Biology subjects

Li, X.

Publications and source records attributed to Li, X..

At least 109 records · Page 6Linked to original sources

bioRxiv2026

Automating scientific annotations for open transcriptomic profiles via multi-stage agents

Public transcriptomic repositories contain millions of samples, yet their large-scale reuse is hindered by heterogeneous and inconsistently reported metadata. In the Gene Expression Omnibus (GEO), key biological information is often distributed across study- and sample-level records, requiring context-dependent interpretation. Here we present GEOMeta, a large language model (LLM)-based multi-stage workflow with task-specialized agents for automated GEO metadata curation. The pipeline separates metadata retrieval, task-specific information extraction, field standardization, ontology mapping and quality control. Using GEOMeta, we generated standardized annotations for approximately 600,000 human bulk RNA-seq samples. To demonstrate its utility, we benchmarked transcriptome representation models for predicting sex, age, tissue and disease from transcriptome embeddings. We further prospectively annotated newly submitted GEO studies and evaluated 22 frontier LLMs. Recent open-source Flash models achieved annotation quality comparable to leading reasoning models while reducing costs by an order of magnitude. GEOMeta provides a scalable resource and reproducible framework for metadata curation.

bioinformatics↗

bioRxiv2026

Endothelial ANGPT2 insufficiency impairs retinal vascularization with ROP-like neovascular tufts

ANGPT2 is widely recognized as a critical regulator of pathological neovascularization. By analyzing scRNA-seq data from neonatal retinas, we demonstrate that Angpt2 transcripts are highly enriched in tip cells relative to other endothelial subtypes, where Angpt1/4 expression is absent. However, mechanisms underlying ANGPT2 function at angiogenic fronts remain inadequately understood. Here, we show that endothelial Angpt2 deletion severely disrupted retinal vascularization, characterized by neovascular tufts and micro-hemorrhage. Similar angiogenic defects also occurred in the brain, but were less evident in other tissues examined. Mechanistically, ANGPT2 insufficiency attenuated retinal tip cell invasion with aberrant mural cell coverage, compromising sprouting into non-vascularized tissues. Retinal RNA-seq analysis revealed that transcripts associated with endothelial migration and junction assembly were reduced in Angpt2 mutants compared to littermate controls, while upregulated genes were enriched in hypoxia-responsive pathways and mural cell development. Notably, abnormal mural-tip cell associations were detected within 48 hours post-Angpt2 deletion, displaying also a hypoxia-driven transcriptomic signature. These closely resemble the vascular pathologies observed in human retinopathy of prematurity. In contrast, Angpt1 insufficiency or Angpt4 deficiency primarily affected venous morphogenesis. Collectively, our findings imply that ANGPT2 is essential for driving tip cell invasion during sprouting angiogenesis, and that its insufficiency triggers hypoxia-driven vascular anomalies.

developmental biology↗

bioRxiv2026

Integrated Post-Translational Modification (PTM) Proteomics Reveals Early Redox and Mitochondrial Remodeling Following Ref-1 Inhibition in Pancreatic Cancer

BackgroundApurinic/apyrimidinic endonuclease 1/redox factor-1 (Ref-1/APE1) is a central regulator of redox-dependent transcriptional signaling that promotes pancreatic ductal adenocarcinoma (PDAC) progression, therapeutic resistance, and metabolic adaptation. While pharmacologic inhibition of Ref-1 suppresses tumor growth and alters cellular metabolism, immediate molecular events linking Ref-1 inhibition to downstream cellular adaptation remain poorly understood. We therefore sought to characterize proteome-wide signaling responses induced by second-generation Ref-1 redox inhibitor, APX2014. MethodsWe applied an integrated multiplexed proteomics workflow to simultaneously quantify global protein abundance together with cysteine oxidation, phosphorylation, and lysine acetylation in Pa03C PDAC cells following acute treatment (30-120 min) with selective Ref-1 redox inhibitor APX2014. Differential post-translational modification (PTM) analysis, pathway enrichment, structural mapping of regulated sites, and functional mitochondrial substrate utilization assays were performed to define early signaling responses. ResultsAPX2014 induced rapid and extensive remodeling of PTM landscape while producing minimal changes in global protein abundance. Cysteine oxidation represented the earliest and most sustained response, accompanied by widespread phosphorylation and delayed lysine acetylation. Integrated pathway analyses identified mitochondrial translation, respiratory electron transport, TCA cycle metabolism, and mitochondrial redox homeostasis as the earliest and most consistently regulated processes. Functional mitochondrial assays confirmed impaired utilization of TCA cycle substrates following APX2014 treatment. Coordinated PTM remodeling was observed on Ref-1-associated signaling proteins, including NF-{kappa}B1 and p53, revealing simultaneous regulation of oxidation, phosphorylation, and acetylation within functionally important domains. Early redox-sensitive protein networks were also associated with subsequent disruption of mitotic organization. ConclusionsIntegrated multi-PTM proteomics reveals that pharmacologic Ref-1 redox inhibition rapidly rewires regulatory signaling networks before detectable changes in protein abundance. Our findings identify mitochondrial redox remodeling as an early consequence of Ref-1 inhibition, providing systems-level insight into how Ref-1-targeted therapies disrupt metabolic and stress-adaptive programs in pancreatic cancer. This work establishes a framework for understanding the molecular basis of Ref-1-directed therapeutics and highlights integrated PTM profiling as a powerful strategy for defining early drug response mechanisms. These findings provide a strong translational rationale for advancing next-generation Ref-1 redox inhibitors such as APX2014, developed from the first-in-class inhibitor APX3330 currently in clinical trials, and underscore the broader therapeutic potential of targeting Ref-1 redox signaling in pancreatic cancer.

cancer biology↗

bioRxiv2026

AI4Loop: an Artificial Intelligence Framework Reveals Increased 3D Chromatin Interactions and Therapeutic Vulnerabilities across 12,000 Cancer Samples

Three-dimensional chromatin interactions shape gene regulation, but their large-scale analysis remains limited by the cost and complexity of experimental assays. Here we present AI4Loop, a deep learning framework that infers genome-wide gene-centered chromatin interaction networks directly from RNA-seq data. Across multiple cell types, AI4Loop recovered interaction patterns consistent with clinical samples and orthogonal chromatin conformation datasets. Applied to 12,347 transcriptomes from 32 cancer types, AI4Loop revealed pervasive increases in gene-centered chromatin interactions in tumors, particularly at oncogene-associated loci. These inferred interaction networks outperformed gene expression alone in cancer classification. Integration with more than 50,000 drug-treated transcriptomes identified compounds predicted to reverse cancer-associated interaction gains. Hi-C experiments confirmed that the oxazolidinone antibiotics eperezolid and radezolid reduce breast cancer-gain chromatin interactions. Together, these results identify increased gene-centered chromatin interactions as a pan-cancer feature and provide a scalable strategy for linking 3D genome dysregulation to therapeutic vulnerabilities.

bioinformatics↗

bioRxiv2026

De novo design of autocatalytically forming intra- and intermolecular isopeptide bonds to construct rigid covalent protein assemblies

Isopeptide bonds are amide bonds between amino acid side chains that can form autocatalytically, notably in the pili of Gram-positive bacteria. Here, we design de novo proteins that form both intramolecular and intermolecular isopeptide bonds entirely autocatalytically. We report over 50 designs that form isopeptide bonds, validated by mass spectrometry and 5 crystal structures. We redesign these constructs as split proteins that form a covalent intermolecular isopeptide crosslink when combined. These split designs are orthogonal to the existing isopeptide-based SpyTag/Catcher system, and their formation can be regulated by temperature, providing control over the timing of crosslinking in protein assemblies. We extend these designs to create rigid domain crosslinks that enable the construction of large well ordered symmetric rings of up to 215 kDa that are irreversibly covalently crosslinked by multiple isopeptide bonds into a single molecule. Our results provide insight into the determinants of isopeptide bond formation, considerably expand the set of isopeptide bond crosslinking systems, and establish a framework to construct fully covalent rigid protein assemblies.

biophysics↗

bioRxiv2026

Spatial Logic Reconciles Gene-signature Methods in Triple Negative Breast Cancer

Triple-Negative Breast Cancer (TNBC) presents a significant clinical challenge due to its heterogeneity and lack of targeted treatment options, with chemotherapy and immunotherapy combinations currently serving as the main therapeutic strategy. Efforts to address TNBC heterogeneity have largely focused on classifying intrinsic cancer subtypes based on differential tumor mRNA expression, a strategy that has proven effective in hormone receptor-positive breast cancers but has yet to yield a clinically useful predictor of survival or treatment response in TNBC. We hypothesize that both the intrinsic characteristics of TNBC and the surrounding immune microenvironment influence treatment outcomes and that immune cell infiltration affects TNBC subtype classification and response variability. To explore this hypothesis, we compared the predictive and prognostic capabilities of cancer subtype-based (TNBC-type) gene signatures and immune cell deconvolution methods (CIBERSORT) within the same TNBC datasets. We found that immune cell abundance outperformed TNBC subtype-signatures and multicellular immune cell aggregates showed the highest performance of all. More specifically, aggregate immune cells associated with tertiary lymphoid structures and tumor associated macrophages/monocytes demonstrated statistically significant predictive value. These findings were confirmed in an independent cohort of 67 TNBC patients treated with neoadjuvant chemotherapy. Further, single-cell RNA sequencing analysis revealed that the predictive power of cancer-subtype could be partially explained by immune- and stromal features. Examination of single-cell resolution spatial transcriptomic data confirmed presence of TLS-like, TAM- and cancer-stromal niches within TNBC biopsy samples that were associated with treatment response. Overall, our results highlight that immune cell aggregates, which capture the spatial organization of the TME, outperform cell-type specific gene signatures in predicting TNBC outcomes. Our novel approach provides a robust framework for interpreting spatial relationships in bulk RNA-seq data, offering a pathway for reconciling past data with current advancements in spatial profiling technologies. This work paves the way for future studies to leverage the multi-cellular complexity of TNBC, enhancing diagnostic precision and facilitating the development of therapies that strategically modulate the tumor microenvironment for improved anti-cancer responses.

cancer biology↗

bioRxiv2026

African Green Monkey Cerebrospinal Fluid miRNome Captures Conserved miRNAs Relevant to Human Neurodegenerative Disease

BackgroundThe African green monkey (AGM) is increasingly used as a model for early-stage Alzheimers disease (AD), with cerebrospinal fluid (CSF) targeted for biomarker discovery and longitudinal disease monitoring of shifts in the central nervous system. MicroRNAs (miRNAs) are particularly informative indicators of early neuropathological change. Despite the complementary value of an early-stage disease model and a molecular marker capable of capturing early change, the miRNA composition (miRNome) of AGM remains undefined. We established the AGM CSF miRNome from antemortem samples using miRNA sequencing and a qRT-PCR-based array. We also developed a hierarchical annotation pipeline to classify miRNAs as either family-conserved or unclassified and to assess sequence alignment across humans and other species. ResultsWe used untargeted miRNA sequencing to characterize the AGM CSF miRNome and identified 205 miRNAs that could be classified into three family-conserved categories: canonical, noncanonical, and 3'-terminal variants. Of these, 150 were also detected using a human-targeted qRT-PCR array, providing independent support for the sequence-derived miRNome. Sequencing abundance and qRT-PCR array Ct values showed significant cross-platform concordance overall, although concordance was lower for 3'-terminal isomiRs than for canonical miRNAs. Comparison with human GTEx tissue-expression data indicated that several human homologs of AGM CSF miRNAs exhibited brain-preferential expression. Notably, predicted targets of many of these miRNAs were enriched for pathways implicated in neurodegenerative disease. Finally, we identified 20 unclassified candidates that could not be assigned to established miRNA families, two of which we propose as putatively novel miRNAs. ConclusionThe AGM CSF miRNome is substantially conserved with the human miRNome but also contains 3'-terminal isomiRs and unclassified miRNA candidates. AGM CSF contains miRNAs homologous to human miRNAs associated with AD and other neuropathologies, highlighting the translational potential of this model. However, our study also reveals challenges related to species-specific sequence variation and reduced cross-platform concordance for isomiRs. Thus, comparative studies will be needed to validate the functional and biomarker relevance of these miRNAs across species. More generally, this initial miRNome provides a reference resource for future studies of miRNAs in AGM across disease-related, physiological, experimental, and evolutionary contexts.

genomics↗

bioRxiv2026

Functional and evolutionary insights into the emerging tet(X4)-carrying non-O1/O139 Vibrio cholerae from retail pork

The tigecycline resistance gene tet(X4) is prevalent in Enterobacteriaceae, particularly in Escherichia coli. To our knowledge, no study has reported the dissemination dynamics of tet(X4) in Vibrio spp. Herein, we isolated and characterized a first tet(X4)-positive non-O1/O139 Vibrio cholerae isolate from retail pork. Genomic sequencing identified a novel tet(X4) variant in the V. cholerae chromosome, harboring a G568A nucleotide substitution that resulted in an Ala190Thr (A190T) amino acid substitution in Tet(X4). While this Tet(X4)-A190T variant conferred lower phenotypic resistance to tetracyclines (including tigecycline) than the wild-type Tet(X4), its overall catalytic efficiency against these antibiotics was paradoxically enhanced despite a reduced substrate affinity. Genomic comparisons revealed that two copies of ISCR2 flanked the variant gene, and the structure was ISCR2-hp-hp-abh-tet(X4)G568A -ISCR2, which is highly homologous to the reported E. coli plasmids carrying tet(X4). In addition, it confirmed the presence of an ISCR2-mediated circular intermediate, proving this modules capacity for horizontal transfer of the tet(X4)G568A variant. Furthermore, the ISCR2-tet(X4) genetic structure carrying the G568A substitution was integrated within a chimeric SXT/R391-like integrative and conjugative element (ICE), which is also serving as a vehicle for genetic dissemination. As per our knowledge, this is the first report on the emergence of SXT/R391-like ICE carrying tet(X4) in Vibrio strains. Our finding demonstrates that the clinically relevant tigecycline resistance gene tet(X4), previously confined mainly to Enterobacterales from humans and livestock, is now actively spreading into environmental Vibrio populations. This cross-species transfer highlights a previously underappreciated ecological and public health concern in aquatic ecosystems.

microbiology↗

bioRxiv2026

Plasma titration provides a physical ruler for cross-platform proteomics

Plasma proteomics is expanding across platforms and cohorts, and integrating these data for AI demands comparability at the protein level, not merely concordant associations1,2. Affinity and MS platforms use distinct probes (antibodies, aptamers, or peptides) and signal readouts, yielding contradictory cross-platform results3,4. Without a known quantitative truth, we cannot distinguish biology from measurement distortion, leaving no gold standard for integration. Here we introduce Plasmix--a plasma reference suite with predefined male:female ratios (M, 1:0; Y, 3:1; P, 1:1; X, 1:3; F, 0:1)--and show that preserving this quantitative titration gradient, not just technical repeatability, predicts cross-platform concordance and identifies protein measurements suitable for integration. Profiling Plasmix across five platforms (Olink, SomaScan, NULISA, AAgAtlas, and MS-DIA) and 12 protocols across 17 batches, we found discordance is dominated by signal generation, not sample identity, and platforms distort signals in a protein-specific manner. Crucially, proteins retaining the titration response showed stronger agreement in an independent cohort; anchoring to the Plasmix midpoint (P) via sample-to-reference ratios reduced distortions, extending harmonizable coverage by 10-20%. Plasmix thus provides a physical ruler to benchmark accuracy, identifying genuinely integrable measurements before pooling datasets or training AI models--a critical bottleneck for plasma proteomics.

molecular biology↗

bioRxiv2026

Hurricane-induced structural disturbance amplifies forest vulnerability to subsequent heatwaves

Sequential hurricane-heatwave events threaten forest resilience via understudied legacy effects. Using Bayesian Structural Time Series, piecewise Structural Equation Modeling, and a 21-event global synthesis, we quantify how structural degradation non-linearly amplifies productivity loss during subsequent heatwaves. Our Hurricane Michael (2018) case study reveals significant negative GPP legacy effects during the 2019 heatwave. Intact, tall and diverse canopies buffer microclimates and moderate thermal sensitivity. Hurricane-induced structural simplification removes this protection, exposing temperature-sensitive shaded leaves to extreme stress. We identified a context-dependent hydraulic trade-off: structural complexity provides shading but exacerbates forest sensitivity to water deficits during peak heat, the vulnerability of which reverses during the recovery phase. Globally, these legacy effects are triggered by heatwave intensity and modulated by soil type, with loamy-soil forests most vulnerable. These findings highlight the critical role of forest structure in forest responses to compound disturbances. Neglecting structural legacies in Earth System Models likely underestimates risks to global carbon sinks.

ecology↗

bioRxiv2026

Structure-aware deep learning predicts influenza antigenicity and guides vaccine strain recommendation

The continuous accumulation of genetic mutations in influenza A viruses (IAVs) drives antigenic drift, necessitating precise antigenic prediction for optimal vaccine strain selection. While sequence-based methods have advanced antigenic surveillance, they neglect the three-dimensional structural context that fundamentally dictates viral antigenicity. Here, we introduce Vir3D, which leverages ESMFold-derived structural information from amino acid sequences to precisely predict viral antigenicity and guide vaccine strain selection. Across both human H3 and highly pathogenic avian H5 subtypes, Vir3D not only accurately discriminates antigenic variants and infers pairwise antigenic distances, but also mechanistically delineates key structural residues driving viral immune evasion. In a decade-long retrospective analysis, Vir3D-prioritized vaccines consistently achieve broader antigenic coverage of circulating strains than World Health Organization (WHO) recommendations. Crucially, Vir3D successfully predicts that the emerging U.S. dairy cattle H5N1 virus (TX/24) remains antigenically stable relative to clade 2.3.4.4b vaccine strains, and subsequent wet-laboratory validation of hemagglutination inhibition (HI) assays definitively corroborates this finding. Overall, Vir3D establishes a powerful, structure-driven framework for proactive influenza surveillance and pandemic preparedness.

bioinformatics↗

bioRxiv2026

Protective pan-betacoronavirus neutralizing antibodies by vaccination

The continued emergence of betacoronaviruses underscores the urgent need for vaccines that provide broadly protective immunity. Here, we present an epitope-focused vaccine strategy targeting the conserved S2 stem-helix region of the spike fusion machinery, a broadly neutralizing antibody-(bnAb) epitope shared across betacoronaviruses yet partially occluded on the native spike. Immunization of non-human primates with engineered S2 stem-helix nanoparticle immunogens, alone or followed by a SARS-CoV-2 BA.1 spike mRNA boost, elicited broadly cross-reactive antibody responses against sarbecoviruses, merbecoviruses, and embecoviruses and neutralized SARS-CoV-2, multiple variants, other sarbecoviruses, and MERS-CoV. Vaccine-elicited monoclonal antibodies displayed broad in-vitro neutralizing activity and protected against both SARS-CoV-2 and MERS-CoV in-vivo. Structural analyses revealed conserved features between rhesus and human stem-helix bnAbs, supporting the translational potential. Overall, our findings provide proof-of-concept that epitope-focused nanoparticle immunogens can target partially occluded, immunoquiescent bnAb epitopes, laying the groundwork for pan-betacoronavirus vaccines that provide broad protection and strengthen pandemic preparedness. ONE SENTENCE SUMMARYEpitope-focused S2 stem-helix nanoparticle immunogens elicit protective broadly neutralizing antibodies (bnAbs) against diverse betacoronaviruses in non-human primates, establishing a framework for development of pan-betacoronavirus vaccines.

immunology↗

bioRxiv2026

Molecular and functional characterization of CYP6AN1 orthologs involved in capsaicin metabolism in two Helicoverpa species

The generalist Helicoverpa armigera and the specialist Helicoverpa assulta are closely related noctuid pests and are among the few insect herbivores capable of feeding on and damaging hot pepper fruits, which contain the defensive compound capsaicin. Cytochrome P450 monooxygenases (P450s) contribute to the metabolism of plant defensive compounds and can facilitate insect adaptation to chemically defended host plants. Here, we identified CYP6AN1 in H. assulta (HassCYP6AN1) and comparatively characterized the CYP6AN1 orthologs from H. armigera (HarmCYP6AN1) and H. assulta. RACE identified one full-length HarmCYP6AN1 transcript and three full-length HassCYP6AN1 transcript isoforms. The HassCYP6AN1 isoforms contained distinct 5' UTRs generated by alternative transcription initiation and splicing but shared an identical coding sequence. Sequence comparisons and phylogenetic analysis supported their assignment as orthologs. Constitutive CYP6AN1 expression was higher in the H. assulta midgut, whereas dietary capsaicin significantly induced CYP6AN1 expression in the H. armigera midgut. Recombinant CYP6AN1 proteins were co-expressed with NADPH-cytochrome P450 reductase in Escherichia coli, and their substrate-metabolizing activities were evaluated using HPLC-based depletion assays. Both orthologs metabolized capsaicin, but HarmCYP6AN1 exhibited an approximately 2.3-fold higher depletion activity than HassCYP6AN1 under the conditions tested. HarmCYP6AN1 also showed P450-content-dependent xanthotoxin depletion, whereas no detectable xanthotoxin metabolism was observed for HassCYP6AN1. These findings establish CYP6AN1 as a component of the capsaicin-metabolizing repertoire of both species and reveal substantial divergence between the orthologs in transcript organization, expression regulation, catalytic activity, and detectable substrate range.

zoology↗

bioRxiv2026

IKKβ as a putative non-covalent and quinone-mediated covalent target of 4-methylcatechol in RANKL/NF-κB signaling: a combined computational and experimental analysis

Excessive osteoclast activity contributes to pathological bone loss in osteoporosis, rheumatoid arthritis, and osteolytic malignancies. The effects of small catechol derivatives on receptor activator of nuclear factor-{kappa}B ligand (RANKL)-induced osteoclastogenesis remain poorly understood. This study investigated the effects of 4-methylcatechol (4-MC) on RANKL-induced NF-{kappa}B activation and osteoclast differentiation. 4-MC reduced RANKL-induced NF-{kappa}B luciferase activity in HEK-293T/RANK cells. 4-MC also suppressed RANKL-induced TRAP activity in RAW264.7 cells in a concentration-dependent manner and reduced the number of TRAP-positive multinucleated osteoclasts, without affecting cell viability. Molecular docking predicted non-covalent binding of 4-MC within the ATP-binding hinge region of IKK{beta} (PDB: 4KIK), forming a close polar contact with Glu97, predicted hydrogen bonds with Cys99, and a hydrophobic contact with Ile165, within the pocket occupied by the co-crystallized inhibitor K252a. Covalent docking predicted that the oxidized quinone form of 4-MC engages Cys179 in the IKK{beta} activation loop. Quantum chemical calculations confirmed a markedly higher electrophilicity index for the oxidized quinone than for the parent catechol, supporting this mechanism. In silico ADMET profiling indicated favorable drug-likeness and safety. These findings identify IKK{beta} as a plausible molecular target of 4-MC through both non-covalent and covalent mechanisms. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/741661v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1d9f82eorg.highwire.dtl.DTLVardef@134a24borg.highwire.dtl.DTLVardef@8aeb91org.highwire.dtl.DTLVardef@6fb85d_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2026

The Fontan EV Score: A Circulating Extracellular Vesicle-Based Risk Stratification Tool for Fontan-Associated Liver Disease

BackgroundFontan-associated liver disease (FALD) is a universal complication of the Fontan palliation characterized by chronic congestion and progressive hepatic fibrosis. Current diagnostics rely on invasive biopsies or non-specific biochemical and imaging biomarkers that fail to capture early fibrogenesis, creating a critical need for non-invasive biomarkers to stratify disease severity. MethodsWe utilized a translational ovine Fontan model (n = 19) to investigate circulating serum extracellular vesicles (sEVs) as reporters of hepatic pathology. Longitudinal serum samples paired with liver elastography were collected, and sEVs were subjected to multi-omic profiling including small RNA sequencing and proteomics. Regularized regression was used to identify transcriptomic predictors, which were integrated with time post-surgery into an ordinal logistic regression framework to construct the Fontan EV Score (FES). Model performance was evaluated on a held-out test cohort and benchmarked against established serological fibrosis indices. To validate the biological relevance of the FES panel, TGF-{beta}-treated human liver organoids were generated and scored miRNA expression was assessed. ResultsThe sEV proteome exhibited robust separation by surgical physiology, while the small RNA cargo was primarily stratified by fibrotic status. Bioinformatic analysis confirmed a high hepatic origin for these transcripts and identified enrichment of inflammatory pathways including Toll-like receptor and Interleukin-17 cascades in fibrotic subjects. The FES, incorporating time post-surgery and eleven small RNA biomarkers, demonstrated high predictive accuracy in the independent testing cohort with an AUC of 0.876 for moderate and 0.963 for severe fibrosis, substantially outperforming APRI (AUC = 0.618) and FIB-4 (AUC = 0.731). In TGF-{beta}-treated human liver organoids, several scoring miRNAs, including miR-125a-5p and miR-193b-5p, were directionally responsive to profibrotic stimulation. ConclusionsCirculating sEVs carry a liver-associated molecular cargo that can be leveraged for the non-invasive prediction of FALD severity. The FES provides a biologically validated scoring system that substantially outperforms existing serological indices and offers a new avenue for early detection and risk stratification of FALD Novelty and SignificanceO_ST_ABSWhat is Known?C_ST_ABSO_LIFontan-associated liver disease (FALD) is a nearly universal consequence of the Fontan circulation, driven by chronic venous hypertension and reduced cardiac output. C_LIO_LICurrent surveillance tools, including transaminases, composite serological indices (APRI, FIB-4), and elastography, have limited sensitivity and specificity for detecting and staging hepatic fibrosis in the Fontan population. C_LIO_LICirculating small extracellular vesicles (sEVs) carry tissue-derived molecular cargo and have shown diagnostic potential in other liver diseases, but their utility in FALD has not been explored. C_LI What New Information Does This Article Contribute?O_LIMulti-omic profiling of circulating sEVs in a translational ovine Fontan model reveals that the small RNA cargo is stratified by fibrotic status and enriched for inflammatory pathways associated with hepatic stellate cell activation. C_LIO_LIThe Fontan EV Score (FES), integrating time post-surgery with eleven circulating small RNA biomarkers, predicts FALD severity with substantially greater accuracy than APRI and FIB-4. C_LIO_LITGF-{beta}-treated human liver organoids confirm that several FES-associated miRNAs are directly responsive to profibrotic stimulation, providing biological validation independent of Fontan hemodynamics. C_LI This study demonstrates that circulating sEVs function as non-invasive reporters of hepatic fibrogenesis in the Fontan circulation and introduces the first EV-based scoring system for FALD risk stratification. The FES achieved an AUC of 0.876 for moderate and 0.963 for severe fibrosis in an independent test cohort, outperforming established serological indices that were originally developed for viral hepatitis but which perform poorly in congestive hepatopathy. By combining molecular biomarker discovery with in vitro functional validation, this work establishes a foundation for developing targeted, non-invasive diagnostics to guide surveillance and clinical decision-making in the growing Fontan patient population.

bioinformatics↗

bioRxiv2026

Multifaceted and evolutionarily dynamic interactions between Caenorhabditis elegans SPO-11 and its cofactors ensure proper formation of meiotic DNA double-strand breaks

DNA double-strand breaks (DSBs) generated during meiotic prophase by the topoisomerase-like protein SPO11 are essential to create crossovers between homologous chromosomes. Since crossovers are required to biorient chromosomes at the first meiotic division, DSB formation is essential for meiosis in most sexually-reproducing organisms. Since excess DSBs have the potential to destabilize the genome, SPO-11 activity must be strictly regulated by many cofactors. Recent studies have established that SPO11 must dimerize to cut DNA, whereas soluble SPO11 and SPO11-TOPOVIBL complexes are predominantly monomeric (1-3). This contrast suggested that a major role of SPO11 cofactors could be to promote SPO11 dimerization, through means such as increasing local concentration or co-orienting SPO11 protomers. However, the mechanism of this regulation is not well-understood. Here, by taking advantage of phylogenomic analysis in the nematode genus Caenorhabditis, we show that the conserved cofactor DSB-1Rec114 evolved to replace TOPOVIBL function in C. elegans. We provide genetic and biochemical evidence that multiple interactions between SPO-11 and DSB-1 stabilize protein complex formation and promote SPO-11 dimerization. Our results shed light on the regulatory mechanism of programmed DSB formation, which ensures crossover formation and meiotic chromosome segregation while protecting genomic stability. Significance StatementProgrammed DNA double-strand breaks catalyzed by SPO11 are essential for meiosis, but how SPO11 and its cofactors cooperate to cut DNA is not understood. SPO11 only cuts DNA as a homodimer, but soluble SPO11, with or without its core component TOPOVIBL, is predominantly monomeric. We show here that DSB-1, a conserved cofactor of C. elegans SPO-11, has evolved to replace TOPOVIBL to make direct, multifaceted interactions with SPO-11. We provide evidence that DSB-1 simultaneously binds both SPO-11 protomers, and this binding is critical for DNA cleavage, implying a major role of DSB-1 in promoting SPO-11 dimerization. Our phylogenetic analysis also highlights the evolutionary flexibility of a conserved, essential protein complex after the loss of one of its members, TOPOVIBL.

cell biology↗

bioRxiv2026

Immunometabolic Reprogramming by Thyroid-Stimulating Antibodies Drives Orbital Adipogenesis via Histone Lactylation in Thyroid Eye Disease

Thyroid eye disease (TED) is conventionally viewed as an autoimmune inflammatory disorder. However, the metabolic determinants driving orbital tissue remodeling remain largely undefined. Here, we uncover a paradigm-shifting mechanism whereby thyroid-stimulating antibodies (TSAbs) instigate profound metabolic reprogramming in orbital fibroblasts (OFs), driving a switch toward glycolysis and markedly elevating lactate production via the CREB/LDHA axis. Critically, we demonstrate that this TSAbs-induced metabolic perturbation is not a mere byproduct but the principal driver of pathology. Mechanistically, lactate functions as a signaling metabolite that directly potentiates adipogenesis via histone lactylation-dependent transcriptional activation of the master adipogenic regulators PPAR{gamma} and C/EBP. Collectively, our findings underscore metabolic reprogramming as a central pathogenic mechanism in TED, whereby autoimmune cues drive disease progression through metabolic-epigenetic crosstalk. This work substantiates the paradigm of TED as an immune- metabolic disorder.

immunology↗

bioRxiv2026

Evolutionary Origins and Synthetic Reconstruction of Gingerols

How new enzymatic activities become integrated with existing metabolic networks to generate lineage-restricted plant chemistry remains a central question in metabolic evolution, exemplified by gingerol biosynthesis in Zingiberaceae, whose complete enzymatic basis has remained elusive. Here, we resolve this problem by elucidating the evolutionary origins and the full biosynthetic pathway of gingerol through single-cell transcriptomics, functional screening, structural biology, comparative genomics and pathway reconstruction. A coordinated metabolic program operates in ginger oil cells, thereby guiding the identification of diketide-CoA synthases, gingerol synthases (GS) and gingerol reductases that together constitute the complete pathway. GS remodels the conserved type III polyketide synthase scaffold to organize a fatty acyl-CoA and a phenylpropanoid-derived intermediate for gingerol formation. Furthermore, GS arose through duplication and limited active-site remodeling of a curcumin synthase-like enzyme, accompanied by coordinated recruitment of precursor-supply and reduction pathways. Translating these principles into yeast achieves the first de novo microbial production of 6-gingerol from glucose at 12.4 mg/L. These findings reveal the evolutionary logic by which plants recruit and coordinate novel enzymatic activities to establish lineage-restricted metabolic program, providing a framework for understanding and engineering specialized metabolism across the plant kingdom.

synthetic biology↗