Biology subjects

Quirk, J. D.

Publications and source records attributed to Quirk, J. D..

5 recordsLinked to original sources

bioRxiv2026

Novel mouse models for perianal fistulizing Crohns disease reveal therapeutic value of interferon-gamma antagonists

Background and AimsPerianal fistulizing Crohns disease (PFCD) is a challenging complication with poorly understood pathogenesis and limited treatment options, largely due to the lack of clinically relevant animal models. Interferon-gamma (IFN-{gamma}) signaling is hyperactivated in human PFCD. We aimed to establish mouse models recapitulating human PFCD and to evaluate IFN-{gamma} as a new therapeutic target. MethodsPerianal fistulas were established in three mouse models with concurrent Crohns disease-like intestinal inflammation: wild-type (WT) mice with 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced proctocolitis, Il10-/-mice, and TNF{Delta}69AU/+ mice. A modified MAGNIFI-CD index was developed for longitudinal fistula assessment in mice. Transcriptomic analysis and flow cytometry were conducted on mouse fistula tissue. Re-analysis of single-cell and spatial transcriptomics of human PFCD tissues was performed. Therapeutic benefits of anti-TNF-, upadacitinib, and IFN-{gamma} pathway antagonists were evaluated in the PFCD models. ResultsAll three PFCD models sustained chronic perianal fistula tracts for at least 5 weeks after wire removal. All three models closely recapitulate the pathological and molecular features of PFCD in patients, as confirmed by clinical examination, MRI, histopathology, immunostaining, flow cytometry, and transcriptomics. IFN-{gamma} signaling emerged as a central and conserved pathway across all three mouse models and human PFCD. Targeting of the IFN-{gamma} pathway promptly improved fistula healing with mitigation of IFN-{gamma} signaling, inflammation, and epithelial-to-mesenchymal transition (EMT). Moreover, combining IFN-{gamma} and TNF- blockade demonstrated augmented therapeutic efficacy compared to anti-TNF- monotherapy. ConclusionsThese PFCD mouse models and imaging tools provide first reliable and clinically relevant platforms for mechanistic studies and therapeutic evaluation. IFN-{gamma} signaling represents a potential therapeutic target warranting clinical investigation.

immunology↗

bioRxiv2026

Automated Ventricle Assessment via Three-dimensional Anatomical Reconstruction (AVA-TAR): a computational toolkit for autonomous lateral ventricle assessment in preclinical hydrocephalus models

IntroductionCurrent workflows for studying hydrocephalus in rodent models rely on manual segmentation or qualitative assessment of ventricular size on small animal magnetic resonance imaging, which are both inefficient and prone to variability. Atlas-based methods enable more streamlined segmentation, but their analysis is limited to morphologically normal samples. ObjectiveThis study aimed to develop and internally validate a deep learning model that performs automated segmentation of lateral ventricles in rodent brain MRIs, allowing for 3D ventricle reconstruction, morphological analysis, and ventriculomegaly detection. MethodsFour U-Net++ neural networks, each with different encoder backbones, were trained using 307 rodent brain MRIs (262 rats, 45 mice), each with manually segmented lateral ventricles serving as the ground truth. Model performance was evaluated using the Dice coefficient, intersection over union (IoU), and Hausdorff index. The most optimal model was evaluated further for its ability to quantify ventricle volume, convexity, surface area, and symmetry. ResultsThe U-Net++ model with an EfficientNet-B1 encoder achieved high accuracy (Dice: 0.823 {+/-} 0.136; IoU: 0.721 {+/-} 0.85). Further assessment of its morphological predictions found strong correlations with manual measurements of ventricular morphology, with Pearson and interclass correlation coefficients exceeding 0.96 across all metrics. The full validated pipeline was packaged into a publicly available application, hosted at https://ava-tar.org. ConclusionThis study introduces a deep learning tool for automated segmentation and morphological analysis of lateral ventricles in rodent MRIs. The tools efficiency and accuracy in quantifying ventricle morphology offers significant utility in preclinical hydrocephalus research with potential future application in the clinical setting.

neuroscience↗

bioRxiv2025

Indirect Deuterium Displacement Exchange Imaging for Non-invasive High-Resolution CSF Production Mapping

Cerebrospinal fluid (CSF) production is central to brain homeostasis, yet existing measurement techniques are invasive, technically demanding, and confounded by intracranial perturbations. Here, we introduce indirect deuterium displacement exchange imaging (CSF-iDDxI), a noninvasive MRI approach for mapping CSF production in vivo. The method leverages intravenously infused deuterium oxide (D2O), which crosses the blood-CSF barrier, replaces existing H2O in CSF, producing concentration-dependent attenuation of proton (1H) signal within CSF spaces. Using high-resolution 3D balanced steady-state free precession MRI in rats, we demonstrate robust and spatially widespread D2O-induced CSF signal loss that is selectively suppressed by acetazolamide, a carbonic anhydrase inhibitor known to suppress CSF production by the choroid plexus. Dynamic imaging during intravenous D2O infusion further revealed that cortical parenchymal signal changes were unaffected by acetazolamide, confirming specificity to CSF production. Exploratory kinetic modeling estimated rapid CSF water turnover (k {approx} 0.09 min-1) under physiological conditions, reduced to k {approx} 0.031 min-1 with acetazolamide suppression, consistent with prior isotope tracer studies. Together, these findings establish CSF-iDDxI as a sensitive, pharmacologically validated tool for quantifying CSF production and turnover.

neuroscience↗

bioRxiv2025

Cerebellum metastasis model of HER2-positive breast cancer unveils key role of IL34-induced Arg1+ macrophages.

Brain metastases occur in up to 40% of Stage IV breast cancer patients. The cerebellum is a frequent location for metastases in HER2-positive breast cancer patients, but the mechanisms for this are unknown. Here, we developed a syngeneic, immunocompetent mouse model for breast cancer brain metastases by stereotactically injecting mouse HER2-overexpressing breast cancer organoids into the cerebellum. Growth of these cerebellar metastases was monitored by MRI and trastuzumab optical imaging using a near-infrared fluorophore conjugated to trastuzumab. Spatial transcriptomics identified interleukin-34 production by breast cancer cells inducing ARG1+ macrophages at the invading edge of the metastasis. Treatment with a blocking antibody to interleukin-34s receptor, CSF1R, produced tumor shrinkage. These findings have immediate translation potential as a CSF1R-blocking antibody is FDA-approved. Further, it demonstrates that cancer-associated inflammation bordering the brain metastasis promotes metastatic growth and offers a molecularly targeted strategy to treat inflammation in brain metastasis. Graphical summary O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/660224v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@9f1a50org.highwire.dtl.DTLVardef@178acc5org.highwire.dtl.DTLVardef@196d803org.highwire.dtl.DTLVardef@3fe631_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2021

Global cerebrospinal fluid circulation mapping using gold nanoparticle enhanced X-ray microtomography reveals region-specific brain and spinal cord CSF pathways

Cerebrospinal fluid (CSF) movement within the brain interstitium is essential for the development and functioning of the brain. However, the interstitium has largely been thought of as a single entity through which CSF circulates, and it is not known whether specific cell populations within the CNS preferentially interact with CSF. Here, we developed a novel technique for CSF tracking, gold nanoparticle enhanced X-ray microtomography, to achieve micrometer-scale resolution visualization of CSF pathways during development. Using this method and subsequent histological analysis, we map global CSF pathways and present novel particle size-dependent circulation patterns through the CNS. We identify an intraparenchymal CSF circulation that targets stem cell-rich and cholinergic neuronal populations. CSF solute distribution to these areas is mediated by CSF flow along projections from the basal cisterns which is altered in posthemorrhagic hydrocephalus. Our study uncovers region-specific patterns in a biologically driven CSF circulation that has implications for normal brain development and the pathophysiology of hydrocephalus and neurodegenerative disorders.

neuroscience↗