Biology subjects

Zhang, L.

Publications and source records attributed to Zhang, L..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

ONC201 in combination with ATR inhibitor ceralasertib exhibits potent synergy in ovarian cancer cells

Ovarian cancer stands out as one of the most lethal gynecological cancers among women in the United States. While patients with ovarian cancer often show positive responses to treatment, it is common for the cancer to reappear and develop resistance to treatment, so it is important to explore and create novel combinations to increase patient survival rates. ATRi (Ataxia telangiectasia and Rad3-related inhibitors) and ONC201 monotherapies have shown efficacy in ovarian cancer in preclinical models. We hypothesized that combining ATRi with ONC201 would enhance this efficacy. ONC201 induces apoptosis through the TRAIL-pathway following activation of the integrated stress response and inactivation of Akt which is upregulated in ovarian cancer. Six human ovarian cancer cell lines were treated alone and with the novel drug combination of ceralasertib (ATRi) and ONC201. We found an IC50 range of 0.88-20.16 microM for ONC201 and IC50 range of 0.55-54.75 microM for ceralasertib. The combination of ONC201 plus ceralasertib resulted in PARP cleavage consistent with apoptosis along with reduction in Bcl-XL, Xiap and p-Akt expression after 72 hours of treatment. Cytokine profiling showed a decrease in markers of inflammation and tumor progression. Our data provide evidence of synergy from the combination of ATRi ceralasertib and ONC201 against Ovarian cancer cells that merits further investigation including clinical translation.

cancer biology↗

bioRxiv2026

Autism genes converge on three functional programs organized by neuronal subclass, developmental timing, and cortical patterning

Our companion sequencing study uncovered 253 genes robustly associated with autism spectrum disorder (ASD), yet the biological programs they impact, and the cellular, developmental, and spatial contexts in which they converge, remain unresolved. Here we systematically contextualize genes associated with ASD across neurodevelopment and cortical areas, integrating developmental single-cell and spatial atlases with gene- and isoform co-expression, regulatory, proteomic, and synaptic networks. Genetic burden concentrates within temporally-resolved neuronal subclasses: newborn excitatory neurons, immature interneurons, and maturing intratelencephalic lineages. Genes associated with ASD converge on three functional programs--gene regulation, neuronal morphogenesis, and synaptic transmembrane signaling machinery--resolved from 28 ASD-associated networks, several of which are directly regulated by ASD genes including MEF2C, SOX11, and FOXP2. These programs are spatially patterned, with risk genes exhibiting an increasing anterior-to-posterior cortical expression gradient, anchored in the primary visual cortex and driven by excitatory neuron gene-regulatory programs. Finally, ASD risk genes associated with more severe developmental phenotypes show broader excitatory neuron enrichment and less interneuron involvement. Together, these findings anchor ASD genetic vulnerability to specific neurodevelopmental lineages, epochs, and molecular substrates, and delineate the features that distinguish ASD from comorbidities with broader developmental impacts.

genomics↗

bioRxiv2026

Maleic acid adjuvates BCG to induce CD4+CD8+ T cells and sterilize tuberculosis

Anti-tuberculosis (TB) immunity typically emphasizes CD4+ T and CD8+ T cells that only provide limited protection against Mycobacterium tuberculosis (Mtb) infection. The anti-TB function of CD4+CD8+ T cells remains unexplored, mostly due to the dogma that ThPOK and Runx3 antagonize each other to block their development and their scarcity. Here, we show that immunization of BCG (Bacillus Calmette-Gu&eacuterin) with Complete Freund's Adjuvant (CFA) markedly induced CD4+CD8+ T cells through the gut microbiota Clostridium butyricum or its metabolite maleic acid. Mtb-specific CD4+CD8+ T cells exhibited a broad T-cell receptor repertoire and sterilized Mtb infection by inducing SLAMF1 and neutrophil responses. Mechanistically, maleic acid interacted with PAK2 to promote STAT5 phosphorylation at Ser127, thus upregulating Ets1 expression. Direct binding of Ets1 to the Runx3 and ThPOK promoters orchestrated their expression to redirect the CD8+ T cell differentiation towards the CD4+CD8+ lineage. Moreover, immunization of BCG plus Clostridium butyricum or maleic acid sterilized Mtb infection in mouse models. These findings establish CD4+CD8+ T cells as superior immune effectors against Mtb, a concept that could fundamentally redirect the current paradigm for anti-TB vaccine development.

microbiology↗

bioRxiv2026

NEMP1 organizes the meiotic telomere LINC interface to control chromosome movement and telomere integrity

Nuclear Envelope Membrane Protein 1 (NEMP1) is highly expressed in oocytes and required for fertility, yet its meiotic function remains poorly understood. Here, we identify NEMP1 as a critical organizer of meiotic telomere-nuclear envelope coupling and chromosome dynamics. Loss of NEMP1 causes telomere aggregation, loss of shelterin protection, telomere shortening, persistent DNA damage, aberrant non-homologous end joining, and chromosome end-to-end fusion, ultimately leading to aneuploidy in mouse oocyte. NEMP1 is required during early fetal meiotic prophase I for telomere-nuclear envelope attachment, bouquet formation, homolog pairing, and synapsis. Live cell imaging revealed robust rapid prophase movements in wild-type meiocytes, which were nearly abolished by NEMP1 loss and restored by NEMP1-GFP re-expression. Mechanistically, NEMP1 associates with telomeric DNA and the SUN1-KASH5 LINC machinery, and SUN1-GFP restores chromosome movement in Nemp1-deficient meiocytes. Together, these findings establish NEMP1 as a nuclear-envelope organizer linking telomere protection, chromosome dynamics, and genome integrity during mammalian oogenesis.

developmental biology↗

bioRxiv2026

An in vivo chemical genetic approach for targeted glycoproteome analysis in Drosophila melanogaster

Glycans impact every aspect of physiology. Despite the rapid increase in relevance and translational potential, there remains a lack of tools for studying glycosylation in vivo. Here, we present FlyMOE, a chemical-genetic platform for targeted glycoprotein profiling in Drosophila melanogaster. Transgenic flies are equipped with biosynthetic capabilities to install bioorthogonally-tagged monosaccharides into the cellular glycoproteome. The genetic tractability of Drosophila allows for versatile application based on developmental stages, genetic drivers and glycosyltransferase enzymes. We employ FlyMOE to create an overview of the glycoproteome of Drosophila tissues and embryos based on mass spectrometry glycoproteomics, and investigate the substrates of individual members of the PGANT glycosyltransferase family in vivo. FlyMOE will allow the detailed investigation of the glycoproteome in Drosophila and similarly genetically modifiable in vivo model systems.

bioengineering↗

bioRxiv2026

Parallel Arg/N-degron recognition systems regulate coenzyme A biosynthesis

Coenzyme A (CoA) is an essential metabolic cofactor whose biosynthesis is controlled by pantothenate kinases (PANKs), the rate-limiting enzymes in CoA synthesis. Although CoA production is extensively regulated, whether PANK abundance is controlled by selective protein degradation remains unknown. Here, we identify PANK1{beta} and PANK3 as substrates of the Arg/N-degron pathway. Two mechanistically distinct E3 ligase systems, UBR4-KCMF1 and MKLN1-CTLH, independently converge on a common N-terminal MK Arg/N-degron to promote PANK degradation and restrict CoA biosynthesis. UBR4-KCMF1 recognizes the MK Arg/N-degron through KCMF1 ZZ domain, whereas CTLH complex employs the B30.2-domain proteins RanBP9 and RanBP10 as previously unrecognized Arg/N-degron recognins. Structural, biochemical, and cellular analyses demonstrate that RanBP9 and RanBP10 recognize both Met-X and canonical Arg/N-degrons through their B30.2 domains, using a mechanism distinct from canonical UBR proteins. Together, these findings establish a new branch of the mammalian Arg/N-degron pathway and reveal ubiquitin-dependent control of PANK abundance in CoA homeostasis.

molecular biology↗

bioRxiv2026

An Oxidative Stress-Associated Seven-Gene Prognostic Signature in Lung Adenocarcinoma: Integrative Transcriptomic Analysis Across Public Cohorts

Lung adenocarcinoma is molecularly heterogeneous, and oxidative-stress programs can support either tumor restraint or tumor adaptation depending on cellular context. This study integrated public lung adenocarcinoma transcriptomic cohorts to identify oxidative-stress-associated expression features and evaluate their prognostic relevance. Expression profiles from The Cancer Genome Atlas, Genotype-Tissue Expression project, and GEO series GSE31210, GSE40791, and GSE30219 were analyzed. Differential expression, weighted gene co-expression network analysis, functional enrichment, univariable Cox regression, and least absolute shrinkage and selection operator Cox modeling were combined to derive a risk signature. Immune-cell enrichment, gene set enrichment analysis, gene set variation analysis, and pan-cancer analyses were used for biological characterization. A total of 1,305 genes differed between tumor and control samples, including 498 upregulated and 807 downregulated genes. Intersection of differentially expressed genes, the oxidative-stress-associated co-expression module, and the oxidative-stress gene set yielded 44 genes enriched in responses to reactive oxygen species and hydrogen peroxide, antioxidant and peroxidase activities, focal adhesion, Rap1 signaling, and PI3K-Akt signaling. A seven-gene signature comprising FBLN5, HBB, FYN, HGF, TFAP2A, PLIN5, and F2RL1 stratified the 523-sample training cohort and the 207-sample internal validation cohort into groups with different overall survival. Time-dependent areas under the receiver operating characteristic curve at 1, 3, and 5 years were 0.677, 0.622, and 0.649 in training and 0.613, 0.691, and 0.706 in internal validation. In the 85-case GSE30219 external cohort, corresponding values were 0.588, 0.661, and 0.631; survival separation followed the expected direction but did not reach statistical significance (log-rank P = 0.100). Seventeen immune-cell signatures differed between risk groups, while high-risk tumors were enriched for cell-cycle, DNA-replication, mismatch-repair, glycolytic, E2F, G2M-checkpoint, MYC-target, and mTORC1-related programs. The signature therefore captures reproducible oxidative-stress-associated transcriptional variation with moderate prognostic discrimination. Its clinical utility requires prospective evaluation, complete clinical adjustment, and experimental validation.

cancer biology↗

bioRxiv2026

Conserved microglial programmes, non-transferable classifiers: boundaries of the single-cell TBI molecular clock

Background: Traumatic brain injury (TBI) pathology evolves over hours to months, and molecular staging could complement clinical and imaging-based assessment. Single-cell transcriptomics captures cell-type-resolved temporal programs, but whether a transcriptional "molecular clock" trained on one injury model can be transferred to others remains unknown. Methods: We compiled four public mouse TBI single-cell/single-nucleus datasets spanning two injury models - controlled cortical impact (GSE277487; CEREBRI) and fluid percussion injury (GSE160763) - plus an independent mild-FPI cohort reserved for validation (GSE247339), totalling 307,991 cells across four pathological stages (control, acute, subacute, chronic). Classifiers were evaluated at cell and sample levels (held-out libraries) against a permutation null, with per-cell-type, strict leave-one-dataset-out (LODO) generalization, glial-only transfer and gene-level SHAP analyses. Results: Within GSE277487, sample-level balanced accuracy reached 0.67 (permutation null 0.32 +/- 0.09; p = 0.001), and the signal was reproduced in the independent mild-FPI cohort (0.40 vs null 0.19 +/- 0.05; p = 0.0010). Cell-level cross-validation overestimated performance by ~0.16, quantifying within-sample leakage. Cross-dataset generalization was poor (strict LODO balanced accuracy 0.20-0.31); the acute immediate-early response was untransferable (recall 0.002) and 80% of chronic (6-month) cells were assigned to the subacute class. Glial-only models raised subacute recall across models (0.91 and 0.75), but precision was indistinguishable from a subacute-only classifier (0.51 vs 0.50; 0.58 vs 0.58) and one-vs-rest AUROC was at or below chance (0.38-0.54) across four classifier families - classifier collapse, not transferable discrimination. The reproducible cross-model component was instead a gene-expression programme: a microglial complement/lysosomal damage programme (Trem2-Apoe axis) was up-regulated across the severe CCI and FPI models (13/13 concordant genes), whereas the immediate-early module was model-specific. Conclusions: A single-cell molecular clock for TBI staging is feasible within datasets once within-sample leakage is controlled, but it does not transfer across datasets as a classifier: apparent cross-model transfer reflected classifier collapse onto the majority class, and the reproducible cross-model component was a microglial complement/lysosomal gene-expression programme. These findings define the boundaries of cross-dataset time inference in TBI and provide evaluation criteria for claims of transferable single-cell classifiers.

neuroscience↗

bioRxiv2026

Brain deviation scores derived from normative modelling identify dimensions of psychopathology in children and adolescents

Psychiatric diagnoses lack neurobiological grounding, and brain based abnormalities correspond poorly to established diagnostic categories. While multivariate algorithms extract transdiagnostic dimensions from brain behavior covariation, most studies rely on conventional structural morphometric measures such as cortical thickness and surface area, which fail to capture atypical developmental trajectories. Normative modeling (NM) quantifies individual-level brain deviation scores by contrasting brain structural features with population derived percentiles, yielding continuous indices of atypical brain development. However, whether these scores can identify transdiagnostic dimensions remains unclear. We applied sparse canonical correlation analysis (sCCA) to investigate covariation between brain deviation scores and psychiatric symptoms in 1095 children and adolescents from the Healthy Brain Network. We identified an emotion-dysregulation dimension (r=0.33). When generalized to the independent cohort, this dimension showed nominal significance (r=0.18, PFDR = 0.05, uncorrectedP=0.01, n=198). By contrast, no significant dimension was detected using conventional structural brain features. Emotion dysregulation was primarily driven by deviations in cortical thickness and surface area, with distinct regional distributions; reductions in cortical surface area in the middle frontal gyrus, cingulate gyrus, superior temporal gyrus, and insula carried the highest weights. Latent brain scores for emotion dysregulation, computed using sCCA weights for brain deviation scores, showed specific correlations with out-of-model emotion dysregulation related phenotypes. In addition, females exhibited significantly higher latent brain scores than males. Collectively, NM based brain deviation scores were more sensitive than conventional structural metrics in identifying transdiagnostic psychiatric dimensions. Furthermore, latent brain scores derived from sCCA estimated weights may serve as a straightforward metric that captures the degree of dimension-specific atypical brain deviation.

neuroscience↗

bioRxiv2026

A peptidomimetic inhibitor blocks Vibrio cholerae adhesin FrhA.

Cholera is a diarrheal disease from colonization of the small intestine by the Gram-negative bacterium Vibrio cholerae. Cholera remains a critical public health concern due to limitations in therapy and rising antibiotic resistance. The peptide-binding domain (PBD) of the adhesion protein FrhA is critical for V. cholerae intestinal colonization and biofilm formation. In a program targeted on blocking cholera infection, antagonists of the FrhA-PBD are described based on a tripeptide motif. Notably, constraint of the N-terminal tryptophan residue using 1,2,3,4-tetrahydro-{beta}-carboline-3-carboxylic acid (Tcc) and co-crystallization of H-(S)-Tcc-Thr-Asp-OH with an FrhA construct has provided structural information to guide inhibitor design. The diastereomer (R)-Tcc-Thr-Asp exhibited nanomolar binding affinity (Kd = 101 {+/-} 30.2 nM). H-(R)-Tcc-Thr-Asp-OH blocked bacterial hemagglutination mediated by FrhA-PBD and reduced biofilm formation in vitro. Moreover, it showed greater resistance to the digestive enzyme chymotrypsin than previously reported inhibitory pentapeptides, offering potential proteolytic stability while blocking FrhA-PBD-mediated adhesion in the intestine.

biochemistry↗

bioRxiv2026

Targeting Macrophage Connexin 43 Hemichannels Suppresses Synovial Inflammation and Osteoarthritis

Osteoarthritis (OA) is the most common chronic joint disease and a leading cause of disability worldwide, yet no disease-modifying therapies are available. Although OA has traditionally been viewed as a cartilage-centered degenerative disease, growing evidence suggests that synovial inflammation is a critical driver of disease progression. However, the upstream mechanisms and actionable targets that govern this inflammatory response remain poorly defined. Connexin 43 (Cx43), a key regulator of musculoskeletal homeostasis that forms both gap junctions and hemichannels (HCs), is upregulated in osteoarthritic cartilage and synovium, but the specific contribution of Cx43 channels remains unclear. Here, we show that selective inhibition of Cx43 HCs attenuates OA progression in a murine post-traumatic OA model. Using adeno-associated virus (AAV)-mediated gene deletion, we found that Cx43 knockdown in joint tissues reduced cartilage erosion, synovial hyperplasia, subchondral bone sclerosis, and OA-associated pain. To dissect HC-specific functions, we developed a monoclonal antibody, Cx43(M1), that blocks Cx43 HCs without affecting junctional communication. Cx43(M1) preserved cartilage integrity, suppressed synovial inflammation, and alleviated pain behaviors, even when treatment was initiated after established cartilage damage. Mechanistically, the antibody preferentially localized to synovial macrophages, where it inhibited HC activity, reduced ATP and PGE2 release, and suppressed pro-inflammatory gene expression. Macrophage-specific Cx43 deletion recapitulated these protective effects, and Cx43 HC blockade in primary human OA synovial macrophages similarly inhibited inflammatory and catabolic responses. These findings identify synovial macrophage Cx43 HCs as upstream drivers of OA and support a paradigm shift from a predominantly chondrocyte-centered view toward synovial macrophage directed intervention.

immunology↗

bioRxiv2026

Cyclic-thiourea ionizable lipids program multilamellar mRNA-LNPs for sustained expression, frozen-storage stability and potent vaccine immunotherapy

Lipid nanoparticles (LNPs) are the leading delivery vehicles for mRNA therapeutics, yet transient expression and limited formulation stability constrain their broader therapeutic application. Here we report the phenotype-driven discovery of an ionizable lipid (HI-62) bearing a 1,3,5-triazinane-2-thione (cyclic-thiourea) headgroup that reproducibly assemble mRNA into onion-like multilamellar nanoparticles. Cryogenic electron microscopy revealed ordered internal lamellae, while molecular-dynamics simulations supported a cooperative assembly model involving pH-responsive electrostatics, headgroup preorganization and short-range directional interactions. The lead HI-62 formulation maintained greater than 95% mRNA encapsulation across N/P ratios of 3-7, prolonged reporter expression for substantially longer durations than benchmark formulations following intravenous and intramuscular delivery, and retains physicochemical integrity and in vivo potency after repeated freeze-thaw cycles and 18 months of storage at -20. In the tumor models, HI-62 elicits robust cellular responses and achieved significant inhibition of tumor growth. These findings establish cyclic-thiourea headgroup chemistry as a design principle for programming lipid-RNA organization into multilamellar architecture, and provide a design principle for next-generation LNPs platform with durable protein expression and superior stability. The HI-62-based formulation has been utilized in mRNA cancer vaccine program which will enter clinical development in months.

bioengineering↗

bioRxiv2026

AnnoAudit: a marker-based protocol for auditing single-cell atlas annotations reveals annotation-driven artifacts in a widely used traumatic brain injury resource

Single-cell atlas annotations are routinely treated as ground truth but rarely validated before use. We present AnnoAudit, a marker-based audit protocol that combines four convergent checks - marker scoring, unsupervised clustering, margin-gated module scoring, and applicability-gated pretrained models - into a composite Annotation Contamination Score (ACS), plus an independent-gene discrimination step that distinguishes genuine mis-assignment from ambient-RNA detection artifacts, and a trajectory-correlation fingerprint tracing suspicious signals to their cell type of origin. Applied to CEREBRI (GSE269748), a widely used single-cell TBI atlas (73 citations; 65 citing works; six re-analysis studies, none of which validated the annotations), the audit shows that contamination is systematic: the official "glutamatergic neuron" label is 97.8% non-excitatory by markers, with at least 67.4% of its cells independently confirmed as non-neuronal (microglia-dominated); the GABAergic (46.6%), OPC (66.1%), and astrocyte (37.7%) labels are likewise contaminated by marker-confirmed microglia, whereas the microglial, oligodendrocyte, endothelial, and pericyte labels are largely clean (85-96% self-confirmed). The contamination is state-dependent: astrocyte and OPC labels are largely correct in uninjured controls (76.0% OPC self-marker; 18.5% discrimination-confirmed contamination for the astrocyte label) but collapse in the acute 24-h window (14-16% self-marker; 57-71% microglia), recovering by 6 months - so the annotation failure concentrates precisely in the window of maximal injury response. This temporal structure generates coherent false signals - a biphasic trajectory for 40 of 307 ion-channel genes, a KCNC3-specific OXPHOS signature, and an inverted KCNC3 trajectory at 7 days - whereas the corrected response is a sustained acute KCNC3 up-regulation conserved across three independent datasets and three injury models. Simulation-calibrated ACS is 82.6% for CEREBRI. In a human ALS atlas (GSE330130), an ambient-aware re-analysis shows that the official neuron labels are largely correct (1.8-6.1% contamination after discrimination), confirming that the audit does not flag well-annotated resources, and that marker-only estimates on snRNA data with high ambient RNA must be interpreted with the discrimination step. AnnoAudit needs only the deposited count matrix and a canonical panel; we propose it as a routine quality step for atlas-based re-analysis.

bioinformatics↗

bioRxiv2026

Metabolic regulation and structural mechanism of glutamine synthetase AMPylation

In bacteria, glutamine synthetase (GS) is the main ammonium assimilation enzyme. Its activity is tightly regulated according to cellular energy status and carbon/nitrogen balance through reversible AMPylation catalyzed by the bifunctional enzyme GlnE, which is controlled by the signal transducer GlnB protein. Although GS AMPylation has been extensively studied, the GlnB:GlnE:GS regulatory pathway exhibits substantial plasticity among bacterial groups, and the structural basis of GS inhibition by AMPylation remains unclear. Here, we describe how carbon, nitrogen, and energy signals regulate GS AMPylation in Herbaspirillum seropedicae and uncover the structural mechanism underlying enzyme inhibition. Our data reveal that GS AMPylation is independent of unmodified GlnB, whereas uridylylated GlnB (GlnB-UMP) inhibits AMPylation under nitrogen-limiting conditions through a GlnB-GlnE complex modulated by 2-oxoglutarate. We further show that GlnE directly senses glutamine under nitrogen-sufficient conditions, with signal integration depending primarily on energy availability. To elucidate the mechanism of AMPylation GS inhibition, we solved Cryo-EM structures of unmodified and AMPylated GS in complex with MgATP and MnADP. Structural comparisons revealed that AMPylation increases the flexibility of the AMP-loop, disrupting a hydrogen-bond network that stabilizes Arg342 in the orientation required to position the ATP {gamma}-phosphate in its catalytic conformation for efficient phosphoryl transfer to glutamate. These findings reveal how metabolic signals are integrated to regulate GS AMPylation and provide the first structural insights into the mechanism underlying bacterial GS inhibition by AMPylation.

microbiology↗

bioRxiv2026

Copine-6 integrates calcium, phosphoinositide and Rab11 signals to coordinate glutamate receptor recycling

Endosomal trafficking is a major pathway that delivers cell-surface proteins, including glutamate receptors, to support neurotransmission and normal brain functions. Activity-dependent insertion of glutamate receptors is essential for synaptic plasticity, learning and memory. Copine-6 is a neuronal-specific calcium (Ca2+) binding protein that mediates activity-induced exocytosis of -amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA)-type glutamate receptors. The activation of N-methyl-D-aspartate (NMDA) receptors triggers Ca2+-dependent translocation of Copine-6 to intracellular endosomal compartments. However, the mechanisms underlying the activity-dependent accumulation of Copine-6 in endosomes remain unknown. Here, we show that Copine-6 exhibits Ca2+-dependent binding to phosphatidylinositol-3-phosphate (PI(3)P) through the C2B domain and displays enhanced interaction with active Rab11a in a Ca2+-independent manner via the vWA domain. Mutations in the C2B that inhibit binding to PI(3)P not only block the activity-induced translocation of Copine-6 to early endosomes, but it also causes an aberrant accumulation of Copine-6 in recycling endosomes. Consequently, loss of Copine-6 expression impairs the efficient coupling of early and recycling endosomes and blocks activity-dependent delivery of both AMPA and NMDA receptors onto the neuronal plasma membrane. These defects can be restored by re-expressing wild-type Copine-6, but not the C2B phospholipid-binding mutant. Together, our findings establish Copine-6 as a molecular bridge that enhances coupling between the early and recycling endosomal membranes, thereby facilitating the activity-dependent forward trafficking of glutamate receptors to the neuronal plasma membrane to maintain synaptic potentiation.

cell biology↗

bioRxiv2026

Peripheral Monocyte-Derived Extracellular Vesicles Establish an Immune-Brain Communication Pathway in Alzheimer's Disease

Alzheimer's disease (AD) is increasingly recognized as a systemic disorder involving both central and peripheral immune dysfunction, yet the mechanisms by which peripheral immune cells influence neurodegeneration remain poorly understood. Here we identify a physiological extracellular vesicle (EV)-mediated route through which peripheral monocytes communicate with neurons and show that AD-associated monocyte remodeling converts this pathway into a mechanism that mediates neuronal injury. Reanalysis of single-cell transcriptomic data revealed pronounced inflammatory and EV-related transcriptional remodeling in circulating monocytes from patients with AD. Using a genetic CD63-based EV tracking mouse, we found that EVs released from peripheral Lyz2-expressing myeloid cells, including monocytes, accessed the healthy brain parenchyma and preferentially associated with neurons. EVs isolated from primary peripheral monocytes of 5xFAD mice were enriched in inflammatory cargo, including IL-1{beta}, and markedly suppressed distal axonal growth. Neutralization of EV-associated IL-1{beta} partially restored axonal growth, identifying IL-1{beta} as an important mediator of EV-induced neuronal injury. A{beta} stimulation reproduced key features of this pathogenic EV phenotype in RAW 264.7 macrophage-like cells and induced coordinated metabolic dysfunction and pro-inflammatory activation in primary peripheral monocytes. Moreover, repeated systemic administration of EVs from A{beta}-stimulated RAW 264.7 cells accelerated behavioral and cognitive decline and reduced hippocampal synaptic integrity in 5xFAD mice without increasing cerebral amyloid plaque burden. Together, these findings reveal a peripheral monocyte-EV-neuron communication axis that operates under homeostatic conditions and can be redirected toward pathogenic signaling in AD. Targeting this EV-mediated pathway may provide a therapeutic strategy complementary to current A{beta}-directed approaches.

neuroscience↗

bioRxiv2026

Avs2 drives non-canonical tetrameric assembly of trypsin-like domain for anti-phage defense

Bacteria have evolved diverse anti-phage defense systems, with the antiviral STAND family (Avs) representing one of the most diverse and widespread, encompassing at least 90 distinct families, yet only Avs3, Avs4, Avs5 and Avs7 have been well characterized. Here, we elucidated the molecular mechanism of Avs2-trypsin-MBL system, where phage terminase recognition by Avs2 triggers coupled activation of the protease and nuclease activities of trypsin-MBL. Cryo-EM structure of Avs2-trypsin-terminase and biochemical analysis reveal that the binding of terminase ATPase domain triggers the assembly of Avs2 into tetramer, with two unique ATP molecules bridging ATPase active-site recognition by TPR domain. This tetramerization drives the fused trypsin into an active C4-symmetric assembly, an architecture distinct from the conventional non-defense trypsin. Our study unravels the activation mechanism of Avs2-trypsin-MBL system, expanding our understanding on commonality and diversity of widespread Avs-mediated anti-phage immunity, alongside the structural and functional adaption of trypsin.

microbiology↗

bioRxiv2026

An inflammation-associated five-gene expression signature stratifies survival and immune states in lung adenocarcinoma: an integrative public-cohort analysis

Background: Inflammation and the tumor immune microenvironment contribute to lung adenocarcinoma (LUAD) progression, but the relationship among inflammation-linked transcriptional heterogeneity, patient survival, and immune-state variation remains incompletely defined. Objective: We aimed to identify inflammation-associated LUAD subtypes, derive a parsimonious survival-stratification signature, and characterize its immune and pathway context across public transcriptomic cohorts. Methods: Expression profiles and clinical data were obtained from TCGA-LUAD, GTEx normal lung, and GEO datasets GSE11969, GSE30219, GSE31210, and GSE40791. A curated set of 596 inflammation-related genes was used for consensus clustering. Differential-expression analysis, functional enrichment, univariate Cox regression, and LASSO-Cox modeling were integrated to construct a gene-expression risk score. The prognostic dataset comprised 730 cases and was randomly divided into training (n=502) and internal-validation (n=228) sets; 85 GSE30219 cases formed an external-validation cohort. Immune-cell enrichment, gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), and pan-cancer analyses were used for biological contextualization. Results: The LUAD-versus-control comparison identified 1,305 differentially expressed genes, including 498 upregulated and 807 downregulated genes. Consensus clustering resolved two inflammation-associated subtypes and 67 subtype-associated genes, of which 64 were higher and 3 were lower in Cluster 1 relative to Cluster 2. Thirty-three genes overlapped between the tumor-control and subtype contrasts. LASSO-Cox regression selected CHRDL1, FDCSP, CXCL13, CYP4B1, and S100P. The 1-, 3-, and 5-year areas under the time-dependent receiver operating characteristic curve were 0.6625, 0.6581, and 0.6658 in the training set; 0.7422, 0.6537, and 0.6761 in internal validation; and 0.6560, 0.6387, and 0.6753 in external validation. Risk groups differed across multiple T-cell, B-cell, natural-killer-cell, myeloid, dendritic-cell, macrophage, and granulocyte signatures. Positive GSEA signals included cell cycle (normalized enrichment score [NES]=2.67; adjusted P=1.42 x 10-), DNA replication (NES=2.52; adjusted P=2.52 x 10-), and mismatch repair (NES=2.20; adjusted P=1.77 x 10-). Conclusions: The five-gene expression score separated LUAD survival groups and captured coordinated proliferative and immune transcriptional states. Its moderate discrimination supports further biological and clinical validation rather than immediate clinical application.

bioinformatics↗