Biology subjects

Cholewa-Waclaw, J.

Publications and source records attributed to Cholewa-Waclaw, J..

11 recordsLinked to original sources

bioRxiv2026

Non-invasive quantification of hepatic necrosis from circulating alanine aminotransferase kinetics in acetaminophen-treated mice in vivo

Histological necrosis is the reference measure of hepatotoxicity but can only be obtained at terminal cull. A time course requires independent cohorts at every timepoint. Circulating alanine aminotransferase (ALT) can be sampled repeatedly in the same animal, and is released in liver injury. We asked whether serial ALT kinetics can be used to estimate histological necrosis in vivo. Forty-five fasted twelve-week-old male C57BL/6J mice received a single intraperitoneal dose of 350 mg/kg acetaminophen (paracetamol). Plasma ALT and microRNA-122 (miR-122) were measured serially from baseline to 48h as cumulative area-under-the-curve (AUC) to cull, against centrilobular necrosis on haematoxylin and eosin sections as reference (range 0 to 59%, mean 32%). A generalised additive model of necrosis on cumulative ALT AUC and time since dosing predicted necrosis with a leave-one-animal-out cross-validated mean absolute error of 7.7% necrotic area (95% CI 5.6 to 10.0; n=49). A panel of traditional regression and machine-learning models all gave equal or larger error, and adding an additional biomarker or regeneration information did not improve prediction. Serial ALT kinetics therefore provide a calibrated, longitudinal measure of hepatic necrosis in vivo and give a more stable estimate of within-group variance for study planning, while supporting reductions in animal use, because one serially-sampled cohort can replace separate cohorts at each timepoint.

pharmacology and toxicology↗

bioRxiv2026

Cross-protocol comparison of iPSC-microglia reveals hypofunction contributes to neuronal vulnerability and synaptic alterations in the MAPT-S305N model of frontotemporal dementia.

Progressive and chronic neuroinflammation is associated with numerous neurodegenerative diseases, including primary tauopathies such as frontotemporal dementia and progressive supranuclear palsy. Unlike Alzheimers disease, there is no clear genetic association implicating microglial dysfunction as a primary driver of tauopathy. As such, the contributions of microglia to tauopathy pathogenesis have been less well defined. Here, we explore the cell autonomous effects of the pathogenic MAPT-S305N variant on microglial function, across two distinct iPSC-microglia protocols, followed by examination of the non-cell autonomous effects of microglial MAPT genotype on neuronal health and function. We find that different protocols produce cells of equivalent microglial identity, but result in microglia in different functional states, thereby influencing reactivity and detectable phenotypes. Regardless, across both protocols we find that MAPT-S305N induces microglial hypoactivity, evidenced by impaired phagocytosis, reduced cytokine release and diminished regulation of synaptic function. We conclude that microglial hypoactivity may be an early event in disease pathogenesis, where MAPT mutation microglia fail to adequately respond to pathogenic stimuli, thereby contributing to subsequent neuronal vulnerability and susceptibility. Further studies are required to understand how and when this initial hypoactive state may switch to a toxic pro-inflammatory state, and whether early detection and correction may be of therapeutic value.

neuroscience↗

bioRxiv2026

Pericyte Loss Reprogrammes Capillary Endothelium and Drives White Matter Injury in Small Vessel Disease

Pericytes are critical regulators of cerebrovascular homeostasis, yet their contribution to small vessel disease (SVD) and white matter injury remains incompletely understood. Here, we use an inducible Atp13a5-driven genetic strategy to selectively label and ablate brain pericytes, enabling integrated morphological, functional, and transcriptomic analyses across the neurogliovascular unit. Single-cell RNA sequencing and tissue-level mapping identified distinct pericyte subtypes distributed along the vascular tree and revealed subtype-specific vulnerability following depletion. Moderate pericyte loss induced transient cerebrovascular dysfunction characterised by reduced cerebral blood flow and increased blood-brain barrier (BBB) permeability, accompanied by delayed white matter abnormalities, including altered diffusion MRI metrics, oligodendrocyte progenitor cell responses, and myelin loss. At the molecular level, pericyte depletion reprogrammed capillary endothelial cells toward an activated venular-like state characterised by VCAM-1 induction, reduced expression of the BBB-associated transporter MFSD2A, and activation of type I interferon signalling pathways. Cross-species analyses revealed enrichment of human white matter hyperintensity-associated SVD gene signatures across endothelial subtypes following pericyte depletion. Together, these findings identify pericyte dysfunction as a driver of endothelial inflammatory remodelling and white matter injury and establish mechanistic links between microvascular pericyte loss and human SVD.

neuroscience↗

bioRxiv2026

Abrupt Pericyte Loss Precedes Endothelial Activation in Cerebral Small Vessel Disease

Cerebral small vessel disease (cSVD) is a leading cause of stroke and vascular cognitive impairment, yet the cellular mechanisms underlying microvascular dysfunction in human disease remain incompletely understood. In particular, the relationship between pericyte alterations and endothelial activation, two key features of blood-brain barrier dysfunction, remains unresolved. Here, we performed a quantitative single-vessel analysis of the human cortical microvasculature across increasing cSVD severity and ageing. Using multiplex immunohistochemistry combined with spectral unmixing and automated image analysis, we analysed 11,409 microvascular fragments from post-mortem brain tissue derived from 20 cases. Endothelial cells, pericytes, and endothelial activation were assessed using PECAM-1, PDGFR{beta}, and VCAM-1, respectively. Microvascular density and diameter differed between cortical grey matter and the underlying white matter, with white matter vessels being less dense and wider in controls. While vessel diameter remained stable across disease stages, microvascular density increased with cSVD severity and age in the white matter. At the molecular level, PDGFR{beta} signal decreased markedly with increasing cSVD severity, consistent with progressive pericyte loss. This reduction was observed in both grey and white matter and correlated with disease severity and age. Notably, intermediate disease groups displayed marked heterogeneity, with vessels exhibiting either preserved or near-complete pericyte coverage, suggesting a potentially bimodal transition. In parallel, endothelial markers PECAM-1 and VCAM-1 increased significantly with disease severity, reflecting endothelial activation. Unsupervised Gaussian mixture clustering of marker expression identified three vascular states characterised by (i) preserved pericytes with low endothelial activation, (ii) marked pericyte loss without endothelial activation, and (iii) combined pericyte depletion and endothelial activation. These clusters broadly aligned with clinical severity but revealed intermediate states not captured by post-mortem diagnosis alone. Together, these findings suggest that pericyte loss and endothelial activation are partially dissociated processes that occur in a sequential progression in human cSVD, supporting pericyte dysfunction as an early event and highlighting it as a potential therapeutic target in microvascular disease.

pathology↗

bioRxiv2026

Live high-content imaging with automated analysis reveals mitochondrial changes during vascular calcification

Mitochondrial dysfunction is implicated in a wide range of disorders, including cancer, neurodegeneration, and cardiovascular diseases. Conventional assays typically assess mitochondrial function by measuring bulk respiration rates across thousands of cells. While informative, these approaches cannot resolve the behavior of individual mitochondria, may overlook rare mitochondrial events, and often lack sensitivity to subtle changes. Fluorescence microscopy provides single-organelle resolution but is usually low throughput; for example, imaging 1000 cells can require from 20 minutes to an entire day depending on imaging mode. Additionally, analysis of fluorescence images frequently relies on manually selected thresholds, introducing potential bias and variability due to differences in signal-to-background ratios across cells. Here, we present a High-throughput Mitochondrial Imaging Platform (H-MIP) combined with a deep learning segmentation model, enabling rapid imaging and automated characterization of mitochondrial morphology in millions of mitochondria from tens of thousands of cells. We demonstrate the utility of H-MIP by assessing mitochondrial morphology following treatment with Mdivi-1, an inhibitor of mitochondrial division. Furthermore, we employ an in vitro disease model (vascular calcification) to show that mitochondria become elongated in vascular smooth muscle cells undergoing pathological calcification. Overall, H-MIP provides a scalable and robust tool for investigating mitochondrial structure, with the potential to accelerate therapeutic discovery targeting mitochondrial health. HighlightsO_LIH-MIP enables high-throughput imaging of mitochondrial morphology and automated single-mitochondrion analysis at scale. C_LIO_LIH-MIP links mitochondrial morphology to an established disease model, with exciting implications for drug discovery. C_LI

cell biology↗

bioRxiv2024

Development of a pipeline to evaluate YAP-TEAD inhibitor potential - direct TEAD inhibition represses cancerous growth in a NF2-mutant model of mesothelioma

As the core, tumorigenic downstream effectors of the Hippo signalling pathway, YAP/TAZ and the TEAD family of transcription factors represent attractive targets for drug discovery efforts within cancer research. This is particularly true within the context of pleural mesothelioma, in which there are many recent preclinical developments and clinical trials evaluating the efficacy of TEAD inhibitors. The range of inhibitors have shown great promise, but comparisons of their performances are so far limited. Here we develop a high content pipeline that enables a comparative analysis of currently developed YAP/TAZ-TEAD inhibitors. We take advantage of isogenic cellular models that enable us to examine inhibitor specificity. We identify genetic compensation of the Hippo pathway transcriptional module, with implications for therapeutic targeting, and implement Cell Painting to develop a detailed morphological profiling pipeline that enables further characterisation, quantification, and analysis of off-target effects. Our pipeline is scalable and allows us to establish specificity and comparative potency within cancer relevant assays in a clinically relevant cellular model.

cancer biology↗

bioRxiv2024

Watch-breaker: establishment of a microwell array-based miniaturized thymic organoid model suitable for high throughput applications.

T-cell development depends critically on the thymic stroma, in particular the diverse array of functionally distinct thymic epithelial cell (TEC) types. However, a robust in vitro thymus model mimicking the native thymus and compatible with medium/high-throughput analyses is currently lacking. Here, we demonstrate a novel high-density microwell array-based miniaturized thymus organoid (mTO) model, that supports T-cell commitment and development, possesses key organizational characteristics of the native thymus and is compatible with live-imaging and medium/high-throughput applications. We establish the minimum cellular input required for functional mTO and show that mTO TEC phenotype and complexity closely mirrors the native thymus. Finally, we use mTO to probe the role of fetal thymic mesenchyme, revealing a requirement beyond maintenance of Foxn1 in differentiation/maintenance of mature TEC subpopulations. Collectively, mTO present a new in vitro model of the native thymus adaptable to medium/high-throughput applications and validated for exploration of thymus- and thymus organoid-biology.

immunology↗

bioRxiv2020

Neuronal non-CG methylation is an essential target for MeCP2 function

SUMMARYDNA methylation is implicated in neuronal biology via the protein MeCP2, mutation of which causes Rett syndrome. MeCP2 recruits the NCOR1/2 corepressor complexes to methylated cytosine in the CG dinucleotide, but also to non-CG methylation, which is abundant specifically in neuronal genomes. To test the biological significance of its dual binding specificity, we replaced the MeCP2 DNA binding domain with an orthologous domain whose specificity is restricted to mCG motifs. Knock-in mice expressing the domain-swap protein displayed severe Rett syndrome-like phenotypes, demonstrating that interaction with sites of non-CG methylation, specifically the mCAC trinucleotide, is critical for normal brain function. The results support the notion that the delayed onset of Rett syndrome is due to the late accumulation of both mCAC and its reader MeCP2. Intriguingly, genes dysregulated in both Mecp2-null and domain-swap mice are implicated in other neurological disorders, potentially highlighting targets of particular relevance to the Rett syndrome phenotype.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genetics↗

bioRxiv2020

SALL4 controls cell fate in response to DNA base composition

SO_SCPLOWUMMARYC_SCPLOWMammalian genomes contain long domains with distinct average compositions of A/T versus G/C base pairs. In a screen for proteins that might interpret base composition by binding to AT-rich motifs, we identified the stem cell factor SALL4 which contains multiple zinc-fingers. Mutation of the domain responsible for AT binding drastically reduced SALL4 genome occupancy and prematurely up-regulated genes in proportion to their AT content. Inactivation of this single AT-binding zinc-finger cluster mimicked defects seen in Sall4-null cells, including precocious differentiation of embryonic stem cells and embryonic lethality in mice. In contrast, deletion of two other zinc-finger clusters was phenotypically neutral. Our data indicate that loss of pluripotency is triggered by down-regulation of SALL4, leading to de-repression of a set of AT-rich genes that promotes neuronal differentiation. We conclude that base composition is not merely a passive by-product of genome evolution, but constitutes a signal that aids control of cell fate. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=190 SRC="FIGDIR/small/179481v2_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1ec4eb9org.highwire.dtl.DTLVardef@1246a36org.highwire.dtl.DTLVardef@1b9134dorg.highwire.dtl.DTLVardef@1a24904_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2020

Quantitative analysis questions the role of MeCP2 in alternative splicing

MeCP2 is an abundant protein in mature nerve cells, where it binds to DNA sequences containing methylated cytosine. Mutations in the MECP2 gene cause the severe neurological disorder Rett syndrome (RTT), provoking intensive study of the underlying molecular mechanisms. Multiple functions have been proposed, one of which involves a regulatory role in splicing. Here we leverage the recent availability of high-quality transcriptomic data sets to probe quantitatively the potential influence of MeCP2 on alternative splicing. Using a variety of machine learning approaches that can capture both linear and non-linear associations, we show that widely different levels of MeCP2 have a minimal effect on alternative splicing in three different systems. Alternative splicing was also apparently indifferent to developmental changes in DNA methylation levels. Our results suggest that regulation of splicing is not a major function of MeCP2. They also highlight the importance of multi-variate quantitative analyses in the formulation of biological hypotheses. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/115154v2_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1842d5eorg.highwire.dtl.DTLVardef@be867corg.highwire.dtl.DTLVardef@6f46a8org.highwire.dtl.DTLVardef@187f83c_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2018

Mathematical modelling reveals how MeCP2 restrains transcriptional elongation in human neurons

Patterns of gene expression are primarily determined by proteins that locally enhance or repress transcription. While many transcription factors target a restricted number of genes, others appear to modulate transcription levels globally. An example is MeCP2, an abundant methylated-DNA binding protein that is mutated in the neurological disorder Rett Syndrome. Despite much research, the molecular mechanism by which MeCP2 regulates gene expression is not fully resolved. Here we integrate quantitative, multi-dimensional experimental analysis and mathematical modelling to show that MeCP2 is a novel type of global transcriptional regulator whose binding to DNA creates "slow sites" in gene bodies. Waves of slowed-down RNA polymerase II formed behind these sites travel backward and indirectly affect initiation, reminiscent of defect-induced shock waves in non-equilibrium physics transport models. This mechanism differs from conventional gene regulation mechanisms, which often involve direct modulation of transcription initiation. Our findings uncover a genome-wide function of DNA methylation that may account for the reversibility of Rett syndrome in mice. Moreover, our combined theoretical and experimental approach provides a general method for understanding how global gene expression patterns are choreographed.

biophysics↗