Biology subjects

Xiao, W.

Publications and source records attributed to Xiao, W..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

O-GlcNAcylation-Ubiquitin Crosstalk of METTL1 Drives m7G Epitranscriptomic Collapse and Lipid Metabolic Reprogramming in Diabetic Cardiomyopathy

BackgroundMetabolic remodelling and memory in cardiomyocytes is a pivotal mechanism underlying cardiomyopathy pathogenesis. Clinical observations demonstrate persistent progression of hyperglycaemia-induced multiorgan damage following blood glucose stabilization, which is predominantly mediated through epigenetic regulation. While prior studies have identified epigenetic contributions to hyperglycaemic myocardial injury, the involvement of RNA methylation-particularly N7-methylguanosine (m7G) modification-in this regulatory network remains undefined. MethodsClinical specimens were collected from diabetic patients, and cardiomyocyte-specific METTL1 and ob/ob knockout murine models were established in parallel. Multiomic profiling (proteomics, glycoproteomics, ubiquitinomics, m7G-MeRIP sequencing, and metabolomics) was systematically conducted. The molecular mechanisms governing METTL1 regulation via O-GlcNAcylation and ubiquitination were elucidated through integrated in vitro and in vivo assays. A DUB siRNA library and computational strategies combining molecular docking with molecular dynamics simulations were employed for screening drugs targeting METTL1 O-GlcNAcylation, followed by in vivo therapeutic validation. ResultsComparative analysis of diabetic murine and human samples revealed strong METTL1 downregulation in cardiomyopathy contexts. Tamoxifen-inducible METTL1 knockout mice presented exacerbated diabetic cardiomyopathy phenotypes, confirming its cardioprotective function. Multiomic integration demonstrated that METTL1-mediated m7G modification critically regulates cardiomyocyte fatty acid metabolism. Mechanistically, hyperglycaemia was found to induce O-GlcNAcylation at the METTL1-T268 residue, suppressing m7G methyltransferase activity by 38% (p < 0.01). Subsequent investigations revealed that USP5 deubiquitinase activity is impaired under hyperglycaemic conditions, leading to accelerated METTL1 degradation. Notably, administration of the first-in-class small drug HIT106265621 significantly attenuated cardiomyopathy-associated pathological alterations in ob/ob mice in vivo. ConclusionHyperglycaemia promotes METTL1 O-GlcNAcylation, which impedes USP5-mediated deubiquitination, consequently reducing cardiomyocyte METTL1 protein levels and m7G modification. METTL1 deficiency drives diabetic cardiomyopathy progression through fatty acid metabolic dysregulation, inflammatory activation, and myocardial hypertrophy. Pharmacological inhibition of the OGT-METTL1 interaction using HIT106265621 has therapeutic potential for metabolic cardiomyopathy intervention.

pathology↗

bioRxiv2025

Multiscale Entropy of Resting-State fMRI Signals Reveals Differences in Brain Complexity in Autism

BackgroundAtypical intrinsic brain activity has been widely observed in autism spectrum disorder (ASD), yet the temporal complexity of these neural signals remains underexplored. This study aimed to characterise differences in resting-state brain signal complexity between individuals with ASD and neurotypical controls using multiscale entropy (MSE). MethodsResting-state fMRI data were obtained from the Autism Brain Imaging Data Exchange I (ABIDE I), a large multi-site dataset including 397 participants (179 with ASC, 218 neurotypical controls; ASD: Mean age 16.43 years old, SD 7.17 years old; CON: Mean age 15.75 years old, SD 5.67 years old). Voxel-wise multiscale entropy (MSE) features were extracted across multiple temporal scales. Group comparisons were conducted using voxel-wise t-tests and mixed-effects models to identify region- and scale-specific alterations in brain signal complexity. ResultsIndividuals with ASD showed reduced MSE in prefrontal regions at coarser time scales and elevated MSE in posterior midline regions, including the posterior cingulate cortex and precuneus, at finer scales, followed by a decline across coarser scales. This pattern suggests a shift toward uncorrelated randomness in posterior regions and reduced long-range complexity in frontal areas. No significant associations were found between MSE features and ADOS scores. ConclusionsThese findings reveal spatially and temporally specific alterations in brain signal complexity in ASD, particularly within the default mode network. Multiscale entropy provides a complementary approach to traditional connectivity and single-scale entropy analyses, offering novel insights into the organisation of intrinsic brain activity in neurodevelopmental conditions.

neuroscience↗

bioRxiv2025

Tissue-wide profiling of human lungs reveals spatial sequestration of macrophages in tuberculosis

The immune response to human tuberculosis (TB), particularly in the context of complex lung pathology, remains incompletely understood. Here, we employed whole-slide spatial proteomics to map immune cell organization in TB-affected human lung tissues. Our analysis revealed pronounced spatial segregation of major immune cell populations in non-necrotizing TB lesions. At the tissue level, macrophages and lymphocytes formed distinct cellular communities associated with specific pathological features. At the lesion level, macrophages and B cells showed an inverse relationship in both abundance and spatial distribution. Proinflammatory T cells preferentially accumulated in macrophage-rich lesions but remained largely separated from macrophages. Interestingly, lesions exhibiting clear segregation between T cells and macrophages were more common in subclinical TB than in active disease. These findings suggest that spatial isolation of macrophages from effector lymphocytes may help temper inflammation and potentially prevent lesion progression to necrosis, while also enabling immune evasion by Mycobacterium tuberculosis. One Sentence SummaryXiao et al. reveal spatial segregation of immune cells in TB-lung tissue and link the microenvironmental dynamics to disease states of tuberculosis.

immunology↗

bioRxiv2025

Metabolic shifts in the heart of hypothyroid mice -- insights from untargeted metabolomics

ABSTRACTSO_ST_ABSIntroductionC_ST_ABSHypothyroidism is a prevalent disorder that affect all systems of body, including the cardiovascular system and control of cardiac function. However, much remains unknown about the metabolic pathways and disorders in the heart induced by hypothyroidism, as well as the metabolic mechanisms involved. ObjectivesThis work aims to investigate the impacts of hypothyroidism on the heart and explore its underlying mechanisms through untargeted metabolomics analysis. MethodsAn experimental model of hypothyroidism was established by giving water containing 0.1% methimazole and 1% potassium perchlorate to 12-week-old C57BL/6J mice for six consecutive weeks. ResultsAfter treatment, hypothyroidism significantly reduced mices heart weight and heart rate. Metabolomics analysis revealed that the different metabolites (DEMs) primarily concentrated in Phospholipids, Lipids or Lipids-like, Carbohydrates and Carbohydrate conjugates. These specific metabolites were mainly enriched in pathways related to lipid metabolism. The hearts of hypothyroid mice exhibited significantly lower levels of lipoyl-carnitine compared to controls, along with markedly higher levels of glycolysis and pentose phosphate pathway (PPP) intermediates. Furthermore, carnitine palmitoyltransferase 1B (CPT1B) and carnitine palmitoyltransferase 2 (CPT2) expressions were significantly decreased in the hypothyroid mouse heart, while lactate dehydrogenase A (LDHA) expressions was significantly increased, according to the immunoblotting assay. ConclusionsResearch indicates that hypothyroidism triggers disruptions in both cardiac energy metabolism and phospholipid metabolism in adult mice, which in turn results in myocardial atrophy. These findings could pave the way for novel therapeutic strategies aimed at treating hypothyroidism-induced myocardial atrophy.

pathology↗

bioRxiv2025

Eyes-closed resting state EEG reveals clearer and more stable group differences between autistic and neurotypical individuals than eyes-open resting state EEG

BackgroundResting-state electroencephalography (rs-EEG) has been widely used to explore neural dynamics in Autism Spectrum Condition (ASC). However, inconsistencies in findings across studies remain a challenge, partly due to variations in brain state, such as eye conditions (eyes-open vs. eyes-closed). This study aims to examine rs-EEG differences between ASC and neurotypical (NT) participants, focusing on the influence of eye condition. MethodsA total of 300 participants (126 ASC) were included. Rs-EEG data were analysed across eyes-open, eyes-closed, and difference between eye conditions, with 726 variables assessed per participant. Linear regression and effect size (2partial) were used to identify group differences, complemented by cluster-based permutation testing and bootstrapped split-half validation for reliability. ResultsGroup differences were most pronounced in the eyes-closed condition, particularly for relative power and multiscale entropy (MSE). Compared to neurotypical participants, ASC participants exhibited reduced frontal coarse-scale MSE, increased delta power, and decreased alpha power, suggesting altered local-global neural dynamics. Cross-validation revealed greater reliability of effects in the eyes-closed condition compared to eyes-open or difference between eye conditions. ConclusionsEye condition plays a critical role in detecting rs-EEG differences between ASC and NT groups, with the eyes-closed condition yielding more consistent and pronounced effects. These findings highlight the importance of controlling brain state in rs-EEG studies and suggest that integrating eye condition effects with other biomarkers may improve identification of neural differences associated with ASC.

neuroscience↗

bioRxiv2025

A novel broad-spectrum antibiotic targets multiple-drug-resistant bacteria with dual binding targets and no detectable resistance

The rapid emergence of difficult-to-treat multidrug-resistant pathogens, combined with the scarcity of antibiotics possessing novel mechanisms, poses a significant threat to global public health. Here, we integrated the synthetic-bioinformatic natural product approach with peptide optimization to unveil the antibiotic-producing potential of Paenibacillaceae bacteria. Our culture-independent approach led to the discovery of paenimycin, a novel 11-mer depsi-lipopeptide featuring an unprecedented dual-binding mechanism. By sequestering the phosphate and hydroxyl groups of lipid A in Gram-negative bacteria, as well as the phosphate groups of teichoic acids in Gram-positive bacteria, paenimycin exhibited potent and broad-spectrum efficacy against MDR pathogens in vitro and in vivo models. Remarkably, paenimycin demonstrates no detectable resistance, favorable pharmacokinetics and low nephrotoxicity, positioning it as a promising candidate for treating serve and urgent MDR infections.

biochemistry↗

bioRxiv2024

Trial-by-trial inter-areal interactions in visual cortex in the presence or absence of visual stimulation

State-of-the-art computational models of vision largely focus on fitting trial-averaged spike counts to visual stimuli using overparameterized neural networks. However, a computational model of the visual cortex should predict the dynamic responses of neurons in single trials across different experimental conditions. In this study, we investigated trial-by-trial inter-areal interactions in the visual cortex by predicting neuronal activity in one area based on activity in another, distinguishing between stimulus-driven and non-stimulus-driven shared variability. We analyzed two datasets: calcium imaging from mouse V1 layers 2/3 and 4, and extracellular neurophysiological recordings from macaque V1 and V4. Our results show that neuronal activity can be predicted bidirectionally between L2/3 and L4 in mice, and between V1 and V4 in macaque monkeys, with the latter interaction exhibiting directional asymmetry. The predictability of neuronal responses varied with the type of visual stimulus, yet responses could also be predicted in the absence of visual stimulation. In mice, we observed a bimodal distribution of neurons, with some neurons primarily driven by visual inputs and others showing predictable activity during spontaneous activity despite lacking consistent visually evoked responses. Predictability also depended on intrinsic neuronal properties, receptive field overlap, and the relative timing of activity across areas. Our findings highlight the presence of both stimulus- and non-stimulus-related components in interactions between visual areas across diverse contexts and underscore the importance of non-visual shared variability between visual regions in both mice and macaques.

neuroscience↗

bioRxiv2024

Loss of PMR4 callose synthase results in salicylic acid-independent and broad-spectrum resistance to clubroot in Arabidopsis and Brassica napus

The clubroot disease caused by protist Plasmodiophora brassicae is one of the most important diseases of Brassica crops. Growing clubroot-resistant cultivars remains the most effective and practical approach to managing clubroot disease. However, resistance gene-mediated immunity is rapidly overcome in the field when new pathotypes arise. In this study, we identified PMR4 as a potential gene target for creating a novel clubroot-resistant source. Recessive PMR4 mutations in Arabidopsis thaliana conferred broad-spectrum resistance to multiple P. brassicae pathotypes, independent of salicylic acid-mediated plant immunity. CRISPR/Cas9-mediated gene-editing was employed to create mutations in two PMR4 orthologs in the B. napus genome, and resulting homozygous mutants exhibited dual resistance to powdery mildew and clubroot. PMR4 is required for the callose deposition at wound and powdery mildew infection sites in leaves. This study reveals that callose deposition in roots is induced by P. brassicae infection and requires PMR4. It appears that the clubroot disease progression is arrested at the primary-to-secondary infection phase in pmr4-1 mutants. Together, this study demonstrates that PMR4-encoded callose synthase is a host susceptibility factor required for P. brassicae to complete its life cycle, and that PMR4 can be targeted against both powdery mildew and clubroot diseases in Brassica crops.

plant biology↗

bioRxiv2024

Pressorum Sensing: Growth-induced Compression Activates cAMP Signaling in Pseudomonas aeruginosa

Bacteria employ various strategies to coordinate population-level behaviors, with quorum sensing being a well-established mechanism. Here, we report a novel population-level regulatory mechanism in Pseudomonas aeruginosa, which we term pressorum sensing. This mechanism allows bacteria to modulate their collective behavior in response to growth-induced mechanical compression in confined spaces. Using a highly sensitive cAMP biosensor in combination with microfluidics, we demonstrate that when compressive forces reach approximately 30 nN, P. aeruginosa cells rapidly increases intracellular cAMP levels via the Pil-Chp chemosensory system. This response leads to up-regulation of the Type III Secretion System, a key virulence factor. Unlike quorum sensing, which relies on diffusible chemical signals, pressorum sensing utilizes mechanical cues to gauge population density and spatial confinement. In bacterial colonies, this mechanism generates striking spatial patterns of cAMP signaling, including traveling rings that coincide with step-like structures in colony morphology. Our findings reveal a previously unknown link between mechanical compression and bacterial virulence, providing new insights into how P. aeruginosa coordinates population-level responses in confined environments. This work also expands our knowledge of mechanogenetics and opens up new possibilities in synthetic biology and bioengineering applications.

microbiology↗

bioRxiv2024

An AINTEGUMENTA phospho-switch controls bilateral stem cell activity during secondary growth

Plant stem cells have the remarkable ability to give rise to distinct tissues and organs throughout development. Two concentric cylinders of actively dividing stem cells are the main drivers of radial thickening during secondary growth, each producing distinct vascular cell types towards the inside and the outside. While the molecular mechanisms underlying their initiation have been well studied, it remains unclear how these stem cell layers determine which cell type is generated. Here, we demonstrate that the cross-talk between the ERECTA (ER) receptor pathway and auxin signalling controls the amount and choice of output tissue in these two stem cell regions. Mechanistically, we show that the ER pathway phosphorylates the transcription factor AINTEGUMENTA, thereby modulating bilateral stem cell activity and favouring the differentiation of only one type of cell. Our results thus show that the phosphorylation status of ANT regulates root girth and biomass accumulation by influencing bilateral stem cell production. This highlights the critical role of post-translational modifications in plant growth and development. SignificanceThis study uncovers a critical regulatory mechanism governing bilateral stem cell activity during plant radial growth. Stem cells in the cambia proliferate and differentiate into specialized tissues like wood and cork, key sites of biomass accumulation. By exploring the interplay between the ERECTA (ER) receptor and auxin signalling, we reveal how these pathways modulate stem cell differentiation and radial thickening through the phosphorylation of the transcription factor AINTEGUMENTA (ANT). Phosphorylation status of ANT modulates stem cell activity, dictating the production of specific vascular cell types like wood thus controlling root girth. This research underscores the importance of post-translational modifications in plant development and provides a novel regulation underpinning stem cell differentiation, with significant implications for enhancing biomass accumulation as wood.

plant biology↗

bioRxiv2024

DeEPsnap: human essential gene prediction by integrating multi-omics data

Essential genes are necessary for the survival or reproduction of a living organism. The prediction and analysis of gene essentiality can advance our understanding of basic life and human diseases, and further boost the development of new drugs. Wet lab methods for identifying cell essential genes are often costly, time-consuming, and laborious. As a complement, computational methods have been proposed to predict essential genes by integrating multiple biological data sources. Most of these methods are evaluated on model organisms. However, prediction methods for human essential genes are still limited and the relationship between human gene essentiality and different biological information still needs to be explored. In addition, exploring suitable deep learning techniques to overcome the limitations of traditional machine learning methods and improve prediction accuracy is also important and interesting. We propose a snapshot ensemble deep neural network method, DeEPsnap, to predict human essential genes. DeEPsnap integrates sequence features derived from DNA and protein sequence data with features extracted or learned from multiple types of functional data, such as gene ontology, protein complex, protein domain, and protein-protein interaction network. More than 200 features from these biological data are extracted/learned which are integrated together to train a series of cost-sensitive deep neural networks by utilizing multiple deep learning techniques. The proposed snapshot mechanism enables us to train multiple models without increasing extra training effort and cost. The experimental results of 10-fold cross-validation show that DeEPsnap can accurately predict human gene essentiality with an average AUROC (Area Under the Receiver Operating Characteristic curve) of 96.1%, the average AUPRC (Area under the Precision-Recall curve) of 93.82%, the average accuracy of 92.21%, and the average F1 measure about 80.62%. In addition, the comparison of experimental results shows that DeEPsnap outperforms several popular traditional machine learning models and deep learning models. We have demonstrated that the proposed method, DeEPsnap, is effective for predicting human essential genes.

bioinformatics↗

bioRxiv2024

Systems Modeling Reveals Shared Metabolic Dysregulation and Novel Therapeutic Treatments in ME/CFS and Long COVID

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) and Long COVID are complex, multisystem conditions that pose significant challenges in healthcare. Accumulated research evidence suggests that ME/CFS and Long COVID exhibit overlapping metabolic symptoms, indicating potential shared metabolic dysfunctions. This study aims to systematically explore shared metabolic disturbances in the muscle tissue of patients. Utilizing genome-wide metabolic modeling, we identified key metabolic irregularities in the muscle of patients with ME/CFS, notably the downregulation of the alanine and aspartate metabolism pathway and the arginine and proline metabolism pathway. Further, in silico knockout analyses suggested that supplementation with aspartate (ASP) or asparagine (ASN) could potentially ameliorate these metabolic deficiencies. In addition, assessments of metabolomic levels in Long COVID patients also showed the significant downregulation of ASP during post-exertional malaise (PEM) in both muscle and blood. Consequently, we propose that a combination of l-ornithine and l-aspartate (LOLA) is a potential candidate to alleviate metabolic symptoms in ME/CFS and Long COVID for future clinical trials.

systems biology↗

bioRxiv2024

Coral hosts actively accumulate inorganic carbon for zooxanthellae to maintain symbiotic relationships

High primary productivity of coral reefs is widely attributed to the mutualistic symbiosis between coral hosts and their microalgal partners (Symbiodiniaceae). Although the mechanisms maintaining this symbiosis have been considerable investigated, how the symbiont microalgae within coral get sufficient CO2 for photosynthesis still remains inadquately explored. Here, we hypothesized that corals may actively accumulate dissolved inorganic carbon (DIC) for microalgae to maintain the symbiosis. Carbon (HCO3- and glucose) supply and consumption were evaluated in the scleractinian coral (Goniopora lobata) and its symbiont under light and dark conditions. Results suggest that Symbiodiniaceae were high DIC consumers, requiring about 2-3 fold more DIC than free-living species. The corals were high DIC producers, with internal concentrations up to 4.2 fold higher than in the surrounding seawater. In the absence of microalgae utilization, the excess DIC they produced appeared detrimental to their own growth. Moreover, transcriptomic analysis identified several DIC enrichment pathways are evolved in corals to attact the Symbiodiniaceae, including CO2 concentrating mechanisms, respiration, calcification and phosphoenolpyruvate carboxylase. Increased the CO2 dosage in seawater may induce coral symbiosis bleaching. Our findings can deeper reveal on the mechanisms sustaining coral symbiosis, and may help to predict how some corals respond to DIC imbalance under climate changes.

ecology↗

bioRxiv2024

Branched chain α-ketoacids aerobically activate HIF1α signaling in vascular cells

Hypoxia-inducible factor 1 (HIF1) is a master regulator of numerous biological processes under low oxygen tensions. Yet, the mechanisms and biological consequences of aerobic HIF1 activation by intrinsic factors, particularly in primary cells remain elusive. Here, we show that HIF1 signaling is activated in several human primary vascular cells under ambient oxygen tensions, and in vascular smooth muscle cells (VSMCs) of normal human lung tissue, which contributed to a relative resistance to further enhancement of glycolytic activity in hypoxia. Mechanistically, aerobic HIF activation is mediated by paracrine secretion of three branched chain -ketoacids (BCKAs), which suppress prolyl hydroxylase domain-containing protein 2 (PHD2) activity via direct inhibition and via lactate dehydrogenase A (LDHA)-mediated generation of L-2-hydroxyglutarate (L2HG). Metabolic dysfunction induced by BCKAs was observed in the lungs of rats with pulmonary arterial hypertension (PAH) and in pulmonary artery smooth muscle cells (PASMCs) from idiopathic PAH patients. BCKA supplementation stimulated glycolytic activity and promoted a phenotypic switch to the synthetic phenotype in PASMCs of normal and PAH subjects. In summary, we identify BCKAs as novel signaling metabolites that activate HIF1 signaling in normoxia and that the BCKA-HIF1 pathway modulates VSMC function and may be relevant to pulmonary vascular pathobiology.

cell biology↗

bioRxiv2024

Ecological drivers of CRISPR immune systems

1CRISPR-Cas is the only known adaptive immune system of prokaryotes. It is a powerful defense system against mobile genetic elements such as bacteriophages. While CRISPR-Cas systems can be found throughout the prokaryotic tree of life, they are distributed unevenly across taxa and environments. Since adaptive immunity is more useful in environments where pathogens persist or reoccur, the density and/or diversity of the host/pathogen community may drive the uneven distribution of CRISPR system. We directly tested hypotheses connecting CRISPR incidence with prokaryotic density/diversity by analyzing 16S rRNA and metagenomic data from publicly available environmental sequencing projects. In terms of density, we found that CRISPR systems are significantly favored in lower abundance (less dense) taxa and disfavored in higher abundance taxa, at least in marine environments. When we extended this work to compare taxonomic diversity between samples, we found CRISPR system incidence strongly correlated with diversity in human oral environments. Together, these observations confirm that, at least in certain types of environments, the prokaryotic ecological context indeed plays a key role in selecting for CRISPR immunity. 2 ImportanceMicrobes must constantly defend themselves against viral pathogens, and a large proportion of prokaryotes do so using the highly effective CRISPR-Cas adaptive immune system. However, many prokaryotes do not. We investigated the ecological factors behind this uneven distribution of CRISPR-Cas immune systems in natural microbial populations. We found strong patterns linking CRISPR-Cas systems to prokaryotic density within ocean environments and to prokaryotic diversity within human oral environments. Our study validates previous within-lab experimental results that suggested these factors might be important and confirms that local environment and ecological context interact to select for CRISPR immunity.

microbiology↗

bioRxiv2024

MYB68 orchestrates cork differentiation by regulating stem cell proliferation and suberin deposition

Plants have developed specialized barriers to protect and isolate the inner tissues from the environment while maintaining homeostasis. Different barriers are present in various organs and at different growth stages. During secondary growth, the periderm acts as the protective tissue, covering roots, stems, and branches as they become thick. The periderm is a dynamic barrier comprising a stem cell niche known as the cork cambium, which bifacially divides to generate the phelloderm inward and the cork outward. Cork cells have a unique cell wall impregnated with suberin and lignin polymers, essential for the barrier function. Despite its importance, the differentiation process that forms new cork cells from the stem cell is largely unknown. In this work, we identify members of the MYB36-subclade transcription factors as key regulators of cork differentiation. On the one hand, this set of transcription factors promotes suberin deposition by inducing the expression of enzymes involved in all steps of suberin biosynthesis, including the recently discovered suberin-polymerizing enzymes GDS Lipases; on the other hand, it represses cork cambium proliferation. Furthermore, we demonstrated that suberin deposition in the cork is a robust process regulated by a complex network of transcription factors, including other MYB transcription factors that activate suberin deposition in the endodermis. However, only members of the MYB36 subclade can repress cell proliferation in different developmental contexts, highlighting general and specific functions for MYB transcription factors. These findings have broad applicability, as tissue-specific manipulation of MYB activity has the potential for improving traits of biotechnological interest, such as thicker periderms and more suberized cork layers, and for assessing how these traits affect plant performance in response to stresses.

plant biology↗

bioRxiv2024

The lncRNA Malat1 is trafficked to the cytoplasm as a localized mRNA encoding a small peptide in neurons.

Synaptic function is modulated by local translation of mRNAs that are transported to distal portions of axons and dendrites. The Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is broadly expressed across cell types, almost exclusively as a nuclear non-coding RNA. We found that in differentiating neurons, a portion of Malat1 RNA redistributes to the cytoplasm. Depletion of Malat1 from neurons stimulated expression of particular pre- and post-synaptic proteins, implicating Malat1 in their regulation. Neuronal Malat1 is localized to both axons and dendrites in puncta that co-stain with Staufen1 protein, similar to neuronal granules formed by locally translated mRNAs. Ribosome profiling of mouse cortical neurons identified ribosome footprints within a region of Malat1 containing short open reading frames. The upstream-most reading frame (M1) of the Malat1 locus was linked to the GFP coding sequence in mouse ES cells. When these gene-edited cells were differentiated into glutamatergic neurons, the M1-GFP fusion protein was expressed. Antibody staining for the M1 peptide confirmed its presence in wildtype neurons, and showed enhancement of M1 expression after synaptic stimulation with KCL. Our results indicate that Malat1 serves as a cytoplasmic coding RNA in the brain that is both modulated by and modulates synaptic function.

molecular biology↗

bioRxiv2023

How to prevent endothelial cells from losing their edge: a simple patterning of development-like matrix guides a microvessel morphogenetic process by self-organization

Microvascular engineering seeks to exploit known cell-cell and cell-matrix interactions in the context of vasculogenesis to restore homeostatic or disease development of reliable capillary models in vitro. However, current systems generally focus on recapitulating microvessels embedded in thick gels of extracellular matrix, overlooking the significance of discontinuous capillaries, which play a vital role in tissue-blood exchanges particularly in organs like the liver. In this work, we introduce a novel method to stimulate the spontaneous organization of endothelial cells into non-embedded microvessels. By creating an anisotropic micropattern at the edge of a development-like matrix dome using Marangoni-flow, we achieved a long, non-random orientation of endothelial cells, laying a premise for stable lumenized microvessels. Our findings revealed a distinctive morphogenetic process leading to mature lumenized capillaries, demonstrated with both murine and human immortalized liver sinusoidal endothelial cell lines (LSECs). The progression of cell migration, proliferation and polarization was clearly guided by the pattern, initiating the formation of a multicellular cord that caused a deformation spanning extensive regions and generated a wave-like folding of the gel, hinged at a laminin depleted zone, enveloping the cord with gel proteins. This event marked the onset of lumenogenesis, regulated by the gradual apico-basal polarization of the wrapped cells, leading to the maturation of vessel tight junctions, matrix remodeling, and ultimately the formation of a lumen--recapitulating the development of vessels in vivo. Furthermore, we demonstrate that the process strongly relies on the initial gel edge topography, while the geometry of the vessels can be tuned, from a curved to a straight structure. We believe our facile engineering method, guiding an autonomous self-organization of vessels without the need for supporting cells or complex prefabricated scaffolds, holds promise for future integration into microphysiological systems featuring discontinuous, fenestrated capillaries. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/564881v2_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@1d6992org.highwire.dtl.DTLVardef@fe1434org.highwire.dtl.DTLVardef@e07d1aorg.highwire.dtl.DTLVardef@3540ab_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗