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Search Results (1,714)

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20 pages, 888 KB  
Review
Role of Genetic and Epigenetic Biomarkers in Treatment-Resistant Depression: A Literature Review
by Petra Sulić, Andrea Ražić Pavičić, Biljana Đapić Ivančić, Tamara Božina, Nada Božina and Maja Živković
Genes 2025, 16(12), 1443; https://doi.org/10.3390/genes16121443 - 2 Dec 2025
Abstract
Background: Treatment-resistant depression (TRD) affects up to 30–40% of patients with major depressive disorder and remains a major therapeutic challenge. Genetic and epigenetic factors are increasingly recognized as key contributors to both vulnerability and treatment response. Methods: We conducted a narrative review of [...] Read more.
Background: Treatment-resistant depression (TRD) affects up to 30–40% of patients with major depressive disorder and remains a major therapeutic challenge. Genetic and epigenetic factors are increasingly recognized as key contributors to both vulnerability and treatment response. Methods: We conducted a narrative review of studies published between 2021 and 2025, focusing exclusively on DNA- and RNA-based biomarkers of TRD. Twelve studies met the inclusion criteria, covering candidate gene analyses, genome-wide association studies (GWAS), neuroimaging–genetic approaches, and microRNA profiling. Results: Genetic investigations consistently implicate neuroplasticity-related genes (BDNF, NTRK2, PTEN, SYN1, MAPK1, and GSK3B) in the risk of TRD and its relapse. Variants in glutamatergic receptor genes (GRIN2A, GRIN2B, GRIA2, GRIA3) were predicted to result in a rapid and sustained response to ketamine. Genomic approaches further demonstrated that composite genetic panels outperform single-variant predictors. In parallel, microRNAs such as miR-1202, miR-16, miR-135, miR-124, miR-223, and miR-146a emerged as dynamic biomarkers of treatment response, particularly in cohorts treated with ketamine or electroconvulsive therapy. Conclusions: DNA- and RNA-based biomarkers provide promising avenues for improving the understanding and management of TRD. Their integration into clinical frameworks could support patient stratification, individualized treatment selection, and real-time monitoring of therapeutic efficacy. Future research should prioritize replication, methodological harmonization, and longitudinal validation to facilitate the translation of findings into precision psychiatry. Full article
(This article belongs to the Special Issue Psychiatric Pharmacogenomics)
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12 pages, 850 KB  
Article
Circulating miR-223-3p as an Independent Biomarker of Recurrent Thrombotic Risk After Ischemic Stroke
by Bence Balczó, Katalin Maricza, Krisztina Molnár, Zsuzsanna Elek, Zsófia Bánlaki, Réka Kovács-Nagy, Gergely Keszler, Zsolt Rónai, Abigél Molnár and Tihamér Molnár
Biomedicines 2025, 13(12), 2961; https://doi.org/10.3390/biomedicines13122961 - 1 Dec 2025
Abstract
Background: Circulating microRNAs (miRNAs) have emerged as potential biomarkers of platelet reactivity and thrombotic risk. Among them, miR-223-3p regulates P2Y12 receptor expression and may influence response to antiplatelet therapy. This study aimed to evaluate the prognostic value of selected circulating miRNAs in post-stroke [...] Read more.
Background: Circulating microRNAs (miRNAs) have emerged as potential biomarkers of platelet reactivity and thrombotic risk. Among them, miR-223-3p regulates P2Y12 receptor expression and may influence response to antiplatelet therapy. This study aimed to evaluate the prognostic value of selected circulating miRNAs in post-stroke patients receiving antiplatelet treatment. Methods: Sixty ischemic stroke survivors were prospectively enrolled and followed for 18 months for recurrent vascular events (stroke, transient ischemic attack, or myocardial infarction). Plasma levels of miR-126-3p, miR-223-3p, miR-24-3p, and miR-199a-5p were quantified using reverse transcription real-time PCR. Clinical data, antiplatelet regimen, statin use, and Essen Stroke Risk Scores (ESRS) were recorded. Logistic regression was applied to identify independent predictors of thrombotic events. Results: Expression of all examined miRNAs differed significantly across treatment groups. The dual antiplatelet therapy (DAPT) group showed the highest levels of miR-126-3p and miR-199a-5p (p < 0.01). Within the statin-naïve DAPT subgroup, lower miR-199a-5p levels (p < 0.001) were observed among patients who experienced ischemic events (n = 7/60; 12%; stroke = 4, TIA = 2, ACS = 1) during 18 months of follow-up. In multivariate analysis, reduced miR-223-3p remained the only independent predictor of recurrent thrombotic events (OR 1.18, 95% CI 1.01–1.37, p = 0.036), independent of ESRS and platelet reactivity. Elevated miR-126-3p and miR-199a-5p were associated with favorable treatment response, particularly among statin users. Conclusions: This study identifies low circulating miR-223-3p as an independent biomarker of thrombotic risk in post-stroke patients, potentially reflecting enhanced platelet activation via P2Y12 signaling. In contrast, higher miR-126-3p and miR-199a-5p levels may indicate more effective antiplatelet response. These findings support the potential utility of miRNA profiling for individualized antiplatelet therapy and long-term risk stratification after ischemic stroke. Full article
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40 pages, 847 KB  
Review
The Growing Significance of microRNAs in Osteoporosis
by Alika Sarkar, Sana Sarkar, Afreen Anwar, Ji Woong Kim, Jae-Hyuck Shim and Aijaz Ahmad John
Cells 2025, 14(23), 1905; https://doi.org/10.3390/cells14231905 - 1 Dec 2025
Abstract
Osteoporosis is an aging-related disease characterized by low bone mineral density and deteriorated bone structure, resulting in an increased risk of fractures. Currently, most osteoporosis therapies target osteoclasts to inhibit bone resorption, while the three FDA-approved anabolic agents include parathyroid hormone, parathyroid hormone-related [...] Read more.
Osteoporosis is an aging-related disease characterized by low bone mineral density and deteriorated bone structure, resulting in an increased risk of fractures. Currently, most osteoporosis therapies target osteoclasts to inhibit bone resorption, while the three FDA-approved anabolic agents include parathyroid hormone, parathyroid hormone-related protein, and anti-sclerostin antibody that promote osteoblast function. However, long-term treatment with these agents is associated with potential adverse effects and decreased therapeutic efficacy. This has prompted exploration of novel therapeutic strategies, including microRNAs (miRNAs), which are emerging as promising candidates. miRNAs have been reported to play important roles in regulating pathways involved in bone formation and resorption. In addition to their direct roles in osteoblasts and osteoclasts, miRNAs also serve as key mediators of communication between these cells, which is essential for maintaining bone homeostasis. The complexity of osteoporosis requires versatile regulators such as miRNAs that can modulate multiple biological pathways. Recent studies have demonstrated the potential of miRNA-based therapy to restore bone homeostasis in osteoporotic models. However, further studies are needed to develop tissue-specific delivery systems and evaluate long-term safety to improve the therapeutic potential of miRNAs as new osteoporosis drugs. Full article
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18 pages, 3122 KB  
Article
Long Non-Coding RNA DUXAP10 Promotes Tumorigenesis and Metastasis in Anaplastic Thyroid Cancer
by Nicole R. DeSouza, Michelle Carnazza, Tara Jarboe, Danielle Quaranto, Kaci Kopec, Anthony J. Centone, Kate Nielsen, Robert Suriano, Augustine Moscatello, Humayun K. Islam, Xiu-Min Li, Jan Geliebter and Raj K. Tiwari
Cancers 2025, 17(23), 3852; https://doi.org/10.3390/cancers17233852 (registering DOI) - 30 Nov 2025
Abstract
Background: Long non-coding RNAs (lncRNAs) are regulatory molecules that have multifaceted impacts on the carcinogenic molecular landscape—with pathologic consequences when aberrantly expressed. Anaplastic thyroid cancer (ATC) is a rapidly progressing and highly lethal malignancy, with mortality rates approaching 100%. The molecular/transcriptomic signature [...] Read more.
Background: Long non-coding RNAs (lncRNAs) are regulatory molecules that have multifaceted impacts on the carcinogenic molecular landscape—with pathologic consequences when aberrantly expressed. Anaplastic thyroid cancer (ATC) is a rapidly progressing and highly lethal malignancy, with mortality rates approaching 100%. The molecular/transcriptomic signature of ATC has significant gaps in understanding; thus, a comprehensive study of ATC non-coding RNA transcript regulation is necessary. Results: The lncRNA Double Homeobox A Pseudogene 10 (DUXAP10) was identified in patient genomic datasets as a highly upregulated transcript in ATC vs. normal thyroid tissue. DUXAP10 expression was transcriptionally repressed with CRISPR-interference (CRISPRi), and data supports an extensive role of DUXAP10 in several cancer-promoting phenotypes in ATC, both in vitro and in vivo. Our two DUXAP10-CRISPRi cell lines significantly reduced the rapid growth and metastatic behaviors characteristic of ATC, affecting proliferation, viability, clonogenicity, apoptosis, invasion, migration, tumorigenesis, and metastasis. Conclusion: Thus, DUXAP10 is a proposed prognostic marker and therapeutic target for ATC disease propagation and progression. Full article
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20 pages, 1788 KB  
Article
miRNA-155-3p and miRNA-3196 as Potential Biomarkers in Liquid Biopsies of Non-Small Cell Lung Cancer Patients
by Daniela Alexandre, Joana Polido, Salete Valente, Daniel Pimenta Rocha, Alexandra R. Fernandes, Pedro V. Baptista and Carla Cruz
Biomedicines 2025, 13(12), 2946; https://doi.org/10.3390/biomedicines13122946 - 29 Nov 2025
Viewed by 62
Abstract
Background/Objectives: Late diagnosis hampers effective treatment of non-small cell lung cancer (NSCLC). This study evaluated whether circulating microRNAs (miRs), miR-155 and miR-3196, measured in liquid biopsy peripheral blood mononuclear cells (PBMCs), can serve as potential non-invasive biomarkers for NSCLC diagnosis, patient stratification, [...] Read more.
Background/Objectives: Late diagnosis hampers effective treatment of non-small cell lung cancer (NSCLC). This study evaluated whether circulating microRNAs (miRs), miR-155 and miR-3196, measured in liquid biopsy peripheral blood mononuclear cells (PBMCs), can serve as potential non-invasive biomarkers for NSCLC diagnosis, patient stratification, therapy monitoring, and prognosis. Methods: RNA was isolated from PBMCs of 136 NSCLC patients and 64 healthy donors. RT–qPCR quantified miR expression in PBMCs after predefined QC filtering: miR-155-3p (NSCLC n = 63; controls n = 28), miR-3196 (NSCLC n = 55; controls n = 28), and miR-155-5p (NSCLC n = 23; controls n = 12). Diagnostic performance was assessed using receiver operating characteristic (ROC) analyses, reporting area under the curve (AUC), and threshold-dependent sensitivity/specificity. Survival was analyzed with Kaplan–Meier/Cox methods. Associations with clinicopathological variables (stage, metastasis, smoking, EGFR, and KRAS status), treatment response (chemotherapy, immunotherapy, TKIs), and survival outcomes were examined. Results: miR-155-3p was upregulated in NSCLC, whereas miR-3196 was downregulated relative to controls; AUCs were 0.881 and 0.784, respectively. At high-sensitivity operating points, specificity was lower (≈29–30%), consistent with PBMC miRs reflecting both immune activation and tumor burden. In adenocarcinoma, miR-155-3p was associated with advanced stage, metastatic disease and smoking history. miR-3196 aligned with features of metastatic progression. During systemic therapy (chemotherapy, immunotherapy, TKIs), circulating levels of both miRs tended to normalize. Notably, normalization of miR-155-3p levels was associated with improved overall survival, supporting its prognostic value and utility for treatment monitoring. Conclusions: Circulating miR-155-3p and miR-3196 in PBMCs are promising screening/monitoring non-invasive candidates rather than stand-alone NSCLC diagnostics at current thresholds. Combining these miRs with additional biomarkers and/or clinical covariates and tuning decision thresholds may enhance specificity for diagnostic use. While preliminary, these findings warrant validation in large, prospective studies with standardized protocols to enable clinical implementation. Full article
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19 pages, 1605 KB  
Review
Toward Personalized Response Monitoring in Melanoma Patients Treated with Immunotherapy and Target Therapy
by Federico Venturi, Elisabetta Magnaterra, Alberto Gualandi, Biagio Scotti, Carlotta Baraldi, Aurora Maria Alessandrini, Leonardo Veneziano, Elena Maria Cama, Barbara Melotti, Paola Valeria Marchese, Daniela Tassone, Simone Ribero, Marco Ardigò and Emi Dika
Diagnostics 2025, 15(23), 3054; https://doi.org/10.3390/diagnostics15233054 - 29 Nov 2025
Viewed by 70
Abstract
Background/Objectives: Immunotherapy and targeted therapy have revolutionized the treatment of advanced cutaneous melanoma. However, predicting individual response and managing resistance remain major challenges. This narrative review aims to evaluate the prognostic and predictive value of treatment-related adverse events (TRAEs) and circulating biomarkers—including lactate [...] Read more.
Background/Objectives: Immunotherapy and targeted therapy have revolutionized the treatment of advanced cutaneous melanoma. However, predicting individual response and managing resistance remain major challenges. This narrative review aims to evaluate the prognostic and predictive value of treatment-related adverse events (TRAEs) and circulating biomarkers—including lactate dehydrogenase (LDH), circulating tumor DNA (ctDNA), and microRNAs (miRNAs)—in anticipating therapeutic outcomes and personalizing treatment strategies. Methods: A comprehensive literature search was conducted across PubMed, Scopus, and Web of Science for studies published between January 2010 and September 2025. Eligible studies included clinical trials, observational cohorts, and translational research evaluating biomarkers or toxicity profiles in melanoma patients receiving immune checkpoint inhibitors or BRAF/MEK inhibitors. Emphasis was placed on dynamic indicators of treatment efficacy and integrative modeling approaches. Results: Evidence indicates that the emergence of low-to-moderate grade TRAEs—especially immune-related events like vitiligo, thyroiditis, and rash—is positively associated with response to immunotherapy. Similarly, pyrexia and dermatologic toxicities may correlate with outcomes under BRAF/MEK inhibition. ctDNA clearance within 6–12 weeks of therapy strongly predicts durable response and precedes radiologic changes. Specific miRNAs (e.g., miR-21-5p, miR-146a-5p) demonstrate dynamic modulation during treatment and may signal response or resistance. Interferon-driven gene expression profiles further stratify tumors into “hot” or “cold” immune phenotypes, refining predictive accuracy. Conclusions: Integrative models combining TRAEs, ctDNA, miRNA signatures, and interferon-related gene expression offer a multi-dimensional framework for early, individualized response monitoring. Prospective validation, harmonization of assays, and incorporation into adaptive clinical workflows are key to translating these insights into personalized melanoma care. Full article
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44 pages, 2533 KB  
Review
Epigenetic and Transcriptional Reprogramming in 3D Culture Models in Breast Cancer
by Laura Cecilia Flores-García, Karla Rubio, Eloisa Ibarra-Sierra, Macrina B. Silva-Cázares, Carlos Palma-Flores and César López-Camarillo
Cancers 2025, 17(23), 3830; https://doi.org/10.3390/cancers17233830 (registering DOI) - 29 Nov 2025
Viewed by 70
Abstract
Breast cancer remains the leading cause of cancer-related death in women worldwide. This disease is characterized by its molecular and phenotypic heterogeneity, which hinders the development of effective therapies. While two-dimensional (2D) monolayer cell cultures are widely used, they are insufficient to reproduce [...] Read more.
Breast cancer remains the leading cause of cancer-related death in women worldwide. This disease is characterized by its molecular and phenotypic heterogeneity, which hinders the development of effective therapies. While two-dimensional (2D) monolayer cell cultures are widely used, they are insufficient to reproduce the characteristics of the tumor microenvironment, thus limiting our understanding of cancer biology. In this context, three-dimensional (3D) models have emerged as representative tools that more accurately reproduce tissue architecture, cell signaling, and nutrients and oxygen gradients. These cellular models offer greater similarity to primary tissues, improving the study of relevant biological processes. Although 3D cultures provide numerous advantages in cancer research, there is no unified model that standardizes the matrix type and parameters such as gelation time or porosity, hindering the reproducibility and interpretability of the data. This review integrates evidence from various studies to evaluate the effect of epigenetic variations generated by 3D culture methods, which are regulated by mechanotransduction and, consequently, by signaling pathways such as integrin/FAK-ILK/Rho-YAP derived from interactions of cells with extracellular matrix-enriched scaffolds. This affects processes such as DNA methylation, histone coding, and the regulation of non-coding RNAs such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in different molecular subtypes of breast cancer. Overall, the evidence highlights that 3D culture methods are not equivalent but rather generate distinct epigenetic signatures at the non-coding RNA level that influence the proliferation, differentiation, therapeutic resistance, and metastatic potential of tumor cells. Furthermore, the evidence suggests that histone coding patterns, primarily through the reduction of acetylation marks, are conserved regardless of the type of 3D culture. In summary, the study highlights that the microarchitectural and compositional characteristics of 3D scaffolds are key determinants of epigenetic plasticity. Full article
(This article belongs to the Special Issue 3D Cultures and Organoids in Cancer Research)
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21 pages, 643 KB  
Review
MicroRNA-221: A Context-Dependent Mediator in Human Diseases—Highlights from Molecular Mechanisms to Clinical Translation
by Qiu-Xiao Ren, Qian Zhao, Na Wu, Wanying Du, Zhaoyue Liu, Weiping J. Zhang and An-Jing Ren
Cells 2025, 14(23), 1896; https://doi.org/10.3390/cells14231896 - 28 Nov 2025
Viewed by 76
Abstract
MicroRNA-221 (miR-221), a conserved small non-coding RNA, acts as a pivotal modulator of biological processes across multiple organ systems, the dysregulation of which is closely linked to the pathogenesis of various human diseases. This review systematically summarizes its multifaceted roles in cancer, cardiovascular [...] Read more.
MicroRNA-221 (miR-221), a conserved small non-coding RNA, acts as a pivotal modulator of biological processes across multiple organ systems, the dysregulation of which is closely linked to the pathogenesis of various human diseases. This review systematically summarizes its multifaceted roles in cancer, cardiovascular diseases (CVDs), neurological disorders, digestive system diseases, respiratory conditions, and adipose-endocrine dysfunction. In cancer, miR-221 exerts context-dependent oncogenic/tumor-suppressive effects by targeting phosphatase and tensin homolog (PTEN), cyclin-dependent kinase inhibitor 1c (CDKN1C/p57), and BCL2 modifying factor (Bmf), thereby regulating cell proliferation, invasion, stemness, and resistance to cancer therapy; it also serves as a non-invasive biomarker for glioma, papillary thyroid carcinoma, and colorectal cancer. In the cardiovascular system, it balances antiviral defense in viral myocarditis, modulates ventricular fibrotic remodeling in heart failure, and regulates endothelial function in atherosclerosis, with cell-type/ventricle-specific effects. In neurological disorders, it protects dopaminergic neurons in Parkinson’s disease and modulates microglial activation in epilepsy. It also regulates hepatic pathogen defense and intestinal mucosal immunity. Mechanistically, miR-221 alters cellular phenotypes by targeting tumor suppressors or signaling components (e.g., PI3K/AKT, TGF-β/suppressor of mothers against decapentaplegic homolog(SMAD), Wnt/β-catenin). Therapeutically, miR-221-targeting strategies show preclinical promise in cancer and CVDs. Despite this progress, further studies are needed to resolve context-dependent functional discrepancies, validate biomarker utility, and develop cell-specific delivery systems. This review provides a framework to understand its pathophysiologcial roles and potential application as a biomarker and therapeutic target. Full article
(This article belongs to the Special Issue The Silent Regulators: Non-Coding RNAs in Cell Function and Disease)
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0 pages, 4208 KB  
Article
Isolation of Red Beet Plant-Derived Nanovesicles, and Characterization of Their Molecular Content and Biological Activities in Human Cells
by Clarissa Zanotti, Antonio Dario Troise, Simona Arena, Giovanni Renzone, Sabrina De Pascale, Rosalia Ferracane, Chiara Pontecorvi, Chiara Niespolo, Angelo Gismondi, Andrea Scaloni and Mauro Marra
Int. J. Mol. Sci. 2025, 26(23), 11261; https://doi.org/10.3390/ijms262311261 - 21 Nov 2025
Viewed by 183
Abstract
Nowadays, growing evidence indicates that plant-derived nanovesicles cross biological barriers between species, including humans, and deliver therapeutic molecules that influence gene expression, affecting various processes such as inflammation, oxidative stress, and cancer. For these reasons, plant-derived nanovesicles are gaining attention as a valuable [...] Read more.
Nowadays, growing evidence indicates that plant-derived nanovesicles cross biological barriers between species, including humans, and deliver therapeutic molecules that influence gene expression, affecting various processes such as inflammation, oxidative stress, and cancer. For these reasons, plant-derived nanovesicles are gaining attention as a valuable substitute for mammalian exosomes as they offer benefits such as reduced immunogenicity, enhanced bioavailability, and the inclusion of beneficial plant metabolites. However, the development of affordable plant-derived nanovesicle-based therapies requires a robust characterization of their molecular structure and cargo, which in turn depends on obtaining sufficient quantities of homogeneous nanovesicle populations. In this study, we used an advanced purification platform combining ultrafiltration and anion exchange chromatography to isolate highly pure plant-derived nanovesicles from a new source, Beta vulgaris L. These particles were characterized in terms of size, charge, and morphology, and their molecular content was analyzed by omic technologies, including proteomics, lipidomics, and miRNomics. Their ability to promote wound healing and reduce inflammation was demonstrated in vitro using human cells. Furthermore, bioinformatic analysis linking the microRNA profile with potential human target genes provides insights into the biochemical pathways that underlie the bioactivity of nanovesicles. Full article
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29 pages, 941 KB  
Review
Nanoparticles Used for the Delivery of RNAi-Based Therapeutics
by Tianrui Ren, Liang Ma, Ping Fu and Chuyue Zhang
Pharmaceutics 2025, 17(11), 1502; https://doi.org/10.3390/pharmaceutics17111502 - 20 Nov 2025
Viewed by 731
Abstract
RNA interference (RNAi) offers programmable, sequence-specific silencing via small interfering RNA (siRNA) and microRNA (miRNA), but clinical translation hinges on overcoming instability, immunogenicity, and inefficient endosomal escape. This review synthesizes advances in non-viral nanocarriers—liposomes, polymeric nanoparticles, and extracellular vesicles (EVs)—that stabilize nucleic acids, [...] Read more.
RNA interference (RNAi) offers programmable, sequence-specific silencing via small interfering RNA (siRNA) and microRNA (miRNA), but clinical translation hinges on overcoming instability, immunogenicity, and inefficient endosomal escape. This review synthesizes advances in non-viral nanocarriers—liposomes, polymeric nanoparticles, and extracellular vesicles (EVs)—that stabilize nucleic acids, tune biodistribution, and enable organ- and cell-selective delivery. We highlight design levers that now define the field: ligand-guided targeting, stimuli-responsive release, biomimicry and endogenous carriers, and rational co-delivery with small molecules. Across major disease areas—cancer and cardiovascular, respiratory, and urological disorders—these platforms achieve tissue-selective uptake (e.g., macrophages, endothelium, and myocardium), traverse physiological barriers (including the blood–brain barrier and fibrotic stroma), and remodel hostile microenvironments or immune programs to enhance efficacy while maintaining favorable safety profiles. Early clinical studies reflect this diversity, spanning targeted nanoparticles, local drug depots, exosome and cellular carriers, and inhaled formulations, e.g., and converge on core phase-I endpoints (safety, maximum tolerated dose, pharmacokinetics/pharmacodynamics, and early activity). Looking ahead, priorities include good manufacturing practice scale, consistent manufacture—especially for EVs; more efficient loading and cargo control; improved endosomal escape and biodistribution; and rigorous, long-term safety evaluation with standardized, head-to-head benchmarking. Emerging directions such as in vivo EVs biogenesis, theragnostic integration, and data-driven formulation discovery are poised to accelerate translation. Collectively, nanoparticle-enabled RNAi has matured into a versatile, clinically relevant toolkit for precise gene silencing, positioning the field to deliver next-generation therapies across diverse indications. Full article
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53 pages, 1390 KB  
Review
Non-Coding RNA in Type 2 Diabetes Cardio–Renal Complications and SGLT2 Inhibitor Response
by Elena Rykova, Elena Shmakova, Igor Damarov, Tatiana Merkulova and Julia Kzhyshkowska
Int. J. Mol. Sci. 2025, 26(22), 11198; https://doi.org/10.3390/ijms262211198 - 19 Nov 2025
Viewed by 301
Abstract
Type 2 diabetes mellitus (T2DM) is characterized by an uncontrolled increase in blood glucose levels and insulin resistance in cells of various tissues. Vascular complications in T2DM have an inflammatory nature. Drugs with different mechanisms of action have been developed and used to [...] Read more.
Type 2 diabetes mellitus (T2DM) is characterized by an uncontrolled increase in blood glucose levels and insulin resistance in cells of various tissues. Vascular complications in T2DM have an inflammatory nature. Drugs with different mechanisms of action have been developed and used to treat T2DM, initially aimed at controlling blood glucose levels. Among them, sodium-glucose cotransporter 2 inhibitors (SGLT2-i) were developed as specific inhibitors of glucose reabsorption in the kidneys, but along with lowering blood glucose levels, they demonstrated multiple (including non-glycemic) positive effects in the treatment of T2DM related to their beneficial effects on the immune system. SGLT2 inhibitors can reduce the risk of diabetic cardiomyopathy (DCM) and chronic kidney disease (CKD) development in patients with and without diabetes. SGLT2-is improve cardio-renal complications through a number of signaling pathways, including those dependent on the involvement of non-coding RNAs (ncRNAs) and their targets. The best-studied classes of ncRNAs are microRNAs, which are short (less than 200 bases) RNAs (miRNAs), long non-coding RNAs (lncRNAs) (more than 200 bases), and circular RNAs (circRNAs). The regulatory effect of ncRNAs has broad physiological significance, and changes in the ncRNAs’ expression are associated with the pathogenesis of different diseases, including T2DM. RNA-seq allows the construction of networks of interactions of lncRNA/circRNA-miRNA-mRNA called competitive endogenous RNA (ceRNA) networks, to identify clinically significant molecular markers, to improve the mechanistic understanding of pathogenesis, and to contribute to the development of new diagnostics and therapies. Our review summarizes the role of non-coding RNA in the action of SGLT2 inhibitors in cardio-renal complications in T2DM. We focus on methods of detection, genetics, and the effects of non-coding RNA. Specific attention is given to the role of non-coding RNAs in the inflammatory reactions of innate immune cells in relation to the SGLT2 inhibitors. Full article
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28 pages, 2510 KB  
Review
Function and Mechanism of Small Nucleolar RNAs (snoRNAs) and Their Host Genes (SNHGs) in Malignant Tumors
by Jiaji Yu, Yingjie Shao and Wendong Gu
Biomolecules 2025, 15(11), 1625; https://doi.org/10.3390/biom15111625 - 19 Nov 2025
Viewed by 343
Abstract
Small nucleolar RNAs (snoRNAs) and their host genes (SNHGs) are non-coding RNAs that are integral to tumorigenesis and progression. snoRNAs contribute to tumor progression primarily through RNA modification and engagement in intracellular signaling, and by serving as precursors for small nucleolar RNA-derived RNAs [...] Read more.
Small nucleolar RNAs (snoRNAs) and their host genes (SNHGs) are non-coding RNAs that are integral to tumorigenesis and progression. snoRNAs contribute to tumor progression primarily through RNA modification and engagement in intracellular signaling, and by serving as precursors for small nucleolar RNA-derived RNAs (sdRNAs) that exert microRNA (miRNA)-like or epigenetic regulatory functions. SNHGs modulate key tumor cell behaviors—including proliferation, metastasis, and resistance to therapy—through competing endogenous RNA (ceRNA)-mediated interactions and epigenetic mechanisms. Their combined influence significantly impacts patient prognosis. Across diverse malignancies such as neurologic, bone, and head and neck cancers, snoRNAs and SNHGs exhibit cancer-specific regulatory dynamics; for instance, in glioblastoma, snoRNAs and their derived fragments (sdRNAs) contribute to intratumoral heterogeneity by mediating both metabolic reprogramming and epigenetic remodeling, while their mediated modulation of cellular proliferation and metastatic potential is evident in breast cancer. Concurrently, several snoRNAs and SNHGs have emerged as potential diagnostic and prognostic biomarkers, as well as therapeutic targets. Preclinical interventions targeting select snoRNAs or SNHGs have demonstrated promising therapeutic outcomes. This study reviews current insights into the oncogenic functions and signaling networks associated with dysregulated snoRNAs and SNHGs in malignancies, while highlighting novel avenues for future investigation in this domain. Full article
(This article belongs to the Section Molecular Genetics)
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22 pages, 685 KB  
Review
miRNA and Its Implications in the Treatment Resistance in Breast Cancer—Narrative Review of What Do We Know So Far
by Isabela Anda Komporaly, Adelina Silvana Gheorghe, Lidia Anca Kajanto, Elena Adriana Iovănescu, Bogdan Georgescu, Raluca Ioana Mihăilă, Andreea Mihaela Radu, Daniela Luminița Zob, Mara Mădălina Mihai, Mihai Teodor Georgescu and Dana Lucia Stănculeanu
Non-Coding RNA 2025, 11(6), 78; https://doi.org/10.3390/ncrna11060078 - 18 Nov 2025
Viewed by 408
Abstract
Breast cancer remains a leading cause of cancer-related mortality worldwide, with treatment resistance and tumor heterogeneity posing major clinical challenges. MicroRNAs (miRNAs), small non-coding RNAs regulating gene expression, have emerged as key players in breast cancer biology, influencing tumor initiation, progression, and therapy [...] Read more.
Breast cancer remains a leading cause of cancer-related mortality worldwide, with treatment resistance and tumor heterogeneity posing major clinical challenges. MicroRNAs (miRNAs), small non-coding RNAs regulating gene expression, have emerged as key players in breast cancer biology, influencing tumor initiation, progression, and therapy resistance. This narrative review synthesizes recent evidence on the involvement of miRNAs in breast cancer subtypes and their impact on treatment response. Notably, miR-155, miR-503, and miR-21 have shown potential as non-invasive biomarkers and modulators of pathways such as PI3K-Akt, MAPK, and TNF signaling. Additionally, exosomal miRNAs may reflect chemoresistance profiles and predict pathological response to neoadjuvant therapy. Emerging data also support the use of specific miRNAs to sensitize tumors to radiotherapy or modulate immune checkpoints like PD-L1 in triple-negative breast cancer. However, challenges persist regarding standardization, sample types, and study heterogeneity. Further translational research is needed to validate miRNA signatures and their utility in guiding personalized treatment. By highlighting mechanistic insights and potential clinical applications, this review aims to contribute to the ongoing efforts of integrating miRNAs into precision oncology for breast cancer. Full article
(This article belongs to the Special Issue Non-coding RNA as Biomarker in Cancer)
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28 pages, 2012 KB  
Review
Role of Anti-Inflammatory and Antioxidant Properties of Natural Products in Curing Cardiovascular Diseases
by Amit Kulkarni, Chaitra Chidambar Kulkarni, Seetur Radhakrishna Pradeep, Jagadeesha Poyya, Avinash Kundadka Kudva, Vijay Radhakrishnan and Ajay Sathyanarayanrao Khandagale
Curr. Issues Mol. Biol. 2025, 47(11), 955; https://doi.org/10.3390/cimb47110955 - 17 Nov 2025
Viewed by 514
Abstract
Cardiovascular diseases (CVDs) remain a leading cause of mortality worldwide. According to the WHO, every year, there is an increase in the rate of death globally due to CVDs, stroke, and myocardial infarction. Several risk factors contribute to the development of CVDs, one [...] Read more.
Cardiovascular diseases (CVDs) remain a leading cause of mortality worldwide. According to the WHO, every year, there is an increase in the rate of death globally due to CVDs, stroke, and myocardial infarction. Several risk factors contribute to the development of CVDs, one of which is hypoxia, defined as a reduction in oxygen levels. This major stressor affects aerobic species and plays a crucial role in the development of cardiovascular disease. Research has uncovered the “hypoxia-inducible factors (HIFs) switch” and investigated the onset, progression, acute and chronic effects, and adaptations of hypoxia, particularly at high altitudes. The hypoxia signalling pathways are closely linked to natural rhythms such as the circadian rhythm and hibernation. In addition to genetic and evolutionary factors, epigenetics also plays an important role in postnatal cardiovascular responses to hypoxia. Oxidized LDL-C initiates atherosclerosis amidst oxidative stress, inflammation, endothelial dysfunction, and vascular remodelling in CVD pathogenesis. Anti-inflammatory and antioxidant biomarkers are needed to identify individuals at risk of cardiovascular events and enhance risk prediction. Among these, C-reactive protein (CRP) is a recognized marker of vascular inflammation in coronary arteries. Elevated pro-atherogenic oxidized LDL (oxLDL) expression serves as an antioxidant marker, predicting coronary heart disease in apparently healthy men. Natural antioxidants and anti-inflammatory molecules protect the heart by reducing oxidative stress, enhancing vasodilation, and improving endothelial function. For instance, the flavonoid quercetin exerts antioxidant and anti-inflammatory effects primarily by activating the Nrf2/HO-1 signaling pathway, thereby enhancing cellular antioxidant defense and reducing reactive oxygen species. Carotenoids, such as astaxanthin, exhibit potent antioxidant activity by scavenging free radicals and preserving mitochondrial integrity. The alkaloid berberine mediates cardiovascular benefits through activation of AMO-activated protein kinase (AMPK) and inhibition of nuclear factor kappa B [NF-kB] signalling, improving lipid metabolism and suppressing inflammatory cytokines. Emerging evidence highlights microRNAs (miRNAs) as potential regulators of oxidative stress via endothelial nitric oxide synthase (eNOS) and silent mating-type information regulation 2 homolog (SIRT1). While the exact mechanisms remain unclear, their benefits are likely to include antioxidant and anti-inflammatory effects, notably reducing the susceptibility of low-density lipoproteins to oxidation. Additionally, the interactions between organs under hypoxia signalling underscore the need for a comprehensive regulatory framework that can support the identification of therapeutic targets, advance clinical research, and enhance treatments, including FDA-approved drugs and those in clinical trials. Promising natural products, including polysaccharides, alkaloids, saponins, flavonoids, and peptides, as well as traditional Indian medicines, have demonstrated anti-hypoxic properties. Their mechanisms of action include increasing haemoglobin, glycogen, and ATP levels, reducing oxidative stress and lipid peroxidation, preserving mitochondrial function, and regulating genes related to apoptosis. These findings emphasise the importance of anti-hypoxia research for the development of effective therapies to combat this critical health problem. A recent approach to controlling CVDs involves the use of antioxidant and anti-inflammatory therapeutics through low-dose dietary supplementation. Despite their effectiveness at low doses, further research on ROS, antioxidants, and nutrition, supported by large multicentre trials, is needed to optimize this strategy. Full article
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Systematic Review
Hypoxia-Induced Extracellular Vesicles and Non-Coding RNAs in Cancer: A Systematic Review of Tumor Dynamics and Therapeutic Implications in Preclinical Animal Models
by Joao Pedro R. Afonso, Simona Taverna, Annalisa Pinsino, Giuseppe Cammarata, Rodrigo A. C. Andraus, Iranse O. Silva, Carlos H. M. Silva, Claudia S. Oliveira, Rodrigo F. Oliveira, Deise A. A. P. Oliveira, Orlando A. Guedes, Luciana P. Maia, Wilson R. Freitas Junior, Elias J. Ilias, Juan J. Uriarte, Giuseppe Insalaco and Luis V. F. Oliveira
Biomedicines 2025, 13(11), 2796; https://doi.org/10.3390/biomedicines13112796 - 17 Nov 2025
Viewed by 330
Abstract
Background: Cancer is a heterogeneous pathology, and among causative factors, gene expression can influence its development. Molecular approaches using extracellular vesicles (EVs) and non-coding RNAs (ncRNAs) offer great value in understanding tumor progression, early diagnosis, and potential therapies. Objectives: This systematic review was [...] Read more.
Background: Cancer is a heterogeneous pathology, and among causative factors, gene expression can influence its development. Molecular approaches using extracellular vesicles (EVs) and non-coding RNAs (ncRNAs) offer great value in understanding tumor progression, early diagnosis, and potential therapies. Objectives: This systematic review was conducted in accordance with the Preferred Items for Reporting of Systematic Reviews and Meta-Analyses guidelines. Its main objective was to evaluate the effects of cellular hypoxia in different types of cancer, exclusively using animal models and highlighting the regulatory role of microRNAs and circular RNAs in tumor development. Methods: A literature review was performed using the PubMed/Medline and Scopus databases without year limitations. The initial search yielded 171 articles. After applying the inclusion and exclusion criteria, 25 studies were included in this review. Data analysis showed that animal models provide detailed insights into different types of cancers under hypoxic conditions. Results: Our analysis identified that specific circRNAs, such as circPFKFB4 in breast cancer and circPDK1 in pancreatic cancer, are consistently associated with a worse prognosis and therapeutic resistance. Similarly, miRNAs such as miR-1287-5p (breast cancer) and miR-133a (colorectal cancer) have frequently been identified as tumor suppressors whose levels are altered by hypoxic conditions. Furthermore, the results suggested that in some cancers, the release of EVs may facilitate tumor progression and metastasis. However, manipulation of ncRNA expression causes significant changes in the tumor response, which suggests a therapeutic response. Conclusions: This study shows that the use of animal models is essential for exploring the molecular mechanisms of cancer and establishing new therapeutic approaches. Full article
(This article belongs to the Special Issue New Insights in Hypoxic Response Modulation)
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