Biology subjects

Schmidt-Ott, K. M.

Publications and source records attributed to Schmidt-Ott, K. M..

8 recordsLinked to original sources

bioRxiv2026

Targeting the Kidneys Osmotic Gradient with AVPR2 Antagonism Limits Inflammation and Fibrosis after Injury

Background: The renal medulla is characterized by a steep osmotic gradient that is essential for urinary concentration but may also influence cellular stress and injury responses. While vasopressin-dependent medullary hyperosmolarity is well established in water homeostasis, its role in shaping kidney injury and repair remains poorly understood. Methods: We pharmacologically reduced vasopressin signaling using the Avpr2 antagonist Tolvaptan and examined the consequences for renal medullary osmolality, tubular stress responses, inflammation, and fibrotic remodeling. Single-nucleus RNA sequencing, bulk transcriptomics, quantitative PCR, and histological analyses were performed in healthy kidneys and following unilateral ischemia-reperfusion injury (IRI) or cisplatin-induced nephropathy. Results: Tolvaptan treatment lowered renal medullary osmolality and suppressed osmotic stress-associated transcriptional programs in medullary collecting duct cells. Following IRI, Tolvaptan-treated mice exhibited attenuated expression of inflammatory and monocyte recruitment genes, reduced macrophage accumulation in the renal medulla, and diminished fibrotic remodeling at later stages. In cisplatin-induced nephropathy, Tolvaptan reduced tubular injury markers and inflammatory activation in the outer stripe of the outer medulla. Conclusions: These findings identify vasopressin-dependent renal medullary hyperosmolarity as a modulator of tubular stress, inflammation, and fibrotic remodeling after kidney injury. Modulation of the medullary osmotic environment influences early injury trajectories and downstream repair responses across distinct models of acute kidney injury.

pathology↗

bioRxiv2026

Cyst-type epithelial heterogeneity shapes therapeutic responsiveness in ADPKD

Autosomal dominant polycystic kidney disease (ADPKD) exhibits substantial interpatient variability in disease course and therapeutic response, but the cellular basis for this variability remains poorly understood. Here, we combine single-nucleus RNA sequencing of human cyst epithelia with machine learning-based histological analysis of >1,800 cysts to resolve three epithelial cyst types--proximal tubule-like, collecting duct-like, and mixed. These cyst types display distinct injury states, metabolic programs, and stromal microenvironments, including a mixed-cyst niche enriched for CCL2-associated inflammatory signaling. Expression of key therapeutic targets was highly cell-type specific with CFTR enriched in proximal-like epithelia, whereas AVPR2 expression was confined to AQP2-positive collecting duct-like cells. Cyst-type composition varied widely across patients and in an orthologous mouse model (Pkd1RC/RC) in which the burden of AQP2-positive cysts correlated with responsiveness to tolvaptan. These findings identify cyst-type heterogeneity as a major determinant of molecular pathway activation and predictability of therapeutic response in ADPKD.

molecular biology↗

bioRxiv2025

Macrophages induce stromal differentiation and endothelialization in iPSC-derived kidney organoids.

Human induced pluripotent stem cell (iPSC) - derived kidney organoids are powerful models of kidney development and disease but lack mature vasculature. Here, we show that co-culture with human monocyte-derived macrophages (MDM) induces robust endothelial and stromal differentiation in iPSC-derived kidney organoids. MDM promoted the formation of lumenized capillary networks, an effect reproduced by iPSC-derived macrophages and the THP-1 monocyte line. In contrast, organoids without MDM displayed only transient endothelial differentiation that coincided with transient VEGFA upregulation and that regressed during maturation. MDM counteracted this transient phase by releasing soluble Neuropilin-1 (sNRP1), which sequestered VEGFA and stabilized late endothelial development, evidenced by sustained CD31 promoter activity. Transcriptomic profiling revealed that MDM redirected mesodermal fate suppressing lateral plate and cardiac mesoderm while promoting paraxial and intermediate mesoderm and the generation of FoxD1 stromal progenitors via CXCL5 (ENA-78) secretion. These stromal cells supported late endothelial maturation and enhanced overall organoid differentiation. Our findings uncover a macrophage-driven mechanism coupling stromal and vascular development, providing a strategy to achieve functional vascularization in kidney organoids and improving their physiological relevance for research applications.

cell biology↗

bioRxiv2024

Canonical Notch2 Signaling Regulates the Development of Iron-recycling Macrophages and Iron Homeostasis

Red pulp macrophages (RPM) and bone marrow macrophages (BMM) are iron-recycling cells involved in iron homeostasis and erythropoiesis. Here, we show, using conditional deletion strategies of Notch signaling components, that the development of RPM and BMM is regulated by canonical Notch2 signaling. Loss of functional Notch2, or its nuclear mediator Rbpj, causes impairment in RPM and BMM and iron overload in the spleen and bone marrow, while prototypic RPM genes required for iron handling are downregulated. This was accompanied by splenic extramedullary hematopoiesis and changes in splenic microarchitecture. Furthermore, early postnatal transfer of bone marrow and fetal liver progenitors rescued the defects in RPM and BMM and iron overload in a Notch2-dependent manner, demonstrating the potential to restore defective tissue resident macrophage niches by Notch-competent progenitors. Thus, canonical Notch2 is required for development and function of iron-recycling macrophages.

immunology↗

bioRxiv2022

Discovery of a non-canonical GRHL1 binding motif using deep convolutional and recurrent neural networks

Transcription factors regulate gene expression by binding to transcription factor binding sites (TFBSs). Most models for predicting TFBSs are based on position weight matrices (PWMs), which require a specific motif to be present in the DNA sequence and do not consider interdependencies of nucleotides. Novel approaches such as Transcription Factor Flexible Models or recurrent neural networks consequently provide higher accuracies. However, it is unclear whether such approaches can uncover novel non-canonical, hitherto unexpected TFBSs relevant to human transcriptional regulation. In this study, we trained a convolutional recurrent neural network with HT-SELEX data for GRHL1 binding and applied it to a set of GRHL1 binding sites obtained from ChIP-Seq experiments from human cells. We identified 46 non-canonical GRHL1 binding sites, which were not found by a conventional PWM approach. Unexpectedly, some of the newly predicted binding sequences lacked the CNNG core motif, so far considered obligatory for GRHL1 binding. Using isothermal titration calorimetry, we experimentally confirmed binding between the GRHL1-DNA binding domain and predicted GRHL1 binding sites, including a non-canonical GRHL1 binding site. Mutagenesis of individual nucleotides revealed a correlation between predicted binding strength and experimentally validated binding affinity across representative sequences. This correlation was neither observed with a PWM-based nor another deep learning approach. Our results show that convolutional recurrent neural networks may uncover unanticipated binding sites and facilitate quantitative transcription factor binding predictions.

bioinformatics↗

bioRxiv2022

The centrosomal protein 83 (CEP83) regulates human pluripotent stem cell differentiation towards the kidney lineage

BackgroundDuring embryonic development, the mesoderm undergoes patterning into diverse lineages including axial, paraxial, and lateral plate mesoderm (LPM). Within the LPM, the so-called intermediate mesoderm (IM) forms kidney and urogenital tract progenitor cells, while remaining LPM forms cardiovascular, hematopoietic, mesothelial and additional progenitor cells. The signals that regulate these early lineage decisions are incompletely understood. Here, we found that the centrosomal protein 83 (CEP83), a centriolar component necessary for primary cilia formation and mutated in pediatric kidney disease, influences the differentiation of human induced pluripotent stem cells (hiPSCs) towards intermediate mesoderm. MethodsWe induced inactivating deletions of CEP83 in hiPSCs and applied a 7 day in vitro protocol of intermediate mesoderm kidney progenitor differentiation, based on timed application of WNT and FGF agonists. We characterized induced mesodermal cell populations using single cell and bulk transcriptomics and tested their ability to form kidney structures in subsequent organoid culture. ResultsWhile hiPSCs with homozygous CEP83 inactivation were normal regarding morphology and transcriptome, their induced differentiation into IM progenitor cells was perturbed. Mesodermal cells induced after 7 days of monolayer culture of CEP83-deficient hiPCS exhibited absent or elongated primary cilia, displayed decreased expression of critical IM genes (PAX8, EYA1, HOXB7) and an aberrant induction of LPM markers (e. g. FOXF1, FOXF2, FENDRR, HAND1, HAND2). Upon subsequent organoid culture, wildtype cells differentiated to form kidney tubules and glomerular-like structures, whereas CEP83-deficient cells failed to generate kidney cell types, instead upregulating cardiomyocyte, vascular, and more general LPM progenitor markers. ConclusionOur data suggest that CEP83 regulates the balance of intermediate mesoderm and lateral plate mesoderm formation from human pluripotent stem cells, identifying a potential link between centriolar or ciliary function and mesodermal lineage induction.

developmental biology↗

bioRxiv2022

Urinary single-cell sequencing captures intrarenal injury and repair processes in human acute kidney injury

Acute kidney injury (AKI) is a major health issue, the outcome of which depends primarily on damage and reparative processes of tubular epithelial cells (TEC). Mechanisms underlying AKI remain incompletely understood, specific therapies are lacking and monitoring the course of AKI in clinical routine is confined to measuring urine output and plasma levels of filtration markers. Here we demonstrate feasibility and potential of a novel approach to assess the cellular and molecular dynamics of AKI by establishing a robust urine-to-single cell RNA sequencing (scRNAseq) pipeline for excreted kidney cells via flow cytometry sorting. We analyzed 42,608 single cell transcriptomes of 40 urine samples from 32 AKI patients and compared our data with reference material from human AKI post-mortem biopsies and published mouse data. We demonstrate that TEC transcriptomes mirror intrarenal pathology and reflect distinct injury and repair processes, including oxidative stress, inflammation, and tissue rearrangement. We also describe an AKI-specific abundant urinary excretion of progenitor-like cells. In conclusion, single cell transcriptomics of kidney cells excreted in urine provides non-invasive, unprecedented insight into cellular processes underlying AKI, thereby opening novel opportunities for target identification, AKI sub-categorization and monitoring of natural disease course and interventions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/479234v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@e7175corg.highwire.dtl.DTLVardef@1aed1e6org.highwire.dtl.DTLVardef@5655f4org.highwire.dtl.DTLVardef@2512a7_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2021

Transcriptomic responses of the human kidney to acute injury at single cell resolution

BackgroundAcute kidney injury (AKI) occurs frequently in critically ill patients and is associated with adverse outcomes. Cellular mechanisms underlying AKI and kidney cell responses to injury remain incompletely understood. MethodsWe performed single-nuclei transcriptomics, bulk transcriptomics, molecular imaging studies, and conventional histology on kidney tissues from 8 individuals with severe AKI (stage 2 or 3 according to Kidney Disease: Improving Global Outcomes (KDIGO) criteria). Specimens were obtained within 1-2 hours after individuals had succumbed to critical illness associated with respiratory infections, with 4 of 8 individuals diagnosed with COVID-19. Control kidney tissues were obtained post-mortem or after nephrectomy from individuals without AKI. ResultsHigh-depth single cell-resolved gene expression data of human kidneys affected by AKI revealed enrichment of novel injury-associated cell states within the major cell types of the tubular epithelium, in particular in proximal tubules, thick ascending limbs and distal convoluted tubules. Four distinct, hierarchically interconnected injured cell states were distinguishable and characterized by transcriptome patterns associated with oxidative stress, hypoxia, interferon response, and epithelial-to-mesenchymal transition, respectively. Transcriptome differences between individuals with AKI were driven primarily by the cell type-specific abundance of these four injury subtypes rather than by private molecular responses. AKI-associated changes in gene expression between individuals with and without COVID-19 were similar. ConclusionThe study provides an extensive resource of the cell type-specific transcriptomic responses associated with critical illness-associated AKI in humans, highlighting recurrent disease-associated signatures and inter-individual heterogeneity. Personalized molecular disease assessment in human AKI may foster the development of tailored therapies.

molecular biology↗