Search Results (336)

Background: Head and neck squamous cell carcinoma (HNSCC) responds poorly (<20%) to immune checkpoint blockade. Since sialylation suppresses anti-tumour immunity through Siglec signalling independently of the PD-L1/PD-1 axis, we mapped its prognostic landscape in HNSCC by integrating prognostic modelling, molecular subtyping, and AI-guided drug discovery. Methods: Transcriptomic data from seven GEO cohorts and TCGA-HNSC (n = 501) were analysed with a 1204-gene sialylation compendium. The Sialylation Niche Index (SNI) was built in TCGA-HNSC from 117 machine-learning algorithm combinations (nominally 101), with survival-based feature selection and model fitting confined to the training set; model selection used TCGA-HNSC and the external model-selection cohort GSE42743 (n = 74 with overall survival), and the three independent test cohorts were scored without re-fitting (E-MTAB-8588, n = 83; GSE65858, n = 270; and GSE41613, n = 97). Key model genes were characterised by single-cell RNA sequencing (168,742 cells), spatial transcriptomics, and AI-guided screening of 249,455 compounds. Results: Thirty-one prognostic sialylation-associated DEGs defined an immunosuppressive subtype (C1) and an immune-active subtype (C2) with divergent survival. The SNI achieved a C-index of 0.88 in TCGA-HNSC, 0.68 in GSE42743, and 0.58–0.62 in the three independent test cohorts and remained independently prognostic after adjustment for age and other clinicopathological variables in multivariable analysis. SHAP analysis identified HSPH1 (risk-associated) and ST6GALNAC1 (protective) as principal contributors with opposing microenvironmental associations. Conclusions: Sialylation constitutes a distinct immunosuppressive axis in HNSCC, complementary to PD-1 blockade. The SNI provides a biologically anchored prognostic framework whose cross-platform transfer requires recalibration; putative candidate compounds require experimental validation. Full article

Aging and cancer form a biological continuum influenced by epigenomic changes, metabolic dysfunction, inflammation, cellular senescence, and loss of tissue homeostasis. Age-related epigenetic alterations can promote cancer, which exploits plasticity for evolution, immune evasion, metastasis, and resistance. Nutrition and metabolism affect this process through one-carbon metabolism, methyl-donor availability, acetyl-CoA and NAD⁺ balance, redox status, microbiome metabolites, and chromatin enzyme activity. Circulating biomarkers such as cell-free DNA methylation, mutation-based ctDNA, fragmentomic features, and non-coding RNAs can detect tumor and host changes linked to aging, inflammation, nutrition, and treatment with minimal invasiveness. This review explores the epigenetic aging–cancer link, how nutrition and metabolism modify pathways, and the potential of circulating biomarkers for diagnosis, prognosis, prediction, and monitoring. The focus is on epigenetic plasticity, drug-tolerant states, resistance, epigenetic drugs, metabolic targeting, and nutritional interventions. New technologies, including single-cell and spatial epigenomics, long-read sequencing, and multimodal computational approaches, aid biomarker discovery and clinical use. Challenges include variability, misclassification, heterogeneity, confounding, reverse causality, overfitting, and limited validation. Clinical applications need standard workflows, representative cohorts, transparent models, and proof that biomarker-guided strategies improve outcomes. Full article

Background: Allergic rhinitis is common and clinically heterogeneous, but the genes whose genetically regulated immune-state expression influences susceptibility remain incompletely resolved. Methods: We integrated dynamic CD4+ T cell eQTL data (46 activation-state profiles) with allergic rhinitis GWAS summary statistics, applying transcriptome-wide Mendelian randomization (MR), colocalization, SMR/HEIDI, metabolite screening, paired single-cell RNA-seq and TCR analysis, and computational follow-up. Colocalization support was prespecified as conditional ratio PP.H4/(PP.H3 + PP.H4) > 0.7; HEIDI at p > 0.05. Results: After MHC-region exclusion, 50,654 gene-profile pairs were tested and 129 MR-significant genes were identified. Colocalization supported 418 pairs (111 genes); 70 genes passed both SMR and HEIDI; and cross-database comparison yielded a nine-gene overlap set. In GSE200107, baseline good-versus-poor responder differences were larger than treatment-induced transcriptional change; patient-level reanalysis found no pair surviving multiple-testing correction (n = 4 vs. 3); these findings are hypothesis-generating. Paired TCR analysis suggested greater clonotype renewal in good responders (descriptive). Structure-guided screening prioritized unvalidated binder candidates for SLC25A46 and TLR1 (TLR1 TIR docking −5.86 kcal/mol; MD RMSD 0.20 nm). Conclusions: An exploratory metabolite screen yielded nominally significant indirect-effect signals, but the candidate metabolite did not colocalize with the disease locus. This framework prioritizes candidate therapeutic targets for allergic rhinitis. Full article

Medicinal plants are major sources of therapeutic natural products, yet the cell-type-specific organization that governs metabolite biosynthesis, transport, and storage remains imperfectly resolved by organ-level omics. This review synthesizes studies published up to June 2026 that used single-cell, single-nucleus, spatial, metabolomic, and epigenomic approaches to medicinal plant systems, following a PRISMA-guided literature search across PubMed, Web of Science, Scopus, and CNKI. Emerging evidence shows that specialized metabolism is organized through discrete and often rare cell populations, including idioblasts, laticifers, glandular trichomes, secretory epidermal cells, internal phloem-associated parenchyma, cork and periderm cells, mesophyll cells, and other biosynthetic niches. Single-cell RNA sequencing has defined these populations and reconstructed developmental trajectories, whereas single-cell metabolomics and mass spectrometry imaging reveal that metabolite accumulation frequently diverges from biosynthetic gene expression because of intercellular transport, storage capacity, and subcellular compartmentation. Single-cell ATAC-seq and multiome profiling further identify cell-type-specific regulatory regions, transcription factors, and candidate promoters controlling metabolic competence. Together, these technologies are reshaping medicinal plant biology from pathway-centric catalogs into spatially and developmentally resolved cellular maps. We highlight how artificial intelligence (AI)-assisted integration can accelerate cell annotation, regulatory network inference, metabolite assignment, and prioritization of biosynthetic genes, transporters, and engineering targets. Future progress will depend on comparative medicinal plant atlases, improved recovery of recalcitrant tissues, matched transcriptomic, metabolomic, and spatial designs, and functional validation of cell-type-specific mechanisms. Full article

Triple-negative breast cancer (TNBC) is an aggressive and clinically heterogeneous breast cancer subtype characterized by the absence of estrogen receptor, progesterone receptor, and HER2 overexpression, limited targeted treatment options, early relapse, and frequent development of therapy resistance. Although TNBC often shows initial sensitivity to chemotherapy, durable responses are commonly undermined by the emergence of adaptive resistant cell states rather than solely by fixed genetic mutations. This review synthesizes the role of epigenetic plasticity as a central mechanism that enables TNBC cells to dynamically reprogram transcriptional identity, survive therapeutic stress, and transition between epithelial, mesenchymal, stem-like, immune-evasive, and drug-tolerant persister phenotypes. Key epigenetic mechanisms include aberrant DNA methylation, histone acetylation and methylation, BET/BRD4-dependent transcriptional regulation, EZH2-mediated repression, SWI/SNF-dependent chromatin remodeling, non-coding RNA networks, and three-dimensional genome reorganization. These processes regulate tumor suppressor silencing, DNA-damage repair, epithelial–mesenchymal plasticity, cancer stem-cell maintenance, metabolic adaptation, immune-checkpoint regulation, and minimal residual disease. The review also highlights the translational relevance of epigenetic biomarkers, including DNA methylation signatures, circulating epigenetic markers, chromatin-accessibility profiles, and single-cell epigenomic approaches for diagnosis, prognosis, therapy prediction, and monitoring resistance evolution. Finally, therapeutic strategies targeting epigenetic plasticity are discussed, including DNMT, HDAC, BET, EZH2, KDM, and LSD1 inhibitors, with emphasis on rational combination approaches involving chemotherapy, PARP inhibitors, immunotherapy, and metabolic targeting. Overall, epigenetic plasticity represents both a major driver of TNBC resistance and a therapeutically exploitable vulnerability, provided those future strategies account for tumor heterogeneity, adaptive cell-state transitions, biomarker-guided patient selection, and combination-based treatment design. Full article

Non-coding RNAs (ncRNAs) are biologically plausible biomarkers in male infertility, but no assay is ready for routine use. This narrative review organizes human evidence by intended clinical decision and defines clinical actionability as a test’s ability to inform a specified decision through analytical reliability, clinical validity, incremental value, decision-level benefit, and feasible implementation. Evidence is most developed for obstructive versus non-obstructive azoospermia (NOA) classification and sperm-retrieval prognosis. Most reports, however, use selected case–control samples, single-center development cohorts, or same-program evaluations. Mixed biospecimens, incompletely specified RNA isoforms and normalization, uncertain cohort independence, imperfect diagnostic references, and protocol-dependent retrieval outcomes limit transportability. No independent geographic validation of a locked ncRNA assay or prospective evaluation of ncRNA-guided management was identified within the retrieved sources. Current guidelines do not recommend routine ncRNA testing. Progress requires prespecified intended uses, locked assays, representative multicenter validation, same-patient comparison with contemporary care, calibrated risk estimates, decision-curve analysis, and patient-important, couple-centered outcomes. Full article

Leaf senescence negatively impacts yield and postharvest quality in non-heading Chinese cabbage (Brassica rapa ssp. chinensis), and the STAY-GREEN (SGR) homologs BcSGR1 and BcSGR2 function as core regulators of chlorophyll degradation. In this study, we constructed CRISPR/Cas9 single- and dual-gene editing vectors using four high-efficiency, high-specificity single-guide RNAs (sgRNAs). By optimizing the transformation system using petiolate cotyledon explants supplemented with 6 mg·L⁻¹ AgNO₃, we obtained a PCR-positive transformation efficiency of 26% (this value reflects transformation efficiency; the actual gene editing efficiency for each mutant line is presented in the target sequencing results) and generated BcSGR1 (YB1) and BcSGR2 (YB2) single mutants and a BcSGR1/BcSGR2 double mutant (DKO). All mutant lines exhibited a pronounced stay-green phenotype and delayed leaf senescence. The DKO line produced 3.15-fold higher chlorophyll and only one-quarter of the wild-type MDA level, indicating an additive enhancement effect of the double knockout. Compared with the wild type (3-day shelf life), YB1, YB2 and DKO extended postharvest longevity to 7, 8 and 11 days, with senescence delayed by 15, 18 and 22 days, respectively. Notably, whereas the YB1 and YB2 displayed mild leaf shriveling at later developmental stages, the DKO maintained normal leaf morphology. Collectively, our findings demonstrate that dual editing of BcSGR1 and BcSGR2 exerts an additive effect on delaying leaf senescence and enhances postharvest shelf life without incurring significant yield penalties under the experimental conditions. This study provides a feasible and effective strategy for breeding stay-green cultivars of non-heading Chinese cabbage. Full article

Background: Dengue has expanded rapidly beyond traditional tropical and subtropical regions, driven by climate change, urbanization, population mobility, and the spread of competent Aedes vectors. Vaccination is an increasingly important component of dengue prevention, but development has been complicated by four viral serotypes, antibody-dependent enhancement, variable baseline serostatus, and the need for balanced and durable tetravalent immunity. Methods: We conducted a narrative review of PubMed/MEDLINE, Google Scholar, ClinicalTrials.gov, and relevant public health and regulatory sources. Evidence on dengue epidemiology, immunopathogenesis, licensed vaccines, advanced candidates, efficacy, immunogenicity, safety, durability, and implementation was critically evaluated. Priority was given to randomized trials, long-term follow-up studies, regulatory assessments, and surveillance data. Evidence was synthesized descriptively without formal meta-analysis or risk-of-bias assessment. Results: CYD-TDV was the first licensed dengue vaccine but is restricted to individuals with documented previous infection because seronegative recipients may experience an increased risk of severe dengue. TAK-003 has demonstrated overall efficacy against virologically confirmed dengue and dengue-related hospitalization in both baseline-seropositive and baseline-seronegative populations. However, protection is heterogeneous by serotype, and evidence remains limited or uncertain for some serotype-by-serostatus strata. Butantan-DV offers a promising single-dose strategy, but broader use requires additional long-term safety, effectiveness, and serotype-specific data. Inactivated, DNA, viral-vectored, virus-like particle, and mRNA vaccines remain investigational. Conclusions: Dengue vaccination should be integrated with surveillance, vector control, clinical preparedness, and risk communication. Population-based vaccination is most appropriate in high-transmission settings, whereas selective, risk-based strategies are preferable in temperate regions. Continued pharmacovigilance and effectiveness monitoring are essential to guide safe and equitable implementation. Full article

Liquid biopsy, the analysis of tumor-derived material in blood, saliva, and other body fluids, is increasingly explored for the diagnosis, surveillance, and molecular characterization of head and neck squamous cell carcinoma (HNSCC). Its performance, however, is not uniform across the disease, and the reason is fundamentally molecular. human papillomavirus (HPV)-positive oropharyngeal cancers carry viral oncogenes that are absent from the host genome and therefore provide a near ideal, tumor specific circulating marker, whereas HPV-negative tumors are driven by a heterogeneous somatic landscape that offers no single universal target. In this narrative review, we adopt a molecular perspective. We first examine the biological origin of circulating tumor DNA and of the other analytes that liquid biopsy can interrogate including circulating tumor HPV DNA, viral transcripts, microRNAs, extracellular vesicles, and methylation signatures. We then consider how analytical platforms, from droplet digital PCR to next generation and ultrasensitive whole-genome sequencing, translate these molecules into measurements. Only afterward do we discuss the clinical questions, organized by clinical objective rather than by individual study: diagnosis and early detection, prognosis and risk stratification, treatment response monitoring, minimal residual disease and surveillance, and biomarker guided de-escalation in HPV-positive disease. Twelve registered clinical trials, involving approximately 1183 patients, are presented as illustrations of these questions. We close on the biological and technical gaps that still separate promising signals from clinical practice, and on the multi analyte and dynamic strategies most likely to bridge them. At present, liquid biopsy should be regarded as a complementary tool rather than as a replacement for established clinicopathological assessment. Full article

Predicting CRISPR-Cas9 guide RNA efficiency and off-target activity is a precondition for precise genome editing. Computational models have progressively incorporated chromatin accessibility and epigenetic descriptors into their feature sets, yet synthesising findings from independently published studies—especially when those studies contradict one another—remains an unresolved methodological gap. Large Language Models (LLMs) have been proposed as a route to automate cross-study synthesis, but their utility depends on a constraint that receives less attention than model architecture: how much of the source text actually reaches the model at inference time. Cloud-based models process 48,000-token corpora without hardware limitations, but at the cost of data leaving the local environment and with limited reproducibility across API versions. Local RAG systems avoid the cloud dependency while fragmenting the input, discarding the global context needed to link biological arguments that are distributed across separate papers. We benchmark these strategies using a corpus of four CRISPR-Cas9 efficiency prediction studies and apply the Reduced Interaction Sampling (RIS) engine—a local sparse attention method—to retain the full sequence within the memory envelope of a laboratory server. Preserving that context uncovers three latent inconsistencies. The static epigenetic markers used in DeepCRISPR (CTCF, DNase I) show near-zero Spearman correlations with off-target cleavage ($\rho \le 0.07$), while nucleosome positioning scores from the Block Decomposition Method reach $\rho =0.388$–$0.423$. The sequence-only Apindel model was published in June 2022 without incorporating nucleosome descriptors reported in the concurrent literature. The benchmark review by Konstantakos et al. attributed 10–20% of rank correlation to epigenetics—a figure that reflects the weak feature subset evaluated, not a ceiling on chromatin influence. These discrepancies are invisible when papers are read individually or retrieved as chunks; they become traceable only when the full corpus is processed as a single context window. An independent empirical analysis of 2000 CRISPR-Cas9 off-target cleavage events provides evidence consistent with this pattern: static epigenetic markers yield $\left|\rho \right|\le 0.11$, whereas computed NuPoP Affinity descriptors reach $r=-0.622$ ($p<{10}^{-210}$). On a 30-question cross-study synthesis benchmark (5 independent seeds), baseline accuracy is 53.33%, RAG 60.00%, and RIS (30 seeds, 3% density) 70.00% ($p<0.0001$, t-test vs. RAG, $\sigma =0.00\%$ for all configurations). Full article

Cancer-associated thrombosis (CAT) is a major cause of morbidity and mortality in patients with malignancy. Biomarkers of hypercoagulability and thromboinflammation may improve risk stratification and support personalised thromboprophylaxis, but evidence remains heterogeneous, particularly in cervical cancer. A systematic review was conducted according to PRISMA 2020. PubMed/MEDLINE, Scopus, Embase, and Web of Science were searched for studies published between January 2009 and March 2025 evaluating biological, molecular, genetic, and imaging biomarkers associated with hypercoagulability and thromboinflammation in women withcervical cancer. Evidence from breast cancer and broader CAT studies was incorporated to provide translational context. Owing to substantial methodological heterogeneity, findings were synthesised qualitatively. Twenty-five cervical cancer studies met eligibility criteria. D-dimer was the most extensively investigated biomarker and was consistently associated with VTE risk, although specificity was limited. Biomarkers of thrombin generation and fibrinolytic activation, including thrombin–antithrombin complexes, prothrombin fragment 1+2, and plasmin–α2-antiplasmin complex, demonstrated greater mechanistic specificity. Multimarker panels integrating coagulation, fibrinolysis, endothelial injury, platelet activation, and inflammation showed superior predictive performance compared with single biomarkers. Emerging biomarkers, including circulating tumour DNA, extracellular vesicles, and microRNAs, further supported tumour-driven thromboinflammation. SERPINE1 and F2 gene variants were associated with thrombotic risk and adverse prognosis. Current evidence supports further evaluation of integrated multimodal biomarker strategies for CAT risk assessment, but prospective, standardised, tumour-specific studies are required before biomarker-guided approaches can be implemented in clinical practice. Full article

Phosphatidylinositol 5-phosphate 4-kinase type 2 alpha (PIP4K2A) is a key oncogenic driver that regulates the PI5P/PIP2 axis to promote metastatic migration in breast cancer. This study aimed to investigate the therapeutic potential of a crude extract from Tamarix aphylla against breast cancer progression and identify its primary active constituents. The crude extract was initially evaluated against MDA-MB-231 and MCF7 breast cancer cell lines using wound healing assays. Bioassay-guided isolation and screening were deployed to isolate individual components, and the most potent lead compound was structurally characterized using preparative HPLC and FTIR. To analyze its interaction with PIP4K2A, in silico molecular docking, MM/GBSA calculations, and 200 ns molecular dynamics simulations were conducted. In vitro validation was subsequently performed via dose-dependent cytotoxicity assays, scratch assays, single-cell tracking, and RT-qPCR expression analysis. Quercetin was identified as the most potent lead inhibitor against PIP4K2A. Computational modeling revealed that quercetin binds tightly within the PIP4K2A ATP-binding pocket, yielding a superior binding affinity of −10.77 kcal/mol and enhanced thermodynamic stability (ΔGMM/GBSA = −42.6 ± 2.1 kcal/mol) compared to the native ligand (ΔG MM/GBSA = −23.3 ± 1.8 kcal/mol). Molecular dynamics simulations confirmed an induced-fit structural transition that locked the complex into an ultra-stable conformation within a deep global energy minimum basin (−10.8 kcal/mol). In vitro assays demonstrated dose-dependent cytotoxicity, with aggressive triple-negative MDA-MB-231 cells exhibiting higher sensitivity (IC₅₀ = 82.23 µg/mL) than luminal MCF7 cells (IC₅₀ = 97.14 µg/mL). Furthermore, scratch and single-cell tracking assays showed a profound suppression of migration speed and wound closure (reduced to ~40%), while RT-qPCR revealed a near-complete transcriptional knockdown of PIP4K2A mRNA expression (down to 0.025-fold). Collectively, these findings elucidate a unique dual-action mechanism for Tamarix aphylla-derived quercetin—characterized by both direct competitive enzymatic inhibition and downstream transcriptional silencing—positioning it as a promising therapeutic scaffold for targeted anti-metastatic breast cancer interventions. Full article

The primary aim of this review is to summarize current evidence from clinical and pre-clinical studies on endogenous molecular biomarkers associated with radiosensitivity and radioresistance in cervical cancer, including patients treated with photon-based radiotherapy, cervical cancer cell lines, and xenograft models, and to evaluate the association of these biomarkers with radiotherapy response, residual disease, recurrence and survival, and experimental measures of radiosensitivity. A systematic literature review was conducted for studies published over the last 10 years that evaluated associations between genomic, epigenetic, or protein biomarkers and radiotherapy response or survival outcomes in cervical cancer. Eligible studies included in the current analysis summarize clinical, translational, and pre-clinical studies in correlation with photon-based radiotherapy. Research focusing exclusively on non-coding RNAs, exogenous radiosensitizers, or non-photon modalities was excluded. In total, 112 studies were identified, and 46 of them met the inclusion criteria. The identified biomarkers clustered into several key biological processes: DNA damage response and cell cycle regulation, cancer stemness, hypoxia and microenvironment, epigenetic and transcriptional regulation, and signaling pathways, including exosome-mediated communication. Most markers were linked to radioresistance and adverse outcomes, whereas a smaller subset was associated with increased radiosensitivity. A limited group of biomarkers was linked to clinical outcomes such as local control, residual disease, or survival, and emerging multi-marker protein signatures suggested that combinatorial approaches may outperform single-marker strategies. Radiosensitivity in cervical cancer is regulated by a network of biological pathways. Validated, integrated biomarker panels that capture DNA repair proficiency, stemness, hypoxia adaptation, and key signaling pathways are needed to improve risk stratification and enable biomarker-guided radiosensitization. Full article

Extracellular vesicles (EVs) have emerged as fundamental pillars of intercellular communication, acting as primary mediators of the bidirectional biochemical crosstalk within the integrated bone–muscle unit. This review provides a comprehensive synthesis of EV-mediated signaling across the bone–muscle axis, offering a side-by-side mapping of vesicular biogenesis, cargo composition, and functional roles in both tissues. Under physiological conditions, skeletal muscle- and bone-derived EVs orchestrate tissue homeostasis, adaptations to physical exercise, myogenesis, and bone remodeling by transferring unique molecular cargos of proteins and specific microRNAs. However, aging induces a profound remodeling of the EV secretome toward a senescent profile characterized by harmful vesicular factors. This dysfunctional vesicular signaling impairs both muscle regeneration and osteogenesis, directly contributing to the pathogenesis of interconnected age-related disorders like sarcopenia, osteoporosis, and osteosarcopenia. Concurrently, circulating EVs represent valuable, minimally invasive biomarkers for early diagnosis. On the therapeutic front, this review critically evaluates emerging EV-based approaches, utilizing mesenchymal stem cell-derived, bioengineered, or biomaterial-incorporated EVs, offering promising, low-immunogenic alternatives to cell transplantation to enhance musculoskeletal tissue repair and restore bone–muscle homeostasis. Despite persisting technical challenges regarding large-scale production and standardization, targeting or leveraging EV-mediated communication represents one of the most innovative and revolutionary strategies to counteract age-related musculoskeletal decline. By unifying physiological mechanisms, age-related molecular reprogramming, and therapeutic engineering across both muscle and bone into a single narrative, this review provides a comprehensive framework to guide future research and clinical translation in musculoskeletal health. Full article

Objective: Vasculogenic mimicry (VM), characterized by the de novo formation of microvascular-like channels derived from aggressive tumor cells without involving traditional endothelial cells, is a pivotal pathological hallmark driving extreme invasiveness and dismal prognosis in hepatocellular carcinoma (HCC). This study aimed to establish a VM-based molecular subtyping system and systematically characterize its associated biological features, thereby providing a potential framework for individualized prognostic assessment and treatment decision-making in HCC. Methods: We integrated curated VM-associated gene sets with single-cell RNA sequencing data to identify malignant epithelial cell-enriched VM-associated candidate genes. Subsequently, univariate Cox regression, LASSO-Cox regression, and multivariate Cox regression were sequentially performed to identify six prognostic VM-related genes: HSPA9, TGFA, MAD2L1, PROM1, AGXT, and GCGR. HCC patients were stratified into VM, Mixed-VM, and Non-VM subtypes according to VM scores. Kaplan–Meier survival analysis, time-dependent ROC analysis, and Cox regression were used to assess prognostic performance. The biological features of the classification system were evaluated using bulk transcriptomic cohorts, spatial transcriptomics, Cytometry by Time-of-Flight (CyTOF), metabolomics, lipidomics, somatic mutation and copy number alteration analyses, and treatment-related HCC cohorts. Results: The VM score-based classification stratified HCC patients into three molecular subtypes with distinct prognostic and biological characteristics. Patients classified as the VM subtype had significantly poorer overall survival than those classified as Mixed-VM or Non-VM subtypes, and this prognostic pattern was validated across independent cohorts. Multi-omics analyses showed that the VM subtype was associated with YAP-TAZ-TEAD-related transcriptional programs, stemness/proliferation-related features, immunoregulatory and exhaustion-like tumor microenvironmental characteristics, and distinct metabolic and lipidomic alterations involving modified nucleosides, keto acid-related metabolites, cholesteryl esters, and sphingolipid-related species. Spatial transcriptomics revealed focal enrichment of VM-score-high regions and their association with YAP-TAZ-TEAD and immune checkpoint-related signatures. In orthotopic HCC mouse models, YAP1 overexpression increased PAS⁺/CD34⁻ VM-like structures, whereas verteporfin treatment reduced these structures. In two treatment-related cohorts, the Non-VM subtype showed higher response rates to sorafenib and transarterial chemoembolization (TACE) than the VM subtype. Connectivity Map (CMap)-based computational drug prioritization and molecular docking analysis prioritized ivermectin as a candidate compound; however, its antitumor activity requires further experimental validation. Conclusions: This study establishes a VM score-based molecular classification framework for HCC and identifies VM-subtype-associated prognostic, spatial, immune, metabolic, genomic, and therapeutic features. These findings provide a candidate framework for molecular risk stratification and subtype-guided therapeutic exploration in HCC. Full article