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Chen, L.

Publications and source records attributed to Chen, L..

At least 91 records · Page 5Linked to original sources

An oncolytic adenovirus armed with anticancer prodrug-activating enzyme offers enhanced tumor killing and antitumor immunity.

Oncolytic viruses are most commonly administered via intratumoral injection; however, their clinical efficacy in achieving tumor eradication remains limited by several challenges, including insufficient penetration into all tumor cells and the inability to elicit robust systemic antitumor immune responses capable of eliminating metastatic microtumors. Here, we report an oncolytic adenovirus, OAd-2B6, with an engineered adenoviral E1 region for tumor selectivity and carrying the prodrug- activating enzyme cytochrome P450 2B6 (CYP2B6) to activate the anticancer prodrug cyclophosphamide (Cytoxan, CTX). OAd-2B6 alone induced dose-dependent tumor cell killing across multiple human tumor cell lines and exhibited strong synergistic antitumor effects when combined with CTX. Importantly, OAd-2B6-mediated local activation of CTX resulted in a potent bystander killing effect that eliminated tumor cells not directly infected by the virus. In a H1299 lung cancer xenograft nude mouse model, intratumoral injection of OAd-2B6 combined with CTX significantly inhibited tumor growth and even achieved complete tumor regression, with markedly superior efficacy compared with monotherapy. In immunocompetent mice bearing 4T1 breast cancer xenografts, OAd-2B6 alone inhibited tumor growth and was accompanied by upregulation of IFN-{gamma} and GzmB expression in the tumor-infiltrated T cells. CTX combination therapy further enhances this anti-tumor immune response, promoting the activation of T cells to suppress non-injected tumors at a distal site. Collectively, this study demonstrates that OAd-2B6 exerts potent antitumor effects through multiple mechanisms, including direct oncolysis, intratumoral prodrug activation leading to bystander killing, and enhancement of systemic antitumor immunity. These findings provide a promising strategy for improving the therapeutic efficacy of oncolytic therapy.

cancer biology↗

Decoding Immune Reconstitution Failure in People Living with HIV through Single-cell Genomics

Immune non-responders (INRs), a subset of people living with HIV (PLWH), fail to achieve full immune reconstitution and remain at increased risk of morbidity, mortality, and non-AIDS-related illnesses. As the mechanisms underlying this impaired immune recovery remain poorly understood, we performed single-cell multi-omics profiling on peripheral blood mononuclear cells from 43 INRs, 47 immune responders and 53 healthy donors. Our dataset comprises 2,744,009 transcriptomes and 1,226,658 chromatin-accessibility profiles across 58 identified immune cell types. INRs exhibited markedly elevated inflammatory signaling, increased apoptotic activity, and dysregulation of immune-activating ligand-receptor interactions. Additionally, we identified 2,996 interaction cis-eGenes and 5,938 cis-caPeaks, and validated key cell type-specific cis-xQTL effects associated with immune reconstitution failure. Furthermore, we identified 3,551 sc-eQTLs and 872 cell-state interaction eQTLs (ieQTLs) in CD4+ T cells. A genotype-specific upregulation of OAS3 in INRs, likely regulated by STAT1, was identified based on these results. We developed scPRISM (single cell Predictive Reconstitution Immune Status Model), a multi-modal framework that integrates scRNA-seq and scATAC-seq data to perform the dual tasks of differentiating disease states and predicting gene expression from chromatin accessibility, thereby deciphering the cell type-specific cis-regulatory basis of the disease. Our study delineates the transcriptional and epigenomic landscape of immune dysregulation in INRs and provides new genetic insights into HIV-associated immune reconstitution failure. These findings offer a foundation for developing biomarkers and precision therapies to restore immune function in PLWH.

genetics↗

PD-1 remodels SHP2 dynamics and drives the non-catalytic inhibition of T cell activation

The inhibitory receptor programmed cell death protein 1 (PD-1) suppresses T cell activation primarily by recruiting the src homology 2 domain-containing phosphatase 2 (SHP2), thereby unleashing its phosphatase activity. However, a purely enzymatic model struggles to fully explain the rapid and robust disruption of proximal T cell receptor (TCR) and CD28 signaling. Here, by integrating X-ray crystallography, single-molecule magnetic tweezers, supported lipid bilayers, TIRF imaging, liquid-liquid phase separation, and cellular assays, we uncover a dual-layered inhibitory mechanism of the PD-1/SHP2 axis. Mechanistically, we determine the crystal structure of SHP2 in complex with dually phosphorylated PD-1 cytoplasmic motifs (pPD-1), revealing a ligand-induced open conformation, which is distinct from the oncogenic E76K-associated state. We further directly resolve the closed-to-open conformational dynamics of individual SHP2 molecules, characterized by an 8-nm transition amplitude, and demonstrate that pPD-1 accelerates the transition by at least 94-fold. Crucially, the pPD-1-mediated highly open conformation exposes the tandem SH2 (t-SH2) domains to function as a biophysical barrier. Independent of phosphatase activity, these domains directly dismantle pTCR and pCD28 signaling condensates to suppress T cell activation. Together, our findings establish a model in which pPD-1 remodels SHP2 structural dynamics and drives a non-catalytic inhibitory mechanism of TCR and CD28 signaling, suggesting next-generation immunotherapy design to reverse T cell suppression.

immunology↗

HSD17B11 maintains FSP1 localization on lipid droplets to support ferroptosis defense

Ferroptosis is a regulated form of cell death driven by iron-dependent lipid peroxidation, and lipid droplets (LDs) are increasingly recognized as important regulators of this process. Consistent with this role, the anti-ferroptotic factor ferroptosis suppressor protein 1 (FSP1) is known localizing on LDs through N-myristoylation-dependent membrane targeting, where it protects LD lipids from peroxidation. Here, we identify the LD protein HSD17B11 as an additional factor required for maintaining both FSP1 localization on LDs and cellular FSP1 abundance. Silver staining followed by mass spectrometry analysis of purified LD proteins identified reduced LD-associated FSP1 in HSD17B11-deficient cells, which was further validated by immunoblotting and imaging analyses. Mechanistically, HSD17B11 physically interacted with FSP1 and was required to preserve FSP1 association with LDs. Mutational analyses further demonstrated that both FSP1 N-myristoylation and an intact HSD17B11 interaction interface are necessary for LD targeting. Correspondingly, HSD17B11 deficiency reduced LD-associated and total cellular FSP1 levels and increased cellular sensitivity to lipid oxidative stress. Together, our findings identify HSD17B11 as a previously unrecognized regulator of LD-associated FSP1 and reveal an additional mechanism controlling compartmentalized ferroptosis defense.

cell biology↗

Multi-resolution Spatial Graphical Regression Models for Hierarchical Spatial Transcriptomics Data

Advances in spatial transcriptomics (ST) technologies enable systematic molecular characterization of tumor microenvironment, tumor gradients and gene regulatory networks. Cancer progression is known to vary along pathological gradients, yet existing network approaches for gene network inference typically ignore hierarchical spatial organization across the tumor. We develop a Bayesian multi-resolution spatial graphical regression (mSGR) framework to infer spatially varying gene networks from multi-resolution ST data. The proposed model allows precision matrices to vary across hierarchically structured spatial domains, capturing both local and global organization within the tumor. To identify spatially varying regulatory relationships, we introduce a spatially structured edge selection strategy that borrows strength across regions according to spatial proximity and pathological gradients, while Gaussian-process priors flexibly model spatial variation in edge strengths. Scalable inference is achieved through an augmented mean-field variational Bayes algorithm with node-wise parallel regressions, enabling efficient estimation in high-dimensional settings. Simulation studies demonstrate improved recovery of network structures compared with competing approaches. Applying mSGR to multi-resolution ST data from kidney cancer reveals stronger regulatory connectivity in transitional regions of epithelial-mesenchymal transition pathway and identifies hub genes along the tumor gradient, illustrating how spatially resolved network analysis can provide key insights into tumor microenvironment organization.

genomics↗

Satellite Glial Cells Drive Homeostatic Synaptic Structural Plasticity in Sympathetic Neurons

Sympathetic neuronal (SN) activity critically regulates the development and function of peripheral organs and tissues. The demonstration of activity-dependent modulation of SN output suggests that compensatory forms of plasticity could contribute to maintaining the stability of sympathetic circuits. Such plasticity mechanisms could act to restrain SN hyperactivity, a key driver of hypertension in humans and in the spontaneously hypertensive rat (SHR). In this study we examined how long-term changes in activity impact synaptic properties in postnatal sympathetic neuron cultures using chemogenetic and pharmacological manipulations and by examining the effects of enhanced activity of SHR neurons. We showed that bidirectional changes in neuronal activity resulted in homeostatic shifts in synaptic density to counteract long-term activity manipulations. In the absence of sympathetic satellite glial cells (SGCs) there was no synaptic compensation in the cultures. Direct chemogenetic activation of SGCs was sufficient to drive a decrease in synaptic sites and neuronal activity, while glial inhibition blocked activity-dependent synaptic compensation, demonstrating a role for the SGCs in homeostatic regulation of synaptic properties. We found that the SGCs responded to cholinergic signaling by downregulating the expression of the synaptic regulators NGF and TNF, suggesting that reciprocal signaling between SNs and SGCs acts to stabilize sympathetic output during long-term changes in circuit activity. Finally, we showed that these plasticity mechanisms are disrupted in postnatal SHR neurons, with an attenuated neuronal response to glia signaling during synapse formation and activity-dependent plasticity. Taken together, this work describes a new homeostatic activity-dependent plasticity mechanism in the peripheral nervous system.

neuroscience↗

xNNPCD identifies regulators of programmed cell death by integrating perturbation transcriptomes with cancer dependency profiles

Programmed cell death (PCD) encompasses multiple regulated processes whose dysregulation shapes cancer fitness, yet current computational studies largely use known PCD genes for prognosis rather than discovering regulators. We developed xNNPCD, an interpretable neural-network framework that links CRISPR-Cas9 perturbation signatures from CMap to gene dependency profiles from DepMap. The model constrains hidden neurons to five PCD pathways and iteratively refines a prior gene-pathway mask matrix derived from GO, KEGG, and Reactome using pathway-neuron ablation. This converts binary gene-pathway relationships into continuous-valued associations and improves dependency prediction over random forests, standard fully connected multi-layer perceptron, and its own non-iterative variant. The learned matrix recovers annotated death regulators and nominates candidate regulators, including RPL23A, HSPA5, SNRPA1, SLC6A2, and ASAH1; combined with dependency scores, it further separates pathway coupling from regulatory direction. Transferring the refined relationship matrix and learned weights to compound-induced perturbation data enables in silico drug screening, identifying BRD-K19103580 and decitabine as targeted therapeutic agents for apoptosis and ferroptosis, respectively. The pathway-resolved drug profiles can facilitate the rational design of combination therapies targeting complementary PCD pathways to overcome single-pathway resistance. Overall, xNNPCD offers a generalizable, interpretable approach for mapping the regulatory landscape and elucidating the molecular processes of PCD in cancer. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/724150v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@e74c0forg.highwire.dtl.DTLVardef@1326f4corg.highwire.dtl.DTLVardef@291e96org.highwire.dtl.DTLVardef@1970f10_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

Somatic-to-germline transmission of horizontally acquired extrachromosomal circular DNA in Brassica graft chimeras

Whether somatically acquired traits can contribute to heritable variation has remained an open question in plant biology for over a century. Here, using graft-induced periclinal chimeras between Brassica juncea and Brassica oleracea, we identified extrachromosomal circular DNA (eccDNA) as mobile genetic elements capable of crossing histological boundaries and entering the germline. We demonstrated that grafting could promote the horizontal transfer of eccDNA between somatic cell layers, enabling its stable maintenance in recipient tissues and permitting transmission through sexual reproduction across multiple generations. We found that transmitted eccDNA is non-randomly distributed across the genome, preferentially originating from gene-dense regions, and enriched for features associated with molecular persistence, such as inverted repeats, hairpin-forming sequences, and autonomously replicating sequence (ARS) consensus motifs. These genetic regions conferred replication competence, as evidenced by autonomous propagation in an ARS-less heterologous yeast system. Sexual progeny carrying graft-acquired eccDNA exhibited reproducible and lineage-dependent alterations in leaf morphology and drought tolerance, accompanied by coordinated transcriptional reprogramming. Notably, a subset of inherited eccDNA remained transcriptionally active in progeny, producing transcripts absent from self-grafted controls. Our findings establish eccDNA as heritable extrachromosomal elements that link graft-mediated somatic genetic transfer with stable germline transmission, thereby expanding the molecular scope of heritable variation in plants and providing a conceptual framework for graft-based trait transmission.

plant biology↗

Histone modifications analysis reveals enhancers reprogramming during maternal-to-zygotic transition

Enhancers are important epigenetic regulatory components that coordinate spatiotemporal gene expression and play a crucial role in mammalian development, gene regulation, and illness. During early mammalian embryogenesis, histone modifications including H3K4me1, a canonical enhancer mark, and H3K27ac, which identifies active enhancers, are still poorly understood. This study profiles the genome-wide H3K4me1 and H3K27ac patterns in mouse oocytes and pre-implantation embryos using low-input CUT&RUN (cleavage under targets and release using nuclease) with input as low as 50 cells. Both markers are enriched in distal regions and exhibit distinct sequence preferences and reprogramming dynamics in pre-implantation embryos. H3K27ac, a mark of active enhancers, is reprogrammed at the 2-cell stage, whereas H3K4me1 is remodeled at the 4-cell stage and overlaps with H3K27ac, coinciding with accessible chromatin regions. Interestingly, H3K4me1 and H3K27ac are co-localized in promoter regions, where they are mutually exclusive to H3K4me3. Enhancers are dynamically remodeled during maternal-to-zygotic transition (MZT). there are three enhancer types: active enhancers (H3K4me1/H3K27ac), primed enhancers (H3K4me1), and poised enhancers (H3K4me1/H3K27me3). Active enhancers increase significantly after zygotic genome activation. Further, super-enhancers are present across the genome and are mainly enriched in promoters. The specific motifs enriched by super-enhancers may be associated with the variations of gene expressions at different stages.

developmental biology↗

Metabolic Coherence of the Mouse Brain

The brains metabolic demands are well established, but how metabolism is coordinated across anatomically distinct regions remains poorly understood. Here, using matrix-assisted laser desorption/ionization (MALDI) imaging integrated with the Allen Brain Atlas and optimal transport-based computational analysis, we map the spatial metabolome across twelve major mouse brain divisions. We define an optimal-transport-derived inter-regional metabolite similarity metric and refer to it as metabolic coherence. This structure is largely preserved in an amyloid mouse model of Alzheimers disease despite widespread changes in individual metabolite and lipid levels. Individual metabolites and lipids shift in a coordinated manner across regions, sustaining inter-regional relationships even as absolute levels change in patterns indicative of mitochondrial dysfunction. To test whether the coherence metric is responsive to local intervention, we targeted the left hippocampus of mice from this model via lentiviral shHIF1 knockdown or neuronal AAV-mediated AOX expression. Both interventions were associated with metabolite normalization at the injection site. More importantly, normalization extended across distal regions sharing high metabolic similarity with the hippocampus and was accompanied by improved social memory in a single behavioral assay. Gene modulation and amyloid plaque reduction localized to the injection site.

neuroscience↗

A lipid-binding protein in black-legged tick saliva selectively recognizes Borrelia burgdorferi lipids

A proteomic analysis of Ixodes scapularis nymph saliva identified 252 proteins, including six tubular lipid-binding proteins (TULIPs). Comparing nymphs fed on mice that were uninfected or infected with Borrelia burgdorferi, twelve salivary proteins showed significant differences in the amounts detected, including XP_040079658.2, which we refer to as TULIP2. Considering the known immunity-related functions of some TULIPs, we expressed and purified TULIP2 from Escherichia coli and analyzed its interaction with B. burgdorferi lipids. The purification of TULIP2 from E. coli presented many obstacles, due to insolubility, which is consistent with previous reports from studies of other TULIP family members. The binding results showed specificity for B. burgdorferi lipids, with evidence for cholesteryl {beta}-galactoside as a major binding target. Molecular modeling of TULIP2 did not show any strong lipid binding sites. We used molecular dynamics simulation of TULIP2 to explore its conformational landscape by thermal unfolding. The earliest unfolding intermediate opened a hydrophobic pocket to which cholesteryl {beta}-galactoside was predicted to bind strongly. We propose that a specific lipid bilayer interaction with TULIP2 triggers the opening of the ligand-binding site.

biochemistry↗

ITK Deficiency Attenuates Alveolar Hemorrhage by Enhancing Regulatory T Cell-Mediated Tissue Resilience

Pulmonary hemorrhage (PH) is a life-threatening manifestation of systemic autoimmunity caused by immune-mediated disruption of the alveolar capillary barrier. Despite high mortality, the molecular checkpoints that shift destructive inflammation toward protective immune regulation remain poorly defined. Here, using the pristane-induced PH model, we identify interleukin-2-inducible T cell kinase (ITK) as a critical regulator of autoimmune lung injury. ITK deficiency (ITK-/- ) conferred near-complete protection from PH and associated multiorgan injury, accompanied by reduced proinflammatory monocytes and neutrophils and increased Foxp3 regulatory T cells (Tregs). Adoptive transfer of ITK-/-; Tregs protected wild-type recipients from PH and suppressed systemic proinflammatory cytokines, identifying Tregs as key mediators of tissue protection. Mechanistically, lung ITK-/- ; Tregs exhibited increased amphiregulin, a mediator of tissue repair. Transcriptomic profiling further showed that ITK loss reprogrammed Tregs toward a metabolically and functionally enhanced state, with enrichment of oxidative phosphorylation, mTORC1 and STAT5 signaling, and tissue-repair programs. These findings establish ITK as a regulator of the balance between pulmonary injury and reparative immunity and support targeting the ITK axis in severe inflammatory lung disease.

immunology↗

Coordinated subpocket engagement underlies nitazene potency at the μ-opioid receptor.

Nitazenes are emerging synthetic opioids that exhibit exceptionally high potency at the {micro}-opioid receptor (MOR) and contribute to rising overdose fatalities worldwide. Despite extensive in vitro profiling, the structural determinants underlying their structure-activity relationships (SARs) remain unresolved. Here, we combine functional profiling with quantum mechanical calculations and molecular dynamics (MD) simulations to establish a MOR structure-based SAR for nitazenes. Across functional assays, systematic variation at the R1, R2, and R3 positions revealed non-additive effects on potency and identified optimal R1 chain length, R2 N-desethylation, and retention of the 5-nitro group as key determinants of high MOR potency. Consistent with this framework, N-desethyl isotonitazene emerged as the most potent analogue. Structural analysis of the cryo-EM MOR-Gi-fluornitrazene complex, together with MD simulations of multiple nitazene analogues, revealed a conserved trivalent binding architecture in which each substituent engages distinct subpockets. N-desethylation at R2 increases the positive electrostatic surface at the protonated amine, reduces steric constraints near transmembrane helix (TM) 7, strengthens R3 interactions, and allosterically modulates R1 engagement in a substituent-dependent manner. Additionally, optimal R1 chain length and shape stabilize the TM5-TM6 interface and influence activation-relevant TM6 dynamics, defining a unified SAR at R1 across nitazene and fentanyl scaffolds. Together, these findings indicate that nitazene potency reflects substituent-dependent coupling among R1, R2, and R3 within the MOR binding pocket, with R3 engagement distinguishing nitazenes from fentanyl. This framework establishes a coherent structural model of nitazene-MOR recognition that accounts for their unusually high potency and efficacy.

molecular biology↗

A telomere-to-telomere (T2T) pig genome assembly reveals Y chromosome diversity and structural variations of Wuzhishan pigs

BackgroudWuzhishan (WZS) pigs are native to Hainan Province of China, and serve as both important agricultural resources and biomedical models. Although the published WZS pig genome (T2T-pig1.0) even achieving telomere-to telomere (T2T) completeness, substantial genetic diversity still exists within the same pig breed, another WZS pig genome named WZS-T2T was assembled in this study. ResultsMultiple sequencing data were used to assemble genome, and finally yielded a [~]2.68 Gb telomere-to-telomere genome, with N50 length [~]142.87 Mb, and annotated protein coding genes of 23,100. Compared to T2T-pig1.0, QV and BUSCO value was higher, and the Y chromosome (ChrY) length was longer in WZS-T2T than that of T2T-pig1.0. ChrY of two WZS pigs shared 11 genes, including sex differentiation-related genes of SHOX, PRKX, and DDX3X, and SRY; however, energy metabolism gene SLC25A4 and the macrophage-related receptor gene CSF2RA of ChrY were specific to WZS-T2T. An inversion SV on chromosome 10 with length [~]33.86 Mb was identified between two WZS pigs, and three proofs were proposed for proving the accuracy sequence orientation of WZS-T2T.The genetic diversity was consistent with LD decay speed in population different analysis. WZS pigs exhibited higher genetic diversity than other four pig populations (Tunchang pigs, Yuxi black pigs, Large White pig, and Duroc pigs) examined in this study, and presented slower LD decay compared to other four breeds. ConclusionsTherefore, WZS-T2T provided a higher-quality assembly, and potential advantages of both agricultural production and biomedical targets for WZS pigs.

genomics↗

Metabolic dehalogenation of halomethanes by mercury methylators

Mercury (Hg) methylators play key roles in the global Hg cycle. Nonetheless, the Hg methylators are widely present in Hg-absent environments and the Hg methylation is a cometabolic process without cell growth, which leave the origin and evolution of the Hg methylation as a mystery. Here, we reported the CCl4/trihalomethane-to-dihalomethane dehalogenation by model Hg methylators in a metabolic way. Heterologously-expressed HgcAB catalyzed both the CCl4 dechlorination and Hg methylation. Halomethanes were shown to sustain the Hg-methylation community without adding external carbon source, electron donor and acceptor. Metadata analyses suggested the halomethane dehalogenation potential of Hg methylators at the global scale. These results, together with much higher global flux and kinetic Vmax of the metabolic halomethanes dehalogenation relative to the co-metabolic Hg methylation, suggested halomethanes as the potential HgcAB substrates for the evolution of Hg methylation.

microbiology↗

Generation of High-Affinity Anti-GIPR Antagonist Antibodies with Sustained and Non-rebound Weight Loss in DIO Mice by AlfaBodY

The glucose-dependent insulinotropic polypeptide receptor (GIPR) is an attractive therapeutic target for metabolic disorders, with GIPR antagonism emerging as a promising strategy for obesity and type 2 diabetes. However, developing functional antibodies against GPCRs remains challenging due to their complex architecture and conformational dynamics. Here, we employed AlfaBodY, an iterative active learning platform integrating structural and sequence information, to in silico design human anti-GIPR antibodies. Through four rounds of optimization, we generated antibodies with high binding affinities. Lead candidates AB106-131 (KD 1.2 nM) and AB106-156 (KD 1.7 nM) exhibited 7 to 10-fold higher affinity than 2G10 (KD 12 nM) while maintaining comparable antagonistic activity in a cAMP reporter assay (IC50 4[~]5 nM). In diet-induced obese mice, AB106-156 alone induced weight loss comparable to that of semaglutide ([~] -15%), while preserving lean mass and achieving sustained weight control after treatment withdrawal. Co-administration with the GLP-1 receptor agonist semaglutide produced synergistic weight reduction (-25.4%) and markedly attenuated the fat-mass rebound observed with semaglutide alone. Our results demonstrate that AI-driven design can generate potent anti-GIPR antibodies with favourable in vivo efficacy, supporting further development of GIPR antagonist for obesity and related metabolic disorders. The AlfaBodY platform enables faster development of more efficacious biologic drugs.

pharmacology and toxicology↗

Revisiting phage-host inference from metagenome-assembled genomes reveals the need for scaffold-level validation

Accurate phage-host prediction underpins ecological interpretation and experimental validation of uncultivated phages, yet most current approaches rely heavily on metagenome-assembled genomes (MAGs). This reliance implicitly assumes that MAG-level quality metrics, such as completeness and contamination, ensure scaffold-level correctness. Here, we demonstrate that this assumption is frequently violated. Tetranucleotide frequency (TNF) analyses reveal that CRISPR-associated regions often diverge compositionally from their host genomes, increasing the risk of misbinning, while experimentally validated phage-host genome pairs show consistent TNF separation between phages and their hosts, challenging compositional binning assumptions. Through controlled simulations, we further show that the incorporation of substantial amounts of TNF-matched, non-host phage sequences into high-quality MAGs does not substantially alter standard completeness and contamination estimates, rendering such errors largely undetectable. Together, these results expose a systematic and underappreciated source of bias in MAG-based phage-host inference and highlight the need for explicit scaffold-level validation beyond conventional genome-quality metrics. We further propose a practical scaffold-level validation framework that integrates structural linkage and taxonomic consistency to improve the reliability of phage-host inference from MAGs.

microbiology↗

Systemic-to-mucosal trafficking of memory B cells contributes to humoral immunity in the upper respiratory tract

Systemic vaccination induces serum antibodies and circulating memory B cells, protects from severe disease, but does not ensure sterilizing immunity in the upper respiratory tract, where many respiratory pathogens initiate infection. How systemic memory B cells contribute to mucosal immunity remains unclear. Using multiparametric flow cytometry, single-cell RNA and V(D)J sequencing, and functional analyses of paired blood and nasal/oropharyngeal samples, we characterized human B cells across systemic and mucosal compartments. Swab-derived B cells transcriptionally overlap with circulating activated memory B cells while exhibiting distinct features of activation, tissue retention, and spontaneous IgA/IgG secretion. Approximately 6% of mucosal B-cell clones were shared with blood, indicating systemic-mucosal connectivity. Both infection and vaccination expanded two circulating antigen-specific activated memory B cells subsets, whereas antigen-specific B cells accumulated in the upper respiratory tract only following local inflammation. The finding that B-cell recruitment is reactive rather than preemptive may explain the limited efficacy of parenteral vaccines and provides a rationale for developing integrated systemic-mucosal vaccination strategies.

immunology↗