Biology subjects

Cao, Y.

Publications and source records attributed to Cao, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Expression of immune checkpoint VISTA represents a differentiated state of cancer cells and plays a role in regulating actin cytoskeleton

Immune checkpoint blockade has revolutionized cancer therapy, but the therapeutic efficacy is limited. Clinical trials on blockade of newly identified immune checkpoints didn't show promising result, suggesting that it might be insufficient to understand the function of immune checkpoints in cancer merely in the context of immunity. Here, we found mutually exclusive expression patterns of the immune checkpoint VISTA (or VSIR) and the neural stemness factor SETDB1, an oncoprotein that promotes immunoevasion, in xenograft tumors, suggesting that cells with high VISTA expression represents a differentiated, and hence, less or non-malignant state in tumor. Non-neural differentiation factors HHEX, MYOD1 and PPARG promote, whereas oncoproteins KRAS (and the mutant KRAS(G12D)) and SOX2, both being embryonic neural factors, repress VISTA expression. This tendency can be inferred from the finding that neural stemness is the core property of cancer cell. Manipulated expression of VISTA in cancer cells generated no significant effect on cell tumorigenicity and differentiation state, but led to change in cell morphology and actin cytoskeleton. Mechanistically, VISTA regulates a key cytoskeleton regulator, WASF2, leading to the change in cell morphology, which might interfere with signal transduction of immune response. The results suggest that 1) high expression of a protein in tumor might represent a less or non-malignant state, targeting of which would leave malignant cells intact, and consequently, leading to weak or even no therapeutic efficacy, a key factor worth considering for target selection; 2) immune checkpoints might play other roles in cells that interfere with regulation of anti-tumor immunity.

cancer biology↗

bioRxiv2026

The transcription factor Bhlhe40 promotes inflammatory functions of ILC2s through inducing GM-CSF while inhibiting IL-10 expression

Group 2 innate lymphoid cells (ILC2s) regulate type 2 immune responses partly by recruiting eosinophils, but the mechanisms underlying this process remain incompletely understood. Although both ILC2s and type 2 T helper (Th2) cells are capable of expressing IL-5, a cytokine critical for recruiting eosinophils, ILC2s are more potent than Th2 cells in this process. Here, we show that the transcription factor Bhlhe40 promotes GM-CSF production in ILC2s, and Bhlhe40 expression in ILC2s is required for efficient eosinophil recruitment during both papain- and helminth-induced type 2 immune responses. However, Bhlhe40 deficiency in ILC2s had no effect on the production of classical type 2 cytokines, including IL-4, IL-5 and IL-13, despite Bhlhe40 being required for type 2 cytokine production by Th2 cells. Furthermore, in contrast to ILC2s, Th2 cells produced little GM-CSF and administration of GM-CSF rescued eosinophil recruitment in ILC2-specific Bhlhe40-deficient mice. In addition to promoting GM-CSF expression, Bhlhe40 repressed IL-10 production in ILC2s as it did in Th2 cells, particularly during chronic inflammation. Single-cell transcriptomic analyses further supported this regulatory network, and the ChIP-Seq data revealed direct binding of Bhlhe40 to the enhancer and promoter regions within the Il10 and Csf2 loci. Collectively, our findings show that Bhlhe40 exerts distinct gene regulatory functions in ILC2s and Th2 cells, and Bhlhe40 modulates the inflammatory and anti-inflammatory functions of ILC2s by promoting GM-CSF while suppressing IL-10 production.

immunology↗

bioRxiv2026

A mechanism-annotated benchmark reveals limited fidelity to drug-response signatures in single-cell perturbation models

Single-cell drug perturbation models are increasingly used to predict how compounds remodel cellular states, but they are still largely assessed by expression reconstruction. Whether high expression similarity reflects preservation of drug-response signatures remains unclear. Here we present scDrugPerturb-Bench, a mechanism-annotated benchmark that links matched control and drug-treated single-cell RNA-sequencing profiles to literature-curated directional key-gene evidence. The resource covers 181 datasets, 423 annotated response cases, 717 unique key genes and 2.5 million cells. We introduce the Mechanism Fidelity Score (MFS) to evaluate key-gene direction, effect-size recovery, gene-set coherence, mechanism specificity and pathway-level response polarity. Across 12 perturbation-prediction models, 3 baselines and 10 data splits, expression-similarity metrics were weakly aligned with MFS and selected different model configurations. Mechanism-aware selection improved early drug retrieval in a transcriptome-based drug design evaluation, indicating that MFS provides practical information beyond benchmark reporting. Systematic benchmarking revealed limited fidelity to drug-response signatures across cell-line and source-integrated settings. Frozen single-cell foundation model embeddings produced local, metric-dependent gains rather than universal improvements, and source context substantially reshaped model assessment. Hard-negative tests further showed that plausible perturbation responses can arise from non-specific transcriptional shortcuts. These results show that expression reconstruction is an insufficient proxy for preserving drug-response signatures and establish scDrugPerturb-Bench as a benchmark for mechanism-aware evaluation of single-cell drug perturbation models.

bioinformatics↗

bioRxiv2026

Subgenome-Level Phylogeny Reveals an Allopolyploid Origin of Chloranthales from Ancestral Monocot and Eudicot Lineages

Angiosperms (flowering plants) represent the most species-rich lineage of land plants, yet deep phylogenetic relationships among their major clades, particularly within mesangiosperms, remain notoriously difficult to resolve. Although hybridization and whole-genome duplication (WGD) are recognized as major evolutionary forces, the contribution of ancient allopolyploidization, which combines hybridization with WGD, to deep-node phylogenetic discordance in mesangiosperms remains poorly understood. Here, we analyzed genomes from seven representative early-diverging angiosperm lineages, each containing no more than one lineage-specific WGD event. Using a comparative phylogenomic framework, we characterized WGD-derived paralogs across five WGD-bearing lineages. In contrast to other polyploid lineages, Chloranthales WGD-derived paralogs rarely formed sister relationships in gene trees. After evaluating alternative explanations, including incomplete lineage sorting, ancient paralogy, and analytical artifacts, we demonstrate that this discordant phylogenetic signal reflects the genomic legacy of an ancient allopolyploidization event. We further resolved the Chloranthales subgenomes by exploiting biased fractionation patterns within conserved syntenic regions. Subgenome-resolved phylogenomic analyses revealed that the dominant Chloranthales subgenome exhibits phylogenetic affinity with eudicots, whereas the recessive subgenome is associated with monocots, indicating a deep reticulate origin involving ancestral lineages related to these major angiosperm clades. Our findings provide subgenome-resolved evidence that ancient allopolyploidization can connect deeply diverged lineages during early angiosperm evolution, highlighting the importance of incorporating reticulate polyploid histories into phylogenomic frameworks for resolving deep evolutionary relationships.

systems biology↗

bioRxiv2026

Lipoproteins modulate the uptake and biological functionof cationic cell-penetrating peptides across the animal lineage.

Cationic cell-penetrating peptides (+CPPs) are pervasive killer peptides produced by all animals and found in innate immune systems, venoms and neurodegenerative diseases. Despite their ubiquity, the mechanisms underlying their uptake remain opaque and intensely debated. Here, we interrogate +CPPs spanning 600 million years of animal evolution and identify endocytosis as a conserved/convergent uptake mechanism across cell types and organisms, at physiological concentrations. By combining multiplex imaging, genetic screening, cryo-electron tomography, and biophysical methods, we uncover that +CPPs seemingly universally enter eukaryote cells via 'hitchhiking' on lipoproteins. We further show that the interaction of +CPPs with lipoproteins modulates their antimicrobial function. Combined, our findings establish a unified molecular framework describing a pan-eukaryote cell penetrance mechanism. As hyperlipidemia is a common comorbidity, our findings have direct implications for human health. Lastly, the insights gleaned from this work highlight design principles that may inform the future engineering of peptide-based therapeutics and delivery vehicles.

cell biology↗

bioRxiv2026

MiRNA let-7a-5p Ameliorates Pulmonary Fibrosis by Suppressing TGFBR1-Mediated Endothelial-to-Mesenchymal Transition

Background Idiopathic Pulmonary Fibrosis (IPF) is a fatal chronic lung disease with limited therapeutic options. While alveolar epithelial injury and fibroblast activation are well-studied, endothelial-mesenchymal transition (EndoMT) is emerging as a critical pathogenic mechanism. The regulatory role of exosomal miRNAs in pulmonary fibrosis remains unclear. This study investigates serum exosomal miRNAs, particularly let-7a-5p, in modulating EndoMT during the onset of pulmonary fibrosis. Methods Clinical cohorts of IPF patients and healthy controls were enrolled. Serum exosomal miRNAs were profiled, followed by differential expression and functional enrichment analyses. In vitro experiments involved human pulmonary artery endothelial cells (HPAECs) transfected with let-7a-5p mimic or inhibitor. Dual-luciferase reporter assays confirmed the binding between let-7a-5p and TGFBR1. HPAECs were co-cultured with lung epithelial cells to examine paracrine signaling. In vivo studies used a bleomycin-induced mouse model with let-7a-5p agomir administration. Assessments included histopathological staining, hydroxyproline content, Western blot, qPCR, micro-CT, and pulmonary function tests. Results Let-7a-5p was significantly downregulated in serum exosomes from IPF patients, correlating with clinical indicators. Mechanistically, let-7a-5p directly bound the TGFBR1 3'UTR to inhibit its expression. Inhibition of let-7a-5p upregulated -SMA, FN1, smad2/3 phosphorylation, and collagen I, while downregulating CD31 and VE-cadherin. Therapeutically, let-7a-5p mimic reversed bleomycin-induced EndoMT and suppressed epithelial-mesenchymal transition (EMT) via paracrine signaling. Mice administered agomir showed reduced fibrosis, improved lung function, and suppressed TGF-{beta}/Smad signaling. Conclusion Serum exosomal let-7a-5p suppresses pulmonary fibrosis by targeting TGFBR1 to inhibit EndoMT. Its downregulation in IPF patients correlates with disease progression, highlighting its biomarker potential.

molecular biology↗

bioRxiv2026

A microbiota-responsive polyfunctional cytotoxic CD4⁺ T-cell state promotes mucosal inflammation in ulcerative colitis

Ulcerative colitis (UC) is characterised by chronic colonic inflammation with marked heterogeneity in disease severity and therapeutic outcomes. Here, we define a spatially organised, polyfunctional cytotoxic CD4 T-cell state associated with mucosal inflammation and adverse therapeutic outcomes in UC. Integrating ex vivo T-cell receptor stimulation with multi-cohort bulk and single-cell transcriptomics and multiparameter flow cytometry, we show that GZMB CD4 T cells are preferentially enriched in inflamed UC mucosa, but not peripheral blood, and co-express cytotoxic molecules, Th1- and Th17-associated cytokines and chemokines, and immunoregulatory receptors. Single-cell analyses implicate inflammatory cytokine and antigen-presentation signals in the acquisition or maintenance of this state. High-resolution spatial profiling localised this programme predominantly to Th17 cells, which were preferentially enriched within multicellular inflammatory and tertiary lymphoid structure-associated niches. Across independent patient cohorts, a transcriptional signature derived from this state increased with endoscopic disease severity and was associated with reduced response to anti-TNF and anti-IL-12/23p40 therapies. Adoptive transfer of Gzma/Gzmb-deficient rather than wild-type CD4 T cells into Rag2-deficient recipient mice markedly attenuated experimental colitis and abrogated the polyfunctional cytokine phenotype, demonstrating that granzyme-dependent effector activity is a key mechanism driving CD4+ T-cell-mediated intestinal inflammation. Finally, human host-microbiome analysis linked this programme to intestinal dysbiosis, while transfer of dysbiotic microbiota promoted the emergence of a corresponding state in vivo. Collectively, these findings define a microbiota-responsive, spatially organised polyfunctional cytotoxic CD4 T-cell programme that contributes to intestinal inflammation and is associated with disease severity and treatment resistance in UC.

immunology↗

bioRxiv2026

Phosphorylation and pocket-binding ligands rewire the coupled networks in multidomain protein condensate

Biomolecular condensates formed by multidomain proteins are increasingly linked to disease and are emerging targets for chemical modulation. Yet most molecular models emphasize intrinsically disordered regions (IDRs), whereas many available ligands bind folded-domain pockets. How IDR modifications and folded-domain ligands are integrated to control condensate organization remains unclear. Here, we address this problem using histone deacetylase 6 (HDAC6), a disease-associated deacetylase whose S22 phosphorylation and catalytic-pocket ligands differentially regulate condensation. Using atomistic-informed Martini 3 coarse-grained simulations, we show that S22 phosphorylation enhances phase separation of the N-terminal IDR1 without compacting isolated chains. Instead, phosphorylation creates a phospho-S22/D26-centered anionic contact node that strengthens dense-phase interactions with Arg/Lys-rich patches. The HDAC6 ligands Nexturastat A and HPOB remodel this IDR network through distinct charged-contact mechanisms: Nexturastat A acts as a focused competitor for cationic patches, whereas HPOB permits partial compensation through alternative charged contacts. In full-length phospho-HDAC6, the assembled network is not IDR1-dominated but is organized by FD3, the C-terminal ZnF-UBP domain. Pocket-bound ligands redirect this folded-domain network from FD3-FD3 association toward pocket-FD3 contacts, with stronger and more persistent remodeling by Nexturastat A. These results reveal a two-layer regulatory mechanism in which phosphorylation rewires IDR electrostatics while pocket-binding ligands redirect folded-domain interactions, suggesting a strategy for modulating multidomain condensates through ligand-induced contact-network remodeling.

biophysics↗

bioRxiv2026

Spatially Organized Tertiary Lymphoid Structures Emerge in Small Cell Lung Cancer and Associate with Improved Survival

Tertiary lymphoid structures (TLS) are ectopic immune aggregates associated with improved prognosis and response to immunotherapy in multiple solid tumors. However, their presence, spatial organization, and functional relevance in small cell lung cancer (SCLC), a malignancy characterized by profound immune evasion, remain poorly understood. Using imaging mass cytometry (IMC) across 320 regions of interest spanning primary lung tumor, tumor-adjacent lung, liver and lymph node metastasis, complemented by Visium HD spatial transcriptomics, we characterized the cellular architecture and molecular programs of TLS-like niches in SCLC. TLS-like niches were identified in a subset of SCLC samples, predominantly primary lung tumor tissues and adjacent lung, spanning a continuum from loose lymphoid aggregates to compact follicle-like immune structures. Organized TLS-like niches contained CD20+ B-cell cores, closely associated with CD4+ and CD8A+ T cells, proliferating lymphocytes, HLA-DR+ antigen-presenting compartments, and SMA+ stromal scaffolds, and were enriched for canonical TLS organizer signals (CXCL13, LTB, FDCSP). Patients with TLS-positive tumors demonstrated improved overall survival, and core TLS-associated transcriptional programs were associated with favorable survival in an independent bulk RNA-seq cohort. To our knowledge, this represents one of the first spatially resolved analyses of TLS-like immune architecture in SCLC, demonstrating that organized lymphoid immunity can emerge in this classically immune-evasive disease and is associated with improved survival.

cancer biology↗

bioRxiv2026

Destabilization of intratumor Tregs by CTLA-4 engagement confers anti-CTLA-4-driven immunotherapy

Immune checkpoint inhibitors (ICI) that are antibodies against CTLA-4 have achieved therapeutic effects on multiple types of cancers 1-4, but the mechanisms underlying the therapy remain incompletely understood. In contrast to the initial theory that the antibody blockades CTLA-4 on T cells is of central importance, it has recently been demonstrated that selective reduction of CD4+Foxp3+ regulatory T cells (Tregs) in the tumor microenvironment by the antibody plays a key role in the anti-tumor effects5-8, although this phenomenon remains under debate in human patients9-12. We show here that anti-CTLA-4 antibody engages CTLA-4 in Tregs specifically in the tumor tissues to reduce their stability and survival and weaken their suppressive function through upregulating TGF-{beta} signaling. This leads to the antibody-mediated - upregulation of CD4+ and CD8+ effector T cell anti-tumor immunity and consequently cancer immunotherapy. Specifically, anti-CTLA-4 antibody directly stimulates CTLA-4 in intratumor Tregs to enhance their TGF-{beta} receptor I (T{beta}RI)-mediated TGF-{beta} signaling13. This results in reduction of IL-2 receptor CD25 expression and downregulation of lactate metabolism in intratumor Tregs to reduce their stability and survival 14-16, and also compromises their suppressive function by inhibiting Foxp3 expression. This activity requires high levels of CTLA-4 expression in the intratumor Tregs and the presence of antibody Fc receptors in the tumor tissues. Strikingly, deletion of T{beta}RI specifically in Tregs completely prevents the reduction of intratumor Tregs and abrogates the anti-CTLA-4-mediated cancer immunotherapy. In contrast to intratumor Tregs, anti-CTLA-4 antibody treatment blocks CTLA-4 in the intratumor CD4+ Foxp3- and CD8+ T effector cells and in the peripheral Tregs to decrease their T{beta}RI expression and increase their expansion due to their relatively low levels of CTLA-4 in the same tumor bearing mice. Significantly, the engagement of CTLA-4 by anti-human CTLA-4 antibody (ipilimumab) also upregulates TGFBR1 but decreases Il2RA expression and lactate metabolism in human Tregs in vitro and in humanized mice in vivo, leading to suppression of tumor progression. We have provided additional mechanism underlying anti-CTLA-4-mediated anti-tumor effects through destabilizing intratumor Tregs by CTLA-4 engagement-mediated TGF-{beta} signaling. This could lay a theoretical foundation for designing optimal immunotherapy based on anti-CTLA-4 antibody in cancer patients.

immunology↗

bioRxiv2026

Tumor-hepatocyte crosstalk drives a hepatic lactate-TGF-β axis of CD8⁺ T cell exhaustion and immunotherapy resistance in small-cell lung cancer liver metastases

PurposeLiver metastases confer poor outcomes and attenuate the benefit of immunotherapy across solid tumors. This study investigated how the hepatic metastatic niche promotes CD8 T cell dysfunction and immunotherapy resistance in small-cell lung cancer (SCLC). Experimental DesignClinical outcomes and tumor gene expression were integrated with multi-region single-cell RNA sequencing of T cells from rapid-autopsy SCLC metastases, together with spatial transcriptomics. SCLC-hepatocyte conditioned-media models were combined with stable-isotope tracing, mass spectrometry, functional and metabolic assays, and ChIP-qPCR to define mechanisms of CD8 T cell suppression. ResultsLiver metastases were associated with inferior survival and reduced benefit from immune checkpoint blockade. Multi-region single-cell analysis showed that CD8 T cells from liver metastases exhibited an exhaustion-associated state enriched for hypoxia, lactate, and TGF-{beta} programs. SCLC-hepatocyte crosstalk generated a lactate- and TGF-{beta}-rich microenvironment that reduced CD8 T cell effector function, proximal T cell receptor signaling, glycolytic fitness, viability, and proliferation. Stable-isotope tracing demonstrated transfer and accumulation of co-culture-derived lactate in recipient CD8 T cells, with limited entry into downstream pyruvate-linked pathways. Lactate accumulation was accompanied by increased H3K18 lactylation at the PDCD1, LAG3, and TGFB1 regulatory loci. In parallel, SCLC-hepatocyte crosstalk increased paracrine TGF-{beta} and activated canonical SMAD2 signaling in CD8 T cells. TGF-{beta} receptor inhibition restored CD8 T cell proliferation. In the phase III IMpower133 cohort, a combined lactate-TGF-{beta} transcriptional program was associated with inferior survival, most strongly in patients with liver metastases. ConclusionsTumor-hepatocyte crosstalk generates convergent lactate and TGF-{beta} signals that drive CD8 T cell dysfunction in liver metastases. This hepatic immune-metabolic circuit provides a potential mechanism for immunotherapy resistance and supports therapeutic strategies targeting TGF-{beta} signaling in liver-metastatic SCLC. Translational RelevancePatients with SCLC liver metastases have poor outcomes and derive limited benefit from immune checkpoint blockade, but actionable mechanisms of hepatic immune resistance remain undefined. We identify an immune-metabolic circuit in which SCLC-hepatocyte crosstalk generate lactate and TGF-{beta} signals that converge on CD8 T cells. Stable-isotope tracing demonstrates the transfer and accumulation of tumor-hepatocyte-derived lactate in recipient T cells, which causes H3K18 lactylation at exhaustion- and TGFB1-associated loci. In parallel, paracrine TGF-{beta} activates canonical SMAD signaling and reinforces proliferative dysfunction. TGF-{beta} receptor inhibition restores CD8 T cell proliferation. In the phase III IMpower133 cohort, a combined lactate-TGF-{beta} program is associated with inferior survival, particularly among patients with liver metastases. These findings provide a mechanistic and biomarker framework for testing TGF-{beta}-directed strategies in liver-metastatic SCLC, a population with substantial unmet clinical need.

cancer biology↗

bioRxiv2026

Proteomic Profiling Identifies CLDN3 as a Tumor-Selective Therapeutic Target in Small Cell Lung Cancer

Small cell lung cancer (SCLC) remains a highly lethal disease with limited targetable surface antigens beyond delta-like ligand 3 (DLL3). We sought to systematically identify and validate tumor-selective cell-surface targets in relapsed SCLC. To this end, we developed an integrated proteogenomic pipeline combining single-cell RNA sequencing, combinatorial optimization, mass spectrometry-based proteomics, and immunohistochemistry to systematically map the SCLC surfaceome of 49 tumors across 25 patients with relapsed SCLC. Using this approach we found claudin-3 (CLDN3) to be a consistently expressed and tumor-selective antigen, with broader coverage than DLL3, which is the current clinical benchmark. CLDN3 was highly expressed across various treatment states, while maintaining low expression in most nonmalignant tissues. Functional validation using a novel CLDN3-specific monoclonal antibody (ABN501) demonstrated NK cell-mediated cytotoxicity in vitro and tumor regression in vivo, as well as a favorable safety profile. These findings support clinical development of CLDN3-directed therapies and demonstrate the utility of integrated proteogenomic approaches for antigen discovery in solid tumors.

cancer biology↗

bioRxiv2026

Antibody evasion and receptor binding of SARS-CoV-2 variants PQ.16.1.1 and RK.1

The recent global expansion of the SARS-CoV-2 variant NB.1.8.1 has driven the emergence of sublineages PQ.16.1.1 and RK.1, which independently acquired the D420N mutation in their receptor-binding domains and and now dominate the Asia-Pacific region. Evaluations utilizing surface plasmon resonance and pseudovirus assays demonstrate that these sublineages exhibit significantly reduced human ACE2 receptor engagement compared to their parental strain. However, this functional cost is offset by a marked ability to evade humoral immunity, specifically demonstrating profound resistance to Class 1 neutralizing monoclonal antibodies and convalescent plasma from Wuhan-Hu-1-primed individuals. This convergent evolution exemplifies a classical viral trade-off, sacrificing receptor binding efficiency to escape population-level immune pressure. Consequently, these findings suggest these variants will soon spread globally and emphasize the critical need for ongoing surveillance to monitor D420N-carrying lineages.

immunology↗

bioRxiv2026

cf-Cabernet: Nick Repair Prior to End Repair Preserves Endogenous DNA Methylation Information in Cell-Free DNA Methylation Sequencing

Cell-free DNA (cfDNA) methylation profiling holds great promise for non-invasive cancer detection, yet accurate methylome analysis is compromised by DNA damage inherent to cfDNA. Standard library preparation workflows involve an end-repair step during which DNA polymerases can initiate synthesis from single-strand breaks (nicks), replacing endogenous methylated nucleotides with unmethylated nucleotides in the 3' direction and systematically erasing methylation information. This artifact is distinct from the terminal jagged-end effect and disproportionately affects cfDNA and FFPE DNA, which harbor abundant nicks. Here, we developed cf-Cabernet, which builds upon the Cabernet framework (Cao et al., 2023) -- an enzymatic methylation sequencing method featuring carrier DNA-assisted sample recovery and amplification-friendly post-conversion processing -- with the addition of a Taq DNA ligase-mediated nick repair step prior to end repair. Using matched cfDNA samples, we compared cf-Cabernet against standard EM-seq and WGBS. cf-Cabernet and EM-seq both substantially outperformed WGBS in alignment rate. Critically, while standard EM-seq exhibited globally reduced methylation levels compared to WGBS, cf-Cabernet yielded methylation levels concordant with WGBS. M-bias analysis revealed that EM-seq libraries showed persistently depressed methylation across the entire read length, whereas cf-Cabernet methylation recovered to the WGBS baseline beyond the terminal [~]40 bp jagged-end region. Nick-induced methylation erasure during end repair is a significant but previously underappreciated source of error in cfDNA methylation sequencing. cf-Cabernet effectively mitigates this artifact through pre-emptive nick ligation, enabling accurate methylome profiling from damaged DNA templates. This method is broadly applicable to cfDNA, FFPE DNA, and other clinical specimens where DNA integrity is compromised, providing a robust foundation for methylation-based liquid biopsy applications.

genetics↗

bioRxiv2026

A Variant-Resistant Linear Epitope in the SARS-CoV-2 Nucleocapsid Protein for Antigen Detection

We previously generated a mouse monoclonal antibody, N179, against the SARS-CoV-2 nucleocapsid (N) protein and developed a colloidal gold-based immunochromatographic test strip. This assay achieved a detection limit of 2 ng/mL and displayed 98% concordance with RT-qPCR results. However, the precise epitope recognized by mAb N179 had not been defined. Using a panel of GST-fused N protein truncation fragments, we mapped the linear B-cell epitope recognized by mAb N179 to the flexible C-terminal tail of the N protein by Western blotting and ELISA. The minimal binding motif required for mAb N179 recognition was identified as 390QTVTLL395. Multiple sequence alignment of 11 representative SARS-CoV-2 lineages, including Alpha, Beta, Gamma, Delta, and Omicron subvariants BA.1, BA.2, and BA.3.2, revealed that this epitope was completely conserved across all variants analyzed. Stringent local pairwise alignment analysis using EMBOSS WATER further showed that the 390QTVTLL395 motif achieved a perfect 6/6 match exclusively in SARS-CoV-2; no identical sequence was detected in the seven common human coronaviruses, four influenza viruses, or five bat coronaviruses examined. Structural prediction analyses indicated that this region is surface-exposed and possesses a strong linear B-cell epitope propensity. Together, these findings identify 390QTVTLL395 as a specific molecular signature of SARS-CoV-2 among the viruses analyzed. Our results provide an epitope-level explanation for the sustained diagnostic reliability of the mAb N179-based assay against emerging variants, clarify the molecular basis for its lack of cross-reactivity, and may inform the rational design of SARS-CoV-2 diagnostics targeting conserved, mutation-resistant epitopes. ImportanceWe identified the exact nucleocapsid protein epitope recognized by monoclonal antibody N179, a diagnostic antibody used in a colloidal gold rapid assay. The identified 390QTVTLL395 motif at residues 390 to 395 was conserved among the SARS-CoV-2 variants analyzed and was not present as an identical continuous sequence in the related respiratory viruses examined. This work supports precise epitope mapping as a useful strategy for evaluating and revalidating diagnostic antibodies as respiratory viruses evolve.

microbiology↗

bioRxiv2026

An integrative single-cell and spatial transcriptomics atlas highlights candidate regulatory factors in the development of gerbera capitulum

In Asteraceae species, the capitulum is a compact inflorescence, featuring a characteristic reproductive structure. Despite the identification of a few key regulatory factors, the transcriptome-level information on the developing capitulum remains limited. Here, we applied single-cell and spatial transcriptome sequencing to investigate the developing Gerbera hybridas capitulum during floret differentiation. We obtained a transcriptomics atlas encompassing different stages of the Gerbera capitulum and analyzed the cellular and spatial dynamics of gene expression. Using marker gene expression and GO enrichment of cluster-specific DEGs, we annotated putative cell types and described changes in gene expression across sampled stages, potentially associated with ongoing developmental processes. We detected activity of previously undescribed MADS-box genes and defined their spatial expression patterns. Notably, the MADS-box gene GAGL12 was found to be enriched in the putative capitulum phloem cells. The GAGL12 protein was shown in yeast two-hybrid assays to interact with several other MADS-domain proteins with hypothesized functions in vasculature development, and further detailed in silico analyses supported a candidate role in the development of capitulum vasculature. Altogether, we provide integrative and dynamic transcriptomic insight into capitulum and floret development and lay a basis for future functional studies of the control and development of this intriguing reproductive structure.

plant biology↗

bioRxiv2026

A Hypothalamic Inhibitory Circuit Encoding the Scalability of Stress Responses

An appropriate stress response is essential for properly responding to, coping with, and subsequently recovering from disturbing environmental stimuli. However, how the brain dynamically encodes the scalability of stress responses remains poorly understood. Here, we found that, GABAergic neurons in the arcuate nucleus (Arc, denoted as ArcGABA neurons) send direct inputs to corticotropin-releasing hormone (CRH) neurons in the paraventricular nucleus of the hypothalamus (PVH, denoted as PVHCRH neurons), the primary regulators of the hypothalamic-pituitary-adrenal (HPA) axis. Although PVHCRH neurons exhibited time-locked activation in response to various environmental stressors, both GABA release onto PVHCRH neurons and the activity of PVHCRH-projecting ArcGABA neurons were selectively reduced during exposure to prolonged, high-intensity stressors, but not following exposure to transient, low-intensity stressors. Notably, GABA release onto PVHCRH neurons was positively correlated with PVHCRH-projecting ArcGABA neuron activity, yet anticorrelated with PVHCRH neuronal activity in response to the same prolonged, high-intensity stressors. Selective silencing of PVHCRH-projecting ArcGABA neurons was sufficient to elevate HPA axis activity and stress levels, phenocopying the effect of direct of PVHCRH neuron activation. Conversely, selective activation of PVHCRH-projecting ArcGABA neurons reduced both HPA axis activity and stress levels, this effect was completely abolished by concurrent excitation of PVHCRH neurons. Molecular identity screening further revealed that these PVHCRH-projecting ArcGABA neurons are not subsets expressing agouti-related peptide (AgRP) and tyrosine hydroxylase (TH) markers. Collectively, these findings indicate that the non-AgRP/TH ArcGABA PVHCRH neurocircuit serves as a critical neural substrate that directly encodes the scalability of stress responses to environmental stressors by modulating inhibitory GABA release in a stimulus intensity-dependent manner.

neuroscience↗

bioRxiv2026

Quasi-static force requirements are not sufficient to explain arolium engagement in climbing Argentine ants

Argentine ants (Linepithema humile) utilize adhesive pads (arolia) to climb smooth surfaces. Previous research found that ants can adjust their individual arolium engagement according to their locomotion mode. However, it remains unclear how they distribute arolium engagement across multiple limbs to climb effectively, and how arolium engagement varies within a climbing step. As the arolium is a well-known adhesive organ, we hypothesized that engagement across different legs is distributed according to the normal forces required for balancing the body during climbing. To test this, we measured Argentine ants arolium engagement on a vertical glass surface using a Frustrated Total Internal Reflection (FTIR) sensor and compared it to the required normal forces from a quasi-static model. Contrary to the required normal force, the measured arolium engagement was asymmetric between upward and downward climbing, and changed over time. Our results indicated that the quasi-static force requirements are not sufficient to explain arolium engagement in climbing Argentine ants, and suggested that other factors, such as body dynamics, ants anatomy and behavioral preferences, should be included.

zoology↗