International Journal of Molecular Sciences

29 pages, 2421 KB

Open AccessArticle

Proteomic Characterization of the Clostridium cellulovorans Cellulosome and Noncellulosomal Enzymes with Sorghum Bagasse

by Mohamed Y. Eljonid, Fumiyoshi Okazaki, Eiji Hishinuma, Naomi Matsukawa, Sahar Hamido and Yutaka Tamaru

Int. J. Mol. Sci. 2025, 26(23), 11728; https://doi.org/10.3390/ijms262311728 - 3 Dec 2025

Abstract

Sorghum, the fifth major global cereal, has potential as a source crop in temperate regions. To completely use sorghum bagasse, the ideal enzyme cocktail aims to identify and select the contributed enzymatic system. This study investigated the enzymatic system of Clostridium cellulovorans cellulosome [...] Read more.

Sorghum, the fifth major global cereal, has potential as a source crop in temperate regions. To completely use sorghum bagasse, the ideal enzyme cocktail aims to identify and select the contributed enzymatic system. This study investigated the enzymatic system of Clostridium cellulovorans cellulosome and noncellulosomal enzymes using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and liquid chromatography–tandem mass spectrometry LC-MS/MS. Enzyme solutions from treated and untreated sorghum bagasse were prepared and compared based on carboxymethyl cellulase (CMCase) activity. As a result, the enzyme solution derived from untreated sorghum bagasse had the highest activity. Protein bands from each C. cellulovorans culture showed distinct patterns on SDS-PAGE examination: three enzyme fractions, including culture supernatants, crystalline cellulose (Avicel) bound, and unbound fractions. These results suggested that untreated sorghum bagasse induced a variety of cellulosomal and uncellulosomal proteins. On the other hand, 5% or 10% sorghum supernatants could not induce Avicel-bound proteins, including the cellulosome, although even 5% sorghum juice induced three major bands: 180 kilodalton (kDa), 100 kDa, and 70 kDa, respectively. In contrast, cellobiose induced three major bands, while the total number of all isolated proteins from the cellobiose medium was the most limited among all culture media. More intriguingly, our investigation detected one cellulosomal protein, hydrophobic protein A (HbpA) and three noncellulosomal enzymes, indicating that glycosyl hydrolase family 130 (GH130) was identified as a biomass-induced enzyme in good accord with previously published proteomic studies. Therefore, the proteomic dataset generated in this study provides us a foundation for future computational approaches, including machine learning-based prediction of optimal enzyme cocktails for target biomass degradation. Full article

(This article belongs to the Special Issue Advanced Research on Enzymes in Biocatalysis)

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21 pages, 1568 KB

Open AccessArticle

Thioester-Containing Protein TEP27 in Culex quinquefasciatus Promotes JEV Infection by Modulating Host Immune Function

by Yutian Huang, Yuwei Liu, Rongrong Li, Xi Zhu, Ruidong Li, Sihao Peng, Xin An, Yuxin Yang, Yuanyuan Liu, Yiping Wen, Qin Zhao, Shan Zhao, Fei Zhao, Rui Wu, Xiaobo Huang, Qigui Yan, Yifei Lang, Yiping Wang, Yajie Hu, Yi Zheng, Sanjie Cao and Senyan Du Show full author list Hide full author list

Int. J. Mol. Sci. 2025, 26(23), 11727; https://doi.org/10.3390/ijms262311727 - 3 Dec 2025

Abstract

Thioester-containing proteins (TEPs), which are distinguished by the thioester motif (GCGEQ), are essential to arthropods’ defense against infections. Although TEPs have been extensively investigated in Anopheles, Aedes, and Drosophila, their functions in Culex mosquitoes remain inadequately explored. Interestingly, we discovered [...] Read more.

Thioester-containing proteins (TEPs), which are distinguished by the thioester motif (GCGEQ), are essential to arthropods’ defense against infections. Although TEPs have been extensively investigated in Anopheles, Aedes, and Drosophila, their functions in Culex mosquitoes remain inadequately explored. Interestingly, we discovered that Culex TEPs exhibit functional antagonism to their orthologs in other species, actively facilitating viral infection in this vector. In this study, we identified nine TEP genes in Culex quinquefasciatus, three of which were found to critically facilitate Japanese encephalitis virus (JEV) infection, with CqTEP27 exhibiting the most pronounced proviral effect. Mechanistically, CqTEP27 may have suppressed the production of several antimicrobial peptides (AMPs), which increased JEV replication. Our work also highlights the potential of targeting susceptibility factors such as CqTEP27 to block pathogen acquisition. Notably, the rate of mosquito infection was significantly decreased by membrane blood feeding antisera against CqTEP27. Therefore, vaccination against CqTEP27 offers a workable method of avoiding JEV infection. According to our research, CqTEP27 is a promising target for the development of vaccines that prevent JEV transmission. By preventing viral infection in mosquitoes that feed on immunized hosts, this approach can directly disrupt the natural transmission cycle, offering a novel strategy to reduce the disease burden. Full article

(This article belongs to the Special Issue Investigating Host-Parasite Interactions for the Discovery of Novel Therapies and Vaccine Targets)

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22 pages, 3200 KB

Open AccessArticle

Remodeling of Perineuronal Nets in the Striato-Cortical Axis in L-DOPA-Induced Dyskinesia Rat Model

by Nedime Tugce Bilbay, Banu Cahide Tel, Gulsum Akkus, Canan Cakir-Aktas, Taha Solakoglu, Gul Yalcin-Cakmakli and Bulent Elibol

Int. J. Mol. Sci. 2025, 26(23), 11726; https://doi.org/10.3390/ijms262311726 - 3 Dec 2025

Abstract

L-DOPA-induced dyskinesia (LID) remains the most challenging complication of dopamine replacement therapy in Parkinson’s disease, correlated with maladaptive plasticity within corticostriatal circuits. Perineuronal nets (PNNs), extracellular matrix structures enwrapping mainly parvalbumin interneurons (PV-INs), are key regulators of neuronal stability and plasticity, yet their [...] Read more.

L-DOPA-induced dyskinesia (LID) remains the most challenging complication of dopamine replacement therapy in Parkinson’s disease, correlated with maladaptive plasticity within corticostriatal circuits. Perineuronal nets (PNNs), extracellular matrix structures enwrapping mainly parvalbumin interneurons (PV-INs), are key regulators of neuronal stability and plasticity, yet their contribution to LID is unknown. Using a unilateral 6-hydroxydopamine rat model of Parkinsonism followed by chronic L-DOPA administration, we quantified PNN–PV associations by Wisteria floribunda agglutinin (WFA) and PV immunolabeling across striatal and motor cortical territories. Dopamine loss markedly reduced PNN density and intensity in the dorsolateral striatum (DLS), which only partially recovered after L-DOPA. In LID, canonical WFA⁺/PV⁺ cells remained low, whereas non-canonical WFA⁻/PV⁺ populations expanded in both DLS and M1 motor cortex (M1), indicating region-specific remodeling toward a high-plasticity state. To assess causality, we used Chondroitinase ABC (ChABC) for PNN degradation. DLS-targeted ChABC exacerbated abnormal involuntary movements and increased local PV density, while M1-ChABC had no behavioral effect but altered PV metrics within the DLS–M1 axis. These findings identify the DLS as a critical node where PNN fragility amplifies dyskinesia, highlight a functional coupling between striatal and cortical PNN–PV remodeling, and suggest that stabilizing extracellular matrix integrity could mitigate maladaptive plasticity underlying LID. Full article

(This article belongs to the Section Molecular Neurobiology)

21 pages, 890 KB

Open AccessArticle

Molecular Response of Simmental Cows to Negative Energy Balance: Regulation of Interleukin-6 and Plasminogen During Early Lactation

by Kalina Wnorowska, Krzysztof Młynek, Paweł Solarczyk, Beata Głowińska, Karol Tucki and Kamila Puppel

Int. J. Mol. Sci. 2025, 26(23), 11725; https://doi.org/10.3390/ijms262311725 - 3 Dec 2025

Abstract

Negative energy balance (NEB) during early lactation links spontaneous lipolysis (SL) with inflammatory signaling, yet the molecular response in dual-purpose breeds remains insufficiently characterized. This study investigated how NEB regulates circulating concentrations of interleukin-6 (IL-6) and plasminogen (PL) in Simmental cows, contextualizing these [...] Read more.

Negative energy balance (NEB) during early lactation links spontaneous lipolysis (SL) with inflammatory signaling, yet the molecular response in dual-purpose breeds remains insufficiently characterized. This study investigated how NEB regulates circulating concentrations of interleukin-6 (IL-6) and plasminogen (PL) in Simmental cows, contextualizing these changes within concurrent metabolic adaptation. Forty-two cows were monitored from approximately two weeks prepartum to 150 days in milk across six defined stages. Energy balance (EB) was calculated from feed intake and energy-corrected milk yield, while daily milk production (DMP), milk composition, body condition score (BCS), β-hydroxybutyrate (BHBA), glucose (GLU), leptin (LEP), selected fatty acids (FAs: C16:0, C18:0, C18:1-t9, C18:2, IL-6), and PL were determined. EB declined progressively as DMP increased (r = −0.689, p ≤ 0.05). During peak NEB (SLII–SLIII), IL-6 increased from 92.16 to 109.59 ng·L⁻¹ and PL from 1.65 to 2.05 ng·L⁻¹, both inversely correlated with EB (r = −0.741 and −0.586, respectively) and positively associated with each other (r = 0.728), indicating coordinated activation of cytokine and fibrinolytic pathways. NEB severity was accompanied by elevated BHBA and LEP, decreased GLU, reduced BCS, and increased circulating FAs; nevertheless, ketosis remained moderate (peak BHBA 1.04 mmol·L⁻¹). These findings demonstrate that Simmental cows display a breed-specific molecular response in which NEB modulates IL-6 and PL in parallel with controlled lipid mobilization and efficient hepatic metabolism, supporting enhanced metabolic resilience during early lactation. Full article

(This article belongs to the Section Molecular Endocrinology and Metabolism)

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24 pages, 1347 KB

Open AccessReview

Endothelial-to-Mesenchymal Transition in Health and Disease: Molecular Insights and Therapeutic Implications

by Ran Kim and Woochul Chang

Int. J. Mol. Sci. 2025, 26(23), 11724; https://doi.org/10.3390/ijms262311724 - 3 Dec 2025

Abstract

Endothelial-to-mesenchymal transition (EndMT) is a cellular program implicated in fibrosis, vascular remodeling, and the tumor microenvironment across multiple organs. We synthesize mechanistic pathways including TGF-β/SMAD, non-canonical (MAPK, PI3K/AKT, Rho/ROCK), Notch, and Wnt/β-catenin cascades. Their crosstalk with hypoxia, inflammatory cues, and epigenetic mechanisms can [...] Read more.

Endothelial-to-mesenchymal transition (EndMT) is a cellular program implicated in fibrosis, vascular remodeling, and the tumor microenvironment across multiple organs. We synthesize mechanistic pathways including TGF-β/SMAD, non-canonical (MAPK, PI3K/AKT, Rho/ROCK), Notch, and Wnt/β-catenin cascades. Their crosstalk with hypoxia, inflammatory cues, and epigenetic mechanisms can drive loss of endothelial identity and acquisition of mesenchymal characteristics. We outline disease contexts in the heart, lungs, kidneys, liver, central nervous system, and cancer, highlighting context-dependent contributory roles of EndMT. Therapeutically, we review pathway-targeted agents, epigenetic inhibitors, microRNA-based strategies, antibodies/biologics, small molecules and natural compounds, and cell- and gene-based interventions. Finally, we outline a translational roadmap that pairs patient-derived iPSC/organoid and organ-on-a-chip platforms to stratify EndMT states and prioritize targets. We also explore combination regimens that integrate multi-pathway modulation with epigenetic and immune approaches, aiming to deliver clinically meaningful anti-fibrotic benefits while better preserving physiological signaling. Full article

(This article belongs to the Special Issue Health Targeting Cardiovascular and Cerebrovascular Diseases: Molecular Aspects)

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12 pages, 2093 KB

Open AccessArticle

Enhancing Secondary Metabolite Production in Actinobacteria Through Over-Expression of a Medium-Sized SARP Regulator

by Elena Heng, Lee Ling Tan, Yi Wee Lim, Winston Koh, Siew Bee Ng, Yee Hwee Lim, Dillon W. P. Tay and Fong Tian Wong

Int. J. Mol. Sci. 2025, 26(23), 11723; https://doi.org/10.3390/ijms262311723 - 3 Dec 2025

Abstract

Natural products hold immense therapeutic potential, yet they remain underexplored due to challenges in activating or producing them in laboratory settings. Here, we investigate the regulatory capabilities of a new medium-sized Streptomyces Antibiotic Regulator Protein (SARP), Fzm_SARP, in comparison to the well-characterized small [...] Read more.

Natural products hold immense therapeutic potential, yet they remain underexplored due to challenges in activating or producing them in laboratory settings. Here, we investigate the regulatory capabilities of a new medium-sized Streptomyces Antibiotic Regulator Protein (SARP), Fzm_SARP, in comparison to the well-characterized small SARP, RedD, across 18 diverse actinobacterial strains. In addition to the conserved DNA-binding domains typical of SARP regulators, the medium-sized Fzm_SARP also contains an additional NTPase domain. Our study revealed that 327 of the 422 metabolites (77%) detected in 18 wild-type actinobacterial strains were up-regulated in the SARP over-expressing strains. Among these 422 metabolites, 55% were up-regulated in the two SARP over-expressing strains whereas 15% and 7% were specifically up-regulated in the RedD and Fzm_SARP over-expressing strains, respectively. Interestingly, 244 metabolites not previously detected in the wild-type strains were detected in the two SARP over-expressing strains, resulting in a 58% increase from 422 to 666 metabolites. 36% of these new 244 metabolites were up-regulated in the two SARP over-expressing strains whereas 37% and 27% of these metabolites were specifically up-regulated in the RedD and Fzm_SARP over-expressing strains, respectively. These regulator-specific metabolites also give rise to distinct bioactivity profiles observed for each SARP. Overall, these findings expand our understanding of SARP family regulators and offer valuable insights for future research and applications in microbial biotechnology and secondary metabolite production. Full article

(This article belongs to the Special Issue Molecular Research on Actinomycetes-Derived Natural Products)

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26 pages, 14851 KB

Open AccessArticle

The Role of Osteoblasts in Phenotypic Variability of Dominant Osteogenesis Imperfecta: Evidence from Patients and Murine Models

by Milena Jovanovic, Apratim Mitra, Chris Stephan, Ka Wai Wong, Sara Talvacchio, Antonella Forlino, Michael To, Kenneth M. Kozloff, Ryan K. Dale and Joan C. Marini

Int. J. Mol. Sci. 2025, 26(23), 11722; https://doi.org/10.3390/ijms262311722 - 3 Dec 2025

Abstract

One of the hallmarks of Osteogenesis Imperfecta (OI) is phenotypic variability among individuals with the same mutation. The aim of our study is to investigate the under-explored role of osteoblast differentiation in OI phenotypic variability by using human and murine OI osteoblasts. This [...] Read more.

One of the hallmarks of Osteogenesis Imperfecta (OI) is phenotypic variability among individuals with the same mutation. The aim of our study is to investigate the under-explored role of osteoblast differentiation in OI phenotypic variability by using human and murine OI osteoblasts. This is the first comparative study of osteoblasts from OI patients vs. healthy pediatric controls. We investigated osteoblasts carrying COL1A1 substitutions Gly352Ser and Gly589Ser, each expressed in two unrelated patients differing in phenotypic severity. Osteoblasts from type III OI patients with both mutations deposited significantly less mineral vs. type IV. RNA-Seq showed osteoblasts from type IV OI patients with different mutations had downregulated mitochondrial pathways, while osteoblasts from type III OI patients showed downregulation of extracellular matrix pathways. Puromycin assay demonstrated osteoblast protein synthesis was significantly upregulated in type III vs. type IV OI patients. UPR PERK and BiP were reduced in osteoblasts with Gly352Ser from type III and IV OI patients and in osteoblasts with Gly589Ser from a type III OI patient, while both proteins were increased in Gly589Ser osteoblasts from the type IV patient. Additionally, in a murine comparative study, Col1a1 Gly349Ser, called Brtl Ser, showed a much more severe skeletal phenotype than Brtl Cys. Brtl Ser calvarial osteoblasts had reduced collagen secretion and folding with abnormal dermal collagen fibrils vs. wildtype. Also, Brtl Ser osteoblasts showed condensed actin filaments but a similar mineral deposition as Brtl Cys. Electron microscopy revealed elongated mitochondria with cristae dropout in patient and mutant murine osteoblasts. Our study yielded novel insights highlighting osteoblast differentiation, mineralization, and a potential role of mitochondria in OI pathology and phenotypic variability. Full article

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

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20 pages, 4124 KB

Open AccessArticle

Modification of Chitosan with (−)-Gossypol and (−)-Gossypol Acetic Acid Using Free-Radical Grafting Method

by Anna Hlukhaniuk, Małgorzata Świętek, Anna Kołodziej, Aleksandra Wesełucha-Birczyńska, Andrii Mahun, Libor Kobera and Daniel Horák

Int. J. Mol. Sci. 2025, 26(23), 11721; https://doi.org/10.3390/ijms262311721 - 3 Dec 2025

Abstract

One of the approaches to increase bioavailability and stability of hydrophobic biologically active compounds is their incorporation into polymer backbone. This work deals with the modification of chitosan (CS) with gossypol (GS), a phenolic compound with confirmed anticancer properties, by the free-radical grafting [...] Read more.

One of the approaches to increase bioavailability and stability of hydrophobic biologically active compounds is their incorporation into polymer backbone. This work deals with the modification of chitosan (CS) with gossypol (GS), a phenolic compound with confirmed anticancer properties, by the free-radical grafting method. The series of the CS derivatives with increasing content of GS were prepared using pure GS or gossypol acetate (GSA) and compared to the control CS (cCS). The starting CS, cCS, and GS-containing derivatives were characterized using Fourier-transform infrared (FTIR), Raman, and ¹³C ssNMR spectroscopies; elemental and thermogravimetric analysis to evaluate the influence of the radicals and GS on the properties of polymers was performed. The Folin–Ciocalteu (F-C) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) methods were used to evaluate antioxidant properties of GS-modified CSs. Additionally, the polymer solubility and the specific viscosity of the solutions were determined. The content of GS in polymers raised proportionally with increasing amount of GS added to the reaction mixture, thereby enhancing the ability to scavenge free radicals. The type of GS used (GS or GSA) in polymers affected the degree of CS crosslinking (higher for pure GS), polymer solubility (lower for pure GS), the amount of grafted GS (~20% higher for GSA), and antioxidant properties in favor of GSA. Full article

(This article belongs to the Special Issue The Chitosan Biomaterials: Advances and Challenges, 3rd Edition)

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24 pages, 2410 KB

Open AccessArticle

Characterization of the Regulatory AAA-ATPase Subunit Rpt3 in Plasmodium berghei as an Activator of Protein Phosphatase 1

by Claudianne Lainé, Caroline De Witte, Alain Martoriati, Amaury Farce, Inès Metatla, Ida Chiara Guerrera, Katia Cailliau, Jamal Khalife and Christine Pierrot

Int. J. Mol. Sci. 2025, 26(23), 11720; https://doi.org/10.3390/ijms262311720 - 3 Dec 2025

Abstract

The 26S proteasome is the main proteolytic machinery involved in protein degradation, thereby contributing to the homeostasis and stress response of eukaryotic cells. This macromolecular complex consists of a 20S core particle assembled with one or two 19S regulatory particles. Here, we describe [...] Read more.

The 26S proteasome is the main proteolytic machinery involved in protein degradation, thereby contributing to the homeostasis and stress response of eukaryotic cells. This macromolecular complex consists of a 20S core particle assembled with one or two 19S regulatory particles. Here, we describe the Plasmodium berghei (Pb) proteasome AAA-ATPase regulatory subunit Rpt3 and demonstrate its binding to the Protein Phosphatase 1 catalytic subunit (PP1c), which is one of the major and essential parasite phosphatases. The PbRpt3 protein enhances the activity of PP1c both in vitro and in a Xenopus oocyte heterologous model. Further investigation of this model suggests that the PbRpt3-PP1c interaction may occur outside of the proteasome, and it reveals that the RVxF motifs of PbRpt3 are involved in its binding and regulatory function. Moreover, the ATP-binding capacity of PbRpt3 may also contribute to its phosphatase regulatory activity. In the parasite, reverse genetic studies suggest an essential role for PbRpt3 during erythrocytic cycle of P. berghei, and an interactome analysis confirmed that PbRpt3 belongs to the 19S regulatory particle of the proteasome and may interact with proteins previously shown to be involved in phospholipid binding. Full article

(This article belongs to the Section Molecular Microbiology)

21 pages, 4070 KB

Open AccessArticle

Fluoro-Functionalized Silsesquioxane Polymer-Based High Hydrophobic Coatings for Enhancing Properties of Kraft Paper

by Mark A. Stepanov, Yuliya I. Bolgova, Olga M. Trofimova and Alexander S. Pozdnyakov

Int. J. Mol. Sci. 2025, 26(23), 11719; https://doi.org/10.3390/ijms262311719 - 3 Dec 2025

Abstract

Paper plays an important role in the packaging industry due to its low cost, light weight, recyclability and biodegradability. However, the use of paper as a packaging material is severely limited due to its hydrophilicity caused by the hydroxyl groups of cellulose. This [...] Read more.

Paper plays an important role in the packaging industry due to its low cost, light weight, recyclability and biodegradability. However, the use of paper as a packaging material is severely limited due to its hydrophilicity caused by the hydroxyl groups of cellulose. This study reports a simple preparation of highly hydrophobic kraft paper by a one-step dip coating method using [3-(2,2,3,3-tetrafluoropropoxy)propyl]silsesquioxane, {3-[(2,2,3,3,4,4,5,5-octafluoropentyl)oxy]propyl}silsesquioxane or {3-[(2,2,3,3,4,4,5,5,6,6,7,7-dodecafluoroheptyl)oxy]propyl}silsesquioxane as hydrophobic agents. As a result of modification of kraft paper, a stable covalently bonded coating is formed on its surface. The coated kraft paper has demonstrated (1) high water resistance (the water contact angle (WCA) values were 124–141°, and the water absorption and the water vapor permeability (WVP) rates were significantly decreased), (2) excellent resistance to aggressive environments and temperature, (3) enhanced mechanical properties (tensile strength increased from 46.8 to 70.8 MPa), and (4) high wear resistance, as confirmed by sandpaper abrasion, bending, and finger-wipe tests. It was shown that the maximum contact angle values were achieved for kraft paper modified with a 5% polymer solution. The results of this study have great potential, given the simplicity of the modification method, for use in the production of paper-based packaging materials with water-repellent, enhanced mechanical and moisture-protective properties. Full article

(This article belongs to the Collection State-of-the-Art Macromolecules in Russia)

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13 pages, 2900 KB

Open AccessArticle

MicroRNA-1 Suppresses Tumor Progression and UHRF1 Expression in Cholangiocarcinoma

by Makoto Muto, Teruhide Ishigame, Takashi Kimura, Naoya Sato, Yasuhide Kofunato, Akira Kenjo, Hiroyuki Yamamoto, Yuhki Yokoyama, Hirofumi Yamamoto and Shigeru Marubashi

Int. J. Mol. Sci. 2025, 26(23), 11718; https://doi.org/10.3390/ijms262311718 - 3 Dec 2025

Abstract

MicroRNAs (miRNAs) have been shown to suppress tumor progression in several cancers, including cholangiocarcinoma; however, their mechanisms and roles remain largely unexplored. In this study, we aimed to identify novel miRNAs and molecules associated with cholangiocarcinoma progression. Using miRNA and mRNA microarrays from [...] Read more.

MicroRNAs (miRNAs) have been shown to suppress tumor progression in several cancers, including cholangiocarcinoma; however, their mechanisms and roles remain largely unexplored. In this study, we aimed to identify novel miRNAs and molecules associated with cholangiocarcinoma progression. Using miRNA and mRNA microarrays from surgically resected specimens, we identified microRNA-1 (miR-1) as significantly downregulated in cholangiocarcinoma tissues and selected it for further analysis. In the in vitro assay, miR-1 was transfected into cholangiocarcinoma cell lines to assess its effect on tumor progression. Proliferation and migration/invasion assays demonstrated significant tumor suppression in miR-1-transfected cells. Additionally, cell cycle and apoptosis assays revealed an increase in cells in the G1 and G2/M phases, a decrease in the S phase, and an elevation in apoptosis rates in miR-1-transfected cells. Further analysis of the miRNA and mRNA microarray data identified ubiquitin-like with plant homeodomain and ring finger domains 1 (UHRF1) as a molecule potentially associated with miR-1. Quantitative RT-PCR and Western blotting analysis confirmed that UHRF1 expression was suppressed following miR-1 transfection. This study demonstrated that cholangiocarcinoma progression was suppressed by restoring miR-1 expression, suggesting that UHRF1 expression is involved in cholangiocarcinoma progression. The results of this study provide new insights into the molecular mechanisms underlying cholangiocarcinoma progression. Full article

(This article belongs to the Special Issue MicroRNA (miRNA) Technology in Cancer)

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21 pages, 1220 KB

Open AccessArticle

Diagnostic and Prognostic Potential of CXCL9 and CXCL10 Chemokines in Alcohol-Associated Liver Disease

by Agnieszka Szczerbinska, Jacek Rolinski, Agata Surdacka and Halina Cichoz-Lach

Int. J. Mol. Sci. 2025, 26(23), 11717; https://doi.org/10.3390/ijms262311717 - 3 Dec 2025

Abstract

Alcohol-associated liver disease (ALD) is the leading cause of liver-related mortality. In ALD, excessive inflammatory response may induce a massive loss of hepatocytes and lead to irreversible liver damage with progressive fibrosis. Chemokines stimulate the migration of immune cells to the site of [...] Read more.

Alcohol-associated liver disease (ALD) is the leading cause of liver-related mortality. In ALD, excessive inflammatory response may induce a massive loss of hepatocytes and lead to irreversible liver damage with progressive fibrosis. Chemokines stimulate the migration of immune cells to the site of inflammation and contribute to the inflammatory cascade that may result in organ failure. We aimed to investigate blood concentrations of CXCL9/MIG, CXCL10/IP-10, and CXCL16 chemokines and their diagnostic and prognostic significance in patients with ALD. In a prospective observational study, 88 individuals were recruited, including 63 patients with ALD (44 men and 19 women, aged 48.49 ± 10.88) and 25 healthy control volunteers matched for age, sex, and ethnicity. In blood samples, concentrations of CXCL9/MIG, CXCL10/IP-10, and CXCL16 were measured using immunoenzymatic ELISAs. Correlations were examined between CXCL levels and (a) traditional inflammatory markers (C-reactive protein, white blood cell count, neutrophil count, lymphocyte count, and neutrophil-to-lymphocyte ratio-NLR) and (b) liver dysfunction severity scores: Child–Turcotte–Pugh (CTP), MELD-NA, MELD 3.0, and modified Maddrey’s discriminant function (mDF). Patients’ survival within 30 days of hospital admission was recorded for analysis. CXCL capabilities in predicting the severity of liver dysfunction and ALD outcome were validated. ALD patients showed significant systemic upregulation of all studied chemokines compared to the control group. Patients with advanced liver disease, classified as MELD-Na ≥ 20, MELD3.0 > 19, and CTP class C, as well as poor short-term outcomes, presented with significantly higher CXCL9 and CXCL10 levels compared to their counterparts. ALD non-survivors had significantly higher concentrations of all studied CXCLs in comparison to controls. Positive correlations between CXCL16 and CRP, leukocytosis, neutrophils, and NLR were confirmed (0.67; 0.46; 0.48; 0.54, respectively). Although none of the chemokines correlated with ALT activity, CXCL9, CXCL10, and CXCL16 showed positive correlations with bilirubin and alkaline phosphatase and inverse correlations with albumin levels. Our findings revealed the diagnostic and prognostic value of the studied CXCLs in ALD. In particular, CXCL9 and CXCL10 may have potential for discrimination of severe liver dysfunction and poor short-term prognosis. Further multicenter studies are required to confirm our results. Full article

(This article belongs to the Special Issue Immune-Liver Axis—from Disease Pathogenesis to Therapeutic Target)

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17 pages, 1689 KB

Open AccessArticle

The Cellular Effects of Di(2-ethylhexyl) Phthalate in Non-Malignant Colonic Epithelia Involve Oxidative Stress

by Zachary S. Bomstein, Kimberly F. Allred and Clinton D. Allred

Int. J. Mol. Sci. 2025, 26(23), 11716; https://doi.org/10.3390/ijms262311716 - 3 Dec 2025

Abstract

Human exposure to Di(2-ethylhexyl) Phthalate (DEHP) occurs through ingestion of contaminated food. Yet, the effects of DEHP on gastrointestinal toxicity at the cellular level are poorly understood and studies conducted to date have used malignant cell lines, limiting our understanding of molecular signaling [...] Read more.

Human exposure to Di(2-ethylhexyl) Phthalate (DEHP) occurs through ingestion of contaminated food. Yet, the effects of DEHP on gastrointestinal toxicity at the cellular level are poorly understood and studies conducted to date have used malignant cell lines, limiting our understanding of molecular signaling in intestinal epithelia of otherwise healthy individuals. The objective of our study was to use a non-transformed, colonic epithelial cell line (Young Adult Mouse Colonocytes; YAMCs) to characterize the in vitro effects of DEHP on non-malignant colonic epithelia. A 72 h DEHP exposure significantly reduced cell number and proliferation while short-term exposure increased: cellular apoptosis, BAX expression, Reactive Oxygen Species (ROS) production, gene expression linked to oxidative stress (NRF2, GCLC, HO-1, CHOP). Antioxidant pretreatment prior to DEHP exposure attenuated the phthalate’s apoptotic effect, suggesting a link between oxidative stress and apoptosis. Using YAMCs with a CRISPR-deleted Aryl Hydrocarbon Receptor (AhR) we further showed that the apoptotic and pro-oxidative effects of the phthalate are partially mediated through AhR. In conclusion, we have demonstrated that DEHP-induced toxicity in non-malignant colonocytes is due to ROS-induced oxidative stress and subsequently, apoptosis. We have further demonstrated that these effects are partly mediated by the AhR, a mechanism that deserves further investigation. Future studies should build on these findings by (a) characterizing the specific mechanisms linking ROS production to apoptosis demonstrated in our model of exposure, (b) measuring the dynamics of the receptor following DEHP exposure and (c) examining these effects over a longer exposure period. Full article

(This article belongs to the Special Issue Inflammatory Bowel Disease: Molecular Advances in Pathogenesis and Therapies)

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21 pages, 1115 KB

Open AccessReview

Hidden Industrial Trans-Fatty Acids: Mechanistic Insights into Dyslipidemia, Cardiovascular Disease, and Metabolic Dysfunction-Associated Steatotic Liver Disease

by Mona A Hegazy, Bojana Vidovic, Shimaa Abobbakr, Aleksandra Zeljkovic, Aleksandra Stefanovic and Jelena Vekic

Int. J. Mol. Sci. 2025, 26(23), 11715; https://doi.org/10.3390/ijms262311715 - 3 Dec 2025

Abstract

Trans-fatty acids (TFAs), particularly industrially produced TFAs (iTFAs), are linked to dyslipidemia, cardiovascular disease (CVD), and metabolic dysfunction-associated steatotic liver disease (MASLD). Despite regulatory efforts, “hidden” TFAs persist in processed foods, posing ongoing health risks. This narrative review synthesizes evidence on the biochemical [...] Read more.

Trans-fatty acids (TFAs), particularly industrially produced TFAs (iTFAs), are linked to dyslipidemia, cardiovascular disease (CVD), and metabolic dysfunction-associated steatotic liver disease (MASLD). Despite regulatory efforts, “hidden” TFAs persist in processed foods, posing ongoing health risks. This narrative review synthesizes evidence on the biochemical and metabolic impacts of the most studied TFAs, focusing on dyslipidemia, CVD, and MASLD, and highlights gaps in research and policy. Available data suggest that iTFAs, which are dominant in modern diets, were associated with elevated low-density lipoprotein cholesterol (LDL-C), triglycerides, and lipoprotein (a), reduced high-density lipoprotein cholesterol (HDL-C), exacerbating atherosclerosis, increasing hepatic lipogenesis, oxidative stress, and inflammation and driving MASLD progression to fibrosis, whereas ruminant TFAs (rTFAs) showed neutral or beneficial effects. Epigenetic modifications (e.g., DNA methylation, miRNA alterations) induced by TFAs may further worsen metabolic dysfunction. Analytical challenges and inconsistent food labeling make it difficult to assess TFAs intake. Global disparities in TFAs regulations persist, but some regions still exceed recommended limits. Hidden iTFAs represent a critical public health issue, necessitating stricter policies, improved labeling, and consumer education. Future research should prioritize human studies on TFA-induced epigenetic changes and develop healthier fat alternatives. Eliminating residual iTFAs from the food supply is essential to mitigate cardiometabolic risks globally. Full article

(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)

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23 pages, 2482 KB

Open AccessReview

Decoding the Kruppel-like Transcription Factors in Atherosclerosis: Insight from Molecular and Translational Perspectives

by Yiyang Cao, Chenyue Wang, Xuzhou Zhu, Meiqian Zhan, Jinhui Xu and Meixiu Jiang

Int. J. Mol. Sci. 2025, 26(23), 11714; https://doi.org/10.3390/ijms262311714 - 3 Dec 2025

Abstract

Atherosclerosis is a leading contributor to cerebrovascular and cardiovascular diseases, which can be driven by multiple pathological processes, including chronic inflammation, lipid dysregulation, and vascular remodeling. Currently, lifestyle intervention and pharmacological intervention, like statins, are recommended in clinical treatments. However, the mortality and [...] Read more.

Atherosclerosis is a leading contributor to cerebrovascular and cardiovascular diseases, which can be driven by multiple pathological processes, including chronic inflammation, lipid dysregulation, and vascular remodeling. Currently, lifestyle intervention and pharmacological intervention, like statins, are recommended in clinical treatments. However, the mortality and morbidity rates caused by atherosclerosis remain high. Kruppel-like transcription factors (KLFs) are zinc-finger-containing transcription factors that are involved in various physiological and pathological processes. By modulating endothelial cell homeostasis, smooth muscle cell phenotypic switching, and inflammatory responses, members of the KLF family—particularly KLF2, KLF4, KLF5, KLF6, and KLF14—emerge as pivotal regulators in the initiation and progression of atherosclerotic lesions. In this review, we constructed a comprehensive network of KLFs in the pathogenesis of atherosclerosis. Based on the molecular mechanism, this review for the first time highlighted newly identified substances that exploit KLF-modulated pathways to attenuate atherosclerosis, and discussed emerging gene therapy and nanotechnology approaches, addressing both the therapeutic promise and challenges associated with targeted KLF modulation. This first offered new avenues for translational and precision medicine in atherosclerotic cardiovascular disease from the perspective of KLF. Full article

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

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22 pages, 1737 KB

Open AccessReview

Twin Small RNAs and Divergent Fates: The Expansive Regulatory Networks of OmrA and OmrB

by Julia Konarska, Karolina Jaworska, Paulina Lipska and Adrianna Raczkowska

Int. J. Mol. Sci. 2025, 26(23), 11713; https://doi.org/10.3390/ijms262311713 - 3 Dec 2025

Abstract

Small RNAs (sRNAs) have emerged as key regulators of bacterial physiology, enabling rapid adaptation to environmental changes through post-transcriptional control. The homologous sRNAs OmrA and OmrB, conserved in Escherichia coli and other Enterobacterales, share sequence similarity yet differ in expression dynamics and [...] Read more.

Small RNAs (sRNAs) have emerged as key regulators of bacterial physiology, enabling rapid adaptation to environmental changes through post-transcriptional control. The homologous sRNAs OmrA and OmrB, conserved in Escherichia coli and other Enterobacterales, share sequence similarity yet differ in expression dynamics and functional outputs. Both act by base-pairing with target mRNAs, a process facilitated by the RNA chaperone Hfq, which promotes duplex formation and influences RNA stability. In some contexts, regulation also depends on RelA, which stabilizes Hfq-RNA complexes and links OmrA/B activity to the stringent response. Together, OmrA and OmrB modulate outer membrane protein synthesis, motility, biofilm formation, iron uptake, and virulence. OmrA is preferentially induced under nutrient limitation and integrates into the σ^S stress regulon, whereas OmrB is more broadly expressed and can engage in context-dependent mechanisms such as target sequestration. This review highlights the molecular mechanisms of OmrA/B regulation and their contribution to global sRNA-mediated regulatory networks that coordinate bacterial adaptation and pathogenicity. Full article

(This article belongs to the Section Molecular Microbiology)

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19 pages, 994 KB

Open AccessArticle

5-Substituted 4-Thiouridines, 4-Thio-2′-deoxyuridines and Their Oligoglycol Carbonate Prodrugs as Promising Antimicrobial Agents

by Dmitry A. Makarov, Maxim V. Jasko, Sergey D. Negrya, Inna L. Karpenko, Elizabeth V. Urbina, Vladimir O. Chekhov, Olga V. Efremenkova, Byazilya F. Vasilyeva, Danila V. Zimenkov, Anastasia I. Ushtanit, Sergey N. Kochetkov and Liudmila A. Alexandrova

Int. J. Mol. Sci. 2025, 26(23), 11712; https://doi.org/10.3390/ijms262311712 - 3 Dec 2025

Abstract

The problem of antibiotic resistance is one of the challenges that science and medicine face in the 21st century. Nucleoside analogs have already proven as antiviral and antitumor agents, and, currently, there are more and more reports on their antibacterial and antifungal activity. [...] Read more.

The problem of antibiotic resistance is one of the challenges that science and medicine face in the 21st century. Nucleoside analogs have already proven as antiviral and antitumor agents, and, currently, there are more and more reports on their antibacterial and antifungal activity. The substitution of an oxygen atom by a sulfur one leads to the emergence of unique properties. Here, we report the synthesis of eight new 4-thioanalogs of 5-substituted (5-alkyloxymethyl and 5-alkyltriazolylmethyl) derivatives of 2′-deoxyuridine and uridine, which were active against Mycobacterium tuberculosis and Gram-positive bacteria. The novel sulfur-containing nucleosides were synthesized via activation of the pyrimidine C4 position, followed by condensation with thioacetic acid and deblocking. To increase the solubility, oligoglycol carbonate depot forms were obtained via activation of the 3′-hydroxyl group using N,N’-carbonyldiimidazole and condensation with triethylene glycol. The highest inhibitory activity was demonstrated by 3′-triethylene glycol depot forms of 4-thio-5-undecyl- and 5-dodecyloxymethyl-2′-deoxyuridine (4a,b) against two strains of M. smegmatis. The most promising compounds were 5-[4-decyl-(1,2,3-triazol-1-yl)methyl]-4-thio-2′-deoxy- and ribouridine (3c,g) and 5-undecyloxymethyl 4-thiouridine (3e) active toward clinical M. intracellulare isolates. Overall, novel sulfur-containing nucleoside analogs were low toxic, demonstrated better inhibitory activity compared to their C4-oxo ones, and, thus, are promising compounds for the development of new antibacterial agents. Full article

(This article belongs to the Special Issue New Insights in Antibiotic Resistance/Tolerance)

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3 pages, 166 KB

Open AccessEditorial

Special Issue: Polymers, Polymer Blends, and Polymeric Drug Release Systems with Antiviral or Antibacterial Effect—2nd Edition

by Piotr Dobrzyński

Int. J. Mol. Sci. 2025, 26(23), 11711; https://doi.org/10.3390/ijms262311711 - 3 Dec 2025

Abstract

Although the crisis stemming from the global pandemic caused by the coronavirus SARS-CoV-2 seems to have subsided, the threats to global health posed by pathogenic viruses and bacteria remain significant [...] Full article

(This article belongs to the Special Issue Polymers, Polymer Blends, and Polymeric Drug Release Systems with Antiviral or Antibacterial Effect—2nd Edition)

21 pages, 1261 KB

Open AccessReview

Anti-Inflammatory Properties of Resveratrol

by Mateusz Wątroba and Dariusz Szukiewicz

Int. J. Mol. Sci. 2025, 26(23), 11710; https://doi.org/10.3390/ijms262311710 - 3 Dec 2025

Abstract

Resveratrol (RSV), a naturally occurring phytoalexin polyphenolic compound, continues to attract the attention of researchers due to its therapeutic potential, including anti-inflammatory effects. The focus of this work is to critically review RSV’s anti-inflammatory effects at cellular and molecular levels and its clinical [...] Read more.

Resveratrol (RSV), a naturally occurring phytoalexin polyphenolic compound, continues to attract the attention of researchers due to its therapeutic potential, including anti-inflammatory effects. The focus of this work is to critically review RSV’s anti-inflammatory effects at cellular and molecular levels and its clinical and physiological implications as elucidated by in vivo and in vitro studies to identify some unresolved issues. Reference was made to the dietary recommendations of RSV, its poor bioavailability, and high metabolism, limiting the therapeutic use of RSV and requiring formulation strategies for improving its clinical usefulness. Issues related to the interpretation of the results of studies on the anti-inflammatory activity of RSV were also discussed. The cellular response to RSV and the probable molecular pathways associated with it were analyzed separately. Another point for further investigation is the fact that not all the effects found in vitro or in animal models are replicated in clinical studies. Full article

(This article belongs to the Special Issue Potential Health Benefits of Resveratrol: Laboratory-Confirmed Mechanisms of Action)

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