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18 pages, 3266 KB  
Article
Application and Effect of Micropeptide miPEP164c on Flavonoid Pathways and Phenolic Profiles in Grapevine “Vinhão” Cultivar
by Mariana Vale, Arnaud Lanoue, Cécile Abdallah, Hernâni Gerós and Artur Conde
Agronomy 2026, 16(1), 97; https://doi.org/10.3390/agronomy16010097 - 29 Dec 2025
Viewed by 527
Abstract
Climate change increasingly challenges viticulture, demanding innovative and sustainable strategies to preserve grapevine productivity and grape quality. MicroRNA-encoded peptides (miPEPs) have emerged as natural regulators of gene expression, providing a novel mechanism for fine-tuning plant metabolism. Here, we evaluated whether exogenous application of [...] Read more.
Climate change increasingly challenges viticulture, demanding innovative and sustainable strategies to preserve grapevine productivity and grape quality. MicroRNA-encoded peptides (miPEPs) have emerged as natural regulators of gene expression, providing a novel mechanism for fine-tuning plant metabolism. Here, we evaluated whether exogenous application of miPEP164c, previously shown to repress VviMYBPA1 in vitro, can modulate flavonoid pathways in field-grown grapevines (Vitis vinifera L. cv. Vinhão). Grape clusters were sprayed with 1 µM miPEP164c before and during véraison, and molecular, biochemical, and metabolomic analyses were performed at harvest. miPEP164c treatment significantly upregulated pre-miR164c transcripts, leading to post-transcriptional silencing of VviMYBPA1 and strong downregulation of the proanthocyanidin-related genes VviLAR1, VviLAR2, and VviANR. Correspondingly, LAR and ANR activities were reduced by up to 75%, and total proanthocyanidin content decreased by nearly 30%. Metabolomic profiling showed reduced flavan-3-ols and moderate shifts in phenolic acids and stilbenoids, while anthocyanins increased slightly. Overall, miPEP164c reprogrammed flavonoid metabolism under vineyard conditions, selectively lowering tannin biosynthesis without affecting other key phenolics. These findings establish miPEPs as promising biostimulants for precise modulation of grape berry composition, offering new tools for urgently needed sustainable and precision viticulture and improved wine quality under climate change and the increasing environmental challenges it poses. Full article
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13 pages, 1306 KB  
Review
Plant-Derived miRNAs as Potential Cross-Kingdom Cancer Regulators
by Aizhan Rakhmetullina, Zuzanna Lubas and Piotr Zielenkiewicz
Genes 2025, 16(12), 1441; https://doi.org/10.3390/genes16121441 - 2 Dec 2025
Cited by 1 | Viewed by 727
Abstract
MicroRNAs (miRNAs) are key posttranscriptional regulators of gene expression that influence cancer initiation, progression, and therapeutic response. While most studies have focused on endogenous miRNAs, emerging evidence has highlighted the role of plant-derived miRNAs as exogenous dietary regulators capable of cross-kingdom gene modulation. [...] Read more.
MicroRNAs (miRNAs) are key posttranscriptional regulators of gene expression that influence cancer initiation, progression, and therapeutic response. While most studies have focused on endogenous miRNAs, emerging evidence has highlighted the role of plant-derived miRNAs as exogenous dietary regulators capable of cross-kingdom gene modulation. This review summarises current knowledge regarding plant-derived miRNAs and their ability to regulate human cancer-related genes. Experimental findings indicate that plant miRNAs can withstand gastrointestinal digestion, enter the circulation, and regulate the expression of oncogenes, tumour suppressors, long noncoding RNAs, and immune checkpoint molecules via canonical RNA-induced silencing mechanisms. Specific examples include miR-156a, miR-159a-3p, miR-166a, miR-167e-5p, miR-171, miR-395e, miR-2911, miR-4995 and miR-5754, which exhibit anticancer activities across various cancer types and modulate key signalling pathways in mammalian cells, highlighting their potential as cross-kingdom regulators with therapeutic relevance. In addition to these characterised miRNAs, certain plant groups, which are rich in bioactive compounds, remain unexplored as sources of functional miRNAs, representing a promising avenue for future research. Collectively, these studies underscore the ability of plant-derived miRNAs to modulate mammalian gene expression and suggest their potential as diet-based or synthetic therapeutic agents. Further investigations into their bioavailability, target specificity, and functional relevance could inform innovative strategies for cancer prevention, integrating nutritional, molecular biological, and therapeutic approaches. Full article
(This article belongs to the Special Issue Function and Regulatory Mechanism of MicroRNAs in Cancers)
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22 pages, 1098 KB  
Review
Circulating microRNAs and Plasma Gelsolin as Biomarkers of Sepsis: Molecular Insights and Prospects for Precision Medicine
by Mircea Stoian, Leonard Azamfirei, Sergio Rares Bandila, Adina Stoian, Dragoș-Florin Babă and Claudia Bănescu
Biomolecules 2025, 15(11), 1621; https://doi.org/10.3390/biom15111621 - 18 Nov 2025
Cited by 1 | Viewed by 991
Abstract
Sepsis is a major medical emergency, characterized by a dysfunctional immune response to infection, which often progresses to multiple organ failure and death. Early diagnosis and prognostic evaluation present significant challenges due to limitations in the specificity and sensitivity of traditional biomarkers. This [...] Read more.
Sepsis is a major medical emergency, characterized by a dysfunctional immune response to infection, which often progresses to multiple organ failure and death. Early diagnosis and prognostic evaluation present significant challenges due to limitations in the specificity and sensitivity of traditional biomarkers. This narrative review summarizes recent evidence on the potential of circulating microRNAs (miRNAs) such as miR-150, miR-146a, miR-223, miR-155, miR-122, and miR-4772-5p and plasma gelsolin (pGSN) as diagnostic and prognostic markers in sepsis. We discuss mechanisms involved and their potential for integration with artificial intelligence (AI) in personalized medicine. PubMed, Embase, and Web of Science databases were searched for relevant literature. Original research, systematic reviews, and meta-analyses focused on the diagnostic or prognostic value of circulating miRNAs or pGSN in sepsis were included; opinion papers and case reports were excluded. Altered expression of certain circulating microRNAs correlates with disease severity and mortality. Among circulating microRNAs (miRNAs), miR-122 and miR-150 have become the most consistently validated biomarkers in clinical studies, associated with sepsis severity and death rates. Additionally, other miRNAs such as miR-146a, miR-155, and miR-223 play roles in modulating immune and endothelial responses, highlighting the complex regulation of sepsis pathophysiology. Low pGSN concentrations at admission are associated with severe sepsis and acute respiratory distress syndrome, and serve as an independent predictor of mortality. Preclinical studies suggest that supplementation with exogenous pGSN could increase survival. AI algorithms show promising results for early sepsis detection and optimization of therapeutic decisions. However, combining circulating miRNAs and plasma gelsolin (pGSN) into AI-based models is still an exploratory idea that needs prospective validation, assay standardization, and multicenter studies before it can be used clinically. Full article
(This article belongs to the Special Issue Mechanisms of RNA Regulation in Inflammation)
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32 pages, 9450 KB  
Systematic Review
Systematic Review and Meta-Analysis of microRNA-7-5p Expression and Biological Significance in Head and Neck Squamous Cell Carcinoma
by Rikki A. M. Brown, Michael Phillips, Andrew J. Woo, Omar Kujan, Stephanie Flukes, Louise N. Winteringham, Larissa C. Dymond, Fiona Wheeler, Brianna Pollock, Dianne J. Beveridge, Elena Denisenko and Peter J. Leedman
Cancers 2025, 17(19), 3232; https://doi.org/10.3390/cancers17193232 - 4 Oct 2025
Viewed by 1494
Abstract
Background: Head and neck squamous cell carcinoma (HNSCC) is a prevalent malignancy with poor clinical outcomes. microRNA-7-5p (miR-7-5p) has been described as both a tumour suppressor and an oncomiR depending on the tissue context, but its role in HNSCC remains unclear. This [...] Read more.
Background: Head and neck squamous cell carcinoma (HNSCC) is a prevalent malignancy with poor clinical outcomes. microRNA-7-5p (miR-7-5p) has been described as both a tumour suppressor and an oncomiR depending on the tissue context, but its role in HNSCC remains unclear. This study aimed to clarify the clinical significance and biological function of miR-7-5p in HNSCC by integrating data from multiple sources. Methods: A systematic review of the literature was conducted to identify studies analysing miRNA expression in human head and neck tissues. A meta-analysis of individual patient data from Gene Expression Omnibus (GEO), ArrayExpress, and The Cancer Genome Atlas (TCGA) was performed to assess miR-7-5p expression in tumours and normal tissues, and its associations with clinical parameters and prognostic outcomes. Bioinformatics analyses were used to predict miR-7-5p target genes, classify hub genes, and perform gene ontology enrichment analysis. MicroRNA in situ hybridisation (miRNA ISH) and real-time quantitative PCR (RT-qPCR) were conducted on tissue samples, HNSCC cell lines, and an in vitro model of oral oncogenesis to validate miR-7-5p expression patterns. Results: miR-7-5p was significantly upregulated in tumours compared to normal tissues and associated with larger tumour size, HPV-negative status, poor disease-specific survival, and shorter progression-free intervals. Bioinformatics analysis highlighted miR-7-5p target genes enriched in pathways related to cell growth, survival, and tumourigenesis. Despite evidence supporting the anti-cancer role of exogenous miR-7-5p in preclinical models, the observed endogenous upregulation in tumours suggests that miR-7-5p expression may represent a compensatory or stress-responsive mechanism during tumourigenesis, rather than acting as a primary oncogenic driver. Conclusions: This study provides new insights into the complex role of miR-7-5p in HNSCC, supporting its potential as both a biomarker and a therapeutic target. Understanding the context-specific functions of miR-7-5p is essential for its development as an RNA-based therapeutic in HNSCC. Full article
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19 pages, 2817 KB  
Article
A Synthetic Sponge System Against miRNAs of the miR-17/92 Cluster Targets Transcriptional MYC Dosage Compensation in Aneuploid Cancer
by Diana M. Bravo-Estupiñan, Carsten Geiß, Jorge L. Arias-Arias, Mariela Montaño-Samaniego, Ricardo Chinchilla-Monge, Christian Marín-Müller, Steve Quirós-Barrantes, Anne Régnier-Vigouroux, Miguel Ibáñez-Hernández and Rodrigo A Mora-Rodríguez
Cells 2025, 14(17), 1384; https://doi.org/10.3390/cells14171384 - 4 Sep 2025
Viewed by 1131
Abstract
Background: Genomic instability, a hallmark of cancer, leads to copy number variations disrupting gene dosage balance and contributing to tumor progression. One of the most affected oncogenes is MYC, whose overexpression is tightly regulated to avoid cytotoxicity. In aneuploid cancer cells, gene dosage [...] Read more.
Background: Genomic instability, a hallmark of cancer, leads to copy number variations disrupting gene dosage balance and contributing to tumor progression. One of the most affected oncogenes is MYC, whose overexpression is tightly regulated to avoid cytotoxicity. In aneuploid cancer cells, gene dosage compensation mechanisms involving microRNAs (miRNAs) from the miR-17/92 cluster contribute in regulating MYC expression. Targeting this miRNA-mediated compensation system represents a promising therapeutic strategy leading to an uncontrolled and lethal MYC overexpression. Results: Synthetic miRNA sponges targeting miR-17, miR-19a, and miR-20a, key regulators of MYC dosage compensation, were designed and validated. Breast cancer cells (MCF7) with stable exogenous MYC overexpression were used to assess the impact of sponge constructs on MYC regulation. Quantitative RT-PCR revealed a significant reduction in miRNA expression and a corresponding increase in endogenous MYC levels upon sponge treatment. Functional assays in multiple colorectal cancer cell lines with varying MYC copy numbers demonstrated a time-dependent increase in cell death following sponge transfection. Cytotoxic effects increased with MYC copy number, confirming a correlation between gene dosage sensitivity and therapeutic response. Conclusions: Our findings demonstrate that miRNA sponges targeting the miR-17/92 cluster can effectively disrupt MYC dosage compensation, leading to selective cytotoxicity in MYC-amplified cancer cells. Full article
(This article belongs to the Special Issue MicroRNAs: Regulators of Cellular Fate)
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18 pages, 3005 KB  
Article
MicroRNA319-TCP19-IAA3.2 Module Mediates Lateral Root Growth in Populus tomentosa
by Jianqiu Li, Hanyu Chen, Zhengjie Zhao, Yao Yao, Jiarui Pan, Hong Wang, Di Fan, Keming Luo and Qin Song
Plants 2025, 14(16), 2494; https://doi.org/10.3390/plants14162494 - 11 Aug 2025
Cited by 2 | Viewed by 878
Abstract
MicroRNA319 (miR319) and its targets TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors are well-characterized regulators of leaf and flower development, yet their role in root development remains elusive. Here, we demonstrated that overexpression of miR319a led to a decrease in the number and density of lateral [...] Read more.
MicroRNA319 (miR319) and its targets TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors are well-characterized regulators of leaf and flower development, yet their role in root development remains elusive. Here, we demonstrated that overexpression of miR319a led to a decrease in the number and density of lateral roots in poplar, while repressing miR319a by short tandem target mimics (STTM) promoted lateral root (LR) development. The auxin signaling repressors IAA3.1 and IAA3.2 were upregulated in miR319a-OE plants but downregulated in miR319a-STTM plants. After exogenous applications of naphthaleneacetic acid (NAA), which exhibited the characteristics and physiological functions of the endogenous auxin indole-3-acetic acid, the number and density of LR in WT increased by 30% and 44%, respectively. In miR319a-OE plants, the LR number increased by 23% and 48%, and the LR density increased by 10% and 26%. NAA treatment can partially compensate for the phenotype of inhibited LR development caused by the overexpression of miR319a. After N-1-naphthylphthalamic acid (NPA) treatment, which is a key inhibitor of the directional (polar) transport of the auxin hormone in plants, the LR number in WT decreased by 70%. In the overexpression plants, the number of lateral roots decreased by 85–87%, and in the STTM plants, the number of lateral roots decreased by about 83%. It was proved that NPA treatment could reverse the phenotype of increased LR number in miR319a-STTM plants. Expression analysis revealed that miR319a significantly inhibited the expression of the key auxin-regulated genes IAA3.1 and IAA3.2, suggesting that auxin signaling might mediate its effects on lateral root formation. Additionally, we compared the fluorescence signal in the reporter line with GFP expression driven by the auxin-responsive DR5 promoter within the genetic backgrounds of WT, miR319a-OE, and miR319a-STTM plants, which revealed that auxin signaling was stronger in the epidermal cells and elongation zone cells in the LR of miR319a-OE plants, whereas in LR of WT and miR319a-STTM plants, auxin signaling was more pronounced in the root tip meristematic cells. Furthermore, transactivation assays and expression analysis indicated that IAA3.2 was a downstream target of TCP19. Chromatin immunoprecipitation coupled with quantitative PCR (ChIP-qPCR) confirmed that TCP19 directly bound to the promoter region of IAA3.2. These findings establish that miR319a targeted and cleaved TCP19, and TCP19 further directly and negatively regulates the expression of IAA3.2, thereby controlling LR development in Populus tomentosa (P. tomentosa). The formation of LR can expand the plant root system, which is of great significance for the vegetative propagation of plants and the in-vitro regeneration of explants. Moreover, the formation of LR is an important strategy for plants to cope with environmental stresses. This study provides a theoretical basis for breeding poplars more suitable for vegetative propagation. Full article
(This article belongs to the Section Plant Molecular Biology)
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19 pages, 24854 KB  
Article
MiR5651, miR170-3p, and miR171a-3p Regulate Cadmium Tolerance by Targeting MSH2 in Arabidopsis thaliana
by Xianpeng Wang, Hetong Wang, Xiuru Sun, Zihan Tang, Zhouli Liu, Richard A. Ludlow, Min Zhang, Qijiang Cao, Wan Liu and Qiang Zhao
Plants 2025, 14(13), 2028; https://doi.org/10.3390/plants14132028 - 2 Jul 2025
Viewed by 759
Abstract
The DNA mismatch repair (MMR) system plays a crucial role in repairing DNA damage and regulating cell cycle arrest induced by cadmium (Cd) stress. To elucidate the mechanism by which miRNAs target AtMSH2 in regulating Arabidopsis’ response to Cd stress, the wild-type [...] Read more.
The DNA mismatch repair (MMR) system plays a crucial role in repairing DNA damage and regulating cell cycle arrest induced by cadmium (Cd) stress. To elucidate the mechanism by which miRNAs target AtMSH2 in regulating Arabidopsis’ response to Cd stress, the wild-type Arabidopsis, Atmsh2 mutant, and three miRNA-overexpressing transgenic lines were grown hydroponically in half-strength MS solution containing cadmium (Cd) at concentrations of 0, 0.5, 1, 2, and 3 mg/L for 5 days. miRNA-seq analysis, bioinformatics prediction, dual-luciferase reporter assays, and qRT-PCR results demonstrated that miR5651, miR170-3p, and miR171a-3p specifically targeted AtMSH2 and their expression levels showed a significant negative correlation. Compared to wild-type (WT) Arabidopsis, Cd stress tolerance was significantly enhanced in miRNA-overexpressing transgenic lines. Moreover, exogenous application of these three miRNAs in half-strength MS liquid medium also markedly improved Cd stress tolerance in wild-type Arabidopsis. Furthermore, the expression of these three miRNAs expression was further upregulated by Cd stress in a dose-dependent manner. Additionally, DNA damage response in miRNA-overexpressing transgenic lines was promoted based on the expression of DNA repair, DNA damage signaling, and cell cycle genes, which differed from both wild-type and Atmsh2 plants. Taken together, miR5651, miR170-3p, and miR171a-3p participated in Cd stress response and improved plant Cd tolerance by mediating the expression of AtMSH2. Our study provides novel insights into the epigenetic mechanisms of Cd tolerance in plants, which sheds light on breeding for stress resilience in phytoremediation. Full article
(This article belongs to the Special Issue In Vivo and In Vitro Studies on Heavy Metal Tolerance in Plants)
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22 pages, 13702 KB  
Article
MicroRNA miR-193b-3p Regulates Esophageal Cancer Progression Through Targeting RSF1
by Yao Lin, Xudong Zhao, Zhenhua Du, Zhili Jia, Siyu Zhou, Gengsheng Cao and Hengbin Wang
Cells 2025, 14(12), 928; https://doi.org/10.3390/cells14120928 - 19 Jun 2025
Cited by 3 | Viewed by 1621
Abstract
Esophageal cancer (ESCA) is the sixth leading cause of cancer-related mortality worldwide. Despite the significant impact, the molecular mechanisms underlying its initiation and progression remain poorly understood. In this study, we identified mircoRNA miR-193b-3p as a critical regulator of ESCA progression and the [...] Read more.
Esophageal cancer (ESCA) is the sixth leading cause of cancer-related mortality worldwide. Despite the significant impact, the molecular mechanisms underlying its initiation and progression remain poorly understood. In this study, we identified mircoRNA miR-193b-3p as a critical regulator of ESCA progression and the Remodeling and Spacing Factor 1 (RSF1) as an essential target of miR-193b-3p. Analysis of the TCGA_ESCA dataset and RT-qPCR experiments revealed that RSF1 levels are significantly elevated in ESCA and inversely correlated with miR-193b-3p levels. Using a dual-luciferase reporter assay, as well as transfection of miR-193-3p mimics or inhibitors, we confirmed RSF1 as a direct target of miR-193b-3p in ESCA cells. Transfection of miR-193b-3p suppresses ESCA cell proliferation, migration, and invasion. These effects were partially reversed by exogenous RSF1 expression. Injection of AgomiR-193b-3p into mice bearing ESCA xenografts impeded tumor growth. These findings underscore the critical role of the miR-193b-3p/RSF1 axis in esophageal cancer progression. Full article
(This article belongs to the Special Issue Epigenetic Mechanisms of Tumorigenesis)
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24 pages, 4372 KB  
Article
PavSPL Expression Dynamics in Fruits and Seeds and in Relation to Endocarp Lignification Status During the Transition from Development to Ripening in Sweet Cherry
by Matías Zavala, Marcela Menares, Orlando Acevedo, Mirna Melo, Carlos Nuñez, Camila Arancibia, Romina Pedreschi, José Manuel Donoso, Lee A. Meisel, Jonathan E. Maldonado and Nathalie Kuhn
Horticulturae 2025, 11(6), 706; https://doi.org/10.3390/horticulturae11060706 - 19 Jun 2025
Cited by 4 | Viewed by 1328
Abstract
The transition to ripening in non-climacteric species is governed by several signals, including hormones that enhance or counteract the abscisic acid (ABA)-promoting effect. The SQUAMOSA Promoter-binding protein-Like (SPL) transcription factors are involved in ripening through the modulation of anthocyanin biosynthesis. In sweet cherry [...] Read more.
The transition to ripening in non-climacteric species is governed by several signals, including hormones that enhance or counteract the abscisic acid (ABA)-promoting effect. The SQUAMOSA Promoter-binding protein-Like (SPL) transcription factors are involved in ripening through the modulation of anthocyanin biosynthesis. In sweet cherry fruits, several miR156-targeted PavSPLs are expressed before and during ripening. Recently, some PavSPLs were found in the transition from development to ripening in cultivars contrasting in maturity time. Additionally, several forms of miR156 were expressed in sweet cherry seeds of an early-season cultivar. In this work, we addressed the relevance of endocarp lignification and PavSPLs expression for the transition to ripening. First, we characterized early- and late-season sweet cherry cultivars, ‘Celeste’ and ‘Regina’, focusing on fruit and seed development, endocarp lignification, and PavSPL expression profile. Fruit growth dynamics revealed an earlier onset of color development and lignification in ‘Celeste’, while ‘Regina’ exhibited a prolonged lag phase and delayed embryo development. Transcript profiling at the light green stage showed a higher expression of PavSPL genes in fruits and identified cultivar-specific expressions, especially between ‘Regina’ and ‘Celeste’ seeds. Co-expression networks linked PavSPLs to genes involved in lignin and anthocyanin biosynthesis. We focused on PavSPL2 and PavSPL9, which were targeted by mtr-miR156a and gma-miR156f. Both PavSPLs and miRNAs were expressed in fruits and seeds at the yellow stage, an advanced point in the transition to ripening in sweet cherry. Exogenous application of auxin-related compounds in the mid-season cultivar ‘Lapins’ modulated endocarp lignification and pigmentation. Notably, p-IBA treatment, which enzymatically targets the lignin pathway, transiently increased anthocyanin accumulation and reduced lignin deposition, effects that correlated with the downregulation of PavSPL gene expression. These findings highlight the interplay between lignification, color evolution, and pigment biosynthesis during the transition from development to ripening in sweet cherry fruits, and suggest a role for PavSPL genes in this transition. Full article
(This article belongs to the Special Issue Fruit Tree Physiology and Molecular Biology)
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29 pages, 899 KB  
Article
A Three-Level Meta-Frontier Framework with Machine Learning Projections for Carbon Emission Efficiency Analysis: Heterogeneity Decomposition and Policy Implications
by Xiaoxia Zhu, Tongyue Feng, Yuhe Shen, Ning Zhang and Xu Guo
Mathematics 2025, 13(9), 1542; https://doi.org/10.3390/math13091542 - 7 May 2025
Cited by 1 | Viewed by 1124
Abstract
This study proposes a three-level meta-frontier framework enhanced with machine learning-driven projection methods to address the dual heterogeneity in carbon emission efficiency analysis arising from regional disparities and industrial diversification. Methodologically, we introduce two novel projection combinations—“exogenous-exogenous-accumulation (E-E-A) and exogenous-exogenous-consistent (E-E-C)”—to resolve the [...] Read more.
This study proposes a three-level meta-frontier framework enhanced with machine learning-driven projection methods to address the dual heterogeneity in carbon emission efficiency analysis arising from regional disparities and industrial diversification. Methodologically, we introduce two novel projection combinations—“exogenous-exogenous-accumulation (E-E-A) and exogenous-exogenous-consistent (E-E-C)”—to resolve the inconsistency of technology gap ratios (TGRs > 1) in traditional nonradial directional distance function (DDF) models. Reinforcement learning (RL) optimizes dynamic direction vectors, whereas graph neural networks (GNNs) encode spatial interdependencies to constrain the TGR within [0, 1]. Empirical analysis of 60 countries reveals that (1) E-E-C eliminates the TGR overestimation by 12–18% in energy-intensive sectors (e.g., reducing Asia’s secondary industry TGR1 from 1.160 to 1.000); (2) industrial heterogeneity dominates inefficiency in Asia (IHI = 0.207), whereas management gaps drive global secondary sector inefficiency (MI = 0.678); and (3) policy simulations advocate for decentralized renewables in Africa, fiscal incentives for Asian coal retrofits, and expanded EU carbon border taxes. Computational enhancements via Apache Spark achieve a 58% runtime reduction. The framework advances environmental efficiency analysis by integrating machine learning with meta-frontier theory, offering both methodological rigor (via regularization and GNN constraints) and actionable decarbonization pathways. Limitations include static heterogeneity assumptions and data granularity gaps, prompting the future integration of IoT-enabled dynamic models. Full article
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16 pages, 7367 KB  
Article
Mitochondrial miRNA miR-134-5p Play Oncogenic Role in Clear Cell Renal Cell Carcinoma
by Tao Shen, Wei Wang, Haiyang Wang, Xinyi Zhu and Guoping Zhu
Biomolecules 2025, 15(3), 445; https://doi.org/10.3390/biom15030445 - 20 Mar 2025
Cited by 1 | Viewed by 1549
Abstract
Mitochondrial miRNAs (mitomiRs), which are miRNAs that located within mitochondria, have emerged as crucial regulators in a variety of human diseases, including multiple types of cancers. However, the specific role of mitomiRs in clear cell renal cell carcinoma (ccRCC) remains elusive. In this [...] Read more.
Mitochondrial miRNAs (mitomiRs), which are miRNAs that located within mitochondria, have emerged as crucial regulators in a variety of human diseases, including multiple types of cancers. However, the specific role of mitomiRs in clear cell renal cell carcinoma (ccRCC) remains elusive. In this study, we employed a combination of experimental and bioinformatic approaches to uncover the diverse and abundant subcellular distribution of miRNAs within mitochondria in ccRCC. Notably, RNA sequencing after mitochondrial fractionation identified miR-134-5p as a miRNA predominantly detected in the mitochondria of 786O cells, and its expression is significantly upregulated compared to that in 293T cells. Differential expression and survival analyses from TCGA reveal that the upregulation of miR-134-5p is prevalent and closely associated with poor survival outcomes in ccRCC patients. Functionally, exogenous overexpression of miR-134-5p mimics promotes migration in both 786O and Caki-1 cells. Mechanistically, overexpressing the miR-134-5p mimic dramatically downregulates the mRNA levels of CHST6, SFXN2, and GRIK3, whereas the miR-134-5p inhibitor markedly upregulates their expression. Notably, these target mRNAs also predominantly detected in the mitochondria of 786O cells. The downregulated expression signatures of CHST6, SFXN2, and GRIK3 are also closely correlated with poor survival outcomes in ccRCC patients. Taken together, our work identifies a novel mitomiR, miR-134-5p, in ccRCC, provides potential targets that could serve as effective biomarkers for ccRCC diagnosis and prognosis, and opens new avenues for understanding the mitomiR-directed regulatory network in ccRCC progression. Full article
(This article belongs to the Special Issue The Role of Non-Coding RNAs in Health and Disease)
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21 pages, 2682 KB  
Article
Non-Canonical Wnt16 and microRNA-145 Mediate the Response of Human Bone Marrow Stromal Cells to Additively Manufactured Porous 3-Dimensional Biomimetic Titanium–Aluminum–Vanadium Constructs
by David. J. Cohen, Michael B. Berger, Jingyao Deng, Thomas W. Jacobs, Barbara D. Boyan and Zvi Schwartz
Cells 2025, 14(3), 211; https://doi.org/10.3390/cells14030211 - 1 Feb 2025
Viewed by 1938
Abstract
Metal 3D printing is increasingly being used to manufacture titanium–aluminum–vanadium (Ti6Al4V) implants. In vitro studies using 2D substrates demonstrate that the osteoblastic differentiation of bone marrow stromal cells (MSCs) on Ti6Al4V surfaces, with a microscale/nanoscale surface topography that mimics an osteoclast resorption pit, [...] Read more.
Metal 3D printing is increasingly being used to manufacture titanium–aluminum–vanadium (Ti6Al4V) implants. In vitro studies using 2D substrates demonstrate that the osteoblastic differentiation of bone marrow stromal cells (MSCs) on Ti6Al4V surfaces, with a microscale/nanoscale surface topography that mimics an osteoclast resorption pit, involves non-canonical Wnt signaling; Wnt3a is downregulated and Wnt5a is upregulated, leading to the local production of BMP2 and semaphorin 3A (sema3A). In this study, it was examined whether the regulation of MSCs in a 3D environment occurs by a similar mechanism. Human MSCs from two different donors were cultured for 7, 14, or 21 days on porous (3D) or solid (2D) constructs fabricated by powder-bed laser fusion. mRNA and secretion of osteoblast markers, as well as factors that enhance peri-implant osteogenesis, were analyzed, with a primary focus on the Wnt family, sema3A, and microRNA-145 (miR-145) signaling pathways. MSCs exhibited greater production of osteocalcin, latent and active TGFβ1, sema3A, and Wnt16 on the 3D constructs compared to 2D, both of which had similar microscale/nanoscale surface modifications. Wnt3a was reduced on 2D constructs as a function of time; Wnt11 and Wnt5a remained elevated in the 3D and 2D cultures. To better understand the role of Wnt16, cultures were treated with rhWnt16; endogenous Wnt16 was blocked using an antibody. Wnt16 promoted proliferation and inhibited osteoblast differentiation, potentially by reducing production of BMP2 and BMP4. Wnt16 expression was reduced by exogenous Wnt16 in 3D cells. Addition of the anti-Wnt16 antibody to the cultures reversed the effects of exogenous Wnt16, indicating an autocrine mechanism. Wnt16 increased miR-145-5p, suggesting a potential feedback mechanism. The miR-145-5p mimic increased Wnt16 production and inhibited sema3A in a 3D porous substrate-specific manner. Wnt16 did not affect sema3A production, but it was reduced by miR-145-5p mimic on the 3D constructs and stimulated by miR-145-5p inhibitor. Media from 7-, 14-, and 21-day cultures of MSCs grown on 3D constructs inhibited osteoclast activity to a greater extent than media from the 2D cultures. The findings present a significant step towards understanding the complex molecular interplay that occurs in 3D Ti6Al4V constructs fabricated by additive manufacturing. In addition to enhancing osteogenesis, the 3D porous biomimetic structure inhibits osteoclast activities, indicating its role in modulating bone remodeling processes. Our data suggest that the pathway mediated by sema3A/Wnt16/miR145-5p was enhanced by the 3D surface and contributes to bone regeneration in the 3D implants. This comprehensive exploration contributes valuable insights to guide future strategies in implant design, customization, and ultimately aims at improving clinical outcomes and successful osseointegration. Full article
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19 pages, 4377 KB  
Article
Genome-Wide Identification and Expression Analysis of the GRF and GIF Gene Families in Prunus avium
by Hongxu Chen, Yangang Pei, Wanjia Tang, Hongfen Li, Yidi Huang, Yizhe Chu, Guanqiong Kou, Wenyi Niu, Runmei He and Ronggao Gong
Agronomy 2025, 15(1), 153; https://doi.org/10.3390/agronomy15010153 - 10 Jan 2025
Cited by 2 | Viewed by 1917
Abstract
Prunus avium is a woody plant of economic importance within the genus Prunus, the family Rosaceae, which is affected by various environmental factors during its long growth period. Growth-regulating factors (GRFs) and GRF-interacting factors (GIFs) are essential in [...] Read more.
Prunus avium is a woody plant of economic importance within the genus Prunus, the family Rosaceae, which is affected by various environmental factors during its long growth period. Growth-regulating factors (GRFs) and GRF-interacting factors (GIFs) are essential in regulating plant growth and development, responding to environmental stresses, and responding to exogenous hormone induction. Genome-wide analysis showed 13 GRF genes on eight chromosomes and three GIF genes on three chromosomes in P. avium, clustered into three and two branches, respectively. Cis-acting element analysis indicated that the PavGRF promoters contained regulatory elements associated with hormones, light stress, and growth development. Therefore, we evaluated the effects of gibberellin and light stress on the GRF and GIF genes in P. avium at different stages. Transcriptome data revealed that five PavGRFs exhibited elevated expression levels during the green ripening and color conversion stages in P. avium, PavGRF9 and PavGIF1 displayed higher expression during the full red stage, and gibberellin treatment led to the upregulation of these five PavGRFs and PavGIF1 during the full red stage. However, light stress did not significantly impact the expression of PavGRFs and PavGIFs. Additionally, miR396 could bind to the PavGRFs, thereby regulating the expression level of PavGIF after transcription. This study revealed the potential roles of the GRF and GIF transcription factor families in P. avium fruit growth and development, exogenous hormone treatment, and light stress, laying the foundation for further research on the roles of the GRF and GIF gene families in P. avium. Full article
(This article belongs to the Section Horticultural and Floricultural Crops)
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26 pages, 5718 KB  
Article
Transcriptome-Wide Identification of miRNAs and Their Targets During Riboflavin-Promoted Dormancy Release in Lilium ‘Siberia’
by Xiaoping Xu, Chenglong Yang, Yiping Zheng, Wenjie Guo, Zhongxiong Lai and Shaozhong Fang
Horticulturae 2025, 11(1), 17; https://doi.org/10.3390/horticulturae11010017 - 29 Dec 2024
Cited by 1 | Viewed by 1339
Abstract
Dormancy release is an important process for improving the quality of cut-flower lily production and promoting the factory production of lily bulbs. However, the regulatory mechanisms of microRNAs (miRNAs) and their target genes during the dormancy release of lily remain elusive. Anatomy, transcriptomic, [...] Read more.
Dormancy release is an important process for improving the quality of cut-flower lily production and promoting the factory production of lily bulbs. However, the regulatory mechanisms of microRNAs (miRNAs) and their target genes during the dormancy release of lily remain elusive. Anatomy, transcriptomic, molecular biology, and transient transformation techniques involving subcellular localization were applied in our study. There were significant results showing that 0.1 mM riboflavin promoted dormancy release and floral bud differentiation and influenced the flowering time of the Lilium ‘Siberia’. Moreover, some differentially expressed miRNAs and their targets (miR395-y: LoAPS1, miR529-z: LoSPL14, miR396-y: LoCFDP1, miR1863-z: LoFBA3, miR399-y: LoDIT1, and miR11525-z: Lopgm) were identified and predicted. Exogenous riboflavin may activate primary metabolic processes and promote dormancy release in Lilium ‘Siberia’ bulbs. Furthermore, riboflavin upregulated genes related to the riboflavin pathway, H3K4me3 methylation, dormancy control, and the flowering pathway and downregulated dormancy maintenance genes. Moreover, riboflavin promoted endogenous riboflavin and acetyl-CoA accumulation. LoPurple acid phosphatase17 (LoPAP17), a pivotal gene of the riboflavin metabolism pathway, was subsequently cloned. LoPAP17 was most closely related to the orthologous genes of Acorus calamus, Asparagus officinalis, and Musa acuminata. The LoPAP17 protein was subcellularly located in the nucleus. Our study revealed that miRNAs and their target genes might regulate the primary metabolic pathway, promote the accumulation of endogenous riboflavin and acetyl-CoA, and affect protein acetylation during the riboflavin-promoted release of dormancy and flower bud differentiation in the Lilium Oriental hybrid ‘Siberia’. Full article
(This article belongs to the Section Floriculture, Nursery and Landscape, and Turf)
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26 pages, 6347 KB  
Article
The Arabidopsis thaliana Double-Stranded RNA Binding Proteins DRB1 and DRB2 Are Required for miR160-Mediated Responses to Exogenous Auxin
by Kim Zimmerman, Joseph L. Pegler, Jackson M. J. Oultram, David A. Collings, Ming-Bo Wang, Christopher P. L. Grof and Andrew L. Eamens
Genes 2024, 15(12), 1648; https://doi.org/10.3390/genes15121648 - 21 Dec 2024
Cited by 1 | Viewed by 1524
Abstract
DOUBLE-STRANDED RNA BINDING (DRB) proteins DRB1, DRB2, and DRB4 are essential for microRNA (miRNA) production in Arabidopsis thaliana (Arabidopsis) with miR160, and its target genes, AUXIN RESPONSE FACTOR10 (ARF10), ARF16, and ARF17, forming an auxin responsive miRNA [...] Read more.
DOUBLE-STRANDED RNA BINDING (DRB) proteins DRB1, DRB2, and DRB4 are essential for microRNA (miRNA) production in Arabidopsis thaliana (Arabidopsis) with miR160, and its target genes, AUXIN RESPONSE FACTOR10 (ARF10), ARF16, and ARF17, forming an auxin responsive miRNA expression module crucial for root development. Methods: Wild-type Arabidopsis plants (Columbia-0 (Col-0)) and the drb1, drb2, and drb12 mutants were treated with the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D), and the miR160-mediated response of these four Arabidopsis lines was phenotypically and molecularly characterized. Results: In 2,4-D-treated Col-0, drb1 and drb2 plants, altered miR160 abundance and ARF10, ARF16, and ARF17 gene expression were associated with altered root system development. However, miR160-directed molecular responses to treatment with 2,4-D was largely defective in the drb12 double mutant. In addition, via profiling of molecular components of the miR160 expression module in the roots of the drb4, drb14, and drb24 mutants, we uncovered a previously unknown role for DRB4 in regulating miR160 production. Conclusions: The miR160 expression module forms a central component of the molecular and phenotypic response of Arabidopsis plants to exogenous auxin treatment. Furthermore, DRB1, DRB2, and DRB4 are all required in Arabidopsis roots to control miR160 production, and subsequently, to appropriately regulate ARF10, ARF16, and ARF17 target gene expression. Full article
(This article belongs to the Special Issue Plant Genetic Diversity and Omics Research)
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