Biology subjects

Liu, X.

Publications and source records attributed to Liu, X..

At least 109 records · Page 6Linked to original sources

bioRxiv2026

Propagation electrodynamics and differential conduction of action potentials in geometrically branched squid giant axons

Classical neuronal cable theory relies on quasi-static electric field approximations and neglects magnetic induction, Lorentz force coupling, and transient electromagnetic currents, limiting its ability to fully characterize action potential propagation within geometrically branched axons and dendrites. This work develops a coupled Maxwell-electromagnetic cable framework by integrating finite-difference time-domain (FDTD) solutions of Maxwells equations with extended Hodgkin-Huxley and Fitzhugh-Nagumo membrane dynamics, incorporating magnetic gating perturbations, electromagnetic trans-membrane currents IEM, and nanoscale quantum corrections for thin neural segments. Controlled propagation experiments are designed to quantify deviations from standard cable predictions across asymmetric and symmetric axonal bifurcation geometries. Numerical results demonstrate that inductive magnetic effects lower the critical branch radius for junction conduction failure and break symmetric action potential invasion in geometrically identical child branches under external transverse magnetic fields. An electromagnetic corrected geometric ratio GREM is proposed to revise impedance-matching conditions at branch points, accounting for size-dependent axial current imbalance induced by magnetic and displacement currents. Parent axon conduction velocity deviates substantially from the canonical [Formula] scaling law when electromagnetic feedback and quantum charge distributions are included, triggering early signal blockage at large cable diameters. Collectively, this study establishes that quasi-static cable models underestimate electromagnetic corrections to propagation speed, waveform shape, and bifurcation transmission fidelity; the coupled Maxwell-cable framework provides a comprehensive multi-physics tool for modeling electrodynamic signal behavior in complex neuronal architectures.

biophysics↗

bioRxiv2026

Primary and higher-order thalamic nuclei make distinct contributions to cortical reorganization in congenital sensory loss

Early sensory loss transforms the functional organization of affected sensory systems, with regions that normally support vision or audition participating in noncanonical perceptual and cognitive functions. Such reorganization requires coordination across distributed networks. Higher-order thalamic nuclei are positioned to support these interactions through their widespread reciprocal cortical connectivity, yet studies of sensory-loss plasticity have focused primarily on cortex and first-order sensory pathways. Here, we combined structural and functional MRI in early blind and early deaf adults to test how reorganization after sensory loss is expressed across thalamocortical networks. In blindness, structural differences were concentrated along the primary input pathway, with reduced lateral geniculate nucleus volume that covaried with areal organization of primary visual cortex. Functional reorganization was more broadly distributed, with visual cortex showing greater similarity with higher-order (association) thalamic nuclei linked to cognitive control, paralleling a shift toward cognitive-control networks across cortex. This pattern was amplified during a nonvisual perceptual judgment task. Across visual cortex, cross-network functional differences were strongest in regions showing the largest structural effects. A related shift toward control-associated higher-order thalamus was observed in deafness, indicating that higher-order thalamic involvement generalizes across sensory modalities. Together, these results indicate that thalamocortical architecture shapes both the developmental consequences of early sensory loss and the capacity for distributed functional reorganization.

neuroscience↗

bioRxiv2026

Modular counterplays shape condensation and signaling of chimeric antigen receptor

Chimeric antigen receptor-engineered T (CAR T) cell therapy has achieved remarkable clinical efficacy against hematological malignancies but exhibits limited therapeutic outcomes in solid tumors, where immune checkpoint signaling is highly active. Here, we demonstrate that the second-generation CD28-CD3{zeta} (28Z) CAR undergoes liquid-liquid phase separation with the Src-family kinase LCK to assemble a signaling condensate crucial for CAR activation. PD-1, but not LAG3 or CTLA4, disrupts these CAR-LCK condensates through competitive binding to CAR rather than through its canonical phosphotase-dependent inhibitory pathway. Incorporation of a CD3{varepsilon} cytoplasmic module into the CAR introduces additional LCK interactions that reinforce CAR-LCK condensation, thus limited PD-1 incorporation and stabilize signalosome assembly. Consequently, the CD3{varepsilon}-engineered CAR (E-CAR) resists PD-1-mediated condensates disassembly, preserves immunological synapse organization, and sustains proximal signaling following PD-L1 engagement. E-CAR T cells are therefore resistant to PD-1-mediated functional suppression and maintain potent antitumor activity against PD-L1-positive solid tumors. Together, these findings identify disruption of CAR signaling condensates as a previously unrecognized mechanism of PD-1-mediated inhibition and establish CD3{varepsilon} modular signalosome engineering as a rational engineering strategy to overcome immune checkpoint suppression.

immunology↗

bioRxiv2026

Gram-scale one-pot enzymatic synthesis of CDP-ribitol by a designed bifunctional fusion enzyme

D-Ribitol-5-phosphate (Rbo5P) plays vital roles in bacterial and mammalian development. In mammals, Rbo5P is an essential component of the O-mannosyl glycan on -dystroglycan, and its defective biosynthesis causes a group of dystroglycanopathies. Supplementation with cytidine diphosphate ribitol (CDP-ribitol, CDP-Rbo) and its analogues has shown therapeutic potential for certain dystroglycanopathies. However, facile and scalable strategies to prepare CDP-Rbo remain unavailable. Here, we report a practical one-pot enzymatic strategy for gram-scale CDP-Rbo production. Starting from inexpensive ribitol, Rbo5P is first generated by L-ribulokinase (AraB) and then converted to CDP-Rbo by CDP-ribitol pyrophosphorylase (TarI) in 90% yield. To streamline the process, AraB and TarI were fused into a single bifunctional biocatalyst, AraB-TarI, which converts ribitol directly into CDP-Rbo on a gram-scale in a one-step reaction. Furthermore, a nucleotide recycling strategy was developed to lower the cost and increase the atom economy from 47% to 75%. This work provides a green and scalable route to CDP-Rbo and a reliable material supply for developing therapeutics against dystroglycanopathies.

biochemistry↗

bioRxiv2026

MetaSplice: an ensemble pathogenicity predictor for intronic splice variants

Splice-altering variants cause an estimated 15-30% of genetic diseases, yet computational tools lose accuracy outside the canonical GT-AG dinucleotides, leaving intronic variants of uncertain significance (VUS) hard to interpret. Here we present MetaSplice, a 53-feature gradient-boosted ensemble integrating deep-learning splice predictions (SpliceTransformer, Pangolin), evolutionary and gene-level constraint, and splicing-regulatory motifs to score single-nucleotide variants across seven non-exonic splice regions: canonical donor and acceptor sites, donor and acceptor regions, the polypyrimidine tract (PPT), branch point, and deep intronic positions. Trained on 381,226 intronic ClinVar SNVs (35,506 pathogenic), MetaSplice achieved an area under the precision-recall curve (auPRC) of 0.995 in five-fold gene-grouped cross-validation. On a temporally held-out ClinVar test set (107,933 variants), it reached auPRC 0.987 (95% CI 0.985-0.989), outperforming SpliceAI (0.950), CADD v1.7 (0.915), SPIDEX (0.767) and S-CAP (0.253), with the largest gains in the PPT, branch-point and deep intronic regions. As a pathogenicity predictor trained on clinical significance, MetaSplice complements mechanism-specific splice-effect tools. Applied to 47,272 ClinVar splice-region VUS, it nominated 22% for functional follow-up. MetaSplice is freely available as a Docker image.

genomics↗

bioRxiv2026

A Germinal Center-Independent Innate-Like Memory B Cell Compartment of B1 Origin

Memory B cells (MBCs) are a critical cellular reservoir for long-term humoral immunity. MBCs display heterogeneous isotypes and surface markers and can arise through both germinal center (GC)-dependent and GC-independent extrafollicular (EF) pathways. Both the mechanisms controlling EF MBC differentiation and the identities of the B cell populations from which EF MBCs derive remain poorly understood. To capture MBC diversity, we applied a broad selection strategy followed by transcriptional profiling, identifying a subset of MBCs characterized by minimal class switching, limited somatic hypermutation, and an innate-like gene signature. Using genetic models, we demonstrated that this subset arises independently of GC responses and derives from innate B1 cells. These innate-like MBCs differentiate into antigen-specific antibody-secreting cells and confer protection against lethal viral infection. Together, our findings define a previously unrecognized arm of MBC responses, demonstrating that innate B1 cells contribute a non-redundant antibody repertoire to protective immunological memory.

immunology↗

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

Pan-Peroxisome Proliferator-Activated Receptor Agonist IVA337 Alleviates Secondary Lymphedema via Inhibiting TGFβ/SMAD2/3 Signaling Pathway

Lymphedema is a chronic disease characterized by impaired lymph drainage and accumulation of protein-rich interstitial fluid, which progresses to develop irreversible fibrosis. Importantly, effective therapies and treatments are lacking to alleviate and mitigate the disease. The pathological inflammation and fibrogenesis underlying lymphedema prompted us to evaluate a preclinical medicine IVA337, a pan-peroxisome proliferator-activated receptor (PPAR) agonist that improves liver fibrosis in patients with metabolic dysfunction-associated steatohepatitis (MASH) by activating three PPAR isoforms (, {beta}/{delta}, {lambda}), which play critical roles in lipid metabolism, anti-inflammation responses, and anti-fibrogenesis. Here, we investigate the therapeutic effects of IVA337 during the early stage of surgery-induced secondary lymphedema in mice and explored the underlying mechanisms. IVA337 administration alleviated lymphedema progression, improved lymphatic drainage, reduced dermal thickness, and resolved lymphatic vessel dilation. Mechanistically, IVA337 suppressed the TGF{beta}/SMAD2/3 signaling pathway, reduced immune cells infiltration, and improves lymphatic vessels integrity. In human dermal lymphatic endothelial cells (HDLECs), IVA337 attenuated TGF{beta} induced SMAD2/3 phosphorylation and preserved the expression of cell junction Claudin5, reduced VE-Cadherin-stained cell-cell gaps. Collectively, our findings demonstrate that IVA337 protects against early stage lymphedema by inhibiting TGF{beta}/SMAD2/3-mediated inflammatory and fibrotic responses. This study provides a potential therapeutic strategy to improve lymphatic function during the early phase of lymphedema and prevent progressive fibrosis in patients with lymphedema and related disorders.

pathology↗

bioRxiv2026

Ribonucleotide Reductase Inhibition Overcomes FLT3 Inhibitor Resistance in Acute Myeloid Leukemia

Internal tandem duplication mutations in FLT3 (FLT3ITD) occur in approximately 30% of patients with acute myeloid leukemia (AML) and are among the most common genetic alterations in this disease. FLT3ITD is a major driver of AML and is associated with poor clinical outcomes. Although FLT3 inhibitors (FLT3is) have significantly improved outcomes for patients with FLT3ITD+ AML, acquired resistance remains a major barrier to durable clinical benefit. Reactivation of RAS/MAPK signaling, often driven by activating NRAS mutations, is a major mechanism of FLT3i resistance in AML; however, effective strategies to overcome this resistance remain lacking. Here, we identify ribonucleotide reductase (RNR) as a critical therapeutic vulnerability in NRAS-driven FLT3i-resistant FLT3ITD+ AML. Activation of RAS signaling through SPRY3 loss or oncogenic NRAS mutations confers robust resistance to FLT3is, whereas pharmacologic inhibition of RNR with multiple inhibitors, as well as siRNA-mediated RNR suppression, reverses FLT3i resistance and restores FLT3i sensitivity across multiple FLT3ITD+ AML models in vitro. In vivo, clofarabine, an FDA-approved RNR inhibitor (RNRi), significantly overcomes NRAS mutation-driven FLT3i resistance. In combination with FLT3 inhibition, clofarabine markedly suppresses the progression of FLT3i-resistant AML and significantly prolongs survival in cell line-derived xenograft (CDX) models. Importantly, the therapeutic efficacy of the gilteritinib/clofarabine combination was independently validated in two genetically distinct patient-derived xenograft (PDX) models harboring different NRAS mutations, demonstrating robust reduction of leukemia burden and confirming the generalizability of RNR inhibition in primary FLT3i-resistant AML. Together, these findings identify a previously unrecognized therapeutic vulnerability in FLT3i-resistant FLT3mut+ AML and establish RNR inhibition as an effective strategy to overcome FLT3i resistance, providing a strong rationale for the clinical evaluation of RNRis in combination with FLT3is in patients with resistant AML. SignificanceAlthough FLT3 inhibitors (FLT3i) are an important therapeutic advance in FLT3ITD+ AML, resistance commonly develops. We identified ribonucleotide reductase (RNR) as a new key vulnerability in NRAS-driven FLT3i-resistant AML and demonstrated that multiple RNRis, including the FDA-approved agent clofarabine, restore FLT3i sensitivity and enhance antileukemic activity, supporting a clinically actionable combination strategy.

cancer biology↗

bioRxiv2026

CXCL12/CXCR4 Governs Lymphatic Valve Formation Through Flow Dependent AKT/FOXO1/FOXC2 Activation

BackgroundLymphatic valves are specialized structures within lymphatic vessels that ensure unidirectional lymph transport. Defective lymphatic valve formation is associated with lymphedema, a chronic disease characterized by impaired lymph drainage and the accumulation of protein-rich interstitial fluid. Lymphatic valves form during late embryonic stages in mice, with oscillatory shear stress implicated in regulating the molecular mechanisms which control lymphatic valve formation. However, the molecular mechanisms governing lymphatic valve formation remain incompletely understood. Although CXCR4 is regulated by shear stress in blood vessels, whether CXCL12/CXCR4 signaling regulates lymphatic valve formation and the underlying molecular mechanisms remain unknown. MethodsTo investigate the roles of CXCR4 in the regulation of lymphatic valve development, we utilized lymphatic endothelial cell (LEC)-specific Cxcr4 knockout (Flt4CreERT2, Cxcr4f/f) mice. To determine the source of CXCL12, major ligand for CXCR4 in the mesentery, we used global Cxcl12-/-, and Cxcl12-DsRed knock-in/knockout (KIKO) reporter mice, as well as conditional Cxcl12 knockout mouse lines. To determine the molecular mechanisms by which CXCL12/CXCR4 regulates lymphatic valve development, primary human dermal LECs were exposed to oscillatory shear stress (OSS) to mimic valve-associated flow, followed by analysis of downstream signaling pathways and valve related gene expression. ResultsLEC-specific loss of CXCR4 displayed impaired lymphatic valve development. Flt4CreERT2, Cxcr4f/f mice showed a significant reduction in valve numbers in embryonic mesenteric lymphatic vessels. Similarly, reduced valve numbers were observed in Cxcl12-/- embryos, indicating CXCL12/CXCR4 is required for embryonic mesentery collecting lymphatic valve formation. Cxcl12-DsRed KIKO mice revealed that blood vessels, opposed to nerves, were the major source of CXCL12 in the embryonic mesentery. In align with this finding, EC-specific Cxcl12 deletion recapitulated defective valve phenotypes observed in Cxcl12-/- embryos. Mechanistically, CXCR4 knockdown in primary human dermal LECs attenuated OSS induced phosphorylation of AKT and FOXO1, leading to increased nuclear localization of FOXO1 and reduced expression of FOXC2, an essential transcription factor governing lymphatic valve development. Consistent with these findings, lymphatic valves of LEC-Cxcr4 deficient mice exhibited increased FOXO1 nuclear localization. Importantly, pharmacological activation of AKT reduced FOXO1 nuclear accumulation and restored lymphatic valve numbers in LEC-Cxcr4 deficient mesenteric lymphatic vessels. ConclusionsOur findings reveal CXCL12/CXCR4 signaling acts as a critical regulator of lymphatic valve development. CXCL12/CXCR4 signaling integrates into the flow dependent AKT/FOXO1/FOXC2 signaling axis to coordinate lymphatic valve development and morphogenesis. Taken together, our study uncovers a previously unknown role of CXCL12/CXCR4 signaling pathway in the regulation of lymphatic valve development. Targeting CXCL12/CXCR4/AKT/FOXO1 axis may represent a promising therapeutic strategy for improving lymphatic valve development to improve lymphatic function for the treatment of lymphedema.

developmental biology↗

bioRxiv2026

Engineering Oncolytic Measles Virus with MG53 Couples Pyroptotic Tumor Killing with Immune Microenvironment Remodeling to Enhance Checkpoint Immunotherapy in Non-small Cell Lung Cancer

Lung cancer is the leading cause of cancer-related mortality worldwide, with only approximately 30% of patients benefiting from current immune checkpoint immunotherapy. Oncolytic virotherapy offers a promising strategy to overcome this resistance; however, achieving both potent tumor cytotoxicity and robust antitumor immune activation remains a major challenge. Here, we engineered oncolytic measles virus expressing the tumor suppressor MG53 (TRIM72), designated rMeV-MG53, and evaluated its therapeutic potential against non-small cell lung cancer (NSCLC). rMeV-MG53 retained replication kinetics comparable to parental MeV while driving significantly greater cytotoxicity than an unarmed control in NSCLC cells. Mechanistically, MG53 arming amplified caspase-3-dependent apoptosis and potentiated Gasdermin E (GSDME) cleavage, engaging GSDME-mediated pyroptosis as a key tumor-killing mechanism; pharmacological inhibition confirmed caspase-dependent apoptosis as the initiating event leading to pyroptosis, while excluding necroptosis and ferroptosis as significant contributors to rMeV-MG53-induced cytotoxicity. MG53 overexpression induced an intrinsic pro-inflammatory transcriptional signature enriched for TNF, NF-{kappa}B, and IL-17 signaling, and rMeV-MG53 elicited significantly stronger type I interferon and pro-inflammatory cytokine induction than the unarmed control. In an immunocompetent, MeV-permissive syngeneic NSCLC model, intratumoral rMeV-MG53 achieved superior tumor growth inhibition, amplified caspase-3/GSDME pyroptosis, selectively upregulated Cxcl10, Ifng, and Il1b, and drove robust CD8 T-cell and Granzyme B effector infiltration. This immune remodeling was accompanied by compensatory PD-L1 upregulation, and combining rMeV-MG53 with anti-PD-L1 blockade achieved the strongest tumor suppression of all treatment groups. These findings establish MG53-armed oncolytic MeV as a strategy coupling GSDME-mediated pyroptosis with antitumor immune remodeling to sensitize immune-resistant NSCLC to checkpoint immunotherapy.

immunology↗

bioRxiv2026

VASP Promotes Aortic Valve Calcification by Interacting with FBLIM1 to Activate the Focal Adhesion Pathway

BackgroundCalcific aortic valve disease (CAVD) is the most prevalent valvular heart disease, yet there is no effective pharmacological therapy to halt or reverse its progression. Focal adhesions (FAs) are dynamic structures that connect cells to the extracellular matrix (ECM), serving not only as mechanical anchors but also as critical signalling hubs that regulate cell adhesion, spreading, migration, differentiation, and mechanotransduction. However, their specific role in CAVD pathogenesis remains largely unknown. MethodsTo identify upregulated hub genes, an integrated analysis of proteomics and RNA sequencing was performed on calcified aortic valves. To investigate functional roles in vitro, we utilized genetic knockdown and overexpression of VASP in valvular interstitial cells (VICs), followed by phenotypic evaluations of osteogenic differentiation, calcification, and elastin (ELN) secretion. Downstream mechanisms were explored using RNA-seq in VASP-overexpressing VICs, alongside pharmacological inhibition of the FA pathway. Finally, protein-protein interaction assays were conducted to map and analyze the physical binding between VASP and the structural domains of FBLIM1. ResultsIntegrated omics analysis identified VASP as a significantly upregulated gene in human calcified aortic valve tissues. Functionally, VASP knockdown inhibited, whereas its overexpression promoted, the osteogenic differentiation of VICs. RNA-seq revealed that VASP overexpression activated the FA pathway, and the pharmacological blockade of this pathway successfully suppressed calcification both in vitro and vivo. Mechanistically, we demonstrated a direct physical interaction between VASP and the third LIM zinc-binding domain of FBLIM1, and knockdown of FBLIM1 effectively reversed the pro-calcific effects of VASP. Finally, VASP overexpression was found to promote the secretion of ELN, which subsequently contributed to the calcification process. ConclusionOur study reveals that the interaction between VASP and FBLIM1 drives CAVD progression by activating the FA pathway, which subsequently leads to excessive ELN secretion. These findings reveal a novel mechanistic pathway and may provide a potential therapeutic target for CAVD intervention. What are the Clinical Implications?We have identified the VASP-FBLIM1-FA-ELN axis as a novel molecular pathway involved in CAVD pathogenesis, greatly enriching our understanding of the complex process of aortic valve calcification. This pathway intricately links cytoskeletal dynamics, cell adhesion signalling, and ECM remodelling, providing a new theoretical framework for pathophysiological research in CAVD. In clinical practice, VASP and its downstream pathway components, particularly FBLIM1 and the FA pathway, may serve as potential biomarkers and therapeutic targets for the early diagnosis and treatment of CAVD. For example, the FA pathway inhibitors PF-573228 and Y15 demonstrated significant anti-calcification effects both in vitro and in vivo, suggesting that targeting this pathway may offer a new nonsurgical intervention strategy for patients with CAVD.

cell biology↗

bioRxiv2026

Expression and Engineering of Conductive Cytochrome Nanowires

Electrically conductive protein nanowires produced by metal-reducing bacteria have attracted interest as sustainable electronic materials, but their study and engineering have been limited by difficulties in expression, purification, and genetic manipulation. Here we establish Shewanella oneidensis as a heterologous host for production of Geobacter sulfurreducens OmcZ nanowires and progress a complementary in vitro assembly strategy that yields highly pure nanowire preparations. This platform enabled systematic engineering of OmcZ, revealing extensive tolerance to sequence variation and faciliating the design of enhanced-conductivity variants. Guided by comparative analysis of environmental OmcZ homologs, we generated a chimeric nanowire, OmcZ+, that exhibited a [~]3.5-fold increase in bulk conductivity while retaining the overall structure of the parent nanowire. Cryo-electron microscopy revealed unexpected architectural plasticity in OmcZ+ wires, including non-linear dendritic and pentameric assemblies mediated by the solvent-exposed heme VII, suggesting previously unrecognized modes of cytochrome nanowire organization. Incorporation of engineered OmcZ variants into water evaporation-induced electricity generators produced power densities up to [~]25.3 W cm-{superscript 2} and enabled high-performance operation in saline environments, including seawater and human sweat. Together, these results establish a versatile platform for the production, structural analysis, and engineering of cytochrome nanowires, providing a foundation for the development of programmable biological electronic materials.

bioengineering↗

bioRxiv2026

Quantifying Cross-Modal Shared Information Between Histomorphology and Spatial Transcriptomics via Spatiotemporal Trajectory Correlation

Histopathological imaging and spatial transcriptomics (ST) provide synergistic morphological and molecular insights into tissue architecture. While conventional downstream analyses predominantly adopt a discrete paradigm, such as segmenting histological images or identifying spatial domains, emerging trajectory reconstruction methods offer a continuous perspective for analyzing these modalities. However, most current studies are confined to single-modality or single-organ analyses, lacking systematic integration across modalities and multiple organs. To address this limitation, we performed trajectory reconstruction on ST-derived gene expression data and on histopathological morphological features extracted using ten widely used pathology pretrained models across multiple cancer samples from six organs. The results demonstrate that trajectory reconstruction, as a continuous analytical framework, effectively bridges spatial transcriptomics and histopathological imaging. More importantly, we propose an innovative framework that uses trajectory pseudotime as a mediating variable to quantify the extent of information sharing between molecular and morphological features. This framework not only provides a new perspective for understanding the intrinsic links between modalities but also establishes a solid theoretical and methodological foundation for future cross-modal translation studies.

pathology↗

bioRxiv2026

PathoBench: an open community-driven benchmark registry for pathogen bioinformatics tools

SummaryThe proliferation of pathogen bioinformatics pipelines has outpaced the communitys ability to compare them on common ground. Self-reported performance numbers, ad-hoc evaluation datasets, and inconsistent metrics make pipeline selection difficult for clinical and public-health researchers. We present PathoBench, an open web platform that addresses this gap through three coordinated mechanisms: (i) a curated registry of 26 standard benchmark datasets across 10 human pathogens, each with persistent identifiers and direct download links; (ii) pathogen-specific evaluation metrics that submissions must report, allowing direct head-to-head comparison only on the same dataset; and (iii) a credibility framework combining mandatory dataset attestation, ORCID-linked attribution, public peer comments, and administrator verification. As a case study, four published Mycobacterium tuberculosis drug-resistance pipelines were evaluated against the WHO TB mutation catalogue, demonstrating the frameworks discriminating power. PathoBench is open for community contributions across all ten supported pathogens. Availability and implementationPathoBench is freely available at https://pathobench.vercel.app. Source code is released under the MIT license at https://github.com/BPHL-Molecular/pathobench. The platform requires no installation for end users; programmatic access is available via a Supabase REST API. Contactyibo.dong@flhealth.gov Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2026

Total Biosynthesis of Pseudomonas aeruginosa-Derived Azabicyclocarbamates Identifies Distinct Dehydrating Condensation Family Proteins

Bacterial azabicyclocarbamates and related pyrrolizidine alkaloids play important roles in microbial interactions, and are scaffolds of therapeutic potential. Their biosynthesis involves a bimodular non-ribosomal peptide synthetase (NRPS), as well as a Baeyer-Villiger monooxygenase and tailoring enzymes, the latter contributing to the structural diversification of these compounds. Azetidomonamide A, a core metabolite produced by the major human opportunistic pathogen Pseudomonas aeruginosa, is a rare 4,7-bicyclocarbamate involved in modulating bacterial virulence that belongs to a unique family of natural products targeting ClpP proteases. In this study, we elucidated the full set of reactions leading to the 7-membered cyclocarbamate warhead, and reconstituted in vitro the biosynthesis of azetidomonamide A. Notably, this approach allowed for detailed characterization of a condensation (C) domain-catalyzed online dehydration via chemical capture of NRPS-tethered intermediates. Furthermore, we identified the dehydratase AzeD as the founding member of a distinct group of standalone proteins of the C domain family. Via combined structural, docking and biochemical analyses, we provided evidence that AzeDs catalytic mechanism is distinct from that of dehydrating C domains, further expanding the known chemistry of these key biosynthetic enzymes.

biochemistry↗

bioRxiv2026

A novel AR molecular glue degrader via bivalent engagement of the N-terminal domain and RNF213-UBE2J2 complex

Targeted protein degradation enables the elimination of disease-relevant proteins through induced proximity between E3 ligases and substrates. Current androgen receptor (AR) therapies act via the ligand-binding domain (LBD) but fail against constitutively active LBD mutants or splice variants such as AR-V7. Here, we identify GZL626, a small-molecule degrader that induces proteasome-dependent degradation of both full-length AR and AR-V7. GZL626 suppresses AR transcriptional activity, inhibits proliferation of AR-positive prostate cancer cells, and blocks SARS-CoV-2 infection. Mechanistically, GZL626 binds the intrinsically disordered AR N-terminal domain (NTD) and promotes formation of a noncanonical RNF213-UBE2J2-AR ternary complex that drives AR ubiquitination and degradation. The AR DNA-binding domain (DBD) acts as a structural hub within this assembly. Distinct from PROTACs or classical molecular glues, GZL626 engages both AR and RNF213 bivalently, remodeling protein interactions to stabilize a functional E3-E2-substrate complex. These findings establish GZL626 as a first-in-class NTD degrader with potential to overcome resistance in advanced prostate cancer.

biophysics↗

bioRxiv2026

Surface electrostatic networks control hydrophobic core remodeling in a pH-dependent switching protein

Communication between protein surfaces and their buried cores is central to protein structure and function, yet this phenomenon remains challenging to predict and control at high resolution. Changes in the protonation of surface ionizable residues communicate with the hydrophobic core, for example, in diverse pH-dependent protein functions. Hisactophilin, a histidine-rich actin- and membrane-binding protein, provides a general model for exploring such communication as it exhibits a finely tuned pH-regulated myristoyl-switching function. Upon reversible proton binding, the myristoyl group shifts between being sequestered in the hydrophobic core and more solvent accessible. In the current study we utilize experimental and computational approaches we uncover how binding of [~]1.5 net protons alters electrostatic interactions involving ionizable residues distributed across much of the protein surface. These changes are transmitted to the hydrophobic core through dynamic communities of ionizable and hydrophobic residues which substantially rearrange upon switching. The effects of mutating individual ionizable residues are weaker than those of core hydrophobic residues, and only combined mutation of multiple ionizable residues caused substantial functional change. Together, these results reveal how communication between surface ionizable residues and the hydrophobic core is mediated by extensive interaction networks that reorganize in response to changes in protonation. These results may provide general insights for understanding protein cooperativity and the coupling of surface and core residues in protein function, disease, evolution, engineering, and design. Significance StatementHow changes on the protein surface, such as proton binding to ionizable amino acids, are communicated to the protein core to regulate protein stability and function remains ill-defined. Synthesis of experimental and computational analyses resolves the distributed networks of surface ionizable residue interactions coupled to the hydrophobic core that control pH-dependent myristoyl switching in hisactophilin. Small changes in protonation that create and alleviate local electrostatic repulsion give rise to protein-wide changes in fluctuating surface-core interactions. This distributed electrostatics-core coupling mechanism may help explain the often underrecognized and long-range impacts of ionizable residues in proteins and provide a framework for interpreting the effects of mutations in fundamental and applied protein science.

biophysics↗