International Journal of Molecular Sciences

15 pages, 1398 KiB

Open AccessArticle

Influence of HLA Class I and II Polymorphisms on COVID-19 Severity in a South Brazilian Population

by Sergio Grava, Matheus Braga, Victor Hugo de Souza, Afonso Carrasco Pepineli, Aléia Harumi Uchibaba Yamanaka, Christiane Maria Ayo, Joana Maira Valentini Zacarias, Andréa Name Colado Simão, Larissa Danielle Bahls Pinto, Quirino Alves de Lima Neto and Jeane Eliete Laguila Visentainer

Int. J. Mol. Sci. 2025, 26(11), 5341; https://doi.org/10.3390/ijms26115341 (registering DOI) - 2 Jun 2025

Abstract

The high variability of human leukocyte antigen (HLA) genes results in each molecule having distinct antigenic peptide binding capacities, potentially influencing the immune response to SARS-CoV-2. This study aimed to investigate associations between HLA class I (A, B) [...] Read more.

The high variability of human leukocyte antigen (HLA) genes results in each molecule having distinct antigenic peptide binding capacities, potentially influencing the immune response to SARS-CoV-2. This study aimed to investigate associations between HLA class I (A, B) and class II (DRB1) polymorphisms and COVID-19 severity in a South Brazilian population, and to evaluate the binding affinity of alleles to viral peptides. A cross-sectional study included 503 unvaccinated patients with RT-qPCR-confirmed COVID-19: 145 non-severe, 129 severe, and 229 critical. HLA typing was performed using PCR-SSO and Luminex™ technology. The DRB1*11 allelic group was significantly associated with protection against severe and critical cases, while DRB1*15 was associated with increased risk; both remained significant after Bonferroni correction. Other allelic groups were associated with disease outcomes but lost significance after correction: B*49 and B*08 (risk); and B*37, B*50, and A*03 (protection). In silico analysis revealed that the DRB1*15 allele group showed a higher proportion of strong binders, mostly from non-structural proteins, while DRB1*11:01 binders, though fewer in number, were concentrated in the M protein. These results suggest functional differences in antigen presentation and reinforce the relevance of class II HLA, particularly DRB1, in modulating COVID-19 severity. Full article

(This article belongs to the Special Issue Role of HLA (Human Leucocyte Antigen) in Human Diseases)

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14 pages, 1099 KiB

Open AccessArticle

Clinical Implications of Lymph Node Thyroglobulin in Papillary Thyroid Carcinoma Metastases: Independent from Thyroglobulin Antibody Interference

by Ping-Chen Kuo, Wen-Chieh Chen, Wei-Che Lin, Shun-Yu Chi, Yi-Hsiang Chiu, Ya-Chen Yang and Chen-Kai Chou

Int. J. Mol. Sci. 2025, 26(11), 5340; https://doi.org/10.3390/ijms26115340 (registering DOI) - 1 Jun 2025

Abstract

Papillary thyroid carcinoma (PTC) frequently involves cervical lymph node (LN) metastases and is a major determinant of prognosis and recurrence. However, cytology alone has limitations. Fine-needle aspiration thyroglobulin (FNA-Tg) has emerged as a promising diagnostic marker, although its cutoff value remains controversial, particularly [...] Read more.

Papillary thyroid carcinoma (PTC) frequently involves cervical lymph node (LN) metastases and is a major determinant of prognosis and recurrence. However, cytology alone has limitations. Fine-needle aspiration thyroglobulin (FNA-Tg) has emerged as a promising diagnostic marker, although its cutoff value remains controversial, particularly in patients with thyroglobulin antibodies (TgAbs). We retrospectively analyzed 63 LNs of 60 patients with PTC at a single medical center. Patients underwent FNA-Tg measurements and concurrent cytological evaluation. Diagnostic performance metrics, including sensitivity, specificity, positive and negative predictive value, and overall accuracy, were evaluated; the cutoff value was determined; and the potential influence of factors such as TgAb on FNA-Tg levels was investigated. A cutoff value of 4.23 ng/mL for FNA-Tg achieved 100% sensitivity and 90.2% specificity, with an overall accuracy of 93.6%. TgAb positivity did not significantly affect the diagnostic performance in patients with FNA-Tg. FNA-Tg might be useful for detecting local LN recurrence and providing valuable diagnostic insights, particularly in patients with residual thyroid tissue or positive TgAbs. Full article

(This article belongs to the Special Issue Thyroid-Related Diseases: Molecular Pathology, Diagnosis and Treatment: 2nd Edition)

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18 pages, 1560 KiB

Open AccessArticle

Heat vs. Fatigue: Hyperthermia as a Possible Treatment Option for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)

by Barbara Hochecker, Katja Matt, Melanie Scherer, Alica Meßmer, Alexander von Ardenne and Jörg Bergemann

Int. J. Mol. Sci. 2025, 26(11), 5339; https://doi.org/10.3390/ijms26115339 (registering DOI) - 1 Jun 2025

Abstract

The aetiology and pathophysiology of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) have not yet been clarified. Its exact diagnosis is also difficult because it has no biomarkers. This lack of knowledge leads to difficulties in treating the disease. In our work, we are attempting [...] Read more.

The aetiology and pathophysiology of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) have not yet been clarified. Its exact diagnosis is also difficult because it has no biomarkers. This lack of knowledge leads to difficulties in treating the disease. In our work, we are attempting to counteract this problem by analysing the central cellular mechanisms in ME/CFS patients and comparing them with those of healthy individuals. This pilot study provides a small glimpse into the journey of nine people with ME/CFS—more specifically, how their peripheral blood mononuclear cells (PBMCs) responded immediately after a session of whole-body hyperthermia (WBH). The clinical effect of WBH has already been investigated in other studies on the treatment of ME/CFS, and these studies have provided valuable insights into its potential benefits. The present study is concerned with the investigation of cellular parameters, namely autophagy, mitochondrial function and mRNA expression, before and after WBH. The results suggest that ME/CFS patients may have higher autophagy-related protein light chain 3 (LC3)-II levels and increased mitochondrial function compared with healthy individuals. A whole-body hyperthermia session could lead to a reduction in LC3-II levels, resulting in a reversion to the levels observed in healthy donors. In the case of mitochondrial parameters, hyperthermia could lead to an increase in the measured parameters. This pilot study is a continuation of a previously published study in which only the isolated cells of ME/CFS patients and a healthy control group were treated with hyperthermia. Full article

(This article belongs to the Special Issue Molecular Pathologies and Treatment for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome)

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33 pages, 1176 KiB

Open AccessReview

GLP-1 Analogues in the Neurobiology of Addiction: Translational Insights and Therapeutic Perspectives

by Juan David Marquez-Meneses, Santiago Arturo Olaya-Bonilla, Samuel Barrera-Carreño, Lucía Catalina Tibaduiza-Arévalo, Sara Forero-Cárdenas, Liliana Carrillo-Vaca, Luis Carlos Rojas-Rodríguez, Carlos Alberto Calderon-Ospina and Jesús Rodríguez-Quintana

Int. J. Mol. Sci. 2025, 26(11), 5338; https://doi.org/10.3390/ijms26115338 (registering DOI) - 1 Jun 2025

Abstract

Glucagon-like peptide-1 receptor agonists, originally developed for the treatment of metabolic disorders, have recently emerged as promising candidates for the management of substance use disorders. This review synthesizes preclinical, clinical, and translational evidence on the effects of glucagon-like peptide-1 receptor agonists across addiction [...] Read more.

Glucagon-like peptide-1 receptor agonists, originally developed for the treatment of metabolic disorders, have recently emerged as promising candidates for the management of substance use disorders. This review synthesizes preclinical, clinical, and translational evidence on the effects of glucagon-like peptide-1 receptor agonists across addiction models involving alcohol, nicotine, psychostimulants, and opioids. In animal studies, glucagon-like peptide-1 receptor agonists consistently reduce drug intake, attenuate dopamine release in reward circuits, and decrease relapse-like behavior. Clinical and observational studies provide preliminary support for these findings, particularly among individuals with comorbid obesity or insulin resistance. However, several translational barriers remain, including limited blood–brain barrier penetration, species differences in pharmacokinetics, and variability in treatment response due to genetic and metabolic factors. Ethical considerations and methodological heterogeneity further complicate clinical translation. Future directions include the development of central nervous system penetrant analogues, personalized medicine approaches incorporating pharmacogenomics, and rigorously designed trials in diverse populations. Glucagon-like peptide-1 receptor agonists may offer a novel therapeutic strategy that addresses both metabolic and neuropsychiatric dimensions of addiction, warranting further investigation to define their role in the evolving landscape of substance use disorder treatment. Full article

(This article belongs to the Special Issue Drug Delivery to the Central Nervous System: From Design, Synthesis, and Evaluation)

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21 pages, 2132 KiB

Open AccessArticle

Phage–Antibiotic Synergy Enhances Biofilm Eradication and Survival in a Zebrafish Model of Pseudomonas aeruginosa Infection

by Ling-Chun Lin, Yu-Chuan Tsai and Nien-Tsung Lin

Int. J. Mol. Sci. 2025, 26(11), 5337; https://doi.org/10.3390/ijms26115337 (registering DOI) - 1 Jun 2025

Abstract

Pseudomonas aeruginosa is a gram-negative opportunistic pathogen that poses a significant threat due to its increasing multidrug resistance, particularly in clinical settings. This study aimed to isolate and characterize a novel bacteriophage, phiLCL12, from hospital wastewater and evaluate its potential in combination with [...] Read more.

Pseudomonas aeruginosa is a gram-negative opportunistic pathogen that poses a significant threat due to its increasing multidrug resistance, particularly in clinical settings. This study aimed to isolate and characterize a novel bacteriophage, phiLCL12, from hospital wastewater and evaluate its potential in combination with antibiotics to combat P. aeruginosa infections and biofilm formation. Transmission electron microscopy revealed that phiLCL12 possesses a long contractile tail. The isolated phage exhibited a broad host range of 82.22% and could adsorb up to 98% of its target within 4 min. It was effective against multidrug-resistant strains at both high and low multiplicities of infection (MOIs) levels in lysis tests. Taxonomic classification was determined using PhaGCN2 and Whole genomic analysis, and the results identified phiLCL12 as a member of the Pbunavirus. In vitro experiments demonstrated that phiLCL12 significantly enhanced biofilm clearance and inhibited biofilm formation when combined with sub-inhibitory concentrations of imipenem. Furthermore, in vivo experiments using a zebrafish model showed that phage–antibiotic synergy (PAS) improved survival rate compared to antibiotic treatment alone. This study demonstrates that phiLCL12 is effective in both eradicating and preventing P. aeruginosa biofilm formation. The combination of phiLCL12 and imipenem provides a synergistic effect, significantly enhancing survival outcomes in a zebrafish model. These findings highlight the potential of phage–antibiotic synergy as a promising therapeutic strategy against biofilm-associated infections. Full article

(This article belongs to the Collection Feature Papers in Molecular Immunology)

55 pages, 2579 KiB

Open AccessReview

Regulation and Function of Tumor-Associated Macrophages (TAMs) in Colorectal Cancer (CRC): The Role of the SRIF System in Macrophage Regulation

by Agnieszka Geltz, Jakub Geltz and Aldona Kasprzak

Int. J. Mol. Sci. 2025, 26(11), 5336; https://doi.org/10.3390/ijms26115336 (registering DOI) - 1 Jun 2025

Abstract

Colorectal cancer (CRC) remains the leading cause of morbidity and mortality for both men and women worldwide. Tumor-associated macrophages (TAMs) are the most abundant immune cells in the tumor microenvironment (TME) of solid tumors, including CRC. These macrophages are found in the pro-inflammatory [...] Read more.

Colorectal cancer (CRC) remains the leading cause of morbidity and mortality for both men and women worldwide. Tumor-associated macrophages (TAMs) are the most abundant immune cells in the tumor microenvironment (TME) of solid tumors, including CRC. These macrophages are found in the pro-inflammatory M1 and anti-inflammatory M2 forms, with the latter increasingly recognized for its tumor-promoting phenotypes. Many signaling molecules and pathways, including AMPK, EGFR, STAT3/6, mTOR, NF-κB, MAPK/ERK, and HIFs, are involved in regulating TAM polarization. Consequently, researchers are investigating several potential predictive and prognostic markers, and novel TAM-based therapeutic targets, especially in combination therapies for CRC. Macrophages of the gastrointestinal tract, including the normal colon and rectum, produce growth hormone-releasing inhibitory peptide/somatostatin (SRIF/SST) and five SST receptors (SSTRs, SST1-5). While the immunosuppressive function of the SRIF system is primarily known for various tissues, its role within CRC-associated TAMs remains underexplored. This review focuses on the following three aspects of TAMs: first, the role of macrophages in the normal colon and rectum within the broader context of macrophage biology; second, the various bioactive factors and signaling pathways associated with TAM function, along with potential strategies targeting TAMs in CRC; and third, the interaction between the SRIF system and macrophages in both normal tissues and the CRC microenvironment. Full article

(This article belongs to the Special Issue The Role of Macrophages in Cancers)

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19 pages, 4768 KiB

Open AccessArticle

Silver Nanoparticles as a Novel Tissue Preservative: A Comparative Study with 10% Neutral Buffered Formalin

by Safa Taha, Amina Ismaeel, Muna Aljishi, Samvel Selvam, Angeleena Esther and Khaled Greish

Int. J. Mol. Sci. 2025, 26(11), 5335; https://doi.org/10.3390/ijms26115335 (registering DOI) - 1 Jun 2025

Abstract

Tissue preservation plays an essential role in biomedical research and histopathological applications. Traditional methods, despite their efficiency, are associated with compromised long-term tissue integrity and probable ecotoxicities. This study explores the application of silver nanoparticles (AgNPs), known for their antimicrobial properties, as a [...] Read more.

Tissue preservation plays an essential role in biomedical research and histopathological applications. Traditional methods, despite their efficiency, are associated with compromised long-term tissue integrity and probable ecotoxicities. This study explores the application of silver nanoparticles (AgNPs), known for their antimicrobial properties, as a potential tissue preservative. In this work, AgNPs were synthesized via a chemical reduction method. Heart, liver, and kidney tissues were obtained from BALB/c mice and preserved using 10% neutral buffered formalin (NBF) and AgNPs solution for 72 h. Preservation efficiency was assessed by quantifying and measuring DNA and RNA integrity, evaluating protein stability, and conducting histopathological examinations. This study aimed to compare the performance of AgNPs against 10% NBF across these parameters to determine their suitability as an alternative fixative. Our results showed that AgNPs solution maintained consistent DNA, RNA, and protein concentrations/quality across all tissues over 72 h, whereas formalin treatment led to degradation over time. Conversely, 10% NBF demonstrated better preservation of tissue morphology. These results highlighted the differential strengths of each fixative, with AgNPs excelling in molecular preservation and NBF in structural integrity. Overall, AgNPs exhibited superior qualitative and quantitative preservation of nucleic acids and intracellular proteins, indicating their potential as an alternative to formalin for molecular testing. Despite their demonstrated efficacy in biomolecular preservation, further studies are needed to optimize tissue morphology preservation. Full article

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

16 pages, 17025 KiB

Open AccessArticle

Bisulfite Pretreatment Improves Enzymatic Digestibility of Oil Palm Empty Fruit Bunch and Poplar Through Changing Its Structure and Lignin Distribution

by Liping Tan, Xuezhi Li, Xianqin Lu and Jian Zhao

Int. J. Mol. Sci. 2025, 26(11), 5334; https://doi.org/10.3390/ijms26115334 (registering DOI) - 1 Jun 2025

Abstract

This paper investigated the changes in anatomy, ultrastructure and lignin distribution of oil palm empty fruit bunch (EFB) by bisulfite pretreatment. It was found that after bisulfite pretreatment, a large number of pores formed in the cell walls, and the removal of part [...] Read more.

This paper investigated the changes in anatomy, ultrastructure and lignin distribution of oil palm empty fruit bunch (EFB) by bisulfite pretreatment. It was found that after bisulfite pretreatment, a large number of pores formed in the cell walls, and the removal of part of the lignin in the cell wall corner, partial middle layer, and other locations made the tissue structure of the EFB looser, which uncovered cellulose and broke the steric hindrance of cellulase access to cellulose in EFB, and also weakened the negative influence of lignin on cellulase. The changes can greatly contribute to the improvement of enzymatic hydrolysis after bisulfite pretreatment, which is consistent with the increased saccharification efficiency of the pretreated EFB. Poplar was also used to compare the differences and similarities between non-wood and wood materials. Full article

(This article belongs to the Special Issue Lignocellulose Bioconversion and High-Value Utilization)

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30 pages, 2629 KiB

Open AccessReview

Pericytes and Diabetic Microangiopathies: Tissue Resident Mesenchymal Stem Cells with High Plasticity and Regenerative Capacity

by Zeinab Shirbaghaee, Christine M. Sorenson and Nader Sheibani

Int. J. Mol. Sci. 2025, 26(11), 5333; https://doi.org/10.3390/ijms26115333 (registering DOI) - 1 Jun 2025

Abstract

Pericytes (PCs), a heterogeneous population of perivascular supporting cells, are critical regulators of vascular stability, angiogenesis, and blood–tissue barrier integrity. Increasing evidence highlights their active role in the pathophysiology of diabetic microangiopathies, including those affecting the retina, kidney, brain, heart, and peripheral nerves. [...] Read more.

Pericytes (PCs), a heterogeneous population of perivascular supporting cells, are critical regulators of vascular stability, angiogenesis, and blood–tissue barrier integrity. Increasing evidence highlights their active role in the pathophysiology of diabetic microangiopathies, including those affecting the retina, kidney, brain, heart, and peripheral nerves. In diabetes, hyperglycemia-induced PC dysfunction is a major contributor to vascular degeneration, impaired tissue repair, and disease progression across multiple organs. Pericytes also share many characteristics with mesenchymal stem cells (MSCs). They exhibit regenerative capacity, immunomodulatory activities, and multipotent capacities. This review explores the emerging role of PCs as tissue resident MSCs, emphasizing their pathophysiological involvement in diabetes complications, and their potential for utilization in regenerative medicine. We also discuss advances in PC-based therapies, tissue engineering strategies, and clinical applications. Thus, PCs are positioned as promising targets for therapeutic intervention and vascular tissue regeneration. Full article

(This article belongs to the Special Issue Diabetes and Metabolic Dysfunction)

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16 pages, 3005 KiB

Open AccessArticle

Pro-Resolving Macrophage-Induced IL-35⁺ but Not TGF-β1⁺ Regulatory B Cell Activation Requires the PD-L1/PD-1 Pathway

by Guoqin Cao, Takumi Memida, Shengyuan Huang, Elaheh Dalir Abdolahinia, Sunniva Ruiz, Sahar Hassantash, Jayant Ari, Satoru Shindo, Jiang Lin, Toshihisa Kawai and Xiaozhe Han

Int. J. Mol. Sci. 2025, 26(11), 5332; https://doi.org/10.3390/ijms26115332 (registering DOI) - 1 Jun 2025

Abstract

The interaction between immune regulatory cells, such as regulatory B cells (Breg) and pro-resolving macrophages (M2 macrophages), plays an important role in the restoration of immune homeostasis during inflammation. PD-L1 is one of the effector molecules that mediates the immune regulation function of [...] Read more.

The interaction between immune regulatory cells, such as regulatory B cells (Breg) and pro-resolving macrophages (M2 macrophages), plays an important role in the restoration of immune homeostasis during inflammation. PD-L1 is one of the effector molecules that mediates the immune regulation function of M2 macrophages. The activation of PD-L1/PD-1 signaling promotes the differentiation of Breg. Previous studies have shown that Breg promoted M2 macrophage polarization and enhanced their function, but little is known about the regulatory function of M2 macrophages on Breg differentiation. This study aims to determine the effect of M2 macrophages on Breg induction and the potential mechanism in vitro. Bone-marrow-derived macrophages were isolated from wild-type (WT) mice and polarized into M2 using IL-4/IL-13. To investigate the role of PD-L1/PD-1 in M2 macrophage-induced Breg differentiation, spleen B cells were isolated from WT or PD-1 knockout (KO) mice and co-cultured with either naïve (M0) or M2 macrophages for 48 h with or without trans-well inserts. The expression of IL-10, IL-35, and TGF-β1 in B cells was evaluated by flow cytometry and immunofluorescence staining. Recombinant PD-L1 was used to stimulate activated B cells, followed by the detection of IL-35 and TGF-β1. The results show that there was no significant difference in IL-10 expression among all groups. However, IL-35 and TGF-β1 expression in B cells was significantly increased in the M2+B, but not in M0+B, compared to B cells alone. Notably, such increases were diminished when M2 and B cells were separated by trans-well inserts. IL-35 expression was not significantly changed when B cells from PD-1 KO mice were co-cultured with M2 compared to the control. However, TGF-β1 expression was significantly increased when PD-1 KO B cells were co-cultured with M2 compared to the control. IL-35 expression in activated B cells was increased upon stimulation with PD-L1. However, TGF-β1 expression in activated B cells was increased regardless of the PD-L1 availability. This study demonstrates that pro-resolving macrophage-induced IL-35⁺ but not TGF-β1⁺ regulatory B cell activation requires the PD-L1/PD-1 pathway. Full article

(This article belongs to the Special Issue Dental Health and Disease: From the Molecular and Pathological Perspectives)

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20 pages, 2187 KiB

Open AccessArticle

The 8-Hydroxyquinoline Derivatives of 1,4-Naphthoquinone: Synthesis, Computational Analysis, and Anticancer Activity

by Arkadiusz Sokal, Roman Wrzalik, Małgorzata Latocha and Monika Kadela-Tomanek

Int. J. Mol. Sci. 2025, 26(11), 5331; https://doi.org/10.3390/ijms26115331 (registering DOI) - 1 Jun 2025

Abstract

Anticancer drug design has been reformed by the creation of heterocyclic hybrids. The introduction of a quinoline scaffold affects the activity, toxicity, and bioavailability of new compounds. The aim of this study was to synthesize and evaluate the biological activity of hybrids of [...] Read more.

Anticancer drug design has been reformed by the creation of heterocyclic hybrids. The introduction of a quinoline scaffold affects the activity, toxicity, and bioavailability of new compounds. The aim of this study was to synthesize and evaluate the biological activity of hybrids of 1,4-naphthoquinone with the 8-hydroxyquinoline moiety. The structure of the new compounds was characterized using spectroscopic methods, such as HR-MS, NMR, and IR. The analysis was supplemented by calculated NMR and IR spectra. The physicochemical properties and bioavailability of the compounds were examined using in silico methods. An analysis of reactivity descriptors showed that the compounds are good electron acceptors and exhibit high reactivity. Bioavailability properties confirm that hybrids could be good oral administration drugs. The biological potential of hybrids was examined by designation of the enzymatic conversion rate of the NQO1 protein and in vitro against cancer cell lines with overexpression of the gene encoding the NQO1 protein. The possibility of interaction between the tested ligand and the NQO1 protein was examined by molecular docking methods. Full article

(This article belongs to the Special Issue Cheminformatics in Drug Discovery and Green Synthesis)

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20 pages, 7253 KiB

Open AccessArticle

Effect of a Constant Magnetic Field on Cell Morphology and Migration Mediated by Cytoskeleton-Bound Magnetic Nanoparticles

by Olga Karavashkova, Artem Minin, Alexandra Maltseva, Pavel Tin, Georgy Nosov, Alexander M. Demin, Nelly S. Chmelyuk, Maxim Abakumov, Valeria Tsvelaya, Victoria Shipunova, Anastasiia Latypova and Ilya Zubarev

Int. J. Mol. Sci. 2025, 26(11), 5330; https://doi.org/10.3390/ijms26115330 (registering DOI) - 1 Jun 2025

Abstract

Cell migration, shape maintenance, and intracellular signaling are closely linked to dynamic changes in cell morphology and the cytoskeleton. These processes involve the reorganization of the cytoskeleton within the cytoplasm, affecting all its key components: intermediate filaments, microtubules, and microfilaments. A promising strategy [...] Read more.

Cell migration, shape maintenance, and intracellular signaling are closely linked to dynamic changes in cell morphology and the cytoskeleton. These processes involve the reorganization of the cytoskeleton within the cytoplasm, affecting all its key components: intermediate filaments, microtubules, and microfilaments. A promising strategy for remotely controlling cellular functions is the use of magnetic nanoparticles, which can influence cellular physiology. This approach, known as magnetogenetics, has been applied in various areas of cell and molecular biology. Applying a magnetic field allows for the non-invasive modulation of biochemical processes, cell migration, and morphological changes in cells containing magnetic nanoparticles. In our study, magnetic nanoparticles were conjugated with antibodies targeting cytoskeletal components, enabling the magnetically induced manipulation and deformation of the cell cytoskeleton. Our research introduces a novel approach to manipulating specific cytoskeletal components and altering cell polarity with spatial precision in vitro using magnetic nanoparticles associated with the cytoskeleton. Full article

(This article belongs to the Section Molecular Nanoscience)

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11 pages, 836 KiB

Open AccessBrief Report

Dizocilpine Does Not Alter NOS1AP Gene Expression in Rats and in Cell Cultures

by Anton B. Matiiv, Tatyana M. Rogoza, Irina A. Razgovorova, Maria I. Zhdanova, Nina P. Trubitsina, Mariya D. Bezgina, Irina G. Isaeva, Alexander G. Markov, Galina A. Zhuravleva and Stanislav A. Bondarev

Int. J. Mol. Sci. 2025, 26(11), 5329; https://doi.org/10.3390/ijms26115329 (registering DOI) - 1 Jun 2025

Abstract

The NOS1AP gene encodes the nitric oxide synthase 1 adaptor protein (NOS1AP), which binds to neuronal nitric oxide synthase (nNOS) and regulates nitric oxide (NO) production by dissociating nNOS from NMDA receptors (NMDARs). Notably, NOS1AP expression is upregulated upon NMDAR activation; however, there [...] Read more.

The NOS1AP gene encodes the nitric oxide synthase 1 adaptor protein (NOS1AP), which binds to neuronal nitric oxide synthase (nNOS) and regulates nitric oxide (NO) production by dissociating nNOS from NMDA receptors (NMDARs). Notably, NOS1AP expression is upregulated upon NMDAR activation; however, there is no available data regarding its production under the receptor inhibition. The NOS1AP gene is also 1 among more than 1000 genes that are presumed to be associated with the development of schizophrenia. Various animal models of this disorder have been developed, some of which are based on the use of NMDAR antagonists such as dizocilpine (MK-801). In this study, we investigated the expression and production of NOS1AP in rats injected with a low dose of dizocilpine (0.1 mg/kg), as well as in SH-SY5Y and HEK293T cell lines treated with varying concentrations of the same compound (10–200 µM). According to our results, neither the expression of the NOS1AP gene nor the production of NOS1AP protein was affected by dizocilpine treatment. Full article

(This article belongs to the Special Issue Schizophrenia: From Molecular Mechanism to Therapy)

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15 pages, 828 KiB

Open AccessReview

Copeptin as a New Blood-Based Marker for Differential Diagnosis in Stroke Patients

by Antonia Ioana Vasile, Sorin Tuță, Cristina Tiu and Corin Badiu

Int. J. Mol. Sci. 2025, 26(11), 5328; https://doi.org/10.3390/ijms26115328 (registering DOI) - 1 Jun 2025

Abstract

Diagnosis in stroke patients is based mainly on clinical and radiological findings; therefore, there is a need for serological markers that can orient the clinician. Copeptin is a new blood marker for diagnosis and prognosis in several neurological conditions, such as ischemic stroke, [...] Read more.

Diagnosis in stroke patients is based mainly on clinical and radiological findings; therefore, there is a need for serological markers that can orient the clinician. Copeptin is a new blood marker for diagnosis and prognosis in several neurological conditions, such as ischemic stroke, hemorrhagic stroke, aneurysmal subarachnoid hemorrhage, and multiple sclerosis. The aim of our study was to highlight the diagnostic value of copeptin in differentiating between stroke subtypes and stroke mimics. We performed a literature review by searching the PubMed and Scopus databases for papers with the following keywords: “stroke AND copeptin AND differential”. The PRISMA criteria were used. We identified 29 papers that met the criteria. We analyzed only original research articles, excluding reviews and only including those in English. Some studies did not find any significant differences between cerebral infarction, intracerebral hemorrhage, and subarachnoid hemorrhage, but one study demonstrated significant correlations. All studies agreed that copeptin levels can help in differentiating stroke patients from stroke-free patients. Copeptin levels were correlated with prognostic scales For stroke mimics, copeptin levels were extremely broad and for vestibular disorders; it was shown that a normal level of copeptin excludes stroke. Copeptin is a new blood marker that can help clinicians in the acute neurological field. It may help in diagnosing stroke, in differentiating between stroke subtypes and stroke mimics, and in evaluating the prognosis of these patients, but further studies are needed. Full article

(This article belongs to the Special Issue Cerebrovascular Diseases: Mediators of the Capillary No-Reflow Phenomenon After Acute Ischemic Stroke)

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13 pages, 2603 KiB

Open AccessArticle

Metabolic Imaging of Hyperpolarized [1-¹³C]Pyruvate in a Ferret Model of Traumatic Brain Injury

by Dirk Mayer, Abubakr Eldirdiri, Amanda L. Hrdlick, Boris Piskoun, Joshua C. Rogers, Aditya Jhajharia, Minjie Zhu, Julie L. Proctor, Ulrich H. Leiste, William L. Fourney, Jody C. Cantu, Gary Fiskum and Molly J. Goodfellow

Int. J. Mol. Sci. 2025, 26(11), 5327; https://doi.org/10.3390/ijms26115327 (registering DOI) - 1 Jun 2025

Abstract

It is increasingly recognized that early perturbation of energy metabolism might have important implications in management and ultimately the neurological outcome in patients with traumatic brain injury (TBI). At the same time, treatments and screening tools successfully developed in preclinical TBI models have [...] Read more.

It is increasingly recognized that early perturbation of energy metabolism might have important implications in management and ultimately the neurological outcome in patients with traumatic brain injury (TBI). At the same time, treatments and screening tools successfully developed in preclinical TBI models have failed to translate to the clinic. As ferrets possess primate-like gyrencephalic brains that may better replicate the human response to neurologic injury, the goal of this study was to noninvasively measure brain energy metabolism after injury in a ferret model of TBI. To this end, metabolic imaging of hyperpolarized (HP) [1-¹³C]pyruvate (Pyr) and its conversion to lactate (Lac) and bicarbonate (Bic) was performed in ferrets before and after combined under-vehicle blast and controlled cortical impact injury. Reduced Bic/Pyr, reflecting reduced pyruvate dehydrogenase activity, was detected 8–10 days post-injury whereas no difference in Lac/Pyr was observed. These results demonstrate the feasibility of using metabolic imaging of HP [1-¹³C]Pyr to measure perturbations in brain energy metabolism in a novel highly translatable animal model of TBI. The method may contribute to both improved understanding of injury mechanisms and more effective drug development. Full article

(This article belongs to the Special Issue New Breakthroughs in Molecular Diagnostic Tools for Human Diseases)

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23 pages, 5396 KiB

Open AccessArticle

De Novo Transcriptome Assembly and Annotation Elucidate the Response to Extreme Temperature Stress in the Intermediate Host Bulinus globosus of Schistosoma haematobium

by Xinyao Wang, Jianfeng Zhang, Ying Yang, Suying Guo, Yinlong Li, Zhiqiang Qin, Hamza Juma, Saleh Juma, Kun Yang, Shizhu Li and Jing Xu

Int. J. Mol. Sci. 2025, 26(11), 5326; https://doi.org/10.3390/ijms26115326 (registering DOI) - 1 Jun 2025

Abstract

Schistosomiasis remains a major global public health challenge. Bulinus serves as an intermediate host for Schistosoma, including S. haematobium, S. intercalatum, and S. guineensis. Emerging evidence suggests that temperature fluctuations associated with global climate change are key factors influencing [...] Read more.

Schistosomiasis remains a major global public health challenge. Bulinus serves as an intermediate host for Schistosoma, including S. haematobium, S. intercalatum, and S. guineensis. Emerging evidence suggests that temperature fluctuations associated with global climate change are key factors influencing the survival and distribution of Bulinus. The ecological shifts in intermediate host snails may significantly influence schistosomiasis transmission dynamics, thereby exacerbating threats to human health. However, the physiological effects of temperature stress on the survival of B. globosus at the molecular level, including gene expression and underlying mechanisms, remain unclear. Our experimental study found that extreme temperature stress significantly reduced the survival rates of Bulinus globosus (B. globosus). De novo transcriptome sequencing revealed key genes associated with lipid metabolism, carbohydrate metabolism, homeostasis regulation, and the antioxidant system. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified significant enrichment of differentially expressed genes (DEGs) in heat shock protein pathways, propanoate metabolism, and N-acylethanolamine metabolism pathways. Overall, this work provides the first transcriptomic characterization of the thermal stress response in B. globosus, extending genomic resources for annotation and stress-related gene discovery. These findings establish a solid foundation for developing control strategies to mitigate climate-driven risks of schistosomiasis transmission. Full article

(This article belongs to the Special Issue Parasite Biology and Host-Parasite Interactions: 2nd Edition)

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13 pages, 8591 KiB

Open AccessReview

IgG4-Related Disease: Current and Future Insights into Pathological Diagnosis

by Marlon Arias-Intriago, Tamar Gomolin, Flor Jaramillo, Adriana C. Cruz-Enríquez, Angie L. Lara-Arteaga, Andrea Tello-De-la-Torre, Esteban Ortiz-Prado and Juan S. Izquierdo-Condoy

Int. J. Mol. Sci. 2025, 26(11), 5325; https://doi.org/10.3390/ijms26115325 (registering DOI) - 1 Jun 2025

Abstract

Immunoglobulin G4-related disease (IgG4-RD) is a systemic fibroinflammatory condition marked by tumefactive lesions, IgG4+ plasma cell-rich infiltrates, storiform fibrosis, and obliterative phlebitis. Its multisystem involvement and overlap with malignancies, infections, and immune disorders complicate diagnosis despite recent classification advances. This study summarizes diagnostic [...] Read more.

Immunoglobulin G4-related disease (IgG4-RD) is a systemic fibroinflammatory condition marked by tumefactive lesions, IgG4+ plasma cell-rich infiltrates, storiform fibrosis, and obliterative phlebitis. Its multisystem involvement and overlap with malignancies, infections, and immune disorders complicate diagnosis despite recent classification advances. This study summarizes diagnostic challenges, highlights the role of histopathology as per the 2019 classification criteria established by the American College of Rheumatology and the European League Against Rheumatism (ACR/EULAR), and explores emerging tools to improve diagnostic accuracy. ACR/EULAR classification emphasizes three cardinal histopathological features (storiform fibrosis, obliterative phlebitis, or dense lymphoplasmacytic infiltrates) combined with an IgG4+/IgG+ plasma cell ratio >40% and organ-specific IgG4+ thresholds. While serum IgG4 levels are often elevated, their poor specificity necessitates confirmatory biopsy. Diagnostic limitations include sampling variability due to patchy fibrosis, interobserver discrepancies in immunohistochemical interpretation, and differentiation from mimics like lymphoma. Emerging solutions incorporate novel biomarkers (plasmablasts, anti-annexin A11) and advanced techniques (flow cytometry, digital pathology). Future research directions should focus on AI-assisted pattern recognition, multi-omics profiling, and organ-specific criteria refinement. While histopathology remains the diagnostic cornerstone, a multidisciplinary approach integrating clinical, radiological, and laboratory data is vital. Innovations in biomarkers promise improved diagnostic accuracy and personalized care, balancing novel advancements with foundational pathological evaluation. Full article

(This article belongs to the Special Issue Rare Diseases: A Diagnostic and Therapeutic Challenge)

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17 pages, 1573 KiB

Open AccessReview

Artificial Intelligence-Assisted Breeding for Plant Disease Resistance

by Juan Ma, Zeqiang Cheng and Yanyong Cao

Int. J. Mol. Sci. 2025, 26(11), 5324; https://doi.org/10.3390/ijms26115324 (registering DOI) - 1 Jun 2025

Abstract

Harnessing state-of-the-art technologies to improve disease resistance is a critical objective in modern plant breeding. Artificial intelligence (AI), particularly deep learning and big model (large language model and large multi-modal model), has emerged as a transformative tool to enhance disease detection and omics [...] Read more.

Harnessing state-of-the-art technologies to improve disease resistance is a critical objective in modern plant breeding. Artificial intelligence (AI), particularly deep learning and big model (large language model and large multi-modal model), has emerged as a transformative tool to enhance disease detection and omics prediction in plant science. This paper provides a comprehensive review of AI-driven advancements in plant disease detection, highlighting convolutional neural networks and their linked methods and technologies through bibliometric analysis from recent research. We further discuss the groundbreaking potential of large language models and multi-modal models in interpreting complex disease patterns via heterogeneous data. Additionally, we summarize how AI accelerates genomic and phenomic selection by enabling high-throughput analysis of resistance-associated traits, and explore AI’s role in harmonizing multi-omics data to predict plant disease-resistant phenotypes. Finally, we propose some challenges and future directions in terms of data, model, and privacy facets. We also provide our perspectives on integrating federated learning with a large language model for plant disease detection and resistance prediction. This review provides a comprehensive guide for integrating AI into plant breeding programs, facilitating the translation of computational advances into disease-resistant crop breeding. Full article

(This article belongs to the Special Issue Latest Reviews in Molecular Plant Science 2025)

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23 pages, 2177 KiB

Open AccessReview

Exosomes: A Promising Cell-Free Therapeutic Tool for Treating Cutaneous Nerve Injuries and Promoting Wound Healing

by Yujie Mu, Ruting Luo, Le Zhao, Danting Chen, Lixin Cao, Zhenkai Jin, Kun Li and Min Wang

Int. J. Mol. Sci. 2025, 26(11), 5323; https://doi.org/10.3390/ijms26115323 (registering DOI) - 1 Jun 2025

Abstract

The skin is the body’s largest organ. It serves various functions, including protection and metabolism. Due to its structure and location, it is more vulnerable to external physical and chemical damage than internal organs. Additionally, certain endogenous diseases can cause pathological changes to [...] Read more.

The skin is the body’s largest organ. It serves various functions, including protection and metabolism. Due to its structure and location, it is more vulnerable to external physical and chemical damage than internal organs. Additionally, certain endogenous diseases can cause pathological changes to appear on the skin and nerves. When skin tissue breaks down or sustains severe trauma, the cells, blood vessels, and nerves across all layers can suffer varying degrees of damage. This often results in pain, itching, sensory disturbances, and other discomforts, causing significant distress to patients. Stem-cell-derived exosome therapy has emerged as a promising treatment for skin injuries due to its safety, non-toxicity, and precision medicine benefits. Research has shown that stem-cell-derived exosomes regulate nerve cells by mediating MicroRNA (miRNA) transport and expression between cells, promoting axon growth. This exosome-driven miRNA exchange serves as a vital mode of intercellular communication, playing a crucial role in nervous system repair. Nerves play a critical role in skin wound healing and tissue regeneration, with sensory and autonomic nerves influencing key skin functions such as inflammation, immune defense, apoptosis, proliferation, and wound repair. Exosomes may aid in treating cutaneous nerve injuries by directly or indirectly promoting axon regeneration, nerve cell proliferation, and the release of protective neurofactors. Full article

(This article belongs to the Section Molecular Neurobiology)

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16 pages, 1684 KiB

Open AccessArticle

The Application of ¹H Nuclear Magnetic Resonance (NMR), Gas Chromatography (GC) and Ultraviolet–Visible (UV-Vis) Spectroscopy Techniques to the Analysis of the Fatty Acid Profile as Quality of Argan Oil

by Patrycja Słomczyńska, Paweł Siudem, Agnieszka Białek, Sławomir Kaźmierski and Katarzyna Paradowska

Int. J. Mol. Sci. 2025, 26(11), 5322; https://doi.org/10.3390/ijms26115322 (registering DOI) - 1 Jun 2025

Abstract

This study utilised the fatty acid (FA) profiles of cosmetic argan oils from various producers obtained from retail outlets in Poland, Turkey and Morocco between November 2022 and November 2023 as an indicator to control the quality (i.e., purity) and origin (i.e., geographical [...] Read more.

This study utilised the fatty acid (FA) profiles of cosmetic argan oils from various producers obtained from retail outlets in Poland, Turkey and Morocco between November 2022 and November 2023 as an indicator to control the quality (i.e., purity) and origin (i.e., geographical origin) of the oils. The fatty acid profile was analysed using gas chromatography (GC), which revealed that the most prevalent fatty acid in argan oil is oleic acid (C18:1), followed by linoleic acid (C18:2) and, in order, palmitic acid (C16:0). Furthermore, the ¹H NMR spectroscopy method was found to be both rapid and precise in identifying characteristic signals indicative of the presence of individual components (fatty acids) in argan oil, without the necessity for additional analyte processing. To analyse the results obtained, a PCA analysis was performed to discriminate between seven purified argan oil samples. Our study demonstrates the feasibility of implementing certain variables as authenticity and quality criteria. In the context of argan oils, the incorporation of limits for trans fatty acids and the capacity to discern origin through fatty acid profiling may prove to be of paramount importance. The results obtained demonstrated highly significant discrimination of five groups by region and three groups by preparation. Full article

(This article belongs to the Special Issue Modern Analytical Strategies for Foodomics: From Nutritional Value to Food Security)

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21 pages, 3324 KiB

Open AccessArticle

Tripeptide-Loaded Liposomes as Multifunctional Components in Topical Formulations

by Michał Dymek, Maria José García-Celma, Elvira Escribano-Ferrer, Dawid Warszycki, Sławomir Kaźmierski, Łukasz Skoczylas, Małgorzata Tabaszewska and Elżbieta Sikora

Int. J. Mol. Sci. 2025, 26(11), 5321; https://doi.org/10.3390/ijms26115321 (registering DOI) - 1 Jun 2025

Abstract

Modern dermocosmetics combine the effectiveness of active substances with the benefits of percutaneous penetration enhancers to address skin issues such as hyperpigmentation. In this study, three bioactive tripeptides (with amino acid sequences CSF, CVL, and CSN) with previously confirmed tyrosinase inhibition activity were [...] Read more.

Modern dermocosmetics combine the effectiveness of active substances with the benefits of percutaneous penetration enhancers to address skin issues such as hyperpigmentation. In this study, three bioactive tripeptides (with amino acid sequences CSF, CVL, and CSN) with previously confirmed tyrosinase inhibition activity were synthesized using the solid-phase synthesis method. The structures of the obtained peptides were determined. In addition, elastase in silico and in vitro inhibition assays were carried out. The tripeptides were subsequently encapsulated into liposomes, for which key physicochemical parameters were determined, including size, zeta potential, and encapsulation efficiency. The average diameter of the prepared liposomes was approximately 100 nm across all samples. The prepared carriers were found to be stable and exhibited no cytotoxicity toward reconstructed human epidermis cells. The peptides achieved an encapsulation efficiency of approximately 20–30%, with no significant differences observed between the cationic and anionic vesicles. Liposomes containing the CSF tripeptide, which showed the strongest tyrosinase-inhibiting effect, did not transport the peptide through the human skin in an ex vivo assay to permit quantification in the receptor solution, but facilitated penetration and retention of the tripeptide within the epidermis (4.65 ± 1.81 μg/cm²). These findings suggest that the prepared liposomes may serve as valuable carriers of bioactive tripeptides in anti-aging cosmetics. Full article

(This article belongs to the Section Bioactives and Nutraceuticals)

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19 pages, 8031 KiB

Open AccessArticle

Exploring Exosome Contributions to Gouty Arthritis: A Proteomics and Experimental Study

by Chengjin Lu, Xiaoxiong Yang, Xue Wang, Yu Wang, Bing Zhang and Zhijian Lin

Int. J. Mol. Sci. 2025, 26(11), 5320; https://doi.org/10.3390/ijms26115320 (registering DOI) - 1 Jun 2025

Abstract

This study investigated the role of exosomes in the pathological processes of gouty arthritis (GA), with the aim of clarifying their mechanistic role and pathological significance in the onset and progression of GA. Using a rat model of GA established through potassium oxonate [...] Read more.

This study investigated the role of exosomes in the pathological processes of gouty arthritis (GA), with the aim of clarifying their mechanistic role and pathological significance in the onset and progression of GA. Using a rat model of GA established through potassium oxonate and yeast gavage combined with intra-articular monosodium urate (MSU) injection, we isolated and characterized plasma exosomes using transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA), and Western blotting. Differential exosomal protein expression was analyzed using 4D label-free proteomics technology, followed by GO and KEGG enrichment analyses, and protein–protein interaction (PPI) network construction to identify core targets. In vivo experiments measured the expression levels of CTSD in synovial tissues and joint fluid, as well as HPRT1 in renal tissues, while in vitro experiments involved co-culturing NRK cells with exosomes to validate target protein expression. The results indicated that serum uric acid levels were significantly elevated in the model group (p < 0.01), accompanied by pronounced joint swelling and inflammation. Exosome characterization confirmed their typical bilayer membrane structure and the expression of marker proteins (CD63/TSG101). Proteomic analysis identified 40 differentially expressed proteins (12 upregulated and 28 downregulated) enriched in pathways such as complement and coagulation cascades, autophagy, lysosomal function, and purine metabolism. In vivo and in vitro experiments demonstrated significantly increased CTSD expression (p < 0.05/p < 0.01) and decreased HPRT1 expression (p < 0.05/p < 0.01) in the model group, suggesting that exosomes are involved in the occurrence and development of GA by regulating purine metabolism and lysosomal dysfunction. These findings offer new insights into disease mechanisms and potential therapeutic targets. Full article

(This article belongs to the Section Molecular Endocrinology and Metabolism)

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25 pages, 985 KiB

Open AccessReview

From Molecular Precision to Clinical Practice: A Comprehensive Review of Bispecific and Trispecific Antibodies in Hematologic Malignancies

by Behzad Amoozgar, Ayrton Bangolo, Maryam Habibi, Christina Cho and Andre Goy

Int. J. Mol. Sci. 2025, 26(11), 5319; https://doi.org/10.3390/ijms26115319 (registering DOI) - 1 Jun 2025

Abstract

Multispecific antibodies have redefined the immunotherapeutic landscape in hematologic malignancies. Bispecific antibodies (BsAbs), which redirect cytotoxic T cells toward malignant targets via dual antigen engagement, are now established components of treatment for diseases such as acute lymphoblastic leukemia (ALL), diffuse large B-cell lymphoma [...] Read more.

Multispecific antibodies have redefined the immunotherapeutic landscape in hematologic malignancies. Bispecific antibodies (BsAbs), which redirect cytotoxic T cells toward malignant targets via dual antigen engagement, are now established components of treatment for diseases such as acute lymphoblastic leukemia (ALL), diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), and multiple myeloma (MM). Clinical trials of agents like blinatumomab, glofitamab, mosunetuzumab, and teclistamab have demonstrated deep and durable responses in heavily pretreated populations. Trispecific antibodies (TsAbs), although still investigational, represent the next generation of immune redirection therapies, incorporating additional tumor antigens or co-stimulatory domains (e.g., CD28, 4-1BB) to mitigate antigen escape and enhance T-cell persistence. This review provides a comprehensive evaluation of BsAbs and TsAbs across hematologic malignancies, detailing molecular designs, mechanisms of action, therapeutic indications, resistance pathways, and toxicity profiles including cytokine release syndrome (CRS), immune effector cell-associated neurotoxicity syndrome (ICANS), cytopenias, and infections. We further discuss strategies to mitigate adverse effects and resistance, such as antigen switching, checkpoint blockade combinations, CELMoDs, and construct optimization. Notably, emerging platforms such as tetrafunctional constructs, checkpoint-integrated multispecifics, and protease-cleavable masking designs are expanding the therapeutic index of these agents. Early clinical evidence also supports the feasibility of applying multispecific antibodies to solid tumors. Finally, we highlight the transformative role of artificial intelligence (AI) and machine learning (ML) in multispecific antibody development, including antigen discovery, biomarker-driven treatment selection, toxicity prediction, and therapeutic optimization. Together, BsAbs and TsAbs illustrate the convergence of molecular precision, clinical innovation, and AI-driven personalization, establishing a new paradigm for immune-based therapy across hematologic and potentially solid tumor malignancies. Full article

(This article belongs to the Special Issue Antibody Therapy for Hematologic Malignancies)

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16 pages, 7776 KiB

Open AccessArticle

Implementation of a CAM Assay Using Fibrosarcoma Spheroids

by Flemming Puscz, Noah Jozsef Hatem, Sonja Verena Schmidt, Felix Reinkemeier, Marius Drysch, Mustafa Becerikli, Yonca Steubing, Marcus Lehnhardt and Christoph Wallner

Int. J. Mol. Sci. 2025, 26(11), 5318; https://doi.org/10.3390/ijms26115318 (registering DOI) - 31 May 2025

Abstract

Fibrosarcomas represent a rare but highly aggressive tumor entity among soft tissue tumors. Due to its rarity, questions regarding its development and pathophysiology remain unclear. The chorioallantoic membrane (CAM) assay represents an easily available method to investigate tumors on a growth membrane, live [...] Read more.

Fibrosarcomas represent a rare but highly aggressive tumor entity among soft tissue tumors. Due to its rarity, questions regarding its development and pathophysiology remain unclear. The chorioallantoic membrane (CAM) assay represents an easily available method to investigate tumors on a growth membrane, live and in ovo. The following study was established to test whether the growth of fibrosarcoma spheroids on the CAM was possible and to critically review their applicability for downstream investigations. The shells of fertilized chicken eggs were opened and the previously prepared HT1080 cell spheroids (50,000, 75,000, and 100,000 cells per spheroid) were applied to the CAM. After 7 days, tumors were examined for size, weight, and vascularization. After 7 days, 80 of 163 chicken eggs showed sufficient tumor growth. Of these 80 eggs with confirmed tumor growth, 32 (40%) were from the 50,000 spheroid group, 18 (22.5%) were from the 75,000 spheroid group, and 30 (37.5%) were from the 100,000 spheroid group. The 100,000-cell spheroid group exhibited the highest weights, with a mean of 110.7 mg, as well as tumor size expansion. This cell number also showed the highest vascularization rates. Tumor growth of fibrosarcoma spheroids could successfully be initiated on the CAM. Consequently, the CAM assay presents a good base for future studies involving human fibrosarcoma cell spheroids. Full article

(This article belongs to the Special Issue Pathogenesis and Novel Therapeutic Approaches for Sarcomas)

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33 pages, 5836 KiB

Open AccessArticle

Molecular Mechanisms of Biochanin A in AML Cells: Apoptosis Induction and Pathway-Specific Regulation in U937 and THP-1

by Pei-Shan Wu, Jui-Hung Yen, Pei-Yi Chen and Ming-Jiuan Wu

Int. J. Mol. Sci. 2025, 26(11), 5317; https://doi.org/10.3390/ijms26115317 (registering DOI) - 31 May 2025

Abstract

Biochanin A, a naturally occurring isoflavone derived from legumes, possesses anti-inflammatory, estrogenic, and anticancer activities. In this study, we investigated the cytotoxic effects and underlying molecular mechanisms of Biochanin A in acute myeloid leukemia (AML) cell lines, U937 and THP-1, using in vitro [...] Read more.

Biochanin A, a naturally occurring isoflavone derived from legumes, possesses anti-inflammatory, estrogenic, and anticancer activities. In this study, we investigated the cytotoxic effects and underlying molecular mechanisms of Biochanin A in acute myeloid leukemia (AML) cell lines, U937 and THP-1, using in vitro cytotoxicity assays, RNA sequencing, and bioinformatic analyses. Biochanin A induced dose-dependent apoptosis, as evidenced by caspase-7 activation and PARP1 cleavage. Over-representation analysis (ORA) revealed that differentially expressed genes (DEGs) were significantly enriched in pathways related to inflammatory responses, DNA replication, and cell cycle regulation. Gene set enrichment analysis (GSEA) further confirmed the upregulation of apoptosis- and inflammation-related pathways and the downregulation of MYC targets, cholesterol biosynthesis, and G2/M checkpoint gene sets. RT-qPCR analysis demonstrated that Biochanin A downregulated oncogenes such as RUNX1, BCL2, and MYC while upregulating CHOP (GADD153), CDKN1A (p21), and SQSTM1 (p62), contributing to apoptosis and cell cycle arrest across both cell lines. Notably, Biochanin A downregulated PLK1 and UHRF1 in THP-1 cells, indicating a disruption of mitotic progression and epigenetic regulation. In contrast, in U937 cells, Biochanin A upregulated TXNIP and downregulated CCND2, highlighting the involvement of oxidative stress and G1/S cell cycle arrest. These findings support the potential of Biochanin A as a promising therapeutic candidate for AML through both shared and distinct regulatory pathways. Full article

(This article belongs to the Special Issue Unraveling Apoptosis: Deciphering Molecular Mechanisms)

22 pages, 7007 KiB

Open AccessArticle

Functionalization of Two-Component Gelatinous Peptide/Reactive Oligomer Hydrogels with Small Molecular Amines for Enhanced Cellular Interaction

by Caroline Kohn-Polster, Benno M. Müller, Jan Krieghoff, Awais Nawaz, Iram Maqsood, Annett Starke, Kirsten Haastert-Talini, Michaela Schulz-Siegmund and Michael Christian Hacker

Int. J. Mol. Sci. 2025, 26(11), 5316; https://doi.org/10.3390/ijms26115316 (registering DOI) - 31 May 2025

Abstract

A platform of two-component cross-linked hydrogel (cGEL) based on gelatinous peptides and anhydride-containing cross-linkers (oPNMA, oPDMA) is extended for use in peripheral nerve regeneration. Hybrid composites with bio-/chemical cues for enhanced biophysical and biochemical properties were fabricated by covalently grafting small molecular, heterobifunctional [...] Read more.

A platform of two-component cross-linked hydrogel (cGEL) based on gelatinous peptides and anhydride-containing cross-linkers (oPNMA, oPDMA) is extended for use in peripheral nerve regeneration. Hybrid composites with bio-/chemical cues for enhanced biophysical and biochemical properties were fabricated by covalently grafting small molecular, heterobifunctional amines including the nerve growth factor mimetic LM11A-31 to the oligomeric cross-linkers prior to hydrogel formation. The cytocompatibility and growth-supportive conditions within the matrix are confirmed for pristine and modified hydrogels using L929 mouse fibroblasts and human adipose-derived stem cells (hASCs). For hASCs, cell behavior depends on the type of cross-linker and integrated amine. In a subsequent step, neonatal rat Schwann cells (SCs) are seeded on pristine and functionalized cGEL to investigate the materials’ capabilities to support SC growth and morphology. Within all formulations, cell viability, adherence, and cell extension are maintained though the cell elongation and orientation vary compared to the two-dimensional control. It is possible to merge adjustable two-component hydrogels with amines as biochemical signals, leading to improved nervous cell proliferation and activity. This indicates the potential of tunable bioactive cGEL as biomaterials in nerve implants, suggesting their use as a foundational component for nerve conduits. Full article

(This article belongs to the Special Issue Biomaterials: From Design, Synthesis and Characterization to Application)

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19 pages, 5614 KiB

Open AccessArticle

Transcriptome and Co-Expression Network Analyses of Resistant and Susceptible Rice Cultivars in Response to Meloidogyne graminicola

by Shirui Zhang, Zitong Xiao, Kexiang Shen, Wentao Lai, Shunbiao Du, Linyan Zhou and Jiansong Chen

Int. J. Mol. Sci. 2025, 26(11), 5315; https://doi.org/10.3390/ijms26115315 (registering DOI) - 31 May 2025

Abstract

Meloidogyne graminicola represents a significant pathogen of rice, with considerable variability in nematode resistance observed across rice germplasms. However, the gene regulatory networks and molecular mechanisms underlying the differential responses of resistant and susceptible cultivars to M. graminicola infection remain poorly understood. To [...] Read more.

Meloidogyne graminicola represents a significant pathogen of rice, with considerable variability in nematode resistance observed across rice germplasms. However, the gene regulatory networks and molecular mechanisms underlying the differential responses of resistant and susceptible cultivars to M. graminicola infection remain poorly understood. To identify potential sources of resistance, 122 indica cultivars were screened under controlled conditions based on gall formation in infected roots. Notably, Indian indica accession 685 exhibited exceptional resistance, characterized by complete suppression of nematode development within root tissue. To investigate the molecular responses of rice cultivars to M. graminicola infection, RNA sequencing was conducted to analyze gene expression profiles at 5 days post-inoculation (dpi) in resistant cultivar 685, moderately susceptible cultivar 1008, and susceptible cultivar 9311. Subsequent differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) identified key biological pathways, including sugar metabolism, autophagic degradation, and phytohormone signal transduction. Additionally, candidate hub genes were identified and validated through RT-qPCR. This study offers new insights into rice–M. graminicola interactions, highlighting critical molecular factors involved in resistance and susceptibility in host plants. Full article

(This article belongs to the Section Molecular Plant Sciences)

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19 pages, 3132 KiB

Open AccessArticle

Juniper Berry Oil as a Functional Additive in Chitosan–Water Kefiran–Paramylon Porous Sponges: Structural, Physicochemical, and Protein Interaction Insights

by Dorota Chelminiak-Dudkiewicz

Int. J. Mol. Sci. 2025, 26(11), 5314; https://doi.org/10.3390/ijms26115314 (registering DOI) - 31 May 2025

Abstract

This study reports on the design and development of novel porous biomaterials based on chitosan, water kefiran, and paramylon, enriched with various concentrations of juniper berry oil (JBO). The materials were obtained by freeze-drying and comprehensively characterized. The analyses included morphological evaluation (SEM [...] Read more.

This study reports on the design and development of novel porous biomaterials based on chitosan, water kefiran, and paramylon, enriched with various concentrations of juniper berry oil (JBO). The materials were obtained by freeze-drying and comprehensively characterized. The analyses included morphological evaluation (SEM and porosity), physicochemical tests (swelling rate, water vapor transmission rate, and roughness), mechanical tests (tensile strength, Young’s modulus, and elongation at break), and biodegradability under physiological conditions. Moreover, the functional behavior of the materials was evaluated by assessing their antioxidant and anti-inflammatory activity, as well as interactions with selected proteins (human serum albumin and fibrinogen) relevant to biological responses. It was found that the presence of JBO affects the internal structure and improves selected properties in a concentration-dependent manner. This study is the first to investigate the combined use of chitosan, water kefiran, and paramylon in a single porous system enriched with JBO. The results confirm the importance of such biopolymer sponges as promising platforms for applications where appropriate physicochemical and bioactive properties are desired. Full article

(This article belongs to the Section Materials Science)

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16 pages, 1197 KiB

Open AccessArticle

Moderate-Low Risk Breast Cancer Gene Expression in a Romanian Population

by Iulian Gabriel Goidescu, Ioana Cristina Rotar, Georgiana Nemeti, Adelina Staicu, Mihai Surcel, Gheorghe Cruciat, Daniel Mureșan, Cerasela Goidescu and Dan Eniu

Int. J. Mol. Sci. 2025, 26(11), 5313; https://doi.org/10.3390/ijms26115313 (registering DOI) - 31 May 2025

Abstract

Multigene panel testing for hereditary breast and ovarian cancer is becoming a standard in medical care. Recent studies highlight the importance of pathogenic variants in genes with moderate or low penetrance. 255 consecutive breast cancer cases who met the criteria for genetic testing [...] Read more.

Multigene panel testing for hereditary breast and ovarian cancer is becoming a standard in medical care. Recent studies highlight the importance of pathogenic variants in genes with moderate or low penetrance. 255 consecutive breast cancer cases who met the criteria for genetic testing were approached by next-generation sequencing. From 104 pathogenic mutations identified, 21 were in moderate-risk genes, three in low-risk genes and eight in the group with insufficient evidence genes. The most frequent PVs in moderate-risk genes were in the CHEK2 gene—Checkpoint kinase 2 gene (13 cases), the ATM gene—Ataxia-telangiectasia Mutated gene (six cases), BARD1—BRCA1-associated ring domain 1 gene (one case) and RAD 51C–radiation sensitive 51 Paralog C—(one case) genes. Among the low-risk genes, we identified only three pathogenic mutations (two in MSH1 gene—melanocyte-stimulating hormone gene—and one in MLH1 gene—MutL homolog 1 gene). Reporting on low-risk mutations and those with insufficient evidence regarding breast cancer risk is valuable to enable a more comprehensive view of genetic factors influencing disease development and improve screening protocols, tailor diagnostic strategies, and individualize treatment plans. This approach also enhances our understanding of BC risk in various populations, potentially leading to new insights into genetic contributions to cancer and the refinement of risk models for patient care. Full article

(This article belongs to the Special Issue Molecular Research and Cellular Biology of Breast Cancer)

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16 pages, 3841 KiB

Open AccessArticle

Construction of SNP Fingerprinting and Genetic Diversity Analysis of Eggplant Based on KASP Technology

by Wuhong Wang, Hongtao Pang, Na Hu, Haijiao Hu, Tianhua Hu, Yaqin Yan, Jinglei Wang, Jiaqi Ai, Chonglai Bao and Qingzhen Wei

Int. J. Mol. Sci. 2025, 26(11), 5312; https://doi.org/10.3390/ijms26115312 (registering DOI) - 31 May 2025

Abstract

Eggplant (Solanum melongena) is a significant vegetable in the Solanaceae family. Significant progress has been made in genetic diversity analysis and fingerprinting construction for crops such as tomatoes and peppers within the same family, but research on eggplants in these aspects [...] Read more.

Eggplant (Solanum melongena) is a significant vegetable in the Solanaceae family. Significant progress has been made in genetic diversity analysis and fingerprinting construction for crops such as tomatoes and peppers within the same family, but research on eggplants in these aspects remains relatively limited. Current germplasm identification using fingerprinting primarily relies on traditional SSR markers, which suffer from limited polymorphism and labor-intensive workflows. This study aimed to identify high-quality single nucleotide polymorphisms (SNPs), develop reliable Kompetitive Allele-Specific PCR (KASP) markers for eggplant genotyping, and then conduct fingerprint construction and genetic diversity analysis. The ultimate goals were to achieve a precise identification of eggplant varieties and deeply explore the genetic background and evolutionary patterns of eggplant germplasm. In this study, 49 representative eggplant accessions were re-sequenced. After data quality control, sequence alignment, and multiple rounds of screening, 224 high-quality SNPs were identified. Based on these SNPs, 96 SNPs were selected to develop KASP markers. These markers can provide abundant genetic markers for eggplant genetic research, which are used to deeply explore the genetic background and conduct genetic diversity analysis. After multiple rounds of rigorous verification, 32 core candidate markers were finally screened out. The average polymorphic information content (PIC) and gene diversity (GD) values were 0.36 and 0.46, respectively. Phylogenetic tree, population structure, and principal component analyses divided the 280 eggplant accessions into eight distinct groups. Through the analysis of minimal core markers and core germplasm, 23 core SNP markers and a subset of 56 core germplasm accessions were identified, leading to the establishment of a comprehensive fingerprinting system for all 280 accessions. Our findings provide a foundational genetic resource for eggplant germplasm identification and offer significant support for future breeding efforts. Full article

(This article belongs to the Special Issue Plant Breeding and Genetics: New Findings and Perspectives)

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Int. J. Mol. Sci., Volume 26, Issue 11 (June-1 2025) – 380 articles

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