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33 pages, 1735 KB  
Review
Epigenetic Plasticity in Triple-Negative Breast Cancer: Mechanisms of Therapy Resistance, Biomarkers, and Therapeutic Vulnerabilities
by Abdel Raman Alaa, Salma A. B. El-Din, Mohannad A. Farrag, Youssef Ahmed, Mohamed E. Abdel Aziz, Shaimaa Abdel-Ghany, Borros Arneth and Hussein Sabit
Biomedicines 2026, 14(9), 2013; https://doi.org/10.3390/biomedicines14092013 - 8 Sep 2026
Abstract
Triple-negative breast cancer (TNBC) is an aggressive and clinically heterogeneous breast cancer subtype characterized by the absence of estrogen receptor, progesterone receptor, and HER2 overexpression, limited targeted treatment options, early relapse, and frequent development of therapy resistance. Although TNBC often shows initial sensitivity [...] Read more.
Triple-negative breast cancer (TNBC) is an aggressive and clinically heterogeneous breast cancer subtype characterized by the absence of estrogen receptor, progesterone receptor, and HER2 overexpression, limited targeted treatment options, early relapse, and frequent development of therapy resistance. Although TNBC often shows initial sensitivity to chemotherapy, durable responses are commonly undermined by the emergence of adaptive resistant cell states rather than solely by fixed genetic mutations. This review synthesizes the role of epigenetic plasticity as a central mechanism that enables TNBC cells to dynamically reprogram transcriptional identity, survive therapeutic stress, and transition between epithelial, mesenchymal, stem-like, immune-evasive, and drug-tolerant persister phenotypes. Key epigenetic mechanisms include aberrant DNA methylation, histone acetylation and methylation, BET/BRD4-dependent transcriptional regulation, EZH2-mediated repression, SWI/SNF-dependent chromatin remodeling, non-coding RNA networks, and three-dimensional genome reorganization. These processes regulate tumor suppressor silencing, DNA-damage repair, epithelial–mesenchymal plasticity, cancer stem-cell maintenance, metabolic adaptation, immune-checkpoint regulation, and minimal residual disease. The review also highlights the translational relevance of epigenetic biomarkers, including DNA methylation signatures, circulating epigenetic markers, chromatin-accessibility profiles, and single-cell epigenomic approaches for diagnosis, prognosis, therapy prediction, and monitoring resistance evolution. Finally, therapeutic strategies targeting epigenetic plasticity are discussed, including DNMT, HDAC, BET, EZH2, KDM, and LSD1 inhibitors, with emphasis on rational combination approaches involving chemotherapy, PARP inhibitors, immunotherapy, and metabolic targeting. Overall, epigenetic plasticity represents both a major driver of TNBC resistance and a therapeutically exploitable vulnerability, provided those future strategies account for tumor heterogeneity, adaptive cell-state transitions, biomarker-guided patient selection, and combination-based treatment design. Full article
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20 pages, 5670 KB  
Review
Biomolecular Condensates Integrate Transcriptional and Epigenetic Responses to Hypoxia
by Chinmaya Kumar Patel, Ahmed Saif and Xiaojun Ren
Int. J. Mol. Sci. 2026, 27(17), 7926; https://doi.org/10.3390/ijms27177926 - 5 Sep 2026
Viewed by 228
Abstract
Hypoxia is a defining feature of physiological stress and the core of solid tumors, where aberrant vascularization limits oxygen delivery; cells respond through mechanisms that extend beyond the canonical stabilization of hypoxia-inducible factors (HIFs). Recent studies suggest that hypoxia can promote the formation [...] Read more.
Hypoxia is a defining feature of physiological stress and the core of solid tumors, where aberrant vascularization limits oxygen delivery; cells respond through mechanisms that extend beyond the canonical stabilization of hypoxia-inducible factors (HIFs). Recent studies suggest that hypoxia can promote the formation of specific biomolecular conden-sates, membraneless compartments generated through liquid–liquid phase separation in which regulatory proteins and RNAs become locally enriched at genomic regions, while chromatin mainly serves as an organizational scaffold. Transcription factors, the coacti-vators p300/CBP, Mediator, and BRD4, chromatin-modifying enzymes, and architectural RNAs such as NEAT1 and MALAT1 partition into these compartments, and their con-densation can help reorganize local chromatin structure and enhancer–promoter interac-tions. Because molecular oxygen is a shared co-substrate for the Jumonji-C histone demethylases and the ten-eleven translocation (TET) DNA dioxygenases, hypoxia reshapes histone methylation and DNA methylation in parallel, and readers that bridge these marks, including UHRF1, may participate in condensate-associated chromatin regulation. Hypoxia-driven condensation of ZHX2 rewires enhancer–promoter contacts and higher-order genome architecture, influencing cell identity, stemness, and metastatic potential, and Polycomb condensates represent another candidate epigenetic compartment that may be influenced by hypoxic signaling. These processes may be particularly important in cancer, where chronic hypoxia provides a sustained stimulus for condensate formation and epigenetic remodeling. Together, these findings support a model in which phase separation and epigenetic reprogramming are not separate layers but one integrated response to low oxygen, offering opportunities to target maladaptive condensates in disease. Full article
(This article belongs to the Special Issue Molecular Regulatory Mechanisms in the Hypoxic Environment)
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28 pages, 1571 KB  
Article
BRD3OS Dysregulation in Antiphospholipid Syndrome: Integrative Network and RNA Structural Analysis of m6A-Related Candidate Regions
by Carlos A. Guzmán-Martín, Yaneli Juárez-Vicuña, Rafael Bojalil, Evelyn Aranda-Cano, Mario Peña-Peña, Yamnia Q. Alvarez-Alvarez, Fengyang Huang, Javier González-Ramírez, Laura Aline Martínez-Martínez and Fausto Sánchez-Muñoz
Biomolecules 2026, 16(9), 1263; https://doi.org/10.3390/biom16091263 - 1 Sep 2026
Viewed by 157
Abstract
Antiphospholipid syndrome (APS) is an autoimmune disorder characterized by thrombotic and inflammatory manifestations whose molecular regulatory mechanisms remain incompletely understood. Long non-coding RNAs (lncRNAs) and N6-methyladenosine (m6A)-related regulation are increasingly recognized as components of immune gene regulation, but their involvement in APS remains [...] Read more.
Antiphospholipid syndrome (APS) is an autoimmune disorder characterized by thrombotic and inflammatory manifestations whose molecular regulatory mechanisms remain incompletely understood. Long non-coding RNAs (lncRNAs) and N6-methyladenosine (m6A)-related regulation are increasingly recognized as components of immune gene regulation, but their involvement in APS remains poorly characterized. This study investigated BRD3OS (LINC00094) expression in APS and explored its molecular and predicted structural context in relation to m6A-associated regulation. An exploratory case–control study was conducted using an initial lncRNA PCR-array discovery cohort followed by targeted RT-qPCR validation in an independent cohort. Candidate prioritization incorporated multiple expression and technical features and was evaluated through sensitivity analyses. BRD3OS expression, selected m6A regulators (METTL3, METTL14, WTAP, and FTO), inflammatory mediators, and global m6A abundance in total peripheral blood mononuclear cell (PBMC) RNA were evaluated. Bioinformatic network analysis was used to contextualize BRD3OS within APS- and m6A-related molecular systems. RNAfold and RNAplfold were used to characterize the predicted structural context and accessibility of DRACH consensus motifs, with additional analyses evaluating fragment-boundary and composite-score robustness. BRD3OS was significantly downregulated in PBMCs from patients with APS in the independent validation cohort. METTL3, METTL14, and WTAP expression was also reduced, whereas global m6A levels in total PBMC RNA were increased. These observations indicate concurrent alterations in BRD3OS expression and the broader m6A-related molecular environment but do not establish transcript-specific methylation of BRD3OS. Bioinformatic network analysis placed BRD3OS within predicted RNA-centered regulatory relationships relevant to APS. DRACH motifs exhibited heterogeneous predicted structural accessibility, with unpaired structural environments showing greater RNAplfold-derived accessibility than paired regions. Quantitative accessibility estimates were highly concordant across overlapping transcript fragments, although sensitivity analyses indicated that the identity of individual highest-ranked candidates depended on the weighting scheme. BRD3OS downregulation represents a reproducible molecular finding in APS. Concurrent alterations in global m6A abundance and selected m6A regulators suggest broader epitranscriptomic dysregulation; however, these measurements cannot establish m6A modification of BRD3OS or a causal relationship between these observations. Structural and network analyses therefore provide a hypothesis-generating framework for prioritizing candidate regions and interactions for future transcript-specific methylation mapping and functional validation. Full article
(This article belongs to the Special Issue Emerging Roles of Non-Coding RNAs in Gene Regulation and Disease)
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26 pages, 6348 KB  
Article
Combined Exendin-4 and Rituximab Treatment Improves β-Cell Function and Delays Disease Progression in NOD Mice
by Yongbin Wang, Shan He, Huan Yang, Jie Zhang, Likun Yu, Jianjun Xiong, Xingnuan Li, Jiashuo Qiu and Baicheng Ma
Biology 2026, 15(17), 1472; https://doi.org/10.3390/biology15171472 - 31 Aug 2026
Viewed by 239
Abstract
Type 1 diabetes mellitus is characterized by immune-mediated pancreatic β-cell loss and progressive impairment of insulin production. This study evaluated the effects of combined rituximab, a B-cell-directed therapy, and exendin-4, a glucagon-like peptide-1 receptor agonist, on β-cell-related function and metabolic outcomes in experimental [...] Read more.
Type 1 diabetes mellitus is characterized by immune-mediated pancreatic β-cell loss and progressive impairment of insulin production. This study evaluated the effects of combined rituximab, a B-cell-directed therapy, and exendin-4, a glucagon-like peptide-1 receptor agonist, on β-cell-related function and metabolic outcomes in experimental type 1 diabetes. Pancreatic islets isolated from NOD-scid mice were used for in vitro assessment of viability, metabolic activity, insulin secretion under high-glucose conditions, and gene expression. Female NOD mice were assigned to control, exendin-4, rituximab, or combination treatment groups and treated for approximately 20 weeks. Combined treatment showed the greatest increases in insulin-related responses in vitro. In vivo, it was associated with more stable fasting blood glucose levels, improved oral glucose tolerance, delayed progression to hyperglycemia, increased circulating insulin and C-peptide levels, and reduced glucagon, HbA1c, and LDL levels. Histological and molecular analyses further demonstrated reduced pancreatic inflammatory damage, reduced apoptosis-associated changes, and increased BrdU- and cytokeratin-18-associated signals within insulin-positive islet regions. These findings support further investigation of combined B-cell-directed and β-cell-supportive strategies for preserving islet function and delaying disease progression in type 1 diabetes. Full article
(This article belongs to the Section Medical Biology)
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27 pages, 29286 KB  
Article
BUB1 and CDK4/6 Dual Inhibition Increases Radiation Sensitivity in Glioblastoma, Lung Cancer, and Triple-Negative Breast Cancer
by Shivani Thoidingjam, Sushmitha Sriramulu, Asya Haider Muratoglu, Rhea Hede-Sakhardande, Sunita Ghosh, Anthony J. Davis, Stephen L. Brown, Farzan Siddiqui, Benjamin Movsas, Corey Speers and Shyam Nyati
Biomedicines 2026, 14(9), 1940; https://doi.org/10.3390/biomedicines14091940 - 29 Aug 2026
Viewed by 433
Abstract
Background: Solid tumors including glioblastoma (GBM), lung cancer (LC), and triple-negative breast cancer (TNBC) exhibit marked radioresistance driven by dysregulated cell-cycle control and genomic instability. Although CDK4/6 inhibitors suppress tumor proliferation, their radiosensitizing capacity is limited by persistent DNA repair. BUB1, a mitotic [...] Read more.
Background: Solid tumors including glioblastoma (GBM), lung cancer (LC), and triple-negative breast cancer (TNBC) exhibit marked radioresistance driven by dysregulated cell-cycle control and genomic instability. Although CDK4/6 inhibitors suppress tumor proliferation, their radiosensitizing capacity is limited by persistent DNA repair. BUB1, a mitotic checkpoint kinase overexpressed in aggressive cancers, has emerged as a regulator of DNA damage signaling. We tested whether co-targeting BUB1 and CDK4/6 enhances radiosensitivity across solid tumors. Methods: GBM, LC, and TNBC cell lines were treated with BUB1 inhibitor BAY1816032, CDK4/6 inhibitors ribociclib and abemaciclib, and radiation. Proliferation, clonogenic survival, immunoblotting, and combination index analyses assessed cytotoxicity and synergy. CDK4/6-resistant models were generated to examine resistance. In vivo efficacy was evaluated using SUM159 xenografts. DNA damage and homologous recombination repair were measured by gH2AX, RAD51, RPA, BrdU foci and comet assay. The resection branchpoint was assessed by phospho-RPA, with ATR inhibition and BLM or EXO1 depletion testing resection dependence. Results: BUB1 inhibition increased cytotoxicity in vitro and improved therapeutic response in vivo. Combined BUB1 and CDK4/6 inhibition showed strong synergy (C.I. < 1) and enhanced radiosensitization in RB+ models. CDK4/6-resistant cells displayed increased BUB1 expression, and BUB1 inhibition partially restored sensitivity. Mechanistically, dual inhibition intensified homologous recombination defects, marked by persistent gH2AX and altered RAD51, RPA, and BrdU dynamics, consistent with sustained single stranded DNA and impaired HR repair. Persistent RPA32 Ser33 phosphorylation reflects ATR-dependent resection that requires BLM and EXO1 at later stages, supporting sustained resection and unresolved repair leading to increased cell death. Conclusions: Dual inhibition of BUB1 and CDK4/6 represents a promising therapeutic strategy for enhancing radiosensitivity in GBM, lung cancer, and TNBC, particularly in Rb-intact settings. Full article
(This article belongs to the Section Cancer Biology and Oncology)
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21 pages, 3279 KB  
Article
Evaluation of a Modified Codend Configuration for a Marine Mammal Bycatch Reduction Device in a Midwater Trawl Gear
by Jung-Mo Jung, Bong-Jin Cha, Kyu-Suk Choi, Min-Seuk Park, Myounghee Kang and Hyun-Young Kim
Fishes 2026, 11(8), 489; https://doi.org/10.3390/fishes11080489 - 20 Aug 2026
Viewed by 288
Abstract
Marine mammal Bycatch Reduction Devices (BRDs) can result in the escape of target fish species. In the present study, a modified single-layer codend configuration developed from previous studies was evaluated using BRDs with guide net angles of 30° and 45°. Catch was collected [...] Read more.
Marine mammal Bycatch Reduction Devices (BRDs) can result in the escape of target fish species. In the present study, a modified single-layer codend configuration developed from previous studies was evaluated using BRDs with guide net angles of 30° and 45°. Catch was collected separately from the codend and the BRD cover to estimate catch loss rates and characteristics. For caught species, catch loss rates based on the number and weight of individuals were 9% and 13% for herring with the 30° guide net and 16% and 18% with the 45° guide net, respectively. For Korean pomfret, catch loss rates were 24% and 23% at 30° and 4% at 45°. These results suggest that further modification of BRD is necessary. In contrast, catch loss rates of mackerel with the 30° guide net reached 56%, whereas hairtail showed loss rates of 60% and 65% with the 45° guide net. Underwater observations indicated that catch loss was influenced by swimming behavior and entanglement with the guide net. Despite the modification of the codend to a single layer, the present study still observed high catch loss rates. However, no bycatch of marine mammals occurred during the experimental operations. Full article
(This article belongs to the Section Fishery Facilities, Equipment, and Information Technology)
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14 pages, 12214 KB  
Article
An Intact PHD Finger and PHD-BRD Interdomain Linker Are Crucial for Binding of the Chromatin Remodeler Factor TIP5 to the Histone Octamer
by Pavel Čabart
Biomolecules 2026, 16(8), 1209; https://doi.org/10.3390/biom16081209 - 19 Aug 2026
Viewed by 356
Abstract
The bromodomain adjacent to zinc finger (BAZ) family protein TIP5 (transcription termination factor I (TTF-I)/interacting protein 5) contains a plant homeodomain (PHD) zinc finger module that recognizes unmodified histone H3 lysine 4. This study demonstrates that the immobilized PHD domain recruits the histone [...] Read more.
The bromodomain adjacent to zinc finger (BAZ) family protein TIP5 (transcription termination factor I (TTF-I)/interacting protein 5) contains a plant homeodomain (PHD) zinc finger module that recognizes unmodified histone H3 lysine 4. This study demonstrates that the immobilized PHD domain recruits the histone octamer complex. Depletion of zinc cations from the finger or disruption via mutagenesis completely abolished this interaction. Interestingly, the binding ability of the depleted protein was partially recovered under high concentrations of KCl. Extending the PHD domain with a PHD-bromodomain (BRD) interdomain linker led to a substantial increase in binding affinity, with the magnitude progressively dependent on the linker length. To gain insight into these preferential binding interfaces, AlphaFold 3 structure predictions were performed. Within the histone octamer complex, histone H3 was identified as a primary, but not sole, binding partner for TIP5 partial proteins. An increase in predicted total van der Waals interactions correlated with the presence of the linker and its extension; however, an anomaly stemming from the calculated stickiness of the short linker version was encountered. Increased hydrogen-bonding in models with the short linker mirrored the observed affinity. Conversely, the long linker reduced predicted hydrogen (H)-bonds below that for the PHD alone. Finally, structural analysis of the disrupted zinc finger motif revealed the fewest hydrogen bonds. Full article
(This article belongs to the Section Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates)
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29 pages, 10497 KB  
Article
Hair Growth-Supporting and Follicle-Protective Potential of a Botanical-Based Supplement Ingredient: In Vitro, Ex Vivo, and Molecular Docking Studies
by Adrián García, Andrea Cavagnino, Pau Navarro, Olivier Gouin, Cristina Guillem, Anaïs Bobier, Cristina Calabuig and Nuria Caturla
Biomolecules 2026, 16(8), 1207; https://doi.org/10.3390/biom16081207 - 18 Aug 2026
Viewed by 1335
Abstract
Hair follicle homeostasis is influenced by hormonal pathways, the scalp microenvironment, and environmental stressors such as pollution, UV radiation, and oxidative stress. Elissara®, a polyphenol-enriched botanical ingredient, has shown benefits for scalp moisturization, barrier function, sebum regulation, and redness. Building on [...] Read more.
Hair follicle homeostasis is influenced by hormonal pathways, the scalp microenvironment, and environmental stressors such as pollution, UV radiation, and oxidative stress. Elissara®, a polyphenol-enriched botanical ingredient, has shown benefits for scalp moisturization, barrier function, sebum regulation, and redness. Building on these scalp-level benefits, we investigated Elissara’s effects on follicular signaling, survival-associated biomarkers, oxidative damage, and androgen-related pathways as potential contributors to follicular health, using in silico, in vitro, and ex vivo models. Molecular docking (AutoDock Vina) of the main Elissara bioactives (oleuropein, hydroxytyrosol, verbascoside, carnosic acid, carnosol, and quercetin) identified SRD5A2 as a favorable predicted target, with individual binding energies ranging from −8.70 to −9.73 kcal/mol, approaching finasteride/dutasteride reference values. As an exploratory approach, simultaneous multi-ligand docking showed favorable global docking outputs for several targets, indicating that multiple bioactives could be structurally accommodated within complementary regions of the binding site. In human follicle dermal papilla cells, Elissara significantly increased BrdU incorporation to 245.70% of control at 0.002% and reduced SRD5A2 protein levels by 18.48% at 0.006%. In human scalp explants, Elissara at 200 µg/mL increased β-catenin, Bcl-2, and collagen IV under basal conditions and counteracted acute PM2.5/UVA-induced alterations in β-catenin, Ki67-positive cells, Bcl-2, IGF-1, collagen IV, and protein carbonylation. Together, these findings support the potential of Elissara as a promising nutricosmetic ingredient for supporting follicular resilience through multiple follicle-relevant pathways. Clinical studies assessing hair growth outcomes are needed to determine whether these preclinical findings translate into measurable benefits. Full article
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23 pages, 5009 KB  
Article
Longitudinal Tumor, Vascular, and Immune Cell Response in Two Rat Prostate Carcinomas After Isoeffective Photon, Proton, and Carbon Ion Irradiation: Impact of Linear Energy Transfer, Dose Level, and Hypoxia
by Michaela Schmitt, Ina Kurth, Christin Glowa, Manuela Dittrich, Rosemarie Euler-Lange, Stephan Brons, Peter Peschke and Christian P. Karger
Cancers 2026, 18(16), 2653; https://doi.org/10.3390/cancers18162653 - 17 Aug 2026
Viewed by 263
Abstract
Background/Objectives: High linear energy transfer (LET) carbon ions achieved more effective and biologically robust tumor control than photons in preclinical prostate cancer models; however, the longitudinal development of histopathological parameters remains insufficiently characterized, limiting the selection of the optimal treatment modality in [...] Read more.
Background/Objectives: High linear energy transfer (LET) carbon ions achieved more effective and biologically robust tumor control than photons in preclinical prostate cancer models; however, the longitudinal development of histopathological parameters remains insufficiently characterized, limiting the selection of the optimal treatment modality in patients. This study analyzed the temporal histological patterns after isoeffective photon, proton, and carbon ion irradiations. Methods: Two Dunning R3327 prostate carcinoma sublines (H, HI) grown subcutaneously in male Copenhagen rats received single-fraction isoeffective curative photon or carbon ion doses. For HI-tumors, the effectiveness of isoeffective curative proton doses and isoeffective subcurative photon and carbon ion doses was additionally investigated. Tumors were collected prior and up to 3 weeks after irradiation and processed for quantitative histology of proliferation (BrdU), DNA damage (γH2AX), hypoxia (pimonidazole), vascular (CD31), and immune cell (CD3, CD68) markers. Results: All modalities induced an early peak in γH2AX+ tumor cells and a pronounced suppression of BrdU+ cells, with more sustained effects after isoeffective carbon ions doses, particularly in the HI-tumors. These findings, however, differed strongly between hypoxic and oxic micro-environments. Vascular parameters, diffusion distances, and global and compartment-specific hypoxic fractions showed distinct temporal dynamics between photons and carbon ions in HI-tumors, whereas H-tumors exhibited more moderate and reversible changes. At curative carbon ion doses, there was a late rebound of BrdU-positive tumor cells and increased CD68+ macrophage accumulation in chronically hypoxic regions. CD3+ T cells showed a biphasic decrease-recovery pattern in HI-tumors largely independent of radiation quality and oxygenation. Conclusions: Longitudinal histology revealed modality- and tumor-line-specific trajectories of tumor, vascular, hypoxic, and immune responses after isoeffective photon, proton, and carbon ion irradiations in prostate carcinoma. The more persistent tumor cell damage and distinct vascular response, together with late proliferative and macrophage rebounds under chronic hypoxia after carbon ions, provide mechanistic support for the increased biological effectiveness and highlight hypoxia-driven repopulation and inflammation as key processes. Full article
(This article belongs to the Special Issue Proton and Light Ion Therapy for Cancer)
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24 pages, 3933 KB  
Article
Physioxia Reprograms Glioblastoma Cells Enhancing Migration and Altering Therapeutic Sensitivity
by Natasha Hockaden, Elise O’Herron, Dylan Zhou, Nicholas Downing, Jacob Kurlander, Margaret Heffernan, Scott Cooper and Angela Richardson
Cancers 2026, 18(16), 2620; https://doi.org/10.3390/cancers18162620 - 14 Aug 2026
Viewed by 677
Abstract
Background/Objectives: Glioblastoma is an aggressive primary brain tumor that develops within a chronically low-oxygen microenvironment, yet most preclinical studies are performed under atmospheric oxygen conditions that poorly reflect in vivo physiology. This study investigated how sustained culture under physiological oxygen tension (physioxia) influences [...] Read more.
Background/Objectives: Glioblastoma is an aggressive primary brain tumor that develops within a chronically low-oxygen microenvironment, yet most preclinical studies are performed under atmospheric oxygen conditions that poorly reflect in vivo physiology. This study investigated how sustained culture under physiological oxygen tension (physioxia) influences glioblastoma cell behavior, signaling, and therapeutic response. Methods: Multiple patient-derived glioblastoma models were cultured under normoxia (21% O2) or sustained physioxia (5% O2) for at least seven days before experimentation. Cell migration, proliferation, cell cycle distribution, expression of the epithelial-to-mesenchymal transition-associated transcription factor Slug (SNAI2), PDGFRβ-associated signaling, and sensitivity to 5-fluorouracil were evaluated using transwell migration assays, cell counting, flow cytometry, RT-qPCR, immunoblotting, and BrdU incorporation assays. To examine the effects of oxygen history, we established and maintained additional patient-derived cultures grown under physioxia. Results: Sustained physioxia consistently increased migration across all glioblastoma models while reducing proliferation in normoxia-adapted cell lines through increased G0/G1 cell cycle arrest. Physioxia significantly increased Slug expression in all models and enhanced PDGFRβ, AKT, and ERK phosphorylation in a cell line-dependent manner. Therapeutic sensitivity to 5-fluorouracil was altered, with physioxia conferring increased resistance in some glioblastoma models but not universally. Patient-derived cell lines cultured continuously under physioxia retained enhanced migratory capacity and exhibited increased proliferation compared to cells grown in normoxia, suggesting that prior oxygen exposure influences proliferative responses while the pro-migratory phenotype remains conserved. Conclusions: Physiological oxygen tension is a major regulator of glioblastoma cell behavior, influencing migration, proliferation, signaling, and therapeutic response. These findings demonstrate that conventional normoxic culture conditions can obscure biologically relevant phenotypes and support the consideration of physioxia in experimental design. Such technical changes may improve the physiological and translational relevance of preclinical glioblastoma research. Full article
(This article belongs to the Section Tumor Microenvironment)
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20 pages, 3571 KB  
Article
Impact of Preweaning Vaccination on Host Gene Expression Patterns Linked to Future Bovine Respiratory Disease Development in Beef Calves
by Hudson R. McAllister, Bradly I. Ramirez, Sarah F. Capik, Kelsey M. Harvey, Paul S. Morley, Robert J. Valeris-Chacin, Brandi B. Karisch, Amelia R. Woolums, Alexis C. Thompson and Matthew A. Scott
Vaccines 2026, 14(8), 694; https://doi.org/10.3390/vaccines14080694 - 12 Aug 2026
Viewed by 349
Abstract
Background/Objectives: Bovine respiratory disease (BRD) remains a major concern in cattle research, and the long-term effects of vaccination on health and immune responses are not well defined. This study compared gene expression in vaccinated (VAX) and unvaccinated (NOVAX) preweaned calves and subsequent BRD [...] Read more.
Background/Objectives: Bovine respiratory disease (BRD) remains a major concern in cattle research, and the long-term effects of vaccination on health and immune responses are not well defined. This study compared gene expression in vaccinated (VAX) and unvaccinated (NOVAX) preweaned calves and subsequent BRD development during backgrounding. Methods: Whole blood was collected at four timepoints (TIME; T1-4; median age 107, 114, 183, and 230, respectively) from 73 bull calves enrolled in a blinded randomized controlled trial; VAX calves received a commercial attenuated multivalent viral vaccine at T1 and T3. Results: Whole-blood transcriptomics was used to quantify mRNA, identifying 5364 differentially expressed genes (DEGs) for TIME, 84 DEGs for vaccination (VAX), and 129 for BRD status using both glmmSeq and QLF testing (glmmSeq only DEGs: 11,068 TIME, 358 VAX, and 9241 BRD). VAX calves at T3 were clustered uniquely with the enrichment of pathways related to the cellular response to stress, neutrophil degranulation, and antigen processing and presentation compared to NOVAX cattle and VAX at other timepoints. Interferon pathways, natural killer cell responses, and neutrophil activity were generally absent across all timepoints, while antigen presentation pathways were persistently enriched. Regardless of vaccination or future BRD diagnosis, immunological development over time was indicated by DEGs related to adaptive immunity, lymphocyte development, and inflammatory resolution. At T4, cattle diagnosed with BRD during backgrounding had differential gene expression related to oxygen transport, hemoglobin function, and metabolic processes compared to cattle that remained healthy. Conclusions: This study provides insights into the possible genomic mechanisms underlying vaccine responses and preclinical BRD susceptibility in preweaned beef cattle. Full article
(This article belongs to the Special Issue Vaccination Against Major Respiratory Pathogens in Livestock Farming)
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28 pages, 3319 KB  
Article
Trifluoromethyl-Benzimidazole-Hydrazone Derivatives as Promising Selective Anticancer Agents: Synthesis, Cytotoxicity, and Molecular Docking Insights
by Musa Özil, Eyüp Önelge, Mustafa Emirik, Kübra Acikalin Coskun and Yusuf Tutar
Pharmaceuticals 2026, 19(8), 1270; https://doi.org/10.3390/ph19081270 - 11 Aug 2026
Viewed by 438
Abstract
Background/Objectives: Benzimidazole and hydrazone scaffolds are widely investigated in anticancer drug discovery because of their structural versatility and capacity to interact with multiple cancer-related targets. This study aimed to synthesize a series of trifluoromethyl-substituted benzimidazole-hydrazone derivatives, evaluate their antiproliferative activity and cancer-cell [...] Read more.
Background/Objectives: Benzimidazole and hydrazone scaffolds are widely investigated in anticancer drug discovery because of their structural versatility and capacity to interact with multiple cancer-related targets. This study aimed to synthesize a series of trifluoromethyl-substituted benzimidazole-hydrazone derivatives, evaluate their antiproliferative activity and cancer-cell selectivity, and explore their potential interactions with breast cancer-associated molecular targets. Methods: A series of benzimidazole-hydrazone derivatives were prepared through a four-step synthetic route using both conventional and microwave-assisted procedures. The structures of the synthesized compounds were characterized using spectroscopic and analytical methods. Antiproliferative activity was evaluated in estrogen receptor-positive MCF-7 human breast cancer cells using the MTT assay after 48 h of exposure. Selected active compounds were additionally tested against non-tumorigenic hTERT cells to determine their selectivity indices. In silico analyses were performed against estrogen receptor alpha in antagonist and selective estrogen receptor degrader conformations, bromodomain-containing protein 4, and the mTOR kinase domain. Results: Microwave irradiation substantially reduced reaction times from 12–24 h to 4–6 min and increased isolated yields by 7–24 percentage points compared with conventional conditions. Compounds 4, 7, 9, and 11 reduced MCF-7 cell viability below 50% at 20 μM. Compound 7 showed the highest antiproliferative activity, with an IC50 value of 7.5 ± 0.8 μM, and the greatest selectivity toward MCF-7 cells over hTERT cells, with a selectivity index of 12.66. Molecular docking, MD simulation, and MM/GBSA calculations predicted that compound 7 would effectively bind to the investigated targets, particularly estrogen receptor alpha, as well as the BRD4 and mTOR kinase domains. Conclusions: Compound 7 represents a selective, mid-micromolar benzimidazole-hydrazone lead against MCF-7 breast cancer cells. Its predicted molecular interactions warrant further target-based, mechanistic, pharmacokinetic, and in vivo evaluation. Full article
(This article belongs to the Special Issue Computer-Aided Drug Design and Drug Discovery, 2nd Edition)
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28 pages, 7917 KB  
Article
Integrated Transcriptomic and Machine-Learning Analyses Identify Shared Na+ Overload-Related Gene Signatures in Inflammatory Bowel Disease and Ankylosing Spondylitis
by Luojin Wu, Chenghao Ou, Xuan Liu, Miaohan Yan, Jinghan Guan, Xinfeng Wang, Liming Mao, Qiuyun Xu and Zhaoxiu Liu
Genes 2026, 17(8), 938; https://doi.org/10.3390/genes17080938 - 11 Aug 2026
Viewed by 339
Abstract
Background: Ankylosing Spondylitis (AS) and inflammatory bowel disease (IBD) exhibit substantial pathophysiological overlap, including dysregulated innate immunity, barrier dysfunction, and Th17-mediated inflammation. However, whether Na+ overload-related genes (NRGs) exhibit shared transcriptional alterations in IBD and AS remains unclear. This study aimed [...] Read more.
Background: Ankylosing Spondylitis (AS) and inflammatory bowel disease (IBD) exhibit substantial pathophysiological overlap, including dysregulated innate immunity, barrier dysfunction, and Th17-mediated inflammation. However, whether Na+ overload-related genes (NRGs) exhibit shared transcriptional alterations in IBD and AS remains unclear. This study aimed to characterize the expression patterns of NRGs across IBD and AS and to identify candidate genes associated with both diseases. Methods: Differential expression analysis was performed to identify differentially expressed NRGs (DE-NRGs) in diseased tissues relative to normal tissues. Shared DE-NRGs between IBD and AS were screened and defined as common differentially expressed NRGs (Co-DE-NRGs). We then analyzed the correlations of these Co-DE-NRGs and explored their relationships with immune cell infiltration in target tissues. Four machine learning algorithms were applied to screen key NRGs associated with both IBD and AS. Potential therapeutic agents targeting these core biomarkers were predicted using drug–gene interaction databases, and molecular docking was conducted for further validation. Results: A total of 32 shared Co-DE-NRGs were identified for IBD and AS, with nine key regulatory NRGs recognized: CALR, CD63, CYBA, DYSF, HYOU1, IL1B, JAK1, MMP9, and STAT3. Exploratory MR analysis identified disease-specific associations between genetically predicted expression of NRGs and CD, UC, and AS. Genetically predicted STAT3 expression showed positive associations with CD and UC but an inverse association with AS and therefore did not represent a consistent risk factor across the three diseases. Furthermore, transcriptome-based drug-response analysis identified four candidate agents shared between AS and at least one IBD dataset: ciclosporin, BCL-LZH-4, BRD-K79669418, and CID-5951923. Exploratory molecular docking generated STAT3 binding poses for BCL-LZH-4 and CID-5951923, with DOCK Grid Scores of −35.321896 and −28.361128, respectively. CID-5951923 was selected for representative visualization of its predicted interaction with STAT3. Single-cell RNA-sequencing analysis identified tissue- and cell-type-specific STAT3 mRNA expression patterns in the analyzed IBD colonic and AS peripheral-blood datasets, with monocytes representing a major cell population exhibiting detected STAT3 expression in the AS dataset. Conclusions: These findings identify shared NRG-related transcriptional alterations in IBD and AS, with STAT3 emerging as a candidate gene associated with both diseases. Further experimental studies are required to determine whether these alterations reflect the involvement of NECSO and to evaluate their potential diagnostic or therapeutic relevance. Full article
(This article belongs to the Special Issue Genetic and Genomic Analysis of Inflammatory Bowel Disease)
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32 pages, 27841 KB  
Article
Proteomic Dynamics Reveal Cell-Cycle and Rho GTPase Remodeling Associated with Transient Senescence Traits in Human Chondrocytes During Sustained IL-1β Signaling
by Hellen Paula Valerio, Thatiana Corrêa de Melo, Mariana Barbosa de Souza Rizzo, Amanda Teixeira de Melo, Miryam Paola Alvarez-Flores and Ana Marisa Chudzinski-Tavassi
Cells 2026, 15(16), 1431; https://doi.org/10.3390/cells15161431 - 8 Aug 2026
Cited by 1 | Viewed by 544
Abstract
Chronic inflammatory signaling contributes to cartilage degeneration across multiple joint diseases, yet the molecular consequences of sustained cytokine exposure remain incompletely understood. We investigated how prolonged interleukin-1β (IL-1β) stimulation remodels the chondrocyte proteome and whether these changes are associated with senescence-associated traits. Primary [...] Read more.
Chronic inflammatory signaling contributes to cartilage degeneration across multiple joint diseases, yet the molecular consequences of sustained cytokine exposure remain incompletely understood. We investigated how prolonged interleukin-1β (IL-1β) stimulation remodels the chondrocyte proteome and whether these changes are associated with senescence-associated traits. Primary human articular chondrocytes were exposed to IL-1β (10 ng/mL) for up to four days. Time-resolved data-independent acquisition (DIA) proteomics was integrated with immunofluorescence, quantitative PCR, multiplex metalloproteinase profiling, BrdU incorporation, growth-curve analysis, and senescence-associated β-galactosidase assays. Sustained IL-1β induced extensive time-dependent proteomic remodeling, with early inflammatory and extracellular matrix responses followed by alterations in cell-cycle regulation and cytoskeletal organization. Prolonged stimulation was associated with persistent downregulation of CDK4, Cyclin D1, DNA replication-associated proteins, and Rho GTPase-associated components, accompanied by actin cytoskeletal remodeling. These molecular changes were associated with impaired proliferation, increased senescence-associated β-galactosidase activity, and transient modulation of p21. Following cytokine withdrawal, BrdU incorporation showed partial recovery. Together, these findings indicate that sustained IL-1β progressively reshapes the chondrocyte cellular state through coordinated remodeling of proliferative, cytoskeletal, and metalloprotease programs while showing some degree of proliferative plasticity under the conditions tested. Full article
(This article belongs to the Section Cellular Pathology)
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15 pages, 673 KB  
Article
A Combined Intranasal and Parenteral Vaccination Strategy Reduces Morbidity and Antimicrobial Treatments Associated with Bovine Respiratory Disease in Danish Commercial Veal Calves
by Henrik Schmidt, Anne Mette Hostrup Kjeldsen, Jonna Hjorth and Henrik Læssøe Martin
Pathogens 2026, 15(8), 826; https://doi.org/10.3390/pathogens15080826 - 6 Aug 2026
Viewed by 442
Abstract
Background: Bovine respiratory disease (BRD) is a major driver of antimicrobial use in veal calf production systems. Although vaccination may reduce disease incidence and antimicrobial treatments, field evidence supporting clinically relevant reductions in antimicrobial use remains limited. This study evaluated the clinical efficacy [...] Read more.
Background: Bovine respiratory disease (BRD) is a major driver of antimicrobial use in veal calf production systems. Although vaccination may reduce disease incidence and antimicrobial treatments, field evidence supporting clinically relevant reductions in antimicrobial use remains limited. This study evaluated the clinical efficacy of a combined intranasal (IN) and parenteral (subcutaneous/intramuscular; SC/IM) vaccination strategy targeting bovine respiratory syncytial virus, Histophilus somni, and Mannheimia haemolytica under commercial conditions. Methods: A randomised controlled field trial was conducted on two Danish veal calf farms between November 2019 and April 2020, including 880 calves allocated to a vaccinated group (n = 445) or an unvaccinated control group (n = 435). Health outcomes included morbidity, antimicrobial use, mortality, growth performance, and slaughterhouse pulmonary and pleural lesions and were analysed using mixed-effects models. Results: Vaccination significantly reduced BRD-associated morbidity across all evaluation periods (from day 5 after arrival to slaughter), with relative reductions of 18.8–24.6% and 30% fewer antimicrobial treatment days. Pulmonary and pleural lesions were significantly less frequent in vaccinated calves (≈36% reduction). No statistically significant differences were observed in growth performance or mortality. Conclusions: Combined IN + SC/IM vaccination was associated with lower BRD-associated morbidity, antimicrobial treatments, and slaughterhouse respiratory lesions under commercial conditions. Full article
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