High-throughput transcriptomic technologies have made differential gene expression analysis a cornerstone of cancer research by generating extensive lists of differentially expressed genes across tumor types and conditions. However, such lists provide limited biological insight without functional and mechanistic interpretation. This review examines the transition from descriptive gene expression profiles to a mechanistic understanding of cancer biology. We discuss integrative approaches that place expression changes within signaling pathways, transcriptional regulatory networks, and protein–protein interaction networks, thereby helping to identify functional modules and candidate upstream regulators. We emphasize the context-dependent nature of gene expression, which is shaped by genetic alterations, epigenetic landscapes, microenvironmental signals, and cellular heterogeneity. We also examine methodological advances, including gene set enrichment analysis, network-based modeling, and integration of genomic, epigenomic, proteomic, metabolomic, and single-cell transcriptomic data. Case studies across cancer types illustrate how mechanistic analyses can reveal context-specific transcriptional programs associated with oncogenic signaling, tumor suppression, metabolic reprogramming, epithelial–mesenchymal transition, and tumor–immune interactions. We highlight potential translational applications, including candidate biomarker discovery, prioritization of druggable targets, rational design of combination therapies, and investigation of therapeutic resistance. Finally, we discuss current challenges and emerging technologies, such as spatial transcriptomics and clustered regularly interspaced short palindromic repeats (CRISPR)-based perturbation screens, that are advancing the field toward dynamic, systems-level models of tumor biology. Integrating computational analyses with experimental validation can help translate transcriptomic data into clinically relevant hypotheses for precision oncology and personalized cancer therapy.

Cerebrospinal fluid leakage and postoperative tissue adhesion are serious complications following dural injury. Current dural substitutes often lack the functional asymmetry of the native dura mater. This study aimed to develop a hydrophilic/hydrophobic Janus polyvinyl alcohol (PVA) hydrogel membrane with a directional structure and dual functionality for effective dural defect repair.

A PVA hydrogel with an aligned porous architecture was fabricated via directional freezing combined with salt leaching, and thermal annealing was applied to enhance mechanical strength and structural stability. The hydrogel was asymmetrically modified to obtain a Janus membrane. Morphology, mechanical properties, degradation, swelling, wettability, in vitro biocompatibility, and cell migration were evaluated by the NIH-3T3 mouse fibroblast cell line. In vivo biocompatibility was assessed using a rat subcutaneous implantation model, including blank control, Durepair®, frozen-salted PVA, and Janus-PVA groups, with 5 rats in each group. Dural repair efficacy was evaluated in a rat cranial dural defect model, including untreated defect control, frozen-salted-annealed PVA, and Janus-PVA groups, with 15 rats in each group.

The Janus membrane exhibited high tensile strength (8.93 ± 1.46 MPa), slow degradation (1.42% mass loss at 28 days), and low swelling (58.13% water content at 28 days). It displayed distinct bilateral wettability, and effectively blocked fibroblast migration on both sides, acting as a physical barrier against fibroblast-driven adhesion. In the rat dural defect model, the Janus membrane reduced cerebrospinal fluid leakage and brain–dura adhesion compared with the untreated defect and frozen-salted-annealed PVA control groups.

The engineered hydrophilic/hydrophobic Janus PVA hydrogel membrane mimics the functional asymmetry of the native dura mater and may serve as a promising candidate for further evaluation as a dural repair material.

Bacterial infection is a key cause of mortality in patients with acute-on-chronic liver failure (ACLF). In this study, we aimed to identify metabolite biomarkers and develop a novel machine learning model for early identification of bacterial infection in ACLF.

Based on a prospective multicenter cohort from 14 centers, 1,314 patients with acute-on-chronic liver disease were enrolled, including those with ACLF and non-ACLF. Plasma samples at admission were collected for metabolomics profiling. Patients were randomly divided into discovery (n = 921) and validation (n = 393) sets. Machine learning was used to develop diagnostic models. The win ratio method was employed to assess the risk stratification capability of the models.

Bacterial infection occurred in 198 of the 451 ACLF patients and 132 of the 863 non-ACLF patients. Infection altered the plasma metabolome, especially in lipid, amino acid, and xenobiotic metabolic pathways. Models for bacterial infection in ACLF (five metabolites) and non-ACLF (six metabolites) demonstrated superior discrimination in the discovery (AUCs: 0.881 and 0.935, respectively) and validation sets (AUCs: 0.835 and 0.889, respectively) compared with C-reactive protein, white blood cell count, procalcitonin, and the best composite clinical model. Metabolic risk stratification based on the models effectively predicted 90-day outcomes (all-cause death, organ failure, sepsis, new-onset acute decompensation, and systemic inflammatory response syndrome).

Our models based on novel metabolic biomarkers enable identification of patients at high risk of bacterial infection and support risk stratification of 90-day outcomes.

Atherosclerosis is a chronic inflammatory vascular disease in which macrophages play central roles in lipid uptake, foam cell formation, plaque progression, plaque instability and, under certain conditions, plaque regression. This narrative review summarizes current knowledge on macrophage biology in atherosclerosis, with emphasis on macrophage phenotypic diversity, monocyte-endothelial interactions, foam cell formation, extracellular matrix remodeling, immune-cell interactions, cytokine signaling, mitochondrial dysfunction and cellular senescence. The review also discusses emerging macrophage-targeted strategies, including modulation of inflammatory activity, macrophage polarization, cholesterol efflux and lipid homeostasis. Although these approaches provide promising mechanistic and therapeutic insights, many remain at the preclinical stage. Further studies are needed to validate macrophage subtype-specific biomarkers, clarify the interaction between mitochondrial dysfunction and senescence, and evaluate safe and effective combination strategies for clinical translation.

The modern intensive care unit (ICU) inundates clinicians with large volumes of data, leading to cognitive overload and a gap between data availability and actionable insight. While artificial intelligence (AI) promises a solution, its clinical adoption is limited by systemic barriers, including algorithmic bias, a lack of trust, and validation failures. This paper argues that a design philosophy that envisions AI as an autonomous decision-maker, rather than an integrated collaborative tool, has hindered its clinical adoption. We propose an alternative: a collaborative framework designed to augment the intensivist’s expertise by offloading specific cognitive burdens. This framework redefines AI’s purpose as managing data-intensive tasks, illustrated through four collaborative example roles: a synthesizer to create coherent clinical narratives, a sentinel for proactive deterioration surveillance, a simulator to forecast patient responses to interventions, and a stratifier to identify meaningful subphenotypes within complex syndromes. By delegating these computational tasks, this collaborative model frees clinicians to focus on complex synthesis, nuanced judgment, and compassionate communication. Realizing this vision requires a deliberate translational pathway focused on robust data infrastructure, human-centered design, and rigorous validation through prospective clinical trials. Ultimately, the successful integration of AI in critical care depends not on replacing clinicians but on empowering them, creating a more functional ICU in which technology supports the delivery of safer, more precise, and more humane care.

Early predictors of 6-month non-recovery in drug-induced liver injury (DILI) remain limited. Genetic variants are stable host characteristics that may complement baseline clinical variables. We aimed to develop and validate an interpretable, clinical-genetic machine learning model for predicting 6-month non-recovery in patients with DILI.

This retrospective, single-center study included 338 patients with DILI, who were classified as recovered (n = 171) or non-recovered (n = 167) at 6 months. Candidate single-nucleotide polymorphisms and baseline clinical variables were collected during initial hospitalization. Features were selected using complementary screening approaches. Multiple machine learning models were developed and compared. Model discrimination, calibration, clinical utility, the incremental value of genetic predictors, and interpretability using SHapley Additive exPlanations (SHAP) were assessed.

Five predictors were consistently retained for model development: rs72631567, rs28521457, alanine aminotransferase, monocyte percentage, and low-density lipoprotein. Among the candidate algorithms, the light gradient boosting machine model showed the best performance, with area under the receiver operating characteristic curve (AUC) values of 0.92 (95% confidence interval [CI] 0.89–0.95) in the training set and 0.81 (95% CI 0.70–0.91) in the validation set. The model showed acceptable calibration and favorable decision-curve performance. In ablation analysis, the clinical-only model showed limited discrimination (AUC 0.57, 95% CI 0.43–0.71). SHAP analysis identified rs72631567 as the most influential predictor.

An interpretable model that integrates host genetic variants with baseline clinical variables demonstrated good internal performance for early prediction of 6-month non-recovery in DILI. These findings support external validation of genotype-informed risk stratification in patients with DILI.