Biology subjects

Stock, J.

Publications and source records attributed to Stock, J..

8 recordsLinked to original sources

bioRxiv2026

GM-CSF Programs Alveolar Macrophages to Maintain Pulmonary Lymphocyte Homeostasis

Pulmonary lymphocytosis is a common feature of chronic lung disease, but the mechanisms governing lymphocyte accumulation within the lung remain poorly understood. Here, we identify granulocyte-macrophage colony-stimulating factor (GM-CSF) as a central regulator of pulmonary lymphocyte homeostasis. Using genetic models, single-nucleus and spatial transcriptomics, cell trafficking analyses, and pulmonary macrophage replacement studies, we show that loss of GM-CSF signaling causes profound pulmonary lymphocytosis characterized by lymphoid follicle formation, local immunoglobulin production, and expansion of multiple lymphocyte lineages. Mechanistically, GM-CSF signaling deficiency blocks terminal alveolar macrophage differentiation and reprograms alveolar macrophages into inflammatory states marked by reduced PU.1 and PPAR{gamma} expression, enhanced NF-{kappa}B signaling, and expression of lymphocyte-recruiting chemokines. These changes promote lymphocyte recruitment, local proliferation, and lymphoid lineage commitment. Restoration of GM-CSF-responsive alveolar macrophages re-established macrophage identity, suppressed inflammatory chemokine programs, and reversed pulmonary lymphocytosis. Together, these findings identify alveolar macrophages as gatekeepers of adaptive immune homeostasis in the lung.

immunology↗

bioRxiv2025

Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods

How genomic changes translate into organismal novelties is often confounded by the multi-layered nature of genome architecture and the long evolutionary timescales over which molecular changes accumulate. Coleoid cephalopods (squid, cuttlefish, and octopus) provide a unique system to study these processes due to a large-scale chromosomal rearrangement in the coleoid ancestor that resulted in highly modified karyotypes, followed by lineage-specific fusions, translocations, and repeat expansions. How these events have shaped gene regulatory patterns underlying the evolution of coleoid innovations, including their large and elaborately structured nervous systems, novel organs, and complex behaviours, remains poorly understood. To address this, we integrate Micro-C, RNA-seq, and ATAC-seq across multiple coleoid species, developmental stages, and tissues. We find that while topological compartments are broadly conserved, hundreds of chromatin loops are species- and context-specific, with distinct regulation signatures and dynamic expression profiles. CRISPR-Cas9 knockout of a putative regulatory sequence within a conserved region demonstrates the role of loops in neural development and the prevalence of long-range, inter-compartmental interactions. We propose that differential evolutionary constraints across the coleoid 3D genome allow macroevolutionary processes to shape genome topology in distinct ways, facilitating the emergence of novel regulatory entanglements and ultimately contributing to the evolution and maintenance of complex traits in coleoids.

evolutionary biology↗

bioRxiv2025

Ectopic, hepatic GLP-1R agonism enhances the weight loss efficacy of GLP-1 analogues.

ObjectiveUnimolecular triagonists drive substantial weight loss in patients with obesity (PwO) by engaging the glucagon-like peptide 1 (GLP-1) and glucose dependent insulinotropic polypeptide (GIP) receptors to reduce food intake (FI) and the hepatic glucagon (Gcg) receptor to enhance energy expenditure (EE). However, their development has been challenged by deleterious cardiovascular (CV) effects including increased heart rate (HR), elongated QTc, and arrhythmia mediated by GcgR agonism. GLP-1R monoagonists on the other hand improve both obesity and CV outcomes with negligible effects on EE. We sought to imbue peptide GLP-1R agonists with an EE enhancing effect by combining them with ectopic GLP-1R expression and agonism in hepatocytes. MethodsWe used an attenuated adenovirus (AAV) to induce the expression of a functional, liver-specific GLP-1R combined with traditional peptide agonist treatment to drive greater body weight loss via reduced energy intake and increased energy expenditure. ResultsAgonism of the ectopic GLP-1R with either semaglutide, a low internalization GLP-1R agonist (Sema584), or a dual GLP-1R/GIPR agonist in wild-type (WT) diet induced obese (DIO) mice led to enhanced EE and improved weight loss compared to agonist treatment alone. ConclusionsThis represents a novel mechanism for achieving polypharmacy to treat obesity. HighlightsO_LIA Glp1r encoding AAV induces expression of a functional receptor mouse livers. C_LIO_LIEndogenous GLP-1R does not mediate semaglutide clearance. C_LIO_LIEctopic GLP-1R mediates semaglutide clearance. C_LIO_LIEctopic, hepatic Glp1r plus semaglutide enhances weight loss in mice. C_LIO_LIEctopic, hepatic Glp1r plus a dual incretin agonist enhances weight loss in mice. C_LI

zoology↗

bioRxiv2021

A self-generated Toddler gradient guides mesodermal cell migration

The sculpting of germ layers during gastrulation relies on coordinated migration of progenitor cells, yet the cues controlling these long-range directed movements remain largely unknown. While directional migration often relies on a chemokine gradient generated from a localized source, we find that zebrafish ventrolateral mesoderm is guided by the uniformly expressed and secreted protein Toddler/ELABELA/Apela, acting as a self-generated gradient. We show that the Apelin receptor, which is specifically expressed in mesodermal cells, has a dual role during gastrulation, acting as a scavenger receptor to generate a Toddler gradient, and as a chemokine receptor to sense this guidance cue. Thus, we uncover a single receptor-based self-generated gradient as the enigmatic guidance cue that can robustly steer the directional migration of mesoderm through the complex and continuously changing environment of the gastrulating embryo. One sentence summaryAplnr has a dual role to self-generate and sense a Toddler gradient directing mesodermal cells during zebrafish gastrulation.

developmental biology↗

bioRxiv2020

Closed-loop fMRI neurofeedback to reduce negative attentional bias in depression

Depressed individuals show an attentional bias toward negatively valenced stimuli and thoughts. Here we present a novel closed-loop neurofeedback procedure that seeks to remediate this bias. Internal attentional states were detected by applying machine learning techniques to fMRI data in real-time, and externalized using a visually presented stimulus that the participant could learn to control. We trained 15 depressed and 12 healthy control participants over three fMRI sessions, preceded and followed by behavioral and clinical assessments. Initially, depressed participants were more likely than non-depressed participants to get "stuck" in negative attentional states, but this diminished with neurofeedback training relative to controls. Depression severity also decreased from pre- to post-training. These results demonstrate that our method is sensitive to the negative attentional bias in depressed individuals, and its reduction after training showcases the potential of this method as a treatment in the future.

neuroscience↗

bioRxiv2020

A novel factor essential for unconventional secretion of chitinase Cts1

Subcellular targeting of proteins is essential to orchestrate cytokinesis in eukaryotic cells. During cell division of Ustilago maydis, for example, chitinases must be specifically targeted to the fragmentation zone at the site of cell division to degrade remnant chitin and thus separate mother and daughter cells. Chitinase Cts1 is exported to this location via an unconventional secretion pathway putatively operating in a lock-type manner. The underlying mechanism is largely unexplored. Here, we applied a forward genetic screen based on UV mutagenesis to identify components essential for Cts1 export. The screen revealed a novel factor termed Jps1 lacking known protein domains. Deletion of the corresponding gene confirmed its essential role for Cts1 secretion. Localization studies demonstrated that Jps1 colocalizes with Cts1 in the fragmentation zone of dividing yeast cells. While loss of Jps1 leads to exclusion of Cts1 from the fragmentation zone and strongly reduced unconventional secretion, deletion of the chitinase does not disturb Jps1 localization. Yeast-two hybrid experiments suggest that the two proteins interact. In essence, we identified a novel component of unconventional secretion that functions in the fragmentation zone to enable export of Cts1. We hypothesize that Jps1 acts as an anchoring factor, supporting the proposed novel lock-type mechanism of unconventional secretion.

microbiology↗

bioRxiv2019

Transfer Learning for Predicting Conversion from Mild Cognitive Impairment to Dementia of Alzheimer Type based on 3D-Convolutional Neural Network

Dementia of Alzheimers Type (DAT) is associated with a devastating and irreversible cognitive decline. As a pharmacological intervention has not yet been developed to reverse disease progression, preventive medicine will play a crucial role for patient care and treatment planning. However, predicting which patients will progress to DAT is difficult as patients with Mild Cognitive Impairment (MCI) could either convert to DAT (MCI-C) or not (MCI-NC). In this paper, we develop a deep learning model to address the heterogeneous nature of DAT development. Structural magnetic resonance imaging was utilized as a single biomarker, and a three-dimensional convolutional neural network (3D-CNN) was developed. The 3D-CNN was trained using transfer learning from the classification of Normal Control and DAT scans at the source task. This was applied to the target task of classifying MCI-C and MCI-NC scans. The model results in 82.4% classification accuracy, which outperforms current models in the field. Furthermore, by implementing an occlusion map approach, we visualize key brain regions that significantly contribute to the prediction of MCI-C and MCI-NC. Results show the hippocampus, amygdala, cerebellum, and pons regions as significant to prediction, which are consistent with current understanding of disease. Finally, the models prediction value is significantly correlated with rates of change in clinical assessment scores, indicating the model is able to predict an individual patients future cognitive decline. This information, in conjunction with the identified anatomical features, will aid in building a personalized therapeutic strategy for individuals with MCI. This model could also be useful for selection of participants for clinical trials.

bioinformatics↗

bioRxiv2019

Systematic analysis of Plasmodium myosins reveals differential expression, localization and function in invasive and proliferative parasite stages

The myosin superfamily comprises of actin-dependent eukaryotic molecular motors important in a variety of cellular functions. Although well studied in many systems, knowledge of their functions in Plasmodium, the causative agent of malaria, is restricted. Previously, six myosins were identified in this genus, including three Class XIV myosins found only in Apicomplexa and some Ciliates. The well characterised MyoA, is a class XIV myosin essential for gliding motility and invasion. Here, we characterize all other Plasmodium myosins throughout the parasite life cycle and show that they have very diverse patterns of expression and cellular location. MyoB and MyoE, the other two Class XIV myosins, are expressed in all invasive stages, with apical and basal locations, respectively. Gene deletion revealed that MyoE is involved in sporozoite motility, MyoF and MyoK are likely essential in the asexual blood stages, and MyoJ and MyoB are not essential. Both MyoB and its essential light chain (MCL-B) are localised at the apical end of ookinetes but expressed at completely different time points. This work provides a better understanding of the role of actomyosin motors in Apicomplexan parasites, particularly in the motile and invasive stages of Plasmodium during sexual and asexual development within the mosquito.

cell biology↗