Biology subjects

Chen, X.

Publications and source records attributed to Chen, X..

At least 379 records · Page 21Linked to original sources

bioRxiv2025

Human microglia in brain assembloids display region-specific diversity and respond to hyperexcitable neurons carrying SCN2A mutation

Microglia critically shape neuronal circuit development and function, yet their region-specific properties and roles in distinct circuits of the human brain remain poorly understood. In this study, we generated region-specific brain organoids (cortical, striatal, and midbrain), each integrated with human microglia, to fill this critical gap. Single-cell RNA sequencing uncovered six distinct microglial subtypes exhibiting unique regional signatures, including a subtype highly enriched for the GABAB receptor gene within striatal organoids. To investigate the contributions of microglia to neural circuitry, we created microglia-incorporated midbrain-striatal assembloids, modeling a core circuit node for many neuropsychiatric disorders including autism. Using chemogenetics to activate this midbrain-striatal circuit, we observed increased calcium signaling in microglia involving GABAB receptors. Leveraging this model, we examined microglial responses within neural circuits harboring an SCN2A nonsense (C959X) mutation associated with profound autism. Remarkably, microglia displayed heightened calcium responses to SCN2A mutation-mediated neuronal hyperactivity, and engaged in excessive synaptic pruning. These pathological effects were reversed by pharmacological inhibition of microglial GABAB receptors. Collectively, our findings establish an advanced platform to dissect human neuroimmune interactions in sub-cortical regions, highlighting the important role of microglia in shaping critical circuitry related to neuropsychiatric disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=188 SRC="FIGDIR/small/657874v1_ufig1.gif" ALT="Figure 1"> View larger version (72K): org.highwire.dtl.DTLVardef@125b36eorg.highwire.dtl.DTLVardef@270079org.highwire.dtl.DTLVardef@903525org.highwire.dtl.DTLVardef@19145c4_HPS_FORMAT_FIGEXP M_FIG C_FIG TeaserModeling regional microglial diversity in sub-cortical regions is challenging. We generated human organoid and assembloid models containing microglia that acquire region-specific heterogeneity. Our work shows dynamic responses of microglia when exposed to hyperexcitable midbrain-striatal circuits, providing an exciting platform to study neuroimmune interactions in human brain development and neuropsychiatric disorders, including SCN2A mutation-mediated monogenic autism. HighlightsO_LI* Single-cell RNA sequencing analyses reveal six distinct microglial subtypes that spontaneously attain unique specialization in human cortical, striatal, and midbrain organoids. C_LIO_LI* Microglia facilitate axonal projections across regional organoids, promoting assembloid formation. C_LIO_LI* Microglia respond to hyperexcitable neurons via calcium signaling and exhibit excessive pruning of neuronal synapses. C_LIO_LI* Blocking microglial GABAB receptors normalizes calcium activity and reduces synaptic pruning, suggesting a potential targeting strategy for synaptic deficits. C_LI

neuroscience↗

bioRxiv2025

Autism-associated SCN2A deficiency disrupts cortico-striatal circuitry in human brain assembloids

Profound autism spectrum disorder (ASD) is frequently attributable to single-gene mutations, with SCN2A (voltage-gated sodium channel NaV1.2) protein-truncating variants (PTVs) being one of the most penetrant. Although cortico-striatal circuitry is implicated as a key node in ASD, the impact of SCN2A deficiency on human neural circuits is unknown. Using the human cortico-striatal assembloid model, we show that the autism-causing PTV SCN2A-C959X impairs long-range cortical axonal projections, reduces striatal spine density, and attenuates excitatory cortical-striatal synaptic transmission. Surprisingly, these assembloids carrying the heterozygous SCN2A nonsense mutation exhibited pronounced network hyperexcitability, a human cell-specific phenotype not observed in Scn2a+/- mice, highlighting a human-specific circuit vulnerability. Collectively, our study unveils human circuit-specific dysfunctions of SCN2A deficiency and SCN2A-mediated ASD. HighlightsO_LIAxonal projections facilitate synapse formation and functional connectivity in human brain assembloids. C_LIO_LINaV1.2 is expressed along neuronal axons, extending to soma and dendrites in human brain assembloids. C_LIO_LISCN2A-C959X disrupts axonal projection patterns, impairs excitatory synaptic transmission, reduces spine density, and results in elevated neuronal excitability. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/657036v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@6d5b1forg.highwire.dtl.DTLVardef@1795ecdorg.highwire.dtl.DTLVardef@13f0d7eorg.highwire.dtl.DTLVardef@8ee059_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefO_ST_ABSSCN2A haploinsufficiency impairs cortico-striatal circuitry.C_ST_ABSSCN2A haploinsufficiency disrupts axon initial segment (AIS) integrity, leading to hyperexcitability (red arrow), reduced axon projections, and impaired synaptic transmission (decreased sEPSCs and altered network firing). These deficits result in dysfunction within the cortico-striatal circuitry.

neuroscience↗

bioRxiv2025

Peptides alleviate cognitive impairment by inhibiting and disassembling amyloid-beta aggregates in Alzheimer disease

Alzheimers disease (AD) is a devasting neurodegenerative disorder characterized by {beta}-amyloid formation, further exacerbated by RIPK1/RIPK3 necrosome-induced programmed necrosis (necroptosis). We previously showed that the RIPK1/RIPK3 necrosome forms a functional amyloid complex using its RIP homotypic interaction motifs (RHIMs). Here, we discovered that the core RIPK1/RIPK3 necrosome shares strikingly structural similarity to the C-terminal region of {beta}-amyloid (A{beta}42), and the RHIM-derived tetrapeptides (IQIG or VQVG) directly inhibit A{beta} aggregation, disassemble preformed A{beta} fibrils (PFFs), and reduce RIPK1 polymerization. Also, the peptides exhibit effective membrane permeability and could reduce A{beta}40 or A{beta}42-induced neural death and TNF-induced necroptosis in SH-SY5Y cells. IQIG and VQVG injected by ICV increase learning and memory abilities by reducing A{beta} plaques and hyperphosphorylated tau in the cortex and hippocampus of APP/PS1 double-transgenic mice. Mechanistically, the peptides directly interact with A{beta} to block A{beta} aggregation and alleviate microglia-mediated neuroinflammation. Strikingly, single-cell RNA sequencing revealed that the peptides-treated AD transgenic mice restored neuronal homeostasis with increased GABAergic neurons and decreased glutamatergic neurons. Furthermore, total cell-cell interaction strength increased while the AD risk gene Apoe expression decreased in the specific oligodendrocyte subtype of peptides-treated AD mice. Thus, our findings revealed that the peptides could improve cognition and memory capabilities and serve as promising structural templates for potential drugs against AD.

neuroscience↗

bioRxiv2025

Electroacupuncture promotes post-stroke motor recovery through miR-124-3p-mediated regulation of NRG1/ErbB4 signaling pathway

ObjectiveElectroacupuncture has demonstrated beneficial effects in post-stroke motor dysfunction, yet the molecular mechanisms underlying its therapeutic efficacy remain incompletely understood. This study aims to investigate whether electroacupuncture promotes post-stroke motor function recovery by modulating the interaction between miR-124-3p and the NRG1/ErbB4 signaling pathway, specifically exploring whether miR-124-3p directly targets NRG1 to regulate neural plasticity in a focal cerebral ischemia rat model. MethodsThe ischemic stroke model was established by middle cerebral artery occlusion/reperfusion (MCAO/R) in adult rats. These rats were randomly divided into sham, model, electroacupuncture and model plus miR-124-3p inhibitor groups. The model group, electroacupuncture group and model plus miR-124-3p inhibitor group received EA intervention 24 h after modelling for 7 consecutive days. Behavioural function was assessed by Zea Longa score and mechanical pain rating. Hippocampal damage was detected by HE staining and neuronal apoptosis was observed by TUNEL staining. IL-1{beta} and IL-18 levels were measured by ELISA. PCR and Western blotting were used to detect the expression of miR-124-3p and inflammatory pathway proteins. The interaction between miR-124-3p and TLR4 was verified by dual-luciferase reporter assay. ResultsElectroacupuncture improved motor function in rat model of MCAO/R, as evidenced by improved Zea Longa scores and decreased mechanical withdrawal thresholds. Electroacupuncture significantly attenuated neuronal damage and also inhibited the inflammatory response by decreasing IL-18 and IL-1{beta} levels (P < 0.001). Notably, electroacupuncture upregulated miR-124-3p expression (P < 0.0001) and activated the NRG1/ErbB4 signaling pathway in the hippocampus. When miR-124-3p was inhibited, NRG1 protein expression decreased while GABA expression tended to increase. Dual-luciferase reporter assays confirmed that miR-124-3p directly targets the 3UTR of NRG1 mRNA and regulates its expression at the translational level. These findings suggest that electroacupuncture may alleviate neuronal and axonal damage by modulating miR-124-3p/NRG1/ErbB4 signalling and regulating GABA release. ConclusionElectroacupuncture can ameliorate motor dysfunction induced after brain I/R injury by targeting and modulating the NRG1-ErbB4 signaling pathway via miR-124-3p. These data are expected to provide new insights into the mechanisms of electroacupuncture for the prevention of potential targets for the recovery of motor dysfunction after stroke.

animal behavior and cognition↗

bioRxiv2025

Nervous Necrosis Virus Capsid Protein Functions as a SUMO E3 Ligase to Activate MAVS-Dependent NF-κB Signaling

Nervous necrosis virus (NNV) is a lethal aquatic pathogen that activates NF-{kappa}B signaling to manipulate host immune responses, yet the underlying molecular mechanisms remain poorly defined. Here, we identify the NNV capsid protein (CP) as a novel viral SUMO E3 ligase that promotes SUMOylation of Lateolabrax japonicus mitochondrial antiviral signaling protein (MAVS) to drive NF-{kappa}B activation. We show that CP induces p65 nuclear translocation and upregulates proinflammatory cytokine expression in a MAVS-dependent manner. Mechanistically, CP interacts with SUMO2 and the E2 conjugating enzyme L. japonicus UBC9 to promote MAVS SUMOylation at lysine 325 (K325), which stabilizes MAVS, facilitates its aggregation, and amplifies downstream NF-{kappa}B signaling. Notably, disruption of this modification via the K325R mutation or SUMOylation inhibition abrogates MAVS aggregation and inflammatory responses. Our findings reveal a previously unrecognized strategy by which NNV hijacks the host SUMOylation machinery to fine-tune MAVS function, promoting immune evasion and viral persistence. SummaryNervous necrosis virus (NNV) is a highly pathogenic virus in aquatic animals that manipulates host immune signaling to promote infection. Here, we identify the NNV capsid protein (CP) as a viral SUMO E3 ligase that modifies the mitochondrial antiviral signaling protein MAVS via SUMOylation at lysine 325. This modification enhances MAVS stability and aggregation, leading to robust activation of the NF-{kappa}B signaling pathway and increase expression of proinflammatory cytokines. Disruption of this modification abolishes CP-mediated immune activation. This study unveils a previously unrecognized mechanism by which NNV exploits host SUMOylation machinery to modulate MAVS function, contributing to immune evasion and facilitating viral persistence. These findings provide valuable insights into virus-host interactions and highlight potential therapeutic targets against NNV infections.

microbiology↗

bioRxiv2025

The potential of 4-Methylumbelliferone to be repurposed for treating liver fibrosis

4-Methylumbelliferone (4-MU) is the active component of hymecromone, a choleretic and antispasmodic drug with an excellent safety profile. In rodent studies, high doses of 4-MU are also used to inhibit the production of hyaluronan (HA), a biomarker of liver fibrosis. Further, 4-MU shows excellent efficacy in inhibiting liver fibrosis of different etiologies in animal studies, eliciting interest in its repurposing for this condition. However, 4-MUs mechanism of action, and whether it inhibits liver fibrosis by impeding HA synthesis, remains unclear. Using several transgenic mouse models with HA overproduction or degradation in different types of liver cells, we found that both directions of perturbation reduced liver fibrosis levels. In addition, degrading HA via hyaluronidase PH20 overexpression impaired liver function manifested by increased serum aminotransferase (ALT) activity levels. These findings challenge both the role of HA modulation in 4-MUs action and the strategy of targeting HA to treat liver fibrosis. Additional mouse models also excluded the possibility that 4-MU modulates intestinal farnesoid X receptor (FXR) to inhibit liver fibrosis. Ablation of gut microbiota partially abolishes 4-MUs anti-liver fibrosis effect. However, the anti-liver fibrosis effect of 4-MU was lost in the lower-dose group, and the high doses effect in reducing ALT disappeared over time despite its liver fibrosis-reducing effect. Based on these findings, we argue that the lack of efficacy of 4-MU at a translatable dose and lack of a clear mechanism that allows further improvement of 4-MUs efficacy make 4-MU impractical for development as an anti-liver fibrosis treatment. HighlightsO_LI4-MU inhibits MASH fibrosis. C_LIO_LIBoth HA overproduction and digestion in the liver reduce liver fibrosis. C_LIO_LIIntestinal epithelial cell FXR is not required for 4-MU to reduce liver fibrosis. C_LIO_LIThe gut microbiota is partially responsible for 4-MUs antifibrotic effect in the liver. C_LIO_LI4-MU lacks the potential to be further developed into anti-liver fibrosis treatment. C_LI

molecular biology↗

bioRxiv2025

Metabolic and ribosomal dysregulation drive developmental arrest of Schistosoma japonicum in non-permissive rats

Parasitic flatworms of the genus Schistosoma infect a wide range of definitive hosts, which are categorized as permissive or non-permissive based on their capacity to support parasite development. Unlike permissive hosts such as mice, Schistosoma japonicum undergoes pronounced developmental arrest in non-permissive hosts like rats; however, the molecular mechanisms underlying this phenomenon remain largely unclear. In this study, we conducted a comprehensive morphological and transcriptomic comparison of S. japonicum derived from mouse and rat hosts at multiple time points post-infection, identifying the period between 12 and 24 days post-infection (dpi) as a critical window for developmental arrest in parasites from rats. Utilizing single-cell RNA sequencing, we constructed a high-resolution cellular atlas of S. japonicum at 14 and 24 dpi from both host species, revealing host-dependent alterations in cell composition and transcriptional programs during parasite development. Functional analyses further demonstrated that impairments in mitochondrial function and anaerobic glycolysis contribute to the developmental arrest observed in parasites from rats. Additionally, downregulation of ribosomal genes was associated with reduced protein synthesis and impaired cell proliferation. Together, these findings suggest that disruptions in energy metabolism and ribosomal function are key drivers of developmental arrest in non-permissive hosts. This study provides novel, parasite-centered insights into host permissiveness and identifies potential molecular targets for schistosomiasis control strategies.

developmental biology↗

bioRxiv2025

Triad-LMF: A Hierarchical Low-Rank Multimodal Fusion Framework for Robust Cancer Subtype Classification Using Multi-Omics Data

Cancer heterogeneity poses a major challenge for accurate molecular subtype classification. Conventional methods often fail to exploit complementary information across multiple omics modalities, leading to overfitting on high-dimensional data and limited representation of subtype heterogeneity. To address this, we propose Triad-LMF, a multiomics integration framework based on low-rank multimodal fusion to improve classification accuracy. Triad-LMF harmonizes heterogeneous omics data and integrates information through a two-stage hierarchical fusion strategy. Local Pairwise Fusion and Global Triadic Fusion are combined via the Two-Feature and Three-Way LMF modules, enabling a gradual transition from local modality interactions to global feature integration. Experimental results show that Triad-LMF consistently outperforms existing methods. UMAP visualization confirms enhanced subtype separability, and SHAP-based analysis highlights biologically meaningful features. Across independent datasets, Triad-LMF demonstrates strong generalization, offering a robust and interpretable framework for multiomics-driven cancer subtype classification.

bioinformatics↗

bioRxiv2025

Engineering novel AAV capsids by global de-targeting and subsequent muscle-specific tropism in mice and NHPs

Recombinant adeno-associated viral (rAAV) vectors are a potent tool, but their clinical application is restricted by insufficient target tissue transduction and liver toxicity. We employed a novel two-step engineering strategy to create novel rAAV capsids with global tissue de-targeting, then produced strong tissue-specific expression by adding a peptide sequence. We created a novel capsid, AAV.Zero1, with globally de-targeted transduction by loop swapping domains from AAV9 into AAV2. Making an R585A substitution (AAV.Zero2) re-targeted tissues but deleting residues 585-587 (AAV.Zero3) abrogated transduction. Inserting a myogenic peptide into AAV.Zero3 produced a novel capsid (AAV.eM) with strong muscle-specific transgene expression while maintaining minimal off-target expression, including in liver, which was conserved in two mouse strains and non-human primates. AAV.eM showed similar expression as the leading myotropic vector MyoAAV.4A but had a more favorable safety profile. Importantly, AAV.eM was able to functionally rescue a mouse model of Duchenne Muscular Dystrophy following systemic delivery of a micro-dystrophin gene. Thus, AAV.eM is an improved myotropic rAAV capsid that de-targets other tissues, especially the liver, and proof-of-concept for a platform to create capsids with specific properties that translate across species by addition of peptides onto low transduction backbones.

bioengineering↗

bioRxiv2025

High-resolution laminar recordings reveal structure-function relationships in monkey V1

The relationship between structural properties of diverse neuronal populations in monkey primary visual cortex (V1) and their in vivo functional responses is not fully understood. We combined high-density Neuropixels recordings across cortical layers of macaque V1 with non-linear dimensionality reduction on waveform shape to delineate nine putative cell classes: 4 narrow-spiking (NS), 4 broad-spiking (BS) and 1 tri-phasic (TP). Using targeted analyses of laminar organization, spike amplitude, multichannel waveforms, functional properties, and network connectivity of these cell classes, we demonstrate four aspects of the V1 microcircuit predicted by anatomical studies but never fully demonstrated in vivo. First, NS neurons were concentrated in layer 4. Second, a large-amplitude NS cell class in layer 4B showed strong direction selectivity. Third, another layer 4B NS class exhibited robust bursting and orientation selectivity. Finally, cross-correlation analysis revealed functional interactions between cells in different layers. Our results highlight how high-resolution electrophysiology can reveal novel relationships between in vivo function of neurons and the underlying circuit. TeaserHigh-resolution electrophysiology used with machine learning reveals links between function and the underlying neural circuitry.

neuroscience↗

bioRxiv2025

Low-Strength Type I Interferon Signaling Promotes CAR T-Cell Treatment Efficacy

CD19-directed chimeric antigen receptor (CAR) T-cell therapy has significantly advanced the treatment landscape for relapsed/refractory diffuse large B-cell lymphoma (r/r DLBCL). However, up to 60% of patients do not achieve a complete response. To uncover determinants of therapeutic efficacy, we analyzed the infusion products of eight r/r DLBCL patients with distinct clinical responses to axicabtagene ciloleucel using single-cell transcriptomics. Compared to patients who exhibited progressive disease, infusion products of complete responders demonstrated enriched signatures of type I interferon (IFN-I) signaling. Based on these findings, we developed a novel strategy to improve CD19-directed CAR T-cell treatment efficacy by incorporating IFN-I as an enhancer during the ex vivo manufacturing process, with IFN-I removal before CAR T-cell infusion to avoid in vivo toxicities. For both CD28- and 4-1BB-costimulated second-generation CARs, we found that low-strength IFN-I signaling enhanced CAR T-cell cytotoxicity and treatment efficacy against B-cell lymphoma and leukemia. Our low-strength IFN-I-enhanced CAR T-cell ex vivo manufacturing approach leverages an existing FDA-approved pharmacologic agent, circumvents in vivo interferon-associated toxicities, and remains fully compatible with current CAR constructs and manufacturing workflows. Together, our results establish IFN-I as a potent and costimulation-independent enhancer of CAR T-cell efficacy and provide a translationally feasible approach to enhance CAR T-cell therapies.

immunology↗

bioRxiv2025

Selective GSK3α Inhibition Promotes Self-Renewal Across Different Stem Cell States

Pan-GSK3/{beta} inhibition promotes stem cell self-renewal through activation of WNT/{beta}-catenin signaling, but its broad effects complicate the precise control of stem cell states. Here, we show that selective inhibition of GSK3 with BRD0705 supports the long-term self-renewal of mouse embryonic stem cells (ESCs), epiblast stem cells (EpiSCs), and neural stem cells (NSCs), independent of {beta}-catenin signaling. When combined with the tankyrase inhibitor IWR1, BRD0705 broadly supports the maintenance of diverse pluripotent stem cell states, including ESCs, EpiSCs, and formative pluripotent stem cells. This BRD0705/IWR1 cocktail enables stable co-culture of naive ESCs and primed EpiSCs while preserving their distinct molecular and functional identities. Single-cell transcriptomics, epigenomic profiling, and functional assays confirm sustained lineage-specific features across stem cell types. These findings demonstrate that selective GSK3 inhibition enhances stemness by buffering against differentiation cues and promoting intrinsic self-renewal capacity. This work identifies GSK3 as a key regulator of self-renewal across distinct stem cell states and establishes a versatile culture system with broad applications. In BriefWang et al. demonstrate that selective GSK3 inhibition with BRD0705 supports self-renewal of pluripotent and neural stem cells. Combined with IWR1, it enables long-term co-culture of naive and primed stem cells while preserving their distinct molecular and functional identities. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=181 HEIGHT=200 SRC="FIGDIR/small/653860v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@4e371eorg.highwire.dtl.DTLVardef@104b287org.highwire.dtl.DTLVardef@164bd96org.highwire.dtl.DTLVardef@daf1ba_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIGSK3 inhibition by BRD0705 promotes self-renewal of ESCs, EpiSCs, and NSCs C_LIO_LIBRD0705/IWR1 enables long-term co-culture of ESCs and EpiSCs C_LIO_LICo-cultured ESCs and EpiSCs retain distinct naive or primed identities C_LIO_LIBRD0705 preserves stem cell states independently of {beta}-catenin signaling C_LI

cell biology↗

bioRxiv2025

The plant-time-bender model: predicting yield through wheat's perception of time

To address challenges in food security, a better understanding of crop performance under varying and changing environmental conditions is required. Plant Time Warping (PTW) is a deep learning model that integrates high-throughput field phenotyping data with genomic and environmental information to predict wheat yield. PTW leverages image time series, genetic markers, and environmental covariates to learn genotype-specific physiological responses to temperature and vapor pressure deficit. Compared to mere genomic prediction models, PTW demonstrates superior performance when predicting yield in unseen environments across 48 year-locations in Europe. The PTW model captures non-linear growth responses varying with phenological stages and identifies distinct patterns associated with yield performance and stability. Specifically, varieties with higher yield stability exhibit reduced sensitivity to vapor pressure deficit around 1.5 kPa and distinctive temperature responses during emergence and senescence. The learned response pattern enable retrospective and prospective yield predictions, providing a foundation for location-specific variety recommendations and targeted breeding strategies. The integration of phenomic, genomic, and enviromic data has the potential to substantially advance research in climate adaptation strategies for crop production by addressing generalization challenges of predictions to novel environmental conditions. HighlightWe present a novel deep learning model that seamlessly combines high-throughput image data, genomic data, and weather data, enabling better crop predictions for future climates.

genomics↗

bioRxiv2025

A Unique Role for the Hippocampus in Cue Integration During Human Spatial Navigation

It is a central question in cognitive neuroscience how the brain integrates diverse sensory inputs to improve cognitive performance. This study investigated this question in the domain of human spatial navigation using high-field fMRI, a novel navigation task, and desktop virtual reality. Participants learned and retrieved spatial locations using landmarks alone (landmark condition), visual self-motion cues alone (i.e., optic flow; self-motion condition), or both cues together (combination condition). Behaviorally, participants benefited from cue integration. fMRI analyses revealed a cue integration effect in the hippocampus, which displayed positional coding only in the combination condition, and only in participants who showed behavioral evidence of cue integration. Notably, the posterior hippocampus exhibited stronger positional coding in the combination condition than in both single-cue conditions. Additionally, positional coding in the hippocampus predominantly reflected actual, rather than self-reported, locations, suggesting relatively early involvement in the cue integration process. These findings suggest that the hippocampus supports precise memory-guided navigation by integrating different spatial cues, a function beyond simple spatial representation. More broadly, this work helps reconcile the longstanding debate regarding the hippocampuss role in spatial navigation versus episodic and relational memory, facilitating a unified understanding of hippocampal function.

neuroscience↗

bioRxiv2025

Trans-kingdom coupling of redox signaling to environmental cell stress responses through multiphase partitioning.

Reactive Oxygen Species (ROS) signaling is a conserved biological process with parallel functions in all evolutionary branches of life. Here, we identify Receptor for Activated C Kinase 1 (RACK1) as a conserved redox-regulated hub that integrates ROS signals to coordinate cellular stress responses. Using cysteine reactivity profiling in intestinal epithelial cells, we demonstrate that RACK1 undergoes NOX1-dependent oxidation at multiple residues, with C286 serving as a key regulatory site. Functional studies reveal that RACK1 negatively regulates NF{kappa}B signaling through redox-dependent interactions with upstream signaling complexes. Upon stress stimulation, RACK1 dynamically redistributes into membrane-less condensates that act as redox-privileged microenvironments enriched for hydrogen peroxide. We find that oxidized RACK1 condensates are conserved through evolution with analogous stress response behavior in bacteria and yeast indicating a ubiquitous and ancient stress sensor-effector system. Functionally, redox-dependent RACK1 activity links environmental stress to translational control, with oxidation promoting inhibition of protein synthesis. Furthermore, RACK1 mediates responses to diverse pathogen-associated stimuli, including viral and bacterial infection, highlighting its role in epithelial innate immune responses. Collectively, these findings establish RACK1 as a cellular node for redox signaling, operating within condensate-based microdomains to spatially encode oxidative signals and regulate environmental stress pathways in cells. Significance StatementThis study defines a mechanism by which cells achieve specificity in redox signaling through compartmentalization within condensates. By identifying RACK1 as a redox sensor-effector, we reveal an ancient and broadly conserved system linking environmental stress to innate immune signaling and translational control. The discovery of redox-privileged condensates provides a conceptual framework for understanding how transient ROS signals are stabilized and interpreted in epithelial biology, with implications for inflammatory diseases, host-pathogen interactions, and fundamental cellular stress responses.

cell biology↗

bioRxiv2025

Spontaneous spiking statistics form unique area-specific fingerprints and reflect the hierarchy of cerebral cortex

The cerebral cortex is hierarchically organised from sensory to higher cognitive areas1-4. Several dynamical5-8 and anatomical1-4,8 measures, such as timescales and neurotransmitter receptor expression, have independently been linked to the cortical hierarchy. However, a systematic and quantitative characterisation of the relationship between spontaneous spiking activity and the cortical hierarchy remains elusive. Here, we test the hypothesis that single-neuron spontaneous spiking statistics uniquely characterise each cortical area, and that they quantitatively correlate with the cortical hierarchy. We study the spontaneous activity of neurons in seven macaque cortical areas (V1, V4, DP, 7A, M1, PMd, PFC)9-12 in the eyes-open and eyes-closed conditions recorded in a dim-lit room. First, we uncover that the firing rate, inter-spike interval variation, and cross-correlation form a unique fingerprint of the cortical areas, but only when considering them in combination. Second, we show that the differences between the spiking statistics correlate with multiple anatomical markers1,2,4,13-17 of the cortical hierarchy. This effect is much stronger in the eyes-closed condition, suggesting that visual input or the expectation thereof modulates the hierarchical organisation of spontaneous activity. We also observe an increase in timescales up the hierarchy, in agreement with previous findings5,18,19. In conclusion, we demonstrate that spontaneous single-neuron spiking activity reflects the hierarchical organisation of the cerebral cortex: distinct spiking statistics for hierarchically distant areas; similar statistics for nearby areas. Our results thus add a new dynamical dimension to the concept of the cortical hierarchy.

neuroscience↗

bioRxiv2025

The effects of E. granulosus PSCs proteins on host immune cells were elucidated through Transcriptomic and Metabolomic analyses

BackgroundEchinococcus granulosus (E. granulosus), a causative agent of zoonotic diseases, is widely prevalent across most regions and primarily affects vital organs such as the liver and lungs. The parasite secretes immunomodulatory substances, and its protoscolex proteins (PSCs) have been identified as potential diagnostic antigens and vaccine candidates. Although transcriptomics and metabolomics approaches have been employed to investigate echinococcosis, the impact of PSCs on the functionality of host immune cells and the expression of immunomodulatory-related genes remains largely unexplored. MethodsIn this study, immunofluorescence analysis was employed to determine the binding of PSCs to lymphocytes. The CCK-8 assay was utilized to evaluate the impact of varying concentrations of PSCs on cell viability, while ELISA was performed to quantify the levels of cytokines such as IL-9 and IL-4. Furthermore, by integrating LC-MS/MS-based metabolomics and RNA-Seq-based transcriptomics technologies, a systematic analysis was conducted to investigate the metabolic reprogramming and differential gene expression in lymphocytes following PSCs treatment, thereby elucidating the molecular mechanisms underlying its immune regulatory effects. ResultsPSCs proteins inhibited lymphocyte proliferation in a concentration-dependent manner, promoted IL-9 secretion at low concentrations, enhanced IL-4 expression at medium concentrations, and continuously up-regulated TGF-{beta} with increasing concentrations. Transcriptomic analysis identified 1,840 differentially expressed genes (991 up-regulated and 849 down-regulated), and KEGG enrichment analysis highlighted metabolic pathways, including phenylalanine metabolism. Gene Ontology (GO) analysis revealed that the functions of these genes were primarily associated with immunometabolic reprogramming and regulation of the intestinal barrier. Metabonomic profiling detected 12 significantly altered metabolites (8 up-regulated and 4 down-regulated). These findings suggest that PSCs reshape the host immune microenvironment via a metabolic-gene network. This study systematically elucidates how PSCs regulate immune cell function and metabolic homeostasis through multiple targets, providing novel insights into the immune escape mechanisms of parasites. ConclusionPSCs can induce host immune metabolic reprogramming, characterized by the activation of pyrimidine metabolism and the inhibition of bilirubin-mediated oxidative stress, through concentration-dependent regulation of Th9 cytokines (IL-9, IL-4/TGF-{beta}) and suppression of the PI3K-Akt signaling pathway. This process remodels the immune tolerance microenvironment. The aim is to elucidate the molecular mechanisms underlying parasite escape via multi-dimensional immunometabolic regulation, thereby providing a novel direction for the targeted treatment of echinococcosis. Author summaryE. granulosus is a zoonotic disease that can cause space-occupying lesions in the liver, lung and other organs, seriously threaten human health and cause economic losses in animal husbandry. It evades immune attack through a variety of mechanisms.This study investigates the regulatory effects of E. granulosus PSCs on host immune cell function, with a focus on their concentration-dependent influence on Th9 cell differentiation and cytokine expression, including IL-9. Through integrative analyses of transcriptomics and metabolomics, we elucidate the molecular mechanisms underlying immunometabolic reprogramming induced by PSCs. Our findings demonstrate that at low concentrations, PSCs promote the secretion of IL-9 associated with Th9 cells, upregulate IL-4/TGF-{beta} signaling, activate pyrimidine metabolism (leading to thymidine accumulation), enhance bile secretion pathways, and increase bilirubin levels to suppress oxidative stress and T-cell function, thereby establishing an immune-tolerant microenvironment. This research provides the first comprehensive illustration of immune microenvironment remodeling mediated by PSCs via multi-omics network regulation, offering novel insights into the treatment of cystic echinococcosis and host-parasite interactions.

immunology↗

bioRxiv2025

Selective RNA sequestration in biomolecular condensates directs cell fate transitions

Recent studies have emphasized the significance of biomolecular condensates in modulating gene expression through RNA processing and translational control. However, the functional roles of RNA condensates in cell fate specification remains poorly understood. Here, we profiled the coding and non-coding transcriptome within intact biomolecular condensates, specifically P-bodies, in diverse developmental contexts, spanning multiple vertebrate species. Our analyses revealed the conserved, cell type-specific sequestration of untranslated RNAs encoding key cell fate regulators. Notably, P-body contents did not directly reflect active gene expression profiles for a given cell type, but rather were enriched for translationally repressed transcripts characteristic of the preceding developmental stage. Mechanistically, microRNAs (miRNAs) direct the selective sequestration of RNAs into P-bodies in a context-dependent manner, and perturbing AGO2 or alternative polyadenylation profoundly reshapes P-body RNA content. Building on these mechanistic insights, we demonstrate that modulating P-body assembly or miRNA activity dramatically enhances both activation of a totipotency transcriptional program in naive pluripotent stem cells as well as the programming of primed human embryonic cells towards the germ cell lineage. Collectively, our findings establish a direct link between biomolecular condensates and cell fate decisions across vertebrate species and provide a novel framework for harnessing condensate biology to expand clinically relevant cell populations.

cell biology↗