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Search Results (613)

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Keywords = miR-124-3p modulation

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26 pages, 2438 KB  
Review
Exosomes in HPV-Associated Cancers: From Biomarkers to Engineered Therapeutics
by Muharrem Okan Cakir, Melis Selek, Betul Yilmaz, Mustafa Ozdogan and G. Hossein Ashrafi
Cancers 2025, 17(20), 3386; https://doi.org/10.3390/cancers17203386 - 21 Oct 2025
Viewed by 270
Abstract
Background/Objectives: Human papillomavirus (HPV) is the main causative agent of cervical cancer and contributes to a significant proportion of other anogenital and oropharyngeal malignancies. The need for better biomarkers and therapeutic approaches in HPV-associated cancers has drawn attention to exosomes, small extracellular vesicles [...] Read more.
Background/Objectives: Human papillomavirus (HPV) is the main causative agent of cervical cancer and contributes to a significant proportion of other anogenital and oropharyngeal malignancies. The need for better biomarkers and therapeutic approaches in HPV-associated cancers has drawn attention to exosomes, small extracellular vesicles known for their stability, biomolecule transport capabilities, and role in cell-to-cell communication. Methods: This review comprehensively evaluates recent literature on the diagnostic, prognostic, and therapeutic applications of small extracellular vesicles, particularly exosomes, in HPV-related cancers. It analyzes findings on exosomal nucleic acids, proteins, and long non-coding RNAs, as well as engineered exosome-based therapies. Results: Exosomal miRNAs (e.g., miR-204-5p, miR-99a-5p, miR-21), proteins (e.g., glycolytic enzymes, HSP90), and lncRNAs (e.g., HOTAIR, DLEU1) have emerged as promising biomarkers for disease detection and monitoring. Exosomal cargo actively participates in HPV-related tumor progression. For example, miRNAs such as miR-21 and miR-146a modulate immune cell polarization and inflammatory signaling, while lncRNAs like HOTAIR promote oncogenic transcriptional programs. Exosomal proteins including HSP90 and ANXA1 facilitate extracellular matrix remodeling and immune evasion, thereby influencing tumor growth and metastasis. In HPV-positive head and neck and cervical cancers, exosomal cargo reflects HPV status, tumor progression, and treatment response. Therapeutic studies demonstrate the utility of exosomes in vaccine delivery, immune modulation, and drug delivery systems, including the use of PROTACs. However, clinical translation faces barriers including isolation protocol standardization, biomarker validation, and scalable production. Conclusions: Exosomes hold great promise for integration into diagnostic and therapeutic workflows for HPV-related cancers. Future research should focus on resolving standardization issues, validating biomarkers in diverse cohorts, and optimizing engineered exosome platforms for targeted therapy. Full article
(This article belongs to the Collection The Development of Anti-cancer Agents)
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17 pages, 5499 KB  
Article
Functional miRNA-mRNA Regulatory Modules in the Head Kidney of Pelteobagrus vachellii in Response to Aeromonas veronii Infection
by Feiyang Li, Xiaoyun Wu, Yeyu Chen, Qiaolin Zou, Pengcheng Li, Mingjiang Song, Quan Gong, Ya Liu, Jiansheng Lai, Luyun Ni and Jun Wang
Fishes 2025, 10(10), 530; https://doi.org/10.3390/fishes10100530 - 18 Oct 2025
Viewed by 128
Abstract
Aeromonas veronii is a major pathogen threatening freshwater aquaculture, yet the molecular mechanisms of Pelteobagrus vachellii’s immune response to this infection remain unclear. This study integrated histopathology, mRNA-seq and small RNA-seq to investigate P. vachellii’s response to A. veronii at 48 [...] Read more.
Aeromonas veronii is a major pathogen threatening freshwater aquaculture, yet the molecular mechanisms of Pelteobagrus vachellii’s immune response to this infection remain unclear. This study integrated histopathology, mRNA-seq and small RNA-seq to investigate P. vachellii’s response to A. veronii at 48 h post-challenge. Histopathologically, infection induced gill epithelial detachment, hepatocyte swelling with cytoplasmic vacuolation, and melanomacrophage centers (MMCs) in the mid-kidney (histological assessment of the head kidney was not feasible due to sampling limitations associated with its small size). Transcriptomic analysis identified 1210 differentially expressed genes (DEGs) in the head kidney (819 downregulated, 391 upregulated), significantly enriched in 11 immune pathways (e.g., NF-κB, Th17 cell differentiation, Complement and coagulation cascades), with key immune genes (e.g., IL-1β, TCRα, CCL4) upregulated. Gene Set Enrichment Analysis (GSEA) revealed activation of the proteasome, ribosome and oxidative phosphorylation pathways, and suppression of the autophagy-animal, FoxO and AMPK pathways. Small RNA-seq identified 544 known and 958 novel miRNAs in the head kidney, with 42 downregulated and 36 upregulated differentially expressed miRNAs (DE miRNAs). The miRNA-mRNA network showed that DE miRNAs (e.g., miR-101-y/z, miR-132-z, miR-3167-y) negatively regulated immune-related target genes (IL-1R1, IRF4, IκBα) in core immune pathways. Collectively, this study clarifies the pathological and miRNA-mRNA regulatory modules of P. vachellii head kidney against A. veronii infection, providing valuable information that enables the further analyses of the defense mechanisms of P. vachellii against A. veronii infection. Full article
(This article belongs to the Special Issue Physiological Response Mechanisms of Aquatic Animals to Stress)
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17 pages, 2346 KB  
Article
Targeted Regulation of AhGRF3b by ahy-miR396 Modulates Leaf Growth and Cold Tolerance in Peanut
by Xin Zhang, Qimei Liu, Xinyu Liu, Haoyu Lin, Xiaoyu Zhang, Rui Zhang, Zhenbo Chen, Xiaoji Zhang, Yuexia Tian, Yunyun Xue, Huiqi Zhang, Na Li, Pingping Nie and Dongmei Bai
Plants 2025, 14(20), 3203; https://doi.org/10.3390/plants14203203 - 18 Oct 2025
Viewed by 209
Abstract
Peanut (Arachis hypogaea L.) is an important oil and cash crop, but its growth and productivity are severely constrained by low-temperature stress. Growth-regulating factors (GRFs) are plant-specific transcription factors involved in development and stress responses, yet their roles in peanut remain poorly [...] Read more.
Peanut (Arachis hypogaea L.) is an important oil and cash crop, but its growth and productivity are severely constrained by low-temperature stress. Growth-regulating factors (GRFs) are plant-specific transcription factors involved in development and stress responses, yet their roles in peanut remain poorly understood. In this study, we identified AhGRF3b as a direct target of ahy-miR396 using degradome sequencing, which demonstrated precise miRNA-mediated cleavage sites within the AhGRF3b transcript. Expression profiling confirmed that ahy-miR396 suppresses AhGRF3b via post-transcriptional cleavage rather than translational repression. Functional analyses showed that overexpression of AhGRF3b in Arabidopsis thaliana promoted leaf expansion by enhancing cell proliferation. Specifically, leaf length, width, and petiole length increased by 104%, 22%, and 28%, respectively (p < 0.05). Under cold stress (0 °C for 7 days), transgenic lines (OE-2 and OE-6) exhibited significantly better growth than Col-0, with fresh weight increased by 158% and 146%, respectively (p < 0.05). Effect size analysis further confirmed these differences (Cohen’s d = 11.6 for OE-2 vs. Col-0; d = 6.3 for OE-6 vs. Col-0). Protein–protein interaction assays, performed using the yeast two-hybrid (Y2H) system and 3D protein–protein docking models, further supported that AhGRF3b interacts with Catalase 1 (AhCAT1), vacuolar cation/proton exchanger 3 (AhCAX3), probable polyamine oxidase 4 (AhPAO4), and ACT domain-containing protein 11 (AhACR11), which are involved in reactive oxygen species (ROS) scavenging and ion homeostasis. These interactions were associated with enhanced CAT and PAO enzymatic activities, reduced ROS accumulation, and upregulation of stress-related genes under cold stress. These findings suggest that the ahy-miR396/AhGRF3b module plays a potential regulatory role in leaf morphogenesis and cold tolerance, providing valuable genetic resources for breeding cold-tolerant peanut varieties. Full article
(This article belongs to the Special Issue Abiotic Stress Responses in Plants—Second Edition)
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24 pages, 2943 KB  
Article
Serum miR-34a as Indicator of Impaired Fibrinolytic Capacity in Pediatric Thrombosis Through Inadequate Regulation of the ACE/PAI-1 Axis
by Iphigenia Gintoni, Kleoniki Baldouni, Athina Dettoraki, Aikaterini Michalopoulou, Ioanna Papathanasiou, Aspasia Tsezou, Dimitrios Vlachakis, Helen Pergantou, George P. Chrousos and Christos Yapijakis
Int. J. Mol. Sci. 2025, 26(20), 10110; https://doi.org/10.3390/ijms262010110 - 17 Oct 2025
Viewed by 134
Abstract
Pediatric thrombosis (PT) represents a rare condition that can manifest from neonatal life to adolescence, encompassing life-threatening complications. Its pathogenesis is attributed to immature hemostasis in conjunction with environmental and genetic factors, predominantly including those resulting in increased levels of plasminogen activator inhibitor [...] Read more.
Pediatric thrombosis (PT) represents a rare condition that can manifest from neonatal life to adolescence, encompassing life-threatening complications. Its pathogenesis is attributed to immature hemostasis in conjunction with environmental and genetic factors, predominantly including those resulting in increased levels of plasminogen activator inhibitor 1 (PAI-1), the principal inhibitor of fibrinolysis, which is subject to upstream regulation by angiotensin-converting enzyme (ACE). Although the implication of microRNAs (miRNAs), epigenetic modulators of gene expression, has been demonstrated in adult thrombosis, evidence is lacking in the pediatric setting. Here, we investigated the involvement of two miRNA regulators of PAI-1 (SERPINE1 gene) in PT, in relation to clinical and genetic parameters that induce PAI-1 fluctuations. Following bioinformatic target-prediction, miRNA expression was assessed by quantitative real-time PCR in serum-samples of 19 pediatric patients with thrombosis (1–18 months post-incident), and 19 healthy controls. Patients were genotyped for the SERPINE1-4G/5G and ACE-I/D polymorphisms by PCR-based assays. Genotypic and thrombosis-related clinical data were analyzed in relation to miRNA-expression. Two miRNAs (miR-145-5p, miR-34a-5p) were identified to target SERPINE1 mRNA, with miR-34a additionally targeting the mRNA of ACE. The expression of miR-34a was significantly decreased in patients compared to controls (p = 0.029), while no difference was observed in miR-145 expression. Within patients, miR-34a expression demonstrated a peak 1–3 months post-thrombosis and was diminished upon treatment completion (p = 0.031), followed by a slight long-term increase. MiR-34a levels differed significantly by thrombosis site (p = 0.019), while a significant synergistic interaction between site and onset type (provoked/unprovoked) was detected (p = 0.016). Finally, an epistatic modification was observed in cerebral cases, since double homozygosity (4G/4G + D/D) led to a miR-34 decrease, with D/D carriership reversing the 4G/4G-induced upregulation of miR-34a (p = 0.006). Our findings suggest that in pediatric thrombosis, downregulation of miR-34a is indicative of impaired fibrinolytic capacity, attributed to deficient regulation of the inhibitory ACE/PAI-1 axis. Full article
(This article belongs to the Collection Feature Papers Collection in Biochemistry)
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26 pages, 3716 KB  
Article
Ligusticum chuanxiong Hort. Targets hsa-miR-10a-5p to Potentially Induce Apoptosis and Modulate Lipid Metabolism in Glioblastoma: A Natural-Product-Based Therapeutic Strategy
by Xiao-Xuan Cai, Hua-Li Zuo, Jing Li, Hsi-Yuan Huang, Li-Ping Li, Jie Ni, Pei-Sen Wu, Xiao-Yuan Xu, Dan Zhang, Yue-Yang Xie, Hsien-Da Huang and Yang-Chi-Dung Lin
Pharmaceuticals 2025, 18(10), 1553; https://doi.org/10.3390/ph18101553 - 15 Oct 2025
Viewed by 260
Abstract
Background/Objectives: Glioblastoma (GBM), the most aggressive primary malignant brain tumor, has a dismal prognosis and limited treatment options. The dried rhizome of Ligusticum chuanxiong Hort. (Chuanxiong, CX) is a traditional Chinese medicinal herb frequently prescribed in formulas intended to invigorate blood circulation. CX [...] Read more.
Background/Objectives: Glioblastoma (GBM), the most aggressive primary malignant brain tumor, has a dismal prognosis and limited treatment options. The dried rhizome of Ligusticum chuanxiong Hort. (Chuanxiong, CX) is a traditional Chinese medicinal herb frequently prescribed in formulas intended to invigorate blood circulation. CX also exhibits anti-glioma activity, but its molecular mechanisms remain incompletely understood. Methods: In this study, we combined transcriptomics and Raman spectroscopy to investigate the effects of reconstituted CX-dispensing granules (hereafter referred to as CXG solution) on U87MG cells, suggesting their dual role in promoting cell death and modulating collagen deposition and lipid metabolism. Results: Mechanistically, we demonstrated that the CXG solution downregulates hsa-miR-10a-5p, which directly targets BCL2L11, known to induce pro-apoptotic effects, as validated by qPCR and dual-luciferase reporter assays. Furthermore, the CXG solution and hsa-miR-10a-5p suppress lipid metabolism through a coherent feed-forward loop via targeting transcription factors SREBF1 and E2F1. An electrophoretic mobility shift assay (EMSA) confirmed E2F1 binds to the hsa-miR-29a promoter, leading to the synergistic repression of hsa-miR-29a-3p by SREBF1 and E2F1. Network pharmacology analysis combined with molecular docking suggested that the ferulic acid and adenosine in CX potentially modulate EGFR-the E2F1-hsa-miR-10a-5p axis. Conclusions: These findings elucidate CX’s multi-target anti-GBM mechanisms and propose a novel therapeutic strategy combining metabolic intervention with miRNA-targeted therapy, providing novel insights into feed-forward loop regulation in miRNA networks. Full article
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23 pages, 3542 KB  
Article
Modulation of Nuclear Factor Kappa B Signaling and microRNA Profiles by Adalimumab in LPS-Stimulated Keratinocytes
by Aleksandra Plata-Babula, Wojciech Kulej, Paweł Ordon, Julia Gajdeczka, Martyna Stefaniak, Artur Chwalba, Piotr Gościniewicz, Tomasz Kulpok and Beniamin Oskar Grabarek
Int. J. Mol. Sci. 2025, 26(20), 10035; https://doi.org/10.3390/ijms262010035 - 15 Oct 2025
Viewed by 156
Abstract
Psoriasis is a chronic inflammatory skin disease characterized by keratinocyte hyperactivation and dysregulated cytokine signaling, with nuclear factor kappa B (NF-κB), a master transcription factor that regulates immune and inflammatory gene expression, playing a central role. Adalimumab, a monoclonal antibody that inhibits tumor [...] Read more.
Psoriasis is a chronic inflammatory skin disease characterized by keratinocyte hyperactivation and dysregulated cytokine signaling, with nuclear factor kappa B (NF-κB), a master transcription factor that regulates immune and inflammatory gene expression, playing a central role. Adalimumab, a monoclonal antibody that inhibits tumor necrosis factor alpha (TNF-α), is widely used in psoriasis therapy, yet its molecular effects on NF-κB-associated genes and microRNAs (miRNAs) in keratinocytes remain insufficiently defined. In this study, immortalized human keratinocytes (HaCaT cells) were exposed to lipopolysaccharide (LPS) to induce inflammatory stress and treated with adalimumab for 2, 8, and 24 h. Transcriptome-wide profiling was performed using messenger RNA (mRNA) and miRNA microarrays, followed by validation with reverse transcription quantitative polymerase chain reaction (RT-qPCR) and enzyme-linked immunosorbent assay (ELISA). Bioinformatic analyses included prediction of miRNA–mRNA interactions, construction of protein–protein interaction (PPI) networks, and gene ontology (GO) enrichment. Adalimumab reversed LPS-induced upregulation of NF-κB-associated genes, including inhibitor of nuclear factor kappa-B kinase subunit beta (IKBKB), interleukin-1 receptor-associated kinase 1 (IRAK1), TNF receptor-associated factor 2 (TRAF2), mitogen-activated protein kinase kinase kinase 7 (MAP3K7), and TNF alpha-induced protein 3 (TNFAIP3), with concordant changes observed at the protein level. Several regulatory miRNAs, notably miR-1297, miR-30a, miR-95-5p, miR-125b, and miR-4329, showed reciprocal expression changes consistent with anti-inflammatory activity. STRING analysis identified IKBKB as a central hub in the PPI network, while GO enrichment highlighted immune regulation, apoptosis, and NF-κB signaling. These findings demonstrate that adalimumab modulates NF-κB activity in keratinocytes through coordinated regulation of gene, protein, and miRNA expression, providing mechanistic insight into TNF-α blockade in psoriasis. Full article
(This article belongs to the Collection Advances in Cell and Molecular Biology)
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20 pages, 1631 KB  
Article
Effects of a Bacillus licheniformis Fermentation Extract and Monensin on the Rumen and Hindgut Microbiota Composition of Lactating Dairy Cows
by Phoebe Hartoonian, Lucille C. Jonas, Shedrack Omale, Sydney Rigert, Catherine Bradley, Erin Horst, Donald Beitz, Stephan Schmitz-Esser and Ranga Appuhamy
Animals 2025, 15(20), 2980; https://doi.org/10.3390/ani15202980 - 15 Oct 2025
Viewed by 320
Abstract
This research reports ruminal and fecal microbiota composition of lactating dairy cows enrolled in a study aimed at investigating the effects of a fermentation extract derived from Bacillus licheniformis (BLFE), monensin (Rumensin®; R), and their interactions on feed efficiency (FE, FE [...] Read more.
This research reports ruminal and fecal microbiota composition of lactating dairy cows enrolled in a study aimed at investigating the effects of a fermentation extract derived from Bacillus licheniformis (BLFE), monensin (Rumensin®; R), and their interactions on feed efficiency (FE, FE = milk yield/DMI). In a completely randomized design, 48 Holstein cows at 108 ± 35 days in milk were matched for parity and assigned to monensin (0 or 17.6 g/kg of DM) and BLFE (0 or 166 mg/kg of DM) in a 2 × 2 factorial arrangement. Treatments were fed daily for 63 d, including a 21 d adaptation period followed by a 42 d measurement period (P2). On d 38 and d 39 of P2, rumen-fluid (RF) and fecal samples were collected. DNA from RF and feces was sequenced using 16S rRNA gene-amplicon sequencing on an Illumina MiSeq platform. Fecal and RF volatile fatty acid (VFA) concentrations were analyzed, and propionate/acetate (P: A) was determined. The BLFE increased milk yield (3.3 kg/d) and FE (1.20 to 1.28), when fed alone rather than with monensin, while monensin increased energy-corrected milk yield (2.5 kg/d, p < 0.05), regardless of the BLFE in the diet. The BLFE tended to increase ruminal Firmicutes/Bacteroidetes (F: B) when fed alone, while alpha and beta diversities remained unmodified. The BLFE increased the abundances of Bifidobacterium (p = 0.02) and Erysipelotrichaceae_UCG-002 (p = 0.01) in RF, whereas monensin increased and decreased the abundances of Oscillospirales_ge (p = 0.02) and an unclassified Clostridia genus (p = 0.03), respectively. The monensin-suppressed Clostridia were negatively associated with ruminal P: A (r = −0.66; p < 0.01) and feed efficiency (r = −0.30; p = 0.04). The BLFE and monensin interactively affected several fecal genera (p < 0.05), but they had negligible or weak correlations with fecal P: A and FE. Overall, the results showed the ability of dietary supplementations of monensin and BLFE to increase milk production performance and FE by modulating ruminal rather than lower-gut microbiota composition, this is predominantly attributed to the ratio between the Firmicutes and Bacteroidetes abundances in lactating dairy cows. Full article
(This article belongs to the Section Animal Nutrition)
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22 pages, 2744 KB  
Review
miR-106b-5p as a Central Regulator of Cancer Progression and Chemotherapy-Induced Cardiotoxicity: From Molecular Mechanisms to Clinical Translation
by Maria del Carmen Asensio Lopez, Miriam Ruiz Ballester, Francisco Jose Bastida Nicolas, Fernando Soler Pardo, Jose Luis Alonso-Romero, Cesar Caro-Martinez, Domingo Pascual Figal and Antonio Lax
Int. J. Mol. Sci. 2025, 26(20), 10002; https://doi.org/10.3390/ijms262010002 - 14 Oct 2025
Viewed by 245
Abstract
MicroRNAs (miRNAs) are critical regulators of gene expression in cancer biology and cardiovascular disease. miR-106b-5p, a member of the miR-106b-25 cluster, has been widely studied for its oncogenic activity in various malignancies. However, its role as a direct molecular driver of anthracycline-induced cardiotoxicity [...] Read more.
MicroRNAs (miRNAs) are critical regulators of gene expression in cancer biology and cardiovascular disease. miR-106b-5p, a member of the miR-106b-25 cluster, has been widely studied for its oncogenic activity in various malignancies. However, its role as a direct molecular driver of anthracycline-induced cardiotoxicity has only recently been uncovered. This finding highlights new therapeutic possibilities at the intersection of oncology and cardiovascular medicine. This review outlines the dual role of miR-106b-5p as a key modulator in both tumor progression and chemotherapy-induced cardiac dysfunction. miR-106b-5p is upregulated in numerous cancers—including breast, prostate, lung, gastric, colorectal, hepatocellular, and esophageal—and promotes tumorigenesis via suppression of tumor suppressors such as PTEN, BTG3, p21, and SMAD7, leading to activation of oncogenic pathways like PI3K/AKT and TGF-β. Importantly, we present the first evidence that miR-106b-5p is significantly upregulated in the myocardium in response to doxorubicin treatment, where it drives left ventricular dysfunction by targeting PR55α, a key regulator of PP2A activity. This pathway results in cytoplasmic HDAC4 accumulation, aberrant activation of the YY1 transcription factor, and upregulation of sST2, a biomarker linked to adverse cardiac remodeling and poor prognosis. In response, we developed AM106, a novel locked nucleic acid antagomir that silences miR-106 b-5p. Preclinical studies demonstrate that AM106 restores PR55α/PP2A activity, reduces sST2 expression, and prevents structural and functional cardiac damage without compromising anti-tumor efficacy. In parallel, artificial intelligence (AI) tools could be leveraged in the future—based on established AI applications in miRNA cancer research—to accelerate the identification of miR-106b-5p-related biomarkers and guide personalized therapy selection. Our findings position miR-106b-5p as a previously unrecognized molecular bridge between cancer and doxorubicin-induced cardiotoxicity. The development of the AM106 antagomir represents a promising approach with potential clinical applicability in cardio-oncology, offering dual benefits: tumor control and cardioprotection. Coupling this innovation with AI-driven analysis of patient data may enable precision risk stratification, early intervention, and improved outcomes. miR-106b-5p thus emerges as a central therapeutic target and biomarker candidate for transforming the clinical management of cancer patients at risk for heart failure. Full article
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18 pages, 2003 KB  
Article
MicroRNA-125b-5p Drives MMP-2 Expression via Activation of RAGE-38MAPK-p65/p50NF-κB Axis: A Novel Mechanism in Human Lung Cancer Cells
by Yusuf Saleem Khan, Aisha Farhana, Mohammed Kuddus, Syed Monowar Alam Shahid, Abdullah Alsrhani, Abuzar Abdulwahab Osman, Ghorashy E. Y. Mohammed, Muhammad Ikram Ullah and Zafar Rasheed
Int. J. Mol. Sci. 2025, 26(20), 9983; https://doi.org/10.3390/ijms26209983 - 14 Oct 2025
Viewed by 210
Abstract
Dysregulated microRNA-mediated control of matrix metalloproteinase-2 (MMP-2) plays a pivotal role in lung cancer (LC) progression, though the inflammatory signaling mechanisms governing its regulation remain poorly understood. This study reveals how S100A4-activated RAGE signaling modulates MMP-2 expression through microRNA-125b-5p (miR-125b-5p) in human LC [...] Read more.
Dysregulated microRNA-mediated control of matrix metalloproteinase-2 (MMP-2) plays a pivotal role in lung cancer (LC) progression, though the inflammatory signaling mechanisms governing its regulation remain poorly understood. This study reveals how S100A4-activated RAGE signaling modulates MMP-2 expression through microRNA-125b-5p (miR-125b-5p) in human LC cells. Potential miRNA target genes were computationally predicted using TargetScan algorithms. Functional interaction between miR-125b-5p and MMP-2 3′UTR was experimentally validated through dual-luciferase reporter assays incorporating full-length MMP-2 3′UTR sequence. Further validation was performed through transfection with miRNA inhibitors or mimics. To delineate the underlying mechanisms, key pathways were inhibited using small-molecule antagonists targeting p38-MAPK and NF-κB. Our analysis identified a conserved miR-125b-5p binding site in the MMP-2 3′UTR. In A549 cells, S100A4 induced reciprocal regulation, simultaneously upregulating MMP-2 and downregulating miR-125b-5p, with luciferase assays confirming direct targeting. Pre-miR-125b-5p transfection effectively reduced endogenous MMP-2 levels, while p38-MAPK/NF-κB activation mediated this regulation by suppressing miR-125b-5p consequently elevating MMP-2 expression. These findings were further validated in another human LC cell, SHP-77. These findings provide the first evidence demonstrating that miR-125b-5p directly regulates MMP-2 in LC, establishing S100A4-RAGE⟶p38/NF-κB⟶miR-125b-5p⟶MMP-2 axis as a novel regulatory pathway. The results position miR-125b-5p as a dual-action biomarker and therapeutic target against MMP-2-driven LC metastasis, offering new insights into critical inflammation-to-cancer connections. Full article
(This article belongs to the Special Issue MicroRNAs as Biomarkers and Therapeutic Targets in Human Diseases)
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16 pages, 1716 KB  
Review
The Impact of Non-Coding RNA on Inflammation and Airway Remodeling in Asthma Related to Obesity: State-of-the-Art and Therapeutic Perspectives
by Maria Kachel, Wojciech Langwiński and Aleksandra Szczepankiewicz
J. Clin. Med. 2025, 14(20), 7161; https://doi.org/10.3390/jcm14207161 - 11 Oct 2025
Viewed by 260
Abstract
Asthma is a chronic respiratory disease affecting over 262 million people worldwide, with obesity-associated asthma emerging as a distinct endotype of increasing prevalence characterized by metabolic inflammation and airway remodeling. Unlike allergic asthma, this phenotype is driven by chronic low-grade inflammation, originating from [...] Read more.
Asthma is a chronic respiratory disease affecting over 262 million people worldwide, with obesity-associated asthma emerging as a distinct endotype of increasing prevalence characterized by metabolic inflammation and airway remodeling. Unlike allergic asthma, this phenotype is driven by chronic low-grade inflammation, originating from hypertrophic and hypoxic adipose tissue. This dysregulated state leads to the activation of pro-inflammatory pathways and the secretion of cytokines, contributing to airway dysfunction and remodeling. Recent evidence highlights non-coding RNAs (ncRNAs) as key regulators of these processes. MicroRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) influence inflammation and remodeling by modulating immune cell polarization, cytokine secretion, extracellular matrix composition, and airway smooth muscle cell (ASMC) proliferation. Notably, H19, MEG3, GAS5, miR-26a-1-3p, and miR-376a-3p have been implicated in both asthma and obesity, suggesting their role in linking metabolic dysfunction with airway pathology. Moreover, ncRNAs regulate Treg/Th17 balance, fibroblast activation, and autophagy-related pathways, further influencing airway remodeling. Our in silico analysis highlighted the IGF1R signaling pathway as a key enriched mechanism, linking selected ncRNAs with metabolic dysregulation and inflammation in obesity-related asthma. This paper reviews how ncRNAs regulate inflammation and airway remodeling in obesity-associated asthma, emphasizing their potential molecular links between metabolic dysfunction and airway pathology. Full article
(This article belongs to the Special Issue New Clinical Advances in Chronic Asthma)
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23 pages, 13395 KB  
Article
Identification and Validation of Iron Metabolism-Related Biomarkers in Endometriosis: A Mendelian Randomization and Single-Cell Transcriptomics Study
by Juan Du, Zili Lv and Xiaohong Luo
Curr. Issues Mol. Biol. 2025, 47(10), 831; https://doi.org/10.3390/cimb47100831 - 9 Oct 2025
Viewed by 369
Abstract
Studies have shown that the iron concentration in the peritoneal fluid of women is associated with the severity of endometriosis. Therefore, investigation of iron metabolism-related genes (IM-RGs) in endometriosis holds significant implications for both prevention and therapeutic strategies in affected patients. Differentially expressed [...] Read more.
Studies have shown that the iron concentration in the peritoneal fluid of women is associated with the severity of endometriosis. Therefore, investigation of iron metabolism-related genes (IM-RGs) in endometriosis holds significant implications for both prevention and therapeutic strategies in affected patients. Differentially expressed IM-RGs (DEIM-RGs) were identified by intersecting IM-RGs with differentially expressed genes derived from GSE86534. Mendelian randomization analysis was employed to determine DEIM-RGs causally associated with endometriosis, with subsequent verification through sensitivity analyses and the Steiger test. Biomarkers associated with IM-RGs in endometriosis were validated using expression data from GSE86534 and GSE105764. Functional annotation, regulatory network construction, and immunological profiling were conducted for these biomarkers. Single-cell RNA sequencing (scRNA-seq) (GSE213216) was utilized to identify distinctively expressed cellular subsets between endometriosis and controls. Experimental validation of biomarker expression was performed via reverse transcription–quantitative polymerase chain reaction (RT-qPCR). BMP6 and SLC48A1, biomarkers indicative of cellular BMP response, were influenced by a medicus variant mutation that inactivated PINK1 in complex I, concurrently enriched by both biomarkers. The lncRNA NEAT1 regulated BMP6 through hsa-mir-22-3p and hsa-mir-124-3p, while SLC48A1 was modulated by hsa-mir-423-5p, hsa-mir-19a-3p, and hsa-mir-19b-3p. Immune profiling revealed a negative correlation between BMP6 and monocytes, whereas SLC48A1 displayed a positive correlation with activated natural killer cells. scRNA-seq analysis identified macrophages and stromal stem cells as pivotal cellular components in endometriosis, exhibiting altered self-communication networks. RT-qPCR confirmed elevated expression of BMP6 and SLC48A1 in endometriosis samples relative to controls. Both BMP6 and SLC48A1 were consistently overexpressed in endometriosis, reinforcing their potential as biomarkers. Moreover, macrophages and stromal stem cells were delineated as key contributors. These findings provide novel insights into therapeutic and preventive approaches for patients with endometriosis. Full article
(This article belongs to the Section Bioinformatics and Systems Biology)
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20 pages, 11715 KB  
Article
Hypercapnia as a Double-Edged Modulator of Innate Immunity and Alveolar Epithelial Repair: A PRISMA-ScR Scoping Review
by Elber Osorio-Rodríguez, José Correa-Guerrero, Dairo Rodelo-Barrios, María Bonilla-Llanos, Carlos Rebolledo-Maldonado, Jhonny Patiño-Patiño, Jesús Viera-Torres, Mariana Arias-Gómez, María Gracia-Ordoñez, Diego González-Betancur, Yassid Nuñez-Beyeh, Gustavo Solano-Sopó and Carmelo Dueñas-Castell
Int. J. Mol. Sci. 2025, 26(19), 9622; https://doi.org/10.3390/ijms26199622 - 2 Oct 2025
Viewed by 444
Abstract
Lung-protective ventilation and other experimental conditions raise arterial carbon dioxide tension (PaCO2) and alter pH. Short-term benefits are reported in non-infectious settings, whereas infection and/or prolonged exposure are typically harmful. This scoping review systematically maps immune-mediated effects of hypercapnia on innate [...] Read more.
Lung-protective ventilation and other experimental conditions raise arterial carbon dioxide tension (PaCO2) and alter pH. Short-term benefits are reported in non-infectious settings, whereas infection and/or prolonged exposure are typically harmful. This scoping review systematically maps immune-mediated effects of hypercapnia on innate immunity and alveolar epithelial repair. Scoping review per Levac et al. and PRISMA Extension for Scoping Reviews (Open Science Framework protocol: 10.17605/OSF.IO/WV85T; post hoc). We searched original preclinical studies (in vivo/in vitro) in PubMed, Web of Science, ScienceDirect, Cochrane Reviews, and SciELO (2008–2023). PaCO2 (mmHg) was prioritized; %Fraction of inspired Carbon Dioxide (%FiCO2) was recorded when PaCO2 was unavailable; pH was classified as buffered/unbuffered. Data were organized by context, PaCO2, and exposure duration; synthesis used heat maps (0–120 h) and a narrative description for >120 h. Mechanistic axes extracted the following: NF-κB (canonical/non-canonical), Bcl-2/Bcl-xL–Beclin-1/autophagy, AMPK/PKA/CaMKKβ/ERK1/2 and ENaC/Na,K-ATPase trafficking, Wnt/β-catenin in AT2 cells, and miR-183/IDH2/ATP. Thirty-five studies met the inclusion criteria. In non-infectious models, a “protective window” emerged, with moderate PaCO2 and brief exposure (65–95 mmHg; ≤4–6 h), featuring NF-κB attenuation and preserved epithelial ion transport. In infectious models and/or with prolonged exposure or higher PaCO2, harmful signals predominated: reduced phagocytosis/autophagy (Bcl-2/Bcl-xL–Beclin-1 axis), AMPK/PKA/ERK1/2-mediated internalization of ENaC/Na,K-ATPase, depressed β-catenin signaling in AT2 cells, impaired alveolar fluid clearance, and increased bacterial burden. Chronic exposures (>120 h) reinforced injury. Hypercapnia is a context-, dose-, time-, and pH-dependent double-edged modulator. The safe window is narrow; standardized, parallel reporting of PaCO2 and pH—with explicit comparisons of buffered vs. unbuffered hypercapnia—is essential to guide clinical translation. Full article
(This article belongs to the Special Issue Cellular and Molecular Mechanisms of Acute Lung Injury)
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18 pages, 1688 KB  
Article
Thymoquinone Upregulates microRNA-199a-3p and Downregulates COX-2 Expression and PGE2 Production via Deactivation of p38/ERK/JNK-MAPKs and p65/p50-NF-κB Signaling in Human Lung Cancer Cells
by Yusuf Saleem Khan, Aisha Farhana, Ghorashy E. Y. Mohammed, Abuzar Abdulwahab Osman, Abdullah Alsrhani, Syed M. A. Shahid, Mohammed Kuddus and Zafar Rasheed
Biology 2025, 14(10), 1348; https://doi.org/10.3390/biology14101348 - 2 Oct 2025
Cited by 1 | Viewed by 426
Abstract
Chronic inflammation driven by Cyclooxygenase-2 (COX-2) overexpression plays a key role in lung cancer (LC) progression, making it a critical therapeutic target. This study explores thymoquinone (TQ), a potent bioactive phytochemical derived from Nigella sativa, known for its anti-inflammatory and anti-cancer effects, focusing [...] Read more.
Chronic inflammation driven by Cyclooxygenase-2 (COX-2) overexpression plays a key role in lung cancer (LC) progression, making it a critical therapeutic target. This study explores thymoquinone (TQ), a potent bioactive phytochemical derived from Nigella sativa, known for its anti-inflammatory and anti-cancer effects, focusing on its ability to suppress lipopolysaccharide (LPS)-induced COX-2 expression via microRNA hsa-miR-199a-3p modulation in LC cells. Using A549 and SHP-77 LC cells, we tested the effect of TQ under LPS stimulation and miRNA inhibition. Advanced techniques like TaqMan qPCR, luciferase reporter gene constructs, and anti-miRNA transfection confirmed that miR-199a-3p directly silences COX-2. Western blot and ELISA assays revealed that TQ dramatically reduces COX-2 protein and PGE2 levels by boosting miRNA-199a-3p. Importantly, TQ also blocked MAPK (p38, JNK, ERK) and NF-κB activation, even when miR-199a-3p was suppressed, proving its multi-targeted action beyond miRNA regulation. These findings reveal a novel anti-inflammatory mechanism, where TQ curbs COX-2-driven inflammation by enhancing miR-199a-3p, simultaneously shutting down pro-cancer MAPK/NF-κB signaling pathways. Given the strong link between chronic inflammation and LC aggressiveness, this study positions TQ as a promising therapeutic candidate, especially for inflammation-mediated lung cancer progression. Its dual ability to modulate miRNA and key signaling cascades makes it a compelling option for future LC treatment strategies. Full article
(This article belongs to the Special Issue Plant Natural Products: Mechanisms of Action for Promoting Health)
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15 pages, 1767 KB  
Article
The Imatinib–miR-335-5p–ARHGAP18 Axis Attenuates PDGF-Driven Pathological Responses in Pulmonary Artery Smooth Muscle Cells
by Yunyeong Lee and Hara Kang
Int. J. Mol. Sci. 2025, 26(19), 9368; https://doi.org/10.3390/ijms26199368 - 25 Sep 2025
Viewed by 374
Abstract
The proliferation and migration of pulmonary artery smooth muscle cells (PASMCs) are key pathological features of vascular remodeling during pulmonary hypertension. Platelet-derived growth factor (PDGF) signaling is a major contributor to these processes. Given the importance of microRNA (miRNA) regulation in the PDGF [...] Read more.
The proliferation and migration of pulmonary artery smooth muscle cells (PASMCs) are key pathological features of vascular remodeling during pulmonary hypertension. Platelet-derived growth factor (PDGF) signaling is a major contributor to these processes. Given the importance of microRNA (miRNA) regulation in the PDGF signaling pathway in PASMCs, we hypothesized that imatinib, a tyrosine kinase inhibitor, modulates the expression levels of miRNAs responsive to PDGF signaling to ameliorate the PDGF signaling-induced PASMC phenotype. In this study, we investigated the role of miR-335-5p in PDGF signaling-induced PASMC proliferation and migration, as well as the involvement of imatinib in the regulatory network of miR-335-5p. miR-335-5p was identified as a critical negative regulator of PDGF signaling. Functional assays revealed that miR-335-5p significantly inhibits PASMC proliferation and migration. Through target prediction and validation, Rho GTPase Activating Protein 18 (ARHGAP18) was identified as a novel direct target of miR-335-5p. In addition, ARHGAP18 was found to play an essential role in regulating PASMC proliferation and migration. Although miR-335-5p was downregulated upon PDGF-BB stimulation, its expression was restored by imatinib. These findings highlight the important role of the imatinib–miR-335-5p–ARHGAP18 axis as a potential therapeutic target for pathological vascular remodeling. Full article
(This article belongs to the Section Molecular Biology)
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24 pages, 3066 KB  
Article
miR-25-3p Modulates Tumor Aggressiveness and Ferroptosis Escape in T24 Bladder Cancer Cells In Vitro
by Andresa Hiromi Sakai, Érica Romão Pereira, Anna Gabriele Prado dos Santos, Débora Hipólito Quadreli, Luan Vitor Alves de Lima, Diego Luis Ribeiro, Samira Rahimirad, Carolina Mathias, Monyse de Nóbrega, Mário Sérgio Mantovani, Glaura Scantamburlo Alves Fernandes, Ilce Mara de Syllos Cólus and Juliana Mara Serpeloni
Pharmaceuticals 2025, 18(9), 1382; https://doi.org/10.3390/ph18091382 - 16 Sep 2025
Viewed by 609
Abstract
Background/Objectives: Urothelial bladder carcinoma (UBC) is one of the most prevalent malignancies worldwide, and efforts have intensified to identify molecular markers that improve the prognosis and reduce treatment costs. Among the regulators of tumor behavior, microRNAs (miRNAs) have emerged as promising biomarkers [...] Read more.
Background/Objectives: Urothelial bladder carcinoma (UBC) is one of the most prevalent malignancies worldwide, and efforts have intensified to identify molecular markers that improve the prognosis and reduce treatment costs. Among the regulators of tumor behavior, microRNAs (miRNAs) have emerged as promising biomarkers for cancer diagnoses and treatment. The modulation of miR-25-3p has been associated with pancreatic, colorectal, and lung cancers; its role in UBC remains poorly explored. In this study, we investigated the effects of miR-25-3p modulation in a high-grade and muscle-invasive bladder cancer (MIBC) cell line (T24), using in vitro functional assays and bioinformatics approaches. Results: Bioinformatics analyses using TCGA-BLCA datasets revealed that miR-25-3p is upregulated in tumor tissues compared to non-tumor tissues, prompting an investigation into its molecular targets and related pathways. The transfection of T24 cells with an miR-25-3p mimic and inhibitor led to respective overexpression (11.16-fold) and downregulation (-2.82-fold) compared to the negative control. Functionally, miR-25-3p overexpression increased cell proliferation, viability, and migration, while its inhibition decreased the cell migration capacity. A gene expression analysis revealed that miR-25-3p overexpression resulted in the downregulation of TP53, AIFM1, NFE2L2, TFRC, ACSL4, SLC7A11, and SLC3A2, whereas MMP9, MMP11, and GPX4 were upregulated, suggesting a role in both migration and ferroptosis regulation. In the inhibitor group, increased SLC3A2 and decreased MMP11 expression further supported this connection. Our results using an in vitro model for MIBC with the transfection of T24 cells suggest that miR-25-3p influences key pathways involved in oxidative stress and cell death, promoting a more aggressive tumor phenotype. Conclusions: The modulation of miR-25-3p impacts the behavior of T24 bladder cancer cells and may indicate its role in disease progression. Our results underscore the potential of miR-25-3p as a prognostic biomarker and support further studies considering its therapeutic relevance in managing high-grade and muscle-invasive bladder cancer. Full article
(This article belongs to the Special Issue Therapeutic Applications of Micro-RNA in Cancer Management)
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