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Lee YC, Lin YC, Wu YS, Tsao YY, Lin YC, Lin HH, Hsu YF, Wu YC, Lin CC, Tzeng HE, Wang PH, Chang WW, Hsiao KY. Nuclear circGUSBP1 promotes cancer stemness via transcriptional coordination with OCT4. Life Sci 2025; 374:123707. [PMID: 40360086 DOI: 10.1016/j.lfs.2025.123707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2025] [Revised: 04/23/2025] [Accepted: 05/06/2025] [Indexed: 05/15/2025]
Abstract
AIMS Endometrial cancer (ECa) is a prevalent gynecological malignancy, with treatment often hindered by metastasis and recurrence driven by cancer stem-like cells. While circular RNAs (circRNAs) are well known for their cytoplasmic roles as microRNA sponges, their nuclear functions remain largely unexplored. This study investigates nuclear circRNAs and their roles in regulating cancer stem-like properties in ECa. MATERIALS AND METHODS Nuclear RNA sequencing data were analyzed to identify nuclear-enriched circRNAs. The subcellular localization of circGUSBP1 and circZNF680 was assessed via nuclear-cytoplasmic fractionation and RT-qPCR. The functional impact of circGUSBP1 was evaluated using tumorsphere formation, migration, and cisplatin sensitivity assays. Transcriptomic profiling and survival analysis were conducted using circGUSBP1-knockdown ECa cells and The Cancer Genome Atlas (TCGA) dataset. KEY FINDINGS CircGUSBP1 exhibited a high circular-to-linear transcript ratio and was preferentially nuclear, independent of intron retention. Its expression correlated with NANOG and OCT4 upregulation. Overexpression of circGUSBP1 enhanced tumorsphere formation, whereas circGUSBP1-knockdown (KD) reduced tumorsphere formation, impaired migration, and increased cisplatin sensitivity. Transcriptomic analysis revealed downregulation of stemness-related genes, supporting its role as a transcriptional co-activator. Notably, 230 circGUSBP1-regulated genes were co-targeted by OCT4, including SUPT16H and SUV39H2, chromatin remodelers linked to poor prognosis in ECa patients. Higher GUSBP1 expression, but not GUSB, correlated with worse survival outcomes in TCGA data. SIGNIFICANCE These findings identify circGUSBP1 as a nuclear regulator of cancer stemness. Through circGUSBP1/OCT4 co-regulation of chromatin modulators, circGUSBP1 promotes aggressive tumor behavior, highlighting its potential as a therapeutic target.
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Affiliation(s)
- Yueh-Chun Lee
- Department of Radiation Oncology, Chung Shan Medical University Hospital, Taichung 402306, Taiwan; School of Medicine, Chung Shan Medical University, Taichung 402306, Taiwan
| | - Ya-Chi Lin
- Big Data Center, China Medical University Hospital, China Medical University, Taichung 404328, Taiwan; Department of Biomedical Informatics, China Medical University, Taichung 404328, Taiwan
| | - Yu-Shiue Wu
- Department of Anesthesiology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi City 60002, Taiwan
| | - Yun-Ya Tsao
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Yun-Chieh Lin
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Hui-Hsuan Lin
- Doctoral Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung 402202, Taiwan
| | - Yu-Feng Hsu
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Yu-Chen Wu
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Chien-Cheng Lin
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan
| | - Huey-En Tzeng
- Department of Oncology and Precision Medicine Center, Taichung Veterans General Hospital, Taichung 407219, Taiwan
| | - Po-Hui Wang
- Institute of Medicine, Chung Shan Medical University, Taichung 402306, Taiwan; Department of Obstetrics and Gynecology, Chung Shan Medical University Hospital, Taichung 402306, Taiwan
| | - Wen-Wei Chang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung 402306, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, Taichung 402306, Taiwan
| | - Kuei-Yang Hsiao
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; Doctoral Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung 402202, Taiwan; Doctoral Program in Translational Medicine, College of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; Rong Hsing Research Center for Translational Medicine, College of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan.
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Liu Y, Yue J, Jiang Y, Tian X, Shu A. The role of circRNA in insulin resistance and its progression induced by adipose inflammation. J Diabetes Complications 2025; 39:109042. [PMID: 40279985 DOI: 10.1016/j.jdiacomp.2025.109042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Revised: 03/18/2025] [Accepted: 04/16/2025] [Indexed: 04/29/2025]
Abstract
CircRNAs refer to a type of closed circular non-coding RNA without a 5' cap or a 3' poly (A) structure. They are largely distributed in the cytoplasm or localized in exosomes and cannot be easily degraded by RNA exonuclease activity. Their stable expression is broadly observed across eukaryotic species. Insulin resistance (IR) refers to the inability of insulin to exert its normal biological function, as manifested by the impairment of glucose utilization in peripheral tissues (e.g., muscle and fat tissues). IR is a key factor in the pathogenesis of Type 2 diabetes (T2D) and is closely associated with obesity. Recent studies have shown that certain circRNAs play critical roles in obesity-induced diabetes by regulating IR and participating in inflammatory processes. CircRNAs, with their multiple microRNA (miRNA) binding sites, act as miRNA sponges to eliminate the inhibitory actions of miRNAs and up-regulate the expression of target genes. CircRNAs play a significant role in regulating obesity-induced diabetes through their interactions with disease-related miRNAs. In the present study, we explored the biological characteristics of circRNAs and extensively discussed the role of circRNAs in the development of inflammation and IR in adipocytes, highlighting their potential as therapeutic targets for obesity-induced diabetes. Specific circRNAs (e.g., circARF3 and circ-ZNF609) have been identified as key players in modulating IR and inflammatory responses in adipose tissue. CircRNAs are emerging as important regulators of IR and inflammation in adipocytes, with significant potential for therapeutic intervention in obesity-induced diabetes. Further research is needed to elucidate the mechanisms underlying their actions and to explore strategies for targeting circRNAs in clinical applications.
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Affiliation(s)
- Yifei Liu
- Department of Anesthesiology, The First College of Clinical Medical Science, China Three Gorges University, Yichang, Hubei Province 443000, China; Yichang Central people's Hospital, Yichang, Hubei Province 443000, China; The Institute of Geriatric Anesthesia, China Three Gorges University, Yichang, Hubei Province, 443000, China
| | - Jie Yue
- Department of Anesthesiology, The First College of Clinical Medical Science, China Three Gorges University, Yichang, Hubei Province 443000, China; Yichang Central people's Hospital, Yichang, Hubei Province 443000, China; The Institute of Geriatric Anesthesia, China Three Gorges University, Yichang, Hubei Province, 443000, China
| | - Yuxia Jiang
- Department of Anesthesiology, The First College of Clinical Medical Science, China Three Gorges University, Yichang, Hubei Province 443000, China; Yichang Central people's Hospital, Yichang, Hubei Province 443000, China; The Institute of Geriatric Anesthesia, China Three Gorges University, Yichang, Hubei Province, 443000, China
| | - Xu Tian
- Department of Anesthesiology, The First College of Clinical Medical Science, China Three Gorges University, Yichang, Hubei Province 443000, China; Yichang Central people's Hospital, Yichang, Hubei Province 443000, China; The Institute of Geriatric Anesthesia, China Three Gorges University, Yichang, Hubei Province, 443000, China
| | - Aihua Shu
- Department of Anesthesiology, The First College of Clinical Medical Science, China Three Gorges University, Yichang, Hubei Province 443000, China; Yichang Central people's Hospital, Yichang, Hubei Province 443000, China; The Institute of Geriatric Anesthesia, China Three Gorges University, Yichang, Hubei Province, 443000, China.
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3
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Wang Z, Su X, Zhan Z, Wang H, Zhou S, Mao J, Xu H, Duan S. miR-660: A novel regulator in human cancer pathogenesis and therapeutic implications. Gene 2025; 953:149434. [PMID: 40120868 DOI: 10.1016/j.gene.2025.149434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2024] [Revised: 03/12/2025] [Accepted: 03/18/2025] [Indexed: 03/25/2025]
Abstract
MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression. Among these, miR-660, located on chromosome Xp11.23, is increasingly studied for its role in cancer due to its abnormal expression in various biological contexts. It is regulated by 8 competing endogenous RNAs (ceRNAs), which adds complexity to its function. miR- 660 targets 19 genes involved in 6 pathways such as PI3K/AKT/mTOR, STAT3, Wnt/β-catenin, p53, NF‑κB, and RAS, influencing cell cycle, proliferation, apoptosis, and invasion/migration. It also plays a role in resistance to chemotherapies like cisplatin, gemcitabine, and sorafenib in lung adenocarcinoma (LUAD), pancreatic ductal adenocarcinoma (PDAC), and hepatocellular carcinoma (HCC), thus highlighting its clinical importance. Additionally, leveraging liposomes as nanocarriers presents a promising avenue for enhancing cancer drug delivery. Our comprehensive study not only elucidates the aberrant expression patterns, biological functions, and regulatory networks of miR-660 and its ceRNAs but also delves into the intricate signaling pathways implicated. We envisage that our findings will furnish a robust framework and serve as a seminal reference for future investigations of miR-660, fostering advancements in cancer research and potentially catalyzing breakthroughs in cancer diagnosis and treatment paradigms.
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Affiliation(s)
- Zehua Wang
- Department of Clinical Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Xinming Su
- Department of Clinical Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Zhiqing Zhan
- Department of Clinical Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Hangxuan Wang
- Department of Clinical Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Shuhan Zhou
- Department of Clinical Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Jiasheng Mao
- Department of Clinical Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Hening Xu
- Department of Clinical Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Shiwei Duan
- Department of Clinical Medicine, Hangzhou City University, Hangzhou, Zhejiang, China.
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Liu Y, Ai H. Circular RNAs in gynecological cancer: From molecular mechanisms to clinical applications (Review). Oncol Lett 2025; 29:291. [PMID: 40271005 PMCID: PMC12015383 DOI: 10.3892/ol.2025.15037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2024] [Accepted: 03/14/2025] [Indexed: 04/25/2025] Open
Abstract
Circular RNAs (circRNAs) have emerged as promising biomarkers and therapeutic targets in gynecological cancer. The present review explored developments in circRNA research in ovarian, endometrial and cervical cancer. circRNA biogenesis, functions and roles in cancer pathogenesis have been discussed, focusing on their potential as diagnostic and prognostic markers. Furthermore, circRNAs mechanisms of action, including miRNA sponging, protein scaffolding and peptide encoding were examined, highlighting specific circRNAs implicated in each cancer type and their clinical significance. The unique properties of circRNAs, such as stability and tissue-specific expression, make them ideal candidates for biomarker development. By synthesizing the currently available literature and identifying future research directions, the present review underscored circRNAs potential to improve gynecological cancer management through novel diagnostic tools, prognostic markers and targeted therapies.
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Affiliation(s)
- Ying Liu
- Department of Gynecology and Obstetrics, The Third Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121000, P.R. China
- Liaoning Provincial Key Laboratory of Follicular Development and Reproductive Health, Jinzhou Medical University, Jinzhou, Liaoning 121000, P.R. China
| | - Hao Ai
- Department of Gynecology and Obstetrics, The Third Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121000, P.R. China
- Liaoning Provincial Key Laboratory of Follicular Development and Reproductive Health, Jinzhou Medical University, Jinzhou, Liaoning 121000, P.R. China
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5
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Wang H, Bian C, Zhang Y, Zhang L, Wang F. Circular RNAs in glioma progression: Fundamental mechanisms and therapeutic potential: A review. Int J Biol Macromol 2025; 313:144360. [PMID: 40388873 DOI: 10.1016/j.ijbiomac.2025.144360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2025] [Revised: 05/14/2025] [Accepted: 05/16/2025] [Indexed: 05/21/2025]
Abstract
Gliomas are the most common primary malignant brain tumors, characterized by aggressive invasion, limited therapeutic options, and poor prognosis. Despite advances in surgery, radiotherapy, and chemotherapy, the median survival of glioma patients remains disappointingly low. Therefore, identifying glioma-associated therapeutic targets and biomarkers is of significant clinical importance. Circular RNAs (circRNAs) are a class of naturally occurring long non-coding RNAs (lncRNAs), notable for their stability and evolutionary conservation. Increasing evidence indicates that circRNA expression is dysregulated in gliomas compared to adjacent non-tumor tissues and contributes to the regulation of glioma-related biological processes. Furthermore, numerous circRNAs function as oncogenes or tumor suppressors, mediating glioma initiation, progression, and resistance to temozolomide (TMZ). Mechanistically, circRNAs regulate glioma biology through diverse pathways, including acting as miRNA sponges, binding RNA-binding proteins (RBPs), modulating transcription, and even encoding functional peptides. These features highlight the potential of circRNAs as diagnostic and prognostic biomarkers, as well as therapeutic targets for glioma. This review summarizes the dysregulation and functions of circRNAs in glioma and explores key mechanisms through which they mediate tumor progression, including DNA damage repair, programmed cell death (PCD), angiogenesis, and metabolic reprogramming. Our aim is to provide a comprehensive perspective on the multifaceted roles of circRNAs in glioma and to highlight their potential for translational application in targeted therapy.
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Affiliation(s)
- Hongbin Wang
- Head and Neck Oncology Ward, West China Hospital of Sichuan University, Chengdu, China
| | - Chenbin Bian
- Head and Neck Oncology Ward, West China Hospital of Sichuan University, Chengdu, China
| | - Yidan Zhang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Li Zhang
- Head and Neck Oncology Ward, West China Hospital of Sichuan University, Chengdu, China
| | - Feng Wang
- Head and Neck Oncology Ward, West China Hospital of Sichuan University, Chengdu, China.
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6
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Zheng S, Hu J, Jiao Z, Wang T, Hu J, Zhang CY. Lighting up three-dimensional nanolantern for circular RNA imaging and precise gene therapy. Biosens Bioelectron 2025; 276:117273. [PMID: 39970724 DOI: 10.1016/j.bios.2025.117273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2024] [Revised: 02/14/2025] [Accepted: 02/14/2025] [Indexed: 02/21/2025]
Abstract
Circular RNAs (circRNAs) are a category of endogenous single-stranded RNAs with covalently closed head-to-tail topology, and they play a crucial part in regulating gene expression at post-transcriptional and transcriptional levels. Herein, we construct a three-dimensional nanolantern for circRNA imaging and precise gene therapy. This assay involves an integrated multi-functionalized lantern-shaped probe. By rationally engineering four vertexes and six edges of DNA dimensional architecture, the integrated nanolantern probe functions not only as a delivery machine for reactants but also as a scaffold for catalytic hybridization reactions. The presence of circCDYL initiates the entropy-driven strand displacement assembly of nanolantern monomer to generate long nanolantern concatemers while releasing small interfering RNAs (siRNAs) for target-stimulated on-site and on-demand gene therapy. Compared with canonical linear probe-based catalytic circuit, this method exhibits significantly improved fluorescence stability and gene therapy efficiency due to the inherent resistance of DNA rigid structure to enzymic digestion. This strategy enables one-step detection of circCDYL with a limit of detection (LOD) of 28.2 aM, and accurate quantification of circCDYL expressions in breast cancer patients and healthy individuals. Importantly, this catalytic circuit can achieve tumor-specific gene silencing with minimal off-target toxicity, holding great potential in tumor diagnosis and precise medicine.
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Affiliation(s)
- Shi Zheng
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 211189, China
| | - Jinping Hu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 211189, China
| | - Zichen Jiao
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, 210000, China
| | - Tao Wang
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, 210000, China.
| | - Juan Hu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 211189, China.
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 211189, China.
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7
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Liu D, Wang X, Zhang Y, Zuo S, Chereda B, Gregory PA, Zhao CX, Goodall GJ. A Dual-Selection System for Enhanced Efficiency and Fidelity of Circular RNA Overexpression. J Mol Biol 2025; 437:169064. [PMID: 40049291 DOI: 10.1016/j.jmb.2025.169064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 02/24/2025] [Accepted: 03/01/2025] [Indexed: 03/16/2025]
Abstract
Circular RNAs (circRNAs) are essential regulators of cellular processes, but are challenging to study using traditional methods. Overexpression approaches, such as the use of linearized plasmids and viral vectors, often result in high rates of false-positive clones, where cells retain selection markers without expressing the target circRNA. This study addresses this limitation by developing a dual-selection circRNA system designed to enhance the accuracy and reliability of circRNA overexpression. Our system integrates a fluorescent reporter gene upstream of the circRNA expression cassette, under a shared promoter, and a downstream antibiotic resistance marker, allowing for both antibiotic selection and flow cytometric cell-sorting to identify and enrich cells with genuine circRNA expression. We successfully incorporated this system into an inducible lentiviral vector for controlled overexpression in various cell types. The dual-selection circRNA system offers a significant advance for circRNA research and studies of other RNA species where accurate and reliable overexpression is essential.
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Affiliation(s)
- Dawei Liu
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia; School of Chemical Engineering, Faculty of Science, Engineering and Technology, The University of Adelaide, Adelaide, SA 5005, Australia.
| | - Xing Wang
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Yali Zhang
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Shiyi Zuo
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Bradley Chereda
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Philip A Gregory
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Chun-Xia Zhao
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia; School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
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Joshi V, Swati, Mishra A, Panda A, Sharma V. The role of circular RNAs in regulating cytokine signaling in cancer. FEBS Open Bio 2025. [PMID: 40356340 DOI: 10.1002/2211-5463.70051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Revised: 03/30/2025] [Accepted: 04/29/2025] [Indexed: 05/15/2025] Open
Abstract
Dysregulation of cytokine signaling is central to the development and progression of cancer. Cytokines are not only involved in promoting cancer development but also regulate anti-tumor immune responses. Circular RNAs (circRNAs) are single-stranded, covalently closed RNA molecules lacking free ends, which have emerged as critical regulators of cytokine signaling. Transcriptional and post-transcriptional regulation of cytokine signaling by circRNAs contributes to cancer pathogenesis. Here, we discuss the emerging role of circRNAs in modulating cytokine signaling pathways that regulate cancer development. In particular, we examine the role of circRNAs in TGF-β, IL-6, IL-10, TNF-α, VEGF, FGF, PDGF, and chemokine signaling in cancer.
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Affiliation(s)
- Vandana Joshi
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, India
| | - Swati
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, India
| | | | - Vivek Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, India
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Wang M, Zheng S, Zhang Y, Zhang J, Lai F, Zhou C, Zhou Q, Li X, Li G. Transcriptome analysis reveals PTBP1 as a key regulator of circRNA biogenesis. BMC Biol 2025; 23:127. [PMID: 40350413 PMCID: PMC12067716 DOI: 10.1186/s12915-025-02233-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 05/02/2025] [Indexed: 05/14/2025] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) are a class of non-coding RNAs generated through back splicing. High expression of circRNAs is often associated with numerous abnormal cellular biological processes. However, the regulatory factors of circRNAs are not fully understood. RESULTS In this study, we identified PTBP1 as a crucial regulator of circRNA biogenesis through a comprehensive analysis of the whole transcriptome profiles across 10 diverse cell lines. Knockdown of PTBP1 led to a significant decrease in circRNA expression, concomitant with a distinct reduction in cell proliferation. To investigate the regulatory mechanism of PTBP1 on circRNA biogenesis, we constructed a minigene reporter based on SPPL3 gene. The results showed that PTBP1 can bind to the flanking introns of circSPPL3, and the mutation of PTBP1 motif impedes the back splicing of circSPPL3. Subsequently, to demonstrate that this observation is not an exception, the comprehensive regulatory effects of PTBP1 on circRNAs were confirmed by miniGFP, reflecting the necessity of the binding site in the flanking introns. Analysis of data from clinical samples showed that both PTBP1 and circRNAs exhibited substantial upregulation in acute myeloid leukemia, further demonstrating a potential role for PTBP1 in promoting circRNA biogenesis under in vivo conditions. Competitive endogenous RNA (ceRNA) network revealed that PTBP1-associated circRNAs participated in biological processes associated with cell proliferation. CONCLUSIONS In summary, our study is the first to identify the regulatory effect of PTBP1 on circRNA biogenesis and indicates a possible link between PTBP1 and circRNA expression in leukemia.
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Affiliation(s)
- Mohan Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming Technology for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shanshan Zheng
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming Technology for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yan Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming Technology for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jingwen Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming Technology for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fuming Lai
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming Technology for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cong Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming Technology for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiangwei Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming Technology for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming Technology for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
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10
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Wang Y, Tu M, Gao H, Deng S. Impacts of Circular RNAs on the Osteogenic Differentiation of Dental Stem Cells. Stem Cells Int 2025; 2025:8338337. [PMID: 40376229 PMCID: PMC12081154 DOI: 10.1155/sci/8338337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2025] [Accepted: 04/11/2025] [Indexed: 05/18/2025] Open
Abstract
Dental stem cells are widely viewed as good options for bone regeneration because of their ease of acquisition, innate ability to renew themselves, and ability to differentiate into different types of cells. However, the process of osteogenic differentiation of dental stem cells is orchestrated by an intricate system of regulatory mechanisms. Recent studies have demonstrated the critical impacts of circular RNAs (circRNAs) on osteogenic differentiation of dental stem cells. Exploring the roles and regulatory pathways of circRNAs in dental stem cells could identify novel targets and approaches for utilizing dental stem cell therapy in clinical settings. This review provides a comprehensive overview of the functions and mechanisms of circRNAs, with a particular focus on their expression patterns and regulatory roles in osteogenic differentiation of various dental stem cell types. Furthermore, this review discusses current research challenges in this field and proposes future directions for advancing our understanding of circRNA-mediated regulation in dental stem cell biology.
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Affiliation(s)
- Yang Wang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, China
| | - Meijie Tu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, China
| | - Huihui Gao
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, China
| | - Shuli Deng
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, China
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11
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Jeong H, Son S, Lee G, Park JH, Yoo S. Biogenesis of circular RNAs in vitro and in vivo from the Drosophila Nk2.1/scarecrow gene. G3 (BETHESDA, MD.) 2025; 15:jkaf055. [PMID: 40071305 PMCID: PMC12060249 DOI: 10.1093/g3journal/jkaf055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 02/21/2025] [Indexed: 03/19/2025]
Abstract
The scarecrow (scro) gene encodes a fly homolog of mammalian Nkx2.1, which is vital for early fly development and for optic lobe development. Previously, scro was reported to produce a circular RNA in addition to traditional mRNAs. In this study, we report 12 different scro circular RNAs, which are either mono or multiexonic forms. The most abundant ones are circScro(2) carrying the second exon (E2) only and bi-exonic circScro(3,4) having both the third (E3) and fourth exon (E4). Levels of circScro(2) show an age-dependent increase in adult heads, supporting a general trend of high accumulation of circular RNAs in aged fly brains. In silico analysis of the introns flanking circular RNA exons predicts 2 pairs of intronic complementary sequences; 1 pair residing in introns 1 and 2 and the other in introns 2 and 4. The first pair was demonstrated to be essential for the circScro(2) production in cell-based assays; furthermore, deletion of the region including intronic complementary sequence components in the intron-2 reduces in vivo production of both circScro(2) and circScro(3,4) by 80%, indicating them to be essential for the biogenesis of the 2 circular RNAs. Besides the intronic complementary sequence, the intron regions immediately abutting exons seem to be responsible for a basal level of circular RNA formation. Moreover, ectopic intronic complementary sequence derived from the laccase2 locus is comparably effective in circScro production, buttressing the importance of the hairpin loop structure formed by intronic complementary sequence for the biogenesis of circular RNA. Last, overexpressed scro alters outcomes of both linear and circular RNAs from the endogenous scro locus, suggesting that Scro plays a direct or indirect role in regulating the expression levels of either or both forms.
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Affiliation(s)
- Hyunjin Jeong
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea
| | - Suhyeon Son
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea
| | - Gyunghee Lee
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Jae H Park
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
- Graduate Program of Genome Science & Technology, University of Tennessee, Knoxville, TN 37996, USA
| | - Siuk Yoo
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea
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12
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Silva JP, Corrales WA, Catalán J, Olave FA, González-Mori PI, Alarcón M, Guarnieri T, Aliaga E, Maracaja-Coutinho V, Fiedler JL. Comprehensive Analysis of circRNA Expression and circRNA-miRNA-mRNA Networks in the Ventral Hippocampus of the Rat: Impact of Chronic Stress and Biological Sex. ACS Chem Neurosci 2025; 16:1720-1737. [PMID: 40257053 DOI: 10.1021/acschemneuro.4c00681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2025] Open
Abstract
This study provides new insights into how sex and chronic stress influence circRNA expression in the rat ventral hippocampus, a region critical for emotional processing. We identified 206 sex-biased circRNAs and 194 stress-responsive circRNAs, highlighting distinct expression profiles. Parental genes of male circRNAs were primarily enriched in synaptic transmission pathways, while those of female circRNAs were associated with axon guidance, emphasizing sex-specific molecular differences. Chronic stress also triggered miRNA changes unique to each sex, revealing divergent regulatory mechanisms. The identified circRNA-miRNA-mRNA axes, modulated under stress, appear to regulate the translation of numerous potential mRNA targets. In males, stress positively regulated neuroprotective pathways, suggesting a compensatory response to mitigate stress-induced damage. In contrast, females exhibited a broader translational network that favored mRNA expression without distinct pathway-specific actions. However, the smaller repressed network in females─characterized by a higher circRNA-to-miRNA and mRNA ratio─may indicate a more selective and targeted regulatory mechanism, with many interactions linked to anti-inflammatory processes. Coexpression analysis revealed two male-specific modules with altered activity under stress. These were associated with processes such as reticulum stress and actin dynamics, the latter linked to dendritic spine loss and depressive-like behaviors, extensively documented in chronically stressed male rats. Conversely, females displayed an activated stress-responsive module, promoting axon guidance and long-term potentiation, which may contribute to improved cognitive outcomes. Among the identified circRNAs, rno-Gabrg3_0001 emerged as stress-sensitive in males. This circRNA exhibited predicted miRNA binding sites and interactions with proteins involved in vesicle trafficking, forming part of a highly active module enriched in genes related to ion transport and membrane protein localization. Overall, these findings uncover sex-dependent regulatory mechanisms driving transcriptomic changes under chronic stress, deepening our understanding of ventral hippocampal molecular functions. Investigating these regulatory networks, which differentially affect the male and female ventral hippocampus, could inform the development of sex-specific therapeutic strategies for stress-related disorders.
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Affiliation(s)
- Juan Pablo Silva
- Laboratory of Neuroplasticity and Neurogenetics, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia 8380492, Santiago, Chile
- Unidad de Genómica Avanzada─UGA, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia 8380492, Santiago, Chile
| | - Wladimir A Corrales
- Laboratory of Neuroplasticity and Neurogenetics, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia 8380492, Santiago, Chile
- Unidad de Genómica Avanzada─UGA, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia 8380492, Santiago, Chile
| | - Julia Catalán
- Laboratory of Neuroplasticity and Neurogenetics, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia 8380492, Santiago, Chile
| | - Felipe A Olave
- Laboratory of Neuroplasticity and Neurogenetics, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia 8380492, Santiago, Chile
| | - Pablo I González-Mori
- Laboratory of Neuroplasticity and Neurogenetics, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia 8380492, Santiago, Chile
| | - Matías Alarcón
- Laboratory of Neuroplasticity and Neurogenetics, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia 8380492, Santiago, Chile
| | - Tatiana Guarnieri
- Laboratory of Neuroplasticity and Neurogenetics, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia 8380492, Santiago, Chile
| | - Esteban Aliaga
- School of Medícal Technology and The Neuropsychology and Cognitive Neurosciences Research Center (CINPSI-Neurocog), Faculty of Health Sciences, Universidad Católica del Maule, Talca 3460000, Chile
| | - Vinicius Maracaja-Coutinho
- Unidad de Genómica Avanzada─UGA, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia 8380492, Santiago, Chile
- Advanced Center for Chronic Diseases─ACCDiS, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia 8380492, Santiago, Chile
- Centro de Modelamiento Molecular, Biofísica y Bioinformática─CM2B2, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia 8380492, Santiago, Chile
| | - Jenny L Fiedler
- Laboratory of Neuroplasticity and Neurogenetics, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia 8380492, Santiago, Chile
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13
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Hsu CY, Bediwi AK, Zwamel AH, Uthirapathy S, Ballal S, Singh A, Sharma GC, Devi A, Almalki SG, Kadhim IM. circRNA/TLR interaction: key players in immune regulation and autoimmune diseases. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2025:10.1007/s00210-025-04221-9. [PMID: 40328911 DOI: 10.1007/s00210-025-04221-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2025] [Accepted: 04/23/2025] [Indexed: 05/08/2025]
Abstract
Circular RNAs are a class of non-coding RNAs with covalently closed loops. They have been revealed to regulate immune responses by affecting gene expression. Although initially considered splicing byproducts, new studies have indicated their role in transcriptional and post-transcriptional control, especially with TLRs. TLRs start inflammatory signaling and let the innate immune system recognize PAMPs. circRNAs interact context-dependently with TLR pathways to influence immune homeostasis and inflammation in either pathogenic or protective roles. In autoimmune diseases, dysregulated circRNA expression can aggravate immune responses and damage tissue. CircRNAs can interact with RNA-binding proteins, function as molecular sponges for miRNAs, and change inflammatory pathways like the NF-κB signaling cascade, influencing immune responses. They control adaptive immunity, function of antigen-presenting cells, and cytokine generation. The stability and presence of circRNAs in many body fluids make them therapeutic targets and biomarkers for inflammatory and autoimmune diseases. The several immune control roles of circRNA-TLR interactions are discussed in this review, as well as their consequences for immunologically mediated disease diagnosis and treatment.
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Affiliation(s)
- Chou-Yi Hsu
- Thunderbird School of Global Management, Arizona State University Tempe Campus, Phoenix, AZ, 85004, USA
| | - Alaa Khalaf Bediwi
- Medical Laboratory Techniques Department, College of Health and Medical Technology, University of Al-Maarif, Anbar, Iraq.
| | - Ahmed Hussein Zwamel
- Department of Medical Analysis, Medical Laboratory Technique College, the Islamic University, Najaf, Iraq.
- Department of Medical Analysis, Medical Laboratory Technique College, the Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq.
- Department of Medical Analysis, Medical Laboratory Technique College, the Islamic University of Babylon, Babylon, Iraq.
| | - Subasini Uthirapathy
- Pharmacy Department, Tishk International University, Erbil, Kurdistan Region, Iraq
| | - Suhas Ballal
- Department of Chemistry and Biochemistry, School of Sciences, JAIN (Deemed to be University), Bangalore, Karnataka, India
| | - Abhayveer Singh
- Centre for Research Impact & Outcome, Chitkara University Institute of Engineering and Technology, Chitkara University, Rajpura, 140401, Punjab, India
| | - Girish Chandra Sharma
- Department of Applied Sciences-Chemistry, NIMS Institute of Engineering & Technology, NIMS University Rajasthan, Jaipur, India
| | - Anita Devi
- Chandigarh Engineering College, Chandigarh Group of Colleges-Jhanjeri, Mohali, 140307, Punjab, India
| | - Sami G Almalki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, 11952, Majmaah, Saudi Arabia
| | - Issa Mohammed Kadhim
- Department of Medical Laboratories Technology, Al-Nisour University College, Nisour Seq. Karkh, Baghdad, Iraq
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14
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Zhou M, Yang J, Huang C. The Functional Diversity of Chromatin-Associated RNA Binding Proteins in Transcriptional and Post-Transcriptional Regulation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2025; 16:e70015. [PMID: 40404282 DOI: 10.1002/wrna.70015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2024] [Revised: 05/06/2025] [Accepted: 05/08/2025] [Indexed: 05/24/2025]
Abstract
RNA-binding proteins (RBPs) are a diverse class of proteins that interact with their target RNA molecules to regulate gene expression at the transcriptional and post-transcriptional levels. RBPs contribute to almost all aspects of RNA processing with sequence-specific, structure-specific, and nonspecific binding modes. Advances in our understanding of the mechanisms of RBP-mediated regulatory networks consisting of DNAs, RNAs, and protein complexes and the association between these networks and human diseases have been made very recently. Here, we discuss the "unconventional" functions of RBPs in transcriptional regulation by focusing on the cutting-edge investigations of chromatin-associated RBPs (ChRBPs). We briefly introduce examples of how ChRBPs influence the genomic features and molecular structures at the level of transcription. In addition, we focus on the post-transcriptional functions of various RBPs that regulate the biogenesis, transportation, stability control, and translation ability of circular RNA molecules (circRNAs). Lastly, we raise several questions about the clinical significance and potential therapeutic utility of disease-relevant RBPs.
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Affiliation(s)
- Min Zhou
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing, China
| | - Jun Yang
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, China
- Center of Plant Functional Genomics and Synthetic Biology, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
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15
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Liu L, Lei X, Wang Z, Meng J, Song B. TransRM: Weakly supervised learning of translation-enhancing N6-methyladenosine (m 6A) in circular RNAs. Int J Biol Macromol 2025; 306:141588. [PMID: 40023417 DOI: 10.1016/j.ijbiomac.2025.141588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2024] [Revised: 02/24/2025] [Accepted: 02/26/2025] [Indexed: 03/04/2025]
Abstract
As our understanding of Circular RNAs (circRNAs) continues to expand, accumulating evidence has demonstrated that circRNAs can interact with microRNAs and RNA-binding proteins to modulate gene expression. More importantly, a subset of circRNAs has been reported to possess coding potential, enabling them to translate into functional proteins. Recent studies also indicate that the N6-methyladenosine (m6A)-modified start codon may function as an Internal Ribosome Entry Site (IRES), influencing the translation of circRNAs. Therefore, elucidating how m6A regulates circRNA translation potential could significantly advance circRNA research, including the development of circRNA-based vaccines. However, to our knowledge, there are currently no computational tools specifically designed for this purpose. To bridge this gap, we have developed the first computational model, termed TransRM, to predict the impact of base-resolution m6A sites on circRNA translation. Our model employs weakly supervised learning with two convolution layers. These layers extract RNA modification features, and a bidirectional gated recurrent unit predicts the contribution of each RNA modification to circRNA translation. Subsequently, the RNA modification features are then integrated with their contribution to assess the probability of circRNA translation using a random forest algorithm. TransRM has demonstrated efficiency in identifying translation-enhancing m6A sites, with an AUROC of 0.9188 and an AUPRC of 0.9371, respectively. We hope that our newly proposed model could help to broaden our understanding of circRNA regulation at the epitranscriptome layer, particularly in identifying translated circRNAs, thereby contributing to the development of more effective circular RNA-based therapeutics.
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Affiliation(s)
- Lian Liu
- School of Computer Science, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an, Shaanxi 710119, China.
| | - Zheng Wang
- School of Computer Science, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Jia Meng
- Department of Biosciences and Bioinformatics, Center for Intelligent RNA Therapeutics, Suzhou Key Laboratory of Cancer Biology and Chronic Disease, School of Science, XJTLU Entrepreneur College, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L7 8TX, United Kingdom
| | - Bowen Song
- Department of Public Health, School of Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
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16
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Zhang J, Zhao F. Circular RNA discovery with emerging sequencing and deep learning technologies. Nat Genet 2025; 57:1089-1102. [PMID: 40247051 DOI: 10.1038/s41588-025-02157-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2024] [Accepted: 03/07/2025] [Indexed: 04/19/2025]
Abstract
Circular RNA (circRNA) represents a type of RNA molecule characterized by a closed-loop structure that is distinct from linear RNA counterparts. Recent studies have revealed the emerging role of these circular transcripts in gene regulation and disease pathogenesis. However, their low expression levels and high sequence similarity to linear RNAs present substantial challenges for circRNA detection and characterization. Recent advances in long-read and single-cell RNA sequencing technologies, coupled with sophisticated deep learning-based algorithms, have revolutionized the investigation of circRNAs at unprecedented resolution and scale. This Review summarizes recent breakthroughs in circRNA discovery, characterization and functional analysis algorithms. We also discuss the challenges associated with integrating large-scale circRNA sequencing data and explore the potential future development of artificial intelligence (AI)-driven algorithms to unlock the full potential of circRNA research in biomedical applications.
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Affiliation(s)
- Jinyang Zhang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Fangqing Zhao
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
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17
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Liu J, Yao D, Zhou F, Li K, Sun W, Wang S, Cai C, Xu X. RBM24-mediated biogenesis of circ23679 protects cardiomyocytes against apoptosis via sponging miR-15b-5p. Int J Biol Macromol 2025; 310:143242. [PMID: 40250678 DOI: 10.1016/j.ijbiomac.2025.143242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Revised: 03/28/2025] [Accepted: 04/15/2025] [Indexed: 04/20/2025]
Abstract
Circular RNAs (circRNAs) have emerged as significant members of gene regulatory networks and play important roles in normal heart biology and cardiac diseases. RNA binding proteins (RBPs) are key regulatory factors in circRNA formation; however, the mechanisms by which RBP regulate circRNA production remain unclear. RNA binding motif protein 24 (RBM24) is essential for alternative splicing of genes related to cardiac function, and its loss leads to dilated cardiomyopathy and heart failure. In this study, we performed circRNA profiling on hearts from wild-type and Rbm24 knockout mice, identifying the differential expression of circRNAs. We demonstrated that RBM24 could directly bind to pre-mRNA, facilitating the inclusion of specific exons to provide a substrate for circ23679 production. Moreover, RBM24-regulated circRNA production depended on its phosphorylation status. Further, we showed that RBM24-mediated circ23679 acted as a sponge of miR-15b-5p, and a deficient in circ23679-mediated 'sponging events' could drive cardiac apoptosis. Conversely, circ23679 overexpression inhibited cardiac apoptosis and alleviated the disease phenotype in mouse models of heart failure. Thus, our study not only proposes a novel model in which RBPs provide the substrate for circRNA formation but also reveals that RBM24-dependent circRNA production is a crucial post-transcriptional regulatory circuit in cardiac pathogenesis.
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Affiliation(s)
- Jing Liu
- The Institute of Stem Cell and Regenerative Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian Province 361100, PR China.
| | - Dongbo Yao
- The Institute of Stem Cell and Regenerative Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian Province 361100, PR China
| | - Fangwen Zhou
- The Institute of Stem Cell and Regenerative Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian Province 361100, PR China
| | - Keyue Li
- The Institute of Stem Cell and Regenerative Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian Province 361100, PR China
| | - Wenhao Sun
- The Institute of Stem Cell and Regenerative Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian Province 361100, PR China
| | - Shanshan Wang
- The Institute of Stem Cell and Regenerative Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian Province 361100, PR China
| | - Can Cai
- The Institute of Stem Cell and Regenerative Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian Province 361100, PR China
| | - Xiuqin Xu
- The Institute of Stem Cell and Regenerative Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian Province 361100, PR China.
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18
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Luo J, Sun T, Jiang S, Yang Z, Xiao C, Deng J, Zhou B, Yang X. Comprehensive analysis of non-coding RNAs in the ovaries of high and low egg production hens. Anim Reprod Sci 2025; 276:107836. [PMID: 40220592 DOI: 10.1016/j.anireprosci.2025.107836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Revised: 04/02/2025] [Accepted: 04/03/2025] [Indexed: 04/14/2025]
Abstract
Egg production performance a critical economic trait in the poultry industry. The regulatory mechanisms underlying egg production performance mediated by non-coding RNAs remain to be characterized. To systematically investigate ovarian lncRNAs, circRNAs, and miRNAs associated with laying efficiency, we conducted comparative transcriptomic analyses using RNA sequencing (RNA-seq) of ovarian tissues from phenotypically divergent groups - high egg production (HEP) and low egg production (LEP) hens. In our study, we identified 675 lncRNAs, 140 circRNAs, and 10 miRNAs that were significantly differentially expressed (DE) between HEP and LEP. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that target genes of DE lncRNAs, DE miRNAs, and the source genes of DE circRNAs are involved in the MAPK signaling pathway, endocytosis, notch signaling pathway, among others. Furthermore, we identified five miRNA-mRNA interactions related to egg production including gga-miR-449c-3p, and five genes (GLI2, TAC1, EML6, THOC3, MMP9). These findings establish the first comprehensive ncRNA interactome driving ovarian efficiency, offering both biomarkers for breeding selection and mechanistic targets for reproductive enhancement.
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Affiliation(s)
- Jintang Luo
- From the College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Tiantian Sun
- From the College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Siyi Jiang
- From the Beijing Royal School, Beijing 102209, China
| | - Zhuliang Yang
- From the College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Cong Xiao
- From the College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jixian Deng
- From the College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Biyan Zhou
- From the College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Xiurong Yang
- From the College of Animal Science and Technology, Guangxi University, Nanning 530004, China; From the Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Naning 530004, China.
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19
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Dou Y, Zhang X, Guo R, Huang X, Song Y, Liu X, Shi J, Li F, Zhang D, Kong P, Nie L, Li H, Zhang F, Han M. Quaking-cZFP609 Axis Remedies Aberrant Plasticity of Vascular Smooth Muscle Cells via Mediating Platelet-Derived Growth Factor Receptor β Degradation. MedComm (Beijing) 2025; 6:e70167. [PMID: 40242156 PMCID: PMC12000678 DOI: 10.1002/mco2.70167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 03/04/2025] [Accepted: 03/06/2025] [Indexed: 04/18/2025] Open
Abstract
Vascular smooth muscle cell (VSMC) plasticity is crucial for the repair after vascular injury. However, the high plasticity of VSMCs may make them transform into pathogenic phenotypes. Here, we show that VSMCs overexpressing Sirtuin 1 (SIRT1) exhibit a reduced phenotypic plasticity in the context of platelet-derived growth factor (PDGF)-BB treatment. SIRT1 activated Quaking (QKI)-cZFP609 axis is involved in the plasticity regulation in the VSMCs. Mechanically, SIRT1 deacetylates K133 and K134 of QKI and mediates its activation. Activated QKI binds the QKI response elements located in the upstream and downstream of the cZFP609-forming exons in ZFP609 pre-mRNA to mediate cZFP609 production. Furthermore, the acetylation of QKI is increased by inhibiting SIRT1 with the selective and potent inhibitor EX527 or deletion of SIRT1, accompanied with parallel decrease in cZFP609 formation. Final, we identify that cZFP609 directs PDGF receptor (PDGFR)β sorting into endosomal/lysosomal pathway and degradation by bridging PDGFRβ and Rab7, resulted in attenuating Raf-MEK-ERK cascade activation downstream of PDGFRβ signaling. Overexpression of cZFP609 remedies aberrant plasticity and overproliferation of VSMCs, and ameliorates neointimal formation. Together, these results highlight that modulating the QKI-cZFP609 axis may help propel repair without stenosis as a therapeutic strategy in vascular injury.
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Affiliation(s)
- Yong‐Qing Dou
- Department of Biochemistry and Molecular BiologyCollege of Basic MedicineShijiazhuangChina
- College of Integrative MedicineHebei University of Chinese MedicineShijiazhuangChina
| | - Xiao‐Yun Zhang
- College of Integrative MedicineHebei University of Chinese MedicineShijiazhuangChina
| | - Rui‐Juan Guo
- Department of Biochemistry and Molecular BiologyCollege of Basic MedicineShijiazhuangChina
- Key Laboratory of Neural and Vascular Biology of Ministry of EducationShijiazhuangChina
- Key Laboratory of Vascular Biology of Hebei ProvinceHebei Medical UniversityShijiazhuangChina
| | - Xiao‐Fu Huang
- Department of Biochemistry and Molecular BiologyCollege of Basic MedicineShijiazhuangChina
| | - Yu Song
- Department of Biochemistry and Molecular BiologyCollege of Basic MedicineShijiazhuangChina
- Key Laboratory of Neural and Vascular Biology of Ministry of EducationShijiazhuangChina
- Key Laboratory of Vascular Biology of Hebei ProvinceHebei Medical UniversityShijiazhuangChina
| | - Xin‐Long Liu
- Department of Biochemistry and Molecular BiologyCollege of Basic MedicineShijiazhuangChina
| | - Jie Shi
- Department of Biochemistry and Molecular BiologyCollege of Basic MedicineShijiazhuangChina
| | - Fan‐Qin Li
- Department of Biochemistry and Molecular BiologyCollege of Basic MedicineShijiazhuangChina
| | - Dan‐Dan Zhang
- Department of Biochemistry and Molecular BiologyCollege of Basic MedicineShijiazhuangChina
- Key Laboratory of Neural and Vascular Biology of Ministry of EducationShijiazhuangChina
- Key Laboratory of Vascular Biology of Hebei ProvinceHebei Medical UniversityShijiazhuangChina
| | - Peng Kong
- Department of Biochemistry and Molecular BiologyCollege of Basic MedicineShijiazhuangChina
- Key Laboratory of Neural and Vascular Biology of Ministry of EducationShijiazhuangChina
- Key Laboratory of Vascular Biology of Hebei ProvinceHebei Medical UniversityShijiazhuangChina
| | - Lei Nie
- Department of Biochemistry and Molecular BiologyCollege of Basic MedicineShijiazhuangChina
- Key Laboratory of Neural and Vascular Biology of Ministry of EducationShijiazhuangChina
- Key Laboratory of Vascular Biology of Hebei ProvinceHebei Medical UniversityShijiazhuangChina
| | - Han Li
- Department of Orthopaedic SurgeryInstitute of Biomechanical Science and Biomechanical Key Laboratory of Hebei ProvinceThird Hospital of Hebei Medical UniversityShijiazhuangChina
| | - Fan Zhang
- Key Laboratory of Neural and Vascular Biology of Ministry of EducationShijiazhuangChina
- Key Laboratory of Vascular Biology of Hebei ProvinceHebei Medical UniversityShijiazhuangChina
| | - Mei Han
- Department of Biochemistry and Molecular BiologyCollege of Basic MedicineShijiazhuangChina
- Key Laboratory of Neural and Vascular Biology of Ministry of EducationShijiazhuangChina
- Key Laboratory of Vascular Biology of Hebei ProvinceHebei Medical UniversityShijiazhuangChina
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20
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Chen T, Wei Y, Kang J, Zhang D, Ye J, Sun X, Hong M, Zhang W, Wu H, Ding Z, Fei G. ADAR1-HNRNPL-Mediated CircCANX Decline Promotes Autophagy in Chronic Obstructive Pulmonary Disease. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2414211. [PMID: 40091520 PMCID: PMC12079403 DOI: 10.1002/advs.202414211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2024] [Revised: 03/05/2025] [Indexed: 03/19/2025]
Abstract
Chronic obstructive pulmonary disease (COPD) is a characteristic chronic airway inflammatory disease that worsens over time, however, there are currently limited clinical therapeutics to suspend its progression. Circular RNAs (circRNAs), which have emerged as functional regulators in various diseases, including COPD, may server as new pharmacological targets in COPD. Here, it is identified a nuclear circRNA, circCANX, that is preferentially decreased in COPD. The linear splicing of CANX pre-mRNA, enhanced by the ADAR1-HNRNPL interaction, is responsible for the circCANX decline. Clinically, the higher circCANX expression is associated with a worse lung function index of FEV1/FVC among patients with COPD. CircCANX suppresses autophagy and stress granule (SG) formation to strengthen inflammation of COPD in vivo and in vitro. Mechanistically, circCANX recruits the tumor suppressor protein P53 (P53) mRNA and RNA helicase upstream frameshift 1 (UPF1) to form a ternary complex, which mediates P53 mRNA degradation through nonsense-mediated mRNA decay (NMD) process. Together, this study reveals an important circCANX-mediated regulatory mechanism in COPD, and provides new insights into the potential of circRNA-based drug and biomarker development for COPD.
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Affiliation(s)
- Ting‐Ting Chen
- Department of Respiratory and Critical Care MedicineFirst Affiliated Hospital of Anhui Medical UniversityHefeiAnhui Province230022China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui ProvinceHefeiAnhui Province230022China
| | - Yuan‐Yuan Wei
- Department of Respiratory and Critical Care MedicineFirst Affiliated Hospital of Anhui Medical UniversityHefeiAnhui Province230022China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui ProvinceHefeiAnhui Province230022China
| | - Jia‐Ying Kang
- Department of Respiratory and Critical Care MedicineFirst Affiliated Hospital of Anhui Medical UniversityHefeiAnhui Province230022China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui ProvinceHefeiAnhui Province230022China
| | - Da‐Wei Zhang
- Department of Respiratory and Critical Care MedicineFirst Affiliated Hospital of Anhui Medical UniversityHefeiAnhui Province230022China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui ProvinceHefeiAnhui Province230022China
| | - Jing‐Jing Ye
- Department of Respiratory and Critical Care MedicineFirst Affiliated Hospital of Anhui Medical UniversityHefeiAnhui Province230022China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui ProvinceHefeiAnhui Province230022China
| | - Xi‐Shi Sun
- Emergency Medicine CenterAffiliated Hospital of Guangdong Medical UniversityZhanjiangGuangdong Province524000China
| | - Mei Hong
- Department of Respiratory and Critical Care MedicineFirst Affiliated Hospital of Anhui Medical UniversityHefeiAnhui Province230022China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui ProvinceHefeiAnhui Province230022China
| | - Wen‐Ting Zhang
- Department of Respiratory and Critical Care MedicineFirst Affiliated Hospital of Anhui Medical UniversityHefeiAnhui Province230022China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui ProvinceHefeiAnhui Province230022China
| | - Hui‐Mei Wu
- Department of Geriatric Respiratory and Critical Care MedicineFirst Affiliated Hospital of Anhui Medical UniversityHefeiAnhui Province230022China
| | - Zhen‐Xing Ding
- Department of Emergency MedicineFirst Affiliated Hospital of Anhui Medical UniversityHefeiAnhui Province230022China
| | - Guang‐He Fei
- Department of Respiratory and Critical Care MedicineFirst Affiliated Hospital of Anhui Medical UniversityHefeiAnhui Province230022China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui ProvinceHefeiAnhui Province230022China
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21
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Mueller NL, Dujsikova A, Singh A, Chen YG. Human and pathogen-encoded circular RNAs in viral infections: insights into functions and therapeutic opportunities. Hum Mol Genet 2025:ddaf031. [PMID: 40304711 DOI: 10.1093/hmg/ddaf031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 02/16/2025] [Accepted: 02/21/2025] [Indexed: 05/02/2025] Open
Abstract
Circular RNAs (circRNAs) are emerging as important regulatory molecules in both host and viral systems, acting as microRNA sponges, protein decoys or scaffolds, and templates for protein translation. Host-derived circRNAs are increasingly recognized for their roles in immune responses, while virus-encoded circRNAs, especially those from DNA viruses, have been shown to modulate host cellular machinery to favor viral replication and immune evasion. Recently, RNA virus-encoded circRNAs were also discovered, but evidence suggests that they might be generated using a different mechanism compared to the circRNAs produced from the host and DNA viruses. This review highlights recent advances in our understanding of both host and virus-derived circRNAs, with a focus on their biological roles and contributions to pathogenesis. Furthermore, we discuss the potential of circRNAs as biomarkers and their application as therapeutic targets or scaffolds for RNA-based therapies. Understanding the roles of circRNAs in host-virus interactions offers novel insights into RNA biology and opens new avenues for therapeutic strategies against viral diseases and associated cancers.
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Affiliation(s)
- Noah L Mueller
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06519, United States
| | - Adela Dujsikova
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06519, United States
| | - Amrita Singh
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06519, United States
| | - Y Grace Chen
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06519, United States
- Department of Genetics, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06519, United States
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22
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Tang M, Li H, Chang S, Li Y, Nie H, Li F. Dysregulated circular RNAs in rheumatoid arthritis: Cellular roles and clinical prospects. Autoimmun Rev 2025; 24:103774. [PMID: 39956349 DOI: 10.1016/j.autrev.2025.103774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 01/27/2025] [Accepted: 02/11/2025] [Indexed: 02/18/2025]
Abstract
Rheumatoid arthritis (RA) is still a healthcare challenge, although current therapeutic strategies have substantially improved its clinical outcomes. The development of novel biomarkers and treatments can increase the likelihood of identification and disease remission in RA patients, especially for patients with seronegative RA and difficult-to-treat RA (D2T RA). Circular RNAs (circRNAs), a novel non-coding RNA species, have been reported to play crucial roles in various biological process of RA. The mechanistic functions of the dysregulated circRNAs in RA are primarily associated with miRNA sponging and regulating transcription. CircRNAs acting as miRNA sponges are further summarized by cell types, including fibroblast-like synoviocytes (FLSs), lymphocytes, macrophages, chondrocytes, and mesenchymal stem cells (MSCs)-/plasma-secreted exosomes. Besides, a description of dysregulated circRNAs in blood, synovial tissue and cartilage tissue suggests their diagnostic potential for RA. In addition, some directions for future research are provided to open the possibility that dysregulated cell- and tissue- specific circRNAs constituting a fresh reservoir of therapeutic targets, and biomarkers for diagnosis, predicting response to therapy, drug selection or patient stratification for RA.
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Affiliation(s)
- Mengshi Tang
- Department of Rheumatology and Immunology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Clinical Medical Research Center for Systemic Autoimmune Disease in Hunan Province, Changsha, Hunan 410011, China
| | - Hongxing Li
- Department of Orthopaedics, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Department of Orthopaedics, the Central Hospital of Shaoyang, Shaoyang, Hunan 422099, China
| | - Siyuan Chang
- Department of Rheumatology and Immunology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Clinical Medical Research Center for Systemic Autoimmune Disease in Hunan Province, Changsha, Hunan 410011, China
| | - Yuanyuan Li
- Department of Rheumatology and Immunology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Clinical Medical Research Center for Systemic Autoimmune Disease in Hunan Province, Changsha, Hunan 410011, China
| | - Huiyu Nie
- Department of Rheumatology and Immunology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Clinical Medical Research Center for Systemic Autoimmune Disease in Hunan Province, Changsha, Hunan 410011, China
| | - Fen Li
- Department of Rheumatology and Immunology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Clinical Medical Research Center for Systemic Autoimmune Disease in Hunan Province, Changsha, Hunan 410011, China.
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23
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Ning Q, Jin Q, Zhao L, Wang Y, Wang J, Yang L, Han Y, Zhi Q, Zheng J, Chen F, Dong D. Transcriptome-scale analysis of functional alternative back-splicing events in colorectal cancer. J Transl Med 2025; 23:468. [PMID: 40275292 PMCID: PMC12020325 DOI: 10.1186/s12967-025-06479-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/11/2025] [Indexed: 04/26/2025] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) are a class of non-polyadenylated RNAs generated from back-splicing of genes. Multiple circRNAs can be generated at a single gene locus through alternative back-splicing events (ABS), sharing the same 5' or 3' back-splice site. To date, how prevalent ABS events are and how they are participated in carcinogenesis of human colorectal cancer (CRC) remains unexplored. METHODS To explore the functional roles of ABS events in CRC carcinogenesis, we analyzed ribosomal RNA-depleted transcriptome sequencing data of 176 CRC samples and characterized the landscape of ABS events in CRC. CRC cancer-related ABS events were identified by comparing paired CRC tumor tissues and adjacent normal tissues. Then, univariate and multivariate Cox regression was used to find prognostic ABS events. Moreover, in vitro and in vivo assays were used to exploring the functional roles of circXPO1-1 and circXPO1-2 in CRC. RESULTS We totally identified 19,611 high confidence circRNAs in CRC, among which 17,874 (91·1%) of circRNAs were found recurrently. The number of ABS circRNAs accounted for 68.8% of all identified high confidence circRNAs, which suggested that ABS events are prevalent in CRC transcriptome. Particularly, 552 ABS circRNAs were found to be aberrantly expressed between paired CRC tumor tissues and adjacent normal tissues, and their parent genes are closely associated with cancer-related hallmarks. In addition, 13 differential ABS circRNAs were identified to be associated with CRC patient survival and could act as independent prognostic indicators. Furthermore, we identified two ABS circRNAs of XPO1 gene (circXPO1-1 and circXPO1-2). The result showed that overexpression of circXPO1-2 inhibited CRC cell proliferation, migration, and invasion in vitro and in vivo, whereas circXPO1-1 is not, indicating that the circularization isoforms of XPO1 gene have different functions in CRC. CONCLUSIONS In conclusion, our work provides the landscape of ABS events in CRC transcriptome and the close association of ABS circRNAs with tumorigenesis offers a new set of targets with potential clinical benefit.
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Affiliation(s)
- Qianqian Ning
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, 99 Huaihai Road, Xuzhou, 221002, Jiangsu, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Qian Jin
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, 99 Huaihai Road, Xuzhou, 221002, Jiangsu, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Lei Zhao
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Medicine, Tongji University, Shanghai, China
| | - Yudi Wang
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Jie Wang
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Lili Yang
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Ye Han
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Qiaoming Zhi
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Junnian Zheng
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, 99 Huaihai Road, Xuzhou, 221002, Jiangsu, China.
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
| | - Feifei Chen
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, 99 Huaihai Road, Xuzhou, 221002, Jiangsu, China.
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
| | - Dong Dong
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, 99 Huaihai Road, Xuzhou, 221002, Jiangsu, China.
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
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24
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Zhou Y, Gao Y, Peng Y, Cai C, Han Y, Chen Y, Deng G, Ouyang Y, Shen H, Zeng S, Du Y, Xiao Z. QKI-induced circ_0001766 inhibits colorectal cancer progression and rapamycin resistance by miR-1203/PPP1R3C/mTOR/Myc axis. Cell Death Discov 2025; 11:192. [PMID: 40263288 PMCID: PMC12015279 DOI: 10.1038/s41420-025-02478-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 02/25/2025] [Accepted: 04/04/2025] [Indexed: 04/24/2025] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer and remains a significant challenge due to high rates of drug resistance and limited therapeutic options. Circular RNAs (circRNAs) are increasingly recognized for their roles in CRC initiation, progression, and drug resistance. However, no circRNA-based therapies have yet entered clinical development, underscoring the need for comprehensive detection and mechanistic studies of circRNAs in CRC. Here, we identified and characterized a circular RNA, circ_0001766 (hsa_circ_0001766), through microarray analysis of CRC tissues. Our results showed that circ_0001766 is downregulated in CRC tissues and closely associated with patient survival and metastasis. Functional experiments demonstrated that circ_0001766 inhibits CRC cell proliferation, migration and invasion both in-vitro and in-vivo. Mechanistically, hypoxia downregulates Quaking (QKI), an RNA-binding protein essential for the biogenesis of circ_0001766 by binding to introns 1 and 3 of PDIA4 pre-mRNA. Reduced QKI expression under hypoxic conditions leads to decreased circ_0001766 levels in CRC. Circ_0001766 acts as a competitive endogenous RNA, sponging miR-1203 to prevent the degradation of PPP1R3C mRNA. Loss of circ_0001766 results in decreased PPP1R3C expression, leading to the activation of mTOR signaling and increased phosphorylation of Myc, which promotes CRC progression and rapamycin resistance. Our study reveals that overexpression of circ_0001766 or PPP1R3C in CRC cells inhibits the mTOR and Myc pathway, thereby resensitizing cells to rapamycin. The combination of circ_0001766 or PPP1R3C with rapamycin markedly inhibits CRC cell proliferation and induces apoptosis by reducing rapamycin-induced Myc phosphorylation. In summary, our study elucidates a critical circ_0001766/miR-1203/PPP1R3C axis that modulates CRC progression and rapamycin resistance. Our findings highlight circ_0001766 as a promising therapeutic target in CRC, providing a new avenue for enhancing the efficacy of existing treatments and overcoming drug resistance.
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Grants
- This study was supported by grants from the National Natural Science Foundation of China (No. 82373275, 81974384, 82173342 & 82203015), the China Postdoctoral Science Foundation (No.2023JJ40942), three projects from the Nature Science Foundation of Hunan Province (No.2021JJ3109, 2021JJ31048, 2023JJ40942), Nature Science Foundation of Changsha (No.73201), CSCO Cancer Research Foundation (No.Y-HR2019-0182 & Y-2019Genecast-043), the Key Research and Development Program of Hainan Province (No.ZDYF2020228 & ZDYF2020125), Natural Science Foundation (Youth Funding) of Hunan Province of China (2022JJ40458), Hunan Provincial Natural Science Foundation of China (2024JJ6662), The Youth Science Foundation of Xiangya Hospital (2023Q01) and Scientific Research Program of Hunan Provincial Health Commission (202203105261). The graphical abstract was created using BioRender (BioRender.com).This study was supported by grants from the National Natural Science Foundation of China (No. 82373275, 81974384, 82173342 & 82203015), the China Postdoctoral Science Foundation (No.2023JJ40942), three projects from the Nature Science Foundation of Hunan Province (No.2021JJ3109, 2021JJ31048, 2023JJ40942), Nature Science Foundation of Changsha (No.73201), CSCO Cancer Research Foundation (No.Y-HR2019-0182 & Y-2019Genecast-043), the Key Research and Development Program of Hainan Province (No.ZDYF2020228 & ZDYF2020125), Natural Science Foundation (Youth Funding) of Hunan Province of China (2022JJ40458), Hunan Provincial Natural Science Foundation of China (2024JJ6662), The Youth Science Foundation of Xiangya Hospital (2023Q01) and Scientific Research Program of Hunan Provincial Health Commission (202203105261). The graphical abstract was created using BioRender (BioRender.com).
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Affiliation(s)
- Yulai Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX, USA
| | - Yan Gao
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Yinghui Peng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Changjing Cai
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ying Han
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yihong Chen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Gongping Deng
- Department of Emergency, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan, China
| | - Yanhong Ouyang
- Department of Emergency, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan, China
| | - Hong Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shan Zeng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yangfeng Du
- Department of Oncology, Changde Hospital, Xiangya School of Medicine, Central South University, Changde, Hunan, China.
| | - Zemin Xiao
- Department of Oncology, Changde Hospital, Xiangya School of Medicine, Central South University, Changde, Hunan, China.
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25
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Kirio K, Patop IL, Anduaga AM, Harris J, Pamudurti N, Su TN, Martel C, Kadener S. Circular RNAs exhibit exceptional stability in the aging brain and serve as reliable age and experience indicators. Cell Rep 2025; 44:115485. [PMID: 40184256 PMCID: PMC12105716 DOI: 10.1016/j.celrep.2025.115485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2024] [Revised: 02/05/2025] [Accepted: 03/07/2025] [Indexed: 04/06/2025] Open
Abstract
Circular RNAs (circRNAs) increase in the brain with age across various animal systems. To elucidate the reasons behind this phenomenon, we profile circRNAs from fly heads at six time points throughout their lifespan. Our results reveal a linear increase in circRNA levels with age, independent of changes in mRNA levels, overall transcription, intron retention, or host gene splicing, demonstrating that the age-related accumulation is due to high stability rather than increased biogenesis. This remarkable stability suggests that circRNAs can serve as markers of environmental experience. Indeed, flies exposed to a 10-day regimen at 29°C exhibit higher levels of specific circRNAs even 6 weeks after returning to standard conditions, indicating that circRNAs can reveal past environmental stimuli. Moreover, half-life measurements show circRNA stability exceeding 20 days, with some displaying virtually no degradation. These findings underscore the remarkable stability of circRNAs in vivo and their potential as markers for stress and life experiences.
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Affiliation(s)
- Ken Kirio
- Biology Department, Brandeis University, Waltham, MA 02454, USA
| | | | | | - Jenna Harris
- Biology Department, Brandeis University, Waltham, MA 02454, USA
| | | | - The Nandar Su
- Biology Department, Brandeis University, Waltham, MA 02454, USA
| | - Claire Martel
- Biology Department, Brandeis University, Waltham, MA 02454, USA
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26
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Li YJ, Liu H, Zhang YD, Li A, Pu LX, Gao Y, Zhang SR, Otecko NO, Liu L, Liu YY, Peng MS, Irwin DM, Yi C, Xie W, Qin Y, Wang Z, Wei HJ, Zhou ZY, Zhang YP. Genome wide analysis of allele-specific circular RNAs in mammals and their role in cell proliferation. Gene 2025; 946:149317. [PMID: 39921049 DOI: 10.1016/j.gene.2025.149317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2024] [Revised: 01/25/2025] [Accepted: 02/04/2025] [Indexed: 02/10/2025]
Abstract
Circular RNAs (circRNAs) are a large class of widely expressed RNAs with covalently closed continuous structures. However, it is currently unknown if circRNAs shows allele-specific expression, as are the consequences of genetic variation on their circularization efficiency and subsequent biological function. Here, we propose a novel pipeline, ASE-circRNA, to accurately quantify both circRNA and their related linear RNA for each allele, and then assess the allele-specificity of the expression of a circular RNA. We identified and analyzed allele-specific circRNAs from human tissue, as well as brains from reciprocal crosses between pairs of highly divergent strains of both mice and pigs by next generation sequencing. Droplet digital PCR (ddPCR) was used to confirm the circularization efficiency measured by next generation sequencing. We found that variation in intron sequences affect the circularization efficiency of circRNAs. Furthermore, we demonstrate that a circRNA, circHK1, regulates the expression of POLR2A to influence the rate of cell proliferation. Our study provides new insight into the molecular mechanisms impacted by variation in genome sequence in the origin of human disease and phenotype.
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Affiliation(s)
- Ying-Ju Li
- State Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China; State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming 650091, Yunnan, China; School of Life Science, Yunnan University, Kunming 650091, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China
| | - Hang Liu
- State Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China
| | - Yue-Dong Zhang
- State Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China; State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming 650091, Yunnan, China; School of Life Science, Yunnan University, Kunming 650091, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China
| | - Aimin Li
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an 710048, Shaanxi, China
| | - Li-Xia Pu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, China
| | - Yun Gao
- State Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
| | - Shu-Run Zhang
- State Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
| | - Newton O Otecko
- State Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China
| | - Lu Liu
- State Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China; Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, Anhui, China
| | - Yu-Yan Liu
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming 650091, Yunnan, China; School of Life Science, Yunnan University, Kunming 650091, Yunnan, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto M5S 1A8, Canada
| | - Chungen Yi
- Beijing Geneway Technology Co., Ltd, Beijing 100007, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yan Qin
- CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Zefeng Wang
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hong-Jiang Wei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650251, China; College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650251, China.
| | - Zhong-Yin Zhou
- State Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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Tao X, Zhai SN, Liu CX, Huang Y, Wei J, Guo YL, Liu XQ, Li X, Yang L, Chen LL. Degradation of circular RNA by the ribonuclease DIS3. Mol Cell 2025; 85:1674-1685.e8. [PMID: 39965568 DOI: 10.1016/j.molcel.2025.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 07/30/2024] [Accepted: 01/15/2025] [Indexed: 02/20/2025]
Abstract
Features of circular RNAs (circRNAs) produced by back-splicing of eukaryotic exon(s) make them resistant to degradation by linear RNA decay machineries. Thus, a general circRNA degradation pathway under normal conditions has remained largely elusive. Here, we report that the endonucleolytic enzyme DIS3 is responsible for the degradation of circRNAs. Depletion of DIS3 leads to the upregulation of more than 60% of circRNAs with little effect on their linear cognates. Such DIS3-mediated circRNA degradation is conserved, occurs in the cytoplasm, and relies on DIS3's endonucleolytic activity but is independent of the RNA exosome complex. Sequence enrichment analyses suggest that DIS3 prefers to degrade circRNAs containing U-rich motifs. Correspondingly, synthesized RNA circles with or without U-rich motifs exhibit decreased or increased stabilities, respectively. Together, these findings suggest a general regulation of circRNA turnover by DIS3.
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Affiliation(s)
- Xiao Tao
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Si-Nan Zhai
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China; Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chu-Xiao Liu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Youkui Huang
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jia Wei
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yi-Lin Guo
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xiao-Qi Liu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiang Li
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Ling-Ling Chen
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China; New Cornerstone Science Laboratory, Shenzhen, China; School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Shanghai Academy of Natural Sciences (SANS), Shanghai 200031, China.
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Li D, Liu M, Lai M, Wang L, Wei L, Wu S, Liang S, Liu S, Zeng X. The regulatory role of the circELMOD3-associated ceRNA network in the progression and prognosis of hepatocellular carcinoma. Front Genet 2025; 16:1521360. [PMID: 40303979 PMCID: PMC12037612 DOI: 10.3389/fgene.2025.1521360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Accepted: 04/07/2025] [Indexed: 05/02/2025] Open
Abstract
Background Our previously research has validated the effect of circELMOD3 on HCC tumor inhibition. However, further investigations are warranted to investigate the prognostic significance of circELMOD3 in HCC and its regulation via the competitive endogenous RNA (ceRNA) network. Methods The gene expression profiles and clinical information were obtained from The Cancer Genome Atlas (TCGA-LIHC) and International Cancer Genome Consortium (ICGC). Base on the circMine, miRWalk and TargetScan database, we constructed circELMOD3-miRNA-mRNA network. Univariate Cox and least absolute shrinkage and selection operator (LASSO) regression analysis was used to constructed the prognostic model. Additionally, Gene set enrichment analysis (GSEA) was conducted for the prognostic-related genes. Finally, the expression levels of genes and proteins were respectively assessed by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting. Results We constructed a ceRNA network comprising circELMOD3, 5 miRNAs, and 274 mRNAs. From this ceRNA network, we identified four prognostication-relation genes to develop a survival prediction model. In the TCGA-LIHC training set, the area under the curve (AUC) values for one-, three- and five-years of survival were 0.734, 0.718 and 0.707, respectively, then we validated the prognostic model in International Cancer Genome Consortium database. Gene set enrichment analysis displayed that these four prognostic genes were primary enriched pathways related to cell cycle regulation. Our finding demonstrated that circELMOD3 could affect the relative expression levels of N-cadherin, E-cadherin, CDK4, CDK6 and CyclinD1 proteins. Conclusion we constructed a novel ceRNA network based on circELMOD3, to comprehensively characterizing the prognosis of HCC, providing valuable insights for the therapy and prognosis of HCC.
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Affiliation(s)
- Deyuan Li
- School of public health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Meiliang Liu
- School of public health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Mingshuang Lai
- School of public health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Lijun Wang
- School of public health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Liling Wei
- School of public health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Siqian Wu
- School of public health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Si Liang
- School of public health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Shun Liu
- School of public health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Xiaoyun Zeng
- School of public health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Nanning, China
- Department of Epidemiological and Health Statistics, School of Public Health, Guilin Medical University, Guilin, Guangxi, China
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Zhao M, Fu W, Zhang Y, Ma J, Yang X, Nie H, Wu W, Gao F, Wu F, Xin M, Yang K, He S. Chronic hypoxia-induced upregulation of hsa_circ_0005255 attenuates myocardial injury via targeting hsa-miR-3916/FTO/m6A axis. Int J Biol Macromol 2025; 310:143228. [PMID: 40246114 DOI: 10.1016/j.ijbiomac.2025.143228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2025] [Revised: 03/19/2025] [Accepted: 04/14/2025] [Indexed: 04/19/2025]
Abstract
Chronic hypoxia initiates compensatory mechanisms to protect the heart. Circular RNAs (circRNAs), a recently identified class of non-coding RNAs, represent a significant portion of mammalian transcriptome. We aimed to explore the underlying mechanisms of circRNA involvement in chronic hypoxia-related cardiovascular diseases. In the presents study, we firstly observed hsa_circ_0005255 was elevated in myocardial samples collected from patients with cyanotic heart disease through using circRNA array sequencing, which was confirmed both in vivo and in vitro. The upregulation of hsa_circ_0005255 reduced the levels of N6-methyladenosine (m6A) modification and protected cardiomyocytes from chronic hypoxia induced injury. Fat mass and obesity-associated protein (FTO), the classic regulator of methylation, was proved to be regulated by hsa_circ_0005255. Further research verified the direct target interactions of hsa_circ_0005255/hsa-miR-3916 and hsa-miR-3916/FTO. Our findings suggested hsa_circ_0005255 played pivotal protective role in cardiomyocytes via hsa-miR-3916/FTO/m6A axis. We also showed that silencing hsa_circ_0005255 increased myocardial apoptosis and worsened ischemia/reperfusion (I/R) injury in vivo. In addition, the expression of hsa_circ_0005255 in clinical myocardial samples showed a significant negative correlation with myocardial enzyme levels and early clinical outcomes. This study elucidates a novel mechanism that hsa_circ_0005255/hsa-miR-3916/FTO-m6A axis is involved in myocardial adaptation to chronic hypoxia, representing a promising therapeutic target for cardiovascular diseases.
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Affiliation(s)
- Maolin Zhao
- Department of Cardiovascular Surgery, The General Hospital of Western Theater Command, College of Medicine, Southwest Jiaotong University, Chengdu 61003l, Sichuan, China
| | - Weijie Fu
- Department of Cardiovascular Surgery, The General Hospital of Western Theater Command, College of Medicine, Southwest Jiaotong University, Chengdu 61003l, Sichuan, China
| | - Yaolei Zhang
- Laboratory animal center, The General Hospital of Western Theater Command, Chengdu 610083, Sichuan, China
| | - Jianwen Ma
- Department of Cardiovascular Surgery, The General Hospital of Western Theater Command, College of Medicine, Southwest Jiaotong University, Chengdu 61003l, Sichuan, China
| | - Xuelin Yang
- Department of Cardiovascular Surgery, The General Hospital of Western Theater Command, College of Medicine, Southwest Jiaotong University, Chengdu 61003l, Sichuan, China
| | - Huwei Nie
- Department of Cardiovascular Surgery, The General Hospital of Western Theater Command, College of Medicine, Southwest Jiaotong University, Chengdu 61003l, Sichuan, China
| | - Wei Wu
- Department of Cardiovascular Surgery, The General Hospital of Western Theater Command, College of Medicine, Southwest Jiaotong University, Chengdu 61003l, Sichuan, China
| | - Feng Gao
- Department of Cardiovascular Surgery, The General Hospital of Western Theater Command, College of Medicine, Southwest Jiaotong University, Chengdu 61003l, Sichuan, China
| | - Fan Wu
- Department of Cardiovascular Surgery, The General Hospital of Western Theater Command, College of Medicine, Southwest Jiaotong University, Chengdu 61003l, Sichuan, China
| | - Mei Xin
- Department of Cardiovascular Surgery, The General Hospital of Western Theater Command, College of Medicine, Southwest Jiaotong University, Chengdu 61003l, Sichuan, China
| | - Ke Yang
- Department of Cardiovascular Surgery, The General Hospital of Western Theater Command, College of Medicine, Southwest Jiaotong University, Chengdu 61003l, Sichuan, China
| | - Siyi He
- Department of Cardiovascular Surgery, The General Hospital of Western Theater Command, College of Medicine, Southwest Jiaotong University, Chengdu 61003l, Sichuan, China.
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Hu PC, Yao JT, Wang KJ, Ye SZ, Meng XY, Chen HC, Yu R, Ma Q. Research progress on circular RNA in the regulation of drug resistance in genitourinary cancers. Cell Mol Life Sci 2025; 82:158. [PMID: 40232412 PMCID: PMC12000500 DOI: 10.1007/s00018-025-05683-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Revised: 03/25/2025] [Accepted: 03/28/2025] [Indexed: 04/16/2025]
Abstract
In recent years, significant progress has been made in the management of genitourinary cancers, primarily due to advancements in surgical techniques, the emergence of targeted therapy and immunotherapy, and the refinement of chemotherapy agents. However, despite the expanding arsenal of treatment modalities, some patients still face challenges associated with drug resistance, which hinders efforts to improve survival rates. Circular RNAs (circRNAs) are covalently closed RNA molecules with a stable structure and a unique ability to form reverse splicing loops. Increasing evidence suggests that abnormal expression of circRNAs is significantly correlated with the occurrence of genitourinay cancers, indicating their potentials as diagnostic and prognostic biomarkers, as well as new targets for treatment. Although research on circRNAs in genitourinary cancers has progressed, it is still in the preliminary stage. This review summarizes the properties and functions of circRNAs, focusing on their molecular and cellular mechanisms involved in mediating cancer-related drug resistance in the genitourinary system, including autophagy, epithelial-mesenchymal transition, and glycolysis, etc. The clinical potential of circRNAs in regulating drug resistance is also carefully discussed.
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Affiliation(s)
- Peng-Cheng Hu
- Health Science Center, Ningbo University, Ningbo, 315101, Zhejiang, China
| | - Jia-Tao Yao
- Health Science Center, Ningbo University, Ningbo, 315101, Zhejiang, China
| | - Ke-Jie Wang
- Translational Research Laboratory for Urology, The First Affiliated Hospital of Ningbo University, #59 Liuting Street, Ningbo, 315010, Zhejiang, China
| | - Sha-Zhou Ye
- Translational Research Laboratory for Urology, The First Affiliated Hospital of Ningbo University, #59 Liuting Street, Ningbo, 315010, Zhejiang, China
| | - Xiang-Yu Meng
- Translational Research Laboratory for Urology, The First Affiliated Hospital of Ningbo University, #59 Liuting Street, Ningbo, 315010, Zhejiang, China
| | - Hai-Chao Chen
- Department of Urology, The First Affiliated Hospital of Ningbo University, #59 Liuting Street, Ningbo, 315010, Zhejiang, China.
| | - Rui Yu
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, #818 Fenghua Road, Ningbo, 315211, Zhejiang, China.
| | - Qi Ma
- Comprehensive Genitourinary Cancer Center, The First Affiliated Hospital of Ningbo University, #59 Liuting Street, Ningbo, 315010, Zhejiang, China.
- Yi-Huan Genitourinary Cancer Group, The First Affiliated Hospital of Ningbo University, #59 Liuting Street, Ningbo, 315010, Zhejiang, China.
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Tang Y, Yuan F, Cao M, Ren Y, Li Y, Yang G, Zhong Z, Liang H, Xiong Z, He Z, Lin N, Deng M, Yao Z. CircRNA-mTOR Promotes Hepatocellular Carcinoma Progression and Lenvatinib Resistance Through the PSIP1/c-Myc Axis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025:e2410591. [PMID: 40231634 DOI: 10.1002/advs.202410591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2024] [Revised: 11/26/2024] [Indexed: 04/16/2025]
Abstract
Circular RNAs (circRNAs) are crucial regulators of targeted drug resistance in hepatocellular carcinoma (HCC). However, the specific mechanisms underlying resistance that significantly hampers the effectiveness of HCC treatments remain unclear. Here, it is found that circRNA-mTOR is highly expressed in HCC and strongly correlated with patient prognosis. Furthermore, circRNA-mTOR enhances the stemness of HCC cells, thereby promoting the progression of HCC and contributing to lenvatinib resistance. Mechanistically, circRNA-mTOR promotes the nuclear translocation of the RNA-binding protein (RBP) PC4 and SRSF1 interacting protein 1 (PSIP1) through specific binding. The enhancement of HCC cell stemness by circRNA-mTOR occurs via the PSIP1/c-Myc signaling pathway, ultimately driving HCC progression and lenvatinib resistance. This study highlights the important role of circRNA-mTOR in HCC progression and the maintenance of lenvatinib resistance and underscores its potential as a biomarker for the diagnosis and prognosis of HCC. In conclusion, this study provides an experimental foundation for targeted drug therapy in HCC and offers novel insights, perspectives, and methodologies for understanding the development and occurrence of this disease. These findings are significant for the development of new diagnostic and therapeutic markers for HCC, with the ultimate goal of reducing drug resistance.
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Affiliation(s)
- Yongchang Tang
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Feng Yuan
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510120, China
| | - Mingbo Cao
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Yupeng Ren
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Yuxuan Li
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Gaoyuan Yang
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Zhaozhong Zhong
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
- Department of Kidney Transplantation, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Hao Liang
- Department of Hepatobiliary and Pancreatic Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Zhiyong Xiong
- Department of Hepatobiliary and Pancreatic Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Zhiwei He
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Nan Lin
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Meihai Deng
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Zhicheng Yao
- Department of Hepatobiliary and Pancreatic Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
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Wu H, Tang H, Han X, Ngando FJ, Shang Y, Guo Y. Identification of circular RNAs as biomarkers for pupal age estimation and postmortem interval in forensically important Sarcophaga peregrina (Diptera: Sarcophagidae). Int J Legal Med 2025:10.1007/s00414-025-03490-6. [PMID: 40227424 DOI: 10.1007/s00414-025-03490-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Accepted: 04/01/2025] [Indexed: 04/15/2025]
Abstract
Accurate estimation of the pupal age in necrophagous flies is vital for determining the postmortem interval (PMI) in forensic entomology. Differential expression of genes (DEGs) exhibits temporal fluctuations across the developmental stages of these flies. This study evaluates circular RNAs (circRNAs) as novel molecular markers and develops a model for predicting pupal development time based on circRNA expression. Transcriptomic analysis of Sarcophaga peregrina pupae at various stages identified four circRNAs (circRNA_0037, circRNA_0531, circRNA_3373, circRNA_2847) showing significant expression differences. Using real-time quantitative PCR and regression analysis, we constructed a model to estimate development time, which accurately predicts intra-puparial periods. Additionally, we examined circRNA degradation patterns in pupae under lethal conditions and identified a clear degradation trend in circRNA_2847, suggesting its potential use for estimating the PMI. This study introduces new molecular markers and insights for estimating necrophagous fly pupal age.
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Affiliation(s)
- Hai Wu
- Department of Forensic Science, Xiangya School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410013, China
| | - Haojie Tang
- Department of Forensic Science, Xiangya School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410013, China
| | - Xing Han
- Department of Forensic Science, Xiangya School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410013, China
| | - Fernand Jocelin Ngando
- Department of Forensic Science, Xiangya School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410013, China
| | - Yanjie Shang
- Department of Forensic Science, Xiangya School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410013, China.
| | - Yadong Guo
- Department of Forensic Science, Xiangya School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410013, China.
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Huang CJ, Choo KB. Frequent dysregulation of multiple circular RNA isoforms with diverse regulatory mechanisms in cancer - Insights from circFNDC3B and beyond: Why unique circular RNA identifiers matter. Biochem Biophys Res Commun 2025; 758:151627. [PMID: 40112536 DOI: 10.1016/j.bbrc.2025.151627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2024] [Revised: 03/09/2025] [Accepted: 03/12/2025] [Indexed: 03/22/2025]
Abstract
Circular RNAs (circRNAs) are post-transcriptional regulators generated through backsplicing of pre-mRNAs, primarily comprising exons of host genes. A single host gene may produce multiple circRNA isoforms with distinct structures and sequences. Dysregulated circRNA expression has been implicated in tumorigenesis. This review aims to investigate the selection and regulatory roles of circRNA isoforms in cancer using the extensively studied hsa_circFNDC3B and thirteen other circRNAs as study models. Interrogation of literature and databases, particularly the circBase, confirms that host genes generate a plethora of circRNA isoforms; however, only a small subset of isoforms is validated as dysregulated in tumor tissues. Notably, two or more isoforms of the same circRNA are frequently dysregulated in cancer. Structurally, short isoforms retaining 5'-proximal exons are preferentially selected, but for long host genes, circRNAs may arise from mid- or 3'-regions. We identify dysregulation of seven circFNDC3B isoforms across twelve cancer types and multi-isoforms in nine of the other thirteen circRNAs also in multiple cancers. MicroRNA sponging appears to be the major regulatory mechanism, but possible biased study designs raise concerns. Using circFNDC3B and circZFR as examples, we show inconsistency and inadequacy in circRNA nomenclature in different databases and the literature, underscoring the urgent need for a universally accepted standardized central circRNA database. As an interim measure, we propose guidelines for circRNA nomenclature in journal publications. Our findings caution against indiscriminate clinical use of specific circRNA isoforms as biomarkers or therapeutic targets without further validation.
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Affiliation(s)
- Chiu-Jung Huang
- Department of Animal Science & Graduate Institute of Biotechnology, College of Environmental Planning & Bioresources (former School of Agriculture), Chinese Culture University, Taipei, 111114, Taiwan.
| | - Kong Bung Choo
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, 11217, Taiwan.
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Wingfield JL, Puthanveettil SV. Decoding the complex journeys of RNAs along neurons. Nucleic Acids Res 2025; 53:gkaf293. [PMID: 40243060 PMCID: PMC12004114 DOI: 10.1093/nar/gkaf293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2024] [Revised: 03/25/2025] [Accepted: 03/28/2025] [Indexed: 04/18/2025] Open
Abstract
Neurons are highly polarized, specialized cells that must overcome immense challenges to ensure the health and survival of the organism in which they reside. They can spread over meters and persist for decades yet communicate at sub-millisecond and millimeter scales. Thus, neurons require extreme levels of spatial-temporal control. Neurons employ molecular motors to transport coding and noncoding RNAs to distal synapses. Intracellular trafficking of RNAs enables neurons to locally regulate protein synthesis and synaptic activity. The way in which RNAs get loaded onto molecular motors and transported to their target locations, particularly following synaptic plasticity, is explored below.
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Affiliation(s)
- Jenna L Wingfield
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, United States
| | - Sathyanarayanan V Puthanveettil
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, United States
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Piergentili R, Sechi S. Targeting Regulatory Noncoding RNAs in Human Cancer: The State of the Art in Clinical Trials. Pharmaceutics 2025; 17:471. [PMID: 40284466 PMCID: PMC12030637 DOI: 10.3390/pharmaceutics17040471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Revised: 03/29/2025] [Accepted: 03/31/2025] [Indexed: 04/29/2025] Open
Abstract
Noncoding RNAs (ncRNAs) are a heterogeneous group of RNA molecules whose classification is mainly based on arbitrary criteria such as the molecule length, secondary structures, and cellular functions. A large fraction of these ncRNAs play a regulatory role regarding messenger RNAs (mRNAs) or other ncRNAs, creating an intracellular network of cross-interactions that allow the fine and complex regulation of gene expression. Altering the balance between these interactions may be sufficient to cause a transition from health to disease and vice versa. This leads to the possibility of intervening in these mechanisms to re-establish health in patients. The regulatory role of ncRNAs is associated with all cancer hallmarks, such as proliferation, apoptosis, invasion, metastasis, and genomic instability. Based on the function performed in carcinogenesis, ncRNAs may behave either as oncogenes or tumor suppressors. However, this distinction is not rigid; some ncRNAs can fall into both classes depending on the tissue considered or the target molecule. Furthermore, some of them are also involved in regulating the response to traditional cancer-therapeutic approaches. In general, the regulation of molecular mechanisms by ncRNAs is very complex and still largely unclear, but it has enormous potential both for the development of new therapies, especially in cases where traditional methods fail, and for their use as novel and more efficient biomarkers. Overall, this review will provide a brief overview of ncRNAs in human cancer biology, with a specific focus on describing the most recent ongoing clinical trials (CT) in which ncRNAs have been tested for their potential as therapeutic agents or evaluated as biomarkers.
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Phiwthong T, Limkul S, Aunkam P, Seabkongseng T, Teaumroong N, Tittabutr P, Boonchuen P. Quaking RNA-Binding protein (QKI) mediates circular RNA biogenesis in Litopenaeus vannamei during WSSV infection. FISH & SHELLFISH IMMUNOLOGY 2025; 159:110178. [PMID: 39921020 DOI: 10.1016/j.fsi.2025.110178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Revised: 02/04/2025] [Accepted: 02/04/2025] [Indexed: 02/10/2025]
Abstract
The Quaking RNA-binding protein (QKI), a member of the STAR family, is considered critical in the formation of circular RNAs (circRNAs), as it aids in catalyzing a back-splicing phenomenon by interacting with RNA precursors. CircRNAs have progressively been revealed to play central roles in the regulation of various biological processes, such as antiviral defense mechanisms. This study identifies a QKI in L. vannamei, referred to as LvQKI, comprised of conserved STAR and KH RNA-binding domains. Analysis through tissue-specific expression using qRT-PCR has revealed a high expression level of LvQKI in the gill - one of the primary regions heavily populated by the white spot syndrome virus (WSSV) - and its activation was triggered during WSSV infection. From an RNA interference-mediated suppression targeting LvQKI, a decrease and increase in survival rates and WSSV copy number were observed, respectively. Notably, circRNA levels were significantly lowered in LvQKI-silenced shrimp, whereas linear RNAs remained stable. Conversely, administration of recombinant LvQKI (rLvQKI) protein before a WSSV challenge not only enhanced survival rates but also reduced viral load, wherein both circRNAs and linear RNAs underwent up-regulation in rLvQKI-treated shrimp. Our results introduce LvQKI as a crucial factor in circRNA biogenesis and immune defense in shrimp, emphasizing the interplay between LvQKI's and circRNAs' roles in fighting viral invasion.
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Affiliation(s)
- Tannatorn Phiwthong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Muang District, Nakhon Ratchasima, 30000, Thailand
| | - Sirawich Limkul
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Muang District, Nakhon Ratchasima, 30000, Thailand
| | - Phirom Aunkam
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Muang District, Nakhon Ratchasima, 30000, Thailand
| | - Tuangrak Seabkongseng
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Muang District, Nakhon Ratchasima, 30000, Thailand
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Muang District, Nakhon Ratchasima, 30000, Thailand
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Muang District, Nakhon Ratchasima, 30000, Thailand
| | - Pakpoom Boonchuen
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Muang District, Nakhon Ratchasima, 30000, Thailand.
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37
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O'Leary E, Jiang Y, Kristensen LS, Hansen TB, Kjems J. The therapeutic potential of circular RNAs. Nat Rev Genet 2025; 26:230-244. [PMID: 39789148 DOI: 10.1038/s41576-024-00806-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2024] [Indexed: 01/12/2025]
Abstract
Over the past decade, research into circular RNA (circRNA) has increased rapidly, and over the past few years, circRNA has emerged as a promising therapeutic platform. The regulatory functions of circRNAs, including their roles in templating protein translation and regulating protein and RNA functions, as well as their unique characteristics, such as increased stability and a favourable immunological profile compared with mRNAs, make them attractive candidates for RNA-based therapies. Here, we describe the properties of circRNAs, their therapeutic potential and technologies for their synthesis. We also discuss the prospects and challenges to be overcome to unlock the full potential of circRNAs as drugs.
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Affiliation(s)
| | - Yanyi Jiang
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | | | | | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark.
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark.
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Srinivasan A, Magner D, Kozłowski P, Philips A, Kajdasz A, Wojciechowski P, Wojciechowska M. Global dysregulation of circular RNAs in frontal cortex and whole blood from DM1 and DM2. Hum Genet 2025; 144:417-432. [PMID: 39903274 PMCID: PMC12003446 DOI: 10.1007/s00439-025-02729-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2024] [Accepted: 01/25/2025] [Indexed: 02/06/2025]
Abstract
Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are autosomal dominant neuromuscular disorders associated with expansions of microsatellites, respectively, in DMPK and CNBP. Their pathogenesis is linked to the global aberrant alternative splicing (AAS) of many genes and marks mostly muscular and neuronal tissues, while blood is the least affected. Recent data in DM1 skeletal muscles indicated that abnormalities in RNA metabolism also include global upregulation of circular RNAs (circRNAs). CircRNAs are a heterogeneous group considered splicing errors and by-products of canonical splicing. To elucidate whether circRNA dysregulation is an inherent feature of the myotonic environment, we perform their analysis in the frontal cortex and whole blood of DM1 and DM2 patients. We find a global elevation of circRNAs in both tissues, and its magnitude is neither correlated with the differences in their parental gene expression nor is associated with AAS published earlier. Aberrantly spliced cassette exons of linear transcripts affected in DM1 and DM2 are not among the circularized exons, which unique genomic features prerequisite back-splicing. However, the blueprint of the AAS of linear RNAs is found in a variety of circRNA isoforms. The heterogeneity of circRNAs also originates from the utilization of exonic and intronic cryptic donors/acceptors in back splice junctions, and intron-containing circRNAs are more characteristic of the blood. Overall, this study reveals circRNA dysregulation in various tissues from DM1 and DM2; however, their levels do not correlate with the AAS in linear RNAs, suggesting a potential independent regulatory mechanism underlying circRNA upregulation in myotonic dystrophy.
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Affiliation(s)
- Arvind Srinivasan
- Department of Rare Diseases, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Dorota Magner
- Department of Rare Diseases, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Department of Biochemistry and Biotechnology, University of Life Sciences, Poznan, Poland
| | - Piotr Kozłowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna Philips
- Department of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Arkadiusz Kajdasz
- Department of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Paweł Wojciechowski
- Laboratory of Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Marzena Wojciechowska
- Department of Rare Diseases, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
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Zhao Y, Wang S, Fu S, Wang X, Zhang J, Chen F. The diagnostic and therapeutic potential of multiple myeloma-associated circular RNAs. Exp Hematol 2025; 144:104709. [PMID: 39756785 DOI: 10.1016/j.exphem.2024.104709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 12/13/2024] [Accepted: 12/19/2024] [Indexed: 01/07/2025]
Abstract
Circular RNA (circRNA) was first discovered in viruses in 1974; they are primarily formed through back splicing, where a downstream splice donor is joined to an upstream splice acceptor, resulting in a closed circRNA transcript. Under normal conditions, most circRNAs are stably expressed; however, in pathological conditions, circRNAs can play critical roles in the disease process of multiple myeloma (MM) through mechanisms such as competing endogenous RNAs (ceRNAs), regulation of transcription and splicing, affecting protein expression and localization, and even direct encoding of peptides. In recent years, there has been increasing interest in the role of circRNAs in MM and their regulatory functions during the disease process. Numerous studies have revealed that circRNAs are involved in the pathogenesis and prognosis of MM, aiding in the identification of reliable prognostic markers and potential therapeutic targets. Therefore, this review summarizes the structural characteristics of circRNAs, and their regulatory roles in MM, and introduces the latest advancements in understanding the novel functions of circRNAs in MM.
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Affiliation(s)
- Yue Zhao
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Shaokun Wang
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Shuang Fu
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Xinxin Wang
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Jihong Zhang
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Fang Chen
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China.
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40
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Feng Y, Zhu Y, Zhu Y, Lu Y, He Y, Wu Y, Jiang L, Weng W. Circular RNA NXN (circNXN) promotes diabetic retinopathy by regulating the miR-338-3p/FGFR1 axis. Arch Physiol Biochem 2025; 131:177-187. [PMID: 39988878 DOI: 10.1080/13813455.2024.2404102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 08/17/2024] [Accepted: 09/09/2024] [Indexed: 02/25/2025]
Abstract
Diabetic retinopathy (DR) is the leading manifestation of diabetic microangiopathy. However, effective biomarkers and therapies are lacking. Circular RNAs (circRNAs) have been implicated in various diseases including DR. However, the role of circRNAs in DR remains elusive. In the present study, circNXN was upregulated in high glucose (HG)-treated human retinal microvascular endothelial cells (hRMECs). circNXN knockdown inhibited the proliferation, migration, and angiogenesis of hRMECs and promoted apoptosis. In addition, circNXN acted as a sponge for miR-338-3p to facilitate the FGFR1 (fibroblast growth factor receptor 1) expression. Furthermore, rescue assays revealed that the reduced promoting effect on hRMECs induced by the knockdown of circNXN could be reversed by a miR-338-3p inhibitor in HG-treated hRMECs. Additionally, in a DR rat model, circNXN downregulation ameliorated retinal vasculature changes. Our findings reveal a new therapeutic strategy for DR that may provide a new approach to clinical DR therapy.
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Affiliation(s)
- Yanbing Feng
- Department of ophthalmology, Jiaxing Hospital of Traditional Chinese Medicine, No.1501 Zhongshan East Road, Jiaxing, Zhejiang, China
| | - Yongwei Zhu
- Department of ophthalmology, Jiaxing Hospital of Traditional Chinese Medicine, No.1501 Zhongshan East Road, Jiaxing, Zhejiang, China
| | - Yixing Zhu
- Department of ophthalmology, Jiaxing Hospital of Traditional Chinese Medicine, No.1501 Zhongshan East Road, Jiaxing, Zhejiang, China
| | - Yanting Lu
- Department of ophthalmology, Jiaxing Hospital of Traditional Chinese Medicine, No.1501 Zhongshan East Road, Jiaxing, Zhejiang, China
| | - Yanyan He
- Department of ophthalmology, Jiaxing Hospital of Traditional Chinese Medicine, No.1501 Zhongshan East Road, Jiaxing, Zhejiang, China
| | - Yibo Wu
- Department of ophthalmology, Jiaxing Hospital of Traditional Chinese Medicine, No.1501 Zhongshan East Road, Jiaxing, Zhejiang, China
| | - Lijun Jiang
- Department of ophthalmology, Jiaxing Hospital of Traditional Chinese Medicine, No.1501 Zhongshan East Road, Jiaxing, Zhejiang, China
| | - Wenqing Weng
- Department of ophthalmology, Jiaxing Hospital of Traditional Chinese Medicine, No.1501 Zhongshan East Road, Jiaxing, Zhejiang, China
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41
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Hatzimanolis O, Sykes AM, Cristino AS. Circular RNAs in neurological conditions - computational identification, functional validation, and potential clinical applications. Mol Psychiatry 2025; 30:1652-1675. [PMID: 39966624 PMCID: PMC11919710 DOI: 10.1038/s41380-025-02925-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 01/11/2025] [Accepted: 02/10/2025] [Indexed: 02/20/2025]
Abstract
Non-coding RNAs (ncRNAs) have gained significant attention in recent years due to advancements in biotechnology, particularly high-throughput total RNA sequencing. These developments have led to new understandings of non-coding biology, revealing that approximately 80% of non-coding regions in the genome possesses biochemical functionality. Among ncRNAs, circular RNAs (circRNAs), first identified in 1976, have emerged as a prominent research field. CircRNAs are abundant in most human cell types, evolutionary conserved, highly stable, and formed by back-splicing events which generate covalently closed ends. Notably, circRNAs exhibit high expression levels in neural tissue and perform diverse biochemical functions, including acting as molecular sponges for microRNAs, interacting with RNA-binding proteins to regulate their availability and activity, modulating transcription and splicing, and even translating into functional peptides in some cases. Recent advancements in computational and experimental methods have enhanced our ability to identify and validate circRNAs, providing valuable insights into their biological roles. This review focuses on recent developments in circRNA research as they related to neuropsychiatric and neurodegenerative conditions. We also explore their potential applications in clinical diagnostics, therapeutics, and future research directions. CircRNAs remain a relatively underexplored area of non-coding biology, particularly in the context of neurological disorders. However, emerging evidence supports their role as critical players in the etiology and molecular mechanisms of conditions such as schizophrenia, bipolar disorder, major depressive disorder, Alzheimer's disease, and Parkinson's disease. These findings suggest that circRNAs may provide a novel framework contributing to the molecular dysfunctions underpinning these complex neurological conditions.
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Affiliation(s)
- Oak Hatzimanolis
- Institute for Biomedicine and Glycomics, Griffith University, Brisbane, QLD, Australia
| | - Alex M Sykes
- Institute for Biomedicine and Glycomics, Griffith University, Brisbane, QLD, Australia
| | - Alexandre S Cristino
- Institute for Biomedicine and Glycomics, Griffith University, Brisbane, QLD, Australia.
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42
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You Q, Yu J, Pan R, Feng J, Guo H, Liu B. Decoding the regulatory roles of circular RNAs in cardiac fibrosis. Noncoding RNA Res 2025; 11:115-130. [PMID: 39759175 PMCID: PMC11697406 DOI: 10.1016/j.ncrna.2024.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 09/04/2024] [Accepted: 11/28/2024] [Indexed: 01/07/2025] Open
Abstract
Cardiovascular diseases (CVDs) are the primary cause of death globally. The evolution of nearly all types of CVDs is characterized by a common theme: the emergence of cardiac fibrosis. The precise mechanisms that trigger cardiac fibrosis are still not completely understood. In recent years, a type of non-coding regulatory RNA molecule known as circular RNAs (circRNAs) has been reported. These molecules are produced during back splicing and possess significant biological capabilities, such as regulating microRNA activity, serving as protein scaffolds and recruiters, competing with mRNA, forming circR-loop structures to modulate transcription, and translating polypeptides. Furthermore, circRNAs exhibit a substantial abundance, notable stability, and specificity of tissues, cells, and time, endowing them with the potential as biomarkers, therapeutic targets, and therapeutic agents. CircRNAs have garnered growing interest in the field of CVDs. Recent investigations into the involvement of circRNAs in cardiac fibrosis have yielded encouraging findings. This study aims to provide a concise overview of the existing knowledge about the regulatory roles of circRNAs in cardiac fibrosis.
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Affiliation(s)
| | | | - Runfang Pan
- Department of Anatomy, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jiaming Feng
- Department of Anatomy, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Haidong Guo
- Department of Anatomy, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Baonian Liu
- Department of Anatomy, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
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Tang X, Feng X, Xu Y, Yang B, Wang Y, Zhou Y, Wang Q, Mao Y, Xie W, Liu T, Tang Q, Liu Y, Wang Y, Xu J, Lu Y. CircZmMED16 delays plant flowering by negatively regulating starch content through its binding to ZmAPS1. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2025; 67:1142-1161. [PMID: 39835885 DOI: 10.1111/jipb.13824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 11/12/2024] [Indexed: 01/22/2025]
Abstract
Circular RNAs (circRNAs), a type of head-to-tail closed RNA molecules, have been implicated in various aspects of plant development and stress responses through transcriptome sequencing; however, the precise functional roles of circRNAs in plants remain poorly understood. In this study, we identified a highly expressed circular RNA, circZmMED16, derived from exon 8 of the mediator complex subunit 16 (ZmMED16) across different maize (Zea mays L.) inbred lines using circRNA-seq analysis. This circRNA is predominantly expressed in maize tassels and functions in the cytoplasm. Overexpression of circZmMED16 resulted in increased expression of ZmMED16/AtMED16 and delayed flowering in both maize and Arabidopsis thaliana, compared with that in wild-type plants. In contrast, overexpression of the parent gene ZmMED16 did not alter the flowering time of transgenic plants in Arabidopsis, suggesting that circZmMED16 plays a specific role in regulating flowering, distinct from that of linear ZmMED16. To further understand the mechanisms underlying the regulation of flowering time by circZmMED16, we performed RNA pull-down, dual-luciferase, RNA interference (RNAi), and ribonuclease protection assays (RPA). These results indicate that circZmMED16 interacts with small subunit 1 of ADP-glucose pyrophosphorylase (APS1) mRNA in both maize and Arabidopsis. The knockdown of circZmMED16 increased the expression of ZmAPS1, whereas the overexpression of circZmMED16 led to the downregulation of ZmAPS1 RNA and protein. By affecting ZmAPS1 expression, circZmMED16 reduced ADP-glucose pyrophosphorylase (AGPase) activity and led to delayed flowering. These results revealed a novel regulatory mechanism for circRNAs in flowering time and shed light on their functional and regulatory roles in plants.
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Affiliation(s)
- Xin Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 610000, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 610000, China
| | - Xiaoju Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 610000, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 610000, China
| | - Yang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 610000, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 610000, China
| | - Bo Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 610000, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 610000, China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 610000, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 610000, China
| | - Yang Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 610000, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 610000, China
| | - Qi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 610000, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 610000, China
| | - Yan Mao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 610000, China
- College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, 610000, China
| | - Wubing Xie
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 610000, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 610000, China
| | - Tianhong Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 610000, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 610000, China
| | - Qi Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 610000, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 610000, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 610000, China
| | - Yao Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 610000, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 610000, China
| | - Jie Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 610000, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 610000, China
| | - Yanli Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 610000, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 610000, China
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Dremel SE, Koparde VN, Arbuckle JH, Hogan CH, Kristie TM, Krug LT, Conrad NK, Ziegelbauer JM. Noncanonical circRNA biogenesis driven by alpha and gamma herpesviruses. EMBO J 2025; 44:2323-2352. [PMID: 40033018 PMCID: PMC12000468 DOI: 10.1038/s44318-025-00398-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/05/2025] [Accepted: 02/14/2025] [Indexed: 03/05/2025] Open
Abstract
Herpesviruses require the host transcriptional machinery, inducing significant changes in gene expression to prioritize viral transcripts. We examined alpha- and gamma-herpesvirus alterations to a type of alternative splicing, namely circular RNA (circRNA) synthesis. We developed "Circrnas in Host And viRuses anaLysis pIpEline" (CHARLIE) to facilitate viral profiling. This method identified thousands of back-splicing variants, including circRNA common to lytic and latent phases of infection. Ours is the first report of Herpes Simplex Virus-1 circRNAs, including species derived from ICP0 and the latency-associated transcript. We characterized back-splicing cis- and trans-elements, and found viral circRNAs resistant to spliceosome perturbation and lacking canonical splice donor-acceptors. Subsequent loss-of-function studies of host RNA ligases (RTCB, RLIG1) revealed instances of decreased viral back splicing. Using eCLIP and 4sU-Sequencing, we determined that the KSHV RNA-binding protein, ORF57, enhanced synthesis for a subset of viral and host circRNAs. Our work explores unique splicing mechanisms driven by lytic infection, and identifies a class of transcripts with the potential to function in replication, persistence, or tumorigenesis.
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Affiliation(s)
- Sarah E Dremel
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Vishal N Koparde
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Advanced Biomedical Computational Sciences, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, 21701, USA
| | - Jesse H Arbuckle
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA
| | - Chad H Hogan
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, 11794, USA
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Thomas M Kristie
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA
| | - Laurie T Krug
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Nicholas K Conrad
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Joseph M Ziegelbauer
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, 20892, USA.
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Ding X, Li R, Xu J, Hu G, Wang W, Lv Q, Wang Y. hsa_circ_0004846 enhances the malignant phenotype of papillary thyroid carcinoma cells via the miR‑142‑3p/PELI1 axis. Oncol Lett 2025; 29:203. [PMID: 40070794 PMCID: PMC11894512 DOI: 10.3892/ol.2025.14949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Accepted: 01/28/2025] [Indexed: 03/14/2025] Open
Abstract
Circular RNAs (circRNAs) are closely associated with human tumorigenesis; however, whether hsa_circ_0004846 serves a role in the progression of papillary thyroid carcinoma (PTC) remains unclear. Therefore, the present study aimed to investigate the effect of hsa_circ_0004846 on PTC. The results demonstrated that circ_0004846 was abnormally upregulated in PTC tissues and thyroid cancer cell lines (BCPAP, TPC-1 and IHH-4). Furthermore, hsa_circ_0004846-overexpressing or -depleted PTC cell lines (TPC-1 and IHH-4) were constructed using a lentiviral vector system. Notably, hsa_circ_0004846 overexpression markedly promoted cell proliferation, migration and invasion, as evidenced by activation of the PI3K/AKT pathway and the upregulation of vimentin, a class-III intermediate filament, which acts by regulating cell attachment and migration. However, hsa_circ_0004846 knockdown displayed the opposite effects. Mechanistically, the regulatory association among hsa_circ_0004846, microRNA (miR)-142-3p and Pellino E3 ubiquitin protein ligase 1 (PELI1) was validated using a dual-luciferase reporter assay. Specifically, the results demonstrated that hsa_circ_0004846 could sponge miR-142-3p, and the expression levels of miR-142-3p were negatively associated with those of hsa_circ_0004846. In addition, PELI1, a cancer-related E3 ubiquitin ligase, was identified as a downstream target of the hsa_circ_0004846/miR-142-3p axis in PTC. Therefore, PELI1 silencing could reverse the hsa_circ_0004846-induced malignant phenotype of PTC cells. Taken together, the results of the current study highlighted the effect of the hsa_circ_0004846/miR-142-3p/PELI1 regulatory network on PTC progression, thus providing a promising target for PTC treatment.
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Affiliation(s)
- Xiaojie Ding
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
- Department of Endocrinology, Anhui No. 2 Provincial People's Hospital, Hefei, Anhui 230041, P.R. China
| | - Ruiqi Li
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Jingya Xu
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Guangquan Hu
- Department of Cardiology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Wenping Wang
- Department of Endocrinology, Anhui No. 2 Provincial People's Hospital, Hefei, Anhui 230041, P.R. China
| | - Qihuan Lv
- Department of International Medical Service, The First Affiliated Hospital of University of Science and Technology of China, Hefei, Anhui 230001, P.R. China
| | - Youmin Wang
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
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Kelly D, Bicker S, Winterer J, Nanda P, Germain PL, Dieterich C, Schratt G. A functional screen uncovers circular RNAs regulating excitatory synaptogenesis in hippocampal neurons. Nat Commun 2025; 16:3040. [PMID: 40155636 PMCID: PMC11953392 DOI: 10.1038/s41467-025-58070-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 03/11/2025] [Indexed: 04/01/2025] Open
Abstract
Circular RNAs (circRNAs) are an expanding class of largely unexplored RNAs which are prominently enriched in the mammalian brain. Here, we systematically interrogate their role in excitatory synaptogenesis of rat hippocampal neurons using RNA interference. Thereby, we identify seven circRNAs as negative regulators of excitatory synapse formation, many of which contain high-affinity microRNA binding sites. Knockdown of one of these candidates, circRERE, promotes the formation of electrophysiologically silent synapses. Mechanistically, circRERE knockdown results in a preferential upregulation of synaptic mRNAs containing binding sites for miR-128-3p. Overexpression of circRERE stabilizes miR-128-3p and rescues exaggerated synapse formation upon circRERE knockdown in a miR-128-3p binding site-specific manner. Overall, our results uncover circRERE-mediated stabilization of miR-128-3p as a means to restrict the formation of silent excitatory synaptic co-clusters and more generally implicate circRNA-dependent microRNA regulation in the control of synapse development and function.
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Affiliation(s)
- Darren Kelly
- Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, Zurich, Switzerland
| | - Silvia Bicker
- Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, Zurich, Switzerland
| | - Jochen Winterer
- Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, Zurich, Switzerland
| | - Prakruti Nanda
- Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, Zurich, Switzerland
| | - Pierre-Luc Germain
- Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, Zurich, Switzerland
- Laboratory of Molecular and Behavioural Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, Zurich, Switzerland
- Lab of Statistical Bioinformatics, IMLS, University of Zürich, Zurich, Switzerland
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Gerhard Schratt
- Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, Zurich, Switzerland.
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Wang J, Zhang C, Zhang Y, Guo J, Xie C, Liu Y, Chen L, Ma L. Circular RNA in liver cancer research: biogenesis, functions, and roles. Front Oncol 2025; 15:1523061. [PMID: 40224186 PMCID: PMC11985449 DOI: 10.3389/fonc.2025.1523061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Accepted: 03/11/2025] [Indexed: 04/15/2025] Open
Abstract
Liver cancer, characterized by its insidious nature, aggressive invasiveness, and propensity for metastasis, has witnessed a sustained increase in both incidence and mortality rates in recent years, underscoring the urgent need for innovative diagnostic and therapeutic approaches. Emerging research indicates that CircRNAs (circular RNAs) are abundantly and stably present within cells, with their expression levels closely associated with the progression of various malignancies, including hepatocellular carcinoma. In the context of liver cancer progression, circRNAs exhibit promising potential as highly sensitive diagnostic biomarkers, offering novel avenues for early detection, and also function as pivotal regulatory factors within the carcinogenic process. This study endeavors to elucidate the biogenesis, functional roles, and underlying mechanisms of circRNAs in hepatocellular carcinoma, thereby providing a fresh perspective on the pathogenesis of liver cancer and laying a robust foundation for the development of more precise and effective early diagnostic tools and therapeutic strategies.
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Affiliation(s)
- Jiayi Wang
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan, China
- School of Rehabilitation Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Congcong Zhang
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan, China
- School of Rehabilitation Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Yinghui Zhang
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Jiaojiao Guo
- School of Rehabilitation Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Chenyu Xie
- School of Rehabilitation Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Yulu Liu
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Lidian Chen
- School of Rehabilitation Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Liangliang Ma
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan, China
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Chi R, Liu Y, Wang P, Yang F, Wang X, He X, Di R, Chu M. Estrogen-induced circFAM171A1 regulates sheep myoblast proliferation through the oar-miR-485-5p/MAPK15/MAPK pathway. Cell Mol Life Sci 2025; 82:123. [PMID: 40105989 PMCID: PMC11923336 DOI: 10.1007/s00018-025-05639-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 02/19/2025] [Accepted: 02/24/2025] [Indexed: 03/22/2025]
Abstract
Estrogen is an important hormone that affects muscle development in female animals. Previous studies have shown that estrogen can protect muscle cells from apoptosis by inhibiting the MAPK signaling pathway. However, the molecular mechanisms by which estrogen-induced MAPK signaling regulates myoblast growth and development remain unclear. In this study, RNA-seq was performed on ovariectomized small-tailed Han (OR-STH) sheep and sham surgery small-tailed Han (STH) sheep to analyze the effects of estrogen on muscle growth and development in female animals. There were 8721 differentially expressed circRNAs (DECs), 143 differentially expressed miRNAs (DEMs) and 2238 differentially expressed mRNAs (DEGs) in the longissimus dorsi between the OR-STH and STH groups. Bioinformatics analysis revealed that the differentially expressed gene MAPK15 was significantly enriched in the MAPK signaling pathway, which is important for muscle development. Therefore, we constructed the ceRNA network circFAM171A1/oar-miR-485-5p/MAPK15 and explored its effect on muscle growth and development. The results of the molecular mechanism experiments indicated that circFAM171A1 can sponge oar-miR-485-5p to regulate MAPK15. The addition of the exogenous hormone estradiol (E2) to sheep myoblasts could induce circFAM171A1, regulate the expression of oar-miR-485-5p and MAPK15, and promote the proliferation of sheep myoblasts. The results showed that MAPK15 and circFAM171A1 significantly promoted the proliferation of myoblasts and inhibited the apoptosis of myoblasts in sheep, whereas oar-miR-485-5p inhibited the expression of MAPK15 and circFAM171A1, inhibited myoblast proliferation and promoted apoptosis. Furthermore, circFAM171A1 attenuated the inhibitory effect of oar-miR-485-5p on myoblasts. In summary, estrogen induced the expression of circFAM171A1 in sheep myoblasts, and circFAM171A1 can act as a sponge for oar-miR-485-5p to promote the expression of the target gene MAPK15 and ultimately regulate the proliferation of sheep myoblasts. This study provides new insights into the molecular mechanism of estrogen regulation of muscle growth and development in female animals.
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Affiliation(s)
- Runqing Chi
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Yufang Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, 230031, China
| | - Peng Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Fan Yang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Xiangyu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Xiaoyun He
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Ran Di
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Rd, Beijing, 100193, China.
| | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Rd, Beijing, 100193, China.
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Karousi P, Kontos CK, Nikou ST, Carell T, Sideris DC, Scorilas A. Discovery of circular transcripts of the human BCL2-like 12 (BCL2L12) apoptosis-related gene, using targeted nanopore sequencing, provides new insights into circular RNA biology. Funct Integr Genomics 2025; 25:66. [PMID: 40106061 PMCID: PMC11923030 DOI: 10.1007/s10142-025-01578-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2024] [Revised: 03/05/2025] [Accepted: 03/11/2025] [Indexed: 03/22/2025]
Abstract
Circular RNAs (circRNAs) constitute an RNA type formed by back-splicing. BCL2-like 12 (BCL2L12) is an apoptosis-related gene comprising 7 exons. In this study, we used targeted nanopore sequencing to identify circular BCL2L12 transcripts in human colorectal cancer cells and investigated the effect of circRNA silencing on mRNA expression of the parental gene. In brief, nanopore sequencing following nested PCR amplification of cDNAs of BCL2L12 circRNAs from 7 colorectal cancer cell lines unraveled 46 BCL2L12 circRNAs, most of which described for the first time. Interestingly, 40 novel circRNAs are likely to form via back-splicing between non-canonical back-splice sites residing in highly similar regions of the primary transcripts. All back-splice junctions were validated using next-generation sequencing (NGS) after circRNA enrichment. Surprisingly, 2 novel circRNAs also comprised a poly(A) tract after BCL2L12 exon 7; this poly(A) tract was back-spliced to exon 1, in both cases. Furthermore, the selective silencing of a BCL2L12 circRNA resulted in a subsequent decrease of BCL2L12 mRNA levels in HCT 116 cells, thus providing evidence of parental gene expression regulation by circRNAs. In conclusion, our study led to the discovery of many circular transcripts from a single human gene and provided new insights into circRNA biogenesis and mode of action.
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Affiliation(s)
- Paraskevi Karousi
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece.
| | - Stavroula T Nikou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Thomas Carell
- Department for Chemistry, Institute for Chemical Epigenetics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Diamantis C Sideris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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50
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Vitiello E, Castagnetti F, Mecarelli LS, D'Ambra E, Tollis P, Ruocco G, Laneve P, Caffarelli E, Mariani D, Bozzoni I. Live-cell imaging of circular and long noncoding RNAs associated with FUS pathological aggregates by Pepper fluorescent RNA. RNA (NEW YORK, N.Y.) 2025; 31:529-548. [PMID: 39779212 PMCID: PMC11912908 DOI: 10.1261/rna.080119.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 12/14/2024] [Indexed: 01/11/2025]
Abstract
Lately, important advancements in visualizing RNAs in fixed and live cells have been achieved. Although mRNA imaging techniques are well-established, the development of effective methods for studying noncoding RNAs (ncRNAs) in living cells is still challenging but necessary, as they show a variety of functions and intracellular localizations, including participation in highly dynamic processes like phase transition, which is still poorly studied in vivo. Addressing this issue, we tagged two exemplary ncRNAs with the fluorescent RNA (fRNA) Pepper. Specifically, we showed that circ-HDGFRP3 interacts with p-bodies and is recruited in pathological FUS aggregates in a dynamic fashion, and we super-resolved its distribution in such condensates via structured illumination microscopy. Moreover, we tracked the long noncoding RNA (lncRNA) nHOTAIRM1, a motor neuron-specific constituent of stress granules, monitoring its behavior throughout the oxidative-stress response in physiological and pathological conditions. Overall, as fRNA development progresses, our work demonstrates an effective use of Pepper for monitoring complex processes, such as phase transition, in living cells through the visualization of circular RNAs (circRNAs) and lncRNAs with super-resolution power.
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Affiliation(s)
- Erika Vitiello
- Center for Human Technologies, Italian Institute of Technology, Genoa, Italy
| | | | - Lorenzo Stufera Mecarelli
- Center for Human Technologies, Italian Institute of Technology, Genoa, Italy
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Eleonora D'Ambra
- Center for Life Nano- and Neuro-Science, Fondazione Italian Institute of Technology, Rome, Italy
| | - Paolo Tollis
- Center for Life Nano- and Neuro-Science, Fondazione Italian Institute of Technology, Rome, Italy
| | - Giancarlo Ruocco
- Center for Life Nano- and Neuro-Science, Fondazione Italian Institute of Technology, Rome, Italy
| | - Pietro Laneve
- Institute of Molecular Biology and Pathology, CNR, Rome, Italy
| | | | - Davide Mariani
- Center for Human Technologies, Italian Institute of Technology, Genoa, Italy
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Irene Bozzoni
- Center for Human Technologies, Italian Institute of Technology, Genoa, Italy
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Rome, Italy
- Center for Life Nano- and Neuro-Science, Fondazione Italian Institute of Technology, Rome, Italy
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