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Early Post-Transplant Recipient Tissue Injury Predicts Allograft Function, Rejection, and Survival in Lung Transplant Recipients, Evidence from Cell-free DNA

Eur Respir J. 2025 Jul 31:2402537. doi: 10.1183/13993003.02537-2024. Online ahead of print.

ABSTRACT

BACKGROUND: Allograft injury in the early post-transplant period is a known risk factor of death after lung transplantation. However, the recipient tissue injury profile and its association with outcomes remain unexplored. This study leverages cell-free DNA (cfDNA) to test this association.

METHODS: The prospective cohort multicenter study included lung transplant recipients (GRAfT, NCT02423070) with serial plasma measurements of recipient-derived (rd)-cfDNA using digital droplet PCR. Non-transplant healthy controls were recruited as the comparator. Whole-genome bisulfite sequencing identified tissue sources of cfDNA. Mean rd-cfDNA levels within 30 days post-transplant was computed. Multivariable regression models were used to assess the association between rd-cfDNA tertiles and the primary outcome of death and secondary outcomes.

RESULTS: The study included 215 patients with 2530 cfDNA values, including 675 cfDNA assessments in the first 30 days. Median rd-cfDNA levels in the first 30 days post-transplant were ∼16-fold higher than cfDNA for healthy controls. Patients in the highest tertile rd-cfDNA group had lower lung function post-transplant, and increased risk of death (HR: 3.15, 95% CI: 1.59-6.24, p<0.001) and acute rejection (HR 2.33, 95% CI: 1.33-4.08, p=0.03), compared to the low/middle tertile group. Tissue-specific cfDNA sources were also distinct cfDNA in the highest versus lowest rd-cfDNA tertiles, with cfDNA from innate immune cells serving as the strongest predictor of mortality.

CONCLUSION: Post-transplant recipient tissue injury varies between lung transplant patients and is associated with increased risk of acute rejection and mortality.

PMID:40744691 | DOI:10.1183/13993003.02537-2024

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NAVIGATOR: A regional multimodal imaging biobank initiative powered by AI tools for precision medicine in oncology

Eur J Radiol. 2025 Jul 22;191:112327. doi: 10.1016/j.ejrad.2025.112327. Online ahead of print.

ABSTRACT

The NAVIGATOR project established an Italian regional imaging biobank and interactive research platform designed to support precision oncology through the integration of multimodal imaging, clinical, and omics data. The platform goes beyond a static repository, offering a secure Virtual Research Environment (VRE) where users can upload data, test AI algorithms, and execute complete analytical pipelines. The platform incorporates artificial intelligence (AI)-driven radiomics and deep learning methodologies to enable biomarker extraction, disease stratification, and predictive modeling. This manuscript presents the development and implementation of the NAVIGATOR infrastructure, including its data governance framework, ethical and legal considerations, and application to three oncological use cases: prostate, rectal, and gastric cancers. To date, the biobank has collected imaging and clinical data from over 700 patients across these cohorts. AI models were deployed within a dedicated VRE to facilitate image analysis, feature extraction, and classification tasks. The project addresses critical challenges related to data harmonization, regulatory compliance, privacy safeguards and fairness in AI systems. NAVIGATOR demonstrates the feasibility of integrating AI methodologies within imaging biobanks and provides a scalable framework to advance oncological research and support clinical decision-making.

PMID:40743874 | DOI:10.1016/j.ejrad.2025.112327

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Liquid biopsy in breast cancer: Redefining precision medicine

J Liq Biopsy. 2025 Jul 16;9:100312. doi: 10.1016/j.jlb.2025.100312. eCollection 2025 Sep.

ABSTRACT

Breast cancer (BC) is the most frequent cancer and the leading cause of cancer-related death among women worldwide. It represents a heterogeneous group of diseases with distinct morphological, immunophenotypic, and molecular profiles, which significantly impact clinical behavior and therapeutic response. Moreover, under treatment pressure, tumor cells may undergo molecular changes and phenotypic plasticity, leading to resistance and therapeutic failure. Although tissue biopsy remains the gold standard for diagnosis and molecular characterization, it has several limitations, including invasiveness, sampling bias, and the inability to dynamically capture tumor evolution over time. Hence, a non-invasive and repeatable approach capable of real-time monitoring is increasingly needed. Liquid biopsy (LB), through the analysis of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), has emerged as a powerful tool to complement tissue biopsy. It allows for longitudinal assessment of tumor burden, detection of minimal residual disease, and identification of molecular alterations relevant to targeted therapies. Despite promising results, the integration of LB into clinical practice is still limited by methodological heterogeneity, standardization gaps, and regulatory issues. Nonetheless, LB represents a key advancement toward precision oncology and may become essential in the personalized management of BC patients. In this review, we explore the current applications, benefits, and technical limitations of LB in different BC settings. We provide a comprehensive overview of the biological and clinical significance of CTCs and ctDNA, emphasizing their diagnostic, prognostic, and predictive roles. Finally, we present an updated summary of ongoing clinical trials that incorporate LB for clinical decision-making.

PMID:40740670 | PMC:PMC12308030 | DOI:10.1016/j.jlb.2025.100312

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Target-Specific Potency and Drug-Ability Profile of Flavonoids Against Lung Cancer: An Integrative Multi-Omics Approach for Lead Identification

Drug Dev Res. 2025 Aug;86(5):e70131. doi: 10.1002/ddr.70131.

ABSTRACT

Since lung cancer accounts for approximately 20% of cancer-related fatalities globally, it is one of the most common and deadly cancers, necessitating the discovery of innovative, potent, and less toxic treatment agents as imperative. Opportunistically, phytoflavonoids (PFs), a specific class of phytochemicals, display promising anticancer activity through their multimodal apoptosis-inducing properties. Based on existing evidence, the present study employs an integrative multi-omics approach to assess the target-specific binding efficacy and drug-ability outlines of PFs against lung cancer. We selected two of the most likely lung cancer targets using the core part of PFs: carbonic anhydrase IX (PDB ID: 3DAZ) and poly(A) binding protein cytoplasmic 1 (PDB ID: 3KUJ). Another two key targets, glutathione S-transferase P1 (PDB ID: 3GSS) and 17β-hydroxysteroid dehydrogenase 1 (HSD17B1, 3HB4), were also included in our study based on recent literature. The potency of 66 PFs against four targets was assessed through a molecular docking study using PyRx 0.8-AutoDock 4.2 software. PF15, PF43, PF6, and PF26 were the lead candidates. Further, physicochemical profiles through standard Lipinski rule of five parameters and toxicity and drug-ability profiles suggested that PF43 (naringenin) is the most ideal lead candidate among them. Molecular dynamics (MD) simulation studies were performed at 200 ns to observe the kinetic behaviors of CA9-PF43 and CA9-U-1014 docking complexes along with the calculated free energy through the MM/PBSA method. From both analyses, PF43 showed higher stability and lower free energy, expressing its potency over the standard drug. We also investigated the structure-activity relationship and frontier molecular orbitals to highlight the drug chemistry of lead PFs. The integrative multi-omics investigation suggested that using PF43 for lung cancer treatment could increase the chances of experimental success. Overall, the systematic computational analyses provide a platform for lead identification and pave the way for precision phytotherapy in current drug discovery.

PMID:40741887 | DOI:10.1002/ddr.70131

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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

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An integrated approach for analyzing spatially resolved multi-omics datasets from the same tissue section

Front Mol Biosci. 2025 Jul 15;12:1614288. doi: 10.3389/fmolb.2025.1614288. eCollection 2025.

ABSTRACT

Recent advances in spatial transcriptomics (ST) and spatial proteomics (SP) technologies have enabled high-dimensional molecular profiling at single-cell resolution, providing deeper insights into the tumour-immune microenvironment. However, these modalities are typically applied to separate tissue sections, limiting direct comparisons across molecular layers. We developed a wet-lab and computational framework to perform and integrate ST and SP from the same tissue section, as demonstrated on human lung cancer samples. Applying ST, SP, and hematoxylin and eosin (H&E) staining from the same section ensured consistency in tissue morphology and spatial context. Computational registration using Weave software allowed accurate alignment and annotation transfer across modalities. This co-registered dataset enabled single-cell level comparisons of RNA and protein expression, revealed segmentation accuracy and transcript-protein correlation analyses within individual cells. Notably, we observed systematic low correlations between transcript and protein levels-consistent with prior findings-now resolved at cellular resolution. Our approach highlights the feasibility and utility of performing spatially-resolved multi-omics analysis on the same section without compromising data quality, facilitating concordance studies and region-specific analysis of immune and tumour markers, and ultimately advancing our understanding of disease heterogeneity at the molecular level.

PMID:40735471 | PMC:PMC12304548 | DOI:10.3389/fmolb.2025.1614288

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Integrative single-cell multi-omics profiling of human pancreatic islets identifies T1D-associated genes and regulatory signals

Cell Rep. 2025 Jul 29;44(8):116065. doi: 10.1016/j.celrep.2025.116065. Online ahead of print.

ABSTRACT

Genome-wide association studies (GWASs) have identified over 100 signals associated with type 1 diabetes (T1D). However, it has been challenging to translate any given T1D GWAS signal into mechanistic insights, such as causal variants, their target genes, and the specific cell types involved. Here, we present a comprehensive multi-omic integrative analysis of single-cell/nucleus resolution profiles of gene expression and chromatin accessibility in human pancreatic islets under baseline and T1D-stimulating conditions. We nominate effector cell types for all T1D GWAS signals and the regulatory elements and genes for three independent T1D signals acting through β cells at the DLK1/MEG3, RASGRP1, and TOX loci. Subsequently, we validated the functional impact of these genes and regulatory regions using isogenic human embryonic stem cells (hESCs). We found that loss of RASGRP1 or DLK1, as well as disruption of their corresponding regulatory regions, led to increased β cell apoptosis. Furthermore, β cells derived from isogenic hESCs carrying the T1D risk allele of rs3783355 associated with DLK1 showed elevated β cell death. Through additional RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) analyses, we identified five genes upregulated in both RASGRP1-/- and DLK1-/- β-like cells, four of which are near T1D GWAS signals. This integrative approach combining single-cell multi-omics, GWASs, and isogenic human pluripotent stem cell (hPSC)-derived β-like cells illuminates cell type context, genes, single nucleotide polymorphisms (SNPs), and regulatory elements underlying T1D-associated signals, providing insights into the biological functions and molecular mechanisms involved.

PMID:40737125 | DOI:10.1016/j.celrep.2025.116065

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The heterogeneity of type 1 diabetes: implications for pathogenesis, prevention, and treatment-2024 Diabetes, Diabetes Care, and Diabetologia Expert Forum

Diabetologia. 2025 Jul 30. doi: 10.1007/s00125-025-06462-y. Online ahead of print.

ABSTRACT

This article summarises the current understanding of the heterogeneity of type 1 diabetes from a June 2024 international Expert Forum organised by the editors of Diabetes, Diabetes Care, and Diabetologia. The Forum reviewed key factors contributing to the development and progression of type 1 diabetes and outlined specific, high-priority research questions. Knowledge gaps were identified and, notably, opportunities to harness disease heterogeneity to develop personalised therapies were outlined. Herein, we summarise our discussions and review the heterogeneity of genetic risk and immunologic and metabolic phenotypes that influence and characterise type 1 diabetes progression (presented as a palette of risk factors). We discuss how these age-related factors determine disease aggressiveness (along gradients) and describe how variable immunogenetic pathways aggregate (into networks) to affect beta cell and other pancreatic pathologies to cause clinical disease at different ages and with variable severity (described as disease-related thresholds). Heterogeneity of pathogenesis and clinical severity opens avenues to prevention and intervention, including the potential of disease-modifying immunotherapy and islet cell replacement. We conclude with a call for (1) continued research to identify more factors contributing to the disease, both overall and in specific subgroups; (2) investigations focusing on both individuals who surpass metabolic and immune thresholds and develop diabetes and those who remain disease free with the same level of immunogenetic risk; and (3) efforts to identify where the current type 1 diabetes staging system may fall short and determine how it can be improved to capture and leverage heterogeneity in prevention and intervention strategies.

PMID:40736750 | DOI:10.1007/s00125-025-06462-y

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Fatty acid-binding proteins in cancers

Int J Surg. 2025 Jul 15. doi: 10.1097/JS9.0000000000003049. Online ahead of print.

ABSTRACT

Fatty acid-binding proteins (FABPs) are intracellular lipid chaperones with molecular weights of approximately 14-15 kDa. By binding and transporting fatty acids and lipid-related molecules, FABPs precisely regulate metabolic pathways, signal transduction, and gene expression, playing a central role in cancer initiation and progression. The 11 identified subtypes (FABP1-FABP12; FABP11 is identical to FABP3) exhibit tissue-specific expression and influence tumor progression through metabolic reprogramming, immune microenvironment modulation, and therapy resistance. Metabolically, FABPs enhance fatty acid uptake, β-oxidation, and synthesis, meeting the high proliferative demands of tumors. In immune regulation, FABP4+ macrophages secrete IL-6 to suppress T cell activity, while FABP6 downregulates MHC-I molecule expression to reduce CD8+ T cell infiltration, fostering an immunosuppressive microenvironment. Regarding therapy resistance, FABP4 enhances mitochondrial β-oxidation to reduce apoptosis in ovarian cancer, and FABP5 promotes chemoresistance in HCC via the HIF-1α pathway. Functional heterogeneity exists among subtypes: FABP7 drives glioblastoma stem cell migration via RXRα signaling, while FABP5 exhibits context-dependent roles, promoting HCC progression but suppressing colorectal cancer (CRC) through mTOR-mediated autophagy. Clinically, FABPs serve as diagnostic biomarkers and therapeutic targets. However, challenges such as insufficient target specificity, cross-cancer heterogeneity, and normal tissue toxicity remain. Future studies should integrate multi-omics and single-cell technologies to elucidate cell-specific mechanisms and develop precise combination therapies for clinical translation.

PMID:40717587 | DOI:10.1097/JS9.0000000000003049

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Protocol update to: High-throughput scNMT protocol for multiomics profiling of single cells from mouse brain and pancreatic organoids

STAR Protoc. 2025 Jul 24;6(3):103980. doi: 10.1016/j.xpro.2025.103980. Online ahead of print.

ABSTRACT

Single-cell nucleosome, methylome, and transcriptome (scNMT) sequencing is a recently developed method that allows multiomics profiling of single cells. In this scNMT protocol, we describe profiling of cells from mouse brain and pancreatic organoids, using liquid handling platforms to increase throughput from 96-well to 384-well plate format. Our approach miniaturizes reaction volumes and incorporates the latest Smart-seq3 protocol to obtain higher numbers of detected genes and genomic DNA (gDNA) CpGs per cell. We outline normalization steps to optimally distribute per-cell sequencing depth. For complete details on the use and execution of this protocol, please refer to Kremer et al. and other works.1,2,3,4,5,6,7 This protocol is an update to Cerrizuela et al.7.

PMID:40711871 | DOI:10.1016/j.xpro.2025.103980

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State Space Models Can Enable AI in Low-Power Edge Computing

At the the 2025 Embedded Vision Summit, Tony Lewis, chief technology officer at BrainChip, presented research done by his company into state space models (SSMs) and how they can provide LLM capabilities with very low power consumption in limited computing environments, such as those found on dashcams, medical devices, security cameras, and even toys.

By Patrick Farry
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PIVOT: an open-source tool for multi-omic spatial data registration

bioRxiv [Preprint]. 2025 Jun 8:2025.06.08.658506. doi: 10.1101/2025.06.08.658506.

ABSTRACT

Advances in spatial profiling have resulted in the generation of multi-omic atlases that span biological scales. In general, multiple workflows are required for image registration, coordinate registration, and spot deconvolution to integrate modalities. To improve the throughput of registration of multi-omic cohorts, we introduce PIVOT, a user-friendly and open-source interface for streamlined nonlinear registration. We demonstrate PIVOT's strengths through registration of three multi-omic datasets, and show comparison of its performance to existing workflows.

PMID:40661390 | PMC:PMC12259011 | DOI:10.1101/2025.06.08.658506

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Personalized molecular signatures of insulin resistance and type 2 diabetes

Muscle samples from over 120 people were analyzed to identify molecular patterns linked to insulin resistance, a key feature of type 2 diabetes. The findings reveal new insights that could help tailor more personalized and effective treatments for the disease.
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High-Sensitive Spatial Proteomics for Pancreatic Cancer Progression Analysis

bioRxiv [Preprint]. 2025 May 5:2025.05.01.651678. doi: 10.1101/2025.05.01.651678.

ABSTRACT

Pancreatic cancer remains as one of the most challenging malignancies to diagnose and treat due to the late development of symptoms and limited early diagnostic options. Intraductal papillary mucinous neoplasms (IPMNs) are non-invasive precursors to invasive pancreatic ductal adenocarcinoma (PDAC)and an understanding of the changes in patterns of protein expression that accompany the progression from normal ductal (ND) cell, to IPMN to PDAC may provide avenues for improved earlier detection. In this study, we present an optimized spatial tissue proteomics workflow, termed SP-Max (Spatial Proteomics Optimized for Maximum Sensitivity and Reproducibility in Minimal Sample), designed to maximize protein recovery and quantification from limited laser micro dissected (LMD) samples. Our workflow enabled the identification of more than 6,000 proteins and the quantification of over 5,200 protein groups from FFPE tissue contours of pancreatic tissues. Comparative analyses across ND, IPMN, and PDAC revealed critical molecular differences in protein pathways and potential markers of progression. SP-Max provides a systematic, reproducible approach that significantly enhances our ability to study precancerous lesions and cancer progression in pancreatic tissues at unprecedented resolution.

PMID:40654937 | PMC:PMC12247709 | DOI:10.1101/2025.05.01.651678

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A 23-gene multi-omics signature predicts prognosis and treatment response in non-small cell lung cancer

Discov Oncol. 2025 Jul 23;16(1):1391. doi: 10.1007/s12672-025-03243-2.

ABSTRACT

We developed the first multi-omics prognostic signature integrating 19 programmed cell death (PCD) pathways and organelle functions (mitochondria, lysosomes, Golgi apparatus) to predict prognosis and immunotherapy response in non-small cell lung cancer (NSCLC). (2) Methods: By combining single-cell RNA-seq, bulk transcriptomics, and deep neural networks (DNN), we identified a 23-gene signature validated across four cohorts (AUC 0.696–0.812). Conducted MR analysis to explore causal links between signature genes and NSCLC incidence, providing biological insights. (3) Results: A prognostic signature was developed, including 23 prognostic genes related to 19 PCD patterns and three organelle functions. The signature demonstrated powerful performance in predicting NSCLC prognosis, immune in-filtration, and therapeutic response. Established DNN models showed high value in predicting risk score groupings of NSCLC. MR analysis for combined SNP information of the 23 prognostic genes suggested a link to the high incidence of NSCLC. Individual MR analysis showed that HIF1A and SQLE expression had a causal effect on NSCLC incidence. (4) Conclusion: This signature stratifies high-risk patients with immunosuppressive microenvironments and predicts enhanced sensitivity to gemcitabine and PD-1 inhibitors, offering a roadmap for personalized NSCLC management.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12672-025-03243-2.

PMID:40699399 | PMC:PMC12287486 | DOI:10.1007/s12672-025-03243-2

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Molecular characterization of breast cancer and multiple primary malignancies: the latest application using unmarked quantitative proteomics

Int J Surg. 2025 Jul 22. doi: 10.1097/JS9.0000000000002999. Online ahead of print.

ABSTRACT

BACKGROUND: Breast cancer remains the most prevalent malignancy among women, and patients presenting with both breast and lung cancer pose significant challenges in clinical diagnosis and treatment. Currently, comprehensive multi-omics analyses for such multiple malignancies are lacking.

METHODS: An integrated multi-omics analysis was performed, incorporating quantitative proteomics and radiomics data from patients with single primary breast cancer as well as those with multiple primary tumors (breast and lung cancer).

RESULTS: Quantitative proteomics analysis revealed four distinct molecular signatures (Types I-IV). Patients with single breast cancer exhibited driving pathways primarily linked to cell proliferation (e.g., HER2), whereas those with multiple breast cancers showed enrichment in ER-related and proliferative pathways. In contrast, patients with multiple lung cancers displayed pathways associated with immune response and immune escape. Additionally, immune subtyping identified three distinct immune landscapes (Types I-III). Radiomic analysis demonstrated strong correlations between these molecular/immune subtypes and imaging findings. Patients with high imaging information scores exhibited pronounced tumor heterogeneity and reduced immune infiltration.

CONCLUSIONS: This study provides new insights into the molecular pathogenesis of multiple primary malignancies, particularly breast and lung cancer.

PMID:40694032 | DOI:10.1097/JS9.0000000000002999

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Liquid Biopsy: Current advancements in clinical practice for bladder cancer

J Liq Biopsy. 2025 Jul 8;9:100310. doi: 10.1016/j.jlb.2025.100310. eCollection 2025 Sep.

ABSTRACT

Bladder cancer is the ninth most common malignancy worldwide, with two clinically distinct forms: non-muscle-invasive disease, characterized by high recurrence and excellent long-term survival, and muscle-invasive disease, associated with poorer outcomes. Current surveillance-cystoscopy and urine cytology-offers high specificity but is invasive, costly, and insensitive to low-grade tumors, underscoring the need for reliable, non-invasive biomarkers. Liquid biopsy approaches in urine and blood have demonstrated promise for real-time assessment of tumor burden, molecular heterogeneity, and early recurrence. Circulating tumor DNA (ctDNA) assays detect tumor-derived genetic and epigenetic alterations, enabling dynamic monitoring of minimal residual disease and treatment response. Methylation-based tests and CpG-targeted sequencing in urine achieve high diagnostic accuracy, potentially reducing dependence on cystoscopy. Molecular classification of bladder tumors into luminal and basal subtypes has refined therapeutic strategies: FGFR inhibitors for luminal-papillary tumors, EGFR-targeted and chemotherapy approaches for basal/squamous cases, and immune-checkpoint inhibitors guided by immune-infiltration profiles. Integration of artificial intelligence with multi-omic liquid biopsy data further enhances predictive modeling for recurrence, treatment response, and minimal residual disease detection. Despite these advances, clinical implementation faces challenges including pre-analytical variability, lack of standardized assays, limited prospective validation, and unclear cost-effectiveness. Harmonized protocols, large multicenter trials, and health-economic evaluations are essential to translate liquid biopsy technologies into routine practice. Future integration with advanced imaging, tissue biopsy, and digital pathology-supported by multidisciplinary collaboration and formal guideline endorsement-holds the potential to personalize bladder cancer management, reduce invasive procedures, and improve patient outcomes.

PMID:40698358 | PMC:PMC12281373 | DOI:10.1016/j.jlb.2025.100310

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Integrated Multi-Omics Profiling Identifies PDZ-Binding Kinase (PBK) as a Novel Prognostic Biomarker in Hepatocellular Carcinoma

J Hepatocell Carcinoma. 2025 Jul 17;12:1453-1469. doi: 10.2147/JHC.S493907. eCollection 2025.

ABSTRACT

BACKGROUND: Hepatocellular carcinoma (HCC) necessitates novel immunotherapeutic targets. PBK, a cancer/testis antigen (CTA), was identified as a pivotal hub gene influencing prognosis, tumor mutation burden (TMB), and immune microenvironment remodeling.

METHODS: PBK was prioritized using weighted gene co-expression network analysis (WGCNA) and differential expression screening in the TCGA-LIHC cohort, intersected with curated CTAs. Analyses assessed correlations with clinicopathological features (TNM stage, survival), genomic characterization (mutation frequencies), and functional validation via siRNA-mediated PBK knockdown in Huh7 cells (migration assay). Single-cell RNA sequencing (scRNA-seq) profiled of the tumor immune microenvironment.

RESULTS: PBK overexpression was significantly correlated with advanced TNM stage (P < 0.05) and poor survival (log-rank P = 0.003). Genomic analysis revealed distinct mutation profiles: high-PBK tumors exhibited increased TP53 mutation frequency (39% vs 17%) but decreased CTNNB1 mutations (20% vs 31%). Patients exhibiting with combined PBK overexpression and high TMB demonstrated the poorest prognosis. Functional validation confirmed that PBK knockdown significantly inhibited Huh7 cell migration capacity (P < 0.05). scRNA-seq analysis showed PBK-enriched tumors contained elevated proportions of immunosuppressive SPP1(+) macrophages (22.33% vs 6.6%, FDR corrected P < 0.001) and CD8(+) SLC4A10(+) MAIT cells (9.82% vs 4.7%, FDR corrected P < 0.001).

CONCLUSION: PBK synergistically drives HCC progression through three synergistic mechanisms: (1) promoting oncogenic mutation accumulation (eg, TP53), (2) increasing metastatic potential, and (3) reprogramming an immune-suppressive microenvironment enriched for SPP1(+) macrophages and CD8(+)SLC4A10(+) MAIT cells. This establishes PBK as a dual-purpose biomarker for prognostic stratification and immunotherapy resistance prediction, providing a mechanistic rationale for developing PBK-targeted therapies in HCC.

PMID:40697330 | PMC:PMC12279550 | DOI:10.2147/JHC.S493907

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Nanobody therapy rescues behavioural deficits of NMDA receptor hypofunction

Nature, Published online: 23 July 2025; doi:10.1038/s41586-025-09265-8

A bivalent biparatopic nanobody penetrates the brain, binds to and potentiates the activity of homodimeric metabotropic glutamate receptor 2, correcting cognitive deficits in two preclinical mouse models with endophenotypes resulting from NMDA receptor hypofunction.
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