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}
Pub Date : 2025-07-06DOI: 10.1016/j.ncrna.2025.07.002
Xia Cai , Hui Shan , Jiaojiao Wang , Jiaxin Qin , Huiling Gong , Jun Cai , Jin He
Small RNAs (sRNAs) are widely used by bacteria to regulate diverse biological processes. Although they are generally considered “non-coding”, some sRNAs (called dual-function sRNAs) have been found to encode small proteins, which are usually less than 50 amino acids in length and have long been overlooked due to significant challenges in their annotation and biochemical detection. However, in the past few decades, an increasing number of small proteins encoded by dual-function sRNAs have been reported. Previous reviews of dual-function sRNAs have mainly focused on their base-pairing nucleic acid functions, with less emphasis on the nature of their translated peptides, resulting in limited understanding of their full functional scope. This article reviews ten small proteins encoded by dual-function sRNAs and introduces their physiological functions, interacting protein partners, and the research methods used, aiming to provide new perspectives and directions for the study of small proteins and enhance understanding of bacterial regulatory mechanisms mediated by dual-function sRNAs.
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Pub Date : 2025-07-03DOI: 10.1016/j.ncrna.2025.07.001
Yina Li , Nan Wang , Jinying Hu, Minlan Luo, Na Zhang, Lili Gao
Aims
This study investigates how plasma exosomal miRNAs regulate core fucosylation (CF)-modified targets to influence autophagy and fibrosis in idiopathic pulmonary fibrosis (IPF), aiming to identify novel therapeutic strategies targeting dysregulated alveolar epithelial cell (AEC) autophagy.
Materials and methods
Plasma exosomes from IPF patients and healthy controls were isolated via ultracentrifugation, validated by TEM, nanoparticle tracking analysis (NTA), and Western blot (CD9/CD81). Exosomal miRNA profiling employed high-throughput sequencing, with TargetScan/miRanda predicting target genes. A549 and MLE-12 cells assessed exosome uptake (PKH67 labeling) and miRNA-mRNA interactions (dual-luciferase assays). CF modification was analyzed via immunoprecipitation/Western blot. In vivo validation used bleomycin (BLM)-induced fibrosis models in alveolar epithelial-specific FUT8-knockout (CKO) mice.
Key findings
IPF plasma exosomes suppressed autophagy and exacerbated fibrosis in AECs. miR-15a-5p was markedly downregulated in IPF exosomes. Overexpression of miR-15a-5p reversed BLM-induced autophagy inhibition and fibrosis. Mechanistically, miR-15a-5p directly targeted IGF1R, a CF-modified protein. Reduced miR-15a-5p elevated IGF1R expression, activating PI3K/AKT to inhibit autophagy and promote fibrosis.
Significance
This study identifies miR-15a-5p as a critical regulator of CF-modified IGF1R in IPF pathogenesis. Its downregulation drives PI3K/AKT-mediated autophagy suppression, accelerating fibrosis. Restoring miR-15a-5p or targeting IGF1R/PI3K/AKT signaling may offer novel therapeutic avenues for IPF.
本研究探讨血浆外泌体mirna如何调节核心聚焦化（CF）修饰的靶点影响特发性肺纤维化（IPF）的自噬和纤维化，旨在确定针对失调肺泡上皮细胞（AEC）自噬的新治疗策略。材料和方法采用超离心分离IPF患者和健康对照的血浆外泌体，通过TEM、纳米颗粒跟踪分析（NTA）和Western blot （CD9/CD81）进行验证。外泌体miRNA分析采用高通量测序，TargetScan/miRanda预测靶基因。A549和MLE-12细胞评估外泌体摄取（PKH67标记）和miRNA-mRNA相互作用（双荧光素酶测定）。通过免疫沉淀/Western blot分析CF修饰。在肺泡上皮特异性fut8敲除（CKO）小鼠中使用博来霉素（BLM）诱导的纤维化模型进行体内验证。关键发现sipf血浆外泌体抑制aec的自噬并加重纤维化。miR-15a-5p在IPF外泌体中明显下调。过表达miR-15a-5p可逆转blm诱导的自噬抑制和纤维化。在机制上，miR-15a-5p直接靶向IGF1R，一种cf修饰的蛋白。miR-15a-5p降低，IGF1R表达升高，激活PI3K/AKT抑制自噬，促进纤维化。本研究发现miR-15a-5p在IPF发病机制中是cf修饰的IGF1R的关键调节因子。其下调驱动PI3K/ akt介导的自噬抑制，加速纤维化。恢复miR-15a-5p或靶向IGF1R/PI3K/AKT信号通路可能为IPF提供新的治疗途径。
{"title":"The mechanism of plasma exosome miR-15a-5p targeting the CF-modified protein IGF1R to regulate alveolar epithelial autophagy and influence pulmonary interstitial fibrosis","authors":"Yina Li , Nan Wang , Jinying Hu, Minlan Luo, Na Zhang, Lili Gao","doi":"10.1016/j.ncrna.2025.07.001","DOIUrl":"10.1016/j.ncrna.2025.07.001","url":null,"abstract":"<div><h3>Aims</h3><div>This study investigates how plasma exosomal miRNAs regulate core fucosylation (CF)-modified targets to influence autophagy and fibrosis in idiopathic pulmonary fibrosis (IPF), aiming to identify novel therapeutic strategies targeting dysregulated alveolar epithelial cell (AEC) autophagy.</div></div><div><h3>Materials and methods</h3><div>Plasma exosomes from IPF patients and healthy controls were isolated via ultracentrifugation, validated by TEM, nanoparticle tracking analysis (NTA), and Western blot (CD9/CD81). Exosomal miRNA profiling employed high-throughput sequencing, with TargetScan/miRanda predicting target genes. A549 and MLE-12 cells assessed exosome uptake (PKH67 labeling) and miRNA-mRNA interactions (dual-luciferase assays). CF modification was analyzed via immunoprecipitation/Western blot. In vivo validation used bleomycin (BLM)-induced fibrosis models in alveolar epithelial-specific FUT8-knockout (CKO) mice.</div></div><div><h3>Key findings</h3><div>IPF plasma exosomes suppressed autophagy and exacerbated fibrosis in AECs. miR-15a-5p was markedly downregulated in IPF exosomes. Overexpression of miR-15a-5p reversed BLM-induced autophagy inhibition and fibrosis. Mechanistically, miR-15a-5p directly targeted IGF1R, a CF-modified protein. Reduced miR-15a-5p elevated IGF1R expression, activating PI3K/AKT to inhibit autophagy and promote fibrosis.</div></div><div><h3>Significance</h3><div>This study identifies miR-15a-5p as a critical regulator of CF-modified IGF1R in IPF pathogenesis. Its downregulation drives PI3K/AKT-mediated autophagy suppression, accelerating fibrosis. Restoring miR-15a-5p or targeting IGF1R/PI3K/AKT signaling may offer novel therapeutic avenues for IPF.</div></div>","PeriodicalId":37653,"journal":{"name":"Non-coding RNA Research","volume":"15 ","pages":"Pages 51-64"},"PeriodicalIF":5.9,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144695462","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 : 2025-06-23DOI: 10.1016/j.ncrna.2025.06.004
Dong-Li Zhu , Yan Zhang , Xiao-Yu Zhang , Zi-Han Qiu , Ke Li , Xiao-Rong Zhou , Zhen-Zhen He , Xiao-Feng Chen , Shan-Shan Dong , Wen Tian , Ya-Kang Wang , Tie-Lin Yang , Bo Yang , Yan Guo
Background
Osteoporosis is a systemic skeletal disorder characterized by reduced bone mass and microarchitectural deterioration of bone tissue. Our previous investigation provided preliminary evidence that single nucleotide polymorphisms (SNPs) may functionally interact with the LINC00339, potentially contributing to the pathogenesis and progression of osteoporosis through undefined molecular pathways. However, the exact mechanistic basis of LINC00339's involvement in osteoporotic bone remodeling remains incompletely characterized and warrants systematic exploration.
Methods
We analyzed the differentially expressed of LINC003339 in different bone tissues by qRT-PCR. ALP and Alizarin red S (ARS) staining were conducted in stably knocked-down and overexpressed of LINC00339 cell lines. RNA fluorescence in situ hybridization (FISH) assays were used to detect the subcellular location of LINC00339. The mechanism of LINC00339 regulating cell division cycle 42 (CDC42) was explored by RNA-protein pull-down, RNA immunoprecipitation (RIP) and Co-IP assays.
Results
This study demonstrated significant upregulation of LINC00339 in bone tissue specimens derived from osteoporosis patients compared to healthy controls. Functional analyses revealed that LINC00339 dysregulation exhibited an inverse correlation with osteogenic differentiation capacity across multiple osteoblast cell models. Subcellular localization analysis via FISH confirmed the predominant cytoplasmic distribution of LINC00339 in bone cells. Mechanistically, RNA-protein pull-down assays combined with RNA immunoprecipitation (RIP) identified poly (ADP-Ribose) polymerase 1 (PARP1) as a direct binding partner of LINC00339. Further investigation established that the LINC00339-PARP1 axis cooperatively modulates transcriptional programs critical to bone homeostasis, potentially driving pathogenic mechanisms underlying osteoporosis progression. Notably, integrated transcriptomic and rescue experiments revealed that LINC00339 and PARP1 coregulate CDC42 expression through post-transcriptional regulatory mechanisms.
Conclusions
The identification of the LINC00339-PARP1-CDC42 regulatory axis elucidates a novel molecular mechanism contributing to osteoporosis pathogenesis. This discovery not only advances our understanding of epigenetic regulation in bone remodeling but also positions the LINC00339-PARP1 interaction as a potential therapeutic target for modulating osteoblast dysfunction. Importantly, these findings establish a conceptual framework for lncRNA-driven interventions in skeletal disorders, highlighting the translational potential of targeting RNA-protein complexes to restore bone homeostasis.
{"title":"Long noncoding RNA LINC00339 promotes osteoporosis development via modulating of regulator CDC42 by binding PARP1","authors":"Dong-Li Zhu , Yan Zhang , Xiao-Yu Zhang , Zi-Han Qiu , Ke Li , Xiao-Rong Zhou , Zhen-Zhen He , Xiao-Feng Chen , Shan-Shan Dong , Wen Tian , Ya-Kang Wang , Tie-Lin Yang , Bo Yang , Yan Guo","doi":"10.1016/j.ncrna.2025.06.004","DOIUrl":"10.1016/j.ncrna.2025.06.004","url":null,"abstract":"<div><h3>Background</h3><div>Osteoporosis is a systemic skeletal disorder characterized by reduced bone mass and microarchitectural deterioration of bone tissue. Our previous investigation provided preliminary evidence that single nucleotide polymorphisms (SNPs) may functionally interact with the LINC00339, potentially contributing to the pathogenesis and progression of osteoporosis through undefined molecular pathways. However, the exact mechanistic basis of LINC00339's involvement in osteoporotic bone remodeling remains incompletely characterized and warrants systematic exploration.</div></div><div><h3>Methods</h3><div>We analyzed the differentially expressed of LINC003339 in different bone tissues by qRT-PCR. ALP and Alizarin red S (ARS) staining were conducted in stably knocked-down and overexpressed of LINC00339 cell lines. RNA fluorescence in situ hybridization (FISH) assays were used to detect the subcellular location of LINC00339. The mechanism of LINC00339 regulating cell division cycle 42 (CDC42) was explored by RNA-protein pull-down, RNA immunoprecipitation (RIP) and Co-IP assays.</div></div><div><h3>Results</h3><div>This study demonstrated significant upregulation of LINC00339 in bone tissue specimens derived from osteoporosis patients compared to healthy controls. Functional analyses revealed that LINC00339 dysregulation exhibited an inverse correlation with osteogenic differentiation capacity across multiple osteoblast cell models. Subcellular localization analysis via FISH confirmed the predominant cytoplasmic distribution of LINC00339 in bone cells. Mechanistically, RNA-protein pull-down assays combined with RNA immunoprecipitation (RIP) identified poly (ADP-Ribose) polymerase 1 (PARP1) as a direct binding partner of LINC00339. Further investigation established that the LINC00339-PARP1 axis cooperatively modulates transcriptional programs critical to bone homeostasis, potentially driving pathogenic mechanisms underlying osteoporosis progression. Notably, integrated transcriptomic and rescue experiments revealed that LINC00339 and PARP1 coregulate CDC42 expression through post-transcriptional regulatory mechanisms.</div></div><div><h3>Conclusions</h3><div>The identification of the LINC00339-PARP1-CDC42 regulatory axis elucidates a novel molecular mechanism contributing to osteoporosis pathogenesis. This discovery not only advances our understanding of epigenetic regulation in bone remodeling but also positions the LINC00339-PARP1 interaction as a potential therapeutic target for modulating osteoblast dysfunction. Importantly, these findings establish a conceptual framework for lncRNA-driven interventions in skeletal disorders, highlighting the translational potential of targeting RNA-protein complexes to restore bone homeostasis.</div></div>","PeriodicalId":37653,"journal":{"name":"Non-coding RNA Research","volume":"15 ","pages":"Pages 18-28"},"PeriodicalIF":5.9,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144654332","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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