International Journal of Molecular Sciences

5 pages, 187 KiB

Open AccessEditorial

Special Issue “Functional Role of Cytokines in Cancer and Chronic Inflammation”

by Daria Potashnikova and Elizaveta Fasler-Kan

Int. J. Mol. Sci. 2025, 26(9), 4048; https://doi.org/10.3390/ijms26094048 (registering DOI) - 25 Apr 2025

Cytokines are a diverse group of signaling proteins that are secreted by a wide range of cell types, including, but not limited to, immune cells [...] Full article

(This article belongs to the Special Issue Functional Role of Cytokines in Cancer and Chronic Inflammation)

13 pages, 689 KiB

Open AccessReview

Obesity- and High-Fat-Diet-Induced Neuroinflammation: Implications for Autonomic Nervous System Dysfunction and Endothelial Disorders

by Galateia Stathori, Nikolaos F. Vlahos, Evangelia Charmandari and Georgios Valsamakis

Int. J. Mol. Sci. 2025, 26(9), 4047; https://doi.org/10.3390/ijms26094047 (registering DOI) - 25 Apr 2025

Abstract

Obesity is a multifactorial condition linked to severe health complications, including cardiovascular diseases and endothelial dysfunction. Both obesity and high-fat diets (HFDs) are strongly associated with neuroinflammation, particularly in the hypothalamus. The autonomic nervous system (ANS), which controls involuntary physiological processes, is critical [...] Read more.

Obesity is a multifactorial condition linked to severe health complications, including cardiovascular diseases and endothelial dysfunction. Both obesity and high-fat diets (HFDs) are strongly associated with neuroinflammation, particularly in the hypothalamus. The autonomic nervous system (ANS), which controls involuntary physiological processes, is critical for maintaining cardiovascular health, and its dysfunction is implicated in endothelial disorders. With its homeostatic control centers located in the hypothalamus and brainstem, a crucial question arises: could obesity- and HFD-induced neuroinflammation disrupt central ANS structures, leading to ANS dysfunction and subsequent endothelial disorders? This review examined whether neuroinflammation caused by obesity and HFD contributes to endothelial dysfunction through the dysregulation of the ANS. Our analysis revealed that hypothalamic inflammation linked to obesity and an HFD is associated with sympathetic hyperactivity and endothelial disorders. Identified molecular mechanisms include the influence of inflammatory cytokines, activation of the NF-κB/IKK-β pathway, microglial activation mediated by angiotensin II, circulating mitochondria triggering cGAS activation, and the stimulation of the TLR4 pathway. Our findings suggest that hypothalamic inflammation may play a central role in the interplay between obesity/an HFD, ANS dysfunction, and endothelial disorders. Full article

(This article belongs to the Special Issue Reproductive Diseases and Modern Lifestyle: From Bench to Bedside)

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16 pages, 2117 KiB

Open AccessArticle

Local and Systemic Endothelial Damage in Patients with CEAP C2 Chronic Venous Insufficiency: Role of Mesoglycan

by Angelo Santoliquido, Claudia Carnuccio, Luca Santoro, Angela Di Giorgio, Alessia D'Alessandro, Francesca Romana Ponziani, Flavia Angelini, Marcello Izzo and Antonio Nesci

Int. J. Mol. Sci. 2025, 26(9), 4046; https://doi.org/10.3390/ijms26094046 - 24 Apr 2025

Abstract

Chronic venous disease (CVD) involves complex pathophysiological mechanisms, particularly an imbalance between matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs), contributing to venous remodeling and varicosities. Elevated MMP-2 and MMP-9 levels are commonly found in tissues affected by venous ulcers. Inflammation plays a [...] Read more.

Chronic venous disease (CVD) involves complex pathophysiological mechanisms, particularly an imbalance between matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs), contributing to venous remodeling and varicosities. Elevated MMP-2 and MMP-9 levels are commonly found in tissues affected by venous ulcers. Inflammation plays a central role in CVD, with higher levels of pro-inflammatory markers present in varicose veins compared to healthy ones. Syndecans, key components of the endothelial glycocalyx, are involved in inflammatory responses. Alterations in the glycocalyx structure are associated with vascular damage in both venous and arterial diseases. This study aimed to investigate inflammatory changes in CVD patients, focusing on glycocalyx damage and the therapeutic role of mesoglycan, a glycosaminoglycan-based drug. A prospective, monocentric study included 23 patients with C2 clinical–etiological–anatomical–pathological (CEAP) CVD. Serum samples were collected before and after mesoglycan treatment. Results showed significantly elevated levels of VCAM-1, MMP-2, MMP-9, SDC-1, IL-6, and IL-8 in blood from varicose veins versus the systemic circulation. Patients received 50 mg of mesoglycan orally every 12 h for 90 days. After treatment, a notable reduction in inflammatory markers was observed. These results support the hypothesis that mesoglycan may alleviate both local and systemic inflammation, providing insights into new therapeutic strategies for CVD management. Full article

(This article belongs to the Special Issue Cellular and Molecular Progression of Cardiovascular Diseases)

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22 pages, 2019 KiB

Open AccessArticle

A Single-Domain VNAR Nanobody Binds with High-Affinity and Selectivity to the Heparin Pentasaccharide Fondaparinux

by Martha Gschwandtner, Rupert Derler, Elisa Talker, Christina Trojacher, Nina Gubensäk, Walter Becker, Tanja Gerlza, Zangger Klaus, Pawel Stocki, Frank S. Walsh, Julia Lynn Rutkowski and Andreas Kungl

Int. J. Mol. Sci. 2025, 26(9), 4045; https://doi.org/10.3390/ijms26094045 - 24 Apr 2025

Abstract

Glycosaminoglycans (GAGs) are key ligands for proteins involved in physiological and pathological processes. Specific GAG-binding patterns are rarely identified, with the heparin pentasaccharide as an Antithrombin-III ligand being the best characterized. Generating glycan-specific antibodies is difficult due to their size, pattern dispersion, and [...] Read more.

Glycosaminoglycans (GAGs) are key ligands for proteins involved in physiological and pathological processes. Specific GAG-binding patterns are rarely identified, with the heparin pentasaccharide as an Antithrombin-III ligand being the best characterized. Generating glycan-specific antibodies is difficult due to their size, pattern dispersion, and flexibility. Single-domain variable new antigen receptors (VNAR nanobodies) from nurse sharks are highly soluble, stable, and versatile. Their unique properties suggest advantages over conventional antibodies, particularly for challenging biotherapeutic targets. Here we have used VNAR semi-synthetic phage libraries to select high-affinity fondaparinux-binding VNARs that did not show cross-reactivity with other GAG species. Competition ELISA and surface plasmon resonance identified a single fondaparinux-selective VNAR clone. This VNAR exhibited an extraordinarily stable protein fold: the beta-strands are stabilized by a robust hydrophobic network, as revealed by heteronuclear NMR. Docking fondaparinux to the VNAR structure revealed a large contact surface area between the CDR3 loop of the antibody and the glycan. Fusing the VNAR with a human Fc domain resulted in a stable product with a high affinity for fondaparinux (Kd = 9.3 × 10⁻⁸ M) that could efficiently discriminate between fondaparinux and other glycosaminoglycans. This novel glycan-targeting screening technology represents a promising therapeutic strategy for addressing GAG-related diseases. Full article

(This article belongs to the Section Biochemistry)

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16 pages, 729 KiB

Open AccessArticle

The Influence of Different Preservation Protocols on the Teeth’s Osteoinductive Characteristics: An In Vitro Study

by Filiberto Mastrangelo, Sara Franceschelli, Ciro Annicchiarico, Alice Annicchiarico, Maria Elena Bizzoca, Federica De Cecco, Rosalba La Gioia, Gabriele Cervino and Mirko Pesce

Int. J. Mol. Sci. 2025, 26(9), 4044; https://doi.org/10.3390/ijms26094044 - 24 Apr 2025

Abstract

The purpose of this study was to evaluate in vitro whether the type of tooth preservation before treatment with the Tooth Transformer^® (TT) device affects the osteoinductive characteristics of the extracted tooth. Forty extracted teeth from healthy non-smoking patients were selected. All [...] Read more.

The purpose of this study was to evaluate in vitro whether the type of tooth preservation before treatment with the Tooth Transformer^® (TT) device affects the osteoinductive characteristics of the extracted tooth. Forty extracted teeth from healthy non-smoking patients were selected. All teeth were cleaned of caries, tartar, and filling material and then roughly sectioned and divided into four experimental groups according to storage type: room-temperature (RT) tooth samples, frozen tooth samples, RIPA tooth samples, and fresh tooth samples. Each sample was minced, demineralized, and disinfected using the TT device. The Enzyme-Linked ImmunoSorbent Assay (ELISA) test revealed the presence of bone morphogenetic protein-2 (BMP-2) and collagen type-I (COL-I) in all of the samples, demonstrating that the fresh teeth retained the most significant amount of osteoinductive protein. In contrast, the tooth samples stored at room temperature (RT) showed the most important loss of BMP-2 and COL-I. A Western Blot analysis demonstrated the presence of the Mineralization Protein LIM-1 (LMP-1) and Transforming Growth Factor-β (TGF-β) in all of the dental samples analyzed. The fresh and frozen dental samples showed significantly higher levels of LMP-1 than those in the other samples. In contrast, the levels of TGF-β were similar in all of the dental samples examined, regardless of the type of storage. These experimental results suggest that an extracted tooth should be treated with the TT device as soon as possible to maximize its osteoinductive potential in surgical bone preservation and regeneration procedures. Full article

(This article belongs to the Section Materials Science)

23 pages, 6218 KiB

Open AccessArticle

Hypoxia-Dependent Upregulation of VEGF Relies on β3-Adrenoceptor Signaling in Human Retinal Endothelial and Müller Cells

by Martina Lucchesi, Lorenza Di Marsico, Lorenzo Guidotti, Matteo Lulli, Luca Filippi, Silvia Marracci and Massimo Dal Monte

Int. J. Mol. Sci. 2025, 26(9), 4043; https://doi.org/10.3390/ijms26094043 (registering DOI) - 24 Apr 2025

Abstract

β-adrenoceptors (BARs) are involved in vascular endothelial growth factor (VEGF) production during retinal neovascularization. Here, using human retinal endothelial and Müller cells (hRECs and MIO-M1, respectively), we evaluated the effects exerted by hypoxia on BARs, hypoxia-inducible factor-1α subunit (HIF-1α) and VEGF, as well [...] Read more.

β-adrenoceptors (BARs) are involved in vascular endothelial growth factor (VEGF) production during retinal neovascularization. Here, using human retinal endothelial and Müller cells (hRECs and MIO-M1, respectively), we evaluated the effects exerted by hypoxia on BARs, hypoxia-inducible factor-1α subunit (HIF-1α) and VEGF, as well as the involvement of BAR3 and nitric oxide synthase (NOS) enzymes in hypoxia-induced VEGF production. We altered oxygen availability through a hypoxic incubator. BARs, HIF-1 α and VEGF levels were evaluated. Cells were treated with the BAR3 antagonist SR59230A, different NOS inhibitors or the NO donor SNAP. The influence of the BAR3/NOS axis on hypoxic VEGF production was assessed. Hypoxia upregulated BAR3, HIF-1α and VEGF in hRECs and MIO-M1 cells. SR59230A counteracted hypoxia-dependent VEGF increase in both cell lines, exerting no effect on HIF-1α upregulation. Treatments with NOS inhibitors prevented the hypoxia-dependent VEGF increase, while SNAP abrogated the effect of SR59230A in reducing hypoxia-induced VEGF upregulation. The present results corroborate the hypothesis that in the hypoxic retina, BAR3 influence on VEGF production is mediated by NO and suggest that, at least in endothelial and Müller cells, BAR3 activity is necessary to allow the HIF-1-mediated VEGF upregulation. Full article

(This article belongs to the Special Issue Molecular and Cellular Mechanisms of Retinal Diseases)

17 pages, 3389 KiB

Open AccessArticle

Genome-Wide Identification and Functional Analysis of C2H2 Zinc Finger Transcription Factor Genes in the Intertidal Macroalga Pyropia haitanensis

by Jiajia Xie, Dehua Ji, Yan Xu, Kai Xu, Chaotian Xie and Wenlei Wang

Int. J. Mol. Sci. 2025, 26(9), 4042; https://doi.org/10.3390/ijms26094042 - 24 Apr 2025

Abstract

The possible regulatory effects of C2H2 zinc finger proteins, which are important transcription factors, on intertidal seaweed responses to abiotic stress are unclear. This study was conducted to comprehensively analyze the C2H2 gene family of a representative intertidal seaweed species (Pyropia haitanensis [...] Read more.

The possible regulatory effects of C2H2 zinc finger proteins, which are important transcription factors, on intertidal seaweed responses to abiotic stress are unclear. This study was conducted to comprehensively analyze the C2H2 gene family of a representative intertidal seaweed species (Pyropia haitanensis) and clarify its genomic characteristics and biological functions. A total of 107 PhC2H2 zinc finger protein-encoding genes distributed on five P. haitanensis chromosomes were identified and divided into three subgroups. The expression levels of 85, 61, 58, 45, and 41 PhC2H2 genes responded in the maturation of filaments, high-temperature, salt, low-irradiance, and dehydration stress, respectively. The PhC2H2 gene family was conserved during Porphyra evolution, with no indications of large-scale genome-wide replication events. On average, PhC2H2 genes had more transposable element (TE) insertions than Pyropia yezoensis and Porphyra umbilicalisC2H2 genes, suggesting that TE insertions may have been the main driver of PhC2H2 gene family expansion. A key gene (PhC2H2.94) screened following a quantitative trait locus analysis was significantly responsive to high-temperature stress and was associated with photosynthesis, peroxisomes, the ubiquitin proteasome pathway, and the endoplasmic reticulum-related protein processing pathway, which contribute to the stress tolerance of P. haitanensis. Additionally, PhC2H2.94 transgenic Chlamydomonas reinhardtii exhibited increased tolerance to heat stress. This study provides new insights and genetic resources for characterizing the molecular mechanism underlying intertidal seaweed responses to abiotic stresses and breeding stress-resistant macroalgae. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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30 pages, 3180 KiB

Open AccessReview

From Defense to Disease: How the Immune System Fuels Epithelial–Mesenchymal Transition in Ovarian Cancer

by Michał Kos, Paulina Mertowska, Sebastian Mertowski, Jacek Roliński, Aleksandra Krasińska-Płachta, Tomasz Urbanowicz, Marek Gogacz and Ewelina Grywalska

Int. J. Mol. Sci. 2025, 26(9), 4041; https://doi.org/10.3390/ijms26094041 - 24 Apr 2025

Abstract

Ovarian cancer is one of the most deadly gynecological cancers, with over 300 thousand new cases per year, most of which are diagnosed in advanced stages. The limited availability of effective biomarkers and lack of characteristic symptoms make early diagnosis difficult, resulting in [...] Read more.

Ovarian cancer is one of the most deadly gynecological cancers, with over 300 thousand new cases per year, most of which are diagnosed in advanced stages. The limited availability of effective biomarkers and lack of characteristic symptoms make early diagnosis difficult, resulting in a five-year survival rate of 30–40%. Mutations in the BRCA1 and BRCA2 genes and abnormalities of signaling pathways such as PI3K/AKT and TP53 play a key role in the progression of ovarian cancer. The immune system, which can act against tumors, often supports tumor development in the ovarian cancer microenvironment through immunoevasion, which is influenced by cytokines such as IL-6, IL-10, and TGF-β. Epithelial-to-mesenchymal transition (EMT) allows cancer cells to acquire mesenchymal characteristics, increasing their invasiveness and metastatic capacity. Immunological factors, including pro-inflammatory cytokines and signals from the tumor microenvironment regulate the EMT process. This review aims to present the role of EMT in ovarian cancer progression, its interactions with the immune system, and potential biomarkers and therapeutic targets. Modulation of the immune response and inhibition of EMT may constitute the basis for personalized therapies, which opens new possibilities for improving the prognosis and efficacy of treatment in patients with ovarian cancer. Full article

(This article belongs to the Special Issue Ovarian Cancer: Pathogenesis, Biomarkers and Treatment)

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11 pages, 2454 KiB

Open AccessArticle

Glibenclamide Serves as a Potent Vasopressor to Treat Vasoplegia After Cardiopulmonary Bypass and Reperfusion in a Porcine Model

by Andreas Winter, Pascal Nepper, Marcus Hermann, Franziska Bayer, Stephanie Riess, Razan Salem, Jan Hlavicka, Anatol Prinzing, Florian Hecker, Tomas Holubec, Kai Zacharowski, Thomas Walther and Fabian Emrich

Int. J. Mol. Sci. 2025, 26(9), 4040; https://doi.org/10.3390/ijms26094040 - 24 Apr 2025

Abstract

The hemodynamic stabilization of patients after complex cardiac surgery is a daily challenge. The use of high doses of catecholamines is common but has potential adverse effects. Glibenclamide, a K_ATP blocker, seems to attenuate vasoplegia in different animal models of septic shock. [...] Read more.

The hemodynamic stabilization of patients after complex cardiac surgery is a daily challenge. The use of high doses of catecholamines is common but has potential adverse effects. Glibenclamide, a K_ATP blocker, seems to attenuate vasoplegia in different animal models of septic shock. Therefore, the aim of this study was to investigate the impact of Glibenclamide on the vasoplegic syndrome after cardiopulmonary bypass in a porcine model. In this experimental study, 20 landrace pigs were randomized into two groups and examined: In the control group, standard medical therapy, including norepinephrine, was used, and in the study group standard medical therapy plus additional Glibenclamide was administered. Following general anesthesia, prolonged cardiopulmonary bypass and aortic cross-clamping was performed. In the study group, Glibenclamide was administered 45 min after weaning from cardiopulmonary bypass. The dosage used was 10 mg/kg as a bolus, followed by a continuous infusion of 10 mg/kg/h. Hemodynamic and laboratory measurements were performed. Glibenclamide had a relevant effect on circulatory parameters. With increasing vascular resistance and blood pressure, norepinephrine was able to be reduced. While the heart rate dropped to physiological levels, the cardiac index decreased as well. The results lead to the conclusion that Glibenclamide was able to break through vasoplegic syndrome and could therefore serve as a potent drug to stabilize patients after cardiac surgery. Full article

(This article belongs to the Special Issue New Molecular Insights into Ischemia/Reperfusion: 2nd Edition)

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34 pages, 1833 KiB

Open AccessArticle

Synergistic Effects of Insulin-like Growth Factor-1 and Platelet-Derived Growth Factor-BB in Tendon Healing

by Julia Rieber, Petra Wolint, Gabriella Meier-Bürgisser, Esteban Ongini, Pietro Giovanoli, Maurizio Calcagni, Jess G. Snedeker and Johanna Buschmann

Int. J. Mol. Sci. 2025, 26(9), 4039; https://doi.org/10.3390/ijms26094039 - 24 Apr 2025

Abstract

Tendon ruptures are common musculoskeletal injuries associated with prolonged healing and complications such as adhesion formation and rerupture. Despite advancements in treatment strategies, full functional recovery remains a challenge. Growth factors (GFs) like insulin-like growth factor-1 (IGF-1) and platelet-derived growth factor-BB (PDGF-BB) play [...] Read more.

Tendon ruptures are common musculoskeletal injuries associated with prolonged healing and complications such as adhesion formation and rerupture. Despite advancements in treatment strategies, full functional recovery remains a challenge. Growth factors (GFs) like insulin-like growth factor-1 (IGF-1) and platelet-derived growth factor-BB (PDGF-BB) play key roles in tendon repair and may have synergistic effects when applied together. To support tendon healing, a bioactive electrospun polymer scaffold made of Degrapol^® (DP) was developed, incorporating IGF-1, PDGF-BB, or both. A range of in vitro and in vivo analyses were performed to assess scaffold structure, cell behavior, gene expression, metabolism, and biomechanical and adhesion outcomes three weeks post-surgery. Interestingly, the combined application of IGF-1 and PDGF-BB did not simply amplify individual effects but showed a complex interaction. Depending on the parameter and time point, the combination led to either enhanced or reduced responses compared to single-factor treatments, indicating a synergistic modulation rather than a purely additive effect. These findings suggest that the combination of IGF-1 and PDGF-BB can modulate key cellular and molecular processes in tendon regeneration, making this approach a promising strategy to improve tendon healing. Full article

(This article belongs to the Section Bioactives and Nutraceuticals)

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20 pages, 976 KiB

Open AccessReview

Hypocrellin-Mediated PDT: A Systematic Review of Its Efficacy, Applications, and Outcomes

by Jakub Fiegler-Rudol, Katarzyna Kapłon, Kornela Kotucha, Magdalena Moś, Dariusz Skaba, Aleksandra Kawczyk-Krupka and Rafał Wiench

Int. J. Mol. Sci. 2025, 26(9), 4038; https://doi.org/10.3390/ijms26094038 - 24 Apr 2025

Abstract

Photodynamic therapy (PDT) is a light-activated treatment that generates reactive oxygen species (ROS) to induce microbial cell death. As resistance to traditional antibiotics intensifies globally, PDT has emerged as a promising alternative or adjunctive antimicrobial strategy. Among various photosensitizers, Hypocrellin, a perylenequinone compound, [...] Read more.

Photodynamic therapy (PDT) is a light-activated treatment that generates reactive oxygen species (ROS) to induce microbial cell death. As resistance to traditional antibiotics intensifies globally, PDT has emerged as a promising alternative or adjunctive antimicrobial strategy. Among various photosensitizers, Hypocrellin, a perylenequinone compound, has shown high ROS yield and broad-spectrum activity against bacteria and fungi. This systematic review evaluated the efficacy, safety, and therapeutic potential of Hypocrellin-mediated antimicrobial photodynamic therapy. Following PRISMA 2020 guidelines, a comprehensive literature search was conducted in PubMed, Embase, Scopus, and the Cochrane Library for studies published between 2015 and 2025. Eligible studies included in vitro and preclinical in vivo research using Hypocrellin as a photosensitizer. Quality and risk of bias were assessed using a structured nine-item checklist. Ten eligible studies, all conducted in China, were included. Hypocrellin-mediated aPDT significantly reduced microbial loads in both planktonic and biofilm states of resistant pathogens such as Candida albicans, Candida auris, Cutibacterium acnes, and Staphylococcus aureus. The treatment acted via ROS-mediated apoptosis, membrane disruption, and mitochondrial dysfunction, with minimal cytotoxicity to mammalian cells. Studies also reported enhanced efficacy when Hypocrellin was incorporated into nanocarriers, polymeric scaffolds, or combined with chemodynamic or photothermal therapies. However, substantial heterogeneity was observed in Hypocrellin concentrations, irradiation parameters, and outcome measures. Hypocrellin-based PDT exhibits potent antimicrobial activity and favorable safety in preclinical settings, supporting its potential as an alternative to conventional antibiotics. However, standardized treatment protocols and robust clinical trials are urgently needed to validate long-term safety and translational feasibility. These findings underscore the broader promise of PDT in addressing drug-resistant infections through a mechanism unlikely to induce resistance. Full article

(This article belongs to the Special Issue Photodynamic Therapy and Photodetection, 2nd Edition)

24 pages, 784 KiB

Open AccessReview

Endocytic Pathways Unveil the Role of Syndecans in the Seeding and Spreading of Pathological Protein Aggregates: Insights into Neurodegenerative Disorders

by Anett Hudák and Tamás Letoha

Int. J. Mol. Sci. 2025, 26(9), 4037; https://doi.org/10.3390/ijms26094037 - 24 Apr 2025

Abstract

Alzheimer’s disease and other neurodegenerative disorders are characterized by the accumulation of misfolded proteins, such as amyloid-beta, tau, and α-synuclein, which disrupt neuronal function and contribute to cognitive decline. Heparan sulfate proteoglycans, particularly syndecans, play a pivotal role in the seeding, aggregation, and [...] Read more.

Alzheimer’s disease and other neurodegenerative disorders are characterized by the accumulation of misfolded proteins, such as amyloid-beta, tau, and α-synuclein, which disrupt neuronal function and contribute to cognitive decline. Heparan sulfate proteoglycans, particularly syndecans, play a pivotal role in the seeding, aggregation, and spreading of toxic protein aggregates through endocytic pathways. Among these, syndecan-3 is particularly critical in regulating the internalization of misfolded proteins, facilitating their propagation in a prion-like manner. This review examines the mechanisms by which syndecans, especially SDC3, contribute to the seeding and spreading of pathological protein aggregates in neurodegenerative diseases. Understanding these endocytic pathways provides valuable insights into the potential of syndecans as biomarkers and therapeutic targets for early intervention in Alzheimer’s disease and other related neurodegenerative disorders. Full article

(This article belongs to the Special Issue Pathogenic Proteins in Neurodegenerative Diseases: From Pathogenesis to Therapeutic Innovations)

17 pages, 4037 KiB

Open AccessArticle

Identification and Exploration of Pyroptosis-Related Genes in Macrophage Cells Reveal Necrotizing Enterocolitis Heterogeneity Through Single-Cell and Bulk-Sequencing

by Peipei Zhang, Ying Li, Panpan Xu, Peicen Zou, Sihan Sheng, Ruiqi Xiao, Pu Xu, Ying Chen, Yue Du, Lishuang Ma and Yajuan Wang

Int. J. Mol. Sci. 2025, 26(9), 4036; https://doi.org/10.3390/ijms26094036 - 24 Apr 2025

Abstract

Necrotizing enterocolitis (NEC) is an acute intestine dysfunction intestinal disorder characterized by inflammation and cell death, including pyroptosis. Previous studies have implicated pyroptosis, particularly via NLRP3 inflammatory activation, and contribute to the development of NEC. However, the genetic and molecular mechanisms underlying pyroptosis [...] Read more.

Necrotizing enterocolitis (NEC) is an acute intestine dysfunction intestinal disorder characterized by inflammation and cell death, including pyroptosis. Previous studies have implicated pyroptosis, particularly via NLRP3 inflammatory activation, and contribute to the development of NEC. However, the genetic and molecular mechanisms underlying pyroptosis in NEC pathogenesis and sequelae remain unclear. Our study aimed to identify the pyroptosis-related cell populations and genes and explore potential therapeutic targets. Single-cell RNA sequencing (scRNA-seq) data were analyzed to identify the cell populations related to NEC and pyroptosis. Weighted gene correlation network analysis (WGCNA) of bulk RNA-seq was performed to identify gene modules associate with pyroptosis. Cell–cell communication was employed to investigate intercellular signaling networks. Gene Set Enrichment Analysis (GSEA) was conducted to compare the pathways enriched in the high and low TREM1-expressing subgroups. Immunofluorescence staining was performed to detect the TREM1⁺CD163⁺ macrophages in the intestines. PCR and Western blot were performed to detect the expression of mRNA and proteins in the intestine tissues and cells. scRNA-seq analysis revealed increased macrophage abundance in NEC, with one macrophage cluster (cluster 4) exhibiting a markedly elevated pyroptosis score. WGCNA identified a gene module (MEbrown) that positively correlated with pyroptosis. Five genes (TREM1, TLN1, NOTCH2, MPZL1, and ADA) within this module were identified as potential diagnostic markers of pyroptosis. Furthermore, we identified a novel macrophage subpopulation, TREM1⁺CD163⁺, in NEC. Cell–cell communication analysis suggested that TREM1⁺CD163⁺ macrophages interact with other cells primarily through the NAMPT/ITGA5/ITGB1 and CCL3/CCR1 pathways. GSEA revealed a significant association between high TREM1 expression and pathways related to pyroptosis, cell proliferation, and inflammation. In vivo and in vitro experiments confirmed an increase in TREM1⁺CD163⁺ macrophages in NEC-affected intestines. TREM1 inhibition in THP-1 cells significantly reduced the expression of pro-inflammatory cytokines and pyroptosis-related genes and proteins. We identified the TREM1⁺CD163+ macrophage population that plays a crucial role in pyroptosis during NEC progression. Our findings elucidate the biological functions and molecular mechanisms of TREM1, demonstrating its upregulation in vivo and pro-pyroptosis effects in vitro. These insights advance our understanding of the role of pyroptosis in NEC pathogenesis and suggest TREM1 is a potential therapeutic target for NEC. Full article

(This article belongs to the Section Molecular Immunology)

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22 pages, 3297 KiB

Open AccessReview

Antiepileptic Drug Combinations for Epilepsy: Mechanisms, Clinical Strategies, and Future Prospects

by Cunjiang Li, Xingyu Wang, Mingzhenlong Deng, Qinggen Luo, Chaoxing Yang, Zhicheng Gu, Shuxian Lin, Yongxiang Luo, Lei Chen, Yan Li and Bin He

Int. J. Mol. Sci. 2025, 26(9), 4035; https://doi.org/10.3390/ijms26094035 - 24 Apr 2025

Abstract

Epilepsy is a chronic neurological disorder characterized by abnormal neuronal discharge, leading to recurrent and unpredictable disruptions in brain function. Despite over 30 antiepileptic drugs (AEDs), 30% of patients develop drug-resistant epilepsy, requiring combination therapy. This review explores epilepsy’s pathogenesis, including neuronal hyperexcitability, [...] Read more.

Epilepsy is a chronic neurological disorder characterized by abnormal neuronal discharge, leading to recurrent and unpredictable disruptions in brain function. Despite over 30 antiepileptic drugs (AEDs), 30% of patients develop drug-resistant epilepsy, requiring combination therapy. This review explores epilepsy’s pathogenesis, including neuronal hyperexcitability, neurotransmitter imbalances, and ion channel dysfunction, alongside genetic, inflammatory, immune, and oxidative stress factors. AEDs are classified by mechanisms like voltage-gated ion channel modulation and GABA/glutamate regulation, tracing their evolution from traditional (e.g., phenobarbital) to modern therapies (e.g., lamotrigine). Combination therapy, using complementary mechanisms (e.g., lacosamide with levetiracetam), enhances efficacy but poses risks like drug interactions and cognitive impairment. Integrating molecular biology and pharmacology advances, this review highlights the need for rational drug selection and individualized strategies to improve epilepsy treatment outcomes and patient quality of life. Future directions include personalized treatments, optimized dosage forms, novel drug targets, and multi-target drugs. Full article

(This article belongs to the Special Issue From Molecular Insights to Novel Therapies: Neurological Diseases)

15 pages, 707 KiB

Open AccessArticle

Fecal Arachidonic Acid: A Potential Biomarker for Inflammatory Bowel Disease Severity

by Muriel Huss, Tanja Elger, Claudia Kunst, Johanna Loibl, Sabrina Krautbauer, Gerhard Liebisch, Arne Kandulski, Martina Müller, Hauke Christian Tews and Christa Buechler

Int. J. Mol. Sci. 2025, 26(9), 4034; https://doi.org/10.3390/ijms26094034 - 24 Apr 2025

Abstract

Arachidonic acid levels are elevated in the colonic mucosa of patients with inflammatory bowel disease (IBD). Fecal metabolites are emerging as valuable diagnostic tools for IBD. This study aimed to investigate associations between 31 fecal fatty acids, including arachidonic acid, to identify potential [...] Read more.

Arachidonic acid levels are elevated in the colonic mucosa of patients with inflammatory bowel disease (IBD). Fecal metabolites are emerging as valuable diagnostic tools for IBD. This study aimed to investigate associations between 31 fecal fatty acids, including arachidonic acid, to identify potential correlations with disease severity. Among the 31 fatty acids analyzed in feces, dihomo-γ-linolenic acid, arachidonic acid, and adrenic acid were significantly increased in patients with IBD compared to controls. In contrast, levels of linoleic acid and γ-linolenic acid, the precursors of arachidonic acid, were similar between both groups. No significant differences in fatty acid levels were observed between patients with Crohn’s disease and ulcerative colitis. Arachidonic acid and adrenic acid levels positively correlated with fecal calprotectin, a clinically established marker of IBD severity, but showed no association with stool consistency or the Gastrointestinal Symptom Rating Scale. This suggests that these fatty acids are linked to disease severity rather than disease-related symptoms. Current IBD-specific medications had no significant impact on the fecal levels of any of the 31 fatty acids. In summary, this study demonstrates elevated fecal levels of dihomo-γ-linolenic acid, arachidonic acid, and adrenic acid in IBD patients. Normal levels of precursor fatty acids suggest that impaired downstream metabolism may contribute to the accumulation of these n-6 polyunsaturated fatty acids. Full article

(This article belongs to the Special Issue Molecular Diagnosis and Treatment of Inflammatory Bowel Disease)

17 pages, 13939 KiB

Open AccessArticle

FAM20B-Catalyzed Glycosylation Regulates the Chondrogenic and Osteogenic Differentiation of the Embryonic Condyle by Controlling IHH Diffusion and Release

by Xiaoyan Chen, Han Liu, Yuhong Huang, Leilei Li, Xuxi Jiang, Bo Liu, Nan Li, Lei Zhu, Chao Liu and Jing Xiao

Int. J. Mol. Sci. 2025, 26(9), 4033; https://doi.org/10.3390/ijms26094033 - 24 Apr 2025

Abstract

Although the roles of proteoglycans (PGs) have been well documented in the development and homeostasis of the temporomandibular joint (TMJ), how the glycosaminoglycan (GAG) chains of PGs contribute to TMJ chondrogenesis and osteogenesis still requires explication. In this study, we found that FAM20B, [...] Read more.

Although the roles of proteoglycans (PGs) have been well documented in the development and homeostasis of the temporomandibular joint (TMJ), how the glycosaminoglycan (GAG) chains of PGs contribute to TMJ chondrogenesis and osteogenesis still requires explication. In this study, we found that FAM20B, a hexokinase essential for attaching GAG chains to the core proteins of PGs, was robustly activated in the condylar mesenchyme during TMJ development. The inactivation of Fam20b in craniofacial neural crest cells (CNCCs) dramatically reduced the synthesis and accumulation of GAG chains rather than core proteins in the condylar cartilage, which resulted in a hypoplastic condylar cartilage by severely promoting chondrocyte hypertrophy and perichondral ossification. In the condyles of Wnt1-Cre;Fam20b^f/f mouse embryos, enlarged Ihh- and COL10-expressing domains indicated premature hypertrophy resulting from an attenuated IHH-PTHRP negative feedback in condylar chondrocytes, while increased osteogenic markers, canonical Wnt activity, and type-H angiogenesis verified the enhanced osteogenesis in the perichondrium. Further ex vivo investigations revealed that the loss of Fam20b decreased the domain area but increased the activity of HH signaling in the embryonic condylar mesenchyme. Moreover, the abrogation of GAG chains in heparan sulfate and chondroitin sulfate proteoglycans led to a rapid up- and then downregulation of HH signaling in condylar chondrocytes, implicating a “slow-release” manner of growth factors controlled by GAG chains. Overall, this study revealed a comprehensive role of the FAM20B-catalyzed GAG chain synthesis in the chondrogenic and osteogenic differentiation of the embryonic TMJ condyle. Full article

(This article belongs to the Special Issue Glycobiology in Human Health and Disease)

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29 pages, 4571 KiB

Open AccessReview

Triplexes Color the Chromaverse by Modulating Nucleosome Phasing and Anchoring Chromatin Condensates

by Alan Herbert

Int. J. Mol. Sci. 2025, 26(9), 4032; https://doi.org/10.3390/ijms26094032 - 24 Apr 2025

Abstract

Genomic sequences that form three-stranded triplexes (TPXs) under physiological conditions (called T-flipons) play an important role in defining DNA nucleosome-free regions (NFRs). Within these NFRs, other flipon types can cycle conformations to actuate gene expression. The transcripts read from the NFR form condensates [...] Read more.

Genomic sequences that form three-stranded triplexes (TPXs) under physiological conditions (called T-flipons) play an important role in defining DNA nucleosome-free regions (NFRs). Within these NFRs, other flipon types can cycle conformations to actuate gene expression. The transcripts read from the NFR form condensates that engage proteins and small RNAs. The helicases bound then trigger RNA polymerase release by dissociating the 7SK ribonucleoprotein. The TPXs formed usually incorporate RNA as the third strand. TPXs made only from DNA arise mostly during DNA replication. Many small RNA types (sRNAs) and long noncoding (lncRNA) can direct TPX formation. TPXs made with circular RNAs have greater stability and specificity than those formed with linear RNAs. LncRNAs can affect local gene expression through TPX formation and transcriptional interference. The condensates seeded by lncRNAs are updated by feedback loops involving proteins and noncoding RNAs from the genes they regulate. Some lncRNAs also target distant loci in a sequence-specific manner. Overall, lncRNAs can rapidly evolve by adding or subtracting sequence motifs that modify the condensates they nucleate. LncRNAs show less sequence conservation than protein-coding sequences. TPXs formed by lncRNAs and sRNAs help place nucleosomes to restrict endogenous retroelement (ERE) expression. The silencing of EREs starts early in embryogenesis and is essential for bootstrapping development. Once the system is set, EREs play a different role, with a notable enrichment of Short Interspersed Nuclear Repeats (SINEs) in Enhancer–Promoter condensates. The highly programmable TPX-dependent processes create a chromaverse capable of many complexities. Full article

(This article belongs to the Collection Feature Papers in Molecular Genetics and Genomics)

17 pages, 3908 KiB

Open AccessArticle

B3 Superfamily in Cucumber (Cucumis sativus L.): Identification, Evolution, Expression Patterns, and Function in Glandular Trichome Development

by Mingming Dong, Lei Sun, Wujun Wang, Yaru Wang, Li Shan, Xingwang Liu and Huazhong Ren

Int. J. Mol. Sci. 2025, 26(9), 4031; https://doi.org/10.3390/ijms26094031 - 24 Apr 2025

Abstract

The B3 transcription factor superfamily, crucial for plant growth and stress adaptation, remains poorly characterized in cucumber (Cucumis sativus), a globally important vegetable crop. Here, we conducted the first genome-wide identification of 52 B3 superfamily genes in cucumber, classifying them into [...] Read more.

The B3 transcription factor superfamily, crucial for plant growth and stress adaptation, remains poorly characterized in cucumber (Cucumis sativus), a globally important vegetable crop. Here, we conducted the first genome-wide identification of 52 B3 superfamily genes in cucumber, classifying them into LAV, ARF, RAV, and REM subfamilies through integrated phylogenetic and structural analyses. These genes exhibited conserved B3 domains with lineage-specific motif architectures and diverse exon–intron organizations, particularly within the structurally divergent REM subfamily. Collinearity analysis revealed segmental duplication as a key driver of family expansion, notably between syntenic REM clusters on chromosomes 2 (CsREM5-7) and 6 (CsREM18-20). Promoter cis-element profiling identified enrichment in hormone-responsive and stress adaptation motifs, suggesting functional diversification in signaling pathways. Furthermore, tissue-specific expression divergence was observed across 10 organs, with ARF members displaying broad regulatory roles and REM genes showing apical meristem enrichment. Strikingly, CsRAV8 exhibited glandular trichome-specific expression, a novel finding, given Arabidopsis RAVs’ lack of trichome-related functions. Spatial validation via in situ hybridization localized CsRAV8 transcripts to trichome glandular head cells. Functional investigation using virus-induced gene silencing (VIGS) demonstrated that CsRAV8 suppression caused significant glandular trichome shriveling, implicating its role in maintaining glandular cavity integrity. This study provides the first comprehensive genomic inventory of B3 transcription factors in cucumber, providing evolutionary insights and functional frameworks for future functional genomics studies. Full article

(This article belongs to the Section Molecular Plant Sciences)

32 pages, 4178 KiB

Open AccessReview

The Impact of Plant-Derived Polyphenols on Combating Efflux-Mediated Antibiotic Resistance

by Anna Duda-Madej, Szymon Viscardi, Piotr Niezgódka, Wiktoria Szewczyk and Katarzyna Wińska

Int. J. Mol. Sci. 2025, 26(9), 4030; https://doi.org/10.3390/ijms26094030 - 24 Apr 2025

Abstract

The global healthcare system is increasingly challenged by the rising prevalence of multidrug-resistant bacteria and the limited therapeutic options for related infections. Efflux-mediated antibiotic resistance represents a significant obstacle, primarily due to the absence of drugs specifically designed to target bacterial efflux pumps. [...] Read more.

The global healthcare system is increasingly challenged by the rising prevalence of multidrug-resistant bacteria and the limited therapeutic options for related infections. Efflux-mediated antibiotic resistance represents a significant obstacle, primarily due to the absence of drugs specifically designed to target bacterial efflux pumps. Recent research has identified polyphenols, a broad class of plant-derived organic compounds, as potential inhibitors of efflux pump activity. This review consolidates data on the inhibitory properties of eight widely distributed polyphenols: curcumin, quercetin, luteolin, tannic acid, naringenin, epigallocatechin-3-gallate, ellagic acid, and resveratrol. These compounds have demonstrated the capacity to inhibit efflux pumps, either through direct interference with bacterial protein function or by downregulating the expression of genes encoding pump subunits. Importantly, several polyphenols exhibit synergistic interactions with antibiotics, including colistin, ciprofloxacin, and tetracycline. For instance, quercetin has shown inhibitory potency comparable to that of established efflux pump inhibitors such as verapamil and reserpine. These findings suggest that polyphenols represent promising candidates for the development of novel efflux pump inhibitors. However, further research is required to validate their efficacy and safety and facilitate their translation into clinical applications for combating antibiotic resistance. Full article

(This article belongs to the Special Issue Drug Treatment for Bacterial Infections)

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