Biomolecules

23 pages, 2986 KiB

Open AccessArticle

Dynamic Mechanical Load as a Trigger for Growth and Proliferation in Porcine Epithelial Cells

by Stefan Kahlert, Constanze Nossol, Marcus Krüger, Sascha Kopp, Daniela Grimm, Simon L. Wuest and Hermann-Josef Rothkötter

Biomolecules 2025, 15(3), 455; https://doi.org/10.3390/biom15030455 - 20 Mar 2025

Viewed by 299

Abstract

The impact of gravity is a basic force determining our existence on Earth. Changes in orientation with respect to the gravity vector trigger alternating mechanical forces on organisms, organs, and cells. In the intestines of mammals, epithelial cells are continuously exposed to changed [...] Read more.

The impact of gravity is a basic force determining our existence on Earth. Changes in orientation with respect to the gravity vector trigger alternating mechanical forces on organisms, organs, and cells. In the intestines of mammals, epithelial cells are continuously exposed to changed orientations to gravity. In this study, we employed dynamic cultivation systems to mimic the load changes and the resulting mechanical forces. The morphological and functional response of non-cancer-derived porcine epithelial cell lines IPEC-1 and IPEC-J2 was analyzed. We found that dynamic growth conditions affect morphology in the enterocyte model IPEC-1 but not in IPEC-J2. Changes in IPEC-1 were accompanied by modifications of the distribution and structure of the F-actin cytoskeleton rather than the amount. The structure of the apical brush border and the tight junction system seemed to be largely unaffected; however, a robust decrease in transepithelial resistance was found in IPEC-1 and partially in IPEC-J2. We further detected an increase in Ki67, pointing towards accelerated proliferation. In line with this finding, we detected a doubling of cellular mitochondrial respiration, which was not linked to a general increase in the respiratory chain capacity. Dynamic cultivation of confluent epithelial cell layers did not evoke signs of senescence. In summary, we identified the mechanical load cycle as a relevant parameter for the modulation of the morphological structure and physiological behaviour of intestinal epithelial cells. Full article

(This article belongs to the Special Issue Effects of Weightlessness on Molecular Changes in Cellular Organisms, Animals and Plants)

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23 pages, 1691 KiB

Open AccessReview

The Role of Long Non-Coding RNAs in Modulating the Immune Microenvironment of Triple-Negative Breast Cancer: Mechanistic Insights and Therapeutic Potential

by Yongcheng Su, Qingquan Bai, Wenqing Zhang, Beibei Xu and Tianhui Hu

Biomolecules 2025, 15(3), 454; https://doi.org/10.3390/biom15030454 - 20 Mar 2025

Viewed by 392

Abstract

Triple-negative breast cancer (TNBC) is a highly heterogeneous and aggressive subtype of breast cancer that faces therapeutic challenges due to a shortage of effective targeted therapies. The complex biology of TNBC renders its clinical management fraught with difficulties, especially regarding the immune microenvironment [...] Read more.

Triple-negative breast cancer (TNBC) is a highly heterogeneous and aggressive subtype of breast cancer that faces therapeutic challenges due to a shortage of effective targeted therapies. The complex biology of TNBC renders its clinical management fraught with difficulties, especially regarding the immune microenvironment of the tumor. In recent years, long non-coding RNAs (lncRNAs) have been recognized as important gene regulators with key roles in tumor development and microenvironmental regulation. Previous studies have shown that lncRNAs play important roles in the immune microenvironment of TNBC, including the regulation of tumor immune escape and the function of tumor-infiltrating immune cells. However, despite the increasing research on lncRNAs, there are still many unanswered questions, such as their specific mechanism of action and how to effectively utilize them as therapeutic targets. Therefore, the aim of this study was to review the mechanisms of lncRNAs in the TNBC immune microenvironment, explore their regulatory roles in tumor immune escape and immune cell infiltration, and explore their prospects as potential therapeutic targets. By integrating the latest research results, this study aims to provide new ideas and directions for future TNBC treatment. Full article

(This article belongs to the Special Issue The Role of Non-Coding RNAs in Health and Disease)

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24 pages, 4293 KiB

Open AccessArticle

Conformational Analyses of the AHD1-UBAN Region of TNIP1 Highlight Key Amino Acids for Interaction with Ubiquitin

by Michael L. Samulevich, Liam E. Carman, Rambon Shamilov and Brian J. Aneskievich

Biomolecules 2025, 15(3), 453; https://doi.org/10.3390/biom15030453 - 20 Mar 2025

Viewed by 288

Abstract

Tumor necrosis factor ɑ (TNFɑ)-induced protein 3 (TNFAIP3)-interacting protein 1 (TNIP1) is genetically and functionally linked to limiting auto-immune and inflammatory responses. We have shown that TNIP1 (alias A20-binding inhibitor of NF-κB 1, ABIN1), functioning as a hub location to coordinate other proteins [...] Read more.

Tumor necrosis factor ɑ (TNFɑ)-induced protein 3 (TNFAIP3)-interacting protein 1 (TNIP1) is genetically and functionally linked to limiting auto-immune and inflammatory responses. We have shown that TNIP1 (alias A20-binding inhibitor of NF-κB 1, ABIN1), functioning as a hub location to coordinate other proteins in repressing inflammatory signaling, aligns with biophysical traits indicative of its being an intrinsically disordered protein (IDP). IDPs move through a repertoire of three-dimensional structures rather than being in one set conformation. Here we employed bioinformatic analysis and biophysical interventions via amino acid mutations to assess and alter, respectively, conformational flexibility along a crucial region of TNIP1, encompassing the ABIN homology domain 1 and ubiquitin-binding domain in ABIN proteins and NEMO (AHD1-UBAN), by purposeful replacement of key residues. In vitro secondary structure measurements were mostly in line with, but not necessarily to the same degree as, expected results from in silico assessments. Notably, changes in single amino acids outside of the ubiquitin-binding region for gain-of-order effects had consequences along the length of the AHD1-UBAN propagating to that region. This is evidenced by differences in recognition of the partner protein polyubiquitin ≥ 28 residues away, depending on the mutation site, from the previously identified key binding site. These findings serve to demonstrate the role of conformational flexibility in protein partner recognition by TNIP1, thus identifying key amino acids likely to impact the molecular dynamics involved in TNIP1 repression of inflammatory signaling at large. Full article

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

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23 pages, 1038 KiB

Open AccessReview

Neuroprotective Properties of Clove (Syzygium aromaticum): State of the Art and Future Pharmaceutical Applications for Alzheimer’s Disease

by Tatevik Sargsyan, Hayarpi M. Simonyan, Lala Stepanyan, Avetis Tsaturyan, Caterina Vicidomini, Raffaele Pastore, Germano Guerra and Giovanni N. Roviello

Biomolecules 2025, 15(3), 452; https://doi.org/10.3390/biom15030452 - 20 Mar 2025

Viewed by 1414

Abstract

This study explores the neuropharmacological potential of various molecular and amino acid components derived from Syzygium aromaticum (clove), an aromatic spice with a long history of culinary and medicinal use. Key bioactive compounds such as eugenol, α-humulene, β-caryophyllene, gallic acid, quercetin, and luteolin [...] Read more.

This study explores the neuropharmacological potential of various molecular and amino acid components derived from Syzygium aromaticum (clove), an aromatic spice with a long history of culinary and medicinal use. Key bioactive compounds such as eugenol, α-humulene, β-caryophyllene, gallic acid, quercetin, and luteolin demonstrate antioxidant, anti-inflammatory, and neuroprotective properties by scavenging free radicals, modulating calcium channels, and reducing neuroinflammation and oxidative stress. Moreover, gallic acid and asiatic acid may exhibit protective effects, including neuronal apoptosis inhibition, while other useful properties of clove phytocompounds include NF-κB pathway inhibition, membrane stabilization, and suppression of pro-inflammatory pathways, possibly in neurons or other relevant cell types, further contributing to neuroprotection and cognitive enhancement. Amino acid analysis revealed essential and non-essential amino acids such as aspartic acid, serine, glutamic acid, glycine, histidine, and arginine in various clove parts (buds, fruits, branches, and leaves). These amino acids play crucial roles in neurotransmitter synthesis, immune modulation, antioxidant defense, and metabolic regulation. Collectively, these bioactive molecules and amino acids contribute to clove’s antioxidant, anti-inflammatory, neurotrophic, and neurotransmitter-modulating effects, highlighting its potential as a preventive and therapeutic candidate for neurodegenerative disorders. While preliminary preclinical studies support these neuroprotective properties, further research, including clinical trials, is needed to validate the efficacy and safety of clove-based interventions in neuroprotection. Full article

(This article belongs to the Special Issue Biomolecular Approaches and Drugs for Neurodegeneration)

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Graphical abstract

22 pages, 1950 KiB

Open AccessReview

Inositol and PIP2/PIP3 Ratio: At the Crossroad of the Biodynamic Interface Between Cells and Their Microenvironment

by Guglielmo Lentini, Alessandro Querqui, Alessandro Giuliani, Roberto Verna and Mariano Bizzarri

Biomolecules 2025, 15(3), 451; https://doi.org/10.3390/biom15030451 - 20 Mar 2025

Viewed by 314

Abstract

Plasma membrane plays a pivotal role in orchestrating motility and invasive processes, as well as mitosis and genome expression. Indeed, specialized regions of the plasma membrane enriched in phosphoinositides—namely PIP2 and PIP3—can accommodate the requirements of the dynamic interface, which mediates the interplay [...] Read more.

Plasma membrane plays a pivotal role in orchestrating motility and invasive processes, as well as mitosis and genome expression. Indeed, specialized regions of the plasma membrane enriched in phosphoinositides—namely PIP2 and PIP3—can accommodate the requirements of the dynamic interface, which mediates the interplay between cells and their microenvironment. The fine-tuned balance between the two phosphoinositides is instrumental in regulating cytoskeleton organization, motility, ion channel activation, and membrane traffic. The balanced expression of PIP2/PIP3 fulfills these functions by activating pathways through several transporter and receptor proteins. These dynamic interactions modulate the interplay with the extracellular environment by decreasing/increasing their exposure on the cell surface. In this way, lipid structures can rapidly either dismiss or recruit specific proteins, eventually favoring their cooperation with membrane receptors and ion channels. Particularly, exposure of proteins can be managed through the internalization of plasma membrane segments, while receptor signaling can be desensitized by their removal from the cell surface. Notably, the equilibrium between PIP2 and PIP3 is largely dependent on inositol availability, as inositol addition enhances PIP2 content while reducing PIP3 via PI3K inhibition. Pharmacological modulation of PIP2/PIP3 balance promises to be an interesting target in different clinical settings. Full article

(This article belongs to the Special Issue Inositol Phosphates in Health and Disease, 2nd Edition)

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24 pages, 3877 KiB

Open AccessReview

Revolutionizing Implantation Studies: Uterine-Specific Models and Advanced Technologies

by Shu-Yun Li and Francesco John DeMayo

Biomolecules 2025, 15(3), 450; https://doi.org/10.3390/biom15030450 - 20 Mar 2025

Viewed by 410

Abstract

Implantation is a complex and tightly regulated process essential for the establishment of pregnancy. It involves dynamic interactions between a receptive uterus and a competent embryo, orchestrated by ovarian hormones such as estrogen and progesterone. These hormones regulate proliferation, differentiation, and gene expression [...] Read more.

Implantation is a complex and tightly regulated process essential for the establishment of pregnancy. It involves dynamic interactions between a receptive uterus and a competent embryo, orchestrated by ovarian hormones such as estrogen and progesterone. These hormones regulate proliferation, differentiation, and gene expression within the three primary uterine tissue types: myometrium, stroma, and epithelium. Advances in genetic manipulation, particularly the Cre/loxP system, have enabled the in vivo investigation of the role of genes in a uterine compartmental and cell type-specific manner, providing valuable insights into uterine biology during pregnancy and disease. The development of endometrial organoids has further revolutionized implantation research. They mimic the native endometrial structure and function, offering a powerful platform for studying hormonal responses, implantation, and maternal-fetal interactions. Combined with omics technologies, these models have uncovered the molecular mechanisms and signaling pathways that regulate implantation. This review provides a comprehensive overview of uterine-specific genetic tools, endometrial organoids, and omics. We explore how these advancements enhance our understanding of implantation biology, uterine receptivity, and decidualization in reproductive research. Full article

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

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22 pages, 2201 KiB

Open AccessArticle

Enhancing Antimicrobial Peptides from Frog Skin: A Rational Approach

by Silvana Aguilar, Daniel Moreira, Ana Laura Pereira Lourenço, Natalia Wilke, Matías A. Crosio, Andreanne Vasconcelos, Eder Alves Barbosa, Elizabete C. I. Bispo, Felipe Saldanha-Araujo, Marcelo H. S. Ramada, Franco M. Escobar, Cristina V. Torres, José R. S. A. Leite and Mariela M. Marani

Biomolecules 2025, 15(3), 449; https://doi.org/10.3390/biom15030449 - 20 Mar 2025

Viewed by 458

Abstract

Antimicrobial resistance is a global health threat, which has been worsened by the slow development of new antibiotics. The rational design of natural-derived antimicrobial peptides (AMPs) offers a promising alternative for enhancing the efficacy of AMPs and accelerating drug discovery. This paper describes [...] Read more.

Antimicrobial resistance is a global health threat, which has been worsened by the slow development of new antibiotics. The rational design of natural-derived antimicrobial peptides (AMPs) offers a promising alternative for enhancing the efficacy of AMPs and accelerating drug discovery. This paper describes the rational design of improved peptide derivatives starting from hylin-Pul3, a peptide previously isolated from the frog Boana pulchella, by optimizing its hydrophobicity, cationicity, and amphipathicity. In silico screening identified six promising candidates: dHP3-31, dHP3-50, dHP3-50.137, dHP3-50.190, dHP3-84, and dHP3-84.39. These derivatives exhibited enhanced activity against Gram-negative bacteria, emphasizing the role of cationicity and the strategic arginine incorporation. Hemolytic assays revealed the derivatives’ improved selectivity, particularly for the derivatives with “imperfect amphipathicity”. In fibroblast assays, dHP3-84 was well-tolerated, while dHP3-84.39 promoted cell proliferation. Antioxidant assays (ABTS assays) highlighted the Trp-containing derivatives’ (dHP3-50.137, dHP3-31) significant activity. The lipid membrane interaction studies showed that hylin-Pul3 disrupts membranes directly, while dHP3-84.39, dHP3-50, and dHP3-50.137 promote vesicle aggregation. Conversely, dHP3-84 did not induce membrane disruption or aggregation, suggesting an intracellular mode of action. Machine learning models were effective in predicting bioactivity, as these predicted AMPs showed enhanced selectivity and potency. Among them, dHP3-84 demonstrated broad-spectrum potential. These findings highlight the value of rational design, in silico screening, and structure–activity studies in optimizing AMPs for therapeutic applications. Full article

(This article belongs to the Special Issue Antimicrobial Peptides in Nature: Inspiration for Rationally Designed Antimicrobials)

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25 pages, 1671 KiB

Open AccessReview

The Regulation of Cellular Senescence in Cancer

by Xianhong Zhang, Yue Gao, Siyu Zhang, Yixiong Wang, Yitian Du, Shuailin Hao and Ting Ni

Biomolecules 2025, 15(3), 448; https://doi.org/10.3390/biom15030448 - 20 Mar 2025

Viewed by 557

Abstract

Cellular senescence is a stable state of cell cycle arrest caused by telomere shortening or various stresses. After senescence, cells cease dividing and exhibit many age-related characteristics. Unlike the halted proliferation of senescence cells, cancer cells are considered to have unlimited growth potential. [...] Read more.

Cellular senescence is a stable state of cell cycle arrest caused by telomere shortening or various stresses. After senescence, cells cease dividing and exhibit many age-related characteristics. Unlike the halted proliferation of senescence cells, cancer cells are considered to have unlimited growth potential. When cells display senescence-related features, such as telomere loss or stem cell failure, they can inhibit tumor development. Therefore, inducing cells to enter a senescence state can serve as a barrier to tumor cell development. However, many recent studies have found that sustained senescence of tumor cells or normal cells under certain circumstances can exert environment-dependent effects of tumor promotion and inhibition by producing various cytokines. In this review, we first introduce the causes and characteristics of induced cellular senescence, analyze the senescence process of immune cells and cancer cells, and then discuss the dual regulatory role of cell senescence on tumor growth and senescence-induced therapies targeting cancer cells. Finally, we discuss the role of senescence in tumor progression and treatment opportunities, and propose further studies on cellular senescence and cancer therapy. Full article

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24 pages, 7946 KiB

Open AccessArticle

Heterologous Expression of Either Human or Soya Bean Ferritins in Budding Yeast Reveals Common Functions Protecting Against Oxidative Agents and Counteracting Double-Strand Break Accumulation

by Nuria Pujol Carrión and Maria Ángeles de la Torre-Ruiz

Biomolecules 2025, 15(3), 447; https://doi.org/10.3390/biom15030447 - 20 Mar 2025

Viewed by 245

Abstract

Ferritins are globular proteins that, upon self-assembly in nanocages, are capable of bio-safely storing huge concentrations of bioavailable iron. They are present in most cell types and organisms; one of the exceptions is yeast. Heterologous expression of either human or vegetal ferritins in [...] Read more.

Ferritins are globular proteins that, upon self-assembly in nanocages, are capable of bio-safely storing huge concentrations of bioavailable iron. They are present in most cell types and organisms; one of the exceptions is yeast. Heterologous expression of either human or vegetal ferritins in Saccharomyces cerevisiae revealed new and unknown functions for soya bean ferritins; validated this model by confirming previously characterized functions in human ferritins and also demonstrated that, like human H chain, vegetal H1, and H2 chains also shown a tendency to localize in the nucleus when expressed in an eukaryotic cell model lacking plastids and chloroplasts. Furthermore, when expressed in the system budding yeast, the four ferritins (human H and L and soya bean H1 and H2 chains) present equivalent and relevant functions as protectors against oxidative damage and against the accumulation of double-strand breaks in the DNA. We present evidence demonstrating that these effects are exclusively observed with oxidative agents that operate through the Fenton reaction, such as H₂O₂. Here, we also discuss the ferritin requirement for N-glycosylation to exert these functions. We believe that our approach might contribute to extending the knowledge around ferritin function and its consequent relevance to human health. Full article

(This article belongs to the Special Issue Recent Insights into Metal Binding Proteins)

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14 pages, 2522 KiB

Open AccessArticle

Structural and Metabolic Changes in Pregnant Rat Uterine and Adipose Tissue Induced by a High-Fat High-Sugar Diet

by Dina Šišljagić, Senka Blažetić, Milorad Zjalić, Irena Labak, Vedrana Ivić, Kálmán Ferenc Szűcs, Róbert Gáspár, Eszter Ducza, Sandor G. Vari, Andrijana Muller and Marija Heffer

Biomolecules 2025, 15(3), 446; https://doi.org/10.3390/biom15030446 - 20 Mar 2025

Viewed by 280

Abstract

Pregnancy presents specific metabolic demands, and disruption caused by a high-fat high-sugar diet (HFHSD) have been associated with significant complications, including maternal health risk, fetal developmental issues, and infertility. Obesity-related changes in the uterine tissues may contribute to these challenges. This study analyzed [...] Read more.

Pregnancy presents specific metabolic demands, and disruption caused by a high-fat high-sugar diet (HFHSD) have been associated with significant complications, including maternal health risk, fetal developmental issues, and infertility. Obesity-related changes in the uterine tissues may contribute to these challenges. This study analyzed structural changes in the uterus and adipose tissue of pregnant rats on gestation day 22 fed an HFHSD using various staining techniques. Hematoxylin and eosin staining showed morphological changes in the adipose tissue and the uterine structure, including the lumen size and the thickness of the myometrium, endometrium, and perimetrium. The amount of collagen in the uterus was determined by PicroSirius red staining, while PAS-D staining was used to observe glycogen content. Key protein expressions, such as insulin and leptin receptors and UCP1 and UCP3, were analyzed by immunohistochemistry. The HFHSD promoted hypertrophy of visceral and gonadal adipocytes, suggesting metabolic alterations. By the end of pregnancy, a significant reduction in uterine lumen size was observed. Additionally, a decrease in insulin and higher leptin receptor expressions in the myometrium indicated significant physiological alteration. These findings offer insight into how an HFHSD affects uterine structure and function during late pregnancy but should be interpreted within the physiological context of gestation-related metabolic changes. Further research is needed to understand the functional consequences of these alterations on reproductive and metabolic health. Full article

(This article belongs to the Section Molecular Medicine)

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16 pages, 7367 KiB

Open AccessArticle

Mitochondrial miRNA miR-134-5p Play Oncogenic Role in Clear Cell Renal Cell Carcinoma

by Tao Shen, Wei Wang, Haiyang Wang, Xinyi Zhu and Guoping Zhu

Biomolecules 2025, 15(3), 445; https://doi.org/10.3390/biom15030445 - 20 Mar 2025

Viewed by 413

Abstract

Mitochondrial miRNAs (mitomiRs), which are miRNAs that located within mitochondria, have emerged as crucial regulators in a variety of human diseases, including multiple types of cancers. However, the specific role of mitomiRs in clear cell renal cell carcinoma (ccRCC) remains elusive. In this [...] Read more.

Mitochondrial miRNAs (mitomiRs), which are miRNAs that located within mitochondria, have emerged as crucial regulators in a variety of human diseases, including multiple types of cancers. However, the specific role of mitomiRs in clear cell renal cell carcinoma (ccRCC) remains elusive. In this study, we employed a combination of experimental and bioinformatic approaches to uncover the diverse and abundant subcellular distribution of miRNAs within mitochondria in ccRCC. Notably, RNA sequencing after mitochondrial fractionation identified miR-134-5p as a miRNA predominantly detected in the mitochondria of 786O cells, and its expression is significantly upregulated compared to that in 293T cells. Differential expression and survival analyses from TCGA reveal that the upregulation of miR-134-5p is prevalent and closely associated with poor survival outcomes in ccRCC patients. Functionally, exogenous overexpression of miR-134-5p mimics promotes migration in both 786O and Caki-1 cells. Mechanistically, overexpressing the miR-134-5p mimic dramatically downregulates the mRNA levels of CHST6, SFXN2, and GRIK3, whereas the miR-134-5p inhibitor markedly upregulates their expression. Notably, these target mRNAs also predominantly detected in the mitochondria of 786O cells. The downregulated expression signatures of CHST6, SFXN2, and GRIK3 are also closely correlated with poor survival outcomes in ccRCC patients. Taken together, our work identifies a novel mitomiR, miR-134-5p, in ccRCC, provides potential targets that could serve as effective biomarkers for ccRCC diagnosis and prognosis, and opens new avenues for understanding the mitomiR-directed regulatory network in ccRCC progression. Full article

(This article belongs to the Special Issue The Role of Non-Coding RNAs in Health and Disease)

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20 pages, 2264 KiB

Open AccessReview

Nanomaterial-Based Molecular Imaging in Cancer: Advances in Simulation and AI Integration

by James C. L. Chow

Biomolecules 2025, 15(3), 444; https://doi.org/10.3390/biom15030444 - 20 Mar 2025

Viewed by 531

Abstract

Nanomaterials represent an innovation in cancer imaging by offering enhanced contrast, improved targeting capabilities, and multifunctional imaging modalities. Recent advancements in material engineering have enabled the development of nanoparticles tailored for various imaging techniques, including magnetic resonance imaging (MRI), computed tomography (CT), positron [...] Read more.

Nanomaterials represent an innovation in cancer imaging by offering enhanced contrast, improved targeting capabilities, and multifunctional imaging modalities. Recent advancements in material engineering have enabled the development of nanoparticles tailored for various imaging techniques, including magnetic resonance imaging (MRI), computed tomography (CT), positron emission tomography (PET), and ultrasound (US). These nanoscale agents improve sensitivity and specificity, enabling early cancer detection and precise tumor characterization. Monte Carlo (MC) simulations play a pivotal role in optimizing nanomaterial-based imaging by modeling their interactions with biological tissues, predicting contrast enhancement, and refining dosimetry for radiation-based imaging techniques. These computational methods provide valuable insights into nanoparticle behavior, aiding in the design of more effective imaging agents. Moreover, artificial intelligence (AI) and machine learning (ML) approaches are transforming cancer imaging by enhancing image reconstruction, automating segmentation, and improving diagnostic accuracy. AI-driven models can also optimize MC-based simulations by accelerating data analysis and refining nanoparticle design through predictive modeling. This review explores the latest advancements in nanomaterial-based cancer imaging, highlighting the synergy between nanotechnology, MC simulations, and AI-driven innovations. By integrating these interdisciplinary approaches, future cancer imaging technologies can achieve unprecedented precision, paving the way for more effective diagnostics and personalized treatment strategies. Full article

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

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40 pages, 2575 KiB

Open AccessSystematic Review

Associations Between Follicular Fluid Biomarkers and IVF/ICSI Outcomes in Normo-Ovulatory Women—A Systematic Review

by Soha Albeitawi, Saif-Ulislam Bani-Mousa, Baraa Jarrar, Ibrahim Aloqaily, Nour Al-Shlool, Ghaida Alsheyab, Ahmad Kassab, Baha’a Qawasmi and Abdalrahman Awaisheh

Biomolecules 2025, 15(3), 443; https://doi.org/10.3390/biom15030443 - 20 Mar 2025

Viewed by 777

Abstract

(1) Background: The follicular fluid (FF) comprises a large portion of ovarian follicles, and serves as both a communication and growth medium for oocytes, and thus should be representative of the metabolomic status of the follicle. This review aims to explore FF biomarkers [...] Read more.

(1) Background: The follicular fluid (FF) comprises a large portion of ovarian follicles, and serves as both a communication and growth medium for oocytes, and thus should be representative of the metabolomic status of the follicle. This review aims to explore FF biomarkers as well as their effects on fertilization, oocyte, and embryo development, and later on implantation and maintenance of pregnancy. (2) Methods: This review was registered in the PROSPERO database with the ID: CRD42025633101. We parsed PubMed, Scopus, and Google Scholar for research on the effects of different FF biomarkers on IVF/ICSI outcomes in normo-ovulatory women. Included studies were assessed for risk of bias using the NOS scale. Data were extracted and tabulated by two independent researchers. (3) Results: 22 included articles, with a sample size range of 31 to 414 and a median of 60 participants, contained 61 biomarkers, including proteins, growth factors, steroid and polypeptide hormones, inflammation and oxidative stress markers, amino acids, vitamins, lipids of different types, and miRNAs. Most of the biomarkers studied had significant effects on IVF/ICSI outcomes, and seem to have roles in various cellular pathways responsible for oocyte and embryo growth, implantation, placental formation, and maintenance of pregnancy. The FF metabolome also seems to be interconnected, with its various components influencing the levels and activities of each other through feedback loops. (4) Conclusions: FF biomarkers can be utilized for diagnostic and therapeutic purposes in IVF; however, further studies are required for choosing the most promising ones due to heterogeneity of results. Widespread adoption of LC-MS and miRNA microarrays can help quantify a representative FF metabolome, and we see great potential for in vitro supplementation (IVS) of some FF biomarkers in improving IVF/ICSI outcomes. Full article

(This article belongs to the Section Molecular Biomarkers)

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19 pages, 1974 KiB

Open AccessArticle

Topical Instillation of N-Acetylcysteine and N-Acetylcysteine Amide Impedes Age-Related Lens Opacity in Mice

by Hidetoshi Ishida, Yu Sasaki, Teppei Shibata, Hiroshi Sasaki, Bhavana Chhunchha, Dhirendra P. Singh and Eri Kubo

Biomolecules 2025, 15(3), 442; https://doi.org/10.3390/biom15030442 - 19 Mar 2025

Viewed by 358

Abstract

Cataracts, the leading cause of blindness globally, are caused by oxidative stress and inflammation, which disrupt lens transparency due to increased accumulation of reactive oxygen species (ROS) as well as protein and DNA damage during aging. Using in vitro, ex vivo, and in [...] Read more.

Cataracts, the leading cause of blindness globally, are caused by oxidative stress and inflammation, which disrupt lens transparency due to increased accumulation of reactive oxygen species (ROS) as well as protein and DNA damage during aging. Using in vitro, ex vivo, and in vivo models, we determined the protective efficacy of N-acetylcysteine amide (NACA) against oxidative stress-induced and aging-induced cataractogenesis. We found that lens epithelial cells exposed to the oxidative stress inducers hydrogen peroxide (H₂O₂) or tert-butyl hydroperoxide showed significant ROS accumulation and reduced cellular viability. These effects were inhibited by NACA via the suppression of ROS and thioredoxin-interacting protein (Txnip) expression, a regulator of oxidative stress-related cellular damage and inflammation. In ex vivo lens experiments, NACA significantly reduced H₂O₂-induced lens opacity and preserved lens integrity. Similarly to NACA-treated lenses ex vivo, the integrity and opacity of aged mouse lenses, when topically instilled with NACA, were preserved and reduced, respectively, and are directly related to reduced Txnip and increased thioredoxin (Trx) expression levels. Overall, our findings demonstrated the protective ability of NACA to abate aberrant redox-active pathways, particularly the ROS/TRX/TXNIP axis, thereby preventing cataractogenesis and preserving eye lens integrity and ultimately impeding aging-related cataracts. Full article

(This article belongs to the Section Molecular Medicine)

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16 pages, 3824 KiB

Open AccessReview

Tissue Resident and Infiltrating Immune Cells: Their Influence on the Demise of Beta Cells in Type 1 Diabetes

by Sophie L. Walker, Pia Leete and Joanne Boldison

Biomolecules 2025, 15(3), 441; https://doi.org/10.3390/biom15030441 - 19 Mar 2025

Viewed by 400

Abstract

Type 1 diabetes (T1D) is an organ-specific autoimmune disease that results in the selective loss of pancreatic beta cells and an eventual deficit in insulin production to maintain glucose homeostasis. It is now increasingly accepted that this dynamic disease process is multifactorial; involves [...] Read more.

Type 1 diabetes (T1D) is an organ-specific autoimmune disease that results in the selective loss of pancreatic beta cells and an eventual deficit in insulin production to maintain glucose homeostasis. It is now increasingly accepted that this dynamic disease process is multifactorial; involves a variety of immune cells which contribute to an inflamed pancreatic microenvironment; and that the condition is heterogenous, resulting in variable rates of subsequent beta cell damage. In this review, we will explore the current understanding of the cellular interactions between both resident and infiltrating immune cells within the pancreatic environment, highlighting key mechanisms which may promote the beta cell destruction and islet damage associated with T1D. Full article

(This article belongs to the Special Issue Immune Responses in Type 1 Diabetes)

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12 pages, 863 KiB

Open AccessArticle

The Exon-Based Transcriptomic Analysis of Parkinson’s Disease

by Sulev Kõks

Biomolecules 2025, 15(3), 440; https://doi.org/10.3390/biom15030440 - 19 Mar 2025

Viewed by 248

Abstract

Parkinson’s disease (PD) is a neurodegenerative disease with a complicated pathophysiology and diagnostics. Blood-based whole transcriptome analysis of the longitudinal PPMI cohort was performed with a focus on the change in the expression of exons to find potential RNA-based biomarkers. At the moment [...] Read more.

Parkinson’s disease (PD) is a neurodegenerative disease with a complicated pathophysiology and diagnostics. Blood-based whole transcriptome analysis of the longitudinal PPMI cohort was performed with a focus on the change in the expression of exons to find potential RNA-based biomarkers. At the moment of diagnosis, the expression of exons was very similar in both control and PD patients. The exon-based analysis identified 27 differentially expressed exons in PD patients three years after the diagnosis compared to the health controls. Moreover, thirteen exons were differentially expressed during the three-year progression of the PD. At the same time, control subjects had only minimal changes that can mostly be attributed to being related to aging. Differentially regulated exons we identified in the PD cohort were mostly related to different aspects of the pathophysiology of PD, such as an innate immune response or lysosomal activity. We also observed a decline in the expression of the OPN1MW3 gene that is related to colour vision, which suggests that colour vision analysis could be a practical biomarker to monitor the progression of PD. Full article

(This article belongs to the Section Molecular Medicine)

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14 pages, 1281 KiB

Open AccessReview

Salivary-Gland-Mediated Nitrate Recirculation as a Modulator for Cardiovascular Diseases

by Baoxing Pang, Xingyun Qi and Huiliang Zhang

Biomolecules 2025, 15(3), 439; https://doi.org/10.3390/biom15030439 - 19 Mar 2025

Viewed by 265

Abstract

Cardiovascular diseases (CVDs), which include multiple disorders of the heart and blood vessels, are the leading causes of death. Nitric oxide (NO) is a vasodilator that regulates vascular tension. Endogenous NO is produced via the L-arginine–nitric oxide synthase (NOS) pathway. In conditions of [...] Read more.

Cardiovascular diseases (CVDs), which include multiple disorders of the heart and blood vessels, are the leading causes of death. Nitric oxide (NO) is a vasodilator that regulates vascular tension. Endogenous NO is produced via the L-arginine–nitric oxide synthase (NOS) pathway. In conditions of cardiovascular dysfunction, NOS activity is impaired, leading to NO deficiency. In turn, the reduction in NO bioactivity exacerbates the pathogenesis of CVDs. Exogenous intake of inorganic nitrate supplements endogenous production via the nitrate–nitrite–NO pathway to maintain the NO supply. Salivary glands play an essential role in the conversion of nitrate to NO, with approximately 25% of circulating nitrate being absorbed and secreted into saliva. As a result, salivary nitrate concentrations can exceed that in the blood by more than tenfold. This recycled nitrate in saliva serves as a reservoir for NO and performs NO-like functions when endogenous NO production is insufficient. In this review, we summarize the emerging benefits of dietary nitrate in CVDs, with a particular focus on salivary-gland-mediated nitrate recirculation in maintaining NO bioavailability and cardiovascular homeostasis. Salivary-gland-mediated nitrate recirculation provides a novel perspective for potential intervention of CVDs. Full article

(This article belongs to the Special Issue Pharmacology of Cardiovascular Diseases)

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23 pages, 8139 KiB

Open AccessArticle

Efficient Fabrication of Human Corneal Stromal Cell Spheroids and Promoting Cell Stemness Based on 3D-Printed Derived PDMS Microwell Platform

by Yuexi Chen, Jianing Gu, Zekai Cui, Xihao Sun, Yuqin Liang, Chunwen Duan, Xiaoxue Li, Zhanyu Su, Bo Zhang, Jiansu Chen and Zheng Wang

Biomolecules 2025, 15(3), 438; https://doi.org/10.3390/biom15030438 - 19 Mar 2025

Viewed by 371

Abstract

Spherical culture could promote the plasticity and stemness of human corneal stromal cells (hCSCs). Here, we introduce a novel three-dimensional (3D) cell culture system based on a polydimethylsiloxane (PDMS) microwell platform composed of many V-bottom microcavities to generate human corneal stromal cell spheroids [...] Read more.

Spherical culture could promote the plasticity and stemness of human corneal stromal cells (hCSCs). Here, we introduce a novel three-dimensional (3D) cell culture system based on a polydimethylsiloxane (PDMS) microwell platform composed of many V-bottom microcavities to generate human corneal stromal cell spheroids and promote cell stemness. We isolated hCSCs from SMILE-derived lenticules and maintained their physiological phenotype by culturing them in a medium supplemented with human corneal stromal extract (hCSE). Utilizing a PDMS microwell platform fabricated through 3D printing technology, we successfully generated 3D corneal stromal cell spheroids (3D-CSC) with uniform size and stable structure, exhibiting increased expression of pluripotency factors, including OCT4, NANOG, SOX2, KLF4, and PAX6. Furthermore, the iPS supernatant of E8-conditioned medium (E8-CM) significantly enhanced the stemness properties of these cells. RNA sequencing and proteomics analyses revealed that 3D-CSCs exhibited superior proliferation, differentiation, cell adhesion, migration, and neurogenesis compared to traditional monolayer cultures, underscoring the role of biophysical cues in promoting hCSCs stemness. In summary, this study presents an effective 3D cell culture platform that mimics the in vivo microenvironment, facilitating the enhancement of stemness properties and providing valuable insights into corneal tissue engineering and regenerative medicine, particularly for treating corneal opacities and diseases. Full article

(This article belongs to the Section Cellular Biochemistry)

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15 pages, 852 KiB

Open AccessArticle

Liver Injury Following Intravenous Methylprednisolone Pulse Therapy in Multiple Sclerosis: The Experience from a Single Academic Liver Center

by Dimitris Kounatidis, Natalia G. Vallianou, Georgios Kontos, Hariklia Kranidioti, Nikolaos Papadopoulos, Alexandros Panagiotopoulos, Krystalia Dimitriou, Vasileios Papadimitropoulos, Melanie Deutsch, Spilios Manolakopoulos, Dimitrios Vassilopoulos and John Koskinas

Biomolecules 2025, 15(3), 437; https://doi.org/10.3390/biom15030437 - 19 Mar 2025

Viewed by 323

Abstract

Intravenous methylprednisolone (IVMP) pulses, widely used for managing multiple sclerosis (MS) exacerbations, can lead to acute liver injury, presenting a diagnostic challenge in distinguishing between drug-induced autoimmune-like hepatitis (DI-ALH) and idiopathic autoimmune hepatitis (AIH). This study aimed to delineate the clinical and biochemical [...] Read more.

Intravenous methylprednisolone (IVMP) pulses, widely used for managing multiple sclerosis (MS) exacerbations, can lead to acute liver injury, presenting a diagnostic challenge in distinguishing between drug-induced autoimmune-like hepatitis (DI-ALH) and idiopathic autoimmune hepatitis (AIH). This study aimed to delineate the clinical and biochemical features of IVMP-induced liver injury, discern its etiology, and evaluate the efficacy of glucocorticoid (GC) therapy in treatment. A retrospective analysis of 13 relapsing MS patients with IVMP-induced liver injury was conducted. Liver injury was classified as hepatocellular, cholestatic, or mixed, with severity assessment guiding liver biopsy in selected cases. Causality was assessed using the Roussel Uclaf Causality Assessment Method (RUCAM) and the Simplified Diagnostic Criteria for AIH. All patients were initially monitored for a minimum of six months, with a mean follow-up period of 4.30 years. The median onset of liver injury was 37.46 days post-IVMP, with a mean peak alanine transaminase (ALT) level of 618.46 U/L. antinuclear antibody (ANA) positivity was observed in 61.53% of cases, with elevated serum immunoglobulin G (IgG) at 15.38%. Hepatocellular injury was universal among patients, and causality assessment predominantly supported DI-ALH. GC therapy was administered in six cases, achieving favorable outcomes in all but one, which necessitated rituximab. Biochemical normalization occurred within a mean of 55.41 days, with GC-treated patients recovering faster (48 days). These findings support the hypothesis that IVMP can induce hepatocellular injury, likely DI-ALH, during MS exacerbations. A tapering GC regimen proved effective in promoting recovery, particularly in severe cases. Additionally, this study introduced a diagnostic and therapeutic algorithm for managing IVMP-induced liver injury, offering a practical framework for clinical application. Full article

(This article belongs to the Special Issue Insights from the Editorial Board Members)

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18 pages, 2931 KiB

Open AccessArticle

Design, Synthesis, and Bioevaluation of Matrine Derivatives as Potential Anti–Hepatitis B Virus Agents

by Ting-Ting Liu, Meng-Fan Xie, Xin Liu, Rong-Tao Li, Yao Bai and Zhi-Jun Zhang

Biomolecules 2025, 15(3), 436; https://doi.org/10.3390/biom15030436 - 18 Mar 2025

Viewed by 375

Abstract

Hepatitis B virus (HBV) is a causative reagent that frequently causes progressive liver diseases, leading to the development of acute hepatitis, chronic hepatitis, cirrhosis, and eventually hepatocellular carcinoma. Despite several antiviral drugs, including interferon-α and nucleotide derivatives, being approved for clinical treatment [...] Read more.

Hepatitis B virus (HBV) is a causative reagent that frequently causes progressive liver diseases, leading to the development of acute hepatitis, chronic hepatitis, cirrhosis, and eventually hepatocellular carcinoma. Despite several antiviral drugs, including interferon-α and nucleotide derivatives, being approved for clinical treatment of HBV, critical issues remain unresolved, e.g., their low-to-moderate efficacy and adverse side effects, as well as resistant strains. In this study, twenty-three matrine derivatives were synthesized, and their antiviral effects against HBV were evaluated. Of these, eleven compounds inhibited HBeAg secretion significantly more than the positive control, lamivudine (3TC). Among the compounds synthesized in this study, compounds 4a and 4d had the most potent inhibitory activity, with IC₅₀ value of 41.78 and 33.68 μM, respectively. Compounds 1h, 4a, and 4d were also subjected to molecular docking studies. These compounds inhibited viral gene expression and viral propagation in a cell culture model. Thus, we believe our compounds could serve as resource for antiviral drug development. Full article

(This article belongs to the Special Issue Natural Products and Their Derivatives with Antiviral Activity)

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12 pages, 2288 KiB

Open AccessArticle

Cryo-EM Structure of the Flagellar Motor Complex from Paenibacillus sp. TCA20

by Sakura Onoe, Tatsuro Nishikino, Miki Kinoshita, Norihiro Takekawa, Tohru Minamino, Katsumi Imada, Keiichi Namba, Jun-ichi Kishikawa and Takayuki Kato

Biomolecules 2025, 15(3), 435; https://doi.org/10.3390/biom15030435 - 18 Mar 2025

Viewed by 473

Abstract

The bacterial flagellum, a complex nanomachine composed of numerous proteins, is utilized by bacteria for swimming in various environments and plays a crucial role in their survival and infection. The flagellar motor is composed of a rotor and stator complexes, with each stator [...] Read more.

The bacterial flagellum, a complex nanomachine composed of numerous proteins, is utilized by bacteria for swimming in various environments and plays a crucial role in their survival and infection. The flagellar motor is composed of a rotor and stator complexes, with each stator unit functioning as an ion channel that converts flow from outside of cell membrane into rotational motion. Paenibacillus sp. TCA20 was discovered in a hot spring, and a structural analysis was conducted on the stator complex using cryo-electron microscopy to elucidate its function. Two of the three structures (Classes 1 and 3) were found to have structural properties typical for other stator complexes. In contrast, in Class 2 structures, the pentamer ring of the A subunits forms a C-shape, with lauryl maltose neopentyl glycol (LMNG) bound to the periplasmic side of the interface between the A and B subunits. This interface is conserved in all stator complexes, suggesting that hydrophobic ligands and lipids can bind to this interface, a feature that could potentially be utilized in the development of novel antibiotics aimed at regulating cell motility and infection. Full article

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

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17 pages, 3256 KiB

Open AccessReview

Chemotaxis and Related Signaling Systems in Vibrio cholerae

by Fuga Omori, Hirotaka Tajima, Sotaro Asaoka, So-ichiro Nishiyama, Yoshiyuki Sowa and Ikuro Kawagishi

Biomolecules 2025, 15(3), 434; https://doi.org/10.3390/biom15030434 - 18 Mar 2025

Viewed by 436

Abstract

The motility and chemotaxis of Vibrio cholerae, the bacterial pathogen responsible for cholera, play crucial roles in both environmental survival and infection. Understanding their molecular mechanisms is therefore essential not only for fundamental biology but also for infection control and therapeutic development. [...] Read more.

The motility and chemotaxis of Vibrio cholerae, the bacterial pathogen responsible for cholera, play crucial roles in both environmental survival and infection. Understanding their molecular mechanisms is therefore essential not only for fundamental biology but also for infection control and therapeutic development. The bacterium’s sheathed, polar flagellum—its motility organelle—is powered by a sodium-driven motor. This motor’s rotation is regulated by the chemotaxis (Che) signaling system, with a histidine kinase, CheA, and a response regulator, CheY, serving as the central processing unit. However, V. cholerae possesses two additional, parallel Che signaling systems whose physiological functions remain unclear. Furthermore, the bacterium harbors over 40 receptors/transducers that interact with CheA homologs, forming a complex regulatory network likely adapted to diverse environmental cues. Despite significant progress, many aspects of these systems remain to be elucidated. Here, we summarize the current understanding to facilitate future research. Full article

(This article belongs to the Special Issue Recent Advances in Supramolecular Motility Machinery of Microorganisms)

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30 pages, 1958 KiB

Open AccessReview

The Balance of MFN2 and OPA1 in Mitochondrial Dynamics, Cellular Homeostasis, and Disease

by Paola Zanfardino, Alessandro Amati, Mirko Perrone and Vittoria Petruzzella

Biomolecules 2025, 15(3), 433; https://doi.org/10.3390/biom15030433 - 18 Mar 2025

Viewed by 631

Abstract

Mitochondrial dynamics, governed by fusion and fission, are crucial for maintaining cellular homeostasis, energy production, and stress adaptation. MFN2 and OPA1, key regulators of mitochondrial fusion, play essential roles beyond their structural functions, influencing bioenergetics, intracellular signaling, and quality control mechanisms such as [...] Read more.

Mitochondrial dynamics, governed by fusion and fission, are crucial for maintaining cellular homeostasis, energy production, and stress adaptation. MFN2 and OPA1, key regulators of mitochondrial fusion, play essential roles beyond their structural functions, influencing bioenergetics, intracellular signaling, and quality control mechanisms such as mitophagy. Disruptions in these processes, often caused by MFN2 or OPA1 mutations, are linked to neurodegenerative diseases like Charcot-Marie-Tooth disease type 2A (CMT2A) and autosomal dominant optic atrophy (ADOA). This review explores the molecular mechanisms underlying mitochondrial fusion, the impact of MFN2 and OPA1 dysfunction on oxidative phosphorylation and autophagy, and their role in disease progression. Additionally, we discuss the divergent cellular responses to MFN2 and OPA1 mutations, particularly in terms of proliferation, senescence, and metabolic signaling. Finally, we highlight emerging therapeutic strategies to restore mitochondrial integrity, including mTOR modulation and autophagy-targeted approaches, with potential implications for neurodegenerative disorders. Full article

(This article belongs to the Section Molecular Biology)

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16 pages, 1209 KiB

Open AccessArticle

Vitamin D Decreases Susceptibility of CD4⁺ T Cells to HIV Infection by Reducing AKT Phosphorylation and Glucose Uptake: A Bioinformatic and In Vitro Approach

by John D. Loaiza, Jose Fernando Gómez, Daniel Muñoz-Escudero, Sandra M. Gonzalez, Timothy Kyle Eubank, Maria T. Rugeles, Ana Lucía Rodríguez-Perea and Wbeimar Aguilar-Jimenez

Biomolecules 2025, 15(3), 432; https://doi.org/10.3390/biom15030432 - 18 Mar 2025

Viewed by 430

Abstract

Activated immune cells are highly susceptible to human immunodeficiency virus (HIV) infection. Vitamin D (VitD) induces antimicrobial responses and reduces cellular activation. We investigated VitD effects on HIV-1 replication, glucose uptake, and gene regulation using computational and in vitro approaches. CD4⁺ T [...] Read more.

Activated immune cells are highly susceptible to human immunodeficiency virus (HIV) infection. Vitamin D (VitD) induces antimicrobial responses and reduces cellular activation. We investigated VitD effects on HIV-1 replication, glucose uptake, and gene regulation using computational and in vitro approaches. CD4⁺ T cells from healthy male donors were treated with VitD and infected with HIV-1. After 72 h, p24 protein was measured to assess viral replication. VitD effects on anti- and pro-HIV genes were analyzed by a Boolean network model based on curated databases and the literature. CCR5 and CXCR4 coreceptor expression, AKT phosphorylation, and glucose uptake were evaluated by flow cytometry, and expression of some model-identified genes was quantified by qPCR. VitD reduced p24 by 53.2% (p = 0.0078). Boolean network modeling predicted that VitD upregulates antiviral, migration, and cell-differentiation related genes, while downregulating genes related to cellular activation, proliferation, glucose metabolism, and HIV replication, notably AKT1, CCNT1, SLC2A1, HIF1A, and PFKL. In vitro, VitD reduced AKT phosphorylation by 26.6% (p = 0.0156), transcription of CCNT1 by 22.7% (p = 0.0391), and glucose uptake by 22.8% (p = 0.0039) without affecting classic antiviral genes or coreceptor expression. These findings suggest an anti-HIV effect of VitD, mediated through AKT and glucose metabolism downmodulation, both involved in cell activation and HIV-1 replication. Full article

(This article belongs to the Special Issue Vitamin D in Health and Disease—Honorary Special Issue Commemorating the Work of Dr. Luminita A. Stanciu)

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19 pages, 8357 KiB

Open AccessArticle

Binding of Pro-Inflammatory Proteins S100A8 or S100A9 to Amyloid-β Peptide Suppresses Its Fibrillation

by Ekaterina A. Litus, Marina P. Shevelyova, Alisa A. Vologzhannikova, Evgenia I. Deryusheva, Andrey V. Machulin, Ekaterina L. Nemashkalova, Maria E. Permyakova, Andrey S. Sokolov, Valeria D. Alikova, Vladimir N. Uversky and Sergei E. Permyakov

Biomolecules 2025, 15(3), 431; https://doi.org/10.3390/biom15030431 - 17 Mar 2025

Viewed by 312

Abstract

Human serum albumin (HSA) is a natural depot of amyloid-β peptide (Aβ), a key player in Alzheimer’s disease (AD). HSA and pro-inflammatory Ca²⁺-binding proteins S100A8 and S100A9 are involved in Aβ metabolism and its deposition in the brain, serving as probable [...] Read more.

Human serum albumin (HSA) is a natural depot of amyloid-β peptide (Aβ), a key player in Alzheimer’s disease (AD). HSA and pro-inflammatory Ca²⁺-binding proteins S100A8 and S100A9 are involved in Aβ metabolism and its deposition in the brain, serving as probable triggers and therapeutic targets in AD, but their interplay with regard to Aβ binding/fibrillation is unclear. To this end, here we explore the in vitro binding of Ca²⁺-bound S100A8 or S100A9 to monomeric Aβ and the influence of the S100 proteins on Aβ fibrillation. The equilibrium dissociation constants of the complexes of dimeric S100A8/S100A9 with Aβ40/42 estimated by biolayer interferometry are 1–5 µM. S100A8 and S100A9 interfere with HSA binding to Aβ. Thioflavin T assay and electron microscopy data show that micromolar S100A8/S100A9 inhibit Aβ40 fibrillation, and the inhibitory effect of S100A8 exceeds that for HSA. The competition for Aβ between HSA and S100A8/S100A9 may contribute to the Aβ-HSA imbalance in the pro-inflammatory conditions in AD. Full article

(This article belongs to the Special Issue Selected Papers From the 3rd International Electronic Conference on Biomolecules)

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13 pages, 3525 KiB

Open AccessArticle

High Dose C6 Ceramide-Induced Response in Embryonic Hippocampal Cells

by Federico Fiorani, Martina Mandarano, Samuela Cataldi, Alessandra Mirarchi, Stefano Bruscoli, Francesco Ragonese, Bernard Fioretti, Toshihide Kobayashi, Nario Tomishige, Tommaso Beccari, Claudia Floridi, Cataldo Arcuri and Elisabetta Albi

Biomolecules 2025, 15(3), 430; https://doi.org/10.3390/biom15030430 - 17 Mar 2025

Viewed by 363

Abstract

Ceramide is a critical molecule in both the physiology and pathology of the central nervous system. The most studied aspect is its effect on embryonic/stem cells. A salient question is whether low doses of ceramide induce neuronal differentiation without interfering with sphingolipid metabolism [...] Read more.

Ceramide is a critical molecule in both the physiology and pathology of the central nervous system. The most studied aspect is its effect on embryonic/stem cells. A salient question is whether low doses of ceramide induce neuronal differentiation without interfering with sphingolipid metabolism and whether high doses can be used in glioblastoma for their cytotoxic effect. Here, we examined the effect of a high dose of ceramide (13 µM) on HN9.10e cells. Interestingly, 13 µM ceramide induced an immediate increase in cell viability, followed by an increase in the number of mitochondria. Microscopic and morphometric analysis revealed a decrease in the number of differentiated cells with 13 µM compared to 0.1 µM but with longer neurites. Furthermore, the lipidomic study demonstrated an increase in the formation of medium–long-chain ceramide and sphingomyelin species and sphingosine 1 phosphate. Sphingolipid modification correlated with SMPD3, ASAH2, and SPHK2 gene expression coding for neutral sphingomyenase 2, ceramidase 2, and sphingosine kinase 2, respectively. Overall, our data show that the variety of responses to ceramide of the same cell type is dependent on the concentration used. Low doses do not affect sphingolipid metabolism, and high doses do so with a different cellular response. Full article

(This article belongs to the Section Cellular Biochemistry)

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16 pages, 4826 KiB

Open AccessArticle

Assembly Formation of P65 Protein, Featured by an Intrinsically Disordered Region Involved in Gliding Machinery of Mycoplasma pneumoniae

by Masaru Yabe, Takuma Toyonaga, Miki Kinoshita, Yukio Furukawa, Tasuku Hamaguchi, Yuhei O. Tahara, Munehito Arai, Katsumi Imada and Makoto Miyata

Biomolecules 2025, 15(3), 429; https://doi.org/10.3390/biom15030429 - 17 Mar 2025

Viewed by 411

Abstract

Mycoplasma pneumoniae is a human pathogen that glides on host cell surfaces by a repeated catch and release mechanism using sialylated oligosaccharides. At a pole, this organism forms a protrusion called an attachment organelle composed of surface structures, including an adhesin complex and [...] Read more.

Mycoplasma pneumoniae is a human pathogen that glides on host cell surfaces by a repeated catch and release mechanism using sialylated oligosaccharides. At a pole, this organism forms a protrusion called an attachment organelle composed of surface structures, including an adhesin complex and an internal core structure. To clarify the structure and function of the attachment organelle, we focused on a core component, P65, which is essential for stabilization of the adjacent surface and core proteins P30 and HMW2, respectively. Analysis of its amino acid sequence (405 residues) suggested that P65 contains an intrinsically disordered region (residues 1–217) and coiled-coil regions (residues 226–247, 255–283, and 286–320). Four protein fragments and the full-length P65 were analyzed by size exclusion chromatography, analytical centrifugation, circular dichroism spectroscopy, small-angle X-ray scattering, limited proteolysis, and negative staining electron microscopy. The results showed that P65 formed a multimer composed of a central globule with 30 and 23 nm axes and four to six projections 14 nm in length. Our data suggest that the C-terminal region of P65 is responsible for multimerization, while the intrinsically disordered N-terminal region forms a filament. These assignments and roles of P65 in the attachment organelle are discussed. Full article

(This article belongs to the Special Issue Recent Advances in Supramolecular Motility Machinery of Microorganisms)

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16 pages, 7285 KiB

Open AccessArticle

S-Nitrosoglutathione Is Not a Substrate of OATP1B1, but Stimulates Its Expression and Activity

by Yulia V. Abalenikhina, Aleksey V. Shchulkin, Olga N. Suchkova, Pelageya D. Ananyeva, Pavel Yu. Mylnikov, Elena N. Yakusheva, Igor A. Suchkov and Roman E. Kalinin

Biomolecules 2025, 15(3), 428; https://doi.org/10.3390/biom15030428 - 17 Mar 2025

Viewed by 322

Abstract

S-nitrosoglutathione (GSNO) is the S-nitrosated derivative of glutathione (GSH). GSNO is an endogenous class of NO donors and a natural NO depot in biological systems. Organic anion transporting polypeptide 1B1 (OATP1B1) is an influx transporter that is expressed in the liver. OATP1B1 plays [...] Read more.

S-nitrosoglutathione (GSNO) is the S-nitrosated derivative of glutathione (GSH). GSNO is an endogenous class of NO donors and a natural NO depot in biological systems. Organic anion transporting polypeptide 1B1 (OATP1B1) is an influx transporter that is expressed in the liver. OATP1B1 plays an important role in the transport of endogenous and exogenous substances. Various pathways for the regulation of OATP1B1 have been described. In the present study, the involvement of OATP1B1 in GSNO transport and the regulation of OATP1B1 by GSNO was examined. For HEK293-OATP1B1, it has been shown that GSNO is not a substrate of OATP1B1, but OATP1B1 can participate in the transport of GSH across the cell membrane. GSNO at concentrations of 1–100 μM and exposure for 3 h do not affect the expression and activity of OATP1B1, but exposure for 24 and 72 h stimulates the expression of the SLCO1B1 gene, OATP1B1, and transporter activity. Up-regulation of OATP1B1 by GSNO is carried out through the NO-cGMP signaling pathway, Nrf2, and LXRa. Full article

(This article belongs to the Section Cellular Biochemistry)

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26 pages, 2166 KiB

Open AccessArticle

Kinetics of Circulating Progenitor Cells and Chemotactic Factors in Full-Term Neonates with Encephalopathy: Indications of Participation in the Endogenous Regenerative Process

by Nikolaos Efstathiou, Georgios Koliakos, Katerina Kantziou, Georgios Kyriazis, Aristeidis Slavakis, Vasiliki Drossou and Vasiliki Soubasi

Biomolecules 2025, 15(3), 427; https://doi.org/10.3390/biom15030427 - 17 Mar 2025

Viewed by 412

Abstract

Preclinical studies have shown that progenitor cells (PCs) are mobilized toward injured tissues to ameliorate damage and contribute to regeneration. The exogenous therapeutic administration of PCs in children affected by neonatal encephalopathy (NE) is a promising, yet underreported, topic. In this prospective study, [...] Read more.

Preclinical studies have shown that progenitor cells (PCs) are mobilized toward injured tissues to ameliorate damage and contribute to regeneration. The exogenous therapeutic administration of PCs in children affected by neonatal encephalopathy (NE) is a promising, yet underreported, topic. In this prospective study, we investigated whether endogenous circulating progenitor cells (CPCs) are involved in intrinsic regeneration mechanisms following neonatal brain injury. Thirteen full-term infants with moderate/severe NE, eleven with perinatal stress, and twelve controls were enrolled. Blood samples were collected on days 1, 3, 9, 18, and 45, as well as at 8 and 24 months of life, and were analyzed with a focus on Endothelial Progenitor Cells, Haematopoietic Stem Cells, and Very Small Embryonic-Like Stem Cells, in addition to chemotactic factors (erythropoietin, IGF-1, and SDF-1). Correlations between CPCs, chemotactic factors, and brain injury were assessed using serum levels of brain injury biomarkers (S100B and neuron-specific enolase), brain MRIs, and Bayley III developmental scores. Increased brain injury biomarkers were followed by the upregulation of SDF-1 receptor and erythropoietin and, finally, by elevated CPCs. These findings suggest a potential endogenous regenerative effort, primarily observed in the moderate encephalopathy group, but this is suppressed in cases of severe brain injury. Mimicking and enhancing endogenous regeneration pathways in cases of failure—regarding cell type and timeframe—could provide a novel therapeutic model. Full article

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14 pages, 2188 KiB

Open AccessArticle

The Prognostic, Predictive and Clinicopathological Implications of KRT81/HNF1A- and GATA6-Based Transcriptional Subtyping in Pancreatic Cancer

by Michael Guenther, Sai Agash Surendran, Lea Margareta Steinke, Iduna Liou, Melanie Alexandra Palm, Volker Heinemann, Michael Haas, Stefan Boeck and Steffen Ormanns

Biomolecules 2025, 15(3), 426; https://doi.org/10.3390/biom15030426 - 17 Mar 2025

Viewed by 490

Abstract

Background: Transcriptional subtypes of pancreatic ductal adenocarcinoma (PDAC) based on the expression of hallmark genes may have prognostic implications and potential predictive functions. The two most employed subtyping markers assess the combined expression of KRT81 and HNF1A or of GATA6 alone, which can [...] Read more.

Background: Transcriptional subtypes of pancreatic ductal adenocarcinoma (PDAC) based on the expression of hallmark genes may have prognostic implications and potential predictive functions. The two most employed subtyping markers assess the combined expression of KRT81 and HNF1A or of GATA6 alone, which can be detected by immunohistochemistry (IHC). This study aimed to determine the prognostic or predictive impact of both subtyping marker panels in two large cohorts of advanced and resected pancreatic ductal adenocarcinoma (PDAC) patients. Methods: Transcriptional subtypes were determined by combining the expression of KRT81/HNF1A or assessing GATA6 expression alone by IHC in samples of two independent PDAC patient cohorts (advanced PDAC n = 139 and resected PDAC n = 411) as well as in 57 matched primary tumors and their corresponding metastases. RNAseq-based expression data of 316 resected PDAC patients was analyzed for validation. Results: Transcriptional subtypes widely overlapped in both marker panels (χ² p < 0.001) but switched during disease progression in up to 31.6% of patients. They had a modest impact on the patients’ prognosis in both cohorts, with longer overall survival (OS) for patients with KRT81−/HNF1A+ or GATA6+ tumors but better progression-free survival (PFS) and disease-free survival (DFS) in patients with KRT81+/GATA6− tumors treated with palliative or adjuvant gemcitabine-based chemotherapy. RNAseq expression data confirmed the findings. Conclusions: Transcriptional subtypes have differential responses to palliative and adjuvant gemcitabine-based chemotherapy and may change during disease progression. Both employed subtyping marker panels are equivalent and may be used to inform clinical therapy decisions. Full article

(This article belongs to the Special Issue Genetic and Genomic Biomarkers in Cancer Diagnosis, Prognosis, and Treatment Prediction)

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Biomolecules, Volume 15, Issue 3 (March 2025) – 144 articles

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