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67 pages, 3389 KB  
Review
Metaflammation’s Role in Systemic Dysfunction in Obesity: A Comprehensive Review
by Ioana-Maria Crasan, Matei Tanase, Corina Elena Delia, Gratiela Gradisteanu-Pircalabioru, Anisoara Cimpean and Elena Ionica
Int. J. Mol. Sci. 2025, 26(21), 10445; https://doi.org/10.3390/ijms262110445 (registering DOI) - 27 Oct 2025
Abstract
Obesity is redefined as a complex systemic disease, transcending mere caloric imbalance, driven by intricate dysregulation across metabolic, neuroendocrine, immunological, and epigenetic axes. Central to its pathology is adipose tissue, which is considered a dynamic endocrine and immune organ. Its dysfunctional expansion fuels [...] Read more.
Obesity is redefined as a complex systemic disease, transcending mere caloric imbalance, driven by intricate dysregulation across metabolic, neuroendocrine, immunological, and epigenetic axes. Central to its pathology is adipose tissue, which is considered a dynamic endocrine and immune organ. Its dysfunctional expansion fuels chronic, low-grade systemic inflammation, termed “metaflammation”, characterised by pathways such as NF-kB and NLRP3 inflammasome activation, as well as pervasive immune cell infiltration. This inflammatory state could profoundly impair insulin signalling and contribute to major complications, including insulin resistance, type 2 diabetes, and cardiovascular disease. Further exacerbating this systemic dysfunction is gut microbiota dysbiosis, which promotes metabolic endotoxemia and neuroendocrine dysregulation, impacting hypothalamic function, central hormone resistance, and reproductive health. Epigenetic modifications also serve as crucial mediators, translating environmental exposures into altered gene expression that perpetuates susceptibility across generations. This review summarises the current understanding of obesity by integrating molecular, neuroendocrine, and immunometabolic underpinnings, reinterpreting it as a comprehensive expression of systemic dysfunction. Through this integrated perspective our hope is to highlight the necessity of a paradigm shift towards personalised, multi-targeted interventions that extend beyond conventional weight management. An integrative, translational approach modulating the immunometabolic network, microbiota, and epigenetics is essential to effectively address the global obesity epidemic and its far-reaching health implications. Full article
20 pages, 1002 KB  
Review
Diet, Exercise, and Lifestyle in Glaucoma: Current Evidence and Future Perspectives
by Akiko Hanyuda, Satoru Tsuda, Noriko Himori, Kota Sato, Naoki Takahashi and Toru Nakazawa
Nutrients 2025, 17(21), 3369; https://doi.org/10.3390/nu17213369 (registering DOI) - 27 Oct 2025
Abstract
Glaucoma is a major ocular neurodegenerative disease and a leading cause of irreversible blindness worldwide, with prevalence projected to exceed 110 million by 2040. Although lowering intraocular pressure (IOP) remains the only proven treatment, glaucoma arises from a complex interplay of genetic, local, [...] Read more.
Glaucoma is a major ocular neurodegenerative disease and a leading cause of irreversible blindness worldwide, with prevalence projected to exceed 110 million by 2040. Although lowering intraocular pressure (IOP) remains the only proven treatment, glaucoma arises from a complex interplay of genetic, local, and systemic factors—including oxidative stress, vascular dysregulation, mitochondrial dysfunction, and neuroinflammation. Emerging evidence suggests that modifiable lifestyle factors may influence these pathogenic pathways. In this review, higher dietary nitrate from leafy greens is consistently associated with lower primary open-angle glaucoma risk, aligning with nitric-oxide-mediated endothelial support and more stable ocular perfusion pressure. Flavonoids (anthocyanins and flavanols), carotenoids (lutein/zeaxanthin), and B vitamins have strong biological rationale for glaucoma prevention but have limited support from long-term, large population-based studies. The effect of polyunsaturated fats on glaucoma remains inconsistent and warrants source-(plant vs. animal) and substitution-based analyses. Consistent protective effects of aerobic exercise and high-quality sleep may be associated with favorable metabolic profiles and ocular perfusion, potentially mitigating retinal ganglion cell loss. Conversely, smoking and alcohol use are frequently coupled with poorer diet quality (e.g., lower vegetable intake) and heightened oxidative stress, which may exacerbate glaucomatous neurodegeneration. However, much of the current literature is constrained by cross-sectional designs, reliance on self-reported food frequency questionnaires, and insufficient use of structural endpoints such as retinal nerve fiber layer imaging. This review focuses on the potential of lifestyle modification and future directions in prevention and treatment strategies for glaucoma, highlighting the need for large-scale, multi-ethnic, genotype-stratified longitudinal studies and randomized controlled trials to establish causality and define optimal intervention strategies. Full article
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18 pages, 1632 KB  
Review
Hematopoietic Stem Cell Aging: Mechanisms, Microenvironment Influences, and Rejuvenation Strategies
by Jiaqi Cui, Xincan Li, Bin Liu, Cheng Dong and Yun Chang
Bioengineering 2025, 12(11), 1166; https://doi.org/10.3390/bioengineering12111166 (registering DOI) - 27 Oct 2025
Abstract
Hematopoietic stem cells (HSCs) are essential for lifelong blood production and immune homeostasis. However, aging induces functional declines in HSCs, leading to hematological disorders, immune dysfunction, and increased susceptibility to malignancies. This review explores the biological underpinnings of HSC aging, highlighting the intrinsic [...] Read more.
Hematopoietic stem cells (HSCs) are essential for lifelong blood production and immune homeostasis. However, aging induces functional declines in HSCs, leading to hematological disorders, immune dysfunction, and increased susceptibility to malignancies. This review explores the biological underpinnings of HSC aging, highlighting the intrinsic and extrinsic factors that drive this process. We discuss the molecular and cellular mechanisms contributing to HSC aging, including genetic instability, epigenetic alterations, metabolic shifts, and inflammation signaling. Additionally, we examine the role of the bone marrow microenvironment in modulating HSC aging, emphasizing the impact of niche interactions, stromal cell dysfunction, and extracellular matrix remodeling. To advance our understanding of HSC aging, pluripotent stem cell differentiation platforms provide a valuable tool for modeling aged HSC phenotypes and identifying potential therapeutic targets. We review current strategies for HSC rejuvenation, including metabolic reprogramming, epigenetic modifications, pharmacological interventions, and niche-targeted approaches, aiming to restore HSC function and improve regenerative potential. Finally, we present emerging perspectives on the clinical implications of HSC aging, discussing potential translational strategies for combating age-associated hematopoietic decline. By integrating insights from stem cell biology, aging research, and regenerative medicine, this review provides a comprehensive overview of HSC aging and its therapeutic potential. Addressing these challenges will be critical for developing interventions that promote hematopoietic health and improve outcomes in aging populations. Full article
(This article belongs to the Special Issue Stem Cell Immunoengineering)
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19 pages, 845 KB  
Systematic Review
Luminescent and Optical Thin Film Coatings in Ophthalmic Lenses: Advances, Clinical Applications, and Future Directions
by Ana Paula Oliveira and Clara Martinez-Perez
Coatings 2025, 15(11), 1246; https://doi.org/10.3390/coatings15111246 (registering DOI) - 27 Oct 2025
Abstract
Ophthalmic lens coatings are increasingly designed to combine optical, mechanical, and biological functions. This systematic review, registered in PROSPERO and conducted according to PRISMA 2020 guidelines, synthesized 54 experimental, preclinical, and clinical studies on coatings for spectacle lenses, contact lenses, and intraocular lenses. [...] Read more.
Ophthalmic lens coatings are increasingly designed to combine optical, mechanical, and biological functions. This systematic review, registered in PROSPERO and conducted according to PRISMA 2020 guidelines, synthesized 54 experimental, preclinical, and clinical studies on coatings for spectacle lenses, contact lenses, and intraocular lenses. Spectacle lens studies consistently showed that anti-reflective and blue-light filtering coatings reduce glare perception, improve contrast sensitivity, and provide UV protection, while laboratory tests demonstrated significant reductions in impact resistance, with fracture energy of CR-39 lenses decreasing by up to 63% when coated. Contact lens research revealed that plasma and polymeric coatings reduce water contact angles from >100° to <20°, enhancing wettability, while antimicrobial strategies such as melamine binding or nanoparticle-based films achieved >80% reductions in bacterial adhesion. Drug-eluting approaches sustained antibiotic or antioxidant release for periods ranging from 24 h to 6 days, with improved ocular bioavailability compared with drops. Intraocular lens studies demonstrated that heparin surface modifications reduced postoperative flare and anterior chamber cells, and phosphorylcholine or alkylphosphocholine coatings suppressed lens epithelial cell proliferation. Drug-loaded coatings with methotrexate, gefitinib, or amikacin significantly inhibited posterior capsule opacification and infection in ex vivo and animal models. Collectively, coatings improve visual comfort, photoprotection, wettability, and biocompatibility, but clinical translation requires solutions to mechanical trade-offs, long-term stability, and regulatory challenges. Full article
(This article belongs to the Special Issue Developments in Optical Coatings and Thin Films)
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22 pages, 1018 KB  
Review
Molecular Pathogenesis of Arrhythmogenic Cardiomyopathy: Mechanisms and Therapeutic Perspectives
by Eliza Popa and Sorin Hostiuc
Biomolecules 2025, 15(11), 1512; https://doi.org/10.3390/biom15111512 (registering DOI) - 25 Oct 2025
Viewed by 51
Abstract
Arrhythmogenic cardiomyopathy (ACM) is a genetic cardiac disease characterized by a progressive loss of cardiomyocytes associated with fibrofatty myocardial replacement, resulting in a heightened risk of ventricular arrhythmias and sudden cardiac death. ACM is a common cause of sudden death in young individuals, [...] Read more.
Arrhythmogenic cardiomyopathy (ACM) is a genetic cardiac disease characterized by a progressive loss of cardiomyocytes associated with fibrofatty myocardial replacement, resulting in a heightened risk of ventricular arrhythmias and sudden cardiac death. ACM is a common cause of sudden death in young individuals, and exercise has been proven to be a factor in disease progression. Current therapeutic strategies, including lifestyle modification, antiarrhythmic pharmacological therapy, catheter ablation, and the placement of implantable cardioverter-defibrillators, remain primarily palliative options rather than addressing the underlying molecular substrate. The pathogenesis of ACM includes complex molecular and cellular mechanisms, linking genetic mutations to structural and electrical anomalies of the ventricle. The lack of targeted therapies contributes to a challenging approach to the disease. It highlights the need for a better understanding of the mechanisms that lead to myocardial remodeling and arrhythmic predisposition. With the help of animal models (especially murine) and induced pluripotent stem cells, there have been advances in understanding the molecular pathogenesis of ACM. In this review, we summarized some of the pathogenic molecular pathways involved in the development of ACM and emerging therapies targeted towards disease modification, not just prevention. Full article
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15 pages, 2608 KB  
Article
The Effect of Nutritional Supplementation in Ex Vivo Lung Perfusion Perfusate on Human Lung Endothelial Cell Function
by Dejan Bojic, Kimberly Main, Tanroop Aujla, Olivia Hough, Shaf Keshavjee and Mingyao Liu
Cells 2025, 14(21), 1668; https://doi.org/10.3390/cells14211668 (registering DOI) - 25 Oct 2025
Viewed by 122
Abstract
Clinical application of ex vivo lung perfusion (EVLP) has increased marginal donor lung utilization. It has been developed as a platform for donor lung reconditioning. However, many of the current repair strategies are limited by a maximum reliable EVLP circuit duration of 12 [...] Read more.
Clinical application of ex vivo lung perfusion (EVLP) has increased marginal donor lung utilization. It has been developed as a platform for donor lung reconditioning. However, many of the current repair strategies are limited by a maximum reliable EVLP circuit duration of 12 h. Past studies have successfully extended EVLP through nutrient supplementation, but the exact components and respective mechanisms by which EVLP is extended remains unknown. As such, the focus of this study was to systematically evaluate the effects of nutritional supplements in EVLP perfusates on cell apoptosis, viability, confluence, and migration. To test this, we developed a high-throughput human lung endothelial cell culture platform where experimental perfusates with various combinations of GlutaMAX (a glutamine dipeptide), Travasol (amino acids), Intralipid (lipids), Multi-12 (vitamins), cysteine, and glycine were tested using the Incucyte Live imaging system. GlutaMAX supplementation alone significantly reduced apoptosis, improved viability and cell migration beyond all other supplements and further outperformed standard endothelial cell culture medium. Travasol offered short-term benefits, while Intralipid offered minimal functional support. Multi-12 improved viability and apoptosis independently and in combination with other supplements. The best experimental perfusate targeted the glutathione synthesis pathway, combining GlutaMAX, cysteine and glycine and further reduced apoptosis compared with GlutaMAX alone. Collectively, these results suggest that nutrient selection during EVLP is critical and highlights the need to systematically evaluate perfusate modifications as opposed to broad-spectrum nutrient delivery. This in vitro model provides a cost-effective platform for preclinical screening of perfusate modifications to enhance organ viability during EVLP. Full article
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23 pages, 6258 KB  
Article
Specific Glutamylation Patterns of the Cytoskeleton Confer Neuroresistance to Lobe X of the Cerebellum in a Model of Childhood-Onset Neurodegeneration with Cerebellar Atrophy
by Carlos Hernández-Pérez, Andrés A. Calderón-García, David Pérez-Boyero, Verónica González-Núñez, Eduardo Weruaga and David Díaz
Int. J. Mol. Sci. 2025, 26(21), 10378; https://doi.org/10.3390/ijms262110378 (registering DOI) - 25 Oct 2025
Viewed by 62
Abstract
The cytoskeleton relies heavily on the dynamic nature of microtubules, regulated by post-translational modifications such as polyglutamylation and deglutamylation. Disruption of its internal balance, particularly through the absence of cytosolic carboxypeptidase 1 (CCP1), leads to cytoskeletal collapse and cell death. An example of [...] Read more.
The cytoskeleton relies heavily on the dynamic nature of microtubules, regulated by post-translational modifications such as polyglutamylation and deglutamylation. Disruption of its internal balance, particularly through the absence of cytosolic carboxypeptidase 1 (CCP1), leads to cytoskeletal collapse and cell death. An example of this occurrence exists in the Purkinje Cell Degeneration (PCD) mouse, a direct animal model for childhood-onset neurodegeneration with cerebellar atrophy (CONDCA) human disease. Both CONDCA patients and PCD mice suffer a dramatic degeneration of Purkinje cells. Intriguingly, lobe X appears less vulnerable to this insult. This study revealed in wild-type mice that lobe X expresses less Ccp1 compared to other lobes, correlating with its delayed degeneration in PCD mice. Further expression analysis of other deglutamylating enzymes (CCP4 and CCP6) and glutamylating enzymes (TTLL1) revealed distinctive patterns: Ccp4 showed minimal relevance in cerebellum, while Ccp6 displayed a compensatory increase during critical stages. Meanwhile, Ttll1 expression remained consistent across lobes, suggesting that the resistance of lobe X may be related to a more dynamic, hyperglutamylated cytoskeleton. Unraveling the neuroresistance mechanisms of Purkinje cells may help mitigate neuronal loss in CONDCA patients and may offer a glimmer of hope for alleviating the symptoms of other neurodegenerative diseases. Full article
(This article belongs to the Special Issue Molecular Mechanisms and Treatments in Neurodegenerative Diseases)
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21 pages, 1260 KB  
Review
COVID-19 Hijacking of the Host Epigenome: Mechanisms, Biomarkers and Long-Term Consequences
by Alena D. Zolotarenko, Hakob M. Poghosyan, Victoria V. Sheptiy and Sergey A. Bruskin
Int. J. Mol. Sci. 2025, 26(21), 10372; https://doi.org/10.3390/ijms262110372 (registering DOI) - 24 Oct 2025
Viewed by 239
Abstract
The epigenetics of COVID-19 is a rapidly expanding field that reveals how the SARS-CoV-2 virus initiates alterations in the host’s genome, influencing the susceptibility to infection, the disease severity, and long-term consequences, known as “long COVID.” In this review, we describe the mechanisms [...] Read more.
The epigenetics of COVID-19 is a rapidly expanding field that reveals how the SARS-CoV-2 virus initiates alterations in the host’s genome, influencing the susceptibility to infection, the disease severity, and long-term consequences, known as “long COVID.” In this review, we describe the mechanisms utilized by the virus to manipulate the host epigenome, suppressing antiviral responses and creating a favorable environment for viral replication. We also highlight virus-induced epigenetic changes across diverse cell populations that contribute to COVID-19 pathogenesis. Notably, the virus reprograms hematopoietic stem and progenitor cells, leading to long-lasting alterations in innate immunity, a phenomenon known as “trained immunity.” These epigenetic modifications are maintained in differentiated daughter cells and may explain the persistent inflammation and other symptoms of long COVID. Furthermore, we discuss emerging epigenetic biomarkers of disease severity, including methylation signatures in genes such as AIM2, HLA-C, and PARP9, as well as dysregulated miRNA profiles. Understanding this complex interplay between the virus and the host’s epigenetic landscape is crucial for developing new therapeutic approaches that target specific epigenetic modifications to suppress pathological processes and improve clinical outcomes for COVID-19 patients. Full article
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30 pages, 5963 KB  
Review
Engineering Inorganic Nanoparticles to Induce Cuproptosis: A New Strategy for Cancer Therapy
by Zhenxing Jiang, Jianwei Dai, Juanjuan Jiang, Shenghe Deng, Junnan Gu, Jun Wang, Mian Chen, Wentai Cai, Ke Wu, Kaixiong Tao, Ke Liu and Kailin Cai
Pharmaceutics 2025, 17(11), 1383; https://doi.org/10.3390/pharmaceutics17111383 (registering DOI) - 24 Oct 2025
Viewed by 365
Abstract
Cuproptosis is a newly identified type of copper (Cu)-dependent programmed cell death (PCD), triggered when Cu directly interacts with the lipoylated components of the tricarboxylic acid (TCA) cycle, and it has shown significant antitumor potential. However, challenges such as insufficient Cu accumulation in [...] Read more.
Cuproptosis is a newly identified type of copper (Cu)-dependent programmed cell death (PCD), triggered when Cu directly interacts with the lipoylated components of the tricarboxylic acid (TCA) cycle, and it has shown significant antitumor potential. However, challenges such as insufficient Cu accumulation in tumor cells, systemic toxicity, and the lack of specific carriers for effectively inducing cuproptosis hinder its practical application. Inorganic nanoparticles (INPs) present a promising solution due to their unique ability to target specific areas, potential for multifunctional modification, and controlled release capabilities. Their distinctive physicochemical properties also enable the integration of synergistic multimodal cancer therapies. Therefore, utilizing INPs to induce cuproptosis represents a promising strategy for cancer treatment. This review systematically elucidates the regulatory mechanisms of Cu homeostasis and the molecular pathways underlying cuproptosis, thoroughly discusses current INP-based strategies designed to trigger cuproptosis, and comprehensively examines the multi-modal synergistic antitumor mechanisms based on cuproptosis. Finally, we also address the current challenges and future perspectives in developing clinically applicable nanoplatforms aimed at harnessing cuproptosis for effective cancer therapy. Full article
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18 pages, 3908 KB  
Article
Repurposed Drugs for Heterotopic Ossification Management: Revitalizing Therapeutic Strategies
by Ana Alonso-Pérez, Eloi Franco-Trepat, María Guillán-Fresco, Miriam López-Fagúndez, Andrés Pazos-Pérez, Verónica López, Antonio Salas, Federico Martinón-Torres, Alberto A. Jorge-Mora and Rodolfo Gómez
Pharmaceuticals 2025, 18(11), 1609; https://doi.org/10.3390/ph18111609 (registering DOI) - 24 Oct 2025
Viewed by 157
Abstract
Background and Objectives: Heterotopic ossification (HO) involves abnormal bone growth in soft tissues. Current treatments are ineffective and prone to adverse effects, suggesting the need for new HO therapies. Intramembranous bone growth is led by osteoblasts. Since osteoblastogenesis and adipogenesis are opposed [...] Read more.
Background and Objectives: Heterotopic ossification (HO) involves abnormal bone growth in soft tissues. Current treatments are ineffective and prone to adverse effects, suggesting the need for new HO therapies. Intramembranous bone growth is led by osteoblasts. Since osteoblastogenesis and adipogenesis are opposed and mutually controlled processes, this study aims to identify a new repurposed therapeutic tool to inhibit osteoblastogenesis through adipogenesis promotion. Methods: We performed docking experiments between peroxisome proliferator-activated receptor-γ and bone metabolism-affecting drugs, namely, thiazolidinediones (rosiglitazone, pioglitazone), indomethacin, and dexamethasone, to test tritherapy antiosteoblastogenic effect. Mouse mesenchymal stem cells (C3H10T1/2), human osteoblast-like cells (SaOS2 and primary preosteoblasts), and mouse chondrocytes (ATDC5) were differentiated in the presence of these compounds. The effects on osteoblastogenesis, adipogenesis, and endochondral ossification were analysed through marker gene expression via RT–qPCR. Additionally, primary human HO cells and a congenital HO patient were treated with the selected drug combination (P-tritherapy). Results: Tritherapy significantly and synergistically promoted the expression of an adipogenic marker (fatty acid-binding protein 4) and decreased the expression of an osteoblastogenic marker (osteopontin). In an endochondral ossification model, it reduced ossification markers (collagen-2α1) expression, and in HO cells, it increased adipogenesis markers’ expression. Clinically, P-tritherapy administration prompted bone resorption in a patient with progressive osseous heteroplasia. Conclusions: Tritherapy induced adipogenesis while inhibiting osteoblastogenesis and endochondral ossification, demonstrating its potential as a new therapeutic tool to prevent abnormal bone growth. These results were consistent with bone turnover modification observed in a congenital HO patient. This concordance underscores tritherapy potential for rapid and safe translation to prevent HO. Full article
(This article belongs to the Section Pharmacology)
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23 pages, 1640 KB  
Article
miR-155-5p Silencing Does Not Alter BTLA Molecule Expression in CLL T Cells: Implications for Targeted Immunotherapy
by Agata Kosmaczewska, Lidia Ciszak, Anna Andrzejczak, Anna Tomkiewicz, Anna Partyka, Zofia Rojek-Gajda, Irena Frydecka, Dariusz Wołowiec, Tomasz Wróbel, Agnieszka Bojarska-Junak, Jacek Roliński and Lidia Karabon
Biomolecules 2025, 15(11), 1499; https://doi.org/10.3390/biom15111499 - 24 Oct 2025
Viewed by 151
Abstract
Given that we have demonstrated that miR-155-5p is increased in CLL PBMCs and that its reduction with inhibitory siRNA partially restores the immune checkpoint BTLA protein level in CLL B cells, risk stratification for using anti-miR-155-based immunotherapy in CLL seems reasonable, particularly with [...] Read more.
Given that we have demonstrated that miR-155-5p is increased in CLL PBMCs and that its reduction with inhibitory siRNA partially restores the immune checkpoint BTLA protein level in CLL B cells, risk stratification for using anti-miR-155-based immunotherapy in CLL seems reasonable, particularly with its potential impact on T cells. Therefore, we aimed to assess the role of miR-155-5p in the epigenetic modification of BTLA levels in CLL T cells, especially since we observed that BTLA expression unfavorably promotes increased proliferative activity and IL-4 secretion in T cells, thus suggesting BTLA malfunction in the CLL T cell subset. Transfection of PBMCs with an inhibitor of miR-155-5p (INH) led to about a ten-fold down-regulation of miR-155-5p levels compared to control siRNA (NC) both in CLL patients and healthy individuals (HC), as assessed by RT-qPCR. Additionally, we did not find any significant differences in BTLA protein expression in T cells after silencing miR-155-5p in either examined group. We demonstrated for the first time that immunotherapy approaches based on systemic administration of anti-miR-155-5p therapeutics would be a favorable strategy in CLL, since they do not affect BTLA expression in T cell populations and could benefit CLL patients with impaired BTLA levels on CLL cells. Full article
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27 pages, 1763 KB  
Review
Molecular Mechanisms of the Ubiquitin-Specific Proteases (USPs) Family in Biliary Tract Cancer and Targeted Intervention Strategies
by Qian Cheng, Delin Ma, Shengmin Zheng, Jialing Hao, Gang Wang, Yanbin Ni and Jiye Zhu
Biomedicines 2025, 13(11), 2586; https://doi.org/10.3390/biomedicines13112586 - 23 Oct 2025
Viewed by 271
Abstract
Biliary tract carcinoma (BTC) is a group of highly heterogeneous malignancies arising from the biliary epithelium. Anatomically, BTC is categorized into gallbladder cancer (GBC) and cholangiocarcinoma (CCA), with the latter further subdivided into intrahepatic (iCCA), perihilar (pCCA), and distal cholangiocarcinoma (dCCA). Epidemiological studies [...] Read more.
Biliary tract carcinoma (BTC) is a group of highly heterogeneous malignancies arising from the biliary epithelium. Anatomically, BTC is categorized into gallbladder cancer (GBC) and cholangiocarcinoma (CCA), with the latter further subdivided into intrahepatic (iCCA), perihilar (pCCA), and distal cholangiocarcinoma (dCCA). Epidemiological studies reveal a dismal five-year survival rate of less than 20% for BTC patients, with limited responses to current chemotherapy regimens, underscoring the urgent need to unravel its complex molecular pathogenesis. Recent research has increasingly focused on the regulatory networks of post-translational modifications, particularly the ubiquitin-proteasome system (UPS), in tumorigenesis. As the largest subfamily of deubiquitinating enzymes (DUBs), ubiquitin-specific proteases (USPs) regulate the stability of key oncoproteins such as phosphatase and tensin homolog (PTEN) and c-Myc, playing pivotal roles in tumor cell proliferation, apoptosis evasion, invasion, and metastasis. This review systematically summarizes the differential expression profiles of USP family members (e.g., USP1, USP3, USP7, USP8, USP9X, USP21, and USP22) in BTC and their clinical significance, with a focus on elucidating how specific USPs regulate tumor progression through key substrates, including poly(ADP-ribose) polymerase 1 (PARP1), dynamin-1-like protein (DNM1L), and O-GlcNAc transferase (OGT). Furthermore, based on recent advances, we discuss the therapeutic potential of small-molecule USP inhibitors in BTC targeted therapy, providing a theoretical foundation for developing novel precision treatment strategies. Full article
(This article belongs to the Special Issue Ubiquitylation and Deubiquitylation in Health and Diseases)
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20 pages, 696 KB  
Review
Ubiquitin E3 Ligases and p53 in Doxorubicin-Induced Cardiotoxicity
by Shingo Tachibana, Yoichiro Otaki, Jun Goto, Tetsu Watanabe and Masafumi Watanabe
Int. J. Mol. Sci. 2025, 26(21), 10252; https://doi.org/10.3390/ijms262110252 - 22 Oct 2025
Viewed by 135
Abstract
Doxorubicin (Dox) is a widely used anti-cancer drug. It has proven efficacy against various cancers, although the clinical application of Dox has been limited due to dose-dependent, irreversible, and fatal Dox-induced cardiotoxicity (DIC). The mechanism of DIC remains unclear. p53 plays a key [...] Read more.
Doxorubicin (Dox) is a widely used anti-cancer drug. It has proven efficacy against various cancers, although the clinical application of Dox has been limited due to dose-dependent, irreversible, and fatal Dox-induced cardiotoxicity (DIC). The mechanism of DIC remains unclear. p53 plays a key role in DIC via cardiomyocyte loss due to cell death and oxidative stress. Its expression is strictly controlled by post-translational modifications, and its suppression in cardiomyocytes reportedly ameliorates DIC. The ubiquitin system regulates biological processes that are fundamental to the development of cardiovascular diseases. The dysregulation of several ubiquitin E3 ligases is reportedly associated with DIC development through the upregulation of p53. Ubiquitin E3 ligases are classified into four groups; all classes of E3 ligases are involved in p53 degradation. In this review, we focus on recently emerging topics regarding the role of E3 ligases in the regulation of p53 degradation. We also provide an overview of the functional roles of E3 ligases in DIC. Recent reports have identified cardioprotective agents for DIC through ubiquitin E3 ligase-mediated p53 suppression. Here, we present some findings regarding the current development of cardioprotective agents for DIC. These agents may serve as a novel therapeutic target for the treatment of DIC. Full article
(This article belongs to the Special Issue Cardioprotection in Drug-Induced Cardiotoxicity)
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15 pages, 3301 KB  
Article
Effect of Copper-Catalyzed Oxidation on the Aggregation of the Islet Amyloid Polypeptide
by Océane Amilca, Phuong Trang Nguyen, Lucie Perquis, Fabrice Collin and Steve Bourgault
Antioxidants 2025, 14(11), 1269; https://doi.org/10.3390/antiox14111269 - 22 Oct 2025
Viewed by 274
Abstract
The islet amyloid polypeptide (IAPP) is a 37-residue peptide hormone secreted by pancreatic β-cells that is known to aggregate into amyloid fibrils. These fibrils accumulate in the pancreatic islets of individuals afflicted with type 2 diabetes and are implicated in β-cell dysfunction. Metal [...] Read more.
The islet amyloid polypeptide (IAPP) is a 37-residue peptide hormone secreted by pancreatic β-cells that is known to aggregate into amyloid fibrils. These fibrils accumulate in the pancreatic islets of individuals afflicted with type 2 diabetes and are implicated in β-cell dysfunction. Metal ions such as copper and zinc are known to modulate IAPP fibrillization, yet the role of metal-induced oxidative modifications in this process remains largely unexplored. This study examines the non-enzymatic post-translational oxidation of IAPP and its effects on aggregation using the biologically relevant Cu/O2/ascorbate system. Mass spectrometry identified residues within the amyloidogenic region (residues 20–29) as the primary targets of oxidation. These oxidative modifications impaired the formation of cross-β-sheet amyloid fibrils and promoted the accumulation of amorphous aggregates. The H18A IAPP derivative, lacking the key metal-binding histidine, was also examined to assess the impact of sequence variation on oxidation and aggregation. Copper-mediated oxidation of H18A resulted in a broader distribution of oxidation sites and impacts fibril formation. These findings provide preliminary mechanistic insights into copper-induced oxidation and its impact on IAPP aggregation pathways. Full article
(This article belongs to the Section Aberrant Oxidation of Biomolecules)
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16 pages, 6472 KB  
Article
Research on the Mechanism of Hypoxia Tolerance of a Hybrid Fish Using Transcriptomics and Metabolomics
by Yuhua Tang, Jiayi Yang, Chunchun Zhu, Hong Zhang, Li Hu, Wenting Rao, Xinxin Yu, Ming Wen, Min Tao and Shaojun Liu
Biology 2025, 14(10), 1462; https://doi.org/10.3390/biology14101462 - 21 Oct 2025
Viewed by 198
Abstract
The novel hybrid fish BTB, derived from crossing blunt snout bream (Megalobrama amblycephala, BSB) and topmouth culter (Culter alburnus, TC), exhibits markedly hypoxia tolerance in aquaculture. In this study, hypoxic treatment experiments confirmed that, comparing to its original parent [...] Read more.
The novel hybrid fish BTB, derived from crossing blunt snout bream (Megalobrama amblycephala, BSB) and topmouth culter (Culter alburnus, TC), exhibits markedly hypoxia tolerance in aquaculture. In this study, hypoxic treatment experiments confirmed that, comparing to its original parent BSB, the tolerance to low oxygen of BTB increased by 20.0%. Furthermore, a comparative analysis of the transcriptome and metabolome was performed using gill tissues from BTB exposed to normoxic and hypoxic conditions. Under hypoxic conditions, BTB displayed adaptive modifications in gill lamellae and hemocytes. Transcriptomic profiling identified 789 differentially expressed genes (DEGs), with 298 upregulated and 491 downregulated, enriched in pathways including apoptosis, NK cell-mediated cytotoxicity, MAPK/TNF/Toll-like receptor signaling, and HIF-1/FoXO signaling pathways. Twelve hypoxia-related candidate genes (egln3, im_7150988, znf395a, hif-1an, mknk2b, pck2, ero1a, igfbp-1a, vhl, bpifcl, egln1a, and ccna1) were screened and validated as potential contributors to hypoxia tolerance. Metabolomics analysis revealed a total of 108 differential metabolites (78 upregulated and 30 downregulated), predominantly linked to Arginine and proline metabolism, Ether lipid metabolism, Arachidonic acid metabolism, and Glycerophospholipid metabolism. Association analysis of transcriptomics and metabolomics revealed that the DEGs and DMs were enriched in the pathways of glycerophospholipid metabolism, ether lipid metabolism, arachidonic acid metabolism, and arginine and proline metabolism. In summary, BTB exhibited relatively high hypoxia tolerance, and 12 candidate genes related to hypoxia tolerance were identified. These findings laid a foundation for further investigation into the mechanisms of hypoxia tolerance improvement in hybrid fish. Full article
(This article belongs to the Special Issue Genetics and Evolutionary Biology of Aquatic Organisms)
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