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From Verification Burden to Trusted Collaboration: Design Goals for LLM-Assisted Literature Reviews
Multimodal Learning for Scalable Representation of High-Dimensional Medical Data
Benchmarking AI Models in Software Engineering: A Review, Search Tool, and Unified Approach for Elevating Benchmark Quality
Understanding Prompt Management in GitHub Repositories: A Call for Best Practices
MetaVoxel: Joint Diffusion Modeling of Imaging and Clinical Metadata
High-Throughput Dissection of Inter-Organ Genetic Networks: A Multi-Omic Systems Biology Approach
SLAS Technol. 2025 Dec 11:100376. doi: 10.1016/j.slast.2025.100376. Online ahead of print.
ABSTRACT
The existing multi-omic analyses are frequently confined to individual tissues, and the regulatory picture of the systemic regulator of complex physiology and disease is hidden. To fill this gap, we have created a unified systems biology model of the high-throughput dissection of inter-organ genetic networks. Our model incorporates transcriptomic, epigenomic and proteomic analysis of five major organs (liver, kidney, heart, lung, brain) using the Multi-Omics Factor Analysis (MOFA+) tool, specifically, cross-tissue coordination. We characterized 27 evidence-heavy cross-tissue modules (FDR < 0.05) that are major hubs such as *HNF4Aenda NRF2cheng8loadmasterregulatingconstitutionembryonicstemcellularinfoncogenes recognize them. One notable observation was liver-kidney metabolic axis, significant cross-talks in hepatocyte organoids are confirmed with CRISPR knockdown, which suppresses the expression of transporters expressed by the kidney. Our work offers a scalable validated framework that goes beyond organ-centric perspectives, which can be used as a potent tool of systemic disease modelling and precision medicine.
PMID:41389879 | DOI:10.1016/j.slast.2025.100376
Stakeholder Criteria for Trust in Artificial Intelligence–Based Computer Perception Tools in Health Care: Qualitative Interview Study
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