Biology subjects

Yao, X.

Publications and source records attributed to Yao, X..

At least 19 recordsLinked to original sources

bioRxiv2026

Serum IgM crosslinks hepatitis B subviral particles into supramolecular immune complexes

Hepatitis B virus (HBV)-infected cells release hepatitis B surface antigen (HBsAg)-rich subviral particles (SVPs) in large excess over infectious virions. SVPs bind antibodies against HBsAg (anti-HBs), including neutralizing antibodies, but the physical products of antibody capture in human blood are uncharacterized. Here we used cryo-electron tomography (cryo-ET) to image HBsAg-enriched serum from a patient with severe acute Hepatitis B and observed three-dimensional assemblies of intact IgM-SVP immune complexes. These associations persisted at a lower particle density and were validated by a spatial-randomization null model. Subtomogram averaging and single-particle cryo-electron microscopy (cryo-EM) identified three serum IgM Fc-core assemblies, IgM-J-CD5L, IgM-J and IgM-J-SC, with cryo-EM maps reaching 2.8 angstrom resolution. Mapping these Fc core assemblies into tomograms revealed full-length IgM engaging individual SVPs through several Fab arms and bridging neighboring particles into immune complex networks containing multiple IgM molecules and SVPs. Thus, serum IgM uses multivalent Fab interactions to crosslink HBsAg-rich SVPs into supramolecular immune complexes. This observation extends the SVP decoy model from passive antibody sequestration to higher-order particle organization.

molecular biology↗

bioRxiv2026

Mode of T cell priming durably shapes the TCR repertoire, effector function and α4β1 integrin expression of human virus-specific CD4+ T cells

The generation of an effective T cell response against an antigen depends on the recognition of the antigen by the T cell receptor (TCR), followed by T cell priming, initiating coordinated biophysical, biochemical and proliferative changes that drive differentiation into effector and memory clones. The immunological environments in which priming occurs, such as natural infection or vaccination, influences the quality and persistence of memory T cells, but the long-term impacts remain incompletely understood. Here, we investigate how the mode of priming shapes durable antigen-specific CD4+ T cell memory, utilising two cohorts 3-4 years after initial antigen encounter: individuals recovered from SARS-CoV-2 infection and infection-naive individuals who received a SARS-CoV-2 vaccination. Using ex vivo single-cell RNA sequencing, paired TCR sequencing and in vitro functional analyses, we characterise the transcriptional, clonal and functional profile of Spike-specific CD4+ T cells. Across both cohorts, CD4+ T cell responses against spike epitopes S166-180, S751-765 and S866-880, were immunodominant, with shared public TCR clonotypes indicating conserved antigen-recognition regardless of mode of priming. Despite this shared specificity, infection-primed individuals exhibited greater TCR repertoire diversity and lower CDR3{beta} sequence convergence. Transcriptionally, infection-primed cells exhibited a more cytotoxic and effector phenotype, while vaccine-primed cells preferentially adopted T follicular helper (Tfh)- and Th1-associated phenotypes. Infection-primed individuals also displayed enrichment of cell adhesion and integrin signalling pathways, with a greater proportion of spike-specific CD4+ T cells expressing 4{beta}1 integrin subunits, consistent with enhanced migratory and effector potential. Collectively, our findings demonstrate that the mode of antigen priming may influence the long-term CD4+ T cell memory states, influencing TCR repertoire diversity, functional differentiation and tissue-homing potential, years after the initial immune response.

immunology↗

bioRxiv2026

Plasma titration provides a physical ruler for cross-platform proteomics

Plasma proteomics is expanding across platforms and cohorts, and integrating these data for AI demands comparability at the protein level, not merely concordant associations1,2. Affinity and MS platforms use distinct probes (antibodies, aptamers, or peptides) and signal readouts, yielding contradictory cross-platform results3,4. Without a known quantitative truth, we cannot distinguish biology from measurement distortion, leaving no gold standard for integration. Here we introduce Plasmix--a plasma reference suite with predefined male:female ratios (M, 1:0; Y, 3:1; P, 1:1; X, 1:3; F, 0:1)--and show that preserving this quantitative titration gradient, not just technical repeatability, predicts cross-platform concordance and identifies protein measurements suitable for integration. Profiling Plasmix across five platforms (Olink, SomaScan, NULISA, AAgAtlas, and MS-DIA) and 12 protocols across 17 batches, we found discordance is dominated by signal generation, not sample identity, and platforms distort signals in a protein-specific manner. Crucially, proteins retaining the titration response showed stronger agreement in an independent cohort; anchoring to the Plasmix midpoint (P) via sample-to-reference ratios reduced distortions, extending harmonizable coverage by 10-20%. Plasmix thus provides a physical ruler to benchmark accuracy, identifying genuinely integrable measurements before pooling datasets or training AI models--a critical bottleneck for plasma proteomics.

molecular biology↗

bioRxiv2026

HDOCK-Multimer: integrating docking and combinatorial assembly for structure prediction of large protein complexes

Deep learning methods, such as AlphaFold and RosettaFold, achieve high accuracy in protein structure prediction. However, predicting the structure of large protein complexes remains challenging due to their large size and intricate multi-chain interactions. Docking-based methods can handle large proteins, but are limited by the huge combinatorial binding space of multichains. Assembly-based approaches offer an alternative, but their accuracy critically relies on the precision of predicted subcomponents. Addressing the challenges, we propose HDOCK-Multimer (HDM), a structure prediction framework of large protein complexes by integrating ab initio docking and combinatorial assembly. HDM can efficiently reduce reliance on subcom-ponent accuracy through docking process, while leveraging the pairwise interactions of subcom-ponents through assembly strategy. HDM is extensively validated on three benchmarks of 35 large heteromeric complexes, 172 large protein complexes, and 7 CASP15 targets, and compared with state-of-the-art methods including MoLPC, CombFold, AlphaFold-Multimer (AFM), and AlphaFold3 (AF3). It is shown that HDOCK-Multimer substantially outperforms the other methods. In addition, HDM also shows ability to predict the stoichiometry and model the complex without stoichiometry input. It is anticipated that HDM will serve as a powerful tool for studying large protein complexes or molecular machines. The HDM package is freely available at https://github.com/huang-laboratory/HDOCK-Multimer/.

bioinformatics↗

bioRxiv2026

Tfh dysfunction underlies poor responses to HBV vaccination

The primary goal of vaccination is to induce durable protection through generation of antigen-specific humoral immunity and cellular immune memory. Yet the same vaccine may elicit durable protection in some and less durable responses in others. Antigen-specific antibody responses arise from germinal centers (GCs), where T follicular helper (Tfh) cells help cognate B cells undergo somatic hypermutation (SHM), affinity maturation to generate humoral protection and cellular immune memory. In humans, however, the mechanisms linking GC dynamics to downstream antibody output remain incompletely characterized. To identify the molecular and cellular events that underlie differential vaccine responsiveness, we leveraged the known, pronounced variability in vaccine antigen-specific antibody concentration and durability observed after Hepatitis B virus (HBV) immunization. We longitudinally profiled 101 healthy adults undergoing either de novo (n=59) or booster (n=42) immunization. We then stratified participants into High (>100 mIU/mL) and Low (<100 mIU/mL) responder groups based on vaccine antigen-specific antibody responses. From this cohort, we obtained core needle biopsies (CNBx) of vaccine-draining lymph nodes from 10 participants (High Responder n=6, Low Responder n=4), 10-21 days post-final vaccination and performed single-cell RNA sequencing with paired antigen receptor sequencing. Lymph node BCR repertoire analysis revealed convergent, semi-public clonotypes across unrelated participants with elevated SHM. Transcriptomic profiling of GC-B cells uncovered stark functional divergence between response groups, with High Responders showing robust activation across both dark zone (DZ) and light zone (LZ) compartments and enrichment of MYC and mTORC1 signaling. In contrast, Low Responders exhibited a contracted LZ compartment and a stalled GC B cell response. This divergence in B cell responses corresponded to changes in the T cell compartment. High Responders harbored an expanded Tfh subset marked by increased expression of CXCL13, ICOS, and GNG4, indicative of their GC localization and capacity to provide B cell help. Moreover, receptor-ligand analysis indicated that these GNG4+Tfh formed coordinated costimulatory networks capable of driving LZ GC-B cell licensing. Low Responders demonstrated a divergent program in which their GNG4+Tfh displayed aberrant inflammatory transcriptional activity. This inflammatory signaling was associated with reduced specificity of BCL6 regulon activity despite maintained expression of canonical Tfh genes. Together, these findings reveal that variable HBV vaccine responsiveness was associated with transcriptional network alterations in the GNG4+Tfh subset, offering a molecular framework for understanding poor vaccine responses. One Sentence SummaryLymph node Tfh dysfunction is associated with poor vaccine responses to Hepatitis B virus vaccination

immunology↗

bioRxiv2026

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

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

microbiology↗

bioRxiv2026

Novel mouse models for perianal fistulizing Crohns disease reveal therapeutic value of interferon-gamma antagonists

Background and AimsPerianal fistulizing Crohns disease (PFCD) is a challenging complication with poorly understood pathogenesis and limited treatment options, largely due to the lack of clinically relevant animal models. Interferon-gamma (IFN-{gamma}) signaling is hyperactivated in human PFCD. We aimed to establish mouse models recapitulating human PFCD and to evaluate IFN-{gamma} as a new therapeutic target. MethodsPerianal fistulas were established in three mouse models with concurrent Crohns disease-like intestinal inflammation: wild-type (WT) mice with 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced proctocolitis, Il10-/-mice, and TNF{Delta}69AU/+ mice. A modified MAGNIFI-CD index was developed for longitudinal fistula assessment in mice. Transcriptomic analysis and flow cytometry were conducted on mouse fistula tissue. Re-analysis of single-cell and spatial transcriptomics of human PFCD tissues was performed. Therapeutic benefits of anti-TNF-, upadacitinib, and IFN-{gamma} pathway antagonists were evaluated in the PFCD models. ResultsAll three PFCD models sustained chronic perianal fistula tracts for at least 5 weeks after wire removal. All three models closely recapitulate the pathological and molecular features of PFCD in patients, as confirmed by clinical examination, MRI, histopathology, immunostaining, flow cytometry, and transcriptomics. IFN-{gamma} signaling emerged as a central and conserved pathway across all three mouse models and human PFCD. Targeting of the IFN-{gamma} pathway promptly improved fistula healing with mitigation of IFN-{gamma} signaling, inflammation, and epithelial-to-mesenchymal transition (EMT). Moreover, combining IFN-{gamma} and TNF- blockade demonstrated augmented therapeutic efficacy compared to anti-TNF- monotherapy. ConclusionsThese PFCD mouse models and imaging tools provide first reliable and clinically relevant platforms for mechanistic studies and therapeutic evaluation. IFN-{gamma} signaling represents a potential therapeutic target warranting clinical investigation.

immunology↗

bioRxiv2026

A chemoinformatics-guided platform for efficient discovery of RNA-binding small molecules: Proof-of-concept for myotonic dystrophy type 1

Structured RNAs cause human diseases but remain challenging to target selectively with small molecules. Here, we report a chemoinformatics-guided discovery framework that integrates fingerprint-based molecular design, experimental validation, and mechanistic profiling to identify small molecules that bind highly structured, disease-associated RNAs. Using an RNA-binder fingerprint derived from known ligands, a Tversky similarity screen of >8 million compounds yielded a 150-member library enriched in chemical space for RNA-active scaffolds. Target engagement and cell-based assays identified multiple selective ligands for the pathogenic expanded triplet repeat, r(CUG)exp, that causes myotonic dystrophy type 1 (DM1) by binding and sequestering the RNA-binding protein muscleblind-like 1 (MBNL1). Biophysical and single-molecule analyses revealed that the small molecules bind the 1x1 nucleotide U/U internal loops formed when r(CUG)exp folds, partially block MBNL1 binding, and modulate RNA folding equilibria. Two optimized scaffolds rescued MBNL1-dependent splicing in patient-derived myotubes with micromolar potency and minimal cytotoxicity. This study establishes a generalizable, data-driven platform for discovering drug-like RNA-binding lead small molecules and demonstrates its application to the toxic repeat expansion RNA underlying DM1. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/723748v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1a87b41org.highwire.dtl.DTLVardef@340a14org.highwire.dtl.DTLVardef@81b583org.highwire.dtl.DTLVardef@1b3ba14_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

bioinformatics↗

bioRxiv2026

NFIC-mediated CaSR endocytosis defines a hyperactive TOMM20highCHGAhigh oxyphil cell state as a pathological driver of autonomous secondary hyperparathyroidism

Secondary hyperparathyroidism (SHPT) is a debilitating complication of chronic kidney disease. Its clinical management is frequently compromised by calcimimetic resistance, a refractory state primarily driven by the progressive downregulation of the membrane calcium-sensing receptor (CaSR). Despite the centrality of CaSR as a therapeutic target, the mechanisms governing its aberrant expression and membrane localization remain incompletely elucidated. Here, we generated a single-cell transcriptomic atlas of human parathyroid tissues from SHPT and primary hyperparathyroidism (PHPT) patients, uncovering a unique stromal-immune niche that is specifically induced by uremic stress in SHPT. Our data also observed a striking dissociation between CaSR mRNA and its abundance as a membrane protein in SHPT tissues. Pseudotime trajectory analysis showed a progressive decline in CaSR pathway activity and a concomitant increase in endo-lysosomal activity along the trajectory, terminating in pathological oxyphil cells as the endpoint of chief cell differentiation in SHPT. Mechanistically, Nuclear Factor I C (NFIC) transcriptionally activated clathrin light chain B (CLTB) and Ras-related protein Rab7a (RAB7A) to trigger clathrin-mediated endocytosis and lysosomal degradation of CaSR, thus reducing its membrane abundance. This degradative program was further validated by multiplex immunofluorescence in TOMM20highCHGAhigh pathological oxyphil cells in human SHPT tissues. To translate these mechanistic findings into a clinically actionable strategy, we repurposed the clinically approved lysosomal inhibitor hydroxychloroquine (HCQ) to block this CaSR degradation pathway. In patient-derived xenograft (PDX) mouse models, co-administration of HCQ and cinacalcet acted synergistically to restore membrane CaSR expression, normalize serum PTH and calcium levels and suppress parathyroid tumor growth more effectively than monotherapies. Collectively, our single-cell-guided study identifies an NFIC-driven endo-lysosomal program as a previously unrecognized mechanism underlying CaSR downregulation and calcimimetic resistance in SHPT, and establishes HCQ repurposing as a clinically tractable therapeutic strategy for patients with refractory SHPT.

cell biology↗

bioRxiv2026

MVCBench: A Multimodal Benchmark for Drug-induced Virtual Cell Phenotypes

Drugs induce coordinated phenotypic changes across multiple modalities, including transcriptional reprogramming and cellular morphological remodeling. Predicting these drug-induced modality changes is central to drug discovery, mechanism-of-action studies and precision therapeutics, however, prediction performance depends critically on how both drug compounds and cellular states are represented. Despite rapid advances in drug molecular and gene representation methods, a systematic evaluation of these methods remains lacking. Herein, we introduce MVCBench, a comprehensive benchmarking framework for evaluating drug molecular and gene representation methods in predicting drug-induced multimodal virtual cell (MVC) phenotypes. MVCBench leverages large-scale transcriptomic and high-content imaging data and systematically evaluates 24 representation methods (12 drug molecular and 12 gene representation methods) across nearly 1.1 million drug-induced profiles, under both in-distribution and out-of-distribution settings spanning unseen compounds, cell lines, assay plates and datasets. Our benchmarking reveals a pronounced modality-dependent asymmetry: advanced drug molecular representations substantially improve the prediction of drug-induced morphological phenotypes but provide only limited gains for gene expression prediction relative to classical fingerprints, whereas task-specific gene representations outperform general-purpose foundation models in predicting drug-induced transcriptomic responses. Predictive performance also deteriorates sharply under distribution shift, highlighting persistent challenges in cross-dataset and cross-platform generalization. We further show that integrating transcriptomic and morphological modalities consistently improves prediction accuracy, and derive practical design principles for MVC architectures, including modality-aware loss calibration and fusion strategies. Together, MVCBench provides a systematic foundation for evaluating representation methods and offers guidance for developing robust MVC models of drug-induced cellular responses.

bioinformatics↗

bioRxiv2026

TIM3+ Tumor Associated M2 Macrophages Impair Antitumor T Cell Immunity and Promote Gastric Cancer Progression and Peritoneal Metastasis

Peritoneal metastases (PM) are the leading cause of cancer-related death in gastric cancer (GC) patients with survival typically < 9 months. Here, we demonstrate that TIM3 and its ligands are increased along the GC continuum and associated with poor survival. Integrated omics analyses and functional studies revealed highly enriched TIM3 in CD163+ tumor associated M2 immunosuppressive macrophages significantly promote tumor cell invasion and tumor growth in vivo, while TIM3 depletion in macrophages reduced tumor cell malignant attributes and increased T cell immunity from PBMCs or CD45+ immune cells of malignant ascites in co-culture system. By cytokine and kinase arrays, we discovered that depletion of TIM3 in macrophages reduced the production of notable secretome of cytokines/chemokines from M2 macrophages; and the protumor function of TIM3+ macrophages rely on the p90RSK1/2/CCL20 axis. Finally, we reveal that TIM3 blockage or genetic KO had superior antitumor activity in combination with anti-PD1 immunotherapy and mitomycin C (MMC) chemotherapy. Together, this study uncovers an important role for TIM3 in tumor associated M2 macrophages and underscores the potential of TIM3 blockage in GC patients with PM. Statement of significanceIn this study, we show TIM3 increases along GC continuum, and highly enriched on tumor associated M2 macrophages that fuel tumor growth; and suppress T cell function via p90RSK1/2/CCL20 axis. TIM3 depletion restores T-cell immunity and curbs tumor growth. TIM3 blockade combined with anti-PD1 and mitomycin C provide a novel therapeutic strategy for GC patients with PM.

immunology↗

bioRxiv2026

Bioorthogonal Catalytic Microneedles Based on a Cytotoxic PEI Matrix for Synergistic Melanoma Therapy

Microneedle (MN) patches have emerged as a highly efficient platform for localized drug delivery, showing great promise in cancer therapy due to their ability to enable precise drug administration. However, conventional MN systems are limited by the low drug-loading capacity of their tips and primarily rely on biologically inert, non-therapeutic matrices for structural support, which restricts further gains in antitumor efficacy. Herein, we present a strategy turning toxicity into therapy by constructing palladium nanoparticle-loaded polyvinyl alcohol/polyethyleneimine (PVA/PEI@Pd) hydrogel microneedles (PPPd-MNs), which exploit the intrinsic cytotoxicity of PEI for synergistic melanoma therapy. The PPPd-MNs efficiently catalyze the deprotection of a doxorubicin prodrug (P-DOX), enabling in situ generation of active doxorubicin (DOX). Notably, the PEI matrix serves a dual function: acting as a robust ligand to stabilize Pd catalysts and functioning as a therapeutic agent that disrupts cancer cell membranes. Both in vitro and in vivo experiments demonstrate that the combination of Pd-mediated bioorthogonal activation of DOX and PEI-induced membrane damage achieves a remarkable synergistic therapeutic outcome in a murine melanoma model, resulting in a tumor inhibition rate of up to 98%. This work repurposes the inherent cytotoxicity of the carrier material as an active therapeutic component, offering a novel paradigm for the design of high-performance bioorthogonal catalytic systems.

bioengineering↗

bioRxiv2026

Fine-tuning STEAP1 protein expression and purification to preserve its conformation and function

Six-transmembrane Epithelial Antigen of the Prostate 1 (STEAP1) has emerged as a promising therapeutic target for prostate cancer. We have optimized the expression and purification conditions of human STEAP1 to maximize the production of its homotrimeric form, which is crucial for metal ion reduction and maintaining cellular redox balance. Proteins obtained from these optimized conditions were complexed with both heme and flavin-adenine dinucleotide (FAD), two cofactors that are fundamental to STEAP functionality, suggesting native folding and interactions of the protein. In addition, we compared the impact of stable and transient expression systems on the protein quality of STEAP1. We found that stable expression promoted heme incorporation, improved expression homogeneity, and ensured correct protein orientation on cell surfaces. Our findings present effective strategies for optimizing the recombinant production of STEAP1, with potential applicability to other STEAP family proteins to facilitate therapeutic discovery.

biochemistry↗

bioRxiv2026

A Single-Cell Temporal Atlas of Mouse Nasal Embryonic Development

The mammals breathe and perceive odors through anatomically and functionally distinct respiratory and olfactory regions of the nose; however, how the early embryo endows this system remains largely unknown. Here, we present a temporal high-resolution single-cell RNA sequencing (scRNA-seq) atlas of mouse nasal development, comprising 183,247 cells collected from 20 embryos spanning embryonic day 10.5 (E10.5) to E18.5. We identified 7 major cell clusters and 52 molecularly defined subtypes, including previously unrecognized rare populations and niche-derived signaling components involved in progenitor cell maintenance. Lineage reconstruction of epithelial and mesenchymal compartments revealed dynamic cell fate transitions and highlighted candidate regulators of lineage specification, including Foxa1 as a regulator of nasal respiratory ciliated epithelium differentiation. Integration with adult nasal epithelium datasets further delineated transcriptional dynamics of olfactory stem cells. This study provides a molecular roadmap of nasal development and offers a valuable resource for future research into nasal biology and regenerative strategies.

developmental biology↗

bioRxiv2026

Asymmetric partition of the O-GlcNAcome in mitosis ensures binary cell fate decision

Many cellular components undergo biased segregation during stem cell division, but whether such order extends to the proteome has remained unknown. Using our real-time O-GlycoTracer, we find that O-GlcNAcylated proteins (the O-GlcNAcome) segregate asymmetrically during Drosophila neuroblast mitosis, predisposing the two daughters to distinct fates. The daughter that preserves stem cell identity inherits most of the O-GlcNAcome. This asymmetric partition requires putative O-GlcNAc readers, notably 14-3-3 proteins. We further identify the nuclear pore complex (NPC) as a major O-GlcNAc substrate in neuroblasts; Nup153, located in the nuclear basket, shows O-GlcNAc-dependent biased inheritance. Perturbing multiple steps in this segregation pathway disrupts neuroblast differentiation, reduces brain size, and causes adult learning deficits. These findings reveal a coordinated O-GlcNAc-driven mechanism for proteome-level asymmetric inheritance during neural stem cell division, with implications for neurodevelopmental disorders linked to OGT or 14-3-3 mutations.

cell biology↗

bioRxiv2026

Multi-Omics Reveals Activated Fibroblasts with Dual Functional Roles in Repair and Negative Barrier in the CD8+ T Cell Cytotoxic Niche for Lung Cancer Neoadjuvant Therapy

A major challenge in elucidating immune activation and tolerance is that single-omics technologies are inherently limited. Since single-cell transcriptomics lacks spatial information and spatial transcriptomics lacks resolution or depth, neither can adequately model the multidimensional tumor immune microenvironment (TiME) features. We present NICHE (Niche Integrated Cellular Heterogeneity Elucidator), an integrative multi-omics framework. By aligning physical cell-cell interactions with single-cell ligand-receptor (L-R) expression, NICHE leverages single-cell transcriptomics, spatial proteomics, and AI modeling to systematically decode the composition, spatial interactions, and communications within immune functional niches. To validate NICHEs capabilities, we applied it to human tonsil tissue. The framework successfully identified key structural and functional units and deeply elucidated the cell-cell interactions and molecular crosstalk within them. Furthermore, these results were validated through orthogonal methods, including single-cell spatial transcriptomics and multiplexed immunofluorescence, which confirmed the accuracy and reproducibility of our analyses. In non-small cell lung cancer (NSCLC) patients undergoing neoadjuvant immunotherapy, CD8+ T cell cytotoxic niches mediate tumor clearance with variable outcomes, to define the cellular and molecular drivers behind this functional spectrum, we utilized NICHE to analyze the TiME from patients with complete versus partial pathological response, both pre- and post-treatment. We found that neoadjuvant immunotherapy may induce the activation of CXCL12+, NECTIN2+, POSTN+, and COL6A1+ fibroblasts through the activation of cytotoxic T cells. Paradoxically, these fibroblasts support tissue repair but also establish an immunosuppressive niche that protects residual tumor cells, ultimately attenuating treatment efficacy. Our work establishes a multidimensional framework for dissecting dynamic immune activity, with direct implications for understanding tumor immunology and identifying novel therapeutic targets.

immunology↗

bioRxiv2026

Coordinate Up-regulation of Both TK1 and TS Expression in Cycling Cells: Mechanistic Basis and Implications for Dual-Targeted Cancer Therapy

Our previous study [2] has revealed that various types of cycling cells undergo rapid proliferation and division. Cycling cells can be broadly categorized into two groups: cycling immune cells (CICs) and cycling non-immune cells (CNICs). Cancer cells represent a special type of cycling cells. Based on a set of 26 marker genes, we proposed a simple method for the rapid identification of cycling-cell types. Comparisons across cycling-cell types uncovered novel gene-regulatory mechanisms underlying the cell cycle, development, and differentiation. Notably, we discovered that the coordinate up-regulation of both TS and TK1 expression is indispensable for securing a robust deoxythymidine triphosphate (dTTP) supply required for DNA replication in cycling cells. The compensatory interplay between salvage and de novo synthesis provides a plausible explanation for resistance to 5-fluorouracil (5-FU), a TS inhibitor for cancer chemotherapy. Consequently, blocking dTTP synthesis requires co-inhibition of TK1 and TS. For the first time, we present the crucial single-cell transcriptome evidence for this coordinate up-regulation, thereby establishing the mechanistic basis for developing TK1/TS as a dual target in cancer therapy.

cancer biology↗

bioRxiv2025

A VSV-vector vaccine simultaneously targeting H5N1 hemagglutinin (HA) and matrix protein 2 (M2) induces robust neutralizing and ADCC antibody responses and provides full protection against lethal H5N1 infection in a mouse model

Human (avian) influenza A viruses, especially highly pathogenic avian influenza (HPAI) viruses, pose a significant public health threat, and a multivalent vaccine is the primary prophylactic measure to control these viruses. To establish such a vaccine, we generated two multivalent vesicular stomatitis virus (VSV)-based vaccine candidates (V-EtM2e/H505 and V-EtM2e/H522) and characterized their ability to induce protective immune responses. Our results revealed that vaccine immunization in mice induced high humoral immune responses against both the HPAI hemagglutinin (HA) protein and the ectodomain of M2 (M2e) protein. Intriguingly, vaccine-immunized mouse sera exhibited highly efficient neutralizing activity against the corresponding H5 pseudovirus and mediated potent and broad antibody-dependent cellular cytotoxicity (ADCC) activity against M2e derived from human and avian influenza H5, H1, H3, and H7 viruses. Furthermore, both intranasal and intramuscular immunization provided efficient protection against HPAI H5N1 virus challenge in mice, with a 100% survival rate and a nondetectable viral load in several tissues. Notably, noninvasive mucosal (IN) delivery of V-EtM2e/H522 achieved protection equal to that of IM delivery at a 100-fold lower immunizing dose. These findings provide strong evidence for the effectiveness of a multivalent VSV-based vaccine against human (avian) influenza A viruses.

microbiology↗