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AI-driven virtual cell models in preclinical research: technical pathways, validation mechanisms, and clinical translation potential
npj Digital Medicine, Published online: 11 December 2025; doi:10.1038/s41746-025-02198-6
AI-driven virtual cell models in preclinical research: technical pathways, validation mechanisms, and clinical translation potentialKidSpeak: A General Multi-purpose LLM for Kids' Speech Recognition and Screening
AI Deception: Risks, Dynamics, and Controls
MedCondDiff: Lightweight, Robust, Semantically Guided Diffusion for Medical Image Segmentation
Life-Code: Central Dogma Modeling with Multi-Omics Sequence Unification
Rethinking Bias in Generative Data Augmentation for Medical AI: a Frequency Recalibration Method
From Efficiency to Adaptivity: A Deeper Look at Adaptive Reasoning in Large Language Models
A Survey on Cache Methods in Diffusion Models: Toward Efficient Multi-Modal Generation
BALR-SAM: Boundary-Aware Low-Rank Adaptation of SAM for Resource-Efficient Medical Image Segmentation
Prospective proteomics for discovering biomarkers in lung adenocarcinoma: a literature review
Transl Cancer Res. 2025 Sep 30;14(9):6102-6117. doi: 10.21037/tcr-2025-1092. Epub 2025 Sep 26.
ABSTRACT
BACKGROUND AND OBJECTIVE: Lung adenocarcinoma (LUAD), as the main subtype of non-small cell lung cancer (NSCLC), faces clinical challenges including molecular heterogeneity, late diagnosis, and aggressive growth, leading to a low 5-year survival rate. Biomarkers are critical for early detection, accurate differentiation of benign/malignant lesions, and guiding personalized treatment strategies. Proteomic technologies using liquid biopsy show potential by analyzing protein changes and post-translational modifications (PTMs) to identify novel biomarkers and unravel cancer mechanisms. This review examines proteomic advances in LUAD, compares platform strengths, lists validated protein markers, and discusses challenges like specificity and regulations. It aims to develop a precision medicine framework by integrating multi-omics data for improved diagnosis and treatment.
METHODS: This study conducted a literature review by searching the PubMed and Web of Science databases for original articles written in English from 2002 to 2025, using the keywords "lung adenocarcinoma" OR "LUAD" AND "biomarkers" AND "proteomics" OR "SomaScan" OR "spatial proteomics" to identify the latest research findings in the field of proteomics technology and LUAD biomarkers. The included studies mainly focused on the current landscape of biomarkers in the diagnosis, treatment, and prognosis of LUAD.
KEY CONTENT AND FINDINGS: This review discusses high-throughput methods for comprehensive protein profiling in accessible biospecimens (tissues, blood, urine) to identify biomarkers for LUAD. We systematically evaluate emerging proteomic strategies, including mass spectrometry (MS), proximity extension assays (PEAs), spatial proteomics techniques, and SomaScan platforms-coupled with innovative computational frameworks have revolutionized biomarkers discovery and their translational potential in developing precision diagnostics and targeted therapies. Additionally, the review addresses challenges in integrating proteomics with genomics, transcriptomics, and metabolomics, offering new methodologies and expanding research in life sciences. As technological advancements continue, it is anticipated that more potential biomarkers will be conducted to validate the broader application in LUAD treatment, addressing early-stage disease complexities and aiding in selecting more effective treatment strategies.
CONCLUSIONS: By synthesizing cutting-edge evidence on proteome-driven LUAD biomarkers, this review elucidates actionable strategies to refine early detection protocols and mechanism-informed personalized treatment frameworks, directly advancing precision oncology initiatives for this prevalent malignancy through biomarker-guided clinical decision-making and multi-omics integration.
PMID:41158224 | PMC:PMC12554480 | DOI:10.21037/tcr-2025-1092
Multi-omics analyses inform mechanisms of immunotherapy response in pancreatic cancer
Front Immunol. 2025 Oct 2;16:1673098. doi: 10.3389/fimmu.2025.1673098. eCollection 2025.
ABSTRACT
INTRODUCTION: Pancreatic ductal adenocarcinoma (PDAC) continues to exhibit resistance to immunotherapy. In this study, we evaluated the efficacy of combining immunotherapy with chemotherapy for the treatment of advanced pancreatic cancer. Additionally, we employed a multimodal analytical approach to elucidate the immune landscape and conduct transcriptomic profiling in PDAC.
METHODS: A retrospective analysis was conducted on the clinical data of 52 patients diagnosed with advanced PDAC who underwent a combined treatment regimen of immunotherapy and chemotherapy. The study evaluated the objective response rate (ORR), disease control rate (DCR), and progression-free survival (PFS). To characterize the immune landscape in treatment-naive pancreatic ductal adenocarcinoma (PDAC) tumors and in the systemic circulation, flow cytometry, multiplex immunohistochemistry (mIHC), and whole transcriptome sequencing were employed.
RESULTS: The study reported an ORR of 32.7%, a DCR of 67.3%, and a 6-month PFS rate of 38.5%, with a median PFS of 5.5 months. Patients treated with a combination of immunotherapy and gemcitabine achieved the longest PFS. The first-line treatment cohort exhibited a significantly higher DCR (79.3% vs. 52.2%, P = 0.038) and a longer median PFS (6.6 vs. 3.5 months, P = 0.032) compared to the second-line treatment cohort. The efficacy of treatment varied depending on the drug combinations used. Flow cytometry analysis revealed a greater frequency of CD45- CD64+ cells in the peripheral blood of patients with progressive disease (PD) compared to those with a partial response (PR). Multiplex immunofluorescence (MIF) analysis indicated an increased intratumoral infiltration of CD8+ T cells and CD137+ CD8+ T cells in patients with PR. Whole transcriptome sequencing (WTSS) identified key genes involved in immune regulation, signal transduction, and digestive function. Hemopexin (HPX) and regulatory factor X-associated protein (RFXAP) were upregulated in PR patients and showed a positive correlation with survival, whereas Interleukin-6 (IL-6) expression was linked to poor prognosis.
CONCLUSIONS: These findings indicate that immunochemotherapy shows potential for the treatment of advanced PDAC. Our study elucidates the immune landscape associated with PDAC and provides critical insights for the identification of prospective therapeutic targets, which could guide the development of innovative combination immunotherapy strategies.
PMID:41112307 | PMC:PMC12528169 | DOI:10.3389/fimmu.2025.1673098
AI chatbots are already biasing research — we must establish guidelines for their use now
Nature, Published online: 09 September 2025; doi:10.1038/d41586-025-02810-5
The academic community has looked at how artificial-intelligence tools help researchers to write papers, but not how they distort the literature scientists choose to cite.New advances in oral microbiology and tumor research
World J Clin Oncol. 2025 Jul 24;16(7):106981. doi: 10.5306/wjco.v16.i7.106981.
ABSTRACT
Cancer remains a major global health concern, with escalating incidence and mortality rates underscoring the urgent need for novel diagnostic and therapeutic strategies. Increasing evidence has identified the oral microbiota as a critical contributor to tumorigenesis, thereby expanding the understanding of cancer pathogenesis beyond conventional risk factors such as tobacco use and genetic predisposition. This review summarizes recent progress in elucidating the complex relationship between the oral microbiota and various malignancies, particularly oral squamous cell carcinoma, esophageal adenocarcinoma, and pancreatic ductal adenocarcinoma. Pathogenic bacteria, including Porphyromonas gingivalis and Fusobacterium nucleatum, have been implicated in promoting tumor progression through mechanisms involving chronic inflammation, the production of metabolic toxins, and immune evasion. The dysbiosis of the oral microbiota, often driven by lifestyle factors such as poor diet, tobacco use, and alcohol consumption, further exacerbates these carcinogenic processes. Emerging therapeutic approaches including probiotics, oral microbiota transplantation, and CRISPR-based bacterial editing are under investigation for their potential to restore microbial homeostasis and suppress pathogenic species. Additionally, saliva-based microbial biomarkers have shown promise for non-invasive cancer screening. The integration of multi-omics technologies and artificial intelligence-driven platforms is further advancing the development of precision oncology. This review aims to consolidate fragmented findings concerning the oral microbiota-cancer axis and address existing gaps in mechanistic understanding. The review's significance lies in the translational potential of microbial research to clinical applications, offering opportunities to reduce the global cancer burden through early detection and microbiota-targeted therapies.
PMID:40741186 | PMC:PMC12304933 | DOI:10.5306/wjco.v16.i7.106981
Complex genetic variation in nearly complete human genomes
Nature, Published online: 23 July 2025; doi:10.1038/s41586-025-09140-6
Using sequencing and haplotype-resolved assembly of 65 diverse human genomes, complex regions including the major histocompatibility complex and centromeres are analysed.The Somatic Mosaicism across Human Tissues Network
Nature, Published online: 02 July 2025; doi:10.1038/s41586-025-09096-7
The Somatic Mosaicism across Human Tissues Network aims to create a reference catalogue of somatic mosaicism across different tissues and cells within individuals.A call for built-in biosecurity safeguards for generative AI tools
Nature Biotechnology, Published online: 28 April 2025; doi:10.1038/s41587-025-02650-8
A call for built-in biosecurity safeguards for generative AI toolsAuthor Correction: π-HuB: the proteomic navigator of the human body
Nature, Published online: 23 December 2024; doi:10.1038/s41586-024-08555-x
Author Correction: π-HuB: the proteomic navigator of the human bodyFerroptosis, necroptosis, pyroptosis, and cuproptosis in cancer: a comparative bibliometric analysis
Cell Death Discovery, Published online: 10 July 2023; doi:10.1038/s41420-023-01542-7
Ferroptosis, necroptosis, pyroptosis, and cuproptosis in cancer: a comparative bibliometric analysis