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Clinical utility of OGN in pan-cancer: diagnostic biomarker and immune microenvironment regulator

12 February 2026 at 19:00

Transl Cancer Res. 2026 Jan 31;15(1):43. doi: 10.21037/tcr-2025-1499. Epub 2026 Jan 27.

ABSTRACT

BACKGROUND: Osteoglycin (OGN), an extracellular matrix protein, has emerging but poorly characterized roles in cancer. This study presents the first pan-cancer investigation of OGN's expression patterns, clinical significance, immune interactions, and functional mechanisms.

METHODS: Multi-omics data from Genotype Tissue Expression (GTEx), Cancer Cell Line Encyclopedia (CCLE), The Cancer Genome Atlas (TCGA), and Human Protein Atlas (HPA) databases were integrated. Differential expression was analyzed in normal tissues and tumor samples. Diagnostic utility was evaluated using area under the curve (AUC) of receiver operating characteristic (ROC) curve. Prognostic value was assessed via Kaplan-Meier [overall survival (OS); disease-specific survival (DSS); disease free interval (DFI); progression-free interval (PFI)] and Cox regression analyses. Immune microenvironment correlations were quantified using ESTIMATE, CIBERSORT, and gene set enrichment. Functional pathways were explored through gene set enrichment analysis (GSEA) and correlation with hallmark cancer signatures.

RESULTS: OGN was broadly expressed in normal tissues (brain, liver, kidney) but significantly downregulated in most tumor types (P<0.05, TCGA; validated at protein level, HPA). OGN demonstrated high diagnostic accuracy in pan-cancer (AUC: 0.703-0.990), achieving near-perfect performance in colon adenocarcinoma (COAD) (AUC: 0.966) and thyroid cancer (THCA) (AUC: 0.920). High OGN expression correlated with improved survival outcomes in thymoma (THYM) (OS/DSS) and cholangiocarcinoma (CHOL) (PFI/DFI), but worse prognosis in lung adenocarcinoma​/liver hepatocellular carcinoma​ (LUAD/LIHC), indicating cancer-type specificity. OGN expression strongly associated with immune cell infiltration (macrophages, natural killer cells, T cells), chemokine signaling, programmed death-ligand 1 (PD-L1) levels, microsatellite instability (MSI), and tumor mutation burden (TMB). GSEA revealed enrichment of OGN-linked genes in epithelial-mesenchymal transition (EMT), angiogenesis, JAK-STAT, and PI3K pathways across cancers.

CONCLUSIONS: Our pan-cancer analysis highlights OGN as a context-dependent regulator linking extracellular matrix (ECM) remodeling with immune and angiogenic signaling. Its pan-cancer dysregulation, diagnostic/prognostic value, and crosstalk with immune evasion mechanisms nominate OGN as a promising multi-functional biomarker and therapeutic target.

PMID:41674945 | PMC:PMC12885879 | DOI:10.21037/tcr-2025-1499

DeKeyNLU: Enhancing Natural Language to SQL Generation through Task Decomposition and Keyword Extraction

arXiv:2509.14507v2 Announce Type: replace Abstract: Natural Language to SQL (NL2SQL) provides a new model-centric paradigm that simplifies database access for non-technical users by converting natural language queries into SQL commands. Recent advancements, particularly those integrating Retrieval-Augmented Generation (RAG) and Chain-of-Thought (CoT) reasoning, have made significant strides in enhancing NL2SQL performance. However, challenges such as inaccurate task decomposition and keyword extraction by LLMs remain major bottlenecks, often leading to errors in SQL generation. While existing datasets aim to mitigate these issues by fine-tuning models, they struggle with over-fragmentation of tasks and lack of domain-specific keyword annotations, limiting their effectiveness. To address these limitations, we present DeKeyNLU, a novel dataset which contains 1,500 meticulously annotated QA pairs aimed at refining task decomposition and enhancing keyword extraction precision for the RAG pipeline. Fine-tuned with DeKeyNLU, we propose DeKeySQL, a RAG-based NL2SQL pipeline that employs three distinct modules for user question understanding, entity retrieval, and generation to improve SQL generation accuracy. We benchmarked multiple model configurations within DeKeySQL RAG pipeline. Experimental results demonstrate that fine-tuning with DeKeyNLU significantly improves SQL generation accuracy on both BIRD (62.31% to 69.10%) and Spider (84.2% to 88.7%) dev datasets.

Hierarchical Retrieval with Out-Of-Vocabulary Queries: A Case Study on SNOMED CT

arXiv:2511.16698v1 Announce Type: cross Abstract: SNOMED CT is a biomedical ontology with a hierarchical representation of large-scale concepts. Knowledge retrieval in SNOMED CT is critical for its application, but often proves challenging due to language ambiguity, synonyms, polysemies and so on. This problem is exacerbated when the queries are out-of-vocabulary (OOV), i.e., having no equivalent matchings in the ontology. In this work, we focus on the problem of hierarchical concept retrieval from SNOMED CT with OOV queries, and propose an approach based on language model-based ontology embeddings. For evaluation, we construct OOV queries annotated against SNOMED CT concepts, testing the retrieval of the most direct subsumers and their less relevant ancestors. We find that our method outperforms the baselines including SBERT and two lexical matching methods. While evaluated against SNOMED CT, the approach is generalisable and can be extended to other ontologies. We release code, tools, and evaluation datasets at https://github.com/jonathondilworth/HR-OOV.

From Passive to Proactive: A Multi-Agent System with Dynamic Task Orchestration for Intelligent Medical Pre-Consultation

arXiv:2511.01445v1 Announce Type: new Abstract: Global healthcare systems face critical challenges from increasing patient volumes and limited consultation times, with primary care visits averaging under 5 minutes in many countries. While pre-consultation processes encompassing triage and structured history-taking offer potential solutions, they remain limited by passive interaction paradigms and context management challenges in existing AI systems. This study introduces a hierarchical multi-agent framework that transforms passive medical AI systems into proactive inquiry agents through autonomous task orchestration. We developed an eight-agent architecture with centralized control mechanisms that decomposes pre-consultation into four primary tasks: Triage ($T_1$), History of Present Illness collection ($T_2$), Past History collection ($T_3$), and Chief Complaint generation ($T_4$), with $T_1$--$T_3$ further divided into 13 domain-specific subtasks. Evaluated on 1,372 validated electronic health records from a Chinese medical platform across multiple foundation models (GPT-OSS 20B, Qwen3-8B, Phi4-14B), the framework achieved 87.0% accuracy for primary department triage and 80.5% for secondary department classification, with task completion rates reaching 98.2% using agent-driven scheduling versus 93.1% with sequential processing. Clinical quality scores from 18 physicians averaged 4.56 for Chief Complaints, 4.48 for History of Present Illness, and 4.69 for Past History on a 5-point scale, with consultations completed within 12.7 rounds for $T_2$ and 16.9 rounds for $T_3$. The model-agnostic architecture maintained high performance across different foundation models while preserving data privacy through local deployment, demonstrating the potential for autonomous AI systems to enhance pre-consultation efficiency and quality in clinical settings.

An eyecare foundation model for clinical assistance: a randomized controlled trial

Nature Medicine, Published online: 28 August 2025; doi:10.1038/s41591-025-03900-7

Trained and validated on multimodal data from 14.5 million images from multicountry datasets, a foundation model is shown to increase diagnostic and referral accuracy of clinicians when used as an assistant in a trial involving 16 ophthalmologists and 668 patients.

Targeting spermine metabolism to overcome immunotherapy resistance in pancreatic cancer

Nat Commun. 2025 Aug 22;16(1):7827. doi: 10.1038/s41467-025-63146-2.

ABSTRACT

While dysregulation of polyamine metabolism is frequently observed in cancer, it is unknown how polyamines alter the tumor microenvironment (TME) and contribute to therapeutic resistance. Analysis of polyamines in the plasma of pancreatic cancer patients reveals that spermine levels are significantly elevated and correlate with poor prognosis. Using a multi-omics approach, we identify Serpinb9 as a vulnerability in spermine metabolism in pancreatic cancer. Serpinb9, a serine protease inhibitor, directly interacts with spermine synthase (SMS), impeding its lysosome-mediated degradation and thereby augmenting spermine production and secretion. Mechanistically, the accumulation of spermine in the TME alters the metabolic landscape of immune cells, promoting CD8+ T cell dysfunction and pro-tumor polarization of macrophages, thus creating an immunosuppressive microenvironment. Small peptides that disrupt the Serpinb9-SMS interaction significantly enhance the efficacy of immune checkpoint blockade therapy. Together, our findings suggest that targeting spermine metabolism is a promising strategy to improve pancreatic cancer immunotherapy.

PMID:40846845 | PMC:PMC12373741 | DOI:10.1038/s41467-025-63146-2

Interplay between gut microbial communities and metabolites modulates pan-cancer immunotherapy responses

Cell Metab. 2025 Jan 28:S1550-4131(24)00495-9. doi: 10.1016/j.cmet.2024.12.013. Online ahead of print.

ABSTRACT

Immune checkpoint blockade (ICB) therapy has revolutionized cancer treatment but remains effective in only a subset of patients. Emerging evidence suggests that the gut microbiome and its metabolites critically influence ICB efficacy. In this study, we performed a multi-omics analysis of fecal microbiomes and metabolomes from 165 patients undergoing anti-programmed cell death protein 1 (PD-1)/programmed death ligand 1 (PD-L1) therapy, identifying microbial and metabolic entities associated with treatment response. Integration of data from four public metagenomic datasets (n = 568) uncovered cross-cohort microbial and metabolic signatures, validated in an independent cohort (n = 138). An integrated predictive model incorporating these features demonstrated robust performance. Notably, we characterized five response-associated enterotypes, each linked to specific bacterial taxa and metabolites. Among these, the metabolite phenylacetylglutamine (PAGln) was negatively correlated with response and shown to attenuate anti-PD-1 efficacy in vivo. This study sheds light on the interplay among the gut microbiome, the gut metabolome, and immunotherapy response, identifying potential biomarkers to improve treatment outcomes.

PMID:39909032 | DOI:10.1016/j.cmet.2024.12.013

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