Biology subjects

Bian, X.

Publications and source records attributed to Bian, X..

At least 19 recordsLinked to original sources

bioRxiv2026

Vascularized Organoids Emerge from a Heart-Foregut-like Intermediate Recapitulating Early Human Development

During early cardiogenesis, the heart regions lie in close contact with foregut endoderm, which supplies essential nutrients and signaling cues to orchestrate primitive heart tube assembly. Here, we show that self-organized heart/foregut like-structures emerge from human pluripotent stem cells (hPSCs). The initial heart/foregut-like structures, termed the Seed, are encased by surrounding supportive cells termed Soil, which provide a matrix microenvironment; the Seed progressively develops into chambered human cardiac organoids (hCOs) containing cardiomyocytes (CMs), epicardial cells, cardiac fibroblasts, and endothelial cells. Optimization of the induction system further enhanced hCO maturation and vascularization. Therefore, this Soil-Seed system provides a model to dissect human early heart/foregut self-organization.

developmental biology↗

bioRxiv2026

Multi-parametric NIR-II fluorescence perfusion imaging towards quantitative stroke evaluation

Preclinical stroke research is severely hampered by the lack of high-throughput, quantitative perfusion imaging tools capable of bridging the gap between functional hemodynamics and structural injury. The emerging second near-infrared (NIR-II) fluorescence imaging offers superior spatial resolution and tissue penetration, but its utility remains restricted by a lack of standardized analysis protocols and inability to resolve in-depth infarct regions. Here, we introduce FIMPA, an integrated analytical framework for standardized, multi-parametric stroke evaluation based on NIR-II fluorescence perfusion imaging. FIMPA systematically processes the image sequence through motion correction and atlas registration to generate an anatomically aligned library of 125 vascular and hemodynamic parameters. Statistical screening identifies 67 stroke-correlated features, enabling objective, data-driven quantification of perfusion deficits. To resolve spatial infarct boundaries, we developed FIMPA-SI (FIMPA Stroke Index), a deep learning-based index utilizing a ViT-UNETR framework. By leveraging self-supervised pre-training with MRI data, FIMPA-SI suppresses dominant vascular signals to translate multi-parametric dynamics into anatomically precise stroke severity maps. Validated in tMCAO mice, FIMPA-SI achieves high spatial concordance with MRI and significantly outperforms conventional laser speckle contrast imaging and single-parameter metrics. FIMPA provides a robust solution for accelerating preclinical therapeutics and advancing optical neuroimaging.

bioengineering↗

bioRxiv2026

Coevolution-driven reconstruction of multi-taxa siderophore interaction networks reveals topological diversity of microbial exploitation

Microbial communities are shaped by secreted metabolites that mediate ecological interactions, yet predicting these interactions from genomic sequences remains difficult, because the specific recognition between co-functional metabolites (CFMs), such as siderophores, and their receptor proteins (Rec) cannot be inferred from gene annotation alone. This difficulty arises from three factors: the prevalence of Rec-mediated exploitation, the lack of high-accuracy functional annotations, and the absence of genomic co-localization between functionally paired CFM-Rec in Gram-positive bacteria. Here we present the Coevolution-based Interaction Model (CIM), an automated framework that maps specific CFM-Rec pairings directly from uncurated genomic datasets. Using a dynamic joint optimization strategy that accounts for exploitation asymmetry and avoids combinatorial explosion, CIM identifies functional pairings solely through evolutionary covariation. We validated this approach by reconstructing macroscale iron scavenging networks across nine bacterial taxa. Experiments confirmed that CIM can bridge genomic distances exceeding 3 Mb in the Gram-positive genus Rhodococcus to identify unlinked cognate receptors, and can accurately predict cross-utilization by exploiter strains despite substantial receptor sequence heterogeneity in Burkholderiaceae and Rhizobiaceae. Finally, topological analysis of the reconstructed networks shows that siderophore exploitation acts as a universal topological glue, fusing fragmented microbial populations into highly connected communities, and that the exploitability of siderophore production reverses depending on network modularity. CIM thus offers a scalable, sequence-to-ecology approach for predicting interactions mediated by secondary metabolites in microbial communities.

systems biology↗

bioRxiv2026

Artificial Recombination of Nonribosomal Peptide Synthetases Rapidly Evolves Natural Products

Efficient engineering of nonribosomal peptide synthetases (NRPSs) is a key strategy for expanding valuable peptide natural products. Current bioinformatics-guided approaches are often constrained by a set of predefined fusion sites, remaining experimentally challenging in most NRPS systems. Here we present the Recombineering Accelerated Evolution (RACE), which harnesses Red/ET recombineering mediated partially matched homologous recombination to recapitulate recombination-driven NRPS evolution on a highly accelerated timescale. Application of RACE to six known NRPS gene clusters generated 830 recombinants and yielded over 600 novel peptides including novel bis-lipopeptides. These recombinants reveal 112 previously unrecognized recombination fusion sites, providing an extensive landscape for NRPS evolution and more useful resources for guiding NRPS engineering. The RACE establishes a new paradigm for programmable NRPS evolution and enables rapid discovery of bioactive peptides.

synthetic biology↗

bioRxiv2025

DNA Framework Nanoreactor for Programmable Membrane Fusion

Membrane fusion is a fundamental yet transient process that has long resisted direct structural and kinetic dissection. Here we introduce a DNA framework vesicle (DFV) nanoreactor that transforms this elusive biological phenomenon into a programmable, visualizable, and quantifiable process-a nanoreaction confined in space yet extended in time. By embedding lipid membranes and SNARE proteins within precisely defined DNA apertures, DFVs convert stochastic vesicle collisions into geometry-controlled fusion events with tunable kinetics. Cryo-electron microscopy resolves a complete sequence of six intermediates, revealing how nanoscale confinement reshapes the energetic landscape of bilayer merger. Quantitative fluorescence and nano-flow cytometry further establish a direct link between spatial design and fusion probability. Extending this concept to living cells, DFVs enable controllable membrane fusion and augmentation on VAMP2-expressing membranes, achieving direct cytosolic delivery of functional siRNA via fusion-driven transfer rather than endocytosis. This framework bridges structural precision and functional mimicry, offering a unified platform to reconstruct, quantify, and harness membrane fusion as a programmable process for synthetic biology and nanomedicine.

bioengineering↗

bioRxiv2025

Human Organoids Reveal PTEN-driven Mesendoderm Specification via Retinoic Acid Signaling Suppression

During early embryogenesis, epiblast cells ingress through the primitive streak (PS) and commit to a mesendoderm (MES) fate, giving rise to both mesodermal and endodermal lineages. Despite advancements in human organoid technology for modeling pre-implantation blastocyst stage, robust systems that accurately recapitulate MES specification and PS formation during the post-implantation stage remain limited. Here, we show that human induced pluripotent stem cells can be used to generate three-dimensional MES organoids that faithfully mimic in vivo human MES specification, particularly from the anterior PS. We demonstrate that MES organoid formation is dependent on PTEN expression and that loss of PTEN severely impairs the formation of mesoderm and definitive endoderm derivatives arising from MES organoids. To elucidate the molecular mechanisms underlying these defects, we conducted an integrative multi-omics analysis, including transcriptome, chromatin accessibility profiling, metabolism, and phosphoproteomics, on wild-type and PTEN-/-MES cells. These analyses revealed that PTEN suppresses retinoic acid (RA) signaling during MES lineage commitment. Furthermore, we identified the RA-degrading enzyme CYP26A1 as a downstream effector of PTEN. Notably, while excessive RA induced by PTEN ablation is detrimental to MES cell generation, physiological levels of RA are necessary. Collectively, our human MES organoids offer a valuable model for dissecting early human development, and our findings identify PTEN as a key regulator of MES fate commitment through inhibition of RA signaling.

developmental biology↗

bioRxiv2025

Changing the initiation unit of nonribosomal peptide synthetases to access underexplored biosynthetic potential

Nonribosomal peptide synthases (NRPSs) are large multimodular enzymes, capable of synthesizing nonribosomal peptides (NRPs) with diverse structures and bioactivities. Genome sequencing revealed a large number of uncharacterized NRPS biosynthetic gene clusters (BGCs) and their products are underexplored. The majority of NRPSs remain silent potentially attributed to factors such as the low activity of the initiation unit or insufficient precursor supply. Exchanging the starter condensation (Cs) domains within initiation unit can change the length of acyl chains of NRPs, hinting at a promising strategy through swapping of a well-studied Cs domain to activate the initiation unit and harness primary metabolites as precursors, which may offer a new option to access silent BGCs. Here, we first pinpointed two highly efficient fusion sites for initiation unit exchanges. Subsequently, they were validated by replacing the initiation region of endopyrrole pathway with a Cs-containing initiation unit for generation of a lipo-endopyrrole derivate. We promptly leveraged this strategy of changing initiation unit to target six previously silent NRPS BGCs, three BGCs were successfully activated and five novel lipopeptides were identified, demonstrating its application to recover silent BGCs. Furthermore, we extended this strategy in more BGCs from different bacteria. Utilizing a heterologous Cs-containing unit to replace the initiation region of chitinimide biosynthetic pathway led to successful incorporation of N-terminal fatty acid chains into chitinimide to create artificial lipo-chitinimides. This study provides a feasible strategy to rationally recover silent BGCs and add fatty acid chains to NRPs, enriching the genome mining and combinatorial biosynthesis approach for bacterial natural products. SignificanceNonribosomal peptide synthetases (NRPSs) represent a valuable yet underexplored reservoir for bioactive natural products, but most of them are silent. This study introduces the concept that changing initiation unit to activate and optimize the functional expression of NRPSs, and successfully access three of six previously silent NRPS pathways, providing a feasible complement to the current genome mining approaches. Moreover, the N-terminal lipid chains are crucial for the activity of lipopeptides. We employed a heterologous Cs (starter condensation domain)-containing initiation unit to replace the original initiation region for creation of artificial nonribosomal lipopeptides, ultimately yielding three novel lipo-derivatives. This work presents a groundbreaking approach for activating and optimizing NRPSs and provides profound insight into the exploration of bacterial NRPS pathways.

synthetic biology↗

bioRxiv2025

3,4-hydroxyphenyl lactic acid from Lactiplantibacillus plantarum prevents alcoholic liver injury in mice

Alcoholic liver disease (ALD) is a major health burden linked to oxidative stress, gut dysbiosis, and disrupted hepatic metabolism. While Lactiplantibacillus plantarum (L. plantarum) has shown potential in alleviating ALD, the specific mechanisms and bioactive components remain unclear. This study investigated the hepatoprotective effects of L. plantarum fermentation liquid (PFL) and its key metabolite, 3,4-hydroxyphenyl lactic acid (HPLA), against alcohol-induced liver injury. Using acute and chronic alcohol intoxication mouse models, we demonstrated that PFL significantly reduced mortality, attenuated hepatocyte damage, and restored alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) activities. UHPLC-QTOF-MS/MS analysis identified HPLA as the primary active component in PFL, exhibiting potent antioxidant properties. In vitro and in vivo experiments revealed that HPLA mitigated oxidative stress by enhancing superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activities, reducing malondialdehyde (MDA) levels, and suppressing lipid accumulation. Mechanistically, network pharmacology and molecular validation highlighted that HPLA alleviated hepatic injury by modulating the EGFR/PPAR- signaling axis, thereby counteracting alcohol-induced oxidative stress and lipid metabolism disorders. These findings elucidate a novel "gut-liver" axis mechanism mediated by HPLA, offering a theoretical foundation for the clinical application of L. plantarum and its metabolites in ALD management. ImportanceNumerous animal studies and clinical trials have demonstrated the effectiveness of probiotics in treating alcoholic liver disease. In this study, we primarily created a mouse model for both acute and chronic alcoholism and discovered that Lactiplantibacillus plantarum fermentation solution significantly decreased the inflammatory response and oxidative stress caused by alcohol. Its key metabolite, 3,4-hydroxyphenyl lactic acid (HPLA), exhibited strong antioxidant properties, helping to reduce oxidative stress by preventing lipid accumulation. This research offers insights into how probiotic interventions can mitigate alcoholic liver damage, enhancing our understanding of the protective effects of Lactiplantibacillus plantarum and emphasizing the potential of its metabolite, HPLA, as a targeted treatment for alcoholic liver disease.

microbiology↗

bioRxiv2024

Incomplete lineage sorting of segmental duplications defines the human chromosome 2 fusion site early during African great ape speciation

All great apes differ karyotypically from humans due to the fusion of chromosomes 2a and 2b, resulting in human chromosome 2. Yet, the structure, function, and evolutionary history of the genomic regions associated with this fusion remain poorly understood. Here, we analyze finished telomere-to-telomere chromosomes in great apes and macaques to show that the fusion was associated with multiple pericentric inversions, segmental duplications (SDs), and the rapid turnover of subterminal repetitive DNA. We characterized the fusion site at single-base-pair resolution and identified three distinct SDs that originated more than 5 million years ago. These three distinct SDs were differentially distributed among African great apes as a result of incomplete lineage sorting (ILS) and lineage-specific duplication. Most conspicuously, one of these SDs shares homology to a hypomethylated SD spacer sequence present in hundreds of copies in the subterminal heterochromatin of chimpanzees and bonobos. The fusion in human was accompanied by a systematic degradation of the three divergent -satellite arrays representing the ancestral centromere creating five distinct structural haplotypes in humans. CRISPR/Cas9-mediated depletion of the fusion site in human cell lines significantly alters the expression of 108 genes, indicating a potential regulatory consequence to this human-specific karyotypic change.

evolutionary biology↗

bioRxiv2024

Spatiotemporal Single-Cell Roadmap of Human Skin Wound Healing

Wound healing is vital for human health, yet the details of cellular dynamics and coordination in human wound repair remain largely unexplored. To address this, we conducted single-cell and spatial transcriptomics analyses on human skin and acute wound tissues through inflammation, proliferation, and remodeling phases of wound repair from the same individuals, monitoring the cellular and molecular dynamics of human skin wound healing at an unprecedented spatiotemporal resolution. This singular roadmap reveals the cellular architecture of the wound margin and identifies FOSL1 as a critical driver of re-epithelialization. It shows that pro-inflammatory macrophages and fibroblasts sequentially support keratinocyte migration like a relay race across different healing stages. Comparison with single-cell data from venous and diabetic foot ulcers uncovers a link between failed keratinocyte migration and impaired inflammatory response in chronic wounds. Additionally, comparing human and mouse acute wound transcriptomes underscores the indispensable value of this roadmap in bridging basic research with clinical innovations. HighlightsO_LIA spatiotemporal atlas to explore human in vivo gene expression across wound healing C_LIO_LIWound margin architecture unveils a model for human re-epithelialization C_LIO_LIDistinct healing challenges in venous ulcers and diabetic foot ulcers C_LIO_LIUnique human healing traits emerge in cellular heterogeneity and gene expression C_LI

cell biology↗

bioRxiv2024

Neuropeptide Y co-opts neuronal ensembles for memory lability and stability

Memory engrams are formed by activity-dependent recruitment of distinct subsets of excitatory principal neurons (or neuronal ensembles) whereas inhibitory neurons pivot memory lability and stability1-5. However, the molecular logic for memory engrams to preferentially recruit specific type of interneurons over other subtypes remains enigmatic. Using activity-dependent single-cell transcriptomic profiling6-8 in mice with training of cued fear memory and extinction, we discovered that neuropeptide Y (NPY)-expressing (NPY+) GABAergic interneurons in the ventral hippocampal CA1 (vCA1) region exert fast GABAergic inhibition to facilitate the acquisition of memory, but bifurcate NPY-mediated slow peptidergic inhibition onto distinct sub-ensembles underlying the extinction of single memory trace. Genetically encoded calcium and NPY sensors revealed that both calcium dynamics of NPY+ neurons and their NPY release in vCA1 ramp up as extinction learning progresses while behavioral state switches from "fear-on" to "fear-off". Bidirectional manipulations of NPY+ neurons or NPY itself demonstrated NPY is both necessary and sufficient to control the rate and degree of memory extinction by acting on two physically non-overlapping sub-ensembles composed of NPY1R- and NPY2R-expressing neurons. CRISPR/Cas9-mediated knockout of NPY2R or NPY1R further unravels that NPY co-opts its actions on these two sub-ensembles to gate early fast and late slow stages of extinction. These findings exemplify the intricate spatiotemporal orchestration of slow peptidergic inhibitions from single subtype of GABAergic interneurons to fine-tune engram lability verse stability of memory.

neuroscience↗

bioRxiv2024

Comparative genomics of macaques and integrated insights into genetic variation and population history

The crab-eating macaques (Macaca fascicularis) and rhesus macaques (M. mulatta) are widely studied nonhuman primates in biomedical and evolutionary research. Despite their significance, the current understanding of the complex genomic structure in macaques and the differences between species requires substantial improvement. Here, we present a complete genome assembly of a crab-eating macaque and 20 haplotype-resolved macaque assemblies to investigate the complex regions and major genomic differences between species. Segmental duplication in macaques is [~]42% lower, while centromeres are [~]3.7 times longer than those in humans. The characterization of [~]2 Mbp fixed genetic variants and [~]240 Mbp complex loci highlights potential associations with metabolic differences between the two macaque species (e.g., CYP2C76 and EHBP1L1). Additionally, hundreds of alternative splicing differences show post-transcriptional regulation divergence between these two species (e.g., PNPO). We also characterize 91 large-scale genomic differences between macaques and humans at a single-base-pair resolution and highlight their impact on gene regulation in primate evolution (e.g., FOLH1 and PIEZO2). Finally, population genetics recapitulates macaque speciation and selective sweeps, highlighting potential genetic basis of reproduction and tail phenotype differences (e.g., STAB1, SEMA3F, and HOXD13). In summary, the integrated analysis of genetic variation and population genetics in macaques greatly enhances our comprehension of lineage-specific phenotypes, adaptation, and primate evolution, thereby improving their biomedical applications in human diseases.

genomics↗

bioRxiv2024

Circular RNA circASH1L(4,5) protects microRNA-129-5p from target-directed microRNA degradation in human skin wound healing

Both circular RNAs (circRNA) and microRNAs (miRNA) have emerged to play important roles in health and disease. To understand their function in tissue repair, we profiled circRNA, linear RNA, and miRNA expression dynamics in human wound-edge keratinocytes across the wound healing process. Our investigation spotlighted circASH1L(4,5) and its engagement with miR-129-5p, both of which levels were increased with wound repair. Unlike conventional miRNA sponging, circASH1L enhanced miR-129 stability and silencing activity by protecting this miRNA from target-directed miRNA degradation (TDMD) triggered by NR6A1 mRNA. TGF-{beta} signaling, pivotal in wound healing, fostered circASH1L expression while suppressing NR6A1, thus enhancing the miR-129 abundance at the post-transcriptional level. Functionally, circASH1L and miR-129 enhanced keratinocyte migration and proliferation, crucial for re-epithelialization of human wounds. Collectively, our study uncovers circRNAs novel role as shields for miRNAs and sheds light on the physiological importance of regulated miRNA degradation in human skin wound healing.

molecular biology↗

bioRxiv2024

Genomic and transcriptomic characteristics of type VI secretion system in Klebsiella pneumoniae

The Type VI secretion system (T6SS) serves as a crucial molecular weapon in interbacterial competition and significantly influences cell-cell interactions. Various bacterial species utilize their T6SSs to execute a multitude of functions, dictated by their ecological niche. However, the characteristics of T6SS in clinical Klebsiella pneumoniae, a common opportunistic nosocomial pathogen, have not been fully elucidated. Here, we conducted a genomic analysis of 65 clinical K. pneumoniae isolates obtained from patients with varying infections. Genes encoding a T6SS cluster were present in all analyzed strains of K. pneumoniae. Strains of identical sequence type (ST) carried structurally and numerically identical T6SS. Our study also highlights the importance of selecting conserved regions in key T6SS genes for effective primer design in PCR identification. We then utilized the predominant ST11 K. pneumoniae HS11286 to investigate the effect of knocking out T6SS marker genes hcp or vgrG. Transcriptome analysis identified a total of 1,298 co-upregulated and 1,752 co-downregulated differentially expressed genes. Additionally, the absence of hcp or vgrG gene suppressed the expression of other T6SS-related genes within the locus I cluster. Pathway analysis showed that the {Delta}hcp mutant exhibited alterations in transport, establishment of localization, localization and cell processes. Furthermore, interbacterial competition experiments showed that hcp and vgrG are essential for competitive ability of ST11 K. pneumoniae HS11286. This study furthers our understanding of the genomic characteristics of T6SS in K. pneumoniae and suggested that the involvement of multiple genes in T6SS of strain HS11286. ImportanceGram-negative bacteria use T6SS to deliver effectors that interact with neighboring cells for niche advantage. K. pneumoniae is an opportunistic nosocomial pathogen that often carriers multiple T6SS loci, the function of which has not yet been elucidated. We performed a genomic analysis of 65 clinical K. pneumoniae strains isolated from various sources, confirming that all strains contained T6SS. We then used transcriptomics to further study changes in gene expression and effect upon interbacterial competition following knockout of key T6SS genes in ST11 K. pneumoniae HS11286. Our findings revealed the distribution and genomic characteristics of T6SS in clinical K. pneumoniae. This study also described the overall transcriptional changes in the predominant Chinese ST11 strain HS11286 upon deletion of crucial T6SS genes. Additionally, this work provides a reference for future research on the identification of T6SS in bacteria.

microbiology↗

bioRxiv2023

Genomic and transcriptomic analysis revealed new insights into the influence of key T6SS genes hcp and vgrG on drug resistance and interbacterial competition in Klebsiella pneumoniae

Type VI secretion systems (T6SSs) act as a molecular weapon in interbacterial competition and play an important role in cell-cell interactions. Different species of bacteria use their T6SSs to perform a variety of functions according to ecological niche. Therefore, it is necessary to better understand the T6SS potential of Klebsiella pneumoniae (K. pneumoniae), a common clinical opportunistic pathogen. Here, we conducted a genomic analysis on the evolution, T6SS, virulence and antimicrobial resistance of 65 K. pneumoniae in patients with different infections. And we combined transcriptome analysis after knockout of key gene in T6SS of this species. Results showed that genes encoding a T6SS were present in all K. pneumoniae in this study, and there was no correlation was found between T6SS cluster and carbapenem resistance and virulence genes. Differentially expressed genes (DEGs) including 1298 co-upregulated and 1714 co-downregulated were identified after hcp or vgrG deletion. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis have demonstrated common changes in quorum sensing, propionate metabolism and other pathways. And we found that the deletion of hcp or vgrG genes up-regulated of beta-lactam (blaKPC-2) and other resistance genes. Interbacterial competition experiments showed that hcp and vgrG are essential genes for competitive ability of ST11 K. pneumoniae. Taken together, the entire study provides further insight into the investigation of T6SS in K. pneumoniae through genomic and transcriptomic analysis. ImportanceGram-negative bacteria use T6SS to deliver toxin effectors to interact with neighboring cells for niche advantage. K. pneumoniae is an opportunistic nosocomial pathogen that often carriers multiple cope T6SSs, but the function of its T6SS has not yet elucidated. Here, we performed a genomic analysis of 65 clinical K. pneumoniae strains, in order to explore the relationship between T6SS and virulence and resistance genes. We also study the repertoire after knockout of key gene in T6SS of this species by transcriptomics. It was suggested that T6SS is associated with drug resistance, and its key genes hcp and vgrG are critical for the interspecies competition of K. pneumoniae.

microbiology↗

bioRxiv2022

Evidence suggesting creatine as a new central neurotransmitter: presence in synaptic vesicles, release upon stimulation, effects on cortical neurons and uptake into synaptosomes and synaptic vesicles

The discovery of a new neurotransmitter, especially one in the central nervous system (CNS), is both important and difficult. We have been searching for new neurotransmitters for 12 years. We detected creatine (Cr) in synaptic vesicles (SVs), at a level lower than glutamate (Glu) and gamma-aminobutyric acid (GABA) but higher than acetylcholine (ACh) and 5-hydroxytryptamine (5-HT). SV Cr was reduced in mice lacking either arginine:glycine amidinotransferase (AGAT, a Cr synthetase) or SLC6A8, a Cr transporter with mutations among the most common causes of intellectual disability (ID) in men. Calcium-dependent release of Cr was detected after stimulation in brain slices. Cr release was reduced in SLC6A8 and AGAT mutants. Cr inhibited neocortical pyramidal neurons. SLC6A8 was necessary for Cr uptake into synaptosomes. Cr was found by us to be taken up into SVs in an ATP dependent manner. Our biochemical, chemical, genetic and electrophysiological results are consistent with the possibility of Cr as a neurotransmitter, though not yet reaching the level of proof for the now classic transmitters. Our novel approach to discover neurotransmitters is to begin with analysis of contents in SVs before defining their function and physiology.

neuroscience↗

bioRxiv2022

Importance of Glutamine in Synaptic Vesicles Revealed by Functional Studies of SLC6A17 and Its Mutations Pathogenic for Intellectual Disability

Human mutations in the gene encoding the solute carrier (SLC) 6A17 caused intellectual disability (ID). The physiological role of SLC6A17 and pathogenesis of Slc6a17-based-ID were both unclear. Here we report learning deficits in SLC6A17 knockout and point mutants. Biochemistry, proteomics and electron microscopy (EM) support SLC6A17 protein localization in synaptic vesicles (SVs). Chemical analysis of SVs by liquid chromatography coupled to mass spectrometry (LC-MS) revealed glutamine (Gln) in SVs containing SLC6A17. Virally mediated overexpression of SLC6A17 increased Gln in SVs. Either genetic or virally mediated targeting of SLC6A17 reduced Gln in SVs. One ID mutation caused SLC6A17 mislocalization while the other caused defective Gln transport. Multidisciplinary approaches with 7 types of genetically modified mice have shown Gln as an endogenous substrate of SLC 6A17, uncovered Gln as a new molecule in SVs, established the necessary and sufficient roles of SLC6A17 in Gln transport into SVs, and suggested SV Gln decrease as the key pathogenetic mechanism in human ID.

neuroscience↗

bioRxiv2022

The injury-induced circular RNA circGLIS3 activates dermal fibroblasts to promote wound healing

Delayed skin wound healing and excessive scarring are consequences of an impaired healing process and represent a major health and economic burden worldwide. Current intervention strategies lack efficacy and suffer from high recurrence rates necessitating the investigation into alternative treatment modalities like circular RNAs (circRNAs). By RNA sequencing, we profiled circRNA expression changes during human skin wound healing as well as in keratinocytes and fibroblasts isolated from donor-matched skin and acute wounds. CircGLIS3 was found to be transiently upregulated in the dermal fibroblasts upon skin injury, which was at least partially due to the activated IL-1 signaling. Similarly, overabundant circGLIS3 expression was detected in human keloid lesions compared to the surrounding healthy skin. We found that circGLIS3 resided mainly in the cytoplasm, where it interacted with and stabilized Procollagen C-endopeptidase enhancer 1 (PCPE-1) protein to enhance TGF-{beta} signaling, fibroblast activation, and production of extracellular matrix - important biological processes required for wound repair. Accordingly, knockdown of circGLIS3 in human ex vivo wounds potently reduced wound contraction and delayed re-epithelialization. Collectively, we have identified a previously uncharacterized circRNA regulator of human skin wound healing that may open an avenue for circRNA-based therapeutics for abnormal scarring or nonhealing wounds. One Sentence SummaryTransient increase of the circular RNA circGLIS3 promotes the wound fibroblast activation and extracellular matrix production to facilitate wound closure.

molecular biology↗