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17 pages, 3892 KB  
Article
Transformer-Driven Semi-Supervised Learning for Prostate Cancer Histopathology: A DINOv2–TransUNet Framework
by Rubina Akter Rabeya, Jeong-Wook Seo, Nam Hoon Cho, Hee-Cheol Kim and Heung-Kook Choi
Mach. Learn. Knowl. Extr. 2026, 8(2), 26; https://doi.org/10.3390/make8020026 (registering DOI) - 23 Jan 2026
Abstract
Prostate cancer is diagnosed through a comprehensive study of histopathology slides, which takes time and requires professional interpretation. To minimize this load, we developed a semi-supervised learning technique that combines transformer-based representation learning and a custom TransUNet classifier. To capture a wide range [...] Read more.
Prostate cancer is diagnosed through a comprehensive study of histopathology slides, which takes time and requires professional interpretation. To minimize this load, we developed a semi-supervised learning technique that combines transformer-based representation learning and a custom TransUNet classifier. To capture a wide range of morphological structures without manual annotation, our method pretrains DINOv2 on 10,000 unlabeled prostate tissue patches. After receiving the transformer-derived features, a bespoke CNN-based decoder uses residual upsampling and carefully constructed skip connections to merge data from many spatial scales. Expert pathologists identified only 20% of the patches in the whole dataset; the remaining unlabeled samples were contributed by using a consistency-driven learning method that promoted reliable predictions across various augmentations. The model received precision and recall scores of 91.81% and 89.02%, respectively, and an accuracy of 93.78% on an additional test set. These results exceed the performance of a conventional U-Net and a baseline encoder–decoder network. All things considered, the localized CNN (Convolutional Neural Network) decoding and global transformer attention provide a reliable method for prostate cancer classification in situations with little annotated data. Full article
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16 pages, 5092 KB  
Article
Evaluating Adjuvant Radiation Therapy Survival Benefit in Early-Stage HER2-Positive Invasive Breast Cancer Following Breast-Conserving Surgery: A National Cohort Aligned with NRG-BR008 HERO Trial
by Jonathon S. Cummock, Ali J. Haider, Mohummad Kazmi, Waqar M. Haque, Andrew M. Farach, E. Brian Butler and Bin S. Teh
Cancers 2026, 18(3), 352; https://doi.org/10.3390/cancers18030352 (registering DOI) - 23 Jan 2026
Abstract
Background and purpose: The role of adjuvant radiation therapy (RT) in early-stage HER2-positive breast cancer treated with breast-conserving surgery (BCS) and systemic therapy remains uncertain in the era of HER2-targeted regimens. This study evaluates the survival impact of RT in patients aligned with [...] Read more.
Background and purpose: The role of adjuvant radiation therapy (RT) in early-stage HER2-positive breast cancer treated with breast-conserving surgery (BCS) and systemic therapy remains uncertain in the era of HER2-targeted regimens. This study evaluates the survival impact of RT in patients aligned with the HERO RT de-escalation trial (NRG-BR008). Materials and methods: We queried the National Cancer Database for patients with early-stage HER2-positive invasive breast carcinoma treated with BCS and systemic therapy, stratified into HERO trial-aligned cohorts: Arm 1 (adjuvant systemic therapy) vs. Arm 2 (neoadjuvant systemic therapy, pathologic complete response). Within each cohort, patients receiving adjuvant RT were compared with those omitting RT. In the primary analysis, patients were propensity score matched (PSM) on demographics, diagnosis years, tumor characteristics, and trial stratification variables. Inverse probability of treatment weighting (IPTW) was additionally performed as a sensitivity analysis. Overall survival was evaluated using Kaplan–Meier, Cox regression, and restricted mean survival time (RMST). Results: In Arm 1 (818 patients, 94 deaths), 5-year OS was 96.9% with RT vs. 88.0% without RT, and 10-year OS was 94.3% vs. 68.5% (log-rank p < 0.001). RT omission was associated with higher mortality in the PSM Cox model (HR, 4.78; 95% CI, 2.84–8.02; p < 0.001), with an RMST advantage favoring RT of +2.86 months at 5 years and +12.55 months at 10 years (p < 0.001). In Arm 2 (176 patients, 10 deaths), 5-year OS was 97.6% with RT vs. 91.1% without RT, and OS at 107 months was 94.8% vs. 91.1% (log-rank p = 0.13). RT omission was not statistically significant in the PSM Cox model (HR, 3.40; 95% CI, 0.82–14.05; p = 0.09), though RMST favored RT (+1.83 months at 5 years, p = 0.004; +3.91 months at 107 months, p = 0.03). IPTW analyses were directionally consistent in Arm 1 (HR, 3.26; 95% CI, 2.52–4.21; p < 0.001) and inconclusive in Arm 2 (HR, 1.78; 95% CI, 0.80–3.95; p = 0.16). Conclusions: In this HERO-aligned national cohort, RT omission was associated with inferior OS in patients treated with adjuvant systemic therapy after BCS. Findings in the neoadjuvant pCR cohort were imprecise and hypothesis-generating. Given the retrospective registry design, lack of recurrence-specific endpoints, and potential residual confounding, results should not be interpreted as causal but support continued RT use outside prospective de-escalation trials. Full article
(This article belongs to the Special Issue Personalized Radiotherapy in Cancer Care (2nd Edition))
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29 pages, 12304 KB  
Article
DyVarMap: Integrating Conformational Dynamics and Interpretable Machine Learning for Cancer-Associated Missense Variant Classification in FGFR2
by Yiyang Lian and Amarda Shehu
Bioengineering 2026, 13(1), 126; https://doi.org/10.3390/bioengineering13010126 - 22 Jan 2026
Abstract
Accurate interpretation of missense variants in cancer-associated genes remains a critical challenge in precision oncology, as most sequence-based predictors lack mechanistic explanations. Receptor tyrosine kinases like FGFR2 exemplify this problem: their function depends on conformational dynamics, yet most variants remain classified as variants [...] Read more.
Accurate interpretation of missense variants in cancer-associated genes remains a critical challenge in precision oncology, as most sequence-based predictors lack mechanistic explanations. Receptor tyrosine kinases like FGFR2 exemplify this problem: their function depends on conformational dynamics, yet most variants remain classified as variants of uncertain significance (VUS). In this paper we present DyVarMap, an interpretable structural-learning framework that integrates AlphaFold2-based ensemble generation with physics-driven refinement, manifold learning, and supervised classification using five biophysically motivated geometric features. Applied to FGFR2, the framework generates diverse conformational ensembles, identifies metastable states through nonlinear dimensionality reduction, and classifies pathogenicity while providing mechanistic attributions via SHAP analysis. External validation on ten kinase-domain variants yields an AUROC of 0.77 with superior calibration (Brier score = 0.108) compared to PolyPhen-2 (0.125) and AlphaMissense (0.132). Feature importance analysis consistently identifies K659–E565 salt-bridge distance and DFG motif dihedral angles as top predictors, directly linking predictions to known activation mechanisms. Case studies of borderline variants (A628T, E608K, L618F) demonstrate the framework’s ability to provide structurally coherent mechanistic explanations. DyVarMap bridges the gap between static structure prediction and dynamics-aware functional assessment, generating testable hypotheses for experimental validation and demonstrating the value of incorporating conformational dynamics into variant effect prediction for precision oncology. Full article
(This article belongs to the Special Issue Machine Learning in Precision Oncology: Innovations and Applications)
26 pages, 582 KB  
Article
Symmetric Double Normal Models for Censored, Bounded, and Survival Data: Theory, Estimation, and Applications
by Guillermo Martínez-Flórez, Hugo Salinas and Javier Ramírez-Montoya
Mathematics 2026, 14(2), 384; https://doi.org/10.3390/math14020384 (registering DOI) - 22 Jan 2026
Abstract
We develop a unified likelihood-based framework for limited outcomes built on the two-piece normal family. The framework includes a censored specification that accommodates boundary inflation, a doubly truncated specification on (0,1) for rates and proportions, and a survival formulation [...] Read more.
We develop a unified likelihood-based framework for limited outcomes built on the two-piece normal family. The framework includes a censored specification that accommodates boundary inflation, a doubly truncated specification on (0,1) for rates and proportions, and a survival formulation with a log-two-piece normal baseline and Gamma frailty to account for unobserved heterogeneity. We derive closed-form building blocks (pdf, cdf, survival, hazard, and cumulative hazard), full log-likelihoods with score functions and observed information, and stable reparameterizations that enable routine optimization. Monte Carlo experiments show a small bias and declining RMSE with increasing sample size; censoring primarily inflates the variability of regression coefficients; the scale parameter remains comparatively stable, and the shape parameter is most sensitive under heavy censoring. Applications to HIV-1 RNA with a detection limit, household food expenditure on (0,1), labor-supply hours with a corner solution, and childhood cancer times to hospitalization demonstrate improved fit over Gaussian, skew-normal, and beta benchmarks according to AIC/BIC/CAIC and goodness-of-fit diagnostics, with model-implied censoring closely matching the observed fraction. The proposed formulations are tractable, flexible, and readily implementable with standard software. Full article
(This article belongs to the Section D1: Probability and Statistics)
19 pages, 7426 KB  
Article
Promoter Methylation–Expression Coupling of Gliogenesis Genes in IDH-Wildtype Glioblastoma: Longitudinal Analysis and Prognostic Value
by Roxana Radu, Ligia Gabriela Tataranu, Anica Dricu and Oana Alexandru
Int. J. Mol. Sci. 2026, 27(2), 1112; https://doi.org/10.3390/ijms27021112 - 22 Jan 2026
Abstract
Glioblastoma (GBM) shows extensive epigenetic heterogeneity. In IDH-wildtype (IDH-WT) GBM, promoter DNA methylation may regulate lineage programs influencing tumor evolution and prognosis; here, we systematically profiled promoter-level methylation dynamics across longitudinal tumors. Genome-wide DNA methylation data were obtained from the [...] Read more.
Glioblastoma (GBM) shows extensive epigenetic heterogeneity. In IDH-wildtype (IDH-WT) GBM, promoter DNA methylation may regulate lineage programs influencing tumor evolution and prognosis; here, we systematically profiled promoter-level methylation dynamics across longitudinal tumors. Genome-wide DNA methylation data were obtained from the publicly available Gene Expression Omnibus (GEO; GSE279073) dataset, comprising a longitudinal cohort of 226 IDH-wildtype glioblastomas profiled on the Illumina Infinium EPIC 850K array across primary and recurrent stages at the University of California, San Francisco. From 333 Gene Ontology gliogenesis-annotated genes (GO:0042063), a 48-gene promoter panel was derived, with ≥2 probes per gene. Promoter methylation was summarized as the median β-value and tested using one-sample Wilcoxon with FDR correction. Functional enrichment, longitudinal variation, and patient-level methylation burden were assessed. Validation analyses were performed using independent IDH-wildtype GBM datasets from The Cancer Genome Atlas (RNA-seq and 450K methylation; n = 347). Promoter hypomethylation predominated across all stages, with 25 genes consistently hypomethylated and 7 hypermethylated. Functional enrichment highlighted gliogenesis, glial cell differentiation, neurogenesis, and Notch-related signaling. In TCGA, promoter methylation inversely correlated with expression for 11 of 33 genes (FDR < 0.05). An Expression Score contrasting hypomethylated and hypermethylated genes was positively associated with improved overall survival, where higher scores predicted better outcome (HR = 0.87, p = 0.016; Q4 vs. Q1 HR = 0.68, p = 0.025), and a complementary Methylation Score showed that higher promoter hypermethylation predicted poorer outcome (HR = 1.73, p < 0.001). CNTN2 and TSPAN2 were adverse prognostic genes (FDR < 0.05). The Expression Score was highest in Proneural tumors and lowest in Mesenchymal tumors (p < 0.001), reflecting a proneural-like state associated with better prognosis. Promoter methylation within gliogenesis genes defines a stable yet prognostically informative epigenetic signature in IDH-WT GBM. Hypomethylation promotes transcriptional activation and a favorable outcome, whereas hypermethylation represses lineage programs and predicts poorer survival. Full article
(This article belongs to the Special Issue Hallmarks of Cancer: Emerging Insights and Innovations)
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15 pages, 647 KB  
Study Protocol
Non-Invasive Detection of Prostate Cancer with Novel Time-Dependent Diffusion MRI and AI-Enhanced Quantitative Radiological Interpretation: PROS-TD-AI
by Baltasar Ramos, Cristian Garrido, Paulette Narváez, Santiago Gelerstein Claro, Haotian Li, Rafael Salvador, Constanza Vásquez-Venegas, Iván Gallegos, Víctor Castañeda, Cristian Acevedo, Gonzalo Cárdenas and Camilo G. Sotomayor
J. Imaging 2026, 12(1), 53; https://doi.org/10.3390/jimaging12010053 (registering DOI) - 22 Jan 2026
Abstract
Prostate cancer (PCa) is the most common malignancy in men worldwide. Multiparametric MRI (mpMRI) improves the detection of clinically significant PCa (csPCa); however, it remains limited by false-positive findings and inter-observer variability. Time-dependent diffusion (TDD) MRI provides microstructural information that may enhance csPCa [...] Read more.
Prostate cancer (PCa) is the most common malignancy in men worldwide. Multiparametric MRI (mpMRI) improves the detection of clinically significant PCa (csPCa); however, it remains limited by false-positive findings and inter-observer variability. Time-dependent diffusion (TDD) MRI provides microstructural information that may enhance csPCa characterization beyond standard mpMRI. This prospective observational diagnostic accuracy study protocol describes the evaluation of PROS-TD-AI, an in-house developed AI workflow integrating TDD-derived metrics for zone-aware csPCa risk prediction. PROS-TD-AI will be compared with PI-RADS v2.1 in routine clinical imaging using MRI-targeted prostate biopsy as the reference standard. Full article
(This article belongs to the Section Medical Imaging)
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12 pages, 804 KB  
Article
Total Neoadjuvant Therapy Versus Conventional Chemoradiotherapy in Rectal Cancer: Impact on Tumor Regression Grade and the Predictive Value of CEA
by Aikaterini Sarafi, Aikaterini Leventi, Klaountia Athitaki, Konstantinos Stamou, Ioannis Papaconstantinou and Dimitrios Korkolis
Medicina 2026, 62(1), 226; https://doi.org/10.3390/medicina62010226 (registering DOI) - 22 Jan 2026
Abstract
Background and Objectives: The introduction of total neoadjuvant therapy (TNT) in the preoperative stage has been associated with improved oncological outcomes. However, TNT may lead to tissue fibrosis and be accompanied by increased difficulty during surgery. Additionally, predicting tumor response to neoadjuvant [...] Read more.
Background and Objectives: The introduction of total neoadjuvant therapy (TNT) in the preoperative stage has been associated with improved oncological outcomes. However, TNT may lead to tissue fibrosis and be accompanied by increased difficulty during surgery. Additionally, predicting tumor response to neoadjuvant therapy is crucial for identifying patients who may achieve a complete pathological response (pCR) or qualify for organ-preserving strategies. The aim of this study is to evaluate the effect of TNT versus conventional chemoradiotherapy (CRT) on tumor regression grade (TRG) and the association between preoperative carcinoembryonic antigen (CEA) levels and good tumor response. A secondary endpoint is to investigate the effect of TNT on surgical difficulty, using indirect indicators like the quality of total mesorectal excision (TME), circumferential resection margin (CRM), and achievement of R0 resection. Materials and Methods: This is a retrospective, single-center study including 93 patients with locally advanced rectal cancer who received either TNT (n = 43) or CRT (n = 50). Results: The TNT group, compared to the CRT group, demonstrated a significantly higher rate of pCR (TRG0) (37.2% vs. 18%, p = 0.038) and good tumor regression (TRG 0–1) (53.5% vs. 28%, p = 0.019). Furthermore, patients with CEA < 5 ng/mL showed significantly higher rates of good tumor response (TRG 0–1) compared to those with CEA ≥ 5 ng/mL (45.3% vs. 16.7%, p = 0.032). When further categorized by treatment type, CEA levels did not demonstrate statistically significant differences Lastly, increased surgical difficulty could not be established, as no significant differences were observed in terms of positive CRM rates, R0 resection, and TME quality between groups. Conclusions: TNT was associated with improved TRG scores compared to CRT without increasing surgical difficulty. Lower pre-treatment CEAs were linked to better tumor response, irrespective of the type of treatment. These findings support the oncological benefit of TNT and suggest that CEA may have some predictive value for treatment response. Full article
(This article belongs to the Special Issue Novel Insights in Laparoscopic Surgery of Colorectal Carcinoma)
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12 pages, 1222 KB  
Article
Impact of Deep-Learning-Based Respiratory Motion Correction on [18F] FDG PET/CT Test–Retest Reliability and Consistency of Tumor Quantification in Patients with Lung Cancer
by Shijia Weng, Limei Jiang, Runze Wu, Yuanyan Cao, Yuan Li and Qian Wang
Biomedicines 2026, 14(1), 245; https://doi.org/10.3390/biomedicines14010245 - 21 Jan 2026
Abstract
Objectives: Respiratory motion degrades the quantitative accuracy and test–retest (TRT) reliability of fluorine-18 fluorodeoxyglucose ([18F] FDG) positron emission tomography (PET)/computed tomography (CT) in lung cancer. This study investigated whether a deep-learning-based respiratory motion correction (RMC) method improves the TRT reliability and [...] Read more.
Objectives: Respiratory motion degrades the quantitative accuracy and test–retest (TRT) reliability of fluorine-18 fluorodeoxyglucose ([18F] FDG) positron emission tomography (PET)/computed tomography (CT) in lung cancer. This study investigated whether a deep-learning-based respiratory motion correction (RMC) method improves the TRT reliability and image quality of [18F] FDG PET tumor quantification compared with non-motion-corrected (NMC) reconstructions. Methods: Thirty-one patients with primary lung cancer underwent three PET acquisitions: whole body free breathing (Scan1), thoracic free breathing (Scan2), and thoracic controlled breathing (ScanCB). Each dataset was reconstructed with and without RMC. Visual assessments of liver motion artifacts, lesion clarity, and PET-CT co-registration were scored. Lung tumors were segmented to derive standardized uptake value max (SUVmax), SUVmean, metabolic tumor volume (MTV), PET-derived lesion length (PLL), and total lesion glycolysis (TLG). Visual image scores and TRT reliability of tumor quantification were compared using Kruskal–Wallis one-way analysis of variance and intraclass correlation coefficients (ICCs). Results: RMC reconstructions achieved higher visual scores of lesion clarity and PET-CT co-registration across all lung lobes and significantly reduced liver motion artifacts compared with NMC reconstructions. Differences in SUVmax, SUVmean, PLL, MTV, and TLG between Scan2 and ScanCB were significantly smaller with RMC than with NMC. ICCs for SUVmax, SUVmean, MTV, and TLG were higher between scans with RMC than NMC reconstructions, indicating improved TRT reliability. Conclusions: The deep-learning-based RMC method improved the image quality and TRT reproducibility of [18F] FDG PET/CT quantification in lung cancer, supporting its potential for routine adoption in therapy-response assessments. Full article
(This article belongs to the Section Molecular and Translational Medicine)
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31 pages, 1700 KB  
Review
Prospective of Colorectal Cancer Screening, Diagnosis, and Treatment Management Using Bowel Sounds Leveraging Artificial Intelligence
by Divyanshi Sood, Surbhi Dadwal, Samiksha Jain, Iqra Jabeen Mazhar, Bipasha Goyal, Chris Garapati, Sagar Patel, Zenab Muhammad Riaz, Noor Buzaboon, Ayushi Mendiratta, Avneet Kaur, Anmol Mohan, Gayathri Yerrapragada, Poonguzhali Elangovan, Mohammed Naveed Shariff, Thangeswaran Natarajan, Jayarajasekaran Janarthanan, Shreshta Agarwal, Sancia Mary Jerold Wilson, Atishya Ghosh, Shiva Sankari Karuppiah, Joshika Agarwal, Keerthy Gopalakrishnan, Swetha Rapolu, Venkata S. Akshintala and Shivaram P. Arunachalamadd Show full author list remove Hide full author list
Cancers 2026, 18(2), 340; https://doi.org/10.3390/cancers18020340 - 21 Jan 2026
Abstract
Background: Colorectal cancer (CRC) is the second leading cause of cancer-related mortality worldwide, accounting for approximately 10% of all cancer cases. Despite the proven effectiveness of conventional screening modalities such as colonoscopy and fecal immunochemical testing (FIT), their invasive nature, high cost, and [...] Read more.
Background: Colorectal cancer (CRC) is the second leading cause of cancer-related mortality worldwide, accounting for approximately 10% of all cancer cases. Despite the proven effectiveness of conventional screening modalities such as colonoscopy and fecal immunochemical testing (FIT), their invasive nature, high cost, and limited patient compliance hinder widespread adoption. Recent advancements in artificial intelligence (AI) and bowel sound-based signal processing have enabled non-invasive approaches for gastrointestinal diagnostics. Among these, bowel sound analysis—historically considered subjective—has reemerged as a promising biomarker using digital auscultation and machine learning. Objective: This review explores the potential of AI-powered bowel sound analytics for early detection, screening, and characterization of colorectal cancer. It aims to assess current methodologies, summarize reported performance metrics, and highlight translational opportunities and challenges in clinical implementation. Methods: A narrative review was conducted across PubMed, Scopus, Embase, and Cochrane databases using the terms colorectal cancer, bowel sounds, phonoenterography, artificial intelligence, and non-invasive diagnosis. Eligible studies involving human bowel sound-based recordings, AI-based sound analysis, or machine learning applications in gastrointestinal pathology were reviewed for study design, signal acquisition methods, AI model architecture, and diagnostic accuracy. Results: Across studies using convolutional neural networks (CNNs), gradient boosting, and transformer-based models, reported diagnostic accuracies ranged from 88% to 96%. Area under the curve (AUC) values were ≥0.83, with F1 scores between 0.71 and 0.85 for bowel sound classification. In CRC-specific frameworks such as BowelRCNN, AI models successfully differentiate abnormal bowel sound intervals and spectral patterns associated with tumor-related motility disturbances and partial obstruction. Distinct bowel sound-based signatures—such as prolonged sound-to-sound intervals and high-pitched “tinkling” proximal to lesions—demonstrate the physiological basis for CRC detection through bowel sound-based biomarkers. Conclusions: AI-driven bowel sound analysis represents an emerging, exploratory research direction rather than a validated colorectal cancer screening modality. While early studies demonstrate physiological plausibility and technical feasibility, no large-scale, CRC-specific validation studies currently establish sensitivity, specificity, PPV, or NPV for cancer detection. Accordingly, bowel sound analytics should be viewed as hypothesis-generating and potentially complementary to established screening tools, rather than a near-term alternative to validated modalities such as FIT, multitarget stool DNA testing, or colonoscopy. Full article
(This article belongs to the Section Methods and Technologies Development)
14 pages, 590 KB  
Article
Behaviour Change for Physical Activity Is Feasible and Effective in Women Living with Metastatic Breast Cancer: A Pilot Two-Arm Randomised Trial
by Mark Liu, Sharon Kilbreath, Jasmine Yee, Jane Beith and Elizabeth Dylke
Cancers 2026, 18(2), 338; https://doi.org/10.3390/cancers18020338 - 21 Jan 2026
Abstract
Background/Objectives: Physical activity benefits women with metastatic breast cancer. Past trials are typically well-resourced and supervised, but home-based interventions may be preferable and more accessible. This pilot trial evaluated the feasibility and preliminary efficacy of a remotely delivered behaviour change intervention aiming to [...] Read more.
Background/Objectives: Physical activity benefits women with metastatic breast cancer. Past trials are typically well-resourced and supervised, but home-based interventions may be preferable and more accessible. This pilot trial evaluated the feasibility and preliminary efficacy of a remotely delivered behaviour change intervention aiming to increase physical activity for women with metastatic breast cancer. Methods: A 12-week, two-arm trial involved 20 women with metastatic breast cancer randomised 1:1 to a generic recommendation group or behaviour change group. Both groups received a physical activity recommendation, Fitbit® watch, diary, and nine phone/video call sessions. The behaviour change group received individualised advice around physical activity benefits, motivation, barriers, and social support; the generic recommendation group completed a recurring symptom questionnaire. Feasibility outcomes were recruitment, retention and adherence rates. Acceptability was evaluated with a structured interview at trial completion. Preliminary efficacy outcomes included 5-day Actigraph wear, 6 min walk distance, 30 s sit-to-stands, and questionnaires for self-reported physical activity, quality-of-life, fatigue, behavioural factors, and patient-specific function. Results: Recruitment, retention, and adherence rates were 63% (n = 20/32), 80% (n = 16/20), and 76% (137/180 sessions), respectively. Participants across both groups reported that participation was acceptable, and their behaviour change was perceived as sustainable. Preliminary change scores for efficacy measures favoured the behaviour change group, except some quality-of-life and behavioural factor subscales. Conclusions: Participants were receptive to the trial, and feasibility and efficacy measures were positive. This indicates that a behaviour change intervention for unsupervised physical activity is acceptable and can be beneficial to women with metastatic breast cancer, warranting further exploration. Full article
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18 pages, 3124 KB  
Article
Diet–Microbiome Relationships in Prostate-Cancer Survivors with Prior Androgen Deprivation-Therapy Exposure and Previous Exercise Intervention Enrollment
by Jacob Raber, Abigail O’Niel, Kristin D. Kasschau, Alexandra Pederson, Naomi Robinson, Carolyn Guidarelli, Christopher Chalmers, Kerri Winters-Stone and Thomas J. Sharpton
Microorganisms 2026, 14(1), 251; https://doi.org/10.3390/microorganisms14010251 - 21 Jan 2026
Abstract
The gut microbiome is a modifiable factor in cancer survivorship. Diet represents the most practical intervention for modulating the gut microbiome. However, diet–microbiome relationships in prostate-cancer survivors remain poorly characterized. We conducted a comprehensive analysis of diet–microbiome associations in 79 prostate-cancer survivors (ages [...] Read more.
The gut microbiome is a modifiable factor in cancer survivorship. Diet represents the most practical intervention for modulating the gut microbiome. However, diet–microbiome relationships in prostate-cancer survivors remain poorly characterized. We conducted a comprehensive analysis of diet–microbiome associations in 79 prostate-cancer survivors (ages 62–81) enrolled in a randomized exercise intervention trial, 59.5% of whom still have active metastatic disease. Dietary intake was assessed using the Diet History Questionnaire (201 variables) and analyzed using three validated dietary pattern scores: Mediterranean Diet Adherence Score (MEDAS), Healthy Eating Index-2015 (HEI-2015), and the Mediterranean-Dash Intervention for Neurodegenerative Delay (MIND) diet score. Gut microbiome composition was characterized via 16S rRNA sequencing. Dimensionality reduction strategies, including theory-driven diet scores and data-driven machine learning (Random Forest, and Least Absolute Shrinkage and Selection Operator (LASSO)), were used. Statistical analyses included beta regression for alpha diversity, Permutational Multivariate Analysis of Variance (PERMANOVA) for beta diversity (both Bray–Curtis and Sørensen metrics), and Microbiome Multivariable Associations with Linear Models (MaAsLin2) with negative binomial regression for taxa-level associations. All models tested interactions with exercise intervention, APOLIPOPROTEIN E (APOE) genotype, and testosterone levels. There was an interaction between MEDAS and exercise type on gut alpha diversity (Shannon: p = 0.0022), with stronger diet–diversity associations in strength training and Tai Chi groups than flexibility controls. All three diet-quality scores predicted beta diversity (HEI p = 0.002; MIND p = 0.025; MEDAS p = 0.034) but not Bray–Curtis (abundance-weighted) distance, suggesting diet shapes community membership rather than relative abundances. Taxa-level analysis revealed 129 genera with diet associations or diet × host factor interactions. Among 297 dietary variables tested for cognitive outcomes, only caffeine significantly predicted Montreal Cognitive Assessment (MoCA) scores after False Discovery Rate (FDR) correction (p = 0.0009, q = 0.014) through direct pathways beneficial to cognitive performance without notable gut microbiome modulation. In cancer survivors, dietary recommendations should be tailored to exercise habits, genetic background, and hormonal status. Full article
(This article belongs to the Special Issue The Interactions Between Nutrients and Microbiota)
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19 pages, 4422 KB  
Article
In Vitro and In Vivo Efficacy of Epithelial Barrier-Promoting Barriolides as Potential Therapy for Ulcerative Colitis
by Jon P. Joelsson, Michael J. Parnham, Laurène Froment, Aude Rapet, Andreas Hugi, Janick Stucki, Nina Hobi and Jennifer A. Kricker
Biomedicines 2026, 14(1), 237; https://doi.org/10.3390/biomedicines14010237 - 21 Jan 2026
Abstract
Background/Objectives: Ulcerative colitis (UC) is an inflammatory bowel disease and a major cause of ulcers and chronic inflammation in the colon and rectum. Recurring symptoms include abdominal pain, rectal bleeding, and diarrhoea, and patients with UC are at a higher risk of [...] Read more.
Background/Objectives: Ulcerative colitis (UC) is an inflammatory bowel disease and a major cause of ulcers and chronic inflammation in the colon and rectum. Recurring symptoms include abdominal pain, rectal bleeding, and diarrhoea, and patients with UC are at a higher risk of developing comorbidities such as colorectal cancer and poor mental health. In UC, the decreased diversity and changed metabolic profile of gut microbiota, along with a diminished mucus layer, leads to disruption of the underlying epithelial barrier, with an ensuing excessive and detrimental inflammatory response. Treatment options currently rely on drugs that reduce the inflammation, but less emphasis has been placed on improving the resilience of the epithelial barrier. Macrolide antibiotics exhibit epithelial barrier-enhancing capacities unrelated to their antibacterial properties. Methods: We investigated two novel barriolides, macrolides with reduced antibacterial effects in common bacterial strains. Gut epithelial cell barrier resistance in the Caco-2 cell line, with and without co-culture with mucus-producing HT-29 cells, was increased when treated with barriolides. Using AXGut-on-Chip technology with inflammatory cytokine-stimulated Caco-2/HT-29 co-cultures, the effectiveness of the barriolides was confirmed. Lastly, we reveal the barrier-enhancing and inflammation-reducing effects of the barriolides in a dextran-sulphate sodium (DSS)-induced colitis mouse model. Results: We show the predictive power of the novel AXGut-on-Chip system and the effectiveness of the novel barriolides. Indications include reduced inflammatory response, increased epithelial barrier and decreased overall clinical score. Conclusions: The results of this study indicate the notion that barriolides could be used as a treatment option for UC. Full article
(This article belongs to the Section Drug Discovery, Development and Delivery)
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16 pages, 8077 KB  
Article
The Senescence-SASP Landscape in Colon Adenocarcinoma: Prognostic and Therapeutic Implications
by Tianyu Ren, Suyouwei Gao, Yangrong Feng, Yangyang Xu, Xinyi Mi, Jite Shi and Man Chu
Curr. Issues Mol. Biol. 2026, 48(1), 114; https://doi.org/10.3390/cimb48010114 - 21 Jan 2026
Abstract
Cellular senescence, characterized by permanent cell cycle arrest, significantly influences cancer development, immune regulation, and progression. However, the precise mechanisms by which senescence contributes to colorectal cancer prognosis remain to be fully elucidated. By integrating expression profiles of senescence-related and prognostic genes in [...] Read more.
Cellular senescence, characterized by permanent cell cycle arrest, significantly influences cancer development, immune regulation, and progression. However, the precise mechanisms by which senescence contributes to colorectal cancer prognosis remain to be fully elucidated. By integrating expression profiles of senescence-related and prognostic genes in colon adenocarcinoma (COAD) patients, we formulated and confirmed a nine-gene cellular senescence-related signature (CSRS) that integrates senescence-associated and prognosis-predictive genes using data from the CellAge, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). A cell senescence-related prognostic formula was developed as follows: CSRS = (CASP2 × 0.2098) + (CDKN2A × 0.1196) + (FOXD1 × 0.1472) + (ING5 × 0.3723) + (OXTR × 0.0786) + (PHGDH × 0.1408) + (SERPINE1 × 0.1127) + (SNAI1 × 0.1034) + (LIMK1 × 0.0747). In a multivariate Cox proportional hazards model, the CSRS score, age and TNM stage were all identified as significant independent indicators for overall survival, affirming their prognostic value in colorectal cancer. The CSRS-high group exhibited significantly up-regulated senescence-associated secretory phenotype (SASP) and immune cell infiltration, whereas the CSRS-low group showed an apparent better response to immune-checkpoint inhibitor therapy. Our findings suggest CSRS score and its constituent genes represent potential biomarkers for prognosis and immunotherapeutic benefit in COAD patients. Extending this nine-gene set into a broader senescence-associated panel should be a next step toward delivering truly individualized treatment plans. Full article
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10 pages, 246 KB  
Article
Transition from Transrectal Systematic to Transperineal Lesion-Focused Prostate Biopsy: A Real-World Comparative Analysis
by Thibaut Long Depaquit, Federica Sordelli, Christopher Agüero, Arthur Peyrottes, Alessandro Uleri, Laurent Daniel, David Chemouni, Cyrille Bastide and Michael Baboudjian
Cancers 2026, 18(2), 332; https://doi.org/10.3390/cancers18020332 - 21 Jan 2026
Abstract
Background/Objectives: The transperineal (TP) approach has progressively replaced the transrectal (TR) approach for prostate biopsy because of its improved safety profile. However, its impact on the detection of clinically significant prostate cancer (csPCa), particularly within modern lesion-focused biopsy strategies that combine targeted and [...] Read more.
Background/Objectives: The transperineal (TP) approach has progressively replaced the transrectal (TR) approach for prostate biopsy because of its improved safety profile. However, its impact on the detection of clinically significant prostate cancer (csPCa), particularly within modern lesion-focused biopsy strategies that combine targeted and perilesional sampling, remains uncertain. We aimed to evaluate the real-world diagnostic impact of transitioning from a TR systematic-based biopsy strategy to a TP lesion-focused approach. Methods: We conducted a retrospective single-centre study including consecutive men who underwent image-guided prostate biopsy between 2018 and 2025. Only patients with a single MRI-visible lesion (PI-RADS ≥ 3) were included. Two biopsy strategies were compared: TR systematic biopsy (TR–SBx), combining targeted and systematic cores, and TP lesion-focused biopsy (TP–LFx), combining targeted and perilesional cores. The primary outcome was the detection of csPCa (Gleason Grade Group ≥ 2). Secondary outcomes included detection of Gleason Grade Group 1 cancer and negative biopsies. Inverse probability of treatment weighting (IPTW) based on a propensity score was applied to adjust for baseline differences. Doubly robust weighted logistic regression models were used, with predefined subgroup and sensitivity analyses. Results: Among 1032 included patients, 931 underwent TR–SBx and 101 TP–LFx. After restriction to the region of common support, 528 patients were retained for IPTW analyses. In the IPTW-adjusted analysis, TP–LFx was associated with higher csPCa detection compared with TR–SBx (adjusted odds ratio [OR] 2.52, 95% confidence interval [CI] 1.40–4.52; p = 0.002) and with lower detection of Gleason Grade Group 1 cancer (OR 0.50, 95% CI 0.27–0.92; p = 0.03). Subgroup analyses suggested a stronger association in patients with prior negative biopsy and in anterior or apical lesions. Conclusions: In routine clinical practice, transitioning from a transrectal systematic-based biopsy strategy to a transperineal lesion-focused approach was associated with improved detection of csPCa and reduced overdiagnosis. These findings support the consideration of transperineal, lesion-focused MRI-guided biopsy strategies in contemporary prostate cancer diagnostics. Full article
11 pages, 495 KB  
Article
Trends in the Management of Bladder Cancer with Emphasis on Frailty: A Nationwide Analysis of More Than 49,000 Patients from a German Hospital Network
by Tobias Klatte, Frederic Bold, Julius Dengler, Michela de Martino, Sven Hohenstein, Ralf Kuhlen, Andreas Bollmann, Thomas Steiner and Nora F. Dengler
Life 2026, 16(1), 169; https://doi.org/10.3390/life16010169 - 21 Jan 2026
Abstract
Background: Bladder cancer (BC) predominantly affects older patients, and their multidisciplinary treatment often includes surgical intervention. Frailty can influence treatment decisions and is associated with poorer outcomes. This study analyses trends in demographics, treatment patterns and frailty in a large, nationwide, real-world inpatient [...] Read more.
Background: Bladder cancer (BC) predominantly affects older patients, and their multidisciplinary treatment often includes surgical intervention. Frailty can influence treatment decisions and is associated with poorer outcomes. This study analyses trends in demographics, treatment patterns and frailty in a large, nationwide, real-world inpatient cohort in Germany. Methods: This retrospective observational study included a total of 49,139 consecutive patients, who received inpatient care for BC at all HELIOS hospitals in Germany between 2016 and 2022. Frailty was assessed using the Hospital Frailty Risk Score (HFRS) and categorised as low (<5), intermediate (5–15), or high (>15). Trends in HFRS, treatment modalities, and demographic variables were analysed using regression models and compared between the periods 2016–2019 and 2020–2022. Results: Of the 49,139 patients, 27,979 were treated between 2016–2019 and 21,160 between 2020–2022. Patients treated in the later period were slightly older but had a lower comorbidity index. The proportion of patients with low frailty increased (73.4% vs. 75.5%, p < 0.01), intermediate frailty decreased (23.5% vs. 21.5%, p < 0.01) and the proportion of highly frail patients remained stable at 3.0% (p = 0.95). Rates of transurethral resection declined over time, whereas rates of RC remained stable (p = 0.12). The use of systemic therapy increased (p = 0.003), particularly among low frailty elderly patients. Early intravesical chemotherapy following transurethral resection declined significantly in 2020–2022 (p < 0.001), particularly among elderly patients with high frailty. Mean length of hospital stay decreased by one day, while ICU admission rates and in-hospital mortality remained stable across time periods. Conclusions: This study shows frailty-specific changes in hospitalisation patterns and inpatient management of BC in Germany, underscoring the value of frailty assessment in population-based research. The proportion of patients classified as having low frailty increased over time. Significant changes in the use of intravesical chemotherapy and systemic therapy were associated with frailty. The decline in early intravesical chemotherapy may have implications for recurrence risk and downstream healthcare utilisation. Full article
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