Biology subjects

Ramirez, D. M.

Publications and source records attributed to Ramirez, D. M..

4 recordsLinked to original sources

bioRxiv2026

Shared Transcriptomic Signatures in Perilesional and Contralesional Cortex

Stroke induces a transient period of heightened plasticity during which functional recovery is most pronounced. Work in rodent models of stroke has identified key mechanisms in both the ipsilesional and contralesional cortex that contribute to functional and structural post-stroke plasticity. To date, most gene expression studies have focused on the infarct core and the immediately surrounding tissue, peri-lesional cortex (PLC). We sought to understand whether the contralesional cortex (CLC), a region that shows robust structural and molecular remodeling despite its distance from the lesion, mounts a distinct transcriptional response to stroke. Direct comparisons of molecular pathways governing these regions, particularly across sexes, are limited. To address this gap, we performed bulk RNA sequencing of the PLC and CLC at 7 days post-stroke, a critical time point for initiating repair, in male and female mice. Our results indicate that despite distinct positions from the lesion, both regions share a robust upregulation of inflammatory signaling, with Gene Ontology enrichment indicating activation of cytokine signaling, leukocyte activation, and gliogenesis pathways. Further analysis of this shared gene expression signature revealed reactive microglia signaling as the dominant pathway. Surprisingly, the CLC did not show a distinct transcriptional response. These findings were consistent across males and females, which also showed similar CLC-derived corticospinal tract axonal sprouting at 6 weeks post-stroke. Together, these findings support a shared microglia-centered neuroinflammatory transcriptional response in the PLC and CLC and suggest that microglial reactivity is a key early process for post-stroke cortical plasticity in both male and female mice.

neuroscience↗

bioRxiv2024

Integrated stress response associated with dark microglia promotes microglial lipogenesis and contributes to neurodegeneration

Microglia, the brains primary resident immune cells, are a heterogeneous population and can assume phenotypes with diverse functional outcomes on brain homeostasis. In Alzheimers disease (AD), where microglia are a leading causal cell type, microglia subsets with protective functions have been well characterized. Yet, the identity of microglia subsets that drive neurodegeneration remains unresolved. Here, we identify a neurodegenerative microglia phenotype that is characterized by a conserved stress signaling pathway, the integrated stress response (ISR). Using mouse models to activate or inhibit ISR in microglia, we show that ISR underlies the ultrastructurally distinct "dark" microglia subset linked to pathological synapse loss. Inducing microglial ISR in murine AD models exacerbates neurodegenerative pathologies, such as Tau pathology and synaptic terminal loss. Conversely, inhibiting microglial ISR in AD models ameliorates these pathologies. Mechanistically, we present evidence that ISR promotes the secretion of toxic long-chain lipids that impair neuron and oligodendrocyte homeostasis in vitro. Accordingly, small molecule-based inhibition of lipid synthesis in AD models ameliorates synaptic terminal loss. Our results demonstrate that activation of ISR within microglia represents a novel pathway contributing to neurodegeneration and suggest that this may be sustained, at least in part, by the secretion of long-chain lipids from ISR-activated microglia.

neuroscience↗

bioRxiv2023

Endogenous pathology in tauopathy mice progresses via brain networks

Neurodegenerative tauopathies are hypothesized to propagate via brain networks. This is uncertain because we have lacked precise network resolution of pathology. We therefore developed whole-brain staining methods with anti-p-tau nanobodies and imaged in 3D PS19 tauopathy mice, which have pan-neuronal expression of full-length human tau containing the P301S mutation. We analyzed patterns of p-tau deposition across established brain networks at multiple ages, testing the relationship between structural connectivity and patterns of progressive pathology. We identified core regions with early tau deposition, and used network propagation modeling to determine the link between tau pathology and connectivity strength. We discovered a bias towards retrograde network-based propagation of tau. This novel approach establishes a fundamental role for brain networks in tau propagation, with implications for human disease. One-Sentence SummaryNovel whole brain imaging of p-tau deposition reveals retrograde-dominant network propagation in a tauopathy mouse model.

neuroscience↗

bioRxiv2021

Milk Exosomes Cross the Blood-Brain Barrier in Murine Cerebral Cortex Endothelial Cells and Promote Dendritic Complexity in the Hippocampus and Brain Function in C57BL/6J Mice

BackgroundHuman milk contains large amounts of exosomes (MEs) and their regulatory microRNA cargos, whereas infant formulas contain only trace amounts of MEs and microRNAs. Breastfeeding has been implicated in optimal brain development but experimental evidence linking ME intake with brain development is limited. ObjectivesWe assessed the transport of MEs across the blood-brain barrier (BBB) and ME accumulation in distinct regions of the brain in brain endothelial cells and suckling mice. We further assessed BME-dependent gene expression profiles and effects on the dendritic complexity of hippocampal granule cells and phenotypes of BME depletion in neonate, juvenile and adult mice. MethodsThe transfer of MEs across the BBB was assessed by using bovine MEs labeled with FM4-64 or loaded with IRDye-labeled miR-34a in murine brain endothelial bEnd.3 cell monolayers and dual chamber systems, and in wild-type newborn pups fostered to exosome and cargo tracking (ECT) dams that express MEs endogenously labeled with a CD63-eGFP fusion protein for subsequent analysis by serial two-photon tomography and staining with anti-eGFP antibodies. Effects of MEs on gene expression and dendritic architecture of granule cells was analyzed in hippocampi from juvenile mice fed exosome and RNA-depleted (ERD) and exosome and RNA-sufficient (ERS) diets by using RNA-sequencing analysis and Golgi-Cox staining followed by integrated neuronal tracing and morphological analysis of neuronal dendrites, respectively. Spatial learning and severity of kainic acid-induced seizures were assessed in mice fed ERD and ERS diets. ResultsbEnd.3 cells internalized MEs by using a saturable transport mechanism and secreted miR-34a across the basal membrane. MEs penetrated the entire brain in fostering experiments; major regions of accumulation included the hippocampus, cortex and cerebellum. Two hundred ninety-five genes were differentially expressed in hippocampi from male mice fed ERD and ERS diets; high-confidence gene networks included pathways implicated in axon guidance and calcium signaling. Only one gene was differentially expressed in females fed the experimental diets. Juvenile pups fed the ERD diet had reduced dendritic complexity of dentate granule cells in the hippocampus, scored nine-fold lower in the Barnes maze test of spatial learning and memory (P < 0.01), and the severity of seizures was 5-fold higher following kainic acid administration in adult mice fed the ERD diet compared to mice fed the ERS diet (P < 0.01). ConclusionsMEs cross the BBB and contribute toward optimal neuronal development, spatial learning and memory, and resistance to kainic acid-induced seizures in mice.

neuroscience↗