International Journal of Molecular Sciences

18 pages, 3134 KiB

Open AccessArticle

A Novel Chemotherapy Combination to Enhance Proteotoxic Cell Death in Hepatocellular Carcinoma Experimental Models Without Killing Non-Cancer Cells

by Carlos Perez-Stable, Alicia de las Pozas, Teresita Reiner, Jose Gomez, Manojavan Nagarajan, Robert T. Foster, Daren R. Ure and Medhi Wangpaichitr

Int. J. Mol. Sci. 2025, 26(14), 6699; https://doi.org/10.3390/ijms26146699 (registering DOI) - 12 Jul 2025

Abstract

Inhibitors of the ubiquitin–proteasome system increase proteotoxic stress and have achieved clinical success for multiple myeloma but not for solid cancers such as hepatocellular carcinoma. Our objective is to identify a combination with proteasome inhibitors that enhances proteotoxic stress and apoptotic cell death [...] Read more.

Inhibitors of the ubiquitin–proteasome system increase proteotoxic stress and have achieved clinical success for multiple myeloma but not for solid cancers such as hepatocellular carcinoma. Our objective is to identify a combination with proteasome inhibitors that enhances proteotoxic stress and apoptotic cell death in hepatocellular carcinoma but with less toxicity to non-cancer cells. We found that rencofilstat, a pan-cyclophilin inhibitor, combined with ixazomib, a proteasome inhibitor, increased apoptotic cell death in hepatocellular carcinoma but not in umbilical vein or dermal fibroblast non-cancer cells. We then analyzed the effects of rencofilstat + ixazomib on XBP1s and PERK, critical factors in the unfolded protein response used by cells to survive proteotoxic stress. Rencofilstat + ixazomib maintained higher expression of XBP1s and genetic models suggested that XBP1s was a pro-survival protein early and pro-death protein at later times. Simultaneously, decreased PERK expression prevented the block in protein synthesis via phospho-eIF2α and likely further amplified proteotoxic stress. Rencofilstat + ixazomib did not have effects on XBP1s or PERK in non-cancer cells. Further genetic experiments revealed the pro-survival roles for cyclophilin A and B in mediating rencofilstat + ixazomib-induced cell death. In the Hep3B xenograft model, rencofilstat + ixazomib significantly inhibited tumor volumes/weights without general toxicity. We conclude that rencofilstat + ixazomib amplified proteotoxic stress in hepatocellular carcinoma past a threshold pro-survival pathways could not tolerate, whereas non-cancer cells were less affected. Full article

(This article belongs to the Special Issue Signaling Pathways Dysregulation in Cancer: Advances and New Therapeutics Hopes)

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37 pages, 2494 KiB

Open AccessReview

A Systems Biology Approach to Memory Health: Integrating Network Pharmacology, Gut Microbiota, and Multi-Omics for Health Functional Foods

by Heng Yuan, Junyu Zhou, Hongbao Li, Suna Kang and Sunmin Park

Int. J. Mol. Sci. 2025, 26(14), 6698; https://doi.org/10.3390/ijms26146698 (registering DOI) - 12 Jul 2025

Abstract

Memory impairment, ranging from mild memory impairment to neurodegenerative diseases such as Alzheimer’s disease, poses an escalating global health challenge that necessitates multi-targeted interventions to prevent progression. Health functional foods (HFFs), which include bioactive dietary compounds that not only provide basic nutrition but [...] Read more.

Memory impairment, ranging from mild memory impairment to neurodegenerative diseases such as Alzheimer’s disease, poses an escalating global health challenge that necessitates multi-targeted interventions to prevent progression. Health functional foods (HFFs), which include bioactive dietary compounds that not only provide basic nutrition but also function beyond that to modulate physiological pathways, offer a promising non-pharmacological strategy to preserve memory function. This review presents an integrative framework for the discovery, evaluation, and clinical translation of biomarkers responsive to HFFs in the context of preventing memory impairment. We examine both established clinical biomarkers, such as amyloid-β and tau in the cerebrospinal fluid, neuroimaging indicators, and memory assessments, as well as emerging nutritionally sensitive markers including cytokines, microRNAs, gut microbiota signatures, epigenetic modifications, and neuroactive metabolites. By leveraging systems biology approaches, we explore how network pharmacology, gut–brain axis modulation, and multi-omics integration can help to elucidate the complex interactions between HFF components and memory-related pathways such as neuroinflammation, oxidative stress, synaptic plasticity, and metabolic regulation. The review also addresses the translational pipeline for HFFs, from formulation and standardization to regulatory frameworks and clinical development, with an emphasis on precision nutrition strategies and cross-disciplinary integration. Ultimately, we propose a paradigm shift in memory health interventions, positioning HFFs as scientifically validated compounds for personalized nutrition within a preventative memory function framework. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Alzheimer’s Disease)

19 pages, 3181 KiB

Open AccessArticle

Overexpression of BDNF and uPA Combined with the Suppression of Von Hippel–Lindau Tumor Suppressor Enhances the Neuroprotective Activity of the Secretome of Human Mesenchymal Stromal Cells in the Model of Intracerebral Hemorrhage

by Stalik S. Dzhauari, Alexandra L. Primak, Nataliya A. Basalova, Natalia I. Kalinina, Anna O. Monakova, Kirill D. Bozov, Arkadiy Ya. Velichko, Maria E. Illarionova, Olga A. Grigorieva, Zhanna A. Akopyan, Vladimir S. Popov, Pavel G. Malkov, Anastasia Yu. Efimenko, Vsevolod A. Tkachuk and Maxim N. Karagyaur

Int. J. Mol. Sci. 2025, 26(14), 6697; https://doi.org/10.3390/ijms26146697 (registering DOI) - 12 Jul 2025

Abstract

Nerve tissue damage is an unsolved problem in modern neurology and neurosurgery, which prompts the need to search for approaches to stimulate neuroprotection and regeneration of neural tissue. Earlier we have shown that the secretome of human mesenchymal stromal cells (MSCs) stimulates rat [...] Read more.

Nerve tissue damage is an unsolved problem in modern neurology and neurosurgery, which prompts the need to search for approaches to stimulate neuroprotection and regeneration of neural tissue. Earlier we have shown that the secretome of human mesenchymal stromal cells (MSCs) stimulates rat survival, reduces the severity of neurological deficits, and decreases the volume of brain damage in a hemorrhagic stroke model. A significant disadvantage of using the MSC secretome is the need to concentrate it (at least 5–10 fold) to achieve appreciable pharmacological activity. This increases the cost of obtaining clinically applicable amounts of secretome and slows down the clinical translation of this technology. Here, we created a number of genetically modified human MSC cultures, including immortalized MSCs and those with hyperexpression of brain-derived neurotrophic factor (BDNF) and urokinase-type plasminogen activator (uPA) and with suppressed expression of Von Hippel–Lindau tumor suppressor (VHL), and we evaluated the pharmacological activity of their secretomes in a model of intracerebral hemorrhage (ICH) in rats. The secretome of MSCs immortalized by hyperexpression of the catalytic subunit of human telomerase (hTERT) revealed neuroprotective activity indistinguishable from that of primary MSC cultures, yet it still required 10-fold concentration to achieve neuroprotective efficacy. The secretome of MSC culture with combined hyperexpression of BDNF and uPA and suppressed expression of Von Hippel–Lindau tumor suppressor even without additional concentration reduced the severity of neurological disorders and decreased brain lesion volume in the ICH model. The secretomes of MSCs with separate overexpression of BDNF and uPA or suppression of VHL had no such effect or, on the contrary, revealed a toxic effect in the ICH model. Presumably, this may be due to an imbalance in the representation of individual growth factors in the secretome of genetically modified MSCs, which individually may lead to undesirable effects in damaged nervous tissue, such as increased permeability of the blood–brain barrier (under the influence of pro-angiogenic factors) or neural cell apoptosis (due to an excess of neurotrophic factors). The obtained data show that genetic modification of MSC cultures can enhance or alter the therapeutic activity of their secretomes, which can be used in the creation of promising sources of biopharmaceutical substances. Full article

(This article belongs to the Special Issue Fundamental and Practical Perspectives in Regenerative Medicine: Proceedings of the VI National Congress of Regenerative Medicine (2024))

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13 pages, 1498 KiB

Open AccessArticle

Evaluation of Ropivacaine and 3-OH-Ropivacaine Pharmacokinetics Following Interpectoral Nerve Block via LC-MS/MS—A Pilot Study

by Mihaela Butiulca, Lenard Farczadi, Silvia Imre, Camil Eugen Vari, Laurian Vlase, Leonard Azamfirei and Alexandra Elena Lazar

Int. J. Mol. Sci. 2025, 26(14), 6696; https://doi.org/10.3390/ijms26146696 (registering DOI) - 12 Jul 2025

Abstract

Regional anesthesia techniques such as the ultrasound-guided PECS II (pectoral nerve block) block are increasingly employed to optimize perioperative analgesia while minimizing systemic anesthetic exposure. Ropivacaine is commonly used for its favorable pharmacological profile; however, clinical data on its pharmacokinetics and systemic metabolite [...] Read more.

Regional anesthesia techniques such as the ultrasound-guided PECS II (pectoral nerve block) block are increasingly employed to optimize perioperative analgesia while minimizing systemic anesthetic exposure. Ropivacaine is commonly used for its favorable pharmacological profile; however, clinical data on its pharmacokinetics and systemic metabolite behavior following interpectoral administration remain limited. This study aimed to characterize the plasma concentration–time profile of ropivacaine and its main active metabolite, 3-OH-ropivacaine, in patients undergoing interpectoral nerve block, using a validated LC-MS/MS (liquid chromatography coupled with mass spectrometry) method. Venous blood samples were collected from 18 patients at predefined time points (0, 1, 3, 6, and 24 h) following a PECS II block performed with a ropivacaine-lidocaine mixture. Plasma concentrations were quantified via a validated LC-MS/MS protocol in accordance with FDA (Food and Drug Administration) and EMA (European Medicines Agency) guidelines. Pharmacokinetic parameters were derived using non-compartmental analysis. Ropivacaine reached a mean peak plasma concentration (Cmax—maximum concentration) of 167.5 ± 28.3 ng/mL at 1.3 ± 0.2 h (Tmax—maximum time). The metabolite 3-OH-ropivacaine peaked at 124.1 ± 21.4 ng/mL at 2.3 ± 0.3 h. The terminal elimination half-life was 19.4 ± 2.8 h for ropivacaine and 29.2 ± 3.1 h for its metabolite. Plasma levels demonstrated prolonged systemic exposure with predictable pharmacokinetics. The PECS II block using ropivacaine results in sustained systemic levels of both the parent drug and its primary metabolite, supporting its role in prolonged perioperative analgesia. These data provide a pharmacokinetic foundation for personalized regional anesthesia protocols. This strategy facilitates the adaptation of anesthetic protocols to the individual characteristics of each patient, aligning with the principles of personalized medicine, particularly in patients with altered metabolic capacity. Full article

(This article belongs to the Special Issue Ion Channels as a Potential Target in Pharmaceutical Designs 2.0)

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17 pages, 3752 KiB

Open AccessArticle

Disease Severity- and Hormonal Status-Dependent Alterations of EGF and MIF in the Serum of Endometriosis Patients

by Norbert Tóth, Réka Brubel, Attila Bokor, Ágnes Kemény, Nelli Farkas, Tibor Pál, Zsuzsanna Helyes and Krisztina Pohóczky

Int. J. Mol. Sci. 2025, 26(14), 6695; https://doi.org/10.3390/ijms26146695 (registering DOI) - 12 Jul 2025

Abstract

Endometriosis is the extrauterine engraftment of endometrium-like tissue, causing chronic pain. Complex sensory–vascular–immune interactions, including growth factors, cytokines, and neuropeptides, are implicated in its pathophysiology, but the mechanisms remain unknown. Here, epidermal growth factor (EGF), vascular endothelial growth factor, interleukins (IL-1β, IL-6, IL-8), [...] Read more.

Endometriosis is the extrauterine engraftment of endometrium-like tissue, causing chronic pain. Complex sensory–vascular–immune interactions, including growth factors, cytokines, and neuropeptides, are implicated in its pathophysiology, but the mechanisms remain unknown. Here, epidermal growth factor (EGF), vascular endothelial growth factor, interleukins (IL-1β, IL-6, IL-8), macrophage migration inhibitory factor (MIF), calcitonin gene-related peptide, and somatostatin were measured in the serum of endometriosis patients with different disease severities, menstruation cycle- and pharmacotherapy-related hormonal status compared with controls. Mediator levels in deep-infiltrating rectosigmoid nodules were also compared with those in non-endometriotic colon tissues. Pain was assessed by the visual analogue scale. Serum EGF was significantly lower in mild endometriosis and in the secretory phase. MIF and IL-6 were higher in stage I–IV endometriosis, with MIF also higher in the secretory phase and in patients not receiving oral contraceptives. Somatostatin was lower in mild endometriosis than that in healthy individuals and the severe endometriosis group. No tissue-level differences were found. A strong positive correlation between serum EGF and somatostatin levels and dysmenorrhea and dysuria was detected in mild cases. It is concluded that certain serum alterations may be related to severity- and hormone status-dependent endometriosis mechanisms, but their diagnostic/prognostic value seems to be limited due to variability and lack of specificity. Full article

(This article belongs to the Special Issue Molecular Mechanisms, Biomarkers, and Therapeutic Targets for Endometriosis)

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16 pages, 1780 KiB

Open AccessPerspective

BRCA2 Pre-mRNA Differential 5′ Splicing: A Rescue of Functional Protein Properties from Pathogenic Gene Variants and a Lifeline for Fanconi Anemia D1 Patients

by Roberto Paredes, Kiran Batta, Daniel H. Wiseman, Reham Gothbi, Vineet Dalal, Christine K. Schmidt, Reinhard Kalb, Stefan Meyer and Detlev Schindler

Int. J. Mol. Sci. 2025, 26(14), 6694; https://doi.org/10.3390/ijms26146694 (registering DOI) - 12 Jul 2025

Abstract

Fanconi anemia (FA) is a DNA repair deficiency disorder associated with genomic and chromosomal instability and a high cancer risk. In a small percentage of cases, FA is caused by biallelic pathogenic variants (PVs) in the BRCA2/FANCD1 gene, defining the FA-D1 subtype. Experimental [...] Read more.

Fanconi anemia (FA) is a DNA repair deficiency disorder associated with genomic and chromosomal instability and a high cancer risk. In a small percentage of cases, FA is caused by biallelic pathogenic variants (PVs) in the BRCA2/FANCD1 gene, defining the FA-D1 subtype. Experimental and epidemiologic data indicate that the complete absence of BRCA2 is incompatible with viability. Therefore, cells from individuals affected with FA caused by biallelic BRCA2 PVs must have a residual BRCA2 function. This activity may be maintained through hypomorphic missense mutations, translation termination–reinitiation associated with a translational stop mutation, or other non-canonical or uncommon translation initiation and elongation events. In some cases, however, residual BRCA2 function is provided by alternatively or aberrantly spliced BRCA2 transcripts. Here, we review and debate aspects of the contribution of splicing in the 5′ segment to BRCA2 functions in the context of PVs affecting this largely intrinsically disordered protein region, with a focus on recent findings in individuals with FA-D1. In this Perspective, we also discuss some of the broader biological implications and open questions that arise from considering 5′-terminal BRCA2 splicing in light of old and new findings from FA-D1 patients and beyond. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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18 pages, 660 KiB

Open AccessReview

Understanding the Insulin-Degrading Enzyme: A New Look at Alzheimer’s Disease and Aβ Plaque Management

by Michele Cerasuolo, Maria Chiara Auriemma, Irene Di Meo, Carmen Lenti, Michele Papa, Giuseppe Paolisso and Maria Rosaria Rizzo

Int. J. Mol. Sci. 2025, 26(14), 6693; https://doi.org/10.3390/ijms26146693 (registering DOI) - 12 Jul 2025

Abstract

Insulin-degrading enzyme (IDE) plays a critical role in regulating insulin levels in various tissues, including the brain, liver, and kidneys. In type 2 diabetes mellitus (T2DM), key features include insulin resistance, elevated insulin levels in the blood, and hyperglycemia. In this context, the [...] Read more.

Insulin-degrading enzyme (IDE) plays a critical role in regulating insulin levels in various tissues, including the brain, liver, and kidneys. In type 2 diabetes mellitus (T2DM), key features include insulin resistance, elevated insulin levels in the blood, and hyperglycemia. In this context, the function of IDE becomes particularly important; however, in T2DM, IDE’s function can be impaired. Notably, individuals with T2DM have a higher risk of developing Alzheimer’s disease (AD), suggesting that impaired IDE function may contribute to both diabetes and neurodegeneration. IDE has been studied for its ability to degrade Amyloid-β peptides, the primary constituents of amyloid plaques in AD. However, its role in Aβ clearance in vivo remains debated due to limited enzymatic efficacy under physiological conditions and differences in subcellular localization between IDE and its putative substrate. Other proteases, such as neprilysin, appear to play a more prominent role in preventing plaque formation. Additionally, the long-standing hypothesis that insulin competes with Aβ for IDE activity has been questioned, as brain insulin levels are too low to inhibit Aβ degradation significantly. Genetic variants in the IDE gene have been associated with increased AD risk, although the mechanisms by which they alter enzyme function are not yet fully understood. A deeper understanding of IDE’s role in the context of both metabolic and neurodegenerative diseases may provide valuable insights for the development of new therapeutic strategies. Full article

(This article belongs to the Special Issue The Role of Amyloid in Neurological Diseases)

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16 pages, 4784 KiB

Open AccessArticle

In Vitro and In Vivo Testing of Decellularized Lung and Pancreas Matrices as Potential Islet Platforms

by Alexandra Bogomolova, Polina Ermakova, Arseniy Potapov, Artem Mozherov, Julia Tselousova, Ekaterina Vasilchikova, Alexandra Kashina and Elena Zagaynova

Int. J. Mol. Sci. 2025, 26(14), 6692; https://doi.org/10.3390/ijms26146692 (registering DOI) - 12 Jul 2025

Abstract

The treatment of type 1 diabetes through pancreatic islet transplantation faces significant limitations, including donor organ shortages and poor islet survival due to post-transplantation loss of extracellular matrix support and inadequate vascularization. Developing biocompatible scaffolds that mimic the native islet microenvironment could substantially [...] Read more.

The treatment of type 1 diabetes through pancreatic islet transplantation faces significant limitations, including donor organ shortages and poor islet survival due to post-transplantation loss of extracellular matrix support and inadequate vascularization. Developing biocompatible scaffolds that mimic the native islet microenvironment could substantially improve transplantation outcomes. This study aimed to create and evaluate decellularized (DCL) matrices from porcine organs as potential platforms for islet transplantation. Porcine lung and pancreatic tissues were decellularized using four different protocols combining detergents (Triton X-100, SDS and SDC) with optimized incubation times. The resulting matrices were characterized through DNA quantification and histological staining (H&E and Van Gieson). Islet viability was assessed in vitro using Live/Dead staining after 3 and 7 days of culture on the matrices. In vivo biocompatibility was evaluated by implanting matrices into rat omentum or peritoneum, with histological analysis at 1-, 4-, and 8 weeks post-transplantation. Protocols 3 (for lung tissue) and 4 (for pancreas tissue) demonstrated optimal decellularization efficiency with residual DNA levels below 8%, while preserving the collagen and elastin networks. In vitro, islets cultured on decellularized lung matrix had maintained 95% viability by day 7, significantly higher than the controls (60%) and pancreatic matrix (83%). The omentum showed superior performance as an implantation site, exhibiting minimal inflammation and fibrosis compared to the peritoneum sites throughout the 8-week study period. These findings establish DCL as a promising scaffold for islet transplantation due to its superior preservation of ECM components and excellent support of islet viability. This work provides a significant step toward developing effective tissue-engineered therapies for diabetes treatment. Full article

(This article belongs to the Special Issue Fundamental and Practical Perspectives in Regenerative Medicine: Proceedings of the VI National Congress of Regenerative Medicine (2024))

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12 pages, 2466 KiB

Open AccessArticle

ROMP and Vinyl Polynorbornenes with Vanadium(III) and Nickel(II) diNHC Complexes

by Katarzyna Halikowska-Tarasek, Elwira Bisz, Dawid Siodłak, Błażej Dziuk and Wioletta Ochędzan-Siodłak

Int. J. Mol. Sci. 2025, 26(14), 6691; https://doi.org/10.3390/ijms26146691 (registering DOI) - 12 Jul 2025

Abstract

The polymerization of norbornene can occur via ring-opening metathesis polymerization (ROMP) or vinyl-addition pathways, each yielding polynorbornene with distinct structures and properties. This study reports on the synthesis and catalytic application of a new class of vanadium(III) and nickel(II) complexes bearing N-heterocyclic [...] Read more.

The polymerization of norbornene can occur via ring-opening metathesis polymerization (ROMP) or vinyl-addition pathways, each yielding polynorbornene with distinct structures and properties. This study reports on the synthesis and catalytic application of a new class of vanadium(III) and nickel(II) complexes bearing N-heterocyclic carbene ligands, based on the IPr* framework, for the polymerization of norbornene. The vanadium(III) complexes, activated by diethylaluminum chloride and in the presence of ethyl trichloroacetate, showed activity in ROMP. In contrast, the nickel(II) complexes, activated by methylaluminoxane, exhibited catalytic activity toward vinyl-addition polymerization. Characterization by GPC, NMR, and FTIR confirmed the formation of both ring-opening metathesis polymerization and vinyl-type-derived polynorbornenes, with vinyl-type polymers showing significantly higher molecular weights. Structural variations in the N-heterocyclic carbene ligands, particularly the linker length between imidazole donors, were found to strongly influence polymer molecular weight and the morphology of polynorbornenes. Full article

(This article belongs to the Section Materials Science)

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13 pages, 20460 KiB

Open AccessArticle

The Effects of AtNCED3 on the Cuticle of Rice Leaves During the Nutritional Growth Period

by Yang Zhang, Yuwei Jia, Hui Chen, Min Wang, Xiaoli Li, Lanfang Jiang, Jianyu Hao, Xiaofei Ma and Hutai Ji

Int. J. Mol. Sci. 2025, 26(14), 6690; https://doi.org/10.3390/ijms26146690 (registering DOI) - 12 Jul 2025

Abstract

The plant cuticle, a protective barrier against external stresses, and abscisic acid (ABA), a key phytohormone, are crucial for plant growth and stress responses. Heterologous expression of AtNCED3 in plants has been widely studied. In this research, by comparing the japonica rice cultivar [...] Read more.

The plant cuticle, a protective barrier against external stresses, and abscisic acid (ABA), a key phytohormone, are crucial for plant growth and stress responses. Heterologous expression of AtNCED3 in plants has been widely studied. In this research, by comparing the japonica rice cultivar Zhonghua 10 and its AtNCED3 over-expressing lines during the vegetative growth stage through multiple methods, we found that AtNCED3 over-expression increased leaf ABA content, enhanced epidermal wax and cutin accumulation, modified wax crystal density, and thickened the cuticle. These changes reduced leaf epidermal permeability and the transpiration rate, thus enhancing drought tolerance. This study helps understand the role of endogenous ABA in rice cuticle synthesis and its mechanism in plant drought tolerance, offering potential for genetic improvement of drought resistance in crops. Full article

(This article belongs to the Special Issue Advance in Plant Abiotic Stress: 3rd Edition)

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17 pages, 3910 KiB

Open AccessArticle

Genome-Wide Identification and Comprehensive Analysis of Ubiquitin-Specific Protease Gene Family in Soybean (Glycine max)

by Cuirong Tan, Dingyue Ban, Haiyang Li, Jinxing Wang, Baohui Liu and Chunyu Zhang

Int. J. Mol. Sci. 2025, 26(14), 6689; https://doi.org/10.3390/ijms26146689 - 11 Jul 2025

Abstract

Deubiquitination plays a pivotal role in regulating plant responses to abiotic stress, growth, and development. Among the deubiquitinase (DUB) families, ubiquitin-specific proteases (UBPs) constitute the largest group. Despite this, limited research has been conducted on the functional characteristics of the UBP gene family [...] Read more.

Deubiquitination plays a pivotal role in regulating plant responses to abiotic stress, growth, and development. Among the deubiquitinase (DUB) families, ubiquitin-specific proteases (UBPs) constitute the largest group. Despite this, limited research has been conducted on the functional characteristics of the UBP gene family in soybean (Glycine max). In this study, we identified 52 UBP gene family members in soybean, all of which harbored UCH (ubiquitin C-terminal hydrolase) domains with short yet evolutionarily conserved Cys-box and His-box. These genes were phylogenetically classified into 14 distinct groups; GmUBP genes within the same group shared analogous patterns of conserved domains and motifs. Moreover, a synteny analysis reveals that the GmUBP family has undergone extensive gene duplication events and shares a close evolutionary relationship with Arabidopsis thaliana. We conducted a focused analysis on GmUBP7, which is a gene exhibiting high expression levels in soybean seeds. Intriguingly, this gene exhibited several haplotypes in natural soybean varieties, with significant differences being observed in relation to seed traits, such as 100-seed weight, total fatty acid content, and protein content among different haplotypes. Collectively, the findings from this study provide a foundation for the functional characterization of GmUBP genes, offering new insights into the regulatory network underlying seed development in soybean. Full article

(This article belongs to the Section Molecular Plant Sciences)

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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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