International Journal of Molecular Sciences

19 pages, 2153 KiB

Open AccessReview

Molecular Mechanisms Regulating Epithelial Mesenchymal Transition (EMT) to Promote Cancer Progression

by Saima Ghafoor, Elizabeth Garcia, Daniel J. Jay and Sujata Persad

Int. J. Mol. Sci. 2025, 26(9), 4364; https://doi.org/10.3390/ijms26094364 (registering DOI) - 3 May 2025

The process of epithelial–mesenchymal transition (EMT) is crucial in various physiological/pathological circumstances such as development, wound healing, stem cell behavior, and cancer progression. It involves the conversion of epithelial cells into a mesenchymal phenotype, which causes the cells to become highly motile. This [...] Read more.

The process of epithelial–mesenchymal transition (EMT) is crucial in various physiological/pathological circumstances such as development, wound healing, stem cell behavior, and cancer progression. It involves the conversion of epithelial cells into a mesenchymal phenotype, which causes the cells to become highly motile. This reprogramming is initiated and controlled by various signaling pathways and governed by several key transcription factors, including Snail 1, Snail 2 (Slug), TWIST 1, TWIST2, ZEB1, ZEB2, PRRX1, GOOSECOID, E47, FOXC2, SOX4, SOX9, HAND1, and HAND2. The intracellular signaling pathways are activated/inactivated by signals received from the extracellular environment and the transcription factors are carefully regulated at the transcriptional, translational, and post-translational levels to maintain tight regulatory control of EMT. One of the most important pathways involved in this process is the transforming growth factor-β (TGFβ) family signaling pathway. This review will discuss the role of EMT in promoting epithelial cancer progression and the convergence/interplay of multiple signaling pathways and transcription factors that regulate this phenomenon. Full article

(This article belongs to the Special Issue Cellular Plasticity and EMT in Cancer and Fibrotic Diseases)

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12 pages, 6355 KiB

Open AccessArticle

Soft-Tissue Sarcomas—A Correlation Among Tumor Margin Infiltration, Immunological Markers, and Survival Rate

by Bogdan Șerban, Adrian Cursaru, Sergiu Iordache, Mihai Costache, Bogdan Cretu, Adrian Dumitru and Catalin Cirstoiu

Int. J. Mol. Sci. 2025, 26(9), 4363; https://doi.org/10.3390/ijms26094363 (registering DOI) - 3 May 2025

Abstract

Early and appropriate diagnosis of soft-tissue sarcomas (STSs) is hampered by their relatively low prevalence and sometimes unusual clinical appearance. It takes a comprehensive diagnostic work-up to differentiate between different types of soft-tissue sarcomas. Determining tumor margins by preoperative imaging is important, especially [...] Read more.

Early and appropriate diagnosis of soft-tissue sarcomas (STSs) is hampered by their relatively low prevalence and sometimes unusual clinical appearance. It takes a comprehensive diagnostic work-up to differentiate between different types of soft-tissue sarcomas. Determining tumor margins by preoperative imaging is important, especially in order to preserve the affected limb and improve quality of life. Misjudgment of tumor margins may increase or decrease the stage of soft-tissue sarcoma and thus influence the patient’s prognosis. The applicability of conventional MRI alone for determining the tumor margin is limited. Additional information regarding the peritumoral tissue, particularly at the cellular level, can be obtained via diffusion-weighted imaging (DWI). However, there are not many publications on employing DWI to evaluate tumor margin infiltration in soft-tissue sarcoma patients. Because the immune system plays a variety of roles during oncogenesis, it can occasionally be difficult to distinguish between tumor invasion and the presence of a reactive inflammatory infiltrate. Clarifying the predictive importance of lymphocyte infiltration in soft-tissue sarcomas was the goal of this investigation. We examined the correlations between expression of CD4, CD8, and CD34 and tumor margin infiltration observed on a DWI sequence. CD4, CD8, and CD34 marker positivity was linked to soft-tissue sarcomas that were less aggressive and did not invade the tumor margins, indicating a higher survival percentage for these individuals. Full article

(This article belongs to the Special Issue Biomarker Discovery and Validation for Precision Oncology)

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16 pages, 2702 KiB

Open AccessReview

Harnessing Azelaic Acid for Acute Myeloid Leukemia Treatment: A Novel Approach to Overcoming Chemoresistance and Improving Outcomes

by Silvia Di Agostino, Anna Di Vito, Annamaria Aloisio, Giovanna Lucia Piazzetta, Nadia Lobello, Jessica Bria and Emanuela Chiarella

Int. J. Mol. Sci. 2025, 26(9), 4362; https://doi.org/10.3390/ijms26094362 (registering DOI) - 3 May 2025

Abstract

Azelaic acid (AZA), an aliphatic dicarboxylic acid (HOOC-(CH2)₇-COOH), is widely used in dermatology. It functions as an inhibitor of tyrosinase, mitochondrial respiratory chain enzymes, and DNA synthesis, while also scavenging free radicals and reducing reactive oxygen species (ROS) production by neutrophils. [...] Read more.

Azelaic acid (AZA), an aliphatic dicarboxylic acid (HOOC-(CH2)₇-COOH), is widely used in dermatology. It functions as an inhibitor of tyrosinase, mitochondrial respiratory chain enzymes, and DNA synthesis, while also scavenging free radicals and reducing reactive oxygen species (ROS) production by neutrophils. AZA has demonstrated anti-proliferative and cytotoxic effects on various cancer cells. However, its therapeutic potential in acute myeloid leukemia (AML) remains largely unexplored. AML is a complex hematologic malignancy characterized by the clonal transformation of hematopoietic precursor cells, involving chromosomal rearrangements and multiple gene mutations. The disease is associated with poor prognosis and high relapse rates, primarily due to its propensity to develop resistance to treatment. Recent studies indicate that AZA suppresses AML cell proliferation by inducing apoptosis and arresting the cell cycle at the G1 phase, with minimal cytotoxic effects on healthy cells. Additionally, AZA exerts antileukemic activity by modulating the ROS signaling pathway, enhancing the total antioxidant capacity in both AML cell lines and patient-derived cells. AZA also sensitizes AML cells to Ara-C chemotherapy. In vivo, AZA has been shown to reduce leukemic spleen infiltration and extend survival. As our understanding of AML biology progresses, the development of new molecularly targeted agents, in combination with traditional chemotherapy, offers the potential for improved treatment outcomes. This review aims to provide a comprehensive synthesis of preclinical evidence on the therapeutic potential of AZA in AML, consolidating current knowledge and identifying future directions for its clinical application. Full article

(This article belongs to the Special Issue Molecular Mechanism of Acute Myeloid Leukemia)

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26 pages, 4704 KiB

Open AccessArticle

CRISPR/Cas9 Ribonucleoprotein Delivery Enhanced by Lipo-Xenopeptide Carriers and Homology-Directed Repair Modulators: Insights from Reporter Cell Lines

by Xianjin Luo, Eric Weidinger, Tobias Burghardt, Miriam Höhn and Ernst Wagner

Int. J. Mol. Sci. 2025, 26(9), 4361; https://doi.org/10.3390/ijms26094361 (registering DOI) - 3 May 2025

Abstract

CRISPR-Cas9 genome editing is a versatile platform for studying and treating various diseases. Homology-directed repair (HDR) with DNA donor templates serves as the primary pathway for gene correction in therapeutic applications, but its efficiency remains a significant challenge. This study investigates strategies to [...] Read more.

CRISPR-Cas9 genome editing is a versatile platform for studying and treating various diseases. Homology-directed repair (HDR) with DNA donor templates serves as the primary pathway for gene correction in therapeutic applications, but its efficiency remains a significant challenge. This study investigates strategies to enhance gene correction efficiency using a T-shaped lipo-xenopeptide (XP)-based Cas9 RNP/ssDNA delivery system combined with various HDR enhancers. Nu7441, a known DNA-PKcs inhibitor, was found to be most effective in enhancing HDR-mediated gene correction. An over 10-fold increase in HDR efficiency was achieved by Nu7441 in HeLa-eGFPd2 cells, with a peak HDR efficiency of 53% at a 5 nM RNP concentration and up to 61% efficiency confirmed by Sanger sequencing. Surprisingly, the total gene editing efficiency including non-homologous end joining (NHEJ) was also improved. For example, Nu7441 boosted exon skipping via NHEJ-mediated splice site destruction by 30-fold in a DMD reporter cell model. Nu7441 modulated the cell cycle by reducing cells in the G1 phase and extending the S and G2/M phases without compromising cellular uptake or endosomal escape. The enhancement in genome editing by Nu7441 was widely applicable across several cell lines, several Cas9 RNP/ssDNA carriers (LAF-XPs), and also Cas9 mRNA/sgRNA/ssDNA polyplexes. These findings highlight a novel and counterintuitive role for Nu7441 as an enhancer of both HDR and total gene editing efficiency, presenting a promising strategy for Cas9 RNP-based gene therapy. Full article

(This article belongs to the Special Issue CRISPR-Cas Systems and Genome Editing—2nd Edition)

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13 pages, 476 KiB

Open AccessArticle

Association Between Periodontal Pathogens and Inflammation in Patients with Acute Coronary Syndromes

by Ioana-Patricia Rodean, Vasile-Bogdan Halațiu, Teodora Maria Popa, Emanuel Blîndu, Theofana Mihăilă, Constantin Țolescu, Andrei Modiga, Imre Benedek and Theodora Benedek

Int. J. Mol. Sci. 2025, 26(9), 4360; https://doi.org/10.3390/ijms26094360 (registering DOI) - 3 May 2025

Abstract

(1) The link between periodontal disease (PD) and acute coronary syndromes (ACSs) is predominantly attributed to the atherosclerotic process, mediated by systemic inflammation. However, the correlation between the severity of PD, characterized by the presence of periodontal pathogens, and systemic inflammation in patients [...] Read more.

(1) The link between periodontal disease (PD) and acute coronary syndromes (ACSs) is predominantly attributed to the atherosclerotic process, mediated by systemic inflammation. However, the correlation between the severity of PD, characterized by the presence of periodontal pathogens, and systemic inflammation in patients with ACS remains inadequately clarified. (2) This study aims to assess the association between the severity of PD and systemic inflammatory biomarkers, along with lipid profiles, in patients with ACS. (3) In total, 42 patients with ACS and concomitant PD were divided into two groups based on the presence of periodontal pathogens belonging to the red or red-orange complexes. Group 1–29 patients displayed pathogens from the red complex (RC) and group 2–13 patients displayed pathogens from the red-orange complex (ROC). All participants underwent a comprehensive dental examination, including DNA sampling from the periodontal pockets for pathogen detection. Systemic inflammation was evaluated alongside assessments of lipid profiles. (4) Inflammatory markers were more pronounced in the RC group compared with the ROC group. Moreover, patients in the RC group showed significantly higher monocyte-to-lymphocyte ratios (0.41 ± 0.20 vs. 0.28 ± 0.12; p = 0.002), platelet-to-lymphocyte ratios (139.50 ± 33.85 vs. 100.90 ± 8.84; p = 0.02), serum C-reactive protein levels (9.34 ± 1.08 mg/L vs. 5.46 ± 1.03 mg/L; p = 0.03), and serum uric acid levels (6.9 ± 0.49 mg/dL vs. 5.4 ± 0.26 mg/dL; p = 0.006). Concerning lipid profiles, the RC group exhibited significantly higher low-density lipoprotein cholesterol (LDL) levels (169.60 ± 12.63 mg/dL vs. 106.70 ± 9.34 mg/dL; p = 0.0007) and significantly lower high-density lipoprotein cholesterol (HDL) levels (29.29 ± 3.50 mg/dL vs. 39.56 ± 2.07 mg/dL; p = 0.002). (5) The severity of PD, indicated by the concomitant presence of pathogens from the red and orange complexes, is associated with an unfavorable lipid profile and elevated inflammatory biomarkers. These findings highlight the potential importance of periodontal intervention in the prevention of ACS. Full article

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

25 pages, 3526 KiB

Open AccessReview

Extracellular Vesicles in Sport Horses: Potential Biomarkers and Modulators of Exercise Adaptation and Therapeutics

by Dominika Milczek-Haduch, Magdalena Żmigrodzka and Olga Witkowska-Piłaszewicz

Int. J. Mol. Sci. 2025, 26(9), 4359; https://doi.org/10.3390/ijms26094359 (registering DOI) - 3 May 2025

Abstract

Significant systemic metabolic benefits result from even a single exercise session by activating multiple metabolic and signaling pathways within the organism. Among these mechanisms, extracellular vesicles (EVs) play a critical role by delivering their molecular cargo to neighboring or distant cells, thereby influencing [...] Read more.

Significant systemic metabolic benefits result from even a single exercise session by activating multiple metabolic and signaling pathways within the organism. Among these mechanisms, extracellular vesicles (EVs) play a critical role by delivering their molecular cargo to neighboring or distant cells, thereby influencing cellular metabolism and function. As research progresses, EVs represent an exciting frontier in exercise science and fitness adaptation processes. There is increasing interest in understanding the physiology of EVs as signaling particles and their use as minimally invasive diagnostic and prognostic biomarkers in the early detection of oxidative stress-related abnormalities. They also show potential to be used in monitoring exercise progress, injury prevention, or recovery, and may provide insights for personalized training programs. This review examines the current understanding of the role of physical activity in generating exercise-responsive EVs. It highlights the potential applications of EVs in exercise science and personalized fitness optimization, not only for human athletes but also for exercising animals such as horses. On the other hand, it also presents potential difficulties that researchers currently working on this topic may encounter due to technical limitations. Full article

(This article belongs to the Special Issue Molecular and Physiological Mechanisms of Exercise)

20 pages, 11032 KiB

Open AccessArticle

Assessment of Catalase Inhibition Under e-Beam Irradiation

by Victoria Ipatova, Ulyana Bliznyuk, Polina Borshchegovskaya, Alexander Chernyaev, Maria Toropygina, Violetta Kim, Alexander Nikitchenko, Aleksandr Kozlov, Dmitry Yurov, Mikhail Beklemishev, Igor Rodin and Elena Kozlova

Int. J. Mol. Sci. 2025, 26(9), 4358; https://doi.org/10.3390/ijms26094358 (registering DOI) - 3 May 2025

Abstract

Catalase serves as a crucial component of the antioxidant defense system by catalyzing the decomposition of hydrogen peroxide into water and molecular oxygen. This study investigated the effects of 1 MeV accelerated electron irradiation on catalase activity in model solutions at doses of [...] Read more.

Catalase serves as a crucial component of the antioxidant defense system by catalyzing the decomposition of hydrogen peroxide into water and molecular oxygen. This study investigated the effects of 1 MeV accelerated electron irradiation on catalase activity in model solutions at doses of 100 Gy and 1000 Gy. Enzyme activity was assessed using two complementary methods: spectrophotometric analysis and the oxygen bubble method. The experimental results demonstrated dose-dependent inhibition of catalase activity, indicating that substantial radiation-induced structural modifications may occur in the enzyme molecule as a result of irradiation. To understand the relationship between the irradiation dose and the catalase inhibition, calibration curves plotting the dependencies of hydrogen peroxide decomposition rate and the delayed appearance of oxygen bubbles after adding hydrogen peroxide to catalase saline solution on the catalase concentration showed a 1.5-fold reduction in catalase activity at 100 Gy and a 40-fold decrease at 1000 Gy. Based on these findings, we propose a novel biodosimetry approach utilizing the oxygen bubble formation delay time as an express assessment tool for detecting high radiation doses absorbed by biological objects, for example, food products. The results obtained in the study have important implications for evaluating radiation effects on biological systems, in particular catalase-containing food products, offering potential applications in radiation safety monitoring and food quality control. Full article

(This article belongs to the Special Issue Antioxidants and Enzyme Inhibitors: Design, Synthesis and Action Mechanisms)

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16 pages, 461 KiB

Open AccessReview

The Emerging Oncogenic Role of RARγ: From Stem Cell Regulation to a Potential Cancer Therapy

by Geoffrey Brown

Int. J. Mol. Sci. 2025, 26(9), 4357; https://doi.org/10.3390/ijms26094357 (registering DOI) - 3 May 2025

Abstract

Retinoic acid receptor (RAR) γ expression is restricted during adult haematopoiesis to haematopoietic stem cells and their immediate offspring and is required for their maintenance. From zebrafish studies, RARγ is selectively expressed by stem cells and agonism in the absence of exogenous all- [...] Read more.

Retinoic acid receptor (RAR) γ expression is restricted during adult haematopoiesis to haematopoietic stem cells and their immediate offspring and is required for their maintenance. From zebrafish studies, RARγ is selectively expressed by stem cells and agonism in the absence of exogenous all-trans retinoic acid blocked stem cell development. Recent findings for the expression of RARγ have revealed an oncogenic role in acute myeloid leukaemia and cholangiocarcinoma and colorectal, head and neck, hepatocellular, ovarian, pancreatic, prostate, and renal cancer. Overexpression and agonism of RARγ enhanced cell proliferation for head and neck, hepatocellular, and prostate cancer. RARγ antagonism, pan-RAR antagonism, and RARγ downregulation led to cell growth which was often followed by cell death for acute myeloid leukaemia, astrocytoma, and cholangiocarcinoma as well as hepatocellular, primitive, neuroectodermal ovarian, and prostate cancer. Histological studies have associated high level RARγ expression with high-grade disease, metastasis, and a poor prognosis for cholangiocarcinoma and ovarian, pancreatic, and prostate cancer. RARγ is expressed by cancer stem cells and is a targetable drive of cancer cell growth and survival. Full article

(This article belongs to the Special Issue The Hallmarks of Cancer Stem Cells)

16 pages, 1207 KiB

Open AccessArticle

Exploring Nepicastat Activity: Beyond DβH

by Rafal Jas, Marta Bauer, Błażej Grodner, Weronika Kończak, Karolina Frączek, Anna K. Laskowska, Małgorzata Milczarek, Wojciech Kamysz and Patrycja Kleczkowska

Int. J. Mol. Sci. 2025, 26(9), 4356; https://doi.org/10.3390/ijms26094356 (registering DOI) - 3 May 2025

Abstract

Recently, an old drug, disulfiram, has been shown to reduce cocaine intake by inhibiting dopamine beta (β)-hydroxylase. Its effectiveness was also reported in opioid treatment, as disulfiram attenuated morphine-induced tolerance and dependence. A similar mechanism of action was evident in a selective inhibitor [...] Read more.

Recently, an old drug, disulfiram, has been shown to reduce cocaine intake by inhibiting dopamine beta (β)-hydroxylase. Its effectiveness was also reported in opioid treatment, as disulfiram attenuated morphine-induced tolerance and dependence. A similar mechanism of action was evident in a selective inhibitor of DβH, nepicastat, particularly in the aspect of cocaine-seeking behavior. Hence, the objective of this study was to verify whether or not nepicastat reproduces disulfiram activity in pain reduction. Moreover, determination of its likely biological effects resulting from interactions with targets other than DβH has been given, in particular acetylcholinesterase. As was found, nepicastat was characterized by the absence of desired antinociceptive activity, though its co-administration with morphine resulted in a dose- and time-dependent enhancement of morphine-induced analgesic effect and attenuation of tolerance. Similarly, nepicastat was found to manifest antimicrobial potency against selected bacterial strains, although the effect was found to be weak. Intriguingly, this compound interacted with acetylcholinesterase through inhibition of its activity. These results clearly indicate nepicastat as a potent molecule that exhibits various biological effects. This, in turn, suggests its possible application in pathological conditions that still require effective treatment. Full article

(This article belongs to the Special Issue Drug Repurposing: Emerging Approaches to Drug Discovery)

20 pages, 1083 KiB

Open AccessReview

The Role of Xenobiotics and Anelloviruses in Colorectal Cancer: Mechanisms and Perspectives

by Francisco Aguayo, Julio C. Tapia, Gloria M. Calaf, Juan P. Muñoz, Julio C. Osorio, Matías Guzmán-Venegas, Carolina Moreno-León, Jorge Levican and Cristian Andrade-Madrigal

Int. J. Mol. Sci. 2025, 26(9), 4354; https://doi.org/10.3390/ijms26094354 (registering DOI) - 3 May 2025

Abstract

Xenobiotics are non-natural chemical compounds to which the human population is exposed. Chronic exposure to certain xenobiotics is associated with various diseases, including cancer development. Anelloviruses (AVs), including Torque Teno Virus (TTV), Torque Teno Mini Virus (TTMV), and Torque Teno Midi Virus (TTMDV), [...] Read more.

Xenobiotics are non-natural chemical compounds to which the human population is exposed. Chronic exposure to certain xenobiotics is associated with various diseases, including cancer development. Anelloviruses (AVs), including Torque Teno Virus (TTV), Torque Teno Mini Virus (TTMV), and Torque Teno Midi Virus (TTMDV), are ubiquitous viruses found in the general population. As no disease has been definitively associated with AVs, they are sometimes referred to as “viruses awaiting a disease”. This review explores the potential roles of xenobiotics and AVs in colorectal cancer (CRC) development and suggests a potential interplay between them. Evidence suggests an association between certain xenobiotics (like pesticides, cigarette smoke components, and dietary factors) and CRC, while such an association is less clear for AVs. The high prevalence of AVs suggests these infections alone may be insufficient to disrupt homeostasis; thus, additional factors might be required to promote disease, potentially including cancer. Full article

(This article belongs to the Special Issue Viral Infections and Cancer: Recent Advances and Future Perspectives)

41 pages, 4411 KiB

Open AccessArticle

Galactooligosaccharides Attenuate Behavioural, Haematological and Immunological Abnormalities and Influence Gut Microbiota in Rats with Amygdala Hyperactivation Induced by Electrical Stimulation

by Jan Ruciński, Ewelina Kurowska-Rucińska, Dorota Myślińska, Beata Grembecka, Natalia Piekarczyk, Agnieszka Necel, Katarzyna Kosznik-Kwaśnicka and Irena Majkutewicz

Int. J. Mol. Sci. 2025, 26(9), 4353; https://doi.org/10.3390/ijms26094353 (registering DOI) - 3 May 2025

Abstract

The amygdala, especially its central nucleus (CeA), is one of the key brain structures regulating fear, anxiety and stress responses and is also involved in gut microbiota signal processing. Amygdala hyperactivity, as well as microbiota alterations, plays an important role in the pathophysiology [...] Read more.

The amygdala, especially its central nucleus (CeA), is one of the key brain structures regulating fear, anxiety and stress responses and is also involved in gut microbiota signal processing. Amygdala hyperactivity, as well as microbiota alterations, plays an important role in the pathophysiology of anxiety disorders, depression or post-traumatic stress disorder (PTSD). The present study determines whether 3 weeks of galactooligosaccharide (GOS) supplementation alleviates behavioural, haematological, immunological and gut microbiota disturbances induced by long-term electrical stimulation of the CeA in rats (Stim). The unsupplemented Stim group showed locomotor hyperactivity and higher anxiety (measured with an actometer and the elevated plus maze, respectively), as well as a decrease in white blood cells (WBCs), lymphocytes (LYMs), red blood cells (RBCs) and platelets (PLTs); an elevation of TNFα; a reduction in IL-10 concentration in plasma; and microbiota alterations as compared to the control (Sham) group. GOS supplementation alleviated all these Stim-induced adverse effects or even normalised them to the sham group level. The effect of GOS was comparable to citalopram and even more effective in WBC and PLT normalisation and IL-10 induction. The obtained results indicate the high therapeutic potential of GOS in anxiety and stress-related disorders. GOS supplementation may support conventional therapy or the prevention of PTSD, depression and anxiety disorders. Full article

(This article belongs to the Special Issue The Role of Specific Alteration in Neurological Disorders: From Molecular Mechanisms to Therapeutic Strategies)

25 pages, 3761 KiB

Open AccessArticle

N-Acetylcysteine Attenuates Aβ-Mediated Oxidative Stress, Blood–Brain Barrier Leakage, and Renal Dysfunction in 5xFAD Mice

by Atcharaporn Ontawong, Geetika Nehra, Bryan J. Maloney, Chutima S. Vaddhanaphuti, Björn Bauer and Anika M. S. Hartz

Int. J. Mol. Sci. 2025, 26(9), 4352; https://doi.org/10.3390/ijms26094352 (registering DOI) - 3 May 2025

Abstract

Alzheimer’s disease (AD) is characterized by amyloid-beta (Aβ) pathology and is closely linked to oxidative stress, which contributes to blood–brain barrier leakage, renal dysfunction, and cognitive decline. We investigated the effects of N-acetyl cysteine (NAC), an FDA-approved antioxidant, on oxidative stress, brain Aβ [...] Read more.

Alzheimer’s disease (AD) is characterized by amyloid-beta (Aβ) pathology and is closely linked to oxidative stress, which contributes to blood–brain barrier leakage, renal dysfunction, and cognitive decline. We investigated the effects of N-acetyl cysteine (NAC), an FDA-approved antioxidant, on oxidative stress, brain Aβ levels, barrier leakage, renal function, and cognition in 5xFAD mice. Eight-week-old 5xFAD mice were fed a rodent diet supplemented with 600 mg/kg_Diet NAC for 4 weeks; wild-type (WT) mice and control 5xFAD mice were fed a regular rodent diet. We detected elevated brain and renal 4-hydroxynonenal(4-HNE) levels, reduced creatinine clearance, and increased plasma S100β levels in untreated 5xFAD mice compared to WT controls. Untreated 5xFAD mice also had higher capillary leakage, reduced P-gp activity, and impaired cognition compared to WT. NAC treatment of 5xFAD mice reduced brain Aβ40 levels, normalized 4-HNE levels to control levels, improved creatinine clearance, decreased capillary leakage, and lowered S100β plasma levels. NAC improved cognitive performance in 5xFAD mice, as shown by Y-maze. Our findings indicate that Aβ-induced oxidative stress contributes to barrier dysfunction, renal impairment, and cognitive deficits in 5xFAD mice. Notably, NAC treatment mitigates these effects, suggesting its potential as an adjunct therapy for AD and other Aβ-related pathologies by reducing oxidative stress. Full article

(This article belongs to the Section Molecular Biology)

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21 pages, 1061 KiB

Open AccessReview

Emerging Frontiers in Zebrafish Embryonic and Adult-Derived Cell Lines

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

Int. J. Mol. Sci. 2025, 26(9), 4351; https://doi.org/10.3390/ijms26094351 (registering DOI) - 3 May 2025

Abstract

Zebrafish (Danio rerio) has become a pivotal vertebrate model in biomedical research, renowned for its genetic similarity to humans, optical transparency, rapid embryonic development, and amenability to experimental manipulation. In recent years, the derivation of cell lines from zebrafish embryos has [...] Read more.

Zebrafish (Danio rerio) has become a pivotal vertebrate model in biomedical research, renowned for its genetic similarity to humans, optical transparency, rapid embryonic development, and amenability to experimental manipulation. In recent years, the derivation of cell lines from zebrafish embryos has unlocked new possibilities for in vitro studies across developmental biology, toxicology, disease modeling, and genetic engineering. These embryo-derived cultures offer scalable, reproducible, and ethically favorable alternatives to in vivo approaches, enabling high-throughput screening and mechanistic exploration under defined conditions. This review provides a comprehensive overview of protocols for establishing and maintaining zebrafish embryonic cell lines, emphasizing culture conditions, pluripotency features, transfection strategies, and recent innovations such as genotype-defined mutant lines generated via CRISPR/Cas9 and feeder-free systems. We also highlight emerging applications in oncology, regenerative medicine, and functional genomics, positioning zebrafish cell lines as versatile platforms bridging animal models and next-generation in vitro systems. Its continued optimization holds promise for improved reproducibility, reduced animal use, and expanded translational impact in biomedical research. Full article

(This article belongs to the Special Issue The Zebrafish Model in Animal and Human Health Research, 2nd Edition)

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12 pages, 1959 KiB

Open AccessArticle

Interactions of CFTR and Arylsulfatase B (ARSB; N-acetylgalactosamine-4-sulfatase) in Prostate Carcinoma

by Sumit Bhattacharyya and Joanne K. Tobacman

Int. J. Mol. Sci. 2025, 26(9), 4350; https://doi.org/10.3390/ijms26094350 (registering DOI) - 3 May 2025

Abstract

Defective CFTR (cystic fibrosis transmembrane conductance regulator) is pathognomonic for cystic fibrosis (CF), which is characterized by an accumulation of tenacious secretions in pulmonary airways, as well as by abnormal ductal secretions in other organs, including the pancreas and prostate. The advent of [...] Read more.

Defective CFTR (cystic fibrosis transmembrane conductance regulator) is pathognomonic for cystic fibrosis (CF), which is characterized by an accumulation of tenacious secretions in pulmonary airways, as well as by abnormal ductal secretions in other organs, including the pancreas and prostate. The advent of CFTR modulating therapies has markedly improved the clinical status and survival of CF patients, primarily attributable to improved lung function. Previous publications reported that a decline in CFTR function was associated with a decline in activity and expression of the enzyme N-acetylgalactosamine-4-sulfatase (Arylsulfatase B; ARSB). ARSB removes 4-sulfate groups from N-acetylgalactosamine 4-sulfate residues and is required for the degradation of chondroitin 4-sulfate (chondroitin sulfate A) and dermatan sulfate, two sulfated glycosaminoglycans which accumulate in cystic fibrosis. Declines in both ARSB and in CFTR have been associated with the development of malignancies, including prostate malignancy. The experiments in this report show that similar effects on invasiveness are present when either CFTR or ARSB is inhibited in human prostate epithelial cells, and these effects resemble findings detected in malignant prostate tissue. The effects of CFTR inhibition are reversed by treatment with recombinant human ARSB in prostate cells. These results suggest that treatment by rhARSB may benefit patients with cystic fibrosis and prostate cancer. Full article

(This article belongs to the Special Issue Molecular Mechanisms and Pathophysiology of Cystic Fibrosis)

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13 pages, 854 KiB

Open AccessArticle

Respiratory Function Improvement and Lifespan Extension Following Immunotherapy with NP001 Support the Concept That Amyotrophic Lateral Sclerosis (ALS) Is an Immuno-Neurologic Disease

by Rongzhen Zhang, Ari Azhir and Michael S. McGrath

Int. J. Mol. Sci. 2025, 26(9), 4349; https://doi.org/10.3390/ijms26094349 (registering DOI) - 3 May 2025

Abstract

Amyotrophic lateral sclerosis (ALS) is a heterogeneous disease that involves progressive loss of voluntary muscle and ultimately, respiratory function, which is the primary cause of death in ALS patients. Respiratory vital capacity (VC) measurements are objective, reproducible, and directly related to survival. Respiratory [...] Read more.

Amyotrophic lateral sclerosis (ALS) is a heterogeneous disease that involves progressive loss of voluntary muscle and ultimately, respiratory function, which is the primary cause of death in ALS patients. Respiratory vital capacity (VC) measurements are objective, reproducible, and directly related to survival. Respiratory function is known to be negatively affected in individuals with excess abdominal fat contributing to a chronic innate immune inflammatory state. To test whether ALS patients might have a body mass index (BMI) related VC response to the innate immune system regulator NP001, clinical results from two NP001 phase 2 trials were evaluated in an intent-to-treat manner, stratified by BMI measurements. Slowing of progressive VC loss and extension of overall survival (OS) occurred primarily in ALS patients who were overweight with a BMI ≥ 25 (70% of patients in the phase 2 trials). Innate immune dysfunction is a characteristic of ALS patients ≤ 65 years of age, and in this group both VC and OS changes in response to NP001 were most significant. This study represents a novel approach to ALS, wherein VC and OS were both significantly improved through immunologic, not neurologic modulation with NP001, a precursor to the dominant regulator of inflammation, taurine chloramine. Full article

(This article belongs to the Special Issue Immunity in Neurodegenerative Diseases: Systemic Immune Imbalance, Neuroinflammation, and Beyond)

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22 pages, 16916 KiB

Open AccessArticle

Engineering an Integrated Bioprocess to Produce Human Dental Pulp Stem Cell-Alginate-Based Bone Organoids

by Mauricio Zamorano, Cristobal Aguilar-Gallardo, Aloyma Lugo, Luis Jimenez, Jorge G. Farias and Athanasios Mantalaris

Int. J. Mol. Sci. 2025, 26(9), 4348; https://doi.org/10.3390/ijms26094348 (registering DOI) - 3 May 2025

Abstract

Bone tissue engineering (BTE) emerged as a practical approach to tackle prosthetic industry limitations. We merge aspects from developmental biology, engineering and medicine with the aim to produce fully functional bone tissue. Mesenchymal stem cells have the capability of self-renewal and specific lineage [...] Read more.

Bone tissue engineering (BTE) emerged as a practical approach to tackle prosthetic industry limitations. We merge aspects from developmental biology, engineering and medicine with the aim to produce fully functional bone tissue. Mesenchymal stem cells have the capability of self-renewal and specific lineage differentiation. Herein lies their potential for BTE. Among MSCs, human dental pulp stem cells have a higher proliferation rate, shorter doubling times, lower cellular senescence, and enhanced osteogenesis than hBM-SCs under specific conditions. In addition, these cells are readily accessible and can be extracted through a subtle extraction procedure. Thus, they garner fewer moral concerns than most MSCs available and embody a promising cell source for BTE therapies able to replace hBM-MSCs. Interestingly, their study has been limited. Conversely, there is a need for their further study to harness their true value in BTE, with special emphasis in the design of bioprocesses able to produce viable, homogenous bone constructs in a clinical scale. Here, we study the osteogenic differentiation of hDPSCs encapsulated in alginate hydrogels under suspended culture in a novel perfusion bioreactor. The system is compared with traditional 3D static and fed-batch culture methodologies. The novel system performed better, producing higher alkaline phosphatase activity, and more homogeneous, dense and functional bone constructs. Additionally, cell constructs produced by the in-house-designed system were richer in mature osteoblast-like and mineralizing osteocyte-like cells. In conclusion, this study reports the development of a novel bioprocess able to produce hDPSC-based bone-like constructs, providing new insights into hDPSCs’ therapeutic potential and a system able to be transferred from the laboratory bench into medical facilities. Full article

(This article belongs to the Special Issue New Trends and Challenges in Polysaccharide Biomaterials)

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27 pages, 2510 KiB

Open AccessArticle

Norfloxacin Oxidative Degradation and Toxicity in Aqueous Media: Reciprocal Effects of Acidity Evolution on Metal Cations and Clay Catalyst Dispersion

by Roumaissa Djidja, David Dewez and Abdelkrim Azzouz

Int. J. Mol. Sci. 2025, 26(9), 4347; https://doi.org/10.3390/ijms26094347 - 2 May 2025

Abstract

The ozonation of norfloxacin (NOF), a widely used fluoroquinolone antibiotic, in the presence of Na⁺, Fe²⁺, Cu²⁺, Ni²⁺, and Co²⁺ cations and their montmorillonite-supported counterparts was investigated. The NOF degradation and the toxicity of [...] Read more.

The ozonation of norfloxacin (NOF), a widely used fluoroquinolone antibiotic, in the presence of Na⁺, Fe²⁺, Cu²⁺, Ni²⁺, and Co²⁺ cations and their montmorillonite-supported counterparts was investigated. The NOF degradation and the toxicity of the ozonized mixtures towards an aquatic organism (Lemna minor) were evaluated in terms of changes in its frond number, chlorophyll content, photosynthesis efficacy, and production of reactive oxygen species (ROS). The evolution over time of the NOF degradation grade and the toxicity were discussed in terms of i. the observed changes in the interactions of the cation and clay catalyst with NOF molecules; ii. the pH decay, during ozonation. Ion-exchange and Lewis acid–base interactions appear to govern NOF adsorption and clay catalyst dispersion in correlation with the progressive formation of acidic species in the aqueous media. These findings reveal promising prospects for tailoring optimum oxidative water treatments with minimum toxicity and for predicting their environmental impacts on aquatic media. Full article

(This article belongs to the Section Materials Science)

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23 pages, 1539 KiB

Open AccessReview

Role and Potential of Artificial Intelligence in Biomarker Discovery and Development of Treatment Strategies for Amyotrophic Lateral Sclerosis

by Yoshihiro Kitaoka, Toshihiro Uchihashi, So Kawata, Akira Nishiura, Toru Yamamoto, Shin-ichiro Hiraoka, Yusuke Yokota, Emiko Tanaka Isomura, Mikihiko Kogo, Susumu Tanaka, Igor Spigelman and Soju Seki

Int. J. Mol. Sci. 2025, 26(9), 4346; https://doi.org/10.3390/ijms26094346 - 2 May 2025

Abstract

Neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), present significant challenges owing to their complex pathologies and a lack of curative treatments. Early detection and reliable biomarkers are critical but remain elusive. Artificial intelligence (AI) has emerged as a transformative tool, enabling advancements in [...] Read more.

Neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), present significant challenges owing to their complex pathologies and a lack of curative treatments. Early detection and reliable biomarkers are critical but remain elusive. Artificial intelligence (AI) has emerged as a transformative tool, enabling advancements in biomarker discovery, diagnostic accuracy, and therapeutic development. From optimizing clinical-trial designs to leveraging omics and neuroimaging data, AI facilitates understanding of disease and treatment innovation. Notably, technologies such as AlphaFold and deep learning models have revolutionized proteomics and neuroimaging, offering unprecedented insights into ALS pathophysiology. This review highlights the intersection of AI and ALS, exploring the current state of progress and future therapeutic prospects. Full article

(This article belongs to the Special Issue New Therapies and Strategies in the Treatment of Neurodegenerative Diseases)

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17 pages, 9850 KiB

Open AccessArticle

m⁶A Methylation Mediated Autophagy and Nucleotide-Binding Oligomerization Domain-like Receptors Signaling Pathway Provides New Insight into the Mitigation of Oxidative Damage by Mulberry Leaf Polysaccharides

by Wenqiang Jiang, Yan Lin, Linjie Qian, Siyue Lu, Zhengyan Gu, Xianping Ge and Linghong Miao

Int. J. Mol. Sci. 2025, 26(9), 4345; https://doi.org/10.3390/ijms26094345 - 2 May 2025

Abstract

m⁶A methylation modification is an important genetic modification involved in biological processes such as sexual maturation, antibacterial, and antiviral in aquatic animals. However, few studies have been conducted in aquatic animals on the relationship between m⁶A methylation modification and [...] Read more.

m⁶A methylation modification is an important genetic modification involved in biological processes such as sexual maturation, antibacterial, and antiviral in aquatic animals. However, few studies have been conducted in aquatic animals on the relationship between m⁶A methylation modification and autophagy-inflammation induced by lipid metabolism disorders. In the present study, a high-fat (HF) group and HF-MLP group (1 g mulberry leaf polysaccharides (MLPs)/1 kg HF diet) were set up. The mid-hind intestines of Megalobrama amblycephala juveniles from the two groups were collected for MeRIP-seq and RNA-seq after an 8-week feeding trial. The m⁶A peaks in the HF and HF-MLP groups were mainly enriched in the 3′ Untranslated Region (3′UTR), Stop codon, and coding sequence (CDS) region. Compared with the HF group, the m⁶A peaks in the HF-MLP group were shifted toward the 5′UTR region. ‘RRACH’ was the common m⁶A methylation motif in the HF and HF-MLP groups. Methyltransferase mettl14 and wtap expression in the intestines of the HF-MLP group were significantly higher compared with the HF group (p < 0.05). A total of 21 differentially expressed genes(DEGs) with different peaks were screened by the combined MeRIP-seq and RNA-seq analysis. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis enriched BCL2 interacting protein 3 (bnip3) to autophagy–animal and mitophagy–animal signaling pathways, etc., and nucleotide-binding domain leucine-rich repeat protein 1 (nlrp1) was enriched to the Nucleotide-binding oligomerization domain (NOD)-like receptor signaling pathway. Combined MeRIP-seq and RNA-seq analysis indicated that the expression pattern of bnip3 was hyper-up and that of nlrp1 was hyper-down. Gene Set Enrichment Analysis (GSEA) analysis confirmed that the intestinal genes of HF-MLP group positively regulate lysosomal and autophagy–animal signaling pathways. In the present study, we demonstrated that m⁶A methylation modification plays a role in regulating autophagy-inflammatory responses induced by HF diets by MLPs, and further explored the molecular mechanisms by which MLPs work from the epigenetic perspective. Full article

(This article belongs to the Special Issue Fish Nutrition Program and Epigenetic Regulation)

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