International Journal of Molecular Sciences

26 pages, 1399 KiB

Open AccessReview

Clinical and Molecular Advances on the Black Yeast Exophiala dermatitidis

by Jakub Suchodolski, Mateusz Parol, Karolina Pawlak, Agata Piecuch and Rafał Ogórek

Int. J. Mol. Sci. 2025, 26(14), 6804; https://doi.org/10.3390/ijms26146804 (registering DOI) - 16 Jul 2025

Exophiala dermatitidis is an emerging black yeast recognized in both superficial and life-threatening infections, including those in immunocompetent hosts. This narrative review focuses on recent developments (mostly between 2019 and 2025) in two major areas. First, we examined the clinical and epidemiological background [...] Read more.

Exophiala dermatitidis is an emerging black yeast recognized in both superficial and life-threatening infections, including those in immunocompetent hosts. This narrative review focuses on recent developments (mostly between 2019 and 2025) in two major areas. First, we examined the clinical and epidemiological background of E. dermatitidis, with particular focus on its involvement in cystic fibrosis and CARD9 deficiency, as well as central nervous system, ocular, and systemic infections. Second, we address the molecular basis of its pathogenicity, with particular attention to melanin production, capsule formation, and metabolic adaptation. We also discuss diagnostic challenges and antifungal susceptibility, highlighting gaps between laboratory studies and clinical outcomes. Full article

(This article belongs to the Special Issue Recent Advances in Molecular Pathology, Drug Resistance and Diagnostics of Human Fungal Diseases)

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16 pages, 4472 KiB

Open AccessArticle

Effect of Low-Level Laser Therapy on Periodontal Host Cells and a Seven-Species Periodontitis Model Biofilm

by Selma Dervisbegovic, Susanne Bloch, Vera Maierhofer, Christian Behm, Xiaohui Rausch-Fan, Andreas Moritz, Christina Schäffer and Oleh Andrukov

Int. J. Mol. Sci. 2025, 26(14), 6803; https://doi.org/10.3390/ijms26146803 (registering DOI) - 16 Jul 2025

Abstract

Low-level laser therapy (LLLT) is gaining attention as an effective adjunct to non-surgical periodontal treatment. This study evaluates the potential of LLLT to reduce bacterial load in a clinically relevant in vitro subgingival biofilm model and its impact on the inflammatory response. A [...] Read more.

Low-level laser therapy (LLLT) is gaining attention as an effective adjunct to non-surgical periodontal treatment. This study evaluates the potential of LLLT to reduce bacterial load in a clinically relevant in vitro subgingival biofilm model and its impact on the inflammatory response. A subgingival biofilm model consisting of seven bacterial species was established. Primary human gingival fibroblasts (GFs) and periodontal ligament cells (PDLs) were cultured. Both biofilms and host cells were treated with the DenLase Diode Laser (980 nm) under various clinically relevant settings. The composition and structure of the seven-species biofilms were evaluated using quantitative PCR and fluorescence microscopy, respectively. The inflammatory response in host cells was analyzed by measuring the gene and protein expression levels of various inflammatory mediators. Laser treatment at power outputs ranging from 0.3 to 2 W had no significant effect on biofilm composition or architecture. LLLT, particularly at higher power settings, reduced the viability in both GFs and PDLs up to 70%. Gene expression levels of inflammatory mediators were only minimally influenced by laser treatment. However, LLLT significantly decreased the secretion of all examined cytokines. These findings suggest that LLLT with a 980 nm diode laser, under clinically relevant conditions, exerts anti-inflammatory rather than antimicrobial effects. Full article

(This article belongs to the Special Issue Periodontal Disease: From Molecular Pathogenesis to Precision Diagnostics and Innovative Therapeutics)

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10 pages, 1668 KiB

Open AccessArticle

Hepatic Inflammation Primes Vascular Dysfunction Following Treatment with LPS in a Murine Model of Pediatric Fatty Liver Disease

by Hong Huang, Robin Shoemaker, Yasir Alsiraj, Margaret Murphy, Troy E. Gibbons and John A. Bauer

Int. J. Mol. Sci. 2025, 26(14), 6802; https://doi.org/10.3390/ijms26146802 (registering DOI) - 16 Jul 2025

Abstract

Obesity and pediatric fatty liver disease are increasingly prevalent, yet the underlying mechanisms linking these conditions to heightened inflammatory and immune responses remain poorly understood. Using a murine model reflecting early-life obesity and hepatic steatosis, we tested the hypothesis that obesity-driven hepatic inflammation [...] Read more.

Obesity and pediatric fatty liver disease are increasingly prevalent, yet the underlying mechanisms linking these conditions to heightened inflammatory and immune responses remain poorly understood. Using a murine model reflecting early-life obesity and hepatic steatosis, we tested the hypothesis that obesity-driven hepatic inflammation intensifies systemic immune responses and exacerbates vascular dysfunction following innate immune activation. Newly weaned C57BL/6 mice were fed either a high-saturated-fat, high-cholesterol diet (HFD) or a control diet (CD) for four weeks, modeling adolescence in humans. HFD-fed mice exhibited hepatic and splenic enlargement, elevated plasma cholesterol levels, increased activity levels of liver enzymes (alanine and aspartate aminotransferases), and higher plasma serum amyloid A (SAA) concentrations. Following a sublethal dose of lipopolysaccharide (LPS), the expression of hepatic inflammatory genes (VCAM-1 and iNOS) was significantly elevated in HFD-fed mice, indicating an exaggerated local immune response. Mice fed an HFD also showed significant impairment in endothelium-dependent vasorelaxation compared to CD mice and saline-treated controls, while endothelium-independent responses remained intact. These vascular changes occurred in the context of hepatic inflammation, suggesting that early-life diet-induced steatosis sensitizes the vasculature to inflammatory insult. These findings suggest that obesity-driven hepatic inflammation primes exaggerated systemic immune responses to innate immune stimuli, potentially contributing to the vascular dysfunction and variable clinical morbidity observed in pediatric inflammatory conditions. Full article

(This article belongs to the Special Issue Obesity: From Molecular Mechanisms to Clinical Aspects)

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21 pages, 3038 KiB

Open AccessArticle

Exploring the Interplay Between Gut Microbiota and the Melatonergic Pathway in Hormone Receptor-Positive Breast Cancer

by Aurora Laborda-Illanes, Soukaina Boutriq, Lucía Aranega-Martín, Daniel Castellano-Castillo, Lidia Sánchez-Alcoholado, Isaac Plaza-Andrades, Jesús Peralta-Linero, Emilio Alba, José Carlos Fernández-García, Alicia González-González and María Isabel Queipo-Ortuño

Int. J. Mol. Sci. 2025, 26(14), 6801; https://doi.org/10.3390/ijms26146801 (registering DOI) - 16 Jul 2025

Abstract

Emerging evidence suggests a bidirectional relationship between gut microbiota, melatonin synthesis, and breast cancer (BC) development in hormone receptor-positive patients (HR+HER2+ and HR+HER2-). This study investigated alterations in gut microbiota composition, the serum serotonin–N-acetylserotonin (NAS)–melatonin axis, fecal short-chain fatty acids (SCFAs) and beta-glucuronidase [...] Read more.

Emerging evidence suggests a bidirectional relationship between gut microbiota, melatonin synthesis, and breast cancer (BC) development in hormone receptor-positive patients (HR+HER2+ and HR+HER2-). This study investigated alterations in gut microbiota composition, the serum serotonin–N-acetylserotonin (NAS)–melatonin axis, fecal short-chain fatty acids (SCFAs) and beta-glucuronidase (βGD) activity, and serum zonulin in HR+ BC patients compared to healthy controls. Blood and fecal samples were analyzed using mass spectrometry for serotonin, NAS, melatonin, and SCFAs; ELISA for AANAT, ASMT, 14-3-3 protein, and zonulin; fluorometric assay for βGD activity; and 16S rRNA sequencing for gut microbiota composition. HR+ BC patients exhibited gut dysbiosis with reduced Bifidobacterium longum and increased Bacteroides eggerthii, alongside elevated fecal βGD activity, SCFA levels (e.g., isovaleric acid), and serum zonulin, indicating increased intestinal permeability. Serum serotonin and N-acetylserotonin (NAS) levels were elevated, while melatonin levels were reduced, with a higher NAS/melatonin ratio in BC patients. AANAT levels were increased, and ASMT levels were decreased, suggesting disrupted melatonin synthesis. Bifidobacterium longum positively correlated with melatonin and negatively with βGD activity, while Bacteroides eggerthii showed a positive correlation with βGD activity. These findings suggested that gut microbiota alterations, disrupted melatonin synthesis, microbial metabolism, and intestinal permeability may contribute to BC pathophysiology. The NAS/melatonin ratio could represent a potential biomarker, necessitating further mechanistic studies to confirm causality and explore therapeutic interventions. Full article

(This article belongs to the Special Issue Interplay Between the Human Microbiome and Diseases)

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37 pages, 18532 KiB

Open AccessArticle

Regeneration of Biomechanically Functional Tendon Tissue Following Injection of Uncultured, Autologous, Adipose-Derived Regenerative Cells into Partial Achilles Tendon Defects in Rabbits

by Christoph Schmitz, Christopher Alt, Tobias Wuerfel, Stefan Milz, Jacqueline Dinzey, Ashley Hill, Katie J. Sikes, Lindsey H. Burton, Jeremiah Easley, Holly L. Stewart, Christian M. Puttlitz, Benjamin C. Gadomski, Kevin M. Labus, David A. Pearce, Nicola Maffulli and Eckhard U. Alt

Int. J. Mol. Sci. 2025, 26(14), 6800; https://doi.org/10.3390/ijms26146800 (registering DOI) - 16 Jul 2025

Abstract

Current treatment strategies for partial tendon tears often lack the capacity to promote true tissue regeneration and improve long-term clinical outcomes. This study tested the hypothesis that treatment of a partial defect in the rabbit common calcaneus tendon (CCT) with uncultured, unmodified, autologous, [...] Read more.

Current treatment strategies for partial tendon tears often lack the capacity to promote true tissue regeneration and improve long-term clinical outcomes. This study tested the hypothesis that treatment of a partial defect in the rabbit common calcaneus tendon (CCT) with uncultured, unmodified, autologous, adipose-derived regenerative cells (UA-ADRCs) enables regenerative healing without scar formation. A full-thickness, 3 mm defect was produced in the midsubstance of the right gastrocnemius tendon, a component of the CCT, in adult female New Zealand white rabbits. Animals received either an injection of 28.3 × 10⁶ UA-ADRCs in 0.5 mL Ringer’s lactated solution (RLS) or saline, or RLS or saline alone as sham treatment. Tendons were analyzed 4 or 12 weeks post-treatment using histology, immunohistochemistry and non-destructive biomechanical testing. UA-ADRC-treated tendons showed newly formed connective tissue consistent with tendon regeneration, whereas sham-treated tendons developed scar tissue. Biomechanical testing showed significantly higher percent relaxation in UA-ADRC-treated tendons compared to sham controls (p < 0.05), indicating greater viscoelasticity characteristic of healthy or well-integrated tissue. Together, these findings suggest that UA-ADRC therapy may provide a regenerative, structure-modifying treatment for partial tendon tears. Full article

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

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17 pages, 3753 KiB

Open AccessArticle

LSA-DDI: Learning Stereochemistry-Aware Drug Interactions via 3D Feature Fusion and Contrastive Cross-Attention

by Shanshan Wang, Chen Yang and Lirong Chen

Int. J. Mol. Sci. 2025, 26(14), 6799; https://doi.org/10.3390/ijms26146799 (registering DOI) - 16 Jul 2025

Abstract

Accurate prediction of drug–drug interactions (DDIs) is essential for ensuring medication safety and optimizing combination-therapy strategies. However, existing DDI models face limitations in handling interactions related to stereochemistry and precisely locating drug interaction sites. These limitations reduce the prediction accuracy for conformation-dependent interactions [...] Read more.

Accurate prediction of drug–drug interactions (DDIs) is essential for ensuring medication safety and optimizing combination-therapy strategies. However, existing DDI models face limitations in handling interactions related to stereochemistry and precisely locating drug interaction sites. These limitations reduce the prediction accuracy for conformation-dependent interactions and the interpretability of molecular mechanisms, potentially posing risks to clinical safety. To address these challenges, we introduce LSA-DDI, a Spatial-Contrastive-Attention-Based Drug–Drug Interaction framework. Our 3D feature extraction method captures the spatial structure of molecules through three features—coordinates, distances, and angles—and fuses them to enhance the model of molecular spatial structures. Concurrently, we design and implement a Dynamic Feature Exchange (DFE) mechanism that dynamically regulates the flow of information across modalities via an attention mechanism, achieving bidirectional enhancement and semantic alignment of 2D topological and 3D spatial structure features. Additionally, we incorporate a dynamic temperature-regulated multiscale contrastive learning framework that effectively aligns multiscale features and enhances the model’s generalizability. Experiments conducted on public drug databases under both warm-start and cold-start scenarios demonstrated that LSA-DDI achieved competitive performance, with consistent improvements over existing methods. Full article

(This article belongs to the Special Issue New Insights in Artificial Intelligence for Drug Design and Target Discovery)

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13 pages, 12136 KiB

Open AccessArticle

Comparative Analysis of Differentially Expressed Long Non-Coding RNA in Pre- and Postmenopausal Fibroids

by Tsai-Der Chuang, Shawn Rysling, Nhu Ton, Daniel Baghdasarian and Omid Khorram

Int. J. Mol. Sci. 2025, 26(14), 6798; https://doi.org/10.3390/ijms26146798 (registering DOI) - 16 Jul 2025

Abstract

Uterine fibroids (leiomyomas) are benign tumors whose growth is influenced by estrogen and progesterone. This study aimed to compare the profiles of differentially expressed long non-coding RNAs (lncRNAs) in fibroids from postmenopausal and premenopausal women to identify hormone-responsive lncRNAs. RNA sequencing was performed [...] Read more.

Uterine fibroids (leiomyomas) are benign tumors whose growth is influenced by estrogen and progesterone. This study aimed to compare the profiles of differentially expressed long non-coding RNAs (lncRNAs) in fibroids from postmenopausal and premenopausal women to identify hormone-responsive lncRNAs. RNA sequencing was performed on six pairs of fibroid (Fib) and adjacent myometrium (Myo) tissues from postmenopausal women. Out of 7876 normalized lncRNAs, 3684 were differentially expressed (≥1.5-fold), with 1702 upregulated and 1982 downregulated in Fib. Comparative analysis with a previously published premenopausal dataset identified 741 lncRNAs that were altered based on their menopausal status, including 62 lncRNAs that were uniquely dysregulated in postmenopausal samples. Overall, 9 lncRNAs were selected for validation by PCR in an expanded cohort of 31 postmenopausal and 84 premenopausal paired samples. Several lncRNAs, including LINC02433, LINC01449, SNHG12, H19, and HOTTIP, were upregulated in premenopausal Fib but not in postmenopausal ones, while ZEB2-AS1 displayed the opposite pattern. CASC15 and MIAT were elevated in Fib from both groups, although the increase was less pronounced in the postmenopausal group. LINC01117 was significantly downregulated in postmenopausal Fib, with no change observed in premenopausal samples. Additionally, analysis based on MED12 mutation status revealed that lncRNAs such as LINC01449, CASC15, and MIAT showed limited or reduced differential expression (mutation-positive vs. mutation-negative) in postmenopausal patients compared to the premenopausal group. These findings indicate that lncRNA expression in fibroids is modulated by menopausal status, likely reflecting hormonal influence. Hormone-responsive lncRNAs may play key roles in fibroid pathogenesis and represent potential targets for therapeutic intervention. Full article

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

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18 pages, 1010 KiB

Open AccessReview

Engineering IsPETase and Its Homologues: Advances in Enzyme Discovery and Host Optimisation

by Tolu Sunday Ogunlusi, Sylvester Sapele Ikoyo, Mohammad Dadashipour and Hong Gao

Int. J. Mol. Sci. 2025, 26(14), 6797; https://doi.org/10.3390/ijms26146797 (registering DOI) - 16 Jul 2025

Abstract

Polyethylene terephthalate (PET) pollution represents a significant environmental challenge due to its widespread use and recalcitrant nature. PET-degrading enzymes, particularly Ideonella sakaiensis PETases (IsPETase), have emerged as promising biocatalysts for mitigating this problem. This review provides a comprehensive overview of recent [...] Read more.

Polyethylene terephthalate (PET) pollution represents a significant environmental challenge due to its widespread use and recalcitrant nature. PET-degrading enzymes, particularly Ideonella sakaiensis PETases (IsPETase), have emerged as promising biocatalysts for mitigating this problem. This review provides a comprehensive overview of recent advancements in the discovery and heterologous expression of IsPETase and closely related enzymes. We highlight innovative approaches, such as in silico and AI-based enzyme screening and advanced screening assays. Strategies to enhance enzyme secretion and solubility, such as using signal peptides, fusion tags, chaperone co-expression, cell surface display systems, and membrane permeability modulation, are critically evaluated. Despite considerable progress, challenges remain in achieving industrial-scale production and application. Future research must focus on integrating cutting-edge molecular biology techniques with host-specific optimisation to achieve sustainable and cost-effective solutions for PET biodegradation and recycling. This review aims to provide a foundation for further exploration and innovation in the field of enzymatic plastic degradation. Full article

(This article belongs to the Special Issue The Characterization and Application of Enzymes in Bioprocesses)

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11 pages, 1288 KiB

Open AccessArticle

Accurate DNA Synthesis Across 8-Oxoadenine by Human PrimPol

by Elizaveta O. Boldinova, Alexander A. Kruchinin, Polina N. Kamzeeva, Andrey V. Aralov and Alena V. Makarova

Int. J. Mol. Sci. 2025, 26(14), 6796; https://doi.org/10.3390/ijms26146796 (registering DOI) - 16 Jul 2025

Abstract

PrimPol is a human DNA primase and DNA polymerase involved in DNA damage tolerance in both nuclei and mitochondria. PrimPol restarts stalled replication forks by synthesizing DNA primers de novo and also possesses DNA translesion activity (TLS activity). PrimPol efficiently and relatively accurately [...] Read more.

PrimPol is a human DNA primase and DNA polymerase involved in DNA damage tolerance in both nuclei and mitochondria. PrimPol restarts stalled replication forks by synthesizing DNA primers de novo and also possesses DNA translesion activity (TLS activity). PrimPol efficiently and relatively accurately bypasses several DNA lesions including 8-oxoguanine, thymine glycol and 5-formyluracil. In this work, we showed that PrimPol possesses efficient and accurate TLS activity across 8-oxoadenine, another common DNA lesion caused by oxidative stress. The accuracy of PrimPol on DNA with 8-oxoA was significantly higher compared to DNA containing 8-oxoG. Replacement of Mg²⁺ ions with Mn²⁺ stimulated activity of PrimPol on DNA with 8-oxoA and 8-oxoG as well as undamaged A in a sequence-dependent manner by the lesion skipping (or template scrunching) mechanism. Altogether, our data support the idea that PrimPol possesses efficient TLS activity across a wide range of DNA lesions caused by oxidative stress. Full article

(This article belongs to the Section Molecular Biology)

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19 pages, 3234 KiB

Open AccessArticle

siRNA Features—Automated Machine Learning of 3D Molecular Fingerprints and Structures for Therapeutic Off-Target Data

by Michael Richter and Alem Admasu

Int. J. Mol. Sci. 2025, 26(14), 6795; https://doi.org/10.3390/ijms26146795 (registering DOI) - 16 Jul 2025

Abstract

Chemical modifications are the standard for small interfering RNAs (siRNAs) in therapeutic applications, but predicting their off-target effects remains a significant challenge. Current approaches often rely on sequence-based encodings, which fail to fully capture the structural and protein–RNA interaction details critical for off-target [...] Read more.

Chemical modifications are the standard for small interfering RNAs (siRNAs) in therapeutic applications, but predicting their off-target effects remains a significant challenge. Current approaches often rely on sequence-based encodings, which fail to fully capture the structural and protein–RNA interaction details critical for off-target prediction. In this study, we developed a framework to generate reproducible structure-based chemical features, incorporating both molecular fingerprints and computationally derived siRNA–hAgo2 complex structures. Using an RNA-Seq off-target study, we generated over 30,000 siRNA–gene data points and systematically compared nine distinct types of feature representation strategies. Among the datasets, the highest predictive performance was achieved by Dataset 3, which used extended connectivity fingerprints (ECFPs) to encode siRNA and mRNA features. An energy-minimized dataset (7R), representing siRNA–hAgo2 structural alignments, was the second-best performer, underscoring the value of incorporating reproducible structural information into feature engineering. Our findings demonstrate that combining detailed structural representations with sequence-based features enables the generation of robust, reproducible chemical features for machine learning models, offering a promising path forward for off-target prediction and siRNA therapeutic design that can be seamlessly extended to include any modification, such as clinically relevant 2′-F or 2′-OMe. Full article

(This article belongs to the Section Biochemistry)

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40 pages, 2429 KiB

Open AccessReview

Hepatocytes as Model for Investigating Natural Senotherapeutic Compounds and Their Effects on Cell Cycle Dynamics and Genome Stability

by Anastasia Fizikova, Anna Prokhorova, Daria Churikova, Zahar Konstantinov, Roman Ivanov, Alexander Karabelsky and Stanislav Rybtsov

Int. J. Mol. Sci. 2025, 26(14), 6794; https://doi.org/10.3390/ijms26146794 (registering DOI) - 16 Jul 2025

Abstract

DNA is inherently unstable and is susceptible to damage from both endogenous sources (such as reactive oxygen species) and exogenous factors (including UV, ionizing radiation, and chemicals). The accumulation of DNA damage manifests as genetic mutations, chromosomal instability, and the stalling of DNA [...] Read more.

DNA is inherently unstable and is susceptible to damage from both endogenous sources (such as reactive oxygen species) and exogenous factors (including UV, ionizing radiation, and chemicals). The accumulation of DNA damage manifests as genetic mutations, chromosomal instability, and the stalling of DNA replication and transcription processes. Accumulated DNA damage influences apoptosis and cell cycle checkpoints, serving as one of the key triggers for the manifestation of the senescent phenotype. Both aging and cancer are associated with the accumulation of mutations in somatic cells. Disruption of cell cycle control and uncontrolled proliferation are fundamental characteristics of any cancer cell, with the majority of anticancer drugs acting as inhibitors of cyclin-dependent kinases, thereby inducing a transition of cells into a senescent state. Consequently, disturbances in the dynamics and regulation of inflammatory responses, oxidative stress, cell proliferation, DNA damage repair, and epigenetic anomalies, along with the influence of retroviruses and transposons, lead to the accumulation of senescent cells within the human body, characterized by blocked replication and cell cycle, as well as a distinct secretory phenotype. The age-related or disease-associated accumulation of these senescent cells significantly alters the physiology of tissues and the organism as a whole. Many secondary metabolites of higher plants exhibit senolytic and senomorphic activities, although most of them are not fully characterized. In this review, we will explore the principal signaling pathways in mammalian cells that govern the cell cycle and cellular senescence, with a particular emphasis on how their dynamics, expression, and regulation have been modified through the application of senotherapeutic compounds. The second section of the review will identify key target genes for the metabolic engineering, primarily aimed at enhancing the accumulation of plant secondary metabolites with potential therapeutic benefits. Lastly, we will discuss the rationale for utilizing liver cells as a model system to investigate the effects of senolytic compounds on human physiology and health, as well as how senotherapeutic substances can be leveraged to improve gene therapy approaches based on CRISPR/Cas9 and prime-editing technologies. Full article

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

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14 pages, 2193 KiB

Open AccessArticle

In Situ Electrochemical Atomic Force Microscopy Study of Interfacial Reactions on a Graphite Negative Electrode for Magnesium-Ion Batteries

by Sungjae Yoon, Paul Maldonado Nogales, Sangyup Lee, Seunga Yang and Soon-Ki Jeong

Int. J. Mol. Sci. 2025, 26(14), 6793; https://doi.org/10.3390/ijms26146793 (registering DOI) - 15 Jul 2025

Abstract

The cointercalation of solvated Mg²⁺ ions into graphite has typically been considered challenging because of concerns regarding the instability of the electrolyte and the potential for structural degradation. However, recent developments in electrolyte design suggest that this process may be reversible under [...] Read more.

The cointercalation of solvated Mg²⁺ ions into graphite has typically been considered challenging because of concerns regarding the instability of the electrolyte and the potential for structural degradation. However, recent developments in electrolyte design suggest that this process may be reversible under appropriate conditions. In this study, the interfacial behavior of graphite in a magnesium-ion system was investigated using in situ electrochemical atomic force microscopy. Electrochemical tests in a triglyme-based electrolyte revealed a reversible capacity of 158 mAh g⁻¹, attributed to the insertion of triglyme-solvated Mg²⁺ ions. Real-time surface imaging of highly oriented pyrolytic graphite revealed the formation of a passivating surface film during the initial cycle, along with nanoscale hill-like (~1 nm) and blister-like (~5 nm) structures, which were partially reversible and showed good correlation with the redox peaks observed in the cyclic voltammetry experiments, suggesting that the surface film enables Mg²⁺ transport while mitigating electrolyte decomposition. These findings demonstrate that stable co-intercalation of solvated Mg²⁺ ions is achievable in the early cycles in graphite and highlight the importance of interfacial engineering and solvation structures in the development of magnesium-ion batteries. Full article

(This article belongs to the Section Physical Chemistry and Chemical Physics)

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17 pages, 4529 KiB

Open AccessArticle

Inhibition of FOXM1 Leads to Suppression of Cell Proliferation, Migration, and Invasion Through AXL/eEF2 Kinase Signaling and Induces Apoptosis and Ferroptosis in GBM Cells

by Ezgi Biltekin, Nermin Kahraman, Ogun Ali Gul, Yasemin M. Akay, Metin Akay and Bulent Ozpolat

Int. J. Mol. Sci. 2025, 26(14), 6792; https://doi.org/10.3390/ijms26146792 (registering DOI) - 15 Jul 2025

Abstract

Glioblastoma multiforme (GBM) is an aggressive and molecularly heterogeneous brain cancer with a poor prognosis. Despite advancements in standard-of-care therapies, including surgery, radiotherapy, and temozolomide (TMZ), the median survival remains approximately 15 months, with a 5-year survival rate of less than 10%. We [...] Read more.

Glioblastoma multiforme (GBM) is an aggressive and molecularly heterogeneous brain cancer with a poor prognosis. Despite advancements in standard-of-care therapies, including surgery, radiotherapy, and temozolomide (TMZ), the median survival remains approximately 15 months, with a 5-year survival rate of less than 10%. We and others have demonstrated that FOXM1 is a critical oncogenic driver of GBM cell proliferation. However, the role of FOXM1 and its interaction with other oncogenic signaling pathways in GBM remains incompletely understood. In this study, we identified FOXM1, AXL, and eEF2K as highly upregulated oncogenes in GBM patient tumors. We demonstrated, for the first time, that FOXM1 directly interacts with AXL and eEF2K, regulating their expression and promoting GBM cell proliferation, migration, and invasion. Knockdown of these genes disrupted cell proliferation, spheroid formation, migration, and invasion, and induced apoptosis and ferroptosis. Additionally, inhibiting the FOXM1–AXL/eEF2K signaling axis sensitized GBM cells to TMZ, further enhancing apoptotic and ferroptotic responses. These findings highlight the critical role of the FOXM1–AXL/eEF2K signaling pathway in GBM progression and suggest that targeting this axis may offer a novel multitargeted therapeutic strategy in GBM. Full article

(This article belongs to the Special Issue Circulating Biomarkers for the Diagnosis of Neurobiological Diseases 2.0)

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28 pages, 1136 KiB

Open AccessReview

Metabolic Disturbances Involved in Cardiovascular Diseases: The Role of Mitochondrial Dysfunction, Altered Bioenergetics and Oxidative Stress

by Donatella Pietrangelo, Caroline Lopa, Margherita Litterio, Maria Cotugno, Speranza Rubattu and Angela Lombardi

Int. J. Mol. Sci. 2025, 26(14), 6791; https://doi.org/10.3390/ijms26146791 (registering DOI) - 15 Jul 2025

Abstract

The study of metabolic abnormalities regarding mitochondrial respiration and energy production has significantly advanced our understanding of cell biology and molecular mechanisms underlying cardiovascular diseases (CVDs). Mitochondria provide 90% of the energy required for maintaining normal cardiac function and are central to heart [...] Read more.

The study of metabolic abnormalities regarding mitochondrial respiration and energy production has significantly advanced our understanding of cell biology and molecular mechanisms underlying cardiovascular diseases (CVDs). Mitochondria provide 90% of the energy required for maintaining normal cardiac function and are central to heart bioenergetics. During the initial phase of heart failure, mitochondrial number and function progressively decline, causing a decrease in oxidative metabolism and increased glucose uptake and glycolysis, leading to ATP depletion and bioenergetic starvation, finally contributing to overt heart failure. Compromised mitochondrial bioenergetics is associated with vascular damage in hypertension, vascular remodeling in pulmonary hypertension and acute cardiovascular events. Thus, mitochondrial dysfunction, leading to impaired ATP production, excessive ROS generation, the opening of mitochondrial permeability transition pores and the activation of apoptotic and necrotic pathways, is revealed as a typical feature of common CVDs. Molecules able to positively modulate cellular metabolism by improving mitochondrial bioenergetics and energy metabolism and inhibiting oxidative stress production are expected to exert beneficial protective effects in the heart and vasculature. This review discusses recent advances in cardiovascular research through the study of cellular bioenergetics in both chronic and acute CVDs. Emerging therapeutic strategies, specifically targeting metabolic modulators, mitochondrial function and quality control, are discussed. Full article

(This article belongs to the Special Issue Molecular Research in Cardiovascular Disease, 3rd Edition)

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22 pages, 1013 KiB

Open AccessArticle

Selection of Stable Reference Genes for Gene Expression Studies in Activated and Non-Activated PBMCs Under Normoxic and Hypoxic Conditions

by Artur Wardaszka, Anna Smolarska, Piotr Bednarczyk and Joanna Katarzyna Bujak

Int. J. Mol. Sci. 2025, 26(14), 6790; https://doi.org/10.3390/ijms26146790 (registering DOI) - 15 Jul 2025

Abstract

Immunotherapy has emerged as a key modality in cancer treatment, yet its effectiveness varies significantly among patients, often due to the metabolic stress imposed by the tumor microenvironment. Hypoxia, a major factor in the tumor microenvironment, results from the high metabolic rate of [...] Read more.

Immunotherapy has emerged as a key modality in cancer treatment, yet its effectiveness varies significantly among patients, often due to the metabolic stress imposed by the tumor microenvironment. Hypoxia, a major factor in the tumor microenvironment, results from the high metabolic rate of tumor cells and inadequate vascularization, impairing immune cells’ function and potentially influencing gene expression profiles. Despite the widespread use of quantitative real-time PCR in immunological studies, to the best of our knowledge, data on reference gene stability in human peripheral blood mononuclear cells under hypoxic conditions is limited. In our study, we assessed the expression stability of commonly used reference genes (S18, HPRT, IPO8, RPL13A, SDHA, PPIA, and UBE2D2) in both non-stimulated and CD3/CD28-activated peripheral blood mononuclear cells cultured under normoxic, hypoxic (1% O₂), and chemically induced hypoxic conditions for 24 h. Analysis using four different algorithms—delta Ct, geNorm, NormFinder, and BestKeeper—identified RPL13A, S18, and SDHA as the most suitable reference genes for human peripheral blood mononuclear cells under hypoxic conditions. In contrast, IPO8 and PPIA were found to be the least suitable housekeeping genes. The study provides essential insights into the stability of reference genes in peripheral blood mononuclear cells under hypoxic conditions, a critical but understudied aspect of immunological research. Given the significant impact of hypoxia on T cell metabolism and function in the tumor microenvironment, selecting reliable reference genes is crucial for accurate gene expression analysis. Our findings will be valuable for future studies investigating hypoxia-driven metabolic reprogramming in immune cells, ultimately contributing to a better understanding of T cell responses in cancer immunotherapy. Full article

(This article belongs to the Section Molecular Immunology)

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20 pages, 1256 KiB

Open AccessReview

Hurdles of Sperm Success: Exploring the Role of DNases

by Jaime Gosálvez, Carmen López-Fernández, Javier Bartolomé-Nebreda and Carlos García de la Vega

Int. J. Mol. Sci. 2025, 26(14), 6789; https://doi.org/10.3390/ijms26146789 (registering DOI) - 15 Jul 2025

Abstract

The incidence of sperm DNA fragmentation (SDF) in the ejaculate has garnered increasing attention in recent years due to its negative impact on reproductive outcomes. SDF involves two primary types of damage to the canonical double helix of DNA: single-strand breaks and double-strand [...] Read more.

The incidence of sperm DNA fragmentation (SDF) in the ejaculate has garnered increasing attention in recent years due to its negative impact on reproductive outcomes. SDF involves two primary types of damage to the canonical double helix of DNA: single-strand breaks and double-strand breaks. Both of these can occur throughout the entire process of gametogenesis. Determining the precise causes of elevated SDF remains challenging, as it is influenced by a wide range of physiological processes and environmental factors. This review comprehensively explores the mechanisms underlying SDF, with a particular emphasis on the critical role of deoxyribonucleases (DNases) across different stages of male gamete development, as well as their relevance in assisted reproductive technologies (ART). Full article

(This article belongs to the Special Issue New Insights into Male Infertility and Sperm Biology)

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16 pages, 2172 KiB

Open AccessArticle

Impact of SOD1 Transcript Variants on Amyotrophic Lateral Sclerosis Severity

by Matteo Bordoni, Eveljn Scarian, Camilla Viola, Francesca Dragoni, Rosalinda Di Gerlando, Bartolo Rizzo, Luca Diamanti, Stella Gagliardi and Orietta Pansarasa

Int. J. Mol. Sci. 2025, 26(14), 6788; https://doi.org/10.3390/ijms26146788 (registering DOI) - 15 Jul 2025

Abstract

Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disease that affects motor neurons of people, leading to death. This pathology can be caused by mutations in different genes, including superoxide dismutase 1 (SOD1). Previous studies have pointed out the presence of [...] Read more.

Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disease that affects motor neurons of people, leading to death. This pathology can be caused by mutations in different genes, including superoxide dismutase 1 (SOD1). Previous studies have pointed out the presence of two transcripts of SOD1, a short one and a long one. The aim of this study was the investigation of these two transcripts both in the SH-SY5Y cell line and in patients’ peripheral blood mononuclear cells. We found that the shortest SOD1 transcript is upregulated under stress conditions in both the cellular model and the patients’ cells. Moreover, we found a potential correlation between the short SOD1 transcript and the severity of the pathology, which also correlates with the age of patients. No correlation was found between SOD1 transcripts and the progression of the disease. These data suggest a toxic effect of short SOD1 transcripts in ALS patients, by affecting the severity of the pathology making it a possible biomarker for this disease. Interestingly, our data suggest that a short SOD1 transcript does not influence and drive disease progression. The finding of a biomarker will have suitable implications as indicators of disease severity and from the perspective of drug development. Full article

(This article belongs to the Special Issue Amyotrophic Lateral Sclerosis: From Molecular Basis to Therapies)

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15 pages, 10930 KiB

Open AccessArticle

Leflunomide-Mediated Immunomodulation Inhibits Lesion Progression in a Vitiligo Mouse Model

by Fang Miao, Xiaohui Li, Liang Zhao, Shijiao Zhang, Mengmeng Geng, Chuhuan Ye, Ying Shi and Tiechi Lei

Int. J. Mol. Sci. 2025, 26(14), 6787; https://doi.org/10.3390/ijms26146787 (registering DOI) - 15 Jul 2025

Abstract

Autoimmune CD8⁺ T cell-driven melanocyte destruction constitutes a key pathogenic mechanism in the development of vitiligo. Therefore, the pharmacological inhibition of CD8⁺ T cell effector functions and skin trafficking is a clinically viable therapeutic strategy. This study investigates leflunomide (LEF), an [...] Read more.

Autoimmune CD8⁺ T cell-driven melanocyte destruction constitutes a key pathogenic mechanism in the development of vitiligo. Therefore, the pharmacological inhibition of CD8⁺ T cell effector functions and skin trafficking is a clinically viable therapeutic strategy. This study investigates leflunomide (LEF), an immunomodulatory drug with established safety in autoimmune diseases, for its therapeutic potential in a tyrosine-related protein (TRP) 2-180-induced vitiligo mouse model. Through flow cytometry, immunofluorescence, ELISA, and histopathological analyses, we systematically evaluated LEF’s effects on T cell regulation, chemokine expression, and cytokine profiles. Key findings demonstrated that LEF (20 mg/kg/day) significantly attenuated depigmentation by reducing CD8⁺ T cell infiltration and suppressing the IFN-γ-driven expression of CXCL9/10. Furthermore, LEF restored CD4⁺/CD8⁺ T cell homeostasis and rebalanced pro-inflammatory (IFN-γ, TNF-α, IL-2) and anti-inflammatory (IL-4, IL-10) cytokines, inducing a shift from Th1 to Th2. These results position LEF as an effective immunomodulator that disrupts the IFN-γ-CXCL9/10 axis and re-establishes immune balance, offering a promising repurposing strategy for halting vitiligo progression. Full article

(This article belongs to the Special Issue Advances in Vitiligo: From Mechanisms to Treatment Innovations)

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18 pages, 6166 KiB

Open AccessArticle

Conserved Yet Divergent Smc5/6 Complex Degradation by Mammalian Hepatitis B Virus X Proteins

by Maya Shofa, Yuri V Fukushima and Akatsuki Saito

Int. J. Mol. Sci. 2025, 26(14), 6786; https://doi.org/10.3390/ijms26146786 (registering DOI) - 15 Jul 2025

Abstract

Hepatitis B virus (HBV), belonging to the genus Orthohepadnavirus, can cause chronic hepatitis and hepatocarcinoma in humans. HBV ensures optimal replication by encoding X, a multifunctional protein responsible for degrading the structural maintenance of chromosomes (Smc) 5/6 complex, an anti-HBV factor in [...] Read more.

Hepatitis B virus (HBV), belonging to the genus Orthohepadnavirus, can cause chronic hepatitis and hepatocarcinoma in humans. HBV ensures optimal replication by encoding X, a multifunctional protein responsible for degrading the structural maintenance of chromosomes (Smc) 5/6 complex, an anti-HBV factor in hepatocytes. Previous studies suggest that degradation of the Smc5/6 complex is conserved among viruses from the genus Orthohepadnavirus. Recently, a novel hepadnavirus in cats, domestic cat HBV (DCHBV), has been identified as genetically close to HBV. However, it remains unclear whether the DCHBV X protein possesses similar Smc5/6 complex-degrading properties. Here, we investigated the degradation of the Smc5/6 complex by X proteins from viruses of the genus Orthohepadnavirus, including DCHBV, in cells derived from primates and cats. We found that the DCHBV X protein degraded the Smc5/6 complex in the cells of several host species, and the degree of its anti-Smc5/6 complex activity differed depending on the host species. Furthermore, the DCHBV X protein degraded Smc6 independently of DNA-binding protein 1 (DDB1), which is a critical host factor for HBV X-mediated Smc6 degradation. Our findings highlight the conserved yet divergent degradation machinery for Smc6 of mammalian hepatitis B virus X proteins. Full article

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

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36 pages, 3091 KiB

Open AccessReview

Lipidome Complexity in Physiological and Pathological Skin Pigmentation

by Emanuela Bastonini, Daniela Kovacs, Vittoria Maresca, Monica Ottaviani, Anna Di Nardo, Enrica Flori, Giorgia Cardinali and Stefania Briganti

Int. J. Mol. Sci. 2025, 26(14), 6785; https://doi.org/10.3390/ijms26146785 (registering DOI) - 15 Jul 2025

Abstract

Skin pigmentation results from complex cellular interactions and is influenced by genetic, environmental, and metabolic factors. Emerging evidence highlights the multiple pathways by which lipids regulate melanogenesis and points to lipid metabolism and signaling as key players in this process. Lipidomics is a [...] Read more.

Skin pigmentation results from complex cellular interactions and is influenced by genetic, environmental, and metabolic factors. Emerging evidence highlights the multiple pathways by which lipids regulate melanogenesis and points to lipid metabolism and signaling as key players in this process. Lipidomics is a high-throughput omics approach that enables detailed characterization of lipid profiles, thus representing a valid tool for evaluating skin lipid functional role in both physiological melanogenesis and pigmentary disorders. The use of lipidomics to gain a deeper comprehension of the role of lipids in skin pigmentation is still an evolving field, but it has allowed the identification of significant lipid dysregulation in several pigmentary pathologies. This review summarizes the current knowledge on the involvement of lipids in skin pigmentation, focusing on lipid profile alterations described in hyper- and hypopigmentary disorders such as post-inflammatory hyperpigmentation, melasma, solar lentigo, and vitiligo. Lipidomic profiling reveals disease-specific alterations supporting the pivotal role of lipid signaling in the physiopathological mechanisms of melanogenesis. These findings provide insights into disease pathogenesis and show promise for the discovery of biomarkers and innovative therapeutic strategies for pigmentary disorders. Full article

(This article belongs to the Special Issue Pigment Cells: From Biology to Medicine)

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30 pages, 3811 KiB

Open AccessArticle

In Vivo and In Vitro Experimental Study Comparing the Effect of a Combination of Sodium Dichloroacetate and Valproic Acid with That of Temozolomide on Adult Glioblastoma

by Rūta Skredėnienė, Donatas Stakišaitis, Angelija Valančiūtė and Ingrida Balnytė

Int. J. Mol. Sci. 2025, 26(14), 6784; https://doi.org/10.3390/ijms26146784 (registering DOI) - 15 Jul 2025

Abstract

To date, there is no effective treatment for glioblastoma (GBM). This study aimed to compare the effectiveness of sodium dichloroacetate (NaDCA), a valproic acid and NaDCA combination (VPA–NaDCA), or temozolomide (TMZ) on U87 and T98G cell tumors on the chick embryo chorioallantoic membrane [...] Read more.

To date, there is no effective treatment for glioblastoma (GBM). This study aimed to compare the effectiveness of sodium dichloroacetate (NaDCA), a valproic acid and NaDCA combination (VPA–NaDCA), or temozolomide (TMZ) on U87 and T98G cell tumors on the chick embryo chorioallantoic membrane (CAM), and on the expression of proliferating cell nuclear antigen (PCNA), polycomb inhibitory complex catalytic subunit 2 (EZH2), and TP53 gene-encoded p53 protein (p53) in tumors on the CAM, and SLC12A2 (gene encoding Na⁺-K⁺-2Cl⁻ (NKCC1) co-tarnsporter), SLC12A5 (gene encoding K⁺-Cl⁻ (KCC2) co-transporter), SLC5A8 (gene encoding Na⁺-dependent monocarboxylate transporter) and CDH1 (gene encoding the E-cadherin protein) and CDH2 (gene encoding the N-cadherin protein) in cells. VPA–NaDCA and TMZ reduced the invasion of U87 and T98G tumors, as well as the expression of PCNA and EZH2 in the tumor. TMZ reduced p53 expression in tumors from both cell lines, whereas VPA–NaDCA did not affect the expression of this marker. VPA–NaDCA, but not TMZ, reduced SLC12A2 expression in T98G cells. However, VPA–NaDCA and TMZ did not affect SLC12A2 expression in U87 cells. VPA–NaDCA increased SLC5A8 expression only in U87 cells, and TMZ did not affect gene expression in either cell line. Only VPA–NaDCA increased CDH1 expression and decreased CDH2 expression in T98G cells, whereas TMZ had no effect on gene expression in the study cells. This study demonstrated that VPA–NaDCA exhibits a more effective anticancer effect than NaDCA. The data suggest that VPA–NaDCA has a more effective impact than TMZ; however, the effect of investigational medicines on carcinogenesis varies depending on the cell line. The study of the efficacy of drugs used to treat tumors on the CAM and cells demonstrates that it is essential to assess the effectiveness of treatment, which should be personalized, before administering chemotherapy. Full article

(This article belongs to the Special Issue New Molecular Mechanisms in the Development of Brain Tumors and Metastases)

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19 pages, 3529 KiB

Open AccessArticle

Sex-Dependent Effects of Aging and Insulin Resistance on Skeletal Muscle Function and Structure in Rats

by Patricia Sosa, Javier Angulo, Alberto Sánchez-Ferrer, Maria Carmen Gómez-Cabrera, Argentina Fernández, Leocadio Rodríguez-Mañas and Mariam El Assar

Int. J. Mol. Sci. 2025, 26(14), 6783; https://doi.org/10.3390/ijms26146783 (registering DOI) - 15 Jul 2025

Abstract

Skeletal muscle function is determinant for maintaining functional performance and independence in older adults. Muscle is a primary target of aging and insulin resistance (IR)—two conditions associated with functional decline. Sex-related differences may influence these effects at structural and functional levels. We aimed [...] Read more.

Skeletal muscle function is determinant for maintaining functional performance and independence in older adults. Muscle is a primary target of aging and insulin resistance (IR)—two conditions associated with functional decline. Sex-related differences may influence these effects at structural and functional levels. We aimed to evaluate the individual and combined effects of aging and IR on the function and structure of extensor digitorum longus (EDL) and soleus muscles in male and female rats. Animals aged 3 and 20 months were studied, with IR induced by 8 weeks of 20% fructose in drinking water. Muscle contractility was assessed alongside histological and hormonal analyses. In males, aging impaired EDL and soleus contractile force, free testosterone levels, and muscle mass. IR decreased muscle function only in young animals. In females, aging led to muscle loss without affecting contractile strength, but the combination of aging and IR reduced muscle contraction, decreased estradiol and exacerbated muscle loss. Both sexes showed aging-related loss of EDL glycolytic fibers, altered regenerative capacity, and increased fibrosis. IR alone reduced glycolytic fibers in young animals of both sexes but increased fibrosis only in males. These results highlight sex-specific effects of aging and IR on muscle function, relevant for targeted strategies to prevent and treat age- and IR-related muscle function decline. Full article

(This article belongs to the Special Issue Molecular Research on Skeletal Muscle Diseases)

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28 pages, 5847 KiB

Open AccessArticle

Platelet-Rich Plasma (PRP) Mitigates Silver Nanoparticle (AgNP)-Induced Pulmonary Fibrosis via iNOS/CD68/CASP3/TWIST1 Regulation: An Experimental Study and Bioinformatics Analysis

by Shaimaa R. Abdelmohsen, Ranya M. Abdelgalil, Asmaa M. Elmaghraby, Amira M. Negm, Reham Hammad, Eleni K. Efthimiadou, Sara Seriah, Hekmat M. El Magdoub, Hemat Elariny, Islam Farrag, Nahla El Shenawy, Doaa Abdelrahaman, Hussain Almalki, Ahmed A. Askar, Marwa M. El-Mosely, Fatma El Zahraa Abd El Hakam and Nadia M. Hamdy

Int. J. Mol. Sci. 2025, 26(14), 6782; https://doi.org/10.3390/ijms26146782 (registering DOI) - 15 Jul 2025

Abstract

Platelet-rich plasma (PRP) has become an increasingly valuable biologic approach for personalized regenerative medicine because of its potent anti-inflammatory/healing effects. It is thought to be an excellent source of growth factors that can promote tissue healing and lessen fibrosis. Although this treatment has [...] Read more.

Platelet-rich plasma (PRP) has become an increasingly valuable biologic approach for personalized regenerative medicine because of its potent anti-inflammatory/healing effects. It is thought to be an excellent source of growth factors that can promote tissue healing and lessen fibrosis. Although this treatment has demonstrated effectiveness in numerous disease areas, its impact on pulmonary fibrosis (PF) caused by silver nanoparticles (AgNPs) via its antiapoptotic effects remains to be explored. AgNPs were synthesized biologically by Bacillus megaterium ATCC 55000. AgNP characterization was carried out via UV‒Vis spectroscopy, X-ray diffraction (XRD), dynamic light scattering (DLS), transmission electron microscopy (TEM), and scanning electron microscopy (SEM) imaging to reveal monodispersed spheres with a mean diameter of 45.17 nm. A total of 48 male Wistar rats divided into six groups, with 8 rats per group, were used in the current study on the basis of sample size and power. The groups used were the PRP donor, control, AgNP, AgNP+PRP, AgNP+dexamethasone (Dexa) rat groups, and a recovery group. Body weights, hydroxyproline (HP) levels, and CASP3 and TWIST1 gene expression levels were assessed. H&E and Sirius Red staining were performed. Immunohistochemical studies for inducible nitric oxide synthase (iNOS) and cluster of differentiation 68 (CD68) with histomorphometry were conducted. A significant reduction in body weight (BWt) was noted in the AgNP group compared with the AgNP+PRP group (p < 0.001). HP, CASP3, and TWIST1 expression levels were significantly increased by AgNPs but decreased upon PRP (p < 0.001) treatment. Compared with those in the control group, the adverse effects of AgNPs included PF, lung alveolar collapse, thickening of the interalveolar septa, widespread lymphocytic infiltration, increased alveolar macrophage CD68 expression, and iNOS positivity in the cells lining the alveoli. This work revealed that PRP treatment markedly improved the histopathological and immunohistochemical findings observed in the AgNP group in a manner comparable to that of the Dexa. In conclusion, these results demonstrated the therapeutic potential of PRP in a PF rat model induced via AgNPs. This study revealed that PRP treatment significantly improved the histopathological and immunohistochemical alterations observed in the AgNP-induced group, with effects comparable to those of the Dexa. In conclusion, these findings highlight the therapeutic potential of PRP in a rat model of AgNP-induced PF. Full article

(This article belongs to the Special Issue New Advances in Cancer Genomics)

12 pages, 1293 KiB

Open AccessArticle

Urinary Titin as a Non-Invasive Biomarker for Sarcopenia Sex Differences in Unresectable Digestive Malignancies: A Retrospective Cohort Study

by Shiho Kaneko, Kazuaki Harada, Masatsugu Ohara, Shintaro Sawaguchi, Tatsuya Yokoyama, Koichi Ishida, Yasuyuki Kawamoto, Satoshi Yuki, Yoshito Komatsu and Naoya Sakamoto

Int. J. Mol. Sci. 2025, 26(14), 6781; https://doi.org/10.3390/ijms26146781 (registering DOI) - 15 Jul 2025

Abstract

The prognosis of sarcopenia is poor in cancer patients. Recently, urinary titin, a biomarker of muscle damage, has been suggested as a potential marker for sarcopenia. However, its utility in patients with unresectable digestive malignancies remains unclear. In addition, sex differences have been [...] Read more.

The prognosis of sarcopenia is poor in cancer patients. Recently, urinary titin, a biomarker of muscle damage, has been suggested as a potential marker for sarcopenia. However, its utility in patients with unresectable digestive malignancies remains unclear. In addition, sex differences have been reported in the association between sarcopenia and urinary titin levels. This study aimed to evaluate urinary titin as a diagnostic marker for unresectable digestive malignancies, focusing on sex differences. This retrospective study enrolled 96 patients (58 males, 38 females; median age 70), and urinary titin was evaluated as a diagnostic biomarker in relation to clinical factors (e.g., age, Eastern Cooperative Oncology Group performance status [ECOG PS], albumin [Alb]) and muscle indicators (e.g., psoas muscle index [PMI], handgrip strength). In male patients, urinary titin levels were significantly higher in the sarcopenia subgroup (5.78 vs. 2.79 pmol/mgCr, p = 0.008), and multivariate analyses identified urinary titin as an independent predictor of sarcopenia (odds ratio 13.4, p = 0.028). The receiver operating characteristic (ROC) analysis demonstrated fair diagnostic performance (area under the curve [AUC] 0.729), with an optimal cutoff value of 3.676 pmol/mgCr. Urinary titin may serve as a useful non-invasive diagnostic biomarker for sarcopenia in patients with unresectable digestive malignancies, particularly in males. These findings suggest that sex-specific approaches are required for sarcopenia assessment with urinary titin. Full article

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

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20 pages, 2355 KiB

Open AccessArticle

Multistage Molecular Simulations, Design, Synthesis, and Anticonvulsant Evaluation of 2-(Isoindolin-2-yl) Esters of Aromatic Amino Acids Targeting GABA_A Receptors via π-π Stacking

by Santiago González-Periañez, Fabiola Hernández-Rosas, Carlos Alberto López-Rosas, Fernando Rafael Ramos-Morales, Jorge Iván Zurutuza-Lorméndez, Rosa Virginia García-Rodríguez, José Luís Olivares-Romero, Rodrigo Rafael Ramos-Hernández, Ivette Bravo-Espinoza, Abraham Vidal-Limon and Tushar Janardan Pawar

Int. J. Mol. Sci. 2025, 26(14), 6780; https://doi.org/10.3390/ijms26146780 (registering DOI) - 15 Jul 2025

Abstract

Epilepsy remains a widespread neurological disorder, with approximately 30% of patients showing resistance to current antiepileptic therapies. To address this unmet need, a series of 2-(isoindolin-2-yl) esters derived from natural amino acids were designed and evaluated for their potential interaction with the GABA [...] Read more.

Epilepsy remains a widespread neurological disorder, with approximately 30% of patients showing resistance to current antiepileptic therapies. To address this unmet need, a series of 2-(isoindolin-2-yl) esters derived from natural amino acids were designed and evaluated for their potential interaction with the GABA_A receptor. Sixteen derivatives were subjected to in silico assessments, including physicochemical and ADMET profiling, virtual screening–ensemble docking, and enhanced sampling molecular dynamics simulations (metadynamics calculations). Among these, compounds derived from the aromatic amino acids, phenylalanine, tyrosine, tryptophan, and histidine, exhibited superior predicted affinity, attributed to π–π stacking interactions at the benzodiazepine binding site of the GABA_A receptor. Based on computational performance, the tyrosine and tryptophan derivatives were synthesized and further assessed in vivo using the pentylenetetrazole-induced seizure model in zebrafish (Danio rerio). The tryptophan derivative produced comparable behavioral seizure reduction to the reference drug diazepam at the tested concentrations. The results implies that aromatic amino acid-derived isoindoline esters are promising anticonvulsant candidates and support the hypothesis that π–π interactions may play a critical role in modulating GABA_A receptor binding affinity. Full article

(This article belongs to the Special Issue Computational Studies in Drug Design and Discovery)

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16 pages, 6242 KiB

Open AccessArticle

IgG:FcγRIIb Signaling on Mast Cells Blocks Allergic Airway Inflammation

by Cynthia Kanagaratham, Yasmeen S. El Ansari, Kameryn N. Furiness and Hans C. Oettgen

Int. J. Mol. Sci. 2025, 26(14), 6779; https://doi.org/10.3390/ijms26146779 (registering DOI) - 15 Jul 2025

Abstract

IgG antibodies, signaling via the inhibitory receptor, FcγRIIb, are potent inhibitors of IgE-mediated mast cell activation. We have previously reported that in addition to blocking mast cell degranulation, inhibitory IgG signals shut down a proinflammatory transcriptional program in which mast cells produce cytokines [...] Read more.

IgG antibodies, signaling via the inhibitory receptor, FcγRIIb, are potent inhibitors of IgE-mediated mast cell activation. We have previously reported that in addition to blocking mast cell degranulation, inhibitory IgG signals shut down a proinflammatory transcriptional program in which mast cells produce cytokines and chemokines known to drive type 2 tissue inflammation. To determine whether such effects of allergen-specific IgG can modulate allergic inflammation in vivo, we examined the airways of mice sensitized to ovalbumin (OVA) by intraperitoneal injection and then challenged with intranasal OVA. Pretreatment with allergen-specific IgG significantly reduced the recruitment of inflammatory cells, including macrophages and eosinophils, into the lungs of OVA-sensitized mice. The bronchoalveolar lavage fluid of OVA-challenged mice contained elevated levels of chemokine ligands (CCL2 and CCL24) and interleukin-5, a response that was markedly blunted in animals receiving allergen-specific IgG. IgG-treated animals exhibited attenuated allergen-induced production of IgE, IL-4, and IL-13, along with impaired OVA-induced goblet cell hyperplasia and Muc5ac expression and suppressed airway hyperresponsiveness, consistent with a shift away from a Th2 response. Using mice with a lineage-specific deletion of FcγRIIb, we demonstrated that each of these protective effects of IgG was dependent upon the expression of this receptor on mast cells. Overall, our findings establish that allergen-specific IgG can reduce allergen-driven airway inflammation and airway hyperresponsiveness and point to a mechanistic basis for the therapeutic benefit of aeroallergen-specific IgG therapy. Full article

(This article belongs to the Special Issue Advances in the Pathogenesis of Allergic Diseases: From Mechanisms to Therapeutics)

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31 pages, 1327 KiB

Open AccessReview

Tumor Microenvironment in Melanoma—Characteristic and Clinical Implications

by Hubert Sikorski, Michał Aleksander Żmijewski and Anna Piotrowska

Int. J. Mol. Sci. 2025, 26(14), 6778; https://doi.org/10.3390/ijms26146778 (registering DOI) - 15 Jul 2025

Abstract

Cutaneous melanoma is an aggressive cancer with an increasing incidence worldwide, highlighting the need for research into its pathogenesis. The tumor microenvironment (TME) plays a critical role in melanoma progression and consists of cellular components and an extracellular matrix (ECM) rich in cytokines [...] Read more.

Cutaneous melanoma is an aggressive cancer with an increasing incidence worldwide, highlighting the need for research into its pathogenesis. The tumor microenvironment (TME) plays a critical role in melanoma progression and consists of cellular components and an extracellular matrix (ECM) rich in cytokines and signaling molecules. The most abundant stromal cells within the TME are cancer-associated fibroblasts (CAFs), which remodel the ECM and modulate immune responses. Among immune cells, tumor-associated macrophages (TAMs) predominate, and their polarization toward the M2 phenotype supports tumor progression. Tumor-infiltrating lymphocytes (TILs) have diverse functions, including cytotoxic T-cells, helper T-cells that modulate immune response, B-cells forming tertiary lymphoid structures (TLS), and regulatory T-cells with immunosuppressive properties. Dendritic cells (DCs) also play a complex role in the TME. A notable subpopulation are mature regulatory dendritic cells (mregDCs), which contribute to immune evasion. All of these TME components may drive tumorigenesis. Advancements in melanoma treatment—including immunotherapy and targeted therapies—have significantly improved outcomes in advanced-stage disease. In parallel, emerging approaches targeting the tumor microenvironment and gut microbiome, as well as personalized strategies such as neoantigen vaccines and cell-based therapies, are under active investigation and may further enhance therapeutic efficacy in the near future. Full article

(This article belongs to the Special Issue Molecular Mechanisms and Therapies for Melanoma)

37 pages, 1341 KiB

Open AccessReview

Molecular Insights into the Potential Cardiometabolic Effects of GLP-1 Receptor Analogs and DPP-4 Inhibitors

by Małgorzata Król, Patrycja Kupnicka, Justyna Żychowska, Patrycja Kapczuk, Izabela Szućko-Kociuba, Eryk Prajwos and Dariusz Chlubek

Int. J. Mol. Sci. 2025, 26(14), 6777; https://doi.org/10.3390/ijms26146777 (registering DOI) - 15 Jul 2025

Abstract

Cardiovascular diseases (CVDs) are the leading cause of global mortality, with type 2 diabetes mellitus (T2DM) and obesity significantly increasing the risk of CVD. Glucagon-like peptide-1 receptor agonists (GLP-1 RAs) and dipeptidyl peptidase-4 inhibitors (DPP-4is) have gained attention for their potential cardioprotective effects. [...] Read more.

Cardiovascular diseases (CVDs) are the leading cause of global mortality, with type 2 diabetes mellitus (T2DM) and obesity significantly increasing the risk of CVD. Glucagon-like peptide-1 receptor agonists (GLP-1 RAs) and dipeptidyl peptidase-4 inhibitors (DPP-4is) have gained attention for their potential cardioprotective effects. Therefore, this review aims to explore the molecular mechanisms underlying the cardiovascular benefits of these agents. A literature review was conducted searching PubMed databases from 1990 to January 2025, including research on the effects of GLP-1 RA and DPP-4i on cardiovascular health, specifically concerning atherosclerosis, coronary artery disease, vascular health, cardiac arrhythmias, myocardial infarction (MI), and heart failure, with a focus on the biochemical and molecular effects of these drugs. We analyzed 131 scientific publications, which indicate that GLP-1 RA and DPP-4i significantly reduce cardiovascular risk and major adverse cardiovascular events (MACEs), including atherosclerosis, myocardial infarction, and cardiac arrhythmias. These clinical outcomes are attributed to the mitigation of oxidative stress, inflammation, and endothelial dysfunction as well as improvement in mitochondrial function and lipid metabolism. GLP-1 RAs offer substantial cardiovascular benefits, making them valuable in managing T2DM and reducing CVD risk. Their integration into treatment regimens for CVD can reduce hospitalization rates, improve quality of life, and extend life expectancy. DPP-4is, while beneficial, are less effective in cardiovascular protection. Further research is needed to optimize therapeutic strategies and broaden the clinical application of these agents in cardiometabolic care. Full article

(This article belongs to the Special Issue Cardiovascular Disease: Molecular Basis, Potential Therapeutic Targets and Translational Research)

24 pages, 1114 KiB

Open AccessReview

Primary Graft Dysfunction in Lung Transplantation: An Overview of the Molecular Mechanisms

by Jitte Jennekens, Sue A. Braithwaite, Bart Luijk, Niels P. van der Kaaij, Nienke Vrisekoop, Saskia C. A. de Jager and Linda M. de Heer

Int. J. Mol. Sci. 2025, 26(14), 6776; https://doi.org/10.3390/ijms26146776 (registering DOI) - 15 Jul 2025

Abstract

Primary graft dysfunction (PGD) remains a major complication after lung transplantation. Donor lung ischemia followed by reperfusion drives oxidative stress and inflammatory responses. The pathophysiology is influenced by various donor-, procedure-, and recipient-related factors, which complicates the identification of biomarkers for evaluation of [...] Read more.

Primary graft dysfunction (PGD) remains a major complication after lung transplantation. Donor lung ischemia followed by reperfusion drives oxidative stress and inflammatory responses. The pathophysiology is influenced by various donor-, procedure-, and recipient-related factors, which complicates the identification of biomarkers for evaluation of donor lung injury or therapeutic interventions to minimize PGD. This review provides an overview of the molecular pathways that contribute to PGD pathophysiology, including those involved in loss of endothelial–epithelial membrane integrity, neutrophil infiltration, and the development of pulmonary edema. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Primary Graft Dysfunction and Acute Rejection in Solid Organ Transplantation)

27 pages, 873 KiB

Open AccessReview

Liposomes and Extracellular Vesicles as Distinct Paths Toward Precision Glioma Treatment

by Wiktoria Fraczek, Maciej Szmidt, Kacper Kregielewski and Marta Grodzik

Int. J. Mol. Sci. 2025, 26(14), 6775; https://doi.org/10.3390/ijms26146775 (registering DOI) - 15 Jul 2025

Abstract

Glioblastoma multiforme (GBM), the most aggressive and therapy-resistant glioma subtype, remains an urgent clinical challenge due to its invasive nature, molecular heterogeneity, and the protective constraints of the blood–brain barrier (BBB). Liposomes and extracellular vesicles (EVs) have emerged as two of the most [...] Read more.

Glioblastoma multiforme (GBM), the most aggressive and therapy-resistant glioma subtype, remains an urgent clinical challenge due to its invasive nature, molecular heterogeneity, and the protective constraints of the blood–brain barrier (BBB). Liposomes and extracellular vesicles (EVs) have emerged as two of the most promising nanocarrier systems capable of overcoming these limitations through improved drug delivery and cellular targeting. Their applications in glioma therapy span chemotherapy, immunotherapy, and gene therapy, each presenting distinct advantages and mechanisms of action. Liposomes offer structural flexibility, controlled release, and a well-established clinical framework, while EVs provide innate biocompatibility, low immunogenicity, and the ability to mimic natural intercellular communication. Both systems demonstrate the capacity to traverse the BBB and selectively accumulate in tumor tissue, yet they differ in scalability, cargo loading efficiency, and translational readiness. Comparative evaluation of their functions across therapeutic modalities reveals complementary strengths that may be leveraged in the development of more effective, targeted strategies for glioma treatment. Full article

(This article belongs to the Special Issue Molecular Advances in Liposome-Based Drug Delivery Systems)

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Int. J. Mol. Sci., Volume 26, Issue 14 (July-2 2025) – 259 articles

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