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Cell
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Multimodal AI generates virtual population for tumor microenvironment modeling
GigaTIME leverages multimodal AI to generate virtual multiplex immunofluorescence (mIF) profiles from standard H&E slides, enabling comprehensive tumor immune microenvironment modeling across a large (>14,000) and diverse patient population. This virtual approach unlocks new opportunities for large-scale clinical discoveries that were previously hindered by the scarcity of mIF data.
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Omics In Lung
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Gut microbial metabolites in cancer immunomodulation
Mol Cancer. 2025 Dec 3. doi: 10.1186/s12943-025-02521-5. Online ahead of print.ABSTRACTGut microbiota-derived metabolites are emerging as systemic "remote immunoregulators" that shape tumor immunity across tissues. Integrating evidence across short-chain fatty acids, tryptophan derivatives, secondary bile acids, polyamines and other metabolites, we advance a metabolite-immune pathway-cancer framework that links receptor-mediated signaling, epigenetic remodeling and metabolic reprogramming to con
Gut microbial metabolites in cancer immunomodulation
Mol Cancer. 2025 Dec 3. doi: 10.1186/s12943-025-02521-5. Online ahead of print.
ABSTRACT
Gut microbiota-derived metabolites are emerging as systemic "remote immunoregulators" that shape tumor immunity across tissues. Integrating evidence across short-chain fatty acids, tryptophan derivatives, secondary bile acids, polyamines and other metabolites, we advance a metabolite-immune pathway-cancer framework that links receptor-mediated signaling, epigenetic remodeling and metabolic reprogramming to context-dependent, bidirectional immune effects. Importantly, in addition to the g protein-coupled receptor / aryl hydrocarbon receptor pathway, the selected microbial small molecule metabolites are the true T-cell receptor ligands of unconventional T cells, directly shaping the tissue resident immune and tumor microenvironment, supplementing the receptor signaling and epigenetic programs in our framework. We synthesize how these metabolites recalibrate the tumor immune microenvironment-modulating antigen presentation, T-cell effector fitness and exhaustion, regulatory T-cell activity, and myeloid polarization-and why the same metabolite can either potentiate immune surveillance or entrench immunosuppression depending on ligand-receptor pairing, dose and tissue niche. We compare tumor-type specific patterns (e.g., colorectal, liver, lung, breast and prostate cancers) to highlight common circuits and organ-restricted idiosyncrasies. Methodologically, we outline how single-cell and spatial multi-omics, imaging mass spectrometry and functional biosensors now enable co-registration of metabolite exposure with immune-cell states in human tumors, providing an actionable basis for biomarker discovery. Given ongoing debate about signals attributed to intratumoral microbiota in low-biomass tumor tissues, we foreground quantifiable, spatially mappable and pharmacologically tractable metabolite-receptor pathways, using microbe-associated molecular patterns / translocation as comparators to judge when chemical signals should be prioritized as intervention targets. Finally, we evaluate precision intervention avenues-including fecal microbiota transplantation, rational bacterial consortia, engineered microbes and nanoparticle-enabled metabolite delivery-and propose stratification rules that pair metabolite/receptor signatures with fit-for-purpose delivery. Together, mapping tissue-specific metabolite-immune circuits and embedding them in robust biomarker frameworks may convert microbial metabolites from correlative markers into therapeutic targets and tools, improving the efficacy and durability of cancer immunotherapy.
PMID:41339918 | DOI:10.1186/s12943-025-02521-5
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Journal of Medical Internet Research
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Embracing the Future of Medical Education With Large Language Model–Based Virtual Patients: Scoping Review
Background: In recent years, large language models (LLMs) have experienced rapid development. LLM-based virtual patients have begun to gain attention, offering new opportunities for simulations in medical education. Objective: This study aims to systematically analyze the current applications, research trends, and challenges of LLM-based virtual patients in medical education and to explore potential future directions for development. Methods: This study adheres to the PRISMA-ScR (Preferred Repor
Embracing the Future of Medical Education With Large Language Model–Based Virtual Patients: Scoping Review
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Nature - Issue - nature.com science feeds
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A whole-slide foundation model for digital pathology from real-world data
Nature, Published online: 22 May 2024; doi:10.1038/s41586-024-07441-wProv-GigaPath, a whole-slide pathology foundation model pretrained on a large dataset containing around 1.3 billion pathology images, attains state-of-the-art performance in cancer classification and pathomics tasks.
A whole-slide foundation model for digital pathology from real-world data
Nature, Published online: 22 May 2024; doi:10.1038/s41586-024-07441-w
Prov-GigaPath, a whole-slide pathology foundation model pretrained on a large dataset containing around 1.3 billion pathology images, attains state-of-the-art performance in cancer classification and pathomics tasks.