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Biomolecules
Volume 15
Issue 5
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Biomolecules, Volume 15, Issue 5 (May 2025) – 132 articles

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27 pages, 1697 KiB  
Review
Multimodal Function of Mesenchymal Stem Cells in Psoriasis Treatment
by Jiaxin Ou, Ziqing Li, Danni Yao, Chuanjian Lu and Xiang Zeng
Biomolecules 2025, 15(5), 737; https://doi.org/10.3390/biom15050737 (registering DOI) - 19 May 2025
Abstract
Psoriasis is a chronic inflammatory disease mediated by the innate and adaptive immune systems, and its pathogenesis involves multiple aspects, including abnormal interleukin (IL)-23–Th17 axis, dysfunction of Tregs and other immune cells, and a complex relationship between keratinocytes and the vascular endothelium. Dysfunction [...] Read more.
Psoriasis is a chronic inflammatory disease mediated by the innate and adaptive immune systems, and its pathogenesis involves multiple aspects, including abnormal interleukin (IL)-23–Th17 axis, dysfunction of Tregs and other immune cells, and a complex relationship between keratinocytes and the vascular endothelium. Dysfunction of mesenchymal stem cells in psoriatic skin may also be the main reason for the dysregulated inflammatory response. Mesenchymal stem cells, a type of adult stem cells with multidifferentiation potential, are involved in the regulation of multiple links and targets in the pathogenesis of psoriasis. Thus, a detailed exploration of these mechanisms may lead to the development of new therapeutic strategies for the treatment of psoriasis. In this paper, the role of mesenchymal stem cells in skin homeostasis, the pathogenesis of psoriasis, and the multimodal function of using mesenchymal stem cells in the treatment of psoriasis are reviewed. Full article
(This article belongs to the Section Cellular Biochemistry)
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18 pages, 1521 KiB  
Article
Chemical Composition, Antioxidant, and Enzyme Inhibitory Activities of Artemisia schmidtiana Maxim. Essential Oil
by Xinyu Zhu and Xu Liu
Biomolecules 2025, 15(5), 736; https://doi.org/10.3390/biom15050736 (registering DOI) - 19 May 2025
Abstract
Artemisia schmidtiana Maxim., a plant belonging to the Asteraceae family, is renowned for its extensive ethnomedicinal applications and distinctive aromatic qualities. This study evaluated the chemical composition, antioxidant capacity, and inhibitory effects on acetylcholinesterase (AChE), α-glucosidase, and β-lactamase of its essential oil (EO). [...] Read more.
Artemisia schmidtiana Maxim., a plant belonging to the Asteraceae family, is renowned for its extensive ethnomedicinal applications and distinctive aromatic qualities. This study evaluated the chemical composition, antioxidant capacity, and inhibitory effects on acetylcholinesterase (AChE), α-glucosidase, and β-lactamase of its essential oil (EO). The major constituents of the EO were identified as germacrene D (16.29%), falcarinol (11.02%), β-caryophyllene (9.43%), α-zingiberene (7.93%), phytol (6.06%), and α-humulene (4.04%). The EO demonstrated radical scavenging activity against DPPH (44.9% at 5 mg/mL) and ABTS (IC50 = 0.72 ± 0.02 mg/mL) radicals, with a FRAP antioxidant capacity of 126.61 ± 0.59 μmol·g−1. Additionally, the EO exhibited modest AChE inhibition (16.7% at 250 μg/mL) and significant inhibition of α-glucosidase and β-lactamase, with IC50 values of 178.80 ± 17.02 μg/mL and 40.06 ± 8.22 μg/mL, respectively. Molecular docking revealed favorable interactions between the major EO compounds and the tested enzymes, providing a theoretical foundation for future drug development. These findings suggest that A. schmidtiana EO holds potential for applications in the food and pharmaceutical industries, warranting further investigation. Full article
(This article belongs to the Section Natural and Bio-derived Molecules)
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11 pages, 1386 KiB  
Article
An Exogenous NO Donor Provokes Mechanical Alternans in Normal Rat Atria and Impairs Sarcomere Contractility in Right Atrial Cardiomyocytes in Atrial Fibrillation
by Xenia Butova, Tatiana Myachina, Polina Mikhryakova, Raisa Simonova, Daniil Shchepkin and Anastasia Khokhlova
Biomolecules 2025, 15(5), 735; https://doi.org/10.3390/biom15050735 (registering DOI) - 17 May 2025
Viewed by 48
Abstract
Atrial fibrillation (AF) is the most common arrhythmia worldwide. AF is associated with a deficiency in nitric oxide (NO) production, which contributes to disturbances in the electrical and mechanical function of the atrial myocardium. NO donors are considered promising for the treatment and [...] Read more.
Atrial fibrillation (AF) is the most common arrhythmia worldwide. AF is associated with a deficiency in nitric oxide (NO) production, which contributes to disturbances in the electrical and mechanical function of the atrial myocardium. NO donors are considered promising for the treatment and prevention of AF, but their effects on atrial contractility are unclear. This study examines the direct impact of a low-molecular-weight NO donor, spermine-NONOate (NOC-22), on the contractile function of atrial cardiomyocytes in paroxysmal AF. To study whether an NO donor-induced increase in NO level causes chamber-specific changes in atrial contractility, we measured sarcomere length (SL) dynamics in contracting single cardiomyocytes from the rat left and right atria (LA, RA) using a 7-day acetylcholine-CaCl2-induced AF model. We showed that in control rats NOC-22 provoked alternans of sarcomere shortening in both LA and RA cardiomyocytes. In AF, NOC-22 decreased the sarcomere-shortening amplitudes and velocities of sarcomere shortening–relengthening and increased the magnitude of sarcomere-shortening alternans only in RA cardiomyocytes. The negative effects of NO donors on RA contractility warrant careful consideration of their use in AF treatment. Full article
(This article belongs to the Section Molecular Medicine)
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23 pages, 3018 KiB  
Article
Uncovering a Novel Role of ROR1 in the Epigenetic Regulation of Tumor Suppressor Gene CREB3L1 in Triple-Negative Breast Cancer Cells
by Victoria L. Reed, Eric Lalu, Leena Yoon, Norman Fultang and Bela Peethambaran
Biomolecules 2025, 15(5), 734; https://doi.org/10.3390/biom15050734 (registering DOI) - 16 May 2025
Viewed by 33
Abstract
A characteristic of triple-negative breast cancer (TNBC) is the epigenetic regulation of tumor suppressor genes, leading to TNBC heterogeneity and treatment resistance in patients. TNBC exhibits high methylation rates, leading to the silencing of numerous tumor suppressor genes. DNA methyltransferase inhibitors (DNMTis) have [...] Read more.
A characteristic of triple-negative breast cancer (TNBC) is the epigenetic regulation of tumor suppressor genes, leading to TNBC heterogeneity and treatment resistance in patients. TNBC exhibits high methylation rates, leading to the silencing of numerous tumor suppressor genes. DNA methyltransferase inhibitors (DNMTis) have shown limited clinical efficacy in TNBC treatment. This study aims to uncover a target that could be used to reverse the epigenetic silencing of tumor suppressor genes in TNBC. The Western blot analysis demonstrated that ROR1 knockdown, an oncofetal gene, reduced DNMT3A and DNMT3B protein expression in the TNBC cell lines MDA-MB-231 and HCC1806, as well as a non-malignant breast cell line, MCF10A. The reduced representation bisulfite sequencing (RRBS) analysis identified differential methylation of CREB3L1 when ROR1 is knocked down in TNBC cell lines. CREB3L1 is a transcription factor that plays tumor-suppressive roles in TNBC and is commonly epigenetically silenced in patients. This study shows that ROR1 requires pSTAT3 activation to upregulate DNMT3A and DNMT3B expression to induce CREB3L1 epigenetic silencing in TNBC. ROR1 knockdown resulted in the re-expression of CREB3L1 in TNBC cells. The data provide evidence that ROR1 inhibition, in combination with DNMTis, could enhance patient outcomes as a therapeutic approach for TNBC. Full article
(This article belongs to the Special Issue Tumour Suppressor Genes: The Guardians of Cell Integrity)
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8 pages, 1487 KiB  
Commentary
Ossification in Normal and Pathological Contexts: The Key Role of Static Osteogenesis vs. Dynamic Osteogenesis in the Etiopathology of Some Skeletal Alterations
by Carla Palumbo, Francesca Paganelli and Marzia Ferretti
Biomolecules 2025, 15(5), 733; https://doi.org/10.3390/biom15050733 - 16 May 2025
Viewed by 40
Abstract
This Commentary is intended to start a discussion in the field of calcification/ossification related to osteogenesis. It highlights that two types of bone formation, static osteogenesis (SO) and dynamic osteogenesis (DO), are temporally followed by each other in bone histogenesis and bone lesion [...] Read more.
This Commentary is intended to start a discussion in the field of calcification/ossification related to osteogenesis. It highlights that two types of bone formation, static osteogenesis (SO) and dynamic osteogenesis (DO), are temporally followed by each other in bone histogenesis and bone lesion repair. Moreover, they also represent the common denominator in the pathological processes of both calcification and peculiar ossifications, such as heterotopic ossification and the formation of supernumerary skeletal segments. The final objective is to propose a different interpretation of certain bone alterations/pathologies, attributable to the two peculiar osteogenesis patterns (SO and DO), occurring in both physiological and pathological conditions. From these reflections, new approaches in the definition of diagnosis and therapies of certain alterations could be derived. Full article
(This article belongs to the Special Issue Tissue Calcification in Normal and Pathological Environments)
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23 pages, 3352 KiB  
Article
Neurologic Deficit Score at 4–5 Days Post-eCPR Predicts Long-Term Brain Dysfunction in Rats Following Cardiac Arrest
by Wolfgang Weihs, Alexandra-Maria Stommel, Andrea Müllebner, Alexander Franz Szinovatz, Matthias Müller, Ingrid Magnet, Michael Holzer, Andrey V. Kozlov, Sandra Högler and J. Catharina Duvigneau
Biomolecules 2025, 15(5), 732; https://doi.org/10.3390/biom15050732 - 16 May 2025
Viewed by 68
Abstract
Cardiac arrest (CA) survivors often develop long-term neurological deficits, but its long-term impact on vulnerable brain regions and neurological outcomes remains unclear. In a previous CA model with conventional cardiopulmonary resuscitation, we found reduced heme oxygenase (HO) activity in the hippocampus and cortex [...] Read more.
Cardiac arrest (CA) survivors often develop long-term neurological deficits, but its long-term impact on vulnerable brain regions and neurological outcomes remains unclear. In a previous CA model with conventional cardiopulmonary resuscitation, we found reduced heme oxygenase (HO) activity in the hippocampus and cortex 14 days post-CA, suggesting its potential as a functional outcome marker. Here, we used a rat model with 6 or 8 min of CA followed by extracorporeal cardiopulmonary resuscitation. While in the 6 min-CA group, 67% survived to day 14, increased mortality within 4 days resulted in only 33% survival in the 8 min group post-ROSC. All animals displayed neurological impairment assessed by daily neurologic deficit scoring (NDS). While deficits declined within the first 3–4 days in the 6 min-CA animals, the 8 min-CA group showed significantly worse neurological outcomes until day 14. Two weeks post-CA, neuroinflammatory and neurodegenerative markers (HO-1, TNF-R1, Iba1, and GFAP) were elevated in the hippocampus, while HO and 2-oxoglutarate dehydrogenase complex activities were reduced in all rats, indicating a decrease in anti-oxidative capacity and mitochondrial capacity for metabolizing glutamate. NDS at day 4–5 strongly correlated with the delayed CA-mediated enzymatic dysfunction determined in the hippocampus. This finding highlights this time point for identifying at-risk individuals and suggests a prolonged therapeutic intervention lasting at least until 4 days post-CA. Full article
(This article belongs to the Collection Feature Papers in Section 'Molecular Medicine')
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39 pages, 6992 KiB  
Article
Silver Nanoparticles (AgNPs) from Lysinibacillus sp. Culture Broths: Antibacterial Activity, Mechanism Insights, and Synergy with Classical Antibiotics
by Carlos Pernas-Pleite, Amparo M. Conejo-Martínez, Irma Marín and José P. Abad
Biomolecules 2025, 15(5), 731; https://doi.org/10.3390/biom15050731 - 16 May 2025
Viewed by 123
Abstract
Antibiotic-resistant bacteria pose problems for infection prevention and treatment, so developing new procedures or substances against infection is mandatory. Silver nanomaterials are among the more promising antibacterial agents. Herein, we describe the biogenic synthesis of silver nanoparticles (AgNPs) using culture broths from an [...] Read more.
Antibiotic-resistant bacteria pose problems for infection prevention and treatment, so developing new procedures or substances against infection is mandatory. Silver nanomaterials are among the more promising antibacterial agents. Herein, we describe the biogenic synthesis of silver nanoparticles (AgNPs) using culture broths from an undescribed species of Lysinibacillus. Culture broths with or without NaCl and from the exponential and stationary growth phases produced four AgNP types. Nanoparticles’ shapes were quasi-spherical, with core sizes of 7.5–14.7 nm and hydrodynamic diameters of 48.5–80.2 nm. All the AgNPs contained Ag0 crystals and some AgCl ones. Moreover, their coronas presented different proportions of carbohydrates, proteins, and aliphatic compounds. The AgNPs were good antibacterial agents against six bacterial species, three Gram-positive and three Gram-negative, with MICs of 0.3–9.0 µg/mL. Their activity was higher against the Gram-negative bacteria and particularly against Pseudomonas aeruginosa. These AgNPs acted synergistically with several of the fifteen tested antibiotics. Interestingly, AgNP combinations with some of these inhibited the growth of antibiotic-resistant bacteria, as in the case of S. epidermidis for streptomycin and S. aureus for colistin. The ROS production by E. coli and S. aureus when treated with most AgNPs suggested different mechanisms for bacterial killing depending on the AgNP. Full article
(This article belongs to the Section Bio-Engineered Materials)
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18 pages, 2856 KiB  
Article
The Influence of Topiramate on Morphine Dependence in Mice
by Adrian Pysiewicz, Antonina Mazur, Jolanta Kotlińska, Irena Baranowska-Bosiacka, Krzysztof Fronc, Małgorzata Łupina, Marta Kruk-Słomka and Joanna Listos
Biomolecules 2025, 15(5), 730; https://doi.org/10.3390/biom15050730 (registering DOI) - 16 May 2025
Viewed by 92
Abstract
Topiramate evokes pharmacological activity via a blockade of voltage-dependent sodium channels, reduction in glutamate release, inhibition of AMPA receptors and kainate receptors, and potentiation of GABAergic neurotransmission. Therefore, it is used not only as an antiseizure drug but is also effective in migraine [...] Read more.
Topiramate evokes pharmacological activity via a blockade of voltage-dependent sodium channels, reduction in glutamate release, inhibition of AMPA receptors and kainate receptors, and potentiation of GABAergic neurotransmission. Therefore, it is used not only as an antiseizure drug but is also effective in migraine prophylaxis, cluster headaches, neuropathic pain, and alcohol dependence. The aim of this study was to investigate the effect of topiramate in morphine dependence in mice, particularly in terms of morphine tolerance, morphine withdrawal signs, and morphine sensitization. In these experiments, topiramate was administered both acutely and chronically. Topiramate significantly reduced the morphine tolerance in the hot-plate test and attenuated naloxone-induced morphine withdrawal signs. Its effect on morphine sensitization to the locomotor activity of mice was poor. The obtained results showed that topiramate might be an effective drug for reducing the physical symptoms of morphine dependence. Full article
(This article belongs to the Special Issue Glutamate and Glutamate Receptors in Health and Diseases, Second Edition)
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15 pages, 531 KiB  
Review
The Role of Substance P in Corneal Homeostasis
by Jastrzębska-Miazga Irmina, Machna Bartosz, Wyględowska-Promieńska Dorota and Smędowski Adrian
Biomolecules 2025, 15(5), 729; https://doi.org/10.3390/biom15050729 - 16 May 2025
Viewed by 105
Abstract
The cornea, a highly innervated and avascular ocular tissue, relies on intricate neuro-immune interactions to maintain homeostasis. Among key neuromediators, substance P (SP)—a neuropeptide belonging to the tachykinin family—plays a dual role in corneal physiology and pathology. This review synthesizes current knowledge on [...] Read more.
The cornea, a highly innervated and avascular ocular tissue, relies on intricate neuro-immune interactions to maintain homeostasis. Among key neuromediators, substance P (SP)—a neuropeptide belonging to the tachykinin family—plays a dual role in corneal physiology and pathology. This review synthesizes current knowledge on SP’s involvement in corneal innervation, epithelial homeostasis, immune regulation, neovascularization, and wound healing, while highlighting its dichotomous effects in both promoting tissue repair and exacerbating inflammation. SP, primarily signaling through the neurokinin-1 receptor (NK1R), influences corneal epithelial proliferation, barrier function, and wound healing by modulating cytokines, chemokines, and growth factors. However, its overexpression is linked to pain sensitization, inflammatory keratitis, and corneal neovascularization, driven by interactions with immune cells (e.g., mast cells, neutrophils) and pro-angiogenic factors (e.g., VEGF). Clinical studies demonstrate altered SP levels in dry eye disease, neurotrophic keratitis, and post-refractive surgery, correlating with nerve damage and ocular surface dysfunction. Emerging therapies targeting SP pathways- such as NK1R antagonists (e.g., fosaprepitant) and SP-IGF-1 combinations-show promise for treating neurotrophic ulcers but face challenges due to SP’s context-dependent actions. Future research should clarify the roles of NK2R/NK3R receptors and optimize SP-based interventions to balance its reparative and inflammatory effects. Understanding SP’s multifaceted mechanisms could advance the development of therapies for corneal diseases, particularly those involving sensory neuropathy and immune dysregulation. Full article
(This article belongs to the Section Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates)
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22 pages, 5584 KiB  
Article
Recovery of Lysosomal Acidification and Autophagy Flux by Attapulgite Nanorods: Therapeutic Potential for Lysosomal Disorders
by Yuanjing Hao, Xinru Fan, Xiaodan Huang, Zhaoying Li, Zhiyuan Jing, Guilong Zhang, Yuxue Xu, Na Zhang and Pengfei Wei
Biomolecules 2025, 15(5), 728; https://doi.org/10.3390/biom15050728 - 16 May 2025
Viewed by 71
Abstract
Dysfunction of the lysosome and autophagy–lysosome pathway is closely associated with various diseases, such as neurodegenerative diseases, non-alcoholic fatty liver disease (NAFLD), etc. Additionally, chloroquine is a clinically widely used drug for treating malaria and autoimmune diseases, but long-term or high-dose administration may [...] Read more.
Dysfunction of the lysosome and autophagy–lysosome pathway is closely associated with various diseases, such as neurodegenerative diseases, non-alcoholic fatty liver disease (NAFLD), etc. Additionally, chloroquine is a clinically widely used drug for treating malaria and autoimmune diseases, but long-term or high-dose administration may lead to significant toxic side effects. Attapulgite (ATT), a natural nanomaterial with excellent adsorption capacity and biocompatibility, herein demonstrated a novel biological function in regulating the lysosomal and autophagy–lysosome pathway. ATT could be effectively internalized into lysosome-related acidic compartments. Further study revealed that ATT could restore lysosomal pH, activate cathepsin D, alleviate autophagy blockage in chloroquine-treated cells, and reduce chloroquine-elicited cell death. In a cell model related to Huntington’s disease, treatment with ATT reinforced the degradation of the mutant huntingtin proteins by increasing cathepsin D maturation and autophagy flux. ATT could also promote lipid droplet clearance in hepatocytes with palmitic acid-induced steatosis, reduce hepatic lipid accumulation, and improve fasting blood glucose in high-fat-diet-induced NAFLD mice. These findings establish ATT as a lysosomal modulator, providing a foundation for its therapeutic potential in mitigating the adverse effects associated with long-term chloroquine use, especially improving neurodegenerative and metabolic disorders. Full article
(This article belongs to the Special Issue Nanomaterials and Their Applications in Biomedicine)
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21 pages, 5182 KiB  
Article
Tropomodulin–Tropomyosin Interplay Modulates Interaction Between Cardiac Myosin and Thin Filaments
by Galina V. Kopylova, Anastasia M. Kochurova, Evgeniia A. Beldiia, Andrey V. Slushchev, Victoria V. Nefedova, Natalia S. Ryabkova, Ivan A. Katrukha, Daria S. Yampolskaya, Alexander M. Matyushenko and Daniil V. Shchepkin
Biomolecules 2025, 15(5), 727; https://doi.org/10.3390/biom15050727 - 16 May 2025
Viewed by 12
Abstract
Tropomodulin (Tmod) is an actin-binding protein that interacts with tropomyosin and the actin filament at the pointed end. The influence of Tmod on the thin filament activation in the myocardium is not clear. We studied the interactions of Tmod1 and Tmod4 with the [...] Read more.
Tropomodulin (Tmod) is an actin-binding protein that interacts with tropomyosin and the actin filament at the pointed end. The influence of Tmod on the thin filament activation in the myocardium is not clear. We studied the interactions of Tmod1 and Tmod4 with the cardiac tropomyosin isoforms Tpm1.1 and Tpm1.2 using size-exclusion chromatography, a pull-down assay, and cross-linking with glutaraldehyde. We found that Tmod1 and Tmod4 form complexes with both Tpm1.1 and Tpm1.2, indicating durable interactions between these proteins. The effects of both Tmods on the actin–myosin interaction were studied using an in vitro motility assay. Tmod did not affect the sliding velocity of bare F-actin. Tmod1 slightly dose-dependently decreased the sliding velocity of F-actin–Tpm1.1 filaments and had no effect on the velocity of F-actin–Tpm1.2 filaments. With ventricular myosin, Tmod1 reduced the calcium sensitivity of the sliding velocity of thin filaments containing Tpm1.1 but did not affect it with filaments containing Tpm1.2. With atrial myosin, Tmod1 decreased the calcium sensitivity of the sliding velocities of thin filaments containing both Tpm1.1 and Tpm1.2. We can conclude that Tmod takes part in the regulation of actin–myosin interactions in the myocardium through interactions with Tpm. The effect of Tmod on the activation of thin filaments depends on the protein isoforms. Full article
(This article belongs to the Section Cellular Biochemistry)
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16 pages, 2164 KiB  
Article
The Hepatoprotective Properties of Gentiopicroside, Sweroside, and Swertiamarin Against Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD)
by Anthony O. Boateng, Vinood B. Patel and S. W. Annie Bligh
Biomolecules 2025, 15(5), 726; https://doi.org/10.3390/biom15050726 - 16 May 2025
Viewed by 64
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) is a metabolic disease characterised by the accumulation of fat in the liver. It is estimated that 30–38% of the world’s adult population have MASLD, making it the most prevalent global chronic liver disease. Due to a [...] Read more.
Metabolic dysfunction-associated steatotic liver disease (MASLD) is a metabolic disease characterised by the accumulation of fat in the liver. It is estimated that 30–38% of the world’s adult population have MASLD, making it the most prevalent global chronic liver disease. Due to a lack of a therapy for MASLD, treatment has been mainly focussed on managing the conditions associated with the disease such as obesity, diabetes mellitus, and hyperlipidaemia. This study aimed to investigate the role played by Gentiana phytochemicals including the following: gentiopicroside, sweroside, and swertiamarin, in promoting hepatocyte protection against the cytotoxic effects of fatty acids. Gentiana species such as lutea, macrophylla, rigescens, and scabra are known to protect and enhance hepatocyte viability via their antioxidant, anti-inflammatory, and bitter components including the following: amarogentin gentianine, iso-orientin, swertiamarin, gentiopicroside, and sweroside. In this study, HepG2 cells pre-treated with phytochemicals gentiopicroside, sweroside, swertiamarin, and silymarin followed by an exposure to arachidonic acid (10, 30, 50 and 80 µM) were assessed for cell viability via MTT, mitochondrial function via seahorse assay, ROS levels via DCF assay, and annexin V-FITC for apoptosis. THLE-2 cells were also assayed for validation. The phytochemicals tested improved ATP production notably gentiopicroside, which improved ATP production by over 60% compared to untreated hepatocytes. Significant hepatocyte protection against lipotoxicity leading to apoptosis was also observed in gentiopicroside in the presence of 30 µM arachidonic acid with apoptosis reduced by over 50%. ROS production was reduced up to 60% by the pre-treatment of HepG2 cells with 20 µM, gentiopicroside, sweroside, swertiamarin, and silymarin, with the highest reduction observed in swertiamarin. It was concluded that phytochemicals gentiopicroside, sweroside, and swertiamarin play key roles in the hepatocyte protection against the cytotoxic effects of fatty acids. This protection is conferred by enhancing mitochondrial function in terms of increasing the maximal respiratory capacity in response to a high influx of fatty acids, promoting ATP production as well as scavenging ROS produced as a result of high fatty acid influx and increased mitochondrial respiration. Highlights: Gentiopicroside may minimise lipotoxicity leading to apoptosis and necrosis in hepatocytes in the presence of arachidonic acid. A pre-treatment of hepatocytes with phytochemicals, namely gentiopicroside, sweroside, and silymarin provides a degree of protection which may be attributed to the enhancement of mitochondrial function. Sweroside, silymarin, and swertiamarin may protect HepG2 and THLE-2 cells by scavenging ROS produced by arachidonic acid and the mitochondrial electron transport chain. Full article
(This article belongs to the Special Issue Nonalcoholic Fatty Liver Disease: From Molecular Mechanisms to Therapeutic Approaches)
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24 pages, 761 KiB  
Review
Unlocking the Potential of Bioactive Compounds in Pancreatic Cancer Therapy: A Promising Frontier
by Silvia Brugiapaglia, Ferdinando Spagnolo and Claudia Curcio
Biomolecules 2025, 15(5), 725; https://doi.org/10.3390/biom15050725 - 15 May 2025
Viewed by 228
Abstract
Pancreatic ductal adenocarcinoma (PDA) is a highly challenging malignancy to treat, with a high mortality rate and limited therapeutic options. Despite advances in cancer research, the prognosis for patients diagnosed with PDA is often poor due to late-stage detection and resistance to conventional [...] Read more.
Pancreatic ductal adenocarcinoma (PDA) is a highly challenging malignancy to treat, with a high mortality rate and limited therapeutic options. Despite advances in cancer research, the prognosis for patients diagnosed with PDA is often poor due to late-stage detection and resistance to conventional therapies. Consequently, there is growing interest in the potential of bioactive compounds as alternative or adjuvant treatments, given their ability to target multiple aspects of cancer biology, offering a more holistic approach to treatment. In the context of PDA, certain bioactive compounds, such as polyphenols (found in fruits, vegetables, and tea), flavonoids, carotenoids and compounds in cruciferous vegetables, have shown potential in inhibiting cancer cell growth, reducing inflammation, and promoting cancer cell apoptosis. This review aims to elucidate the mechanisms, by which these bioactive compounds exert their effects, modulating the oxidative stress, influencing inflammatory pathways and regulating cell survival and death. It also highlights current clinical trials that are paving the way toward incorporating these natural agents into mainstream treatment strategies, with the goal of boosting the efficacy of conventional therapies for PDA. Full article
(This article belongs to the Special Issue Design and Synthesis of Bioactive Compounds for Therapeutic Applications)
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16 pages, 2496 KiB  
Article
High Bendability of Short RNA-DNA Hybrid Duplex Revealed by Single-Molecule Cyclization and Molecular Dynamics Simulations
by Bin Wu, Fujia Tian, Yajun Yang, Liang Dai and Xinghua Zhang
Biomolecules 2025, 15(5), 724; https://doi.org/10.3390/biom15050724 - 15 May 2025
Viewed by 158
Abstract
R-loops are nucleic acid structures composed of an RNA-DNA hybrid (RDH) duplex and a displaced single-stranded DNA (ssDNA), which are fundamentally involved in key biological functions, including transcription and the preservation of genome stability. In an R-loop, the RDH duplex is bent by [...] Read more.
R-loops are nucleic acid structures composed of an RNA-DNA hybrid (RDH) duplex and a displaced single-stranded DNA (ssDNA), which are fundamentally involved in key biological functions, including transcription and the preservation of genome stability. In an R-loop, the RDH duplex is bent by the folded secondary structures of the displaced ssDNA. Previous experiments and simulations indicated the high bendability of DNA below the persistence length. However, the bendability of a short RDH duplex remains unclear. Here, we report that an RDH duplex exhibits higher bendability than a DNA duplex on the short length scale using single-molecule cyclization experiments. Our molecular dynamics simulations show that an RDH duplex has larger intrinsic curvature and structural fluctuations and more easily forms kinks than DNA, which promote the bending flexibility of RDH from unlooped structures. Interestingly, we found that an RDH duplex composed of a C-rich DNA strand and a G-rich RNA strand shows significantly higher bendability than that composed of a G-rich DNA strand and a C-rich RNA strand in the same CpG island promoter regions, which may contribute to the formation of an R-loop. These findings shape our understanding towards biological processes involving R-loops through the high and sequence-dependent bendability of an RDH duplex. Full article
(This article belongs to the Section Molecular Biophysics: Structure, Dynamics, and Function)
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13 pages, 2564 KiB  
Article
Viable Cryopreservation Strategy for Extending the Timeframe of Circulating Tumor Cell Detection in Breast Cancer Clinical Trials
by Cristina Sánchez-Quesada, Estefanía Toledo, José Juan Jiménez-Moleón and José Juan Gaforio
Biomolecules 2025, 15(5), 723; https://doi.org/10.3390/biom15050723 - 15 May 2025
Viewed by 121
Abstract
Circulating tumor cells (CTCs) hold recognized prognostic value in various cancers, including breast cancer, where their presence correlates with survival outcomes. However, the typical 24 h window for blood processing and CTC isolation poses a logistical challenge, particularly for multicenter studies. This study [...] Read more.
Circulating tumor cells (CTCs) hold recognized prognostic value in various cancers, including breast cancer, where their presence correlates with survival outcomes. However, the typical 24 h window for blood processing and CTC isolation poses a logistical challenge, particularly for multicenter studies. This study aimed to evaluate cryopreservation at different stages of CTC isolation and immunocytological detection to extend the blood sample processing period. Using spiked peripheral blood samples with MDA-MB-231, SKBR3, and MCF7 breast cancer cell lines, four distinct cryopreservation points were assessed: following Ficoll gradient separation, immunomagnetic separation, cytocentrifugation, and cytokeratin labeling. Our findings demonstrated that cryopreservation of the mononuclear and granulocytic cell fraction after double-density Ficoll gradient separation was the only viable method for subsequent CTC detection. This approach allowed for consistent recovery of CK+ CTCs, with an average recovery rate of over 81% after one year of cryopreservation. In contrast, cryopreservation at later stages resulted in undetectable CTCs or only cellular debris. In conclusion, cryopreservation following density gradient centrifugation is a feasible strategy for delaying CTC isolation and immunocytological analysis in breast cancer research, facilitating its application in multicenter clinical trials. Full article
(This article belongs to the Section Molecular Medicine)
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17 pages, 15016 KiB  
Article
Baicalin Alleviates Piglet Immunosuppression Induced by Glaesserella parasuis via Promoting CD163/Tumor Necrosis Factor-like Weak Inducer of Apoptosis-Mediated Autophagy
by Shulin Fu, Ronghui Luo, Jingyang Li, Yunjian Fu, Qiaoli Dong, Siyu Liu, Yamin Sun, Ling Guo, Jin Hu and Yinsheng Qiu
Biomolecules 2025, 15(5), 722; https://doi.org/10.3390/biom15050722 - 15 May 2025
Viewed by 149
Abstract
Glaesserella parasuis (G. parasuis) causes vascular inflammation in piglets, resulting in vascular damage. However, the mechanism causing vascular inflammation remains unclear. Baicalin possesses an anti-inflammatory function. Tumor necrosis factor-like weak inducer of apoptosis (TWEAK) has been implicated in immunosuppression. CD163, a [...] Read more.
Glaesserella parasuis (G. parasuis) causes vascular inflammation in piglets, resulting in vascular damage. However, the mechanism causing vascular inflammation remains unclear. Baicalin possesses an anti-inflammatory function. Tumor necrosis factor-like weak inducer of apoptosis (TWEAK) has been implicated in immunosuppression. CD163, a scavenger receptor expressed on macrophages that acts as a decoy receptor for TWEAK, plays a crucial role in the regulation of autophagy and inflammation. This research investigated the efficacy of baicalin in reducing immunosuppression elicited by G. parasuis through the regulation of CD163/TWEAK-mediated autophagy. The data demonstrated that G. parasuis altered routine blood indicators and biochemical parameters, increased cytokine production, and induced blood vessel tissue damage. G. parasuis reduced the CD3+ T cell proportion, CD3+CD4+ T cell proportion, and CD3+CD8+ T cell proportion in piglet blood. The proteomic analysis revealed that CD163 was differentially expressed in the blood vessels of challenged piglets. Baicalin was found to regulate CD163/TWEAK axis expression, inhibit Notch/Wnt signaling pathway activation, promote autophagy, and reduce NLRP3/Caspase 1 signaling pathway activation. Baicalin also decreased cytokine production and alleviated pathological tissue damage in the blood vessels of G. parasuis-challenged piglets. Taken together, this study indicates that baicalin alleviates G. parasuis-induced immunosuppression and might promote CD163/TWEAK-mediated autophagy. This finding suggests that baicalin could serve as a potential therapeutic agent to control G. parasuis infection and related vascular inflammation. Full article
(This article belongs to the Topic Recent Advances in Veterinary Pharmacology and Toxicology)
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16 pages, 503 KiB  
Review
Embryonic Origins of Cancer: Insights from Double Homeobox 4 Regulation
by Bo Fu, Hong Ma, Liang Wang, Zhenhua Guo, Fang Wang, Di Liu and Dongjie Zhang
Biomolecules 2025, 15(5), 721; https://doi.org/10.3390/biom15050721 - 14 May 2025
Viewed by 149
Abstract
Embryogenesis and tumorigenesis share several key biological characteristics, such as rapid cell proliferation, high plasticity, and immune evasion. This similarity indicates that developmental pathways can be hijacked, leading to the formation of malignant cell states. With regard to this, cancer can be regarded [...] Read more.
Embryogenesis and tumorigenesis share several key biological characteristics, such as rapid cell proliferation, high plasticity, and immune evasion. This similarity indicates that developmental pathways can be hijacked, leading to the formation of malignant cell states. With regard to this, cancer can be regarded as a stem cell disease. On the contrary, a fetus, in many ways, has similar characteristics to the “ideal tumor”, such as immune evasion and rapid growth. Therefore, deciphering the molecular mechanisms beneath these phenomena will help us to understand the embryonic origins of cancer. This review discusses the relationship between embryogenesis and tumorigenesis, highlighting the potential roles played by DUX4. DUX4 is involved in the activation of the zygote genome and then facilitates the establishment of totipotency in pre-implantation embryos, whereas the misexpression of DUX4 is associated with different types of cancer. Taken together, this indicates that DUX4 performs analogous functions in these two processes and connects embryogenesis and tumorigenesis. Through examining DUX4, this review underscores the importance of developmental mechanisms in cancer biology, suggesting that the insights gained from studying embryonic processes may provide novel therapeutic strategies. As we continue to explore the complex relationship between cancer and embryogenesis, elucidating the role of DUX4 in linking these two processes will be critical for developing targeted therapies that exploit developmental pathways. Full article
(This article belongs to the Section Molecular Biology)
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13 pages, 5029 KiB  
Article
Crystal Structure of the Multidomain Pectin Methylesterase PmeC5 from Butyrivibrio fibrisolvens D1T
by Vincenzo Carbone, Kerri Reilly, Carrie Sang, Linley R. Schofield, William J. Kelly, Ron S. Ronimus, Graeme T. Attwood and Nikola Palevich
Biomolecules 2025, 15(5), 720; https://doi.org/10.3390/biom15050720 - 14 May 2025
Viewed by 116
Abstract
Pectin is a dynamic and complex polysaccharide that forms a substantial proportion of the primary plant cell wall and middle lamella of forage ingested by grazing ruminants. Pectin methylesterases (PMEs) are enzymes that belongs to the carbohydrate esterase family 8 (CE8) and catalyze [...] Read more.
Pectin is a dynamic and complex polysaccharide that forms a substantial proportion of the primary plant cell wall and middle lamella of forage ingested by grazing ruminants. Pectin methylesterases (PMEs) are enzymes that belongs to the carbohydrate esterase family 8 (CE8) and catalyze the demethylesterification of pectin, a key polysaccharide in cell walls. Here we present the crystal structure of the catalytic domain of PmeC5 that is associated with a gene from Butyrivibrio fibrisolvens D1T that encodes a large secreted pectinesterase family protein (2089 aa) determined to a resolution of 1.33 Å. Protein in silico modelling of the secreted pectinesterase confirmed the presence of an additional pectate lyase (PL9) and adhesin-like domains. The structure of PmeC5 was the characteristic right-handed parallel β-helical topology and active site residues of Asp231, Asp253, and Arg326 typical of the enzyme class. PmeC5 is a large modular enzyme that is characteristic of rumen B. fibrisolvens megaplasmids and plays a central role in degrading plant cell wall components and releasing methanol in the rumen environment. Such secreted PMEs are significant contributors to plant fiber digestion and methane production, making them attractive targets for both methane mitigation strategies and livestock productivity enhancement. Full article
(This article belongs to the Topic Design, Synthesis and Biological Evaluation of Novel Small Molecules as Multi-target Enzyme Inhibitors)
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25 pages, 3667 KiB  
Review
Nicotinamide N-Methyltransferase (NNMT) and Liver Cancer: From Metabolic Networks to Therapeutic Targets
by Shi-Yan Lai, Xiao-Juan Zhu, Wei-Dong Sun, Shuang-Zhou Bi, Chen-Ying Zhang, An Liu and Jiang-Hua Li
Biomolecules 2025, 15(5), 719; https://doi.org/10.3390/biom15050719 - 14 May 2025
Viewed by 190
Abstract
Hepatocellular carcinoma (HCC), the predominant form of primary liver cancer, remains a global health challenge with limited therapeutic options and high mortality rates. Despite advances in understanding its molecular pathogenesis, the role of metabolic reprogramming in HCC progression and therapy resistance demands further [...] Read more.
Hepatocellular carcinoma (HCC), the predominant form of primary liver cancer, remains a global health challenge with limited therapeutic options and high mortality rates. Despite advances in understanding its molecular pathogenesis, the role of metabolic reprogramming in HCC progression and therapy resistance demands further exploration. Nicotinamide N-methyltransferase (NNMT), a metabolic enzyme central to NAD+ and methionine cycles, has emerged as a critical regulator of tumorigenesis across cancers. However, its tissue-specific mechanisms in HCC—particularly in the context of viral hepatitis and methionine cycle dependency—remain understudied. This review systematically synthesizes current evidence on NNMT’s dual role in HCC: (1) driving NAD+ depletion and homocysteine (Hcy) accumulation via metabolic dysregulation, (2) promoting malignant phenotypes (proliferation, invasion, metastasis, and drug resistance), and (3) serving as a prognostic biomarker and therapeutic target. We highlight how NNMT intersects with epigenetic modifications, immune evasion, and metabolic vulnerabilities unique to HCC. Additionally, we critically evaluate NNMT inhibitors, RNA-based therapies, and non-pharmacological strategies (e.g., exercise) as novel interventions. By bridging gaps between NNMT’s molecular mechanisms and clinical relevance, this review provides a roadmap for advancing NNMT-targeted therapies and underscores the urgency of addressing challenges in biomarker validation, inhibitor specificity, and translational efficacy. Our work positions NNMT not only as a metabolic linchpin in HCC but also as a promising candidate for precision oncology. Full article
(This article belongs to the Section Molecular Biology)
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18 pages, 1035 KiB  
Review
Erythrocyte Membrane Fingerprints in the Veterinary Field: The Importance of Membrane Profiling and Its Application in Companion Animals
by Benedetta Belà, Alessandro Gramenzi, Paraskevi Prasinou and Carla Ferreri
Biomolecules 2025, 15(5), 718; https://doi.org/10.3390/biom15050718 - 14 May 2025
Viewed by 223
Abstract
The importance of lipid molecules present at the level of cell membranes is already well known. They can act as secondary messengers, participating in signal transduction processes that regulate various organ functions; furthermore, their nature significantly influences cellular properties and functions. Recent studies [...] Read more.
The importance of lipid molecules present at the level of cell membranes is already well known. They can act as secondary messengers, participating in signal transduction processes that regulate various organ functions; furthermore, their nature significantly influences cellular properties and functions. Recent studies have seen how the lipid composition of cell membranes is connected to the animal lifespan and the onset of several pathological conditions. While numerous studies have been conducted aimed at characterizing the membrane lipidomic profile in the human field, in the animal field, especially in pets, the number of studies is very limited. In recent years, preliminary analyses have been conducted to provide initial information on the composition of membrane fatty acids in healthy pets and those with chronic enteropathy. The results of these studies are very interesting as they highlight differences in fatty acid composition between the two groups of animals. Obviously, a greater number of works is needed to obtain more reliable results and to analyze how the membrane lipid composition can vary in different breeds and sizes of dogs and cats in an attempt to understand the mechanisms underlying it. The present review is divided into three main parts: the first one examines the close influence of fatty acids on membrane properties/functions, the second one presents the main lipidomic analyses conducted so far on companion animals, and the third and final part summarizes the latest works on the link between membrane lipid profiles and animal lifespans, also focusing on dietary and non-dietary strategies able to influence it. Membrane lipidomics allows us to obtain a concrete overview of an animal’s metabolism and nutrition; furthermore, lipid alterations could be used as biomarkers for the early diagnosis of pathologies. This represents an innovative tool in the veterinary field to monitor the metabolic/health status of animals. Full article
(This article belongs to the Section Lipids)
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14 pages, 1624 KiB  
Article
Factors Determining Kinesin Motors in a Predominant One-Head-Bound or Two-Heads-Bound State During Its Stepping Cycle
by Xiao-Xuan Shi, Yu-Ru Liu and Ping Xie
Biomolecules 2025, 15(5), 717; https://doi.org/10.3390/biom15050717 - 13 May 2025
Viewed by 186
Abstract
At physiological or saturating ATP concentrations, some families of kinesin motors, such as kinesin-1 and kinesin-2, exhibit a predominant two-heads-bound (2HB) state during their stepping cycle on microtubules, while others, such as kinesin-3, exhibit a predominant one-head-bound (1HB) state. An interesting but unclear [...] Read more.
At physiological or saturating ATP concentrations, some families of kinesin motors, such as kinesin-1 and kinesin-2, exhibit a predominant two-heads-bound (2HB) state during their stepping cycle on microtubules, while others, such as kinesin-3, exhibit a predominant one-head-bound (1HB) state. An interesting but unclear issue is what factors determine a kinesin motor in the predominant 1HB and 2HB states. Here, on the basis of the general chemomechanical pathway of the kinesin motors, a theory is given on fractions of 1HB and 2HB states. With the theory, the factors affecting a kinesin motor in the predominant 1HB and 2HB states are determined. The results about the effects of ATP concentration, ADP concentration and external load on the fractions of 1HB and 2HB states are presented. Furthermore, the theory is applied to kinesin-1, kinesin-2, kinesin-3, kinesin-5 and kinesin-13 motors, with the theoretical results agreeing well with published experimental data. Full article
(This article belongs to the Section Molecular Biophysics: Structure, Dynamics, and Function)
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26 pages, 1575 KiB  
Review
CXCR Family and Hematologic Malignancies in the Bone Marrow Microenvironment
by Yanquan Liu and Huanwen Tang
Biomolecules 2025, 15(5), 716; https://doi.org/10.3390/biom15050716 - 13 May 2025
Viewed by 137
Abstract
Malignant hematologic diseases, also referred to as hematologic tumors, encompass a series of malignant proliferative disorders of the lymphopoietic system, including leukemia, lymphoma, multiple myeloma, and myeloproliferative neoplasms. The dysregulation of inflammatory factors or chronic inflammatory responses plays an indispensable role in the [...] Read more.
Malignant hematologic diseases, also referred to as hematologic tumors, encompass a series of malignant proliferative disorders of the lymphopoietic system, including leukemia, lymphoma, multiple myeloma, and myeloproliferative neoplasms. The dysregulation of inflammatory factors or chronic inflammatory responses plays an indispensable role in the onset and progression of these tumors. The C-X-C motif chemokine receptor (CXCR) serves as a key mediator of immune-inflammatory responses. Through its specific regulatory mechanisms, CXCR is involved in the transduction and activation of various signaling pathways, thereby mediating the malignant biological characteristics of blood tumor cells, such as uncontrolled proliferation, differentiation, invasion, migration, autophagy, and apoptosis. In the bone marrow microenvironment, CXCR plays a pivotal role. This review systematically analyzes and elucidates the roles and mechanisms of the CXCR family in hematologic malignancies, aiming to provide new insights into the biological mechanisms and clinical significance of these diseases. The CXCR family holds great potential as a molecular marker for both fundamental research and the clinical diagnosis and treatment of hematologic malignancies. Full article
(This article belongs to the Topic Advances in Molecular Pathogenesis and Targeted Therapies for Multiple Myeloma)
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13 pages, 467 KiB  
Review
OX40–OX40L Axis in Cutaneous T-Cell Lymphomas: Pathogenic, Prognostic, and Potential Therapeutic Perspectives
by Alba Guglielmo, Alessandro Borghi, Corrado Zengarini, Bianca Maria Piraccini, Monica Corazza and Alessandro Pileri
Biomolecules 2025, 15(5), 715; https://doi.org/10.3390/biom15050715 - 13 May 2025
Viewed by 149
Abstract
Mycosis fungoides (MF) and Sézary syndrome (SS) are the most prevalent forms of cutaneous T-cell lymphoma (CTCL) and are characterized by the proliferation of CD4+ T-helper cells. The pathogenesis of CTCLs involves a critical interaction between neoplastic cells and the tumor microenvironment. [...] Read more.
Mycosis fungoides (MF) and Sézary syndrome (SS) are the most prevalent forms of cutaneous T-cell lymphoma (CTCL) and are characterized by the proliferation of CD4+ T-helper cells. The pathogenesis of CTCLs involves a critical interaction between neoplastic cells and the tumor microenvironment. This interaction is driven not only by cytokines but also by surface proteins that mediate cell–cell contact. One such protein, OX40 (also known as CD134), is a member of the TNF receptor superfamily and serves as an induced costimulatory molecule that facilitates the interaction between T-cells and antigen-presenting cells. In this narrative review, we explore the literature surrounding the OX40–OX40L interaction in CTCLs, highlighting its pathogenic and prognostic significance. Additionally, we compare the expression and function of OX40–OX40L in chronic inflammatory skin diseases, such as atopic dermatitis and psoriasis, with their role in CTCLs. Finally, we provide an overview of the current state of therapeutic research, discussing the potential of targeting the OX40–OX40L axis in CTCL treatment. Full article
(This article belongs to the Section Molecular Biomarkers)
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13 pages, 1023 KiB  
Article
Hydroxytyrosyl Eicosapentaenoate as a Potential Antioxidant for Omega-3 Fatty Acids: Improved Synthesis and Comparative Evaluation with Other Natural Antioxidants
by Natalia García-Acosta, Rosa Cert, Marta Jordán, Luis Goya, Raquel Mateos and Jose Luis Espartero
Biomolecules 2025, 15(5), 714; https://doi.org/10.3390/biom15050714 - 13 May 2025
Viewed by 246
Abstract
Hydroxytyrosol (HT), the primary phenolic compound in virgin olive oil, has notable cardiovascular benefits, particularly in preventing low-density lipoprotein (LDL) oxidation. However, its hydrophilicity limits its solubility and integration into lipid-based formulations. This study aimed to enhance its lipophilicity by synthesizing hydroxytyrosyl eicosapentaenoate [...] Read more.
Hydroxytyrosol (HT), the primary phenolic compound in virgin olive oil, has notable cardiovascular benefits, particularly in preventing low-density lipoprotein (LDL) oxidation. However, its hydrophilicity limits its solubility and integration into lipid-based formulations. This study aimed to enhance its lipophilicity by synthesizing hydroxytyrosyl eicosapentaenoate (HT-EPA), a derivative of HT and eicosapentaenoic acid (EPA), using a one-step enzymatic catalysis with lipase B from Candida antarctica (CALB). The reaction, performed as a suspension of HT in ethyl eicosapentaenoate (Et-EPA) (1:9 molar ratio) under vacuum, achieved higher yields and shorter reaction times than previously reported, with a purity exceeding 98%, confirmed by 1H-NMR. For the first time, the antioxidant capacity of HT-EPA in comparison with other natural antioxidants was assessed using the FRAP assay, while its oxidative stability in an omega-3-rich oil matrix was evaluated via the Rancimat method. HT-EPA and hydroxytyrosyl acetate (HT-Ac) displayed antioxidant activity comparable to HT but significantly higher than α-tocopherol, a common food antioxidant. Given the scarcity of effective lipid-soluble antioxidants, HT-EPA represents a promising candidate for omega-3 nutraceuticals, offering enhanced stability and potential health benefits. This study provides a simple, efficient, and scalable strategy for developing functional lipid-based formulations with cardioprotective potential by improving HT solubility while preserving its antioxidant properties. Full article
(This article belongs to the Section Lipids)
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29 pages, 2758 KiB  
Review
Past, Present and Future Perspectives of Forensic Genetics
by Itzae Adonai Gutiérrez-Hurtado, Mayra Elizabeth García-Acéves, Yolanda Puga-Carrillo, Mariano Guardado-Estrada, Denisse Stephania Becerra-Loaiza, Víctor Daniel Carrillo-Rodríguez, Reynaldo Plazola-Zamora, Juliana Marisol Godínez-Rubí, Héctor Rangel-Villalobos and José Alonso Aguilar-Velázquez
Biomolecules 2025, 15(5), 713; https://doi.org/10.3390/biom15050713 - 13 May 2025
Viewed by 388
Abstract
Forensic genetics has experienced remarkable advancements over the past decades, evolving from the analysis of a limited number of DNA segments to comprehensive genome-wide investigations. This progression has significantly improved the ability to establish genetic profiles under diverse conditions and scenarios. Beyond individual [...] Read more.
Forensic genetics has experienced remarkable advancements over the past decades, evolving from the analysis of a limited number of DNA segments to comprehensive genome-wide investigations. This progression has significantly improved the ability to establish genetic profiles under diverse conditions and scenarios. Beyond individual identification, forensic genetics now enables the inference of physical traits (e.g., eye, hair, and skin color, as well as body composition), biogeographic ancestry, lifestyle habits such as alcohol and tobacco use, and even the transfer of genital microbiomes post-coitus, among other characteristics. Emerging trends point to a future shaped by the integration of cutting-edge technologies, including CRISPR-Cas systems, artificial intelligence, and machine learning, which promise to further revolutionize the field. This review provides a thorough exploration of forensic genetics, tracing its evolution from its foundational methods (past) to its diverse modern applications (present) and offering insights into its potential future directions. Full article
(This article belongs to the Collection Feature Papers in Molecular Genetics)
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22 pages, 683 KiB  
Review
Interplay Between Vascular Dysfunction and Neurodegenerative Pathology: New Insights into Molecular Mechanisms and Management
by Avanthika Mekala and Hongyu Qiu
Biomolecules 2025, 15(5), 712; https://doi.org/10.3390/biom15050712 - 13 May 2025
Viewed by 201
Abstract
Vascular dysfunction frequently coexists with neurodegenerative disorders such as dementia and Alzheimer’s disease (AD) in older individuals; however, the cause-and-effect relationship remains unclear. While AD is primarily characterized by neural tissue degeneration, emerging evidence suggests that aging-induced vascular dysfunction contributes to both the [...] Read more.
Vascular dysfunction frequently coexists with neurodegenerative disorders such as dementia and Alzheimer’s disease (AD) in older individuals; however, the cause-and-effect relationship remains unclear. While AD is primarily characterized by neural tissue degeneration, emerging evidence suggests that aging-induced vascular dysfunction contributes to both the onset and progression of cognitive impairment and dementia by decreasing cerebral blood flow (CBF) and disrupting the blood–brain barrier (BBB). This challenges the traditional notion and underscores vascular dysfunction as an early pathogenic stimulus; thus, targeting vascular pathologies could be a promising strategy to slow dementia progression and potentially prevent AD. Conversely, aging-related neurodegeneration exacerbates vascular dysfunction, accelerating dementia pathology through oxidative stress and inflammation as well as deposition of neurotoxic substances such as beta-amyloid (Aβ) and tau in vascular walls. This bidirectional interaction creates a vicious cycle that worsens cognitive decline, underscoring the complexity of these diseases. This review aims to highlight recent advances in research on the mechanisms of aging-related vascular dysfunction in neurodegenerative diseases, focusing on vascular contributions to cognitive impairment and dementia (VCID) and AD. Additionally, we will explore the reciprocal effects and intricate relationship between vascular dysfunction and neurodegenerative pathologies, enhancing our understanding of relative disease pathogenesis and guiding the development of innovative prevention and treatment strategies. Full article
(This article belongs to the Special Issue The Role of Vascular Dysfunction in Neuronal Degeneration and Cognitive Impairment (2nd Edition))
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14 pages, 6294 KiB  
Article
Vitamin D and Retinoic Acid Require Protein Kinase C Activity and Reactive Oxygen Species as Opposing Signals Regulating PEIG-1/GPRC5A Expression in Caco-2 and T84 Colon Carcinoma Cells
by Pablo A. Iglesias González, Consuelo Mori, Ángel G. Valdivieso and Tomás A. Santa Coloma
Biomolecules 2025, 15(5), 711; https://doi.org/10.3390/biom15050711 - 13 May 2025
Viewed by 253
Abstract
PEIG-1/GPRC5A (phorbol ester induced gene-1/G-protein Coupled Receptor Class C Group 5 Member A) was the first identified member of the orphan G protein-coupled receptor family GPRC5. Deregulation of its expression is associated with the development and progression of various types of tumours, particularly [...] Read more.
PEIG-1/GPRC5A (phorbol ester induced gene-1/G-protein Coupled Receptor Class C Group 5 Member A) was the first identified member of the orphan G protein-coupled receptor family GPRC5. Deregulation of its expression is associated with the development and progression of various types of tumours, particularly colon carcinoma. In this work, we study the effects of vitamin D (VD, cholecalciferol) and retinoic acid (RA) on GPRC5A mRNA expression in the colorectal cancer cell lines Caco-2 and T84. Both VD (10 µM) and all-trans retinoic acid (ATRA, atRA, RA) (10 µM) increased GPRC5A mRNA levels. Protein kinase C (PKC) inhibition with Gö6983 (10 µM) completely abolished the effects of VD and RA on GPRC5A expression. In parallel, VD and RA increased cytosolic and mitochondrial ROS levels (cROS and mtROS). However, the antioxidants NAC (10 mM) and MitoTEMPO (10 µM) raised GPRC5A gene expression levels in the presence of VD or RA, suggesting that elevated ROS may inhibit GPRC5A expression. In conclusion, both VD and RA stimulate GPRC5A expression. The mechanisms involve a common and essential PKC signalling pathway, as Gö6983 inhibited both VD- and RA-induced signalling. Full article
(This article belongs to the Special Issue Biomolecules and Their Impact on Biology and Translational Applications: Celebrating the Pioneering Work of Prof. Ho Jeong Kwon)
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22 pages, 5907 KiB  
Article
A Novel Ashwagandha (Withania somnifera) Formulation Mitigates Sleep Deprivation-Induced Cognitive Impairment and Oxidative Stress in a Rat Model
by Besir Er, Busra Ozmen, Emre Sahin, Cemal Orhan, Nurhan Sahin, Abhijeet A. Morde, Muralidhara Padigaru and Kazim Sahin
Biomolecules 2025, 15(5), 710; https://doi.org/10.3390/biom15050710 - 12 May 2025
Viewed by 225
Abstract
Ashwagandha (Withania somnifera) is a well-known adaptogenic herb traditionally used to enhance sleep quality and mitigate stress-induced cognitive decline. This study investigated the effects of different doses of ashwagandha root extract (AE) formulations on cognitive function, oxidative stress, and neuronal plasticity [...] Read more.
Ashwagandha (Withania somnifera) is a well-known adaptogenic herb traditionally used to enhance sleep quality and mitigate stress-induced cognitive decline. This study investigated the effects of different doses of ashwagandha root extract (AE) formulations on cognitive function, oxidative stress, and neuronal plasticity in a rat model of sleep deprivation (SD). Forty-nine rats were randomly assigned to seven groups: control, wide platform (WP), SD, SD + A1 (15 mg/kg AE 1.5%), SD + A2 (30 mg/kg AE 1.5%), SD + A3 (5.5 mg/kg AE 8.0%), and SD + A4 (11 mg/kg AE 8.0%). The extract was administered orally for four weeks. SD induced via a modified wide platform model significantly impaired spatial memory, increased oxidative stress, and suppressed GABA receptor activity. Treatment with all AE doses, except 15 mg/kg AE 1.5%, considerably reduced serum corticosterone (12% for SD + A2, 15% for SD + A3, and 32% for SD + A4), CRH (11% for SD + A2, 14% for SD + A3, and 17% for SD + A4), ACTH (22% for SD + A2, 26% for SD + A3, and 38% for SD + A4), and MDA levels (31% for SD + A2, 34% for SD + A3, and 46% for SD + A4) (p < 0.05). All doses improved antioxidant enzyme activity and memory performance, while AE 8.0% doses notably increased serotonin (19% for SD + A3 and 33% for SD + A4) and dopamine levels (40% for SD + A3 and 50% for SD + A4). Moreover, AE treatment enhanced markers of neuronal plasticity and partially improved GABAergic function. These findings suggest that AE formulations, particularly at higher concentrations, exert neuroprotective effects against SD-induced cognitive impairment by modulating oxidative stress, neurotransmitter balance, and neuroplasticity, indicating their potential application in managing stress-related neurological disorders. Full article
(This article belongs to the Special Issue Design and Synthesis of Bioactive Compounds for Therapeutic Applications)
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37 pages, 2972 KiB  
Review
Role of Tumor Necrosis Factor in Tuberculosis
by Fedor D. Kireev, Julia A. Lopatnikova, Alina A. Alshevskaya and Sergey V. Sennikov
Biomolecules 2025, 15(5), 709; https://doi.org/10.3390/biom15050709 - 12 May 2025
Viewed by 144
Abstract
Tumor necrosis factor (TNF) is a key immunoregulatory cytokine with a dual role in the host response to Mycobacterium tuberculosis. While essential for granuloma formation, macrophage activation, and containment of latent infection, TNF can also contribute to tissue damage and immune pathology. [...] Read more.
Tumor necrosis factor (TNF) is a key immunoregulatory cytokine with a dual role in the host response to Mycobacterium tuberculosis. While essential for granuloma formation, macrophage activation, and containment of latent infection, TNF can also contribute to tissue damage and immune pathology. This review systematically analyzes over 300 peer-reviewed studies published between 1980 and 2024, highlighting the molecular and cellular mechanisms of TNF action in tuberculosis (TB). Particular attention is given to TNF receptor signaling pathways, the balance between protective and pathological immune responses, and the modulation of TNF activity during anti-TNF therapy in patients with autoimmune diseases. We discuss how different TNF inhibitors vary in their capacity to interfere with host defense mechanisms, with monoclonal antibodies carrying a higher reactivation risk than receptor-based agents. To enhance conceptual clarity, we provide newly developed schematic representations that integrate current knowledge on TNF-driven immune dynamics, including its interaction with other cytokines, effects on granuloma stability, and role in intracellular bacterial control. Understanding the pleiotropic functions of TNF in tuberculosis pathogenesis is crucial for developing safe immunomodulatory strategies and optimizing the clinical management of patients at risk of latent TB reactivation. Full article
(This article belongs to the Section Biological Factors)
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17 pages, 4071 KiB  
Article
Examining the Effects of the RUNX1 p.Leu43Ser Variant on FPD/AML Phenotypes Using a CRISPR/Cas9-Generated Knock-In Murine Model
by Ana Marin-Quilez, Ignacio García-Tuñón, Rocío Benito, José Luis Ordoñez, Lorena Díaz-Ajenjo, Ana Lama-Villanueva, Carmen Guerrero, Jesús Pérez-Losada, José Ramón González-Porras, Jesús María Hernández-Rivas, Mónica del Rey and José María Bastida
Biomolecules 2025, 15(5), 708; https://doi.org/10.3390/biom15050708 - 12 May 2025
Viewed by 133
Abstract
Germline heterozygous variants in RUNX1 lead to Familial Platelet Disorder with Myeloid Leukemia Predisposition (FPD/AML). Cellular and/or animal models are helpful to uncovering the role of a variant in disease progression. Twenty-five mice per genotype (RUNX1WT/WT, RUNX1WT/L43S, RUNX1L43S/L43S [...] Read more.
Germline heterozygous variants in RUNX1 lead to Familial Platelet Disorder with Myeloid Leukemia Predisposition (FPD/AML). Cellular and/or animal models are helpful to uncovering the role of a variant in disease progression. Twenty-five mice per genotype (RUNX1WT/WT, RUNX1WT/L43S, RUNX1L43S/L43S), previously generated by CRISPR/Cas9, and nine sub-lethally irradiated mice per genotype were investigated. Peripheral blood (PB), bone marrow (BM), and spleen samples were analyzed by flow cytometry and histopathology. Deregulated genes were analyzed by RNA-seq in BM. An aberrant myeloid Mac1+Sca1+ckit− population in the PB, BM, and spleen of two homozygous and one heterozygous mouse was observed, as well as BM hypercellularity. No Mac1+Sca1+ckit− cells were detected in any RUNX1WT/WT mice. Moreover, the spleen of both homozygous mice showed destruction of the white/red pulp and the presence of apoptotic cells. The aberrant population was also detected in four irradiated mice, two heterozygous and two homozygous, in their PB, BM, and spleen. RNA-seq studies showed 698 genes significantly deregulated in the three non-irradiated Mac1+Sca1+ckit− mice vs. six healthy mice, highlighting the alteration of genes involved in apoptosis and DNA repair. These results indicate that the homozygous form of the variant p.Leu43Ser may contribute to the pathogenesis of aberrant cells. Full article
(This article belongs to the Special Issue Molecular Advances in Platelet Disease, Thrombosis and Hemostasis)
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