect to a single exiting nephric duct with this connection forming with the early distal nephron prior to nephron segmentation. Using constitutional reporter lines, we show that the nephrons arise from the nephric progenitors and fuse with the nephric duct while the nephric duct progenitors form a single common duct without any branching. The stromal component of the nephric duct progenitor population also contributes to the medullary stroma surrounding the nephrons. Such modular assembloids address the challenge of nephron unification in an engineered kidney tissue model.

bioengineering↗

bioRxiv2021

Enhanced metanephric specification to functional proximal tubule enables toxicity screening and infectious disease modelling in kidney organoids

While pluripotent stem cell-derived kidney organoids are now being used to model renal disease, the proximal nephron remains immature with limited evidence for key functional solute channels. This may reflect early mispatterning of the nephrogenic mesenchyme and/or insufficient maturation. Here we show that enhanced specification to metanephric nephron progenitors results in elongated and radially aligned proximalised nephrons with distinct S1 - S3 proximal tubule cell types. Such PT-enhanced organoids possess improved albumin and organic cation uptake, appropriate KIM-1 upregulation in response to cisplatin, and improved expression of SARS-CoV-2 entry factors resulting in increased viral replication. The striking proximo-distal orientation of nephrons resulted from localized WNT antagonism originating from the organoid stromal core. PT-enhanced organoids represent an improved model to study inherited and acquired proximal tubular disease as well as drug and viral responses.

bioengineering↗

bioRxiv2021

DevKidCC allows for robust classification and direct comparisons of kidney organoid datasets

Kidney organoids provide a valuable resource to understand kidney development and disease. Clustering algorithms and marker genes fail to accurately and robustly classify cellular identity between human pluripotent stem cell (hPSC)-derived organoid datasets. Here we present a new method able to accurately classify kidney cell subtypes, a hierarchical machine learning model trained using comprehensive reference data from single cell RNA-sequencing of human fetal kidney (HFK). We demonstrate the tools (DevKidCC) performance by application to all published kidney organoid datasets and a novel dataset. DevKidCC is available on Github and can be used on any kidney single cell RNA-sequence data.

bioinformatics↗

bioRxiv2020

Draft Genome Assemblies and Annotations of Agrypnia vestita Walker, and Hesperophylaxmagnus Banks Reveal Substantial Repetitive Element Expansion in Tube Case-making Caddisflies (Insecta: Trichoptera)

Trichoptera (caddisflies) play an essential role in freshwater ecosystems; for instance, larvae process organic material from the water and are food for a variety of predators. Knowledge on the genomic diversity of caddisflies can facilitate comparative and phylogenetic studies thereby allowing scientists to better understand the evolutionary history of caddisflies. While Trichoptera are the most diverse aquatic insect order, they remain poorly represented in terms of genomic resources. To date, all long-read based genomes have been sequenced from individuals in the retreat-making suborder, Annulipalpia, leaving [~]275 Ma of evolution without high-quality genomic resources. Here, we report the first long-read based de novo genome assemblies of two tube case-making Trichoptera from the suborder Integripalpia, Agrypnia vestita Walker and Hesperophylax magnus Banks. We find that these tube case-making caddisflies have genome sizes that are at least three-fold larger than those of currently sequenced annulipalpian genomes and that this pattern is at least partly driven by major expansion of repetitive elements. In H. magnus, long interspersed nuclear elements (LINEs) alone exceed the entire genome size of some annulipalpian counterparts suggesting that caddisflies have high potential as a model for understanding genome size evolution in diverse insect lineages. SignificanceThere is a lack of genomic resources for aquatic insects. So far, only three high-quality genomes have been assembled, all from individuals in the retreat-making suborder Annulipalpia. In this article, we report the first high-quality genomes of two case-making species from the suborder Integripalpia, which are essential for studying genomic diversity across this ecologically diverse insect order. Our research reveals larger genome sizes in the tube case-makers (suborder Integripalpia, infraorder Phryganides), accompanied by a disproportionate increase of repetitive DNA. This suggests that genome size is at least partly driven by a major expansion of repetitive elements. Our work shows that caddisflies have high potential as a model for understanding how genomic diversity might be linked to functional diversification and forms the basis for detailed studies on genome size evolution in caddisflies. Data depositionThis project has been deposited at NCBI under the Bioproject ID: PRJNA668166

genomics↗

bioRxiv2018

Fate-mapping within human kidney organoids reveals conserved mammalian nephron progenitor lineage relationships.

While mammalian kidney morphogenesis has been well documented, human kidney development is poorly understood. Here we combine reprogramming, CRISPR/Cas9 gene-editing and organoid technologies to study human nephron lineage relationships in vitro. Early kidney organoids contained a SIX2+ population with a transcriptional profile akin to human nephron progenitors. Lineage-tracing using gene-edited induced pluripotent stem cell (iPSC) lines revealed that SIX2-expressing cells contribute to nephron formation but not to the putative collecting duct epithelium. However, Cre-mediated temporal induction of the SIX2+ lineage revealed a declining capacity for these cells to contribute to nephron formation over time. This suggests human kidney organoids, unlike the developing kidney in vivo, lack a nephron progenitor niche capable of both self-renewal and ongoing nephrogenesis. Nonetheless, human iPSC-derived kidney tissue maintains previously identified lineage relationships supporting the utility of pluripotent stem cell-derived kidney organoids for interrogating the molecular and cellular basis of early human development.

cell biology↗