Adv Sci (Weinh). 2026 Apr 3:e17640. doi: 10.1002/advs.202517640. Online ahead of print.

ABSTRACT

The embryonic coelomic mesothelium acts as a critical progenitor hub during mammalian organogenesis, undergoing epithelial-to-mesenchymal transition (EMT) to drive vascular growth and parenchymal development in visceral organs. A prominent example is the epicardium, which plays an essential role during heart development. The principles of gene regulation in the coelomic mesothelium remain poorly defined. Specifically, it is unclear how cis-regulatory elements, including enhancers, orchestrate the spatiotemporal patterns of gene expression required for mesothelial identity and function. Here, a multi-omic approach was used to identify trans- and cis-regulatory elements that regulate mesothelial gene expression in three organs: heart, lung, and pancreas. This analysis uncovers a cardiac-specific regulatory circuit in which the transcription factor (TF) TBX20 selectively activates epicardial enhancers to orchestrate essential developmental programs. In contrast, TF MAF orchestrates pan-mesothelial gene expression via conserved CREs, which are absent in non-mesothelial lineages. Our integrated genomic analysis reveals MAF as a central custodian of mesothelial identity, a role underscored by its negative correlation with EMT, evolutionary conservation, and dynamic regulatory activity throughout development. Our work establishes a foundational blueprint of the gene regulatory landscape governing the coelomic mesothelium, defining both conserved principles and organ-specific mechanisms of spatiotemporal gene expression during early mammalian development.

PMID:41933934 | DOI:10.1002/advs.202517640

Future Sci OA. 2026 Dec;12(1):2653101. doi: 10.1080/20565623.2026.2653101. Epub 2026 Apr 3.

ABSTRACT

BACKGROUND: Clarification of the molecular mechanism of malignant tumor progression, identification of the key signaling pathways and molecules involved in the processes of invasion and metastasis, and identification of new targets and strategies for effective tumor treatment are extremely important for scientific research and clinical application prospects.

METHODS: Based on large-sample data mining, we first evaluated the expression and mutation profiles of SPRR family genes across cancers and then focused on the molecular functions of SPRR2D across cancers.

RESULTS: Multi-omics experiments revealed that SPRR2D is significantly overexpressed in various tumors, especially in LUSC. ROC curve analysis revealed that SPRR2D demonstrated significant diagnostic efficacy across cancers. Cox regression analysis revealed that the expression of SPRR2D was associated with the survival time of patients with various tumors. Moreover, the expression of SPRR2D is closely related to tumor immune infiltration. GDSC data analysis revealed that the expression levels of SPRR1A, SPRR1B, SPRR2A, SPRR3, and SPRR2D are negatively correlated with the sensitivity to gefitinib, trametinib, bosutinib, afatinib, lapatinib, and erlotinib.

CONCLUSIONS: From a multi-omics perspective, it was revealed that SPRR2D plays a significant role in regulating tumorigenesis and drug sensitivity in tumors.

PMID:41933926 | PMC:PMC13051589 | DOI:10.1080/20565623.2026.2653101

Adv Sci (Weinh). 2026 Apr 3:e17640. doi: 10.1002/advs.202517640. Online ahead of print.

ABSTRACT

The embryonic coelomic mesothelium acts as a critical progenitor hub during mammalian organogenesis, undergoing epithelial-to-mesenchymal transition (EMT) to drive vascular growth and parenchymal development in visceral organs. A prominent example is the epicardium, which plays an essential role during heart development. The principles of gene regulation in the coelomic mesothelium remain poorly defined. Specifically, it is unclear how cis-regulatory elements, including enhancers, orchestrate the spatiotemporal patterns of gene expression required for mesothelial identity and function. Here, a multi-omic approach was used to identify trans- and cis-regulatory elements that regulate mesothelial gene expression in three organs: heart, lung, and pancreas. This analysis uncovers a cardiac-specific regulatory circuit in which the transcription factor (TF) TBX20 selectively activates epicardial enhancers to orchestrate essential developmental programs. In contrast, TF MAF orchestrates pan-mesothelial gene expression via conserved CREs, which are absent in non-mesothelial lineages. Our integrated genomic analysis reveals MAF as a central custodian of mesothelial identity, a role underscored by its negative correlation with EMT, evolutionary conservation, and dynamic regulatory activity throughout development. Our work establishes a foundational blueprint of the gene regulatory landscape governing the coelomic mesothelium, defining both conserved principles and organ-specific mechanisms of spatiotemporal gene expression during early mammalian development.

PMID:41933934 | DOI:10.1002/advs.202517640

Future Sci OA. 2026 Dec;12(1):2653101. doi: 10.1080/20565623.2026.2653101. Epub 2026 Apr 3.

ABSTRACT

BACKGROUND: Clarification of the molecular mechanism of malignant tumor progression, identification of the key signaling pathways and molecules involved in the processes of invasion and metastasis, and identification of new targets and strategies for effective tumor treatment are extremely important for scientific research and clinical application prospects.

METHODS: Based on large-sample data mining, we first evaluated the expression and mutation profiles of SPRR family genes across cancers and then focused on the molecular functions of SPRR2D across cancers.

RESULTS: Multi-omics experiments revealed that SPRR2D is significantly overexpressed in various tumors, especially in LUSC. ROC curve analysis revealed that SPRR2D demonstrated significant diagnostic efficacy across cancers. Cox regression analysis revealed that the expression of SPRR2D was associated with the survival time of patients with various tumors. Moreover, the expression of SPRR2D is closely related to tumor immune infiltration. GDSC data analysis revealed that the expression levels of SPRR1A, SPRR1B, SPRR2A, SPRR3, and SPRR2D are negatively correlated with the sensitivity to gefitinib, trametinib, bosutinib, afatinib, lapatinib, and erlotinib.

CONCLUSIONS: From a multi-omics perspective, it was revealed that SPRR2D plays a significant role in regulating tumorigenesis and drug sensitivity in tumors.

PMID:41933926 | PMC:PMC13051589 | DOI:10.1080/20565623.2026.2653101

Transl Oncol. 2026 Apr 3;67:102748. doi: 10.1016/j.tranon.2026.102748. Online ahead of print.

ABSTRACT

BACKGROUND: Epithelial ovarian cancer (EOC) encompasses five major histological subtypes with marked genetic, immunological, and clinical heterogeneity. While genome-wide association studies (GWAS) have identified subtype-specific risk loci, a critical gap remains in understanding how plasma proteins influence immune-cell traits and contribute to EOC pathogenesis.

METHODS: We integrated subtype-stratified GWAS data from two EOC cohorts with plasma proteomics and immune-cell traits to construct protein-immune-EOC regulatory landscapes using a three-stage Mendelian randomization framework. Single-cell RNA-seq and multiplex immunofluorescence were employed to delineate the cellular distribution and spatial context of causal proteins. Subsequent analyses characterized immune infiltration, macrophage polarization, and clinicopathological associations. Drug-gene correlations were used to identify potential therapeutic targets, and transcriptomic analyses were applied to delineate the underlying transcriptional landscape.

RESULTS: We identified 20 subtype-specific protein-immune-EOC regulatory axes, with FCGR2B emerging as a causal plasma protein in immune regulation and high-grade serous ovarian cancer (HGSOC) progression. FCGR2B was highly expressed in tumor-associated macrophages and was associated with an M2-like polarization phenotype. Functional characterization revealed that FCGR2B was associated with shorter progression-free survival and an immunosuppressive tumor microenvironment. Transcriptomic analyses revealed altered NF-κB signaling upon FCGR2B knockdown, and drug-response data suggested a potential association between high FCGR2B expression and sensitivity to NF-κB inhibitors.

CONCLUSIONS: These findings delineate subtype-specific genetically informed protein-immune regulatory landscapes in EOC and identify FCGR2B as a key immunoregulatory and prognostic biomarker in HGSOC, suggesting FCGR2B as a potential therapeutic vulnerability that warrants further investigation.

PMID:41934917 | DOI:10.1016/j.tranon.2026.102748

Clin Chim Acta. 2026 Mar 31;588:120992. doi: 10.1016/j.cca.2026.120992. Online ahead of print.

ABSTRACT

Bladder cancer diagnosis and surveillance remain anchored in cystoscopy and urine cytology, despite their invasiveness, operator dependence, and limited sensitivity for low-grade or flat lesions. These constraints have accelerated interest in liquid biopsy approaches that provide noninvasive, real-time molecular insights into tumor biology. This narrative review examines emerging evidence on three key classes of circulating biomarkers, namely, circulating tumor DNA (ctDNA), exosomes, and circulating tumor cells (CTCs), and their expanding roles in diagnosis, prognosis, and treatment guidance. ctDNA reflects tumor-specific genomic alterations and shows particular strength in detecting minimal residual disease, identifying early molecular relapse, and monitoring therapeutic response, although its diagnostic sensitivity remains moderate. Urinary exosomes demonstrate some of the highest diagnostic accuracies among liquid biopsy platforms, with multimarker RNA panels achieving sensitivities and specificities above 90%, while their diverse cargo of miRNAs, mRNAs, and lncRNAs provides robust prognostic information linked to recurrence and survival. CTCs, although technically challenging to isolate owing to their phenotypic heterogeneity, offer valuable insights into tumor aggressiveness, metastatic potential, and treatment responsiveness, especially in muscle-invasive disease. Advances in ultrasensitive sequencing, microfluidic CTC capture, and multi-omics integration are accelerating clinical translation. Collectively, circulating biomarkers are poised to complement and, in selected contexts, transform bladder cancer management by enabling earlier detection, individualized risk stratification, and more precise therapeutic decision-making.

PMID:41933678 | DOI:10.1016/j.cca.2026.120992

Adv Sci (Weinh). 2026 Apr 3:e17640. doi: 10.1002/advs.202517640. Online ahead of print.

ABSTRACT

The embryonic coelomic mesothelium acts as a critical progenitor hub during mammalian organogenesis, undergoing epithelial-to-mesenchymal transition (EMT) to drive vascular growth and parenchymal development in visceral organs. A prominent example is the epicardium, which plays an essential role during heart development. The principles of gene regulation in the coelomic mesothelium remain poorly defined. Specifically, it is unclear how cis-regulatory elements, including enhancers, orchestrate the spatiotemporal patterns of gene expression required for mesothelial identity and function. Here, a multi-omic approach was used to identify trans- and cis-regulatory elements that regulate mesothelial gene expression in three organs: heart, lung, and pancreas. This analysis uncovers a cardiac-specific regulatory circuit in which the transcription factor (TF) TBX20 selectively activates epicardial enhancers to orchestrate essential developmental programs. In contrast, TF MAF orchestrates pan-mesothelial gene expression via conserved CREs, which are absent in non-mesothelial lineages. Our integrated genomic analysis reveals MAF as a central custodian of mesothelial identity, a role underscored by its negative correlation with EMT, evolutionary conservation, and dynamic regulatory activity throughout development. Our work establishes a foundational blueprint of the gene regulatory landscape governing the coelomic mesothelium, defining both conserved principles and organ-specific mechanisms of spatiotemporal gene expression during early mammalian development.

PMID:41933934 | DOI:10.1002/advs.202517640

Phytomedicine. 2026 Mar 27;155:158126. doi: 10.1016/j.phymed.2026.158126. Online ahead of print.

ABSTRACT

BACKGROUND: Mitochondrial damage can induce the release of mitochondrial DNA (mtDNA), leading to oxidative stress and activation of immune responses. Targeting mitochondrial dysfunction may thus represent a therapeutic strategy for gastric cancer. Isobavachalcone (IBC), a prenylated chalcone derived from Psoralea corylifolia L., has demonstrated antitumor activity, but its mechanism of action remains unclear, limiting its clinical application.

PURPOSE: This study aimed to investigate the antitumor effects of IBC in gastric cancer and to elucidate the underlying molecular mechanisms, with a focus on mitochondrial damage and immune activation.

STUDY DESIGN: The study combined in vitro and in vivo assays with multi-omics sequencing and network pharmacology to identify IBC's therapeutic target and downstream signaling pathways.

METHODS: Gastric cancer cells and mouse models were treated with IBC to assess its inhibitory effects. Multi-omics approaches and network pharmacology were used to identify potential targets. ROS production, mitochondrial membrane integrity, and immune pathway activation were evaluated via biochemical and molecular assays.

RESULTS: IBC significantly suppresses gastric cancer growth both in vitro and in vivo. Integrated analysis identifies dihydroorotate dehydrogenase (DHODH) as a direct target of IBC. DHODH deficiency can induce mitochondrial membrane remodeling and STING pathway activation. Inhibition of DHODH by IBC induces ROS accumulation, mitochondrial membrane remodeling, and activation of the STING pathway, promoting antitumor immune responses. This study demonstrates that IBC enhances antitumor immunity in gastric cancer through mitochondrial damage-mediated mechanisms.

CONCLUSION: IBC exerts dual antitumor and immunostimulatory effects in gastric cancer by targeting DHODH, inducing mitochondrial damage, and activating the STING pathway, highlighting its promising therapeutic potential in gastric cancer.

PMID:41931998 | DOI:10.1016/j.phymed.2026.158126

Gastroenterology. 2026 Apr 1:S0016-5085(26)00312-4. doi: 10.1053/j.gastro.2026.03.020. Online ahead of print.

ABSTRACT

The burden of chronic liver disease is rapidly increasing worldwide, driven primarily by metabolic dysfunction-associated steatotic liver disease (MASLD), metabolic and alcohol-associated liver disease (MetALD), and alcohol-associated liver disease (ALD). Genetic predisposition contributes substantially to variability in disease onset, progression, and outcomes, and recent advances in genomic discovery have brought polygenic risk scores (PRS) and targeted sequencing closer to clinical relevance. This review summarizes the role of genetic testing in clinical hepatology, including monogenic drivers of disease and the growing role of common variants and PRS. Specific populations, including cryptogenic cirrhosis and lean MASLD patients, may be enriched for monogenic drivers of disease. In addition, patients with chronic liver disease may benefit from incorporation of genetic risk scores including PNPLA3, TM6SF2, HSD17B13, and other key variants in determining risk for fibrosis progression and cirrhosis. Across MASLD and ALD, PRS demonstrate modest improvements in predicting fibrosis progression and liver-related events, especially when integrated with clinical risk factors and comorbidities. However, their performance remains limited for population-level screening. Similarly, PRS alone has limited diagnostic accuracy for hepatocellular carcinoma and more complex models with clinical features and multi-omic biomarkers are likely needed. Emerging therapies targeting PNPLA3 and HSD17B13 variants represent a paradigm shift toward genetically informed treatment. Yet challenges remain, including limited ancestral diversity in genomic datasets, pleiotropic effects of variants, cost-effectiveness, and the need for integration with other omics and electronic medical records. As evidence matures, combining genetic risk with clinical and environmental factors may enable more personalized approaches to prognostication and therapy in liver disease.

PMID:41932449 | DOI:10.1053/j.gastro.2026.03.020

Am J Hum Genet. 2026 Apr 2;113(4):828-841. doi: 10.1016/j.ajhg.2026.03.008.

ABSTRACT

Reliable reference transcriptome prediction models are key to accurate multi-ancestry transcriptome-wide association studies (TWASs). We propose three methods leveraging functionally informed variants (FIVs) for transcriptome prediction models to improve multi-ancestry TWASs. We trained models on 1,287 multi-ancestry participants from the Trans-Omics for Precision Medicine (TOPMed) program Multi-Ethnic Study of Atherosclerosis (MESA) with RNA sequencing (RNA-seq) data from peripheral blood mononuclear cells (PBMCs). We validated models' prediction accuracy on two external independent datasets, Geuvadis and Jackson Heart Study. To test robustness of our methods for TWASs, we integrated models with three multi-ancestry GWASs from blood cell, lipid, and pulmonary function traits, respectively. Our methods presented similar prediction accuracy while using a smaller and functionally informed set of variants compared to the benchmark method, elastic net (EN). Overall, our methods achieved higher power and accuracy (with average improved accuracy of 24% over EN) for TWASs. However, no single proposed method outperformed all GWAS traits. To further improve TWAS performance, we propose an omnibus approach that aggregates TWAS summary statistics from our methods. The omnibus approach yielded the highest number of Bonferroni-significant TWAS genes for all GWAS traits, and it further improved TWAS power and accuracy for blood cell traits. Additionally, the omnibus approach detected some trait-relevant important genes that the EN missed. Our study demonstrates the value of including FIVs in multi-ancestry transcriptome prediction models for improving TWAS performance. Further, the observed TWAS improvement depends on the GWAS trait's relevance to the PBMCs used to build our transcriptome prediction models.

PMID:41932314 | DOI:10.1016/j.ajhg.2026.03.008

Phytomedicine. 2026 Mar 27;155:158126. doi: 10.1016/j.phymed.2026.158126. Online ahead of print.

ABSTRACT

BACKGROUND: Mitochondrial damage can induce the release of mitochondrial DNA (mtDNA), leading to oxidative stress and activation of immune responses. Targeting mitochondrial dysfunction may thus represent a therapeutic strategy for gastric cancer. Isobavachalcone (IBC), a prenylated chalcone derived from Psoralea corylifolia L., has demonstrated antitumor activity, but its mechanism of action remains unclear, limiting its clinical application.

PURPOSE: This study aimed to investigate the antitumor effects of IBC in gastric cancer and to elucidate the underlying molecular mechanisms, with a focus on mitochondrial damage and immune activation.

STUDY DESIGN: The study combined in vitro and in vivo assays with multi-omics sequencing and network pharmacology to identify IBC's therapeutic target and downstream signaling pathways.

METHODS: Gastric cancer cells and mouse models were treated with IBC to assess its inhibitory effects. Multi-omics approaches and network pharmacology were used to identify potential targets. ROS production, mitochondrial membrane integrity, and immune pathway activation were evaluated via biochemical and molecular assays.

RESULTS: IBC significantly suppresses gastric cancer growth both in vitro and in vivo. Integrated analysis identifies dihydroorotate dehydrogenase (DHODH) as a direct target of IBC. DHODH deficiency can induce mitochondrial membrane remodeling and STING pathway activation. Inhibition of DHODH by IBC induces ROS accumulation, mitochondrial membrane remodeling, and activation of the STING pathway, promoting antitumor immune responses. This study demonstrates that IBC enhances antitumor immunity in gastric cancer through mitochondrial damage-mediated mechanisms.

CONCLUSION: IBC exerts dual antitumor and immunostimulatory effects in gastric cancer by targeting DHODH, inducing mitochondrial damage, and activating the STING pathway, highlighting its promising therapeutic potential in gastric cancer.

PMID:41931998 | DOI:10.1016/j.phymed.2026.158126

Gastroenterology. 2026 Apr 1:S0016-5085(26)00312-4. doi: 10.1053/j.gastro.2026.03.020. Online ahead of print.

ABSTRACT

The burden of chronic liver disease is rapidly increasing worldwide, driven primarily by metabolic dysfunction-associated steatotic liver disease (MASLD), metabolic and alcohol-associated liver disease (MetALD), and alcohol-associated liver disease (ALD). Genetic predisposition contributes substantially to variability in disease onset, progression, and outcomes, and recent advances in genomic discovery have brought polygenic risk scores (PRS) and targeted sequencing closer to clinical relevance. This review summarizes the role of genetic testing in clinical hepatology, including monogenic drivers of disease and the growing role of common variants and PRS. Specific populations, including cryptogenic cirrhosis and lean MASLD patients, may be enriched for monogenic drivers of disease. In addition, patients with chronic liver disease may benefit from incorporation of genetic risk scores including PNPLA3, TM6SF2, HSD17B13, and other key variants in determining risk for fibrosis progression and cirrhosis. Across MASLD and ALD, PRS demonstrate modest improvements in predicting fibrosis progression and liver-related events, especially when integrated with clinical risk factors and comorbidities. However, their performance remains limited for population-level screening. Similarly, PRS alone has limited diagnostic accuracy for hepatocellular carcinoma and more complex models with clinical features and multi-omic biomarkers are likely needed. Emerging therapies targeting PNPLA3 and HSD17B13 variants represent a paradigm shift toward genetically informed treatment. Yet challenges remain, including limited ancestral diversity in genomic datasets, pleiotropic effects of variants, cost-effectiveness, and the need for integration with other omics and electronic medical records. As evidence matures, combining genetic risk with clinical and environmental factors may enable more personalized approaches to prognostication and therapy in liver disease.

PMID:41932449 | DOI:10.1053/j.gastro.2026.03.020

Eur J Cancer. 2026 Mar 19;239:116676. doi: 10.1016/j.ejca.2026.116676. Online ahead of print.

ABSTRACT

BACKGROUND: Circulating tumor DNA (ctDNA) is a promising biomarker in melanoma, with higher sensitivity for tumor burden detection than conventional diagnostics. While well established in research, clinical routine implementation remains pending. Key global questions concern optimal clinical applications and barriers to adoption.

METHODS: A web-based survey of 116 members of the Melanoma World Society Study Group assessed international expert opinions on ctDNA utility across predefined clinical scenarios. The questionnaire included 18 general questions on ctDNA use and 5 clinical vignettes with de-identified patient data and retrospectively obtained ctDNA results.

RESULTS: ctDNA was rated most valuable for detecting minimal residual disease (mean score 3.63), surveillance of recurrent disease (3.85), and stage IV melanoma (3.82), with limited utility in early stages. Experts considered ctDNA superior to S100 and LDH for early relapse detection and identifying progressive disease. Most participants (80%) agreed that ctDNA correlates with radiographic response, and 82% favored its integration into routine follow-ups. In urgent high-tumor-burden settings, 82.8% would initiate BRAFi/MEKi therapy based on ctDNA if tissue analysis was pending, and 93.9% if unavailable. For central nervous system lesions, 62% did not support blood ctDNA, while 66% considered cerebrospinal fluid valuable. Pragmatic approaches with small to mid-size targeted panels and short turnaround times were preferred. Major barriers included the need for prospective trials (85%), standardized guidelines (83%), and reimbursement policies (82%).

CONCLUSION: Key opinion leaders regarded ctDNA as a valuable adjunct selected melanoma scenarios. Validation through prospective studies, guideline development, and reimbursement frameworks are essential for broader clinical implementation.

PMID:41932032 | DOI:10.1016/j.ejca.2026.116676

ESMO Real World Data Digit Oncol. 2026 Jan 14;11:100652. doi: 10.1016/j.esmorw.2025.100652. eCollection 2026 Mar.

ABSTRACT

BACKGROUND: Malignant tumors release circulating tumor DNA (ctDNA) into the bloodstream, providing insights into tumor-specific mutations and pathways driving cancer progression. ctDNA testing is currently approved as a type of liquid biopsy to monitor disease burden and detect minimal residual disease (MRD). This study aimed to evaluate the adoption of ctDNA testing in a community oncology practice and assess the overall diagnostic performance of ctDNA and its association with disease progression in stage IV colorectal cancer (CRC), as determined by imaging studies.

PATIENTS AND METHODS: This retrospective study analyzed the medical records of 88 patients with gastrointestinal cancers (80 CRC, 5 gastric, 3 esophageal) who underwent ctDNA molecular testing between January 2020 and April 2022. Electronic medical records from patients aged ≥21 years who had two or more ctDNA tests with concurrent imaging studies or a pathology-confirmed CRC, gastric cancer, or esophageal cancer diagnosis were evaluated.

RESULTS: At baseline, 47 (53.4%) patients had negative and 41 (46.6%) had positive results. Most patients had CRC (90.1%). In stage IV CRC, ctDNA was increasing before radiologic progression in all documented cases (100%), with a median lead time of 2.5 months (range 0.5-15 months). In early-stage CRC (I-III), ctDNA preceded radiologic progression in 40% of cases, with a median lead time of 6 months (range 6-10 months).

CONCLUSIONS: Using real-world data, we report the first-time results of the ctDNA testing adoption in a community oncology setting among patients with gastrointestinal cancers, predominantly CRC. Our findings suggest that integration of ctDNA testing may support disease monitoring in routine clinical practice.

PMID:41930304 | PMC:PMC13040887 | DOI:10.1016/j.esmorw.2025.100652

Eur J Cancer. 2026 Mar 24;239:116699. doi: 10.1016/j.ejca.2026.116699. Online ahead of print.

ABSTRACT

INTRODUCTION: The latest generation of liquid biopsies incorporates multi-omic features, including genomics, methylomics, and fragmentomics. Machine learning (ML) approaches have been proposed to synthesize these complex biological data for the development of diagnostic classifiers. This study aims to evaluate the integration of ML with circulating cell-free DNA (cfDNA) analysis for early cancer detection.

METHODS: Medline, Embase, Cochrane, and Web of Science were searched in July 2025. Eligible studies combined ML and cfDNA features to distinguish cancer patients (stages I-III) from non-cancer controls. Summary diagnostic performance metrics and their 95% confidence intervals (CI) were calculated.

RESULTS: The study included 109 articles permitting analyses for lung (n = 34), liver (n = 29), colorectal (n = 28), pancreatic (n = 16), breast (n = 17), esophageal (n = 12), ovarian (n = 13), gastric (n = 9), head and neck (n = 4), and mixed (n = 27) cancer types. Specificity was consistently high across all tumor types and stages (94%-99%). Sensitivity ranged from 72% to 92% for stage I-III, 44-91% for stage I, 71-98% for stage II and 83-99% for stage III. In the pooled study population, neural networks (90%, 95% CI: 81%-95%), random forest (86%, 95% CI: 77%-92%) and heterogeneous ensemble learning (85%, 95% CI: 79%-89%) demonstrated the highest sensitivity. The stratified analysis by classifier feature revealed 86% (95% CI: 80%-90%) sensitivity for fragmentation and 81% (95% CI: 76%-85%) for methylation, with 92%-96% specificity.

CONCLUSION: ML and cfDNA profiling show potential for early cancer detection, with ensemble methods, neural networks and random forests achieving the best overall performance. Fragmentomic features provide the highest sensitivity.

PMID:41930854 | DOI:10.1016/j.ejca.2026.116699

Front Immunol. 2026 Mar 18;17:1791707. doi: 10.3389/fimmu.2026.1791707. eCollection 2026.

ABSTRACT

BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy with a complex tumor ecosystem that contributes to its progression. Deubiquitinases (DUBs) are vital regulators in cancer. However, the overall activity of DUBs and their role in driving PDAC progression within immune microenvironment remain largely unknown.

METHODS: We employed an integrative multi-omics strategy combining machine learning (ML) on bulk transcriptomic data, single-cell RNA sequencing and spatial transcriptomic profiling. We applied Coxnet and Fuzzy SVM for prognostic modeling, inferCNV for malignant cell identification, SCENIC for transcription factor regulon analysis, LIANA⁺ for inferring inter-cellular communication networks and cell2location for spatial deconvolution. USP54 expression was detected by real-time quantitative PCR, western blotting and immunohistochemistry. USP54 function was validated through in vitro and in vivo assays.

RESULTS: ML-based pathway analysis revealed post-translational modification as a major prognostic category, within which elevated DUBs activity emerged as an independent adverse prognostic factor. At the single-cell level, USP54 was upregulated along the trajectory of malignant ductal cells and correlated with an inflamed tumor microenvironment. Cell-cell communication analysis predicted signaling from monocytes/macrophages to tumor cells via the THBS1-integrin ligand-receptor pair. This immune-derived signaling potentially converged on KLF5-positive tumor cells, with KLF5 identified as a putative transcriptional activator of USP54. Spatial transcriptomics validated the co-localization of USP54 expression, elevated DUB activity, and KRAS signaling within specific tumor niches adjacent to THBS1-enriched immune regions. High USP54 expression was frequently observed in PDAC tissues and associated with poor patient survival. More importantly, in both BxPC-3 and PANC-1 cell lines, USP54 knockdown suppressed cell proliferation and metastasis, whereas its overexpression enhanced these malignant phenotypes. Subcutaneous xenograft growth and tail vein injection experiments validated these findings in vivo.

CONCLUSIONS: Our comprehensive multi-omics analysis and experimental validation identify the deubiquitinase USP54 as a novel promoter of PDAC progression within a spatially organized tumor-immune microenvironment. These findings suggest USP54 as both a candidate prognostic biomarker and a potential therapeutic target for this lethal malignancy.

PMID:41929495 | PMC:PMC13038871 | DOI:10.3389/fimmu.2026.1791707

J Physiol Pharmacol. 2026 Feb;77(1):xxx. doi: 10.26402/jpp.2026.1.04. Epub 2026 Apr 2.

ABSTRACT

Helicobacter pylori infection remains one of the most common chronic bacterial infections worldwide and represents a major etiological factor in diseases of the upper gastrointestinal tract, including chronic gastritis, peptic ulcer disease, and gastric cancer. Despite continuous refinement of eradication regimens based on antibiotics and proton pump inhibitors, treatment efficacy has progressively declined, primarily due to increasing antimicrobial resistance and the ability of H. pylori to form biofilm structures. Accumulating evidence indicates that biofilm formation, bacterial virulence, and modulation of host immune responses constitute an interconnected network of mechanisms that collectively promote bacterial persistence and therapeutic failure. This review outlines an integrated pathogenic framework for H. pylori, focusing on the functional interplay between key virulence determinants - including CagA, VacA, neutrophil-activating protein (NAP), high-temperature requirement A (HtrA), IceA, DupA, urease, catalase, and adhesins - and their contribution to biofilm development, epithelial barrier disruption, and sustained gastric inflammation. Biofilm formation is highlighted as a central adaptive strategy that not only limits antibiotic penetration but also induces metabolic dormancy, enhances efflux pump activity, and increases tolerance to oxidative stress and immune-mediated clearance, thereby significantly reducing the effectiveness of standard eradication therapies. In addition, the review incorporates novel insights derived from recent high-throughput omics approaches, including genomics, transcriptomics, proteomics, and metabolomics, which have advanced the understanding of H. pylori pathogenicity, adaptive responses, and resistance mechanisms at a systems level. A major emphasis is placed on recent advances in therapeutic strategies that extend beyond conventional antibiotic-based regimens. The review summarizes current pharmacological approaches, including the use of more potent acid-suppressive agents such as vonoprazan, susceptibility-guided and personalized eradication therapies, and emerging anti-biofilm interventions, including antimicrobial peptides, phytochemicals, small-molecule inhibitors, and enzymatic degradation of the extracellular polymeric matrix. In addition, nanotechnology-based drug delivery systems are discussed as promising tools to improve antibiotic stability, bioavailability, and targeted release within the hostile gastric environment. In conclusion, effective management of H. pylori infection requires a mechanistically informed and multidisciplinary approach that integrates bacterial virulence, biofilm biology, host immune modulation, and regional antimicrobial resistance profiles. The combination of established pharmacological therapies with innovative anti-biofilm and nanomedicine-based strategies represents a promising direction for improving eradication outcomes and limiting the further development of antimicrobial resistance.

PMID:41931732 | DOI:10.26402/jpp.2026.1.04

PLoS One. 2026 Apr 3;21(4):e0346173. doi: 10.1371/journal.pone.0346173. eCollection 2026.

ABSTRACT

Cancer remains a leading cause of mortality worldwide and a significant barrier to improving quality of life across all populations. The protein kinase D family, including PRKD3, has been demonstrated to play a crucial role in cancer development through its involvement in regulating key cellular processes. Although growing evidence highlights the role of PRKD3 in the tumorigenesis of certain cancers, a comprehensive pan-cancer analysis of PRKD3 remains unavailable. To address this, we performed an integrative pan-cancer analysis of PRKD3 using multi-omics datasets from The Cancer Genome Atlas, the Genotype-Tissue Expression project, and cBioPortal. We examined PRKD3 expression, copy number variation, mutation, and DNA methylation, and evaluated their associations with clinicopathological features, patient survival, and diagnostic potential across 33 cancer types. Immune relevance was further assessed through correlations with immune infiltration, checkpoint gene expression, and immunotherapy response-related genomic biomarkers. Our results revealed that PRKD3 expression was highly heterogeneous, showing significant upregulation in liver cancer, gastric cancer, and adrenocortical carcinoma, and downregulation in others. Elevated expression was consistently associated with poor prognosis and increased stromal, neutrophil, and cancer-associated fibroblast infiltration in adrenocortical carcinoma, liver cancer, and stomach cancer, whereas paradoxical associations with favorable outcomes were observed in kidney clear cell carcinoma. PRKD3 expression also correlated with immune checkpoint molecules including PD-1, PD-L1, and CTLA-4, supporting an immunosuppressive role, while context-dependent associations with TMB and MSI highlighted its potential influence on tumor immunogenicity and responsiveness to immune checkpoint blockade. Collectively, these findings identify PRKD3 as a potential context-dependent modulator of tumor biology, prognosis, and immune interactions, underscoring its potential as a biomarker of diagnostic, prognostic, and therapeutic relevance in precision oncology.

PMID:41931575 | PMC:PMC13048501 | DOI:10.1371/journal.pone.0346173

Eur J Cancer. 2026 Mar 24;239:116699. doi: 10.1016/j.ejca.2026.116699. Online ahead of print.

ABSTRACT

INTRODUCTION: The latest generation of liquid biopsies incorporates multi-omic features, including genomics, methylomics, and fragmentomics. Machine learning (ML) approaches have been proposed to synthesize these complex biological data for the development of diagnostic classifiers. This study aims to evaluate the integration of ML with circulating cell-free DNA (cfDNA) analysis for early cancer detection.

METHODS: Medline, Embase, Cochrane, and Web of Science were searched in July 2025. Eligible studies combined ML and cfDNA features to distinguish cancer patients (stages I-III) from non-cancer controls. Summary diagnostic performance metrics and their 95% confidence intervals (CI) were calculated.

RESULTS: The study included 109 articles permitting analyses for lung (n = 34), liver (n = 29), colorectal (n = 28), pancreatic (n = 16), breast (n = 17), esophageal (n = 12), ovarian (n = 13), gastric (n = 9), head and neck (n = 4), and mixed (n = 27) cancer types. Specificity was consistently high across all tumor types and stages (94%-99%). Sensitivity ranged from 72% to 92% for stage I-III, 44-91% for stage I, 71-98% for stage II and 83-99% for stage III. In the pooled study population, neural networks (90%, 95% CI: 81%-95%), random forest (86%, 95% CI: 77%-92%) and heterogeneous ensemble learning (85%, 95% CI: 79%-89%) demonstrated the highest sensitivity. The stratified analysis by classifier feature revealed 86% (95% CI: 80%-90%) sensitivity for fragmentation and 81% (95% CI: 76%-85%) for methylation, with 92%-96% specificity.

CONCLUSION: ML and cfDNA profiling show potential for early cancer detection, with ensemble methods, neural networks and random forests achieving the best overall performance. Fragmentomic features provide the highest sensitivity.

PMID:41930854 | DOI:10.1016/j.ejca.2026.116699

J Intern Med. 2026 Apr 3. doi: 10.1111/joim.70092. Online ahead of print.

ABSTRACT

Tuberculosis (TB) remains a major global health challenge, with multi-drug antibiotic regimens as the current standard of care. While effective at killing Mycobacterium tuberculosis, these treatments do not resolve persistent inflammation, prevent lung damage, or reverse immune dysregulation that contribute to poor outcomes and disease recurrence. Precision medicine offers a promising alternative but requires deeper insight into disease mechanisms to enable tailored interventions. This comprehensive review introduces the concept of immune endotyping to define the underlying disease mechanisms as tools to decode clinical and immunological heterogeneity in TB. TB displays a wide spectrum of clinical phenotypes, from latent or asymptomatic infection to mild or severe disease with characteristic non-cavitary or cavitary lung pathology. Instead, distinct immune endotypes capture the diverse biological pathways that shape disease progression and treatment response. Similar clinical presentations may arise from different immune dysfunctions, underscoring the need to move beyond broad phenotypic classifications. Advances in multi-omics and computational analyses uncover immune signatures that enable stratification for host-directed therapies (HDTs) targeting hyperinflammation, immunosuppression, coagulopathy or metabolic exhaustion. Integrating clinical, radiological, and immunological data through multimodal profiling is essential for developing personalized interventions. We also explore how endotyping has transformed treatment in other diseases, offering valuable insights for TB. Additionally, we present examples of how putative immune endotypes may be targeted with appropriate HDTs. In summary, this review underscores the potential of immune endotypes to advance precision medicine in TB, moving beyond one-size-fits-all treatment to improve outcomes, especially in severe and drug-resistant cases.

PMID:41930636 | DOI:10.1111/joim.70092