Biology subjects

Zhang, L.

Publications and source records attributed to Zhang, L..

At least 91 records · Page 5Linked to original sources

bioRxiv2026

Adipose GPD2 Couples Glycolytic Signals to Epigenetic Control of Metabolic Homeostasis

The glycerol-3-phosphate shuttle (G3PS) is a classic reducing equivalent transferring system, yet its role in adipose metabolism remains poorly understood. Here, we identify mitochondrial glycerol-3-phosphate dehydrogenase (GPD2), the core enzyme of G3PS, as a critical orchestrator of adipose thermogenesis and systemic metabolic homeostasis. Adipocyte-specific GPD2 knockout mice exhibited impaired thermogenic capacity and energy expenditure, rendering them susceptible to obesity and metabolic dysfunction. Mechanistically, GPD2 deficiency elevated cytosolic NADH, which suppressed glycolysis and decreased the levels of key metabolites, such as acetyl-CoA, thereby diminishing H3K27ac at thermogenic gene loci and silencing these genes. NADH depletion with an NADH oxidase rescued both glycolysis and thermogenic gene expression. In support of this mechanism, we defined a previously undescribed enhancer of Ucp1 whose H3K27ac was tightly controlled by GPD2. Remarkably, replenishing the acetyl-CoA pool or directly restoring H3K27ac at the Ucp1 enhancer reversed UCP1 expression in GPD2-deficient adipocytes. Importantly, we find that human adipose GPD2 expression is inversely correlated with BMI, WHR, and HOMA-IR, underscoring its clinical relevance. Collectively, our findings establish GPD2 as an essential node in the metabolic-epigenetic axis that governs thermogenic activation and energy balance.

biochemistry↗

bioRxiv2026

Pan-cancer NET-associated immunothrombosis coupling identifies a neutrophil-linked but neutrophil-irreducible tumor ecology

BackgroundNeutrophil extracellular traps (NETs) connect innate immunity with thrombosis, metastasis and immune escape, but bulk-tumor NET-associated signatures may mainly report neutrophil abundance. We tested whether an established NETs score also captures a neutrophil-irreducible tumor ecology. MethodsWe reanalysed a published 19-gene NETs score in 9,496 TCGA tumors across 32 cancer types. Tumor-stratified correlations mapped Hallmark and custom immunothrombosis modules. Within each cancer type, the score was residualized against a curated neutrophil proxy and partitioned into four median-defined ecological quadrants. Clinical survival and two independent immune-checkpoint-blockade cohorts provided outcome context. ResultsRaw NETs score was positively associated with TNF-alpha/NF-kB signaling in 32/32 cancers (median Spearman rho=0.404; FDR<0.05 in 30) and hypoxia in 32/32 (median rho=0.394; FDR<0.05 in 31). After neutrophil residualization, hypoxia (median rho=0.206; positive in 30/32) and TNF-alpha/NF-kB signaling (median rho=0.165; positive in 29/32) remained dominant. NETs-high/neutrophil-low tumors retained myeloid-inflammatory, immunothrombotic and hypoxic enrichment. Residual NETs score was associated with adverse overall survival in eight of 23 evaluable cancers after available clinical adjustment. It did not discriminate response in IMvigor210 (AUC=0.519, P=0.642) or GSE91061 (AUC=0.527, P=0.808), although it differed across IMvigor210 immune phenotypes (P=0.045). ConclusionsThe published NETs score contains a neutrophil-linked yet incompletely neutrophil-reducible component that organizes hypoxic, inflammatory and immunothrombotic tumor ecology. Its translational value is context dependent rather than that of a universal standalone immunotherapy biomarker.

cancer biology↗

bioRxiv2026

Conditional Deletion of All Neurexins Defines Diversity of Essential Synaptic Organizer Functions for Neurexins

Presynaptic neurexins are key regulators of synapse properties that arguably represent the best-studied synaptic adhesion molecules. Despite thousands of papers, however, no direct comparison of overall neurexin functions in different types of synapses is available. A decade ago, we provided such an analysis but we recently retracted this paper because four images contained microduplications that, although without discernible impact on the paper's conclusions, could not be corrected. As a result, the scientific community lost access to primary data that established the fundamental principle that neurexins perform profoundly different functions in different types of synapses. In the present study, we have therefore reanalyzed the original raw data and expanded their conclusions with new experiments to document, in a single study, the basic contributions of neurexins to different synapses. We used triple conditional knockout mice targeting all neurexins except for Neurexin-1r and applied neuron-specific manipulations combined with slice electrophysiology, two-photon Ca2+-imaging, and immunohistochemistry. With this approach, we focused on excitatory climbing-fiber synapses in the cerebellum and on inhibitory synapses formed by parvalbumin- or somatostatin-positive neurons in the cerebellum, hippocampus, and medial prefrontal cortex. Our results show that pan-neurexin deletions produce dramatically different phenotypes in synapses, ranging from modest to massive impairments in synapse assembly (climbing-fiber and parvalbumin-positive synapses) to severe but selective decreases in action potential-induced presynaptic Ca2+-transients (somatostatin-positive synapses). Thus, neurexins perform powerful but distinct context-dependent roles in different synapses that shape the brain's circuits.

neuroscience↗

bioRxiv2026

Single-nuclear RNA sequencing reveals an ATF3-independent sensory-neuron program after surgical incision

BackgroundAcute postoperative pain is common and often treated with opioids, but which sensory-neuron changes are responsible for the peripheral drive of pain is poorly defined. Skin incision induces activating transcription factor 3 (ATF3), the canonical marker of nerve injury, in dorsal root ganglion (DRG) neurons, and ATF3 marks the neurons that remain hyperexcitable. Whether ATF3 is required for postoperative pain is unknown. MethodsAdult mice of both sexes underwent hind-paw plantar incision. Postoperative nociceptive behavior was compared between sensory-neuron-specific ATF3 conditional-knockout mice (AvilCre/+; Atf3fl/fl) and littermate controls using assays that probe distinct primary-afferent modalities (von Frey; Hargreaves; dynamic light touch) together with an operator-independent index of spontaneous injury behavior. Single-nucleus RNA sequencing of wild-type and ATF3-null DRG sensory neurons (naive and postoperative day 1) characterized the initiating injury program; transcription-factor-activity inference, RNAscope, and phospho-c-Jun immunostaining examined c-Jun; and the oral dual leucine zipper kinase (DLK) inhibitor GNE-3511, given at the time of incision, was tested behaviorally. ResultsIncision transiently induced ATF3 in a subset of DRG neurons, returning to baseline by day 14, in parallel with the two-week course of nociceptive behavior. Deleting ATF3 in sensory neurons did not change the onset or resolution of nociceptive behavior on any readout, in either sex, across mechanical, thermal, and tactile modalities. Single-nucleus profiling showed a broad surgery-responsive nociceptor program in which ATF3 was the most strongly induced gene, yet only 23% of surgery-responsive neurons expressed it. Without ATF3, the program was remodeled but not abolished, and transcription-factor-activity inference nominated c-Jun as a candidate ATF3-independent factor; incision induced c-Jun in vivo. Systemic inhibition of DLK, which activates c-Jun pathway, lowered c-Jun phosphorylation and reduced evoked nociceptive hypersensitivity. ConclusionsOur results indicate that ATF3 marks part of the injured sensory neuron but does not drive acute post-surgical nociceptive behavior, and that it is not required for the postsurgical pain behaviors across afferent modalities carried by molecularly distinct nociceptor classes. The underlying injury program is broader than ATF3 and is nominated to depend on c-Jun. Because DLK inhibition, given at the time of incision, reduced evoked hypersensitivity, we propose the DLK-JNK-c-Jun axis as a candidate perioperative non-opioid target, which will require further genetic validation.

neuroscience↗

bioRxiv2026

Pluripotency and Transcriptional Pausing Disrupt Circadian Rhythms to Facilitate the Enrichment of Cancer Stem Cells

Triple negative breast cancer (TNBC) is the most aggressive breast cancer subtype, enriched for cancer stem cells (CSCs), which are the cause of tumor recurrence. CSCs are responsible for tumor initiation and propagation; however, the molecular mechanisms underlying their formation remain largely unclear. We show that carboplatin treated TNBC cells lose their circadian rhythms and promote the enrichment of CSCs. Notably, genetic ablation of the circadian clock by itself, without carboplatin treatment, facilitated the formation of CSCs along with their ability to generate 3D tumorspheres and mouse tumors enriched with CSCs. Mechanistically, we identified an antagonistic interplay between the circadian clock and pluripotency, whereby the core pluripotent factor OCT4 disrupts the expression of circadian timekeeping genes to disable the circadian clock. Furthermore, we uncovered a transcriptional pausing program, controlling the circadian clock, to be perturbed in carboplatin treated TNBC cells. Concordantly, based on gene expression analysis from The Cancer Genome Atlas (TCGA), we found that the uncoupling of transcriptional pausing and the circadian clock correlated with low survivability across diverse cancer types. Moreover, cancer patients with poor prognosis exhibit low expression of the core timekeeping genes Clock, Npas2, Bmal1 and Rorc. Lastly, we restored circadian rhythms in Oct4 deficient TNBC cells and impaired their ability to generate tumorspheres and decreased the number of CSCs in mouse tumors. Overall, our findings demonstrate an unprecedented mechanism for the formation of CSCs that is dependent on the loss of circadian rhythms and thereby has eminent implications for developing new cancer therapies.

cancer biology↗

bioRxiv2026

Spatial Glyco-Codes Define Human Liver Pathology and Progression

Glycosylation is a fundamental process regulating cellular function, tissue organization, and disease progression. However, comprehensive glycan profiling at single-cell spatial resolution remains largely inaccessible, particularly in clinical archival tissues. Here we develop spatial-GPT, a multimodal platform for simultaneous profiling of glycans, proteins, and/or transcripts in archival formalin-fixed paraffin-embedded (FFPE) tissues. Using a panel of 30 DNA-encoded lectins recognizing major mammalian glycan motifs and structural classes, sequencing-based spatial-GPT (DBiT-GPT) mapped the spatial glycome, proteome, and transcriptome across 16 human liver specimens encompassing steatosis, fibrosis, cirrhosis, and hepatocellular carcinoma (HCC), leading to identification of spatial glyco-codes - combinatorial glycan states associated with distinct cellular identities, tissue features, and pathological processes. Unexpectedly, glyco-codes alone were sufficient to resolve major cell types, disease states, and HCC subtypes, revealing a previously unappreciated level of biological information encoded within the tissue glycome. Spatial glycomics uncovered tumor-like glyco-codes in premalignant regions, suggesting that glycan reprogramming may precede overt malignant transformation. Using imaging-based single-cell spatial glycan-protein profiling (CODEX-GP), we track glyco-codes across the whole-tissue architecture of 3 representative HCC samples. We further examined the glyco-codes across more than 300 patient specimens and quantified cell-type- and disease-specific glyco-codes as well as glycan-defined immune-evasion, T-cell-exhaustion, and steato-fibrotic niches. Together, these findings establish spatial glyco-codes as a previously unrecognized layer of tissue organization that encodes cellular identity, tissue function, and disease progression. The ability of glyco-codes to distinguish major liver pathologies across independent patient cohorts further highlights their potential as a new class of molecular histopathology biomarkers.

pathology↗

bioRxiv2026

Senescence-associated loss of intestinal α1,2-fucose disrupts a modifiable host-microbiome homeostasis axis in people with HIV

BackgroundPeople with HIV (PWH), despite effective antiretroviral therapy (ART), experience disrupted intestinal homeostasis characterized by microbial dysbiosis and impaired intestinal barrier integrity, which contribute to chronic inflammation and aging-associated comorbidities. However, tractable mechanisms contributing to this dysfunction remain poorly defined. ObjectiveTo determine whether acquired loss of intestinal 1,2-fucose, a host-derived intrinsic prebiotic glycan that supports colonization by short-chain fatty acid (SCFA)-producing bacteria essential for intestinal barrier integrity, contributes to microbiome disruption, impaired epithelial resilience, inflammation, and biological aging in PWH. DesignIleal and colonic biopsies, isolated crypts, stool, and blood from PWH on ART and controls underwent multi-omic analyses. Findings were mechanistically interrogated using stool anaerobic fermentation assays and 3D intestinal organoid models of stress-mediated epithelial disruption. ResultsIn intestinal tissues, PWH exhibited reduced 1,2-fucosylation and increased senescence-associated expression of the fucose-degrading enzyme -L-fucosidase. Lower 1,2-fucose tracked with depletion of SCFA-producing bacteria, increased inflammation, and premature biological aging. In anaerobic fermentations, stool from PWH produced fewer SCFAs than controls, whereas supplementation with the human-milk-oligosaccharide-derived 1,2-fucose donor 2'-fucosyllactose restored SCFA production and improved intestinal organoid resilience to stress-mediated disruption. ConclusionThese findings identify acquired loss of intestinal 1,2-fucose as a modifiable host-microbiome mechanism linking epithelial senescence, microbial metabolic dysfunction, impaired barrier resilience, inflammation, and biological aging in treated HIV infection. SUMMARY BOXO_ST_ABSWhat is already known on this topicC_ST_ABSPeople with HIV on suppressive antiretroviral therapy frequently have persistent intestinal barrier dysfunction, microbial dysbiosis, chronic inflammation, and accelerated biological aging, but the host mechanisms that maintain this disrupted mucosal state remain incompletely defined. What this study addsThis study identifies acquired loss of intestinal 1,2-fucosylation as a feature of treated HIV infection and links this defect to a host fucosidase-high, senescence-enriched mucosal niche, depletion of SCFA-producing bacteria, impaired tight junction-associated barrier signatures, inflammation, and biological aging phenotypes. How this study might affect research, practice or policyThese findings support intestinal glycan ecology as a modifiable host-microbiome axis and provide a rationale for testing 1,2-fucose-replenishing strategies, such as 2'-fucosyllactose, to restore microbial metabolic output and improve epithelial resilience in people with HIV.

microbiology↗

bioRxiv2026

Long-Timescale Molecular Dynamics Reveal a Coordination-Biased Conformational Selection Mechanism for Sorcin Activation

Sorcin is a dimeric penta-EF-hand Ca2+-binding protein that regulates intracellular Ca2+ homeostasis through Ca2+-dependent conformational activation and target recognition, and it has also been implicated in multidrug resistance in cancer. Although crystal structures have defined the apo inactive and Ca2+-bound active states of Sorcin, the transition pathways connecting these states and the conformational ensembles populated under each condition remain poorly understood. Here, we used long-timescale all-atom molecular dynamics simulations on Anton 3, totaling [~]90 s, to define the Ca2+-coupled conformational landscape of dimeric human Sorcin at atomic resolution. Starting from the Ca2+-bound structure, we directly observed the transition from the active to the inactive state following Ca2+ removal, demonstrating that loss of Ca2+ coordination is sufficient to drive inactivation on the microsecond timescale. Simulations initiated from the Ca2+-bound crystal structure with retained ions unexpectedly revealed ultrafast Ca2+ dissociation and rebinding at all EF-hand sites, indicating weak intrinsic Ca2+ affinity and highly dynamic ion exchange. In complementary simulations initiated from the apo structure, Sorcin spontaneously sampled active-like conformations even in the absence of stable Ca2+ binding, supporting a conformational selection mechanism in which Ca2+ shifts the population toward pre-existing active states rather than inducing the transition de novo. Across all conditions, we also observed pronounced and persistent structural asymmetry between the two protomers, revealing that the Sorcin homodimer is dynamically heterogeneous despite its symmetric crystal structures. Together, these results support a coordination-biased conformational selection model for Sorcin activation, in which weak and rapidly exchanging Ca2+ binding stabilizes, rather than induces, the active state. This work provides a dynamic framework for understanding Sorcin function as a fast Ca2+ sensor and offers broader mechanistic insight into activation principles of EF-hand Ca2+-binding proteins.

biophysics↗

bioRxiv2026

Culture-Free Rapid Phenotypic Antimicrobial Susceptibility Testing for Helicobacter pylori Based on Fluorescence Rapid On-Site Evaluation Technology: A Preliminary Study

BackgroundPhenotypic antibiotic susceptibility testing (AST) for Helicobacter pylori (H. pylori) has relied on bacterial culture for three decades, requiring 5-7 days to yield results. Genotypic rapid tests can only detect known resistance mutations and fail to reliably identify amoxicillin resistance. To our knowledge, no culture-free rapid phenotypic AST method for H. pylori has been previously reported. MethodsWe developed a phenotypic AST method based on fluorescence rapid on-site evaluation (ROSE) technology that completely bypasses bacterial culture. Gastric mucosal biopsy specimens from 40 H. pylori-positive patients were homogenized and co-incubated with an acridine orange/ethidium bromide (AO/EB)-based viability staining reagent and three first-line antibiotics--amoxicillin, clarithromycin, and levofloxacin--at concentrations corresponding to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints for H. pylori, at 37 {degrees}C for 1 hour. Fluorescence intensity was measured using a microplate reader. A reduction in fluorescence relative to an antibiotic-free control indicated susceptibility, whereas no significant reduction indicated resistance. Conventional culture-based AST (E-test) served as the reference method. The overall concordance rate, sensitivity, specificity, and Cohens kappa coefficient were calculated. ResultsFourteen of the 40 samples had unsuccessful culture and were excluded, leaving 26 samples for statistical analysis of each antibiotic. The overall concordance rates between the ROSE method and culture-based AST were 84.6% (22/26) for amoxicillin, 76.9% (20/26) for levofloxacin, and 69.2% (18/26) for clarithromycin. Cohens kappa coefficients indicated moderate agreement for all three antibiotics ({kappa} = 0.523, 0.539, and 0.412, respectively). Unlike genotypic methods, the ROSE method successfully assessed amoxicillin susceptibility in all 40 patients--a critical first-line antibiotic for which no reliable genetic resistance marker currently exists. The turnaround time was approximately 1 hour (55-65 minutes), compared with 5-7 days for culture-based methods; preliminary estimates indicated a cost reduction of approximately 3,000-5,000 Chinese yuan (CNY) per patient, mainly attributable to the elimination of culture media, prolonged incubation, and repeat clinic visits. ConclusionsThis study reports, for the first time, a culture-free 1-hour phenotypic AST for H. pylori. The method enables same-day, susceptibility-guided treatment decisions, addressing an unmet clinical need spanning three decades. Algorithm optimization and a prospective randomized controlled trial are currently underway to further improve diagnostic accuracy and validate clinical utility.

microbiology↗

bioRxiv2026

Linguistic Analysis of Chinese Oral Performance in Different Tasks of Chinese Second Language Learners and Native Speakers

This study investigated how different forms of task influence the oral performance of Chinese second-language learners and native speakers. By analyzing data from 40 Chinese second-language learners and 40 native speakers through picture description tasks, formal and informal questions, and questions with different emotions (happy and unhappy), it was found that different task characteristics significantly affected language performance. Short picture tasks led to higher communication efficiency and noun rates but more errors, while long story tasks showed higher verb rates, function word rates, etc. Formal questions had more characters and nouns but lower communication efficiency compared to informal ones. Also, happy emotion questions resulted in fewer characters, sentences, and errors than unhappy emotion questions. These findings contribute to the theoretical understanding of task-based language performance in Chinese as a second language and offer practical implications for teaching, textbook compilation, and student evaluation.

scientific communication and education↗

bioRxiv2026

PACAPergic BAC engages basolateral amygdalar and anterodorsal thalamic networks during looming-threat learning and memory in a labyrinth

The bed nucleus of the anterior commissure (BAC) is a small pituitary adenylate cyclase-activating polypeptide (PACAP)-rich glutamatergic cell population located at the intersection of the anterior commissure, stria terminalis, stria medullaris, and fornix. Here, we provide functional neuroanatomical characterization of the BAC using PACAP-Cre mice and Cre-dependent viral tracing. BAC axons traverse these major forebrain conduits to engage distributed limbic and diencephalic networks, with dense innervation of the posterior basolateral amygdala (pBLA) and anterior dorsal thalamic nucleus (AD), both implicated in emotional processing and spatial orientation. To determine the functional significance of the BAC, we developed a novel looming-threat memory test (LTMT) paradigm in which mice learned the location of a shelter within a dual-maze labyrinth before exposure to an overhead looming stimulus. Chemogenetic inhibition of BAC PACAP neurons impaired shelter-directed escape, increased freezing behavior, prolonged escape trajectories, and disrupted efficient safety-seeking responses. Selective deletion of PACAP from BAC neurons also blocked key aspects of the looming-induced behavioral phenotype. Fos mapping revealed robust neuronal activation by the looming stimulus, within the AD, pBLA, and dorsal periaqueductal gray (dPAG). BAC silencing blocked Fos induction. PACAPBAC depletion blocked fos induction in AD, but not in pBLA or dPAG. Preliminary ex-vivo recordings further indicated that PACAP modulates the intrinsic excitability of AD (and pBLA) neurons. Together, these findings identify the BAC as a previously unrecognized PACAPergic forebrain hub that links emotional and spatial-orientation networks to coordinate looming-threat learning, memory, and adaptive defensive behavior.

neuroscience↗

bioRxiv2026

Genetically informed single-cell and spatial mapping of metabolic programs in human health and disease

Defining cell-type-specific endogenous metabolic features, the spatial distribution of cell-level metabolic states and cellular responses to exogenous metabolites is very important for understanding disease mechanisms. However, existing transcriptome-based metabolic models primarily infer intracellular reaction or pathway-level activities, and therefore cannot directly assess associations between individual metabolite levels and cellular states, particularly for metabolites that act extracellularly as signalling molecules rather than entering cells as metabolic substrates. To overcome this problem, we introduce the gmMAP (Genetically informed metabolite trait mapping across single-cell and spatial tissues), a framework that integrates metabolite GWAS summary statistics with single-cell and spatial transcriptomes to map metabolic programmes at cellular and spatial resolution. Notably, the gmMAP enables the prediction of endogenous metabolic process activation while also revealing intrinsic associations between exogenous metabolites and diverse cellular functional states. To further capture the connectivity of cellular metabolic networks, we incorporated a constraint-based metabolic flux model to evaluate global metabolic activity. To evaluate the accuracy and generalizability of gmMAP, we applied the framework across representative biological contexts spanning human development, physiological homeostasis, inflammation and cancer. In human kidney development, the gmMAP captured dynamic metabolic programmes, which was validated using paired transcriptomic and metabolomic reference datasets, supporting its reliability in metabolite identification and metabolic-flow inference. At the organ level, the gmMAP reconstructed spatial metabolite distribution patterns across 17 mouse organs under homeostatic and autoimmune inflammatory conditions, and further extension of gmMAP to 24 normal human tissues generated a multi-scale metabolic atlas at both organ and cellular resolutions. In disease settings, gmMAP revealed metabolic reprogramming across 29 pan-cancer cell populations, and identified potential links between exogenous metabolites and inflammation-associated stromal metabolic remodelling in ulcerative colitis. Together, gmMAP can consistently connect genetically informed metabolite traits with cell states, spatial tissue organization and disease pathology.

genomics↗

bioRxiv2026

The Two-Component System CrdRS Mediates Sub-inhibitory Antibiotic-Induced Biofilm Formation in Helicobacter pylori via Bidirectional Regulation of Transporters PlpA and GlnP

Biofilm formation by Helicobacter pylori is a major driver of antibiotic tolerance and treatment failure, yet the signaling pathways that trigger biofilm development under sub-inhibitory antibiotic pressure remain poorly understood. Here, we show that sub-MIC levels of metronidazole, amoxicillin, and ciprofloxacin potently induce dense H. pylori biofilms. Through transcriptomic and genetic analyses, we identify the two-component system CrdRS as a central signaling hub that orchestrates this response via the bidirectional regulation of two ATP-binding cassette (ABC) transporters. Phosphorylated CrdR binds to AC-rich promoter motifs to directly activate plpA, which encodes a substrate-binding protein that drives exopolysaccharide secretion and matrix assembly. Concomitantly, CrdR represses glnP, which encodes an inner-membrane permease, thereby relieving transcriptional inhibition of the L-asparaginase gene ansB. This derepression triggers aberrant reactive oxygen species (ROS) accumulation, which promotes oxidative stress-dependent biofilm maturation. Through phenotypic analysis of crdRS deletion mutants, phosphorylation-defective point mutants (CrdRD53A and CrdSH173A), and exogenous hydrogen peroxide (H2O2) induction, we demonstrate that CrdRS specifically responds to antibiotic-induced stress signals in a manner genetically separable from ROS sensing. Collectively, our findings establish a dual-mechanism model in which CrdRS orchestrates antibiotic-induced biofilm formation by simultaneously controlling matrix production and intracellular ROS generation. Notably, glnP expression was significantly lower in clinical multidrug-resistant isolates than in drug-sensitive ones, whereas plpA showed the opposite trend. These findings provide a mechanistic foundation for developing CrdRS-targeted strategies to combat biofilm-associated H. pylori infections.

microbiology↗

bioRxiv2026

Peri-Locus Coeruleus Controls Endothelial Cell Heterogeneity in Enriched Environments via Region-Specific Norepinephrine Signaling

The brain acts as a central integrator that enables organisms to interpret environmental stimuli and coordinate adaptive responses across the body. While enriched environments are known to enhance neural plasticity and cognitive function, their impact on peripheral organ systems remains less understood. Here, we show that enriched environmental conditions activate a peri-locus coeruleus (peri-LC) neuronal ensemble that preserves CD31hiEMCNhi type H endothelium, a specialized bone-associated endothelial subtype, against age-associated decline, thereby enhancing femoral bone density. Chemogenetic activation and ablation experiments further revealed that this peri-LC ensemble is functionally distinct from other sympathetic regulatory brain regions in its control of bone endothelial heterogeneity and skeletal mass. Three-dimensional bone clearing and spatial analyses showed that CD31hiEMCNhi endothelium is closely associated with sympathetic nerve terminals. The peri-LC mediates this process through sympathetic signaling and {beta}2-adrenergic receptors on bone vascular endothelial cells. In vivo imaging further demonstrated that norepinephrine release is spatially restricted, with sprouting endothelial cells near the growth plate exhibiting the highest sensitivity. Together, these findings reveal a refined brain-periphery regulatory logic in which distinct sympathetic brain circuits engage spatially restricted norepinephrine signaling to coordinate organ-specific vascular and skeletal adaptations.

neuroscience↗

bioRxiv2026

Pulse-driven and persistent antimicrobial resistance markers in a transboundary Great Lakes connecting channel: pulse-week-stratified water-quality thresholds for One Health surveillance

Surface waters in urban watersheds receive episodic inputs of wastewater, runoff, and road-salt residues during spring, yet the contribution of these short hydrological windows to antibiotic resistance gene (ARG) loading remains poorly resolved. Weekly samples were collected from offshore and nearshore sites in the Detroit River, a Great Lakes transboundary connecting channel, from February to December 2025. Five clinically relevant ARGs encoding resistance to carbapenems, methicillin, and colistin, alongside the fecal marker pepper mild mottle virus (PMMoV), were quantified by qPCR and paired with ten conventional water-quality variables. blaNDM, mcr-1, and blaVIM-7 were not detected while blaKPC occurred as discrete pulses. One week (5 May) accounted for 37.2% of annual offshore blaKPC loading, and three weeks in late April to early May accounted for 72.8%, with peak concentrations reaching 5.4 x 103 and 7.2 x 103 copies L{square}{superscript 1}. mecA was detected in nearly all samples without a dominant pulse. PMMoV normalization showed blaKPC did not vary seasonally (Kruskal-Wallis p = 0.198), consistent with diluted wastewater during spring precipitation events rather than an emergent source. mecA/PMMoV varied seasonally (p = 0.003) and was lowest in spring, implicating non-wastewater inputs in summer and autumn. Seven water-quality variables were significantly elevated during blaKPC pulse weeks. PCA distinguished pulse from background conditions, explaining 81.3% of variance. A random forest classifier achieved leave-one-out AUC of 0.917; ROC AUC reached 0.943 for total phosphorus, 0.924 for chloride, and 0.974 for the multivariate model. These results demonstrate that blaKPC and mecA operate through distinct source pathways and that routine water-quality monitoring can flag elevated blaKPC risk without additional sampling infrastructure.

microbiology↗

bioRxiv2026

Fitness and immune-escape within germinal centers shape premalignant evolution toward lymphoma

Germinal centers (GCs) support physiological B-cell mutagenesis and are considered lymphoma-permissive; nevertheless, lymphoma development is uncommon. Human in situ follicular neoplasia (ISFN) captures this paradox: premalignant B-cells can persist within GCs for prolonged periods without progressing to overt lymphoma. We found that human ISFN, but not normal GCs, are infiltrated by CD8 T-cells, suggesting that premalignant GC B-cells are locally immune-surveilled. Using mouse models that separate early premalignant fitness from lymphoma-associated evolution, we show that fitness-enhanced premalignant GC B-cells expand transiently but are selectively eliminated by infiltrating cytotoxic CD8 T-cells, while normal GC B-cells are spared. By contrast, evolved premalignant GC B-cells retain their fitness but disable productive CD8 T-cell cytotoxic differentiation, allowing persistence and lymphoma-like transcriptional and genomic evolution. These findings establish GCs as active immune-surveillance sites and show that progression from premalignancy to lymphoma requires both enhanced GC fitness and escape from local immune control. Key findingsGCs undergo active immune-surveillance to detect premalignant B-cells. Premalignant GC B-cells trigger cytotoxic CD8 T-cell responses. Lymphoma-associated evolution enables immune-escape within GCs. Fitness and immune-escape drive evolution from premalignancy to lymphoma. BlurbGerminal centers are considered lymphoma-permissive; however, progression from premalignancy is uncommon. Using models of human in situ follicular neoplasia, Zhang et al. demonstrate that infiltrating CD8 T-cells actively eliminate premalignant GC B-cells. Co-occurrence of lymphoma-like alterations blocks this cytotoxic T-cell response, driving immune escape and lymphoma evolution.

cancer biology↗

bioRxiv2026

Conversion of a Viral Glycan Shield into a Binding Anchor via Causal-Driven Antibody Optimization

Therapeutic antibodies are challenged by rapidly evolving pathogens that exploit glycosylation to shield epitopes. SARS-CoV-2 JN.1 exemplifies this, escaping antibodies through the N354-linked glycan. However, targeting glycosylated epitopes remains vacant, as scarce and heterogeneous glycan structures render existing approaches ineffective. Here, we introduce the Antibody Evolution Nexus with Causal-Driven Simulation (AENCS), integrating molecular simulation with causal inference. Applying AENCS to restore S309 efficacy against JN.1, we identified ACC01, exhibiting [~]24-fold improved neutralization. With limited prior knowledge of the N354 glycosylation site, ACC01 stabilized this glycan conformation, facilitating the determination of its cryo-EM structure. Causal dissection revealed how this glycan shield is functionally inverted into a binding anchor through multi-layered interactions. This mechanistic conversion, combined with the conservation of N354 glycosylation, enabled ACC01 to maintain potent activity against the latest variant NB.1.8.1. Collectively, AENCS demonstrates causal-driven antibody engineering can illuminate cryptic glycosylated epitopes, providing viable paradigms for exploring this vacant frontier.

bioengineering↗

bioRxiv2026

Beyond statistical significance: ranking transcription factor binding motifs by effect size

Chromatin immunoprecipitation-sequencing (ChIP-seq) has wide use in identifying transcription factor binding sites. DNA sequence motifs specific to a targeted transcription factor occur more frequently near ChIP-seq peak centres. The most common approach to quantifying relative motif enrichment ranks motifs by p-value. Because sample sizes can vary substantially across examined motifs, p-value magnitudes may reflect this heterogeneity rather than the biological effect of interest. As alternatives, we considered four ranking methods based on effect sizes: (a) a modified Cliffs delta, (b) the lower bound of a frequentist asymptotic confidence interval, (c) the lower bound of a frequentist finite-sample confidence interval, and (d) the lower bound of a Bayesian credible region. Through extensive simulations, the four alternatives better recovered the simulated central-enrichment ordering under heterogeneous sample sizes. Using published ChIP-seq data for GATA3, the effect size methods ranked the known targeted motif highest, even compared to highly similar motifs for other GATA family members, while p-value ranking did not. In a separate SRF application, all four alternative methods also consistently ranked the known motif highest. We recommend the asymptotic confidence interval lower bound for its simplicity, ease of implementation, and intuitive interpretation. The software is freely available (https://github.com/ScottMastro/motif-ranking).

bioinformatics↗