Biology subjects

Ma, K.

Publications and source records attributed to Ma, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Neutrophil Extracellular Trap Deposition Establishes an Immunosuppressive Environment in Non-metastatic Lymph Nodes and Facilitates Heterologous Metastatic Outgrowth

Metastasis accounts for most cancer-related mortality, and regional lymph nodes (LNs) are among the earliest sites of dissemination for many solid tumours. Yet tumour-draining lymph nodes (TDLNs) are also sites of adaptive immune activation, raising the question of how these immune organs become permissive to metastatic growth. We investigated whether neutrophil extracellular traps (NETs), which accumulate in TDLNs before detectable tumour-cell arrival, contribute to immune conditioning of histologically tumour-negative nodes and whether the consequences of this conditioning extend beyond the initiating tumour. Using multiplex immunofluorescence and spatial transcriptomic profiling of TDLNs from 19 patients with gastroesophageal adenocarcinoma, we found that NET positivity in non-metastatic TDLNs was associated with inferior overall survival and a distinct immunoregulatory state characterized by closer NET-Treg spatial relationships, coordinated increases in Treg-associated transcriptional programs, altered immune composition and redistribution of CD8 T cells away from Tregs. NET-positive nodes also showed reduced CD8 naive/stem-like transcription, while greater peri-Treg CD8 redistribution was associated with lower cytotoxic-effector transcription. In vitro, direct NET exposure shifted human T cells toward regulatory and dysfunction-associated phenotypes and impaired tumour-cell control. NET-conditioned Tregs further suppressed CD8 T cell proliferation and granzyme B expression, while depletion of Tregs attenuated NET-associated CD8 apoptosis. In tumour-bearing mice, neutrophil elastase inhibition altered activated Treg distribution across tumour-draining and contralateral LNs. Importantly, prior H59 tumour conditioning increased susceptibility to a subsequent heterologous MC38 metastatic challenge after removal of the initiating tumour; this phenotype was attenuated by TDLN resection and PAD4 deficiency. Adoptive transfer of contralateral-LN T cells from conditioned donors further identified a transferable component of this metastasis-permissive state that was sensitive to NET-directed intervention. These findings support a model in which NET-associated nodal immune conditioning alters Treg and CD8 T cell organization and function before overt nodal metastasis. The consequences of this conditioning extend beyond the draining node and can shape host susceptibility to a subsequent heterologous tumour challenge, broadening the premetastatic-niche concept toward conditioning of the host immune state.

cancer biology↗

bioRxiv2026

High-plex protein imaging across thick tissue by synchronized amplification

High-plex protein imaging is essential for decoding complex tissue organization, yet it remains largely confined to thin sections. Current approaches in millimeter-thick samples suffer from poor signal penetration and depth-dependent, uneven signal amplification. Even with specialized instrumentation to facilitate probe diffusion, iterative millimeter-thick tissue workflows can take more than four days per staining round, and reported eleven-marker experiments extend beyond a month. We introduce Amplification by Cyclic Extension (ACE), a DNA-barcoded, synchronized in situ amplification strategy that uses thermally controlled cyclic extension to coordinate DNA concatemer growth across tissue depths. By synchronously activating and coordinating reaction progression throughout the sample, ACE enables controlled, uniform signal amplification across tissue depths. Using ACE, we demonstrate 63-plex protein and RNA imaging in thin sections, 22-plex protein imaging in 200 m mouse brain sections, and 16-plex protein imaging in 1 mm-thick brain tissue encompassing over three million cells. For millimeter-thick tissues, ACE reduces per-round target-switching time from multiple days to less than eight hours, shifting volumetric high-plex protein imaging from months to days. Together, these results establish ACE as a synchronized amplification strategy that enables scalable high-plex protein imaging in thick tissues.

bioengineering↗

bioRxiv2026

RORγ Inverse Agonism Redirects Tumour-Conditioned Emergency Myelopoiesis and Attenuates Established Tumour Progression

Systemic inflammation is associated with poor outcomes in gastroesophageal adenocarcinoma (GEA), but how it contributes to disease progression remains unclear. We investigated retinoic acid receptor-related orphan receptor gamma (ROR{gamma}) as a regulator of tumour-conditioned myeloid responses. In treatment-naive GEA patients, elevated circulating neutrophil-to-lymphocyte ratio (cNLR) tracked with circulating ROR{gamma} positive neutrophils and tumoural spatial organization of ROR{gamma} positive myeloid cells, rather than neutrophil abundance. In syngeneic tumour models, pharmacologic ROR{gamma} inverse agonism altered marrow progenitor composition before tumour-growth divergence and remodeled myeloid organization across bone marrow, tumour and lung despite no endpoint change in circulating neutrophil proportions, which did not capture the earlier marrow response or subsequent tumour trajectory. ROR{gamma} perturbation enhanced longitudinal tumour control with PD-L1 blockade, whereas effects on metastatic establishment depended on tumour conditioning and treatment timing. These findings identify ROR{gamma} associated myeloid programming as a therapeutically tractable, context-dependent regulator linking systemic inflammation, hematopoiesis, tissue immune organization, and cancer progression.

cancer biology↗

bioRxiv2026

Substrate recognition and ion coupling mechanism of the human VIAAT

Inhibitory neurotransmission, essential for neural circuit homeostasis and proper neurological function, depends on the efficient sequestration of {gamma}-aminobutyric acid (GABA) and glycine into synaptic vesicles. This critical process is mediated exclusively by the vesicular inhibitory amino acid transporter (VIAAT). Despite extensive biochemical and physiological investigation, the molecular mechanism governing VIAAT-mediated transport has remained incompletely understood. Here, we determined structures of human VIAAT in multiple functional states, including apo, GABA-bound, and glycine-bound states, as well as apo state in chloride-free condition. VIAAT adopts a classical LeuT-fold and we elucidated how its large, electronegative binding pocket accommodates both GABA and glycine. Moreover, we resolved two previously unidentified chloride-binding sites. Through integrative molecular dynamics simulations and functional mutagenesis, our results support roles for chloride and the conserved residue E213 in substrate binding and proton-coupled transport. Together, our findings establish a structural framework for VIAAT-mediated inhibitory neurotransmitter transport that illuminates the molecular basis of inhibitory synaptic transmission and provides a foundation for understanding VIAAT dysfunction in epilepsy and related neurodevelopmental disorders.

neuroscience↗

bioRxiv2026

A Measurable Systemic Immune Phenotype Links Circulating Myeloid Dysfunction to Tumour Spatial Organization in Gastroesophageal Adenocarcinoma

Background: Both static and longitudinal measures of circulating neutrophil-to-lymphocyte ratio (cNLR) are prognostic markers across solid malignancies, including gastroesophageal adenocarcinoma (GEA). Despite this consistency, cNLR remains poorly integrated into clinical decision-making and is generally regarded as a nonspecific inflammatory or disease-burden signal rather than a defined biological state. Analysis of a large, prospectively assembled GEA cohort showed that cNLR was only weakly associated with tumour burden or pathological response, yet both baseline and postoperative cNLR independently predicted outcome. Methods: These observations prompted a retrospective biological investigation of what host biology cNLR captures. Using available clinically linked biospecimens, we performed multiscale analyses across complementary patient subsets encompassing peripheral-blood immune function and soluble signalling, tumour single-cell transcriptional programmes, and spatial myeloid organization within tissue. Results: High baseline cNLR was associated with reduced circulating cytotoxic and immune-trafficking mediators, elevated angiogenesis-associated factors, neutrophil-mediated suppression of lymphocyte proliferation, impaired tumour-cell killing, and enhanced spontaneous neutrophil extracellular trap formation. Single-cell profiling identified coordinated transcriptional differences across tumour compartments, including innate, cytokine and myeloid programmes. Spatial profiling showed that myeloid abundance and organization varied across anatomical compartments; greater tumour-periphery PDL1 positive myeloid clustering was associated with inferior recurrence-free survival. Baseline cNLR showed little relationship with static myeloid abundance, whereas pretreatment cNLR dynamics were associated with altered cross-compartment spatial relationships between CD8 positive cells and myeloid cells. Notably, higher early postoperative cNLR was associated with greater PDL1 positive myeloid clustering at the tumour periphery, linking the spatial architecture of the resected tumour with a systemic myeloid phenotype persisting after surgery. Conclusions: The data identify a prognostic, multilevel myeloid-associated host phenotype in GEA that is incompletely explained by tumour burden. Integrating systemic immune function, tumour single cell transcriptomics and spatial myeloid organization demonstrates that these biological domains provide distinct, yet convergent views of the host immune phenotype captured by cNLR. These findings establish a biological framework for the clinical utility of cNLR and highlight myeloid-associated immune processes as promising targets for therapeutic intervention.

cancer biology↗

bioRxiv2026

Functional niche attributes shape species interaction roles in ecological networks

Identifying how species interact in ecological networks is key to understanding species' contributions to ecosystem functioning, but can be difficult to establish in species-rich communities. Functional niches, which capture broader ecological strategies, are often easier to assess and could help approximate species' interaction roles. We tested this by integrating species interaction and leaf functional trait data of tree species and leaf-associated interaction types from a large-scale forest biodiversity experiment. We found that identity, variability, and similarities of functional niches shaped corresponding aspects of interaction roles. Interestingly, however, this association inversed in the case of functional niche variability, which decreased instead of increased the variability of species interactions. This suggests a potential trade-off between processes that determine variability in functional and interaction space. Furthermore, effects were not constrained within aspects, with similarities of interactions being particularly responsive to most tested niche aspects, indicating that interaction-based competition among plants is particularly sensitive to functional niche differences. Moreover, many effects of functional niches depended on tree species biomass and tree species richness, highlighting the importance of the larger ecological context for determining species interaction roles. Together, our findings show that species' interaction roles, while clearly altered by, are not simply a consequence of functional niches. Instead, interaction roles integrate multiple aspects of functional niches depending on species performances and community composition and can therefore be crucial for anticipating ecosystem change.

ecology↗

bioRxiv2026

CLEAR-ST: Physics-informed probabilistic decontamination of spatial transcriptomics by modeling mRNA lateral diffusion

Spatial transcriptomics is a rapidly evolving technology that allows for the measurement of gene expression in a spatially resolved manner. However, one technical problem that occurs for many sequencing-based spatial transcriptomics platforms is the presence of mRNA lateral diffusion, where mRNA from one spot can bind to probes in another spot, leading to contamination and inaccurate gene expression measurements. In Visium-like assays, this artifact is often visible as structured out-of-tissue signal and boundary-associated expression halos, yet its magnitude, spatial decay, and directional bias vary substantially across samples. Here, we present CLEAR-ST, a physics-informed probabilistic framework for correcting diffusion-like contamination in spatial transcriptomics data. CLEAR-ST infers a latent clean expression field using a denoising autoencoder and links it to the observed counts through a graph-Laplacian forward contamination model with learnable diffusion parameters, finally evaluated with a selectable count likelihood. We first conducted a comprehensive comparison between 10X official and independently generated Visium samples, demonstrating that out-of-tissue count profiles are highly related to nearby in-tissue expression, more concentrated near tissue boundaries, and diffusion directions across genes are likely coherent. Across real samples with varying contamination burden, CLEAR-ST improved spatial domain recovery, increased gene-level spatial autocorrelation, and enhanced the biological specificity of downstream analyses such as marker gene discovery, pathway identification and cell type deconvolution. Compared to benchmark methods, CLEAR-ST showed consistent gains in clustering quality and concordance with manual annotations. Together, CLEAR-ST provides an interpretable and practical approach for diffusion-aware correction of capture-based spatial transcriptomics data.

bioinformatics↗

bioRxiv2026

Comprehensive Mapping of SGCA Variant Effects Reveals Domain-Specific Constraints Relevant to Sarcoglycanopathies

Pathogenic variants in SGCA, encoding -sarcoglycan, cause an autosomal recessive limb-girdle muscular dystrophy, LGMDR3/2D, yet clinical interpretation of SGCA variants remains challenging due to the high prevalence of rare missense variants. -sarcoglycan is an essential component of the sarcoglycan complex at the muscle cell membrane, and pathogenic variants frequently impair its membrane localization. Here, we systematically assess the effects of all possible single-nucleotide variants across the SGCA coding sequence using a saturation mutagenesis-based experimental assay that quantifies -sarcoglycan surface expression. We generate a comprehensive functional atlas that distinguishes tolerated and damaging variants, aligning with independent genetic and clinical evidence, and reveals domain-specific properties of the cytoplasmic region, in which C-terminal truncating variants retain membrane localization, suggesting possible pathogenic mechanisms beyond impaired trafficking. This work provides a scalable functional framework to support genetic diagnosis and variant interpretation in sarcoglycanopathies. Graphical AbstractSchematic overview of saturation mutagenesis-based functional mapping of SGCA. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/740214v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@19be841org.highwire.dtl.DTLVardef@ad2e49org.highwire.dtl.DTLVardef@1b9cb61org.highwire.dtl.DTLVardef@d77317_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2026

FMRP prevents Me31B/DDX6-associated repression of long neurodevelopmental mRNAs

Long, dosage-sensitive mRNAs encoding neurodevelopmental regulators are selectively dependent on fragile X messenger ribonucleoprotein (FMRP) for efficient translation across animal systems, but the mechanism underlying this length-dependent requirement remains unclear. Here, we show that FMRP maintains translation of long target mRNAs by preventing their inappropriate sequestration into a Me31B/DDX6-dependent P-body repression pathway. In Drosophila oocytes, loss of FMRP caused target mRNAs, but not bulk polyadenylated RNA, to accumulate in Me31B-marked P-bodies. Improved individual-nucleotide resolution crosslinking and immunoprecipitation (iiCLIP) revealed that FMRP and Me31B co-occupy many long coding sequences, suggesting that FMRP targets are intrinsically vulnerable to repressive Me31B-associated machinery. A screen targeting [~]120 candidate genes, followed by proteomic analysis, identified an FMRP-associated ribonucleoprotein (RNP) assembly containing the stress granule-linked proteins Rin/G3BP, Lig/UBAP2L, and Capr/Caprin1. These factors supported translation or localization of distinct FMRP target subsets. Finally, inhibition of Me31B-dependent repressive complex assembly restored translation of the majority of FMRP targets in FMRP-deficient oocytes, supporting a model in which translational failure results from excessive repression. Together, these findings reveal a cytoplasmic RNP assembly that safeguards mRNAs by antagonizing promiscuous P-body repression and provide a mechanistic explanation for the selective vulnerability of long neurodevelopmental transcripts to FMRP loss.

molecular biology↗

bioRxiv2026

Noncanonical Circular RNAs and Potential Functions

Circular RNAs (circRNAs) are ubiquitous in eukaryotes; dysregulated circRNA expression is linked to diseases, including lung cancer. In contrast to canonical circRNAs arising from exon-intron boundaries, noncanonical circRNAs originating within exonic, intronic, and intergenic regions have typically been dismissed as transcriptional noise or technical artifacts. To explore circRNA diversity and appreciate their functions, we developed an algorithm to identify both canonical and noncanonical circRNAs without relying on genome annotation, enabling the identification of circRNAs of all types and in newly sequenced or poorly annotated species. Results from lung cancer cells revealed that noncanonical circRNAs constituted over two-thirds of the circRNA population and were expressed more abundantly than canonical circRNAs, and genes with fewer and shorter exons were hotspots for noncanonical circRNA and circRNA isoform production. Further analyses showed that many noncanonical circRNAs were indeed endogenous circRNAs transcribed within cells rather than experimental artifacts, were potentially translated into proteins or peptides, and were conserved across species. Moreover, we validated 65 noncanonical circRNAs in NCI-H23 cells using multiple bioassays and demonstrated that both exonic and intergenic noncanonical circRNAs influenced cell viability. CircRNA profiles in tumor and tumor-adjacent tissues of lung cancer patients revealed tissue-specific expression and differentially expressed canonical and noncanonical circRNAs from cognate genes involved in cancer-related pathways, indicating their potential clinical relevance. This study confirmed the authenticity of noncanonical circRNAs and provided the first experimental evidence that noncanonical circRNAs influence cancer cell phenotypes. These findings broaden our understanding of circRNA biology, highlighting their widespread genomic distribution, diverse functions, and potential clinical relevance.

molecular biology↗

bioRxiv2026

High glucose confers senescence resistance via GLUT1 epigenetic rewiring to blunt immunotherapy responses in esophageal squamous cell carcinoma

Therapeutic resistance and undefined predictive biomarkers severely hinder the clinical popularization of immunotherapy in esophageal squamous cell carcinoma (ESCC). Herein, we identify the glucose transporter 1 (GLUT1) as a critical determinant of immunotherapy resistance. Elevated expression of GLUT1 correlates with poor immunotherapy response and unfavorable prognosis in ESCC patients. GLUT1 deletion or inhibition enhances CD8 T cell infiltration and cytotoxicity, and sensitizes ESCC tumors to anti-PD-1 (-PD1) therapy. Importantly, dietary glucose restriction exhibits equivalent antitumor efficacy to GLUT1 inhibition when combined with -PD1. Mechanistically, GLUT1 establishes a positive feedback loop with HAT1 and FOXM1, which epigenetically remodels chromatin accessibility to suppress tumor cell senescence, thereby impeding CD8 T cell-mediated antitumor immunity. Our findings highlight GLUT1 as a predictive biomarker of immunotherapy resistance and suggest dietary glucose restriction as a viable strategy to potentiate immunotherapy efficacy in ESCC. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=188 HEIGHT=200 SRC="FIGDIR/small/738372v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@c2c5d5org.highwire.dtl.DTLVardef@14a34c7org.highwire.dtl.DTLVardef@cf05e4org.highwire.dtl.DTLVardef@18bc354_HPS_FORMAT_FIGEXP M_FIG C_FIG SHORT SUMMARYDong et al. identify glucose transporter 1 (GLUT1) as a predictor of poor response to immunotherapy in esophageal squamous cell carcinoma. GLUT1 promotes immune evasion by forming a positive feedback loop with the HAT1/FOXM1 anti-senescence axis, thereby epigenetically remodeling chromatin accessibility. GLUT1 inhibition or dietary glucose restriction restores CD8 T-cell-mediated antitumor immunity and improves the efficacy of anti-PD-1 therapy in preclinical models.

cancer biology↗

bioRxiv2026

Multitrophic interaction networks mediate biodiversity effects on ecosystem multifunctionality

Biodiversity loss threatens the multifunctionality of ecosystems on which human well-being ultimately depends. Changes in multitrophic species interactions may be key to explaining the ecological consequences of biodiversity loss, but research explicitly linking species interactions and ecosystem multifunctionality remains rare. To assess interaction-mediated biodiversity effects and underlying mechanisms, characterizing the structure of species interaction networks is invaluable. Using comprehensive species interaction and ecosystem functioning data from a large-scale tree biodiversity experiment, we find consistent effects of the structure of species interaction networks on ecosystem multifunctionality across multiple types of antagonistic and mutualistic interactions. While positive effects of network size align with expected positive effects of multitrophic species diversity, positive effects of niche overlap among interacting species and negative effects of highly connected species (i.e. high linkage density) reveal additional, interaction-mediated drivers of multifunctionality. Specifically, the effects of niche overlap suggest benefits of functionally similar species, and the effects of linkage density underscore the importance of specialized interactions in promoting ecosystem multifunctionality. These findings emphasize that to effectively safeguard ecosystem service provisioning, ecosystem management and biodiversity conservation not only need to account for biodiversity changes at multiple trophic levels, but also explicitly for how species interact among each other.

ecology↗

bioRxiv2026

Circadian Clock Control of Muscle Stem Cells Through Temporal Coordination of Notch and Wnt Signaling

The circadian clock regulates stem cell responses during tissue remodeling and repair. In skeletal muscle regeneration, successful regenerative myogenesis requires a temporally coordinated transition from Notch- to Wnt-driven signaling. However, the mechanisms governing this timing event remain poorly understood. Here, we show that circadian clock activity marks the cycling population of regeneration-activated myogenic progenitors that is induced in concert with Notch signaling. We identify key components of the Notch pathway as direct circadian clock targets and demonstrate that the clock coordinates Notch and Wnt signaling to drive myogenic progression. Genetic activation of the clock in satellite cells, as well as pharmacological clock stimulation, enhanced both proliferative expansion and subsequent differentiation of myogenic progenitors during regeneration. These effects were mediated by early activation of Notch signaling followed by increased Wnt pathway activity at later regenerative stages. Notably, both clock-dependent mechanisms remained functional in dystrophin-deficient mouse muscle and human myoblasts. Furthermore, clock-activating compounds enhanced regenerative myogenesis following acute injury and improved regeneration in dystrophic muscle. Collectively, these findings establish the circadian clock as a temporal regulator of regenerative signaling programs that orchestrate muscle repair with potential for targeted interventions.

cell biology↗

bioRxiv2026

Novel mouse models for perianal fistulizing Crohns disease reveal therapeutic value of interferon-gamma antagonists

Background and AimsPerianal fistulizing Crohns disease (PFCD) is a challenging complication with poorly understood pathogenesis and limited treatment options, largely due to the lack of clinically relevant animal models. Interferon-gamma (IFN-{gamma}) signaling is hyperactivated in human PFCD. We aimed to establish mouse models recapitulating human PFCD and to evaluate IFN-{gamma} as a new therapeutic target. MethodsPerianal fistulas were established in three mouse models with concurrent Crohns disease-like intestinal inflammation: wild-type (WT) mice with 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced proctocolitis, Il10-/-mice, and TNF{Delta}69AU/+ mice. A modified MAGNIFI-CD index was developed for longitudinal fistula assessment in mice. Transcriptomic analysis and flow cytometry were conducted on mouse fistula tissue. Re-analysis of single-cell and spatial transcriptomics of human PFCD tissues was performed. Therapeutic benefits of anti-TNF-, upadacitinib, and IFN-{gamma} pathway antagonists were evaluated in the PFCD models. ResultsAll three PFCD models sustained chronic perianal fistula tracts for at least 5 weeks after wire removal. All three models closely recapitulate the pathological and molecular features of PFCD in patients, as confirmed by clinical examination, MRI, histopathology, immunostaining, flow cytometry, and transcriptomics. IFN-{gamma} signaling emerged as a central and conserved pathway across all three mouse models and human PFCD. Targeting of the IFN-{gamma} pathway promptly improved fistula healing with mitigation of IFN-{gamma} signaling, inflammation, and epithelial-to-mesenchymal transition (EMT). Moreover, combining IFN-{gamma} and TNF- blockade demonstrated augmented therapeutic efficacy compared to anti-TNF- monotherapy. ConclusionsThese PFCD mouse models and imaging tools provide first reliable and clinically relevant platforms for mechanistic studies and therapeutic evaluation. IFN-{gamma} signaling represents a potential therapeutic target warranting clinical investigation.

immunology↗

bioRxiv2026

The widely used eGFP sequence produces an unintended protein product

Plasmids are widely used for gene expression, yet their coding potential beyond the intended coding sequence (CDS) is often poorly characterized. Here, we explored putative hidden open reading frames (hidden ORFs) embedded within non-canonical reading frames of plasmid sequences through a computational workflow for their identification. Using enhanced green fluorescent protein (eGFP) as a target gene, we observed unexpectedly uninterrupted ORFs in both the +2 coding frame and the reverse frame. Immunoblotting detected stable expression of the +2 frame-derived protein, but not the reverse-frame ORF. Motivated by these observations, we developed a computational pipeline and analyzed 6,308 eGFP-containing plasmids, identifying putative hidden ORFs in approximately 6% of constructs. Approximately 94% of hidden ORFs occurred in the +2 frame, with the remainder occurring in the reverse frame. The same analytical pipeline, if utilized for plasmids beyond eGFP plasmids, can contribute to avoiding unintended outcomes, in applications such as gene replacement therapy.

molecular biology↗

bioRxiv2026

Therapeutic targeting of fibrin-microglia interactions ameliorates Alzheimer disease-related hyperexcitability and brain network dysfunction

Brain network dysfunction--including hyperexcitability, altered oscillations, and sleep disruption--is prominent in Alzheimers disease (AD), but the contribution of vascular-neuroimmune processes to these alterations remains unclear. Here, we blocked the pro-inflammatory interaction of the blood protein fibrin with microglia using genetic (Fgg{gamma}390-396A mice) and antibody-based (5B8 and THN392) strategies to test its role in AD-related network dysfunction. The 5xFAD model of AD exhibited network hyperexcitability associated with oscillatory slowing, sleep states, and disrupted sleep-circadian rhythms. These deficits were largely attenuated by blocking fibrin-microglia interactions in 5xFAD;Fgg{gamma}390-396A mice. Notably, pharmacological interventions after disease onset with both anti-fibrin antibodies similarly attenuated these AD-related network deficits and behavioral abnormalities. We conclude that vascular-neuroimmune processes driven by fibrin-microglia interactions promote AD-related network dysfunction and that targeting the fibrin-microglia axis--currently under clinical evaluation with the humanized antibody THN391-- represents a promising therapeutic strategy for AD. There is a companion manuscript submitted to bioRxiv (Yan et al., 2026).110 HIGHLIGHTSO_LIFibrin promotes AD-related network hyperexcitability and oscillatory slowing in 5xFAD mice C_LIO_LIFibrin promotes AD-related disruption of sleep and circadian rhythms in 5xFAD mice C_LIO_LIGenetic blocking of fibrin-microglia interactions rescues AD-related brain network dysfunction C_LIO_LIAnti-fibrin antibodies (5B8 and THN392) show acute and chronic therapeutic benefit C_LI

neuroscience↗

bioRxiv2026

Quercetin and Fisetin activate circadian clock via RORα and inhibit adipocyte growth

The circadian clock maintains temporal control of metabolic processes and exerts a key role in adipocyte development. Discovery of clock-modulatory compounds may provide new avenues for metabolic disease therapy. Here we report the identification of flavonoid compounds, Quercetin and Fisetin, as clock-activating molecules with direct inhibitory action on adipogenesis and adipocyte lipid metabolism. Quercetin and Fisetin displayed robust ROR agonism that promoted clock oscillation with induction of clock genes. Treating preadipocytes with these compounds blocked their adipogenic differentiation. In mature adipocytes, Quercetin and Fisetin suppressed lipid accumulation by inhibiting lipogenic enzymes. Furthermore, activation of ROR by a synthetic agonist or ectopic expression were sufficient to inhibit adipogenesis. In mice treated with Quercetin or Fisetin, ROR was markedly induced in adipose depots with strong suppression of the adipogenic and lipogenic programs. While quercetin significantly attenuated lipid storage in adipose tissue in vivo accompanied with lowering of free fatty acids and improved insulin sensitivity, fisetin displayed a less robust effect with differential regulation of lipolytic pathway. Collectively, these findings uncovered the clock-activating properties of quercetin and fisetin that prevent adipocyte maturation and hypertrophy to limit adipose tissue expansion. These actions contribute, at least in part, to their beneficial effects on metabolic disorders.

cell biology↗

bioRxiv2026

ExMODE: A Multi-Omics Repository for Extremophile Adaptation and Bioprospecting

Extreme environments, though hostile to most life forms, host specialized extremophile communities that have redefined biological cognition and emerged as vital biotechnological resources, with their unique adaptive traits and bioactive molecules driving advances in multiple scientific and industrial fields. However, research on extremophiles is hindered by limitations in culture-based methods, fragmented multi-omics data with non-uniform annotation standards across repositories, the lack of cross-extreme comparative research in existing resources, and the singularity of data dimensionality that neglects key structural information, all of which restrict the functional interpretation of extremophile microbes and the exploitation of their bioprospecting potential. To tackle these challenges, we developed ExMODE (https://db.genomics.cn/exmode/), a comprehensive multi-omics database platform dedicated to extremophiles. It centrally integrates multi-omics data from diverse extreme habitats with a standardized annotation framework, resolving data fragmentation and enabling systematic cross-environment comparative analyses to elucidate extremophile adaptive mechanisms. Moreover, ExMODE aggregates multi-dimensional datasets including genes, genomes, secondary metabolite sequences and protein structures, overcoming the constraints of single-dimensional data and significantly improving the efficiency of biotechnological resource discovery from extreme microorganisms.

microbiology↗