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Keywords = lysosome selectivity

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19 pages, 3112 KiB  
Article
Development of a Lentiviral Vector for High-Yield Production of Synthetic and Recombinant GCase for Gaucher Disease Therapy
by Ana Carolina Coelho, Claudia Emília Vieira Wiezel, Alline Cristina de Campos, Lílian Louise Souza Figueiredo, Gabriela Aparecida Marcondes Suardi, Juliana de Paula Bernardes, Daniela Pretti da Cunha Tirapelli, Vitor Marcel Faça, Kuruvilla Joseph Abraham, Carlos Gilberto Carlotti-Júnior, Velia Siciliano, Ron Weiss, Stanton Gerson and Aparecida Maria Fontes
Int. J. Mol. Sci. 2025, 26(15), 7089; https://doi.org/10.3390/ijms26157089 - 23 Jul 2025
Viewed by 199
Abstract
Gaucher disease (GD) is an autosomal recessive disorder caused by the deficient activity of the lysosomal enzyme glucocerebrosidase (GCase). Although enzyme replacement therapy (ERT) remains the standard of care for non-neuropathic GD patients, its high cost significantly limits accessibility. To enhance production efficiency, [...] Read more.
Gaucher disease (GD) is an autosomal recessive disorder caused by the deficient activity of the lysosomal enzyme glucocerebrosidase (GCase). Although enzyme replacement therapy (ERT) remains the standard of care for non-neuropathic GD patients, its high cost significantly limits accessibility. To enhance production efficiency, we developed a lentiviral system encoding a codon-optimized GCase gene driven by the human elongation factor 1a (hEF1α) promoter for stable production in human cell lines. A functional lentiviral vector, LV_EF1α_GBA_Opt, was generated at a titer of 7.88 × 108 LV particles/mL as determined by qPCR. Six transduction cycles were performed at a multiplicity of infection of 30–50. The transduced heterogeneous human cell population showed GCase-specific activity of 307.5 ± 53.49 nmol/mg protein/h, which represents a 3.21-fold increase compared to wild-type 293FT cells (95.58 ± 16.5 nmol/mg protein/h). Following single-cell cloning, two clones showed specific activity of 763.8 ± 135.1 and 752.0 ± 152.1 nmol/mg/h (clones 15 and 16, respectively). These results show that codon optimization, a lentiviral delivery system, and clonal selection together enable the establishment of stable human cell lines capable of producing high levels of biologically active, synthetic recombinant GCase in vitro. Further studies are warranted for the functional validation in GD patient-derived fibroblasts and animal models. Full article
(This article belongs to the Special Issue Gaucher Disease: From Molecular Mechanisms to Treatments)
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30 pages, 3013 KiB  
Review
Inter-Organelle Crosstalk in Oxidative Distress: A Unified TRPM2-NOX2 Mediated Vicious Cycle Involving Ca2+, Zn2+, and ROS Amplification
by Esra Elhashmi Shitaw, Maali AlAhmad and Asipu Sivaprasadarao
Antioxidants 2025, 14(7), 776; https://doi.org/10.3390/antiox14070776 - 24 Jun 2025
Viewed by 562
Abstract
Reactive oxygen species (ROS) are critical signalling molecules, but their overproduction leads to oxidative stress (OS), a common denominator in the pathogenesis of numerous non-communicable diseases (NCDs) and aging. General antioxidant therapies have largely been unsuccessful, highlighting the need for a deeper understanding [...] Read more.
Reactive oxygen species (ROS) are critical signalling molecules, but their overproduction leads to oxidative stress (OS), a common denominator in the pathogenesis of numerous non-communicable diseases (NCDs) and aging. General antioxidant therapies have largely been unsuccessful, highlighting the need for a deeper understanding of ROS amplification mechanisms to develop targeted interventions. This review proposes a unified, self-amplifying “vicious cycle” of inter-organelle crosstalk that drives pathological ROS elevation and cellular damage. We outline a pathway initiated by extracellular stressors that co-activate plasma membrane TRPM2 channels and NADPH oxidase-2. This synergy elevates cytoplasmic Ca2+, leading to lysosomal dysfunction and permeabilization, which in turn releases sequestered Zn2+. Mitochondrial uptake of this labile Zn2+ impairs electron transport chain function, particularly at Complex III, resulting in mitochondrial fragmentation, loss of membrane potential and a burst of mitochondrial ROS (mtROS). These mtROS diffuse to the nucleus, activating PARP-1 and generating ADPR, which further stimulates TRPM2, thereby perpetuating the cycle. This “circular domino effect” integrates signals generated across the plasma membrane (Ca2+), lysosomes (Zn2+), mitochondria (ROS) and nucleus (ADPR), leading to progressive organelle failure, cellular dysfunction, and ultimately cell death. Understanding and targeting specific nodes within this TRPM2-NOX2-Ca2+-Zn2+-mtROS-ADPR axis offers novel therapeutic avenues for NCDs by selectively disrupting pathological ROS amplification while preserving essential physiological redox signalling. Full article
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35 pages, 2933 KiB  
Review
NEU1-Mediated Extracellular Vesicle Glycosylation in Alzheimer’s Disease: Mechanistic Insights into Intercellular Communication and Therapeutic Targeting
by Mohd Adnan, Arif Jamal Siddiqui, Fevzi Bardakci, Malvi Surti, Riadh Badraoui and Mitesh Patel
Pharmaceuticals 2025, 18(6), 921; https://doi.org/10.3390/ph18060921 - 19 Jun 2025
Viewed by 630
Abstract
Alzheimer’s disease (AD), a progressive neurodegenerative disorder, is marked by the pathological accumulation of amyloid-β plaques and tau neurofibrillary tangles, both of which disrupt neuronal communication and function. Emerging evidence highlights the role of extracellular vesicles (EVs) as key mediators of intercellular communication, [...] Read more.
Alzheimer’s disease (AD), a progressive neurodegenerative disorder, is marked by the pathological accumulation of amyloid-β plaques and tau neurofibrillary tangles, both of which disrupt neuronal communication and function. Emerging evidence highlights the role of extracellular vesicles (EVs) as key mediators of intercellular communication, particularly in the propagation of pathological proteins in AD. Among the regulatory factors influencing EV composition and function, neuraminidase 1 (NEU1), a lysosomal sialidase responsible for desialylating glycoproteins has gained attention for its involvement in EV glycosylation. This review explores the role of NEU1 in modulating EV glycosylation, with particular emphasis on its influence on immune modulation and intracellular trafficking pathways and the subsequent impact on intercellular signaling and neurodegenerative progression. Altered NEU1 activity has been associated with abnormal glycan profiles on EVs, which may facilitate the enhanced spread of amyloid-β and tau proteins across neural networks. By regulating glycosylation, NEU1 influences EV stability, targeting and uptake by recipient cells, primarily through the desialylation of surface glycoproteins and glycolipids, which alters the EV charge, recognition and receptor-mediated interactions. Targeting NEU1 offers a promising therapeutic avenue to restore EV homeostasis and reduces pathological protein dissemination. However, challenges persist in developing selective NEU1 inhibitors and effective delivery methods to the brain. Furthermore, altered EV glycosylation patterns may serve as potential biomarkers for early AD diagnosis and monitoring. Overall, this review highlights the importance of NEU1 in AD pathogenesis and advocates for deeper investigation into its regulatory functions, with the aim of advancing therapeutic strategies and biomarker development for AD and related neurological disabilities. Full article
(This article belongs to the Special Issue Pharmacotherapy for Alzheimer’s Disease)
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16 pages, 9639 KiB  
Article
Immunomodulatory Effects of Pulmonarom®: In Vitro Induction of TLR and Cytokine Expression in Human Dendritic Cells
by Juan A. Hernández-Aceves, Sandra Georgina Solano-Gálvez, Arturo A. Wilkins-Rodríguez, José Delgado-Domínguez, Alberto Garcia Lozano, Carlos Cabello-Gutierrez, Lidia Flor Estela Huerta, Gladis Fragoso, Laila Gutiérrez-Kobeh and Rosalino Vázquez-López
Pharmaceuticals 2025, 18(6), 885; https://doi.org/10.3390/ph18060885 - 13 Jun 2025
Viewed by 942
Abstract
Background: Bacterial lysates are known to modulate the immune response against respiratory infections. However, the effects of the commercial bacterial lysate Pulmonarom® on dendritic cells—particularly human monocyte-derived dendritic cells (moDCs)—have not been studied. Additionally, limited data are available on the expression of [...] Read more.
Background: Bacterial lysates are known to modulate the immune response against respiratory infections. However, the effects of the commercial bacterial lysate Pulmonarom® on dendritic cells—particularly human monocyte-derived dendritic cells (moDCs)—have not been studied. Additionally, limited data are available on the expression of Toll-like receptors (TLRs) and cytokines following stimulation with bacterial lysates. Methods: Human monocytes were isolated from buffy coats and differentiated into moDCs. Pulmonarom® was lyophilized, quantified, and used to stimulate moDCs. Ultrastructural changes were evaluated using transmission electron microscopy. The expression of TLRs and selected cytokines was analyzed by flow cytometry. Results: Pulmonarom® stimulation induced morphological changes in moDCs, including an increased number of dendrites and lysosomes. It also led to the upregulation of MHC class II molecules and TLRs 2, 3, 6, and 7. Additionally, the production of IL-4, IL-6, IL-8, and MCP-1 was significantly increased. Conclusions: Pulmonarom® promotes moDC maturation, characterized by enhanced antigen presentation capabilities and lysosomal activity, along with increased expression of specific TLRs and cytokines. These features suggest a trained immunity phenotype in moDCs, potentially improving their ability to initiate adaptive immune responses against respiratory pathogens. To our knowledge, this is the first study to investigate the immunomodulatory effects of Pulmonarom® on human moDCs, providing novel insights into its potential as an immunotherapeutic adjuvant. Full article
(This article belongs to the Section Biopharmaceuticals)
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7 pages, 191 KiB  
Technical Note
Characterization of Dried Blood Spot Quality Control Materials for Lysosomal Enzyme Activity Assays Using Digital Microfluidic Fluorometry to Detect Lysosomal Storage Disorders in Newborns
by Paul Dantonio, Tracy Klug, Golriz Yazdanpanah, Christopher Haynes, Hui Zhou, Patrick Hopkins, Robert Vogt, Rachel Lee, Carla Cuthbert and Konstantinos Petritis
Int. J. Neonatal Screen. 2025, 11(2), 44; https://doi.org/10.3390/ijns11020044 - 10 Jun 2025
Viewed by 523
Abstract
Newborn bloodspot screening for one or more lysosomal storage disorders (NBS-LSD) is currently performed by many public health NBS laboratories globally. The screening tests measure activities of selected lysosomal enzymes on dried blood spot (DBS) specimens collected from newborns by the heel stick [...] Read more.
Newborn bloodspot screening for one or more lysosomal storage disorders (NBS-LSD) is currently performed by many public health NBS laboratories globally. The screening tests measure activities of selected lysosomal enzymes on dried blood spot (DBS) specimens collected from newborns by the heel stick method Because these assays measure enzyme activity, the quantitative results are dependent on the particular analytical method. DBS quality control (DBS QC) materials with assay-specific certified values that span the relevant range from typical to LSD-affected newborns are an important component of quality assurance in NBS laboratories. The Newborn Screening Quality Assurance Program (NSQAP) at the U.S. Centers for Disease Control and Prevention (CDC) provides public health NBS laboratories with DBS QC sets for NBS-LSD comprising four admixtures of pooled umbilical cord blood and a base pool made from leukodepleted peripheral blood and heat-inactivated serum. To evaluate the suitability of these materials for use with digital microfluidics fluorometry (DMF) assays which can currently measure the activity of four enzymes (acid α-galactosidase (GLA); acid β-glucocerebrosidase (GBA); acid α-glucosidase (GAA); and iduronidase (IDUA)), CDC collaborated with the Newborn Screening Unit at the Missouri State Public Health Laboratory (MSPHL). Using MSPHL criteria, we found that the certified results from each of two DBS QC lots collectively spanned the range from typical (screen negative) to enzyme deficient (screen positive) newborn DBS levels for each of the four lysosomal enzymes measured. The range included borderline results that would require repeat screening of the newborn under the MSPHL protocol. We conclude that these DBS QC preparations are suitable for use as external quality control materials for DMF assays used to detect LSDs in newborns. Full article
12 pages, 2647 KiB  
Article
Decursin Suppresses Esophageal Squamous Cell Carcinoma Progression via Orchestrated Cell Cycle Deceleration, Apoptotic Activation, and Oncoprotein Degradation
by Chen Fang, Lin Wu, Xiangzhe Yang, Kai Xie, Peng Zhang, Yu Feng, Haitao Ma and Xing Tong
Int. J. Mol. Sci. 2025, 26(11), 5391; https://doi.org/10.3390/ijms26115391 - 4 Jun 2025
Viewed by 522
Abstract
Esophageal squamous cell carcinoma (ESCC) remains a lethal malignancy with limited therapeutic options. This study investigated the antitumor efficacy and mechanisms of decursin, a natural pyranocoumarin derivative, against ESCC. In vitro analyses demonstrated that decursin selectively inhibited ESCC cell viability (IC50: 14.62 ± [...] Read more.
Esophageal squamous cell carcinoma (ESCC) remains a lethal malignancy with limited therapeutic options. This study investigated the antitumor efficacy and mechanisms of decursin, a natural pyranocoumarin derivative, against ESCC. In vitro analyses demonstrated that decursin selectively inhibited ESCC cell viability (IC50: 14.62 ± 0.61–26.20 ± 2.11 μM across TE-1, KYSE-30, and KYSE-150 cell lines) without affecting normal esophageal epithelial cells (Het-1A). Decursin (10 μM) suppressed colony formation, impaired wound healing (p < 0.001 at 48 h), and reduced Transwell migration/invasion in KYSE-150 cells. Subcutaneous xenograft models revealed significant tumor growth inhibition (p < 0.01) with decursin treatment (10 mg/kg, intraperitoneal), accompanied by no systemic toxicity. Mechanistically, decursin induced G0/G1 cell cycle deceleration (p < 0.01) and apoptosis through ubiquitin–proteasome-mediated degradation of oncoproteins TP63 and SOX2. Time- and dose-dependent protein suppression was reversed by proteasome inhibitor MG-132, but unaffected by lysosomal inhibition. These findings establish decursin as a promising therapeutic agent for ESCC, functioning via proteasomal degradation of key oncogenic drivers, and provide a rationale for decursin’s further development as a targeted monotherapy or chemosensitizer in multimodal regimens. Full article
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22 pages, 5103 KiB  
Article
Exploring Multivalent Architectures for Binding and Stabilization of N-Acetylgalactosamine 6-Sulfatase
by Maria Giulia Davighi, Francesca Clemente, Giampiero D’Adamio, Macarena Martínez-Bailén, Alessio Morano, Andrea Goti, Amelia Morrone, Camilla Matassini and Francesca Cardona
Molecules 2025, 30(10), 2222; https://doi.org/10.3390/molecules30102222 - 20 May 2025
Viewed by 644
Abstract
Morquio A syndrome is a lysosomal disorder caused by the deficiency of the lysosomal enzyme N-acetylgalactosamine 6-sulfatase (GALNS, EC 3.1.6.4). Currently, enzyme replacement therapy (ERT) is used to treat Morquio A through the infusion of the recombinant enzyme VIMIZIM® (elosulfase alfa, [...] Read more.
Morquio A syndrome is a lysosomal disorder caused by the deficiency of the lysosomal enzyme N-acetylgalactosamine 6-sulfatase (GALNS, EC 3.1.6.4). Currently, enzyme replacement therapy (ERT) is used to treat Morquio A through the infusion of the recombinant enzyme VIMIZIM® (elosulfase alfa, BioMarin). Unfortunately, the recombinant enzyme exhibits low conformational stability in vivo. A promising approach to address this issue is the coadministration of recombinant human GALNS (rhGALNS) with a pharmacological chaperone (PC), a molecule that selectively binds to the misfolded protein, stabilizes its conformation, and assists in the restoration of the impaired function. We report in this work the synthesis of a library of multivalent glycomimetics exploiting the copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction between several dendrimeric scaffolds armed with terminal alkynes and azido ending iminosugars of different structures (pyrrolidines, piperidines, and pyrrolizidines) or simple azido ending carbohydrates as bioactive units. The biological evaluation identified pyrrolidine-based nonavalent dendrimers 1 and 36 as the most promising compounds, able both to bind the native enzyme with IC50 in the micromolar range and to act as enzyme stabilizers toward rhGALNS in a thermal denaturation study, thus identifying promising compounds for a combined PC/ERT therapy. Full article
(This article belongs to the Special Issue Glycomimetics: Design, Synthesis and Bioorganic Applications)
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12 pages, 839 KiB  
Article
A Novel Screening Approach for Familial Hypercholesterolemia: A Genetic Study on Patients Detected Using Preexisting Centralized Analytics
by Joaquín Sánchez-Prieto, Fernando Sabatel, Fátima Moreno, Miguel A. Arias and Luis Rodríguez-Padial
J. Clin. Med. 2025, 14(8), 2780; https://doi.org/10.3390/jcm14082780 - 17 Apr 2025
Viewed by 552
Abstract
Introduction and Objectives: Familial hypercholesterolemia (FH) is an autosomal dominant genetic disorder of lipid metabolism that is characterized by elevated low-density lipoprotein cholesterol (LDL-C) levels and a high risk of atherosclerotic cardiovascular disease. Familial hypercholesterolemia is typically caused by mutations in the LDL [...] Read more.
Introduction and Objectives: Familial hypercholesterolemia (FH) is an autosomal dominant genetic disorder of lipid metabolism that is characterized by elevated low-density lipoprotein cholesterol (LDL-C) levels and a high risk of atherosclerotic cardiovascular disease. Familial hypercholesterolemia is typically caused by mutations in the LDL receptor gene (LDLR), although other alterations may be found. The aim of this study was to perform a genetic study on a population identified through a new population-based diagnostic screen program for FH. Methods: Genetic variants in LDLR, apolipoprotein B (APOB), apolipoprotein E (APOE), proprotein convertase subtilisin/kexin type 9 (PCSK9), signal transducing Adaptor Family Member 1 (STAP1), low density lipoprotein receptor adaptor protein 1 (LDLRAP1) and lipase A, and lysosomal acid type lipase A (LIPA), as well as a genetic risk score, were evaluated in 84 individuals with a clinical diagnosis of FH based on the Dutch Lipid Clinics Network criteria (DLCN ≥ 6). These individuals were selected from a cohort of 752 patients with an abnormal lipid profile, obtained by screening existing centralized analytics. Results: A clinical diagnosis of FH was established in 17.9% of the patients evaluated, with mean LDL-C levels of 305.7 mg/dL (95% CI 250.4–360.9). Genetic variants were detected in 70.2% of these patients, with 50 different mutations identified, mainly in the LDLR. The most frequent pathogenic variants were c.1342C>T and c.313+1G>C. Null variants exhibited a more severe phenotype, and the risk score indicates that patients carrying genetic alterations have a 42% higher risk of developing cardiovascular disease. Conclusions: A high rate of genetic alterations was detected in patients with severe FH. In most cases, the phenotypic findings did not predict the genetic results, which provide important information regarding the cardiovascular risk of patients. Full article
(This article belongs to the Section Cardiovascular Medicine)
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12 pages, 1410 KiB  
Article
Mutation-Specific Cardiomyocyte Lines from Patients with Fabry Disease: A Sustainable In Vitro Model to Investigate Structure, Function, and Disease Mechanisms
by Kathleen Nicholls, Andrea Wise, David Elliot, Menno ter Huurne, Maria Fuller and Sharon Ricardo
Int. J. Transl. Med. 2025, 5(2), 15; https://doi.org/10.3390/ijtm5020015 - 15 Apr 2025
Viewed by 922
Abstract
Background: Fabry disease (FD) results from pathogenic GLA variants, causing lysosomal α-galactosidase A (α-GalA) deficiency and sphingolipid ceramide trihexoside (Gb3 or THC) accumulation. Disease phenotype varies widely but cardiomyopathy is commonly life-limiting. As a multisystemic disorder, FD initiates at the cellular level; however, [...] Read more.
Background: Fabry disease (FD) results from pathogenic GLA variants, causing lysosomal α-galactosidase A (α-GalA) deficiency and sphingolipid ceramide trihexoside (Gb3 or THC) accumulation. Disease phenotype varies widely but cardiomyopathy is commonly life-limiting. As a multisystemic disorder, FD initiates at the cellular level; however, the mechanism/s underlying Gb3-induced cell dysfunction remains largely unknown. This study established an in vitro mutation-specific model of Fabry cardiomyopathy using human-induced pluripotent stem cell (iPSC)-derived cardiomyocytes to explore underlying cell pathology. Methods: Skin biopsies from consenting Fabry patients and normal control subjects were reprogrammed to iPSCs then differentiated into cardiomyocytes. The GLA mutations in Fabry cell lines were corrected using CRISP-Cas9. Phenotypic characteristics, α-Gal A activity, Gb3 accumulation, functional status, and lipid analysis were assessed. Cardiomyocytes derived from two patients with severe clinical phenotype and genotypes, GLAc.851T>C, GLAc.1193_1196del, and their respective corrected lines, GLAcorr c.851T>C, GLAcorr c.1193_1196del, were selected for further studies. Results: Cardiomyocytes derived from individuals with FD iPSCs exhibited stable expression of cardiomyocyte markers and spontaneous contraction, morphological features of FD, reduced α-Gal A activity, and accumulation of Gb3. Lipidomic profiling revealed differences in the Gb3 isoform profile between the control and FD patient iPSC-derived cardiomyocytes. Contraction strength was unchanged but relaxation after contraction was delayed, mimicking the diastolic dysfunction typical of Fabry cardiomyopathy. Conclusions: iPSC-derived cardiomyocytes provide a useful model to explore aspects of Fabry cardiomyopathy, including disruptions in sphingolipid pathways, proteomics, and multigene expression that together link genotype to phenotype. The platform potentially offers broad applicability across many genetic diseases and offers the prospect of testing and implementation of individualised therapies. Full article
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28 pages, 4577 KiB  
Article
Cell-Free DNA (cfDNA) Regulates Metabolic Remodeling in the ES-2 Ovarian Carcinoma Cell Line, Influencing Cell Proliferation, Quiescence, and Chemoresistance in a Cell-of-Origin-Specific Manner
by Isabel Lemos, Catarina Freitas-Dias, Ana Hipólito, José Ramalho, Fabrizio Carteni, Luís G. Gonçalves, Stefano Mazzoleni and Jacinta Serpa
Metabolites 2025, 15(4), 244; https://doi.org/10.3390/metabo15040244 - 2 Apr 2025
Viewed by 729
Abstract
Background: The cell-free DNA (cfDNA) is an extracellular fragmented DNA found in body fluids in physiological and pathophysiological contexts. In cancer, cfDNA has been pointed out as a marker for disease diagnosis, staging, and prognosis; however, little is known about its biological role. [...] Read more.
Background: The cell-free DNA (cfDNA) is an extracellular fragmented DNA found in body fluids in physiological and pathophysiological contexts. In cancer, cfDNA has been pointed out as a marker for disease diagnosis, staging, and prognosis; however, little is known about its biological role. Methods: The role of cfDNA released by ES-2 ovarian cancer cells was investigated, along with the impact of glucose bioavailability and culture duration in the cfDNA-induced phenotype. The effect of cfDNA on ES-2 cell proliferation was evaluated by proliferation curves, and cell migration was assessed through wound healing. We explored the impact of different cfDNA variants on ES-2 cells’ metabolic profile using nuclear magnetic resonance (NMR) spectroscopy and cisplatin resistance through flow cytometry. Moreover, we assessed the protein levels of DNA-sensitive Toll-like receptor 9 (TLR9) by immunofluorescence and its colocalization with lysosome-associated membrane protein 1 (LAMP1). Results: This study demonstrated that despite inducing similar effects, different variants of cfDNA promote different effects on cells derived from the ES-2 cell line. We observed instant reactions of adopting the metabolic profile that brings back the cell functioning of more favorable culture conditions supporting proliferation and resembling the cell of origin of the cfDNA variant, as observed in unselected ES-2 cells. However, as a long-term selective factor, certain cfDNA variants induced quiescence that favors the chemoresistance of a subset of cancer cells. Conclusions: Therefore, different tumoral microenvironments may generate cfDNA variants that will impact cancer cells differently, orchestrating the disease fate. Full article
(This article belongs to the Special Issue Insights into Tumor Cell Metabolism and Epigenetics)
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23 pages, 8711 KiB  
Article
Cell-Free DNA (cfDNA) Regulates Metabolic Remodeling, Sustaining Proliferation, Quiescence, and Migration in MDA-MB-231, a Triple-Negative Breast Carcinoma (TNBC) Cell Line
by Isabel Lemos, Catarina Freitas-Dias, Ana Hipólito, José Ramalho, Fabrizio Carteni, Luís G. Gonçalves, Stefano Mazzoleni and Jacinta Serpa
Metabolites 2025, 15(4), 227; https://doi.org/10.3390/metabo15040227 - 27 Mar 2025
Cited by 1 | Viewed by 867
Abstract
Background: The clinical relevance of circulating cell-free DNA (cfDNA) in oncology has gained significant attention, with its potential as a biomarker for cancer diagnosis and monitoring. However, its precise role in cancer biology and progression remains unclear. cfDNA in cancer patients’ blood has [...] Read more.
Background: The clinical relevance of circulating cell-free DNA (cfDNA) in oncology has gained significant attention, with its potential as a biomarker for cancer diagnosis and monitoring. However, its precise role in cancer biology and progression remains unclear. cfDNA in cancer patients’ blood has been shown to activate signaling pathways, such as those mediated by toll-like receptors (TLRs), suggesting its involvement in cancer cell adaptation to the tumor microenvironment. Methods: This impact of cfDNA released from MDA-MB-231, a triple-negative breast cancer (TNBC) cell line was assessed, focusing on glucose availability and culture duration. The impact of cfDNA on the proliferation of MDA-MB-231 cells was investigated using proliferation curves, while cellular migration was evaluated through wound healing assays. The metabolic alterations induced by distinct cfDNA variants in MDA-MB-231 cells were investigated through nuclear magnetic resonance (NMR) spectroscopy, and their effect on cisplatin resistance was evaluated using flow cytometry. Furthermore, the expression levels of DNA-sensitive Toll-like receptor 9 (TLR9) were quantified via immunofluorescence, alongside its colocalization with lysosome-associated membrane protein 1 (LAMP1). Results: This study indicates that cfDNA facilitates metabolic adaptation, particularly under metabolic stress, by modulating glucose and glutamine consumption, key pathways in tumor cell metabolism. Exposure to cfDNA induced distinct metabolic shifts, favoring energy production through oxidative phosphorylation. The anti-cancer activity of cfDNA isolated from conditioned media of cells cultured under stressful conditions is influenced by the culture duration, emphasizing the importance of adaptation and se-lection in releasing cfDNA that can drive pro-tumoral processes. Additionally, cfDNA exposure influenced cell proliferation, quiescence, and migration, processes linked to metastasis and treatment resistance. These findings underscore cfDNA as a key mediator of metabolic reprogramming and adaptive responses in cancer cells, contributing to tumor progression and therapy resistance. Furthermore, the activation of TLR9 signaling suggests a mechanistic basis for cfDNA-induced phenotypic changes. Conclusions: Overall, cfDNA serves as a crucial signaling molecule in the tumor microenvironment, orchestrating adaptive processes that enhance cancer cell survival and progression. Full article
(This article belongs to the Special Issue Insights into Tumor Cell Metabolism and Epigenetics)
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20 pages, 12976 KiB  
Article
1′-Acetoxychavicol Acetate Selectively Downregulates Tumor Necrosis Factor Receptor-Associated Factor 2 (TRAF2) Expression
by Chihiro Moriwaki, Shingo Takahashi, Nhat Thi Vu, Yasunobu Miyake and Takao Kataoka
Molecules 2025, 30(6), 1243; https://doi.org/10.3390/molecules30061243 - 10 Mar 2025
Viewed by 694
Abstract
1′-Acetoxychavicol acetate (ACA) is a natural compound derived from rhizomes of the Zingiberaceae family that suppresses the nuclear factor κB (NF-κB) signaling pathway; however, the underlying mechanisms remain unclear. Therefore, the present study investigated the molecular mechanisms by which ACA inhibits the NF-κB [...] Read more.
1′-Acetoxychavicol acetate (ACA) is a natural compound derived from rhizomes of the Zingiberaceae family that suppresses the nuclear factor κB (NF-κB) signaling pathway; however, the underlying mechanisms remain unclear. Therefore, the present study investigated the molecular mechanisms by which ACA inhibits the NF-κB signaling pathway in human lung adenocarcinoma A549 cells. The results obtained showed ACA decreased tumor necrosis factor (TNF)-α-induced intercellular adhesion molecule-1 (ICAM-1) expression in A549 cells. It also inhibited TNF-α-induced ICAM-1 mRNA expression and ICAM-1 promoter-driven and NF-κB-responsive luciferase reporter activities. Furthermore, the TNF-α-induced degradation of the inhibitor of NF-κB α protein in the NF-κB signaling pathway was suppressed by ACA. Although ACA did not affect TNF receptor 1, TNF receptor-associated death domain, or receptor-interacting protein kinase 1 protein expression, it selectively downregulated TNF receptor-associated factor 2 (TRAF2) protein expression. The proteasome inhibitor MG-132, but not inhibitors of caspases or lysosomal degradation, attenuated ACA-induced reductions in TRAF2 expression. ACA also downregulated TRAF2 protein expression in human fibrosarcoma HT-1080 cells. This is the first study to demonstrate that ACA selectively downregulates TRAF2 protein expression. Full article
(This article belongs to the Special Issue Natural Products with Pharmaceutical Activities)
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29 pages, 3347 KiB  
Article
Integration of Global Lipidomics and Gonad Histological Analysis via Multivariate Chemometrics and Machine Learning: Identification of Potential Lipid Markers of Ovarian Development in the Blue Mussel (Mytilus edulis)
by Vincenzo Alessandro Laudicella, Stefano Carboni, Cinzia De Vittor, Phillip D. Whitfield, Mary K. Doherty and Adam D. Hughes
Lipidology 2025, 2(1), 5; https://doi.org/10.3390/lipidology2010005 - 10 Mar 2025
Viewed by 1371
Abstract
Background/Objectives: Gonad histological analysis (GHA) is the traditional method for assessing the gonad maturation status of blue mussels (Mytilus edulis). GHA has some operational disadvantages, such as limited processing outputs, subjectivity in the assessment of transitional stages of gonadal maturation and [...] Read more.
Background/Objectives: Gonad histological analysis (GHA) is the traditional method for assessing the gonad maturation status of blue mussels (Mytilus edulis). GHA has some operational disadvantages, such as limited processing outputs, subjectivity in the assessment of transitional stages of gonadal maturation and the need for experienced and trained operators. Lipids could become important indicators of gonadal maturation as they cover many essential functions during such processes in mussels. In this work, blue mussel ovary (BMO) ultrastructure is integrated with liquid chromatography coupled with mass spectrometry (LC-MS) lipidomics fingerprinting to identify suitable markers for ovarian maturation through the application of chemometrics and machine learning approaches. Methods: BMOs are classified here as ripe or non-ripe by means of GHA and the gamete volume fraction (GVF). Receiving operating characteristic (ROC) curves were used to classify the results of the different statistics according to their area under the curve (AUC), and the functional role of important lipids was assessed by lipid ontology enrichment (LiOn) analysis. Results: This approach allowed for the selection of a panel of 35 lipid molecules (AUC > 0.8) that can distinguish non-ripe from ripe BMOs. Ceramide phosphoethanolamine (CerPE) 40:2 was the molecule with the highest classification ability (AUC 0.905), whereas glycerophosphoserine (PS) was the class mostly changing between the two groups. LiOn analysis indicated significant differences in the functional roles of these lipids, highlighting enrichment terms associated with membrane lipids, lysosomes and highly unsaturated triglycerides (TGs) in non-ripe ovaries, whereas terms associated with storage lipids and low-saturated TG characterised ripe BMOs. Full article
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18 pages, 7059 KiB  
Article
Analysis of the Expression Patterns of piRNAs in Response to Microsporidian Invasion in Midgut of Workers (Apis cerana cerana)
by Yiqiong Zhang, Mengyi Wang, Wenhua Xu, He Zang, Tizhen Yan, Tao Wu, Kaifei Huang, Dafu Chen, Qingming Luo, Rui Guo and Jianfeng Qiu
Int. J. Mol. Sci. 2025, 26(6), 2402; https://doi.org/10.3390/ijms26062402 - 7 Mar 2025
Viewed by 700
Abstract
Piwi-interacting RNAs (piRNAs) play an essential part in transposon suppression, DNA methylation, and antiviral responses. The current understanding of the roles of piRNAs in honeybees is very limited. This study aims to analyze the expression pattern and regulatory role of piRNAs in the [...] Read more.
Piwi-interacting RNAs (piRNAs) play an essential part in transposon suppression, DNA methylation, and antiviral responses. The current understanding of the roles of piRNAs in honeybees is very limited. This study aims to analyze the expression pattern and regulatory role of piRNAs in the Asian honeybee (Apis cerana) responding to infection by Nosema ceranae, based on previously gained small RNA-seq data. Here, 450 and 422 piRNAs were respectively identified in the midgut tissues of Apis cerana cerana workers at 7 and 10 days post-inoculation (dpi) with N. ceranae, including 539 non-redundant ones. Additionally, one up-regulated (piR-ace-1216942) and one down-regulated (piR-ace-776728) piRNA were detected in the workers’ midgut at 7 dpi, targeting 381 mRNAs involved in 31 GO terms, such as metabolic processes, catalytic activity, and organelles, as well as 178 KEGG pathways, including lysosome, MAPK signaling pathway, and purine metabolism. A total of 35 up-regulated and 11 down-regulated piRNAs were screened from the workers’ midgut at 10 dpi, targeting 13,511 mRNAs engaged in 50 GO terms, such as biological regulation, transporter activity, and membrane, as well as 389 KEGG pathways, including the JAK-STAT signaling pathway, Hippo signaling pathway, and nitrogen metabolism. Further analysis indicated that 28 differentially expressed piRNAs (DEpiRNAs) in the midgut at 10 dpi could target 299 mRNAs annotated to three cellular immune pathways (lysosome, endocytosis, and phagosome), while 24 DEpiRNAs could target 205 mRNAs relevant to four humoral immune pathways (FoxO, JAK-STAT, NF-κB, and MAPK signaling pathway). Through Sanger sequencing and RT-qPCR, the expression of six randomly selected DEpiRNAs was verified. Moreover, the dual-luciferase reporter gene assay confirmed the binding relationships between piR-ace-446232 and CRT as well as between piR-ace-1008436 and EGFR. Our findings not only contribute to enrich our understanding of the role of piRNAs in honeybees but also provide a basis for exploring the host response to N. ceranae infection mediated by piRNAs. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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22 pages, 6244 KiB  
Article
Targeting Glucosylceramide Synthase: Innovative Drug Repurposing Strategies for Lysosomal Diseases
by Giorgia Canini, Elena Mazzinelli, Giuseppina Nocca, Wanda Lattanzi and Alessandro Arcovito
Int. J. Mol. Sci. 2025, 26(5), 2195; https://doi.org/10.3390/ijms26052195 - 28 Feb 2025
Cited by 1 | Viewed by 647
Abstract
Sphingolipidoses, a subgroup of lysosomal storage diseases (LSDs), are rare and debilitating disorders caused by defects in sphingolipid metabolism. Despite advancements in treatment, therapeutic options remain limited. Miglustat, a glucosylceramide synthase EC 2.4.1.80 (GCS) inhibitor, is one of the few available pharmacological treatments; [...] Read more.
Sphingolipidoses, a subgroup of lysosomal storage diseases (LSDs), are rare and debilitating disorders caused by defects in sphingolipid metabolism. Despite advancements in treatment, therapeutic options remain limited. Miglustat, a glucosylceramide synthase EC 2.4.1.80 (GCS) inhibitor, is one of the few available pharmacological treatments; however, it is associated with significant adverse effects that impact patients’ quality of life. Drug repurposing offers a promising strategy to identify new therapeutic agents from approved drugs, expanding treatment options for rare diseases with limited therapeutic alternatives. This study aims to identify potential alternative inhibitors of GCS through a drug-repurposing approach, using computational and experimental methods to assess their therapeutic potential for sphingolipidoses. A library of approved drugs was screened using advanced computational techniques, including molecular docking, molecular dynamics simulations, and metadynamics, to identify potential GCS inhibitors. Promising candidates were selected for further in vitro validation to evaluate their inhibitory activity and potential as therapeutic alternatives to Miglustat. Computational screening identified several potential GCS inhibitors, with Dapagliflozin emerging as the most promising candidate. Experimental validation confirmed its efficacy, revealing a complementary mechanism of action to Miglustat while potentially offering a more favorable side effect profile. This study underscores the utility of computational and experimental methodologies in drug repurposing for rare diseases. The identification of Dapagliflozin as a potential GCS inhibitor provides a foundation for further preclinical and clinical evaluation, supporting its potential application in the treatment of sphingolipidoses. Full article
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