Biology subjects

An, J.

Publications and source records attributed to An, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Sex hormones gate the neuronal control of dendritic cell migration and immunity

How endocrine states modulate local immune responses is a fundamental question in immunology. Sexual dimorphism is a striking example: females generally mount stronger immune responses than males, yet how sex hormones intersect with local signals is poorly understood. Here, we identify an endocrine-neuro-immune circuit in which sex hormones determine whether immune cells respond to nociceptor signals. In female skin, nociceptor-derived CGRP promotes dendritic cell (DC) migration and T cell priming indirectly through inflammatory monocytes. CGRP induces monocyte production of Activin A, which upregulates CXCR4 on DCs and promotes migration to draining lymph nodes. In males, androgen receptor signaling suppresses monocyte Activin A and silences this circuit. Disrupting the relay abolishes enhanced female immunity, whereas deleting androgen receptor in male monocytes restores neuronal control. Thus, sex hormones regulate immunity by determining how immune cells interpret neuronal signals, revealing how endocrine state can gate local neuroimmune communication to generate sex-specific immune responses.

immunology↗

bioRxiv2026

PIAS1 loss and INHBA gain define a TGFβ-driven EMT state in OSCC progression

Oral squamous cell carcinoma (OSCC), a highly aggressive subtype of head and neck cancer, remains a major clinical challenge with limited therapeutic options and poor survival outcomes. The Protein Inhibitor of Activated STAT1 (PIAS1), a SUMO E3 ligase involved in transcriptional regulation, DNA repair, and epithelial-mesenchymal transition (EMT), exhibits cancer type-specific roles, but its function in OSCC has not been well characterized. Here, we investigated the molecular and functional role of PIAS1 in OSCC progression and prognosis. All patient cohorts analysed here comprise HPV-negative disease. Analysis across multiple cohorts revealed that PIAS1 mRNA expression is significantly lower in tumor tissues than in normal oral cavity squamous epithelium, including in a cohort of 60 patient-matched tumor and normal pairs. Within the tumor compartment, protein abundance of PIAS1 correlated positively with patient survival. Functional assays using OSCC cell lines demonstrated that PIAS1 acts in a SUMO E3-dependent manner to suppress TGF{beta}-induced migration and invasion. Transcriptomic profiling of PIAS1-depleted cells revealed alterations in expression of genes with relevance in TGF{beta} signaling and pro-invasive cellular responses. Further analyses showed that 46 of these differentially altered hits intersected with The Cancer Genome Atlas (TCGA)-OSCC datasets, where four of these genes, including INHBA, associated with cell stemness-pathway. Spatial analysis of the mRNA abundance of INHBA within OSCC-derived surgical specimens showed increased abundance at the invasive front, and positively associated with aggressive tumor phenotypes, poor patients' outcomes, and resistance to immunotherapy. Single-cell RNA-seq analyses of INHBA revealed increased levels within tumor cells and cancer-associated fibroblasts (CAFs), suggesting potential tumor-intrinsic and extrinsic (tumor microenvironment) sources and hence actions. Collectively, our findings establish PIAS1 as a tumor suppressor in OSCC that restrains TGF{beta}-driven aggressive behaviour. Furthermore, we identify INHBA as a potential therapeutic target, among other genes characterized by spatially restricted, invasive tumor phenotypes.

cancer biology↗

bioRxiv2026

Electrodeposited Biocompatible Coatings for 3D Electrodes on Retinal Prostheses

Photovoltaic subretinal prosthesis, PRIMA, provides central vision to patients blinded by age-related macular degeneration, with acuity matching the 100 m pixel size. Further miniaturization requires pillar electrodes to position the stimulating surfaces closer to the inner retinal neurons. While such structures can be electroplated in gold and coated on their tops with SIROF, the exposed gold sidewalls are not biocompatible. Sputtering or atomic layer deposition of protective coatings are unsuitable for selectively passivating the pillar structures without also coating the photosensitive regions and return electrodes of the implant. Here, we present a strategy for biocompatible coating of pillar sidewalls while preserving surrounding implant functionality. The approach combines non-critical photoresist lithography to protect planar return electrodes with electrodeposition of TiO2; or Pt onto gold pillar sidewalls. In-vivo studies demonstrated that both TiO2 and Pt coatings are biocompatible and prevent adverse reactions of the retinal tissue to gold. Since specific capacitance of electroplated TiO2 (25 F/cm2) is much lower than that of Pt (240 F/cm2), the former better limits the current from the side walls and ensures that charge injection occurs predominantly through the pillar tops coated with SIROF (~6 mF/cm2). Electrodeposition, combined with noncritical photolithography provides a scalable wafer-level solution for fabrication of biocompatible three-dimensional electro-neural interfaces, addressing a critical bottleneck in bioelectronics.

bioengineering↗

bioRxiv2026

Transcriptomic analysis of cecal mucosal immunity in SPF White Leghorn chicks infected with precocious and parent strains of Eimeria tenella

Eimeria tenella (E. tenella) preferentially invades the cecum of young chickens and causes enormous economic losses to the global poultry industry. In this study, chick infection models of virulent parent strain and precocious attenuated line were established with schizogony (2 dpi) and gametogony (6 dpi) as two critical sampling time points. Combined with pathogenicity detection, transcriptome sequencing, mucosal immune index measurement and homologous challenge protection assays, we systematically deciphered the differential molecular mechanisms underlying pathogenicity and immune regulation between the two strains. Pathogenicity results showed that increased infection dosages suppressed weight gain and aggravated bloody diarrhea and oocyst shedding in both strains. In particular, infection with 1 x 105 sporulated oocysts of the parent strain caused massive chick mortality, while the precocious line exhibited markedly lower virulence. Transcriptomic data revealed that gametogony (6 dpi) represented the peak of host immune response. The parent strain persistently overactivated the NF- {kappa}B - mediated positive feedback cascade of coagulation and complement as well as ECM remodeling, triggering steroid metabolic disorder and antioxidant exhaustion, which ultimately induced severe hemorrhagic necrosis of the cecum. By contrast, the precocious line specifically activated the PPAR - {gamma} signaling pathway to negatively restrain excessive inflammation, accompanied by enriched TLR signaling and leukocyte transendothelial migration pathways, thereby forming an immune cascade of "lipid anti - inflammation - pathogen elimination - mucosal repair". Immunoprotection trials verified that priming with 1 x 104 sporulated oocysts of the precocious line significantly alleviated cecal lesions and reduced oocyst output upon secondary challenge, conferring stable mucosal immune protection. The expression trends of seven hub genes (PPARG, PLIN1, CYP1A1, THBS1, FMO4, CYP2C18, CYP14) detected via qRT - PCR were consistent with RNA - seq data. This study identified a dual regulatory paradigm consisting of NF - {kappa}B - mediated tissue injury and PPAR - {gamma} - dependent anti - inflammatory responses, refined the mucosal immune theoretical framework for commercially available precocious attenuated strains, and provided candidate molecular targets for targeted anti - coccidial intervention in chickens.

microbiology↗

bioRxiv2026

Cardiovascular Benefits of Menopause Hormone Treatment is Age-Dependent

BackgroundHormone therapy (HT) has not consistently reduced atherosclerotic cardiovascular disease (ASCVD) events in post-menopausal women, yet the underlying mechanisms remain poorly understood. MethodsFemale Ldlr-/- mice with established atherosclerosis were subjected to surgical menopause and treated with 17{beta}-estradiol (E2) following lipid normalization. Studies were performed in aging and young mice. To determine whether inflammation mediates the age-dependent response to HT, a cohort of aging mice underwent transplantation with Ifn{gamma}-/- bone marrow (BM) before hormone treatments. Metabolic parameters, HDL function, systemic inflammation, atherosclerotic burden, liver metabolic and oxidative stress signaling, and hepatic estrogen receptor signaling were evaluated. ResultsIn aging mice, menopause E2 treatment failed to reduce established atherosclerosis as shown in sham operated mice during lipid normalization. Instead, E2 treatment increased circulating IFN{gamma} and IL-6, impaired HDL antioxidant and cholesterol efflux functions, and promoted inflammatory and vulnerable plaque phenotypes. Suppression of inflammation through Ifn{gamma}-/-BM transplantation restored HDL function and significantly reduced atherosclerosis in E2-treated aging mice. In contrast to aging mice, young mice exhibited reduced systemic and plaque inflammation, improved HDL functions and atherosclerosis following E2 treatment. Liver RNA sequencing and qPCR validation identified activation of inflammatory, oxidative stress, and lipid metabolic pathways in aging E2-treated mice, which were largely attenuated following Ifn{gamma}-/-bone marrow transplantation as well as in young mice. Compared to young mice, aging mice presented hepatic estrogen receptor remodeling characterized by reduced estrogen receptor (ER) expression and increased G-protein coupled estrogen receptor (GPER) expression. Constitutive GPER activation was accompanied by induction of NOX1-dependent oxidative stress, which was further exacerbated by E2 treatment, leading to persistent inflammation. ConclusionsThe cardiovascular effects of estrogen therapy are fundamentally age dependent. Aging shifts estrogen signaling toward hepatic oxidative stress and inflammation through increased GPER. While E2 treatment preserves both metabolic and cardiovascular protection in young mice, aging exacerbates GPER-NOX1-mediated oxidative stress, resulting in impaired HDL function and persistent residual ASCVD risk. These findings identify inflammation-driven, non-lipid mechanisms as potential therapeutic targets to improve cardiovascular outcomes during hormone therapy in postmenopausal women.

physiology↗

bioRxiv2026

Gut Microbiota Dysbiosis Drives Myocardial Hypertrophy Through GBP2b/GBP1-Mediated Immune Reprogramming and Exosomal Signaling in Chronic Colitis

BACKGROUNDPatients with inflammatory bowel disease (IBD) are at increased risk of cardiovascular disease, yet the mechanisms linking chronic intestinal inflammation to cardiac dysfunction remain poorly understood. IBD is characterized by profound gut microbiota dysbiosis, which we hypothesize drives systemic immune dysregulation and contributes to cardiac dysfunction. METHODSA chronic colitis mouse model was used to assess gut microbiota dysbiosis, systemic immune cell metabolism, and cardiac remodeling. Cardiac outcomes were evaluated by echocardiography, histology, and molecular analyses. Mechanisms were examined using fecal microbiota transplantation, immune cell depletion, exosome transfer, bone marrow chimeras, RNA-seq, co-immunoprecipitation, confocal microscopy, and siRNA-mediated gene silencing. RESULTSChronic DSS colitis induced cardiac dysfunction, hypertrophy, and fibrosis in mice. These changes were accompanied by sustained gut microbiota dysbiosis, metabolic reprogramming, and mitochondrial dysfunction in circulating immune cells. Fecal microbiota transfer experiments demonstrated that colitis-associated microbiota were sufficient to reprogram systemic immune cells and promote cardiac dysfunction. Immune cell depletion studies identified macrophages as key mediators of colitis-associated cardiac injury. Colitis increased systemic lipopolysaccharide (LPS) translocation, bone marrow chimera experiments demonstrated that hematopoietic TLR4 signaling was required for immune cell metabolic remodeling and cardiac dysfunction during chronic colitis. Transcriptomic analysis identified guanylate-binding protein 2b (GBP2b/GBP1, hereafter referred to as GBP1) as a key downstream effector of LPS-TLR4 signaling. Upon LPS stimulation, GBP1 localized to mitochondria, where it interacted with DRP1 and FIS1 to promote mitochondrial fission, oxidative stress, and enhanced immune cell migration into the heart. In addition, GBP1 was secreted via exosomes, which were taken up by cardiomyocytes and contributed to hypertrophic remodeling, and cardiac dysfunction. CONCLUSIONSThese findings establish the LPS-TLR4-GBP1 axis as a key driver of colitis-associated cardiovascular dysfunction and highlight this pathway as a promising therapeutic target for reducing cardiovascular risk in patients with IBD. Novelty and SignificanceO_ST_ABSWhat Is Known?C_ST_ABSO_LIPatients with inflammatory bowel disease have an increased risk of cardiovascular dysfunction that cannot be fully explained by traditional cardiovascular risk factors. C_LIO_LIGut microbiota dysbiosis and chronic innate immune activation are hallmarks of inflammatory bowel disease, but their direct contribution to cardiac remodeling remains unclear. C_LI What New Information Does This Article Contribute?O_LIChronic colitis-associated gut microbiota dysbiosis induces systemic immune cell metabolic and mitochondrial reprogramming that is sufficient to drive cardiomyocyte hypertrophy and cardiac dysfunction. C_LIO_LIHematopoietic Toll-like receptor 4 signaling links colitis associated gut microbiota to immune metabolic dysfunction and cardiac impairment, establishing a causal gut-immune-heart axis. C_LIO_LIGuanylate-binding protein 2b (GBP2b/GBP1) is identified as a critical downstream effector that promotes mitochondrial fission, oxidative stress, immune cell cardiac infiltration, and exosome-mediated cardiac remodeling. C_LI

pathology↗

bioRxiv2026

Targeting CD73-A2aR-Mediated Adenosine Signaling at the Tumor-Immune Interface Overcomes Radioresistance

BackgroundRadiotherapy efficacy is constrained by an immunosuppressive tumor microenvironment (TME) enriched in extracellular adenosine and suppressive myeloid populations that attenuate cytotoxic T-cell responses. The CD73-adenosine-A2a/A2b receptor axis represents a key metabolic immune checkpoint; however, the relative contributions of tumor cell-intrinsic versus host-derived adenosine signaling to radiotherapy response remain incompletely defined. MethodsUsing orthotopic murine breast carcinoma models, we interrogated radiation-induced adenosine dynamics and downstream immune remodeling through quantitative adenosine measurements, bulk RNA sequencing, and multiparameter flow cytometry. Genetically engineered models were employed to dissect the roles of tumor-derived CD73 and host A2a/A2b receptors in regulating radiosensitivity. Therapeutic studies evaluated combinatorial targeting of CD73 and A2a/A2b receptors with radiotherapy and anti-PD-1, followed by comprehensive immune profiling in breast carcinomas. ResultsTumor cell-intrinsic CD73 and host A2A receptor signaling cooperatively drive radioresistance and tumor progression. Radiotherapy induces a rapid surge in intratumoral adenosine, triggering transcriptional and cellular programs consistent with myeloid-mediated immunosuppression and lymphocyte dysfunction. Although T-cell infiltration increases at later time point post-irradiation, effector function remains constrained. Pharmacologic inhibition of CD73 and A2a/A2b receptors partially restores T-cell functionality but is insufficient for durable tumor control as monotherapy. In contrast, concurrent blockade of adenosine signaling during radiotherapy, followed by adjuvant PD-1 inhibition, amplifies adaptive antitumor immunity and significantly enhances tumor control. ConclusionsThese findings define a mechanistic link between radiation-induced adenosine signaling and immune dysfunction in the TME. Targeting the CD73-A2a/A2b axis in combination with radiotherapy and checkpoint blockade represents a rational strategy to overcome radioresistance and improve antitumor immunity. STATEMENT OF SIGNIFICANCEThe tumor and immune cell contributions to adenosine signaling play a central role in shaping the therapeutic outcomes of tumor irradiation. Therapeutic targeting of the adenosine signaling axis improves radiosensitivity and efficacy of checkpoint blockade.

cancer biology↗

bioRxiv2026

Task-space dimensions guide human exploration in complex environments

Efficient exploration is essential for rapid learning in high-dimensional environments, where rewards depend on a sparse and unknown subset of task dimensions. Here, we developed a multidimensional value-learning task in which participants explored without explicit knowledge of the underlying structure. Across multiple task designs, participants consistently demonstrated successful learning under structural uncertainty. Behavioral analyses revealed that over half of participants adopted a structured exploration strategy--Full Dimension Scan (FDS)--with three key properties. First, participants systematically isolated and sampled one candidate dimension at a time, effectively reducing search complexity. Second, FDS was temporally persistent within dimensions while maintaining diverse sampling of feature values, enabling efficient local inference. Third, participants sequentially deployed FDS across dimensions, achieving broad coverage of the task space. Importantly, this strategy transferred across tasks: prior experience in lower-dimensional environments promoted stronger FDS use and improved performance in higher-dimensional settings. Consistent with these findings, a dimension-guided exploration model incorporating dimension-level attentional control best captured human behavior. Together, these results identify dimension-guided exploration as a core principle that transforms high-dimensional search into tractable, structured learning, providing new insight into adaptive behavior in complex environments.

animal behavior and cognition↗

bioRxiv2026

Multiscale transcriptomic organization of the human brain with DigitalBrain

The human brain varies across anatomical regions, cell types, development, aging and disease states, yet existing single-cell transcriptomic resources remain fragmented and difficult to integrate into a unified biological model. Here we present DigitalBrain, a human brain-specific atlas and foundation-model framework for organizing diverse and fragmented human brain transcriptomic data across scales. We first built DigitalBrain-Atlas, a harmonized whole-brain single-cell resource comprising 16.35 million transcriptomes from 2,143 donors across 165 brain regions, spanning the human lifespan and multiple neurological and clinical conditions. We then developed DigitalBrain-M1, a Transformer-based model that jointly encodes gene identity and expression magnitude to learn a shared embedding space for cells and genes. Across held-out datasets, DigitalBrain supported robust single-cell integration, clustering and cell-type annotation while preserving major biological structure and reducing technical fragmentation. Beyond these benchmarks, the learned embeddings revealed emergent large-scale hierarchical organization of the human brain, linking anatomically distinct regions into higher-order patterns consistent with known functional systems. Applied to human hippocampal aging, DigitalBrain identified cell-type-specific aging sensitive gene sets, highlighted dentate gyrus granule cells as a particularly age-sensitive population, and discovered selective reorganization of gene programs related to synaptic transmission, postsynaptic structure, membrane excitability and axon guidance during aging. Cross-dataset convergence was strongest at the level of functional modules and recurrent aging sensitive genes. Together, these results demonstrate that DigitalBrain is a brain-specific framework for mapping human brain organization across scales, and as an early step towards a complete virtual organ for the human brain.

bioinformatics↗

bioRxiv2026

Intestinal intraepithelial lymphocyte migration and tissue homeostasis are dictated by Gα13

Intestinal intraepithelial lymphocytes (IEL), including conventional CD8{beta} T resident memory (Trm) cells and unconventional CD8 T cells, promote tissue integrity. Here, we studied the G-protein coupled receptor signals regulating IEL positioning, homeostasis, and function. Deficiency in heterotrimeric G-protein subunit G13 or its effector Arhgef1 caused an intestine-specific loss of all types of CD8+ TCR{beta} and TCR{gamma}{delta} IEL. G13-deficient IEL exhibited restricted intraepithelial movement and impaired maturation. Induction of intestinal CD8{beta}+ Trm upon infection was intact in the absence of G13-signaling, but the cells had poor access to the villous niche and defective survival that could be rescued by increasing TGF{beta}+ or interleukin (IL)15. In vivo CRISPR/Cas9 screening identified GPR132 as a G13-coupled receptor that regulates CD8{beta}+ IEL homeostasis and migration to lysophosphatidylcholine. Mice bearing G13-deficient T cells suffered more severe colitis and increased colorectal tumor growth. The selective requirement for G13-signaling for IEL positioning and survival in the villous niche has implications for therapeutic intervention.

immunology↗

bioRxiv2026

Ketosis rescues frataxin deficiency and corrects disease phenotypes in an FRDA animal model

Friedreich ataxia (FRDA) is an autosomal recessive neurodegenerative disease caused by deficiency of the mitochondrial protein frataxin. Effective therapeutic options remain limited for FRDA. We previously demonstrated that frataxin regulates ketone body metabolism by modulating 3-Oxoacid CoA-Transferase 1 (OXCT1), the rate-limiting enzyme in ketone body catabolism. However, the mechanisms governing frataxin-dependent control of OXCT1 turnover as well as the contribution of frataxin deficiency-induced OXCT1 reduction to FRDA pathogenesis, have remained unclear. Here, we demonstrate that frataxin regulates OXCT1 protein turnover by inhibiting its ubiquitination and subsequent proteasomal degradation. The N-terminal 40 amino acids of frataxin mediate such events, as overexpression of this region alone blocks ubiquitin-proteasome system (UPS)-dependent OXCT1 degradation. To evaluate the impact of OXCT1 deficiency on FRDA phenotypes, we enhanced OXCT1 reduction by introducing a 50% OXCT1 knockout into frataxin-deficient KIKO mice (KIKO/OXCT1/-). While OXCT1 deficiency potentiates cell death in vitro in control and FRDA patient fibroblasts, further OXCT1 reduction in KIKO mice induces ketosis, increases frataxin levels, and improves neurobehavioral performance. The increase in frataxin does not reflect elevated FXN gene transcription but rather enhanced mitochondrial biogenesis, evidenced by increased biogenesis markers, restored mitochondrial morphology and size, and increased mitochondrial gene expression. Fasting-which promotes ketosis-similarly increases frataxin levels and mitochondrial biogenesis markers in older KIKO/OXCT1+/- mice. {beta}-hydroxybutyrate administration in FRDA iPSC-derived cardiomyocytes elevates frataxin levels and mitochondrial biogenesis markers, further supporting the beneficial effect of ketosis on frataxin expression and mitochondrial biogenesis. Collectively, our findings demonstrate that ketosis partially restores frataxin levels and ameliorates FRDA-related phenotypes, providing a potential therapeutic strategy for FRDA.

biochemistry↗

bioRxiv2026

ABCC1 protects skin dendritic cells from FITC-induced toxicity by efflux and extracellular glutathione buffering

Dendritic cell (DC) migration is critical for initiating adaptive immune responses. Previous work suggested a role for ATP-binding cassette transporter C1 (ABCC1) in skin DC migration following cutaneous fluorescein isothiocyanate (FITC) exposure, but the precise mechanism involved was unclear. Here we establish that the primary contribution of ABCC1 to skin DC function following FITC exposure is not modulation of migration, but enhancement of survival. Our findings demonstrate that ABCC1 operates on a dual level: intracellularly, by transporting toxic FITC and fluorescein out of DCs, and extracellularly, by contributing to a glutathione (GSH) buffer zone that protects surrounding cells. DCs are particularly susceptible to FITC-mediated toxicity, possibly due to their high endocytic activity. This study elucidates the critical dependence of DCs on ABCC1 and extracellular GSH for resistance to toxic organic molecules and thereby identifies potential therapeutic avenues targeting ABCC1 to modulate immune responses. Significance StatementAdaptive immunity is critically dependent on dendritic cells (DCs) and their ability to take up foreign molecules for processing and presentation to T cells. DCs in the skin are exposed to a diversity of environmental chemicals and whether they have mechanisms to protect themselves from chemical-induced toxicity has been unclear. In this work we investigate the role of the multi-drug resistance transporter ABCC1 (MRP1) in DC biology. We reveal that ABCC1 shields DCs from chemical poisoning following skin exposure to fluorescein isothiocyanate (FITC). ABCC1 is needed both cell intrinsically and cell extrinsically to achieve the full protective effect. This discovery underscores a previously unrecognized reliance of DCs on ABCC1 function and opens new opportunities for therapeutic manipulation of these cells.

immunology↗

bioRxiv2025

ZIKV NS5-mediated STAT2 degradation as a determinant of immune evasion and pathogenicity

Type I interferon (IFN) signaling is a central antiviral defense, with STAT2 driving the expression of IFN-stimulated genes (ISGs) to restrict viral infection. Many flaviviruses, including Zika virus (ZIKV), evade this pathway through non-structural protein 5 (NS5)-mediated ubiquitination and proteasomal degradation of STAT2, yet the contribution of this immune evasion strategy to viral fitness and pathogenesis remains incompletely defined. Here, using a multi-step mutational scanning strategy that jointly assessed STAT2 degradation and viral RNA replication, we identified a single NS5 residue, L162, as uniquely permissive to substitution that abolishes STAT2 degradation without compromising intrinsic replication functions. Substitution of L162 with alanine or glycine (L162A or L162G) selectively disrupted NS5 recruitment of the ZSWIM8-CUL3 E3 ubiquitin ligase, thereby preserving STAT2 stability and restoring IFN signaling. Recombinant ZIKV carrying these mutations exhibited reduced replication and enhanced ISG induction in human cells, defects fully rescued by STAT2 knockout. In A129 mice (type I IFN receptor deficient), mutant and WT viruses replicated comparably, but in human STAT2 knock-in mice, ZIKV-NS5L162G exhibited markedly reduced viral loads and disease. Notably, infection with ZIKV-NS5L162G elicited robust neutralizing antibody and T cell responses that conferred protection against WT challenge. Together, these findings establish NS5-mediated STAT2 degradation as a central determinant of ZIKV immune evasion, viral fitness and pathogenesis, and highlight disruption of NS5-STAT2 antagonism as a promising strategy for antiviral intervention and rational attenuation.

microbiology↗

bioRxiv2025

From Ions to Chaos: exploring a whole-brain modelling framework in the mouse

Computational neuroscience offers powerful tools for understanding brain function in both healthy and diseased states. However, detailed data on microscale mechanisms--such as those involved in genetics and pharmacology--are often derived from mouse experiments and further lack integration into whole-brain models. In this work, we bridge microscale ion-channel dynamics and macroscale network behavior by employing the Larter-Breakspear neural mass model on The Virtual Brain platform with a mouse brain connectome. Our simulations reproduced key findings from prior computational studies with the Larter-Breakspear model, demonstrating its cross-species translation to the mouse. This included the emergence of chaotic dynamics and network synchrony as a function of coupling and delay parameters. Furthermore, we demonstrate that Calcium, Sodium, and Potassium-related parameters each critically shape the global dynamic regimes and that the response to external stimuli is highly sensitive to calcium concentrations. This work represents the first integration of the Larter-Breakspear model into a mouse-scale connectome, validating previous results in a new context. In addition, it establishes a framework for a detailed exploration of synchrony, ion dependency, and stimulus reactivity. By linking molecular simulations, genetic data, and mouse electrophysiology, this approach holds promise for mechanistic insights into neuropsychiatric disorders, such as schizophrenia and epilepsy.

neuroscience↗

bioRxiv2025

Network Adaptability Governs Resilience and Susceptibility to Social Defeat

Stress resilience is defined as the ability to maintain mental health after adversity. In humans, resilience is marked by threat-safety discrimination and extinction of fear, whereas susceptibility involves fear generalization and extinction resistance. Using a translational mouse model of chronic social defeat stress combined with preregistered multimodal brain imaging, we investigated structural and network-level markers of resilience, susceptibility, and threat learning. Resilience was characterized by preserved dentate gyrus integrity, greater microstructural complexity in prefrontal regions, and signatures consistent with enhanced inhibitory gating within amygdalar circuits. Susceptibility, in contrast, involved reduced dentate gyrus complexity and diminished microstructural flexibility, with a weaker but parallel pattern in the basolateral amygdala. Impaired threat learning was linked to compromised CA1/CA2 integrity and reduced pons connectivity, highlighting hippocampal-brainstem interactions in memory consolidation. Overall, these findings show that resilience emerges from adaptive network reorganization, whereas susceptibility and impaired learning reflect distinct dysfunctions, underscoring individual coping differences even among genetically identical animals.

neuroscience↗

bioRxiv2025

β-Nicotinamide mononucleotide: a novel broad-spectrum CRISPR inhibitor

CRISPR-Cas systems have revolutionized genome editing with their precision and versatility, enabling transformative applications in various fields, especially in the treatment of genetic diseases. However, the clinical translation of this technology is hindered by challenges such as off-target effects and uncontrolled nuclease activity. At the same time, it has the possibility of causing biosecurity risks, underscoring the urgent need for reliable regulatory tools. Existing CRISPR inhibitors, primarily anti-CRISPR protein or exogenously synthesized small molecules, are limited by their specificity or bioavailability and long research period, unable to address the diverse CRISPR nucleases used in research and therapy. Based on the phenomena obtained from various in vitro and cell experiments, combining molecular dynamics simulation and bio - layer interferometry (BLI) analysis, here we report a naturally occurring small-molecule {beta}-nicotinamide mononucleotide (NMN), the first known endogenous metabolite with broad-spectrum inhibitory activity against multiple CRISPR-associated proteins (Cas9, Cas12, and Cas13) through various mechanisms. Our findings establish NMN as a dual-purpose tool, which reduces cell damage caused by gene editing and mitigates risks of unintended genetic modifications in research and clinical settings. This discovery further shortens the distance between basic medicine and translational medicine, providing a new approach for developing endogenous regulatory molecules in genome engineering.

genetics↗

bioRxiv2025

The cryo-EM-delineated mechanism underlying mimicry of CXCR4 agonism enables widespread stem cell neuroprotection in a mouse model of ALS

G-protein coupled receptors (GPCRs) are transmembrane proteins that mediate a range of signaling functions and, therefore, offer targets for a number of therapeutic interventions. Chemokine receptor CXCR4, a GPCR, plays versatile roles in normal and abnormal physiological processes. Synthetic CXCR4 antagonists have been extensively studied and approved for the clinical treatment of cancer and other diseases. We recently elucidated the structural mechanisms underlying CXCR4 antagonism using cryogenic electron microscopy (cryo-EM). CXCR4 agonism by synthetic molecules is an unanticipated therapeutic intervention we recently unveiled. The structural mechanisms underlying those actions remain poorly understood yet could help elucidate a new class of drugs. Here we demonstrate a synthetic dual-moiety strategy that combines simplified agonistic and antagonistic moieties taken from natural agonistic and antagonistic chemokines, respectively, to design de novo peptide mimics of biological function of natural CXCR4 agonist SDF-1. Two peptides so generated, SDV1a and SDVX1 were shown to mimic the action of SDF-1 in activating CXCR4 signaling pathways and cell migration. The structural mechanism of these peptides in the mimicry of CXCR4 agonism was illustrated by cryo-EM structures of CXCR4 bound and activated by the peptides in the presence of G protein, revealing common interactions with the receptor by these peptides in comparison with SDF-1 that explain their close mimicry and conformational changes leading to CXCR4 signal activation. The therapeutic benefit of one of these peptides, SDV1a, was demonstrated in the SOD1G93A mouse model of the spinal motor neuron degenerative disease, amyotrophic lateral sclerosis (ALS) wherein the success of neuroprotective actions of transplanted human neural stem cells (hNSCs) is directly correlated with the expanse of diseased neuroaxis traversed by the donor cells; SDV1a enabled broader neuroprotective coverage while also permitting a much less invasive route of cell administration for extending life. Taken together, these results provide insights into the structural determinants of therapeutic CXCR4 agonism which may allow the design of adjunctive drugs that improve cell-based treatments of central nervous system (CNS) diseases.

neuroscience↗

bioRxiv2025

Amorphous silicon resistors enable smaller pixels in photovoltaic retinal prosthesis

ObjectiveClinical trials of the photovoltaic subretinal prosthesis PRIMA demonstrated feasibility of prosthetic central vision with resolution matching its 100{micro}m pixel size. To improve prosthetic acuity further, pixel size should be decreased. However, there are multiple challenges, one of which is related to accommodating a compact shunt resistor within each pixel that discharges the electrodes between stimulation pulses and helps increase the contrast of the electric field pattern. Unfortunately, standard materials used in integrated circuit resistors do not match the resistivity required for small photovoltaic pixels. Therefore, we used a novel material - doped amorphous silicon (a-Si) and integrated it into photovoltaic arrays with pixel sizes down to 20{micro}m. ApproachTo fit within a few {micro}m2 area of the pixels and provide resistance in the M{Omega} range, the material should have sheet resistance of a few hundred k{Omega}/sq, which translates to resistivity of a few {Omega}*cm. The a-Si layer was deposited by low-pressure chemical vapor deposition (LPCVD) and its resistivity was adjusted by PH3 doping before encapsulating the resistors between SiO2 and SiC for stability in-vivo. Main ResultsHigh-resolution retinal implants with integrated shunt resistors were fabricated with values ranging from 0.75 to 4 M{Omega} on top of the photovoltaic pixels of 55, 40, 30 and 20 {micro}m in size. Photoresponsivity with all pixel sizes was approximately 0.53 A/W, as high as in the arrays with no shunt resistor. The shunts shortened electrodes discharge time, with the average electric potential in electrolyte decreasing by only 21-31% when repetition rate increased from 2 to 30 Hz, as opposed to a 54-55% decrease without a shunt. Similarly, contrast of a Landolt C pattern increased from 16-22% with no shunt to 22-34% with a shunt. Further improvement in contrast is expected with pillar electrodes and local returns within each pixel. SignificanceMiniature shunt resistors in a MOhm range can be fabricated from doped a-Si in a process compatible with manufacturing of photovoltaic arrays. The shunt resistors improved current injection and spatial contrast at video frame rates, without compromising the photoresponsivity. These advances are critical for scaling pixel sizes below 100 {micro}m to improve visual acuity of prosthetic vision.

neuroscience↗