Biomolecules

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24 pages, 2125 KB

Open AccessEditor’s ChoiceArticle

Enhanced Anti-Nociception by Novel Dual Antagonists for 5-HT2AR and mGluR5 in Preclinical Models of Pain

by Daekyu Choi, Hyun Jin Heo, Haeyoung Shin, Jayzoon Im, Geonho Lee, Ah Hyun Kim, Kwang-Hyun Hur, Yoonmi Nho, Choon-Gon Jang and Hanmi Lee

Biomolecules 2025, 15(10), 1456; https://doi.org/10.3390/biom15101456 - 15 Oct 2025

Cited by 1 | Viewed by 1582

Abstract

Extensive research has focused on developing anti-nociceptive therapy by targeting specific molecular pathways. Among these, the serotonin 2A receptor (5-HT2AR) and metabotropic glutamate receptor 5 (mGluR5) are recognized as key mediators of neuropathic pain. However, the therapeutic potential of their simultaneous inhibition remains [...] Read more.

Extensive research has focused on developing anti-nociceptive therapy by targeting specific molecular pathways. Among these, the serotonin 2A receptor (5-HT2AR) and metabotropic glutamate receptor 5 (mGluR5) are recognized as key mediators of neuropathic pain. However, the therapeutic potential of their simultaneous inhibition remains largely unexplored. In this study, we evaluated the efficacy of dual antagonism of 5-HT2AR and mGluR5 using spinal nerve ligation (SNL) and formalin-induced pain models in male Sprague–Dawley rats. Co-administration of selective antagonists significantly enhanced anti-allodynic and anti-nociceptive effects, as evidenced by increased withdrawal thresholds and reduced pain-related behaviors compared to monotherapy. The analgesic efficacy of dual antagonism was comparable to that of gabapentin and morphine. Additionally, novel small molecules designed to concurrently inhibit 5-HT2AR and mGluR5 exerted dose-dependent anti-nociceptive effects by suppressing excitatory postsynaptic responses and inhibiting the phosphorylation of ERK and AKT signaling molecules. Importantly, unlike morphine, repeated administration of the dual antagonist maintained anti-allodynic efficacy with a low potential of abuse. These findings may indicate the promise of simultaneous 5-HT2AR and mGluR5 antagonism as a novel and potentially safer strategy for managing chronic neuropathic pain. Full article

(This article belongs to the Section Molecular Medicine)

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26 pages, 3377 KB

Open AccessEditor’s ChoiceArticle

Charge Neutralization During Peptide Transport in the Bacterial SecYEG Translocon

by Laura Nübl, Ekaterina Sobakinskaya and Frank Müh

Biomolecules 2025, 15(10), 1442; https://doi.org/10.3390/biom15101442 - 12 Oct 2025

Viewed by 1038

Abstract

The driving force behind protein translocation across the cell membrane is not yet fully understood. In bacteria, there is an electrochemical potential across the cell membrane, which can interact with charged residues in the translocation substrate. In this study, the protonation states of [...] Read more.

The driving force behind protein translocation across the cell membrane is not yet fully understood. In bacteria, there is an electrochemical potential across the cell membrane, which can interact with charged residues in the translocation substrate. In this study, the protonation states of lysine and glutamate, serving as test residues in a peptide translocating across the bacterial channel SecYEG, are investigated by applying Poisson–Boltzmann continuum electrostatic free energy calculations and Monte Carlo titrations to snapshots of molecular dynamics (MD) simulations. A clear shift in protonation probability towards the uncharged state is found for both test residues as they move deeper into the channel. Thus, charge neutralization occurs irrespective of whether the original charge of the test residue is positive (lysine) or negative (glutamate). Electrostatic interactions of acidic and basic residues of SecYEG with the peptide cancel out. The main determinants of the test residue’s protonation state are the dielectric properties of its surroundings and interactions with non-titrating charges in the channel. Crucially, the membrane protein—including its water-filled pore—is assigned a low dielectric constant. The results are discussed in the context of the limitations inherent to continuum electrostatics and MD simulations with fixed protonation states. Full article

(This article belongs to the Special Issue Advances in Membrane Proteins: From Structure to Function and Molecular Engineering)

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24 pages, 2986 KB

Open AccessEditor’s ChoiceArticle

Transcriptional Profiling Defines Unique Subtypes of Transit Amplifying Neural Progenitors Within the Neonatal Mouse Subventricular Zone

by Rebecca Zaritsky, Ekta Kumari, Fernando Janczur Velloso, Alexander Lemenze, Seema Husain and Steven W. Levison

Biomolecules 2025, 15(10), 1438; https://doi.org/10.3390/biom15101438 - 11 Oct 2025

Cited by 2 | Viewed by 1512

Abstract

While significant progress has been made in understanding the heterogeneity of Neural Stem Cells (NSCs), our understanding of similar heterogeneity among the more abundant transit amplifying progenitors is lagging. Our work on the neural progenitors (NPs) of the neonatal subventricular zone (SVZ) began [...] Read more.

While significant progress has been made in understanding the heterogeneity of Neural Stem Cells (NSCs), our understanding of similar heterogeneity among the more abundant transit amplifying progenitors is lagging. Our work on the neural progenitors (NPs) of the neonatal subventricular zone (SVZ) began over a decade ago, when we used antibodies to the four antigens, CD133, LeX, CD140a, and NG2 to perform Fluorescence-activated cell sorting to classify subsets of the neonatal mouse SVZ as either multi-potential (MP1, MP2, MP3, MP4 and PFMPs), glial-restricted (GRP1, GRP2, and GRP3), or neuron-astrocyte restricted (BNAP). Using RNA sequencing, we have characterized the distinctive molecular fingerprints of four SVZ neural progenitor subtypes and compared their gene expression profiles to those of the NSCs. We performed bioinformatic analyses to provide insights into each NP type’s unique interactome and the transcription factors regulating their development. Overall, we identified 1581 genes upregulated in at least one NP subset compared to the NSCs. Of these genes, 796 genes were upregulated in BNAP/GRP1 compared to NSCs; 653 in GRP2/MP3; 440 in GRP3; and 527 in PFMPs. One gene that emerged from our analysis that can be used to distinguish the NPs from the NSCs is Etv1, also known as Er81. Also notable is that the NSCs downregulated cilia formation genes as they differentiated to become multipotential progenitors. Among the NPs, both PFMP and GRP3 subtypes differentially expressed genes related to neuron and oligodendrocyte development, including Matn4, Lhfpl3 and Olig2. GRP3s uniquely expressed Etv5, a transcription factor known to promote glial cell fate specification, while PFMPs uniquely expressed Lhx6, a transcription factor that regulates interneuron specification. PFMPs also expressed transcripts for olfactory receptors. Unlike the other NPs, the GRP1 and GRP2 NPs upregulated expression of genes for proteins involved in immune function. The present work will serve as an important resource for investigators interested in further defining the transit amplifying progenitors of the mammalian SVZ. Full article

(This article belongs to the Special Issue Cellular and Molecular Biology of Neurodevelopment)

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17 pages, 2467 KB

Open AccessEditor’s ChoiceArticle

The Discovery of α-Adrenoceptor Antagonists as a Potential New Treatment Option for Uveal Melanoma

by Yilan He, Hongtao Liu, Ulrike Hendgen-Cotta, Tienush Rassaf, Nikolaos E. Bechrakis and Utta Berchner-Pfannschmidt

Biomolecules 2025, 15(10), 1436; https://doi.org/10.3390/biom15101436 - 10 Oct 2025

Cited by 1 | Viewed by 1331

Abstract

Uveal melanoma (UM) is the most common primary intraocular tumor in adults. Because of its high potential for spreading and its limited response to treatment, UM remains a clinical challenge. Previous studies suggest that clinical adrenergic receptor (AR) antagonists might be effective in [...] Read more.

Uveal melanoma (UM) is the most common primary intraocular tumor in adults. Because of its high potential for spreading and its limited response to treatment, UM remains a clinical challenge. Previous studies suggest that clinical adrenergic receptor (AR) antagonists might be effective in the treatment of UM. This study reports the antitumor activity of α-blocker in UM spheroids generated from α_1A- and α_2A-AR-positive UM cell lines. These cell lines were derived from primary tumors or hepatic metastases and differed in their genetic risk status for metastasis. Drug screening with UM spheroids revealed that prazosin and doxazosin dose-dependently reduced viability, whereas terazosin, alfuzosin, silodosin, tamsulosin, and phenoxybenzamine were found to be inefficient. Prazosin induced apoptosis, resulting in the disintegration of UM spheroid morphology and growth inhibition. Additionally, prazosin prevented UM spheroid cell outgrowth and long-term survival, indicating potential for tumor control. Like the selective α_1A-AR antagonist RS17053, prazosin inhibited the formation and growth of UM spheroids stimulated by the α_1-agonist phenylephrine. This suggests a tumor-preventive effect through the blockade of α_1A-AR. The present study highlights the responses of UM spheroids to α-AR antagonists and demonstrates that prazosin, doxazosin, or RS17053 may be a treatment option for preventing UM tumor recurrence or metastasis. Full article

(This article belongs to the Section Molecular Medicine)

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16 pages, 5174 KB

Open AccessEditor’s ChoiceArticle

Glucocorticoids Induce an Opposite Metabolic Switch in Human Monocytes Contingent upon Their Polarization

by Elisa Peruzzi, Sophia Heidenreich, Lucas Klaus, Angela Boshnakovska, Agathe Amouret, Tobias Legler, Sybille D. Reichardt, Fred Lühder and Holger M. Reichardt

Biomolecules 2025, 15(10), 1422; https://doi.org/10.3390/biom15101422 - 7 Oct 2025

Cited by 1 | Viewed by 1262

Abstract

Background: Monocytes can commit to different phenotypes associated with specific features required in inflammation and homeostasis. Classical and alternative activation are two extremes of monocyte polarization and are both influenced by glucocorticoids (GCs). Methods: Human monocytes were sorted from the blood of healthy [...] Read more.

Background: Monocytes can commit to different phenotypes associated with specific features required in inflammation and homeostasis. Classical and alternative activation are two extremes of monocyte polarization and are both influenced by glucocorticoids (GCs). Methods: Human monocytes were sorted from the blood of healthy individuals and activated with LPS or IL-4 and IL-13, either in the absence or presence of dexamethasone (Dex). Metabolic adjustments were analyzed using Seahorse stress tests, SCENITH, and RT-qPCR. Results: LPS enhanced glycolysis and also, to a lesser extent, oxidative phosphorylation (OXPHOS), whereas addition of Dex induced a metabolic switch in favor of the latter. In contrast, activation of monocytes with IL-4 and IL-13 exclusively stimulated OXPHOS, which was suppressed by concomitant Dex treatment. The glycolytic function of monocytes matched alterations in gene expression of glucose transporters and metabolic enzymes, which were upregulated by LPS and inhibited by Dex via interference with the mTORC1 pathway but remained unaltered in response to IL-4 and IL-13. Although the dependency of classically and alternatively activated monocytes on OXPHOS and glucose usage markedly differed, modulation by GCs was limited to the latter polarization state. Conclusions: Our findings unravel a highly selective regulation of human monocyte energy metabolism by different activating stimuli as well as by GCs. Full article

(This article belongs to the Special Issue Transcription Factors in Hematopoiesis and Immunity: From Development to Therapeutic Targeting)

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13 pages, 2439 KB

Open AccessEditor’s ChoiceArticle

2-Hydroxymelatonin Induces Husk-Imposed Vivipary in the Transgenic Rice Overexpressing Melatonin 2-Hydroxylase

by Kyungjin Lee and Kyoungwhan Back

Biomolecules 2025, 15(10), 1412; https://doi.org/10.3390/biom15101412 - 4 Oct 2025

Cited by 1 | Viewed by 1202

Abstract

Pre-harvest sprouting (PHS) reduces the quality and quantity of crop seeds. PHS can be imposed through the embryo or husk pathway of cereal crops. Most reported PHS seeds are imposed via the embryo pathway. Here, we generated transgenic rice plants overexpressing rice melatonin [...] Read more.

Pre-harvest sprouting (PHS) reduces the quality and quantity of crop seeds. PHS can be imposed through the embryo or husk pathway of cereal crops. Most reported PHS seeds are imposed via the embryo pathway. Here, we generated transgenic rice plants overexpressing rice melatonin 2-hydroxylase (OsM2H), which catalyzes the hydroxylation of melatonin to 2-hydroxymelatonin (2-OHM). OsM2H overexpression (M2H-OE) showed PHS under paddy conditions. Germination assays revealed that intact seeds harvested at 26 and 36 days after heading (DAH) showed PHS, whereas dehusked seeds did not, indicating husk-imposed PHS. Overproduction of 2-OHM was observed in M2H-OE seeds compared to wild-type control. In addition, M2H-OE lines produced more hydrogen peroxide than the wild-type. 2-OHM-induced reactive oxygen species resulted in the induction of OsGA3ox2, a gibberellin (GA) biosynthesis gene, and repression of OsGA2ox3, a GA degradation gene, in caryopses at 2 DAH, but in the induction of the ABA degradation gene OsABA8ox3 in intact seeds at 26 DAH. In addition, M2H-OE seedlings were longer and showed increased levels of hydrogen peroxide and OsGA3ox2 expression versus the wild-type. This is the first report showing that 2-OHM can induce PHS via the husk pathway in rice seeds through the induction of GA biosynthetic and ABA degradation genes. Full article

(This article belongs to the Special Issue New Insights into Hormonal Control of Plant Growth and Development)

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18 pages, 1240 KB

Open AccessEditor’s ChoiceArticle

Short-Chain Fatty Acid Profiles in Amyotrophic Lateral Sclerosis: Longitudinal Effects of Disease and Mediterranean Diet Intervention

by Anca Moțățăianu, Valentin Ion, Mihai Dumitreasă, Ioana Ormenișan, Lenard Farczadi, Sebastian Andone, Rodica Bălașa and Medeea Maria Roman

Biomolecules 2025, 15(10), 1380; https://doi.org/10.3390/biom15101380 - 28 Sep 2025

Cited by 1 | Viewed by 1434

Abstract

Background: Amyotrophic lateral sclerosis (ALS) evolution is influenced by many dietary factors, biochemical and hormonal inter-relations and gut microbiota. This study focuses on dynamics by conducting a plasmatic quantitative analysis of six of the main short-chain fatty acids (SCFAs) for ALS patients [...] Read more.

Background: Amyotrophic lateral sclerosis (ALS) evolution is influenced by many dietary factors, biochemical and hormonal inter-relations and gut microbiota. This study focuses on dynamics by conducting a plasmatic quantitative analysis of six of the main short-chain fatty acids (SCFAs) for ALS patients and the shifts in circulating SCFA profiles during ALS progression as well as their potential responsiveness or change due to dietary modulation. Methods: A 12-month prospective study in parallel with control group determinations was conducted. The patients diagnosed with ALS were evaluated at the start of the study (T0) followed by a six-month observation time frame (T1) and after another six months of a Mediterranean diet intervention (T2). Plasma SCFAs were determined using liquid chromatography coupled to mass spectrometry to showcase the plasmatic profiles. Correlation between plasma levels of SCFAs and patients’ clinical characteristics next to correlations between plasma SCFA levels at T1 and T2 were performed. Results: A significant increase between control group and patients at T0 was observed for acetic, propionic, butyric and hydroxy-butyric acid. Hexanoic acid levels stagnated and 4-methyl-valeric acid concentrations decreased. Evolutions from T1 and T2 impacted acetate, propionate and 4-methyl-valerate. Conclusions: The study offers a better understanding regarding the differences in SCFA levels in ALS patients. The Mediterranean diet may impact the levels of acetic and propionic acid, indicating the modulation of SCFA production by gut microbiota. Full article

(This article belongs to the Section Bioinformatics and Systems Biology)

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14 pages, 2453 KB

Open AccessEditor’s ChoiceArticle

Patterny: A Troupe of Decipherment Helpers for Intrinsic Disorder, Low Complexity and Compositional Bias in Proteins

by Paul M. Harrison

Biomolecules 2025, 15(9), 1332; https://doi.org/10.3390/biom15091332 - 18 Sep 2025

Cited by 1 | Viewed by 2253

Abstract

Intrinsically disordered regions (IDRs) are sometimes considered parts of the ‘dark proteomes’, i.e., protein parts that have been largely under-appreciated, as are the overlapping phenomena of low-complexity or compositionally biased regions (LCRs/CBRs). Experimentalists and computationalists alike are still learning how to decrypt the [...] Read more.

Intrinsically disordered regions (IDRs) are sometimes considered parts of the ‘dark proteomes’, i.e., protein parts that have been largely under-appreciated, as are the overlapping phenomena of low-complexity or compositionally biased regions (LCRs/CBRs). Experimentalists and computationalists alike are still learning how to decrypt the functionally meaningful features of such regions. Here, I report the creation of the support troupe Patterny to aid such protein cryptanalysis. The current troupe members are named Blocky, Bandy, Moduley, Repeaty, and Runny. To discern important features, protein regions are compared to ideal assortments wherein everything is sampled proportionally and dispersed randomly. Blocky discerns the segregation of amino-acids by type, and scores them for it. Bandy is focused on picking out compositional bands and calculating their evenness. Moduley labels the boundaries of optimized compositional modules (‘CModules’) and other possible boundary sets for compositionally biased regions. Repeaty concisely summarizes repetitiveness using an information entropy of amino-acid interval diversity. Runny enumerates homopeptide content and assesses its significance. Both original whole sequences and CModules from Moduley, are fed into the other Patterny members. Patterny is applied to some illustrative sample data from yeast proteome and the DISPROT database. It is available at Github, and might aid those aiming to intensify light-shedding and hypothesis generation for protein regions with function encoded in a distributed manner, such as IDRs and LCRs/CBRs more generally. Full article

(This article belongs to the Special Issue Advances in Computational Biology of Intrinsically Disordered Proteins)

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17 pages, 1742 KB

Open AccessEditor’s ChoiceArticle

Pinocembrin Downregulates Vascular Smooth Muscle Cells Proliferation and Migration Leading to Attenuate Neointima Formation in Balloon-Injured Rats

by Hyeonhwa Kim, Jihye Jung, Young-Bob Yu, Dong-Hyun Choi, Leejin Lim and Heesang Song

Biomolecules 2025, 15(9), 1325; https://doi.org/10.3390/biom15091325 - 17 Sep 2025

Viewed by 1492

Abstract

The abnormal proliferation and migration of vascular smooth muscle cells (VSMCs) are a primary cause of cardiovascular diseases such as atherosclerosis and restenosis after angioplasty. Pinocembrin (5,7-dihydroxyflavanone, PCB), a natural flavonoid compound found abundantly in propolis, has been reported to have antibacterial, anti-inflammatory, [...] Read more.

The abnormal proliferation and migration of vascular smooth muscle cells (VSMCs) are a primary cause of cardiovascular diseases such as atherosclerosis and restenosis after angioplasty. Pinocembrin (5,7-dihydroxyflavanone, PCB), a natural flavonoid compound found abundantly in propolis, has been reported to have antibacterial, anti-inflammatory, antioxidant, and anticancer effects, and cardiac function improvement in ischemic heart disease. In this study, the protective effects of PCB against the migration and proliferation of VSMCs were investigated. MTT and BrdU assays were performed to estimate the cytotoxicity and cell proliferative activity of PCB, respectively. Rat aortic VSMC migrations and neointima formation were evaluated using wound healing, boyden chamber assays, and in balloon-injured (BI) rat, respectively. PCB suppressed the phosphorylated levels of p38 in PDGF-BB-induced VSMCs followed by reducing the expression of MMP2 and 9. PCB downregulated the expression levels of cell cycle regulatory proteins such as PCNA, CDK2, CDK4, and Cyclin D1. Furthermore, the phosphorylated levels of FAK at Y397 and Y925 sites and the expression levels of FAK-related proteins such as Integrin β1, Paxillin, Talin, and Vinculin were significantly reduced by PCB in PDGF-BB-induced VSMCs. The neointima formation was markedly decreased by PCB administration in the carotid artery of a balloon-injured rat. In conclusion, PCB inhibits the proliferation and migration of VSMCs by stimulation of PDGF-BB through the regulation of the p38 and FAK signaling pathway. Therefore, PCB may be a promising therapeutic candidate for preventing and treating cardiovascular diseases such as atherosclerosis and restenosis. Full article

(This article belongs to the Section Cellular Biochemistry)

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18 pages, 3750 KB

Open AccessEditor’s ChoiceArticle

LRRK2-Mediated Neuroinflammation Induces Neuronal Dysfunctions in a Parkinson’s and Alzheimer’s Disease Cellular Model

by Veronica Mutti, Giulia Carini, Moira Marizzoni, Alice Filippini, Federica Bono, Chiara Fiorentini, Samantha Saleri, Floriana De Cillis, Annamaria Cattaneo, Massimo Gennarelli, Paolo Martini and Isabella Russo

Biomolecules 2025, 15(9), 1322; https://doi.org/10.3390/biom15091322 - 16 Sep 2025

Cited by 4 | Viewed by 2281

Abstract

Chronic neuroinflammation plays a crucial role in the progression of neurodegenerative diseases (NDs), including Parkinson’s disease (PD) and Alzheimer’s disease (AD). Leucine-Rich Repeat Kinase 2 (LRRK2), a gene linked to familial and sporadic PD, has been positively associated with neuroinflammation in both in [...] Read more.

Chronic neuroinflammation plays a crucial role in the progression of neurodegenerative diseases (NDs), including Parkinson’s disease (PD) and Alzheimer’s disease (AD). Leucine-Rich Repeat Kinase 2 (LRRK2), a gene linked to familial and sporadic PD, has been positively associated with neuroinflammation in both in vitro and in vivo systems. These observations suggest that LRRK2 might actively contribute to neuronal damage and degeneration in NDs. Based on these premises, we explored the impact of LRRK2-mediated neuroinflammation on neurons in a PD- and AD-related context. We set up a cellular model composed of human induced pluripotent stem cell (hiPSC)-derived neurons (dopaminergic for PD and cholinergic for AD) exposed to inflamed glial medium [α-synuclein pre-formed fibrils (α-syn pffs) for PD and amyloid-β (Aβ)_1–42 fibrils for AD] for several days. To dissect the effect of neuroinflammation, and specifically, the role of LRRK2, on neuronal functions, we first performed transcriptome analysis, and then, we validated the results at functional levels. Interestingly, we found that LRRK2-dependent neuroinflammation contributes to neuronal dysfunctions and death in both ND contexts and that LRRK2 kinase inhibition prevents these detrimental effects. Overall, our results suggest that lowering neuroinflammation through LRRK2 pharmacological inhibition might limit the progression of NDs and thus be neuroprotective. Full article

(This article belongs to the Section Molecular Medicine)

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24 pages, 5096 KB

Open AccessEditor’s ChoiceArticle

Coming Clean and Avoiding Bubble Trouble–Using Detergents Wisely in the Purification of Membrane Proteins for Cryo-EM Studies

by Bowen Chen, Peter Harrison, Vasileios Kargas, Naomi Pollock, Robert C. Ford, Stephen M. Prince and Richard F. Collins

Biomolecules 2025, 15(9), 1315; https://doi.org/10.3390/biom15091315 - 12 Sep 2025

Viewed by 5479

Abstract

Detergent solubilisation remains the most commonly used but potentially problematic method to extract membrane proteins from lipid bilayers for Cryo-EM studies. Although recent advances have introduced excellent alternatives—such as amphipols, nanodiscs and SMALPs—the use of detergents is often necessary for intermediate steps. In [...] Read more.

Detergent solubilisation remains the most commonly used but potentially problematic method to extract membrane proteins from lipid bilayers for Cryo-EM studies. Although recent advances have introduced excellent alternatives—such as amphipols, nanodiscs and SMALPs—the use of detergents is often necessary for intermediate steps. In this paper, we share our experiences working with detergent-solubilised samples within the modern Cryo-EM structural pipeline from the perspective of an EM specialist. Our aim is to inform novice users about potential challenges they may encounter. Drawing on specific examples from a variety of biological membrane systems, including Magnesium channels, lipopolysaccharide biosynthesis, and the human major facilitator superfamily transporters, we describe how the intrinsic properties of detergent-extracted samples can affect protein purification, Cryo-EM grid preparation (including the formation of vitreous ice) and the reconstitution of proteins into micelles. We also discuss how these unique characteristics can impact different stages of structural analysis and lead to complications in single-particle averaging software analysis. For each case, we present our insights into the underlying causes and suggest possible mitigations or alternative approaches. Full article

(This article belongs to the Special Issue Structural Biology of Protein)

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17 pages, 3984 KB

Open AccessEditor’s ChoiceArticle

PARP1 and PARG Are the Draft Horses for Polycomb-Trithorax Chromatin Regulator Machinery

by Guillaume Bordet and Alexei V. Tulin

Biomolecules 2025, 15(9), 1314; https://doi.org/10.3390/biom15091314 - 12 Sep 2025

Viewed by 1392

Abstract

During tissue differentiation, gene expression patterns are committed to the epigenetic cellular memory machinery, including Polycomb and Trithorax groups (PcG and TrxG), which label chromatin with repressive or active histone marks. Histone marks recruit effector proteins that then execute local chromatin repression or [...] Read more.

During tissue differentiation, gene expression patterns are committed to the epigenetic cellular memory machinery, including Polycomb and Trithorax groups (PcG and TrxG), which label chromatin with repressive or active histone marks. Histone marks recruit effector proteins that then execute local chromatin repression or activation. The effectors of TrxG have remained largely unknown. Here we report that the Poly (ADP-ribose) Polymerase 1 (PARP1) and Poly (ADP-ribose) Glycohydrolase (PARG) function as critical effectors of TrxG and PcG, respectively. We found that PARP1 binds TrxG-generated histone marks with high affinity in vitro, completely colocalizing with them genome-wide, and controls the expression of loci modified by TrxG. Conversely, PARG preferentially associates with PcG-occupied loci. We propose a model in which TrxG complexes prime chromatin for PARP1 recruitment, leading to poly (ADP-ribose) generation to maintain an open chromatin state essential for transcription. Full article

(This article belongs to the Section Biological Factors)

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26 pages, 3890 KB

Open AccessEditor’s ChoiceArticle

Gene Duplication, Translocation, and Molecular Evolution of Dmrt1 and Related Sex-Determining Genes in Anurans

by Sagar S. Shinde, Paris Veltsos and Wen-Juan Ma

Biomolecules 2025, 15(9), 1306; https://doi.org/10.3390/biom15091306 - 11 Sep 2025

Viewed by 1984

Abstract

Sex determination, the developmental process that directs embryos toward male or female fates, is controlled by master sex-determining genes whose origins and evolutionary dynamics remain poorly understood outside of a few model systems. In contrast to the highly differentiated sex chromosomes of mammals, [...] Read more.

Sex determination, the developmental process that directs embryos toward male or female fates, is controlled by master sex-determining genes whose origins and evolutionary dynamics remain poorly understood outside of a few model systems. In contrast to the highly differentiated sex chromosomes of mammals, birds, and Drosophila, most anurans (frogs and toads) maintain homomorphic sex chromosomes that exhibit a rapid turnover, even among closely related species. Master sex-determining genes evolve via gene duplication or via allelic diversification, and sex chromosome turnover is driven by gene translocation or novel mutations in the existing genes involved in the sexual developmental pathway. To uncover the mechanisms underlying the emergence of master sex-determining genes and sex chromosome turnover, we analyzed 53 published anuran genomes and one caecilian genome (>200 Mya divergence) and available transcriptomes. We asked how often master sex-determining genes arise by gene duplication, whether and how often gene translocation associates with sex chromosome turnover, and if master sex-determining genes evolve under positive selection. We find that chromosome-level synteny is remarkably conserved, with only a few fusions or fissions and no evidence for translocation of four candidate master sex-determining genes (Dmrt1, Foxl2, Bod1l, and Sox3). Only Dmrt1 duplicated in 3 out of 50 species (excluding tetraploid Xenopus), and it showed strong testis-biased expression in all 8 species with available gonadal expression data. While Dmrt1 has evolved under purifying selection, Dmrt1 duplicates exhibit elevated nonsynonymous substitution rates and tendency towards positive selection. Lineage-specific amino acid changes were observed in the conserved DM domain of Dmrt1. These results demonstrate that, in anurans, master sex-determining genes rarely arise via gene duplication, and more likely evolve via allelic diversification. Sex chromosome turnover is not associated with gene translocation and is more likely driven by mutations on genes involved in sexual developmental pathways. All candidate sex-determining genes were under strong purifying selection, with the exception of duplications which are linked to positive selection. Our results suggest future research on anuran sex determination and sex chromosome evolution should focus on identifying allelic diversification and novel mutations on genes involved in sexual developmental pathways. Full article

(This article belongs to the Special Issue Molecular Insights into Sex and Evolution)

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14 pages, 791 KB

Open AccessEditor’s ChoiceArticle

Assessment of Cardiorenal Involvement in Systemic Sclerosis Patients

by Chiara Pellicano, Giancarlo D’Ippolito, Annalisa Villa, Ottavio Martellucci, Umberto Basile, Valeria Carnazzo, Valerio Basile, Edoardo Rosato, Mariapaola Marino and Antonietta Gigante

Biomolecules 2025, 15(9), 1297; https://doi.org/10.3390/biom15091297 - 9 Sep 2025

Viewed by 1397

Abstract

Systemic sclerosis (SSc) is an autoimmune disease associated with a high burden of morbidity and mortality due to organ complications. Pulmonary arterial hypertension (PAH) and cardiac involvement, characterized by chronic right ventricular (RV) pressure overload with consequent RV dysfunction and ultimately right heart [...] Read more.

Systemic sclerosis (SSc) is an autoimmune disease associated with a high burden of morbidity and mortality due to organ complications. Pulmonary arterial hypertension (PAH) and cardiac involvement, characterized by chronic right ventricular (RV) pressure overload with consequent RV dysfunction and ultimately right heart failure (HF), are among these. A common comorbidity in SSc is chronic kidney disease (CKD). CKD is often present at the time of PAH diagnosis or a decline in renal function may occur during the course of the disease. CKD is strongly and independently associated with mortality in patients with PAH and HF. The cardiovascular and renal systems are closely interconnected, and disruption of this balance may result in cardiorenal syndrome (CRS). Type 2 CRS refers to CKD as a consequence of chronic HF. In clinical practice, non-specific markers such as troponin, B-type natriuretic peptide (BNP), N-terminal pro-BNP (NT-proBNP), and serum creatinine aid in CRS diagnosis. More specific biomarkers, including cystatin C (CysC), neutrophil gelatinase-associated lipocalin (NGAL), galectin-3, and soluble urokinase plasminogen activator receptor (suPAR), have shown value for diagnosis and prognosis in CRS. This study aimed to evaluate comprehensively heart/kidney damage markers related to CRS in SSc patients compared with healthy controls (HC) and to examine their association with renal and cardiac ultrasound parameters. SSc patients showed significantly higher CRS markers than HC (p < 0.001). SSc patients with clinically diagnosed CRS had significantly elevated galectin-3, suPAR, sNGAL, and uNGAL levels (p < 0.05) than SSc patients without CRS. Positive correlations were found between renal resistive index (RRI) and NT-proBNP (r = 0.335, p < 0.05), and between RRI and suPAR (r = 0.331, p < 0.05). NT-proBNP, suPAR, galectin-3, sNGAL, and uNGAL emerge as promising biomarkers for the early detection of cardiac and renal involvement in SSc patients. Full article

(This article belongs to the Special Issue Cellular and Molecular Mechanisms in Cardiorenal Syndrome)

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18 pages, 2244 KB

Open AccessEditor’s ChoiceArticle

Metabolic Adaptations Determine the Evolutionary Trajectory of TOR Signaling in Diverse Eukaryotes

by Kyle Johnson, Dellaraam Pourkeramati, Ian Korf and Ted Powers

Biomolecules 2025, 15(9), 1295; https://doi.org/10.3390/biom15091295 - 8 Sep 2025

Cited by 1 | Viewed by 2810

Abstract

Eukaryotes use diverse nutrient acquisition strategies, including autotrophy, heterotrophy, mixotrophy, and symbiosis, which shape the evolution of cell regulatory networks. The Target of Rapamycin (TOR) kinase is a conserved growth regulator that in most species functions within two complexes, TORC1 and TORC2. TORC1 [...] Read more.

Eukaryotes use diverse nutrient acquisition strategies, including autotrophy, heterotrophy, mixotrophy, and symbiosis, which shape the evolution of cell regulatory networks. The Target of Rapamycin (TOR) kinase is a conserved growth regulator that in most species functions within two complexes, TORC1 and TORC2. TORC1 is broadly conserved and uniquely sensitive to rapamycin, whereas the evolutionary distribution of TORC2 is less well-defined. We built a sensitive hidden Markov model (HMM)-based pipeline to survey core TORC1 and TORC2 components across more than 800 sequenced eukaryotic genomes spanning multiple major supergroups. Both complexes are present in early-branching lineages, consistent with their presence in the last eukaryotic common ancestor, followed by multiple lineage-specific losses of TORC2 and, more rarely, TORC1. A striking pattern emerges in which TORC2 is uniformly absent from photosynthetic autotrophs derived from primary endosymbiosis and frequently lost in those derived from secondary or tertiary events. In contrast, TORC2 is consistently retained in mixotrophs, which obtain carbon from both photosynthesis and environmental uptake, and in free-living obligate heterotrophs. These findings suggest that TORC2 supports heterotrophic metabolism and is often dispensable under strict autotrophy. Our results provide a framework for the evolutionary divergence of TOR signaling and highlight metabolic and ecological pressures that shape TOR complex retention across eukaryotes. Full article

(This article belongs to the Section Bioinformatics and Systems Biology)

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31 pages, 2529 KB

Open AccessEditor’s ChoiceArticle

Synthesis and Bioevaluation of Chalcones as Broad-Spectrum Antiviral Compounds Against Single-Stranded RNA Viruses

by Lorael K. M. Kirton, Nasser N. Yousef, Griffith D. Parks and Otto Phanstiel IV

Biomolecules 2025, 15(9), 1285; https://doi.org/10.3390/biom15091285 - 5 Sep 2025

Cited by 5 | Viewed by 1451

Abstract

Chalcones are flavonoid compounds containing an α,β-unsaturated ketone core that are often found in plants and have diverse biological activities including antiviral activity. For example, chalcone 8o was previously shown to have antiviral activity against human cytomegalovirus (HCMV) and human immunodeficiency virus (HIV); [...] Read more.

Chalcones are flavonoid compounds containing an α,β-unsaturated ketone core that are often found in plants and have diverse biological activities including antiviral activity. For example, chalcone 8o was previously shown to have antiviral activity against human cytomegalovirus (HCMV) and human immunodeficiency virus (HIV); two viruses that use a nuclear phase to complete their growth cycle. Here, we synthesized ten new derivatives of 8o and tested them for antiviral activity against four RNA viruses that replicate exclusively in the cytoplasm, including prototype members of the paramyxovirus, flavivirus, bunyavirus, and coronavirus families. For example, chalcones 8o and 8p showed potent inhibition of PIV5 replication with minimal cytotoxicity in human fibroblast cultures. Time-of-addition studies showed that these chalcones inhibit an early stage of viral replication and prevent viral spread through cell cultures. Most importantly, our top performing chalcones showed potent in vitro antiviral activity against Zika virus, La Crosse Virus, and the coronavirus OC43. These studies offer mechanistic insight into chalcone-mediated inhibition of viral replication, demonstrate the influence of functional group changes of chalcone scaffolds on their efficacy as antivirals, and support the development of chalcones as broad-spectrum antiviral compounds. Full article

(This article belongs to the Section Natural and Bio-derived Molecules)

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11 pages, 201 KB

Open AccessEditor’s ChoiceArticle

Human Stem Cell-Based Embryo Models in Implantation Research: Regulation, Consistency and Potential

by Søren Holm

Biomolecules 2025, 15(9), 1287; https://doi.org/10.3390/biom15091287 - 5 Sep 2025

Viewed by 2810

Abstract

The use of human stem cell-based embryo models (hSCBEM) in implantation research is developing rapidly. This raises regulatory and ethical issues as these models become more complex and get closer to morphological and functional identity with human embryos. This paper provides an analysis [...] Read more.

The use of human stem cell-based embryo models (hSCBEM) in implantation research is developing rapidly. This raises regulatory and ethical issues as these models become more complex and get closer to morphological and functional identity with human embryos. This paper provides an analysis of two possible approaches to resolving the regulatory issues. The first approach is to try to achieve consistency with current regulation of embryo research, and the second approach is to elaborate the regulation of hSCBEMs based on their developmental potential. It is shown that both approaches are problematic. The consistency approach is problematic because the current regulation of embryo research is best understood as being the result of a historical, political compromise in most jurisdictions. And the approach based on assessment of developmental potential is problematic because of unavoidable epistemic uncertainty about the potential of a new hSCBEM, and because of problems in determining what constitutes a particular model, and what changes to a model makes it into a different model. Full article

(This article belongs to the Special Issue Embryo Implantation: New Molecular Insights in Endometrial Receptivity, Trophoblast Invasion and Signaling)

16 pages, 2527 KB

Open AccessEditor’s ChoiceArticle

Molecular and Computational Studies Reveal That Per- and Polyfluoroalkyl Substances Can Impair Protamine–DNA Interaction, Potentially Inducing DNA Damage

by Federica Musella, Maria Grazia Guarnieri, Simona Amore, Luigi Montano, Francesco Bertola, Salvatore Micali, Francesco Paolo Busardò, Carmen Di Giovanni, Gennaro Lettieri and Marina Piscopo

Biomolecules 2025, 15(9), 1279; https://doi.org/10.3390/biom15091279 - 4 Sep 2025

Cited by 9 | Viewed by 2070

Abstract

Interactions between protamines and DNA are essential for the correct structure of human sperm chromatin. Reproductive health can be adversely affected by environmental pollutants like per- and polyfluoroalkyl substances (PFAS). We previously reported that exposure to PFAS in the Veneto region causes alterations [...] Read more.

Interactions between protamines and DNA are essential for the correct structure of human sperm chromatin. Reproductive health can be adversely affected by environmental pollutants like per- and polyfluoroalkyl substances (PFAS). We previously reported that exposure to PFAS in the Veneto region causes alterations in sperm nuclear basic proteins (SNBP), along with reduced seminal antioxidant activity and increased lipoperoxides. This study analysed the protamine-to-histone ratio in SNBP and quantified the extent of DNA damage induced by SNBP in subjects in Veneto with serum perfluorooctanoic acid (PFOA) levels above the reference threshold. We found that all individuals with serum PFOA above the threshold exhibited grade three DNA damage, regardless of the protamine–histone ratio, which was generally altered but consistently shifted toward protamines. This indicate that exposure to PFAS can alter the protamine–histone ratio in these subjects. Moreover, SNBPs from these individuals showed reduced DNA-protective capacity under pro-oxidant conditions, suggesting a role in oxidative damage. To rationalize these effects, in this cross sectional study, we investigated the potential interactions between PFAS and human protamines by molecular docking analyses which showed that PFAS can form stable complexes with DNA through hydrophobic and polar interactions, especially with thymine pyrimidine rings. Further, docking analyses revealed that fluorine atoms in PFAS may interact with guanidinium groups in protamine P1 via electrostatic and van der Waals forces, competing with DNA for binding sites and potentially disrupting chromatin organisation. A ternary PFAS–DNA–protamine adduct may underpin the observed DNA damage. These results suggest that PFAS induce oxidative stress, which could affect male fertility. Full article

(This article belongs to the Special Issue Sperm Nuclear BASIC Proteins: From Chromatin Remodeling to Drug Development and Innovative Clinical Applications)

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17 pages, 1083 KB

Open AccessEditor’s ChoiceArticle

Zinc Therapy in Mild Cognitive Impairment: Cognitive Stabilization in Pharmacodynamically Responsive Patients in the ZINCAiD Trial

by Rosanna Squitti, Alberto Benussi, Silvia Fostinelli, Andrea Geviti, Jasmine Rivolta, Mariacarla Ventriglia, Alessandra Micera, Mauro Rongioletti, Roberta Ghidoni, Matteo Santilli, Alberto Granzotto, Alberto Albanese, Giuliano Binetti, Stefano L. Sensi and Barbara Borroni

Biomolecules 2025, 15(9), 1268; https://doi.org/10.3390/biom15091268 - 1 Sep 2025

Cited by 5 | Viewed by 2638

Abstract

Dysregulation contributes to Alzheimer’s disease (AD) pathophysiology. Zinc therapy promotes enterocyte copper sequestration, potentially reducing systemic copper. Individual biological responses may vary. Methods: ZINCAiD was a 24-week, randomized, double-blind, placebo-controlled phase II trial assessing zinc therapy in individuals with mild cognitive impairment (MCI) [...] Read more.

Dysregulation contributes to Alzheimer’s disease (AD) pathophysiology. Zinc therapy promotes enterocyte copper sequestration, potentially reducing systemic copper. Individual biological responses may vary. Methods: ZINCAiD was a 24-week, randomized, double-blind, placebo-controlled phase II trial assessing zinc therapy in individuals with mild cognitive impairment (MCI) due to AD (EudraCT No.: 2019-000604-15; registered on 26 March 2020). Participants were randomized 2:1 to receive elemental zinc (135 mg/day for 12 weeks, then 65 mg/day) or placebo. Ceruloplasmin was measured at predefined intervals for safety monitoring, blinded to the investigators. Post hoc, “Zinc Responders” were defined by ≥20% reduction in ceruloplasmin at week 12. The primary cognitive endpoint was the Cognitive Composite 2 scale (CC2); secondary endpoints included MMSE and CDR-Sob. Findings: Of the 48 participants randomized, 9 discontinued, primarily due to unrelated clinical deterioration; 39 had complete ceruloplasmin data. Two serious adverse events occurred in the Placebo group. Mild gastrointestinal symptoms occurred in eight participants, with only four leading to dropout. In the primary zinc vs. placebo analysis, no significant differences emerged in cognitive outcomes. A post hoc exploratory analysis stratified participants by pharmacodynamic response: 12 individuals with MCI due to AD (31%) met the criteria for “Zinc Responder,” defined by ≥20% reduction in serum ceruloplasmin at week 12. Only Zinc Responders maintained cognitive stability over 24 weeks, whereas the combined group of Zinc Non-Responders and placebo-treated participants showed a significant decline. For the composite cognitive score (CC2), the interaction between visit and response group was significant (p = 0.030), with deterioration observed only in the Non-Responder + Placebo group (Δ = –2.72, p < 0.0001 vs. –0.71, p = 0.35 in Responders). Similar patterns were observed for CDR-Sob (interaction p = 0.017) and MMSE (trend p = 0.09). Interpretation: Zinc therapy stabilized cognition in a pharmacodynamically defined MCI subgroup. These exploratory findings suggest serum ceruloplasmin as a feasible biomarker of target engagement. Larger trials are needed for confirmation. Full article

(This article belongs to the Section Chemical Biology)

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21 pages, 2229 KB

Open AccessEditor’s ChoiceArticle

A Multi-Ingredient Supplement Improves Body Re-Composition, Ovarian Aging Markers, and Reproductive Success in Young and Middle-Aged Female Mice

by Alessandra Chiarot, Mahek Minhas, Nicoletta M. de Maat, Jenny Doan, Mats I. Nilsson, Bart P. Hettinga, Mehrnoosh Faghih, Michael S. Neal, Joshua P. Nederveen and Mark A. Tarnopolsky

Biomolecules 2025, 15(9), 1258; https://doi.org/10.3390/biom15091258 - 30 Aug 2025

Cited by 1 | Viewed by 3201

Abstract

Ovarian aging is characterized by mitochondrial dysfunction, oxidative stress, and inflammation. The development of adjunctive treatments that mitigate age-related subfertility is warranted. We examined the benefits of nutraceutical supplementation (FE; Fertility Enhancer) with mitochondrial antioxidants, anti-inflammatory agents, metabolic activators, vitamins and minerals, and [...] Read more.

Ovarian aging is characterized by mitochondrial dysfunction, oxidative stress, and inflammation. The development of adjunctive treatments that mitigate age-related subfertility is warranted. We examined the benefits of nutraceutical supplementation (FE; Fertility Enhancer) with mitochondrial antioxidants, anti-inflammatory agents, metabolic activators, vitamins and minerals, and amino acids on ovarian aging, metabolic activity, and reproductive success in young (Y; 6-month-old) and middle-aged (O; 11-month-old) female C57BL/6J mice. The mice were fed calorie- and macronutrient-matched diets w/wo the FE supplement for three months and harem mated twice. Daily FE supplementation promoted significant body re-composition, including loss of white adipose tissue (gWAT: −36% vs. CON, p < 0.001), gain of skeletal muscle (SkM: +67% vs. CON, p < 0.001), and improved SkM/gWAT ratio (+185% vs. CON, p < 0.001). Metabolic testing showed enhanced fat oxidation (+38%, p < 0.01) and energy expenditure (+7%, p = 0.051) in FE mice. Breeding and immunoblotting data demonstrated improved reproductive success (Y-CON: 44%, Y-FE: 89%, O-CON: 0%, O-FE: 18%) and a modest attenuation of ovarian aging markers in both FE groups. We surmise that a multi-ingredient supplement, such as the Fertility Enhancer, may improve body re-composition, metabolic activity, and markers of ovarian aging, thus enhancing reproductive health and fertility in females. Full article

(This article belongs to the Special Issue Molecular Aspects of Female Infertility)

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15 pages, 919 KB

Open AccessEditor’s ChoiceArticle

Modulating Effect of Carbohydrate Antigen 125 on the Prognostic Value of High-Sensitivity C-Reactive Protein in Heart Failure

by Enrique Santas, Arancha Martí-Martínez, Elena Revuelta-López, Sandra Villar, Rafael de la Espriella, Patricia Palau, Pau Llàcer, Gema Miñana, Enrique Rodriguez-Borja, Arturo Carratalá, Arantxa Gonzalez, Antoni Bayés-Genís, Juan Sanchis and Julio Núñez

Biomolecules 2025, 15(9), 1260; https://doi.org/10.3390/biom15091260 - 30 Aug 2025

Cited by 1 | Viewed by 1462

Abstract

Inflammation and congestion are key pathophysiological processes in heart failure (HF). Our aim was to evaluate the potential modulatory effect of carbohydrate antigen 125 (CA125) on inflammation, assessed by high-sensitivity C-reactive protein (hs-CRP). We analyzed a cohort of 4043 consecutive patients in whom [...] Read more.

Inflammation and congestion are key pathophysiological processes in heart failure (HF). Our aim was to evaluate the potential modulatory effect of carbohydrate antigen 125 (CA125) on inflammation, assessed by high-sensitivity C-reactive protein (hs-CRP). We analyzed a cohort of 4043 consecutive patients in whom hs-CRP and CA125 levels were measured during a hospitalization for acute HF. Multivariate Cox regression models were applied to assess the association between the biomarkers and all-cause mortality and death/HF rehospitalization at 6 months. In multivariable analysis, a significant interaction between hs-CRP and CA125 was observed for both outcomes (p-value for interaction = 0.036 and <0.001, respectively). hs-CRP was significantly associated with an increased risk of death (HR = 1.27; 95% CI 1.16–1.41; p < 0.001) and death/HF rehospitalization (HR = 1.18; 95% CI 1.09–1.28; p < 0.001) if CA125 > 35 U/mL. In contrast, hs-CRP was not predictive of events when CA125 ≤ 35 U/mL. In conclusion, in patients with acute HF, the association between hs-CRP and clinical outcomes was modulated by CA125 levels. hs-CRP was associated with a higher risk of events only in patients with elevated CA125. These findings support a potential modulatory and amplifying role for CA125 in the inflammatory response in HF. Full article

(This article belongs to the Special Issue Biomolecules in Myocarditis and Inflammatory Heart Disease)

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27 pages, 9028 KB

Open AccessEditor’s ChoiceArticle

Neuromuscular Defects in a Drosophila Model of the Congenital Disorder of Glycosylation SLC35A2-CDG

by Kazuyoshi Itoh, Masaki Kurogochi, Tadashi Kaname, Jun-ichi Furukawa and Shoko Nishihara

Biomolecules 2025, 15(9), 1256; https://doi.org/10.3390/biom15091256 - 29 Aug 2025

Viewed by 2194

Abstract

SLC35A2-CDG is a congenital disorder of glycosylation caused by mutations in the SLC35A2 gene encoding a Golgi-localized UDP-galactose transporter. This transporter plays an essential role in glycan synthesis by transporting UDP-galactose from the cytoplasm into the Golgi lumen. Its dysfunction leads to impaired [...] Read more.

SLC35A2-CDG is a congenital disorder of glycosylation caused by mutations in the SLC35A2 gene encoding a Golgi-localized UDP-galactose transporter. This transporter plays an essential role in glycan synthesis by transporting UDP-galactose from the cytoplasm into the Golgi lumen. Its dysfunction leads to impaired galactose-containing glycans and various neurological symptoms, although the underlying mechanisms remain largely unknown. We identified a novel SLC35A2-CDG patient carrying a pathogenic variant (c.617_620del, p.(Gln206ArgfsTer45)) who exhibited neurological abnormalities including bilateral ventriculomegaly. To investigate the disease mechanism, we established the first Drosophila model of SLC35A2-CDG. Knockout of Ugalt, the fly ortholog of SLC35A2, resulted in embryonic lethality, indicating its essential role. Knockdown of Ugalt reduced mucin-type O-glycans on muscles and neuromuscular junctions (NMJs), without affecting N-glycans. Ugalt knockdown larvae exhibited mislocalized NMJ boutons accompanied by a deficiency in basement membrane components on muscles. This phenotype resembles that of mutants of dC1GalT1 and dGlcAT-P, both involved in mucin-type O-glycosylation. Genetic interaction between Ugalt and dC1GalT1 was confirmed through double knockdown and double heterozygous analyses. Given that Drosophila NMJs are widely used as a model for mammalian central synapses, our findings suggest that Ugalt regulates NMJ architecture via mucin-type O-glycosylation and provide insights into the molecular basis of neurological abnormalities in SLC35A2-CDG. Full article

(This article belongs to the Special Issue Drosophila as a Model System to Study Metabolism)

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17 pages, 3302 KB

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Consequences of Adhesion Molecule Close Homolog of L1 Deficiency for Neurons and Glial Cells in the Mouse Spinal Cord After Injury

by Igor Jakovcevski, Ayse Acar, Benjamin Schwindenhammer, Mohammad I. K. Hamad, Gebhard Reiss, Eckart Förster and Melitta Schachner

Biomolecules 2025, 15(9), 1247; https://doi.org/10.3390/biom15091247 - 28 Aug 2025

Viewed by 1584

Abstract

After spinal cord injury, pathological changes predominantly proceed caudal to the site of injury. To what extent these changes contribute to abnormalities during regeneration is poorly understood. Here, we addressed this question with a low-thoracic compression injury mouse model. The total numbers of [...] Read more.

After spinal cord injury, pathological changes predominantly proceed caudal to the site of injury. To what extent these changes contribute to abnormalities during regeneration is poorly understood. Here, we addressed this question with a low-thoracic compression injury mouse model. The total numbers of immunohistochemically stained neuronal and glial cell types in the lumbar spinal cord were stereologically determined 6 weeks after injury. We also investigated injured mice deficient in close homolog of L1 (CHL1), which had been reported to recover better after injury than their wild-type littermates. We here report that there were no differences between genotypes in uninjured animals. In both injured CHL1-deficient and wild-type littermates, gray and white matter volumes were decreased as compared with uninjured mice. Numbers of motoneurons and parvalbumin-expressing interneurons were also reduced in both genotypes. Numbers of interneurons in injured mutant mice were lower than in wild-type littermates. Whereas injury did not affect numbers of astrocytes and oligodendrocytes in the gray matter, numbers of microglia/macrophages were increased. In the mutant white matter, numbers of oligodendrocytes were reduced, with no changes in numbers of astrocytes and microglia. A loss of motoneurons and interneurons was observed in both genotypes, but loss of interneurons was more prominent in the absence of CHL1. We propose that, after injury, CHL1 deficiency causes deficits in structural outcome not seen after injury of wild-type mice. Full article

(This article belongs to the Collection Feature Papers in Section 'Molecular Medicine')

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23 pages, 4058 KB

Open AccessEditor’s ChoiceArticle

Inhibition of Astrocyte Reactivity by Mdivi-1 After Status Epilepticus in Rats Exacerbates Microglia-Mediated Neuroinflammation and Impairs Limbic–Cortical Glucose Metabolism

by Francisca Gómez-Oliver, Rubén Fernández de la Rosa, Mirjam Brackhan, Pablo Bascuñana, Miguel Ángel Pozo and Luis García-García

Biomolecules 2025, 15(9), 1242; https://doi.org/10.3390/biom15091242 - 27 Aug 2025

Cited by 2 | Viewed by 1710

Abstract

The lithium–pilocarpine rat model of status epilepticus (SE) is a well-established paradigm for studying epileptogenesis. Astrocyte reactivity has been implicated in modulating seizure susceptibility and neuroinflammation, yet its functional role in early epileptogenesis remains unclear. Herein, we evaluated the effects of Mdivi-1, a [...] Read more.

The lithium–pilocarpine rat model of status epilepticus (SE) is a well-established paradigm for studying epileptogenesis. Astrocyte reactivity has been implicated in modulating seizure susceptibility and neuroinflammation, yet its functional role in early epileptogenesis remains unclear. Herein, we evaluated the effects of Mdivi-1, a pharmacological inhibitor of mitochondrial fission protein Drp1, for its ability to modulate astrocytic mitochondrial dynamics and for its reported preventive neuroprotective properties. Mdivi-1 was administered shortly after SE onset, and we assessed brain glucose metabolism using [¹⁸F]FDG PET, alongside histological markers of neurodegeneration, astrocyte reactivity, and microglial activation, at 3 days post-SE. As expected, SE induced widespread brain hypometabolism measured by a VOI analysis, hippocampal neurodegeneration, and glial activation. Post-SE Mdivi-1 administration reduced hippocampal astrogliosis but neither conferred neuroprotection nor rescued glucose metabolism. On the contrary, Mdivi-1 exacerbated limbic–cortical hypometabolism when evaluated by SPM and normalized to whole brain tracer uptake and microglia-mediated neuroinflammation. These findings challenge the assumption that early astrocyte inhibition confers neuroprotection. Furthermore, early suppression of astrocyte reactivity after the damage has occurred may shift the neuroinflammatory response toward maladaptive microglial activation. Thus, while Mdivi-1 holds promise as a preventive neuroprotective agent, its use post-SE may have unintended adverse effects on the brain’s response to SE. Full article

(This article belongs to the Special Issue Biomolecular Approaches and Drugs for Neurodegeneration—2nd Edition)

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17 pages, 2356 KB

Open AccessEditor’s ChoiceArticle

Obesity Risk Factors Promote Metabolic Reprogramming and Viral Infection in Airways with Type 1 High Inflammation

by Paige Hartsoe, Niccolette Schaunaman, Taylor Nichols, Diana Cervantes, Stephanie Dawrs, Fernando Holguin and Hong Wei Chu

Biomolecules 2025, 15(9), 1229; https://doi.org/10.3390/biom15091229 - 26 Aug 2025

Viewed by 1571

Abstract

Obesity is a significant health issue, as it is related to human diseases such as asthma and respiratory viral infections. Asthma patients with obesity have more severe diseases, which can be presented with type 1 (e.g., IFN-γ) high inflammation. The interactions of obesity [...] Read more.

Obesity is a significant health issue, as it is related to human diseases such as asthma and respiratory viral infections. Asthma patients with obesity have more severe diseases, which can be presented with type 1 (e.g., IFN-γ) high inflammation. The interactions of obesity or saturated fatty acids (e.g., palmitic acid, PA) with IFN-γ in airway viral infections have not been clear. In this study, we determined the role of obesity risk factors high-fat diet (HFD) and PA in rhinovirus infection in the context of IFN-γ stimulation in mice and cultured human tracheobronchial epithelial cells. We further examined the therapeutic effect of a glycolytic inhibitor on metabolic reprogramming and viral infection in our experimental models. In mice, HFD in combination with IFN-γ significantly increased lung rhinovirus levels as well as neutrophilic inflammation. Similarly, PA and IFN-γ combination increased viral infection in mice, but HFD or PA alone had a minimal effect on viral infection. Mouse model data were confirmed in cultured primary healthy human airway epithelial cells where PA and IFN-γ together increased viral load. Mechanistically, HFD or PA in combination with IFN-γ up-regulated the glycolytic pathway and generated metabolites favoring viral replication. Inhibition of glycolysis by 2-DG effectively reduced viral infection in human airway epithelial cells. Our data suggest that hosts with obesity along with type 1 high inflammation may be at an increased risk of respiratory viral infections. Intervention of the glycolytic pathway or its metabolites may reduce the severity of viral infection. Full article

(This article belongs to the Section Molecular Medicine)

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14 pages, 1711 KB

Open AccessEditor’s ChoiceArticle

A De Novo DNM1L Mutation in Twins with Variable Symptoms, Including Paraparesis and Optic Neuropathy

by Alessia Nasca, Alessia Catania, Andrea Legati, Rossella Izzo, Carola D’onofrio, Teresa Ciavattini, Eleonora Lamantea, Costanza Lamperti and Daniele Ghezzi

Biomolecules 2025, 15(9), 1230; https://doi.org/10.3390/biom15091230 - 26 Aug 2025

Viewed by 1546

Abstract

Mitochondrial network dynamics, encompassing processes like fission, fusion, and mitophagy, are crucial for mitochondrial function and overall cellular health. Dysregulation of these processes has been linked to various human diseases. Particularly, pathogenic variants in the gene DNM1L can lead to a broad range [...] Read more.

Mitochondrial network dynamics, encompassing processes like fission, fusion, and mitophagy, are crucial for mitochondrial function and overall cellular health. Dysregulation of these processes has been linked to various human diseases. Particularly, pathogenic variants in the gene DNM1L can lead to a broad range of clinical phenotypes, ranging from isolated optic atrophy to severe neurological conditions. DNM1L encodes DRP1 (dynamin-1-like protein), which is a key player in mitochondrial and peroxisomal fission. This study describes two twin sisters with a de novo heterozygous variant in DNM1L, due to possible paternal germline mosaicism identified through clinical exome sequencing. The two twins showed a variable clinical presentation, including paraparesis and optic neuropathy. Functional studies of patient-derived fibroblasts revealed altered mitochondrial and peroxisomal morphology, along with dysregulated DNM1L transcript levels, indicating the deleterious effect of the variant. These findings allowed us to reclassify the identified variant from a variant of uncertain significance to a likely pathogenic variant. Our report provides insight into the phenotypic spectrum of DNM1L-related disorders and highlights the need to combine genetic and functional analyses to accurately diagnose rare mitochondrial diseases. Full article

(This article belongs to the Special Issue Mitochondria and Central Nervous System Disorders: 3rd Edition)

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19 pages, 3290 KB

Open AccessEditor’s ChoiceArticle

From Corncob By-Product to Functional Lignins: Comparative Analysis of Alkaline and Organosolv Extraction Followed by Laccase Treatment

by Elise Martin, Swarnima Agnihotri, Fabrice Audonnet, Eric Record, Pascal Dubessay, Mohammad J. Taherzadeh and Philippe Michaud

Biomolecules 2025, 15(9), 1226; https://doi.org/10.3390/biom15091226 - 26 Aug 2025

Cited by 1 | Viewed by 2310

Abstract

Corncobs, produced globally at over 200 million tons annually with 11–18% lignin content, represent an abundant and underexploited lignocellulosic resource for sustainable lignin valorization. In this study, two distinct extraction methodologies, alkaline treatment using sodium hydroxide and an organosolv process with a 50:50 [...] Read more.

Corncobs, produced globally at over 200 million tons annually with 11–18% lignin content, represent an abundant and underexploited lignocellulosic resource for sustainable lignin valorization. In this study, two distinct extraction methodologies, alkaline treatment using sodium hydroxide and an organosolv process with a 50:50 ethanol/water mixture, were systematically compared for their efficiency in isolating lignin from corncobs. Both protocols achieved high yields, up to 82% for alkaline and 84% for organosolv extraction under optimized conditions. The resulting lignins displayed notable differences in chemical structure and physical properties, as revealed by spectroscopic and thermal analyses, highlighting their divergent potential for downstream applications. To evaluate the suitability of these lignins to biocatalytic upgrading, post-extraction enzymatic treatment was performed using Pycnoporus cinnabarinus laccase (EC 1.10.3.2). Significant structural modifications were observed in alkaline-extracted lignin, as determined by FTIR spectroscopy, while organosolv lignin remained largely unaltered, a difference attributed to its lower aqueous solubility at the enzyme’s optimal pH. These results demonstrate the critical impact of extraction conditions on lignin reactivity and suitability for enzymatic tailoring. This work underscores the potential for holistic corncob valorization within integrated biorefinery frameworks. Selective extraction and targeted enzymatic modification not only facilitate efficient by-product utilization but also expand the prospects for producing versatile bio-based materials, thereby advancing the transition toward a sustainable, circular bioeconomy. Full article

(This article belongs to the Special Issue Recent Advances in Laccases and Laccase-Based Bioproducts: 2nd Edition)

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21 pages, 4387 KB

Open AccessEditor’s ChoiceArticle

Comparative Analysis of Aggregation of β- and γ-Synucleins in Vertebrates

by Maria Carmela Bonaccorsi di Patti, Martina Meoni and Mattia Toni

Biomolecules 2025, 15(9), 1231; https://doi.org/10.3390/biom15091231 - 26 Aug 2025

Cited by 1 | Viewed by 1430

Abstract

This study explores the structural transitions and aggregation behaviour of recombinant β- and γ-synucleins from five vertebrate species—Cyprinus carpio, Danio rerio, Xenopus laevis, Anolis carolinensis, and Homo sapiens—using thioflavin T fluorescence and circular dichroism spectroscopy, with and without [...] Read more.

This study explores the structural transitions and aggregation behaviour of recombinant β- and γ-synucleins from five vertebrate species—Cyprinus carpio, Danio rerio, Xenopus laevis, Anolis carolinensis, and Homo sapiens—using thioflavin T fluorescence and circular dichroism spectroscopy, with and without copper ions. Although synucleins are well-conserved proteins among vertebrates, species-specific differences in amino acid composition and predicted secondary structures were observed, particularly within β-strand-forming regions. During a six-day incubation, human β-synuclein exhibited a time-dependent increase in β-sheet-rich structures, while non-mammalian β-synucleins showed limited variation. In contrast, γ-synucleins from all species displayed greater aggregation propensity, with variations in kinetics and magnitude. The presence of copper reduced the rate of aggregation in human β-synuclein, likely due to high-affinity metal-binding sites, whereas γ-synuclein aggregation was only mildly affected. Notably, copper enhanced late-phase aggregation in A. carolinensis β-synuclein. These findings suggest that sequence divergence among synuclein isoforms may underlie species-specific aggregation mechanisms and metal sensitivity. The differential aggregation behaviour observed across taxa may reflect evolutionary adaptations in synuclein function and folding propensity, with implications for understanding the molecular basis of synucleinopathies and their potential modulation by metal ions. Full article

(This article belongs to the Section Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates)

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19 pages, 6650 KB

Open AccessEditor’s ChoiceArticle

Protective Effect of Low 2-O, 3-O Desulfated Heparin (ODSH) Against LPS-Induced Acute Lung Injury in Mice

by Joyce Gonzales, Rahul S. Patil, Thomas P. Kennedy, Nagavedi S. Umapathy, Rudolf Lucas and Alexander D. Verin

Biomolecules 2025, 15(9), 1232; https://doi.org/10.3390/biom15091232 - 26 Aug 2025

Viewed by 1941

Abstract

Background: Acute lung injury (ALI) and its severe form, acute respiratory distress syndrome (ARDS), are critical conditions lacking effective pharmacologic therapies. Lipopolysaccharide (LPS), a bacterial endotoxin, is a well-established trigger of ALI. Emerging evidence suggests that heparin derivatives may attenuate lung injury, but [...] Read more.

Background: Acute lung injury (ALI) and its severe form, acute respiratory distress syndrome (ARDS), are critical conditions lacking effective pharmacologic therapies. Lipopolysaccharide (LPS), a bacterial endotoxin, is a well-established trigger of ALI. Emerging evidence suggests that heparin derivatives may attenuate lung injury, but their mechanisms remain unclear. Methods: This study evaluated the protective effects of 2-O, 3-O desulfated heparin (ODSH) in a murine model of LPS-induced ALI. Mice received LPS intratracheally with or without ODSH pre-treatment. Lung injury was assessed by bronchoalveolar lavage fluid (BALF) analysis, Evans blue dye albumin EBDA) extravasation, and histopathology. Results: ODSH treatment significantly reduced BALF protein concentration, inflammatory cell infiltration, and EBDA leakage. ODSH preserved endothelial barrier function in vitro, as evidenced by transendothelial electrical resistance (TER) measurements in human lung microvascular endothelial cell (HLMVEC) monolayers. Histological assessment (H&E staining) and myeloperoxidase (MPO) staining demonstrated reduced lung injury and neutrophil infiltration in the ODSH group. ODSH also downregulated pro-inflammatory mediators (NF-κB, IL-6, p38 MAPK) and upregulated the anti-inflammatory cytokine IL-10. Conclusions: ODSH mitigates LPS-induced ALI by reducing vascular permeability, neutrophilic inflammation, and pro-inflammatory signaling while enhancing IL-10 expression. These findings suggest ODSH may offer a novel therapeutic approach for treating ALI. Full article

(This article belongs to the Special Issue Lung Disease: From Molecular Mechanism to Therapeutic Opportunities)

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14 pages, 668 KB

Open AccessEditor’s ChoiceArticle

Serum Growth Differentiation Factor 15 (GDF15) Levels Reflect Ischemic Etiology in Heart Failure Patients with Iron Deficiency: A Cross-Sectional Study

by Marta Tajes, Maria del Mar Ras-Jiménez, Josefa Girona, Raúl Ramos-Polo, Montse Guardiola, José Manuel García-Pinilla, Josep Ribalta, Marta Cobo-Marcos, Lluís Masana, Javier de Juan-Bagudá, Cândida Fonseca, Cristina Enjuanes, Manuel Vázquez-Carrera, Josep Comin-Colet and Ricardo Rodríguez-Calvo

Biomolecules 2025, 15(9), 1234; https://doi.org/10.3390/biom15091234 - 26 Aug 2025

Cited by 1 | Viewed by 1691

Abstract

Heart failure (HF), particularly of an ischemic etiology, is steadily increasing worldwide. Non-anemic iron deficiency (ID) is highly prevalent among HF patients, and it has been related to worse outcomes. Growth differentiation factor 15 (GDF15) has been related to atherosclerotic cardiovascular (CV) disease, [...] Read more.

Heart failure (HF), particularly of an ischemic etiology, is steadily increasing worldwide. Non-anemic iron deficiency (ID) is highly prevalent among HF patients, and it has been related to worse outcomes. Growth differentiation factor 15 (GDF15) has been related to atherosclerotic cardiovascular (CV) disease, HF and iron pathophysiology. Nevertheless, the specific potential role of GDF15 in HF patients with ID has not been fully explored. In this cross-sectional study we determined serum GDF15 levels in 60 HF patients with ID from the IRON-PATH II study. The discriminative capacity of GDF15 in logistic regression models for classifying these patients according to ischemic etiology was defined as the primary endpoint. Additionally, relationships between GDF15 levels and impaired right ventricle function, impaired functional capacity and HF were included as secondary endpoints. GDF15 was inversely related to tricuspid annular plane systolic excursion (TAPSE) and the six-minute walking test (6MWT), and positively related to hallmarks of HF [i.e., N-terminal prohormone of brain natriuretic peptide (NT-proBNP)] and other molecules influenced by HF progression [i.e., creatinine and ferritin]. Moreover, GDF15 was inversely related to hemoglobin, suggesting a potential link to iron homeostasis. Furthermore, GDF15 showed good classification capacity and improved the accuracy of a logistic regression model for ischemic HF classification in patients with ID. Overall, the findings of this study propose serum GDF15 levels as a potential tool for the classification of HF patients with ID according to the ischemic etiology. Full article

(This article belongs to the Special Issue Chronic Heart Failure: From Molecular Mechanisms to Therapies Strategies)

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14 pages, 2001 KB

Open AccessEditor’s ChoiceArticle

Icatibant Acts as a Balanced Ligand of MRGPRX2 in Human Skin Mast Cells

by Zhuoran Li, Jean Schneikert, Gürkan Bal, Torsten Zuberbier and Magda Babina

Biomolecules 2025, 15(9), 1224; https://doi.org/10.3390/biom15091224 - 25 Aug 2025

Cited by 2 | Viewed by 2517

Abstract

MRGPRX2 (Mas-related G protein-coupled receptor member X2) is implicated in mast cell (MC)-driven disorders due to its ability to bind diverse ligands, which may be G-protein-biased or balanced, with the latter activating both G-proteins and the β-arrestin pathway. Icatibant, a peptide drug, produces [...] Read more.

MRGPRX2 (Mas-related G protein-coupled receptor member X2) is implicated in mast cell (MC)-driven disorders due to its ability to bind diverse ligands, which may be G-protein-biased or balanced, with the latter activating both G-proteins and the β-arrestin pathway. Icatibant, a peptide drug, produces injection-site reactions in most patients and is used experimentally to probe MRGPRX2 function in skin tests. While reported to be G-protein-biased, it is unknown how skin MCs respond to icatibant, although these are the primary target cells during therapy. We therefore compared responses to icatibant with those induced by the balanced agonist substance P (SP) in skin MCs. Degranulation and desensitization were assessed via β-hexosaminidase release, receptor internalization by flow cytometry, and downstream signaling by immunoblotting. Skin MCs degranulated in response to SP and icatibant, relying on Gi proteins and calcium channels; Gq and PI3K (Phosphoinositide 3-kinase) contributed more strongly to exocytosis following icatibant, while JNK (c-Jun n-terminal kinase) was more relevant for SP. Both agonists activated ERK, PI3K/AKT, and (weakly) p38. Surprisingly, and in contrast to the LAD2 (Laboratory of Allergic Diseases 2 mast cell line) MC line, icatibant was at least as potent as SP in eliciting MRGPRX2 internalization and (cross-)desensitization in skin MCs. These findings suggest that icatibant functions differently in primary versus transformed MCs, acting as a fully balanced ligand in the former by triggering not only degranulation but also receptor internalization and desensitization. Therefore, not only the ligand but also the MRGPRX2-expressing cell plays a decisive role in whether a ligand is balanced or biased. These findings are relevant to our understanding of icatibant’s clinical effects on edema and itch. Full article

(This article belongs to the Special Issue Molecular Basis of Mast Cells Activation and Medical Implications)

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17 pages, 4158 KB

Open AccessEditor’s ChoiceArticle

Exploring the Role of Ferroptosis in the Pathophysiology and Circadian Regulation of Restless Legs Syndrome

by Maria Paola Mogavero, Giovanna Marchese, Giovanna Maria Ventola, Giuseppe Lanza, Oliviero Bruni, Luigi Ferini-Strambi and Raffaele Ferri

Biomolecules 2025, 15(8), 1184; https://doi.org/10.3390/biom15081184 - 18 Aug 2025

Cited by 8 | Viewed by 1991

Abstract

The study objectives were to investigate the role of ferroptosis, the mechanism linking iron accumulation, oxidative stress, and dopaminergic dysfunction, in restless legs syndrome (RLS), and to explore its connection with circadian regulation, a key feature of RLS and a known modulator of [...] Read more.

The study objectives were to investigate the role of ferroptosis, the mechanism linking iron accumulation, oxidative stress, and dopaminergic dysfunction, in restless legs syndrome (RLS), and to explore its connection with circadian regulation, a key feature of RLS and a known modulator of ferroptosis. We conducted pathway and gene expression analyses in 17 RLS patients and 39 controls, focusing on pathways related to ferroptosis, oxidative stress, iron metabolism, dopaminergic signaling, circadian rhythms, and immune responses. Enrichment analysis, differential gene expression, and cross-pathway gene overlaps were assessed. Ferroptosis and efferocytosis pathways were significantly upregulated in RLS, while oxidative phosphorylation, phosphatidylinositol signaling, PI3K-Akt, FoxO, and adipocytokine pathways were downregulated. The circadian rhythm pathway was markedly suppressed, with 12 circadian genes downregulated, suggesting that circadian disruption may drive ferroptosis activation. Decreased expression of protective pathways, including antioxidant responses and autophagy, was associated with increased iron accumulation, oxidative stress, and inflammation. Dopaminergic synapse genes were upregulated, possibly as a compensatory response to neuronal damage. Several genes overlapped across ferroptosis, circadian, and dopaminergic pathways, indicating a shared pathogenic mechanism. Our findings support a model in which circadian disruption promotes ferroptosis in RLS, contributing to iron overload, oxidative damage, and dopaminergic dysfunction. This pathogenic cascade may also enhance immune activation and inflammation. Circadian regulation and ferroptosis emerge as promising therapeutic targets in RLS. Further studies in larger cohorts are warranted to validate these mechanistic insights. Full article

(This article belongs to the Special Issue Biomolecules and Materials Based Approaches in Biomedical Field: 2nd Edition)

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31 pages, 4259 KB

Open AccessEditor’s ChoiceArticle

Neuronal Count, Brain Injury, and Sustained Cognitive Function in 5×FAD Alzheimer’s Disease Mice Fed DHA-Enriched Diets

by Cristina de Mello-Sampayo, Mafalda Soares Pádua, Maria Rosário Silva, Maria Lourenço, Rui M. A. Pinto, Sandra Carvalho, Jorge Correia, Cátia F. Martins, Romina Gomes, Ana Gomes-Bispo, Cláudia Afonso, Carlos Cardoso, Narcisa Bandarra and Paula A. Lopes

Biomolecules 2025, 15(8), 1164; https://doi.org/10.3390/biom15081164 - 14 Aug 2025

Cited by 3 | Viewed by 2988

Abstract

Alzheimer’s disease (AD) is the most common form of dementia, affecting over 50 million people globally. Since 1906, efforts to understand this neurodegenerative disease and to develop effective treatments have continued to this day. Recognizing docosahexaenoic acid (DHA, 22:6n-3) as a safe, inexpensive [...] Read more.

Alzheimer’s disease (AD) is the most common form of dementia, affecting over 50 million people globally. Since 1906, efforts to understand this neurodegenerative disease and to develop effective treatments have continued to this day. Recognizing docosahexaenoic acid (DHA, 22:6n-3) as a safe, inexpensive and vital nutrient for brain health and cognitive protection due to its key role in brain development and function, this study explores novel, sustainable non-fish sources as potential dietary supplements to prevent or mitigate AD, within a blue biotechnology framework. Forty 5×FAD male mice, five weeks old, were allocated to five body weight-matched dietary groups (n = 8) and fed isocaloric diets based on AIN-93M standard chow for 6 months. Each diet, except the control feed (non-supplemented group), enclosed a modified lipid fraction supplemented with 2% of the following: (1) linseed oil (LSO, rich in alpha-linolenic acid (ALA,18:3n-3)); (2) cod liver oil (fish oil, FO, rich in both DHA and eicosapentaenoic acid (EPA, 20:5n-3)); (3) Schizochytrium sp. microalga oil (Schizo) with 40% of DHA; and (4) commercial DHASCO oil (DHASCO) with 70% of DHA. The different diets did not affect (p > 0.05) growth performance criteria (e.g., final body weight, daily feed intake, and body weight gain) suggesting no effect on the overall caloric balance or mice growth, but n-3 long-chain polyunsaturated-fatty acid (n-3 LCPUFA) supplementation significantly reduced total cholesterol (p < 0.001) and total lipids (p < 0.001). No systemic inflammation was detected in 5×FAD mice. In parallel, a beneficial modulation of lipid metabolism by DHA-enriched diets was observed, with polyunsaturated fatty acid incorporation, particularly DHA, across key metabolic tissues, such as the liver (p < 0.001) and the brain (p < 0.001). No behavioural variations were detected using an open-field test after 6 months of diet (p > 0.05). While mice fed a standard diet or LSO diet showed cognitive deficit, the incorporation of FO, Schizo or DHASCO oils into dietary routine showed promising protective effects on the working memory (p < 0.05) and the last two diets also on the recognition memory (p < 0.05) Increased neuronal count (p < 0.05), reflecting neuronal survival, was clearly observed with the fish oil diet. In turn, the number of TAU-positive cells (p < 0.05) was reduced in the Schizo diet, while β-amyloid deposition (p < 0.01) and the neuroinflammatory marker, IBA1 (p < 0.05), were decreased across all DHA-enriched diets. These promising findings open new avenues for further studies focused on the protective effects of DHA derived from sustainable and underexploited Schizochytrium sp. microalga in the prevention of AD. Full article

(This article belongs to the Section Cellular Biochemistry)

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20 pages, 4584 KB

Open AccessEditor’s ChoiceArticle

Systemic Lonp1 Haploinsufficiency Mitigates Cardiac Mitochondrial Dysfunction Induced by Cardiomyocyte-Specific Lonp1 Haploinsufficiency via Potential Inter-Organ Crosstalk

by Sakthijothi Muthu, Zinnia Tran, Ramasamy Saminathan, Pratikshya Shrestha and Sundararajan Venkatesh

Biomolecules 2025, 15(8), 1159; https://doi.org/10.3390/biom15081159 - 13 Aug 2025

Cited by 1 | Viewed by 1806

Abstract

Efficient mitochondrial matrix protein quality control (mPQC), regulated by the mitochondrial matrix protease LONP1, is essential for preserving cardiac bioenergetics, particularly in post-mitotic cardiomyocytes, which are highly susceptible to mitochondrial dysfunction. While cardiac mPQC defects could impair heart function, it remains unclear whether [...] Read more.

Efficient mitochondrial matrix protein quality control (mPQC), regulated by the mitochondrial matrix protease LONP1, is essential for preserving cardiac bioenergetics, particularly in post-mitotic cardiomyocytes, which are highly susceptible to mitochondrial dysfunction. While cardiac mPQC defects could impair heart function, it remains unclear whether such defects can be mitigated through inter-organ crosstalk by modulating mPQC in extra-cardiac tissues, a potentially valuable strategy given the challenges of directly targeting the heart. To investigate this, we examined two mouse models of Lonp1 haploinsufficiency at young adulthood: a cardiomyocyte-specific heterozygous knockout (Lonp1^CKO-HET) and a whole-body heterozygous knockout (Lonp1^GKO-HET). Despite similar reductions in Lonp1 mRNA expression in the hearts, Lonp1^GKO-HET mice exhibited no cardiac dysfunction, whereas Lonp1^CKO-HET mice showed mild cardiac dysfunction accompanied by activation of the mitochondrial stress response, including induction of genes such as Clpx, Spg7, Hspa9, and Hspd1, increased mitochondrial dynamics (Pink1, Dnm1l), reduced mitochondrial biogenesis, and compensatory upregulation of the mtDNA transcriptional regulator Tfam, all occurring without overt structural remodeling. These alterations were absent in Lonp1^GKO-HET hearts. Our findings reveal a novel adaptive mechanism in which systemic mPQC deficiency can buffer mitochondrial dysfunction in the heart through inter-organ communication that is lost with cardiomyocyte-specific mPQC disruption. This study identifies systemic modulation of Lonp1-mediated mitochondrial stress pathways as a promising strategy to promote cardiac resilience through protective inter-organ signaling. Full article

(This article belongs to the Special Issue Mitochondrial Proteins: From Import and Biogenesis to Complex Functional Network)

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17 pages, 8538 KB

Open AccessEditor’s ChoiceArticle

Thermodynamic and Kinetic Aspects of Calcium Oxalate Crystallization and Renal Lithiasis

by Jaume Dietrich, Antònia Costa-Bauza and Félix Grases

Biomolecules 2025, 15(8), 1141; https://doi.org/10.3390/biom15081141 - 7 Aug 2025

Cited by 4 | Viewed by 3253

Abstract

Thermodynamic factors (supersaturation of substances that form crystals) and kinetic factors (heterogeneous nucleants and crystallization inhibitors) affect the formation of crystals and stones in the urinary tract. We studied the effect of five different polyhydroxycarboxylic acids and phytate on the formation of calcium [...] Read more.

Thermodynamic factors (supersaturation of substances that form crystals) and kinetic factors (heterogeneous nucleants and crystallization inhibitors) affect the formation of crystals and stones in the urinary tract. We studied the effect of five different polyhydroxycarboxylic acids and phytate on the formation of calcium oxalate crystals in artificial urine. All tested molecules are known to inhibit the crystallization of this calcium salt, and to also form complexes with calcium ions. Considering the typical concentration of polyhydroxycarboxylic acids in urine (similar to that of the calcium ion) and their ability to inhibit crystallization, their most important effect is the capacity to complex calcium—a thermodynamic effect. For phytate and its metabolites, which are present in concentrations much lower than that of the calcium ion, the most important effect is as a crystallization inhibitor—a kinetic effect. Among the five polyhydroxycarboxylic acids examined here, hydroxycitrate had the strongest complexing capacity, and the addition of phytate to hydroxycitrate led to greater inhibition of crystallization. Therefore, because oral consumption of hydroxycitrate does not increase the urinary pH, it is likely that the combined consumption of hydroxycitrate and phytate can provide certain benefits for patients with increased risk of developing calcium oxalate stones. We also discussed the effects of these different molecules on the different calcium oxalate stones, including papillary calcium oxalate monohydrate stones, cavity calcium oxalate monohydrate stones, calcium oxalate dihydrate stones, and mixed calcium oxalate dihydrate/hydroxyapatite stones. Full article

(This article belongs to the Section Molecular Medicine)

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16 pages, 1318 KB

Open AccessEditor’s ChoiceArticle

Aptamer-Coated PLGA Nanoparticles Selectively Internalize into Epithelial Ovarian Cancer Cells In Vitro and In Vivo

by Gregory Benedetto, Anthony Fowler, Dan Langdon, Maya Raine, Molly Lynne White, Joshua Ogle, Corey Garmon, Craig Ogle and Christine Richardson

Biomolecules 2025, 15(8), 1123; https://doi.org/10.3390/biom15081123 - 4 Aug 2025

Cited by 4 | Viewed by 1810

Abstract

Ovarian cancer is a deadly gynecological malignancy that will affect about 21,000 women and result in almost 153,000 deaths in the United States in 2025. New clinical tools that facilitate early diagnosis and treatment of ovarian malignancies will significantly help reduce mortality and [...] Read more.

Ovarian cancer is a deadly gynecological malignancy that will affect about 21,000 women and result in almost 153,000 deaths in the United States in 2025. New clinical tools that facilitate early diagnosis and treatment of ovarian malignancies will significantly help reduce mortality and improve current long-term survival rates. We utilized a previously identified single-strand DNA aptamer RLA01 that binds and internalizes into target epithelial ovarian cancer cells to label PLGA-based nanoparticles and determine their ability to selectively target EOC cells and deliver payloads for cellular internalization. Nanoparticles labeled with RLA01 significantly enhanced cellular uptake 20–85% by receptor-mediated endocytosis into target EOC Caov-3 cells and inhibited cellular uptake in non-target HOSE 6-3 cells. Further, labeling of paclitaxel-loaded nanoparticles with RLA01 significantly decreased cell proliferation and induced apoptosis. A preliminary pilot study looking at the in vivo stability of aptamers demonstrated their ability to promote retention and honing of nanoparticles at tumors. These data demonstrate the effective combinatorial use of aptamer RLA01 and nanoparticle technologies for the direct targeting of tumor cell populations both in vitro and in vivo. Full article

(This article belongs to the Section Bio-Engineered Materials)

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24 pages, 2279 KB

Open AccessEditor’s ChoiceArticle

Dual Oxytocin Signals in Striatal Astrocytes

by Elisa Farsetti, Sarah Amato, Monica Averna, Diego Guidolin, Marco Pedrazzi, Guido Maura, Luigi Francesco Agnati, Chiara Cervetto and Manuela Marcoli

Biomolecules 2025, 15(8), 1122; https://doi.org/10.3390/biom15081122 - 4 Aug 2025

Cited by 2 | Viewed by 1779

Abstract

The ability of the neuropeptide oxytocin to affect glial cell function is receiving increasing attention. We previously reported that oxytocin at a low nanomolar concentration could inhibit both astrocytic Ca²⁺ signals and glutamate release. Here, we investigate the ability of oxytocin receptors [...] Read more.

The ability of the neuropeptide oxytocin to affect glial cell function is receiving increasing attention. We previously reported that oxytocin at a low nanomolar concentration could inhibit both astrocytic Ca²⁺ signals and glutamate release. Here, we investigate the ability of oxytocin receptors to couple both inhibitory and stimulatory pathways in astrocytes, as already reported in neurons. We assessed the effects of oxytocin at concentrations ranging from low to high in the nanomolar range on intracellular Ca²⁺ signals and on the glutamate release in astrocyte processes freshly prepared from the striatum of adult rats. Our main findings are as follows: oxytocin could induce dual responses in astrocyte processes, namely the inhibition and facilitation of both Ca²⁺ signals and glutamate release; the inhibitory and the facilitatory response appeared dependent on activation of the G_i and the G_q pathway, respectively; both inhibitory and facilitatory responses were evoked at the same nanomolar oxytocin concentrations; and the biased agonists atosiban and carbetocin could duplicate oxytocin’s inhibitory and facilitatory response, respectively. In conclusion, due to the coupling of striatal astrocytic oxytocin receptors to different transduction pathways and the dual effects on Ca²⁺ signals and glutamate release, oxytocin could also play a crucial role in neuron–astrocyte bi-directional communication through a subtle regulation of striatal glutamatergic synapses. Therefore, astrocytic oxytocin receptors may offer pharmacological targets to regulate glutamatergic striatal transmission, which is potentially useful in neuropsychiatric disorders and in neurodegenerative diseases. Full article

(This article belongs to the Special Issue Neuron–Astrocyte Interactions in Neurological Function and Disease)

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32 pages, 20583 KB

Open AccessEditor’s ChoiceArticle

Application of Prodigiosin Extracts in Textile Dyeing and Novel Printing Processes for Halochromic and Antimicrobial Wound Dressings

by Cátia Alves, Pedro Soares-Castro, Rui D. V. Fernandes, Adriana Pereira, Rui Rodrigues, Ana Rita Fonseca, Nuno C. Santos and Andrea Zille

Biomolecules 2025, 15(8), 1113; https://doi.org/10.3390/biom15081113 - 1 Aug 2025

Cited by 4 | Viewed by 2511

Abstract

The textile industry’s reliance on synthetic dyes contributes significantly to pollution, highlighting the need for sustainable alternatives like biopigments. This study investigates the production and application of the biopigment prodigiosin, which was produced by Pseudomonas putida with a yield of 1.85 g/L. Prodigiosin [...] Read more.

The textile industry’s reliance on synthetic dyes contributes significantly to pollution, highlighting the need for sustainable alternatives like biopigments. This study investigates the production and application of the biopigment prodigiosin, which was produced by Pseudomonas putida with a yield of 1.85 g/L. Prodigiosin was prepared under acidic, neutral, and alkaline conditions, resulting in varying protonation states that influenced its affinity for cotton and polyester fibers. Three surfactants (anionic, cationic, non-ionic) were tested, with non-ionic Tween 80 yielding a promising color strength (above 4) and fastness results with neutral prodigiosin at 1.3 g/L. Cotton and polyester demonstrated good washing (color difference up to 14 for cotton, 5 for polyester) and light fastness (up to 15 for cotton, 16 for polyester). Cellulose acetate, used in the conventional printing process as a thickener, produced superior color properties compared to commercial thickeners. Neutral prodigiosin achieved higher color strength, and cotton fabrics displayed halochromic properties, distinguishing them from polyester, which showed excellent fastness. Prodigiosin-printed samples also exhibited strong antimicrobial activity against Pseudomonas aeruginosa and retained halochromic properties over 10 pH cycles. These findings suggest prodigiosin as a sustainable dye alternative and pH sensor, with potential applications in biomedical materials, such as antimicrobial and pH-responsive wound dressings. Full article

(This article belongs to the Special Issue Applications of Biomaterials in Medicine and Healthcare)

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16 pages, 2742 KB

Open AccessEditor’s ChoiceArticle

miRNA408 from Camellia japonica L. Mediates Cross-Kingdom Regulation in Human Skin Recovery

by Soll Jin, Jae-Goo Kim, Hye Jin Kim, Ji Young Kim, Sang Hoon Kim, Hee Cheol Kang and Mi Jung Kim

Biomolecules 2025, 15(8), 1108; https://doi.org/10.3390/biom15081108 - 1 Aug 2025

Cited by 4 | Viewed by 1657

Abstract

Wound healing is a complex and dynamic process involving several stages of tissue repair. This study has shown that extracellular vesicles (EVs) derived from the callus of Camellia japonica L. and their associated microRNAs (miRNAs) possess significant wound healing activities. In human fibroblasts, [...] Read more.

Wound healing is a complex and dynamic process involving several stages of tissue repair. This study has shown that extracellular vesicles (EVs) derived from the callus of Camellia japonica L. and their associated microRNAs (miRNAs) possess significant wound healing activities. In human fibroblasts, EVs from C. japonica L. stimulated wound healing and upregulated collagen gene expression. The EVs also decreased inflammation levels in human keratinocytes, supporting wound healing. Among the miRNAs identified, miR408, one of the abundant miRNAs in the EVs, also showed similar wound healing efficacy. These findings suggest that both EVs and miR408 from the callus of C. japonica L. play a pivotal role in promoting wound healing. Additionally, this study shows that the regulation of miRNAs between different kingdoms can be achieved and suggests a new direction for the utilization of plant-derived components. Full article

(This article belongs to the Section Molecular Biophysics: Structure, Dynamics, and Function)

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24 pages, 2944 KB

Open AccessEditor’s ChoiceArticle

Oral Pharmacokinetic Evaluation of a Microemulsion-Based Delivery System for Novel A190 Prodrugs

by Sagun Poudel, Chaolong Qin, Rudra Pangeni, Ziwei Hu, Grant Berkbigler, Madeline Gunawardena, Adam S. Duerfeldt and Qingguo Xu

Biomolecules 2025, 15(8), 1101; https://doi.org/10.3390/biom15081101 - 30 Jul 2025

Viewed by 2178

Abstract

Peroxisome proliferator-activated receptor alpha (PPARα) is a key regulator of lipid metabolism, making its agonists valuable therapeutic targets for various diseases, including chronic peripheral neuropathy. Existing PPARα agonists face limitations such as poor selectivity, sub-optimal bioavailability, and safety concerns. We previously demonstrated that [...] Read more.

Peroxisome proliferator-activated receptor alpha (PPARα) is a key regulator of lipid metabolism, making its agonists valuable therapeutic targets for various diseases, including chronic peripheral neuropathy. Existing PPARα agonists face limitations such as poor selectivity, sub-optimal bioavailability, and safety concerns. We previously demonstrated that A190, a novel, potent, and selective PPARα agonist, effectively alleviates chemotherapy-induced peripheral neuropathy and CFA-induced inflammatory pain as a non-opioid therapeutic agent. However, A190 alone has solubility and permeability issues that limits its oral delivery. To overcome this challenge, in this study, four new-generation ester prodrugs of A190; A190-PD-9 (methyl ester), A190-PD-14 (ethyl ester), A190-PD-154 (isopropyl ester), and A190-PD-60 (cyclic carbonate) were synthesized and evaluated for their enzymatic bioconversion and chemical stability. The lead candidate, A190-PD-60, was further formulated as a microemulsion (A190-PD-60-ME) and optimized via Box–Behnken design. A190-PD-60-ME featured nano-sized droplets (~120 nm), low polydispersity (PDI < 0.3), and high drug loading (>90%) with significant improvement in artificial membrane permeability. Crucially, pharmacokinetic evaluation in rats demonstrated that A190-PD-60-ME reached a 16.6-fold higher Cmax (439 ng/mL) and a 5.9-fold increase in relative oral bioavailability compared with an A190-PD-60 dispersion. These findings support the combined prodrug-microemulsion approach as a promising strategy to overcome oral bioavailability challenges and advance PPARα-targeted therapies. Full article

(This article belongs to the Special Issue Advancing Innovations in Biomedical Research for Translational Applications)

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23 pages, 4653 KB

Open AccessEditor’s ChoiceArticle

Zinc-Induced Folding and Solution Structure of the Eponymous Novel Zinc Finger from the ZC4H2 Protein

by Rilee E. Harris, Antonio J. Rua and Andrei T. Alexandrescu

Biomolecules 2025, 15(8), 1091; https://doi.org/10.3390/biom15081091 - 28 Jul 2025

Cited by 2 | Viewed by 2040

Abstract

The ZC4H2 gene is the site of congenital mutations linked to neurodevelopmental and musculoskeletal pathologies collectively termed ZARD (ZC4H2-Associated Rare Disorders). ZC4H2 consists of a coiled coil and a single novel zinc finger with four cysteines and two histidines, from which the protein [...] Read more.

The ZC4H2 gene is the site of congenital mutations linked to neurodevelopmental and musculoskeletal pathologies collectively termed ZARD (ZC4H2-Associated Rare Disorders). ZC4H2 consists of a coiled coil and a single novel zinc finger with four cysteines and two histidines, from which the protein obtains its name. Alpha Fold 3 confidently predicts a structure for the zinc finger but also for similarly sized random sequences, providing equivocal information on its folding status. We show using synthetic peptide fragments that the zinc finger of ZC4H2 is genuine and folds upon binding a zinc ion with picomolar affinity. NMR pH titration of histidines and UV–Vis of a cobalt complex of the peptide indicate its four cysteines coordinate zinc, while two histidines do not participate in binding. The experimental NMR structure of the zinc finger has a novel structural motif similar to RANBP2 zinc fingers, in which two orthogonal hairpins each contribute two cysteines to coordinate zinc. Most of the nine ZARD mutations that occur in the ZC4H2 zinc finger are likely to perturb this structure. While the ZC4H2 zinc finger shares the folding motif and cysteine-ligand spacing of the RANBP2 family, it is missing key substrate-binding residues. Unlike the NZF branch of the RANBP2 family, the ZC4H2 zinc finger does not bind ubiquitin. Since the ZC4H2 zinc finger occurs in a single copy, it is also unlikely to bind DNA. Based on sequence homology to the VAB-23 protein, the ZC4H2 zinc finger may bind RNA of a currently undetermined sequence or have alternative functions. Full article

(This article belongs to the Special Issue Functional Peptides and Their Interactions (3rd Edition))

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22 pages, 1822 KB

Open AccessEditor’s ChoiceArticle

Increased Concentration of Anti-Egg Albumin Antibodies in Cerebrospinal Fluid and Serum of Patients with Alzheimer’s Disease—Discussion on Human Serpins’ Similarity and Probable Involvement in the Disease Mechanism

by Dionysia Amanatidou, Magdalini Tsolaki, Vasileios Fouskas, Ioannis Gavriilidis, Maria Myriouni, Anna Anastasiou, Efthimia Papageorgiou, Diona Porfyriadou, Zoi Parcharidi, Eleftheria Papasavva, Maria Fili and Phaedra Eleftheriou

Biomolecules 2025, 15(8), 1085; https://doi.org/10.3390/biom15081085 - 27 Jul 2025

Viewed by 2186

Abstract

Alzheimer’s Disease (AD) is a multifactorial process. Amyloid plaque formation constitutes the main characteristic of the disease. Despite the identification of numerous factors associated with AD, the mechanism remains unclear in several aspects. Disturbances in intestinal and blood–brain barrier (BBB) penetration, observed in [...] Read more.

Alzheimer’s Disease (AD) is a multifactorial process. Amyloid plaque formation constitutes the main characteristic of the disease. Despite the identification of numerous factors associated with AD, the mechanism remains unclear in several aspects. Disturbances in intestinal and blood–brain barrier (BBB) penetration, observed in AD, may facilitate immunologic response to food-derived antigens. In the present study, antibodies against egg albumin, bovine-casein, and N-Glycolyl-Neuraminic acid (Neu5Gc) were measured in the cerebrospinal fluid (CSF) and serum of the patients using an enzyme-linked immunosorbent assay (ELISA). Zero anti-Neu5Gc and low concentrations of anti-casein antibodies were detected. Increased anti-native egg albumin antibodies were present in the serum of patients of all stages with 65% positivity (p < 0.001) in mild disease and a higher percentage in females (81.9%, p < 0.001). Lower serum positivity to anti-denatured egg albumin antibodies was observed, showing a gradual increase with severity and higher prevalence also in females. In the CSF, anti-native and anti-denatured egg albumin antibodies were mainly observed in severely ill patients with accumulative positivity to either antigen, reaching 61.8% in severe vs. 15% in mild disease (p < 0.001). Increased values were mainly observed in males. Anti-egg albumin antibodies may be implicated in the disease mechanism through sequence/structural similarity with human proteins, mainly serpins, and it would be worth consideration in further investigations and therapeutic strategies. Full article

(This article belongs to the Special Issue Food, Microbe, Viral and Parasite-Derived Antibodies in Autoimmune and Chronic Diseases)

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20 pages, 17373 KB

Open AccessEditor’s ChoiceArticle

The Memory Gene, Murashka, Is a Regulator of Notch Signalling and Controls the Size of the Drosophila Germline Stem Cell Niche

by Thifeen Deen, Hideyuki Shimizu, Marian B. Wilkin and Martin Baron

Biomolecules 2025, 15(8), 1082; https://doi.org/10.3390/biom15081082 - 26 Jul 2025

Viewed by 1356

Abstract

We identified Murashka, a RING finger protein, in an oogenesis screen as a regulator of Drosophila ovary germline stem cell niche development. Mutant alleles of murashka exhibited an enlarged niche phenotype reminiscent of increased Notch signalling and displayed genetic interactions with Notch alleles, [...] Read more.

We identified Murashka, a RING finger protein, in an oogenesis screen as a regulator of Drosophila ovary germline stem cell niche development. Mutant alleles of murashka exhibited an enlarged niche phenotype reminiscent of increased Notch signalling and displayed genetic interactions with Notch alleles, and with polychaetoid, a regulator of Notch during niche development. These interactions uncovered both positive and negative impacts on Notch in different genetic backgrounds. In S2 cells, Murashka formed a complex with Notch and colocalised with Notch in the secretory pathway. Murashka expression in S2 cells down-regulated Notch signalling levels but could result in increased fold induction due to the proportionally greater decrease in basal ligand-independent activity. In vivo Murashka expression had different outcomes on different Notch target genes. We observed a decrease in the expression of vestigial along the anterior/posterior boundary of the wing imaginal disc, but not of wingless at the dorsal/ventral boundary. Instead, weak ectopic wingless was observed, which was synergistically increased by the coexpression of Deltex, a positive regulator of ligand-independent signalling. Our results identify a novel developmental role for murashka, a gene previously only associated with a function in long-term memory, and indicate a regulatory role for Murashka through a physical interaction with Notch that has context-dependent outcomes. Murashka adds to a growing number of ubiquitin ligase regulators which interact with Notch at different locations within its secretory and endocytic trafficking pathways. Full article

(This article belongs to the Special Issue Notch and Its Regulation in Health and Disease)

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17 pages, 13173 KB

Open AccessEditor’s ChoiceArticle

High-Resolution Imaging and Interpretation of Three-Dimensional RPE Sheet Structure

by Kevin J. Donaldson, Micah A. Chrenek, Jeffrey H. Boatright and John M. Nickerson

Biomolecules 2025, 15(8), 1084; https://doi.org/10.3390/biom15081084 - 26 Jul 2025

Viewed by 1566

Abstract

The retinal pigment epithelium (RPE), a monolayer of pigmented cells, is critical for visual function through its interaction with the neural retina. In healthy eyes, RPE cells exhibit a uniform hexagonal arrangement, but under stress or disease, such as age-related macular degeneration (AMD), [...] Read more.

The retinal pigment epithelium (RPE), a monolayer of pigmented cells, is critical for visual function through its interaction with the neural retina. In healthy eyes, RPE cells exhibit a uniform hexagonal arrangement, but under stress or disease, such as age-related macular degeneration (AMD), dysmorphic traits like cell enlargement and apparent multinucleation emerge. Multinucleation has been hypothesized to result from cellular fusion, a compensatory mechanism to maintain cell-to-cell contact and barrier function, as well as conserve resources in unhealthy tissue. However, traditional two-dimensional (2D) imaging using apical border markers alone may misrepresent multinucleation due to the lack of lateral markers. We present high-resolution confocal images enabling three-dimensional (3D) visualization of apical (ZO-1) and lateral (α-catenin) markers alongside nuclei. In two RPE damage models, we find that seemingly multinucleated cells are often single cells with displaced neighboring nuclei and lateral membranes. This emphasizes the need for 3D analyses to avoid misidentifying multinucleation and underlying fusion mechanisms. Lastly, images from the NaIO₃ oxidative damage model reveal variability in RPE damage, with elongated, dysmorphic cells showing increased ZsGreen reporter protein expression driven by EMT-linked CAG promoter activity, while more regular RPE cells displayed somewhat reduced green signal more typical of epithelial phenotypes. Full article

(This article belongs to the Section Molecular Biophysics: Structure, Dynamics, and Function)

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15 pages, 8667 KB

Open AccessEditor’s ChoiceArticle

A Novel Synthetic Tag Induces Palmitoylation and Directs the Subcellular Localization of Target Proteins

by Jun Ka, Gwanyeob Lee, Seunghyun Han, Haekwan Jeong and Suk-Won Jin

Biomolecules 2025, 15(8), 1076; https://doi.org/10.3390/biom15081076 - 25 Jul 2025

Viewed by 2085

Abstract

Proper subcellular localization is essential to exert the designated function of a protein, not only for endogenous proteins but also transgene-encoded proteins. Post-translational modification is a frequently used method to regulate the subcellular localization of a specific protein. While there are a number [...] Read more.

Proper subcellular localization is essential to exert the designated function of a protein, not only for endogenous proteins but also transgene-encoded proteins. Post-translational modification is a frequently used method to regulate the subcellular localization of a specific protein. While there are a number of tags that are widely used to direct the target protein to a specific location within a cell, these tags often fail to emulate the dynamics of protein trafficking, necessitating an alternative approach to the direct subcellular localization of transgene-encoded proteins. Here, we report the development of a new synthetic polypeptide protein tag comprised of ten amino acids, which promotes membrane localization of a target protein. This short synthetic peptide tag, named “Palmito-Tag”, induces ectopic palmitoylation on the cysteine residue within the tag, thereby promoting membrane localization of the target proteins without affecting their innate function. We show that the target proteins with the Palmito-Tag are incorporated into the membranous organelles within the cells, including the endosomes, as well as extracellular vesicles. Given the reversible nature of palmitoylation, the Palmito-Tag may allow us to shift the subcellular localization of the target protein in a context-dependent manner. With the advent of therapeutic applications of exosomes and other extracellular vesicles, we believe that the ability to reversibly modify a target protein and direct its deposition to the specific subcellular milieu will help us explore more effective venues to harness the potential of extracellular vesicle-based therapies. Full article

(This article belongs to the Special Issue Feature Papers in Cellular Biochemistry)

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20 pages, 547 KB

Open AccessEditor’s ChoiceArticle

Empirical Assessment of Sequence-Based Predictions of Intrinsically Disordered Regions Involved in Phase Separation

by Xuantai Wu, Kui Wang, Gang Hu and Lukasz Kurgan

Biomolecules 2025, 15(8), 1079; https://doi.org/10.3390/biom15081079 - 25 Jul 2025

Cited by 2 | Viewed by 2103

Abstract

Phase separation processes facilitate the formation of membrane-less organelles and involve interactions within structured domains and intrinsically disordered regions (IDRs) in protein sequences. The literature suggests that the involvement of proteins in phase separation can be predicted from their sequences, leading to the [...] Read more.

Phase separation processes facilitate the formation of membrane-less organelles and involve interactions within structured domains and intrinsically disordered regions (IDRs) in protein sequences. The literature suggests that the involvement of proteins in phase separation can be predicted from their sequences, leading to the development of over 30 computational predictors. We focused on intrinsic disorder due to its fundamental role in related diseases, and because recent analysis has shown that phase separation can be accurately predicted for structured proteins. We evaluated eight representative amino acid-level predictors of phase separation, capable of identifying phase-separating IDRs, using a well-annotated, low-similarity test dataset under two complementary evaluation scenarios. Several methods generate accurate predictions in the easier scenario that includes both structured and disordered sequences. However, we demonstrate that modern disorder predictors perform equally well in this scenario by effectively differentiating phase-separating IDRs from structured regions. In the second, more challenging scenario—considering only predictions in disordered regions—disorder predictors underperform, and most phase separation predictors produce only modestly accurate results. Moreover, some predictors are broadly biased to classify disordered residues as phase-separating, which results in low predictive performance in this scenario. Finally, we recommend PSPHunter as the most accurate tool for identifying phase-separating IDRs in both scenarios. Full article

(This article belongs to the Collection Feature Papers in Bioinformatics and Systems Biology Section)

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23 pages, 36719 KB

Open AccessEditor’s ChoiceArticle

The Impact of Hybrid Bionanomaterials Based on Gold Nanoparticles on Liver Injury in an Experimental Model of Thioacetamide-Induced Hepatopathy

by Mara Filip, Simona Valeria Clichici, Mara Muntean, Luminița David, Bianca Moldovan, Vlad Alexandru Toma, Cezar Login and Şoimița Mihaela Suciu

Biomolecules 2025, 15(8), 1068; https://doi.org/10.3390/biom15081068 - 24 Jul 2025

Cited by 1 | Viewed by 1345

Abstract

The present study aimed to evaluate the therapeutic benefits of a hybrid material based on gold nanoparticles and natural extracts on an experimental model of thioacetamide-induced (TAA) liver injury in rats. The nanomaterials were synthesized using a green method, with Cornus sanguinea L. [...] Read more.

The present study aimed to evaluate the therapeutic benefits of a hybrid material based on gold nanoparticles and natural extracts on an experimental model of thioacetamide-induced (TAA) liver injury in rats. The nanomaterials were synthesized using a green method, with Cornus sanguinea L. extract as a reducing and capping agent (NPCS), and were then mixed with Vaccinium myrtillus L. (VL) extract in order to achieve a final mixture with enhanced properties (NPCS-VL). NPCSs were characterized using UV–vis spectrophotometry and transmission electron microscopy (TEM), which demonstrated the formation of spherical, stable gold nanoparticles with an average diameter of 20 nm. NPCS-VL’s hepatoprotective effects were evaluated through an analysis of oxidative stress, inflammation, hepatic cytolysis, histology assays, and TEM in comparison to silymarin on an animal model of thioacetamide (TAA)-induced toxic hepatitis. TAA administration determined hepatotoxicity, as it triggered redox imbalance, increased proinflammatory cytokine levels and alanine aminotransferase (ALAT) activity, and induced morphological and ultrastructural changes characteristic of liver fibrosis. In rats treated with NPCS-VL, all these pathological processes were attenuated, suggesting a potential antifibrotic effect of this hybrid bionanomaterial. Full article

(This article belongs to the Special Issue Bionanomaterials: Synthesis, Characterization, Toxicity and Biomedical Applications, 3rd Edition)

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16 pages, 2130 KB

Open AccessEditor’s ChoiceArticle

A Distinct miRNA Profile in Intimal Hyperplasia of Failed Arteriovenous Fistulas Reveals Key Pathogenic Pathways

by Carmen Ciavarella, Francesco Vasuri, Alessio Degiovanni, Lena Christ, Raffaella Mauro, Mauro Gargiulo and Gianandrea Pasquinelli

Biomolecules 2025, 15(8), 1064; https://doi.org/10.3390/biom15081064 - 23 Jul 2025

Cited by 2 | Viewed by 1436

Abstract

Intimal hyperplasia (IH) compromises the patency of arteriovenous fistula (AVF) vascular access in patients with end-stage kidney disease. Uncontrolled cell proliferation and migration, driven by inflammation, shear stress and surgery, are well-known triggers in IH. Recently, microRNAs (miRNAs) have emerged as regulators of [...] Read more.

Intimal hyperplasia (IH) compromises the patency of arteriovenous fistula (AVF) vascular access in patients with end-stage kidney disease. Uncontrolled cell proliferation and migration, driven by inflammation, shear stress and surgery, are well-known triggers in IH. Recently, microRNAs (miRNAs) have emerged as regulators of core mechanisms in cardiovascular diseases and as potential markers of IH. This study was aimed at identifying a specific miRNA panel in failed AVFs and clarifying the miRNA involvement in IH. miRNA profiling performed in tissues from patients with IH (AVFs) and normal veins (NVs) highlighted a subset of four miRNAs significantly deregulated (hsa-miR-155-5p, hsa-miR-449a-5p, hsa-miR-29c-3p, hsa-miR-194-5p) between the two groups. These miRNAs were analyzed in tissue-derived cells (NVCs and AVFCs), human aortic smooth muscle cells (HAOSMCs) and human umbilical vein endothelial cells (HUVECs). The panel of hsa-miR-449a-5p, hsa-miR-155-5p, hsa-miR-29c-3p and hsa-miR-194-5p was up-regulated in AVFCs, HAOSMCs and HUVEC under inflammatory stimuli. Notably, overexpression of hsa-miR-449a-5p exacerbated the proliferative, migratory and inflammatory features of AVFCs. In vitro pharmacological modulation of these miRNAs with pioglitazone, particularly the down-regulation of hsa-miR-155-5p and hsa-miR-29c-3p, suggested their involvement in IH pathogenesis and a potential translational application. Overall, these findings provide new insights into the pathogenesis of AVF failure, reinforcing the miRNA contribution to IH detection and prevention. Full article

(This article belongs to the Section Molecular Biology)

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13 pages, 1988 KB

Open AccessEditor’s ChoiceArticle

Genetic Diversity in the Suppressyn Gene Sequence: From Polymorphisms to Loss-of-Function Mutations

by Jun Sugimoto, Danny J. Schust, Takeshi Nagamatsu, Yoshihiro Jinno and Yoshiki Kudo

Biomolecules 2025, 15(7), 1051; https://doi.org/10.3390/biom15071051 - 21 Jul 2025

Cited by 1 | Viewed by 1526

Abstract

The suppressive regulator of cell fusion, suppressyn, is specifically expressed in the human placenta and is thought to play a crucial role in trophoblast fusion or syncytialization. Previous studies have suggested that alterations in its expression are associated with aberrant placental development, [...] Read more.

The suppressive regulator of cell fusion, suppressyn, is specifically expressed in the human placenta and is thought to play a crucial role in trophoblast fusion or syncytialization. Previous studies have suggested that alterations in its expression are associated with aberrant placental development, such as the immature placental morphology observed in Down syndrome, and may contribute to the pathogenesis of fetal growth restriction. While syncytialization in trophoblasts is an essential process for normal placental development, the precise molecular causes of its dysregulation remain poorly understood. In the present study, we aimed to elucidate the potential contribution of genomic variation to the loss of suppressyn function, extending previous analyses of expression abnormalities in perinatal disorders. Through sequence analysis, (1) we identified six polymorphisms within the coding region of the suppressyn gene, and (2) discovered that certain deletions and specific amino acid substitutions result in a complete loss of suppressyn-mediated inhibition of cell fusion. Although these mutations have not yet been reported in disease-associated genomic databases, our findings suggest that comprehensive genomic studies of perinatal and other disorders may reveal pathogenic variants of suppressyn, thereby uncovering novel genetic contributions to placental dysfunction. It is also anticipated that these findings might direct the development of therapeutic strategies targeting loss-of-function mutations. Full article

(This article belongs to the Special Issue Recent Advances in Retroviruses and Endogenous Retroviruses (ERVs) in Mammalian Placenta and Beyond 2025)

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17 pages, 1772 KB

Open AccessEditor’s ChoiceArticle

Exploration of the Possible Relationships Between Gut and Hypothalamic Inflammation and Allopregnanolone: Preclinical Findings in a Post-Finasteride Rat Model

by Silvia Diviccaro, Roberto Oleari, Federica Amoruso, Fabrizio Fontana, Lucia Cioffi, Gabriela Chrostek, Vera Abenante, Jacopo Troisi, Anna Cariboni, Silvia Giatti and Roberto Cosimo Melcangi

Biomolecules 2025, 15(7), 1044; https://doi.org/10.3390/biom15071044 - 18 Jul 2025

Cited by 4 | Viewed by 7470

Abstract

Background: Finasteride, a 5α-reductase inhibitor commonly prescribed for androgenetic alopecia, has been linked to persistent adverse effects after discontinuation, known as post-finasteride syndrome (PFS). Symptoms include neurological, psychiatric, sexual, and gastrointestinal disturbances. Emerging evidence suggests that PFS may involve disruption of sex steroid [...] Read more.

Background: Finasteride, a 5α-reductase inhibitor commonly prescribed for androgenetic alopecia, has been linked to persistent adverse effects after discontinuation, known as post-finasteride syndrome (PFS). Symptoms include neurological, psychiatric, sexual, and gastrointestinal disturbances. Emerging evidence suggests that PFS may involve disruption of sex steroid homeostasis, neuroactive steroid deficiency (notably allopregnanolone, ALLO), and gut–brain axis alterations. Objective: This study aimed to investigate the effects of finasteride withdrawal (FW) in a rat model and evaluate the potential protective effects of ALLO on gut and hypothalamic inflammation. Methods: Adult male Sprague Dawley rats were treated with finasteride for 20 days, followed by one month of drug withdrawal. A subgroup received ALLO treatment during the withdrawal. Histological, molecular, and biochemical analyses were performed on the colon and hypothalamus. Gut microbiota-derived metabolites and markers of neuroinflammation and blood–brain barrier (BBB) integrity were also assessed. Results: At FW, rats exhibited significant colonic inflammation, including a 4.3-fold increase in Mφ1 levels (p < 0.001), a 2.31-fold decrease in butyrate concentration (p < 0.01), and elevated hypothalamic GFAP and Iba-1 protein expression (+360%, p < 0.01 and +100%, p < 0.01, respectively). ALLO treatment rescued these parameters in both the colon and hypothalamus but only partially restored mucosal and BBB structural integrity, as well as the NF-κB/PPARγ pathway. Conclusions: This preclinical study shows that FW causes inflammation in both the gut and hypothalamus in rats. ALLO treatment helped reduce several of these effects. These results suggest ALLO could have a protective role and have potential as a treatment for PFS patients. Full article

(This article belongs to the Section Molecular Medicine)

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