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Inverting the Shield: Systematically Generating Safety Tests from Policy Specifications
ADMFormer: An Adaptive-Decomposition Transformer with Time-Varying Masked Spatial Attention for Traffic Forecasting
PHGNet: Prototype-Guided Hypergraph Construction for Heterogeneous Spatiotemporal Forecasting
MindAlign: Bridging EEG, Vision, and Language for Zero-Shot Visual Decoding
What Are We Actually Decoding? Source Attribution for Non-Invasive Brain-to-Language Retrieval
Rethinking the Comparison Unit in Sequence-Level Reinforcement Learning: An Equal-Length Paired Training Framework from Loss Correction to Sample Construction
Internalizing Outcome Supervision into Process Supervision: A New Paradigm for Reinforcement Learning for Reasoning
CoopGuard: Stateful Cooperative Agents Safeguarding LLMs Against Evolving Multi-Round Attacks
Embedding Enhancement via Fine-Tuned Language Models for Learner-Item Cognitive Modeling
Justified or Just Convincing? Error Verifiability as a Dimension of LLM Quality
Trace2Skill: Distill Trajectory-Local Lessons into Transferable Agent Skills
Doxorubicin promotes the production of inflammatory cytokines in tumor-associated macrophages through activating lactate dehydrogenase A
Cell Death Discovery, Published online: 31 March 2026; doi:10.1038/s41420-026-03014-0
Doxorubicin promotes the production of inflammatory cytokines in tumor-associated macrophages through activating lactate dehydrogenase AMulti-omics analysis reveals AR as a potential prognostic factor and immune-related therapeutic target in gastric cancer
Biochem Biophys Rep. 2026 Mar 16;46:102537. doi: 10.1016/j.bbrep.2026.102537. eCollection 2026 Jun.
ABSTRACT
BACKGROUND: Although studies have shown that the androgen receptor (AR) is associated with tumor progression and malignant regulation, its role in the tumor immune microenvironment and predictive value for prognosis and immunotherapy response in various cancer types have not been systematically analyzed.
METHODS: In this paper, multi-omics techniques was used to analyze AR comprehensively.
RESULTS: A comprehensive pan-cancer analysis revealed that the AR was expressed in a variety of tumors, especially as a risk factor for poor prognosis in gastric cancer. In addition, gene set enrichment analysis showed that the AR promotes cell proliferation and tumor cell invasion and regulates anti-tumor response. Immune score, immune cell infiltration, and anticancer immune cycle analysis showed that high AR levels were correlated with low infiltration of CD4+ T cells and NKT cells, high infiltration of Th2 cells and MDSCs, negatively correlated with antigen-presenting molecules, and positively correlated with various immune-negative regulatory molecules. Single-cell sequencing highlighted the heterogeneous expression of ARs in different cell types, particularly in epithelial cells, where high AR levels were associated with the enhanced activity of tumor-promoting pathways.
CONCLUSIONS: In conclusion, this study highlights the potential of the AR as a novel biomarker for gastric cancer prognosis and immunotherapy efficacy, expanding its applicability in the development of new antitumor drugs.
PMID:41890218 | PMC:PMC13014673 | DOI:10.1016/j.bbrep.2026.102537
SVNeoPP: A Workflow for Structural-Variant-Derived Neoantigen Prediction and Prioritization Using Multi-Omics Data
Biology (Basel). 2026 Mar 19;15(6):492. doi: 10.3390/biology15060492.
ABSTRACT
BACKGROUND: Tumor neoantigens are key targets for personalized vaccines and T-cell therapies, yet most pipelines focus on neoantigens derived from SNV/small indel and often yield a limited number of high-quality candidates. SVs are prevalent in tumors and can generate novel chimeric sequences and neopeptides, making them a promising additional source of neoantigens. However, SV-derived neoantigen prediction remains challenging due to breakpoint uncertainty, isoform-dependent coding inference, and limited integration of multi-dimensional evidence and reproducibility.
METHODS: We developed SVNeoPP (Structural Variant Neoantigen Prediction and Prioritization), an end-to-end workflow for SV-derived neoantigen analysis. SVNeoPP takes WGS and RNA-seq as inputs, performs SV calling and annotation, and reconstructs altered transcripts and coding sequences in a traceable, isoform-aware manner to generate candidate peptides. Candidates are prescreened by integrating antigen-processing features with HLA binding prediction, and then hierarchically filtered and prioritized based on transcript expression, LC-MS/MS proteomics evidence, immunogenicity predictions, and sequence similarity to experimentally validated neoantigen databases. SVNeoPP is implemented in Snakemake to enable modular extension, checkpoint-based restarts, and end-to-end reproducibility.
RESULTS: Using a hepatocellular carcinoma (HCC) multi-omics dataset as a proof of concept, we demonstrated the performance of SVNeoPP and obtained a high-priority shortlist of candidate peptides. Compared with other methods, SVNeoPP substantially expanded the candidate search space for SV-derived neoantigens and showed more favorable distributions of antigen-processing and HLA binding features.
CONCLUSIONS: SVNeoPP provides a reusable, traceable, and interpretable multi-dimensional evidence-driven framework for SV-derived neoantigens. As a complementary module to SNV/small-indel pipelines, it broadens the neoantigen candidate repertoire and generates ranked candidates with interpretable evidence to facilitate downstream prioritization and decision-making.
PMID:41892252 | PMC:PMC13024079 | DOI:10.3390/biology15060492
Suicidal Thoughts and Behaviors Among Chinese Adolescents in Relation to Negative Life Events, Internet Addiction, and Sexual Abuse: Cross-Sectional Study
Spatial Omics in Gastrointestinal Oncology: Recent Advances, Therapeutic Insights, and Clinical Translation
J Cancer. 2026 Jan 30;17(3):515-523. doi: 10.7150/jca.127381. eCollection 2026.
ABSTRACT
Gastrointestinal (GI) cancers remain a leading cause of cancer-related morbidity and mortality worldwide, largely due to their molecular heterogeneity, complex tumor microenvironment (TME), and variable treatment responses. In recent years, the emergence of spatially resolved omics technologies-encompassing spatial transcriptomics, proteomics, metabolomics, and epigenomics-has revolutionized the ability to interrogate tumor architecture with unprecedented resolution. These methods enable precise mapping of cellular and molecular interactions within intact tissue contexts, thereby uncovering spatially defined niches that influence tumor progression, immune evasion, and therapeutic resistance. In GI malignancies such as colorectal, gastric, and esophageal cancers, spatial omics have provided critical insights into cancer-stromal-immune crosstalk, identified predictive biomarkers for immunotherapy and targeted agents, and guided the development of novel therapeutic strategies. This review synthesizes the latest advances in spatial omics applied to GI oncology over the past five years, with an emphasis on their integration into early diagnosis, treatment stratification, and real-time monitoring of therapeutic efficacy. We also discuss current challenges, including standardization, data integration, and clinical validation, as well as future directions for incorporating spatial profiling into routine oncology practice. By bridging the gap between bench discoveries and bedside applications, spatial omics hold transformative potential for achieving truly personalized treatment in gastrointestinal cancers.
PMID:41869445 | PMC:PMC13003551 | DOI:10.7150/jca.127381
Assembly of helper NLR resistosome clusters upon activation of a coiled-coil NLR
Nature, Published online: 11 March 2026; doi:10.1038/s41586-026-10215-1
SUMM2, a coiled-coil NLR, promotes the assembly of higher-order resistosome clusters to initiate cell death in plants.