Biology subjects

Song, H.

Publications and source records attributed to Song, H..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

CA19-9 induces microenvironment remodeling in pancreatic ductal adenocarcinoma

Durable therapeutic efficacy remains a major barrier to improving outcomes for patients with pancreatic ductal adenocarcinoma (PDAC). An immunosuppressive tumor microenvironment (TME) is a hallmark of PDAC and has been demonstrated to be a dominant driver of therapeutic resistance. The aberrant glycan CA19-9 is prevalent in PDAC and drives tumor progression, but the paracrine mechanisms by which it contributes to TME remodeling are unknown. To address this, we mapped TME changes and performed functional analyses using a genetically engineered mouse model (GEMM) harboring KrasG12D mutation and inducible CA19-9 expression. Elevation of CA19-9 led to expansion of antigen-presenting cancer associated fibroblasts (apCAFs) and regulatory T cells (Tregs), which can drive immunosuppression. Antibody blockade of CA19 -9 resulted in significant restoration of normal histology and decreased apCAF and Treg populations. We dissected the paracrine signaling mechanisms that drive this TME remodeling in vitro using mouse and human organoid mono- and co-culture models as well as in vivo using GEMMs and syngeneic orthotopic transplantation models. CA19-9 induced IL1a and TGFb expression, reprogramming pancreatic mesothelial cells into apCAFs in vitro, which in turn directly ligated naive Cd4+ T cells resulting in Treg differentiation in co-cultures. Antibody blockade of IL1a and TGFb in mice led to reduced apCAF and Treg differentiation. We previously reported that CA19-9 modification of the secreted Fbln3 protein increased Egfr engagement and now find that the induction of IL1a and TGFb expression by CA19-9 is dependent on Fbln3 hyperactivation of EGFR signaling. Genetic depletion of Fbln3 led to reduced tumor progression and increased Cd8+ T cell infiltration in mice. Together these findings identify a previously unknown signaling axis driving immunosuppressive phenotypes in PDAC, uncovering multiple potential nodes to relieve the immunosuppressive pressures within the PDAC TME.

cancer biology↗

bioRxiv2026

Genetic canalization of nutrient resorption: evidence from a widespread grass under effective salt stress

Nutrient resorption is a key plant strategy for nutrient conservation, yet whether it responds plastically to non-nutrient stressors such as salinity remains unresolved. Using a common garden experiment with 110 genotypes of the cosmopolitan grass Phragmites australis, we first established that the imposed salinity treatment induced strong multi-level stress responses: above-ground biomass declined by >60%, sodium accumulated 3- to 5-fold across all leaf stages, and 484 metabolites showed significant differential accumulation, including canonical markers of osmotic and oxidative stress. Against this backdrop of confirmed stress, we found that nutrient resorption efficiency (NuRE) remained largely unaffected by salinity. Instead, NuRE was strongly correlated with phylogeographic lineage, ecotype, and latitude of origin, demonstrating evolutionary canalization rather than short-term acclimation. Element-specific regulatory patterns were also evident: while phosphorus resorption followed concentration-dependent control regardless of stress, nitrogen control was disrupted under salinity, and potassium resorption showed no such dependence. Our findings reveal that intraspecific variation in nutrient resorption is predominantly shaped by historical adaptation and geographic context, not by plasticity to salinity. This genetic canalization of a key functional trait implies that predictions of nutrient cycling under global change must account for the phylogeographic composition of plant populations.

ecology↗

bioRxiv2026

Neural dynamics of updating social impressions during movie watching

Updating impressions of others is essential to navigating social life. As we get to know an individual, we update our impressions of them in accordance with new information. How the brain dynamically revises impressions in real time under naturalistic conditions remains unclear. Here, we address this question using functional magnetic resonance imaging (fMRI) and natural language analysis in a naturalistic social cognition paradigm. Across 10 runs, participants viewed a character-driven TV episode, reported moments of insight, and described their impressions of the characters. Results reveal that impressions progressively evolved over time. Individuals with more similar existing impressions exhibit greater neural synchrony during movie-watching, which predicts convergence in post-movie impressions. Neural synchrony in the right superior temporal sulcus (STS) mediates the influence of initial similarity on later alignment. Insight moments accompany neural pattern shifts widespread across cortical regions, including the temporoparietal junction (TPJ), dorsomedial prefrontal cortex (dmPFC) and STS, and the magnitude of the shifts tracks the degree of impression updating. Specifically, distinct forms of insight selectively update complementary components of impressions: character insight updates person-centered representations, whereas non-character insight shapes social-event structure. Together, these findings show that people update their impressions of others through dynamic shifts in distributed brain activity patterns at moments of insight, providing a novel and ecologically grounded neural account of social cognition. Significance statementPeople do not simply form first impressions and keep them. As we learn new things about others, our judgments change--sometimes gradually, sometimes in a flash of insight. By tracking brain activity while people watched a TV show and described how their impressions of the characters evolved, we found that people who saw a character in more similar ways also show more similar brain responses when watching them onscreen, which in turn leads to convergence in subsequent impressions. Such updating is closely tied to "aha" moments, when a person is suddenly understood in a new way. These moments were marked by rapid shifts in the brain representational patterns, and larger shifts predicted greater changes in impressions. These findings offer a more naturalistic account of how the brain revises our understanding of other people in everyday life.

neuroscience↗

bioRxiv2026

Apparent generalism in Pseudomonas aeruginosa is underpinned by Convergent, Cryptic Specialization

Microbes that span environmental reservoirs and diverse human infections are often described as generalists or as ubiquitous, yet ecological theory predicts generalism should be unstable when specialists outperform within any one niche. Here we show that Pseudomonas aeruginosas apparent ecological breadth reflects convergent, cryptic specialism (CCS) - repeatable, environment-linked genomic differentiation that is not confined to deep lineages - rather than strict specialism or generalism. An analysis of 6,627 genomes with source-environment metadata reveals that environments are broadly dispersed across the phylogeny, inconsistent with lineage-locked specialization. Despite this shallow phylogenetic structure, genome content predicted environment-of-isolation across nine genotype-discernible environments, including under cross-validation that blocks phylogenetic relatedness. Interpretable feature profiles recovered both shared and environment-specific signals, including genomic signatures distinguishing distinct chronic and acute human infections. Finally, phenotypes from 47 diverse strains clustered more strongly by environmental source than by phylogenetic relatedness. Together, these results indicate that widely distributed bacterial "generalists" can comprise mixtures of cryptic, convergent specialists. By mapping genotype-defined ecological structure, our approach can identify when apparent generalists harbor hidden structure relevant to infection risk.

microbiology↗

bioRxiv2026

MagNet: Computational Methods for Constructing High-Confidence Protein-Protein Interaction Networks in Magnaporthe oryzae

Magnaporthe oryzae, the rice blast fungus, plays a role as a model organism for molecular plant-microbe interaction research. Studies on the pathogenic mechanism of this fungus revealed many genes involved in signaling pathways. As multi-omics data are being available, genomic-level researches have been conducted to uncover the underlying biological processes during the pathogenesis of M. oryzae. Identifying the genome-wide protein-protein interaction (PPI) network is one of the omics-level approaches, which helps to understand signaling and regulatory pathways. However, existing biological network resources of M. oryzae are not sufficient to decipher pathogenesis mechanisms due to the abundance of false positives/negatives. In this study, a reliable PPI network database of M. oryzae, MagNet, was constructed with three methods, including homology-based Interolog search, co-expression network construction, and domain-domain interaction (DDI)-based prediction. With three approaches altogether, the pan-network with 5,600,976 interactions was generated, including 217,531 highly confident interactions supported by all three methods. Experimental data on M. oryzae PPIs supported that our PPI network can predict PPIs with higher accuracy compared to the previously constructed databases. MagNet would provide integrated biological network data, which can help to understand the molecular mechanisms of the rice blast fungus. The PPI data can be accessed via https:/magnet.scnu.ac.kr.

genomics↗

bioRxiv2026

Defining state-selective lipid binding to brain GPCRs - introducing REVEAL

Membrane lipids are central regulators of G protein-coupled receptor (GPCR) function. Defining receptor-specific lipid interactions in native, fully modified mammalian systems remains challenging. Extensive post-translational modifications generate heterogeneous proteoforms that confound conventional mass spectrometry approaches. Here we introduce REVEAL (REceptor enVironment Elucidation by Activated Lipid-release), an automated native top-down mass spectrometry strategy that discriminates specifically bound lipids from background. Applied here to intact, heterogeneous mammalian membrane protein complexes, incubated with a brain polar lipid extract (>1000 components), we define receptor-specific lipid-binding for two neuronal class C GPCRs. We show that agonism remodels lipid occupancy, selectively enriching a reduced repertoire of bound lipids. Plasmalogen lipids emerge as persistent binders across all conformational states of the metabotropic glycine receptor and are preferentially depleted under oxidative stress, implying a protective role at the receptor surface. These findings position lipids as dynamic regulators of both function and response to the cellular redox environment.

biophysics↗

bioRxiv2026

Task-induced topological and geometrical changes in whole-brain dynamics predict cognitive individual differences

Across the last three decades, functional magnetic resonance imaging (fMRI) research - through both resting-state (rsfMRI) and task-based (tfMRI) studies - has greatly advanced our understanding regarding the neural basis of cognition. Yet the mechanistic relationship between rsfMRI and tfMRI is still poorly understood. In particular, it remains unclear how and why the brain activation patterns observed during the resting state are linked to cognitive functioning and individual differences present during task performance. Here, we test a unifying computational account which postulates that task contexts modulate the nonlinear attractor landscape and associated dynamical properties of the brain present under resting conditions, and further that the nature of this modulation is impacted by meaningful cognitive individual differences. To test this account, we develop a joint rsfMRI-tfMRI modeling and analysis framework called Mesoscale Individualized NeuroDynamics with eXogenous inputs (MINDy-X) and apply it to resting and N-back working memory task data from the Human Connectome Project. We first validated that the joint model can simulate and predict both rsfMRI and tfMRI data accurately, consistent with a common underlying dynamical system. Analyses of this joint model revealed that task-related modulation bifurcated the predominantly multistable attractor dynamics present during the resting state towards a predominantly monostable dynamics observed during N-back task states. This topological shift was also accompanied by a geometric reconfiguration, with the task state characterized by an enrichment of dynamical attractor "motifs" clustered around the frontoparietal (FPN) and default mode (DMN) networks. Task-related modulations of this attractor landscape were further subject to clear individual differences, such that individuals who did not exhibit a shift in attractor topology were more error-prone and less cautious in responding, while closer geometric proximity to the FPN and DMN motifs explained additional aspects of task performance. N-back behavior was best characterized by the combination of topological and geometric properties present in both task and rest states, suggesting that they each account for unique aspects of individual variability. The current work supports a novel computational framework for understanding the whole-brain neural activity patterns observed during rsfMRI and tfMRI as reflecting different states within a common non-linear dynamical system. This framework provides a new vocabulary for characterizing cognitive functioning in terms of the unique geometric and topological configuration of the associated attractor landscapes, with the potential for wide application in many domains of basic and clinical neuroscience research.

neuroscience↗

bioRxiv2026

Natively entangled proteins are linked to human disease and pathogenic mutations likely due to a greater misfolding propensity

A recently discovered class of protein misfolding involving native entanglements could be a widespread mechanism by which loss-of-function diseases arise. Here, we test that hypothesis by examining if there is any statistical association between proteins predisposed to misfold in this way and a database of gene-disease relationships. We find that globular proteins containing non-covalent lasso entanglements (NCLEs) in their native structure, which are more prone to misfolding, are 61% more likely to be associated with disease, 68% more likely to harbor pathogenic missense mutations, and their misfolding-prone entangled regions are 64% more likely to harbor pathogenic missense mutations. Protein refolding simulations indicate that these disease associated, natively entangled proteins are 2.5-times more likely to misfold than comparable non-disease proteins that lack native NCLEs. These results indicate that native entanglement misfolding, especially in the presence of missense mutations, have the potential to contribute to a wide variety of diseases. More broadly, these findings open an entirely new space of therapeutic targets in which drugs are designed to avoid these misfolded states and increase the amount of folded, functional protein.

bioinformatics↗

bioRxiv2026

Detecting misfolded non-covalent lasso entanglements in protein structures, simulation trajectories, and mass spectrometry data

A previously overlooked class of protein entanglements, non-covalent lasso entanglements (NCLEs), has been found to play a role in widespread protein misfolding. However, understanding the influence NCLEs have on biological processes is hindered by the absence of dedicated algorithms and computational tools to detect and characterize these geometries in protein structures, molecular dynamics simulations, and in comparison to experimental data from limited proteolysis (LiP) and cross-linking (XL) mass spectrometry (MS). Here, we present EntDetect, a software tool designed to: (1) identify non-redundant NCLEs in protein structures, (2) detect misfolded states by comparing NCLE changes through pairwise comparisons of structures, (3) extract structural ensembles consistent with experimental signals from LiP-MS and XL-MS, and (4) investigate proteome-wide protein misfolding using high-throughput MS data. We demonstrate the utility of EntDetect on a simulated structural ensemble of phosphoglycerate kinase (PGK), alongside corresponding LiP- and XL-MS experimental data. Additionally, we detail the application of EntDetect to detect misfolding associated with native NCLEs on a proteome-wide MS dataset and select candidate proteins for further investigation. This protocol is intended for biophysicists, structural biologists, and molecular biologists with domain knowledge of protein structure, mass spectrometry proteomics data, and beginner experience with Python who want to interpret their experimental observations and computer simulations results through the presence and potential misfolding of NCLE topologies. EntDetect is open-source and freely available (https://github.com/obrien-lab-psu/EntDetect). NCLEweb is also available which is a webserver that identifies NCLEs within a given user-uploaded structure (https://www.ncleweb.org/).

molecular biology↗

bioRxiv2026

An optimized three-laser 27-color spectral flow cytometry panel for multi-organ profiling in mice

While high-dimensional flow cytometry plays critical roles in resolving complex cellular networks, there remains a scarcity of comprehensive panels for the simultaneous profiling of diverse mouse cell types, primarily due to the inherent difficulty of multiplexing. To address this technical gap and resolve diverse cell populations in murine models, we designed a 27-color flow cytometry panel optimized for 3-laser spectral flow cytometers. This optimized panel enables broad and simultaneous detection of 16 distinct cell subsets from both lymphoid and myeloid lineages--including T cells, B cells, plasma cells, NK cells, innate lymphoid cells, dendritic cells, monocytes, macrophages, neutrophils, eosinophils, basophils, mast cells--along with non-immune cells, such as epithelial, endothelial, fibroblast, and neuronal cells. The panel has been successfully applied to various tissues, including spleen, thymus, bone marrow, peripheral blood, mesenteric lymph nodes, peritoneal lavage fluid, gut epithelium, and lamina propria. Applying this panel to a poly(I:C) model, we successfully tracked dynamic shifts in monocyte and neutrophil populations and identified a previously unrecognized, glucocorticoid-producing cell subset via reporter expression. This panel will facilitate high-dimensional immune profiling on standard 3-laser cytometers, providing a robust tool for dissecting cellular dynamics across diverse contexts.

immunology↗

bioRxiv2026

Molecular dissection of protein complexes isolated from sections of human brain

Molecular studies of brain receptors and transporters have typically relied on recombinant systems, limiting insight into their organization in native tissue. Here, we develop nanobody-based immunoprecipitation coupled with native mass spectrometry to interrogate endogenous protein assemblies from post-mortem mouse and human brain sections. We exemplify our approach by characterizing the synaptic proteins VGluT1 and mGluR2. From a single mouse brain, we discover mGluR2/3 heterodimers, alongside mGluR2 homodimers. Considering regions of human brain heterodimeric mGluR2/3 is highly abundant in the OFC and sgACC ([~]70% and 50%, respectively) and forms regional-specific interactions with additional synaptic proteins. In a modest cohort of biobanked human tissue, associated with depression and suicide, we find increased mGluR2/3 in the OFC. Consistent with this, mice exhibit similar associations between heterodimer levels and stress-susceptibility. Overall, our approach provides a direct means for establishing molecular-behavioural links at the level of receptor organization in brain.

biochemistry↗

bioRxiv2026

CA19-9 promotes liver metastasis of pancreatic cancer through E-selectin mediated extravasation

Pancreatic ductal adenocarcinoma (PDAC) frequently metastasizes to the liver, which drives patient mortality. CA19-9 is elevated in most PDAC tumors and is widely used as a clinical biomarker. Elevated serum levels are associated with poor outcomes. However, whether CA19-9 functionally contributes to metastatic progression has not been fully defined, in part because mice lack endogenous CA19-9 expression. Here, using syngeneic murine PDAC cells engineered to express CA19-9, we investigated its functional role in liver metastasis. In splenic injection models, CA19-9 expression markedly increased liver metastatic burden by promoting both metastatic seeding and subsequent metastatic outgrowth. In vitro, CA19-9 enhanced tumor cell adhesion to endothelial cells through interaction with E-selectin. Metastatic seeding of CA19-9-expressing cells was reduced by genetic deletion of E-selectin or antibody neutralization of either CA19-9 or E-selectin in vivo. Therapeutic targeting of CA19-9 with a neutralizing antibody markedly reduced liver metastatic burden after metastatic seeding. CA19-9 expression increased AKT signaling in PDAC cells and liver metastases, and CA19-9 levels correlated with AKT activation in human PDAC tissues. These findings show that CA19-9 promotes PDAC liver metastasis through E-selectin-dependent metastatic seeding and AKT-associated metastatic outgrowth, highlighting CA19-9 as a functional mediator of PDAC metastasis and a potential therapeutic target.

cancer biology↗

bioRxiv2026

Vitamin D3 attenuates nitrogen mustard-induced dermal toxicity by enhancing microbial butyrate production via the intestinal VDR-α-defensin signaling pathway

Nitrogen mustard (NM)-caused severe cutaneous damage lacks effective targeted therapies. Vitamin D3 (VD3) shows promise as a therapy for NM-induced dermal toxicity; however, the underlying mechanisms remain elusive. Herein, we initially confirmed that NM induced gut flora dysbiosis, characterized by a decrease of Akkermansia muciniphila (AKK) abundance, thereby leading to butyrate reduction. Antibiotics (ABX) significantly promoted NM-induced skin injury, whereas fecal microbiota transplantation of the controls feces (HC-FMT) or AKK administration attenuated NM-induced dermal toxicity. HC-FMT or AKK significantly increased butyrate levels in feces and serum of NM-treated mice. Butyrate notably attenuated ABX-caused acceleration of NM-induced skin injury. Meanwhile, NM markedly decreased the expression of -defensins, MMP7, and VDR. NM failed to further decrease AKK abundance and BA contents in intestinal MMP7-deficient mice, which was abolished by human alpha defensin 5 (HD5) overexpression. And intestinal MMP7 deficiency enhanced NM-caused skin injury, which was markedly attenuated by HD5 overexpression, AKK transplantation, or BA supplementation. Moreover, NM also failed to further reduce MMP7 and -defensin expression, AKK abundance, and butyrate levels in intestinal VDR-silenced mice. Finally, VD3 remodeled the gut microbiome particularly enriching AKK, increased butyrate contents and promoted the expression of -defensins, MMP7, and VDR, thereby attenuating NM-induced skin damage. The protective effect of VD3 against NM-caused dermal toxicity was abolished by either ABX or intestinal-specific knockdown of MMP7 or VDR in mice; however, this impairment was reversed by butyrate or AKK. In conclusion, VD3 attenuated NM-caused dermal toxicity by promoting BA production via remodeling the gut microbiota, and this effect was partially mediated by the intestinal VDR--defensin signaling pathway. These highlight that targeting the gut flora or supplementing with BA could be potential therapies for NM-induced dermal toxicity.

molecular biology↗

bioRxiv2026

A single-cell and spatial atlas of prostate cancer reveals the combinatorial nature of gene modules underlying lineage plasticity and metastasis

Prostate cancer encompasses a spectrum of disease states driven by complex cellular heterogeneity. To delineate the transcriptional programs underlying lineage plasticity and metastasis, we constructed a comprehensive single-cell atlas of 128 patients, spanning localized, castration-resistant, and metastatic disease. Lineage plasticity was prevalent in localized disease, with subsets of tumor cells adopting distinct basal-like and club-like states. Luminal-like cancer cells also displayed extensive lineage infidelity, defined not by a binary loss of identity but by the combinatorial erosion of luminal gene modules associated with higher grade and stage. In the metastatic setting, gene program association analysis (GPAS) identified a broad induction of cell-cycle gene modules across organ sites as well as an induction of organ-specific gene modules, including osteomimetic signaling in bone, neuro-migratory genes in brain, and erythroid-like transitions in liver. Neuroendocrine prostate cancers (NEPCs) were not monolithic but defined by combinations of NE-associated gene modules including a novel HES6 program. Notably, these modules were detected at intermediate levels in localized samples, suggesting molecular plasticity precedes histological transformation. We also developed a refined NE signature that could distinguish NEPC tumors more accurately than previously published signatures. Within the tumor microenvironment (TME), we observed an elevation of pro-inflammatory Th17 T-cells in African American patients and identified a rare Schwann cell population. Finally, we present PCformer, a transformer-based foundation model trained on >500,000 cells to automate cell-state classification. Together, this comprehensive atlas demonstrates the complex nature of gene modules underlying lineage infidelity and plasticity in cancer cells and highlights distinct immune and stromal populations within the tumor ecosystem.

genomics↗

bioRxiv2026

Rearing, dissection, and temporal transcriptomic profiling protocols to study density-dependent phenotypic plasticity in Schistocerca (Insecta: Orthoptera)

This protocol generates gregarious and solitarious density-dependent phenotypes in multiple Schistocerca species under controlled environmental conditions. It describes cage setup, feeding, animal handling, and sterile dissection workflows to isolate nervous, chemosensory, gut, fat body, and female reproductive tissues from nymphs and adults. It emphasizes rapid tissue stabilization and RNase-control practices for downstream single-tissue DNA and RNA analyses. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/705994v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@59afdaorg.highwire.dtl.DTLVardef@283b72org.highwire.dtl.DTLVardef@156fa13org.highwire.dtl.DTLVardef@13bf71b_HPS_FORMAT_FIGEXP M_FIG C_FIG

zoology↗

bioRxiv2026

In vivo deuteration reveals pronounced variation in myelin lipid turnover rates and reduced myelin renewal with ageing

Myelin turnover is essential for its structural and functional integrity, yet how this particularly lipid-rich membrane is renewed and why it deteriorates with ageing remain unresolved. Combining deuterium oxide administration in mice with high resolution lipidomics, we establish that brain lipid turnover rates are highly heterogeneous, differ by brain region, and depend primarily on lipid class. Half-lives of common glycerophospholipids in purified myelin were under 2 months whereas many sphingolipids exhibited half-lives exceeding 8 months, dependent on acyl chain length and saturation. Myelin sphingolipid and cholesterol replacement rates in the corpus callosum decreased markedly between 3 and 12 months of age, while disrupting lipid trafficking through ApoE ablation preferentially impaired cholesterol turnover and incorporation into myelin. Our results establish that myelin renewal occurs through continual replacement of individual lipid constituents in a manner that depends on lipid class, hydrophobicity, and ApoE-dependent trafficking, and that this process slows significantly with ageing.

biochemistry↗

bioRxiv2026

Microtubule Stabilization and Biomaterial Guidance Synergize to Enhance CST Regeneration and Motor Recovery After Chronic SCI.

Spinal cord injury (SCI) results in loss of sensory and motor function below the level of damage, with chronic injuries presenting unique challenges for regenerative therapies. While multichannel biomaterial interventions have shown promise in promoting axonal regeneration, circuit restoration, and motor recovery in acute SCI, achieving similar outcomes in chronic injury models remains challenging due to a combination of intrinsic and extrinsic factors. These include the reduced capacity of the neuronal cell body to sustain a growth-activated state and the formation of a physical and chemical barrier at the injury site, preventing axonal growth. To address these challenges and promote motor recovery after chronic injury, we investigated the combinatorial effect of two regenerative approaches: 1) the implantation of poly (lactide-co-glycolide) (PLG) biomaterial bridge to guide axonal growth through the injury site, and 2) the delivery of Epothilone B (EpoB), a microtubule stabilizer that strengthens axons to promote regrowth. We used a transgenic mouse model that selectively expresses a red fluorescent protein variant (tdTomato) reporter throughout the corticospinal tract (CST) under control of the Crym promoter (Crym-tdTomato). We demonstrated that the combination of bridge implantation 60 days after surgical hemisection at C5 with EpoB improved locomotor function. At 12 weeks post-bridge implantation, immunohistology revealed axon regeneration in mice receiving implantation, but not EpoB or no-implant controls. The addition of EpoB significantly increased the volume of both total and CST axons regenerating through the biomaterial channels. Diffusion tensor magnetic resonance imaging (DTI) analysis identified enhanced fractional anisotropy (FA), axial diffusivity (AD), and mean diffusivity (MD) in the bridge region in the combination treatment group, consistent with new intact axons. Furthermore, EpoB enhanced the myelination of regenerated axons in the bridge. Finally, we investigated the proteomic profile of corticospinal neurons ipsilateral and contralateral to the SCI lesion and bridge, comparing the effect of EpoB treatment. Mass spectrometry-based analysis of laser-captured cells in this paradigm identified activation of a regeneration program by corticospinal neurons. These findings present a novel approach to enhance regenerative neural repair and locomotor recovery in chronic SCI.

neuroscience↗

bioRxiv2026

Spatial mapping of RNA turnover kinetics and regulatory landscapes of mRNA stability in the mammalian brain

Spatial and activity-dependent gene regulation in the mammalian brain requires coordinated control of RNA synthesis and degradation 1,2, yet spatially resolved measurement of RNA turnover kinetics in complex tissues remains technically challenging 3. Here, we present spatial NT-seq, an approach that integrates transgenesis-free metabolic RNA labeling with in situ chemical recoding to spatially co-map RNA abundance and turnover kinetics in the mouse brain. By distinguishing newly synthesized from pre-existing RNAs, this method reveals spatially resolved transcriptional and post-transcriptional responses to electroconvulsive stimulation (ECS), a treatment for refractory depression. We uncover pronounced spatial heterogeneity in RNA turnover, with the dentate gyrus (DG) exhibiting elevated basal RNA turnover and robust ECS-induced responses. These findings reveal a "kinetics scaling" mechanism of coordinated regulation of RNA synthesis and decay, by which DG cells can rapidly remodel their transcript pools in responses to external stimuli or differentiation signals 4,5. Machine learning applied to in vivo RNA kinetics landscapes further identifies sequence features and post-transcriptional regulators underlying region-and cell-type-specific control of mRNA stability. Together, this integrated experimental and computational framework, in vivo Timescope, enables transcriptome-wide mapping of RNA turnover kinetics and the regulatory architecture of RNA stability across spatial and cellular contexts, providing new insights into the spatiotemporal regulation of RNA dynamics in brain function and disease.

genomics↗