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Search Results (2,231)

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Keywords = miR-133b

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24 pages, 10124 KB  
Article
Cold Exposure Induces Swine Brown Adipocytes to Display an Island-like Distribution with Atypical Characteristics
by Zhenhua Guo, Lei Lv, Hong Ma, Liang Wang, Bo Fu, Fang Wang, Shuo Yang, Di Liu and Dongjie Zhang
Int. J. Mol. Sci. 2025, 26(20), 9871; https://doi.org/10.3390/ijms26209871 (registering DOI) - 10 Oct 2025
Abstract
The original purpose of this study was to compare human and pig scRNA-seq data to determine why pigs do not have brown adipocytes. However, during the experiment, we identified brown adipocytes in pigs. Therefore, we aimed to confirm that these adipocytes were brown [...] Read more.
The original purpose of this study was to compare human and pig scRNA-seq data to determine why pigs do not have brown adipocytes. However, during the experiment, we identified brown adipocytes in pigs. Therefore, we aimed to confirm that these adipocytes were brown adipocytes via a comparative analysis using typical mouse brown adipose tissue sections. We found that swine brown adipocytes were distributed in an island-like pattern, with three typical characteristics: (1) numerous mitochondria and small lipid droplets, (2) a cellular volume smaller than that of white adipocytes, and (3) expression of specific marker genes (EBF2 and ATP2B4). The expression levels of the thermogenesis-related genes UCP2/3 were not significantly increased. Thus, we conducted ceRNA network analysis, revealing that high expression of the key microRNA miR-10383 increased the thermogenic efficiency of UCP3 in the cold exposure group. In addition, the epigenetic memory of UCP3 was disrupted. Chromatin accessibility and Whole-Transcriptome Sequencing of Groin Adiposesibility results revealed peaks in the promoter regions of the UCP2/3 genes. In our discussion of the study’s limitations, we explain how to repeat the experiment to significantly increase the UCP2/3 protein content. This study fills a research gap regarding brown fat in pigs and can provide a reference for future studies on fat metabolism. Full article
(This article belongs to the Section Molecular Biology)
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27 pages, 3121 KB  
Article
MicroRNA Deregulation and Immune Checkpoint Interactions in Common Variable Immunodeficiency and CLL-Associated Secondary Immunodeficiency
by Paulina Mertowska, Sebastian Mertowski, Milena Czosnek, Barbara Sosnowska-Pasiarska, Aleksandra Krasińska-Płachta, Zbigniew Krasiński, Tomasz Urbanowicz, Krzysztof Bojarski, Mansur Rahnama-Hezavah and Ewelina Grywalska
Cells 2025, 14(20), 1577; https://doi.org/10.3390/cells14201577 - 10 Oct 2025
Abstract
Background: Immunodeficiencies are a heterogeneous group of disorders classified etiologically as primary (congenital) or secondary (acquired). Primary immunodeficiencies (PIDs), such as common variable immunodeficiency (CVID), result from genetic mutations that impair the development and function of lymphocytes. Secondary immunodeficiencies (SIDs) arise as a [...] Read more.
Background: Immunodeficiencies are a heterogeneous group of disorders classified etiologically as primary (congenital) or secondary (acquired). Primary immunodeficiencies (PIDs), such as common variable immunodeficiency (CVID), result from genetic mutations that impair the development and function of lymphocytes. Secondary immunodeficiencies (SIDs) arise as a consequence of chronic diseases, lymphoid malignancies, or immunosuppressive therapies. Aim of the study: The purpose of this study was to assess the serum expression profile of selected microRNAs (miRNAs) in patients with CVID and in those with chronic lymphocytic leukemia (CLL) and coexisting SID, compared to healthy individuals. Methods: Digital PCR (dPCR) was applied to quantify the serum expression levels of selected miRNAs in patients with CVID, patients with CLL and SID, and in healthy controls. Results: dPCR revealed significantly reduced levels of miR-16, miR-30c, miR-181a, miR-29a, miR-150, and miR-326 in the CVID group, potentially reflecting impaired regulatory mechanisms of the immune system. In contrast, elevated levels of miR-21, miR-125b, and miR-155 were observed in the CLL group with SID, suggesting their role in tumorigenesis and secondary immunosuppression. Correlations between miRNA levels and the expression of immune checkpoints (PD-1, CTLA-4, CD200) indicated the involvement of a complex regulatory network encompassing both humoral and cellular immune mechanisms. Conclusions: The results provide preliminary evidence that selected miRNAs could reflect disease-specific immune dysregulation patterns and may hold potential as diagnostic and prognostic biomarkers in both PIDs and SIDs. Full article
(This article belongs to the Special Issue MicroRNAs: Regulators of Cellular Fate)
18 pages, 28866 KB  
Article
The Zebrafish miR-183 Family Regulates Endoderm Convergence and Heart Development via S1Pr2 Signaling Pathway
by Ting Zeng, Ling Liu, Jinrui Lv, Hao Xie, Qingying Shi, Guifang Tao, Xiaoying Zheng, Lin Zhu, Lei Xiong and Huaping Xie
Biomolecules 2025, 15(10), 1434; https://doi.org/10.3390/biom15101434 - 10 Oct 2025
Abstract
MicroRNA (miRNA), as a key post-transcriptional regulatory factor, plays a crucial role in embryonic development. The coordination of endoderm cell convergence and cardiac precursor cell (CPC) migration is critical for cardiac tube fusion. Defects in endoderm can impair the normal migration of CPCs [...] Read more.
MicroRNA (miRNA), as a key post-transcriptional regulatory factor, plays a crucial role in embryonic development. The coordination of endoderm cell convergence and cardiac precursor cell (CPC) migration is critical for cardiac tube fusion. Defects in endoderm can impair the normal migration of CPCs towards the midline, leading to cardia bifida. Although the role of the microRNA-183 family (miR-183, miR-96 and miR-182) in cardiovascular diseases has been reported, the mechanism by which they regulate early heart development remains unclear. In this study, we used zebrafish as a model to elucidate the roles of the microRNA-183 family in early heart development. miRNA mimics were injected into Tg (cmlc2: eGFP) and Tg (sox17: eGFP) transgenic embryos to overexpress the miR-183 family. The results showed that, at 36 hpf, single or co-injection of miR-183/96/182 mimics caused defects in endoderm convergence, with a hole in the endoderm, and a significant down-regulation of the endoderm marker gene sox32. Additionally, embryos with single or co-injection of miR-183/96/182 mimics exhibited cardia bifida and tail blisters, with significantly down-regulated expression levels of genes related to heart development, including cmlc2, vmhc, amhc, nppa, gata4, gata5, nkx2.5, bmp2b, and bmp4. The phenotype caused by overexpression of the miR-183 family is highly consistent with loss of the sphingosine 1-phosphate receptor S1Pr2. Bioinformatics analysis result found that miR-183 can bind to 3′-UTR of the s1pr2 to regulate its expression; overexpression of miR-183 led to a significant decrease in the expression of the s1pr2 gene. Dual luciferase assay results suggest that s1pr2 is a bona fide target of miR-183. In summary, the miR-183 family regulates endoderm convergence and cardiac precursor cell migration via the S1Pr2 signaling pathway. This study reveals that the miR-183 family is a key regulatory factor in endoderm convergence and cardiac precursor cell migration during the early zebrafish development, elucidating the molecular mechanisms underlying early cardiac precursor cell and endoderm cell movement. Full article
(This article belongs to the Section Molecular Biology)
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24 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
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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18 pages, 6821 KB  
Article
Multi-Omics Integration Reveals PBDE-47 as an Environmental Risk Factor for Intracranial Aneurysm via F2R-Mediated Metabolic and Epigenetic Pathways
by Hongjun Liu, Jinliang You, Junsheng Bai, Dilaware Khan and Sajjad Muhammad
Brain Sci. 2025, 15(10), 1091; https://doi.org/10.3390/brainsci15101091 - 9 Oct 2025
Abstract
Background: Intracranial aneurysm (IA) rupture is a life-threatening cerebrovascular event with a mortality rate of up to 40%, affecting approximately 500,000 people globally each year. Although environmental pollutants such as 2,2′,4,4′-tetrabromodiphenyl ether (PBDE-47) have been implicated in the pathogenesis of IA, the causal [...] Read more.
Background: Intracranial aneurysm (IA) rupture is a life-threatening cerebrovascular event with a mortality rate of up to 40%, affecting approximately 500,000 people globally each year. Although environmental pollutants such as 2,2′,4,4′-tetrabromodiphenyl ether (PBDE-47) have been implicated in the pathogenesis of IA, the causal relationship and underlying mechanisms remain unclear. This study aims to systematically explore the potential causal role of PBDE-47 in the development of IA by integrating multi-omics approaches. Methods: We utilized the UK Biobank Drug Proteomics Project (UKB-PPP) genome-wide association study (GWAS) data, including 2940 plasma proteins and 1400 metabolites, along with IA genetic data from 456,348 individuals, to perform a two-sample Mendelian randomization (MR) analysis. Instrumental variables were selected based on genome-wide significance (p < 5 × 10−8) or suggestive thresholds (p < 5 × 10−5). Analytical methods included inverse variance weighting (IVW), MR-Egger, weighted median, MR-PRESSO, and Steiger filtering for sensitivity analysis. Molecular docking and 100-nanosecond molecular dynamics simulations were used to evaluate interactions between PBDE-47 and proteins. Mediation analysis assessed the roles of plasma metabolites and miRNAs, and SMR-HEIDI tests were used to verify causal relationships. Results: MR analysis identified 93 plasma proteins potentially causally associated with IA, including 53 protective factors and 40 risk factors. By integrating PBDE-47 targets, IA-related genes, and metabolite-related genes, we identified 15 hub genes. Molecular docking revealed potential binding between PBDE-47 and F2R (binding energy: −5.516 kcal/mol), and SMR-HEIDI testing supported F2R as a potential causal risk factor for IA. Molecular dynamics simulations indicated the stability of the complex structure. Mediation analysis suggested that F2R may influence IA risk through eight plasma metabolites, and miR-130b-3p may indirectly promote IA development by upregulating F2R. Conclusions: Our findings suggest that exposure to PBDE-47 may have a potential causal relationship with IA risk, potentially mediated through the “PBDE–47–F2R–metabolite–miRNA” regulatory axis. These results provide preliminary evidence for early diagnostic biomarkers and targeted interventions for IA. The multi-omics analytical framework established in this study offers new insights into environmental determinants of neurovascular diseases, although further validation is needed to address potential limitations. Full article
(This article belongs to the Section Environmental Neuroscience)
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24 pages, 3057 KB  
Article
Venous Thrombogenesis and Cervical Cancer: Plasma MicroRNAs as Prognostic Indicators of Tumor Behavior
by Mariana Teixeira Costa, Beatriz Vieira Neto, José Brito da Silva, Luísa Carvalho, Lurdes Salgado, Deolinda Pereira, Filomena Adega, Valéria Tavares and Rui Medeiros
Int. J. Mol. Sci. 2025, 26(19), 9796; https://doi.org/10.3390/ijms26199796 - 8 Oct 2025
Viewed by 240
Abstract
Cervical cancer (CC) is the fourth most common cancer among women globally, with venous thromboembolism (VTE) representing a life-threatening complication. Cancer-associated thrombosis (CAT) arises from tumor-driven activation of hemostasis, worsening prognosis. Recently, circulating microRNAs (miRNAs) have emerged as potential biomarkers for both CAT [...] Read more.
Cervical cancer (CC) is the fourth most common cancer among women globally, with venous thromboembolism (VTE) representing a life-threatening complication. Cancer-associated thrombosis (CAT) arises from tumor-driven activation of hemostasis, worsening prognosis. Recently, circulating microRNAs (miRNAs) have emerged as potential biomarkers for both CAT and cervical tumorigenesis. Thus, this study aimed to assess the implications of five miRNAs—miR-20a-5p, -23a-3p, -125b-5p, -145-5p, and -616-3p—in CC-related VTE context. These miRNAs were quantified by RT-qPCR in plasma from 69 CC patients before treatment. Briefly, VTE occurred in nine patients, decreasing overall survival (OS) [log-rank test, p = 0.005; hazard ratio (HR) = 4.78; 95% confidence interval (CI), 1.42–16.05]. Lower miR-20a-5p levels predicted VTE (ꭓ2 test, p = 0.027) and, in subgroup analyses, they were linked to cervical squamous cell carcinoma (CSCC) and older age (ꭓ2 test, p = 0.003 and p = 0.043, respectively). In VTE patients, miR-145-5p downregulation was associated with improved OS (log-rank test, p = 0.018), an effect also observed in the adenocarcinoma (ADC) subgroup (log-rank test, p = 0.039). The remaining miRNAs showed subtype-specific links to clinicopathological features and survival. These findings highlight the potential value of circulating miRNAs in thrombotic risk and prognosis assessment in CC. Full article
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17 pages, 2080 KB  
Article
Identification of Proteins and MicroRNAs with Prognostic Value for Assisted Reproduction Technology Outcomes in Follicular Fluid of Women with Endometriosis: A Pilot Study
by Ana Catarina Neto, Cláudia Freitas, Ângela Ribeiro, Adriana R. Rodrigues, João L. Silva-Carvalho, Henrique Almeida and Delminda Neves
Int. J. Mol. Sci. 2025, 26(19), 9752; https://doi.org/10.3390/ijms26199752 - 7 Oct 2025
Viewed by 135
Abstract
This study aims to identify molecular markers with prognostic value for biochemical pregnancy in follicular fluid (FF) samples from women with endometriosis after assisted reproductive technology (ART) intervention. Levels of growth differentiation factor-9 (GDF-9), bone morphogenetic protein-15 (BMP-15), and anti-Mullerian hormone (AMH) proteins [...] Read more.
This study aims to identify molecular markers with prognostic value for biochemical pregnancy in follicular fluid (FF) samples from women with endometriosis after assisted reproductive technology (ART) intervention. Levels of growth differentiation factor-9 (GDF-9), bone morphogenetic protein-15 (BMP-15), and anti-Mullerian hormone (AMH) proteins were semi-quantified by Western blotting and microRNAs 20a_1, 145_1, 320a_1, 125-b-5p, 212-3p, and 199_a by qPCR in FF samples from women submitted to ART with a previous diagnosis of endometriosis (n = 20) or male factor infertility (controls) (n = 44). An increase in GDF-9 and BMP-15 and a decrease in AMH mature protein were observed, as well as an increase in miR20a_1 (p = 0.04), miR145_1 (p = 0.003), and miR320a_1 (p = 0.006) in FF samples collected from women with endometriosis compared with controls. A reduction was observed in miR125b-5p (p = 0.004) and 212-3p (p = 0.02) in endometriosis. Receiver operating characteristic (ROC) curve analysis indicated that miR125b-5p, miR212-3p, and miR-145_1 are potential predictors of endometriosis, and miR145_1 and miR320a_1 of biochemical pregnancy in controls. Although limited by a small sample size, the current study demonstrated alterations in AMH, BMP-15, GDF-9, and specific miRNA levels in FF samples harvested from women with endometriosis, emphasizing their potential roles in endometriosis-related infertility. These microRNAs, dysregulated in women with endometriosis, unveil their biomarker properties and their predictive value for ART success. Full article
(This article belongs to the Special Issue Endometriosis and Infertility)
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30 pages, 1628 KB  
Review
RNA Therapeutics: Delivery Problems and Solutions—A Review
by Natalia Pozdniakova, Evgenii Generalov, Alexei Shevelev and Olga Tarasova
Pharmaceutics 2025, 17(10), 1305; https://doi.org/10.3390/pharmaceutics17101305 - 7 Oct 2025
Viewed by 425
Abstract
RNA-based therapeutics offer transformative potential for treating devastating diseases. However, current RNA delivery technologies face significant hurdles, including inefficient tissue targeting, insufficient selectivity, and severe side effects, leading to the termination of many clinical trials. This review critically assesses the landscape of RNA-derived [...] Read more.
RNA-based therapeutics offer transformative potential for treating devastating diseases. However, current RNA delivery technologies face significant hurdles, including inefficient tissue targeting, insufficient selectivity, and severe side effects, leading to the termination of many clinical trials. This review critically assesses the landscape of RNA-derived medicines, examining world-renowned mRNA vaccines (Spikevax, BNT162b2/Comirnaty) and RNA-based therapeutics like Miravirsen (anti-miR-122). It details the composition and clinical trial results of numerous modified short RNA drugs (e.g., siRNAs, miRNA mimetics/inhibitors) targeting various conditions. Prospects for RNA-based medicines are analysed for diseases with substantial societal impact, such as cancer, autoimmune disorders, and infectious diseases, with a focus on evolving delivery methods, including lipid nanoparticles, viral vectors, and exosomes. RNA-mediated macrophage reprogramming emerges as a promising strategy, potentially enhancing both delivery and clinical efficacy. This review highlights that while approved RNA therapies primarily target rare diseases due to delivery limitations, novel approaches in RNA modification, targeted delivery systems, and enhanced understanding of molecular mechanisms are crucial for expanding their application to prevalent diseases and unlocking their full therapeutic potential. Full article
(This article belongs to the Special Issue RNA-Based Vaccines and Therapeutics)
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17 pages, 3749 KB  
Article
Exploring Low Energy Excitations in the d5 Iridate Double Perovskites La2BIrO6 (B = Zn, Mg)
by Abhisek Bandyopadhyay, Dheeraj Kumar Pandey, Carlo Meneghini, Anna Efimenko, Marco Moretti Sala and Sugata Ray
Condens. Matter 2025, 10(4), 53; https://doi.org/10.3390/condmat10040053 - 6 Oct 2025
Viewed by 270
Abstract
We experimentally investigate the structural, magnetic, transport, and electronic properties of two d5 iridate double perovskite materials La2BIrO6 (B = Mg, Zn). Notably, despite similar crystallographic structure, the two compounds show distinctly different magnetic behaviors. The M [...] Read more.
We experimentally investigate the structural, magnetic, transport, and electronic properties of two d5 iridate double perovskite materials La2BIrO6 (B = Mg, Zn). Notably, despite similar crystallographic structure, the two compounds show distinctly different magnetic behaviors. The M = Mg compound shows an antiferromagnetic-like linear field-dependent isothermal magnetization below its transition temperature, whereas the M = Zn counterpart displays a clear hysteresis loop followed by a noticeable coercive field, indicative of ferromagnetic components arising from a non-collinear Ir spin arrangement. The local structure studies authenticate perceptible M/Ir antisite disorder in both systems, which complicates the magnetic exchange interaction scenario by introducing Ir-O-Ir superexchange pathways in addition to the nominal Ir-O-B-O-Ir super-superexchange interactions expected for an ideally ordered structure. While spin–orbit coupling (SOC) plays a crucial role in establishing insulating behavior for both these compounds, the rotational and tilting distortions of the IrO6 (and MO6) octahedral units further lift the ideal cubic symmetry. Finally, by measuring the Ir-L3 edge resonant inelastic X-ray scattering (RIXS) spectra for both the compounds, giving evidence of spin–orbit-derived low-energy inter-J-state (intra t2g) transitions (below ~1 eV), the charge transfer (O 2p → Ir 5d), and the crystal field (Ir t2geg) excitations, we put forward a qualitative argument for the interplay among effective SOC, non-cubic crystal field, and intersite hopping in these two compounds. Full article
(This article belongs to the Section Quantum Materials)
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16 pages, 1370 KB  
Review
The Prognostic Power of miR-21 in Breast Cancer: A Systematic Review and Meta-Analysis
by Luana Conte, Maria Rosaria Tumolo, Giorgio De Nunzio, Ugo De Giorgi, Roberto Guarino, Donato Cascio and Federico Cucci
Int. J. Mol. Sci. 2025, 26(19), 9713; https://doi.org/10.3390/ijms26199713 - 6 Oct 2025
Viewed by 156
Abstract
Breast cancer (BC) is one of the most common malignancies among women worldwide. Despite advances in early detection and treatment, prognosis remains highly variable. Molecular biomarkers, such as microRNAs (miRNAs), have emerged as promising tools to refine prognostic assessment. Among them, miR-21 is [...] Read more.
Breast cancer (BC) is one of the most common malignancies among women worldwide. Despite advances in early detection and treatment, prognosis remains highly variable. Molecular biomarkers, such as microRNAs (miRNAs), have emerged as promising tools to refine prognostic assessment. Among them, miR-21 is consistently overexpressed in solid tumors and implicated in key oncogenic pathways. This systematic review and meta-analysis aimed to clarify the prognostic significance of miR-21 in BC and explore its molecular mechanisms through bioinformatic analyses. A systematic search of PubMed, Scopus, and Web of Science up to April 2025 identified 18 eligible observational studies. Pooled analyses showed that high miR-21 expression was significantly associated with poorer overall survival (OS) (HR = 2.37, 95% CI: 1.42–3.98) and recurrence-related outcomes (DFS/RFS) (HR = 2.10, 95% CI: 1.32–3.34). Subgroup analyses confirmed robust associations across different cut-off definitions and revealed particularly strong effects in triple-negative BC (HR = 5.69) and mixed subtypes (HR = 2.55), but no significant association in HER2-positive BC. Bioinformatic analysis identified target genes such as PTEN, BCL2, STAT3, and MYC, involved in apoptosis regulation, proliferation, NF-κB signaling, and immune modulation. These findings provide consistent evidence that miR-21 is a promising minimally invasive prognostic biomarker in BC, particularly in aggressive subtypes, and support its integration into future multimodal prognostic models. Full article
(This article belongs to the Special Issue Non-Coding RNA in Physiology and Pathophysiology: Second Edition)
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25 pages, 1559 KB  
Review
Anticoagulation Therapies and microRNAs in Heart Failure
by Lucia Spartano, Maria Lombardi and Chiara Foglieni
Biomolecules 2025, 15(10), 1411; https://doi.org/10.3390/biom15101411 - 3 Oct 2025
Viewed by 245
Abstract
Heart Failure (HF) remains a major cause of mortality despite the advances in pharmacological treatment. Anticoagulation therapies, including Clopidogrel, Aspirin, Warfarin, and novel oral anticoagulants (NOACs) such as Apixaban, Rivaroxaban, Edoxaban, and Dabigatran, are frequently administered to HF patients to prevent thromboembolism and [...] Read more.
Heart Failure (HF) remains a major cause of mortality despite the advances in pharmacological treatment. Anticoagulation therapies, including Clopidogrel, Aspirin, Warfarin, and novel oral anticoagulants (NOACs) such as Apixaban, Rivaroxaban, Edoxaban, and Dabigatran, are frequently administered to HF patients to prevent thromboembolism and adverse, life-threatening outcomes (e.g., stroke and myocardial infarction). In these settings, drug resistance and variability in responsivity to therapeutic approaches are challenging issues. Recent studies suggest that non-coding RNAs, particularly microRNAs (miRs) may play a modulatory role in HF therapy context, affecting drug efficacy. Specific miRs have been associated with resistance to Clopidogrel (e.g., miR-223 and miR-26a), Aspirin (e.g., miR-19b-1-5p and miR-92a) and Warfarin (e.g., miR-133 and miR-137). Moreover, Digoxin, a cardiac glycoside acting also over bleeding risk, upregulates miR-132, which is involved in HF-associated cardiac alteration and hypertrophy. Evidence linking miR expression to NOAC pharmacodynamics, cardiac remodeling and regulation of the coagulation is growing. These findings highlight the need of deeply harnessing the potential of miRs as predictive biomarkers or therapeutic targets in HF. Improving the knowledge on the relationship between miR and anticoagulant drugs in HF patients will contribute to personalization of the anticoagulant therapies, aimed at enhancing patient responsivity and minimizing adverse effects, ultimately improving patient life quality. Full article
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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 246
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
Viewed by 297
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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17 pages, 1488 KB  
Communication
Significant Association Between Abundance of Gut Microbiota and Plasma Levels of microRNAs in Individuals with Metabolic Syndrome and Their Potential as Biomarkers for Metabolic Syndrome: A Pilot Study
by Sanghoo Lee, Jeonghoon Hong, Yiseul Kim, Hee-Ji Choi, Jinhee Park, Jihye Yun, Yun-Tae Kim, Kyeonghwan Choi, SaeYun Baik, Mi-Kyeong Lee and Kyoung-Ryul Lee
Genes 2025, 16(10), 1161; https://doi.org/10.3390/genes16101161 - 30 Sep 2025
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Abstract
Background/Objectives: The relationship between gut microbiota (GM) and microRNAs (miRs) related to lipid metabolism in individuals with metabolic syndrome (MetS) remains unclear. This pilot study examined the relationship between Bacteroidetes and Firmicutes abundance at the phylum level and the plasma levels of miR-122 [...] Read more.
Background/Objectives: The relationship between gut microbiota (GM) and microRNAs (miRs) related to lipid metabolism in individuals with metabolic syndrome (MetS) remains unclear. This pilot study examined the relationship between Bacteroidetes and Firmicutes abundance at the phylum level and the plasma levels of miR-122 and miR-370, both of which are associated with lipid metabolism, in Korean individuals with MetS and in healthy controls. We also evaluated the potential of these miRs as biomarkers for MetS. Methods: This study enrolled 7 individuals with MetS and 8 controls. The abundance of GM was analyzed by 16S rRNA amplicon sequencing. To evaluate the relationship between the dominant phyla in the 2 groups, the log ratio of Firmicutes to Bacteroidetes (F/B) was calculated using a centered log-ratio (CLR) transformation. The abundance of the 2 plasma miRs was also quantified by real-time quantitative PCR (RT-qPCR). Pearson’s and Spearman’s correlation analyses were then performed to evaluate the relationship between Bacteroidetes and Firmicutes abundance, the clinical parameters, and plasma levels of the 2 miRs. Additionally, the area under the curve (AUC) value of the receiver operating characteristic (ROC) curve was calculated to evaluate the potential of the 2 miRs as MetS biomarkers. Results: The 2 most abundant phyla were Bacteroidetes and Firmicutes. Bacteroidetes made up an average of 24.7% in the MetS group and 69.7% in the control group. Meanwhile, the average abundance of Firmicutes was 69.8% in the MetS group and 26.5% in the control group. The log F/B ratios in the MetS and control groups were 0.7 ± 0.5 and −0.4 ± 0.1 (p < 0.001), respectively. FDR analysis revealed significant correlations between Bacteroidetes abundance and BMI, DBP, FBG, total chol, insulin and HOMA-IR (FDR-adjusted p < 0.05), as well as between Firmicutes abundance and BMI, FBG, total chol, insulin and HOMA-IR (FDR-adjusted p < 0.05). Plasma levels of the 2 miRs differed significantly between the MetS and control groups: miR-122 (1.43 vs. 0.73; p = 0.0065) and miR-370 (1.39 vs. 0.83; p = 0.0089). The AUC values for miR-122 and miR-370 were 0.946 (p < 0.001) and 0.964 (p < 0.001), respectively. Pearson’s and Spearman’s correlation analyses revealed significant negative correlations between Bacteroidetes abundance and levels of miR-122 (p = 0.0048 and p = 0.0045, respectively) and miR-370 (p = 0.0003 and p < 0.0001, respectively), as well as significant positive correlations between Firmicutes abundance and levels of miR-122 (p = 0.0038 and p = 0.0027, respectively) and miR-370 (p = 0.0004 and p < 0.0001, respectively). However, as our exploratory findings were based on a small sample size, the high correlation results may partly reflect the separation between the MetS and control groups. Conclusions: Our exploratory findings suggest that the GM abundances of individuals with MetS may be significantly associated with plasma levels of miR-122 and miR-370, which are related to lipid metabolism. These miRs may therefore serve as potential MetS biomarkers. Full article
(This article belongs to the Section RNA)
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18 pages, 3955 KB  
Systematic Review
Liquid Biopsy for Cerebral Aneurysms: Circulating RNA as Diagnostic and Prognostic Tools—A Systematic Review of Current Evidence and Perspectives
by Matteo Palermo, Alessandro Olivi and Carmelo Lucio Sturiale
Cells 2025, 14(19), 1525; https://doi.org/10.3390/cells14191525 - 30 Sep 2025
Viewed by 443
Abstract
Intracranial aneurysms (IAs) are potentially devastating cerebrovascular lesions, and predicting rupture risk remains a major clinical challenge. Conventional radiological and clinical scores offer only partial risk stratification, highlighting the need for complementary approaches. Liquid biopsy represents a promising non-invasive strategy to identify circulating [...] Read more.
Intracranial aneurysms (IAs) are potentially devastating cerebrovascular lesions, and predicting rupture risk remains a major clinical challenge. Conventional radiological and clinical scores offer only partial risk stratification, highlighting the need for complementary approaches. Liquid biopsy represents a promising non-invasive strategy to identify circulating biomarkers that reflect aneurysm biology and instability. We conducted a systematic review according to PRISMA 2020 guidelines, screening PubMed, Scopus, and Web of Science up to August 2025. Forty-eight eligible studies, encompassing 3515 IA patients, evaluated circulating RNA species, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in serum, plasma, blood, or cerebrospinal fluid. Multiple candidates emerged as consistently dysregulated: upregulation of miR-21, miR-126, and miR-200a-3p, and downregulation of miR-143 and let-7b-5p were recurrently observed across independent cohorts. LncRNAs, such as MALAT1 and MIAT, and circRNAs, including circ_0000690 and circ_0021001, demonstrated diagnostic and prognostic potential, with some correlating with rupture status and clinical severity indices. Despite encouraging findings, heterogeneity in study design, sample handling, and analytic methods limits reproducibility. Large-scale, multicenter validation studies are essential to translate these biomarkers into clinical practice. Full article
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