Biology subjects

Chen, X.

Publications and source records attributed to Chen, X..

At least 361 records · Page 20Linked to original sources

bioRxiv2025

Computational Design of Next-Gen Peptide Biopesticides: Targeting the Nicotinic Acetylcholine Receptor in Rice Pests Class

The brown planthopper (Nilaparvata lugens) threatens global rice production, and conventional pesticides face resistance and environmental challenges. We present a computational framework integrating AlphaFold3-predicted structure of the nicotinic acetylcholine receptor 3 subunit (nAChR-3) with multi-force-field molecular dynamics (MD) refinements to design peptide biopesticides. Crucially, we introduce "Dipeptide Probing", a high-throughput MD-based screening strategy employing 20 phenylalanine-containing dipeptides (F-X) to map dynamic binding sites. Unlike rigid docking or static free energy calculations, this approach captures transient interactions and cooperative binding phenomena, identifying Phe-Met (FM) as the top binder through hydrophobic contacts and multiple hydrogen bonding, while{pi} -stacking contributed minimally to complex stability, contradicting conventional paradigms. Additionally, MD simulations revealed an unexpected Aggregation-Induced Hydrophobicity Binding (AIHB) mechanism: FM dipeptides self-assemble via hydrogen bonds, orienting hydrophilic groups toward solvent and exposing hydrophobic surfaces to the target, thereby stabilizing complex formation to the helix bundle surface of nAChR-3. This cooperative behavior, undetectable by docking (e.g., AutoDock Vina failed to predict FM binding) or static energy methods, resolves limitations of reductionist approaches. Our work establishes "Dipeptide Probing" as a generalizable paradigm for dynamic binding-site mapping and underscores AIHBs potential to revolutionize peptide-based agrochemical design by leveraging emergent intra-/intermulti-molecule interactions.

plant biology↗

bioRxiv2025

Evolution of antibody cross-reactivity to influenza H5N1 neuraminidase from an N2-specific germline

The ongoing spread of highly pathogenic avian influenza H5N1 clade 2.3.4.4b virus in animals and its occasional spillover to humans have raised concerns about a potential H5N1 pandemic. Although recent studies have shown that pre-existing human antibodies can recognize H5N1 neuraminidase, the molecular basis of how this cross-reactivity develops remains poorly understood. In this study, we used a phage display antibody library derived from 245 healthy donors to isolate an antibody, HB420, that cross-reacts with neuraminidases of human H3N2 and avian H5N1 clade 2.3.4.4b viruses and confers protection in vivo. Cryo-EM analysis reveals that HB420 targets the neuraminidase active site by mimicking sialic acid binding through a single Asp residue. Furthermore, the inferred germline of HB420 is N2-specific but acquires cross-reactivity to H5N1 neuraminidase through somatic hypermutation. Overall, our findings provide insights into how neuraminidase antibody evolves breadth, which has important implications for the development of broadly protective influenza vaccines.

immunology↗

bioRxiv2025

ContrastQA: A Label-guided Graph Contrastive Learning-based approach for protein complex structure quality assessment

Despite recent progress, the Estimation of Model Accuracy (EMA) for protein complexes remains less advanced compared to that for protein monomers. A key challenge lies in effectively integrating both interface-specific and global structural information to accurately assess the quality of protein complexes. Here, we introduce ContrastQA, the first EMA framework for protein complexes that incorporates the proposed label-guided graph contrastive learning based on interface quality. By integrating a geometric graph neural network to model global structural features, ContrastQA effectively captures both local (interface-level) and global (structure-level) information for accurate model quality estimation. ContrastQA achieved ranking losses of 0.123 and 0.116 on the TMscore and GDT-TS metrics on the CASP16 dataset, which are 0.015 (10.9%) and 0.012 (8.7%) lower than the second-best EMA method with ranking losses of 0.138 and 0.128. Furthermore, for the more challenging CASP16 hard targets, our method achieved a TMscore ranking loss of 0.131, which is 0.023 (14.9%) lower than that of the second-best EMA method with a ranking loss of 0.154. Our study demonstrates the strong effectiveness of the label-guided graph contrastive learning module. These findings suggest that our graph contrastive learning framework serves as a valuable pre-training strategy for learning protein structure representations. The source code is available at https://github.com/Cao-Labs/ContrastQA. Significance StatementHigh-quality proteins generated by high-precision structural prediction methods for protein complexes helping biologists prioritize models for drug discovery and understanding disease mechanisms. Recent advances in predicting protein complex structures (like AlphaFold3) still struggle to match experimental precision. A critical bottleneck lies in accurately estimating the quality of predicted models-known as Estimation of Model Accuracy (EMA). Here, we introduce ContrastQA, implementing label-guided graph contrastive learning framework to explore the generalization of high-quality proteins. Our method demonstrates outstanding performance, provides an effective solution for assessing the structural quality of protein complexes.

bioinformatics↗

bioRxiv2025

Sialic Acid Identity Modulates Host Tropism of Sialoglycan-binding Viridans Group Streptococci

Microbial interactions with multiple species may expand the range of potential hosts, supporting both pathogen reservoirs and zoonotic spillover. Viridans group streptococci interact with host cells by engaging protein-attached glycosylations capped with terminal sialic acids (sialoglycans). One potential origin for host tropism of these streptococci arises because humans exclusively synthesize the N-acetylneuraminic acid (Neu5Ac) form of sialic acid, while non-human mammals synthesize both Neu5Ac and a hydroxylated N-glycolylneuraminic acid (Neu5Gc). However, the link between binding preference for these sialic acids and preference for host has not been tested experimentally. Here, we investigate sialoglycan-binding by Neu5Ac/Neu5Gc cross-reactive Siglec-like binding regions (SLBRs) from two strains of streptococci, Streptococcus gordonii strain Challis (SLBRHsa) and Streptococcus sanguinis strain SK36 (SLBRSrpA). Structural and computational analyses of SLBRHsa identified molecular details for the binding of disaccharides capped in Neu5Ac or Neu5Gc. Engineering SLBRHsa and SLBRSrpA for narrow selectivity to synthetic Neu5Gc-terminated glycans shifted the binding preference from authentic human plasma receptors to plasma receptors from rat sources. However, host receptor preference did not fully recapitulate purified Neu5Ac/Neu5Gc-capped sialoglycan preference. These findings suggest that sialic acid identity modulates, but does not uniquely determine, host preference by these streptococci. This work refines our understanding of host specificity and challenges prevailing assumptions about the relative role of sialic acids in host tropism.

pathology↗

bioRxiv2025

A spatial atlas of chemoradiation therapy in pancreatic cancer identifies cellular and microenvironmental determinants of persister populations

The molecular pathways involved in the response to radiation therapy in pancreatic ductal adenocarcinoma (PDAC) remain poorly understood. We aimed to elucidate the adaptive mechanisms and cellular interactions within PDAC to radiation therapy (RT). We constructed a transcriptomic landscape of the cellular subtypes and spatially resolved neighborhoods from 50 patient samples, including 16 longitudinally matched single cell RNA sequencing and 34 spatial transcriptomics specimens. To resolve shortcomings of cell-type mixtures in spatial data, we developed a novel statistical method called SpaCCI (spatially aware analysis of cell-cell interactions) to profile cell-cell interactions and ligand-receptor enrichment. This revealed CXCL12/TGF{beta}-driven persister cell niches where activated fibroblasts reprogram tumor- associated macrophages and spatially exclude stress-response CD8 T cells after RT. Persister cancer cells displayed transcriptional evidence of recalcitrance to metal-induced cell death pathways of ferroptosis and cuproptosis which were recapitulated in preclinical models. Our study reveals the selective pressures experienced by PDAC following RT that may help provide insight for future multimodal therapeutic strategies.

cancer biology↗

bioRxiv2025

Linear scaling reveals low-dimensional structure in observable microbial dynamics

Microbial communities often exhibit apparently complex dynamics driven by myriad interactions among community members and with their environments. Yet, practical modeling and control are often based on limited number of observables, raising a fundamental question: to what extent are these observed dynamics predictable given unobserved background complexity? Here, we report an emergent simplicity that the temporal dynamics of observable microbial populations can be captured by low- dimensional representations. Using variational autoencoders (VAEs), we define a critical latent dimension (Ec) that quantifies the minimal number of variables required to represent observable microbial dynamics. We find that Ec scales linearly with the number of observables, despite the complexity of unobserved background dynamics. This principle holds across simulations of ecological, spatial, and gene-transfer models, experiments with engineered and environment-derived communities, and human microbiomes. Our findings establish a scaling law for microbial community dynamics and demonstrate observable dynamics alone contain sufficient information for prediction and control, even without full knowledge of the community.

systems biology↗

bioRxiv2025

Nanopore Sequencing Unveils Somatic Structural Variations as Biomarkers in Laryngeal squamous cell carcinoma Genomes

Laryngeal squamous cell carcinoma (LSCC) is an aggressive cancer with poor quality of life, largely due to the absence of reliable molecular biomarkers for early diagnosis and prognosis. While somatic structural variations (SVs) have been documented in LSCC, conventional short-read sequencing approaches are inherently limited in detecting of large-scale somatic SVs, which are critical to understanding tumorigenesis. Here, we presented SomaGauss-SV, a somatic SVs detection workflow leveraging nanopore long-read sequencing data. Benchmarking against five paired tumor cell line datasets showed SomaGauss-SV consistently achieves a balanced high precision and recall. SomaGauss-SV applied to 15 paired LSCC tumor-blood samples uncovered a comprehensive SVs landscape and a significant positive correlation between somatic deletion burden and smoking intensity. Furthermore, a high-frequency somatic simple repeat expansion was identified in 20/27 (74.1%) of LSCC patients, upregulating the expression of genes TP53BP2 and FBXO28 through spatial proximity. These findings underscore the potential of long-read sequencing and SomaGauss-SV in uncovering previously unexplored genomic rearrangements in LSCC, providing valuable resources for biomarker discovery.

bioinformatics↗

bioRxiv2025

Cryo-EM Structure of the Erlin1/2 Complex Reveals a Dynamic Scaffold for Membrane Protein Sequestration and Microdomain Assembly

The SPFH (Stomatin, Prohibitin, Flotillin, and HflK/C) family of proteins are key scaffolding components involved in the organization of functional membrane microdomains (FMMs) across various subcellular membranes, including those of the endoplasmic reticulum (ER) and mitochondria, which are characterized by a low content of saturated lipids. Among this protein family, the erlin1/2 complex is specifically located on the ER membrane. Previous studies have shown that the erlin1/2 complex plays an essential role in the ER-associated degradation (ERAD) pathway, mediating the ubiquitin-dependent degradation of various proteins such as inositol 1,4,5-trisphosphate receptors (InsP3Rs), which are important calcium ion transporters on the ER membrane. However, the molecular mechanisms underlying erlin-mediated FMMs organization and its role in ERAD remain poorly understood. In this study, we determined the single-particle cryo-electron microscopy (cryo-EM) structure of the erlin1/2 complex under different detergent conditions. Our findings reveal that the erlin1/2 complex forms a 26-mer cage-like structure, composed of alternating erlin1 and erlin2 subunits. The erlin1/2 complex defines a nanodomain on the ER membrane, which could recruit various types of proteins to both the interior and exterior membrane regions of the cage. By caging cargo proteins, the erlin1/2 complex physically secludes them from their binding partners, leading to a potential halt in their function. Moreover, individual cages can further interact with one another, facilitating the organization of FMMs of different sizes on the ER membrane. These dynamic properties may play a general and critical role in various processes occurring on the ER, including viral replication, positioning the erlin1/2 complex as a promising new target for antiviral drug development.

biophysics↗

bioRxiv2025

Multiplexed Neuromodulatory-Type-Annotated EM-Reconstruction of Larval Zebrafish

Diverse neuromodulatory systems confer functional flexibility upon the hardwired sensorimotor pathways of the brain1-6. Among these, the evolutionarily conserved locus coeruleus (LC)-norepinephrinergic (NE) system integrates and broadcasts information globally7-9. While previous studies have primarily focused on its axonal outputs and effects on neural processing, the organizational logic of its synaptic inputs, enabling it to sense global brain states and in turn shape its activity dynamics for appropriate neuromodulation10,11, remains poorly explored. To address this, we mapped the synaptic input architecture of individual LC-NE neurons by establishing Fish-X, a whole-brain microscale reconstruction of larval zebrafish with neuron-type annotations. This dataset encompasses the retina, brain and anterior spinal cord, capturing >240,000 cells and >25 million synapses. Monoaminergic (including NE, dopaminergic, and serotonergic), hypocretinergic, and glycinergic neurons were resolved by multiplexed subcellular APEX2 labeling, while glutamatergic and GABAergic identities were inferred via morphology comparison with a zebrafish mesoscopic atlas12,13. Compared with other neuronal populations, LC-NE neurons display distinct perisomatic features and high dendritic indegrees. Reconstruction of near-complete dendritic inputs to individual LC-NE neurons reveals their broad yet sparse synaptic convergence across the brain. These synaptic inputs are not randomly distributed but instead organized according to sensory/motor modality, excitatory/inhibitory identity, and synaptic strength. Individual LC-NE neurons share common inputs, a feature conserved within and across monoaminergic systems, suggesting a co-innervation mechanism for coordinated neuromodulation. Thus, our study uncovers multi-level principles governing the spatial organization of LC-NE neurons broad-yet-sparse inputs and provides a pivotal resource for deciphering the microscale architecture of neuromodulatory systems.

neuroscience↗

bioRxiv2025

Directional growth of developing myelin mediated by Wnt gradient and required for proper axon functions

Axon-wrapping myelin sheaths formed by oligodendrocytes are essential for proper functions of the central nervous system. Although much is known about oligodendrocyte development, how the myelin dynamically forms remains unclear. Here we show the preferentially unidirectional extension of developing myelin mediated by Wnt gradient and required for proper axon functions. Using larval zebrafish as an in vivo model, we found that developing myelin in the spinal cord preferentially extends to the anterior end, and this process is dependent on an anterior-to-posterior Wnt4b gradient. Taking advantage of the large size of Mauthner-cell axons, we further showed that disruption of this directional extension impairs the even length distribution of myelin sheaths and faithful transduction of action potentials along the axon, and reduces the reliability of escape behavior. Thus, our study reveals a novel process for precise regulation of myelination, providing a new insight into myelin structuring and functioning.

neuroscience↗

bioRxiv2025

Synergistic Control of Mitochondrial Dynamics and Function by ERAD and Autophagy in Brown Adipocytes

Mitochondrial quality control is essential for maintaining cellular energy homeostasis, particularly in brown adipocytes where dynamic mitochondrial remodeling supports thermogenesis. Although the SEL1L-HRD1 endoplasmic reticulum (ER)-associated degradation (ERAD) pathway and autophagy are two major proteostatic systems, how these pathways intersect to regulate mitochondrial integrity in metabolically active tissues remains poorly understood. Here, using adipocyte-specific genetic mouse models combined with high-resolution 2D and 3D ultrastructural imaging technologies, we reveal an unexpected synergy between SEL1L-HRD1 ERAD and autophagy in maintaining mitochondrial structure and function in brown adipocytes. Loss of ERAD alone triggers compensatory autophagy, whereas combined deletion of both pathways (double knockout, DKO) results in severe mitochondrial abnormalities, including the accumulation of hyperfused megamitochondria penetrated by ER tubules, even under basal room temperature conditions. These phenotypes are absent in mice lacking either pathway individually or in SEL1L-IRE1 DKO, highlighting the pathway-specific coordination between ERAD and autophagy. Mechanistically, dual loss of ERAD and autophagy induces ER expansion, excessive ER-mitochondria contact, upregulation of mitochondria-associated membrane (MAM) tethering proteins, impaired calcium transfer, and defective mitochondrial turnover. As a result, DKO adipocytes accumulate dysfunctional mitochondria, exhibit respiratory deficits, and fail to sustain thermogenesis. Collectively, our study uncovers a cooperative and previously unrecognized mechanism of mitochondrial surveillance, emphasizing the critical role of ERAD-autophagy crosstalk in preserving mitochondrial integrity and thermogenic capacity in brown fat. One-sentence summaryOur study uncovers a previously unrecognized synergy between SEL1L-HRD1 ERAD and autophagy that is essential for preserving mitochondrial integrity and thermogenic capacity in brown adipocytes, revealing new opportunities for targeting mitochondrial dysfunction in metabolic disease.

cell biology↗

bioRxiv2025

Oblique Thick Light-Sheet Microscopy with Spatiotemporal 3D Localization for RNA Imaging in Intact 50 μm-Thick Sections

Neuron typing in intact brain sections demands 3D imaging reconciling thickness compatibility with large-area coverage--a persistent challenge for RNA imaging methods limited by either restricted fields-of-view (<1 mm2) or thin-section constraints (<20 m). Here we introduce oblique thick light-sheet microscopy integrated with spatiotemporal 3D localization, enabling multiplexed RNA imaging across 50 m-thick tissue sections and centimeter-scale regions. The 45{degrees} illumination geometry achieves optical-interference-free imaging in >100 m-thick tissues during single-plane scans, while a spatiotemporal localization algorithm recovers submicron resolution by pinpointing fluorescence in situ hybridization (FISH) spots within volumetric excitation. This strategy reveals layer-spanning neuronal distributions and region-specific expression gradients unattainable with conventional RNA imaging approaches. By resolving the historical trade-off between imaging depth and spatial coverage, our platform advances whole-brain transcriptomics, enabling 3D neuron typing capability critical for deciphering brain-wide cellular architectures.

biophysics↗

bioRxiv2025

Highly accurate protein structure prediction-based virtual docking pipeline accelerating the identification of anti-schistosomal compounds

Schistosomiasis is a major neglected tropical disease that lacks an effective vaccine and faces increasing challenges from praziquantel resistance, underscoring the urgent need for novel therapeutics. Target-based drug discovery (TBDD) is a powerful strategy for drug development. In this study, we utilized AlphaFold to predict the structures of target proteins from Schistosoma mansoni and Schistosoma japonicum, followed by virtual molecular screening to identify potential inhibitors. Among 202 potential therapeutic targets, we identified 37 proteins with high-accuracy structural predictions suitable for molecular docking with 14,600 compounds. This screening yielded 268 candidate compounds, which were further evaluated in vitro for activity against both adult and juvenile S. mansoni and S. japonicum. Seven compounds exhibited strong anti-schistosomal activity, with HY-B2171A (Carubicin hydrochloride, CH) emerging as the most potent. CH was predicted to target the splicing factor U2AF65, and knockdown of its coding gene Smp_019690 resulted in a phenotype similar to CH treatment. RNA sequencing revealed that both CH treatment and Smp_019690 RNAi disrupted splicing events in the parasites. Further studies demonstrated that CH impairs parasite viability by inhibiting U2AF65 function in mRNA splicing regulation. By integrating RNAi-based target identification with structure-based virtual screening, alongside in vitro phenotypic and molecular analyses of compound-treated schistosomes, our study provides a comprehensive framework for anti-schistosomal drug discovery and identifies promising candidates for further preclinical development. Author SummarySchistosomiasis is a debilitating disease caused by parasitic worms and affects over 230 million people worldwide. For decades, control of the disease has relied on a single drug, praziquantel, which is less effective against juvenile parasites and increasingly threatened by the risk of drug resistance. To accelerate the discovery of new treatments, we integrated advanced computational tools with molecular validation. Using AlphaFold-predicted structures of 37 key schistosome proteins, we performed large-scale virtual screening to identify promising drug candidates. Over 200 compounds were prioritized for phenotypic screening on two major human-infective schistosome species, leading to the discovery of seven with potent anti-parasitic activity. Among them, Carubicin hydrochloride showed strong efficacy by targeting a critical splicing factor, U2AF65. Inhibiting this protein--either chemically or through gene silencing-- disrupted parasite movement, suppressed cell proliferation, and altered splicing events. Our work highlights the power of integrating AI-based protein modeling with phenotypic and mechanistic validation to accelerate drug discovery for neglected tropical diseases like schistosomiasis.

pathology↗

bioRxiv2025

Transposon-plasmid nesting enables fast response to fluctuating environments

Mobile genetic elements (MGEs) play a critical role in shaping the response and evolution of microbial populations and communities. Despite distinct maintenance mechanisms, different types of MGEs can form nested structures. Using bioinformatics analysis of 14,338 plasmids in the NCBI RefSeq database, we found transposons to be widespread and significantly enriched on plasmids relative to chromosomes, highlighting the prevalence of transposon-plasmid nesting. We hypothesized that this nested structure provides unique adaptive advantages by combining transposition-driven genetic mobility with plasmid-mediated copy number amplification. Using engineered transposon systems, we demonstrated that nesting enables rapid and tunable responses of transposon-encoded genes in fluctuating environments. Specifically, transposition maintains a reservoir of the encoded genes, while plasmid copy number fluctuations further amplify the dynamic range of gene dosage, thus enhancing the response speed and stability of transposon-encoded traits. Our findings demonstrate an adaptive benefit of transposon-plasmid nesting and provide insights into their ecological persistence and evolutionary success.

systems biology↗

bioRxiv2025

PQBP1-dependent alternative RNA splicing underlies high calorie diet-induced cognitive impairment

High calorie-high fat diet (HFD) has been implicated as a pathological modifier of brain diseases including neurodegenerative dementias, but the detailed molecular mechanisms remain largely unknown. Here we report that HFD suppresses PPAR{gamma}-mediated transcriptional expression of PQBP1, a RNA splicing factor implicated in human intellectual disability and Alzheimers disease. RNAseq-based comprehensive analyses of alternative RNA splicing (AS) in HFD-fed mice for 1 or 6 weeks and in PQBP1-cKO mice reveal their common changes, which weigh on synapse-related genes. Betweenness-based extraction of core molecules from the common changes reveals CASK, Cacnb1 and Cyfip2 as key molecules of the network. Both CASK and Cacnb1 regulate STXBP1, a causative gene for infantile epilepsy syndrome and an essential factor for synapse vesicle release, via their direct interaction. In addition, our analysis suggests that Syt1 plays a role specifically in HFD for 1 week. HFD-induced AS isoforms of CASK, Cacnb1, Cyfip2 and Syt1 impair pre-synapse vesicle release in primary neurons. AAV-PQBP1, AAV-CASK, AAV-Cacnb1, AAV-Cyfip2 or AAV-Syt1 rescues synapse and/or cognitive dysfunctions in HFD mice, genetically supporting the pathological PQBP1-presynase axis in HFD. Moreover, immunohistochemistry experiments suggest that the pathological axis plays roles not only in excitatory neurons, but also in inhibitory neurons of the brain. Collectively, our results unravel a novel molecular mechanism for brain dysfunction when mice are exposed to a HFD.

neuroscience↗

bioRxiv2025

Gene therapies alleviate absence epilepsy associated with Scn2a deficiency in DBA/2J mice

Mutations in the voltage-gated sodium channel gene SCN2A, which encodes the NaV1.2 channel, cause severe epileptic seizures. Patients with SCN2A loss-of-function (LoF) mutations, such as protein-truncating mutations, often experience later-onset and drug-resistant epilepsy, highlighting an urgent unmet clinical need for new therapies. We previously developed a gene-trap Scn2a (Scn2agt/gt) mouse model with a global NaV1.2 reduction in the widely used C57BL/6N (B6) strain. Although these mice display multiple behavioral abnormalities, EEG recordings indicated only mild epileptiform discharges, possibly attributable to the seizure-resistant characteristics associated with the B6 strain. To enhance the epileptic phenotype, we derived congenic Scn2agt/gt mice in the seizure-susceptible DBA/2J (D2J) strain. Notably, we found that these mice exhibit prominent spontaneous absence seizures, marked by both short and long spike-wave discharges (SWDs). Restoring NaV1.2 expression in adult mice substantially reduced their SWDs, suggesting the possibility of SCN2A gene replacement therapy during adulthood. RNA sequencing revealed significant alterations in gene expression in the Scn2agt/gt mice, in particular a broad downregulation of voltage-gated potassium channel (KV) genes, including KV1.1. The reduction of KV1.1 expression was further validated in human cerebral organoids with SCN2A deficiency, highlighting KV1.1 as a promising therapeutic target for refractory seizures associated with SCN2A dysfunction. Importantly, delivery of exogenous human KV1.1 expression via adeno-associated virus (AAV) in D2J Scn2agt/gt mice substantially reduced absence seizures. Together, these findings underscore the influence of mouse strain on seizure severity and highlight the potential of targeted gene therapies for treating SCN2A deficiency-related epilepsies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/657652v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@35374eorg.highwire.dtl.DTLVardef@1c22197org.highwire.dtl.DTLVardef@2b4582org.highwire.dtl.DTLVardef@e06e68_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefScn2a deficiency leads to absence seizures in D2J mice and neuronal hyperexcitability with compensatory KV reduction; restoring NaV1.2 or introducing human KV1.1 reduces seizure burden. HighlightsO_LIScn2a deficiency induces robust absence seizures in the DBA/2J but not the C57BL/6N strain. C_LIO_LICortical neurons in adult DBA/2J mice with Scn2a deficiency exhibit intrinsic hyperexcitability. C_LIO_LISevere Scn2a deficiency leads to downregulation of multiple potassium channel genes. C_LIO_LIGenetic restoration of NaV1.2 expression alleviates spike-wave discharges (SWDs). C_LIO_LIAAV-mediated human KV1.1 delivery substantially reduced absence seizures, demonstrating the therapeutic potential of targeted gene therapy. C_LI

neuroscience↗

bioRxiv2025

Macrophage-derived reactive oxygen species promote Salmonella aggresome formation contributing to bacterial antibiotic persistence

In this study, we reveal that macrophage-derived reactive oxygen species (ROS) can trigger the rapid formation of Salmonella aggresomes, which substantially contribute to the increased frequency of persisters induced by phagocytosis. Salmonella containing aggresomes exhibited a dormant phenotype characterized by reduced adenosine triphosphate (ATP) levels and decreased metabolic activity. Furthermore, these dormant bacteria showed upregulated expression of Salmonella pathogenicity island 1 (SPI-1)-encoded type III secretion system (T3SS)-related genes, followed by later expression of SPI-2 T3SS-related genes when macrophages ROS production declined. Our results demonstrate that Salmonella containing aggresomes can enter a dormant state to escape antibiotic attack, while crucially maintaining the ability to resuscitate when the stress environment is improved. Research on bacterial aggresomes could potentially provide therapeutic strategies to combat bacterial antibiotic persistence. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/657582v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@7e5f1forg.highwire.dtl.DTLVardef@970a39org.highwire.dtl.DTLVardef@204449org.highwire.dtl.DTLVardef@632c47_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

The intratumoral microbiome is negatively associated with malignancy in dermatofibrosarcoma protuberans

In recent years, growing evidence demonstrated the critical roles of intratumoral microbes in tumors. However, the characteristics of intratumoral microbiome in dermatofibrosarcoma protuberans (DFSP) and their associations with tumor malignancy remains unexplored. Here, 106 whole-genome sequencing (WGS) data of the paired biopsy and blood samples from 53 DFSP patients were utilized, in which we extracted high-quality non-human reads to assign microbial taxonomic annotation by Kraken2 and PlusPF database. Meanwhile, significantly elevated non-human reads, microbial abundance, and bacterial load were detected in tumor compared to blood samples. To minimize the impact of contaminants and noise, we conducted a series of filtering procedures and treated blood samples as negative controls. Notably, we found that over 98% of intratumor microbes belonged to bacteria, and that the dominant taxa and alpha-diversity of intratumoral bacteria all exhibited significantly negative correlations with Ki67 expression in tumors. Specifically, the 84 key intratumoral species were identified to be associated with the reduced tumor malignancy, as evidenced by the diminished Ki67 expression, decreased tumor volume, and fewer COL1A1-PDGFB fusion events. These findings highlighted the tumor-suppressive potential of intratumoral microbiome, thereby providing a novel insight into DFSP pathogenesis and clinical management. IMPORTANCETo our knowledge, this is the first study to explore the intratumoral microbiome in DFSP. Microbial DNA signatures could be detected by whole-genome sequencing (WGS) and enabled a comprehensive view of the microbial landscape, thus we analyzed 106 WGS data of the paired biopsy and blood samples from 53 DFSP patients. Our analysis revealed that the dominant taxa and alpha-diversity of intratumoral microbiome all showed significantly negative correlations with Ki67 expression of tumor samples. This study indicated the tumor-suppressive role of intratumoral microbiome in DFSP and highlighted the potential clinical significance in understanding DFSP pathogenesis and guiding therapeutic management strategies.

microbiology↗