International Journal of Molecular Sciences

23 pages, 1608 KiB

Open AccessArticle

Multi-Layered Analysis of TGF-β Signaling and Regulation via DNA Methylation and microRNAs in Astrocytic Tumors

by Klaudia Skóra, Damian Strojny, Dawid Sobański, Rafał Staszkiewicz, Paweł Gogol, Mateusz Miller, Przemysław Rogoziński, Nikola Zmarzły and Beniamin Oskar Grabarek

Int. J. Mol. Sci. 2025, 26(16), 7798; https://doi.org/10.3390/ijms26167798 (registering DOI) - 12 Aug 2025

Abstract

Astrocytic tumors are a heterogeneous group of glial neoplasms characterized by marked differences in biological behavior and patient prognosis. Transforming growth factor-beta (TGF-β) signaling plays a pivotal role in astrocytoma pathogenesis; however, the extent and mechanisms of its epigenetic regulation remain poorly understood. [...] Read more.

Astrocytic tumors are a heterogeneous group of glial neoplasms characterized by marked differences in biological behavior and patient prognosis. Transforming growth factor-beta (TGF-β) signaling plays a pivotal role in astrocytoma pathogenesis; however, the extent and mechanisms of its epigenetic regulation remain poorly understood. This study aimed to investigate how promoter methylation and microRNA-mediated mechanisms regulate key genes within the TGF-β signaling pathway across various astrocytoma grades. Tumor tissue samples from 65 patients with WHO grade II–IV astrocytomas were analyzed using Affymetrix gene expression and microRNA microarrays. Promoter methylation of TGF-β signaling genes was assessed using methylation-specific polymerase chain reaction (MSP). Gene expression was validated by reverse transcription quantitative polymerase chain reaction (RT-qPCR), and protein levels were quantified using enzyme-linked immunosorbent assay (ELISA). MicroRNA targets were predicted using bioinformatic tools, and survival analyses were conducted using Kaplan–Meier and Cox regression models. Six genes—SMAD1, SMAD3, SKIL, BMP2, SMAD4, and MAPK1—showed significant upregulation in high-grade tumors (fold change > 5.0, p < 0.05), supported by RT-qPCR and protein-level data. Promoter hypomethylation and reduced expression of regulatory microRNAs (e.g., hsa-miR-145-5p targeting SMAD3) were more common in higher-grade tumors. Protein–protein interaction analysis indicated strong functional interconnectivity among the overexpressed genes. High protein levels of SMAD1, SMAD3, and SKIL were significantly associated with shorter overall survival (p < 0.001). This multi-level analysis reveals that astrocytic tumor progression involves epigenetic derepression and microRNA-mediated dysregulation of TGF-β signaling. Elevated expression of SMAD1, SMAD3, and SKIL emerged as strong prognostic indicators, underscoring their potential as biomarkers and therapeutic targets in astrocytic tumors. Full article

(This article belongs to the Special Issue Cancer Biology: From Genetic Aspects to Treatment, 2nd Edition)

31 pages, 1874 KiB

Open AccessReview

Natural Polymorphic Variants in the CYP450 Superfamily: A Review of Potential Structural Mechanisms and Functional Consequences

by Rafał Prost and Wojciech Płaziński

Int. J. Mol. Sci. 2025, 26(16), 7797; https://doi.org/10.3390/ijms26167797 (registering DOI) - 12 Aug 2025

Abstract

Cytochrome P450 (CYP450) enzymes play an essential role in the metabolism of drugs, particularly in phase I metabolic reactions. In this article, we present a comprehensive review of fifteen selected enzymes belonging to the CYP450 family. The enzymes included in this analysis are [...] Read more.

Cytochrome P450 (CYP450) enzymes play an essential role in the metabolism of drugs, particularly in phase I metabolic reactions. In this article, we present a comprehensive review of fifteen selected enzymes belonging to the CYP450 family. The enzymes included in this analysis are CYP7A1, CYP3A4, CYP3A5, CYP2D6, CYP2E1, CYP2C8, CYP2C18, CYP2C9, CYP2C19, CYP2B6, CYP2A6, CYP2A13, CYP1B1, CYP1A1, and CYP1A2. We examined the influence of natural, polymorphic variations within their primary amino acid sequences on their enzymatic function and mechanisms of action. To begin, we compiled a dataset of naturally occurring polymorphic variants for these enzymes. This was achieved through a detailed analysis of entries in the UniProt database, as well as an extensive review of the current scientific literature. For each variant, we included commentary regarding its potential impact on enzyme activity or drug response, based on evidence observed in in vitro experiments, in vivo studies, or clinical trials. Particular emphasis was placed on how such polymorphisms might alter the metabolism of xenobiotics, thereby potentially affecting pharmacological outcomes. In this respect, the work represents the first comprehensive source in the scientific literature that systematically gathers and organizes data on CYP450 polymorphisms, including an assessment of their potential significance in processes mediated by these enzymes. A more detailed comparison of the polymorphism-related in vitro studies is devoted to CYP3A4, an enzyme that displays the largest fraction of clinically significant polymorphs. Secondly, we aimed to establish possible molecular explanations for why specific polymorphisms exhibit clinically or experimentally observable effects. To explore this, we performed a qualitative structural analysis of the enzymes, focusing on shared structural characteristics among the examined members of the CYP450 family. The results of this analysis demonstrate that there is no single universal mechanism by which polymorphisms influence the function of CYP450 enzymes. Instead, the mechanisms vary and may include alterations in the orientation of the enzyme within the lipid membrane, changes affecting the association or dissociation of substrates and products at the active site, structural stabilization or destabilization of the enzyme’s reactive centers, modifications in the way the enzyme interacts with its ligand, or alterations in the character of the interface involved in contact with its redox partner (electron transfer protein). Furthermore, among the polymorphisms that significantly impact enzyme function, mutations involving the substitution of arginine residues for other amino acids appear to be overrepresented. Full article

(This article belongs to the Collection Latest Review Papers in Macromolecules)

26 pages, 6716 KiB

Open AccessArticle

When Two-Fold Is Not Enough: Quantifying Uncertainty in Low-Copy qPCR

by Stephen A. Bustin, Sara Kirvell, Tania Nolan, Reinhold Mueller and Gregory L. Shipley

Int. J. Mol. Sci. 2025, 26(16), 7796; https://doi.org/10.3390/ijms26167796 (registering DOI) - 12 Aug 2025

Abstract

Accurate interpretation of qPCR data continues to present significant challenges, particularly at low target concentrations where technical variability, stochastic amplification, and efficiency fluctuations confound quantification. The widespread assumption that qPCR outputs are intrinsically reliable, coupled with inconsistent adherence to best-practice guidelines, has exacerbated [...] Read more.

Accurate interpretation of qPCR data continues to present significant challenges, particularly at low target concentrations where technical variability, stochastic amplification, and efficiency fluctuations confound quantification. The widespread assumption that qPCR outputs are intrinsically reliable, coupled with inconsistent adherence to best-practice guidelines, has exacerbated issues of reproducibility and contributed to misleading conclusions. This may distort pathogen load quantification in diagnostic settings, whilst in gene expression studies, it can lead to overinterpretation of small fold changes. This study presents a systematic, cross-platform evaluation of qPCR performance across a wide dynamic range using defined reaction mixes and technical replicates. We show that calculated copy numbers can closely match expected values over more than three orders of magnitude, but that variability increases markedly at low input concentrations, often exceeding the magnitude of biologically meaningful differences. We conclude that establishing and reporting confidence intervals from the data itself is essential for transparency and for distinguishing reliable quantification from technical noise. Full article

(This article belongs to the Special Issue Advancing Molecular Science Through Reproducible qPCR: MIQE Guidelines and Beyond)

19 pages, 1103 KiB

Open AccessReview

Therapeutic Potential of Chimeric Antigen Receptor-Expressing Mesenchymal Stem Cells in the Treatment of Inflammatory and Autoimmune Diseases

by Vladislav Volarevic, Carl Randall Harrell, Crissy Fellabaum, Valentin Djonov and Ana Volarevic

Int. J. Mol. Sci. 2025, 26(16), 7795; https://doi.org/10.3390/ijms26167795 (registering DOI) - 12 Aug 2025

Abstract

Chimeric antigen receptor-engineered mesenchymal stem cells (CAR-MSCs) represent a novel and highly adaptable platform for the targeted treatment of inflammatory and autoimmune diseases. By integrating the inflammation-homing and immunomodulatory properties of mesenchymal stem cells (MSCs) with the antigen-specific recognition and activation potential of [...] Read more.

Chimeric antigen receptor-engineered mesenchymal stem cells (CAR-MSCs) represent a novel and highly adaptable platform for the targeted treatment of inflammatory and autoimmune diseases. By integrating the inflammation-homing and immunomodulatory properties of mesenchymal stem cells (MSCs) with the antigen-specific recognition and activation potential of chimeric antigen receptors (CARs), CAR-MSCs enable site-specific delivery of therapeutic agents directly to inflamed or diseased tissues. This dual functionality enhances therapeutic precision while minimizing off-target effects and systemic toxicity. Recent preclinical studies have demonstrated the efficacy of CAR-MSCs in modulating pathogenic immune responses, reducing local inflammation, and promoting tissue repair in various disease models. CAR-MSCs have been engineered to recognize and interact with disease-specific antigens or inflammatory markers, allowing them to selectively suppress the activation and proliferation of autoreactive immune cells. This targeted immunosuppression offers a promising strategy for restoring immune tolerance without the risks associated with systemic immunosuppression. In this review, we provide a comprehensive overview of recent developments in CAR-MSC design, highlight mechanisms by which CARs enhance MSC functionality, and discuss key challenges, including safety, scalability, and regulatory considerations. Collectively, these emerging approaches hold substantial promise for reshaping future therapies for inflammatory and autoimmune diseases. Full article

(This article belongs to the Special Issue Therapeutic Uses of Adult Stem Cells)

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18 pages, 6039 KiB

Open AccessArticle

Neutrophil Gelatinase-Associated Lipocalin: A Shared Early Biomarker of Remote Organ Dysfunction in Blast-Induced Extremity Trauma

by Cassie J. Rowe, Uloma Nwaolu, Philip J. Spreadborough and Thomas A. Davis

Int. J. Mol. Sci. 2025, 26(16), 7794; https://doi.org/10.3390/ijms26167794 (registering DOI) - 12 Aug 2025

Abstract

Polytrauma is a critical global health concern characterized by immune dysregulation and a high risk of multiple organ dysfunction syndrome (MODS). Early molecular mechanisms linking trauma severity to organ injury are poorly understood. We used two rat blast-polytrauma models: a tourniquet-induced ischemia/reperfusion injury [...] Read more.

Polytrauma is a critical global health concern characterized by immune dysregulation and a high risk of multiple organ dysfunction syndrome (MODS). Early molecular mechanisms linking trauma severity to organ injury are poorly understood. We used two rat blast-polytrauma models: a tourniquet-induced ischemia/reperfusion injury (tIRI) model and a non-ischemia/reperfusion injury (non-IRI) model. Naïve animals served as controls. RT-qPCR of 120 inflammatory genes in the lung, kidney, and liver, combined with STRING protein–protein interaction analysis, revealed distinct yet overlapping inflammatory gene signatures across all the organs. A core set of genes (Il6, Lbp, Nos2, and Lcn2) was consistently upregulated, indicating shared inflammatory pathways. Transcriptomic responses were most pronounced in the tIRI group, with greater magnitude and altered temporal dynamics, uniquely amplifying pro-inflammatory cytokines, immune cell activators, chemokines, and tissue damage markers. Lipocalin-2 (Lcn2/NGAL) emerged as a shared hub gene across all the organs within 24 h post-injury. Its expression significantly correlated with MODS activity and adverse outcomes, independent of the injury model. At 168 h, Lcn2 expression correlated with increased liver damage and NGAL levels correlated with tissue trauma severity. These findings elucidate distinct pro-inflammatory mediators and networks underlying secondary organ dysfunction, highlighting NGAL as a potential universal biomarker of trauma-induced inflammation and MODS activity, suggesting it as a therapeutic target. Full article

(This article belongs to the Section Molecular Biology)

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18 pages, 4336 KiB

Open AccessArticle

Development of an Antibacterial Poly(Lactic Acid)/Poly(ε-Caprolactone)/Tributyl Citrate Film Loaded with Staphylococcus aureus Bacteriophages Using a Sodium Alginate Coating

by Seulgi Imm, Jaewoo Bai and Yoonjee Chang

Int. J. Mol. Sci. 2025, 26(16), 7793; https://doi.org/10.3390/ijms26167793 (registering DOI) - 12 Aug 2025

Abstract

Biodegradable poly(lactic acid) (PLA)/poly(ε-caprolactone) (PCL) composite films were prepared with a compatibilizer (tributyl citrate, TBC) using a solvent casting method. Incorporation of 5% TBC (w/v, of PCL weight) improved tensile strength and elongation at break (21.93 ± 2.33 MPa [...] Read more.

Biodegradable poly(lactic acid) (PLA)/poly(ε-caprolactone) (PCL) composite films were prepared with a compatibilizer (tributyl citrate, TBC) using a solvent casting method. Incorporation of 5% TBC (w/v, of PCL weight) improved tensile strength and elongation at break (21.93 ± 2.33 MPa and 21.02 ± 1.54%, respectively) and reduced water vapor permeability (from 0.12 ± 0.01 to 0.098 ± 0.01 g·mm·m²·h·kPa), indicating improved compatibility between PLA and PCL. Staphylococcus aureus phage PBSA08 demonstrated rapid and persistent bacteriolytic activity for up to 24 h, suggesting its potential as a promising antibacterial biological agent. To impart antibacterial properties to the developed PLA/PCL/TBC film, PBSA08 was loaded into sodium alginate (SA) and coated on the film surface. The optimal composition was 3% (w/v) SA and 3% (w/v) glycerol, which exhibited suitable dynamic behavior as a coating solution and excellent adhesion to the film surface. The phage-coated antibacterial films demonstrated progressive and significant inhibition against S. aureus starting from 10 to 24 h, with controlled phage-release properties. Overall, the developed active film might exert sustained and remarkable antibacterial effects through controlled release of biological agents (phage) under realistic packaging conditions. Full article

(This article belongs to the Special Issue Molecular Biology of Foodborne Pathogens: Pathogenesis and Control Strategies)

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25 pages, 1555 KiB

Open AccessArticle

Reliable New Biomarkers of Mitochondrial Oxidative Stress and Neuroinflammation in Cerebrospinal Fluid and Plasma from Alzheimer’s Disease Patients: A Pilot Study

by Rosa Di Lorenzo, Chiara Zecca, Guglielmina Chimienti, Tiziana Latronico, Grazia Maria Liuzzi, Vito Pesce, Maria Teresa Dell’Abate, Francesco Borlizzi, Alessia Giugno, Daniele Urso, Giancarlo Logroscino and Angela Maria Serena Lezza

Int. J. Mol. Sci. 2025, 26(16), 7792; https://doi.org/10.3390/ijms26167792 (registering DOI) - 12 Aug 2025

Abstract

Mitochondrial oxidative stress and neuroinflammation are involved in the onset and progression of Alzheimer’s disease (AD). Novel reliable, circulating biomarkers related to these processes were searched in cerebrospinal fluid (CSF) and plasma samples. Paired CSF and plasma samples from 20 subjective memory complaints [...] Read more.

Mitochondrial oxidative stress and neuroinflammation are involved in the onset and progression of Alzheimer’s disease (AD). Novel reliable, circulating biomarkers related to these processes were searched in cerebrospinal fluid (CSF) and plasma samples. Paired CSF and plasma samples from 20 subjective memory complaints (SMC) subjects, 20 mild cognitive impairment (MCI) due to AD subjects, and 20 Alzheimer’s dementia (ADd) patients were analyzed. Protein amounts of manganese-containing superoxide dismutase 2 (SOD2), cell-free mitochondrial DNA (cf-mtDNA) level, DNase I, and matrix metalloproteinases 2 and 9 (MMP-2 and MMP-9) activities were determined. As for SOD2, an MCI male-specific significant increase in both biofluids and an ADd male-specific significant decrease in plasma were found. No significant differences were demonstrated in cf-mtDNA level. An ADd-specific significant increase in plasma DNase I and MMP-2 activities was found. A SMC female-specific significant higher value in CSF MMP-9 activity in comparison to male counterparts was demonstrated. The present results suggest a male patient-specific (MCI and ADd) regulation of SOD2 expression in plasma and support an ADd-specific increase in plasma DNase I and MMP-2 activities. Therefore, the potential of SOD2 amount, DNase I, and MMP-2 activities in plasma as new markers of ADd should be explored. The SMC female-specific high activity of MMP-9 might contribute to AD female-sex bias. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Alzheimer’s Disease)

21 pages, 5863 KiB

Open AccessArticle

Therapeutic Effects of Sulforaphane on Helicobacter pylori-Infected Mice: Insights from High-Coverage Metabolomics and Lipidomics Analyses of Serum and Liver

by Shuling He, Lvyun Sun, Jiali Chen, Yixin Li, Ying Pan, Amei Su, Qiuyao Mao, Jiaqian Hu, Disheng Feng and Yang Ouyang

Int. J. Mol. Sci. 2025, 26(16), 7791; https://doi.org/10.3390/ijms26167791 (registering DOI) - 12 Aug 2025

Abstract

Sulforaphane, a natural isothiocyanate predominantly found in cruciferous vegetables, has shown potential in preventing and treating Helicobacter pylori infection. However, the underlying metabolic mechanisms remain largely unclear. This study employed high-coverage metabolomics and lipidomics methods to comprehensively investigate the effects of sulforaphane on [...] Read more.

Sulforaphane, a natural isothiocyanate predominantly found in cruciferous vegetables, has shown potential in preventing and treating Helicobacter pylori infection. However, the underlying metabolic mechanisms remain largely unclear. This study employed high-coverage metabolomics and lipidomics methods to comprehensively investigate the effects of sulforaphane on the serum and liver metabolic profiles of H. pylori-infected mice. Metabolomics and lipidomics analysis revealed that H. pylori infection disrupted multiple metabolic pathways, leading to perturbations in amino acids, fatty acids, bile acids, and various lipid species. Sulforaphane treatment can ameliorate these disruptions, notably reversing alterations in serum glycerophospholipids and restoring hepatic levels of amino acids, bile acids, glycerophospholipids, ceramides, and peptides. Key metabolic pathways implicated included glutathione metabolism and glycine and serine metabolism, which are associated with antioxidant defense and host resistance to pathogenic infections. These findings offer a comprehensive metabolic basis for understanding the therapeutic effects of sulforaphane against H. pylori infection. Full article

(This article belongs to the Topic Nutrients, Food Bioactives, and Functional Foods in Gastrointestinal and Metabolic Disorders)

36 pages, 3105 KiB

Open AccessArticle

Identification of Key Differentially Expressed Genes in Arabidopsis thaliana Under Short- and Long-Term High Light Stress

by Aleksandr V. Bobrovskikh, Ulyana S. Zubairova and Alexey V. Doroshkov

Int. J. Mol. Sci. 2025, 26(16), 7790; https://doi.org/10.3390/ijms26167790 (registering DOI) - 12 Aug 2025

Abstract

Nowadays, with the accumulation of large amounts of stress-response transcriptomic data in plants, it is possible to clarify the key genes and transcription factors (TFs) involved in these processes. Here, we present the comprehensive transcriptomic meta-analysis of the high light (HL) response in [...] Read more.

Nowadays, with the accumulation of large amounts of stress-response transcriptomic data in plants, it is possible to clarify the key genes and transcription factors (TFs) involved in these processes. Here, we present the comprehensive transcriptomic meta-analysis of the high light (HL) response in photosynthetic tissues of Arabidopsis thaliana (L.) Heynh., offering new insights into adaptation mechanisms of plants to excessive light and involved gene regulatory networks. We analyzed 21 experiments covering 58 HL conditions in total, yielding 218,000 instances of differentially expressed genes (DEGs) corresponding to 19,000 unique genes. Based on these data, we developed the publicly accessible AraLightDEGs resource, which offers multiple search filters for experimental conditions and gene characteristics, and we conducted a detailed meta-analysis using our R pipeline, AraLightMeta. Our meta-analysis highlighted distinct transcriptional programs between short- and long-term HL responses in leaves, revealing novel regulatory interactions and refining the understanding of key DEGs. In particular, long-term HL adaptation involves key TFs such as CRF3 and PTF1 regulating antioxidant and jasmonate signaling; ATWHY2, WHY3, and emb2746 coordinating chloroplast and mitochondrial gene expression; AT2G28450 governing ribosome biogenesis; and AT4G12750 controlling methyltransferase activity. We integrated these findings into a conceptual scheme illustrating transcriptional regulation and signaling processes in leaf cells responding to long-term HL stress. Full article

(This article belongs to the Special Issue Plant Molecular Regulatory Networks and Stress Responses)

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25 pages, 3899 KiB

Open AccessArticle

Exploring the Heterogeneity of Cancer-Associated Fibroblasts via Development of Patient-Derived Cell Culture of Breast Cancer

by Anna Ilyina, Anastasia Leonteva, Ekaterina Berezutskaya, Maria Abdurakhmanova, Mikhail Ermakov, Sergey Mishinov, Elena Kuligina, Sergey Vladimirov, Maria Bogachek, Vladimir Richter and Anna Nushtaeva

Int. J. Mol. Sci. 2025, 26(16), 7789; https://doi.org/10.3390/ijms26167789 (registering DOI) - 12 Aug 2025

Abstract

Cancer-associated fibroblasts (CAFs) constitute a heterogeneous population of cells within the tumor microenvironment and are associated with cancer development and drug resistance. The absence of a universal classification for CAFs hinders their research and therapeutic targeting. To define CAF phenotypes, we developed patient-derived [...] Read more.

Cancer-associated fibroblasts (CAFs) constitute a heterogeneous population of cells within the tumor microenvironment and are associated with cancer development and drug resistance. The absence of a universal classification for CAFs hinders their research and therapeutic targeting. To define CAF phenotypes, we developed patient-derived cell cultures of breast cancer (BC) and validated and characterized four distinct CAF subtypes (S1–S4) by Costa’s classification. Three out of five primary cell cultures of BC demonstrated different functional features rather than fixed cellular states due to the plasticity of the CAF phenotype. CAF crosstalk with cancer cells supported their survival in the presence of anticancer drugs. Based on the analysis of the cytotoxic effect of doxorubicin, cisplatin and tamoxifen, it was demonstrated that CAF-S4 and CAF-S1 cells were sensitive to the action of all drugs investigated, despite the fact that they possessed different mechanisms of action. CAF-S2 cells exhibited the highest level of resistance to the antitumour agents. Homotypic and heterotypic spheroids with CAFs could be used to model the fibrotic area of BC in vitro. The patient-derived cell cultures of CAFs formed spheroids. Hypoxia-activated CAF-S4 have been shown to stimulate the metastatic potential of triple-negative BC cells in a heterotypic spheroid model. Consequently, this study could be a starting point for the development of novel therapeutic strategies that target CAFs and their interactions with cancer cells. Full article

(This article belongs to the Special Issue Advancements in Cancer Biomarkers)

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18 pages, 10021 KiB

Open AccessCommunication

External Glands of Nepenthes Traps: Structure and Potential Function

by Bartosz J. Płachno, Małgorzata Kapusta, Marcin Feldo, Piotr Stolarczyk, Karol Małota and Krzysztof Banaś

Int. J. Mol. Sci. 2025, 26(16), 7788; https://doi.org/10.3390/ijms26167788 (registering DOI) - 12 Aug 2025

Abstract

Nepenthes L. species (tropical pitcher plants) are a classic example of carnivorous plants. The Nepenthes traps are highly specialized pitchers with a zoned structure. On the outer surface of the pitcher, there are nectaries and various types of trichomes, including glandular trichomes. The [...] Read more.

Nepenthes L. species (tropical pitcher plants) are a classic example of carnivorous plants. The Nepenthes traps are highly specialized pitchers with a zoned structure. On the outer surface of the pitcher, there are nectaries and various types of trichomes, including glandular trichomes. The main aim of our study was to examine these glandular trichome structures and check the distribution of the homogalacturonans (HGs) and hemicelluloses in the cell wall of trichome cells. The structure of Nepenthes bicalcarata Hook. f. and Nepenthes albomarginata T.Lobb ex Lindl. trichomes was analyzed using light and electron microscopy. The antibodies were used against the wall components [anti-pectic homogalacturonans (HGs): JIM5 (low methylesterified HGs), LM19 (low methylesterified HGs), CCRC-M38 (a fully de-esterified HGs), JIM7 (highly esterified HGs), LM20 (esterified HGs), LM5 (galactan) and anti-hemicelluloses: LM25 (xyloglucan), LM15 (galactoxyloglucan), CCRC-M138 (xylan), and LM10 antibody (xylan)]. The localization of the examined compounds was determined using immunohistochemistry techniques. The presence of endodermal and transfer cells supports the idea that peltate trichomes actively transport solutes. Also, the presence of pectic homogalacturonans and hydrophilic hemicelluloses indicates that water or aqueous solutions are transported through the trichomes’ cell walls. Our study supports the idea that these trichomes may act as hydathodes or hydropotes. Full article

(This article belongs to the Special Issue Complex Interactions of Plants with Other Organisms: Particular Attention to Carnivorous and Parasitic Plants)

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67 pages, 6308 KiB

Open AccessReview

A Reassessment of Sarcopenia from a Redox Perspective as a Basis for Preventive and Therapeutic Interventions

by Alessia Arcaro, Alessio Lepore, Giovanni Paolo Cetrangolo, Gianluca Paventi, Paul Richard Julian Ames and Fabrizio Gentile

Int. J. Mol. Sci. 2025, 26(16), 7787; https://doi.org/10.3390/ijms26167787 (registering DOI) - 12 Aug 2025

Abstract

The use of a wide variety of antioxidants has been advocated as a means to prevent, delay the progression of, or counteract the adverse consequences of sarcopenia, such as loss of muscle strength, muscle quantity/quality, and physical performance. However, these proposals do not [...] Read more.

The use of a wide variety of antioxidants has been advocated as a means to prevent, delay the progression of, or counteract the adverse consequences of sarcopenia, such as loss of muscle strength, muscle quantity/quality, and physical performance. However, these proposals do not always appear to be supported in the literature by a thorough understanding of the contribution of redox perturbations to the pathogenesis of sarcopenia, nor of the biochemical properties, mechanism of action, pharmacokinetics, and pharmacodynamics of different antioxidants. This review discusses these aspects, aiming to provide a rationale for the selection and use of antioxidants in sarcopenia. After providing a definition of sarcopenia in the context of frailty, we distinguish between oxidative eustress as a physiological response of muscle cells to mild stimulation, such as moderate exercise, mediating their capacity for adaptation and regeneration, and oxidative distress as a pathophysiological response to muscle cell damage and death. The role of oxidative damage to biological macromolecules, both direct and mediated by advanced lipid peroxidation end products and advanced glycation/glycoxidation end products, is examined in detail. Next, we discuss antioxidant defense mechanisms, both enzymatic and non-enzymatic, including redox-sensitive gene regulatory events presided over by nuclear factor erythroid 2-related factor 2, the master regulator of enzymatic antioxidants. The review then discusses criteria for a rational classification of non-enzymatic antioxidants. This is followed by a review of some of the main radical-trapping antioxidants, both phenolic and non-phenolic, whose characteristics are compared. Full article

(This article belongs to the Section Molecular Biology)

16 pages, 8469 KiB

Open AccessCase Report

IgG4-Mediated Sclerosing Riedel Thyroiditis: A Multidisciplinary Case Study and Literature Review

by Dumitru Ioachim, Mihai Alin Publik, Dana Terzea, Carmen Adina Cristea, Adina Mariana Ghemigian, Anda Dumitrascu, Eugenia Petrova, Alexandra Voinea, Romeo Smarandache and Mihail Ceausu

Int. J. Mol. Sci. 2025, 26(16), 7786; https://doi.org/10.3390/ijms26167786 (registering DOI) - 12 Aug 2025

Abstract

Riedel thyroiditis (RT) is a rare immune-mediated inflammatory disease that destroys the thyroid parenchyma, replacing it with storiform fibrosis extending to the extrathyroidal tissue. Secondary fibrotic lesions can be associated as parts of the systemic IgG4-related disease. We present the case of a [...] Read more.

Riedel thyroiditis (RT) is a rare immune-mediated inflammatory disease that destroys the thyroid parenchyma, replacing it with storiform fibrosis extending to the extrathyroidal tissue. Secondary fibrotic lesions can be associated as parts of the systemic IgG4-related disease. We present the case of a 52-year-old female patient who presented initially with subacute thyroiditis when corticosteroid treatment was initiated. After a year, compressive respiratory symptoms and dysphagia appear, and fine-needle aspiration cytology is performed to rule out malignancy, but without results. Thyroidectomy is performed, and histopathology shows scleroatrophic thyroiditis, with chronic inflammatory infiltrate containing eosinophils extending in the neighboring tissue, rare atrophic follicles, and obliterative vasculitis. Immunohistochemistry proves abundant plasma cells with IgG4 secretion; the macrophage is mainly the M2 subtype. RT is diagnosed, and a CT (computed tomography) scan is performed to detect peritracheal fibrosis and subtle pulmonary modifications. A literature review was performed that situates our findings in the context of the current literature. The last part discusses the immuno-inflammatory mechanisms behind IgG4-related diseases. Full article

(This article belongs to the Special Issue Role of Immune Cells in Non-infectious Inflammatory Diseases and Cancers)

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13 pages, 974 KiB

Open AccessArticle

Mechanism of H₂S in Inhibiting the Senescence and Browning of Fresh-Cut Potatoes

by Zixu Lu, Nannan Liu, Wanjie Li, Lisheng Guan, Gaifang Yao, Hua Zhang and Kangdi Hu

Int. J. Mol. Sci. 2025, 26(16), 7785; https://doi.org/10.3390/ijms26167785 (registering DOI) - 12 Aug 2025

Abstract

The market for fresh-cut fruits and vegetables is gradually expanding and is popular among consumers, but fresh-cut fruits and vegetables are highly susceptible to browning, causing a decrease in their quality and nutrition. Although anti-browning reagents and cryopreservation methods are often used for [...] Read more.

The market for fresh-cut fruits and vegetables is gradually expanding and is popular among consumers, but fresh-cut fruits and vegetables are highly susceptible to browning, causing a decrease in their quality and nutrition. Although anti-browning reagents and cryopreservation methods are often used for fresh-cut fruits and vegetables, the effects are not satisfactory. In this paper, hydrogen sulfide (H₂S) donor NaHS solution was used for fumigation of fresh-cut potatoes to explore the mechanism of H₂S signaling on the browning of fresh-cut potatoes at the biochemical level. Fresh-cut potatoes were fumigated with H₂S and it was found that H₂S treatment maintained better color compared with the browning of water control. Then, total phenolic content, reactive oxygen species-related metabolites hydrogen peroxide (H₂O₂) and superoxide anion (·O₂⁻), along with malondialdehyde (MDA), the activities of antioxidant enzymes, and the browning-related enzymes polyphenol oxidase (PPO), catalase (CAT), peroxidase (POD), and phenylalanine amine lyase (PAL) were determined. The results of both principal component analysis (PCA) and correlation analyses consistently indicated that CAT activity showed a strong positive correlation with the browning degree of fresh-cut potatoes. The data indicated that H₂S reduced the degree of browning, increased the total phenolic content, inhibited the accumulation of reactive oxygen species (ROS) content, inhibited POD, PPO, and PAL activities, and increased CAT activity. Full article

(This article belongs to the Special Issue Signaling and Stress Adaptation in Plants)

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16 pages, 1103 KiB

Open AccessArticle

Sex-Dependent Regulation of Liver Fibrosis in Primary Sclerosing Cholangitis: The Role of miR-125b, Androgen Receptors, TGF-β, and Apelin Signalling

by Joanna Abramczyk, Malgorzata Milkiewicz, Alicja Łaba, Piotr Milkiewicz, Jesus M. Banales and Agnieszka Kempinska-Podhorodecka

Int. J. Mol. Sci. 2025, 26(16), 7784; https://doi.org/10.3390/ijms26167784 (registering DOI) - 12 Aug 2025

Abstract

Primary sclerosing cholangitis (PSC) is a cholestatic liver disease with male predominance. This study investigated the role of microRNA-125b in PSC-related liver fibrosis, focusing on its interaction with transforming growth factor beta (TGF-β), androgen receptors (ARs), and apelin. Elevated serum and hepatic levels [...] Read more.

Primary sclerosing cholangitis (PSC) is a cholestatic liver disease with male predominance. This study investigated the role of microRNA-125b in PSC-related liver fibrosis, focusing on its interaction with transforming growth factor beta (TGF-β), androgen receptors (ARs), and apelin. Elevated serum and hepatic levels of miR-125b were observed in PSC patients, particularly in males and those with advanced fibrosis, and correlated with increased liver injury markers and FibroScan stiffness. miR-125b expression negatively correlated with apelin and TGF-β levels, while it positively correlated with AR expression. In vitro, miR-125b overexpression induced ARs and suppressed p53 and apelin, whereas lipopolysaccharide stimulation reduced miR-125b and enhanced pro-inflammatory genes, including TNF-α and TGF-β. Notably, ursodeoxycholic acid therapy significantly decreased serum miR-125b levels. These findings suggest that miR-125b contributes to inflammation and fibrogenesis in PSC, partly through the modulation of TGF-β, ARs, and apelin signalling. Moreover, the observed sex-based differences in miR-125b expression underscore the influence of androgens in PSC pathogenesis. Full article

(This article belongs to the Special Issue Liver Fibrosis: Molecular Pathogenesis, Diagnosis and Treatment)

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22 pages, 12838 KiB

Open AccessArticle

CO and NO Coordinate Developmental Neuron Migration

by Sabine Knipp, Arndt Rohwedder and Gerd Bicker

Int. J. Mol. Sci. 2025, 26(16), 7783; https://doi.org/10.3390/ijms26167783 (registering DOI) - 12 Aug 2025

Abstract

Similarly to the short-lived messenger nitric oxide (NO), the more stable carbon monoxide (CO) molecule can also activate soluble guanylyl cyclase (sGC) to increase cGMP levels. However, CO-induced cGMP production is much less efficient. Using an accessible invertebrate model, we dissect a potential [...] Read more.

Similarly to the short-lived messenger nitric oxide (NO), the more stable carbon monoxide (CO) molecule can also activate soluble guanylyl cyclase (sGC) to increase cGMP levels. However, CO-induced cGMP production is much less efficient. Using an accessible invertebrate model, we dissect a potential interaction between the canonical NO/sGC/cGMP and CO signalling pathways during development. The embryonic midgut of locusts is innervated by neurons that migrate in four discrete chains on its outer surface. Transcellular diffusing NO stimulates enteric neuron migration via cGMP signalling. The application of an NO donor results in virtually all enteric neurons being cGMP-immunoreactive while CO increases cGMP production only in approximately 33% of the migrating neurons. Cellular CO release appears to act as a slow down signal for motility. We quantify how CO specifically increases the interneuronal distance during chain migration. Moreover, time-lapse microscopy shows that CO reduces the directionality of the migrating neurons. These findings support the function of NO and CO as antagonistic signals for the coordination of collective cell migration during the development of the enteric nervous system. These experiments and the resulting insights into basic scientific questions prove once more that locust embryos are not only preparations for basic research, but also relevant models for screening of drugs targeting NO and CO signalling pathways as well as for isolating compounds affecting neuronal motility in general. Full article

(This article belongs to the Collection New Advances in Molecular Toxicology)

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19 pages, 3393 KiB

Open AccessArticle

Integrated Phytochemical Profiling, UPLC-HRMS Characterization, and Bioactivity Evaluation of Zingiber officinale and Piper nigrum

by Aicha Boubker, Abdemollah El Ouardi, Taha El Kamli, Mohammed Kaicer, Faouzi Kichou, Khaoula Errafii, Adnane El Hamidi, Rachid Ben Akame and Aicha Sifou

Int. J. Mol. Sci. 2025, 26(16), 7782; https://doi.org/10.3390/ijms26167782 (registering DOI) - 12 Aug 2025

Abstract

The phytochemical profiles, antioxidant capacities, mineral composition, and antibacterial activities of Zingiber officinale (Z. officinal) and Piper nigrum (P. nigrum) were explored through aqueous, ethanolic, and methanolic extractions. The extracts were analyzed for polyphenols, flavonoids, and tannins, and their [...] Read more.

The phytochemical profiles, antioxidant capacities, mineral composition, and antibacterial activities of Zingiber officinale (Z. officinal) and Piper nigrum (P. nigrum) were explored through aqueous, ethanolic, and methanolic extractions. The extracts were analyzed for polyphenols, flavonoids, and tannins, and their antioxidant potential was assessed using the DPPH assay. UPLC-HRMS identified major bioactive compounds, including 6-gingerol and shogaol in Z. officinale, and piperine and piperlonguminine in P. nigrum. Mineral analysis showed that P. nigrum was particularly rich in essential elements, including calcium (Ca), magnesium (Mg), and iron (Fe). In antibacterial testing, P. nigrum demonstrated wider zones of inhibition against E. coli, whereas Z. officinale was more active at lower concentrations, showing MICs as low as 3.91 µg/mL against Salmonella and S. aureus. PCA analysis revealed strong correlations between phenolic content and biological effects. These results underscore the potential of both spices as effective natural agents for use in food preservation and health-promoting applications. Full article

(This article belongs to the Special Issue Bioactive Compounds and Their Antioxidant Role: 2nd Edition)

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22 pages, 8184 KiB

Open AccessArticle

Porphyromonas gingivalis GroEL Accelerates Abdominal Aortic Aneurysm Formation by Induction of M1 Polarization in Macrophages

by Yi-Wen Lin, Yi-Ting Tsai, Ming-Jen Cheng, Chun-Ming Shih, Chun-Yao Huang, Chien-Sung Tsai, Shih-Ying Sung, Ze-Hao Lai, Chen-Wei Liu and Feng-Yen Lin

Int. J. Mol. Sci. 2025, 26(16), 7781; https://doi.org/10.3390/ijms26167781 (registering DOI) - 12 Aug 2025

Abstract

Abdominal aortic aneurysm (AAA) is a life-threatening vascular disease characterized by chronic inflammation, extracellular matrix degradation, and smooth muscle cell apoptosis. Porphyromonas gingivalis (P. gingivalis), a key periodontal pathogen, has been implicated in the progression of cardiovascular diseases, including AAA, but [...] Read more.

Abdominal aortic aneurysm (AAA) is a life-threatening vascular disease characterized by chronic inflammation, extracellular matrix degradation, and smooth muscle cell apoptosis. Porphyromonas gingivalis (P. gingivalis), a key periodontal pathogen, has been implicated in the progression of cardiovascular diseases, including AAA, but the underlying mechanisms remain unclear. In this study, we investigated the role of GroEL, a bacterial heat shock protein 60 homolog derived from P. gingivalis, in AAA development. We employed a CaCl₂-induced AAA mouse model to evaluate the in vivo effects of GroEL. Mice received periaortic CaCl₂ application followed by intravenous injections of recombinant GroEL. Histological analyses were performed to assess aneurysmal dilation, elastin degradation, and inflammatory cell infiltration. Flow cytometry and immunohistochemistry were used to determine macrophage phenotypes, while cytokine profiles were quantified via ELISA. In vitro, THP-1 monocytes were treated with GroEL to evaluate its impact on macrophage polarization and cytokine expression. Our results showed that GroEL administration significantly enhanced aortic diameter expansion and elastin breakdown, accompanied by increased infiltration of M1-like macrophages and elevated levels of pro-inflammatory cytokines such as TNF-α and IL-6. In vitro findings confirmed that GroEL promotes M1 polarization and inhibits M2 marker expression in THP-1-derived macrophages. These findings suggest that P. gingivalis-derived GroEL plays a pathogenic role in AAA by modulating macrophage polarization toward a pro-inflammatory phenotype. Targeting microbial components such as GroEL may offer new therapeutic strategies for AAA management. Full article

(This article belongs to the Special Issue Periodontal Disease, Association with Systemic Conditions and Periodontal Pathogens: 2nd Edition)

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17 pages, 4312 KiB

Open AccessArticle

Precision-Cut Liver Slices: A Valuable Preclinical Tool for Translational Research in Liver Fibrosis

by Meritxell Perramón, Manuel Macías-Herranz, Rocío García-Pérez, Wladimiro Jiménez and Guillermo Fernández-Varo

Int. J. Mol. Sci. 2025, 26(16), 7780; https://doi.org/10.3390/ijms26167780 (registering DOI) - 12 Aug 2025

Abstract

Halting liver fibrosis progression is a key goal in treating liver disease, yet effective antifibrotic drugs remain unavailable. This study explores the use of precision-cut liver slices (PCLS) as an ex vivo model to evaluate new therapies. Researchers tested how different oxygen levels [...] Read more.

Halting liver fibrosis progression is a key goal in treating liver disease, yet effective antifibrotic drugs remain unavailable. This study explores the use of precision-cut liver slices (PCLS) as an ex vivo model to evaluate new therapies. Researchers tested how different oxygen levels affect viability, tissue integrity, and inflammatory response in PCLS from healthy and fibrotic rats. Fibrotic PCLS maintained their pathological gene signature under 40% oxygen and responded to inflammatory stimuli, indicating preserved functionality. Exposure to high oxygen levels increased oxidative stress and pro-inflammatory gene expression. Cirrhotic PCLS showed early signs of reduced viability and the upregulation of fibrosis-related genes including Col1α2, Col3α1, αSMA, Timp1, Timp2, Mmp2, Pdgfrβ, Nos2, Cox2, and Il6. Lipopolysaccharide (LPS) exposure induced the marked overexpression of Nos2 and Il1β mRNA and confirmed the model’s responsiveness to external injury. Fibrotic PCLS retained fibrogenic activity for at least 48 h. Additionally, the adenoviral delivery of a dominant-negative soluble PDGFRβ effectively blocked fibrotic signaling. Human fibrotic PCLS also remained viable for 72 h and showed an increased mRNA expression of fibrosis markers such as COL1A1, αSMA, and MMP2. These results highlight the potential of PCLS as a promising platform for future therapeutic testing, pending further validation with functional interventions. Full article

(This article belongs to the Special Issue Liver Fibrosis: Molecular Pathogenesis, Diagnosis and Treatment)

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