Biology subjects

Mathew, R.

Publications and source records attributed to Mathew, R..

10 recordsLinked to original sources

bioRxiv2026

Neutrophil remodeling is associated with human meibomian gland dysfunction and enables IFN-γ- and PAD4-dependent gland obstruction in mice

Meibomian gland dysfunction (MGD), a disorder of the eyelid's modified sebaceous glands, is the leading cause of dry eye disease and ocular surface morbidity, yet the immune mechanisms driving gland obstruction remain poorly defined. In a cross-sectional study of 66 patients with ocular surface inflammation, we used meibography and spectral flow cytometry of tear washes to identify a disease-associated, remodeled neutrophil state whose abundance is associated with gland atrophy. Using single-cell transcriptomics in a murine model of immune-mediated MGD, we revealed a disease-associated neutrophil state that exhibited ocular surface-enrichment, CD14 and ICAM-1 expression, and elevated IFN-{gamma} response and inflammatory signatures. Spatial transcriptomics localized IFN-{gamma} signaling and neutrophil migration signatures to the periglandular compartment. The remodeled neutrophils exhibited PAD4-dependent histone citrullination, with Padi4 deletion reducing NET-associated obstructive plugging, thus identifying PAD4-dependent NETotic activity as their disease-producing output. Inhibition of IFN-{gamma} signaling phenocopied Padi4 deficiency, yet combined disruption of these pathways provided no additive protection, indicating that IFN-{gamma} and PAD4 function as separable required inputs. Remodeled neutrophils accumulated under both conditions, uncoupling disease severity from cell abundance alone. Our findings support immune-mediated obstructive MGD as a mechanistic endotype driven by the IFN-{gamma}- and PAD4-dependent effector output of a remodeled neutrophil state.

immunology↗

bioRxiv2026

Plaque-associated oligodendrocyte proteostatic failure underlies myelin loss in Alzheimers disease

Alzheimers disease (AD) features amyloid-{beta} plaques and tau pathology, yet the mechanism underlying early and clinically significant myelin loss remains unresolved. Here, we report human iPSC-derived forebrain organoids with doxycycline-inducible expression of SOX10, OLIG2, and NKX6-2 (SON), which generate robust, mature oligodendrocytes and compact myelin in vitro and in vivo. Introducing amyloid precursor protein (APP) pathogenic mutations produces extracellular amyloid-{beta} plaques and phosphorylated tau, accompanied by reduced myelin basic protein (MBP) expression and disrupted myelin ultrastructure. Single-cell and spatial transcriptomics combined with amyloid plaque imaging reveal that oligodendrocytes in plaque-dense regions show pathological changes in calcium signaling, immune activation, lipid remodeling, and protein catabolic pathways. Notably, MBP protein is reduced despite elevated myelin-related transcription, suggesting plaque-induced degradation of myelin proteins. Consistent with this, proteasomal inhibition restores MBP protein levels and improves compact myelin ultrastructure in AD organoids. In human AD brain tissue, protein catabolic pathways are similarly upregulated with increasing plaque density. Together, these findings identify plaque-associated oligodendrocyte proteostatic failure as a candidate mechanism of myelin loss and a potential therapeutic pathway in AD.

neuroscience↗

bioRxiv2025

High-density extracellular recordings from the interior of intact brain organoids enable automated high-throughput functional assay

Bridging the gap between preclinical screening and clinical outcomes remains a major challenge in drug development for neurological disorders. Brain organoids, derived from human induced pluripotent stem cells, offer a scalable and physiologically relevant platform to model human neural circuits. We develop a fully automated system to record neural activity from the interior of intact human cortical organoids using a high-density microfabricated probe. The robotic system completes insertion within minutes while preserving organoid integrity and enables immediate recording of spontaneous spikes. We extract physiologically grounded and deterministic spike features, and train a long short-term memory classifier to distinguish between organoids derived from healthy individuals and those harboring familial Alzheimers disease (AD) mutations in the amyloid precursor protein. Despite intra-class variability, the classifier differentiates between organoid classes with 100% accuracy. The model classifies AD organoids treated with a drug candidate that reduces amyloid-{beta} levels as retaining an AD-like electrophysiological phenotype, demonstrating that functional readout can contradict molecular markers. The findings establish a high-throughput functional framework that may complement and extend existing drug screening assays.

neuroscience↗

bioRxiv2025

The Cornea Harbors a Tricellular Neuro-Immune Niche that Underpins Touch Sensation

Piezo2 is a mechanosensitive ion channel essential for touch and proprioception, yet the mechanisms that maintain this sensory modality in adult tissues are unknown. Using multiphoton imaging of the cornea in live mice, we discovered that the Cx3cr1Cre locus targets not only macrophages, but also a distinct subset of nerves. Spatial-RNAseq resolved that Cx3cr1Cre-driven labeling was uniquely enriched in Piezo2-expressing neurons, a result of temporal Cx3cr1 expression during development. Through lineage tracing, scRNAseq, and imaging, we identified a novel tripartite cellular niche at the epithelial basement membrane, comprised of monocyte-derived macrophages, nerves, and Schwann cells. Additional scRNAseq and genetic studies revealed that Schwann cell-derived IL34 maintained corneal macrophages. Through pharmacologic and genetic perturbations, we also demonstrate corneal macrophages selectively maintained the structure-function of Piezo2-enriched nerve endings, with disruption of this niche causing specific deficits in mechanosensation while preserving other sensory modalities. Altogether, we describe a novel tricellular niche in the cornea required for Piezo2-mediated touch sensation, suggesting new directions for investigating mechanosensory circuits including proprioception.

immunology↗

bioRxiv2025

Resident Tissue Macrophages Govern Intraocular Pressure Homeostasis

Intraocular pressure is tightly regulated by the conventional outflow tissues, preventing ocular hypertension that leads to neurodegeneration of the optic nerve, or glaucoma. Although macrophages reside throughout the conventional outflow tract, their role in regulating intraocular pressure remains unknown. Using macrophage lineage tracing approaches, we uncovered a dual macrophage ontogeny with distinct spatial organizations across the mouse lifespan. Long-lived, resident tissue macrophages concentrated in the trabecular meshwork and Schlemms canal, whereas short-lived monocyte-derived macrophages, instead, were abundant around distal vessels. Specific depletion of resident tissue macrophages triggered elevated intraocular pressure and outflow resistance, linked to aberrant extracellular matrix turnover in the resistance-generating tissues of the trabecular meshwork. This dysregulated physiology and tissue remodeling were not observed when we depleted monocyte-derived macrophages. Results show ontogeny and tissue-specific macrophage function within the outflow tract, uncovering the integral homeostatic role of resident tissue macrophages in resistance-generating tissues whose dysfunction is responsible for glaucoma.

immunology↗

bioRxiv2024

Stimulus-modulated approach to steady-state: A new paradigm for event-related fMRI.

Functional MRI (fMRI) studies discard the initial volumes acquired during the approach of the magnetization to its steady-state value. Here, we leverage the higher temporal signal-to-noise ratio (tSNR) of these initial volumes to increase the sensitivity of event-related fMRI experiments. To do this, we introduce Acquisition Free Periods (AFPs) that allow for the full recovery of the magnetization, followed by task or baseline acquisition blocks (AB) of fMRI volumes. An appropriately placed stimulus in the AFP produces a Blood Oxygenation-Level-Dependent (BOLD) response that peaks during the initial high tSNR phase of the AB, yielding up to a [~]50% reduction in the number of trials needed to achieve a given statistical threshold relative to conventional fMRI. The silent AFP can be exploited for the presentation of auditory stimuli or uncontaminated electrophysiological recording and its variable duration allows aperiodic stimulus or response-locked signal averaging as well as gating to physiology or motion.

physiology↗

bioRxiv2023

Microglia at Sites of Atrophy Restrict the Progression of Retinal Degeneration via Galectin-3 and Trem2 Interactions

Degenerative diseases of the outer retina, including age-related macular degeneration (AMD), are characterized by atrophy of photoreceptors and retinal pigment epithelium (RPE). In these blinding diseases, macrophages are known to accumulate ectopically at sites of atrophy, but their ontogeny and functional specialization within this atrophic niche remain poorly understood, especially in the human context. Here, we uncovered a transcriptionally unique profile of microglia, marked by galectin-3 upregulation, at atrophic sites in mouse models of retinal degeneration and in human AMD. Using disease models, we found that conditional deletion of galectin-3 in microglia led to defects in phagocytosis and consequent augmented photoreceptor death, RPE damage and vision loss, suggestive of a protective role. Mechanistically, Trem2 signaling orchestrated the migration of microglial cells to sites of atrophy, and there, induced galectin-3 expression. Moreover, pharmacologic Trem2 agonization led to heightened protection, but only in a galectin-3-dependent manner, further signifying the functional interdependence of these two molecules. Likewise in elderly human subjects, we identified a highly conserved population of microglia at the transcriptomic, protein and spatial levels, and this population was enriched in the macular region of postmortem AMD subjects. Collectively, our findings reveal an atrophy-associated specialization of microglia that restricts the progression of retinal degeneration in mice and further suggest that these protective microglia are conserved in AMD. One Sentence SummaryA common neuroprotective response of microglia at the site of retinal atrophy is identified in mice and humans.

immunology↗

bioRxiv2021

Midbrain microglia exhibit early proliferative and inflammatory responses during aging that are modulated by CX3CR1 and microglial ablation and repopulation

During aging, microglia produce inflammatory factors, show reduced tissue surveillance, altered interactions with synapses, and prolonged responses to insults, positioning these cells to have profound impact on the functional integrity of nearby neurons. We and others recently showed that microglial attributes differ significantly across brain regions and CNS insults in young adult mice. However, the degree to which microglial properties vary during aging is largely unexplored. Here, we analyze and manipulate microglial aging within the basal ganglia, brain circuits that exhibit prominent regional microglial heterogeneity and where neurons are vulnerable to functional decline and neurodegenerative disease. We demonstrate that microglia in the ventral tegmental area (VTA) and substantia nigra pars compacta (SNc) exhibit unique and premature responses to aging, compared to microglia elsewhere. This is associated with pockets of VTA/SNc neuroinflammation that are likely to compromise local synaptic function as early as middle age. Surprisingly, these early aging responses of VTA and SNc microglia do not appear to be driven by systemic inflammation, local neuron death, or early responses of astrocytes to aging. Finally, CX3CR1 receptor knockout can exacerbate and microglial ablation/repopulation can suppress early VTA microglial aging; these manipulations have been shown to affect brain-wide microglial aging, and our data demonstrate that their impact is not uniform throughout the CNS. Our findings reveal a previously unappreciated regional variation in the onset and magnitude of microglial aging responses and suggest that there may be important links between local microglial aging and vulnerability of nearby neurons to functional decline and disease.

neuroscience↗

bioRxiv2020

Mucosal Associated Invariant T (MAIT) Cell Responses Differ by Sex in COVID-19

Sexual dimorphisms in immune responses contribute to coronavirus disease 2019 (COVID-19) outcomes, yet the mechanisms governing this disparity remain incompletely understood. We carried out sex-balanced sampling of peripheral blood mononuclear cells from confirmed COVID-19 inpatients and outpatients, uninfected close contacts, and healthy controls for 36-color flow cytometry and single cell RNA-sequencing. Our results revealed a pronounced reduction of circulating mucosal associated invariant T (MAIT) cells in infected females. Integration of published COVID-19 airway tissue datasets implicate that this reduction represented a major wave of MAIT cell extravasation during early infection in females. Moreover, female MAIT cells possessed an immunologically active gene signature, whereas male counterparts were pro-apoptotic. Collectively, our findings uncover a female-specific protective MAIT profile, potentially shedding light on reduced COVID-19 susceptibility in females.

immunology↗

bioRxiv2020

Transcytosis via the late endocytic pathway as a cell morphogenetic mechanism

Plasma membranes fulfil many physiological functions. In polarized cells, different membrane compartments take on specialized roles, each being allocated correct amounts of membrane. The Drosophila tracheal system, an established tubulogenesis model, contains branched terminal cells with subcellular tubes formed by apical plasma membrane invagination. We show that apical endocytosis and late endosome-mediated trafficking determine the membrane allocation to the apical and basal membrane domains. Basal plasma membrane growth stops if endocytosis is blocked, whereas the apical membrane grows excessively. Plasma membrane is initially delivered apically, and then continuously endocytosed, together with apical and basal cargo. We describe an organelle carrying markers of late endosomes and multivesicular bodies (MVBs) that is abolished by inhibiting endocytosis, and which we suggest acts as transit station for membrane destined to be redistributed both apically and basally. This is based on the observation that disrupting MVB formation prevents growth of both compartments.

cell biology↗