International Journal of Molecular Sciences

20 pages, 1227 KiB

Open AccessArticle

Interleukin Dynamics and Their Correlation with Tumor Aggressiveness in Colorectal Carcinoma

by Elena-Teodora Tâlvan, Liviuta Budișan, Călin Ilie Mohor, Valentin Grecu, Ioana Berindan-Neagoe, Victor Cristea, George Oprinca and Adrian Cristian

Int. J. Mol. Sci. 2025, 26(14), 7027; https://doi.org/10.3390/ijms26147027 - 21 Jul 2025

Viewed by 343

Abstract

Colorectal cancer (CRC) is a major global health concern, with tumor progression closely influenced by inflammatory mechanisms and cytokine signaling. This study investigates the serum expression levels of interleukins IL-8, IL-17A, and IL-33 in patients with colon cancer, analyzing their association with tumor [...] Read more.

Colorectal cancer (CRC) is a major global health concern, with tumor progression closely influenced by inflammatory mechanisms and cytokine signaling. This study investigates the serum expression levels of interleukins IL-8, IL-17A, and IL-33 in patients with colon cancer, analyzing their association with tumor grade and depth of invasion. The cohort included 42 patients stratified by tumor differentiation (G1–G3) and various invasion types. ELISA assays revealed that IL-8 levels were highest in well-differentiated tumors and in cases of submucosal and serosal invasion, suggesting a key role in early stage inflammation and angiogenesis. IL-17A and IL-33 levels declined progressively with tumor dedifferentiation and increased invasion depth, indicating immune suppression in advanced stages. Multiple regression analyses highlighted a nonlinear, significant relationship between IL-8 and IL-17A, whereas IL-33 showed no direct correlation with other interleukins. A combined model incorporating IL-8, IL-17A, IL-33, and tumor grade accounted for over 70% of IL-17A variability, underscoring their interactive role in CRC biology. These findings support the potential utility of interleukins as biomarkers and therapeutic targets for stratified CRC management. Full article

(This article belongs to the Special Issue Molecular Diagnosis and Treatment of Colorectal Cancer)

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30 pages, 3285 KiB

Open AccessReview

Curcumin and Dementia: A Systematic Review of Its Effects on Oxidative Stress and Cognitive Outcomes in Animal Models

by Samuel Abiodun Kehinde, Wai Phyo Lin, Bo Bo Lay, Khin Yadanar Phyo, Myat Mon San, Rinrada Pattanayaiying and Sasitorn Chusri

Int. J. Mol. Sci. 2025, 26(14), 7026; https://doi.org/10.3390/ijms26147026 - 21 Jul 2025

Viewed by 259

Abstract

Dementia is marked by progressive cognitive decline linked to oxidative stress, neuroinflammation, and synaptic dysfunction. Curcumin, a natural compound from Curcuma longa, has shown promising neuroprotective effects. This systematic review analyzed 29 preclinical studies using rodent models of dementia induced by chemical, genetic, [...] Read more.

Dementia is marked by progressive cognitive decline linked to oxidative stress, neuroinflammation, and synaptic dysfunction. Curcumin, a natural compound from Curcuma longa, has shown promising neuroprotective effects. This systematic review analyzed 29 preclinical studies using rodent models of dementia induced by chemical, genetic, or dietary methods. The review focused on curcumin’s effects on oxidative stress, inflammation, and cognitive outcomes. All studies assessing malondialdehyde (MDA) reported significant reductions, indicating reduced oxidative stress. Superoxide dismutase (SOD) activity increased in all measured cases, while glutathione (GSH) levels rose in about one-third of studies. A literature search was comprehensively conducted using PubMed, Scopus, AMED, and LILACS databases through April 2024. Curcumin also demonstrated anti-inflammatory properties, with over 80% of studies showing reduced levels of pro-inflammatory cytokines such as TNF-α, IL-6, and IL-1β. Additionally, 40% of studies noted increases in anti-inflammatory markers like IL-4 and IGF-1. Cognitive performance improved in around 80% of studies, especially in spatial learning and memory. Some studies also reported behavioral improvements, including reduced anxiety and enhanced locomotion. Curcumin demonstrated potent antioxidative, anti-inflammatory, and cognitive-enhancing effects across diverse dementia models. Its ability to modulate multiple pathological pathways highlights its potential as a bioactive compound for mitigating cognitive decline associated with neurodegenerative diseases. However, variability in study design and curcumin formulations suggests the need for standardized protocols and further high-quality research to facilitate clinical translation. Full article

(This article belongs to the Special Issue Autophagy, Cellular Senescence and Oxidative Stress in Ageing and Age-Related Diseases)

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19 pages, 1388 KiB

Open AccessArticle

Lipid Oxidation of Stored Brown Rice Changes Ileum Digestive and Metabolic Characteristics of Broiler Chickens

by Beibei He, Xueyi Zhang, Weiwei Wang, Li Wang, Jingjing Shi, Kuanbo Liu, Junlin Cheng, Yongwei Wang and Aike Li

Int. J. Mol. Sci. 2025, 26(14), 7025; https://doi.org/10.3390/ijms26147025 - 21 Jul 2025

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Abstract

Long-term storage may induce lipid oxidation in brown rice and impact its utilization in animal diets. One-day-old male Ross 308 broiler chickens (with an initial body weight of 20 g) were randomly divided into three groups: corn-based diet (Corn), fresh brown rice-based diet [...] Read more.

Long-term storage may induce lipid oxidation in brown rice and impact its utilization in animal diets. One-day-old male Ross 308 broiler chickens (with an initial body weight of 20 g) were randomly divided into three groups: corn-based diet (Corn), fresh brown rice-based diet (BR1) and stored brown rice-based diet (BR6), with 8 replicates of 10 birds per pen, in a 42-day feeding trial. The results showed that lipid oxidation indexes increased and fatty acid composition changed significantly in BR6 (p < 0.05). The dietary replacement of corn with brown rice showed no effects on growth performance of broilers (p > 0.05). However, palmitic acid and oleic acid increased, and stearic acid, linoleic acid and docosadienoic acid decreased in the broiler breast muscle of the BR1 and BR6 groups (p < 0.05). Ileum antioxidant enzyme activities increased in the BR1 and BR6 groups compared to the Corn group (p < 0.05), and the activities of α-amylase, trypsin, chymotrypsin and lipase decreased in the BR6 group compared to the BR1 and Corn groups (p < 0.05). Also, compared to the BR1 group, the overall expression of metabolites involved in drug metabolism—cytochrome P450, GnRH secretion and the estrogen signaling pathway in broiler ileum were down-regulated in the BR6 group (p < 0.05). In conclusion, the lipid oxidation of stored brown rice decreased digestive enzyme activities and changed metabolic characteristics in the ileum of broilers. While replacing corn with brown rice did not affect broiler growth performance, it reduced the contents of unsaturated and essential fatty acids in breast muscle and enhanced the ileal antioxidant functions of broilers. Full article

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

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17 pages, 11573 KiB

Open AccessArticle

IFNγ Expression Correlates with Enhanced Cytotoxicity in CD8+ T Cells

by Varsha Pattu, Elmar Krause, Hsin-Fang Chang, Jens Rettig and Xuemei Li

Int. J. Mol. Sci. 2025, 26(14), 7024; https://doi.org/10.3390/ijms26147024 - 21 Jul 2025

Viewed by 193

Abstract

CD8+ T lymphocytes (CTLs) act as serial killers of infected or malignant cells by releasing large amounts of interferon-gamma (IFNγ) and granzymes. Although IFNγ is a pleiotropic cytokine with diverse immunomodulatory functions, its precise spatiotemporal regulation and role in CTL-mediated cytotoxicity remain incompletely [...] Read more.

CD8+ T lymphocytes (CTLs) act as serial killers of infected or malignant cells by releasing large amounts of interferon-gamma (IFNγ) and granzymes. Although IFNγ is a pleiotropic cytokine with diverse immunomodulatory functions, its precise spatiotemporal regulation and role in CTL-mediated cytotoxicity remain incompletely understood. Using wild-type and granzyme B-mTFP knock-in mice, we employed a combination of in vitro approaches, including T cell isolation and culture, plate-bound anti-CD3e stimulation, degranulation assays, flow cytometry, immunofluorescence, and structured illumination microscopy, to investigate IFNγ dynamics in CTLs. IFNγ expression in CTLs was rapid, transient, and strictly dependent on T cell receptor (TCR) activation. We identified two functionally distinct IFNγ-producing subsets: IFNγ^high (IFNγ^hi) and IFNγ^low (IFNγ^lo) CTLs. IFNγ^hi CTLs exhibited an effector/effector memory phenotype, significantly elevated CD107a surface expression (a marker of lytic granule exocytosis), and higher colocalization with cis-Golgi and granzyme B compared to IFNγ^lo CTLs. Furthermore, CRTAM, an early activation marker, correlated with IFNγ expression in naive CTLs. Our findings establish a link between elevated IFNγ production and enhanced CTL cytotoxicity, implicating CRTAM as a potential regulator of early CTL activation and IFNγ induction. These insights provide a foundation for optimizing T cell-based immunotherapies against infections and cancers. Full article

(This article belongs to the Section Molecular Immunology)

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26 pages, 1216 KiB

Open AccessReview

Neurosteroids, Microbiota, and Neuroinflammation: Mechanistic Insights and Therapeutic Perspectives

by Amal Tahri, Elena Niccolai and Amedeo Amedei

Int. J. Mol. Sci. 2025, 26(14), 7023; https://doi.org/10.3390/ijms26147023 - 21 Jul 2025

Viewed by 357

Abstract

The gut–brain axis (GBA) represents a complex bidirectional communication network that links the gut microbiota (GM) and the central nervous system (CNS). Recent research has revealed that neurosteroids (NSs) play crucial roles in modulating neuroinflammatory responses and promoting neuroprotection. Meanwhile, GM alterations have [...] Read more.

The gut–brain axis (GBA) represents a complex bidirectional communication network that links the gut microbiota (GM) and the central nervous system (CNS). Recent research has revealed that neurosteroids (NSs) play crucial roles in modulating neuroinflammatory responses and promoting neuroprotection. Meanwhile, GM alterations have been associated with various neuroinflammatory and neurodegenerative conditions, such as multiple sclerosis, Alzheimer’s disease, and amyotrophic lateral sclerosis. This review aims to provide a comprehensive overview of the intricate interactions between NS, GM, and neuroinflammation. We discuss how NS and metabolites can influence neuroinflammatory pathways through immune, metabolic, and neuronal mechanisms. Additionally, we explore how GM modulation can impact neurosteroidogenesis, highlighting potential therapeutic strategies that include probiotics, neuroactive metabolites, and targeted interventions. Understanding these interactions may pave the way for innovative treatment approaches for neuroinflammatory and neurodegenerative diseases, promoting a more integrated view of brain health and disease management. Full article

(This article belongs to the Collection Feature Paper Collection in Molecular Endocrinology and Metabolism)

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31 pages, 4667 KiB

Open AccessArticle

Harnessing Plant-Based Nanoparticles for Targeted Therapy: A Green Approach to Cancer and Bacterial Infections

by Mirela Claudia Rîmbu, Daniel Cord, Mihaela Savin, Alexandru Grigoroiu, Mirela Antonela Mihăilă, Mona Luciana Gălățanu, Viorel Ordeanu, Mariana Panțuroiu, Vasilica Țucureanu, Iuliana Mihalache, Oana Brîncoveanu, Adina Boldeiu, Veronica Anăstăsoaie, Carmen Elisabeta Manea, Roxana-Colette Sandulovici, Marinela Chirilă, Adina Turcu-Știolică, Emilia Amzoiu, Victor-Eduard Peteu, Cristiana Tănase, Bogdan Firtat and Carmen-Marinela Mihăilescu Show full author list Hide full author list

Int. J. Mol. Sci. 2025, 26(14), 7022; https://doi.org/10.3390/ijms26147022 - 21 Jul 2025

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Abstract

This study investigates the antioxidant, antimicrobial, and antitumor activities of Taraxacum officinale (Dandelion) and Artemisia annua (Sweet Wormwood) extracts, along with their role in the green synthesis of gold (AuNPs) and silver nanoparticles (AgNPs). Bioreduction was achieved using aqueous and ethanolic extracts (100 [...] Read more.

This study investigates the antioxidant, antimicrobial, and antitumor activities of Taraxacum officinale (Dandelion) and Artemisia annua (Sweet Wormwood) extracts, along with their role in the green synthesis of gold (AuNPs) and silver nanoparticles (AgNPs). Bioreduction was achieved using aqueous and ethanolic extracts (100 mg/mL), enabling solvent-dependent comparisons. Nanoparticles were characterized using ultraviolet–visible spectroscopy (UV–Vis), fluorescence spectroscopy, scanning electron microscopy (SEM), dynamic light scattering (DLS), high-resolution transmission electron microscopy (HRTEM), and zeta potential analysis. Each technique revealed complementary aspects of nanoparticle morphology, size, and stability, with UV–Vis indicating aggregation states and DLS confirming solvent-related size variation even at 3–5% ethanol. Gold nanoparticles synthesized from Dandelion showed strong antibacterial activity against Staphylococcus aureus, while silver nanoparticles from both plants were effective against Escherichia coli. Cytotoxicity assays indicated that silver nanoparticles obtained from ethanolic Dandelion extract containing 3% ethanol in aqueous solution (AgNPsE_ETOH3%-D) significantly reduced LoVo (p = 4.58 × 10⁻³) and MDA-MB-231 (p = 7.20 × 10⁻⁵) cell viability, with high selectivity indices (SI), suggesting low toxicity toward normal cells. Gold nanoparticles synthesized from aqueous Dandelion extract (AuNPsEaq-D) also showed favorable SI values (2.16 for LoVo and 8.41 for MDA-MB-231). Although some formulations demonstrated lower selectivity (SI < 1.5), the findings support the therapeutic potential of these biogenic nanoparticles. Further in vivo studies and pharmacokinetic evaluations are required to validate their clinical applicability. Full article

(This article belongs to the Special Issue Molecular Characterization and Applications of Nanomaterials in Nanomedicine and Cancer Therapy)

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23 pages, 13635 KiB

Open AccessArticle

Cytochalasins Suppress 3D Migration of ECM-Embedded Tumoroids at Non-Toxic Concentrations

by Klara Beslmüller, Lieke J. A. van Megen, Timo Struik, Daisy Batenburg, Elsa Neubert, Tom M. J. Evers, Alireza Mashaghi and Erik H. J. Danen

Int. J. Mol. Sci. 2025, 26(14), 7021; https://doi.org/10.3390/ijms26147021 - 21 Jul 2025

Viewed by 245

Abstract

Migrastatic strategies are considered as candidate therapeutic approaches to suppress cancer invasion into local surrounding tissues and metastatic spread. The F-actin cytoskeleton is responsible for key properties regulating (cancer) cell migration. The cortical F-actin network controls cell stiffness, which, in turn, determines cell [...] Read more.

Migrastatic strategies are considered as candidate therapeutic approaches to suppress cancer invasion into local surrounding tissues and metastatic spread. The F-actin cytoskeleton is responsible for key properties regulating (cancer) cell migration. The cortical F-actin network controls cell stiffness, which, in turn, determines cell migration strategies and efficiency. Moreover, the dynamic remodeling of F-actin networks mediating filopodia, lamellipodia, and F-actin stress fibers is crucial for cell migration. Here, we have used a conditional knockout approach to delete cofilin, an F-actin-binding protein that controls severing. We find that the deletion of cofilin prevents the migration of cancer cells from tumoroids into the surrounding extracellular matrix without affecting their viability. This identifies cofilin as a candidate target to suppress metastatic spread. Pharmacological inhibitors interfering with F-actin dynamics have been developed but their effects are pleiotropic, including severe toxicity, and their impact on 3D tumor cell migration has not been tested or separated from this toxicity. Using concentration ranges of a panel of inhibitors, we select cytochalasins based on the suppression of 2D migration at non-toxic concentrations. We then show that these attenuate the escape of tumor cells from tumoroids and their migration into the surrounding extracellular matrix without toxicity in 3D cultures. This effect is accompanied by suppression of cell stiffness at such non-toxic concentrations, as measured by acoustic force spectroscopy. These findings identify cytochalasins B and D as candidate migrastatic drugs to suppress metastatic spread. Full article

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

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13 pages, 2987 KiB

Open AccessCommunication

Improved Degradome Sequencing Protocol via Reagent Recycling from sRNAseq Library Preparations

by Marta Puchta-Jasińska, Jolanta Groszyk and Maja Boczkowska

Int. J. Mol. Sci. 2025, 26(14), 7020; https://doi.org/10.3390/ijms26147020 - 21 Jul 2025

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Abstract

One of the key elements in the analysis of gene expression and its post-translational regulation is miRNAs. Degradome-seq analyses are performed to analyze the cleavage of target RNAs in the transcriptome. This work presents the first degradome-seq library preparation protocol that enables successful [...] Read more.

One of the key elements in the analysis of gene expression and its post-translational regulation is miRNAs. Degradome-seq analyses are performed to analyze the cleavage of target RNAs in the transcriptome. This work presents the first degradome-seq library preparation protocol that enables successful construction of libraries, even from highly degraded RNA samples with RIN below 3, thus significantly expanding the possibilities for research when working with low-quality material. The developed protocol improves the efficiency of library preparation in degradome-seq analysis used to identify miRNA targets, reduces library preparation time, and lowers the cost of purchasing reagents by using reagents from the RNA-seq library preparation kit and proprietary-designed primers. A crucial feature of this new protocol is optimizing the purification step for short library fragments, which increases the yield of correctly sized fragments compared to previously used methods. This is achieved by implementing an original method involving tube-spin purification with gauze and precipitation using sodium acetate with glycogen, greatly enhancing recovery efficiency—a factor especially critical when working with degraded RNA. Cloning to a plasmid and sequencing of the inserted fragment verified the correctness of the library preparation using the developed protocol. This protocol represents a groundbreaking tool for degradome research, enabling the construction and sequencing of degradome libraries, even from degraded samples previously considered unsuitable for such analyses. This is due to the use of residues from the sRNA-seq library kit. It noticeably reduces the cost of library construction. The precision of the excised fragment after electrophoresis was performed during the procedure to isolate fragments of the correct length, which was improved using additional size markers. Compared to previously used methods, optimizing the purification method of degradome-seq libraries allowed an increase in the yield of fragments obtained. Full article

(This article belongs to the Special Issue Advances in Seed Development and Germination)

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21 pages, 3038 KiB

Open AccessArticle

Glycerol Biosynthesis Pathways from Starch Endow Dunaliella salina with the Adaptability to Osmotic and Oxidative Effects Caused by Salinity

by Huiying Yao, Yi Xu, Huahao Yang, Yihan Guo, Pengrui Jiao, Dongyou Xiang, Hui Xu and Yi Cao

Int. J. Mol. Sci. 2025, 26(14), 7019; https://doi.org/10.3390/ijms26147019 - 21 Jul 2025

Viewed by 204

Abstract

Dunaliella salina, a unicellular and eukaryotic alga, has been found to be one of the most salt-tolerant eukaryotes with a wide range of practical applications. To elucidate the underlying molecular mechanisms of D. salina in response to salinity stress, we performed transcriptome [...] Read more.

Dunaliella salina, a unicellular and eukaryotic alga, has been found to be one of the most salt-tolerant eukaryotes with a wide range of practical applications. To elucidate the underlying molecular mechanisms of D. salina in response to salinity stress, we performed transcriptome sequencing on samples under different stress conditions. A total of 82,333 unigenes were generated, 4720, 1111 and 2611 differentially expressed genes (DEGs) were identified under high salt stress, oxidative stress and hypertonic stress, respectively. Our analysis revealed that D. salina responds to salinity stress through a complex network of molecular mechanisms. Under high salt stress, starch degradation is regulated by AMY (α-amylase) and PYG (glycogen phosphorylase) with alternative expression patterns. This process is hypothesized to be initially constrained by low ATP levels due to impaired photosynthesis. The clustering analysis of DEGs indicated that starch and sucrose metabolism, as well as glycerol metabolism, are specifically reprogrammed under high salt stress. Glycerol metabolism, particularly involving GPDHs, plays a crucial role in maintaining osmotic balance under salinity stress. Key glycerol metabolism genes were up-regulated under salinity conditions, indicating the importance of this pathway in osmotic regulation. The G3P shuttle, involving mitochondrial GPDHs (c25199_g1 and c23777_g1), contributes to redox imbalance management under high salt, oxidative and hypertonic stresses. Notably, c23777_g1 is involved in the G3P shuttle under high salt, oxidative and hypertonic stresses, while c25199_g1 is specifically induced by hypertonic stress. The R2R3-MYB gene (c23845_g1) may respond to different effects of salinity stress by regulating the transcription of ROS-related genes. Our study provides a detailed understanding of the molecular responses of D. salina to salinity stress. We reveal the critical roles of starch and sucrose metabolism, glycerol metabolism and transcription factors in the D. salina adaptation to salinity. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 3rd Edition)

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17 pages, 7080 KiB

Open AccessArticle

Impact of Food Exposome on Atherosclerotic Plaque Stability: Metabolomic Insights from Human Carotid Endarterectomy Specimen

by Emilie Doche, Barbara Leclercq, Constance Sulowski, Ellen Magoncia, Catherine Tardivel, Ljubica Svilar, Gabrielle Sarlon-Bartoli, Jean-Charles Martin, Michel Bartoli, Alexandre Rossillon and Laurent Suissa

Int. J. Mol. Sci. 2025, 26(14), 7018; https://doi.org/10.3390/ijms26147018 - 21 Jul 2025

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Abstract

Carotid atherosclerotic stenosis (CAS) is a leading cause of ischemic stroke. Current understanding of plaque vulnerability remains largely confined to histopathological characterization. Consequently, identifying molecular determinants of plaque stability represents a major challenge to advance prevention strategies. Untargeted metabolomic analysis was performed using [...] Read more.

Carotid atherosclerotic stenosis (CAS) is a leading cause of ischemic stroke. Current understanding of plaque vulnerability remains largely confined to histopathological characterization. Consequently, identifying molecular determinants of plaque stability represents a major challenge to advance prevention strategies. Untargeted metabolomic analysis was performed using mass spectrometry coupled to liquid chromatography on carotid plaques removed from patients with CAS undergoing endarterectomy. To identify factors influencing plaque stability, we compared 42 asymptomatic with 30 symptomatic CAS patients. Associations between each annotated metabolite in plaques and asymptomatic CAS status were assessed using logistic regression models. Asymptomatic patients exhibited lower plasmatic levels of C-reactive protein (CRP) and higher HDL-cholesterol. Within the plaques, caffeine and its catabolites, paraxanthine and methylxanthine, were associated with plaque stability and were correlated with HDL-cholesterol. Additional plant-based diet biomarkers including N5-acetylornithine, gentisic acid, proline betaine, and homostachydrine were also associated with plaque stability. In contrast, N-methylpyridone carboxamides, reflecting niacin excess, involved in vascular inflammatory processes, were both associated with plaque vulnerability and also correlated with higher CRP. Our findings provide molecular evidence that plant-based diets, including coffee, promote carotid plaque stability, while excessive niacin intake, linked to processed foods, may be detrimental. Metabolomics offers new insights into food exposome-related vascular risk. Full article

(This article belongs to the Special Issue Bioactive Compounds from Foods Against Diseases)

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13 pages, 961 KiB

Open AccessArticle

Molecular Landscape of Metastatic Lung Adenocarcinoma in Bulgarian Patients—A Prospective Study

by George Dimitrov, Vladislav Nankov, Natalia Chilingirova, Zornitsa Kamburova and Savelina Popovska

Int. J. Mol. Sci. 2025, 26(14), 7017; https://doi.org/10.3390/ijms26147017 - 21 Jul 2025

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Abstract

Lung adenocarcinoma exhibits a heterogeneous molecular landscape shaped by key oncogenic drivers and tumor suppressor gene alterations. Mutation frequencies vary geographically, influenced by genetic ancestry and environmental factors. However, the molecular profile of lung adenocarcinoma in Bulgarian patients remains largely uncharacterized. We conducted [...] Read more.

Lung adenocarcinoma exhibits a heterogeneous molecular landscape shaped by key oncogenic drivers and tumor suppressor gene alterations. Mutation frequencies vary geographically, influenced by genetic ancestry and environmental factors. However, the molecular profile of lung adenocarcinoma in Bulgarian patients remains largely uncharacterized. We conducted a prospective study of 147 Bulgarian patients with metastatic lung adenocarcinoma, analyzing clinicopathologic features and somatic mutation frequencies using next-generation sequencing. Key mutations and their prevalence were assessed and compared with published data from other populations. The cohort included predominantly male patients (68.0%) with a median age of 67 years. TP53 mutations were most frequent (41.5%), followed by EGFR alterations (19.0%) and KRAS c.34G>T (p.Gly12Cys) (17.0%). Over half of the patients (51.0%) harbored two or more gene mutations. Mutation frequencies aligned closely with European cohorts, exhibiting a lower prevalence of EGFR mutations compared to East Asian populations. This study characterizes the molecular landscape of lung adenocarcinoma in Bulgaria, highlighting the predominance of TP53 and KRAS mutations. The findings emphasize the need for comprehensive molecular profiling to inform targeted therapies and support precision oncology approaches tailored to the Bulgarian population. Further research is needed to validate these results and improve clinical outcomes. Full article

(This article belongs to the Special Issue Advances in Lung Cancer: From Genetic Landscape to Treatment)

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16 pages, 285 KiB

Open AccessArticle

Correlation and Risk Assessment of Inflammation-Based Parameters on Cardiovascular Parameters and Clinical Events in Giant Cell Arteritis: A Retrospective Study

by Leyla Schweiger, Andreas Meinitzer, Dieter Szolar, Marianne Brodmann, Christian Dejaco, Franz Hafner and Philipp Jud

Int. J. Mol. Sci. 2025, 26(14), 7016; https://doi.org/10.3390/ijms26147016 - 21 Jul 2025

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Abstract

This study investigated associations of inflammation-based biomarkers with endothelial dysfunction and lipids and their predictive value for clinical outcome parameters in patients with giant cell arteritis (GCA). A total of 138 patients with inactive GCA were retrospectively analyzed to investigate potential differences in [...] Read more.

This study investigated associations of inflammation-based biomarkers with endothelial dysfunction and lipids and their predictive value for clinical outcome parameters in patients with giant cell arteritis (GCA). A total of 138 patients with inactive GCA were retrospectively analyzed to investigate potential differences in inflammatory biomarkers regarding clinical GCA subtypes and potential correlations between inflammatory parameters with markers of endothelial dysfunction and lipid parameters. Additionally, the predictive role of inflammatory biomarkers for clinical outcomes, including disease relapse, all-cause mortality, cardiovascular events, and glucocorticoid adverse effects, was analyzed. GCA individuals without concomitant symptoms of polymyalgia rheumatica and those who received initial glucocorticoid pulse therapy exhibited significantly higher levels of white blood cells and neutrophils (all with p < 0.05). No other significant differences were observed between inflammatory biomarkers and clinical GCA subtypes. Additionally, significant correlations were identified between selected inflammation-based ratios and specific markers of endothelial dysfunction and lipid parameters (all with p < 0.05). Elevated white blood cells and neutrophils were significant and independent predictors of disease relapse in GCA (all with p < 0.05) in multiple logistic regression analysis. No significant associations were found between any other inflammatory biomarker and the occurrence of cardiovascular events, mortality, or glucocorticoid-related adverse effects. In patients with inactive GCA, selected inflammatory parameters correlated with endothelial dysfunction and dyslipidemia and may be predictive of disease relapse. Full article

(This article belongs to the Special Issue Forward in Vasculitis: Genetics and Beyond)

21 pages, 3372 KiB

Open AccessArticle

Advanced Research on Biological Properties—A Study on the Activity of the Apis mellifera Antioxidant System and the Crystallographic and Spectroscopic Properties of 7-Diethylamino-4-hydroxycoumarin

by Klaudia Rząd, Iwona Budziak-Wieczorek, Aneta Strachecka, Patrycja Staniszewska, Adam Staniszewski, Anna Gryboś, Alicja Matwijczuk, Bożena Gładyszewska, Karolina Starzak, Anna A. Hoser, Maurycy E. Nowak, Małgorzata Figiel, Sylwia Okoń and Arkadiusz Paweł Matwijczuk

Int. J. Mol. Sci. 2025, 26(14), 7015; https://doi.org/10.3390/ijms26147015 - 21 Jul 2025

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Abstract

The search for substances that increase the immunity of bees is becoming a necessity in the era of various environmental threats and the declining immunocompetence of these insects. Therefore, we tested the biological and physicochemical properties of 7-diethylamino-4-hydroxycoumarin (7DOC). In a cage test, [...] Read more.

The search for substances that increase the immunity of bees is becoming a necessity in the era of various environmental threats and the declining immunocompetence of these insects. Therefore, we tested the biological and physicochemical properties of 7-diethylamino-4-hydroxycoumarin (7DOC). In a cage test, two groups of bees were created: a control group fed with sugar syrup and an experimental group fed with sugar syrup with the addition of 7DOC. In each group, the longevity of the bees was determined and the protein concentrations and antioxidant activities in the bees’ hemolymph were determined. The bees fed with 7DOC lived 2.7 times longer than those in the control group. The protein concentrations and activities of SOD, CAT, GPx and GST, as well as the TAC levels, were significantly higher in the hemolymph of the supplemented workers. To confirm these potent biological properties of 7DOC, the UV-Vis spectra, emission and excitation of fluorescence, synchronous spectra and finally the fluorescence lifetimes of this compound were measured using the time-correlated single photon counting method, in various environments differing in polarity and in the environment applied in bee research. This compound was shown to be sensitive to changes in solvent polarity. The spectroscopic assays were complemented with crystallographic tests of the obtained monocrystals of the aforementioned compounds, which attested to the aggregation effects observed in the spectra measurements for the selected coumarin. The research results confirm that this compound has the potential to be implemented in apiary management, which will be our application goal, but further research into apiary conditions is required. Full article

(This article belongs to the Section Bioactives and Nutraceuticals)

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17 pages, 8756 KiB

Open AccessArticle

A Diet Rich in Essential Amino Acids Inhibits the Growth of HCT116 Human Colon Cancer Cell In Vitro and In Vivo

by Giovanni Corsetti, Claudia Romano, Silvia Codenotti, Evasio Pasini, Alessandro Fanzani, Tiziano Scarabelli and Francesco S. Dioguardi

Int. J. Mol. Sci. 2025, 26(14), 7014; https://doi.org/10.3390/ijms26147014 - 21 Jul 2025

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Abstract

The metabolic hyperactivity of tumor cells demands a substantial amount of energy and molecules to build new cells and expand the tumor, diverting these resources from healthy cells. Amino acids (AAs) are the only totipotent and essential molecules for protein construction. Previous in [...] Read more.

The metabolic hyperactivity of tumor cells demands a substantial amount of energy and molecules to build new cells and expand the tumor, diverting these resources from healthy cells. Amino acids (AAs) are the only totipotent and essential molecules for protein construction. Previous in vitro studies in human and murine cancer cells, along with in vivo studies in mice, have shown that an excess of essential amino acids (EAAs) exerts an inhibitory effect on tumor proliferation by promoting apoptosis and autophagy. In this study, both in vitro and in vivo, we evaluated whether a mixture based on EAA can influence the development of human colon cancer (HCT116). To this end, in vitro, we assessed the proliferation of HCT116 cells treated with a special mix of EAA. In vivo, immunosuppressed athymic nude mice, injected with HCT116 cells subcutaneously (s.c.) or intraperitoneally (i.p.), were given a modified EAAs-rich diet (EAARD) compared to the standard laboratory diet (StD). In vitro data showed that the EAA mix impairs cancer growth by inducing apoptosis and autophagy. In vivo, the results demonstrated that EAARD-fed mice developed s.c. tumors significantly smaller than those of StD-fed mice (total mass 3.24 vs. 6.09 g, respectively). Mice injected i.p. and fed with EAARD showed a smaller and more limited number of intra-peritoneal tumors than StD-fed mice (total mass 0.79 vs. 4.77 g, respectively). EAAs prevents the growth of HCT116 cells by inducing autophagy and apoptosis, increasing endoplasmic reticulum stress, and inhibiting inflammation and neo-vascularization. In addition, the EAARD-fed mice, maintained muscle mass and white and brown adipose tissues. A diet with an excess of EAAs affects the survival and proliferative capacity of human colon cancer cells, maintaining anabolic stimuli in muscular cells. Full article

(This article belongs to the Special Issue Innovative Research on Nutrition and Epigenetics in Cancer)

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36 pages, 1807 KiB

Open AccessReview

Thriving or Withering? Plant Molecular Cytogenetics in the First Quarter of the 21st Century

by Elzbieta Wolny, Luis A. J. Mur, Nobuko Ohmido, Zujun Yin, Kai Wang and Robert Hasterok

Int. J. Mol. Sci. 2025, 26(14), 7013; https://doi.org/10.3390/ijms26147013 - 21 Jul 2025

Viewed by 184

Abstract

Nearly four decades have passed since fluorescence in situ hybridisation was first applied in plants to support molecular cytogenetic analyses across a wide range of species. Subsequent advances in DNA sequencing, bioinformatic analysis, and microscopy, together with the immunolocalisation of various nuclear components, [...] Read more.

Nearly four decades have passed since fluorescence in situ hybridisation was first applied in plants to support molecular cytogenetic analyses across a wide range of species. Subsequent advances in DNA sequencing, bioinformatic analysis, and microscopy, together with the immunolocalisation of various nuclear components, have provided unprecedented insights into the cytomolecular organisation of the nuclear genome in both model and non-model plants, with crop species being perhaps the most significant. The ready availability of sequenced genomes is now facilitating the application of state-of-the-art cytomolecular techniques across diverse plant species. However, these same advances in genomics also pose a challenge to the future of plant molecular cytogenetics, as DNA sequence analysis is increasingly perceived as offering comparable insights into genome organisation. This perception persists despite the continued relevance of FISH-based approaches for the physical anchoring of genome assemblies to chromosomes. Furthermore, cytogenetic approaches cannot currently rival purely genomic methods in terms of throughput, standardisation, and automation. This review highlights the latest key topics in plant cytomolecular research, with particular emphasis on chromosome identification and karyotype evolution, chromatin and interphase nuclear organisation, chromosome structure, hybridisation and polyploidy, and cytogenetics-assisted crop improvement. In doing so, it underscores the distinctive contributions that cytogenetic techniques continue to offer in genomic research. Additionally, we critically assess future directions and emerging opportunities in the field, including those related to CRISPR/Cas-based live-cell imaging and chromosome engineering, as well as AI-assisted image analysis and karyotyping. Full article

(This article belongs to the Collection Feature Papers in Molecular Plant Sciences)

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19 pages, 12443 KiB

Open AccessArticle

Multivalent Immune-Protective Effects of Egg Yolk Immunoglobulin Y (IgY) Derived from Live or Inactivated Shewanella xiamenensis Against Major Aquaculture Pathogens

by Jing Chen, Pan Cui, Huihui Xiao, Xiaohui Han, Ziye Ma, Xiaoqing Wu, Juan Lu, Guoping Zhu, Yong Liu and Xiang Liu

Int. J. Mol. Sci. 2025, 26(14), 7012; https://doi.org/10.3390/ijms26147012 - 21 Jul 2025

Viewed by 112

Abstract

Egg yolk immunoglobulin Y (IgY) possesses advantages such as low cost, easy availability, simple preparation, high antigen specificity, absence of drug residues, and compliance with animal welfare standards, making it an environmentally friendly and safe alternative to antibiotics. This research utilizes IgY antibody [...] Read more.

Egg yolk immunoglobulin Y (IgY) possesses advantages such as low cost, easy availability, simple preparation, high antigen specificity, absence of drug residues, and compliance with animal welfare standards, making it an environmentally friendly and safe alternative to antibiotics. This research utilizes IgY antibody technology to develop a multivalent passive immune vaccine for major pathogenic bacteria in aquaculture. In this study, IgY antibodies against live Shewanella xiamenensis (LSX-IgY) and inactivated S. xiamenensis (ISX-IgY) were prepared by immunizing laying hens, and passive immunization protection experiments were conducted in Carassius auratus infected with S. xiamenensis and Aeromonas hydrophila. The passive immunization protection rates of LSX-IgY and ISX-IgY against S. xiamenensis were 63.64% and 72.73%, respectively, and the passive cross-protection rates against A. hydrophila were 50% and 71.43%, respectively. Further, C. auratus sera could specifically bind to S. xiamenensis or A. hydrophila in vitro, and the phagocytic activity of leukocytes was increased. LSX-IgY and ISX-IgY could reduce the bacterial load in the C. auratus kidneys. Meanwhile, they could significantly reduce the levels of antioxidant factors in serum and inhibit the mRNA expression of inflammation-related factors in the kidneys and spleens. Additionally, histopathology and immunofluorescence analysis showed that both IgY preparations preserved tissue integrity and reduced the expression of apoptosis factor (p53) and DNA damage factor (γH2A.X) of visceral organs, respectively. In summary, LSX-IgY and ISX-IgY can combat various bacterial infections, with no significant difference between the two. Additionally, inactivated bacterial immunization is more aligned with animal welfare standards for laying hens. Therefore, ISX-IgY is expected to serve as a multivalent vaccine against major aquaculture pathogens. Full article

(This article belongs to the Section Molecular Microbiology)

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23 pages, 8387 KiB

Open AccessArticle

Solvent Fractionation of Polygonum cuspidatum Sieb. et Zucc. for Antioxidant, Biological Activity, and Chromatographic Characterization

by Yuchen Cheng, Yuri Kang and Woonjung Kim

Int. J. Mol. Sci. 2025, 26(14), 7011; https://doi.org/10.3390/ijms26147011 - 21 Jul 2025

Viewed by 185

Abstract

This study investigated the natural bioactive compounds in Polygonum cuspidatum Sieb. et Zucc. (P. cuspidatum) by fractionating a 70% ethanol extract using n-hexane, chloroform, ethyl acetate, n-butanol, and water. The total polyphenol and flavonoid contents of each fraction were [...] Read more.

This study investigated the natural bioactive compounds in Polygonum cuspidatum Sieb. et Zucc. (P. cuspidatum) by fractionating a 70% ethanol extract using n-hexane, chloroform, ethyl acetate, n-butanol, and water. The total polyphenol and flavonoid contents of each fraction were determined, and their antioxidant activities were evaluated using DPPH, ABTS, and FRAP assays. Additionally, the anti-diabetic potential was assessed via α-glucosidase inhibitory activity, while anti-obesity activity was evaluated using lipase inhibitory activity. The fractions were also tested for tyrosinase and elastase inhibitory activities to assess their skin-whitening and anti-wrinkle potential, and their antibacterial activity against Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa was determined using the agar diffusion method. Finally, bioactive compounds were identified and quantified using HPLC and GC–MSD. The results showed that the ethyl acetate fraction possessed the highest total polyphenol content (0.53 ± 0.01 g GAE/g) and total flavonoid content (0.19 ± 0.02 g QE/g). It also exhibited strong antioxidant activity, with the lowest DPPH radical scavenging IC₅₀ (0.01 ± 0.00 mg/mL), ABTS radical scavenging IC₅₀ (0.06 ± 0.00 mg/mL), and the highest FRAP value (6.02 ± 0.30 mM Fe²⁺/mg). Moreover, it demonstrated potent enzyme inhibitory activities, including tyrosinase inhibitory activity (67.78 ± 2.50%), elastase inhibitory activity (83.84 ± 1.64%), α-glucosidase inhibitory activity (65.14 ± 10.29%), and lipase inhibitory activity (85.79 ± 1.04%). In the antibacterial activity, the ethyl acetate fraction produced a clear inhibitory zone of 19.50 mm against Staphylococcus aureus, indicating notable antibacterial activity. HPLC-PDA and GC–MSD analyses identified tannic acid and emodin as the major bioactive constituents. These findings suggest that the ethyl acetate fraction of P. cuspidatum extract, rich in polyphenol and flavonoid compounds, is a promising natural source of bioactive ingredients for applications in the food, pharmaceutical, and cosmetic industries. Further research is needed to explore its mechanisms and therapeutic applications. Full article

(This article belongs to the Special Issue Cytotoxicity, Antioxidant and Anticancer Activity of Natural Products, 2nd Edition)

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18 pages, 2571 KiB

Open AccessArticle

Selective MicroRNA Packaging Reveals Distinct Core Signatures in Human Mesenchymal-Stromal-Cell-Derived Extracellular Vesicles

by Rachel E. Crossland, Clara Sanjurjo-Rodríguez, Monica Reis, Anne M. Dickinson, Elena Jones and Xiao-Nong Wang

Int. J. Mol. Sci. 2025, 26(14), 7010; https://doi.org/10.3390/ijms26147010 - 21 Jul 2025

Viewed by 173

Abstract

Mesenchymal stromal cells (MSCs) have demonstrated therapeutic efficacy across numerous clinical applications, with evidence suggesting their paracrine effects, particularly through extracellular vesicles (EVs), possibly driving functional outcomes. In this study we perform the comprehensive characterization of microRNA expression profiles in human MSC-derived EVs [...] Read more.

Mesenchymal stromal cells (MSCs) have demonstrated therapeutic efficacy across numerous clinical applications, with evidence suggesting their paracrine effects, particularly through extracellular vesicles (EVs), possibly driving functional outcomes. In this study we perform the comprehensive characterization of microRNA expression profiles in human MSC-derived EVs (MSC-EV) compared to their parental cells, cultured under clinically relevant xeno-free conditions. MSCs were isolated from the bone marrows of healthy donors and characterised according to the International Society for Cellular Therapy criteria, while MSC-EVs were isolated using differential ultracentrifugation and validated according to the International Society for Extracellular Vesicle guidelines. NanoString profiling identified 590 mature microRNAs expressed across both populations, with 42 being significantly differentially expressed between MSC-EVs and parental MSCs. Five microRNAs were distinctly highly expressed in MSCs and five in MSC-EVs, while fifteen of the top twenty most abundant microRNAs showed high expression in both populations. MicroRNA expression patterns were validated in an independent cohort. Functional pathway analysis of differentially expressed microRNAs showed enrichment of key biological processes including cell proliferation, differentiation, and immune regulation. This standardised profiling approach develops our understanding of MSC/MSC-EV microRNA cargo, using a transparent methodological approach that allows for the improved comparability of datasets for the development and advancement of MSC-EV therapeutics. Full article

(This article belongs to the Special Issue MicroRNA Regulation in Human Health and Diseases)

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18 pages, 12574 KiB

Open AccessArticle

A Framework Integrating GWAS and Genomic Selection to Enhance Prediction Accuracy of Economical Traits in Common Carp

by Zhipeng Sun, Yuhan Fu, Xiaoyue Zhu, Ruixin Zhang, Yongjun Shu, Xianhu Zheng and Guo Hu

Int. J. Mol. Sci. 2025, 26(14), 7009; https://doi.org/10.3390/ijms26147009 - 21 Jul 2025

Viewed by 109

Abstract

Common carp (Cyprinus carpio) is one of the most significant fish species worldwide, with its natural distribution spanning Europe and Asia. To conduct a genome-wide association study (GWAS) and compare the prediction accuracy of genomic selection (GS) models for the growth [...] Read more.

Common carp (Cyprinus carpio) is one of the most significant fish species worldwide, with its natural distribution spanning Europe and Asia. To conduct a genome-wide association study (GWAS) and compare the prediction accuracy of genomic selection (GS) models for the growth traits of common carp in spring and autumn at 2 years of age, a total of 325 carp individuals were re-sequenced and phenotypic measurements were taken. Three GWAS methods (FarmCPU, GEMMA, and GLM) were applied and their performance was evaluated in conjunction with various GS models, using significance levels based on p-values. GWAS analyses were performed on eight traits (including the body length, body weight, fat content of fillet, and condition factor) for both spring and autumn seasons. Eleven different GS models (such as Bayes A, Bayes B, and SVR-linear) were combined to evaluate their performance in genomic selection. The results demonstrate that the FarmCPU method consistently exhibits superior stability and predictive accuracy across most traits, particularly under higher SNP densities (e.g., 5K), where prediction accuracies frequently exceed 0.8. Notably, when integrated with Bayesian approaches, FarmCPU achieves a substantial performance boost, with the prediction accuracy reaching as high as 0.95 for the autumn body weight, highlighting its potential for high-resolution genomic prediction. In contrast, GEMMA and GLM exhibited a more variable performance at lower SNP densities. Overall, the integration of FarmCPU with genomic selection (GS) models offers one of the most reliable and efficient frameworks for trait prediction, particularly for complex traits with substantial genetic variation. This approach proves especially powerful when coupled with Bayesian methodologies, further enhancing its applicability in advanced breeding programs. Full article

(This article belongs to the Special Issue Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs and Challenges)

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15 pages, 1351 KiB

Open AccessReview

Unraveling the Complexity of Plant Trichomes: Models, Mechanisms, and Bioengineering Strategies

by Tiantian Chen, Yanfei Ma and Jiyan Qi

Int. J. Mol. Sci. 2025, 26(14), 7008; https://doi.org/10.3390/ijms26147008 - 21 Jul 2025

Viewed by 242

Abstract

Trichomes—microscopic appendages on the plant epidermis—play vital roles as both protective barriers and specialized biosynthetic factories. Acting as the first line of defense against environmental stressors, they also produce a wide range of pharmaceutically valuable secondary metabolites. This mini-review highlights recent advances in [...] Read more.

Trichomes—microscopic appendages on the plant epidermis—play vital roles as both protective barriers and specialized biosynthetic factories. Acting as the first line of defense against environmental stressors, they also produce a wide range of pharmaceutically valuable secondary metabolites. This mini-review highlights recent advances in understanding the development, structure, and function of trichomes, with a focus on glandular secretory trichomes (GSTs) in key species such as Artemisia annua and Solanum lycopersicum. We explore how insights from these systems are driving innovation in plant synthetic biology, including modular genetic engineering and metabolic channeling strategies. These breakthroughs are paving the way for scalable, plant-based platforms to produce high-value compounds. By integrating molecular mechanisms with emerging technologies, this review outlines a forward-looking framework for leveraging trichomes in sustainable agriculture, natural product discovery, and next-generation biomanufacturing. Full article

(This article belongs to the Special Issue Transcription Factors in Plant Gene Expression Regulation, 2nd Edition)

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17 pages, 1743 KiB

Open AccessArticle

Prioritized SNP Selection from Whole-Genome Sequencing Improves Genomic Prediction Accuracy in Sturgeons Using Linear and Machine Learning Models

by Hailiang Song, Wei Wang, Tian Dong, Xiaoyu Yan, Chenfan Geng, Song Bai and Hongxia Hu

Int. J. Mol. Sci. 2025, 26(14), 7007; https://doi.org/10.3390/ijms26147007 - 21 Jul 2025

Viewed by 152

Abstract

Genomic prediction has emerged as a powerful tool in aquaculture breeding, but its effectiveness depends on the careful selection of informative single nucleotide polymorphisms (SNPs) and the application of appropriate prediction models. This study aimed to enhance genomic prediction accuracy in Russian sturgeon [...] Read more.

Genomic prediction has emerged as a powerful tool in aquaculture breeding, but its effectiveness depends on the careful selection of informative single nucleotide polymorphisms (SNPs) and the application of appropriate prediction models. This study aimed to enhance genomic prediction accuracy in Russian sturgeon (Acipenser gueldenstaedtii) by optimizing SNP selection strategies and exploring the performance of linear and machine learning models. Three economically important traits—caviar yield, caviar color, and body weight—were selected due to their direct relevance to breeding goals and market value. Whole-genome sequencing (WGS) data were obtained from 971 individuals with an average sequencing depth of 13.52×. To reduce marker density and eliminate redundancy, three SNP selection strategies were applied: (1) genome-wide association study (GWAS)-based prioritization to select trait-associated SNPs; (2) linkage disequilibrium (LD) pruning to retain independent markers; and (3) random sampling as a control. Genomic prediction was conducted using both linear (e.g., GBLUP) and machine learning models (e.g., random forest) across varying SNP densities (1 K to 50 K). Results showed that GWAS-based SNP selection consistently outperformed other strategies, especially at moderate densities (≥10 K), improving prediction accuracy by up to 3.4% compared to the full WGS dataset. LD-based selection at higher densities (30 K and 50 K) achieved comparable performance to full WGS. Notably, machine learning models, particularly random forest, exceeded the performance of linear models, yielding an additional 2.0% increase in accuracy when combined with GWAS-selected SNPs. In conclusion, integrating WGS data with GWAS-informed SNP selection and advanced machine learning models offers a promising framework for improving genomic prediction in sturgeon and holds promise for broader applications in aquaculture breeding programs. Full article

(This article belongs to the Special Issue Advances in Traits in Animals and Aquatic Species, and Their Improvement Technologies)

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23 pages, 4463 KiB

Open AccessReview

Stargardt’s Disease: Molecular Pathogenesis and Current Therapeutic Landscape

by Kunal Dayma, Kalpana Rajanala and Arun Upadhyay

Int. J. Mol. Sci. 2025, 26(14), 7006; https://doi.org/10.3390/ijms26147006 - 21 Jul 2025

Viewed by 163

Abstract

Stargardt’s disease (STGD1) is an autosomal recessive juvenile macular degeneration caused by mutations in the ABCA4 gene, impairing clearance of toxic retinoid byproducts in the retinal pigment epithelium (RPE). This leads to lipofuscin accumulation, oxidative stress, photoreceptor degeneration, and central vision loss. Over [...] Read more.

Stargardt’s disease (STGD1) is an autosomal recessive juvenile macular degeneration caused by mutations in the ABCA4 gene, impairing clearance of toxic retinoid byproducts in the retinal pigment epithelium (RPE). This leads to lipofuscin accumulation, oxidative stress, photoreceptor degeneration, and central vision loss. Over 1200 pathogenic/likely pathogenic ABCA4 variants highlight the genetic heterogeneity of STGD1, which manifests as progressive central vision loss, with phenotype influenced by deep intronic variants, modifier genes, and environmental factors like light exposure. ABCA4 variants also show variable penetrance and geographical prevalence. With no approved treatment, investigational therapies target different aspects of disease pathology. Small-molecule therapies target vitamin A dimerization (e.g., ALK-001), inhibit lipofuscin accumulation (e.g., soraprazan), or modulate the visual cycle (e.g., emixustat hydrochloride). Gene therapy trials explore ABCA4 supplementation including strategies like RNA exon editing (ACDN-01) and bioengineered ambient light-activated OPSIN. RORA gene therapy (Phase 2/3) addresses oxidative stress, inflammation, lipid metabolism, and complement system dysregulation. Trials like DRAGON (Phase 3, tinlarebant), STARLIGHT (phase 2, bioengineered OPSIN) show promise, but optimizing efficacy remains challenging. With the key problem of establishing genotype–phenotype correlations, the future of STGD1 therapy may rely on approaches targeting oxidative stress, lipid metabolism, inflammation, complement regulation, and genetic repair. Full article

(This article belongs to the Special Issue Molecular Research in Retinal Degeneration)

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18 pages, 1366 KiB

Open AccessReview

Review of Recent Medicinal Applications of Rhenium(I) Tricarbonyl Complexes

by Erick Kipngetich Towett, Vuyelwa J. Tembu, Douglas Kemboi, Moses K. Langat and Amanda-Lee E. Manicum

Int. J. Mol. Sci. 2025, 26(14), 7005; https://doi.org/10.3390/ijms26147005 - 21 Jul 2025

Viewed by 113

Abstract

The use of metal-based complexes is currently taking centre stage in the field of nanomedicine for the treatment and control of various ailments. Rhenium(I) tricarbonyl complexes have frequently been evaluated in vitro for their anticancer activities, and a few have advanced to in [...] Read more.

The use of metal-based complexes is currently taking centre stage in the field of nanomedicine for the treatment and control of various ailments. Rhenium(I) tricarbonyl complexes have frequently been evaluated in vitro for their anticancer activities, and a few have advanced to in vivo and clinical trials, owing to the distinct application characteristics of these complexes. Their inception in drug development is key. This study explores a detailed chronological overview of the medical applications of Re(I) tricarbonyl complexes over the past six years (2019–2024), focusing on their applications and clinical tests in the control and management of various ailments. An in-depth examination of their activities in anticancer treatments, Chagas disease, antifungal infections, antimalarial, and microbial infections was conducted, comparing the complexes to various standard antibiotics, conventional antimalarial drugs, antifungals, and standard anticancer agents. Full article

(This article belongs to the Section Molecular Pharmacology)

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14 pages, 3713 KiB

Open AccessArticle

Titin’s Intrinsically Disordered PEVK Domain Modulates Actin Polymerization

by Áron Gellért Altorjay, Hedvig Tordai, Ádám Zolcsák, Nikoletta Kósa, Tamás Hegedűs and Miklós Kellermayer

Int. J. Mol. Sci. 2025, 26(14), 7004; https://doi.org/10.3390/ijms26147004 - 21 Jul 2025

Viewed by 113

Abstract

The multi-domain muscle protein titin provides elasticity and mechanosensing functions to the sarcomere. Titin’s PEVK domain is intrinsically disordered due to the presence of a large number of prolines and highly charged residues. Although PEVK does not have canonical actin-binding motifs, it has [...] Read more.

The multi-domain muscle protein titin provides elasticity and mechanosensing functions to the sarcomere. Titin’s PEVK domain is intrinsically disordered due to the presence of a large number of prolines and highly charged residues. Although PEVK does not have canonical actin-binding motifs, it has been shown to bind F-actin. Here, we explored whether the PEVK domain may also affect actin assembly. We cloned the middle, 733-residue-long segment (called PEVKII) of the full-length PEVK domain, expressed in E. coli and purified by using His- and Avi-tags engineered to the N- and C-termini, respectively. Actin assembly was monitored by the pyrene assay in the presence of varying PEVKII concentrations. The structural features of PEVKII-associated F-actin were studied with atomic force microscopy. The added PEVKII enhanced the initial and log-phase rates of actin assembly and the peak F-actin quantity in a concentration-dependent way. However, the critical concentration of actin polymerization was unaltered. Thus, PEVK accelerates actin polymerization by facilitating its nucleation. This effect was highlighted in the AFM images of F-actin–PEVKII adsorbed to the supported lipid bilayer. The sample was dominated by radially symmetric complexes of short actin filaments. PEVK’s actin polymerization-modulating effect may, in principle, have a function in regulating sarcomeric actin length and turnover. Altogether, titin’s PEVK domain is not only a non-canonical actin-binding protein that regulates sarcomeric shortening, but one that may modulate actin polymerization as well. Full article

(This article belongs to the Special Issue Biomolecular Structure, Function and Interactions: 2nd Edition)

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14 pages, 1077 KiB

Open AccessArticle

Identification of Molecular Subtypes of B-Cell Acute Lymphoblastic Leukemia in Mexican Children by Whole-Transcriptome Analysis

by Norberto Sánchez-Escobar, María de los Ángeles Romero-Tlalolini, Haydeé Rosas-Vargas, Elva Jiménez-Hernández, Juan Carlos Núñez Enríquez, Angélica Rangel-López, José Manuel Sánchez López, Daniela Rojo-Serrato, América Mariana Jasso Mata, Efraín Abimael Márquez Aguilar, Janet Flores-Lujano, Juan Carlos Bravata-Alcántara, Jorge Alfonso Martín-Trejo, Silvia Jiménez-Morales, José Arellano-Galindo, Aurora Medina Sanson, Jose Gabriel Peñaloza Gonzalez, Juan Manuel Mejía-Aranguré and Minerva Mata-Rocha

Int. J. Mol. Sci. 2025, 26(14), 7003; https://doi.org/10.3390/ijms26147003 - 21 Jul 2025

Viewed by 117

Abstract

B-lineage acute lymphoblastic leukemia (B-ALL) is classified into more than 20 molecular subtypes, and next-generation sequencing has facilitated the identification of these with high sensitivity. Bulk RNA-seq analysis of bone marrow was realized to identify molecular subtypes in Mexican pediatric patients with B-ALL. [...] Read more.

B-lineage acute lymphoblastic leukemia (B-ALL) is classified into more than 20 molecular subtypes, and next-generation sequencing has facilitated the identification of these with high sensitivity. Bulk RNA-seq analysis of bone marrow was realized to identify molecular subtypes in Mexican pediatric patients with B-ALL. High hyperdiploidy (27.3%) was the most frequent molecular subtype, followed by DUX4 (13.6%), TCF3::PBX1 (9.1%), ETV6::RUNX1 (9.1%), Ph-like (9.1%), ETV6::RUNX1-like (9.1%), PAX5alt (4.5%), Ph (4.5%), KMT2A (4.5%), and ZNF384 (4.5%), with one patient presenting both the PAX5alt and low hypodiploidy subtypes (4.5%). The genes TYK2, SEMA6A, FLT3, NRAS, SETD2, JAK2, NT5C2, RAG1, and SPATS2L harbor deleterious missense variants across different B-ALL molecular subtypes. The Ph-like subtype exhibited mutations in STAT2, ADGRF1, TCF3, BCR, JAK2, and NRAS with overexpression of the CRLF2 gene. The DUX4 subtype showed mutually exclusive missense variants in the PDGRFA gene. Here, we have demonstrated the importance of using RNA-seq to facilitate the differential diagnosis of B-ALL with successful detection of gene fusions and mutations. This will aid both patient risk stratification and precision medicine. Full article

(This article belongs to the Special Issue Novel Agents and Molecular Research in Multiple Myeloma)

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23 pages, 2202 KiB

Open AccessArticle

Afucosylated IgG Promote Thrombosis in Mouse Injected with SARS-CoV-2 Spike Expressing Megakaryocytes

by Meryem Mabrouk, Farah Atifi, Hicham Wahnou, Afaf Allaoui, Nabil Zaid, Abdallah Naya, Ejaife O. Agbani, Loubna Khalki, Meriem Khyatti, Youssef Tijani, Khadija Akarid, Damien Arnoult, Haissam Abou-Saleh, Othman El Faqer, Salma Labied, Mounia Ammara, Fadila Guessous, Farid Jalali and Younes Zaid

Int. J. Mol. Sci. 2025, 26(14), 7002; https://doi.org/10.3390/ijms26147002 - 21 Jul 2025

Viewed by 228

Abstract

Despite the prevalence of fucosylated IgG in plasma, specific IgGs with low core fucosylation sporadically emerge in response to virus infections and blood cell alloantigens. This low fucosylation of IgG is implicated in the pathogenesis of SARS-CoV-2 and dengue infections. In COVID-19, the [...] Read more.

Despite the prevalence of fucosylated IgG in plasma, specific IgGs with low core fucosylation sporadically emerge in response to virus infections and blood cell alloantigens. This low fucosylation of IgG is implicated in the pathogenesis of SARS-CoV-2 and dengue infections. In COVID-19, the presence of IgGs with low core fucosylation (afucosylated IgGs) targeting spike protein predicts disease progression to a severe form and actively mediates this progression. This study reveals that SARS-CoV-2 infection of megakaryocytes promotes the generation of pathogenic afucosylated anti-spike IgGs, leading to outcomes, such as pulmonary vascular thrombosis, acute lung injury, and mortality in FcγRIIa-transgenic mice. Platelets from mice injected with virus-infected human megakaryocytes express significant activation biomarkers, indicating a direct link between the immune response and platelet activation. Mice injected with virus-infected human megakaryocytes demonstrate an elevated rate of thrombus formation induced by FeCl₃ (4%) and a reduction in bleeding time, emphasizing the intricate interplay of viral infection, immune response, and hemostatic complications. Treatment with inhibitors targeting FcγRIIa, serotonin, or complement anaphylatoxins of mice injected with spike-expressing MKs successfully prevents observed platelet activation, thrombus formation, and bleeding abnormalities, offering potential therapeutic strategies for managing severe outcomes associated with afucosylated IgGs in COVID-19 and related disorders. Full article

(This article belongs to the Special Issue The Molecular Role of Platelets in Human Diseases)

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16 pages, 1668 KiB

Open AccessArticle

Vitamin D₃ Modulates Inflammatory and Antimicrobial Responses in Oral Epithelial Cells Exposed to Periodontitis-Associated Bacteria

by Fadime Karaca, Susanne Bloch, Fabian L. Kendlbacher, Christian Behm, Christina Schäffer and Oleh Andrukhov

Int. J. Mol. Sci. 2025, 26(14), 7001; https://doi.org/10.3390/ijms26147001 - 21 Jul 2025

Viewed by 129

Abstract

The oral epithelium is essential for maintaining oral health and plays a key role in the onset and progression of periodontitis. It serves as both a mechanical and immunological barrier and possesses antimicrobial activity. Vitamin D₃, a hormone with known immunomodulatory [...] Read more.

The oral epithelium is essential for maintaining oral health and plays a key role in the onset and progression of periodontitis. It serves as both a mechanical and immunological barrier and possesses antimicrobial activity. Vitamin D₃, a hormone with known immunomodulatory functions, may influence oral epithelial responses. This study investigated the effects of two vitamin D₃ metabolites on key immunological and antimicrobial functions of oral epithelial cells, both under basal conditions and during bacterial challenge. Ca9-22 oral epithelial cells were treated with 1,25(OH)₂D₃ or 25(OH)D₃ in the presence or absence of Tannerella forsythia, Fusobacterium nucleatum, or Porphyromonas gingivalis. Inflammatory responses were assessed by measuring gene and protein expression of IL-1β and IL-8. Antimicrobial activity was evaluated via expression of LL-37, hBD-2, and hBD-3, as well as direct bacterial killing assays. Expression of epithelial integrity markers E-cadherin and ICAM-1 was also analyzed. Vitamin D₃ metabolites reduced IL-8 expression and significantly increased LL-37 expression and production in Ca9-22 cells. Both forms enhanced antimicrobial activity against all tested pathogens and modulated epithelial integrity markers. Vitamin D₃ positively regulates antimicrobial and barrier functions in oral epithelial cells, suggesting a potential role in supporting oral health and preventing periodontitis progression. Full article

(This article belongs to the Special Issue Oral and Dental Infectious Diseases: Molecular Pathology, Diagnosis and Therapy)

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21 pages, 3528 KiB

Open AccessArticle

Confocal Laser Scanning Microscopy of Light-Independent ROS in Arabidopsis thaliana (L.) Heynh. TROL-FNR Mutants

by Ena Dumančić, Lea Vojta and Hrvoje Fulgosi

Int. J. Mol. Sci. 2025, 26(14), 7000; https://doi.org/10.3390/ijms26147000 - 21 Jul 2025

Viewed by 139

Abstract

Thylakoid rhodanese-like protein (TROL) serves as a thylakoid membrane hinge linking photosynthetic electron transport chain (PETC) complexes to nicotinamide adenine dinucleotide phosphate (NADPH) synthesis. TROL is the docking site for the flavoenzyme ferredoxin-NADP⁺ oxidoreductase (FNR). Our prior work indicates that the TROL-FNR [...] Read more.

Thylakoid rhodanese-like protein (TROL) serves as a thylakoid membrane hinge linking photosynthetic electron transport chain (PETC) complexes to nicotinamide adenine dinucleotide phosphate (NADPH) synthesis. TROL is the docking site for the flavoenzyme ferredoxin-NADP⁺ oxidoreductase (FNR). Our prior work indicates that the TROL-FNR complex maintains redox equilibrium in chloroplasts and systemically in plant cells. Improvement in the knowledge of redox regulation mechanisms is critical for engineering stress-tolerant plants in times of elevated global drought intensity. To further test this hypothesis and confirm our previous results, we monitored light-independent ROS propagation in the leaves of Arabidopsis wild type (WT), TROL knock-out (KO), and TROL ΔRHO (RHO-domain deletion mutant) mutant plants in situ by using confocal laser scanning microscopy with specific fluorescent probes for the three different ROS: O₂^·−, H₂O₂, and ¹O₂. Plants were grown under the conditions of normal substrate moisture and under drought stress conditions. Under the drought stress conditions, the TROL KO line showed ≈32% less O₂^·− while the TROL ΔRHO line showed ≈49% less H₂O₂ in comparison with the WT. This research confirms the role of dynamical TROL-FNR complex formation in redox equilibrium maintenance by redirecting electrons in alternative sinks under stress and also points it out as promising target for stress-tolerant plant engineering. Full article

(This article belongs to the Special Issue Molecular Insight into Oxidative Stress in Plants)

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16 pages, 3373 KiB

Open AccessArticle

Automated Workflow for High-Throughput LC–MS/MS-Based Therapeutic Monitoring of Cannabidiol and 7-Hydroxy-cannabidiol in Patients with Epilepsy

by Michela Palmisani, Francesca Dattrino, Paola Rota, Federica Tacchella, Guido Fedele, Ludovica Pasca, Carlo Alberto Quaranta, Valentina De Giorgis, Thomas Matulli Cavedagna, Chiara Cancellerini, Anna Butti, Gloria Castellazzi, Emilio Russo, Cristina Tassorelli, Pierluigi Nicotera and Valentina Franco

Int. J. Mol. Sci. 2025, 26(14), 6999; https://doi.org/10.3390/ijms26146999 - 21 Jul 2025

Viewed by 103

Abstract

This study describes the development and validation of a fully automated workflow for serum sample preparation, enabling the quantitative determination of cannabidiol (CBD) and its active metabolite, 7-hydroxy-CBD, via liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) analysis. Implemented on an automated platform, [...] Read more.

This study describes the development and validation of a fully automated workflow for serum sample preparation, enabling the quantitative determination of cannabidiol (CBD) and its active metabolite, 7-hydroxy-CBD, via liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) analysis. Implemented on an automated platform, the workflow performs key steps such as solvent dispensing, mixing, centrifugation, filtration, and supernatant transfer, producing 96-well plates ready for analysis. Human serum samples were obtained from patients with epilepsy treated with CBD. All samples were processed using both manual and automated methods to evaluate method agreement. Quantification was performed by LC–MS/MS with CBD-d₃ as the internal standard (IS). Method validation was conducted in accordance with European Medicine Agency (EMA) guidelines, confirming that the automated protocol meets the recommended acceptance criteria for both intraday and interday precision and accuracy. Calibration curves demonstrated excellent linearity across the concentration ranges. Comparative analysis using Passing–Bablok regression and Bland–Altman plots demonstrated strong agreement between the methods. These findings support the clinical applicability of the automated method for the therapeutic drug monitoring (TDM) of CBD and 7-hydroxy-CBD, and its robust performance and scalability provide a solid foundation for the development of an expanded analytical panel covering a broader range of antiseizure medications (ASMs), enabling more standardized TDM protocols in clinical practice. Full article

(This article belongs to the Special Issue Application of Mass Spectrometry and Chromatography in Drug Monitoring)

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Open AccessArticle

Characterization and Expression of TGF-β Proteins and Receptor in Sea Cucumber (Holothuria scabra): Insights into Potential Applications via Molecular Docking Predictions

by Siriporn Nonkhwao, Jarupa Charoenrit, Chanachon Ratanamungklanon, Lanlalin Sojikul, Supawadee Duangprom, Sineenart Songkoomkrong, Jirawat Saetan, Nipawan Nuemket, Prateep Amonruttanapun, Prasert Sobhon and Napamanee Kornthong

Int. J. Mol. Sci. 2025, 26(14), 6998; https://doi.org/10.3390/ijms26146998 - 21 Jul 2025

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Abstract

Holothuria scabra has long been acknowledged in traditional medicine for its therapeutic properties. The transforming growth factor-beta (TGF-β) superfamily is crucial in regulating cellular processes, including differentiation, proliferation, and immune responses. This study marks the first exploration of the gene expression localization, sequence [...] Read more.

Holothuria scabra has long been acknowledged in traditional medicine for its therapeutic properties. The transforming growth factor-beta (TGF-β) superfamily is crucial in regulating cellular processes, including differentiation, proliferation, and immune responses. This study marks the first exploration of the gene expression localization, sequence conservation, and functional roles of H. scabra TGF-β proteins, specifically activin (HolscActivin), inhibin (HolscInhibin), and the TGF-β receptor (HolscTGFBR), across various organs. In situ hybridization indicated that HolscActivin and HolscInhibin are expressed in the intestine, respiratory tree, ovary, testis, and inner body wall. This suggests their roles in nutrient absorption, gas exchange, reproduction, and extracellular matrix remodeling. Notably, HolscTGFBR demonstrated a similar tissue-specific expression pattern, except for its absence in the respiratory tree. Bioinformatics analysis reveals that HolscTGFBR shares significant sequence similarity with HomsaTGFBR, especially in regions essential for signal transduction and inhibition. Molecular docking results indicate that HolscActivin may promote receptor activation, while HolscInhibin functions as a natural antagonist, reflecting the signaling mechanisms of human TGF-β proteins. Interestingly, cross-species ternary complex docking with human TGF-β receptors further supports these findings, showing that HolscActivin moderately engages the receptors, whereas HolscInhibin exhibits strong binding, suggestive of competitive inhibition. These results indicate that H. scabra TGF-β proteins retain the structural and functional features of vertebrate TGF-β ligands, supporting their potential applications as natural modulators in therapeutic and functional food development. Full article

(This article belongs to the Section Molecular Biology)

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Int. J. Mol. Sci., Volume 26, Issue 14 (July-2 2025) – 482 articles

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