International Journal of Molecular Sciences

30 pages, 1468 KiB

Open AccessReview

The Role of Cytokines in Orthodontic Tooth Movement

by Hideki Kitaura, Fumitoshi Ohori, Aseel Marahleh, Jinghan Ma, Angyi Lin, Ziqiu Fan, Kohei Narita, Kou Murakami and Hiroyasu Kanetaka

Int. J. Mol. Sci. 2025, 26(14), 6688; https://doi.org/10.3390/ijms26146688 - 11 Jul 2025

Abstract

A challenge in orthodontic treatment is the long time taken to move teeth, which extends the long treatment period. Accordingly, various treatment protocols and orthodontic materials have been developed to shorten the orthodontic treatment period. However, controlling biological reactions is considered necessary to [...] Read more.

A challenge in orthodontic treatment is the long time taken to move teeth, which extends the long treatment period. Accordingly, various treatment protocols and orthodontic materials have been developed to shorten the orthodontic treatment period. However, controlling biological reactions is considered necessary to further shorten this treatment period. Orthodontic force results in compression of the periodontal ligament in the direction of tooth movement, resulting in various reactions in the periodontal ligament that induce osteoclast development, alveolar bone absorption, and teeth movement. The aforementioned reactions include immune reactions. Cytokines are substances responsible for intercellular communication and are involved in various physiological actions, including immune and inflammatory reactions. They cause various cellular responses, including cell proliferation, differentiation, cell death, and functional expression. Various cytokines are involved in biological reactions during orthodontic tooth movement (OTM). It is important to understand the role of cytokines during OTM in order to elucidate their biological response. This review discusses the role of cytokines during OTM. Full article

(This article belongs to the Special Issue Regulatory Network of Bone Metabolism)

41 pages, 3033 KiB

Open AccessReview

Analyzing Molecular Determinants of Nanodrugs’ Cytotoxic Effects

by Alicia Calé, Petra Elblová, Hana Andělová, Mariia Lunova and Oleg Lunov

Int. J. Mol. Sci. 2025, 26(14), 6687; https://doi.org/10.3390/ijms26146687 - 11 Jul 2025

Abstract

Nanodrugs hold great promise for targeted therapies, but their potential for cytotoxicity remains a major area of concern, threatening both patient safety and clinical translation. In this systematic review, we conducted a systematic investigation of nanotoxicity studies—identified through an AI-assisted screening procedure using [...] Read more.

Nanodrugs hold great promise for targeted therapies, but their potential for cytotoxicity remains a major area of concern, threatening both patient safety and clinical translation. In this systematic review, we conducted a systematic investigation of nanotoxicity studies—identified through an AI-assisted screening procedure using Scopus, PubMed, and Elicit AI—to establish the molecular determinants of nanodrug-induced cytotoxicity. Our findings reveal three dominant and linked mechanisms that consistently act in a range of nanomaterials: oxidative stress, inflammatory signaling, and lysosomal disruption. Key nanomaterial properties like chemical structure, size, shape, surface charge, tendency to aggregate, and biocorona formation control these pathways, modulating cellular uptake, reactive oxygen species generation, cytokine release, and subcellular injury. Notably, the most frequent mechanism was oxidative stress, which often initiated downstream inflammatory and apoptotic signaling. By linking these toxicity pathways with particular nanoparticle characteristics, our review presents necessary guidelines for safer, more biocompatible nanodrug formulation design. This extensive framework acknowledges the imperative necessity for mechanistic toxicity assessment in nanopharmaceutical design and underscores the strength of AI tools in driving systematic toxicology studies. Full article

(This article belongs to the Special Issue Molecular Research on Nanotoxicology)

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10 pages, 4102 KiB

Open AccessArticle

Silencing of the Alkaline α-Galactosidase Gene CsAGA1 Impairs Root and Gall Development in Cucumber upon Meloidogyne incognita Infection

by Tingting Ji, Xingyi Wang, Xueyun Wang, Lihong Gao, Yongqiang Tian and Si Ma

Int. J. Mol. Sci. 2025, 26(14), 6686; https://doi.org/10.3390/ijms26146686 - 11 Jul 2025

Abstract

Meloidogyne incognita (M. incognita) is a devastating root-knot nematode that parasitizes a broad range of crop species by inducing the formation of giant cells (GCs) in host roots, thereby facilitating nutrient acquisition. This process profoundly alters host sugar metabolism, yet the [...] Read more.

Meloidogyne incognita (M. incognita) is a devastating root-knot nematode that parasitizes a broad range of crop species by inducing the formation of giant cells (GCs) in host roots, thereby facilitating nutrient acquisition. This process profoundly alters host sugar metabolism, yet the molecular regulators underlying sugar dynamics during infection remain poorly understood in cucumber. In this study, we investigated the role of the cucumber alkaline α-galactosidase gene (CsAGA1) in M. incognita-infected roots. Histochemical analysis of proCsAGA1::GUS transgenic lines demonstrated that CsAGA1 is spatially localized to nematode-induced feeding sites, with its expression markedly induced in GCs and phloem-adjacent tissues during infection. Functional analyses revealed that silencing CsAGA1 impaired root and gall development. CsAGA1-silenced plants exhibited increased gall numbers (per gram root) but significantly reduced root growth and smaller galls compared to controls. These results indicate that CsAGA1 is required for proper gall expansion and root growth during M. incognita infection. This study provides novel insight into the sugar-mediated regulation of host–nematode interactions, and CsAGA1 emerges as a potential target for the biological control of M. incognita. Full article

(This article belongs to the Special Issue Biotic and Abiotic Stress Responses of Vegetable Crops)

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18 pages, 9838 KiB

Open AccessArticle

TGF-β Promotes Endothelial-to-Mesenchymal Transition and Alters Corneal Endothelial Cell Migration in Fuchs Endothelial Corneal Dystrophy

by Judy Yan, Brooke Lim, Narisa Dhupar, Kathrine Bhargava, Lina Chen, Greg Moloney and Stephan Ong Tone

Int. J. Mol. Sci. 2025, 26(14), 6685; https://doi.org/10.3390/ijms26146685 - 11 Jul 2025

Abstract

Fuchs endothelial corneal dystrophy (FECD) is a progressive corneal disease characterized by corneal endothelial cell (CEC) loss and guttae formation. Elevated levels of Transforming Growth Factor-Beta 1 and 2 (TGF-β1/-β2) have been reported in the aqueous humor (AH) of FECD patients and have [...] Read more.

Fuchs endothelial corneal dystrophy (FECD) is a progressive corneal disease characterized by corneal endothelial cell (CEC) loss and guttae formation. Elevated levels of Transforming Growth Factor-Beta 1 and 2 (TGF-β1/-β2) have been reported in the aqueous humor (AH) of FECD patients and have been implicated with abnormal extracellular matrix (ECM) production, endothelial-to-mesenchymal transition (EndoMT), the unfolded protein response, and cell death. However, how TGF-β signaling affects cell migration in FECD remains to be elucidated. In this study, we found that TGF-β2 levels were significantly elevated in the AH of FECD patients compared to controls. We performed bulk RNA sequencing on FECD CECs treated with TGF-β1 or TGF-β2 and identified the epithelial-to-mesenchymal (EMT) pathway as one of the top dysregulated pathways. We found that TGF-β1 and TGF-β2 increased EMT markers, filamentous-actin (F-actin) expression and produced more EMT-like phenotype in FECD and control CECs. We also observed that TGF-β1 and TGF-β2 significantly increased FECD CEC migration speed as detected by scratch assay and individual cell tracking and promoted individual cellular migration behavior. This study provides novel insight into FECD pathogenesis and how increased TGF-β signaling promotes EndoMT and alters cellular migration in FECD CECs. Full article

(This article belongs to the Special Issue Functional Roles of Epithelial and Endothelial Cells)

17 pages, 1584 KiB

Open AccessArticle

Association of First-Trimester Maternal Biomarkers with Preeclampsia and Related Maternal and Fetal Severe Adverse Events

by Ana Camacho-Carrasco, Jorge Montenegro-Martínez, María Luisa Miranda-Guisado, Rocío Muñoz-Hernández, Rocío Salsoso, Daniel Fatela-Cantillo, Lutgardo García-Díaz, Pablo Stiefel García-Junco, Alfonso Mate, Carmen M. Vázquez, Verónica Alfaro-Lara, Antonio J. Vallejo-Vaz and Luis M. Beltrán-Romero

Int. J. Mol. Sci. 2025, 26(14), 6684; https://doi.org/10.3390/ijms26146684 - 11 Jul 2025

Abstract

To assess the association between known (PlGF, sFlt-1, betaHCG, PAPPA) and novel (cell-free DNA, cfDNA, and total endothelial and platelet microvesicles, MVs) maternal blood biomarkers measured at the first trimester with the later development of preeclampsia (PE) and PE-related severe adverse events (SAE), [...] Read more.

To assess the association between known (PlGF, sFlt-1, betaHCG, PAPPA) and novel (cell-free DNA, cfDNA, and total endothelial and platelet microvesicles, MVs) maternal blood biomarkers measured at the first trimester with the later development of preeclampsia (PE) and PE-related severe adverse events (SAE), we conducted a retrospective case–control study including women with an established diagnosis of preeclampsia (cases) and healthy pregnant women (controls). Biomarkers were measured from first-trimester blood samples stored in a hospital biobank. A total of 89 women, 54 women with PE and 35 controls were included. PlGF showed good performance for diagnosing overall preeclampsia (AUC: 0.71; 95% CI 0.59–0.82), early-onset preeclampsia (AUC 0.80; 95% CI 0.68–0.9) and fetal-neonatal SAEs (AUC: 0.73; 95% CI 0.63–0.84). Multivariate models including clinical variables, PlGF and other biomarkers showed good to very good discrimination for the development of PE, early-onset PE and fetal-neonatal SAEs (AUCs of 0.87, 0.89 and 0.79, respectively). Platelet-derived MVs were the best isolated biomarker for late-onset PE and, combined with systolic blood pressure, showed good discrimination (AUC: 0.81; 95% CI 0.71–0.92). For maternal SAEs, a model incorporating cfDNA and sFlt-1 provided excellent discrimination (AUC 0.92; 95% CI 0.82–1.00). Our findings suggest that multivariate models incorporating both clinical variables and first-trimester biomarkers may improve risk stratification for PE, especially for late-onset PE and for identifying women at risk of severe maternal or fetal complications. Notably, the inclusion of novel biomarkers such as cfDNA and MVs added value in clinical scenarios where the predictive performance of existing tools remains suboptimal. Full article

(This article belongs to the Special Issue Recent Molecular Research on Preeclampsia)

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17 pages, 1948 KiB

Open AccessArticle

Overexpression of Circular PRMT1 Transcripts in Colorectal Adenocarcinoma Predicts Recurrence and Poor Overall Survival

by Panagiotis Kokoropoulos, Spyridon Christodoulou, Panagiotis Tsiakanikas, Panteleimon Vassiliu, Christos K. Kontos and Nikolaos Arkadopoulos

Int. J. Mol. Sci. 2025, 26(14), 6683; https://doi.org/10.3390/ijms26146683 - 11 Jul 2025

Abstract

Colorectal cancer (CRC) is one of the most prevalent and deadly neoplasms globally; this fact puts emphasis on the need for accurate molecular biomarkers for early detection and accurate prognosis. Circular RNAs (circRNAs) have recently emerged as very promising cancer biomarkers. In this [...] Read more.

Colorectal cancer (CRC) is one of the most prevalent and deadly neoplasms globally; this fact puts emphasis on the need for accurate molecular biomarkers for early detection and accurate prognosis. Circular RNAs (circRNAs) have recently emerged as very promising cancer biomarkers. In this study, we thoroughly examined whether the expression levels of circular transcripts of the protein arginine methyltransferase 1 (PRMT1) gene can predict the prognosis of patients diagnosed with colorectal adenocarcinoma, the most frequent type of CRC. Hence, a highly sensitive quantitative PCR (qPCR) assay was developed and applied to quantify circ-PRMT1 expression in cDNAs from 210 primary colorectal adenocarcinoma tissue specimens and 86 paired normal colorectal mucosae. Extensive biostatistical analysis was then performed to assess the potential prognostic power of circ-PRMT1. Significant overexpression of this molecule was observed in colorectal adenocarcinoma tissue samples in contrast to their non-cancerous counterparts. Moreover, higher circ-PRMT1 expression was correlated with poorer disease-free survival (DFS) and worse overall survival (OS) in colorectal adenocarcinoma patients. Interestingly, multivariate Cox regression analysis revealed that the prognostic value of the expression of this circRNA does not depend on other established prognostic factors included in the prognostic model. Furthermore, the stratification of patients based on TNM staging revealed that higher circ-PRMT1 levels were significantly related to shorter DFS and OS intervals, particularly in patients with colorectal adenocarcinoma of TNM stage II or III. In summary, this original research study provides evidence that circ-PRMT1 overexpression represents a promising molecular biomarker of poor prognosis in colorectal adenocarcinoma, not depending on other established prognostic factors such as TNM staging. Full article

(This article belongs to the Special Issue New Molecular Aspects of Colorectal Cancer)

20 pages, 1556 KiB

Open AccessArticle

Polyclonal LC3B Antibodies Generate Non-Specific Staining in the Nucleus of Herpes Simplex Virus Type 1-Infected Cells: Caution in the Interpretation of LC3 Staining in the Immunofluorescence Analysis of Viral Infections

by Inés Ripa, Sabina Andreu, Daniel Galdo, Oliver Caballero, Raquel Bello-Morales and José Antonio López-Guerrero

Int. J. Mol. Sci. 2025, 26(14), 6682; https://doi.org/10.3390/ijms26146682 - 11 Jul 2025

Abstract

The most common marker used to monitor autophagy is the microtubule-associated protein light chain 3 (LC3). Upon induction of autophagy, LC3 is conjugated to phosphatidylethanolamine and targeted to autophagic membranes, which can be easily detected by immunofluorescence. However, this technique has some limitations. [...] Read more.

The most common marker used to monitor autophagy is the microtubule-associated protein light chain 3 (LC3). Upon induction of autophagy, LC3 is conjugated to phosphatidylethanolamine and targeted to autophagic membranes, which can be easily detected by immunofluorescence. However, this technique has some limitations. During the early stages of HSV-1 infection, strong LC3B nuclear staining is observed within the viral replication compartments. This staining is only detected when using polyclonal antibodies. It is noteworthy that monoclonal antibodies or the GFP-LC3 plasmid do not reveal any nuclear LC3 staining. Interestingly, LC3B is not detected in the nuclear fraction of infected cells by Western blotting, even when polyclonal antibodies are used. In infected LC3B knockout cells, nuclear staining is still observed when using polyclonal LC3B antibodies. This suggests that polyclonal LC3B antibodies generate non-specific nuclear staining in infected cells, which could result in misinterpretation and erroneous conclusions. These findings raise questions about the reliability of LC3-immunofluorescence assays in herpesvirus infections. It is imperative that the methodology employed for monitoring autophagy by immunofluorescence in viral infections be reviewed and updated, and that the specificity of anti-LC3B antibodies be tested before use. To ensure the accuracy of the results, it is essential to validate this technique with additional assays, such as by immunoblot analysis or via the use of autophagy-deficient cell lines. Full article

(This article belongs to the Special Issue Viral Infections: Physiology, Pathophysiology, Pathogenesis, Diagnosis and Treatment)

18 pages, 3194 KiB

Open AccessArticle

Identification and Characterization of the Complete Genome of the TGF-β Gene Family in Tupaia belangeri: Expression and Function of Adipose Tissue Under Cold Acclimation Conditions

by Lijie Du, Wanlong Zhu and Lin Zhang

Int. J. Mol. Sci. 2025, 26(14), 6681; https://doi.org/10.3390/ijms26146681 - 11 Jul 2025

Abstract

The transforming growth factor beta (TGF-

β

) gene family is widely distributed across the animal kingdom, playing a crucial role in various cellular processes and maintaining overall health and homeostasis. The present study identified 34 TGF-

β

family genes based on the [...] Read more.

The transforming growth factor beta (TGF-

β

) gene family is widely distributed across the animal kingdom, playing a crucial role in various cellular processes and maintaining overall health and homeostasis. The present study identified 34 TGF-

β

family genes based on the genome sequence in Tupaia belangeri, which were classified into the TGF-

β

, bone morphogenetic protein (BMP), growth differentiation factor (GDF), glial cell-derived neurotrophic factor (GDNF), and Activin/Inhibin subfamilies. A phylogenetic analysis revealed the evolutionary relationships among members of the TGF-

β

family in T. belangeri and their homologous genes in Homo sapiens, Mus musculus, and Pan troglodytes, indicating a high degree of conservation throughout evolution. A chromosomal distribution and collinearity analysis demonstrated the localization of these genes within the genome of T. belangeri and their collinearity with genes from other species. A gene structure and motif analysis further illustrated the conservation and diversity among TGF-

β

family members. A protein interaction network analysis highlighted the central roles of TGFB1, TGFB3, BMP7, and BMP2 in signal transduction. A functional enrichment analysis underscored the significance of the TGF-

β

signaling pathway in the biological processes of T. belangeri, particularly in cell proliferation, differentiation, and apoptosis. We assessed the impact of cold acclimation treatment on the expression of TGF-

β

family proteins in the adipose tissue (white adipose tissue [WAT] and brown adipose tissue [BAT]) of T. belangeri using ELISA technology, finding that protein expression levels in the experimental group were significantly higher than those of in the control group. These results suggested that cold acclimation may enhance the adaptability of T. belangeri to cold environments by modulating the expression of TGF-

β

family genes. This study offers new insights into the role of the TGF-

β

family in the cold acclimation adaptation of T. belangeri, providing a scientific foundation for future genetic improvements and strategies for cold acclimation. Full article

(This article belongs to the Section Molecular Biology)

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19 pages, 2517 KiB

Open AccessArticle

In Silico Analysis of Post-COVID-19 Condition (PCC) Associated SNP rs9367106 Predicts the Molecular Basis of Abnormalities in the Lungs and Brain Functions

by Amit K. Maiti

Int. J. Mol. Sci. 2025, 26(14), 6680; https://doi.org/10.3390/ijms26146680 - 11 Jul 2025

Abstract

Long- or post-COVID-19 syndrome, which is also designated by WHO as Post COVID-19 Condition (PCC), is characterized by the persistent symptoms that remain after recovery from SARS-CoV-2 infection. A worldwide consortium of Long COVID-19 Host Genetics Initiative (Long COVID-19 HGI) identified an SNP [...] Read more.

Long- or post-COVID-19 syndrome, which is also designated by WHO as Post COVID-19 Condition (PCC), is characterized by the persistent symptoms that remain after recovery from SARS-CoV-2 infection. A worldwide consortium of Long COVID-19 Host Genetics Initiative (Long COVID-19 HGI) identified an SNP rs9367106 (G>C; chr6:41,515,652, GRCh38, p = 1.76 × 10⁻¹⁰, OR = 1.63, 95% CI: 1.40–1.89) that is associated with PCC. Unraveling the functional significance of this SNP is of prime importance to understanding the development of the PCC phenotypes and their therapy. Here, in Silico, I explored how the risk allele of this SNP alters the functional mechanisms and molecular pathways leading to the development of PCC phenotypes. Bioinformatic methods include physical interactions using HI-C and Chia-PET analysis, Transcription Factors (TFs) binding ability, RNA structure modeling, epigenetic, and pathway analysis. This SNP resides within two long RNA genes, LINC01276 and FOXP4-AS1, and is located at ~31 kb upstream of a transcription factor FOXP4. This DNA region, including this SNP, physically interacts with FOXP4-AS1 and FOXP4, implying that this regulatory SNP could alter the normal cellular function of FOXP4-AS1 and FOXP4. Furthermore, rs9367106 is in eQTL with the FOXP4 gene in lung tissue. rs9367106 carrying DNA sequences act as distant enhancers and bind with several transcription factors (TFs) including YY1, PPAR-α, IK-1, GR-α, and AP2αA. The G>C transition extensively modifies the RNA structure that may affect the TF bindings and enhancer functions to alter the interactions and functions of these RNA molecules. This SNP also includes an ALU/SINE sequence and alteration of which by the G>C transition may prevent IFIH1/MDA5 activation, leading to suppression of host innate immune responses. LINC01276 targets the MED20 gene that expresses mostly in brain tissues, associated with sleep disorders and basal ganglia abnormalities similar to some of the symptoms of PCC phenotypes. Taken together, G>C transition of rs9367601 may likely alter the function of all three genes to explain the molecular basis of developing the long-term symptomatic abnormalities in the lungs and brain observed after COVID-19 recovery. Full article

(This article belongs to the Special Issue Genetic Variations in Human Diseases: 2nd Edition)

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22 pages, 2320 KiB

Open AccessReview

Use of Radiomics in Characterizing Tumor Hypoxia

by Mohan Huang, Helen K. W. Law and Shing Yau Tam

Int. J. Mol. Sci. 2025, 26(14), 6679; https://doi.org/10.3390/ijms26146679 - 11 Jul 2025

Abstract

Tumor hypoxia involves limited oxygen supply within the tumor microenvironment and is closely associated with aggressiveness, metastasis, and resistance to common cancer treatment modalities such as chemotherapy and radiotherapy. Traditional methodologies for hypoxia assessment, such as the use of invasive probes and clinical [...] Read more.

Tumor hypoxia involves limited oxygen supply within the tumor microenvironment and is closely associated with aggressiveness, metastasis, and resistance to common cancer treatment modalities such as chemotherapy and radiotherapy. Traditional methodologies for hypoxia assessment, such as the use of invasive probes and clinical biomarkers, are generally not very suitable for routine clinical applications. Radiomics provides a non-invasive approach to hypoxia assessment by extracting quantitative features from medical images. Thus, radiomics is important in diagnosis and the formulation of a treatment strategy for tumor hypoxia. This article discusses the various imaging techniques used for the assessment of tumor hypoxia including magnetic resonance imaging (MRI), positron emission tomography (PET), and computed tomography (CT). It introduces the use of radiomics with machine learning and deep learning for extracting quantitative features, along with its possible clinical use in hypoxic tumors. This article further summarizes the key challenges hindering the clinical translation of radiomics, including the lack of imaging standardization and the limited availability of hypoxia-labeled datasets. It also highlights the potential of integrating radiomics with multi-omics to enhance hypoxia visualization and guide personalized cancer treatment. Full article

(This article belongs to the Special Issue Emerging Advances in Cancer Biomarkers: Machine Learning, Radiomics, Genomics, and More)

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27 pages, 3715 KiB

Open AccessReview

Network Pharmacology as a Tool to Investigate the Antioxidant and Anti-Inflammatory Potential of Plant Secondary Metabolites—A Review and Perspectives

by Anna Merecz-Sadowska, Arkadiusz Sadowski, Hanna Zielińska-Bliźniewska, Karolina Zajdel and Radosław Zajdel

Int. J. Mol. Sci. 2025, 26(14), 6678; https://doi.org/10.3390/ijms26146678 - 11 Jul 2025

Abstract

Plant secondary metabolites possess significant antioxidant and anti-inflammatory properties, but their complex polypharmacological mechanisms remain poorly understood. Network pharmacology has emerged as a powerful systems-level approach for investigating multi-target interactions of natural products. This review systematically analyzes network pharmacology applications in elucidating the [...] Read more.

Plant secondary metabolites possess significant antioxidant and anti-inflammatory properties, but their complex polypharmacological mechanisms remain poorly understood. Network pharmacology has emerged as a powerful systems-level approach for investigating multi-target interactions of natural products. This review systematically analyzes network pharmacology applications in elucidating the antioxidant and anti-inflammatory mechanisms of plant metabolites, evaluating concordance between computational predictions and experimental validation. A comprehensive literature search was conducted across major databases (2015–2025), focusing on network pharmacology studies with experimental validation. Analysis revealed remarkable convergence toward common molecular mechanisms, despite diverse chemical structures. For antioxidant activities, the Nrf2/KEAP1/ARE pathway emerged as the most frequently validated mechanism, along with PI3K/AKT, MAPK, and NF-κB signaling. Anti-inflammatory mechanisms consistently involved NF-κB, MAPK, and PI3K/AKT pathways. Key targets, including AKT1, TNF-α, COX-2, NFKB1, and RELA, were repeatedly identified. Flavonoids, phenolic acids, and terpenoids dominated as bioactive compounds. Molecular docking studies supported predicted interactions, with experimental validation showing good concordance for pathway modulation and cytokine regulation. Network pharmacology provides a valuable framework for investigating the complex bioactivities of plant metabolites. The convergence toward common regulatory hubs suggests that natural compounds achieve protective effects by modulating central nodes that integrate redox balance and inflammatory responses. Despite limitations, including database dependency, integrating network pharmacology with experimental validation accelerates mechanistic understanding in natural-product drug discovery. Full article

(This article belongs to the Special Issue In Silico Methods of Assessing the Therapeutic Potential of Natural Substances)

20 pages, 7239 KiB

Open AccessArticle

Genomic Insights into Vaccinium spp. Endophytes B. halotolerans and B. velezensis and Their Antimicrobial Potential

by Ingrida Mažeikienė, Birutė Frercks, Monika Kurgonaitė, Neringa Rasiukevičiūtė and Irena Mačionienė

Int. J. Mol. Sci. 2025, 26(14), 6677; https://doi.org/10.3390/ijms26146677 - 11 Jul 2025

Abstract

Plant microbiota contributes to nutrient absorption, and the production of hormones and vitamins, and plays a crucial role in responding to environmental stress. We hypothesized that Vaccinium spp. harbour a unique microbiota that enables them to coexist in extreme environments such as saline, [...] Read more.

Plant microbiota contributes to nutrient absorption, and the production of hormones and vitamins, and plays a crucial role in responding to environmental stress. We hypothesized that Vaccinium spp. harbour a unique microbiota that enables them to coexist in extreme environments such as saline, nutrient-poor, and waterlogged conditions. Upon examining Bacillus spp. endophytes isolated from blueberries, cranberries and lingonberries in vitro, we identified B. halotolerans (Bil-LT1_1, Bil-LT1_2) and B. velezensis (Cran-LT1_8, Ling-NOR4_15) strains that inhibit the growth of five pathogenic fungi and five foodborne bacteria. Whole-genome sequencing provided insights into genome organization and plasticity, helping identify mobile elements and genes potentially acquired through horizontal gene transfer. Functional annotation identified genes associated with plant colonization, stress tolerance, biocontrol activity, and plant growth promotion. Comparative genomic analyses revealed key biosynthetic gene clusters (BGCs) responsible for producing antifungal metabolites, including lipopeptides and polyketides. Genes supporting plant nutrition, growth, and environmental adaptation were present also in these strains. Notably, isolated endophytes exhibited particularly high levels of genomic plasticity, likely due to horizontal gene transfer involving gene ontology (GO) pathways related to survival in polymicrobial and foreign environments. Full article

(This article belongs to the Special Issue Microbial Omics: Decoding Microbial Life)

16 pages, 1020 KiB

Open AccessArticle

Circulating microRNAs as Potential Diagnostic Tools for Asthma and for Indicating Severe Asthma Risk

by Elena V. Vorobeva, M. Aref Kyyaly, Collin L. Sones, Peijun J. W. He, S. Hasan Arshad, Tilman Sanchez-Elsner and Ramesh J. Kurukulaaratchy

Int. J. Mol. Sci. 2025, 26(14), 6676; https://doi.org/10.3390/ijms26146676 - 11 Jul 2025

Abstract

Asthma places a significant burden at individual and societal levels, but there remains no gold-standard objective test for asthma diagnosis or asthma severity risk prediction. MicroRNAs (miRNAs) are short non-coding RNA sequences that are attracting interest as biological signatures of health and disease [...] Read more.

Asthma places a significant burden at individual and societal levels, but there remains no gold-standard objective test for asthma diagnosis or asthma severity risk prediction. MicroRNAs (miRNAs) are short non-coding RNA sequences that are attracting interest as biological signatures of health and disease status. We sought to construct serum miRNA panels that could serve as potential biomarkers to aid in the diagnosis of asthma and predict asthma severity. Thirty-five asthma-related miRNAs were screened in the serum of three patient groups (never-asthma, mild-asthma, and severe-asthma; n = 50/group) drawn from two well-characterised cohorts. miRCURY LNA technology was used, followed by GeneGlobe analysis. The associations of miRNA expression with clinical outcomes of interest and diagnostic value of the proposed miRNA panels were assessed. We identified an asthma diagnosis panel comprising upregulated miR-223-3p, miR-191-5p, and miR-197-3p (area under curve (AUC) = 0.813, sensitivity 76% and specificity 72%). Compared with mild-asthma individuals, we also identified an asthma severity risk panel comprising upregulated miR-223-3p plus downregulated miR-30a-5p, miR-660-5p, and miR-125b-5p (AUC = 0.759, sensitivity 78%, specificity 64%). Individual miRNAs showed associations with worse clinical asthma severity and impaired quality of life. miRNA panels with high sensitivity and specificity offer potential as biomarkers for asthma diagnosis and asthma severity. Full article

(This article belongs to the Special Issue Circulating Non-Coding RNAs as Diagnostic and Prognostic Markers of Human Diseases: 3rd Edition)

22 pages, 4817 KiB

Open AccessArticle

LightSpot Fluorescent Conjugates as Highly Efficient Tools for Lysosomal P-gp Quantification in Olaparib-Treated Triple-Negative Breast Cancer Cells

by Antoine Goisnard, Pierre Daumar, Maxime Dubois, Elodie Gay, Manon Roux, Marie Depresle, Frédérique Penault-Llorca, Emmanuelle Mounetou and Mahchid Bamdad

Int. J. Mol. Sci. 2025, 26(14), 6675; https://doi.org/10.3390/ijms26146675 - 11 Jul 2025

Abstract

P-glycoprotein (P-gp) is a key element of cancer treatment resistance, actively extruding cytotoxic drugs from cells and diminishing their efficacy. While its role at the plasma membrane is well established, its intracellular localization, particularly on lysosomes, is increasingly recognized as a critical contributor [...] Read more.

P-glycoprotein (P-gp) is a key element of cancer treatment resistance, actively extruding cytotoxic drugs from cells and diminishing their efficacy. While its role at the plasma membrane is well established, its intracellular localization, particularly on lysosomes, is increasingly recognized as a critical contributor to drug resistance. This study investigates four innovative LightSpot fluorescent compounds to detect and quantify both membrane and lysosomal P-gp in Triple-Negative Breast Cancer (TNBC) SUM1315 and DU4475 cell lines. Results highlighted lysosomal P-gp staining by the LightSpot-FL-1, LightSpot-BrX-1, and LightSpot-BdO-1 fluorescent compounds (Mander’s coefficients > 0.8 overlapping with LAMP2 immunostaining). After both cell lines were exposed to Olaparib, a significant increase in P-gp expression level and lysosomal distribution of P-gp was detected. Indeed, after 100 µM Olaparib exposure, LightSpot-FL-1 allowed us to quantify an increase in P-gp-positive lysosome number of 1293 and 334% for SUM1315 and DU4475 cells, respectively, compared to the control. Findings suggest that P-gp may relocate to lysosomes upon drug exposure, highlighting a dual resistance mechanism involving both membrane and lysosomal P-gp. This study demonstrated the potential of LightSpot fluorescent compounds to evaluate P-gp-mediated cell resistance to treatment and emphasized the need to assess global cell P-gp expression to improve cancer diagnosis. Full article

(This article belongs to the Special Issue Molecular Mechanisms and Therapeutic Strategies to Overcome Drug Resistance in Cancer)

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46 pages, 7993 KiB

Open AccessReview

Quantum Dot-Based Luminescent Sensors: Review from Analytical Perspective

by Alissa Loskutova, Ansar Seitkali, Dinmukhamed Aliyev and Rostislav Bukasov

Int. J. Mol. Sci. 2025, 26(14), 6674; https://doi.org/10.3390/ijms26146674 - 11 Jul 2025

Abstract

Quantum Dots (QDs) are small semiconductor nanoparticles (<10 nm) with strong, relatively stable, and tunable luminescent properties, which are increasingly applied in the sensing and detection of various analytes, including metal ions, biomarkers, explosives, proteins, RNA/DNA fragments, pesticides, drugs, and pollutants. In this [...] Read more.

Quantum Dots (QDs) are small semiconductor nanoparticles (<10 nm) with strong, relatively stable, and tunable luminescent properties, which are increasingly applied in the sensing and detection of various analytes, including metal ions, biomarkers, explosives, proteins, RNA/DNA fragments, pesticides, drugs, and pollutants. In this review, we critically assess recent developments and advancements in luminescent QD-based sensors from an analytical perspective. We collected, tabulated, and analyzed relevant data reported in 124 peer-reviewed articles. The key analytical figures of merit, including the limit of detection (LOD), excitation and emission wavelengths, and size of the particles were extracted, tabulated, and analyzed with graphical representations. We calculated the geometric mean and median LODs from those tabulated publications. We found the following geometric mean LODs: 38 nM for QD-fluorescent-based sensors, 26 nM for QD-phosphorescent-based sensors, and an impressively low 0.109 pM for QD-chemiluminescent-based sensors, which demonstrate by far the best sensitivity in QD-based detection. Moreover, AI-based sensing methods, including the ATTBeadNet model, optimized principal component analysis(OPCA) model, and Support Vector Machine (SVM)-based system, were reviewed as they enhance the analytical performance of the detection. Despite these advances, there are still challenges that include improvements in recovery values, biocompatibility, stability, and overall performance. This review highlights trends to guide the future design of robust, high-performance, QD-based luminescent sensors. Full article

(This article belongs to the Special Issue Properties and Applications of Nanoparticles and Nanomaterials: 2nd Edition)

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23 pages, 677 KiB

Open AccessArticle

The Effects of Psychotherapy on Single and Repeated Ketamine Infusion(s) Therapy for Treatment-Resistant Depression: The Convergence of Molecular and Psychological Treatment

by Sofia Sakopoulos and McWelling Todman

Int. J. Mol. Sci. 2025, 26(14), 6673; https://doi.org/10.3390/ijms26146673 - 11 Jul 2025

Abstract

Ketamine infusion therapy has gained recognition as an innovative treatment for treatment-resistant depression (TRD), demonstrating rapid and robust antidepressant effects. Its therapeutic promise is increasingly understood to involve molecular and neurobiological processes that promote neural plasticity and cognitive flexibility. These changes may create [...] Read more.

Ketamine infusion therapy has gained recognition as an innovative treatment for treatment-resistant depression (TRD), demonstrating rapid and robust antidepressant effects. Its therapeutic promise is increasingly understood to involve molecular and neurobiological processes that promote neural plasticity and cognitive flexibility. These changes may create a unique window for psychotherapeutic interventions to take deeper effect. This retrospective chart review examined the clinical outcomes of individuals with TRD who received either single or repeated ketamine infusion(s), with or without weekly psychotherapy. Depression severity, measured by Beck Depression Inventory scores, was assessed pre-treatment and 30 days post-infusion(s). The results showed significant symptom reduction across all groups, with the most pronounced effects observed in those who received concurrent psychotherapy. While infusion number did not significantly alter outcomes, the integration of ketamine with psychotherapy appeared to enhance treatment response. Full article

(This article belongs to the Special Issue Unveiling Mental Disorders: Molecular Mechanisms and Innovative Therapies)

27 pages, 1246 KiB

Open AccessReview

Exploring Recent Developments in the Manifestation, Diagnosis, and Treatment of Patients with Smith–Lemli–Opitz Syndrome: From Molecular Pathways to Clinical Innovations

by Aleksandra Żukowska, Małgorzata Król, Patrycja Kupnicka, Katarzyna Bąk, Kamil Janawa and Dariusz Chlubek

Int. J. Mol. Sci. 2025, 26(14), 6672; https://doi.org/10.3390/ijms26146672 - 11 Jul 2025

Abstract

Smith–Lemli–Opitz syndrome (SLOS) is a rare, autosomal recessive genetic disorder caused by mutations in the DHCR7 gene, which encodes the enzyme responsible for the final step in cholesterol biosynthesis. Impaired enzyme function leads to cholesterol deficiency, affecting the development and function of the [...] Read more.

Smith–Lemli–Opitz syndrome (SLOS) is a rare, autosomal recessive genetic disorder caused by mutations in the DHCR7 gene, which encodes the enzyme responsible for the final step in cholesterol biosynthesis. Impaired enzyme function leads to cholesterol deficiency, affecting the development and function of the entire organism. The accumulation of cholesterol precursors enhances the formation of oxysterols, which are involved in the pathomechanism of neurological, ophthalmological, and vascular changes in patients. This review analyzes 53 studies published between 2020 and 2025 on the molecular mechanisms underlying the clinical features of SLOS, including cholesterol deficiency, oxysterol accumulation, and the latest diagnostic methods, including LC-MS/MS chromatography and biomarkers such as GFAP for monitoring disease progression. MRI is discussed as a supportive tool for neuroimaging, along with advances in prenatal diagnostics, such as the detection of cholesterol precursors in neonatal hair. Therapeutic options are also reviewed, with particular emphasis on cholesterol supplementation, cholic acid, and experimental treatments such as vitamin E supplementation, statin therapy, gene therapy, and liver transplantation. Current research indicates that expanding knowledge in this area not only improves patient prognosis but also provides hope for the development of effective therapies in the future. Full article

(This article belongs to the Special Issue Recent Progress in Metabolic Diseases)

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21 pages, 4391 KiB

Open AccessArticle

Thermal Cycling-Hyperthermia Attenuates Rotenone-Induced Cell Injury in SH-SY5Y Cells Through Heat-Activated Mechanisms

by Yu-Yi Kuo, Guan-Bo Lin, You-Ming Chen, Hsu-Hsiang Liu, Fang-Tzu Hsu, Yi Kung and Chih-Yu Chao

Int. J. Mol. Sci. 2025, 26(14), 6671; https://doi.org/10.3390/ijms26146671 - 11 Jul 2025

Abstract

Parkinson’s disease (PD) is the second most prevalent neurodegenerative disease. It is characterized by mitochondrial dysfunction, increased reactive oxygen species (ROS), α-synuclein (α-syn) and phosphorylated-tau protein (p-tau) aggregation, and dopaminergic neuron cell death. Current drug therapies only provide temporary symptomatic relief and fail [...] Read more.

Parkinson’s disease (PD) is the second most prevalent neurodegenerative disease. It is characterized by mitochondrial dysfunction, increased reactive oxygen species (ROS), α-synuclein (α-syn) and phosphorylated-tau protein (p-tau) aggregation, and dopaminergic neuron cell death. Current drug therapies only provide temporary symptomatic relief and fail to stop or reverse disease progression due to the severe side effects or the blood–brain barrier. This study aimed to investigate the neuroprotective effects of an intermittent heating approach, thermal cycling-hyperthermia (TC-HT), in an in vitro PD model using rotenone (ROT)-induced human neural SH-SY5Y cells. Our results revealed that TC-HT pretreatment conferred neuroprotective effects in the ROT-induced in vitro PD model using human SH-SY5Y neuronal cells, including reducing ROT-induced mitochondrial apoptosis and ROS accumulation in SH-SY5Y cells. In addition, TC-HT also inhibited the expression of α-syn and p-tau through heat-activated pathways associated with sirtuin 1 (SIRT1) and heat-shock protein 70 (Hsp70), involved in protein chaperoning, and resulted in the phosphorylation of Akt and glycogen synthase kinase-3β (GSK-3β), which inhibit p-tau formation. These findings underscore the potential of TC-HT as an effective treatment for PD in vitro, supporting its further investigation in in vivo models with focused ultrasound (FUS) as a feasible heat-delivery approach. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Neurological and Psychiatric Disease: A Decade of Progress)

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22 pages, 13466 KiB

Open AccessArticle

FR-BINN: Biologically Informed Neural Networks for Enhanced Biomarker Discovery and Pathway Analysis

by Yangkun Cao, Chaoyi Yin, Xinsen Zhou and Yonghe Zhao

Int. J. Mol. Sci. 2025, 26(14), 6670; https://doi.org/10.3390/ijms26146670 - 11 Jul 2025

Abstract

Chronic inflammation plays a pivotal role in human health, with certain inflammatory conditions significantly increasing the risk of cancer, while others do not. However, the molecular mechanisms underlying this divergent risk remain poorly understood. In this study, we propose FR-BINN, a biologically informed [...] Read more.

Chronic inflammation plays a pivotal role in human health, with certain inflammatory conditions significantly increasing the risk of cancer, while others do not. However, the molecular mechanisms underlying this divergent risk remain poorly understood. In this study, we propose FR-BINN, a biologically informed neural network framework for disease prediction and interpretability. Incorporating Fenton reaction (FR)-related biological priors and leveraging multiple interpretability methods, FR-BINN identifies key genes driving cancer-prone and non-cancer-prone chronic inflammatory diseases. The experimental results demonstrate that FR-BINN achieves superior classification performance while offering biologically interpretable insights. Moreover, attribution results derived from different explainable techniques show high consistency, and intra-method results exhibit distinct patterns across disease categories. We further combine large language models with feature attributions to identify candidate biomarkers, and independent datasets confirm the robustness of these findings. Notably, genes such as NCOA1 and SDHB are identified as being associated with cancer susceptibility. The framework further reveals distinct patterns in energy metabolism, oxidative stress, and pH regulation between cancer-prone and non-cancer-prone inflammatory diseases. These insights enhance our understanding of inflammation-associated tumorigenesis and contribute to the identification of potential biomarkers and therapeutic targets. Full article

(This article belongs to the Special Issue Machine Learning Applications in Bioinformatics and Biomedicine: 3rd Edition)

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