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Legal implications of AI standard of care integration on patients’ informed consent: lessons from surgery
npj Digital Medicine, Published online: 13 December 2025; doi:10.1038/s41746-025-02157-1
Legal implications of AI standard of care integration on patients’ informed consent: lessons from surgeryApplication progress of spatial omics in hepatobiliary tumor research
Hepatobiliary Surg Nutr. 2025 Dec 1;14(6):1028-1030. doi: 10.21037/hbsn-2025-aw-862. Epub 2025 Nov 25.
NO ABSTRACT
PMID:41383666 | PMC:PMC12690317 | DOI:10.21037/hbsn-2025-aw-862
Exploring the role of lipid metabolism genes in gastric cancer prognosis and tumor immune microenvironment
J Int Med Res. 2025 Dec;53(12):3000605251403252. doi: 10.1177/03000605251403252. Epub 2025 Dec 11.
ABSTRACT
BackgroundGastric cancer remains a major global health challenge due to its high mortality rate and complex pathophysiological mechanisms. Emerging evidence highlights that dysregulated lipid metabolism contributes to gastric cancer progression and prognosis, but the associations between lipid metabolism-associated genes, gastric cancer patient survival, and tumor immune microenvironment remodeling are not fully elucidated.MethodsWe analyzed publicly available omics and clinical data, including RNA sequencing data from 371 gastric cancer samples in The Cancer Genome Atlas database and 433 gastric cancer samples in the Gene Expression Omnibus database. We first curated the top 100 lipid metabolism-associated genes based on relevance scores. Then, univariate Cox regression was used to identify genes significantly associated with overall survival. Consensus clustering was applied to these survival-related genes to define gastric cancer molecular subtypes. Copy number variation analysis was performed to assess genomic alterations of these genes in tumor samples. A prognostic risk model was constructed using least absolute shrinkage and selection operator regression and validated via multivariate Cox regression. Immune infiltration analysis using CIBERSORT and ESTIMATE algorithms was conducted to explore associations between lipid metabolism-associated genes and tumor immune microenvironment characteristics.ResultsA total of 3911 differentially expressed genes were identified between gastric cancer and adjacent normal tissues. Among the top 100 lipid metabolism-associated genes, 43 were significantly linked to patient survival, most of which were considered as poor prognostic factors. Copy number variation analysis revealed frequent copy number gains of these genes in tumor samples. Consensus clustering stratified patients into two molecular subtypes (LMAGcluster A and LMAGcluster B), with LMAGcluster A showing significantly worse survival outcomes (median survival: 2.6 years vs. 8.3 years in LMAGcluster B, p < 0.001). LMAGcluster A was also characterized by elevated infiltration of pro-tumor immune cells, such as regulatory T cells and follicular helper T cells. The prognostic model based on 14 key lipid metabolism-associated genes exhibited robust predictive performance, with area under the receiver operating characteristic curve values of 0.702-0.761 in The Cancer Genome Atlas cohort and 0.621-0.638 in the Gene Expression Omnibus cohort for 1-, 3-, and 5-year survival.ConclusionLipid metabolism-associated genes are closely associated with gastric cancer prognosis and tumor immune microenvironment remodeling. The identified gene-based molecular subtypes and prognostic model provide novel insights into gastric cancer progression, and the 14 key genes may serve as potential biomarkers and therapeutic targets.
PMID:41381057 | DOI:10.1177/03000605251403252
Trump’s AI executive order promises ‘one rulebook’ — startups may get legal limbo instead
Minimal Residual Disease Detection: Bridging Molecular and Clinical Strategies for Recurrence Prevention in Gynecologic Cancers
Int J Mol Sci. 2025 Dec 3;26(23):11708. doi: 10.3390/ijms262311708.
ABSTRACT
Gynecologic cancers remain a major global health burden, particularly in low- and middle-income countries, with high incidence and mortality rates around 45-50%. The detection of minimal residual disease (MRD) is transforming the management of recurrence risk in gynecologic cancers through highly sensitive molecular technologies. MRD encompasses small populations of residual cancer cells or post-treatment molecular traces but remain undetectable by conventional methods. Its detection relies on circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and advanced next-generation sequencing (NGS), with ctDNA-based MRD assays having sensitivity levels between 85% and over 99%. Other technologies, such as liquid biopsies and digital PCR, are also in development. MRD status has demonstrated high predictors of recurrence and survival with positive MRD strongly associated with poor outcomes and negative MRD indicates sustained remission. However, MRD detection faces significant limitations, such as tumor heterogeneity, inconstant ctDNA levels, technical issues of false-negative results, and limited clinical accessibility. Therefore, this review presents current evidence regarding the molecular detection of MRD in gynecologic malignancies and assesses its prognostic and predictive relevance. Ultimately, MRD continuous integration into clinical practice offers a promising modality to enable early relapse detection, more precise therapeutic decision-making, and the improvement of personalized medicine access to gynecologic cancers worldwide.
PMID:41373852 | PMC:PMC12692091 | DOI:10.3390/ijms262311708
Mind the Gap! Pathways Towards Unifying AI Safety and Ethics Research
Robust AI Security and Alignment: A Sisyphean Endeavor?
Phythesis: Physics-Guided Evolutionary Scene Synthesis for Energy-Efficient Data Center Design via LLMs
IoTEdu: Access Control, Detection, and Automatic Incident Response in Academic IoT Networks
MedXAI: A Retrieval-Augmented and Self-Verifying Framework for Knowledge-Guided Medical Image Analysis
Are ultrasensitive ctDNA assays ready for clinical use in early-stage NSCLC?
Macrophage-targeted immunocytokine leverages myeloid, T, and NK cell synergy for cancer immunotherapy
D2M: A Decentralized, Privacy-Preserving, Incentive-Compatible Data Marketplace for Collaborative Learning
Pancreatic Cancer Organoids: Modeling Disease and Guiding Therapy
Cancers (Basel). 2025 Nov 30;17(23):3850. doi: 10.3390/cancers17233850.
ABSTRACT
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies. An unmet need exists for reliable biomarkers and in vitro models capable of predicting patient drug response to advance personalized medicine. Traditional models fail to represent the tumor's complexity and the role of the stromal environment in chemoresistance. Patient-derived organoids (PDOs) overcome these limitations, enabling multi-omics profiling and reliable drug testing for functional precision medicine. This review provides a comprehensive overview of PDAC PDO research, emphasizing the following major areas: (i) the genetic and phenotypic fidelity of PDOs, (ii) their predictive value for drug response and chemoresistance, (iii) the integration of the extracellular matrix and tumor microenvironment (TME) components, and (iv) emerging technologies. Studies confirm that PDOs faithfully represent the primary tumor's specific genetic features and retain intratumoral heterogeneity. PDO-based platforms have demonstrated a strong correlation between in vitro drug sensitivity and in vivo efficacy in xenograft models, validating their utility for identifying drug candidates, repurposing existing drugs, and determining effective combinations. Efforts are ongoing to integrate crucial TME components, like cancer-associated fibroblasts, using innovative co-culture platforms such as fused PDOs and InterOMaX, to better model desmoplasia and chemoresistance mechanisms. Furthermore, PDO technology is converging with microphysiological systems and artificial intelligence tools to facilitate high-throughput drug screening and dynamic, real-time monitoring of therapeutic effects. The integration of PDOs into biobanks and advanced screening platforms holds the potential to accelerate drug discovery and improve therapeutic outcomes for PDAC patients, if challenges related to protocol standardization and regulatory acceptance are addressed.
PMID:41375051 | PMC:PMC12690986 | DOI:10.3390/cancers17233850
Hierarchical Dataset Selection for High-Quality Data Sharing
Integrative network pharmacology, transcriptomics, and microbiomics elucidate the therapeutic mechanism of <em>Polygala tenuifolia</em> Willd water extract in chronic obstructive pulmonary disease
Front Microbiol. 2025 Nov 25;16:1703853. doi: 10.3389/fmicb.2025.1703853. eCollection 2025.
ABSTRACT
BACKGROUND: Polygala tenuifolia Willd (PT) is a plant with both medicinal and edible values. Traditionally, it has been used for sedation, enhancing cognition, resolving phlegm, and relieving cough. However, its protective effects and mechanisms against chronic obstructive pulmonary disease (COPD) remain unclear.
AIM OF THE STUDY: This study aims to observe the protective effects of the water extract of Polygala tenuifolia Willd (WEPT) on COPD, and to preliminarily elucidate its potential therapeutic mechanisms by integrating network pharmacology, molecular docking, multi-omics analysis, and molecular experiments.
METHODS AND MATERIALS: HPLC quantified WEPT constituents. COPD mice models established via chronic smoke exposure underwent WEPT treatment, and the therapeutic effect was evaluated by lung function test, histopathology and cytokine profiling. Integrated multi-omics analyses (network pharmacology, transcriptomics, microbiomics) identified bioactive compounds, therapeutic targets, pathway regulations, and microbiota dynamics. Molecular docking validated compound-target interactions, while immunohistochemical/fluorescence assays confirmed key protein expression in lung tissues.
RESULTS: WEPT administration effectively reduced inflammatory cytokine levels in COPD mice, improved lung function, and alleviated histopathological damage like alveolar structural injury and airway inflammation. Network pharmacology and transcriptomic analyses identified Norhyoscyamine and Onjixanthone I as key active components, targeting PIK3CA and AKT1 via PI3K-AKT pathway regulation. Microbiome analysis showed WEPT restored gut microbiota balance. Molecular docking confirmed strong binding of bioactive compounds to core targets, while immunostaining assays demonstrated WEPT suppressed p-PI3K and p-AKT protein expression.
CONCLUSION: WEPT may exert its intervention effects on COPD through a multi-target and multi-level comprehensive regulatory mechanism.
PMID:41377050 | PMC:PMC12685879 | DOI:10.3389/fmicb.2025.1703853
AI-driven virtual cell models in preclinical research: technical pathways, validation mechanisms, and clinical translation potential
npj Digital Medicine, Published online: 11 December 2025; doi:10.1038/s41746-025-02198-6
AI-driven virtual cell models in preclinical research: technical pathways, validation mechanisms, and clinical translation potentialPotential for Algorithmic Bias in Clinical Decision Instrument Development
npj Digital Medicine, Published online: 10 December 2025; doi:10.1038/s41746-025-02119-7
Potential for Algorithmic Bias in Clinical Decision Instrument Development