Biomolecules

27 pages, 1321 KB

Open AccessReview

Dysregulated Sialylation in Cancer: From Immunosuppressive Microenvironment to Siglec-Targeted Therapeutics

by Yuecheng Zhang, Zhengyao Gao, Yuhan Zhang, Siqin Ai, Wenyan Li and Lingbo Sun

Biomolecules 2025, 15(10), 1375; https://doi.org/10.3390/biom15101375 (registering DOI) - 27 Sep 2025

Sialic acid, typically positioned at the terminal ends of glycoprotein or glycolipid chains via glycosyltransferase activity, is indispensable for intercellular recognition and signal transduction. Aberrant sialylation has been implicated in disrupted cell communication and oncogenic signaling, contributing to carcinogenesis. Consequently, targeting sialic acid [...] Read more.

Sialic acid, typically positioned at the terminal ends of glycoprotein or glycolipid chains via glycosyltransferase activity, is indispensable for intercellular recognition and signal transduction. Aberrant sialylation has been implicated in disrupted cell communication and oncogenic signaling, contributing to carcinogenesis. Consequently, targeting sialic acid metabolism has emerged as a promising strategy for cancer diagnosis and therapy. This review first delineates the physiological biosynthesis of sialic acid and molecular mechanisms underlying its pathological dysregulation. We then examine the sialic acid–Siglec axis as an immune checkpoint in cancer immunotherapy, highlighting its functional convergence and divergence from the PD-1/PD-L1 pathway. Furthermore, we elucidate how aberrant sialylation drives malignant transformation. Finally, we synthesize current therapeutic strategies targeting the sialic acid–Siglec axis, with particular emphasis on implementing nanomaterial-based platforms in clinical translation. These advances may yield novel diagnostic tools and therapeutic targets for glycobiology-guided precision medicine. Full article

(This article belongs to the Section Molecular Biology)

20 pages, 2797 KB

Open AccessArticle

Age-Dependent Redistribution of the Life-Important Enzyme in the Retina: Adult Müller Glial Cells’ Endfeet Lack Spermine Synthase Expression

by Astrid Zayas-Santiago, Christian J. Malpica-Nieves, José M. Santiago, Yanitza Hernández, David E. Rivera-Aponte, Miguel Méndez-González, Rüdiger W. Veh, Legier V. Rojas and Serguei N. Skatchkov

Biomolecules 2025, 15(10), 1374; https://doi.org/10.3390/biom15101374 (registering DOI) - 27 Sep 2025

Abstract

Polyamine (PA) spermine (SPM) (i) plays an essential role in the function of neurons, while (ii) accumulating predominantly in glial cells by an unknown mechanism. In addition, the translocation of SPM synthesis and redistribution in the developing and maturating retinas remains unclear. Therefore, [...] Read more.

Polyamine (PA) spermine (SPM) (i) plays an essential role in the function of neurons, while (ii) accumulating predominantly in glial cells by an unknown mechanism. In addition, the translocation of SPM synthesis and redistribution in the developing and maturating retinas remains unclear. Therefore, the expression of the SPM-synthesizing enzyme, spermine synthase (SpmS), was compared in rat retinas on postnatal days 3, 21, and 120 using immunocytochemistry, Western blot (WB), and ImageJ analyses. The anti-glutamine synthetase (GS) antibody identified glial cells, and DAPI labeled the cell nuclei. At postnatal day 3 (P3), the neonatal retina shows widespread SpmS expression throughout most neuroblast cells, but absent in the developing synaptic layers and Müller cell (MCs) processes. By day 21 (P20), SpmS becomes strongly expressed in neurons, and not in glia. On day 120 (P120), SpmS was observed in synaptic areas, with significantly less presence in neuronal soma and still none in MCs. WBs showed a decrease in SpmS expression during maturation. Therefore, glial cells do not synthesize SPM, and the accumulation of SPM in MCs found earlier suggests that glial cells take up SPM via a hypothetical high-affinity SPM transporter. In glia, SPM regulates glial connexin (Cx43) and potassium (Kir4.1) channels, being a key player in CNS diseases and aging. Full article

(This article belongs to the Section Cellular Biochemistry)

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24 pages, 524 KB

Open AccessReview

Advances in Computational Drug Repurposing, Driver Genes, and Therapeutics in Lung Adenocarcinoma

by Sajjad Nematzadeh and Arzu Karaul

Biomolecules 2025, 15(10), 1373; https://doi.org/10.3390/biom15101373 (registering DOI) - 27 Sep 2025

Abstract

This review catalogs candidate LUAD driver genes and their roles, recent discoveries, and therapeutic avenues. Beyond experimental repurposing, we evaluate modern computational methods and how they complement bench work. We conclude by appraising recent LUAD repurposing studies through a computational lens, emphasizing practical [...] Read more.

This review catalogs candidate LUAD driver genes and their roles, recent discoveries, and therapeutic avenues. Beyond experimental repurposing, we evaluate modern computational methods and how they complement bench work. We conclude by appraising recent LUAD repurposing studies through a computational lens, emphasizing practical integration into translational research. Highlights: Overview of drug repurposing methods: We provide a list of six experimental and a brief taxonomy of eight computational drug repurposing method families. Recent insights into LUAD driver genes: We present a curated panel of LUAD drivers mapped to pathways, with alteration types, functions, and therapeutic implications. LUAD-focused computational repurposing studies: We provide a synthesis of recent LUAD studies presenting clear method families, highlighting exemplar pipelines, prioritized candidate drugs, and datasets. Full article

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

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22 pages, 1229 KB

Open AccessArticle

Enhancing the Stability of Fungal Lipases by Immobilization onto Accurel MP 1000 Support and Additional Glutaraldehyde Crosslinking

by Alexandra Kovács-Kotogán, Tamás Papp, Csaba Vágvölgyi and Miklós Takó

Biomolecules 2025, 15(10), 1372; https://doi.org/10.3390/biom15101372 - 26 Sep 2025

Abstract

Commercial fungal lipases from Rhizopus oryzae, Rhizopus niveus, Aspergillus niger, Rhizomucor miehei, and Candida rugosa were immobilized via physical adsorption onto Accurel MP 1000, a hydrophobic polypropylene support. The effects of enzyme concentration, pH, temperature, and glutaraldehyde post-treatment were [...] Read more.

Commercial fungal lipases from Rhizopus oryzae, Rhizopus niveus, Aspergillus niger, Rhizomucor miehei, and Candida rugosa were immobilized via physical adsorption onto Accurel MP 1000, a hydrophobic polypropylene support. The effects of enzyme concentration, pH, temperature, and glutaraldehyde post-treatment were systematically evaluated. Immobilization generally enhanced enzyme stability, which was further improved in several cases by glutaraldehyde crosslinking. The immobilized preparations retained over 50% of their initial activity for 3–6 cycles, and 7–10 cycles following glutaraldehyde treatment. While soluble enzymes lost nearly all activity within three months at 5 °C and 25 °C and retained only 5–20% at −20 °C, the immobilized forms preserved 50–100% of their activity under all storage conditions tested. Immobilized lipases also exhibited improved thermal stability at 60 °C by general increments between 1.3 and 1.8 times compared to soluble lipases. Increased tolerance to pH fluctuations was observed in most immobilized enzymes, particularly from R. oryzae, R. niveus, R. miehei, and C. rugosa. Organic solvent tolerance of the immobilized enzymes showed highest stability in hexane (66–100% residual activity after 4 h incubation). Glutaraldehyde treatment affected solvent stability of immobilized lipases in enzyme and solvent dependent manner. These findings demonstrate the improved stability and applicability of the produced biocatalysts in varying reaction environments. Full article

(This article belongs to the Special Issue Recent Advances in the Enzymatic Synthesis of Bioactive Compounds)

16 pages, 1218 KB

Open AccessArticle

Natural Oils as Green Solvents for Reactive Extraction of 7-Aminocephalosporanic Acid: A Sustainable Approach to Bioproduct Recovery in Environmental Biotechnology

by Delia Turcov, Madalina Paraschiv, Alexandra Cristina Blaga, Alexandra Tucaliuc, Dan Cascaval and Anca-Irina Galaction

Biomolecules 2025, 15(10), 1371; https://doi.org/10.3390/biom15101371 (registering DOI) - 26 Sep 2025

Abstract

The growing need for environmentally friendly separation processes has motivated the search for alternative solvents to petroleum-derived chemicals for the recovery of biosynthesized products. Although effective, conventional petroleum-based solvents pose major environmental and sustainability concerns, including pollution, ecotoxicity, human health risks, and high [...] Read more.

The growing need for environmentally friendly separation processes has motivated the search for alternative solvents to petroleum-derived chemicals for the recovery of biosynthesized products. Although effective, conventional petroleum-based solvents pose major environmental and sustainability concerns, including pollution, ecotoxicity, human health risks, and high costs and energy demands for recycling. Consequently, current research and industrial practice increasingly focus on their replacement with safer and more sustainable alternatives. This study investigates the use of natural oils (i.e., grapeseed, sweet almond, and flaxseed oils) as renewable, biodegradable, and non-toxic diluents in reactive extraction systems for the separation of 7-aminocephalosporanic acid (7-ACA). The combination of these oils with tri-n-octylamine (TOA) as extractant enabled high extraction efficiencies, exceeding 50%. The system comprising 120 g/L tri-n-octylamine in grapeseed oil, an aqueous phase pH of 4.5, a contact time of 1 min, and a temperature of 25 °C resulted in a 7-ACA extraction efficiency of 63.4%. Slope analysis suggests that complex formation likely involves approximately one molecule each of tri-n-octylamine and 7-ACA, although the apparent order of the amine is reduced in systems using natural oils. This study highlights the potential of natural oil-based reactive extraction as a scalable and environmentally friendly method for 7-ACA separation, aligning with the principles of green chemistry and environmental biotechnology. Full article

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

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30 pages, 1177 KB

Open AccessReview

Traditional and New Views on MSI-H/dMMR Endometrial Cancer

by Chuqi Liu, Huiyu Ping, Mengmeng Yao, Xinru Li, Qingxin Li, Ruotong Hu, Yawen Xu, Kaidi Meng, Fei Gao and Kai Meng

Biomolecules 2025, 15(10), 1370; https://doi.org/10.3390/biom15101370 - 26 Sep 2025

Abstract

MSI-H/dMMR endometrial cancer (EC) is closely linked to the mismatch repair (MMR) pathway, and its pathogenesis is associated with microsatellite instability (MSI) caused by abnormalities in the core genes of the conventional MMR system. This cancer exhibits a distinct immune microenvironment, which makes [...] Read more.

MSI-H/dMMR endometrial cancer (EC) is closely linked to the mismatch repair (MMR) pathway, and its pathogenesis is associated with microsatellite instability (MSI) caused by abnormalities in the core genes of the conventional MMR system. This cancer exhibits a distinct immune microenvironment, which makes it suitable for treatment with immune checkpoint inhibitors (ICIs). This cancer type demonstrates heterogeneity, encompassing Lynch syndrome (LS)-associated EC (characterized by germline mutations), sporadic EC (attributed to MLH1 promoter hypermethylation), and Lynch-like EC (driven by somatic mutations). Research indicates that these three dMMR EC subtypes possess different immune microenvironments, which may influence the therapeutic efficacy of ICIs. However, the impact of somatic mutations in traditional MMR genes on EC has often been overlooked. Furthermore, over 50% of patients with MSI exhibit no response to ICIs, potentially due to abnormalities in nontraditional MMR genes. This review discusses the role of traditional and nontraditional MMR genes in dMMR EC and related treatment strategies, highlights key issues in the current diagnosis and treatment of dMMR EC, and aims to enhance understanding of its heterogeneity and advance precision diagnosis and treatment. Full article

(This article belongs to the Special Issue Human Reproductive Biology: Uncertainties and Controversies)

21 pages, 1015 KB

Open AccessReview

Research Advances in Cancer-Associated Fibroblasts in Prostate Cancer Progression

by Zhonghao Tang, Si Shen, Chenwei Gu, Sixin Li, Yan Qin and Yuanyuan Mi

Biomolecules 2025, 15(10), 1369; https://doi.org/10.3390/biom15101369 - 26 Sep 2025

Abstract

The tumor microenvironment (TME) is crucial for tumor growth and progression, within which cancer-associated fibroblasts (CAFs) play a central role in regulating cancer cell proliferation, metastasis, and therapy resistance through various mechanisms. Although early-stage prostate cancer (PCa) has a high cure rate, advanced [...] Read more.

The tumor microenvironment (TME) is crucial for tumor growth and progression, within which cancer-associated fibroblasts (CAFs) play a central role in regulating cancer cell proliferation, metastasis, and therapy resistance through various mechanisms. Although early-stage prostate cancer (PCa) has a high cure rate, advanced disease often becomes difficult to manage due to resistance to standard therapies such as androgen deprivation therapy (ADT). Therefore, a deep understanding of the interaction mechanisms between CAFs and PCa cells is essential for developing novel therapeutic strategies targeting resistant advanced PCa. This review systematically summarizes key signaling pathways and molecular mechanisms through which CAFs promote PCa progression, as recently discovered, evaluates the potential of CAFs as prognostic biomarkers, and discusses novel CAF-based therapeutic targets and intervention strategies for PCa. Full article

(This article belongs to the Special Issue Molecular Advances in Drug Resistance and Novel Therapies for Cancer)

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14 pages, 838 KB

Open AccessArticle

A Safety Evaluation of N-Acetylglucosamine Produced by Bacillus subtilis BNZR 2-7: A Comprehensive In Vitro and In Vivo Genotoxicity Assessment

by Liangliang Zhang, Jiahui Hao, Xuefang Liu, Kualian Yang, Lina Bai, Qingping Hu and Saisai Feng

Biomolecules 2025, 15(10), 1368; https://doi.org/10.3390/biom15101368 - 26 Sep 2025

Abstract

N-acetylglucosamine (GlcNAc) is an important functional monosaccharide that serves as a key component in macromolecules such as cell walls and chitin. It has a wide range of applications in medicine, health supplements, and the chemical industry, leading to a growing market demand. This [...] Read more.

N-acetylglucosamine (GlcNAc) is an important functional monosaccharide that serves as a key component in macromolecules such as cell walls and chitin. It has a wide range of applications in medicine, health supplements, and the chemical industry, leading to a growing market demand. This study evaluated the potential genotoxicity of GlcNAc produced by Bacillus subtilis BNZR 2-7 through a comprehensive assessment in vitro and in vivo assays. GlcNAc was non-mutagenic in the Ames test using Salmonella typhimurium and Escherichia coli. Meanwhile, GlcNAc was non-genotoxic in the in vitro micronucleus assay using Chinese hamster ovary cells. In the in vivo assays, GlcNAc was non-genotoxic in the in vivo mammalian erythrocyte micronucleus test and spermatocyte chromosome aberration test in mice. These studies provide additional evidence that GlcNAc produced by Bacillus subtilis BNZR 2-7 is not genotoxic at the doses tested, supporting its safety for use in foods. Full article

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

17 pages, 722 KB

Open AccessArticle

Association of Plasma Placental Growth Factor with White Matter Hyperintensities in Alzheimer’s Disease

by Kazuya Igarashi, Tamao Tsukie, Kazuo Washiyama, Kiyoshi Onda, Yuki Miyagi, Shoya Inagawa, Soichiro Shimizu, Akinori Miyashita, Osamu Onodera, Takeshi Ikeuchi and Kensaku Kasuga

Biomolecules 2025, 15(10), 1367; https://doi.org/10.3390/biom15101367 - 26 Sep 2025

Abstract

Autopsy studies have shown that Alzheimer’s disease (AD) often coexists with cerebrovascular injury, affecting cognitive outcomes and the effectiveness of anti-amyloid-beta (Aβ) drugs. No fluid biomarkers of cerebrovascular injury have been identified yet. We investigated the association between white matter hyperintensities (WMH) severity [...] Read more.

Autopsy studies have shown that Alzheimer’s disease (AD) often coexists with cerebrovascular injury, affecting cognitive outcomes and the effectiveness of anti-amyloid-beta (Aβ) drugs. No fluid biomarkers of cerebrovascular injury have been identified yet. We investigated the association between white matter hyperintensities (WMH) severity and fluid biomarkers, including cerebrospinal fluid (CSF) neurofilament light chain and plasma placental growth factor (PlGF) levels. This study included 242 patients from memory clinics. Magnetic Resonance Imaging (MRI), CSF, and plasma samples were collected. Patients were classified as AD+ or non-AD based on the CSF Aβ42/Aβ40 ratio. In the discovery cohort (79 AD+ and 20 non-AD patients with 3D-T1 images), we analyzed the association between WMH volume and plasma PlGF. In the validation cohort (54 AD+ patients without 3D-T1 images), we analyzed the association between WMH grading and plasma PlGF. Among AD+ patients in the discovery cohort, plasma PlGF levels remained significantly associated with WMH volume and grading after adjusting for age, sex, and global cognition. Among the AD+ patients in the validation cohort, the high-PlGF (above median) group had significantly greater WMH volumes and a higher number of patients with a high WMH grading than the low-PlGF (below median) group. Plasma PlGF is a promising marker of cerebrovascular injury in AD. Full article

(This article belongs to the Special Issue Biomarkers in Neurodegenerative Diseases: Shaping the Future of Diagnosis and Treatment)

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22 pages, 9257 KB

Open AccessArticle

A Dual Regulatory Mechanism of Hormone Signaling and Fungal Community Structure Underpin Dendrobine Accumulation in Dendrobium nobile

by Yongxia Zhao, Nian Xiong, Xiaolong Ji, Dongliang Zhang, Qi Jia, Lin Qin, Xingdong Wu, Daopeng Tan, Jian Xie and Yuqi He

Biomolecules 2025, 15(10), 1366; https://doi.org/10.3390/biom15101366 - 26 Sep 2025

Abstract

(1) Objective: The biosynthesis of medicinal secondary metabolites in Dendrobium nobile Lindl. is regulated by complex environmental, hormonal, and microbial interactions. However, the mechanisms by which subtle variations in plant elevation shape metabolite accumulation through plant–microbe–hormone networks remain largely unexplored. (2) Methods: We [...] Read more.

(1) Objective: The biosynthesis of medicinal secondary metabolites in Dendrobium nobile Lindl. is regulated by complex environmental, hormonal, and microbial interactions. However, the mechanisms by which subtle variations in plant elevation shape metabolite accumulation through plant–microbe–hormone networks remain largely unexplored. (2) Methods: We conducted a multi-omics investigation of D. nobile cultivated under simulated wild conditions at four elevation gradients (347–730 m) in Chishui, China. High-throughput transcriptome sequencing and ITS-based fungal community profiling were combined with hormone quantification and functional prediction (FUNGuild), enabling integrated analysis of hormone pathway activation, microbial structure–function dynamics, and dendrobine levels. (3) Reults: This study systematically investigated D. nobile cultivated under simulated wild conditions across four elevation gradients (347–730 m) in the Danxia region of Chishui, China. We identified a dual regulatory mechanism underlying the elevation-dependent accumulation of dendrobine alkaloids, involving both plant hormone signaling and endophytic fungal communities. Transcriptomic analyses revealed coordinated upregulation of key hormone pathway genes, including DELLA, PYR/PYL, SnRK2, COI1-JAZ-MYC2, and NPR1-TGA, particularly in CY01Y samples at 670 m elevation from ChiYan base in Chishui city, which corresponded to the highest dendrobine content. Concurrently, functional prediction of the ITS-based fungal sequencing data revealed that CY01Y harbored a stable, functionally enriched fungal community dominated by saprotrophs, fungal parasites, and plant pathogens. (4) Conclusions: Through integrative hormone profiling, gene expression, and microbial function analysis, we propose that elevation-induced environmental cues reshape hormone pathways both directly and indirectly via microbial feedback. Specific microbial taxa were identified as potential modulators of hormone signaling and secondary metabolism. The coordinated interaction between plant hormones and endophytic fungi supports a hormone–microbiome–metabolite network that dynamically regulates dendrobine biosynthesis in response to micro-elevation variation. Full article

(This article belongs to the Section Biological Factors)

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21 pages, 4606 KB

Open AccessArticle

Targeting a Tau Kinase Cdk5, Cyclin-Dependent Kinase: A Blood-Based Diagnostic Marker and Therapeutic Earmark for Alzheimer’s Disease

by Sakshi Kumari, Abhinay Kumar Singh, Mukesh Kumar, Rashmita Pradhan, Abhijith R. Rao, Yudhishthir Yadav, Pramod Kumar, Partha Haldar, Punit Kaur and Sharmistha Dey

Biomolecules 2025, 15(10), 1365; https://doi.org/10.3390/biom15101365 - 26 Sep 2025

Abstract

Protein kinases are important molecules of Alzheimer’s Disease (AD), driving neuronal demise and the emergence of the disease’s destructive hallmarks. Cdk5 has recently been highlighted as a key therapeutic target for AD. This study evaluated the expression levels of Cdk5 and Mcl1 (Cdk5’s [...] Read more.

Protein kinases are important molecules of Alzheimer’s Disease (AD), driving neuronal demise and the emergence of the disease’s destructive hallmarks. Cdk5 has recently been highlighted as a key therapeutic target for AD. This study evaluated the expression levels of Cdk5 and Mcl1 (Cdk5’s substrate) in blood samples of 61 AD, 55 Mild Cognitive Impairment (MCI), and 57 Geriatric Controls (GC), and explored the in vitro inhibition of Cdk5. The serum levels of Cdk5 and Mcl1 were measured by Surface Plasmon Resonance (SPR) and verified by Western blot and RT-PCR. Molecular modeling and simulation studies were used to identify a potent hit targeting Cdk5 and validated by binding studies using SPR. The peptide rescue effect was analyzed by MTT assay in the AD cellular model. SPR analysis revealed a significant change in Cdk5 and Mcl1 levels in the serum samples of AD and MCI compared to GC. Results were validated by Western blot and RT-PCR. Binary logistic regression analysis revealed that the concentration of both Cdk5 and Mcl1 was independently associated with disease after adjusting for certain parameters. ROC analysis established an optimum diagnostic cutoff value for Cdk5 [24.97 ng/µL (AUC-0.90)] and Mcl1 [23.08 ng/µL (AUC-0.94)] with high sensitivity and specificity. The peptide YCWS strongly binds to Cdk5′s ATP binding site, confirmed by molecular modeling and SPR. In the AD cellular model, peptide YCWS rescued neurotoxicity, increased Mcl1 levels, and reduced destructive hallmarks by inhibiting Cdk5. It can be concluded that Cdk5 is a promising molecule as a circulatory biomarker for the diagnosis of the early stages of AD, and its peptide inhibitor YCWS is a potential therapeutic agent. Full article

(This article belongs to the Special Issue Biomarkers in Neurodegenerative Diseases: Shaping the Future of Diagnosis and Treatment)

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18 pages, 686 KB

Open AccessArticle

ET-1, MMPs, ZAG, and APN Link Reduced Ocular Perfusion to Glaucoma

by Maren Kasper, Kai Rothaus, Lasse Schopmeyer, Dirk Bauer, Swaantje Grisanti, Carsten Heinz, Karin Loser and Claudia Lommatzsch

Biomolecules 2025, 15(10), 1364; https://doi.org/10.3390/biom15101364 - 25 Sep 2025

Abstract

Purpose: This study sets out to analyze the correlation of ET-1, a vasoactive peptide, along with various cytokines and vascular factors, with clinical parameters and OCT/OCT-A measurements in glaucoma participants. Methods: Eyes of participants with cataract (n = 30) or glaucoma [...] Read more.

Purpose: This study sets out to analyze the correlation of ET-1, a vasoactive peptide, along with various cytokines and vascular factors, with clinical parameters and OCT/OCT-A measurements in glaucoma participants. Methods: Eyes of participants with cataract (n = 30) or glaucoma (n = 87) were examined with optical coherence tomography (OCT) and OCT angiography (OCT-A). Aqueous humor (AqH) from the examined eye and plasma were sampled during cataract or glaucoma surgery and analyzed by means of ELISA and Luminex assay to determine their levels of ET-1 and 35 proteins deemed relevant for regulation of the AqH outflow pathway, ocular perfusion (OP), and glucose metabolism. Results: Glaucomatous eyes are characterized by reductions in RNFL thickness and OP, reflected by reduced vessel density. Furthermore, significantly elevated peripheral ET-1 levels were detected in participants with glaucoma. In addition, significantly elevated AqH levels of MMP-2, MMP-3, ET-1, sEMMPRIN, ZAG, sLOX-1, follistatin, cortisol, endostatin, sTIE-2, and PDGF-BB were detected in the glaucomatous eyes, with correlation to reduced VD for APN, C3a, MMP-3, resistin, sTIE-2, and ZAG. Multivariable analysis showed a correlation of AqH APN levels with the reduced VD in glaucomatous eyes. Conclusions: The peripheral ET-1 level and the intraocular levels of APN, C3a, MMP-3, resistin, sTIE-2, and ZAG are associated with impaired OP in glaucoma. Furthermore, elevated intraocular levels of MMP-3, ZAG, and APN were identified as biomarkers for impaired perfusion in glaucoma. Full article

(This article belongs to the Topic Advances in Adiponectin)

20 pages, 2154 KB

Open AccessArticle

Evaluating the Influence of CHI3L1 and PI3 Methylation in Allergic and Nonallergic Asthma

by Selene Baos, Lucía Cremades-Jimeno, María Ángeles de Pedro, María López-Ramos, Rubén Fernández-Santamaría, Cristina Rosales-Ariza, Joaquín Quiralte, Fernando Florido, Nicolás González-Mangado, María Jesús Rodríguez-Nieto, Germán Peces-Barba, Joaquín Sastre and Blanca Cárdaba

Biomolecules 2025, 15(10), 1363; https://doi.org/10.3390/biom15101363 - 25 Sep 2025

Abstract

Previously, we defined CHI3L1 and PI3 as genes related with asthma and severity by analysis of differential gene expression. In this study, we investigated the role of DNA methylation in their regulation, and their relationship with protein levels and clinical parameters. Peripheral blood [...] Read more.

Previously, we defined CHI3L1 and PI3 as genes related with asthma and severity by analysis of differential gene expression. In this study, we investigated the role of DNA methylation in their regulation, and their relationship with protein levels and clinical parameters. Peripheral blood mononuclear cells (PBMCs) and sera were collected from healthy controls (HCs), nonallergic asthmatic (NA), and allergic asthmatic (AA) patients. RNA and DNA were extracted from PBMCs using the trizol method. Gene expression was assessed by qRT-PCR, and DNA methylation of CpG sites near the promoters was analyzed using sodium bisulfite treatment followed by PCR amplification. DNA methylation analysis was performed using the Sequenom EpiTYPER platform. Protein levels were quantified by ELISA, and statistical analyses were carried out using GraphPad software. Consistent with previous findings, CHI3L1 and PI3 gene expression were significantly lower in asthmatic patients compared to controls. Conversely, CHI3L1 protein levels were higher in both patient groups, while PI3 protein showed no significant changes. DNA methylation analysis revealed higher overall DNA methylation percentages in NA and AA patients for both genes compared to HCs. Despite this, no significant correlations were observed between DNA methylation and gene or protein expression, although some correlations were observed with clinical parameters. In conclusion, CHI3L1 and PI3 represent potential asthma biomarkers, whose regulation may be partially influenced by DNA methylation, a mechanism more pronounced in asthmatic patients than in healthy subjects. Full article

(This article belongs to the Special Issue Molecular Pathology, Diagnostics, and Therapeutics of Lung Disease)

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15 pages, 4179 KB

Open AccessArticle

The Respiratory Burst of Human Granulocytes Is Mostly Independent of Potassium

by Iryna Mahorivska, Martin Geltinger, Gustavo Chaves, Sebastian Lobmann, Martin Jakab, Katharina Helm and Boris Musset

Biomolecules 2025, 15(10), 1362; https://doi.org/10.3390/biom15101362 - 25 Sep 2025

Abstract

Reactive oxygen species (ROS) are among the most effective tools of the innate immune response against pathogenic microbes. The respiratory burst (RB) of polymorphonuclear leukocytes (PMNs) generates an electron current that reduces molecular oxygen to superoxide. Superoxide reacts to form hydrogen peroxide as [...] Read more.

Reactive oxygen species (ROS) are among the most effective tools of the innate immune response against pathogenic microbes. The respiratory burst (RB) of polymorphonuclear leukocytes (PMNs) generates an electron current that reduces molecular oxygen to superoxide. Superoxide reacts to form hydrogen peroxide as a precursor to the highly bactericidal hypochlorous acid. Here, we investigated whether alterations in extracellular potassium concentration impact H₂O₂ production. Such changes may occur, for example, during massive cell death due to necrosis or due to trauma injuries when potassium diffuses out of the cells. We recorded H₂O₂ release over a 2 h period of RB under varying potassium concentrations. Except for 100 mM potassium chloride, which increased the time delay before detectable H₂O₂ production, none of the potassium concentrations had a substantial effect on RB. We further examined whether this effect depended on the specific monovalent ion species. When sodium or methanesulfonate was used instead of potassium or chloride, respectively, no changes in H₂O₂ production were observed. Cell volume measurements under different potassium concentrations showed that only 100 mM potassium chloride significantly shrank the cells. We propose that hypertonic stress is crucial for delaying RB in human granulocytes, whereas the RB itself is independent of the tested ionic species. Additionally, the conducted hypertonic stress experiments revealed an unexpected time-dependence during the course of the RB, showing that the first 6 min were almost inert to hyperosmotic stress. Full article

(This article belongs to the Special Issue Advances in Cellular Biophysics: Transport and Mechanics)

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21 pages, 2253 KB

Open AccessArticle

Anticancer Activity of Jania rubens in HCT-116 Cells via EMT Suppression, TET Downregulation, and ROS-Mediated Cytotoxicity

by Zeina Radwan, Rayan Kassir, Fouad Al Feghaly, Rouaa Zaiter, Mira Abou Daher, Rabih Roufayel, Ziad Fajloun, Hiba Mawlawi, Marwan El-Sabban and Zeina Dassouki

Biomolecules 2025, 15(10), 1361; https://doi.org/10.3390/biom15101361 - 25 Sep 2025

Abstract

The red seaweed Jania rubens (J. rubens) is prevalent along the Lebanese coast and has drawn attention for its notable antineoplastic properties. Our previous data showed that its dichloromethane–methanol (DM) extract possesses antioxidant, cytotoxic, and anti-migratory effects on colon cancer cells. [...] Read more.

The red seaweed Jania rubens (J. rubens) is prevalent along the Lebanese coast and has drawn attention for its notable antineoplastic properties. Our previous data showed that its dichloromethane–methanol (DM) extract possesses antioxidant, cytotoxic, and anti-migratory effects on colon cancer cells. In the present study, a GC-MS analysis of DM extract identified a diverse profile of bioactive compounds, including flavonoids and pyrazole derivatives with antioxidant and anticancer activities. In vitro assays demonstrated that the DM extract exerts significant cytotoxic activity against various cancer cell lines, including colon, breast, and cervical types. Further investigation into the underlying molecular mechanisms revealed that the extract induces G2/M cell cycle arrest and reduces the expression of EMT (epithelial–mesenchymal transition) markers, N-cadherin and Twist. In addition, the extract showed anti-metastatic properties through its ability to decrease MMP-2 and MMP-9 activity. Mechanistically, DM caused a substantial reduction in Ten-Eleven Translocation (TET) enzymes TET-1, TET-2, and TET-3, which are essential DNA demethylation regulators, thus decreasing their enzymatic product 5-hydroxymethylcytosine (5-hmC). Interestingly, despite a significant increase in intracellular ROS (reactive oxygen species), suggesting a contribution to cytotoxicity, no substantial change in the biogenesis of promyelocytic leukemia nuclear bodies (PML-NBs) was detected. These findings demonstrate that J. rubens DM extract contains bioactive compounds with multiple anticancer effects, thus making it a promising candidate for developing new therapeutic agents. Full article

(This article belongs to the Special Issue The Value of Natural Compounds as Therapeutic Agents: 3rd Edition)

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20 pages, 49146 KB

Open AccessArticle

Predicted IL-18/IL-18R Binding Improvement Through Protein Interface Modification with Computer-Aided Design

by Napat Prompat, Chariya Peeyatu, Jirakrit Saetang, Niran Roongsawang, Surasak Sangkhathat and Varomyalin Tipmanee

Biomolecules 2025, 15(10), 1360; https://doi.org/10.3390/biom15101360 - 25 Sep 2025

Abstract

Cytokine-mediated immunotherapy has rapidly emerged as an effective alternative approach for cancer treatment by modulating the anti-tumor response. Interleukin-18 (IL-18) is considered as a promising cancer therapeutic agent due to the ability of cytokines to inhibit cancer by enhancing natural killer (NK) cell [...] Read more.

Cytokine-mediated immunotherapy has rapidly emerged as an effective alternative approach for cancer treatment by modulating the anti-tumor response. Interleukin-18 (IL-18) is considered as a promising cancer therapeutic agent due to the ability of cytokines to inhibit cancer by enhancing natural killer (NK) cell and cytotoxic T cell responses. Since the activity of IL-18 is required for the specific binding to IL-18 receptors, the modification of binding residue at the protein interface is an attractive strategy for IL-18 activity enhancement. The aim of this study was to design and predict mutations increasing the activity of IL-18 through computational structure-based energy calculation and molecular dynamic simulations. Four candidate mutations, E6M, E6M+N111S+R131G, E6M+K129M+R131G, and E6M+N111S+K129M+R131G, could affect/facilitate the receptor binding and stability compared to the wild-type via electrostatic interaction. MD simulations demonstrated that the predicted mutation on IL-18 had no influence on the overall conformation stability, but increased flexibility in the β8–β9 hairpin loop. Furthermore, the dynamic behavior suggested that these candidates could be an alternative for the improvement of IL-18 biological activity, though the full simulation of the IL-18 complex remains necessary. In summary, this study offered a computer-aided design strategy which was of beneficial use in the design and development of IL-18 to increase its cytokine potency and efficiency. Full article

(This article belongs to the Special Issue Protein Structure Prediction in Drug Discovery: 2nd Edition)

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13 pages, 722 KB

Open AccessArticle

An In Vivo Drug Screen Reveals That Sirtuin 2 Activity Promotes Spinal Cord Neurogenesis in Developing Zebrafish

by Laura González-Llera, Álvaro J. Arana, Laura Sánchez and Antón Barreiro-Iglesias

Biomolecules 2025, 15(10), 1359; https://doi.org/10.3390/biom15101359 - 24 Sep 2025

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Abstract

Given the central role of neurogenesis in building a functional nervous system, we recently developed a zebrafish-based drug-screening protocol to uncover molecules and signalling pathways regulating spinal cord neurogenesis. In this study, we have expanded this drug screen and discovered a previously unknown [...] Read more.

Given the central role of neurogenesis in building a functional nervous system, we recently developed a zebrafish-based drug-screening protocol to uncover molecules and signalling pathways regulating spinal cord neurogenesis. In this study, we have expanded this drug screen and discovered a previously unknown role of deacetylase sirtuin 2 (SIRT2) in promoting the generation of serotonergic interneurons in the spinal cord. Treatments with specific SIRT2 inhibitors reduced the generation of serotonergic neurons in the spinal cord, which led to locomotor deficits. Our data suggest that SIRT2 regulates mitotic activity in progenitor cells to promote the generation of serotonergic neurons in developing animals. Together, our results uncover SIRT2 as a key regulator of spinal cord neurogenesis and position it as a promising target for strategies aimed at neural repair in spinal cord disorders. Full article

(This article belongs to the Section Cellular Biochemistry)

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17 pages, 895 KB

Open AccessReview

Proteomic Signatures of Hippocampal Nonsynaptic and Synaptosome-Enriched Mitochondria in Rats Resilient to Chronic Social Isolation

by Dragana Filipović and Christoph W. Turck

Biomolecules 2025, 15(10), 1358; https://doi.org/10.3390/biom15101358 - 24 Sep 2025

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Abstract

Chronic social isolation (CSIS), a known risk factor for the development of major depressive disorders, is associated with hippocampal dysfunction. In rodent models, CSIS produces two phenotypes: CSIS-susceptible, which develop depressive- and anxiety-like behaviors, and CSIS-resilient, which maintain normal behavior despite stress. However, [...] Read more.

Chronic social isolation (CSIS), a known risk factor for the development of major depressive disorders, is associated with hippocampal dysfunction. In rodent models, CSIS produces two phenotypes: CSIS-susceptible, which develop depressive- and anxiety-like behaviors, and CSIS-resilient, which maintain normal behavior despite stress. However, the biological mechanisms underlying resilience to stress remain elusive. Mitochondria, as central regulators of neuronal energy metabolism and redox balance, are potential mediators of stress susceptibility and resilience. This review summarizes comparative proteomic analyses of hippocampal nonsynaptic mitochondria (NSM) and synaptosome-enriched mitochondria from CSIS-susceptible and CSIS-resilient rats along with controls. In NSM of resilient rats relative to susceptible rats, remodeling enhanced energy production, limited reactive oxygen species, stabilized phosphate transport, and promoted removal of damaged components. Compared with controls, these changes optimized energy production, and selectively downregulated oxidative stress-promoting proteins. Conversely, synaptosome-enriched mitochondria from resilient rats showed downregulation of proteins related to synaptic energy metabolism and redox balance relative to CSIS-susceptible rats, but demonstrated upregulation of bioenergetic and antioxidant enzymes, molecular chaperones, and neuroprotective factors compared with controls. These proteomic signatures both highlight mitochondrial adaptability in promoting stress resilience and identify mitochondria as promising targets for the development of novel antidepressant therapies. Full article

(This article belongs to the Special Issue Insights into Mitochondria in Psychiatric Disorders)

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18 pages, 2871 KB

Open AccessArticle

Staphylococcal Enterotoxin M Exhibits Thrombin-like Enzymatic Activity

by Qian Huang, Shuang-Hua Luo, Wan-Fan Tian, Jun-Ni Tang and Ji Liu

Biomolecules 2025, 15(10), 1357; https://doi.org/10.3390/biom15101357 - 24 Sep 2025

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Abstract

To express and purify staphylococcal enterotoxin M (SEM) using immobilized metal affinity chromatography (IMAC), a signal peptide-truncated (ΔNsp) wild-type SEM (SEM_WT) was N-terminally fused in pET-28a(+) to a polyhistidine tag (His_6×-) and thrombin cleavage site (TCS; LVPR↓GS), generating His [...] Read more.

To express and purify staphylococcal enterotoxin M (SEM) using immobilized metal affinity chromatography (IMAC), a signal peptide-truncated (ΔNsp) wild-type SEM (SEM_WT) was N-terminally fused in pET-28a(+) to a polyhistidine tag (His_6×-) and thrombin cleavage site (TCS; LVPR↓GS), generating His_6×-TCS-ΔNspSEM_WT. Unexpectedly, 4 °C desalting reduced the fusion protein’s molecular weight by ~2.0 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). N-terminal sequencing and mass spectrometry identified cleavage specifically at the arginine (R) and glycine (G) peptide bond (R–G bond) within the TCS motif. AlphaFold 3 revealed an exposed serine protease catalytic triad: histidine 172, serine 178, and aspartic acid 212 (H₁₇₂/S₁₇₈/D₂₁₂) in the β-grasp domain, suggesting intrinsic thrombin-like activity (TLA). Sequential IMAC and size-exclusion high-performance liquid chromatography (SE-HPLC) purification eliminated contaminant concerns, while chromogenic substrate S-2238 (S-2238) assays demonstrated increasing specific activity and purification fold, supporting intrinsic TLA. Critically, the mutation of serine at position 178 to alanine (His_6×-TCS-ΔNspSEM_S178A) abolished TLA but preserved the secondary/tertiary structure, confirming the activity’s origin within the wild-type construct. Molecular dynamics (MD) simulations probed the atomistic mechanism for specific R–G bond cleavage. This work establishes a foundation for understanding ΔNspSEM_WT’s TLA. Full article

(This article belongs to the Section Enzymology)

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17 pages, 7798 KB

Open AccessArticle

Dendritic Cell-Cytokine-Induced Killer Cells Co-Loaded with WT1/MUC1/Poly(I:C) Enhance Antitumor Immune Responses In Vitro and In Vivo

by Huimin Liu, Chenlong Wang, Hongtao Chang, Liangliang Dong, Guoqing Yang, Cailing Tong and Lin Mao

Biomolecules 2025, 15(10), 1356; https://doi.org/10.3390/biom15101356 - 24 Sep 2025

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Abstract

Dendritic cell-cytokine-induced killer (DC-CIK) therapy faces limitations due to antigenic heterogeneity and suboptimal immune activation. In this study, we developed a multi-antigen-loaded DC-CIK (Ag-DC-CIK) system that co-targets Wilms’ tumor 1 (WT1), mucin-1 (MUC1), and the TLR3 agonist poly(I:C) to improve therapeutic outcomes. Utilizing [...] Read more.

Dendritic cell-cytokine-induced killer (DC-CIK) therapy faces limitations due to antigenic heterogeneity and suboptimal immune activation. In this study, we developed a multi-antigen-loaded DC-CIK (Ag-DC-CIK) system that co-targets Wilms’ tumor 1 (WT1), mucin-1 (MUC1), and the TLR3 agonist poly(I:C) to improve therapeutic outcomes. Utilizing umbilical cord blood-derived DC and CIK cells, we demonstrated that Ag-DC-CIK significantly enhanced cytotoxicity, as evidenced by the lactate dehydrogenase (LDH) assay, and increased apoptosis induction, indicated by elevated Bax and reduced Bcl-2 expression, in various tumor cell lines (HeLa, HCT116, MKN45) and organoids generated from a gastric cancer patient. Furthermore, Ag-DC-CIK effectively suppressed tumor cell migration and reduced the viability of the organoid. In MKN45 xenograft models, Ag-DC-CIK treatment inhibited tumor growth without inducing systemic toxicity, as shown by decreased Ki67 cell proliferation. This tripartite strategy synergistically enhances DC-CIK therapy by expanding antigen recognition and augmenting immune responses, presenting a promising translational approach for the treatment of gastric cancer. Full article

(This article belongs to the Section Cellular Biochemistry)

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18 pages, 1558 KB

Open AccessArticle

Oral Microbiota Taxa and Pri-miRNA Expression in Bipolar Disorder: A Case–Control Study

by Diego Primavera, Mauro Giovanni Carta, Massimo Tusconi, Goce Kalcev, Laura Atzori, Caterina Ferreli, Rober Romero Ramirez, Letizia Peddio, Cinzia Casu, Sara Fais, Germano Orrù and Alessandra Scano

Biomolecules 2025, 15(10), 1355; https://doi.org/10.3390/biom15101355 - 24 Sep 2025

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Abstract

Background/Objectives: Emerging evidence suggests a role for oral microbiota in mood disorders, particularly bipolar disorder (BD), complementing established links between gut dysbiosis and psychiatric symptoms. This study investigates the composition of oral microbial taxa and the expression of inflammation-related pri-miRNAs (146a and 155) [...] Read more.

Background/Objectives: Emerging evidence suggests a role for oral microbiota in mood disorders, particularly bipolar disorder (BD), complementing established links between gut dysbiosis and psychiatric symptoms. This study investigates the composition of oral microbial taxa and the expression of inflammation-related pri-miRNAs (146a and 155) in individuals with BD, aiming to explore their potential as biomarkers in the oral–gut–brain axis. Methods: A matched case–control design was implemented, recruiting 25 BD patients and 46 controls matched by age and sex. Salivary samples were collected, and microbial profiling was conducted via real-time qPCR targeting major bacterial phyla and genera. Pri-miRNA 146a and 155 expression was evaluated through RT-qPCR using validated primers. Statistical comparisons between groups were performed using Fisher’s exact test and non-parametric tests for continuous variables. Results: Microbial analysis revealed significant reductions (p < 0.01) in α-Proteobacteria, γ-Proteobacteria, and Actinobacteria in BD patients versus controls. A shift toward a higher Firmicutes/Bacteroidetes ratio was observed in the BD cohort, suggesting differences in the oral biotic status between the two groups. However, pri-miRNA 146a and 155 expression levels did not differ significantly between the groups and exhibited high inter-individual variability. Conclusions: The findings indicate that oral microbiota composition differs in BD patients, potentially influencing systemic homeostasis through interactions with gut microbial communities and SCFA pathways. These findings should be interpreted as preliminary and hypothesis-generating given the modest sample size. While pri-miRNAs 146a and 155 did not distinguish BD status, the observed microbial taxa alterations should be regarded as exploratory and hypothesis-generating. Larger, longitudinal studies are required to clarify their potential role in BD pathogenesis and risk assessment. Full article

(This article belongs to the Special Issue Biomarkers and Molecular Basis of Psychiatry)

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23 pages, 2820 KB

Open AccessArticle

Mitochondrial Translation Inhibition Triggers an Rst2-Controlled Transcriptional Reprogramming of Carbon Metabolism in Stationary-Phase Cells of Fission Yeast

by Ying Luo, Shaimaa Hassan, Saniya Raut and Jürg Bähler

Biomolecules 2025, 15(10), 1354; https://doi.org/10.3390/biom15101354 - 24 Sep 2025

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Abstract

Mitochondria possess their own genome, which encodes subunits of the electron transport chain, rendering mitochondrial protein translation essential for cellular energy metabolism. Mitochondrial dysfunction affects nuclear transcription through the retrograde response. We applied RNA-seq to investigate whether and how the inhibition of mitochondrial [...] Read more.

Mitochondria possess their own genome, which encodes subunits of the electron transport chain, rendering mitochondrial protein translation essential for cellular energy metabolism. Mitochondrial dysfunction affects nuclear transcription through the retrograde response. We applied RNA-seq to investigate whether and how the inhibition of mitochondrial translation by chloramphenicol (CAP) affects transcriptome regulation in proliferating or stationary-phase cells of Schizosaccharomyces pombe growing in fermentative or respiratory media. Stationary-phase cells in glucose medium exhibited the strongest transcriptome response to CAP, characterized by expression signatures similar to those observed under other stresses, including the retrograde response. The induced genes were also significantly enriched in cytoplasmic carbon metabolism pathways, reflecting a transcriptional reprogramming from respiration to fermentation. The transcription factors Scr1 and Rst2, regulators of carbon catabolite repression (CCR), controlled a common set of carbon metabolism genes in CAP-treated stationary-phase cells, and they showed opposing effects on the lifespan of these cells. Rst2 was required for the induction of carbon metabolism genes and maintained nuclear localization in CAP-treated stationary-phase cells. A systematic genetic interaction screen revealed functional relationships of Rst2 with processes related to stress and starvation responses. These findings uncover a complex transcriptional program in stationary-phase cells that adapt to inhibited mitochondrial translation, including stress- and retrograde-like responses, contributions of the CCR factors Scr1 and Rst2, and adjustment of carbon metabolism to deal with mitochondrial dysfunction. Full article

(This article belongs to the Special Issue Cellular Quiescence and Dormancy)

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22 pages, 8043 KB

Open AccessArticle

METTL3-Driven m6A Epigenetic Remodeling of lncRNA-AU020206 Stabilizes SLC7A11 via YTHDC2 Attenuates Apoptosis and Ferroptosis in Cerebral Ischemia/Reperfusion Injury

by Hao Zhang, Yajin Guan, Meng Li, Yilin Wu and Xiaoou Sun

Biomolecules 2025, 15(10), 1353; https://doi.org/10.3390/biom15101353 - 24 Sep 2025

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Abstract

Cerebral ischemia/reperfusion (I/R) injury is a devastating neurological disorder with limited treatment options. Emerging evidence suggests that the N6-methyladenosine (m6A) modification and its regulatory factors play pivotal roles in the pathophysiology of I/R. This study aimed to elucidate the function of METTL3-mediated m6A [...] Read more.

Cerebral ischemia/reperfusion (I/R) injury is a devastating neurological disorder with limited treatment options. Emerging evidence suggests that the N6-methyladenosine (m6A) modification and its regulatory factors play pivotal roles in the pathophysiology of I/R. This study aimed to elucidate the function of METTL3-mediated m6A modification of the long non-coding RNA (lncRNA) AU020206 in ferroptosis during cerebral I/R injury and to identify potential molecular targets for neuroprotection. A murine model of middle cerebral artery occlusion/reperfusion (MCAO/R) and N2a cells subjected to oxygen–glucose deprivation/reoxygenation (OGD/R) were established to assess m6A levels and ferroptosis-related changes. Effects of METTL3 overexpression and lncRNA-AU020206 silencing on neuronal apoptosis, inflammation, and ferroptosis were investigated in vitro and in vivo. The interaction between lncRNA-AU020206 and YTHDC2 and the resulting regulation of SLC7A11 mRNA stability and GPX4 expression were evaluated using molecular and biochemical assays. Both MCAO/R mice and OGD/R-treated N2a cells exhibited decreased m6A levels and upregulation of lncRNA-AU020206 accompanied by enhanced ferroptosis. METTL3 overexpression increased the m6A modification of AU020206, promoting its degradation and attenuating neuronal injury, whereas silencing AU020206 or overexpressing YTHDC2 decreased SLC7A11 mRNA stability and enhanced ferroptosis. Restoring the expression of SLC7A11/GPX4 can enhance cell viability, alleviate neuronal apoptosis, and reduce Fe²⁺ overload. Disruption of the METTL3–AU020206–YTHDC2 axis abolished these neuroprotective effects. METTL3-mediated m6A modification of lncRNA-AU020206 restrained ferroptosis and neuronal injury in cerebral I/R by maintaining the stability of the SLC7A11/GPX4 axis via interactions with YTHDC2. Targeting this epitranscriptomic signalling pathway may represent a promising therapeutic strategy for the treatment of ischemic stroke and related neurological disorders. Full article

(This article belongs to the Section Molecular Medicine)

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18 pages, 1641 KB

Open AccessArticle

The ExPAND Study: A Prospective Association Study into Endometriosis-Associated Pain, Neurosteroid Synthesis, and TRPM3

by Eleonora Persoons, Celine Bafort, Pilar Van Mechelen, Martina Ciprietti, Katrien Luyten, Melissa Benoit, Arne Vanhie, Thomas Voets, Carla Tomassetti and Joris Vriens

Biomolecules 2025, 15(10), 1352; https://doi.org/10.3390/biom15101352 - 23 Sep 2025

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Abstract

Endometriosis-associated pain has debilitating effects on the quality of life of patients. Despite its high prevalence in reproductive-aged women, the pathophysiology is still unknown, impeding the development of targeted treatment approaches. The prospective ExPAND study proposes the neurosteroids pregnenolone sulphate (PS) and dehydroepiandrosterone [...] Read more.

Endometriosis-associated pain has debilitating effects on the quality of life of patients. Despite its high prevalence in reproductive-aged women, the pathophysiology is still unknown, impeding the development of targeted treatment approaches. The prospective ExPAND study proposes the neurosteroids pregnenolone sulphate (PS) and dehydroepiandrosterone sulphate (DHEAS) as potential contributors to endometriosis-associated pain, due to their agonistic action at the pain-related ion channel TRPM3. To this end, endometrium, deep endometriosis lesions, and peritoneal fluid were prospectively collected in four demarcated patient groups, which were characterised based on their pain symptoms, as scored via the WERF-EPHect questionnaire, i.e., (1) control (n = 44), (2) endometriosis patients with no pain symptoms (n = 24), (3) with only severe dysmenorrhea (n = 54), or (4) with both severe dysmenorrhea and non-cyclic pelvic pain (n = 78). Tissue mRNA expression levels of steroidogenic enzymes were investigated and showed significantly increased levels of CYP17A1 in the endometrium of patients with severe pain symptoms compared to control tissue. In addition, liquid chromatography with tandem mass spectrometry (LC-MS/MS) was performed to investigate neurosteroid concentrations in the peritoneal fluid. Both neurosteroids PS and DHEAS were present in the peritoneal fluid at concentrations that are known to stimulate TRPM3 activity in vitro. Finally, using microfluorimetric Ca²⁺ imaging, we demonstrate that both DHEAS and PS stimulate human stem-cell-derived sensory neurons in a TRPM3-dependent manner. Taken together, these data indicate a potential contribution of steroidogenesis and TRPM3 in endometriosis-associated pain. Full article

(This article belongs to the Special Issue Role of Neuroactive Steroids in Health and Disease: 2nd Edition)

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41 pages, 3105 KB

Open AccessReview

The Effects and Mechanisms of Low-Intensity Pulsed Ultrasound on Bone Remodeling: From Laboratory to Clinic

by Bo Zong, Weikang Sun, Chao Cai and Peng Shang

Biomolecules 2025, 15(10), 1351; https://doi.org/10.3390/biom15101351 - 23 Sep 2025

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Abstract

Decades of research and applications have demonstrated that low-intensity pulsed ultrasound (LIPUS) has a certain therapeutic effect on diseases involving bone remodeling. LIPUS operates in a pulsed-wave mode at low intensity, ensuring efficient transmission of acoustic energy to target tissues, thereby providing non-invasive [...] Read more.

Decades of research and applications have demonstrated that low-intensity pulsed ultrasound (LIPUS) has a certain therapeutic effect on diseases involving bone remodeling. LIPUS operates in a pulsed-wave mode at low intensity, ensuring efficient transmission of acoustic energy to target tissues, thereby providing non-invasive physical stimulation for therapeutic purposes. Bone remodeling refers to the dynamic renewal process of bone tissue that is jointly completed by multiple cells in the bone metabolic microenvironment. LIPUS influences the basic biological processes of bone remodeling in the skeletal system through mechanical, piezoelectric, and thermal effects on bone tissue, triggering a series of biochemical reactions. This article begins with the discovery of ultrasound and research on bone remodeling, introduces the basic parameters and application devices of LIPUS, and reviews the clinical applications of and basic research on LIPUS in bone remodeling disorders. Focusing on the intersection and integration of biomedical fundamentals and ultrasound science, it analyzes the biological and physical mechanisms of LIPUS in research on and applications of bone remodeling disorders and investigates the basic research questions and clinical transformation application scenarios in this field. Full article

(This article belongs to the Special Issue Advances in Cellular Biophysics: Transport and Mechanics)

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12 pages, 2249 KB

Open AccessArticle

Critical Role of RPS4X in Modulating SCF Complex Formation and Cell Survival

by Satsuki Ryu, Min Ji Kim, Shuya Bando, Yuka Tanaka, Risa Mukai, Yasuhiro Ishihara, Takashi Tominaga and Takayuki Ohshima

Biomolecules 2025, 15(10), 1350; https://doi.org/10.3390/biom15101350 - 23 Sep 2025

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Abstract

Ribosomal proteins have long been recognized as vital components of ribosomes that are involved in protein synthesis. However, emerging evidence indicates that some ribosomal proteins exhibit extraribosomal functions. In this study, we investigated the role of the ribosomal protein S4 X-linked (RPS4X) in [...] Read more.

Ribosomal proteins have long been recognized as vital components of ribosomes that are involved in protein synthesis. However, emerging evidence indicates that some ribosomal proteins exhibit extraribosomal functions. In this study, we investigated the role of the ribosomal protein S4 X-linked (RPS4X) in the regulation of the Skp1–Cullin1–F-box (SCF) ubiquitin ligase complex and apoptosis. We found that RPS4X expression interfered with SCF complex formation by disrupting the interaction between Cullin1 and Skp1. This disruption suppressed ubiquitination of multiple SCF complex substrates, including the anti-apoptotic proteins myeloid cell leukemia 1 (MCL1) and HS1-associated protein X1 (HAX1). Stabilization of MCL1 and HAX1 by RPS4X led to increased resistance of HeLa cells to doxorubicin-induced apoptosis. These findings suggest that RPS4X contributes to the regulation of protein homeostasis and apoptotic pathways by modulating SCF complex activity, providing new insights into the extraribosomal roles of ribosomal proteins. Full article

(This article belongs to the Section Molecular Biology)

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29 pages, 2729 KB

Open AccessReview

Applications of Isothermal Titration Calorimetry in Studying Biomimetic Nanocarriers

by Martin Guerrero, Colby Braden and Yuping Bao

Biomolecules 2025, 15(10), 1349; https://doi.org/10.3390/biom15101349 - 23 Sep 2025

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Abstract

Biomimetic nanocarriers, particularly membrane-based systems, have emerged as promising platforms for drug delivery. A thorough understanding of the molecular interactions that govern their assembly, stability, and cargo-loading efficiency is essential for optimizing their design and performance. Equally important are their interactions with biological [...] Read more.

Biomimetic nanocarriers, particularly membrane-based systems, have emerged as promising platforms for drug delivery. A thorough understanding of the molecular interactions that govern their assembly, stability, and cargo-loading efficiency is essential for optimizing their design and performance. Equally important are their interactions with biological components such as proteins, lipids, nucleotides, and cells, which significantly influence delivery efficacy. Among various techniques for characterizing these nanocarriers, isothermal titration calorimetry (ITC) has proven to be an invaluable tool to study their molecular interactions. ITC enables direct quantification of key thermodynamic parameters, such as binding affinity, stoichiometry, enthalpy, and entropy changes, without the need for molecular labeling or immobilization. This review highlights the application of ITC in the study of biomimetic nanocarriers, focusing on solid lipid nanoparticles, liposomes, extracellular vesicles, cell-derived vesicles and live cells. For each type of nanocarrier, the ITC applications in specific areas and the resulting information are discussed. For example, ITC was used to characterize drug interaction and protein adsorption for solid nanoparticles. In contrast, many aspects of liposomes were explored by ITC, including membrane solubilization and stabilization, peptide interactions, and macromolecule and protein adsorption. Overall, this review aims to provide a conceptual and practical framework for employing ITC in the investigation of biomimetic nanocarrier systems, facilitating their rational design and improved therapeutic performance. Furthermore, the discussion encourages further development of strategies to increase the application in cell-derived vesicles and live cells. Full article

(This article belongs to the Special Issue Advances in Nano-Based Drug Delivery: Unveiling the Next Frontier)

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Biomolecules, Volume 15, Issue 10 (October 2025) – 27 articles

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