Biology subjects

Yu, J.

Publications and source records attributed to Yu, J..

At least 91 records · Page 5Linked to original sources

bioRxiv2026

Targeting Circulating FABP4 Ameliorates Obesity-Associated Hepatic Steatosis

Obesity is a major driver of hepatic steatosis, yet the molecular link between excess adiposity and hepatocellular lipid accumulation remains incompletely defined. Here, we identify circulating fatty acid-binding protein 4 (FABP4) as a key mediator of adipocyte-hepatocyte lipid crosstalk in obesity. Analyses of human liver specimens and mouse models reveal aberrant accumulation of FABP4 protein--but not transcript--in hepatocytes during steatosis, indicating an extrinsic source. Genetic deletion of FABP4, specifically in adipocytes, protects against high fat diet-induced hepatic steatosis without altering obesity or systemic lipid levels. Mechanistically, circulating FABP4 directly binds to hepatocytes, facilitating free fatty acid uptake. Furthermore, we developed a high-affinity humanized monoclonal antibody that selectively neutralizes circulating FABP4, blocks hepatocyte binding, suppresses fatty acid uptake, and markedly attenuates hepatic steatosis in multiple obese mouse models. These findings establish circulating FABP4 as a pathogenic lipid chaperone and a promising therapeutic target for obesity-associated hepatic steatosis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=180 SRC="FIGDIR/small/701451v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@5b91d5org.highwire.dtl.DTLVardef@1c34892org.highwire.dtl.DTLVardef@1d17ea9org.highwire.dtl.DTLVardef@d2b43c_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIHepatocytic accumulation of extrinsic FABP4 links adiposity to liver lipid deposition. C_LIO_LISpecific deletion of FABP4 in adipocytes prevents hepatic steatosis without affecting systemic lipid levels or obesity. C_LIO_LICirculating FABP4 derived from adipocytes directly binds hepatocytes to facilitate free fatty acid transfer. C_LIO_LIBlocking circulating FABP4 with a high-affinity anti-FABP4 monoclonal antibody inhibits hepatocyte lipid uptake and attenuates steatosis in multiple obese mouse models. C_LI

pathology↗

bioRxiv2026

Expression Levels of the Attachment Protein G Differ Between Strains of a Murine Pneumovirus and Determine the Virulence

Pneumonia virus of mice (PVM), the mouse homolog to respiratory syncytial virus (RSV), is increasingly used as surrogate model to study pneumovirus pathogenesis in a more natural pathogen-host relation. Two major strains of PVM, strain 15 and J3666 are currently used in laboratories, with preferences for either one or the other based on the well-documented isolation history of strain 15 or the suggested higher virulence of strain J3666. Using conventional and long read sequencing, we found that the PVM strain J3666 represents two distinct virus populations, which are defined by sequence and structure of the G and SH genes encoding the putative attachment and small hydrophobic proteins, in addition to further nucleotide polymorphisms. Specifically, a nucleotide polymorphism at position 65 in the G gene results in either an upstream open reading frame (uORF) preceding the main ORF in frame, or an extension of the major G ORF by 18 codons. The impact of the different forms of the J3666-G genes on PVM was examined by generating recombinant PVMs differing exclusively in the distinctive 5 portion of the respective G gene. This revealed that the population expressing a G protein with an extended main G ORF was more virulent, whereas the presence of a uORF attenuated virulence. The virulence of PVM correlated with increased expression levels of G, whereas attenuation was rather associated with downregulated expression of G due to the presence of a uORF. Thus, modulation of G protein levels may be an important mechanism by which pneumoviruses modulate virulence. ImportanceThe pneumonia virus of mice strain J3666 is considered a more virulent and more suitable model for severe lower respiratory tract infections. The organization of the gene for the attachment protein G is reported to contain a small upstream open reading frame (uORF) preceding the main G ORF in frame. The translated G protein is predicted to comprise 396 amino acids. We report that this virus strain may be a mixture of two different populations, each with differing virulence. The more virulent population encodes a G protein of potentially 414 amino acids instead of a small uORF. This G gene organization is associated with an increased G protein expression. Importantly, this organization of the G gene is in line with that of several newly identified pneumoviruses, i.e., canine and swine pneumoviruses. These viruses may comprise a distinct group within the Pneumoviridae family.

microbiology↗

bioRxiv2026

Non-viral vasculogenic reprogramming restores cognition and mitigates pathology in Alzheimer's disease

Alzheimers Disease (AD) is characterized by progressive cognitive decline associated with amyloid-beta (A{beta}) plaques, neurofibrillaiy tangles, inflammation, synaptic loss, and profuse neuronal death. Accumulating evidence demonstrates that cerebrovascular impairment precedes the emergence of neuropathological hallmarks, implicating vascular dysfunction as an early contributor to AD onset and progression. We investigated a non-viral strategy to generate pro-vasculogenic fibroblasts by transiently overexpressing Et{upsilon}2, Foxc2, and Flii (EFF) as a potential cell-based therapy for neurovascular deficits in AD. To assess therapeutic potential, FFF-primc[d] fibroblasts were injected into a mouse model of AD (3xTg-AD) and wild-type controls via the intracerebroventricular (ICV) route, followed by cognitive assessments and subsequent brain tissue analyses. Our findings demonstrate that FFF-primed fibroblasts acquire vasculogenic properties, enhance cerebral blood flow (CBF), and alleviate spatial memory deficits in 3xTg-AD mice. Moreover, transplanted FFF-primed fibroblasts exhibited long-term survival, integrated into the brain vasculature, and promoted cortical vascular remodeling in the AD brain. Notably, ICV deployment of these cells is also correlated with reduced cortical amyloid-beta load, suggesting potential therapeutic benefits in reducing AD pathology. Transcriptomic analysis identified the activation of genes involved in fatty acid oxidation, such as Ppar, known for its anti-amyloidogenic and anti-inflammatory effects. Collectively, these findings highlight non- viral, reprogramming-based vasculogenic cell therapy as a promising strategy for Alzheimers disease, capable of alleviating cognitive decline and addressing AD pathology across cellular and tissue scales.

neuroscience↗

bioRxiv2026

BRD8 Disruption Unlocks Retrotransposon-Driven Tumor-Intrinsic Immunogenicity via Redistribution of Histone Acetylation in Liver Cancer

Overall response rate for immune checkpoint blockade (ICB) therapy remains limited in advanced hepatocellular carcinoma (HCC). Epigenetic perturbation has been shown to enhance tumor-intrinsic immunogenicity and thus reverse resistance to immunotherapy in multiple cancer types. Here, through domain-focused CRISPR/Cas9 genetic screens targeting chromatin regulators, we identified the bromodomain-containing protein 8 (BRD8) as a novel epigenetic factor that functions to suppress tumor-intrinsic immunity through BRD8/EP400 chromatin remodeling complex in HCC. Depletion of BRD8 potently induces anti-tumor immune responses and sensitizes tumors to ICB therapy in mouse tumor models. Mechanistically, BRD8 knockout leads to partial redistribution of H3K27ac to repetitive elements, activating double-stranded RNA (dsRNA) accumulation and subsequent type I interferon (IFN) response, leading to tumor rejection via remodeling the tumor microenvironment. The first-in-class selective chemical probe DN02 targeting the bromodomain of BRD8 also exhibits immunomodulatory and anti-tumor effects. In line with these findings, low BRD8 expression correlated with enriched interferon signatures, elevated immune cell infiltration, and prolonged survival in HCC patients. Together, this study reveals BRD8 as a selective epigenetic vulnerability for promoting tumor immunogenicity, and its bromodomain as a druggable target to overcome immunotherapy resistance in liver cancer patients. SignificanceThe induction of viral mimicry by epigenetic interference could trigger tumor-intrinsic immune response and enhance immunotherapy efficacy. Here, through domain-focused CRISPR/Cas9 screening, we identify BRD8 complex as a regulator involved in the suppression of repetitive elements by controlling H3K27ac distribution and propose BRD8 as a novel target to enhance anti-tumor immunity.

cancer biology↗

bioRxiv2026

Identification and Functional Characterization of CXCL17 Orthologs in Amphibians

C-X-C motif chemokine ligand 17 (CXCL17) has recently been identified as an agonist of the poorly characterized G protein-coupled receptor 25 (GPR25). Although GPR25 orthologs are widely distributed across vertebrates, non-mammalian CXCL17 orthologs have only been identified in some fish species in our recent studies. In this study, we systematically searched public databases for amphibian CXCL17 orthologs based on conserved C-terminal motif, gene synteny, and genomic architecture. Using this approach, we identified up to eighteen CXCL17 orthologs from diverse amphibian species. These amphibian CXCL17s exhibit no significant overall sequence similarity to known mammalian or fish CXCL17s, thus they were previously classified as uncharacterized proteins or even unannotated. Compared with known mammalian or fish CXCL17s, most amphibian CXCL17s display distinctive features, including four cysteine residues in their mature peptide and an additional residue following the conserved C-terminal Xaa-Pro-Yaa motif. A representative ortholog from the tropical clawed frog (Xenopus tropicalis) was recombinantly expressed and functionally characterized using cell-based assays, inducing ligand-receptor binding, {beta}-arrestin recruitment, and chemotactic cell migration. The recombinant amphibian CXCL17 directly bound to and efficiently activated its cognate GPR25 receptor and induced chemotactic migration of the transfected human embryonic kidney (HEK) 293T cells, but deletion of four C-terminal residues largely abolished its activity, indicating that all CXCL17 orthologs employ a conserved mechanism for receptor binding and activation. These findings establish the presence of a functional CXCL17-GPR25 signaling system in amphibians and provide new insights into the phylogenetic distribution and sequence diversity of CXCL17 orthologs across vertebrate lineages.

biochemistry↗

bioRxiv2026

Fusion gene discovery in single cells from high throughput long read single cell transcriptomes

High throughput long-read single cell RNA sequencing allows for fusion gene discovery in thousands of cells in parallel, which is however constrained by the lack of robust computational tools. Here, we develop LongFUSE that employs the XOR logic operation and stringent filtering criteria for the accurate detection of cell-specific fusion genes and their splicing isoforms. LongFUSE outperforms existing tools in both simulation and real data, demonstrating high accuracy and robustness.

bioinformatics↗

bioRxiv2026

dia-PASEF Enables Rapid Profiling of the Human Secretome for Deeper Insights into Cellular Dynamics and Inflammatory Mechanisms

Protein secretion is a fundamental mechanism for cellular coordination and signalling, with its dysregulation leading to widespread physiological dysfunction and disease. Immunoassay formats that utilise secondary antibody readouts are the current gold standard for measuring secreted proteins, offering high specificity and sensitivity, but relying on predefined protein panels that constrain the discovery of novel biology. We present a scalable mass spectrometry-based workflow that combines data-independent acquisition with ion mobility and parallel fragmentation to deliver rapid, global profiling of the secretome. Using a translationally relevant human iPSC-derived macrophage model, our approach identified over 1200 proteins in under 15 minutes of acquisition time, delivering exceptional reproducibility across a large sample set. We applied this approach to profile pro-inflammatory phenotypes, confirming robust identification of key cytokines and chemokines whilst revealing non-canonical immune responses absent from both targeted panels and the intracellular proteome. In particular, we identified a unique cholesterol efflux signature, marked by the secretion of APOA1 and PON1, in response to Mycobacterium Tuberculosis, consistent with the metabolic reprogramming that takes place during infection. Furthermore, temporal profiling of macrophage responses to lipopolysaccharide over 24 hours resolved dynamic secretion trajectories that distinguish between acute and chronic inflammatory states. The extended time period facilitated the observation of distinct cytokine-dependent secretion phenotypes, with early secretion of TNF and IL6 initiating downstream signalling cascades that resulted in the delayed secretion of chemokines such as CXCL10 and CCL8. Collectively, these findings establish a robust, scalable platform for global characterisation of secretory networks. Beyond macrophage biology, this workflow offers broad utility for biomarker discovery, mechanistic studies of disease progression and evaluation of new therapeutic interventions, providing a powerful tool for advancing precision medicine.

immunology↗

bioRxiv2026

Graft-Induced Reprogramming Under Arterial Hemodynamic Stress is Associated with a Shared Proteomic Phenotype in Arterial and Venous Conduits Following Coronary Artery Bypass Grafting

BackgroundAutologous venous conduits remain the mainstay of coronary artery bypass grafting (CABG); however, their long-term patency is limited by adverse vascular remodeling. While arterial and venous grafts undergo structural and molecular adaptation to arterial hemodynamics, the mechanisms underlying successful adaptation remain poorly characterized owing to the scarcity of functioning human graft tissues. MethodsWe analyzed bypass grafts explanted en bloc during orthotopic heart transplantation, comprising patent vein grafts (VGP, n=19), occluded vein grafts (VGO, n=9), and patent arterial grafts (AGP, n=13), alongside freshly harvested controls (vein, n=23; artery, n=11). Quantitative histomorphometry, label-free LC-MS/MS proteomics, pathway analysis, and immunohistochemistry were performed. ResultsWhile patent arterial and venous grafts exhibited medial elastin reinforcement, adventitial neovascularization, and organized intimal remodeling, occluded vein grafts demonstrated elastic layer disruption, medial degeneration, and collagen-dense fibrosis. Proteomic analysis revealed a convergent adaptive signature in patent grafts enriched for RNA metabolism, protein synthesis, cytoskeletal dynamics, and extracellular matrix organization, with shared activation of NR4A3, STAT1, and EGFR signaling. Vein-specific adaptation involved SRC-PTGES activation with concomitant STAT3 suppression, whereas arterial grafts engaged IGF1-RUNX2-associated proliferative programs. Failed venous grafts exhibited angiotensin-driven fibroinflammatory remodeling. Endothelial nitric oxide synthase expression was markedly upregulated in the luminal endothelium and adventitial neovessels of patent grafts. ConclusionsDespite distinct vascular origins, arterial and venous grafts converged toward a shared adaptive phenotype characterized by structural maturation and vasoprotective signaling. Targeting common adaptive pathways--including NR4A3, STAT1, EGFR, and adventitial eNOS--may offer therapeutic strategies to enhance long-term graft durability. WHAT ARE THE CLINICAL IMPLICATIONS?This study provides human tissue-based evidence that patent coronary bypass grafts share a common adaptive remodeling program, irrespective of whether the conduit is arterial or venous. Rather than simple venous "arterialization," successful grafts converged on a phenotype characterized by coordinated biosynthetic activity, structural maturation, and vasoprotective signaling, whereas occluded vein grafts exhibited a distinct angiotensin-driven fibroinflammatory remodeling program. Importantly, patent grafts demonstrated conserved upregulation of NR4A3, STAT1, EGFR, and endothelial nitric oxide synthase (eNOS) in both luminal and adventitial endothelial compartments, identifying molecular features that distinguish adaptive from maladaptive remodeling in humans. These findings are clinically relevant because they highlight shared, potentially targetable pathways that may support graft durability across conduit types and provide mechanistic support for surgical strategies that preserve perivascular adipose tissue during vein harvesting. Moreover, the association of graft failure with angiotensin-centered extracellular matrix remodeling suggests a modifiable biological axis that warrants further investigation. Together, this work establishes a human molecular framework for graft adaptation that may inform future biomarker development, therapeutic targeting, and precision strategies aimed at improving outcomes after coronary artery bypass grafting.

pathology↗

bioRxiv2026

Plant Kelch phosphatases are Ser/Thr phosphatases involved in cell cycle regulation

Brassinosteroids (BRs) are plant steroid hormones sensed by the membrane receptor kinase BRI1. Activation of BRI1 leads to the dephosphorylation of BZR1/BES1 transcription factors. Overexpression of the Kelch phosphatase BRI1 SUPPRESSOR 1 (BSU1) rescued the growth defects of bri1 mutants. Subsequent studies identified BSU1 as a protein tyrosine phosphatase, which promotes BR signaling by dephosphorylating a phosphotyrosine in the glycogen synthase kinase 3 BIN2. Crystal structures of the BSU1 phosphatase domain now reveal a high degree of structural similarity to protein phosphatase 1 (PP1), a eukaryotic serine/threonine phosphatase. Consistently, BSU1 efficiently dephosphorylated phosphothreonine- and phosphoserine-containing substrate peptides, but showed no detectable activity toward BIN2 and other phosphotyrosine substrates. A catalytically inactive BSU1 phosphatase domain suppresses the growth phenotypes of the Arabidopsis bri1-5 mutant and binds the BSU1 homologs BSL1-3. bsu1 and bsu1 bsl1 bsl2/3 loss-of-function mutants display wild-type-like BR responses, but exhibit stomatal patterning and fertility defects. Importantly, the PP1-like C-terminal tail of BSU1 is phosphorylated at Thr785 by a cyclin-dependent kinase complex. The phosphorylated tail binds to the BSU1 substrate-binding grooves, blocking access to the active site. Mutation of Thr785 to alanine activates BSU1, suggesting that Kelch phosphatases and PP1 share a common regulatory mechanism. Deletion of the Marchantia polymorpha Kelch phosphatase MpBSLM results in an undifferentiated cell mass phenotype, associated with the over-activation of a cell cycle reporter. Taken together, our experiments suggest that plant Kelch phosphatases act as PP1-like cell cycle regulators, rather than as tyrosine phosphatases in brassinosteroid signaling. (243 words) Significance StatementBrassinosteroid hormones initiate a well-characterized signaling pathways in plants. While the early signaling events at the plasma membrane have been thoroughly examined, the precise sequence of molecular events that comprise the cytoplasmic signaling cascade is less well-understood. Here, the molecular function of the Kelch protein phosphatase BSU1 is re-evaluated. Previous reports have indicated that BSU1 dephosphorylates the GSK3 kinase BIN2 on a central tyrosine residue. However, structural, quantitative enzyme kinetic, and genetic analyses now suggest that BSU1 is a PP1-like serine/threonine phosphatase involved in cell cycle control rather than a tyrosine phosphatase involved in BIN2 de-phosphorylation. The regulation of BSU1 by a cyclin-dependent kinase complex and the role of Kelch phosphatases in cell cycle progression in Marchantia polymorpha are experimentally characterized. (121 words)

plant biology↗

bioRxiv2026

On-virion structural dynamics reveal temperature- and receptor-coordinated activation of an alphacoronavirus spike

Human alphacoronaviruses primarily infect the human upper respiratory tract, yet how physiological temperature and receptor-binding coordinate viral spike (S) protein activation remain unclear. Using cryo-electron tomography and subtomogram averaging, we directly visualized the structural dynamics of S on human coronavirus 229E (HCoV-229E) virions under physiologically relevant temperatures and in the presence of the host receptor human aminopeptidase N (hAPN). We identified two prefusion S2 conformations, compact and loose, that interconvert reversibly by temperature, revealing intrinsic S2 "breathing" on virions. Receptor-binding domain (RBD)-up conformations are rare on apo virions but are promoted at physiological temperature and stabilized upon receptor binding. hAPN can bind bivalently to neighboring S, forming Gemini S-hAPN complexes. Receptor incubation further promotes conversion from prefusion to postfusion S, an effect enhanced at 33. Together, our results demonstrate an optimized temperature for the HCoV-229E viral fitness, establish temperature and receptor binding as synergistic regulators of alphacoronavirus S activation and define an integrated, on-virion model of S conformational transitions during viral entry. These findings provide a structural framework for understanding alphacoronavirus infectivity.

microbiology↗

bioRxiv2026

Microglia stabilize sleep homeostasis via adenosine A3 receptor signaling

Sleep homeostasis maintains the sleep-wake balance through sleep pressure, a process orchestrated by the accumulation of extracellular adenosine (eADO). Microglial Ca{superscript 2} activity has been implicated in sleep regulation, but the mechanism whereby microglia sense sleep pressure remains unclear. Here we show that microglia regulate sleep homeostasis through brain state-dependent Ca2+ activity driven by adenosine A3 receptor (A3R) signaling. Using miniaturized two-photon microscopy (mTPM) in freely behaving mice, we demonstrate that microglial Ca{superscript 2} activity is rapidly altered by brain-state transitions. Pharmacological experiments reveal that microglial Ca2+ dynamics are predominantly mediated by A3R in response to brain state-dependent eADO oscillations. Microglia-specific deletion of A3R attenuates these state-dependent Ca2+ dynamics, impairs microglial morphological plasticity across sleep-wake cycles, and leads to sleep fragmentation by increasing transitions between wakefulness and non-rapid eye movement (NREM) sleep. Together, these findings establish that microglia regulate sleep homeostasis by stabilizing both wakefulness and NREM sleep, a process critically dependent on eADO-A3R signaling.

neuroscience↗

bioRxiv2026

CAR-T-drug conjugate against solid tumor

Chimeric antigen receptor (CAR)-T cell therapy has been clinically successful in hematologic cancers but faces challenges in solid tumors, primarily due to limited tumor infiltration, immunosuppressive tumor microenvironments (TME), and antigen heterogeneity. While combining CAR-T cell therapy with chemotherapy can enhance antitumor activity, this often leads to substantial systemic toxicity. In this study, we introduce CAR-T-drug conjugate (CAR-T-D-C), a new class of dual-functional therapeutics that effectively addresses these obstacles by integrating click chemistry for precise conjugation of cytotoxic agents onto antigen-specific CAR-T cells. By transforming the hostile TME into an ally, this approach facilitates localized delivery of cytotoxic payload directly to the tumor site, enhancing the overall effectiveness of CAR-T therapy in solid tumors. CAR-T-D-Cs with different CAR-T cell binders exhibit robust antitumor activity across diverse solid tumor models, including both human tumor xenografts and syngeneic models. Spatial transcriptomic studies reveals that CAR-T-D-C achieves improved CAR-T tumor infiltration and functional activation within the TME. Compared to conventional CAR-T therapy, CAR-T-D-C markedly enhances immune cell infiltration, augments effector functions, promotes antigen spreading, amplifies systemic immune responses, and improves overall anti-tumor immunity. CAR-T-D-C represents a versatile therapeutic concept that combines the potency of small molecule drugs and the specificity of CAR-T cells as a 2-in-1 immunochemotherapy for treatment of solid tumors.

immunology↗

bioRxiv2025

The Hippo Pathway Regulates Corneal Endothelial Regeneration

Corneal endothelial cells (CECs) have limited regeneration capacity in primates while display a potent restorative capability in some species such as rodents after wounding. The mechanism which determines the regenerative capability of CECs remains poorly understood. Here, we identify that the Hippo signaling pathway is inhibited and the downstream effector YAP is activated during CEC wound healing in rabbit and mouse. Knockdown of Yap1 and pharmacological inhibition of YAP suppresses CECs wound healing in rodents in both in vitro and in vivo models. XMU-MP-1, a specific small molecular inhibitor for Hippo signaling pathway, can promote the corneal endothelial regeneration in rodents and corneal endothelial proliferation in cultured primate CECs, as well as in vivo non-human primate CEC wounding model. These findings suggest that Hippo pathway serves as a conserved signal to regulate corneal endothelial regeneration among various species, providing a novel target for non-invasive treatment of corneal endothelium decompensation.

cell biology↗

bioRxiv2025

Discovery of Abundant Nano-scale Lymphatic-like Vessels in Brains

As one of the most metabolically active organs, the brain requires an exceptionally efficient system for waste clearance to sustain its high metabolic demands. However, whether such a system exists--and, if so, what structural features enable its efficiency--remains incompletely understood. More than a decade ago, the "glymphatic system" was proposed to describe neurofluid transport through cerebrospinal fluid (CSF) and perivascular spaces (PVS), in conjunction with dural and meningeal lymphatic pathways. Nevertheless, it remains unresolved whether neurofluid transport is organized as a structured, vessel-like flow network. Moreover, in stark contrast to the dense network of blood capillaries in the brain, only a sparse population of lymphatic vessels has been identified, raising doubts as to whether the currently recognized lymphatic architecture alone can support efficient metabolic waste clearance. By combining expansion microscopy with CRANAD-3, a pan-{beta}-amyloid fluorescent probe, we discovered abundant nanoscale lymphatic-like vessels (NLVs) within the brain parenchyma of both mice and humans. The majority of these structures have diameters below 1,000 nm and exhibit moderate positivity for multiple lymphatic markers, including LYVE-1, Prox-1, PDPN, and VEGFR3. NLVs frequently coil around blood vessels, and putative connections between vascular structures were observed. Notably, some NLVs traverse multiple cortical layers and display distinct orientation patterns that vary across cortical laminae. This discovery reveals a previously "hidden" vascular network in the brain parenchyma and raises the possibility that an abundant, highly organized system of nanoscale tubular structures may provide an efficient conduit for metabolic waste clearance. Such a system could represent a critical, previously unrecognized component supporting the brains extraordinary metabolic demands.

neuroscience↗

bioRxiv2025

Density-based longitudinal neuron tracking in high-density electrophysiological recordings

Tracking single neurons across days in high-density extracellular recordings is essential for establishing neural mechanisms of learning, memory, and post-injury recovery. However, in weeks-long recordings, identifying cross-day matches among thousands of units is confounded by changes in spike waveforms, unit turnover, and representational drift in neural responses. We introduce DANT (Density-based Across-day Neuron Tracking), an unsupervised framework that jointly estimates probe motion and neuron identity by alternating between density-based clustering in feature space and probe-motion correction inferred from provisional matches. Estimated drift is used to re-register spike waveforms across sessions, after which clustering is recomputed; this iterative loop continues until the set of matches stabilizes. In parallel, DANT learns a decision boundary from match and non-match assignments derived from the clustering results, enabling it to reject low-similarity candidate pairs. Applied to weeks-long Neuropixels recordings from the cortex and striatum in freely moving rats during stable behavior and task switching, DANT substantially increases match yield and reduces false negatives while maintaining a low false-positive rate relative to existing approaches. Together, these results indicate that DANT provides a general, unsupervised solution for longitudinal tracking in chronic, high-density recordings. The bigger pictureModern high-density probes such as Neuropixels record hundreds of units per session. When chronically implanted, many of these units can be stably recorded over extended periods, opening the door to tracking how large neural populations change over days to weeks, a question central to learning, memory, internal states, and recovery from brain injury. Yet, small shifts in probe position, changes in spike waveforms, and drifts in firing properties mean that linking units across sessions is challenging. DANT (Density-based Across-day Neuron Tracking) addresses this problem by providing an unsupervised framework that combines density-based clustering and iterative motion correction to identify cross-day matches with minimal subjective decisions. Applied to chronic Neuropixels recordings from freely moving, task-performing rats, DANT recovers longer and more complete chains of putative same neurons than existing approaches, while keeping the false-positive rate low. By making cross-day tracking more sensitive, scalable, and reproducible, DANT enables a wider range of neuroscience studies to examine the longitudinal behavior of single neurons and neural populations.

neuroscience↗

bioRxiv2025

Spatial Navigation Training Enhances Large-Scale and Small-Scale Spatial Abilities through Different Neural Mechanisms

Elucidating the relationship between large-scale and small-scale spatial abilities is fundamental to advancing our understanding of spatial cognition, with training transfer effects across tasks offering a direct means of exploration. This study investigated how large-scale spatial navigation training influences both large- and small-scale spatial abilities and their underlying neural mechanisms. Participants completed 20 days of real-world campus navigation training and performed large-scale (distance judgment) and small-scale (paper folding) spatial tasks before and after training. The training group showed significant improvements in both tasks, whereas the control group did not. Brain imaging revealed increased activation in the right middle frontal gyrus (MFG) and bilateral posterior cingulate cortex (PCC) during large-scale task performance after training. In contrast, improvements in the small-scale task were associated with reduced deactivation in the right postcentral gyrus (PoCG), right precuneus, and left superior temporal gyrus (STG). Overall, these findings indicate that large-scale navigation training enhances spatial ability across scales through distinct neural mechanisms, supporting the partial dissociation model and highlighting the contribution of negatively activated regions to spatial processing.

neuroscience↗

bioRxiv2025

Neocortical temporal patterning by a two-layered regulatory network

In the developing neocortex, a diverse array of neurons with defined types and abundances are systematically generated by a limited population of radial glial progenitors (RGPs) as they undergo successive fate changes. The molecular regulation behind this intricate temporal patterning remains elusive. We undertook in-depth single-cell multi-omics analyses, discovering a two-layered regulatory framework at the core of this process. Central to this are global temporal regulators positioned above a temporal network, consisting of series of transcriptional factor (TF) hub groups under sequential state transitions. This temporal network operates not by restricting TF expressions to discrete temporal windows, but through coordinated transcriptional and chromatin-accessibility dynamics that modulate transient TF regulatory activity. Moreover, global temporal regulators specify the duration of each cascading stage and, consequently, the number of progenies generated at each stage. Loss of global temporal regulators protracts RGP lineage progression, whereas their increased activity accelerates it. These findings suggest a two-layer temporal regulatory system controlling RGP lineage progression and neural progeny output duality in mammalian neocortical development.

neuroscience↗

bioRxiv2025

Reconstructing physiological oxygen gradients reveals the role of hypoxia in colon epithelial organization

Oxygen gradients organize tissue architecture and metabolism1,2, yet their precise spatial profiles and mechanistic roles remain poorly understood because both in vivo measurement and in vitro control are technically challenging3,4. Here, we quantify the oxygen landscape of the mammalian intestine using microscale sensors, revealing a steep luminal-basal gradient of approximately 10-60 {micro}M mm-1 that collapses under antibiotic perturbation. We then recreate this physiological range ex vivo with a submerged chemostat microfluidic platform that fixes the oxygen boundary condition by coupling an oxygen-permeable PDMS chip to an external scavenger reservoir and integrating embedded optical sensors for real-time readout. This architecture suppresses ambient oxygen ingress and sustains programmable gradients of 10-20 {micro}M mm-1 across three-dimensional colorectal cancer organoid cultures while remaining compatible with live imaging and endpoint retrieval. The platform bridges quantitative in vivo oxygen mapping with controlled ex vivo modeling, establishing a generalizable approach to interrogate how spatial oxygen dynamics govern epithelial organization and disease progression.

bioengineering↗