Pub Date : 2025-08-29DOI: 10.1016/j.ncrna.2025.08.009
Min Li , Jiawei Li , Hongbo Wen , Jun Li , Song Wang , Jianran Guo , Dongyan Zhang , Anqi Zhang , Chuanyou Cui , Rong Fu , Meng An , Wei Zhang , Bo Fu
Breast cancer brain metastasis (BCBM) remains fatal with elusive mechanisms. Here, we unveil the first circRNA m5C methylation landscape in BCBM through MeRIP-seq (methylated RNA immunoprecipitation next-generation sequencing) identifying 7465 BCBM-specific m5C peaks versus 5929 in primary breast cancer (BC). A total of 48 hypermethylated and 128 hypomethylated m5C sites in BCBM (231-BR) were identified compared to BC. Bioinformatics enrichment analysis revealed hypermethylated circRNAs enriched in ERBB/VEGF signaling pathways. Among 8 validated differentially methylated circRNAs, hsa_circ_0004516 was consistently upregulated in BCBM tissues/cells and exhibited NSUN2-dependent m5C modification. Mechanistically, NSUN2-mediated m5C methylation enhanced hsa_circ_0004516 stability, evidenced by significantly shortened half-life upon NSUN2 depletion. Crucially, catalytic mutant NSUN2 (C271A/C321A) abolished this effect. Functional assays demonstrated that hsa_circ_0004516 knockdown in 231-BR cells suppressed proliferation, migration, and invasion by reducing p-AKT (Ser473) levels. The AKT activator SC79 reversed these phenotypic impairments, definitively linking hsa_circ_0004516-driven metastasis to AKT signaling activation. Our study establishes the NSUN2-m5C-hsa_circ_0004516-AKT axis as a novel therapeutic target and biomarker for BCBM.
{"title":"NSUN2-mediated m5C hypermethylation of hsa_circ_0004516 promotes breast cancer brain metastasis by activating AKT signaling","authors":"Min Li , Jiawei Li , Hongbo Wen , Jun Li , Song Wang , Jianran Guo , Dongyan Zhang , Anqi Zhang , Chuanyou Cui , Rong Fu , Meng An , Wei Zhang , Bo Fu","doi":"10.1016/j.ncrna.2025.08.009","DOIUrl":"10.1016/j.ncrna.2025.08.009","url":null,"abstract":"<div><div>Breast cancer brain metastasis (BCBM) remains fatal with elusive mechanisms. Here, we unveil the first circRNA m5C methylation landscape in BCBM through MeRIP-seq (methylated RNA immunoprecipitation next-generation sequencing) identifying 7465 BCBM-specific m5C peaks versus 5929 in primary breast cancer (BC). A total of 48 hypermethylated and 128 hypomethylated m5C sites in BCBM (231-BR) were identified compared to BC. Bioinformatics enrichment analysis revealed hypermethylated circRNAs enriched in ERBB/VEGF signaling pathways. Among 8 validated differentially methylated circRNAs, <em>hsa_circ_0004516</em> was consistently upregulated in BCBM tissues/cells and exhibited NSUN2-dependent m5C modification. Mechanistically, NSUN2-mediated m5C methylation enhanced <em>hsa_circ_0004516</em> stability, evidenced by significantly shortened half-life upon NSUN2 depletion. Crucially, catalytic mutant NSUN2 (C271A/C321A) abolished this effect. Functional assays demonstrated that <em>hsa_circ_0004516</em> knockdown in 231-BR cells suppressed proliferation, migration, and invasion by reducing p-AKT (Ser473) levels. The AKT activator SC79 reversed these phenotypic impairments, definitively linking <em>hsa_circ_0004516</em>-driven metastasis to AKT signaling activation. Our study establishes the NSUN2-m5C-<em>hsa_circ_</em>0004516-AKT axis as a novel therapeutic target and biomarker for BCBM.</div></div>","PeriodicalId":37653,"journal":{"name":"Non-coding RNA Research","volume":"14 ","pages":"Pages 177-190"},"PeriodicalIF":4.7,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145009944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-29DOI: 10.1016/j.ncrna.2025.08.008
Haixia Wang , Ting Gao , Bin Ma , Yuanmin Jia , Hui Wei , Danyang Li , Junlian Gu , Ou Chen , Shouwei Yue
Emerging evidence suggests that aerobic exercise exerts beneficial effects on asthma. Previous studies have demonstrated that cell communication can drive the formation of macrophage extracellular traps (METs). However, the potential of aerobic exercise to mediate communication between airway epithelial cells and macrophages, thereby influencing MET formation, remains unexplored. Our data reveal that the upregulation of circular RNA METTL9 (circMETTL9), derived from methyltransferase-like protein 9 (METTL9) in airway epithelial cells, promotes the formation of METs. Notably, aerobic exercise was found to downregulate the expression of circMETTL9, thereby facilitating communication between airway epithelial cells and macrophages and inhibiting METs formation. Mechanistically, circMETTL9 and insulin-like growth factor binding protein 3 (IGFBP3) compete for binding to the DEXDc domain of eukaryotic translation initiation factor 4A3 (EIF4A3), which regulates METs via the C-X-C motif chemokine ligand 12(CXCL12) -C-X-C chemokine receptor type 4(CXCR4) signaling axis. This study provides robust molecular evidence supporting aerobic exercise as a foundational pulmonary rehabilitation strategy for lung protection in asthma. Targeting circMETTL9, mimicking this exercise-mediated pathway, represents a promising therapeutic approach. These insights offer a direct mechanistic rationale for refining exercise-based rehabilitation protocols and developing novel targeted therapies.
{"title":"Aerobic exercise alleviates allergic airway inflammation by suppressing circMETTL9-mediated formation of macrophage extracellular traps","authors":"Haixia Wang , Ting Gao , Bin Ma , Yuanmin Jia , Hui Wei , Danyang Li , Junlian Gu , Ou Chen , Shouwei Yue","doi":"10.1016/j.ncrna.2025.08.008","DOIUrl":"10.1016/j.ncrna.2025.08.008","url":null,"abstract":"<div><div>Emerging evidence suggests that aerobic exercise exerts beneficial effects on asthma. Previous studies have demonstrated that cell communication can drive the formation of macrophage extracellular traps (METs). However, the potential of aerobic exercise to mediate communication between airway epithelial cells and macrophages, thereby influencing MET formation, remains unexplored. Our data reveal that the upregulation of circular RNA <em>METTL9</em> (<em>circMETTL9</em>), derived from methyltransferase-like protein 9 (<em>METTL9</em>) in airway epithelial cells, promotes the formation of METs. Notably, aerobic exercise was found to downregulate the expression of <em>circMETTL9</em>, thereby facilitating communication between airway epithelial cells and macrophages and inhibiting METs formation. Mechanistically, <em>circMETTL9</em> and insulin-like growth factor binding protein 3 (IGFBP3) compete for binding to the DEXDc domain of eukaryotic translation initiation factor 4A3 (EIF4A3), which regulates METs via the C-X-C motif chemokine ligand 12(CXCL12) -C-X-C chemokine receptor type 4(CXCR4) signaling axis. This study provides robust molecular evidence supporting aerobic exercise as a foundational pulmonary rehabilitation strategy for lung protection in asthma. Targeting <em>circMETTL9</em>, mimicking this exercise-mediated pathway, represents a promising therapeutic approach. These insights offer a direct mechanistic rationale for refining exercise-based rehabilitation protocols and developing novel targeted therapies.</div></div>","PeriodicalId":37653,"journal":{"name":"Non-coding RNA Research","volume":"15 ","pages":"Pages 156-171"},"PeriodicalIF":4.7,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145048416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-22DOI: 10.1016/j.ncrna.2025.08.005
Rebecca Nobili , Cristina Barbagallo , Marco Ragusa , Jasmine Genovese , Valentina D'Agostino , Andrea Diociaiuti , Daniele Castiglia , Teresa Odorisio , Giovanna Zambruno , May El Hachem , Angelo Giuseppe Condorelli
Recessive dystrophic epidermolysis bullosa (RDEB) is a rare and severe skin fragility disease due to loss-of-function mutations in the COL7A1 gene. RDEB patients suffer from relentless mucocutaneous blisters that evolve into chronic wounds with inflammation and progressive fibrosis, which heavily impacts the disease course. RDEB-associated fibrosis is the result of a complex dialogue among different cell types, signalling pathways and epigenetic players that are still poorly characterized. The expression levels of over 750 mature microRNAs were investigated in primary fibroblasts from patients with RDEB (RDEB-FBs) and healthy donors using TaqMan Low-Density Arrays. Among deregulated molecules, only the miR-129-1-3p was down-regulated in RDEB-FBs. Therefore, the role of miR-129-1-3p in regulating the fibrotic features of RDEB-FBs was explored by biochemical and functional assays in cells transfected with a miR-129-1-3p mimic or a small interfering RNA specific for BAG3 (BAG cochaperone 3), a newly identified miR-129-1-3p target. BAG3 expression levels were significantly increased in RDEB-FBs grown under basal conditions and reduced in response to their transfection with a miR-129-1-3p mimic. In RDEB-FBs, the over-expression of miR-129-1-3p or BAG3 silencing markedly impaired cell contractility, a typical feature of activated/pro-fibrotic fibroblasts, decreased phospho-AKT (Ser473) levels, and reduced the ability to synthetize and deposit collagen in the extracellular matrix. Treatment of patients' fibroblasts with the AKT inhibitor perifosine (KRX-0401) recapitulated the effects observed with the mimic molecule of miR-129-1-3p and BAG3 silencing. Our results highlight the role of the miR-129-1-3p/BAG3/AKT axis in RDEB pathogenesis, complementing and expanding the knowledge on non-coding RNAs involved in fibrosis-related processes. Taken together, these findings may contribute to enlarge the toolkit of molecules and pathways that can be exploited as therapeutic targets in skin fibrosis.
{"title":"miR-129-1-3p down-regulation promotes BAG cochaperone 3 (BAG3)-driven pro-fibrotic processes in primary fibroblasts from patients with recessive dystrophic epidermolysis bullosa","authors":"Rebecca Nobili , Cristina Barbagallo , Marco Ragusa , Jasmine Genovese , Valentina D'Agostino , Andrea Diociaiuti , Daniele Castiglia , Teresa Odorisio , Giovanna Zambruno , May El Hachem , Angelo Giuseppe Condorelli","doi":"10.1016/j.ncrna.2025.08.005","DOIUrl":"10.1016/j.ncrna.2025.08.005","url":null,"abstract":"<div><div>Recessive dystrophic epidermolysis bullosa (RDEB) is a rare and severe skin fragility disease due to loss-of-function mutations in the <em>COL7A1</em> gene. RDEB patients suffer from relentless mucocutaneous blisters that evolve into chronic wounds with inflammation and progressive fibrosis, which heavily impacts the disease course. RDEB-associated fibrosis is the result of a complex dialogue among different cell types, signalling pathways and epigenetic players that are still poorly characterized. The expression levels of over 750 mature microRNAs were investigated in primary fibroblasts from patients with RDEB (RDEB-FBs) and healthy donors using TaqMan Low-Density Arrays. Among deregulated molecules, only the miR-129-1-3p was down-regulated in RDEB-FBs. Therefore, the role of miR-129-1-3p in regulating the fibrotic features of RDEB-FBs was explored by biochemical and functional assays in cells transfected with a miR-129-1-3p mimic or a small interfering RNA specific for BAG3 (BAG cochaperone 3), a newly identified miR-129-1-3p target. BAG3 expression levels were significantly increased in RDEB-FBs grown under basal conditions and reduced in response to their transfection with a miR-129-1-3p mimic. In RDEB-FBs, the over-expression of miR-129-1-3p or BAG3 silencing markedly impaired cell contractility, a typical feature of activated/pro-fibrotic fibroblasts, decreased phospho-AKT (Ser473) levels, and reduced the ability to synthetize and deposit collagen in the extracellular matrix. Treatment of patients' fibroblasts with the AKT inhibitor perifosine (KRX-0401) recapitulated the effects observed with the mimic molecule of miR-129-1-3p and BAG3 silencing. Our results highlight the role of the miR-129-1-3p/BAG3/AKT axis in RDEB pathogenesis, complementing and expanding the knowledge on non-coding RNAs involved in fibrosis-related processes. Taken together, these findings may contribute to enlarge the toolkit of molecules and pathways that can be exploited as therapeutic targets in skin fibrosis.</div></div>","PeriodicalId":37653,"journal":{"name":"Non-coding RNA Research","volume":"15 ","pages":"Pages 142-155"},"PeriodicalIF":4.7,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144931923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-20DOI: 10.1016/j.ncrna.2025.08.003
Ioannis Kyriakidis , Zacharias Papadovasilakis , Georgios Papoutsoglou , Iordanis Pelagiadis , Helen A. Papadaki , Charalampos Pontikoglou , Eftichia Stiakaki
Despite significant advancements in overall survival rates for childhood acute lymphoblastic leukemia (ALL), relapse continues to pose a major challenge. MicroRNAs have proven valuable for improving diagnosis, treatment, and survival outcomes, establishing themselves as key biomarkers. Using RNA-seq data from 123 ALL patients and employing predictive modeling via automated machine learning (AutoML) alongside causal-inspired biomarker discovery, we identified highly predictive microRNA signatures linked to high-risk strata and clinical features in unfavorable cases. We further identified predictive signatures for each genetic subtype of childhood ALL, highlighting shared miRNAs throughout the study. A thorough literature review of the relationships between miRNA differential expression and key high-risk features in childhood ALL [immunophenotype, elevated white blood cell counts at diagnosis, central nervous system involvement, measurable residual disease (MRD), and chemoresistance] confirmed the signatures generated in this study. Our results revealed a highly predictive signature distinguishing B- and T-ALL, associated with apoptosis, confirming the reported difference between the two immunophenotypes. Additionally, miR-223 emerged as crucial for high-risk stratification and chemoresistant MRD-positive cases. These findings demonstrate the potential of AutoML tools to reveal novel biological insights in pediatric ALL, driving future advancements.
{"title":"AutoML identification of microRNA biomarkers in high-risk pediatric acute lymphoblastic leukemia","authors":"Ioannis Kyriakidis , Zacharias Papadovasilakis , Georgios Papoutsoglou , Iordanis Pelagiadis , Helen A. Papadaki , Charalampos Pontikoglou , Eftichia Stiakaki","doi":"10.1016/j.ncrna.2025.08.003","DOIUrl":"10.1016/j.ncrna.2025.08.003","url":null,"abstract":"<div><div>Despite significant advancements in overall survival rates for childhood acute lymphoblastic leukemia (ALL), relapse continues to pose a major challenge. MicroRNAs have proven valuable for improving diagnosis, treatment, and survival outcomes, establishing themselves as key biomarkers. Using RNA-seq data from 123 ALL patients and employing predictive modeling via automated machine learning (AutoML) alongside causal-inspired biomarker discovery, we identified highly predictive microRNA signatures linked to high-risk strata and clinical features in unfavorable cases. We further identified predictive signatures for each genetic subtype of childhood ALL, highlighting shared miRNAs throughout the study. A thorough literature review of the relationships between miRNA differential expression and key high-risk features in childhood ALL [immunophenotype, elevated white blood cell counts at diagnosis, central nervous system involvement, measurable residual disease (MRD), and chemoresistance] confirmed the signatures generated in this study. Our results revealed a highly predictive signature distinguishing B- and T-ALL, associated with apoptosis, confirming the reported difference between the two immunophenotypes. Additionally, miR-223 emerged as crucial for high-risk stratification and chemoresistant MRD-positive cases. These findings demonstrate the potential of AutoML tools to reveal novel biological insights in pediatric ALL, driving future advancements.</div></div>","PeriodicalId":37653,"journal":{"name":"Non-coding RNA Research","volume":"15 ","pages":"Pages 120-131"},"PeriodicalIF":4.7,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144917613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-13DOI: 10.1016/j.ncrna.2025.08.002
Yusi Chen , Tengteng Zhu , Fang Li , Yingjie Tan , Tianyu Wang , Xiaoqin Luo , Jun Luo , Yi Tang , Jianqiang Peng , Jiang Li
Introduction
tRNA-derived small RNAs (tsRNAs) are emerging as noninvasive biomarkers of cellular damage. However, their role in pulmonary arterial hypertension (PAH) remains unclear.
Methods
Plasma i-tRF-15:31-Lys-CTT-1 levels were quantified in a discovery cohort (n = 141 PAH patients; n = 50 controls) and a verification cohort (n = 254 PAH patients; n = 70 controls). Diagnostic performance was assessed using receiver operating characteristic analysis, and survival outcomes were evaluated with Kaplan-Meier curves and multivariable Cox regression models.
Results
In discovery cohort, the median age was 41 years (IQR 27–54), with 65.9 % female and a median REVEAL 2.0 score of 7 (IQR 6–8). In verification cohort, the median age was 36 years (IQR 31–52), with 63.4 % female and a median REVEAL 2.0 score of 6 (IQR 4–7). i-tRF-15:31-Lys-CTT-1 showed the greatest fold change among tsRNAs in idiopathic PAH (P < 0.0001). Levels of i-tRF-15:31-Lys-CTT-1 were significantly lower in the high-risk REVEAL group (P < 0.0001). The area under the curve (AUC) of i-tRF-15:31-Lys-CTT-1 for idiopathic PAH diagnosis was 0.90 in discovery cohort and 0.81 in verification cohort. Kaplan-Meier analysis revealed that lower i-tRF-15:31-Lys-CTT-1 levels correlated with poorer prognosis (P < 0.0001). After adjusting for age, sex, and BMI, patients in the highest quartile had a significantly lower incidence of clinical events compared to those in the lowest quartile (HR = 0.08; 95 % CI 0.032–0.18; P < 0.001). Incorporating i-tRF-15:31-Lys-CTT-1 into the REVEAL 2.0 model improved predictive accuracy (AUC from 0.67 to 0.75, P < 0.0001).
Conclusions
i-tRF-15:31-Lys-CTT-1 levels are decreased in PAH, correlate with disease severity, and are promising to improve clinical diagnosis and risk stratification.
{"title":"Identification of plasma tRNA-derived small RNA i-tRF-15:31-Lys-CTT-1 as a biomarker for diagnosis and prognosis of pulmonary arterial hypertension","authors":"Yusi Chen , Tengteng Zhu , Fang Li , Yingjie Tan , Tianyu Wang , Xiaoqin Luo , Jun Luo , Yi Tang , Jianqiang Peng , Jiang Li","doi":"10.1016/j.ncrna.2025.08.002","DOIUrl":"10.1016/j.ncrna.2025.08.002","url":null,"abstract":"<div><h3>Introduction</h3><div>tRNA-derived small RNAs (tsRNAs) are emerging as noninvasive biomarkers of cellular damage. However, their role in pulmonary arterial hypertension (PAH) remains unclear.</div></div><div><h3>Methods</h3><div>Plasma i-tRF-15:31-Lys-CTT-1 levels were quantified in a discovery cohort (n = 141 PAH patients; n = 50 controls) and a verification cohort (n = 254 PAH patients; n = 70 controls). Diagnostic performance was assessed using receiver operating characteristic analysis, and survival outcomes were evaluated with Kaplan-Meier curves and multivariable Cox regression models.</div></div><div><h3>Results</h3><div>In discovery cohort, the median age was 41 years (IQR 27–54), with 65.9 % female and a median REVEAL 2.0 score of 7 (IQR 6–8). In verification cohort, the median age was 36 years (IQR 31–52), with 63.4 % female and a median REVEAL 2.0 score of 6 (IQR 4–7). i-tRF-15:31-Lys-CTT-1 showed the greatest fold change among tsRNAs in idiopathic PAH (P < 0.0001). Levels of i-tRF-15:31-Lys-CTT-1 were significantly lower in the high-risk REVEAL group (P < 0.0001). The area under the curve (AUC) of i-tRF-15:31-Lys-CTT-1 for idiopathic PAH diagnosis was 0.90 in discovery cohort and 0.81 in verification cohort. Kaplan-Meier analysis revealed that lower i-tRF-15:31-Lys-CTT-1 levels correlated with poorer prognosis (P < 0.0001). After adjusting for age, sex, and BMI, patients in the highest quartile had a significantly lower incidence of clinical events compared to those in the lowest quartile (HR = 0.08; 95 % CI 0.032–0.18; P < 0.001). Incorporating i-tRF-15:31-Lys-CTT-1 into the REVEAL 2.0 model improved predictive accuracy (AUC from 0.67 to 0.75, P < 0.0001).</div></div><div><h3>Conclusions</h3><div>i-tRF-15:31-Lys-CTT-1 levels are decreased in PAH, correlate with disease severity, and are promising to improve clinical diagnosis and risk stratification.</div></div>","PeriodicalId":37653,"journal":{"name":"Non-coding RNA Research","volume":"15 ","pages":"Pages 108-119"},"PeriodicalIF":4.7,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144864570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-08DOI: 10.1016/j.ncrna.2025.08.001
Erryk S. Katayama , Jonathan J. Hue , Alexander W. Loftus , Semmer A. Ali , Hallie J. Graor , Luke D. Rothermel , Eric Londin , Mehrdad Zarei , Jordan M. Winter
Purpose
To verify the stability and reliability of circulating microRNA (miRNA) profiles in plasma and serum under different processing and storage conditions to inform future applications to circulating biomarker analyses.
Background
The development of blood-based methods for early disease detection has become increasingly desirable across various medical fields. RNA profiles have been investigated but have been a challenge due to rapid degradation of the analyte by ubiquitous RNases. miRNAs are short, non-coding regulatory RNAs that are believed to be more stable under certain conditions, large in number, and specific to cell type and disease state. Thus, circulating miRNA profiles hold significant promise as diagnostic biomarkers for a range of conditions, including cancer, autoimmune, liver, neurological, metabolic, and cardiovascular diseases. However, to realize their full potential in clinical applications, it is crucial to thoroughly characterize the stability of miRNAs under various blood collection, processing, and storage conditions prior to their investigation and large-scale application in disease-specific biomarker discovery studies.
Methods
Plasma or serum were extracted from whole blood of healthy volunteers. Samples were stored at different temperatures (4 °C or 25 °C, room temperature) for varying periods (0–24 h) to mimic possible delays in processing encountered in routine clinical settings. miRNA was extracted and profiles were assessed with RT-qPCR or small RNA-sequencing techniques.
Results
Mean Cq values of specific miRNAs, such as miR-15b, miR-16, miR-21, miR-24, and miR-223, remained consistent between 0 and 24 h when serum and plasma were stored on ice. Minimal changes were observed in mean Cq values over 24 h when serum was left at room temperature as well. Similar trends were observed when miRNAs from plasma were analyzed. Small-RNA sequencing detected approximately ∼650 different miRNA signals in plasma, with over 99 % of the miRNA profile unchanged even when blood draw tubes were left at room temperature for 6 h prior to processing.
Conclusions
These data demonstrate remarkable stability of miRNAs over time, which should withstand variability in handling and processing that can occur with routine clinical lab draws. Considering the large diversity of miRNAs, this analyte class should be thoroughly investigated as a non-invasive biomarker of diverse disease states.
{"title":"Stability of microRNAs in serum and plasma reveal promise as a circulating biomarker","authors":"Erryk S. Katayama , Jonathan J. Hue , Alexander W. Loftus , Semmer A. Ali , Hallie J. Graor , Luke D. Rothermel , Eric Londin , Mehrdad Zarei , Jordan M. Winter","doi":"10.1016/j.ncrna.2025.08.001","DOIUrl":"10.1016/j.ncrna.2025.08.001","url":null,"abstract":"<div><h3>Purpose</h3><div>To verify the stability and reliability of circulating microRNA (miRNA) profiles in plasma and serum under different processing and storage conditions to inform future applications to circulating biomarker analyses.</div></div><div><h3>Background</h3><div>The development of blood-based methods for early disease detection has become increasingly desirable across various medical fields. RNA profiles have been investigated but have been a challenge due to rapid degradation of the analyte by ubiquitous RNases. miRNAs are short, non-coding regulatory RNAs that are believed to be more stable under certain conditions, large in number, and specific to cell type and disease state. Thus, circulating miRNA profiles hold significant promise as diagnostic biomarkers for a range of conditions, including cancer, autoimmune, liver, neurological, metabolic, and cardiovascular diseases. However, to realize their full potential in clinical applications, it is crucial to thoroughly characterize the stability of miRNAs under various blood collection, processing, and storage conditions prior to their investigation and large-scale application in disease-specific biomarker discovery studies.</div></div><div><h3>Methods</h3><div>Plasma or serum were extracted from whole blood of healthy volunteers. Samples were stored at different temperatures (4 °C or 25 °C, room temperature) for varying periods (0–24 h) to mimic possible delays in processing encountered in routine clinical settings. miRNA was extracted and profiles were assessed with RT-qPCR or small RNA-sequencing techniques.</div></div><div><h3>Results</h3><div>Mean Cq values of specific miRNAs, such as miR-15b, miR-16, miR-21, miR-24, and miR-223, remained consistent between 0 and 24 h when serum and plasma were stored on ice. Minimal changes were observed in mean Cq values over 24 h when serum was left at room temperature as well. Similar trends were observed when miRNAs from plasma were analyzed. Small-RNA sequencing detected approximately ∼650 different miRNA signals in plasma, with over 99 % of the miRNA profile unchanged even when blood draw tubes were left at room temperature for 6 h prior to processing.</div></div><div><h3>Conclusions</h3><div>These data demonstrate remarkable stability of miRNAs over time, which should withstand variability in handling and processing that can occur with routine clinical lab draws. Considering the large diversity of miRNAs, this analyte class should be thoroughly investigated as a non-invasive biomarker of diverse disease states.</div></div>","PeriodicalId":37653,"journal":{"name":"Non-coding RNA Research","volume":"15 ","pages":"Pages 132-141"},"PeriodicalIF":4.7,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144920242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-05DOI: 10.1016/j.ncrna.2025.07.007
Adil Husain , Firoz Ahmad , Sandeep Pandey , Tarun Kumar Upadhyay , Sojin Kang , Min Choi , Jinwon Choi , Moon Nyeo Park , Bonglee Kim
Glioblastoma (GB) remains a major challenge owing to its extremely aggressive nature and resistance to conventional therapies. This review focuses on the intricate roles of progenitor cells, microglia, and non-coding RNAs (ncRNAs) in orchestrating GB pathogenesis and therapy resistance. Glioma stem cells (GSCs), derived from progenitor cells, are important drivers of tumor initiation and recurrence and exhibit remarkable plasticity and resistance to treatment. Microglia, the immune cells of the brain, are hijacked by GB cells to create an immunosuppressive microenvironment that supports tumor growth and resistance to therapy. Non-coding RNAs, including microRNAs and long noncoding RNAs, regulate multiple resistance mechanisms by modulating gene expression and influencing the interactions between progenitor cells and microglia. This review highlights new insights into these interconnected signaling pathways and explores potential therapeutic strategies targeting these molecular players to overcome treatment resistance and improve outcomes in patients with GB.
{"title":"Progenitor cells, microglia, and non-coding RNAs: Orchestrators of glioblastoma pathogenesis and therapeutic resistance","authors":"Adil Husain , Firoz Ahmad , Sandeep Pandey , Tarun Kumar Upadhyay , Sojin Kang , Min Choi , Jinwon Choi , Moon Nyeo Park , Bonglee Kim","doi":"10.1016/j.ncrna.2025.07.007","DOIUrl":"10.1016/j.ncrna.2025.07.007","url":null,"abstract":"<div><div>Glioblastoma (GB) remains a major challenge owing to its extremely aggressive nature and resistance to conventional therapies. This review focuses on the intricate roles of progenitor cells, microglia, and non-coding RNAs (ncRNAs) in orchestrating GB pathogenesis and therapy resistance. Glioma stem cells (GSCs), derived from progenitor cells, are important drivers of tumor initiation and recurrence and exhibit remarkable plasticity and resistance to treatment. Microglia, the immune cells of the brain, are hijacked by GB cells to create an immunosuppressive microenvironment that supports tumor growth and resistance to therapy. Non-coding RNAs, including microRNAs and long noncoding RNAs, regulate multiple resistance mechanisms by modulating gene expression and influencing the interactions between progenitor cells and microglia. This review highlights new insights into these interconnected signaling pathways and explores potential therapeutic strategies targeting these molecular players to overcome treatment resistance and improve outcomes in patients with GB.</div></div>","PeriodicalId":37653,"journal":{"name":"Non-coding RNA Research","volume":"15 ","pages":"Pages 85-99"},"PeriodicalIF":4.7,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144852387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-07-25DOI: 10.1016/j.ncrna.2025.07.006
Venkata Ramana Mallela , Marie Rajtmajerová , Esraa Ali , Lenka Červenková , Andriy Trailin , Petr Hošek , Richard Pálek , Ondřej Daum , Václav Liška , Kari Hemminki , Filip Ambrozkiewicz
Background & Aims
Hepatocellular carcinoma (HCC) is the third deadliest cancer worldwide. Its high mortality is primarily attributed to late-stage diagnosis. While mutations in driver genes, such as those encoding β-catenin (CTNNB1), tumor protein p53 (TP53), and telomerase reverse transcriptase promoter (TERTp) are well-documented in the literature, dysregulation of microRNAs (miRNAs), small non-coding RNAs that serve as crucial translational regulators, remains poorly understood.
Methods
We conducted microRNA profiling by microarrays in 45 paired (tumor and non-tumor adjacent tissue) samples from non-viral HCC patients. We performed clinical correlation, ROC analysis and survival analysis of time to recurrence (TTR), disease-free survival (DFS) and overall survival.
Results
We identified 23 significantly dysregulated miRNAs (p ≤ 0.05, fold change ≥2). We investigated their differential expression and its relationship with clinical and pathological variables. Further, we found that miRNA-1972 may serve as an important positive prognostic marker because its high levels were associated with longer TTR and DFS. Significant positive results were obtained in receiver operating characteristic analysis for miR-1972, miR-3651 and miR-486–5p.
Conclusion
miRNA-1972 is a strong prognostic marker in non-viral HCC. Dysregulation of several other miRNAs relates to pathological variables such as amount of stroma within tumor, microvascular invasion and micronodularity.
{"title":"Non-viral HCC miRNA profiling reveals miR-1972 as a potential positive prognostic marker","authors":"Venkata Ramana Mallela , Marie Rajtmajerová , Esraa Ali , Lenka Červenková , Andriy Trailin , Petr Hošek , Richard Pálek , Ondřej Daum , Václav Liška , Kari Hemminki , Filip Ambrozkiewicz","doi":"10.1016/j.ncrna.2025.07.006","DOIUrl":"10.1016/j.ncrna.2025.07.006","url":null,"abstract":"<div><h3>Background & Aims</h3><div>Hepatocellular carcinoma (HCC) is the third deadliest cancer worldwide. Its high mortality is primarily attributed to late-stage diagnosis. While mutations in driver genes, such as those encoding β-catenin (CTNNB1), tumor protein p53 (TP53), and telomerase reverse transcriptase promoter (TERTp) are well-documented in the literature, dysregulation of microRNAs (miRNAs), small non-coding RNAs that serve as crucial translational regulators, remains poorly understood.</div></div><div><h3>Methods</h3><div>We conducted microRNA profiling by microarrays in 45 paired (tumor and non-tumor adjacent tissue) samples from non-viral HCC patients. We performed clinical correlation, ROC analysis and survival analysis of time to recurrence (TTR), disease-free survival (DFS) and overall survival.</div></div><div><h3>Results</h3><div>We identified 23 significantly dysregulated miRNAs (p ≤ 0.05, fold change ≥2). We investigated their differential expression and its relationship with clinical and pathological variables. Further, we found that miRNA-1972 may serve as an important positive prognostic marker because its high levels were associated with longer TTR and DFS. Significant positive results were obtained in receiver operating characteristic analysis for miR-1972, miR-3651 and miR-486–5p.</div></div><div><h3>Conclusion</h3><div>miRNA-1972 is a strong prognostic marker in non-viral HCC. Dysregulation of several other miRNAs relates to pathological variables such as amount of stroma within tumor, microvascular invasion and micronodularity.</div></div>","PeriodicalId":37653,"journal":{"name":"Non-coding RNA Research","volume":"15 ","pages":"Pages 100-107"},"PeriodicalIF":4.7,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144861167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-07-14DOI: 10.1016/j.ncrna.2025.07.004
Zhuohong Xu , Lihao Liu , Xiaoxi Dai , Xuyue Zhou , Lihao Chen , Hongying Chen , Chao Luan , Dan Huang , Jiaan Zhang , Yu Hu , Kun Chen , Heng Gu
tRNA-derived small RNAs (tsRNAs), a class of non-coding RNAs (ncRNAs), have garnered increasing research interest for their potential roles in various biological processes. Among these, 5′tiRNA-Glu-TTC has been implicated in aging, but its role in skin photoaging remains elusive. This study aimed to elucidate the impact of 5′tiRNA-Glu-TTC on skin photoaging. RT-qPCR analysis revealed that 5′tiRNA-Glu-TTC expression increased in human dermal fibroblasts (HDFs), human skin tissues, and mouse skin tissues following UVB irradiation. In HDFs, transfection of a 5′tiRNA-Glu-TTC mimic induced photoaging phenotypes, while its inhibitor alleviated UVB-induced photoaging. This study found that 5′tiRNA-Glu-TTC participates in photoaging through binding to TRPV3. Overexpression of TRPV3 rescued the photoaging effects induced by the 5′tiRNA-Glu-TTC mimic. Furthermore, 5′tiRNA-Glu-TTC influences photoaging also by activating the PI3K/AKT signaling pathway, an effect that was reversed by TRPV3 overexpression. In vivo studies in nude mice showed that intradermal injection of 5′tiRNA-Glu-TTC adeno-associated virus alleviated UVB-induced skin aging phenotypes, including epidermal thickening, dermal collagen reduction, and increased transepidermal water loss (TEWL). Collectively, our findings demonstrate that 5′tiRNA-Glu-TTC mediates photoaging by targeting TRPV3 and activating the PI3K/AKT pathway.
{"title":"5′tiRNA-Glu-TTC targets TRPV3 and activates the PI3K/AKT signaling pathway to modulate skin photoaging","authors":"Zhuohong Xu , Lihao Liu , Xiaoxi Dai , Xuyue Zhou , Lihao Chen , Hongying Chen , Chao Luan , Dan Huang , Jiaan Zhang , Yu Hu , Kun Chen , Heng Gu","doi":"10.1016/j.ncrna.2025.07.004","DOIUrl":"10.1016/j.ncrna.2025.07.004","url":null,"abstract":"<div><div>tRNA-derived small RNAs (tsRNAs), a class of non-coding RNAs (ncRNAs), have garnered increasing research interest for their potential roles in various biological processes. Among these, 5′tiRNA-Glu-TTC has been implicated in aging, but its role in skin photoaging remains elusive. This study aimed to elucidate the impact of 5′tiRNA-Glu-TTC on skin photoaging. RT-qPCR analysis revealed that 5′tiRNA-Glu-TTC expression increased in human dermal fibroblasts (HDFs), human skin tissues, and mouse skin tissues following UVB irradiation. In HDFs, transfection of a 5′tiRNA-Glu-TTC mimic induced photoaging phenotypes, while its inhibitor alleviated UVB-induced photoaging. This study found that 5′tiRNA-Glu-TTC participates in photoaging through binding to TRPV3. Overexpression of TRPV3 rescued the photoaging effects induced by the 5′tiRNA-Glu-TTC mimic. Furthermore, 5′tiRNA-Glu-TTC influences photoaging also by activating the PI3K/AKT signaling pathway, an effect that was reversed by TRPV3 overexpression. In vivo studies in nude mice showed that intradermal injection of 5′tiRNA-Glu-TTC adeno-associated virus alleviated UVB-induced skin aging phenotypes, including epidermal thickening, dermal collagen reduction, and increased transepidermal water loss (TEWL). Collectively, our findings demonstrate that 5′tiRNA-Glu-TTC mediates photoaging by targeting TRPV3 and activating the PI3K/AKT pathway.</div></div>","PeriodicalId":37653,"journal":{"name":"Non-coding RNA Research","volume":"15 ","pages":"Pages 29-43"},"PeriodicalIF":5.9,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144695460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-07-11DOI: 10.1016/j.ncrna.2025.07.003
Zhe Li , Bo Zhang , Yanru Pan , Qiuyan Weng , Kefeng Hu
Programmed cell death (PCD), which includes various forms such as apoptosis, autophagy, necroptosis, pyroptosis, and ferroptosis, plays a pivotal role in disease pathogenesis and progression. tRNA-derived small RNAs (tsRNAs) have emerged as crucial regulators of these processes, influencing cellular fate and disease outcomes. Research has revealed diverse expression profiles of tsRNAs across various diseases, emphasizing their roles in modulating PCD pathways and their potential value in diagnosis and treatment. Specific tsRNAs can either promote or inhibit apoptosis; for example, tsRNA-3043a promotes ovarian granulosa cell apoptosis in premature ovarian insufficiency, whereas tsRNA-04002 prevents apoptosis in nucleus pulposus cells to delay intervertebral disc degeneration. Furthermore, tsRNAs serve as potential biomarkers for early disease detection, with emerging detection technologies enhancing their clinical utility. Therapeutically, tsRNA-targeted strategies, such as RNA interference and exosome-based drug delivery, offer new avenues for modulating PCD in diseases such as cancer, cardiovascular disorders, and neurodegenerative diseases. Despite challenges in understanding tsRNA biogenesis and functional diversity, their roles in regulating PCD highlight their strong potential in advancing disease diagnostics, treatment strategies, and personalized medicine.
{"title":"Emerging roles of tsRNAs in programmed cell death and disease therapeutics: challenges, opportunities, and future directions","authors":"Zhe Li , Bo Zhang , Yanru Pan , Qiuyan Weng , Kefeng Hu","doi":"10.1016/j.ncrna.2025.07.003","DOIUrl":"10.1016/j.ncrna.2025.07.003","url":null,"abstract":"<div><div>Programmed cell death (PCD), which includes various forms such as apoptosis, autophagy, necroptosis, pyroptosis, and ferroptosis, plays a pivotal role in disease pathogenesis and progression. tRNA-derived small RNAs (tsRNAs) have emerged as crucial regulators of these processes, influencing cellular fate and disease outcomes. Research has revealed diverse expression profiles of tsRNAs across various diseases, emphasizing their roles in modulating PCD pathways and their potential value in diagnosis and treatment. Specific tsRNAs can either promote or inhibit apoptosis; for example, tsRNA-3043a promotes ovarian granulosa cell apoptosis in premature ovarian insufficiency, whereas tsRNA-04002 prevents apoptosis in nucleus pulposus cells to delay intervertebral disc degeneration. Furthermore, tsRNAs serve as potential biomarkers for early disease detection, with emerging detection technologies enhancing their clinical utility. Therapeutically, tsRNA-targeted strategies, such as RNA interference and exosome-based drug delivery, offer new avenues for modulating PCD in diseases such as cancer, cardiovascular disorders, and neurodegenerative diseases. Despite challenges in understanding tsRNA biogenesis and functional diversity, their roles in regulating PCD highlight their strong potential in advancing disease diagnostics, treatment strategies, and personalized medicine.</div></div>","PeriodicalId":37653,"journal":{"name":"Non-coding RNA Research","volume":"15 ","pages":"Pages 65-73"},"PeriodicalIF":4.7,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144772509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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