Biology subjects

Yao, X.

Publications and source records attributed to Yao, X..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

LDscore: a scalable, Python 3-powered web platform for LD score regression analysis

Linkage disequilibrium score regression (LDSC) is an important analytical tool for quantifying heritability and estimating genetic correlations between complex traits. However, the LDSC original implementation relies on an outdated Python 2 framework and deploying the standard command-line tools requires significant setup, data access, and computational expertise, creating a barrier for many researchers. To overcome these limitations, we developed LDscore, a significant technical and accessibility upgraded version of LDSC that allows for rapid analysis of GWAS data. The core advancement is the recoding of the LDSC framework in Python 3, enabling computational optimization and ensuring long-term sustainability. Built on top of this improved foundation, LDscore is implemented as a free, publicly available web application integrated within the popular NCI LDlink framework. LDscore can accelerate scientific research by providing an intuitive graphical interface for heritability estimation, genetic correlation, and LD score calculation, including access to an expanded range of reference populations for online analysis. Notably, our results show that selecting the most appropriate reference population LD panel, even at the subcontinental ancestry group level, is essential for minimizing population stratification bias in heritability estimation. By leveraging cloud computing for superior scalability and eliminating the need for local installation, LDscore adheres to FAIR principles, improving access, traceability, and reproducibility across an expanded set of reference populations, and effectively widens access to researchers worldwide providing support for in-depth genetic analyses. Brief summaryLinkage disequilibrium score regression (LDSC), a widely-used method for quantifying heritability and genetic correlation, is limited by an outdated Python 2 framework and complex command-line deployment. We developed LDscore, a significant technical upgrade built on Python 3 for sustainability and computational optimization. LDscore is a free, cloud-based web application integrated into NCI LDlink. LDscore eliminates installation barriers, offering an intuitive interface for computing heritability estimates, LD scores, and genetic correlation. Crucially, LDscore expands the range of reference populations available in LDSC, which can reduce population-stratification-based bias. Leveraging cloud computing, LDscore accelerates and widens global researcher access to LDSC-based genetic computation. AvailabilityLDscore is freely available within LDlink at https://ldlink.nih.gov/ldscore. Source code for the updated LDSC Python3 framework is available at https://github.com/CBIIT/ldsc under the GNU General Public License v3.0 and the webtool code is at https://github.com/CBIIT/nci-webtools-dceg-linkage (webtool code) under the MIT license.

genomics↗

bioRxiv2025

Identification of SASP-associated biomarkers and regulatory mechanisms in diabetic foot ulcers based on transcriptomics and experimental validation

BackgroundDiabetic foot ulcers (DFU) constitute a major complication arising from diabetes mellitus. Emerging research findings have underscored the pivotal contribution of cellular senescence to the pathophysiological development of wounds exhibiting delayed healing; nevertheless, the molecular regulatory networks governing this process in DFU pathogenesis remain incompletely elucidated MethodsDFU-related transcriptomic datasets were acquired from public databases. Biomarkers were identified through machine learning algorithms combined with expression validation. To evaluate the diagnostic predictive capacity of identified biomarkers for DFU, a nomogram prediction model was developed and validated. Further analyses included Gene Set Enrichment Analysis (GSEA), molecular network regulation, immune infiltration profiling, and drug prediction. Subsequently, the expression profiles of these biomarkers were quantitatively assessed through reverse transcription quantitative PCR (RT-qPCR) methodology. ResultsFour feature genes were identified using machine learning. Among them, CXCR2 and SIGLEC7 passed expression validation and were significantly up-regulated in DFU groups across two datasets (p < 0.05), confirming their potential as biomarkers. A nomogram constructed based on these two biomarkers demonstrated high discriminative accuracy and good calibration (decision curve net benefit > 0, AUC = 0.99). GSEA indicated that CXCR2 and SIGLEC7 were both enriched in the cytokine-cytokine receptor interaction pathway as well as other functionally associated pathways. Molecular regulatory network analysis indicated that both CXCR2 and SIGLEC7 were predicted to be regulated by transcription factors (TFs) such as SOX2. Immune infiltration analysis showed a significant strong positive correlation between CXCR2 and activated mast cells (correlation coefficient (cor) = 0.72, p < 0.001), and between SIGLEC7 and macrophages M0 (cor = 0.71, p < 0.001). Drug prediction identified 12 drugs targeting CXCR2 (e.g., Indoprofen) and one drug targeting SIGLEC7 (N-acetyl-alpha-D-glucosamine). Validation through Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR) revealed that CXCR2 and SIGLEC7 expression levels were markedly increased in the DFU group, showing statistically significant differences (p<0.05), which aligned with the bioinformatics analysis outcomes ConclusionThis study identified CXCR2 and SIGLEC7 as SASPRG-related biomarkers in DFU through bioinformatic analysis, providing new theoretical support and a basis for early diagnosis and treatment of DFU.

genomics↗

bioRxiv2025

Revisiting the in vivo Functions of Coilin in Mice

Cajal bodies (CBs), first identified in the early 20th century, are classic nuclear structures organized primarily by the protein coilin. Although CBs have long been implicated in snRNA modification and maturation, their precise roles in mice remain unclear. Here, we revisit the functions of CBs by using genome editing to generate mice that lack nearly the entire coilin protein, retaining only the first seven amino acids. Mass-spectrometry analyses showed reduced 2'-O-methylation of U2 snRNA in coilin mutant liver; however, these reductions had minimal impact on overall gene expression and pre-mRNA splicing patterns. Additionally, detailed analysis recapitulated previously reported testicular size reductions and newly revealed decreased proportions of high-quality sperm. We also identified novel coilin-containing condensates distinct from genuine CBs in the nuclear pocket of elongating spermatids. Our findings implicate that coilin orchestrates membraneless organelles in various compartments, playing multifunctional roles beyond classical CB formation.

molecular biology↗

bioRxiv2025

Overexpression of TPM4 promotes cancer progression through EMT in anaplastic thyroid cancer

Anaplastic thyroid cancer (ATC) is an undifferentiated tumour originating from thyroid follicular epithelium and represents the most malignant subtype of thyroid cancer. However, the mechanisms underlying ATC development are not fully understood. This study aimed to investigate the mechanisms driving ATC invasion and metastasis to provide novel insights into its aggressive behavior. Through an integrated bioinformatics analysis of the GEO database, we identified Tropomyosin 4 (TPM4) as a differentially expressed gene in ATC. Bioinformatic correlation and pathway enrichment analyses suggested that TPM4 expression is potentially linked to tumor cell invasion and lymph node metastasis. We showed that TPM4 was highly expressed in both ATC tissues and cell lines, and its expression levels were positively correlated with enhanced cell migration and invasion. Mechanistic studies indicated that TPM4 likely enhances tumour cell migration and invasion by facilitating cytoskeletal remodeling and promoting the epithelial-mesenchymal transition (EMT). Our findings suggest that TPM4 represents a promising diagnostic and therapeutic biomarker for ATC.

cancer biology↗

bioRxiv2025

Uncovering structural determinants of peptide recognition by public and private T-cell receptors

Public T cell receptors (TCRs) recurrently emerge across individuals in response to common pathogens, yet the structural and biophysical basis distinguishing public from private clonotypes remains incompletely defined. Here, we combine epitope mapping, single-cell TCR sequencing, and single-particle cryo-electron microscopy to dissect CD8+ T cell responses to the immunodominant SARS-CoV-2 ORF3a(207-215) epitope presented by HLA-A*01:01. Among responding clonotypes, we identify a shared public TCR (TCRpub) and an individual-specific private TCR (TCRpriv) that use nearly identical TRBV5-1 {beta} chains but distinct chains. Both clonotypes exhibit comparable micromolar affinity and functional avidity, yet their structures reveal different antigen-recognition modes. We determined cryo-EM structures of the TCRpub and TCRpriv in complex with ORF3a(207-215)/ HLA-A*01:01 at [~]3 [A] resolution. Despite targeting the same epitope, the two receptors engaged the peptide-MHC complex with distinct CDR-loop orientations and contact footprints: TCRpub engages the peptide through a peptide-centric AGDL CDR3{beta} motif and focuses interactions on the MHC 2-helix, whereas TCRpriv distributes contacts across both MHC -helices via a canonical CDR3{beta} configuration. These findings illustrate how near-identical {beta} chains can yield divergent recognition strategies to recognise the same pMHC ligand through alternative -chain pairing. More broadly, this work establishes cryo-EM as a robust approach for resolving physiological-affinity TCR/pMHC complexes, providing mechanistic insight into how public TCRs emerge and persist in antiviral immunity.

immunology↗

bioRxiv2025

YAP1 Depletion Enhances TAZ and its Complexation with TEAD4 and AP-1 Heterodimer C-JUN/FOSB to Promote Gastric Cancer Progression and Metastases

BackgroundDysregulation of the Hippo signaling pathway, characterized by aberrant activation of the transcriptional coactivators YAP1 and TAZ, drives tumour progression, immunosuppression and metastasis. Hippo pathway components are emerging therapeutic targets in several solid tumours, however, the expression profiles of Hippo coactivators YAP1, TAZ and their transcriptional factors TEAD1-4 in gastric cancer peritoneal metastases (GCPMs) and their therapeutic value are unknown. ObjectiveTo determine expression status of YAP1, TAZ and TEAD1-4 in GCPMs; and to evaluate whether dual targeting of YAP1 and TAZ provides superior antitumour activity compared with inhibition of either coactivator alone. DesignExpression of YAP1, TAZ and TEAD1-4 was examined in GCPMs by single-cell RNA sequencing and co-immunofluorescent staining. Functional studies using genetic knockout and antisense oligonucleotide (ASO) inhibition of YAP1 or TAZ were performed to assess antineoplastic effects in vitro and in vivo. Co-immunoprecipitation and luciferase reporter assays were used to characterize YAP1/TAZ interactions with TEADs and AP-1 components (JUN and FOSB) and to quantify transcriptional activity. Antitumour efficacy was validated in patient-derived xenograft (PDX) and KP-Luc2 syngeneic models. ResultsYAP1, TAZ, and TEADs1- 4 were highly coexpressed in GCPMs and correlated with poor survival. YAP1 inhibition alone elicited compensatory upregulation of TAZ, while combined inhibition of both coactivators maximally repressed cell proliferation and invasion in vitro, and tumor growth in vivo. Increased TAZ complexation with TEAD4 and AP-1 (c-JUN and FOSB) heterodimer was observed following YAP1 knockdown or pharmacological ASO inhibition. Dual inhibition of YAP1 and TAZ was required to maximally suppress YAP1/TAZ expression and reduce their nuclear accumulation, transactivation of TEAD, and activation of downstream genes. ConclusionsThese findings show that combined YAP1 and TAZ inhibition holds promise for the treatment of GCPMs, a highly lethal disease with an urgent need for novel treatment options. WHAT IS ALREADY KNOWN ON THIS TOPICO_LIGastric cancer with peritoneal metastasis (GCPM), occurring in > 45% of gastric cancer (GC) patients, is a highly lethal malignancy with limited therapeutic options. C_LIO_LIThe Hippo pathway mediator Yes-associated protein 1 (YAP1) is intimately involved in chemoresistance, cancer stemness properties, and the epithelial-to-mesenchymal transition in gastric and other cancers. C_LIO_LIWhile YAP1 represents a promising therapeutic target, clinical trial of YAP1 antisense oligonucleotides has been disappointing. C_LI WHAT THIS STUDY ADDSO_LIHippo coactivators YAP1, TAZ and their main transcription factors TEAD1-4 are markedly upregulated in GCPMs and associated with poor prognosis. C_LIO_LIAntisense targeting of YAP1 results in compensatory upregulation of its paralog TAZ. C_LIO_LIUpon YAP1 depletion, TAZ forms transcriptional complexes with TEAD4 and the AP-1 heterodimer (JUN and FOSB). C_LIO_LIDual targeting of YAP1 and TAZ, by oligonucleotides, achieves maximal suppression of tumour growth in vitro and in vivo. C_LI HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE OR POLICYO_LIThese findings provide a strong mechanistic rationale for co-targeting YAP1 and TAZ as a therapeutic approach in metastatic gastric cancer. C_LIO_LIDual Hippo coactivator inhibition could inform the design of future clinical trials aimed at improving outcomes for patients with GCPMs. C_LI

cancer biology↗

bioRxiv2025

Task-similarity dependent reconfiguration of compositional modules and geometry in frontal cortex

Task rules critically shape how neural populations encode information and generalize across cognitive demands, yet the mechanisms linking rule structure, neural dynamics, and behavior remain poorly understood. Here we investigate how rule congruence modulates neural-ensemble compositionality, geometry and cross-task generalizability in mouse anterior lateral motor cortex (ALM). Mice switched between tactile and auditory delayed-response tasks where sensory-motor contingencies were either aligned (congruent) or conflicting (incongruent). Recording from 11,000 ALM neurons revealed rule dependent compositional coding of stimulus, choice, and outcome. In contrast to congruent switching, incongruent rules reduced cross-task generalizability of sensory, choice and outcome representations, expanded population dimensionality, increased reliance on nonlinear mixed-selectivity, and produced more complex coding geometry. These neural changes paralleled behavioral costs during task transitions. Moreover, congruence dependent reconfiguration of sensory-choice subspaces in ALM predicted differences in transition costs, implicating ALM in adaptively resolving conflicting contingencies. Together, these results show that task congruence regulates neural coding geometry and population dynamics, linking rule-switching complexity to dimensionality of neural resource allocation and to cognitive flexibility.

neuroscience↗

bioRxiv2025

A multi-tissue atlas of genetic regulatory effects in sheep

Characterizing the impact of genomic variants on genome function and ultimately complex traits in livestock is essential for the development of sustainable precision agriculture and comparative genomics. Here, as part of the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we present the pilot phase of the SheepGTEx resource through analyzing 6,761 RNA-sequencing samples of 51 primary tissues in a multi-breed population of sheep. We identify millions of regulatory variants associated with seven types of molecular phenotypes, and fine-map 322,468 primary and 114,017 non-primary effects, revealing a high degree of regulatory allelic heterogeneity. We systematically characterize the pleiotropic effects of these variants on molecular phenotypes, assess their context-specific regulatory patterns across tissues, breeds, sexes, and developmental stages, as well as explore their evolutionary constraints across mammals. Finally, we demonstrate the substantial potential of the SheepGTEx resource (https://sheepgtex.farmgtex.org), by providing examples of regulatory mechanisms underpinning 34 complex traits, population divergence between European and Asian breeds, and adaptive evolution in sheep over the past ten millennia.

genomics↗

bioRxiv2025

RNA reinforces condensate nucleation on chromatin to amplify oncogenic transcription

Aberrant chromatin-associated condensates have emerged as drivers of transcriptional dysregulation in cancer. Although extensive studies have elucidated intrinsic protein sequence features governing their formation, how extrinsic factors within the chromatin environment modulate their assembly and pathogenic function remains poorly understood. Gain-of-function mutations in the histone acetylation reader ENL, found in pediatric leukemia and Wilms tumor, drive oncogenesis by inducing condensate formation at highly selective genomic loci. Here, we uncover a critical role for locally produced gene transcripts in reinforcing the nucleation, chromatin engagement, and oncogenic activity of ENL mutant condensates. Mutant ENL binds RNA in part through a conserved basic patch within its YEATS domain, and this interaction enhances condensate formation both in vitro and across diverse cellular contexts. Using a chemically inducible condensate displacement and re-nucleation system, we show that blocking ENL-RNA interactions or transcription impairs condensate reformation at endogenous targets. RNA interactions preferentially enhance mutant ENL occupancy at top-bound, condensate-permissive loci, leading to increased transcriptional bursting and robust gene activation at the single-cell and single-allele level. In mouse models, disrupting ENL-RNA interactions reduces condensate formation and oncogenic transcription in hematopoietic stem and progenitor cells, thereby suppressing ENL mutant-driven leukemogenesis. Together, these findings demonstrate that locally produced RNA transcripts can promote locus-specific nucleation of pathogenic condensates on chromatin, which in turn drive persistent and hyperactive transcription of oncogenic targets and lead to tumorigenesis.

molecular biology↗

bioRxiv2025

scRNA + TCR + BCR-seq Reveals the proportion and characteristics of dual TCR T cells and dual BCR B cells in mice infected with Echinococcus granulosus

Cystic echinococcosis (CE) is a zoonotic parasitic disease caused by Echinococcus granulosus, and the T and B cell responses and regulatory mechanisms in CE remain unclear. In this study, we analyzed the data of peripheral blood and spleen of mice infected with Echinococcus granulosus(EG) by scRNA+TCR+BCR-seq, and made the following novel findings: (1) Peripheral blood of Echinococcus granulosus (EG)-infected mice contained a higher proportion of dual TCR(T cell receptor) T cells with higher clonality than uninfected mice; (2) There was a bias in V gene usage between single TCR T and dual TCR T cells, as well as between single BCR(B cell receptor) B cells and dual BCR B cells in EG-infected mice; (3) Dual TCR Tregs, dual TCR effector CD8 T cells, dual BCR Bregs, and dual BCR memory/dividing B cells exhibited relatively high clonal expansion in EG-infected mice; (4) Shared CDR3 sequences and consistently highly expressed mRNA molecules exist between single receptor T/B and dual receptor T/B cells in EG-infected mice. KEGG enrichment analysis revealed that dual BCR B cells are closely related to the expression of factors associated with pathways such as "Th1/Th2 differentiation" and "antigen processing and presentation". These results suggest that dual TCR T and dual BCR B cells may be involved in the specific responses and regulation of EG-infected mice, providing a novel perspective for the adaptive immune response mechanisms and targeted therapy of parasitic infections. Author summaryEchinococcosis is a zoonotic disease currently prevalent mainly in various parts of Africa. At present, it cannot be completely cured; treatment relies solely on medication to alleviate symptoms. The immunoregulatory mechanisms underlying the disease remain unclear. Using single-cell RNA sequencing, we have identified a novel T- and B-cell subpopulation that may play a role in the immune response to the parasite. This finding opens a new avenue for researchers investigating parasitic diseases.

immunology↗

bioRxiv2025

Cell-Free Protein Crystallization Enables Rapid Structure Determination of Disaccharides and Trisaccharides Using Galectin-10 Crystals

It is critical to understand the conformational selection and dynamics of flexible saccharides via protein-ligand interactions in efforts to elucidate their biofunctional roles. Protein crystals can serve as scaffolds to immobilize small molecules, enabling structural and dynamic analysis of saccharides that are difficult to study by conventional approaches. However, constructing versatile scaffold crystals for high-throughput structural analysis remains challenging because this work involves laborious protein production and crystallization workflows. Here, we report rapid crystallization and structural analysis of saccharide-bound scaffolds by applying cell-free protein crystallization (CFPC) to galectin-10 (Gal-10), a lectin known to crystallize spontaneously in vivo. Using CFPC-generated Gal-10 crystals, we obtained the first atomic-resolution structures of melezitose, one of the trisaccharide, bound to the protein scaffold, revealing binding modes inaccessible by conventional approaches. Normalized B-factor analysis combined with molecular dynamics simulations reveals how the binding-site architecture modulates saccharide flexibility and immobilization. This platform can be extended to other flexible ligands and fragment-based screening.

biophysics↗

bioRxiv2025

PepPCBench is a Comprehensive Benchmark for Protein-Peptide Complex Structure Prediction with AlphaFold3

Peptides mediate up to 40% of protein-protein interactions (PPIs), offering high specificity and the ability to target binding sites inaccessible to small molecules, making them promising candidates for drug development. Accurate modeling of protein-peptide complexes is crucial for understanding fundamental biological processes and for advancing peptide-based drug design. However, due to the high conformational flexibility of peptides, predicting their interactions with proteins remains a significant challenge. Recent advancements in artificial intelligence (AI), exemplified by all-atom protein folding neural networks (PFNNs) such as AlphaFold3 (AF3), have expanded predictive capabilities beyond proteins to encompass protein-peptide complexes. Nevertheless, existing evaluations of these methods are often limited in scope and lack systematic, multi-dimensional, and fair comparisons of PFNN performance in protein-peptide complex prediction. Here, we introduce PepPCBench, a comprehensive benchmark framework specifically developed to evaluate AF3s capabilities in predicting protein-peptide complexes. This study utilizes a carefully curated dataset named PepPCSet, which is excluded from the AF3s training or validation sets. This dataset includes 261 protein-peptide complexes with peptide lengths ranging from 5 to 30 residues. Our benchmark results indicate that AF3 outperforms other PFNNs in prediction accuracy and structural validation. However, its performance remains insufficient for practical peptide drug discovery, indicating room for improvement. It is expected that PepPCBench can provide some valuable insights into the enhancement of protein-peptide complex structure prediction and the development of peptide-based therapeutics. The dataset and pipeline protocols are available at https://github.com/zhaisilong/PepPCBench.

bioinformatics↗

bioRxiv2025

Influence of Macrocyclization Strategies on DNA-Encoded Cyclic Peptide Libraries

Discovery of cyclic peptide hits using DNA-encoded libraries (DELs) has recently been extensively researched, with significant efforts directed toward developing DEL-compatible macrocyclization methods. To investigate how different cyclic linkers influence DEL selection outcomes, we constructed eight distinct sub-libraries and screened them against two protein targets, MDM2 and GIT1, resulting in two representative yet contrasting scenarios. Validation studies for MDM2 revealed that structural similarity patterns observed across multiple sub-libraries could enhance confidence in the authenticity of identified hits. Notably, cmp-10 demonstrated potent inhibitory activity, exhibiting an inhibition constant of 11 nM. In contrast, selections against GIT1 produced discrete enrichment patterns. From these outcomes, two exemplary compounds were selected and validated through both on-DNA and off-DNA modes. cmp-17 was confirmed to bind specifically to the desired binding pocket, displaying a dissociation constant of 1.22 M. Furthermore, ITC experiments using mutant GIT1 proteins (GIT1L271A/L279A and GIT1L271L/L279L) provided additional insights into the mechanism by which cmp-17 disrupts the interaction between GIT1 and {beta}-Pix.

biochemistry↗

bioRxiv2025

CDK9 degradation Inhibits Gastroesophageal Cancer growth and Overcomes Radiation Resistance by Increasing Chromatin Accessibility and Downregulating YAP1/TEAD signaling

BackgroundGastroesophageal cancer (GEAC) remains a major health burden and urgently needs novel therapeutic targets. The inhibition of CDK9s activity holds the potential to be a highly effective anti-cancer therapeutic. However, the functional role of CDK9, and its potential targeting in GEAC, remain largely unknown. ObjectiveWe aim to evaluate the potential of degradation CDK9 in GEAC treatment and explore its mechanisms. DesignWe evaluated the expression and distribution of CDK9 in GEAC tissue. We designed and synthesized novel CDK9 degraders using proteolysis targeting chimeras (PROTACs) strategy and selected the promising one for further anti-tumor activity evaluation both in vitro and in vivo. We evaluated the effects of CDK9 degradation on epigenetic reactivation, gene expression and chromatin accessibility. We evaluated the co-targeting of CDK9 and YAP/Tead signaling for GEAC treatment, especially for radiation-resistant tumor treatment. ResultsWe demonstrated significantly elevated CDK9 expression in primary GEAC tumor tissues compared to normal tissues, in association with poor survival. We developed a novel CDK9 degrader, YX0597, reducing RNA Pol II Serine 2 phosphorylation, and inhibition MCL-1; this was accompanied by potent inhibition of GEAC cell growth, especially in radiation-resistant tumor cells. Mechanistically, YX0597 strongly enhanced chromatin accessibility, activating epigenetically silenced genes; and dramatically inhibited YAP/TEAD signaling. CDK9 closely interacts with YAP/TEAD signaling, and co-targeting these two mediators could be a novel treatment strategy for the treatment of GEAC. ConclusionOur studies reveal a new avenue for targeting CDK9-hyperactivated GEAC tumors, especially in combination with YAP1/TEAD inhibition in radiation-resistant GEAC tumors. What is already known on this subject?Gastroesophageal cancer (GEAC), the third-leading cause of global cancer death and urgently needs novel targeted therapies. Targeted protein degradation has emerged as an attractive strategy to fight cancer, complementing the activity of traditional small-molecule inhibitors. Cyclin-dependent kinase 9 (CDK9) has been implicated in various cancers. Recently, CDK9 degraders have now been developed for future clinical benefit in targeting tumors with highly activated CDK9. What are the new findings?In this study, we show that CDK9 expression was significantly elevated in primary GEAC tumor tissues including PDXs compared to normal tissues, in association with poor survival. We developed a novel CDK9 degrader XY0597 and proved that it inhibits the progression of GEAC by increasing chromatin accessibility and down-regulating YAP/Tead signaling. We also proved a strong connection between CDK9 and YAP/TEAD signaling and Co-targeting them synergistically inhibits GEAC tumor cell growth, especially in tumors with high YAP signaling activity, such as radiation-resistant cancer. How might it impact on clinical practice in the foreseeable future?Our data suggests that CDK9 is a viable anticancer target in GEAC. We demonstrate that a novel CDK9 degrader, YX0597, has high potential clinical application for GEAC treatment, especially in radiation-resistant cancer. We reveal the crosstalk of CDK9 and YAP/TEAD signaling, and that co-targeting these two mediators could be a new avenue for targeting CDK9-hyperactivated GEAC primary and radiation-resistant tumors.

cancer biology↗

bioRxiv2025

Investigating the Mechanisms and Potential Therapeutic Targets of Vestibular Migraine

BackgroundVestibular Migraine (VM) is a complex neurological disorder with recurrent headaches and various vestibular symptoms. Although it severely affects patients quality of life, its causes and pathophysiology are still unclear, and effective treatments are scarce. The lack of data emphasizes the need for bioinformatics to find key genes and pathways in VM, which could help develop new diagnostic and treatment methods. MethodThe GSE109558 dataset was acquired from the Gene Expression Omnibus (GEO) database. To identify VM - related differentially expressed genes, screening was carried out through limma and Weighted Correlation Network Analysis (WGCNA).The functional analysis of VM - related differentially expressed genes was conducted using three bioinformatics approaches: Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and Gene Set Enrichment Analysis (GSEA). Feature selection was further refined using lasso regression and random forest. Also, CIBERSORT was utilized to analyze the infiltration of immune cells, and Spearmans correlation analysis was employed to explore the correlations between diagnostic differentially expressed genes and immune cells.Finally, the Comparative Toxicogenomics Database (CTD) was utilized to search for corresponding drugs, and molecular docking was performed to explore potential therapeutic targets. ResultSix key feature genes (CABIN1, IFIT3, HEATR1, ARHGDIA, RAB11FIP4, and ZNF444) were identified as potential diagnostic markers for VM. Among these, CABIN1 demonstrated the highest diagnostic potential based on ROC curve performance, highlighting its promise as a diagnostic biomarker.Functional annotation of DEGs revealed their enrichment in biological processes related to inflammation, calcium ion channel regulation, and other pathways likely involved in VM pathophysiology. Through the CTD, drugs like Acetaminophen, bisphenol A, and Phenylephrine were identified. Molecular docking simulation was used to explore their potential therapeutic mechanisms for VM. ConclusionThis study offers important insights into the molecular mechanisms of VM and identifies six key feature genes, with CABIN1 standing out as a potential diagnostic marker.These findings pave the way for further research to validate the diagnostic and therapeutic implications of these genes and pathways.

genetics↗

bioRxiv2025

Optimized antibody with W32I mutation enhances antiviral efficacy against influenza

The influenza virus has caused a global pandemic with significant morbidity and mortality, highlighting the need to optimize antibodies for improved antiviral efficacy. The 3E1 antibody effectively neutralizes influenza subtypes H1 and H5 by inhibiting acid-induced conformational changes of hemagglutinin (HA). This study aimed to optimize the antibodys bioactivity by modifying amino acid residues, resulting in single-point mutants (3E1-L [W32I], 3E1-H [F103I]) and a double mutant (3E1-H+L [F103I, W32I]). The binding affinity, neutralizing activity, and antiviral mechanisms of the mutants were evaluated. Notably, the 3E1-L mutant showed significantly enhanced antiviral activity against H1N1 and H3N2 compared to wild-type 3E1, inhibiting both viral entry and release. The prophylactic and therapeutic efficacy of the 3E1-L mutant was validated. Molecular dynamics simulations of the 3E1-L/HA complex showed that the W32I mutation reduces steric hindrance between tryptophan at position 32 and the complementarity-determining region (CDR) L1 loop of HA. In conclusion, the W32I substitution enhances the antiviral activity of wild-type 3E1, making the optimization of 3E1-L a promising strategy for developing more effective influenza therapies.

immunology↗

bioRxiv2024

scRNA+TCR-seq Reveals the Proportion and Characteristics of Dual TCR Treg Cells in Mouse Lymphoid and Non-lymphoid Tissues

The rearrangement of TCR germline V(D)J genes during T cell development, including allelic exclusion and tolerance selection, ensures the clonal selection theory, which states that "a lymphocyte expresses only one type of antigen receptor" This forms the basis for T cell-specific responses. However, The existence of "dual TCR T cells" has consistently been supported by specific experimental evidence. detailed reports on the origin, proportion, tissue distribution, and CDR3 characteristics of "dual TCR Treg cells" are currently lacking. In this study, we utilized scRNA+TCR-seq technology to achieve in-depth analysis of single TCR T and dual TCR T pairings, along with their mRNA expressions, from over 5,000 T cells in each sample. Through comparative studies with shared databases, we provided a detailed analysis of the proportions and characteristics of dual TCR Tregs in mouse lymphoid and non-lymphoid tissues (such as iLN, mLN, blood, and skin). Our findings revealed a high proportion of dual TCR Tregs across various mouse tissues, with their TCR pairing patterns, V(D)J usage, and mRNA expression showing both homogeneity and certain differences compared to single TCR Tregs, as well as heterogeneity across different tissue sites. This research provides new insights and technical approaches for studying the origins, characteristics, effects, and mechanisms of Treg cells in different tissue locations.

immunology↗

bioRxiv2024

Assessment of DNA methylation from a single genomic region of ELOV2 is sufficient to predict chronological age

Estimation of chronological age is particularly informative in forensic contexts. Assessment of DNA methylation status allows for the prediction of age, though the accuracy and ease of manipulation may vary across different models. In this study, we started with a carefully designed discovery cohort recruiting more elderly subjects than other age categories, to diminish the effect of epigenetic drifting. We analyzed DNA methylation from a single genomic region of ELOV2, which was sufficient to construct an age-prediction model comprising 15 CpG sites. This model is further validated by an independent cohort as well as a multi-center test using trace dried bloodstains. The nature of our analytical pipeline, when combined the assessment of a single genomic locus with high-throughput sequencing, can easily be scaled up with low cost. Taken together, we propose a new age-prediction model featuring accuracy, ease of manipulation, high-throughput, and low cost. This model can be readily applied in both classic and newly emergent forensic contexts that require age estimation.

genetics↗