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Search Results (576)

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14 pages, 3998 KB  
Article
Dysregulation of microRNAs in the Brains of Mice Infected with Powassan Virus
by Amany Elsharkawy, Komal Arora, Hamid Reza Jahantigh and Mukesh Kumar
Viruses 2025, 17(10), 1288; https://doi.org/10.3390/v17101288 - 23 Sep 2025
Viewed by 186
Abstract
microRNAs (miRNAs) are known to play critical roles in the regulation of gene expression during neurodegenerative diseases and neurotropic viral infections. However, their specific contribution to the pathogenesis of Powassan virus (POWV) infection in the brain remains poorly understood. Understanding miRNA dynamics in [...] Read more.
microRNAs (miRNAs) are known to play critical roles in the regulation of gene expression during neurodegenerative diseases and neurotropic viral infections. However, their specific contribution to the pathogenesis of Powassan virus (POWV) infection in the brain remains poorly understood. Understanding miRNA dynamics in the brain during POWV infection may reveal novel insights into viral neuropathogenesis and host antiviral responses. Therefore, in the present study, we analyzed miRNA expression profiles in the mouse brain at different time points following a peripheral POWV infection. A total of 599 miRNAs were examined at day 3, 6, and 9 post-infection. Infection with POWV resulted in the modulation of several miRNAs in the brain at all time points. There was a progressive increase in the number of dysregulated miRNAs over the course of infection. This correlated with POWV dissemination into the brain with a progressive increase in viral RNA levels that peaked at day 9 post-infection. There was an early upregulation of miR-1983, miR-19a, and miR-216b that persisted until day 9 post-infection. POWV infection also resulted in the downregulation of miR-500 at all examined time points. Using IPA, we determined the significant canonical pathways affected by miRNA dysregulation. POWV infection modulated the activation of the thyroid hormone receptor and retinoid X receptor (TR/RXR) and the regulation of the phosphatase and tensin homolog (PTEN). Additionally, macrophage classical activation and growth arrest and DNA damage-inducible 45 (GADD45) signaling were activated as early as day 3 post-infection and persisted until day 9 post-infection. Furthermore, our analysis revealed the activation of cell death pathways such as necrosis and apoptosis and the inhibition of cell cycle progression, as well as leukopoiesis. To our knowledge, this is the first study to evaluate the modulation of miRNAs in the brain following POWV infection. Full article
(This article belongs to the Special Issue Tick-Borne Viruses 2026)
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12 pages, 1507 KB  
Article
Identification of Riboflavin Metabolism Pathway in HepG2 Cells Expressing Genotype IV Swine Hepatitis E Virus ORF3 Protein
by Jing Tu, Shengping Wu, Lingjie Wang, Chi Meng, Gengxu Zhou, Jianhua Guo, Jixiang Li, Liting Cao, Zhenhui Song and Hanwei Jiao
Vet. Sci. 2025, 12(9), 912; https://doi.org/10.3390/vetsci12090912 - 19 Sep 2025
Viewed by 256
Abstract
(1) Background: Hepatitis E (HE) is a novel zoonotic disease caused by hepatitis E virus (HEV). In particular, swine hepatitis E virus (SHEV) genotype IV is one of the main genotypes that infect humans. Open reading frame 3 (ORF3) is an important virulence [...] Read more.
(1) Background: Hepatitis E (HE) is a novel zoonotic disease caused by hepatitis E virus (HEV). In particular, swine hepatitis E virus (SHEV) genotype IV is one of the main genotypes that infect humans. Open reading frame 3 (ORF3) is an important virulence protein of SHEV, which is involved in virus assembly, release, and regulation of host cell signaling pathways. Circular RNAs (circRNAs), as a type of competitive endogenous RNA (ceRNA), have a closed-loop structure and are special non-coding RNA molecules. They participates in the regulation of multiple biological processes by adsorbing microRNAs (miRNAs). Riboflavin, also known as vitamin B2, is a component of the coenzyme of flavoenzymes in the body. When there is a deficiency of riboflavin, it will affect the biological oxidation process of the host, leading to metabolic disorders. In addition, riboflavin can also affect the synthesis, transportation and decomposition of lipids in the body. It mainly maintains the normal transportation process of fat in the liver. Therefore, the deficiency of riboflavin will lead to the disorder of lipid metabolism in the body. Thus, viral hepatitis is closely related to riboflavin metabolism. However, there are very few reports on SHEV ORF3 affecting the riboflavin metabolism of target cells and thereby influencing viral infection. Therefore, this study investigates this highly significant scientific issue. (2) Methods: In the previous research of our group, adenovirus was used to mediate the overexpression of SHEV ORF3 genotype IV in HepG2 cells. Total RNA was extracted for high-throughput sequencing of circRNAs and transcriptome. KEGG functional enrichment analysis was performed on the data to identify the differentially expressed circRNAs and miRNAs after SHEV infection, and the relevant circRNA-miRNA network in the riboflavin metabolism pathway in HepG2 cells was found. (3) Results: We identified 4 circRNAs in the riboflavin metabolism pathway of HepG2 cells expressing the ORF3 protein of SHEV genotype IV and successfully found 26 relevant circRNA-miRNA networks. (4) Conclusion: We successfully screened and identified circRNAs related to riboflavin metabolism, further identifying the circRNA-miRNA network and its functional targets. For the first time, we investigated the key mechanism by which ORF3 protein influences riboflavin metabolic pathways in target cells through circRNAs, preliminarily revealing that ariboflavinosis can lead to lipid metabolic disorder in the organism. This indicates a close association between viral HE and riboflavin metabolism. Full article
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26 pages, 2624 KB  
Review
The Dual Role of RASSF4 in Tumorigenesis: Mechanisms and Epigenetic Targeting Strategies
by Rui Tian, Yixin Wu, Wenbin Yuan, Lingli Tian, Rui Zhang, Hao Lyu, Shuai Xiao, Dong Guo, Qi Zhang, Declan William Ali, Marek Michalak, Cefan Zhou, Jingfeng Tang and Xing-Zhen Chen
Biology 2025, 14(9), 1289; https://doi.org/10.3390/biology14091289 - 18 Sep 2025
Viewed by 348
Abstract
RASSF4 is a key member of the Ras-associated domain family (RASSF) that exhibits dual functionality in tumorigenesis, playing critical yet context-dependent roles in various malignancies. Its expression is epigenetically regulated through promoter hypermethylation, histone modifications, and microRNAs including miR-155 and miR-196a-5p, which directly [...] Read more.
RASSF4 is a key member of the Ras-associated domain family (RASSF) that exhibits dual functionality in tumorigenesis, playing critical yet context-dependent roles in various malignancies. Its expression is epigenetically regulated through promoter hypermethylation, histone modifications, and microRNAs including miR-155 and miR-196a-5p, which directly target its 3′ untranslated region. In most cancers, such as non-small cell lung cancer (NSCLC) and gastric adenocarcinoma (GAC), RASSF4 acts as a tumor suppressor by inhibiting the RAS/MAPK pathway while activating the Hippo signaling cascade, ultimately inducing cell cycle arrest and apoptosis. Conversely, in aRMS, RASSF4 is upregulated by the PAX3-FOXO1 fusion oncoprotein and promotes tumor growth through MST1 inhibition and subsequent YAP activation. This review systematically analyzes current evidence regarding RASSF4’s complex regulatory mechanisms and clinical significance. We propose targeted therapeutic strategies including epigenetic reactivation, gene intervention, and combination therapies. Furthermore, we identify RASSF4 as a promising diagnostic biomarker and therapeutic target based on integrated mechanistic and clinical evidence. Future research should focus on elucidating context-dependent regulatory switches, developing targeted delivery systems, and validating clinical utility through prospective trials. Full article
(This article belongs to the Special Issue Signalling Pathways in Cancer and Disease)
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30 pages, 875 KB  
Review
MicroRNA Landscape in Hepatocellular Carcinoma: Metabolic Re-Wiring, Predictive and Diagnostic Biomarkers, and Emerging Therapeutic Targets
by Dimitris Liapopoulos, Panagiotis Sarantis, Theodora Biniari, Thaleia-Eleftheria Bousou, Eleni-Myrto Trifylli, Ioanna A. Anastasiou, Stefania Kokkali, Dimitra Korakaki, Spyridon Pantzios, Evangelos Koustas, Ioannis Elefsiniotis and Michalis V. Karamouzis
Biomedicines 2025, 13(9), 2243; https://doi.org/10.3390/biomedicines13092243 - 11 Sep 2025
Viewed by 990
Abstract
Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality, in part due to late diagnosis and limited prognostic tools. In recent years, microRNAs, small, non-coding regulators of gene expression, have emerged as key modulators of tumor metabolism, microenvironmental crosstalk, and therapeutic response [...] Read more.
Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality, in part due to late diagnosis and limited prognostic tools. In recent years, microRNAs, small, non-coding regulators of gene expression, have emerged as key modulators of tumor metabolism, microenvironmental crosstalk, and therapeutic response in HCC. This narrative review synthesizes evidence published from January 2000 through April 2025, focusing on four interrelated themes: (1) miRNA-driven metabolic rewiring; (2) circulating and exosomal miRNAs as diagnostic and (3) predictive biomarkers; (4) miRNA-based therapeutic strategies. We conducted a targeted PubMed search using terms related to HCC, miRNA biology, biomarkers, metabolism, and therapy, supplemented by manual reference mining. Preclinical and clinical studies reveal that loss of tumor-suppressor miRNAs and gain of oncomiRs orchestrate glycolysis, lipid and glutamine metabolism, and stromal-immune remodeling. Circulating miRNA signatures, including single- and multimarker panels, demonstrate diagnostic AUCs up to 0.99 for early-stage HCC and distinguish HCC from cirrhosis more accurately than alpha-fetoprotein. Predictively, miRNAs such as miR-21 and miR-486-3p correlate with sorafenib resistance, while tissue and exosomal miRNAs forecast recurrence and survival after curative therapy. Therapeutic manipulation, restoring tumor-suppressor miRNAs via mimics or AAV vectors and inhibiting oncomiRs with antagomirs or LNA oligonucleotides, yields potent anti-tumor effects in models, affecting cell cycle, apoptosis, angiogenesis, and immune activation. Despite technical and delivery challenges, early-phase trials validate target engagement and inform safety optimization. In this review, we highlight opportunities to integrate miRNA biomarkers into surveillance algorithms and combine miRNA therapeutics with existing modalities, charting a roadmap toward precision-guided management of HCC. Full article
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20 pages, 3290 KB  
Article
MiRNA Profiling in Premalignant Lesions and Early Glottic Cancer
by Anna Rzepakowska, Agnieszka Zajkowska, Marta Mękarska, Julia Śladowska, Aleksandra Borowy and Maciej Małecki
Cancers 2025, 17(17), 2883; https://doi.org/10.3390/cancers17172883 - 2 Sep 2025
Viewed by 536
Abstract
Background: miRNA profiling across different stages of laryngeal carcinogenesis explores dysregulated molecules relevant to engaged gene pathways and identifies markers for differential diagnosis and prognosis in early mucosal lesions of the larynx. Methods: Tissue samples were prospectively collected from 28 patients [...] Read more.
Background: miRNA profiling across different stages of laryngeal carcinogenesis explores dysregulated molecules relevant to engaged gene pathways and identifies markers for differential diagnosis and prognosis in early mucosal lesions of the larynx. Methods: Tissue samples were prospectively collected from 28 patients with hypertrophic vocal fold lesions: no dysplasia (ND), low-grade dysplasia (LGD), high-grade dysplasia (HGD), and invasive cancer (IC), as well as from 3 patients with vocal fold polyps. miRNA profiling of the samples was performed using microfluidic cards—TaqMan® Human MicroRNA Array A. A comparative analysis of ΔCt (dCt) miRNA expression levels was conducted between groups. Results: hsa-miR-216a-5p and hsa-miR-488-3p were selectively expressed in control tissues, while hsa-miR-105-5p and hsa-miR-516a-5p were exclusively detected in HGD and IC samples. Significant differences in miRNA expression were identified across 4, 16, 17, and 38 miRNA types between control and ND, LGD, HGD, and IC groups, respectively. hsa-miR-185-5p and hsa-miR-21-5p showed significantly altered expression between ND and LGD, HGD, and IC (p = 0.026, 0.001, 0.002; and p = 0.021, 0.002, 0.001, respectively). Twenty-five miRNAs were differentially expressed between LGD and both HGD and IC, while eleven miRNAs distinguished HGD from IC. Notably, hsa-miR-503-5p expression decreased progressively with increasing histological severity. Conclusions: Distinct miRNA expression profiles are associated with progressive stages of laryngeal mucosal lesions. Specific miRNAs may serve as valuable biomarkers for early detection, risk stratification, and prognosis in vocal fold carcinogenesis. Full article
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11 pages, 1399 KB  
Article
MicroRNA Regulation in the Freeze-Tolerant Heart of Dryophytes versicolor
by Saif Rehman, Sarah A. Breedon, Imane Rhzali and Kenneth B. Storey
Genes 2025, 16(9), 997; https://doi.org/10.3390/genes16090997 - 25 Aug 2025
Viewed by 582
Abstract
Background: Freeze tolerance is an uncommon but highly effective strategy that allows certain vertebrates to survive prolonged exposure to subzero temperatures in a frozen, ischemic state. While past studies have characterized the metabolic and biochemical adaptations involved, including cryoprotectant accumulation and metabolic rate [...] Read more.
Background: Freeze tolerance is an uncommon but highly effective strategy that allows certain vertebrates to survive prolonged exposure to subzero temperatures in a frozen, ischemic state. While past studies have characterized the metabolic and biochemical adaptations involved, including cryoprotectant accumulation and metabolic rate suppression, the contribution of post-transcriptional gene regulation by microRNAs (miRNAs) remains largely unexplored. This study investigated freeze-responsive miRNAs in cardiac tissue of the gray tree frog, Dryophytes versicolor, to better understand the molecular mechanisms that support ischemic survival and tissue preservation. Methods: Adult frogs were subjected to controlled freezing at −2.5 °C, and cardiac tissue was collected from frozen and control animals. Total RNA was extracted and analyzed via small RNA sequencing to identify differentially expressed miRNAs, followed by target gene prediction and KEGG pathway enrichment analysis. Results: A total of 3 miRNAs were differentially expressed during freezing, with significant upregulation of miR-93-5p and let-7b-5p and downregulation of miR-4485-3p. Predicted targets of upregulated miRNAs included genes involved in immune signaling pathways (e.g., cytokine–cytokine receptor interaction), steroid hormone biosynthesis, and neuroactive ligand–receptor interaction, suggesting suppression of energetically costly signaling processes. Downregulation of miRNAs targeting cell cycle, insulin signaling, and WNT pathways indicates possible selective preservation of cytoprotective and repair functions. Conclusion: Overall, these results suggest that D. versicolor employs miRNA-mediated regulatory networks to support metabolic suppression, maintain essential signaling, and prevent damage during prolonged cardiac arrest. This work expands our understanding of freeze tolerance at the molecular level and may offer insights into biomedical strategies for cryopreservation and ischemia–reperfusion injury. Full article
(This article belongs to the Section RNA)
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24 pages, 4238 KB  
Article
Hydrothermal Magnesium Alloy Extracts Modulate MicroRNA Expression in RAW264.7 Cells: Implications for Bone Remodeling
by Viviana Costa, Lavinia Raimondi, Daniele Bellavia, Angela De Luca, Pasquale Guglielmi, Angela Cusanno, Luca Cattini, Lia Pulsatelli, Matteo Pavarini, Roberto Chiesa and Gianluca Giavaresi
J. Funct. Biomater. 2025, 16(8), 303; https://doi.org/10.3390/jfb16080303 - 21 Aug 2025
Viewed by 648
Abstract
Magnesium (Mg) alloys, particularly Mg AZ31, have emerged as promising biomaterials for orthopedic applications due to their biodegradability and favorable mechanical characteristics. Among these, the Mg AZ31+SPF alloy, subjected to hydrothermal (HT) treatment, has demonstrated enhanced bioactivity. Our previous research established that this [...] Read more.
Magnesium (Mg) alloys, particularly Mg AZ31, have emerged as promising biomaterials for orthopedic applications due to their biodegradability and favorable mechanical characteristics. Among these, the Mg AZ31+SPF alloy, subjected to hydrothermal (HT) treatment, has demonstrated enhanced bioactivity. Our previous research established that this surface modification supports the osteogenic differentiation of human mesenchymal stem cells (hMSCs) by modulating both canonical and non-canonical signaling pathways, including those implicated in osteogenesis, hypoxic response, exosome biogenesis, and lipid metabolism. In the present study, we extended our investigation to assess the effects of Mg AZ31+SPF+HT and Mg AZ31+SPF extracts on murine pre-osteoclasts (RAW 264.7 cells) over 3- and 6-day treatment periods. The primary objectives were to evaluate biocompatibility and to investigate potential impacts on osteoclastogenesis induction and miRNA expression profiles. Methods: To assess cytocompatibility, metabolic activity, DNA integrity, and morphological alterations in RAW 264.7 cells were evaluated. Osteoclast differentiation was quantified using TRAP staining, alongside the assessment of osteoclastogenic marker expression by qRT-PCR and ELISA. The immunomodulatory properties of the extracts were examined using multiplex BioPlex assays to quantify soluble factors involved in bone healing. Additionally, global miRNA expression profiling was performed using a specialized panel targeting 82 microRNAs implicated in bone remodeling and inflammatory signaling. Results: Mg AZ31+SPF+HT extract exhibited high biocompatibility, with no observable adverse effects on cell viability. Notably, a significant reduction in the number of TRAP-positive and multinucleated cells was observed relative to the Mg AZ31+SPF group. This effect was corroborated by the downregulation of osteoclast-specific gene expression and decreased MMP9 protein levels. Cytokine profiling indicated that Mg AZ31+SPF+HT extract promoted an earlier release of key cytokines involved in maintaining the balance between bone formation and resorption, suggesting a beneficial role in bone healing. Furthermore, miRNA profiling revealed a distinct regulatory signature in Mg AZ31+SPF+HT-treated cells, with differentially expressed miRNAs associated with inflammation, osteoclast differentiation, apoptosis, bone resorption, hypoxic response, and metabolic processes compared to Mg AZ31+SPF-treated cells. Conclusions: Collectively, these findings indicate that hydrothermal treatment of Mg AZ31+SPF (resulting in Mg AZ31+SPF+HT) attenuates pre-osteoclast activation by influencing cellular morphology, gene and protein expression, as well as post-transcriptional regulation via modulation of miRNAs. The preliminary identification of miRNAs and the activation of their regulatory networks in pre-osteoclasts exposed to hydrothermally treated Mg alloy are described herein. In the context of orthopedic surgery—where balanced bone remodeling is imperative—our results emphasize the dual significance of promoting bone formation while modulating bone resorption to achieve optimal implant integration and ensure long-term bone health. Full article
(This article belongs to the Special Issue Metals and Alloys for Biomedical Applications (2nd Edition))
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19 pages, 2983 KB  
Article
Detecting the Type and Severity of Mineral Nutrient Deficiency in Rice Plants Based on an Intelligent microRNA Biosensing Platform
by Zhongxu Li and Keyvan Asefpour Vakilian
Sensors 2025, 25(16), 5189; https://doi.org/10.3390/s25165189 - 21 Aug 2025
Viewed by 754
Abstract
The early determination of the type and severity of stresses caused by nutrient deficiency is necessary for taking timely measures and preventing a remarkable yield reduction. This study is an effort to investigate the performance of a machine learning-based model that identifies the [...] Read more.
The early determination of the type and severity of stresses caused by nutrient deficiency is necessary for taking timely measures and preventing a remarkable yield reduction. This study is an effort to investigate the performance of a machine learning-based model that identifies the type and severity of nitrogen, phosphorus, potassium, and sulfur in rice plants by using the plant microRNA data as model inputs. The concentration of 14 microRNA compounds in plants exposed to nutrient deficiency was measured using an electrochemical biosensor based on the peak currents produced during the probe–target microRNA hybridization. Subsequently, several machine learning models were utilized to predict the type and severity of stress. According to the results, the biosensor used in this work exerted promising analytical performance, including linear range (10−19 to 10−11 M), limit of detection (3 × 10−21 M), and reproducibility during microRNA measurement in total RNA extracted from rice plant samples. Among the microRNAs studied, miRNA167, miRNA162, miRNA169, and miRNA395 exerted the largest contribution in predicting the nutrient deficiency levels based on feature selection methods. Using these four microRNAs as model inputs, the random forest with hyperparameters optimized by the genetic algorithm was capable of detecting the type of nutrient deficiency with an average accuracy, precision, and recall of 0.86, 0.94, and 0.87, respectively, seven days after the application of the nutrient treatment. Within this period, the optimized machine was able to detect the level of deficiency with average MSE and R2 of 0.010 and 0.92, respectively. Combining the findings of this study and the results we reported earlier on determining the occurrence of salinity, drought, and heat in rice plants using microRNA biosensors can be useful to develop smart biosensing platforms for efficient plant health monitoring systems. Full article
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25 pages, 1455 KB  
Article
Expression Analysis of miR-519a-3p and miR-379-5p in Colorectal Cancer Patients: A Combined Experimental and Bioinformatic Approach
by Turkan Gurer, Mehmet Emin Kizakoglu, Alper Aytekin and Rusen Avsar
Diagnostics 2025, 15(16), 2023; https://doi.org/10.3390/diagnostics15162023 - 13 Aug 2025
Viewed by 531
Abstract
Background/Objectives: Colorectal cancer (CRC) is one of the most common malignancies worldwide. microRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression post-transcriptionally and have emerged as important regulators in cancer biology. This study aimed to investigate the roles of miR-379-5p and [...] Read more.
Background/Objectives: Colorectal cancer (CRC) is one of the most common malignancies worldwide. microRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression post-transcriptionally and have emerged as important regulators in cancer biology. This study aimed to investigate the roles of miR-379-5p and miR-519a-3p in CRC using Quantitative Real-Time PCR (RT-qPCR) and comprehensive bioinformatic analyses. Methods: Tumor tissues and matched adjacent normal tissues were collected from 54 patients with CRC. The expression levels of miR-379-5p and miR-519a-3p in these tissues were determined using the RT-qPCR method. To investigate the functional roles of differently expressed miRNAs, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to construct miRNA–transcription factor (TF)–target gene–disease interaction networks. Results: It was found that the expression level of miR-379-5p was statistically significantly increased in tumor tissues compared to normal tissues, while miR-519a-3p was decreased (p < 0.05). GO analysis revealed enrichment in several important biological processes, including cellular protein metabolic processes, biosynthetic processes, response to stress, and nucleic acid binding TF activity. KEGG analysis exhibited that dysregulated miRNAs were associated with important pathways related to carcinogenesis, such as p53 signaling, TGF-beta signaling, and FoxO signaling pathways. Additionally, the miRNAs-TFs-Genes-Diseases Networks analysis identified ESR1 and FOXA1 as common target TFs of dysregulated miRNAs. Network analyses showed that dysregulated miRNAs interact with CRC-associated genes (Caspase 3 (CASP3), Adenomatous polyposis coli (APC), and AKT serine/threonine kinase 3 (AKT3)). Conclusions: The present study indicates that miR-379-5p and miR-519a-3p may be involved in CRC progression, with miR-379-5p being upregulated and miR-519a-3p being downregulated in tumor tissues. However, further functional studies are required to clarify their potential roles in tumor biology. The findings of the study suggest that miR-379-5p and miR-519a-3p may be associated with regulatory pathways related to CRC. These miRNAs have the potential to serve as diagnostic biomarkers or therapeutic targets in CRC. Full article
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15 pages, 646 KB  
Review
A Brief Review of MicroRNA Profiling in Human Prostate Cancer Tissues and Plasma
by Georgios Kallinikas, Amin M. Ektesabi, Chirag M. Vaswani, Georgios Haronis, Eirini Kallinika, Diomidis Kozyrakis, Evangelos Rodinos, Athanasios Filios, Panagiotis Filios, Despoina Mityliniou, Konstantinos Safioleas, Dimitrios Bozios, Athanasios Karmogiannis, Vasileios Konstantinopoulos, Anna Maria Konomi and James N. Tsoporis
Biomolecules 2025, 15(8), 1156; https://doi.org/10.3390/biom15081156 - 12 Aug 2025
Viewed by 780
Abstract
(1) Background: The gold standard, prostate-specific antigen (PSA) screening lacks the sensitivity and specificity required for confident, early prostate-cancer detection. MicroRNAs (miRNAs) are small, highly stable, non-coding RNAs whose expression changes reproducibly in malignancy and therefore offer promise as minimally invasive biomarkers. Although [...] Read more.
(1) Background: The gold standard, prostate-specific antigen (PSA) screening lacks the sensitivity and specificity required for confident, early prostate-cancer detection. MicroRNAs (miRNAs) are small, highly stable, non-coding RNAs whose expression changes reproducibly in malignancy and therefore offer promise as minimally invasive biomarkers. Although prostate cancer biopsies are the gold standard for prostate cancer diagnosis, limitations in the field continue to persist. Since circulating fluids can also be a source of miRNA biomarkers, we investigated the overlap between miRNAs enriched in prostate cancer tissue and those isolated from the plasma of patients with prostate cancer. (2) Methods: We synthesized the published literature (PubMed, Google Scholar, ResearchGate, 2005–April 2025) and re-analyzed three Gene Expression Omnibus (GEO) datasets (GSE54516, GSE21032—tissue; GSE206793—plasma) to identify miRNAs consistently dysregulated in prostate cancer tissue and circulation. (3) Results: Of the 318 screened full-text articles, 24 met the inclusion criteria. From the GEO reanalysis (false-discovery-rate < 0.05, |log2FC| ≥ 1), 219 and 326 miRNAs were differentially expressed in tissue, whereas 12 were altered in plasma. Two miRNAs—miR-449b and miR-455-3p—were common in both compartments, highlighting their translational potential as liquid biopsy surrogates of tumor biology. (4) Conclusions: We summarize functional evidence for leading tumor-suppressive (e.g., miR-205, miR-23b, miR-455-3p) and oncogenic (e.g., miR-21, miR-182, miR-449b) candidates, discuss their intersection with the androgen-receptor, TGF-β, WNT/β-catenin, and PI3K-AKT signaling, and outline outstanding requirements for the clinical qualification of miRNA panels in prostate cancer. Full article
(This article belongs to the Collection Molecular Biology: Feature Papers)
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16 pages, 1298 KB  
Article
Genetic Effects of Chicken Pre-miR-3528 SNP on Growth Performance, Meat Quality Traits, and Serum Enzyme Activities
by Jianzhou Shi, Jinbing Zhao, Bingxue Dong, Na Li, Lunguang Yao and Guirong Sun
Animals 2025, 15(15), 2300; https://doi.org/10.3390/ani15152300 - 6 Aug 2025
Viewed by 409
Abstract
The aim was to investigate the genetic effects of a SNP located in the precursor region of gga-miR-3528. (1) Single-nucleotide polymorphisms within precursor regions of microRNAs play crucial biological roles. (2) Utilizing a Gushi–Anka F2 resource population (n = 860), [...] Read more.
The aim was to investigate the genetic effects of a SNP located in the precursor region of gga-miR-3528. (1) Single-nucleotide polymorphisms within precursor regions of microRNAs play crucial biological roles. (2) Utilizing a Gushi–Anka F2 resource population (n = 860), we screened and validated miRNA SNPs. A SNP mutation in the miR-3528 precursor region was identified. Specific primers were designed to amplify the polymorphic fragment. Genotyping was performed for this individual SNP across the population, using the MassArray system. Association analyses were conducted between this SNP and chicken growth and body measurement traits, carcass traits, meat quality traits, and serum enzyme activities. (3) The rs14098602 (+12 bp A > G) was identified within the precursor region of gga-miR-3528. Significant associations (p < 0.05) were observed between this SNP and chicken growth traits (body weight at the age of 0 day, body weight at the age of 2 weeks, and body weight at the age of 4 weeks), carcass traits (evisceration weight), meat quality traits (subcutaneous fat rate and pectoral muscle density), and serum enzyme activities (total protein, albumin, globulin, cholinesterase, and lactate dehydrogenase). (4) These findings suggest that the polymorphism at rs14098602 may influence chicken growth, meat quality, and serum biochemical indices, through specific mechanisms. The gga-miR-3528 gene likely plays an important role in chicken development. Therefore, this SNP can serve as a molecular marker for genetic breeding and auxiliary selection of growth-related traits, facilitating the rapid establishment of elite chicken populations with superior genetic resources. Full article
(This article belongs to the Section Poultry)
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14 pages, 1343 KB  
Article
Role of Plasma-Derived Exosomal MicroRNAs in Mediating Type 2 Diabetes Remission
by Sujing Wang, Shuxiao Shi, Xuanwei Jiang, Guangrui Yang, Deshan Wu, Kexin Li, Victor W. Zhong and Xihao Du
Nutrients 2025, 17(15), 2450; https://doi.org/10.3390/nu17152450 - 27 Jul 2025
Viewed by 719
Abstract
Objective: This study aimed to identify plasma exosomal microRNAs (miRNAs) associated with weight loss and type 2 diabetes (T2D) remission following low-calorie diet (LCD) intervention. Methods: A 6-month dietary intervention targeting T2D remission was conducted among individuals with T2D. Participants underwent a 3-month [...] Read more.
Objective: This study aimed to identify plasma exosomal microRNAs (miRNAs) associated with weight loss and type 2 diabetes (T2D) remission following low-calorie diet (LCD) intervention. Methods: A 6-month dietary intervention targeting T2D remission was conducted among individuals with T2D. Participants underwent a 3-month intensive weight loss phase consuming LCD (815–835 kcal/day) and a 3-month weight maintenance phase (N = 32). Sixteen participants were randomly selected for characterization of plasma-derived exosomal miRNA profiles at baseline, 3 months, and 6 months using small RNA sequencing. Linear mixed-effects models were used to identify differentially expressed exosomal miRNAs between responders and non-responders. Pathway enrichment analyses were conducted using target mRNAs of differentially expressed miRNAs. Logistic regression models assessed the predictive value of differentially expressed miRNAs for T2D remission. Results: Among the 16 participants, 6 achieved weight loss ≥10% and 12 achieved T2D remission. Eighteen exosomal miRNAs, including miR-92b-3p, miR-495-3p, and miR-452b-5p, were significantly associated with T2D remission and weight loss. Pathway analyses revealed enrichment in PI3K-Akt pathway, FoxO signaling pathway, and insulin receptor binding. The addition of individual miRNAs including miR-15b-3p, miR-26a-5p, and miR-3913-5p to base model improved the area under the curve values by 0.02–0.08 at 3 months and by 0.02–0.06 at 6 months for T2D remission. Conclusions: This study identified exosomal miRNAs associated with T2D remission and weight loss following LCD intervention. Several exosomal miRNAs might serve as valuable predictors of T2D remission in response to LCD intervention. Full article
(This article belongs to the Special Issue Nutrition for Patients with Diabetes and Clinical Obesity)
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16 pages, 1490 KB  
Article
Mir-16 Decreases the Expression of VTI1B and SMPD1, Genes Involved in Membrane-Protein Trafficking in Melanoma
by Adi Layani, Tal Meningher, Yechezkel Sidi, Dror Avni and Raya Leibowitz
Cancers 2025, 17(13), 2197; https://doi.org/10.3390/cancers17132197 - 29 Jun 2025
Viewed by 594
Abstract
Introduction: The interface between T cells and the tumor microenvironment, termed the ‘immunological synapse’, consists of multiple checkpoint protein pairs co-expressed on both sides of the synapse. mir-16, a microRNA from a widely known tumor-suppressor family of miRNAs, was previously shown by us [...] Read more.
Introduction: The interface between T cells and the tumor microenvironment, termed the ‘immunological synapse’, consists of multiple checkpoint protein pairs co-expressed on both sides of the synapse. mir-16, a microRNA from a widely known tumor-suppressor family of miRNAs, was previously shown by us to be downregulated in melanoma. As other miRNAs from this family have been shown to directly target checkpoint proteins, here we investigated whether miR-16 influences the expression patterns of checkpoint proteins in melanoma. Methods: Single-cell gene expression data from the melanoma microenvironment were retrieved from a public database. Melanoma cell lines were established from metastatic lesions and transiently transfected with an hsa-miR-16-5p-mimic RNA or a mir-16-expressing plasmid. The mRNA expression profiles were analyzed using an Affymetrix microarray. Direct targets of miR-16 were identified by luciferase reporter assays. Protein levels were assessed by Western blotting. Results: Bioinformatic analysis revealed that the expression levels of eight checkpoint mRNAs, known to be present on the melanoma side of the immunological synapse, were highly correlated. Four of these mRNAs contained putative binding sites for the miR-15/16 family. miR-16 expression was significantly reduced in melanoma cells, compared to normal melanocytes. Luciferase reporter assays demonstrated that miR-16 directly targets the 3′ untranslated regions (3′UTRs) of CD40, CD80. The mRNAs downregulated following miR-16 overexpression were highly enriched for genes involved in autophagy, vesicle-mediated transport, and the regulation of protein membrane localization. Among these, VTI1B and SMPD1 were confirmed to be direct targets of miR-16. Transient overexpression of miR-16 resulted in a significant reduction in SMPD1 and VTI1B levels in melanoma cell lines. Conclusions: Our findings suggest that miR-16 potentially modulates melanoma tumorigenesis, metastasis and immunogenicity by altering the composition of checkpoint proteins at the immunological synapse and by regulating cellular pathways associated with intracellular trafficking and transmembrane protein presentation. Full article
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29 pages, 2018 KB  
Review
Neutrophil Spatiotemporal Regulatory Networks: Dual Roles in Tumor Growth Regulation and Metastasis
by Pengcheng Li, Feimu Fan, Bixiang Zhang, Chaoyi Yuan and Huifang Liang
Biomedicines 2025, 13(6), 1473; https://doi.org/10.3390/biomedicines13061473 - 14 Jun 2025
Cited by 1 | Viewed by 1303
Abstract
Neutrophils, accounting for 50–70% of circulating leukocytes, exhibit remarkable plasticity in tumor biology. Depending on tumor type and microenvironmental cues, they can exert either anti-tumor or pro-tumor effects. During tumor initiation, neutrophils exposed to chronic inflammation secrete cytokines and oncogenic microRNAs that promote [...] Read more.
Neutrophils, accounting for 50–70% of circulating leukocytes, exhibit remarkable plasticity in tumor biology. Depending on tumor type and microenvironmental cues, they can exert either anti-tumor or pro-tumor effects. During tumor initiation, neutrophils exposed to chronic inflammation secrete cytokines and oncogenic microRNAs that promote genomic instability and malignant transformation. In tumor progression, neutrophils adopt context-dependent phenotypes and execute diverse functions, including polarization into anti-tumor (N1) or pro-tumor (N2) subsets; secretion of inflammatory and angiogenic mediators; formation of neutrophil extracellular traps (NETs); production of reactive oxygen and nitrogen species (e.g., H2O2 and nitric oxide); and modulation of immune cell infiltration and function within the tumor microenvironment. During metastasis, neutrophils facilitate cancer dissemination through three principal mechanisms: (1) promoting epithelial–mesenchymal transition (EMT) via inflammatory signaling, adhesion molecule interactions, and lipid metabolic support; (2) establishing pre-metastatic niches by remodeling distant organ stroma through NETs and matrix metalloproteinases; and (3) reactivating dormant tumor cells in response to chronic inflammation, viral infection, or stress hormones. Collectively, neutrophils function as central regulators across all stages of tumor evolution, influencing cancer growth, immune evasion, and metastatic progression. This review aims to provide a comprehensive synthesis of neutrophil-mediated mechanisms in the tumor microenvironment and highlight emerging strategies for neutrophil-targeted cancer therapy. Full article
(This article belongs to the Section Cancer Biology and Oncology)
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19 pages, 2651 KB  
Article
Temporal Shifts in MicroRNAs Signify the Inflammatory State of Primary Murine Microglial Cells
by Keren Zohar, Elyad Lezmi, Fanny Reichert, Tsiona Eliyahu, Shlomo Rotshenker, Marta Weinstock and Michal Linial
Int. J. Mol. Sci. 2025, 26(12), 5677; https://doi.org/10.3390/ijms26125677 - 13 Jun 2025
Viewed by 836
Abstract
The primary function of microglia is to maintain brain homeostasis. In neurodegenerative diseases like Alzheimer’s, microglia contribute to neurotoxicity and inflammation. In this study, we exposed neonatal murine primary microglial cultures to stimuli mimicking pathogens, injury, or toxins. Treatment with benzoyl ATP (bzATP) [...] Read more.
The primary function of microglia is to maintain brain homeostasis. In neurodegenerative diseases like Alzheimer’s, microglia contribute to neurotoxicity and inflammation. In this study, we exposed neonatal murine primary microglial cultures to stimuli mimicking pathogens, injury, or toxins. Treatment with benzoyl ATP (bzATP) and lipopolysaccharide (LPS) triggered a coordinated increase in interleukin and chemokine expression. We analyzed statistically significant differentially expressed microRNAs (DEMs) at 3 and 8 h post-activation, identifying 33 and 57 DEMs, respectively. Notably, miR-155, miR-132, miR-3473e, miR-222, and miR-146b showed strong temporal regulation, while miR-3963 was sharply downregulated by bzATP. These DEMs regulate inflammatory pathways, including TNFα and NFκB signaling. We also examined the effect of ladostigil, a neuroprotective agent known to reduce oxidative stress and inflammation. At 8 h post-activation, ladostigil induced upregulation of anti-inflammatory miRNAs, such as miR-27a, miR-27b, and miR-23b. Our findings suggest that miRNA profiles reflect microglial responses to inflammatory cues and that ladostigil modulates these responses. This model of controlled microglial activation offers a powerful tool with which to study inflammation in the aging brain and the progression of neurodegenerative diseases. Full article
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