Biology subjects

Sierra, A.

Publications and source records attributed to Sierra, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Multidimensional diffusion MRI reveals heterogeneous microstructural remodeling associated with amyloid pathology

Alzheimer's disease (AD) pathology involves amyloid deposition, reactive gliosis, and localized tissue alterations that coexist within the same brain regions, creating heterogeneous microstructural environments within individual imaging voxels. Conventional diffusion MRI averages these environments into aggregate measures, potentially obscuring their distinct contributions. Frequency-dependent multidimensional MRI ({omega}MD-MRI) resolves distributions of water components with different diffusion length scales, anisotropies, and relaxation properties, providing sensitivity to microstructural restriction, heterogeneity, and shape-size correlations within a voxel. Whether these measurements reveal microstructural complexity associated with AD pathology remains unclear. Here, we performed {omega}MD-MRI on ex vivo brain specimens from approximately 8-month-old 5xFAD and wild-type mice and interpreted the imaging findings alongside complementary histology. {omega}MD-MRI revealed widespread but spatially nonuniform differences between 5xFAD and wild-type brains. Measurements sensitive to microstructural restriction, heterogeneity, and shape-size correlations consistently indicated greater microstructural heterogeneity in 5xFAD brains, with the most prominent differences in the hippocampal formation and major cerebral white matter tracts. Complementary qualitative histology demonstrated extensive amyloid deposition and glial activation in affected regions, while overall cytoarchitecture and myelin organization remained largely preserved. Thus, the {omega}MD-MRI abnormalities occurred in tissue characterized by multiple coexisting pathological and relatively preserved microstructural environments rather than widespread structural degeneration. These findings demonstrate that {omega}MD-MRI can reveal the spatial and microstructural heterogeneity associated with amyloid pathology and provide a more comprehensive characterization of AD-related tissue alterations.

neuroscience↗

bioRxiv2026

Autoencoders for unsupervised analysis of rat myeloarchitecture

Quantitative assessment of brain histology is often constrained by predefined feature sets and labor-intensive manual annotations. To overcome these limitations, we employed unsupervised deep learning to automatically extract and quantify tissue organizational patterns from myelin-stained rat brain sections without the need for prior labeling. We evaluated nonlinear convolutional autoencoders (AEs) against linear principal component analysis (PCA) for feature representation, followed by clustering with Gaussian mixture models. Compared to PCA, AEs better preserved fine axonal architecture and produced more consistent and interpretable tissue clusters across hierarchical levels. The resulting clusters revealed anatomically meaningful tissue organization, including different white matter densities and grey matter subregions. When applied to tissue from sham and mild traumatic brain injury animals, AE-derived features also captured pathology-related alterations, such as white matter loss and injury-specific microstructural changes. These findings demonstrate that unsupervised deep learning can automatically characterize tissue organization at multiple scales and detect pathological changes, offering a scalable, unbiased approach to quantitative neuropathology.

neuroscience↗

bioRxiv2025

Epigenetic control of microglial developmental milestones from proliferative progenitors to efficient phagocytes

Early immune perturbations increase the risk of neurodegenerative and neurodevelopmental disorders, yet the mechanisms underlying the maturation of microglia, the resident immune cells of the brain parenchyma, remain poorly defined. Specifically, how proliferation, morphological differentiation, and phagocytosis are coordinated among microglia progenitors as they colonize the embryonic brain remains unclear. Here, we combined mathematical modeling with spatiotemporal analyses of the murine hippocampus and cerebellum from postnatal day 2 (P2) to P60 to reconstruct the trajectory of microglial development. We identified a proliferative-to-quiescent (P/Q) switch around P3/P4 that preceded the acquisition of morphological complexity and efficient phagocytosis and was accompanied by coordinated shifts in cell-cycle dynamics and metabolic state. Strikingly, this P/Q switch was recapitulated in repopulation contexts in mice and in the human fetal brain, where later stages displayed enhanced phagocytic function coupled to reduced proliferation. Perturbing the proliferative phase through pharmacological or genetic disruption of CSF1R signaling impaired subsequent microglial complexity and phagocytosis efficiency, revealing an unexpected reliance of phagocytosis on proliferation-driven colonization. Finally, we show that microglia stepwise maturation during development is associated with chromatin remodeling and driven by the epigenetic regulator Ikaros. Together, these findings uncover the sequential milestones of microglial development, revealing a potential period of early vulnerability and establishing an unexpected linkage between proliferation and phagocytosis essential to understanding how these processes are coordinated in neurodegenerative disorders.

neuroscience↗

bioRxiv2025

Metabolic and transcriptional adaptations to phagocytosis in microglia sustain their functionality and regenerative properties

Phagocytosis of apoptotic cells, or efferocytosis, is a tightly regulated process that ensures tissue homeostasis and prevents mounting inflammatory responses. In the brain parenchyma, it is executed by microglia, which are encumbered by large numbers of apoptotic debris generated during development, in adult neurogenic niches, aging, and brain diseases. Emerging evidence suggest that phagocytosis is not limited to garbage disposal, but triggers adaptations in the phagocytes that may have a functional impact. To test it we developed an in vivo model of superphagocytosis induced by low cranial irradiation (LCI, 2Gy) that specifically induced apoptosis in the neurogenic niche of the adult hippocampus, synchronizing microglia in a phagocytic state within 6h and leading to full clearance by 24h. Single cell RNA sequencing and metabolomics revealed an unexpected oxidative stress in post-phagocytic microglia, accompanied by catabolic shutdown, mitochondrial remodeling, increased expression of galectin 3, and production of polyamines that led to cell death and compensatory proliferation. To test whether these changes impaired subsequent microglial phagocytosis, we used a glioblastoma model treated with sequential irradiation to induce tumor cell apoptosis. The phagocytosis efficiency of tumor-associated microglia/macrophages was comparable in the first and second apoptotic challenge, suggesting that the metabolic remodeling induced by phagocytosis was adaptive and destined to sustain their functionality. Finally, we assessed the functional impact of post-phagocytosis adaptations using galectin 3 deficient mice under LCI. We found that the recovery of the neurogenic niche after LCI strongly depended on galectin 3, demonstrating the regenerative capacity of post-phagocytic microglia. Overall, our data unveils the complexity of post-phagocytosis adaptations in microglia, underscoring their unexplored therapeutic potential in brain disorders.

neuroscience↗

bioRxiv2025

MIF-induced CD74+ microglia/macrophages are clinically relevant disease-associated subpopulations in brain metastasis and other CNS disorders

The upregulation of CD74, a chaperone involved in MHC-II antigen processing 1,2, has been broadly reported in virtually all brain disorders analyzed by single-cell RNA sequencing 3-6. However, its expression is usually interpreted as indicative of antigen presentation. In parallel, CD74 expression has also been described in cancer cells across multiple tumor types, but interestingly in glioma its expression has been mainly identified in the microenvironment. However, the functional contribution of CD74 to disease progression in the brain, and specifically in secondary brain tumors, has not been directly addressed. Here we described that, in contrast to what it has been assumed, the presence of CD74+ microglia/macrophages, which is induced by increased levels of interferon gamma in the brain affected by metastases, does not relate to its canonical pathway. Instead, CD74s alternative function as cytokine receptor is pivotal. Rewired by increasing levels of its ligand MIF, produced by proliferating cancer cells, the CD74 receptor, upon binding to this ligand, translocates to the nucleus activating a NF-{kappa}B-dependent program promoting metastasis progression. A brain metastasis-associated CD74 signature involves a more aggressive progression of the local disease in patients, while it has no clinical correlation with the matched primary tumor. Furthermore, we identified the CD74+ myeloid population in additional brain disorders including Alzheimers disease and multiple sclerosis, which shared a pan-disease non-canonical signature with clinical relevance. The brain-penetrant drug ibudilast, which prevents the binding of MIF to CD74, decreases brain metastases in experimental models in vivo and in patient-derived organotypic cultures ex vivo in a primary tumor-agnostic manner. Our findings suggest that MIF/CD74-induced reprogramming of myeloid cells in brain disorders is a novel vulnerability that could be exploited therapeutically against brain metastases, and possibly other brain disorders, guided by a non-invasive molecular strategy.

cancer biology↗

bioRxiv2025

Frequency-dependent diffusion tensor distribution imaging in the evaluation of ischemic stroke

Non-invasive MRI is widely used to assess and monitor ischemic stroke, yet conventional approaches often lack sensitivity to subtle microstructural changes and struggle to evaluate tissue viability across lesion, penumbra, and distal regions. In this study, frequency dependent diffusion tensor distribution imaging ({omega}DTD) was combined with clustering of diffusion tensor distributions D({omega}) and multivariate regression modeling to characterize ischemic tissue alterations in a whole brain section. Ex vivo {omega}DTD and histology were performed in rats subjected to middle cerebral artery occlusion (MCAO) or sham surgery (P = 17) 24 hours after reperfusion. Lesions showed cell loss and an increased presence of smaller, likely glial, cells. A random forest (RF) model was used to explain and predict histological parameters from diffusion tensor imaging (DTI), manually bin resolved {omega}DTD features, and cluster resolved {omega}DTD parameters. Model performance was evaluated using leave one animal out cross validation (LOO CV). {omega}DTD features better represented cell number than DTI metrics ({omega}DTD R2 = 0.73 vs. DTI R2 = 0.49), with similar advantages for nuclear area and circularity ({omega}DTD R2 = 0.64 and 0.61 vs. DTI R2 = 0.40 and 0.35). The RF model further proved beneficial in capturing complex, nonlinear relationships between MRI parameters and tissue characteristics. Overall, these results indicate that {omega}DTD provides richer microstructural information than standard DTI, and that combining {omega}DTD with advanced machine learning methods enhances interpretation of ischemic tissue damage.

neuroscience↗

bioRxiv2025

Multimodal approach to characterize surgically removed epileptogenic zone from patients with focal drug-resistant epilepsy: from operating room to wet lab

ObjectiveWe have established a comprehensive sample handling protocol designed for the multiscale assessment of epileptogenic tissue. This protocol aims to identify novel therapeutic targets and enhance the diagnosis and stratification of patients with drug-resistant epilepsy, thereby optimizing their treatment with anti-seizure medications and surgical interventions. MethodsPatients with drug-resistant focal epilepsy, recommended for surgical treatment, are recruited after detailed multidisciplinary preoperative evaluation at the Epilepsy Center at Kuopio University Hospital in Finland. A day before the resective surgery, patients undergo magnetic resonance imaging (MRI) including advanced methodologies. During the surgery, each piece of resected tissue is placed under oxygenation on ice-cold artificial cerebral spinal fluid-solution. The pieces are then immediately transported to the laboratory, assessed by a neuropathologist, and sliced for both clinical diagnosis and research. Two adjacent slices are provided for research and are sent to the University of Eastern Finland. ResultsThe developed sample handling protocol provides the opportunity for detailed characterization of the tissue from the same patient using emerging imaging, electrophysiology, and molecular biology technologies. We have optimized the conditions for preserving the resected tissue alive for electrophysiological measurements and simultaneously making possible ex vivo studies including multi-omics acquisition, electron microscopy, histology, and MRI. Our protocol enables the mapping of functional readouts to structural and molecular alterations in human tissue. Our goal is to integrate multimodal data and co-register the resected tissues within the whole brains in vivo MRI space. This approach aims to enhance the characterization and localization of epileptogenic zones and refine surgical treatment targets by identifying abnormalities in global connectivity and structural patterns. SignificanceWe have successfully developed a systematic protocol for the collection and analysis of multimodal data. This protocol aims to elucidate the structural, functional, and molecular characteristics that render tissue epileptogenic, thereby enhancing the diagnosis and subsequent care of patients with epilepsy. Key pointsO_LIIntroducing a systematic sample handling protocol to assess tissue epileptogenicity at structural, functional and molecular levels. C_LIO_LIA multimodal approach integrating advanced technology with detailed characterization of epileptogenic tissue properties to obtain patient-specific data. C_LIO_LICorrelation of data from preoperative MRI and resected tissue to predict tissue pathology from clinical MRI. C_LI

neuroscience↗

bioRxiv2025

Data-driven classification of tissue water populations by massively multidimensional diffusion-relaxation correlation MRI

Massively multidimensional diffusion-relaxation correlation MRI provides detailed information on tissue microstructure by analyzing water populations at a sub-voxel level. This method correlates frequency-dependent tensor-valued diffusion MRI with longitudinal and transverse relaxation rates, generating nonparametric D({omega})-R1-R2 distributions. Traditionally, D({omega})-R1-R2 distributions are separated using manual binning of the diffusivity and anisotropy space to differentiate white matter (WM), gray matter (GM), and free water (FW) in brain tissue. However, while effective, this approach oversimplifies complex tissue fractions and does not fully utilize all available diffusion-relaxation parameters. In this study, we implemented an unsupervised clustering approach to automatically classify WM, GM, and FW and explore additional water populations using all components in the D({omega})-R1-R2 distributions on ex vivo and in vivo rat brain, and in vivo human brain. Results showed that a basic separation of WM, GM, and FW is possible using unsupervised clustering even under different multidimensional diffusion-relaxation protocols of rat brain and human brain. Additionally, when there is high frequency-dependent diffusion range, it is possible to obtain a cluster characterized by restriction localized in specific high cell density regions such as the dentate gyrus and cerebellum of rat brain. These findings were compared with rat histological sections of myelin and Nissl stainings. We demonstrated that unsupervised clustering of diffusion-relaxation MRI data can reveal tissue complexity beyond traditional WM, GM, and FW segmentation in rat and human brain without parameter assumptions. The unsupervised cluster approach could be used in other body parts (e.g., prostate and breast cancer) without requiring pre-defined bin limits. Furthermore, the characterization of the clusters by diffusivities, anisotropy, and relaxation rates can provide a better understanding of the subtle changes in different cellular fractions in tissue-specific pathologies.

neuroscience↗

bioRxiv2025

Ex vivo massively multidimensional diffusion-relaxation correlation MRI: scan-rescan reproducibility and caveats

Massively multidimensional diffusion-relaxation correlation MRI (MMD-MRI) provides information beyond the traditional voxel-averaged metric that may better characterize the microstructural characteristics of biological tissues. MMD-MRI reproducibility has been established in clinical settings, but has yet to be thoroughly evaluated under preclinical conditions, where superior hardware and modulated gradient waveforms enhance its performance. In this study, we investigate the reproducibility of MMD-MRI on a micro-imaging system using ex vivo mouse brains. Notably, the estimated signal fractions of intra-voxel spectral components in the MD-MRI distribution, corresponding to white and gray matter, along with the frequency-dependent parameters, demonstrated high reproducibility. We identified bias between scan and rescan in some of the metrics, which we attribute to the time gap between repeated scans pointing to a long-time progressive fixation effect. We compare our results with in vivo results from clinical scanners and show the reproducibility of diffusion frequency-dependent metrics to benefit from the improved gradient hardware on our preclinical setup. Our results inform future micro-imaging ex vivo MMD-MRI studies of the reproducibility of MMD-MRI metrics and their dependence on fixation time.

biophysics↗

bioRxiv2025

Microelectrode array scaled for recording human hippocampal slices

Temporal lobe epilepsy (TLE) is a prevalent neurological disorder characterized by recurrent seizures originating from the cortex, amygdala and especially hippocampus. While two-thirds of TLE patients achieve seizure control through medication, approximately one-third remain refractory to pharmacological interventions. For these individuals, surgical resection offers a potential curative option, with approximately 70% achieving seizure freedom. However, the pathogenesis of TLE remains incompletely understood, necessitating further investigation. Therefore, resected brain tissue obtained during the surgery provides a valuable resource for ex vivo study of pathological neuronal activity. Currently, microelectrode array (MEA) technology is widely used for electrophysiological studies. However, commercially available MEAs are limited in their ability to record from large tissue samples, such as an entire hippocampal section. To address this limitation, we have developed a custom MEA and sample chamber compatible with commercially available headstages. This system enables recording of extracellular action potentials (EAPs) and local field potentials (LFPs) across human hippocampal tissue, providing a valuable tool for investigating the neurophysiological mechanisms underlying TLE. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/640534v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@188e42corg.highwire.dtl.DTLVardef@3c10c6org.highwire.dtl.DTLVardef@17145a5org.highwire.dtl.DTLVardef@19369eb_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIA custom microelectrode array and chamber created for human hippocampal slices C_LIO_LIThe custom array recorded action potentials from human hippocampal slices C_LIO_LIThe custom array recorded local field potentials from human hippocampal slices C_LI

neuroscience↗

bioRxiv2024

A bottom-up approach identifies the antipsychotic and antineoplastic trifluoperazine and the ribose derivative deoxytubercidin as novel microglial phagocytosis inhibitors.

Phagocytosis is an indispensable function of microglia, the brain professional phagocytes. Microglia are particularly efficient phagocytosing cells that undergo programmed cell death (apoptosis) in physiological conditions. However, mounting evidence suggests microglial phagocytosis dysfunction in multiple brain disorders. These observations prompted us to search for phagocytosis modulators (enhancers or inhibitors) with therapeutic potential. We used a bottom-up strategy that consisted on the identification of phagocytosis modulators using phenotypic high throughput screenings (HTSs) in cell culture and validation in organotypic cultures and in vivo. We performed two complementary HTS campagnes: at Achucarro, we used primary cultures of mouse microglia and compounds of the Prestwick Chemical Library; at Roche, we used human iPSC derived macrophage-like cells and a proprietary chemo-genomic library with 2,200 compounds with known mechanism-of-action. Next, we validated the more robust compounds using hippocampal organotypic cultures and identified two hits: trifluoperazine, a dopaminergic and adrenergic antagonist used as an antipsychotic and antineoplastic; and deoxytubercidin, a ribose derivative. Finally, we tested whether these compounds were able to modulate phagocytosis of apoptotic newborn cells in the adult hippocampal neurogenic niche in vivo by administering them into the mouse hippocampus using osmotic minipumps. We confirmed that both trifluoperazine and deoxytubercidin have anti-phagocytic activity in vivo, and validated our bottom-up strategy to identify novel phagocytosis modulators. These results show that chemical libraries with anotated mechanism of action are an starting point for the pharmacological modulation of microglia in drug discovery projects aiming at the therapeutic manipulation of phagocytosis in brain diseases. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC="FIGDIR/small/599284v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@13ed994org.highwire.dtl.DTLVardef@13ea710org.highwire.dtl.DTLVardef@4a1c7dorg.highwire.dtl.DTLVardef@1945f00_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

In vivo rat-brain mapping of multiple gray matter water populations using nonparametric D(omega)-R1-R2 distributions MRI

Massively Multidimensional Diffusion MRI combines tensor-valued encoding, oscillating gradients, and diffusion-relaxation correlation to provide multicomponent sub-voxel parameters depicting the tissue microstructure. This method was successfully implemented ex vivo in micro-imaging systems and in clinical conditions but with a reduced diffusion frequency ({omega}) range due to the use of classical tensor-valued encoding. We demonstrate here its preclinical in vivo implementation with a protocol of 389 contrast images probing a wide diffusion frequency range of 18 to 92 Hz at b-values up to 2.1 ms/{micro}m2 enabled by the use of modulated gradient waveforms and combined with multislice high-resolution and low-distortion EPI acquisition with segmented and full reversed phase-encode acquisition. This framework allows the identification of diffusion{omega} -dependence in the rat cerebellum and olfactory bulb gray matter (GM) and the parameter distributions are shown to resolve two water pools in GM with different diffusion coefficients, shapes,{omega} -dependence, relaxation rates, and spatial repartition whose attribution to specific microstructure could modify the current understanding of the origin of restriction in GM.

biophysics↗

bioRxiv2024

Frequency-dependence in multidimensional diffusion-relaxation correlation MRI of the brain: overfitting or meaningful parameter?

Time- or frequency-dependent ("restricted") diffusion potentially provides useful information about cellular-scale structures in the brain but is challenging to interpret because of the intravoxel tissue heterogeneity. Frequency-dependence was recently incorporated in a multidimensional diffusion-relaxation correlation MRI framework relying on tensor-valued diffusion encoding at multiple frequencies, as well as variable echo and repetition times, to give model-free characterization of intravoxel heterogeneity by Monte Carlo data inversion into nonparametric distributions of frequency-dependent diffusion tensors and nuclear relaxation rates. While microimaging equipment with high-amplitude magnetic field gradients allows exploration of frequencies from tens to hundreds of Hz, clinical scanners with more moderate gradient capabilities are limited to a narrow frequency range, which may be insufficient to observe effects of restricted diffusion for brain tissues. We here investigate the effects of including or omitting frequency-dependence in the data inversion from isotropic and anisotropic liquids, excised tumor tissue, ex vivo mouse brain, and in vivo human brain. For microimaging measurements covering a wide frequency range, from 35 to 320 Hz at b-values over 4{middle dot}109 sm-2, the inclusion of frequency-dependence drastically reduces the fit residuals and avoids bias in the diffusion metrics for tumor and brain voxels with micrometer-scale structures. Conversely, for the case of in vivo human brain investigated in the narrow frequency range from 5 to 11 Hz at b = 3{middle dot}109 sm-2, analyses with and without inclusion of frequency-dependence yield similar fit residuals and diffusion metrics for all voxels. These results indicate that frequency-dependent inversion may be generally applied to diffusion-relaxation correlation MRI data with and without observable effects of restricted diffusion.

biophysics↗

bioRxiv2023

IRF5 regulates microglial myelin clearance and cholesterol metabolism after demyelination

Interferon regulatory factor 5 (IRF5), a transcription factor highly involved in innate immunity that drives microglia/macrophage towards a pro-inflammatory state, has been associated to multiple sclerosis susceptibility but its role in MS pathogenesis is unknown. Here we analysed the role of IRF5 in multiple sclerosis animal models. Irf5-/- mice showed exacerbated damage in the chronic phase of experimental autoimmune encephalomyelitis (EAE) mice, despite an initial delay in its onset, as well as after lysolecithin injection into the spinal cord. Transcriptomic and lipidomic analysis evidence a role of this transcription factor in myelin metabolism and cholesterol homeostasis. Indeed, Irf5-/- mice showed an aberrant accumulation of myelin debris and lipidic structures, such as CE-containing lipid droplets and cholesterol crystals, suggesting that myelin-derived lipids are not properly processed. Cholesterol crystal accumulation leads to an aberrant inflammatory response, which block oligodendrocyte migration into the core of demyelinated lesion and remyelination. Pharmacologically facilitating cholesterol transport reduces lipid droplet accumulation and ameliorates EAE exacerbated damage in Irf5-/- mice. These results reveal for the first time the role of Irf5, a transcription factor necessary to orchestrate the immune responses, in phagocytes lipid metabolism which could be pivotal in regenerative responses such as remyelination.

neuroscience↗

bioRxiv2023

The RNA binding protein IMP1/ZBP1 drives mRNA local translation in microglia and mediates polarized migration and phagocytosis in response to inflammation

Polarized cells in the brain, such as neurons and glia, rely on the asymmetric distribution of their proteins compartmentalizing the function of dendrites, axons, glial projections and endfeet. Subcellular proteomes can be assembled either by the transport of proteins synthesized in the cell soma or by the delivery of mRNAs to target compartments where they are locally translated into protein. This latter mechanism is known as local protein synthesis or local translation, and it has been best studied in neurons. Increasing evidence suggest it is also required to maintain local protein homeostasis in glial cells, however, in microglia, local translation remains largely unexplored. Given the scant evidence, we aimed at exploring the existence of local translation in peripheral microglial processes (PeMPs) and unravel its functional significance in response to inflammation, a major hallmark of neurodegenerative diseases. We report that local translation in PeMPs is enhanced by triggering a microglial inflammatory response with bacterial lipopolysaccharides (LPS). We found that Actb mRNA polarizes to PeMPs and is locally translated upon LPS exposure. mRNA localization in eukaryotic cells is driven by RNA binding proteins. Interestingly, downregulation of the Actb binding protein IMP1/ZBP1 impaired Actb mRNA polarization and its localized translation, and led to defects in filopodia distribution, PeMP motility, lamellar directed migration and phagocytosis in microglia. Thus, our work contributes to recent findings that mRNA localization and localized translation occur in microglia and gives a mechanistic insight into the relevance of this molecular mechanism in fundamental microglial functions in response to inflammation.

neuroscience↗

bioRxiv2023

Circulating tumor extracellular vesicles to monitor metastatic prostate cancer genomics and transcriptomic evolution

Extracellular vesicles (EVs) secreted by tumors are abundant in plasma, but their potential for interrogating the molecular features of tumors through multi-omic profiling remains widely unexplored. Genomic and transcriptomic profiling of circulating EV-DNA and EV-RNA isolated from a range of in-vitro and in-vivo models of metastatic prostate cancer (mPC) revealed a high contribution of tumor material to EV-loaded DNA/RNA. Findings were validated in a cohort of longitudinal plasma samples collected from mPC patients during androgen receptor signaling inhibitor (ARSI) therapy. EV-DNA genomic features recapitulated matched-patient biopsies and associated with clinical progression. We developed a novel approach to enable the transcriptomic profiling of EV-RNA (RExCuE). We report how the transcriptomic profile in mPC EV-RNA is enriched for tumor-associated transcripts when compared to same patient blood RNA and healthy individuals EV-RNA, and reflect early on-therapy tumor adaptation changes. Altogether, we show that EV profiling enables longitudinal transcriptomic and genomic profiling of mPC in liquid biopsy.

cancer biology↗

bioRxiv2022

Microglia and meningeal macrophages depletion delay the onset of experimental autoimmune encephalomyelitis

In multiple sclerosis and the experimental autoimmune encephalomyelitis (EAE) model, both resident microglia and infiltrating macrophages contribute to demyelination as well as spontaneous remyelination. Nevertheless, the specific roles of microglia versus macrophages are unknown. We investigated the influence of microglia in EAE using the colony stimulating factor 1 receptor (CSF-1R) inhibitor, PLX5622, to deplete microglial population and Ccr2RFP/+fmsEGFP/+ mice, to distinguish peripheral macrophages and microglia. PLX5622 treatment depleted microglia and meningeal macrophages, and provoked a massive infiltration of CCR2+ macrophages into demyelinating lesions and spinal cord parenchyma. PLX5622 treatment did not alter EAE chronic phase. In contrast, microglia and meningeal macrophages depletion reduced the expression of CD80 co-stimulatory molecule in dendritic and myeloid cells and reduced T cell reactivation and proliferation in the spinal cord parenchyma, inducing a significant delay in EAE onset. Altogether, these data points to a specific role of CNS microglia meningeal macrophages in antigen presentation and T cell reactivation at initial stages of the EAE model.

neuroscience↗

bioRxiv2022

Mind the gap: Nodes of Ranvier are remodeled by chronic psychosocial stress and neuronal activity

Differential expression of myelin-related genes and changes in myelin thickness have been demonstrated in mice after chronic psychosocial stress, a risk factor for anxiety disorders. To determine whether and how stress affects structural remodeling of nodes of Ranvier, another form of myelin plasticity, we developed a 3D reconstruction analysis of node morphology in C57BL/6NCrl and DBA/2NCrl mice. We identified strain-dependent effects of chronic stress on node morphology, including elongation of paranodes in the medial prefrontal cortex (mPFC) in DBA/2NCrl mice. Furthermore, chronic chemogenetic activation of the ventral hippocampus-to-mPFC pathway resulted in increased risk assessment behavior and shortened paranodes specifically in stimulated axons, providing a direct link between anxiety-like behavior and remodeling of the nodes. Altogether, our data demonstrate genetic regulation of nodal remodeling in stress and suggest an activity-dependent regulation of paranodes in anxiety-related circuits. Nodal remodeling may thus contribute to the aberrant circuit function associated with anxiety disorders.

neuroscience↗