1
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Hsu CY, Faisal A, Jumaa SS, Gilmanova NS, Ubaid M, Athab AH, Mirzaei R, Karampoor S. Exploring the impact of circRNAs on cancer glycolysis: Insights into tumor progression and therapeutic strategies. Noncoding RNA Res 2024; 9:970-994. [PMID: 38770106 PMCID: PMC11103225 DOI: 10.1016/j.ncrna.2024.05.001] [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: 02/19/2024] [Revised: 04/18/2024] [Accepted: 05/04/2024] [Indexed: 05/22/2024] Open
Abstract
Cancer cells exhibit altered metabolic pathways, prominently featuring enhanced glycolytic activity to sustain their rapid growth and proliferation. Dysregulation of glycolysis is a well-established hallmark of cancer and contributes to tumor progression and resistance to therapy. Increased glycolysis supplies the energy necessary for increased proliferation and creates an acidic milieu, which in turn encourages tumor cells' infiltration, metastasis, and chemoresistance. Circular RNAs (circRNAs) have emerged as pivotal players in diverse biological processes, including cancer development and metabolic reprogramming. The interplay between circRNAs and glycolysis is explored, illuminating how circRNAs regulate key glycolysis-associated genes and enzymes, thereby influencing tumor metabolic profiles. In this overview, we highlight the mechanisms by which circRNAs regulate glycolytic enzymes and modulate glycolysis. In addition, we discuss the clinical implications of dysregulated circRNAs in cancer glycolysis, including their potential use as diagnostic and prognostic biomarkers. All in all, in this overview, we provide the most recent findings on how circRNAs operate at the molecular level to control glycolysis in various types of cancer, including hepatocellular carcinoma (HCC), prostate cancer (PCa), colorectal cancer (CRC), cervical cancer (CC), glioma, non-small cell lung cancer (NSCLC), breast cancer, and gastric cancer (GC). In conclusion, this review provides a comprehensive overview of the significance of circRNAs in cancer glycolysis, shedding light on their intricate roles in tumor development and presenting innovative therapeutic avenues.
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Affiliation(s)
- Chou-Yi Hsu
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan City, 71710, Taiwan
- Thunderbird School of Global Management, Arizona State University Tempe Campus, Phoenix, Arizona, 85004, USA
| | - Ahmed Faisal
- Department of Pharmacy, Al-Noor University College, Nineveh, Iraq
| | - Sally Salih Jumaa
- College of Pharmacy, National University of Science and Technology, Dhi Qar, Iraq
| | - Nataliya Sergeevna Gilmanova
- Department of Prosthetic Dentistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), Russia, Moscow
| | - Mohammed Ubaid
- Medical Technical College, Al-Farahidi University, Baghdad, Iraq
| | - Aya H. Athab
- Department of Pharmacy, Al-Zahrawi University College, Karbala, Iraq
| | - Rasoul Mirzaei
- Venom & Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sajad Karampoor
- Gastrointestinal & Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
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2
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Korsgaard U, García-Rodríguez JL, Jakobsen T, Ahmadov U, Dietrich KG, Vissing SM, Paasch TP, Lindebjerg J, Kjems J, Hager H, Kristensen LS. The Transcriptional Landscape of Coding and Noncoding RNAs in Recurrent and Nonrecurrent Colon Cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2024:S0002-9440(24)00163-9. [PMID: 38704091 DOI: 10.1016/j.ajpath.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/15/2024] [Accepted: 04/05/2024] [Indexed: 05/06/2024]
Abstract
A considerable number of colon cancer patients with local or local advanced disease suffer from recurrence and there is an urgent need for better prognostic biomarkers in this setting. Here, the transcriptomic landscape of mRNAs, long noncoding RNAs, snRNAs, small nucleolar RNAs (snoRNAs), small Cajal body-specific RNAs, pseudogenes, and circular RNAs, as well as RNAs denoted as miscellaneous RNAs, was profiled by total RNA sequencing. In addition to well-known coding and noncoding RNAs, differential expression analysis also uncovered transcripts that have not been implicated previously in colon cancer, such as RNA5SP149, RNU4-2, and SNORD3A. Moreover, there was a profound global up-regulation of snRNA pseudogenes, snoRNAs, and rRNA pseudogenes in more advanced tumors. A global down-regulation of circular RNAs in tumors relative to normal tissues was observed, although only a few were expressed differentially between tumor stages. Many previously undescribed transcripts, including RNU6-620P, RNU2-20P, VTRNA1-3, and RNA5SP60, indicated strong prognostic biomarker potential in receiver operating characteristics analyses. In summary, this study unveiled numerous differentially expressed RNAs across various classes between recurrent and nonrecurrent colon cancer. Notably, there was a significant global up-regulation of snRNA pseudogenes, snoRNAs, and rRNA pseudogenes in advanced tumors. Many of these newly discovered candidates demonstrated a strong prognostic potential for stage II colon cancer.
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Affiliation(s)
- Ulrik Korsgaard
- Department of Clinical Pathology, Vejle Hospital, Vejle, Denmark; Danish Colorectal Cancer Center South, Vejle Hospital, Vejle, Denmark
| | | | | | - Ulvi Ahmadov
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | | | | | | | - Jan Lindebjerg
- Department of Clinical Pathology, Vejle Hospital, Vejle, Denmark; Danish Colorectal Cancer Center South, Vejle Hospital, Vejle, Denmark
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark; Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C, Denmark
| | - Henrik Hager
- Department of Clinical Pathology, Vejle Hospital, Vejle, Denmark; Danish Colorectal Cancer Center South, Vejle Hospital, Vejle, Denmark; Department of Pathology, Aarhus University Hospital, Aarhus N, Denmark
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3
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Qiu M, Chen Y, Zeng C. Biological functions of circRNA in regulating the hallmarks of gastrointestinal cancer (Review). Int J Oncol 2024; 64:49. [PMID: 38488023 PMCID: PMC10997371 DOI: 10.3892/ijo.2024.5637] [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: 11/04/2023] [Accepted: 02/06/2024] [Indexed: 03/19/2024] Open
Abstract
Circular RNA (circRNA) was first observed in the cytoplasm of eukaryotic cells in 1979, but it was not characterized in detail until 2012, when high‑throughput sequencing technology was more advanced and available. Consequently, the mechanism of circRNA formation and its biological function have been progressively elucidated by researchers. circRNA is abundant in eukaryotic cells and exhibits a certain degree of organization, timing and disease‑specificity. Additionally, it is poorly degradable, meeting the characteristics of an ideal clinical biomarker. In the present review, the recent research progress of circRNAs in digestive tract malignant tumors was primarily discussed. This included the roles, biological functions and clinical significance of circRNA, providing references for its research value and clinical potential in gastrointestinal cancer.
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Affiliation(s)
- Mengjun Qiu
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Youxiang Chen
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Chunyan Zeng
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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4
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Cui YH, Liu CQ, Song XL, Yi WZ, Liu Q, Liu JM, Wu YN, Chen JY, Yang LJ, He HY, Meng J, Pan HW. Integrative Analysis of miRNA and circRNA Expression Profiles and Interaction Network in HSV-1-Infected Primary Corneal Epithelial Cells. Curr Eye Res 2024; 49:368-379. [PMID: 38164922 DOI: 10.1080/02713683.2023.2297345] [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: 09/23/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
PURPOSE Circular RNAs (circRNAs) are products of alternative splicing with roles as competitive endogenous RNAs or microRNA sponges, regulating gene expression and biological processes. However, the involvement of circRNAs in herpes simplex keratitis remains largely unexplored. METHODS This study examines circRNA and miRNA expression profiles in primary human corneal epithelial cells infected with HSV-1, compared to uninfected controls, using microarray analysis. Bioinformatic analysis predicted the potential function of the dysregulated circRNAs and microRNA response elements (MREs) in these circRNAs, forming an interaction network between dysregulated circRNAs and miRNAs. RESULTS A total of 332 circRNAs and 16 miRNAs were upregulated, while 80 circRNAs and six miRNAs were downregulated (fold change ≥2.0 and p < 0.05). Gene ontology (GO) and KEGG pathway analyses were performed on parental genes of dysregulated circRNAs to uncover potential functions in HSV-1 infection. Notably, miR-181b-5p, miR-338-3p, miR-635, and miR-222-3p emerged as pivotal miRNAs interacting with multiple dysregulated circRNAs. CONCLUSIONS This comprehensive study offers insights into differentially expressed circRNAs and miRNAs during HSV-1 infection in corneal epithelial cells, shedding light on circRNA-miRNA interactions' potential role in herpes simplex keratitis pathogenesis.
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Affiliation(s)
- Yu-Hong Cui
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Chao-Qun Liu
- Department of Ophthalmology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Xi-Ling Song
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Wan-Zhao Yi
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Qi Liu
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Jing-Min Liu
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Ya-Ni Wu
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Jian-Ying Chen
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Lv-Jun Yang
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Hui-Ying He
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Jing Meng
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Hong-Wei Pan
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
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5
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Li R, Wang J, Xie Z, Tian X, Hou J, Wang D, Qian H, Shen H, Xu W. CircUSP1 as a novel marker promotes gastric cancer progression via stabilizing HuR to upregulate USP1 and Vimentin. Oncogene 2024; 43:1033-1049. [PMID: 38366146 PMCID: PMC10978489 DOI: 10.1038/s41388-024-02968-8] [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: 10/08/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/18/2024]
Abstract
Circular RNAs (circRNAs) play a crucial role in regulating various tumors. However, their biological functions and mechanisms in gastric cancer (GC) have not been well understood. Here, we discovered a stable cytoplasmic circRNA named circUSP1 (hsa_circ_000613) in GC. CircUSP1 upregulation in GC tissues was correlated with tumor size and differentiation. We observed that circUSP1 promoted GC growth and metastasis. Mechanistically, circUSP1 mainly interacted with the RRM1 domain of an RNA-binding protein (RBP) called HuR, stabilizing its protein level by inhibiting β-TrCP-mediated ubiquitination degradation. The oncogenic properties of HuR mediated promotive effects of circUSP1 in GC progression. Moreover, we identified USP1 and Vimentin as downstream targets of HuR in post-transcriptional regulation, mediating the effects of circUSP1. The parent gene USP1 also enhanced the viability and mobility of GC cells. Additionally, tissue-derived circUSP1 could serve as an independent prognostic factor for GC, while plasma-derived circUSP1 showed promise as a diagnostic biomarker, outperforming conventional markers including serum alpha-fetoprotein (AFP), carcinoembryonic antigen (CEA) and carbohydrate antigen 199 (CA19-9). Our study highlights that circUSP1 promotes GC progression by binding to and stabilizing oncogenic HuR, thereby facilitating the upregulation of USP1 and Vimentin at the post-transcriptional level. These findings suggest that circUSP1 could be a potential therapeutic target and a diagnostic and prognostic biomarker for GC.
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Affiliation(s)
- Rong Li
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, Jiangsu, 210008, China
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China
| | - Junyi Wang
- Centre of Clinical Laboratory, the First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou, Jiangsu, 215006, China
| | - Zhenfan Xie
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China
| | - Xinyu Tian
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, Jiangsu, 210008, China
| | - Jie Hou
- Department of Clinical Laboratory, People's Hospital of Yangzhong City, 235 Yangzi Middle Road, Zhenjiang, Jiangsu, 212200, China
| | - Dongli Wang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China
| | - Hui Qian
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China
| | - Han Shen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, Jiangsu, 210008, China.
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China.
| | - Wenrong Xu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China.
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6
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Niu M, Wang C, Chen Y, Zou Q, Qi R, Xu L. CircRNA identification and feature interpretability analysis. BMC Biol 2024; 22:44. [PMID: 38408987 PMCID: PMC10898045 DOI: 10.1186/s12915-023-01804-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: 07/29/2023] [Accepted: 12/18/2023] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) can regulate microRNA activity and are related to various diseases, such as cancer. Functional research on circRNAs is the focus of scientific research. Accurate identification of circRNAs is important for gaining insight into their functions. Although several circRNA prediction models have been developed, their prediction accuracy is still unsatisfactory. Therefore, providing a more accurate computational framework to predict circRNAs and analyse their looping characteristics is crucial for systematic annotation. RESULTS We developed a novel framework, CircDC, for classifying circRNAs from other lncRNAs. CircDC uses four different feature encoding schemes and adopts a multilayer convolutional neural network and bidirectional long short-term memory network to learn high-order feature representation and make circRNA predictions. The results demonstrate that the proposed CircDC model is more accurate than existing models. In addition, an interpretable analysis of the features affecting the model is performed, and the computational framework is applied to the extended application of circRNA identification. CONCLUSIONS CircDC is suitable for the prediction of circRNA. The identification of circRNA helps to understand and delve into the related biological processes and functions. Feature importance analysis increases model interpretability and uncovers significant biological properties. The relevant code and data in this article can be accessed for free at https://github.com/nmt315320/CircDC.git .
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Affiliation(s)
- Mengting Niu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic University, Shenzhen, 518055, China
- Postdoctoral Innovation Practice Base, Shenzhen Polytechnic University, Shenzhen, 518055, China
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Chunyu Wang
- Faculty of Computing, Harbin Institute of Technology, Harbin, 150000, Heilongjiang, China
| | - Yaojia Chen
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, No.4 Block 2 North Jianshe Road, Chengdu, 610054, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, No.4 Block 2 North Jianshe Road, Chengdu, 610054, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
| | - Ren Qi
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China.
| | - Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic University, Shenzhen, 518055, China.
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7
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Barbosa DF, Oliveira LS, Nachtigall PG, Valentini Junior R, de Souza N, Paschoal AR, Kashiwabara AY. cirCodAn: A GHMM-based tool for accurate prediction of coding regions in circRNA. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 139:289-334. [PMID: 38448139 DOI: 10.1016/bs.apcsb.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Studies focusing on characterizing circRNAs with the potential to translate into peptides are quickly advancing. It is helping to elucidate the roles played by circRNAs in several biological processes, especially in the emergence and development of diseases. While various tools are accessible for predicting coding regions within linear sequences, none have demonstrated accurate open reading frame detection in circular sequences, such as circRNAs. Here, we present cirCodAn, a novel tool designed to predict coding regions in circRNAs. We evaluated the performance of cirCodAn using datasets of circRNAs with strong translation evidence and showed that cirCodAn outperformed the other tools available to perform a similar task. Our findings demonstrate the applicability of cirCodAn to identify coding regions in circRNAs, which reveals the potential of use of cirCodAn in future research focusing on elucidating the biological roles of circRNAs and their encoded proteins. cirCodAn is freely available at https://github.com/denilsonfbar/cirCodAn.
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Affiliation(s)
- Denilson Fagundes Barbosa
- Programa de Pós-Graduação Associado em Bioinformática (UFPR/UTFPR), Departamento Acadêmico de Computação (DACOM), Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Paraná, Brazil; Instituto Federal de Educação, Ciência e Tecnologia de Santa Catarina (IFSC), Canoinhas, Santa Catarina, Brazil
| | - Liliane Santana Oliveira
- Programa de Pós-Graduação Associado em Bioinformática (UFPR/UTFPR), Departamento Acadêmico de Computação (DACOM), Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Paraná, Brazil
| | - Pedro Gabriel Nachtigall
- Laboratório de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, SP, Brazil; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Rodolpho Valentini Junior
- Programa de Pós-Graduação Associado em Bioinformática (UFPR/UTFPR), Departamento Acadêmico de Computação (DACOM), Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Paraná, Brazil
| | - Nayane de Souza
- Programa de Pós-Graduação Associado em Bioinformática (UFPR/UTFPR), Departamento Acadêmico de Computação (DACOM), Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Paraná, Brazil
| | - Alexandre Rossi Paschoal
- Programa de Pós-Graduação Associado em Bioinformática (UFPR/UTFPR), Departamento Acadêmico de Computação (DACOM), Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Paraná, Brazil
| | - André Yoshiaki Kashiwabara
- Programa de Pós-Graduação Associado em Bioinformática (UFPR/UTFPR), Departamento Acadêmico de Computação (DACOM), Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Paraná, Brazil.
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8
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Zahin T, Shi Q, Zang XC, Shao M. Accurate Assembly of Circular RNAs with TERRACE. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579380. [PMID: 38370635 PMCID: PMC10871327 DOI: 10.1101/2024.02.09.579380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Circular RNA (circRNA) is a class of RNA molecules that forms a closed loop with its 5' and 3' ends covalently bonded. Due to this specific structure circRNAs are more stable than linear RNAs, admit distinct biological properties and functions, and have been proven to be promising biomarkers. Circular RNAs were severely overlooked previously owing to the biases in the RNA-seq protocols and in the detection algorithms, but recently gained tremendous attentions in both aspects. However, most existing methods for assembling circRNAs heavily rely on the annotated transcriptomes, and hence exhibit unsatisfactory accuracy when a high-quality transcriptome is unavailable. Here we present TERRACE, a new algorithm for full-length assembly of circRNAs from paired-end total RNA-seq data. TERRACE uses the splice graph as the underlying data structure to organize the splicing and coverage information. We transform the problem of assembling circRNAs into finding two paths that "bridge" the three fragments in the splice graph induced by back-spliced reads. To solve this formulation, we adopted a definition for optimal bridging paths and a dynamic programming algorithm to calculate such paths, an approach that was proven useful for assembling linear RNAs. TERRACE features an efficient algorithm to detect back-spliced reads that are missed by RNA-seq aligners, contributing to its much improved sensitivity. It also incorporates a new machine-learning approach that is trained to assign a confidence score to each assembled circRNA, which is shown superior to using abundance for scoring. TERRACE is compared with leading circRNA detection methods on both simulations and biological datasets. Our method consistently outperforms by a large margin in sensitivity while maintaining better or comparable precision. In particular, when the annotations are not provided, TERRACE can assemble 123%-412% more correct circRNAs than state-of-the-art methods on human tissues. TERRACE presents a major leap on assembling full-length circRNAs from RNA-seq data, and we expect it to be widely used in the downstream research on circRNAs.
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Affiliation(s)
- Tasfia Zahin
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Qian Shi
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Xiaofei Carl Zang
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Mingfu Shao
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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9
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Li F, Du WW, Li X, Xu J, Wu N, Awan FM, Yang Y, Alashti FA, Wang S, Yang BB. A Novel Circular RNA circITGa9 Predominantly Generated in Human Heart Disease Induces Cardiac Remodeling and Fibrosis. RESEARCH (WASHINGTON, D.C.) 2024; 7:0303. [PMID: 38323094 PMCID: PMC10845611 DOI: 10.34133/research.0303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/27/2023] [Indexed: 02/08/2024]
Abstract
Recent studies have highlighted the pivotal roles of circular RNAs (circRNAs) in cardiovascular diseases. Through high-throughput circRNA sequencing of both normal myocardial tissues and hypertrophic patients, we unveiled 32,034 previously undiscovered circRNAs with distinct cardiac expression patterns. Notably, circITGa9, a circRNA derived from integrin-α9, exhibited substantial up-regulation in cardiac hypertrophy patients. This elevation was validated across extensive sample pools from cardiac patients and donors. In vivo experiments revealed heightened cardiac fibrosis in mice subjected to transverse aortic constriction (TAC) after circITGa9 injection. We identified circITGa9 binding proteins through circRNA precipitation followed by liquid chromatography tandem-mass spectrometry. Furthermore, circRNA pull-down/precipitation assays demonstrated that increased circITGa9 expression facilitated binding with tropomyosin 3 (TPM3). Specific binding sites between circITGa9 and TPM3 were identified through computational algorithms and further validated by site-directed mutagenesis. We further showed that circITGa9 induced actin polymerization, characteristic of tissue fibrosis. Finally, we developed approaches that improved cardiac function and decreased fibrosis by delivering small interfering RNA targeting circITGa9 or blocking oligo inhibiting the interaction of circITGa9 and TPM3 into TAC mice, which is amenable for further preclinical and translational development. We conclude that elevated circITGa9 levels drive cardiac remodeling and fibrosis. By pinpointing circITGa9 as a therapeutic target, we open doors to innovative interventions for mitigating cardiac remodeling and fibrosis.
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Affiliation(s)
- Feiya Li
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, ON, Canada
| | - William W. Du
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, ON, Canada
| | - Xiangmin Li
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, ON, Canada
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Institute of Microbiology,
Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Jindong Xu
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, ON, Canada
- Department of Anesthesiology, Guangdong Cardiovascular Institute,
Guangdong Provincial People’s Hospital & Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China
| | - Nan Wu
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, ON, Canada
| | - Faryal Mehwish Awan
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, ON, Canada
- Department of Medical Lab Technology,
The University of Haripur, Haripur, Pakistan
| | - Yang Yang
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, ON, Canada
| | - Fariborz Asghari Alashti
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, ON, Canada
| | - Sheng Wang
- Department of Anesthesiology, Beijing Anzhen Hospital,
Capital Medical University, Beijing, China
| | - Burton B. Yang
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, ON, Canada
- Institute of Medical Sciences,
University of Toronto, Toronto, ON, Canada
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10
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Li Y, Zhang Q, Zhao J, Wang Z, Zong X, Yang L, Zhang C, Zhao H. Mechanical behavior and microstructure of porcine brain tissues under pulsed electric fields. Biomech Model Mechanobiol 2024; 23:241-254. [PMID: 37861916 DOI: 10.1007/s10237-023-01771-w] [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: 05/03/2023] [Accepted: 08/29/2023] [Indexed: 10/21/2023]
Abstract
Pulsed electric fields are extensively utilized in clinical treatments, such as subthalamic deep brain stimulation, where electric field loading is in direct contact with brain tissue. However, the alterations in brain tissue's mechanical properties and microstructure due to changes in electric field parameters have not received adequate attention. In this study, the mechanical properties and microstructure of the brain tissue under pulsed electric fields were focused on. Herein, a custom indentation device was equipped with a module for electric field loading. Parameters such as pulse amplitude and frequency were adjusted. The results demonstrated that following an indentation process lasting 5 s and reaching a depth of 1000 μm, and a relaxation process of 175 s, the average shear modulus of brain tissue was reduced, and viscosity decreased. At the same amplitude, high-frequency pulsed electric fields had a smaller effect on brain tissue than low-frequency ones. Furthermore, pulsed electric fields induced cell polarization and reduced the proteoglycan concentration in brain tissue. As pulse frequency increased, cell polarization diminished, and proteoglycan concentration decreased significantly. High-frequency pulsed electric fields applied to brain tissue were found to reduce impedance fluctuation amplitude. This study revealed the effect of pulsed electric fields on the mechanical properties and microstructure of ex vivo brain tissue, providing essential information to promote the advancement of brain tissue electrotherapy in clinical settings.
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Affiliation(s)
- Yiqiang Li
- School of Mechanical & Aerospace Engineering, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
- Key Laboratory of CNC Equipment Reliability, Ministry of Education, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
| | - Qixun Zhang
- School of Mechanical & Aerospace Engineering, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
- Key Laboratory of CNC Equipment Reliability, Ministry of Education, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
- Chongqing Research Institute, Jilin University, Chongqing, 401100, People's Republic of China
| | - Jiucheng Zhao
- School of Mechanical & Aerospace Engineering, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
- Key Laboratory of CNC Equipment Reliability, Ministry of Education, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
| | - Zhaoxin Wang
- School of Mechanical & Aerospace Engineering, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
- Key Laboratory of CNC Equipment Reliability, Ministry of Education, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
| | - Xiangyu Zong
- School of Mechanical & Aerospace Engineering, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
- Key Laboratory of CNC Equipment Reliability, Ministry of Education, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
| | - Li Yang
- School of Mechanical & Aerospace Engineering, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, People's Republic of China
| | - Chi Zhang
- School of Mechanical & Aerospace Engineering, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China.
- Key Laboratory of CNC Equipment Reliability, Ministry of Education, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China.
| | - Hongwei Zhao
- School of Mechanical & Aerospace Engineering, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China.
- Key Laboratory of CNC Equipment Reliability, Ministry of Education, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China.
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11
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Zhou M, Li S, Huang C. Physiological and pathological functions of circular RNAs in the nervous system. Neural Regen Res 2024; 19:342-349. [PMID: 37488888 PMCID: PMC10503630 DOI: 10.4103/1673-5374.379017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/20/2023] [Accepted: 05/29/2023] [Indexed: 07/26/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of covalently closed single-stranded RNAs that are expressed during the development of specific cells and tissues. CircRNAs play crucial roles in physiological and pathological processes by sponging microRNAs, modulating gene transcription, controlling the activity of certain RNA-binding proteins, and producing functional peptides. A key focus of research at present is the functionality of circRNAs in the nervous system and several advances have emerged over the last 2 years. However, the precise role of circRNAs in the nervous system has yet to be comprehensively reviewed. In this review, we first summarize the recently described roles of circRNAs in brain development, maturity, and aging. Then, we focus on the involvement of circRNAs in various diseases of the central nervous system, such as brain cancer, chronic neurodegenerative diseases, acute injuries of the nervous system, and neuropathic pain. A better understanding of the functionality of circRNAs will help us to develop potential diagnostic, prognostic, and therapeutic strategies to treat diseases of the nervous system.
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Affiliation(s)
- Min Zhou
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Shi Li
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, China
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12
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Tan J, Sahaer P, Li H, Han W, Sun H. The expression, function, and network regulation of circDNAJB6 in chicken macrophages under lipopolysaccharide (LPS) stimulation. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 151:105095. [PMID: 37951323 DOI: 10.1016/j.dci.2023.105095] [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: 07/03/2023] [Revised: 10/06/2023] [Accepted: 11/06/2023] [Indexed: 11/13/2023]
Abstract
Circular RNAs (circRNA) originate from back-splicing events that link a downstream 5'splice site to an upstream 3' splice site. Circular RNA has been shown to be involved in gene expression, interacting with microRNA and RNA binding proteins to affect transcription, splicing, translation, and other processes. However, little is known about the potential function of chicken circRNAs that trigger the pathogenesis. In a previous study, a circular RNA DNAJB6 (circDNAJB6) was identified as a typical covalently closed circular RNA that is abundant in chicken macrophages upon bacterial infection. It was identified that circDNAJB6 was formed by reverse splicing of exons 2 to 5 of the DNAJB6 gene by PCR amplification, Sanger sequencing, and RNase R exonuclease treatment. Moreover, circDNAJB6 had ability to exacerbate the lipopolysaccharides (LPS) induced cellular injury via reducing cell viability, increasing NO product and pro-inflammatory cytokines. In addition, bioinformatic analysis showed that five miRNAs were identified to interact with circDNAJB6, potentially targeting 75 genes, which were significantly enriched in the pathways of autophagy-animal and MAPK signaling. This study has provided and broadened a better understanding the function of circDNAJB6, which may exert potential biomarkers and act as potential targets for the treatment of bacterial infection.
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Affiliation(s)
- Jishuang Tan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Paizelaiti Sahaer
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Huan Li
- School of Biological and Chemical Engineering, Yangzhou Polytechnic College, Yangzhou, China
| | - Wei Han
- The Poultry Research Institute of Chinese Academy of Agricultural Sciences, Yangzhou, China
| | - Hongyan Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China; Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China.
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13
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Masante L, Susin G, Baudet ML. Droplet Digital PCR for the Detection and Quantification of Bona Fide CircRNAs. Methods Mol Biol 2024; 2765:107-126. [PMID: 38381336 DOI: 10.1007/978-1-0716-3678-7_6] [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: 02/22/2024]
Abstract
CircRNAs are covalently closed RNA molecules gaining increasing attention over the years. Initially considered mere splicing errors, circRNAs are now recognized as a novel class of endogenous, conserved RNAs, expressed in many different species. The unique structure, the low levels of expression, and the almost complete sequence overlap with the cognate linear RNA make their detection and quantification challenging. Moreover, it has become crucial to prove the circular nature of the targeted transcript and unequivocally distinguish the circRNA from its linear counterpart. Nowadays, the most widely used technique to quantify circRNA expression is real-time quantitative PCR (qPCR). However, in the particular case of quantification of circles, it shows several technical shortcomings which affect the accuracy of the quantification. To precisely assess circRNA expression level, droplet digital PCR (ddPCR) is rapidly taking over for the more popular qPCR. In this chapter, we describe the detailed procedure based on droplets partitioning to quantify both linear and circRNA abundancy and demonstrate the circularity of the transcript under study with high precision, in a single experiment.
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Affiliation(s)
- Linda Masante
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Giorgia Susin
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Marie-Laure Baudet
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy.
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14
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Pan X, Zhao Z, Huang X, Cen X. Circ-Slain2 Alleviates Cartilage Degradation and Inflammation of TMJOA. J Dent Res 2023; 102:1498-1506. [PMID: 37817544 DOI: 10.1177/00220345231198448] [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: 10/12/2023] Open
Abstract
Temporomandibular joint osteoarthritis (TMJOA) is a degenerative disease with the cessation of matrix anabolism and aggravation of inflammation, which results in severe pain and impaired joint function. However, the mechanisms are not well understood. Circular RNAs (circRNAs) are reported to have various biological functions and participate in the development, diagnosis, prognosis, and treatment of different diseases. This study aimed to investigate the roles and mechanisms of circ-slain2 in TMJOA. We first established TMJOA mouse models and found circ-slain2 was lowly expressed in the cartilage of TMJOA through sequencing data. We observed that circ-slain2 is predominantly localized in the cytoplasm and downregulated in mouse condylar chondrocytes (mCCs) treated with tumor necrosis factor α (TNFα) and interferon γ (IFNγ). Micro-computed tomography and histological examination showed that intra-articular injection of circ-slain2 overexpressing adeno-associated virus could alleviate cartilage catabolism and synovial inflammation to relieve TMJOA in vivo. In addition, elevated circ-slain2 also showed anticatabolic and anti-inflammatory effects on IFNγ- and TNFα-stimulated mouse condylar chondrocytes (mCCs). Functional enrichment analysis indicated that protein processing in endoplasmic reticulum (ER) was associated with TMJOA, and further functional experiments confirmed that circ-slain2 could suppress ER stress in OA mCCs. RNA binding protein immunoprecipitation assay revealed an overt interaction between activating transcription factor 6 (ATF6) and circ-slain2. Inhibition of the expression of both ATF6 and circ-slain2 resulted in dilation of the ER and enhanced the expression of ER stress markers, whose ER stress level was higher than inhibition of ATF6 but lower than knockdown of circ-slain2 expression. Collectively, our research demonstrated that circ-slain2 could regulate ATF6 to relieve ER stress, reducing temporomandibular joint cartilage degradation and synovial inflammation. These findings provide prospects for developing novel osteoarthritis therapies based on circ-slain2 by focusing on reducing the inflammation of synovium and the imbalance between matrix synthesis and degradation.
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Affiliation(s)
- X Pan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Z Zhao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - X Huang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - X Cen
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Temporomandibular joint, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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15
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Samavarchi Tehrani S, Goodarzi G, Panahi G, Maniati M, Meshkani R. Multiple novel functions of circular RNAs in diabetes mellitus. Arch Physiol Biochem 2023; 129:1235-1249. [PMID: 34087083 DOI: 10.1080/13813455.2021.1933047] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022]
Abstract
Circular RNAs (circRNAs), as an emerging group of non-coding RNAs (ncRNAs), have received the attention given evidence indicating that these novel ncRNAs are implicated in various biological processes. Due to the absence of 5' and 3' ends in circ-RNAs, their two ends are covalently bonded together, and they are synthesised from pre-mRNAs in a process called back-splicing, which makes them more stable than linear RNAs. There is accumulating evidence showing that circRNAs play a critical role in the pathogenesis of diabetes mellitus (DM). Moreover, it has been indicated that dysregulation of circRNAs has made them promising diagnostic biomarkers for the detection of DM. Recently, increasing attention has been paid to investigate the mechanisms underlying the DM process. It has been demonstrated that there is a strong correlation between the expression of circRNAs and DM. Hence, our aim is to discuss the crosstalk between circRNAs and DM and its complications.
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Affiliation(s)
- Sadra Samavarchi Tehrani
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Golnaz Goodarzi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ghodratollah Panahi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmood Maniati
- English Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Reza Meshkani
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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16
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Anchesi I, Schepici G, Mazzon E. LncRNAs and CircRNAs as Strategies against Pathological Conditions Caused by a Hypoxic/Anoxic State. Biomolecules 2023; 13:1622. [PMID: 38002304 PMCID: PMC10669691 DOI: 10.3390/biom13111622] [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: 09/26/2023] [Revised: 10/26/2023] [Accepted: 10/28/2023] [Indexed: 11/26/2023] Open
Abstract
Brain damage can be induced by oxygen deprivation. It is known that hypoxic or anoxic conditions can lead to changes in the expression levels of non-coding RNAs (ncRNAs), which, in turn, can be related to Central Nervous System (CNS) injuries. Therefore, it could be useful to investigate the involvement of non-coding RNAs (ncRNAs), as well as the underlying mechanisms which are able to modulate them in brain damage induced by hypoxic or anoxic conditions. In this review, we focused on recent research that associates these conditions with long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). The results of this review demonstrate that the expression of both lncRNAs and circRNAs can be influenced by oxygen deprivation conditions and so they can contribute to inducing damage or providing neuroprotection by affecting specific molecular pathways. Furthermore, several experimental studies have shown that ncRNA activity can be regulated by compounds, thus also modifying their transcriptomic profile and their effects on CNS damages induced by hypoxic/anoxic events.
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Affiliation(s)
| | | | - Emanuela Mazzon
- IRCCS Centro Neurolesi “Bonino-Pulejo”, Via Provinciale Palermo, Strada Statale 113, Contrada Casazza, 98124 Messina, Italy
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17
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Zeng M, Yan S, Yang P, Li Q, Li J, Fan X, Liu X, Yao Y, Wang W, Chen R, Han G, Yang Y, Tang Z. Circular RNA transcriptome across multiple tissues reveal skeletal muscle-specific circPSME4 regulating myogenesis. Int J Biol Macromol 2023; 251:126322. [PMID: 37591436 DOI: 10.1016/j.ijbiomac.2023.126322] [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: 05/03/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
There are significant differences in meat production, growth rate and other traits between Western commercial pigs and Chinese local pigs. Comparative transcriptome approaches have identified many coding and non-coding candidate genes associated various traits. However, the expression and function of circular RNAs (circRNAs) in different pig tissues are largely unknown. In this study, we conducted a comprehensive analysis of the genome-wide circRNA expression profile across ten tissues in Luchuan (a Chinese local breed) and Duroc (a Western commercial breed) pigs. We identified a total of 56,254 circRNAs, of which 42.9 % were not previously annotated. We found that 33.7 % of these circRNAs were differentially expressed. Enrichment analysis revealed that differentially expressed circRNAs might contribute to the phenotypic differentiation between Luchuan and Duroc pigs. We identified 538 tissue-specific circRNAs, most of which were specifically expressed in the brain and skeletal muscle. Competitive endogenous RNA network analysis suggested that skeletal muscle-specific circPSME4 was co-expressed with MYOD1 and targeted by ssc-miR-181d-3p. Functional analysis revealed that circPSME4 knockdown could promote the proliferation and differentiation of myoblasts. Together, our findings provide valuable resources of circRNAs for animal breeding and biomedical research. We demonstrated that circPSME4 is a novel regulator of skeletal muscle development.
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Affiliation(s)
- Mu Zeng
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Shanying Yan
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Peng Yang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Qiaowei Li
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; School of Veterinary Medicine, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Jiju Li
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xinhao Fan
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiaoqin Liu
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yilong Yao
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Wei Wang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ruipu Chen
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Guohao Han
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yalan Yang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
| | - Zhonglin Tang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
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18
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He T, Chen Q, Yuan Z, Yang Y, Cao K, Luo J, Dong G, Peng X, Yang Z. Effects of maternal high-fat diet on fetal growth, placental nutrient transporters and circular RNA expression profiles. Food Funct 2023; 14:9391-9406. [PMID: 37791601 DOI: 10.1039/d3fo02202a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Epidemiological and experimental studies suggest that there is a strong correlation between maternal high-fat diet and fetal-placental development. The current study aims to investigate the effects of maternal high-fat diet on fetal growth, placental nutrient transporters and circular RNA expression profiles in a mouse model. Forty C57BL/6 female mice were randomly assigned to two groups, fed either a control (10% fat for energy) diet (CON) or a high-fat (60% fat for energy) diet (HFD) for 4 weeks before mating and throughout pregnancy, and were killed on day 19.5 of pregnancy. The serum glucose, total cholesterol and low-density lipoprotein, the glucolipid metabolism-related hormones, and the insulin resistance index were significantly increased. High-throughput sequencing showed that differentially expressed circRNAs (DE circRNAs) in the placenta can regulate various biological processes, cellular components, and molecular functions through various energy metabolism pathways, and mmu-let-7g-5p was found to target and bind to multiple DE circRNAs. In addition, this study also predicted that various circRNAs with protein coding functions can regulate maternal placental nutrient transport. In general, the ceRNA (circRNAs-miRNAs-mRNAs) regulatory network of maternal placental nutrient transport constructed in this study is of great significance for further understanding the effect of maternal nutrition on fetal growth in the future.
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Affiliation(s)
- Tianle He
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Qingyun Chen
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Zhidong Yuan
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Yulian Yang
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Kai Cao
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Ju Luo
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Guozhong Dong
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Xie Peng
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Zhenguo Yang
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
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19
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Ayyildiz D, Bergonzoni G, Monziani A, Tripathi T, Döring J, Kerschbamer E, Di Leva F, Pennati E, Donini L, Kovalenko M, Zasso J, Conti L, Wheeler VC, Dieterich C, Piazza S, Dassi E, Biagioli M. CAG repeat expansion in the Huntington's disease gene shapes linear and circular RNAs biogenesis. PLoS Genet 2023; 19:e1010988. [PMID: 37831730 PMCID: PMC10617732 DOI: 10.1371/journal.pgen.1010988] [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: 03/06/2022] [Revised: 10/31/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
Alternative splicing (AS) appears to be altered in Huntington's disease (HD), but its significance for early, pre-symptomatic disease stages has not been inspected. Here, taking advantage of Htt CAG knock-in mouse in vitro and in vivo models, we demonstrate a correlation between Htt CAG repeat length and increased aberrant linear AS, specifically affecting neural progenitors and, in vivo, the striatum prior to overt behavioral phenotypes stages. Remarkably, a significant proportion (36%) of the aberrantly spliced isoforms are not-functional and meant to non-sense mediated decay (NMD). The expanded Htt CAG repeats further reflect on a previously neglected, global impairment of back-splicing, leading to decreased circular RNAs production in neural progenitors. Integrative transcriptomic analyses unveil a network of transcriptionally altered micro-RNAs and RNA-binding proteins (Celf, hnRNPs, Ptbp, Srsf, Upf1, Ythd2) which might influence the AS machinery, primarily in neural cells. We suggest that this unbalanced expression of linear and circular RNAs might alter neural fitness, contributing to HD pathogenesis.
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Affiliation(s)
- Dilara Ayyildiz
- Bioinformatic facility, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
- Biomedical Sciences and Biotechnology, University of Udine, Udine, Italy
| | - Guendalina Bergonzoni
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Alan Monziani
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Takshashila Tripathi
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Jessica Döring
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Emanuela Kerschbamer
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Francesca Di Leva
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Elia Pennati
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Luisa Donini
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Marina Kovalenko
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jacopo Zasso
- Laboratory of Stem Cell Biology, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Luciano Conti
- Laboratory of Stem Cell Biology, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Vanessa C. Wheeler
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Neurology Harvard Medical School, Boston, Massachusetts, United States of America
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Silvano Piazza
- Bioinformatic facility, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Marta Biagioli
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
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20
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Zuniga G, Frost B. Selective neuronal vulnerability to deficits in RNA processing. Prog Neurobiol 2023; 229:102500. [PMID: 37454791 DOI: 10.1016/j.pneurobio.2023.102500] [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: 05/02/2023] [Revised: 06/30/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Emerging evidence indicates that errors in RNA processing can causally drive neurodegeneration. Given that RNA produced from expressed genes of all cell types undergoes processing (splicing, polyadenylation, 5' capping, etc.), the particular vulnerability of neurons to deficits in RNA processing calls for careful consideration. The activity-dependent transcriptome remodeling associated with synaptic plasticity in neurons requires rapid, multilevel post-transcriptional RNA processing events that provide additional opportunities for dysregulation and consequent introduction or persistence of errors in RNA transcripts. Here we review the accumulating evidence that neurons have an enhanced propensity for errors in RNA processing alongside grossly insufficient defenses to clear misprocessed RNA compared to other cell types. Additionally, we explore how tau, a microtubule-associated protein implicated in Alzheimer's disease and related tauopathies, contributes to deficits in RNA processing and clearance.
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Affiliation(s)
- Gabrielle Zuniga
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX, USA; Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, TX, USA; Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Bess Frost
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX, USA; Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, TX, USA; Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA.
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21
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Pisignano G, Michael DC, Visal TH, Pirlog R, Ladomery M, Calin GA. Going circular: history, present, and future of circRNAs in cancer. Oncogene 2023; 42:2783-2800. [PMID: 37587333 PMCID: PMC10504067 DOI: 10.1038/s41388-023-02780-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 08/18/2023]
Abstract
To date, thousands of highly abundant and conserved single-stranded RNA molecules shaped into ring structures (circRNAs) have been identified. CircRNAs are multifunctional molecules that have been shown to regulate gene expression transcriptionally and post-transcriptionally and exhibit distinct tissue- and development-specific expression patterns associated with a variety of normal and disease conditions, including cancer pathogenesis. Over the past years, due to their intrinsic stability and resistance to ribonucleases, particular attention has been drawn to their use as reliable diagnostic and prognostic biomarkers in cancer diagnosis, treatment, and prevention. However, there are some critical caveats to their utility in the clinic. Their circular shape limits their annotation and a complete functional elucidation is lacking. This makes their detection and biomedical application still challenging. Herein, we review the current knowledge of circRNA biogenesis and function, and of their involvement in tumorigenesis and potential utility in cancer-targeted therapy.
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Affiliation(s)
- Giuseppina Pisignano
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| | - David C Michael
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Tanvi H Visal
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Radu Pirlog
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Ladomery
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Frenchay, Bristol, BS16 1QY, UK
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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22
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Gao D, Wang X, Yan YL, Li C, Tan YP, Liu QC, Zhang MY, Zhang JV, Sun QY, Cao ZB, Zhang YH. CircKDM5B sponges miR-128 to regulate porcine blastocyst development by modulating trophectoderm barrier function. Mol Hum Reprod 2023; 29:gaad027. [PMID: 37471586 DOI: 10.1093/molehr/gaad027] [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: 03/29/2023] [Revised: 07/05/2023] [Indexed: 07/22/2023] Open
Abstract
Circular RNAs (circRNAs), which exert critical functions in the regulation of transcriptional and post-transcriptional gene expression, are found in mammalian cells but their functions in mammalian preimplantation embryo development remain poorly understood. Here, we showed that circKDM5B mediated miRNA-128 (miR-128) to regulate porcine early embryo development. We screened circRNAs potentially expressed in porcine embryos through an integrated analysis of sequencing data from mouse and human embryos, as well as porcine oocytes. An authentic circRNA originating from histone demethylase KDM5B (referred to as circKDM5B) was abundantly expressed in porcine embryos. Functional studies revealed that circKDM5B knockdown not only significantly reduced blastocyst formation but also decreased the number of total cells and trophectoderm (TE) cells. Moreover, the knockdown of circKDM5B resulted in the disturbance of tight junction assembly and impaired paracellular sealing within the TE epithelium. Mechanistically, miR-128 inhibitor injection could rescue the early development of circKDM5B knockdown embryos. Taken together, the findings revealed that circKDM5B functions as a miR-128 sponge, thereby facilitating early embryonic development in pigs through the modulation of gene expression linked to tight junction assembly.
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Affiliation(s)
- Di Gao
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong Shenzhen Hospital, Shenzhen, China
- Research Center for Reproduction and Health Development, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advance Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xin Wang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Ye-Lian Yan
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Chao Li
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Yong-Peng Tan
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Qiu-Chen Liu
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Meng-Ya Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Jian V Zhang
- Research Center for Reproduction and Health Development, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advance Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Qing-Yuan Sun
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Zu-Bing Cao
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yun-Hai Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
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23
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Wang Y, Cheng J, Xu C, Jin J, Bao W, Wu S, Wu Z. Genome-wide analysis of circRNA regulation during spleen development of Chinese indigenous breed Meishan pigs. BMC Genomics 2023; 24:477. [PMID: 37612620 PMCID: PMC10463621 DOI: 10.1186/s12864-023-09612-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: 05/10/2023] [Accepted: 08/22/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Numerous circular RNAs (circRNAs) have been recently identified in porcine tissues and cell types. Nevertheless, their significance in porcine spleen development is yet unelucidated. Herein, we reported an extensive overlook of circRNA expression profile during spleen development in Meishan pigs. RESULTS Overall, 39,641 circRNAs were identified from 6,914 host genes. Among them, many circRNAs are up- or down-regulated at different time points of pig spleen development. Using WGCNA analysis, we revealed two essential modules for protein-coding genes and circRNAs. Subsequent correlation analysis revealed 67 circRNAs/co-expressed genes that participated in immnue-associated networks. Furthermore, a competing endogenous RNA (ceRNA) network analysis of circRNAs revealed that 12 circRNAs modulated CD226, MBD2, SAMD3, SIT1, SRP14, SYTL3 gene expressions via acting as miRNA sponges. Moreover, the circRNA_21767/miR-202-3p axis regulated SIT1 expression in a ceRNA manner, which is critical for the immune-based regulation of spleen development in Meishan pigs. CONCLUSIONS Overall, our results demonstrated that the circRNAs were differentially expressed during different stages of porcine spleen development, meanwhile the circRNAs interacted with immune-related genes in a ceRNA-based fashion. Moreover, we presented biomedical researchers with RNAseqTools, a user-friendly and powerful software for the visualization of transcriptome profile data.
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Affiliation(s)
- Yifu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Jinhua Cheng
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Chao Xu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Jian Jin
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Wenbin Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Shenglong Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Zhengchang Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009, China.
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24
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Yu H, Wen B, Lu Y, Xie B, Yu F, Zhang M, Ma C, Cong B, Wen D, Bi H. The Role of circTmeff-1 in Morphine Addiction Memory of Mice. Cells 2023; 12:1985. [PMID: 37566064 PMCID: PMC10417613 DOI: 10.3390/cells12151985] [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: 06/06/2023] [Revised: 07/13/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
In addition to the essential pharmacological effects of opioids, situational cues associated with drug addiction memory are key triggers for drug seeking. CircRNAs, an emerging hotspot regulator in crown genetics, play an important role in central nervous system-related diseases. However, the internal mediating mechanism of circRNAs in the field of drug reward and addiction memory remains unknown. Here, we trained mice on a conditional place preference (CPP) model and collected nucleus accumbens (NAc) tissues from day 1 (T0) and day 8 (T1) for high-throughput RNA sequencing. QRT-PCR analysis revealed that circTmeff-1 was highly expressed in the NAc core but not in the NAc shell, suggesting that it plays a role in addiction memory formation. Meanwhile, the down-regulation of circTmeff-1 by adeno-associated viruses in the NAc core or shell could inhibit the morphine CPP scores. Subsequently, the GO and KEGG analyses indicated that circTmeff-1 might regulate the addiction memory via the MAPK and AMPK pathways. These findings suggest that circTmeff-1 in NAc plays a crucial role in morphine-dependent memory formation.
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Affiliation(s)
- Hailei Yu
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, College of Forensic Medicine, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang 050000, China; (H.Y.); (B.W.); (Y.L.); (B.X.); (F.Y.); (C.M.); (B.C.)
| | - Boyang Wen
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, College of Forensic Medicine, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang 050000, China; (H.Y.); (B.W.); (Y.L.); (B.X.); (F.Y.); (C.M.); (B.C.)
| | - Yun Lu
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, College of Forensic Medicine, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang 050000, China; (H.Y.); (B.W.); (Y.L.); (B.X.); (F.Y.); (C.M.); (B.C.)
| | - Bing Xie
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, College of Forensic Medicine, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang 050000, China; (H.Y.); (B.W.); (Y.L.); (B.X.); (F.Y.); (C.M.); (B.C.)
| | - Feng Yu
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, College of Forensic Medicine, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang 050000, China; (H.Y.); (B.W.); (Y.L.); (B.X.); (F.Y.); (C.M.); (B.C.)
| | - Minglong Zhang
- Department of Biogenetics, Qiqihar Medical University, Qiqihar 161000, China;
| | - Chunling Ma
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, College of Forensic Medicine, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang 050000, China; (H.Y.); (B.W.); (Y.L.); (B.X.); (F.Y.); (C.M.); (B.C.)
| | - Bin Cong
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, College of Forensic Medicine, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang 050000, China; (H.Y.); (B.W.); (Y.L.); (B.X.); (F.Y.); (C.M.); (B.C.)
| | - Di Wen
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, College of Forensic Medicine, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang 050000, China; (H.Y.); (B.W.); (Y.L.); (B.X.); (F.Y.); (C.M.); (B.C.)
| | - Haitao Bi
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, College of Forensic Medicine, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang 050000, China; (H.Y.); (B.W.); (Y.L.); (B.X.); (F.Y.); (C.M.); (B.C.)
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25
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Tian W, Liu Y, Zhang W, Nie R, Ling Y, Zhang B, Zhang H, Wu C. CircDOCK7 facilitates the proliferation and adipogenic differentiation of chicken abdominal preadipocytes through the gga-miR-301b-3p/ACSL1 axis. J Anim Sci Biotechnol 2023; 14:91. [PMID: 37408086 DOI: 10.1186/s40104-023-00891-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/07/2023] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND Abdominal fat deposition depends on both the proliferation of preadipocytes and their maturation into adipocytes, which is a well-orchestrated multistep process involving many regulatory molecules. Circular RNAs (circRNAs) have emergingly been implicated in mammalian adipogenesis. However, circRNA-mediated regulation in chicken adipogenesis remains unclear. Our previous circRNA sequencing data identified a differentially expressed novel circRNA, 8:27,886,180|27,889,657, during the adipogenic differentiation of chicken abdominal preadipocytes. This study aimed to investigate the regulatory role of circDOCK7 in the proliferation and adipogenic differentiation of chicken abdominal preadipocytes, and explore its molecular mechanisms of competing endogenous RNA underlying chicken adipogenesis. RESULTS Our results showed that 8:27,886,180|27,889,657 is an exonic circRNA derived from the head-to-tail splicing of exons 19-22 of the dedicator of cytokinesis 7 (DOCK7) gene, abbreviated as circDOCK7. CircDOCK7 is mainly distributed in the cytoplasm of chicken abdominal preadipocytes and is stable because of its RNase R resistance and longer half-life. CircDOCK7 is significantly upregulated in the abdominal fat tissues of fat chickens compared to lean chickens, and its expression gradually increases during the proliferation and adipogenic differentiation of chicken abdominal preadipocytes. Functionally, the gain- and loss-of-function experiments showed that circDOCK7 promoted proliferation, G0/G1- to S-phase progression, and glucose uptake capacity of chicken abdominal preadipocytes, in parallel with adipogenic differentiation characterized by remarkably increased intracellular lipid droplet accumulation and triglyceride and acetyl coenzyme A content in differentiated chicken abdominal preadipocytes. Mechanistically, a pull-down assay and a dual-luciferase reporter assay confirmed that circDOCK7 interacted with gga-miR-301b-3p, which was identified as an inhibitor of chicken abdominal adipogenesis. Moreover, the ACSL1 gene was demonstrated to be a direct target of gga-miR-301b-3p. Chicken ACSL1 protein is localized in the endoplasmic reticulum and mitochondria of chicken abdominal preadipocytes and acts as an adipogenesis accelerator. Rescue experiments showed that circDOCK7 could counteract the inhibitory effects of gga-miR-301b-3p on ACSL1 mRNA abundance as well as the proliferation and adipogenic differentiation of chicken abdominal preadipocytes. CONCLUSIONS CircDOCK7 serves as a miRNA sponge that directly sequesters gga-miR-301b-3p away from the ACSL1 gene, thus augmenting adipogenesis in chickens. These findings may elucidate a new regulatory mechanism underlying abdominal fat deposition in chickens.
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Affiliation(s)
- Weihua Tian
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ye Liu
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Wenhui Zhang
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ruixue Nie
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yao Ling
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Changxin Wu
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
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26
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Yu Z, Xu X, Ai N, Wang K, Zhang P, Li X, LiuFu S, Liu X, Jiang J, Gu J, Gao N, Ma H. Integrated analysis of circRNA, lncRNA, miRNA and mRNA to reveal the ceRNA regulatory network of postnatal skeletal muscle development in Ningxiang pig. Front Cell Dev Biol 2023; 11:1185823. [PMID: 37465009 PMCID: PMC10350537 DOI: 10.3389/fcell.2023.1185823] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/22/2023] [Indexed: 07/20/2023] Open
Abstract
Introduction: The development of skeletal muscle is regulated by regulatory factors of genes and non-coding RNAs (ncRNAs). Methods: The objective of this study was to understand the transformation of muscle fiber type in the longissimus dorsi muscle of male Ningxiang pigs at four different growth stages (30, 90, 150, and 210 days after birth, n = 3) by histological analysis and whole transcriptome sequencing. Additionally, the study investigated the expression patterns of various RNAs involved in muscle fiber transformation and constructed a regulatory network for competing endogenous RNA (ceRNA) that includes circular RNA (circRNA)/long non-coding RNA (lncRNA)-microRNA (miRNA)-messenger RNA (mRNA). Results: Histomorphology analysis showed that the diameter of muscle fiber reached its maximum at 150 days after birth. The slow muscle fiber transformation showed a pattern of initial decrease followed by an increase. 29,963 circRNAs, 2,683 lncRNAs, 986 miRNAs and 22,411 mRNAs with expression level ≥0 were identified by whole transcriptome sequencing. Furthermore, 642 differentially expressed circRNAs (DEc), 505 differentially expressed lncRNAs (DEl), 316 differentially expressed miRNAs (DEmi) and 6,090 differentially expressed mRNAs (DEm) were identified by differential expression analysis. Functions of differentially expressed mRNA were identified by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). GO enrichment analysis indicates that 40 known genes and 6 new genes are associated with skeletal muscle development. Additionally, KEGG analysis shows that these genes regulate skeletal muscle development via MAPK, FoxO, Hedgehog, PI3K-Akt, Notch, VEGF and other signaling pathways. Through protein-protein interaction (PPI) and transcription factor prediction (TFP), the action mode of skeletal muscle-related genes was explored. PPI analysis showed that there were stable interactions among 19 proteins, meanwhile, TFP analysis predicted 22 transcription factors such as HMG20B, MYF6, MYOD1 and MYOG, and 12 of the 19 interacting proteins were transcription factors. The regulatory network of ceRNA related to skeletal muscle development was constructed based on the correlation of various RNA expression levels and the targeted binding characteristics with miRNA. The regulatory network included 31 DEms, 59 miRNAs, 667 circRNAs and 224 lncRNAs. conclusion: Overall, the study revealed the role of ceRNA regulatory network in the transformation of skeletal muscle fiber types in Ningxiang pigs, which contributes to the understanding of ceRNA regulatory network in Ningxiang pigs during the skeletal muscle development period.
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Affiliation(s)
- Zonggang Yu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xueli Xu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Nini Ai
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Kaiming Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Peiwen Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xintong Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Sui LiuFu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xiaolin Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Jun Jiang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Jingjing Gu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Ning Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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Yuan H, Liu F, Long J, Duan G, Yang H. A review on circular RNAs and bacterial infections. Int J Biol Macromol 2023:125391. [PMID: 37321437 DOI: 10.1016/j.ijbiomac.2023.125391] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023]
Abstract
Bacterial infections and related diseases have been a major burden on social public health and economic stability around the world. However, the effective diagnostic methods and therapeutic approaches to treat bacterial infections are still limited. As a group of non-coding RNA, circular RNAs (circRNAs) that were expressed specifically in host cells and played a key regulatory role have the potential to be of diagnostic and therapeutic value. In this review, we systematically summarize the role of circRNAs in common bacterial infections and their potential roles as diagnostic markers and therapeutic targets.
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Affiliation(s)
- Haitao Yuan
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fang Liu
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Jinzhao Long
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Guangcai Duan
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Haiyan Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China.
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Wang D, Xie D, Zhang J, Cai B, Yang B, Zhou L, Huang X. Comprehensive analysis of the coding and non-coding RNA transcriptome expression profiles of hippocampus tissue in tx-J animal model of Wilson's disease. Sci Rep 2023; 13:9252. [PMID: 37286730 DOI: 10.1038/s41598-023-36503-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 06/05/2023] [Indexed: 06/09/2023] Open
Abstract
Wilson's disease (WD) is an autosomal recessive disorder with a genetic basis. The predominant non-motor symptom of WD is cognitive dysfunction, although the specific genetic regulatory mechanism remains unclear. Tx-J mice, with an 82% sequence homology of the ATP7B gene to the human gene, are considered the most suitable model for WD. This study employs deep sequencing to investigate the differences in RNA transcript profiles, both coding and non-coding, as well as the functional characteristics of the regulatory network involved in WD cognitive impairment. The cognitive function of tx-J mice was evaluated using the Water Maze Test (WMT). Long non-coding RNA (lncRNA), circular RNA (circRNA), and messenger RNA (mRNA) profiles were analyzed in the hippocampal tissue of tx-J mice to identify differentially expressed RNAs (DE-RNAs). Subsequently, the DE-RNAs were used to construct protein-protein interaction (PPI) networks, as well as DE-circRNAs and lncRNAs-associated competing endogenous RNA (ceRNA) expression networks, and coding-noncoding co-expression (CNC) networks. To elucidate their biological functions and pathways, the PPI and ceRNA networks were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. A total of 361 differentially expressed mRNAs (DE-mRNAs), comprising 193 up-regulated and 168 down-regulated mRNAs, 2627 differentially expressed long non-coding RNAs (DE-lncRNAs), consisting of 1270 up-regulated and 1357 down-regulated lncRNAs, and 99 differentially expressed circular RNAs (DE-circRNAs), consisting of 68 up-regulated and 31 down-regulated circRNAs, were observed in the tx-J mice group when compared to the control mice group. Gene Ontology (GO) and pathway analyses revealed that DE-mRNAs were enriched in cellular processes, calcium signaling pathways, and mRNA surveillance pathways. In contrast, the DE-circRNAs-associated competing endogenous RNA (ceRNA) network was enriched for covalent chromatin modification, histone modification, and axon guidance, whereas the DE-lncRNAs-associated ceRNA network was enriched for dendritic spine, regulation of cell morphogenesis involved in differentiation, and mRNA surveillance pathway. The study presented the expression profiles of lncRNA, circRNA, and mRNA in the hippocampal tissue of tx-J mice. Furthermore, the study constructed PPI, ceRNA, and CNC expression networks. The findings are significant in comprehending the function of regulatory genes in WD associated with cognitive impairment. These results also offer valuable information for the diagnosis and treatment of WD.
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Affiliation(s)
- Dan Wang
- College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, No. 1 Qianjiang Road, Xinzhan District, Hefei, 230012, People's Republic of China
| | - Daojun Xie
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Shushan District, Hefei, 230031, People's Republic of China.
| | - Juan Zhang
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Shushan District, Hefei, 230031, People's Republic of China
| | - Biao Cai
- College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, No. 1 Qianjiang Road, Xinzhan District, Hefei, 230012, People's Republic of China
| | - Bo Yang
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Shushan District, Hefei, 230031, People's Republic of China
| | - Lei Zhou
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Shushan District, Hefei, 230031, People's Republic of China
| | - Xiaofeng Huang
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Shushan District, Hefei, 230031, People's Republic of China
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Farina FM, Weber C, Santovito D. The emerging landscape of non-conventional RNA functions in atherosclerosis. Atherosclerosis 2023; 374:74-86. [PMID: 36725418 DOI: 10.1016/j.atherosclerosis.2023.01.009] [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: 08/02/2022] [Revised: 12/15/2022] [Accepted: 01/12/2023] [Indexed: 01/22/2023]
Abstract
Most of the human genome is transcribed into non-coding RNAs (ncRNAs), which encompass a heterogeneous family of transcripts including microRNAs (miRNAs), long ncRNAs (lncRNAs), circular RNAs (circRNAs), and others. Although the detailed modes of action of some classes are not fully elucidated, the common notion is that ncRNAs contribute to sculpting gene expression of eukaryotic cells at multiple levels. These range from the regulation of chromatin remodeling and transcriptional activity to post-transcriptional regulation of messenger RNA splicing, stability, and decay. Many of these functions ultimately govern the expression of coding and non-coding genes to affect diverse physiological and pathological mechanisms in vascular biology and beyond. As such, different classes of ncRNAs emerged as crucial regulators of vascular integrity as well as active players in the pathophysiology of atherosclerosis from the early stages of endothelial dysfunction to the clinically relevant complications. However, research in recent years revealed unexpected findings such as small ncRNAs being able to biophysically regulate protein function, the glycosylation of ncRNAs to be exposed on the cell surface, the release of ncRNAs in the extracellular space to act as ligands of receptors, and even the ability of non-coding portion of messenger RNAs to mediate structural functions. This evidence expanded the functional repertoire of ncRNAs far beyond gene regulation and highlighted an additional layer of biological control of cell function. In this Review, we will discuss these emerging aspects of ncRNA biology, highlight the implications for the mechanisms of vascular biology and atherosclerosis, and discuss possible translational implications.
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Affiliation(s)
- Floriana Maria Farina
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU), Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU), Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany; Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
| | - Donato Santovito
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU), Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany; Institute for Genetic and Biomedical Research (IRGB), Unit of Milan, National Research Council, Milan, Italy.
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Zhang W, Lin S, Jiao Z, An L, Xie T, Wu J, Zhang L. The Mouse CircGHR Regulates Proliferation, Differentiation and Apoptosis of Hepatocytes and Myoblasts. Genes (Basel) 2023; 14:1207. [PMID: 37372387 DOI: 10.3390/genes14061207] [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: 03/27/2023] [Revised: 05/14/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
The anterior pituitary gland of animals secretes growth hormone (GH) to bind to the growth hormone receptor (GHR) on the liver cell membrane through the blood circulation, thereby promoting the downstream gene insulin-like growth factor-1 (IGF1) expression, which is the canonical GH-GHR-IGF1 signaling pathway. Therefore, the amount of GHR and the integrity of its structure will affect animal growth and development. In the previous study, we found that the mouse GHR gene can transcribe a circular transcript named circGHR. Our group cloned the full-length of the mouse circGHR and analyzed its spatiotemporal expression profile. In this study, we further predicted the open reading frame of circGHR with bioinformatics, subsequently constructed a Flag-tagged protein vector and preliminarily verified its coding potential with western blot. Additionally, we found that circGHR could inhibit the proliferation of NCTC469 cells and has a tendency to inhibit cell apoptosis, while for C2C12 cells, it showed a tendency to inhibit cell proliferation and promote its differentiation. Overall, these results suggested that the mouse circGHR had the potential to encode proteins and affect cell proliferation, differentiation and apoptosis.
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Affiliation(s)
- Weilu Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Shudai Lin
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Zhenhai Jiao
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Lilong An
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Tingting Xie
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Jiang Wu
- Experimental Teaching Center, Guangdong Ocean University, Zhanjiang 524088, China
| | - Li Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
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Watts ME, Oksanen M, Lejerkrans S, Mastropasqua F, Gorospe M, Tammimies K. Circular RNAs arising from synaptic host genes during human neuronal differentiation are modulated by SFPQ RNA-binding protein. BMC Biol 2023; 21:127. [PMID: 37237280 DOI: 10.1186/s12915-023-01627-w] [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: 10/27/2022] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Circular RNA (circRNA) molecules, generated through non-canonical back-splicing of exon-exon junctions, have recently been implicated in diverse biological functions including transcriptional regulation and modulation of protein interactions. CircRNAs are emerging as a key component of the complex neural transcriptome implicated in brain development. However, the specific expression patterns and functions of circRNAs in human neuronal differentiation have not been explored. RESULTS Using total RNA sequencing analysis, we identified expressed circRNAs during the differentiation of human neuroepithelial stem (NES) cells into developing neurons and discovered that many circRNAs originated from host genes associated with synaptic function. Interestingly, when assessing population data, exons giving rise to circRNAs in our dataset had a higher frequency of genetic variants. Additionally, screening for RNA-binding protein sites identified enrichment of Splicing Factor Proline and Glutamine Rich (SFPQ) motifs in increased circRNAs, several of which were reduced by SFPQ knockdown and enriched in SFPQ ribonucleoprotein complexes. CONCLUSIONS Our study provides an in-depth characterisation of circRNAs in a human neuronal differentiation model and highlights SFPQ as both a regulator and binding partner of circRNAs elevated during neuronal maturation.
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Affiliation(s)
- Michelle E Watts
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Marika Oksanen
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, NIH, Baltimore, MD, USA
| | - Sanna Lejerkrans
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Francesca Mastropasqua
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, NIH, Baltimore, MD, USA
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden.
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden.
- Karolinska Institutet, BioClinicum J9:30, Visionsgatan 4, 171 56, Solna, Sweden.
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Jiang W, Long X, Li Z, Hu M, Zhang Y, Lin H, Tang W, Ouyang Y, Jiang L, Chen J, He P, Ouyang X. The Role of Circular RNAs in Ischemic Stroke. Neurochem Res 2023:10.1007/s11064-023-03935-7. [PMID: 37126193 DOI: 10.1007/s11064-023-03935-7] [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: 11/25/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 05/02/2023]
Abstract
Ischemic stroke (IS), a devastating condition characterized by intracranial artery stenosis and middle cerebral artery occlusion leading to insufficient oxygen supply to the brain, is a major cause of death and physical disability worldwide. Recent research has demonstrated the critical role of circular RNAs (circRNAs), a class of covalently enclosed noncoding RNAs that are widespread in eukaryotic cells, in regulating various physiological and pathophysiological cellular processes, including cell apoptosis, autophagy, synaptic plasticity, and neuroinflammation. In the past few years, circRNAs have attracted extensive attention in the field of IS research. This review summarizes the current understanding of the mechanisms underlying the involvement of circRNAs in IS development. A better understanding of circRNA-mediated pathogenic mechanisms in IS may pave the way for translating circRNA research into clinical practice, ultimately improving the clinical outcomes of IS patients.
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Affiliation(s)
- Weiwei Jiang
- Department of Organ Transplantation, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiongquan Long
- Department of Gastroenterology, The First Affiliated Hospital of Hunan Normal University, Hunan Normal University, Changsha, Hunan, China
| | - Zhicheng Li
- Collage of Pharmacy, University of South China, Hengyang, Hunan, China
| | - Mi Hu
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, Hunan, China
| | - Yangkai Zhang
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, Hunan, China
| | - Huiling Lin
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, Hunan, China
| | - Wanying Tang
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, Hunan, China
| | - Yuxin Ouyang
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, Hunan, China
| | - Liping Jiang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
| | - Jinzhi Chen
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, Hunan, China
| | - Pingping He
- The Research Center of Reproduction and Translational Medicine of Hunan Province, Department of Physiology, Medical College, Hunan Normal University, Changsha, 410081, Hunan Province, China
| | - Xinping Ouyang
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, Hunan, China.
- The Research Center of Reproduction and Translational Medicine of Hunan Province, Department of Physiology, Medical College, Hunan Normal University, Changsha, 410081, Hunan Province, China.
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Feng H, Deng Z, Peng W, Wei X, Liu J, Wang T. Circular RNA EPHA3 suppresses progression and metastasis in prostate cancer through the miR-513a-3p/BMP2 axis. J Transl Med 2023; 21:288. [PMID: 37118847 PMCID: PMC10148471 DOI: 10.1186/s12967-023-04132-4] [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: 11/03/2022] [Accepted: 04/13/2023] [Indexed: 04/30/2023] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) may regulate the onset and progression of human malignancies by competitively binding to microRNA (miRNA) sponges, thus regulating the downstream genes. However, aberrant circRNA expression patterns and their biological functions in prostate cancer (PCa) warrant further studies. Our research sought to shed further light on the possible role and molecular mechanism of circEPHA3 action in controlling the growth and metastasis of PCa cells. MATERIALS AND METHODS circEPHA3 (has_circ_0066596) was initially screened from a previous circRNA microarray and identified following Actinomycin D and RNase R assays. Fluorescence in situ hybridization, biotin-coupled probe RNA pulldown, and dual-luciferase reporter gene assays were performed to examine the relationship between circEPHA3 and miR-513a-3p. The biological role of circEPHA3 in PCa was assessed by CCK8, wound healing, Transwell assays, and animal experiments. RESULTS We identified a novel circular RNA, circEPHA3 (has_circ_0066596), which was down-regulated in high-grade PCa tissues and cell lines. The outcomes of CCK8, wound healing, Transwell assays, and animal experiments revealed that circEPHA3 prohibited the progression and metastasis of PCa in vivo and in vitro. Mechanistically, circEPHA3 was directly bound to miR-513a-3p and regulated the downstream gene, BMP2, thereby serving as a tumor suppressor in PCa. CONCLUSIONS As a tumor suppressor, circEPHA3 inhibited the proliferation and metastasis of PCa cells through the miR-513a-3p/BMP2 axis, suggesting that circEPHA3 might be a potential therapeutic target for PCa.
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Affiliation(s)
- Huan Feng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong, China
| | - Zhiyao Deng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong, China
| | - Wei Peng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xian Wei
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jihong Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tao Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong, China.
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Seeler S, Andersen MS, Sztanka-Toth T, Rybiczka-Tešulov M, van den Munkhof MH, Chang CC, Maimaitili M, Venø MT, Hansen TB, Pasterkamp RJ, Rybak-Wolf A, Denham M, Rajewsky N, Kristensen LS, Kjems J. A Circular RNA Expressed from the FAT3 Locus Regulates Neural Development. Mol Neurobiol 2023; 60:3239-3260. [PMID: 36840844 PMCID: PMC10122638 DOI: 10.1007/s12035-023-03253-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/28/2023] [Indexed: 02/26/2023]
Abstract
Circular RNAs (circRNAs) are key regulators of cellular processes, are abundant in the nervous system, and have putative regulatory roles during neural differentiation. However, the knowledge about circRNA functions in brain development is limited. Here, using RNA-sequencing, we show that circRNA levels increased substantially over the course of differentiation of human embryonic stem cells into rostral and caudal neural progenitor cells (NPCs), including three of the most abundant circRNAs, ciRS-7, circRMST, and circFAT3. Knockdown of circFAT3 during early neural differentiation resulted in minor transcriptional alterations in bulk RNA analysis. However, single-cell transcriptomics of 30 and 90 days differentiated cerebral organoids deficient in circFAT3 showed a loss of telencephalic radial glial cells and mature cortical neurons, respectively. Furthermore, non-telencephalic NPCs in cerebral organoids showed changes in the expression of genes involved in neural differentiation and migration, including FAT4, ERBB4, UNC5C, and DCC. In vivo depletion of circFat3 in mouse prefrontal cortex using in utero electroporation led to alterations in the positioning of the electroporated cells within the neocortex. Overall, these findings suggest a conserved role for circFAT3 in neural development involving the formation of anterior cell types, neuronal differentiation, or migration.
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Affiliation(s)
- Sabine Seeler
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
- Department of Biomedicine, The Skou Building, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
| | - Maria Schertz Andersen
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
| | - Tamas Sztanka-Toth
- Berlin Institute for Medical Systems Biology (BIMSB), MDC Berlin-Mitte, 10115, Berlin, Germany
| | - Mateja Rybiczka-Tešulov
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, 3584 CG, Utrecht, Netherlands
| | - Marleen H van den Munkhof
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, 3584 CG, Utrecht, Netherlands
| | - Chi-Chih Chang
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
| | - Muyesier Maimaitili
- Department of Biomedicine, The Skou Building, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
- Danish Research Institute of Translational Neuroscience, Nordic EMBL Partnership for Molecular Medicine, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
| | - Morten Trillingsgaard Venø
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
- Omiics ApS, 8200 Aarhus N, Aarhus, Denmark
| | - Thomas Birkballe Hansen
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, 3584 CG, Utrecht, Netherlands
| | - Agnieszka Rybak-Wolf
- Berlin Institute for Medical Systems Biology (BIMSB), MDC Berlin-Mitte, 10115, Berlin, Germany
| | - Mark Denham
- Department of Biomedicine, The Skou Building, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
- Danish Research Institute of Translational Neuroscience, Nordic EMBL Partnership for Molecular Medicine, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology (BIMSB), MDC Berlin-Mitte, 10115, Berlin, Germany
| | - Lasse Sommer Kristensen
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Aarhus, Denmark.
- Department of Biomedicine, The Skou Building, Aarhus University, 8000 Aarhus C, Aarhus, Denmark.
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Aarhus, Denmark.
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Ribeiro V, Martins SG, Lopes AS, Thorsteinsdóttir S, Zilhão R, Carlos AR. NFIXing Cancer: The Role of NFIX in Oxidative Stress Response and Cell Fate. Int J Mol Sci 2023; 24:ijms24054293. [PMID: 36901722 PMCID: PMC10001739 DOI: 10.3390/ijms24054293] [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: 01/27/2023] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
NFIX, a member of the nuclear factor I (NFI) family of transcription factors, is known to be involved in muscle and central nervous system embryonic development. However, its expression in adults is limited. Similar to other developmental transcription factors, NFIX has been found to be altered in tumors, often promoting pro-tumorigenic functions, such as leading to proliferation, differentiation, and migration. However, some studies suggest that NFIX can also have a tumor suppressor role, indicating a complex and cancer-type dependent role of NFIX. This complexity may be linked to the multiple processes at play in regulating NFIX, which include transcriptional, post-transcriptional, and post-translational processes. Moreover, other features of NFIX, including its ability to interact with different NFI members to form homodimers or heterodimers, therefore allowing the transcription of different target genes, and its ability to sense oxidative stress, can also modulate its function. In this review, we examine different aspects of NFIX regulation, first in development and then in cancer, highlighting the important role of NFIX in oxidative stress and cell fate regulation in tumors. Moreover, we propose different mechanisms through which oxidative stress regulates NFIX transcription and function, underlining NFIX as a key factor for tumorigenesis.
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Affiliation(s)
- Vanessa Ribeiro
- cE3c-CHANGE, Department of Animal Biology, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Susana G. Martins
- cE3c-CHANGE, Department of Animal Biology, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Ana Sofia Lopes
- cE3c-CHANGE, Department of Animal Biology, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
- Centro Hospitalar de Lisboa Ocidental (CHLO), 1449-005 Lisbon, Portugal
| | - Sólveig Thorsteinsdóttir
- cE3c-CHANGE, Department of Animal Biology, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Rita Zilhão
- cE3c-CHANGE, Department of Plant Biology, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Ana Rita Carlos
- cE3c-CHANGE, Department of Animal Biology, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
- Correspondence:
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Papageorgiou G, Amoah SK, Pierotti C, Otero M, Eckel S, Coffey K, Allan AM, Caldwell KK, Mellios N. Prenatal alcohol exposure results in brain region- and sex-specific changes in circHomer1 expression in adult mouse brain. Front Neurosci 2023; 17:1087950. [PMID: 36875647 PMCID: PMC9983553 DOI: 10.3389/fnins.2023.1087950] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/16/2023] [Indexed: 02/19/2023] Open
Abstract
Circular RNAs (circRNAs) are a novel category of covalently-closed non-coding RNAs mainly derived from the back-splicing of exons or introns of protein-coding genes. In addition to their inherent high overall stability, circRNAs, have been shown to have strong functional effects on gene expression via a multitude of transcriptional and post-transcriptional mechanisms. Furthermore, circRNAs, appear to be particularly enriched in the brain and able to influence both prenatal development and postnatal brain function. However, little is known about the potential involvement of circRNAs in the long term influence of prenatal alcohol exposure (PAE) in the brain and their relevance for Fetal Alcohol Spectrum Disorders (FASD). Using circRNA-specific quantification, we have found that circHomer1, an activity-dependent circRNA derived from Homer protein homolog 1 (Homer1) and enriched in postnatal brain, is significantly down-regulated in the male frontal cortex and hippocampus of mice subjected to modest PAE. Our data further suggest that the expression of H19, an imprinted embryonic brain-enriched long non-coding RNA (lncRNA), is significantly up-regulated in the frontal cortex of male PAE mice. Furthermore, we show opposing changes in the developmental- and brain region specific- expression of circHomer1 and H19. Lastly, we show that knockdown of H19 results in robust increases in circHomer1 but not linear HOMER1 mRNA expression in human glioblastoma cell lines. Taken together, our work uncovers notable sex- and brain region-specific alterations in circRNA and lncRNA expression following PAE and introduces novel mechanistic insights with potential relevance to FASD.
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Affiliation(s)
- Grigorios Papageorgiou
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Stephen K. Amoah
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Caroline Pierotti
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Madison Otero
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Sophie Eckel
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Kacie Coffey
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Andrea M. Allan
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Kevin K. Caldwell
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Nikolaos Mellios
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, United States
- Autophagy, Inflammation, and Metabolism (AIM) Center, Albuquerque, NM, United States
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Zhang Y, Zhang X, Shen Z, Qiu Q, Tong X, Pan J, Zhu M, Hu X, Gong C. BmNPV circular RNA-encoded peptide VSP39 promotes viral replication. Int J Biol Macromol 2023; 228:299-310. [PMID: 36563818 DOI: 10.1016/j.ijbiomac.2022.12.173] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/23/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
CircRNAs are covalently closed single-stranded circular RNA molecules, which are not easily degraded by endonucleases and play vital roles in many biological processes. Currently, most studies on circRNAs focus on endogenous circRNAs in cells, and there are few studies on virus-encoded circRNAs. In this study, a viral circRNA (circRNA-000010) derived from the region (-/bp: 114514-115,319) of the complementary strand of Bombyx mori Nucleopolyhedrovirus (BmNPV) genome was identified with the circRNA-sequencing. The authenticity of viral circRNA-000010 was further confirmed by reverse transcription PCR, reverse transcription-rolling circle amplification (TCA), in situ hybridization, immunofluorescent staining, and Northern blotting. The results of overexpression and knockdown experiments showed that circRNA-000010 promoted viral replication. Furthermore, a viral small peptide VSP39 with 39 amino acid residues translated by circRNA-000010 but not its linear molecule was confirmed. Finally, VSP39 was found to promote viral replication. Our findings indicated that a viral circRNA encoded by BmNPV promoted viral replication. These findings will provide new clues for further understanding coding information of the BmNPV genome and open a new insight for investigating host-virus interactions.
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Affiliation(s)
- Yaxin Zhang
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Xing Zhang
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Zeen Shen
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Qunnan Qiu
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Xinyu Tong
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Jun Pan
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Min Zhu
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Xiaolong Hu
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China; Institute of Agricultural Biotechnology and Ecological Research, Soochow University, Suzhou 215123, China.
| | - Chengliang Gong
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China; Institute of Agricultural Biotechnology and Ecological Research, Soochow University, Suzhou 215123, China.
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Yu X, Liu H, Chang N, Fu W, Guo Z, Wang Y. Circular RNAs: New players involved in the regulation of cognition and cognitive diseases. Front Neurosci 2023; 17:1097878. [PMID: 36816112 PMCID: PMC9932922 DOI: 10.3389/fnins.2023.1097878] [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: 11/14/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Circular RNAs (circRNAs), a type of covalently closed endogenous single-stranded RNA, have been regarded as the byproducts of the aberrant splicing of genes without any biological functions. Recently, with the development of high-throughput sequencing and bioinformatics, thousands of circRNAs and their differential biological functions have been identified. Except for the great advances in identifying circRNA roles in tumor progression, diagnosis, and treatment, accumulated evidence shows that circRNAs are enriched in the brain, especially in the synapse, and dynamically change with the development or aging of organisms. Because of the specific roles of synapses in higher-order cognitive functions, circRNAs may not only participate in cognitive functions in normal physiological conditions but also lead to cognition-related diseases after abnormal regulation of their expression or location. Thus, in this review, we summarized the progress of studies looking at the role of circRNA in cognitive function, as well as their involvement in the occurrence, development, prognosis, and treatment of cognitive-related diseases, including autism, depression, and Alzheimer's diseases.
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Affiliation(s)
- Xiaohan Yu
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Haoyu Liu
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Ning Chang
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Weijia Fu
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Zhiwen Guo
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yue Wang
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China,*Correspondence: Yue Wang,
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39
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Recent insights into the roles of circular RNAs in human brain development and neurologic diseases. Int J Biol Macromol 2023; 225:1038-1048. [PMID: 36410538 DOI: 10.1016/j.ijbiomac.2022.11.166] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/16/2022] [Indexed: 11/20/2022]
Abstract
Circular RNAs (circRNAs) are a novel class of non-coding RNAs. They are single-stranded RNA transcripts characterized with a closed loop structure making them resistant to degrading enzymes. Recently, circRNAs have been suggested with regulatory roles in gene expression involved in controlling various biological processes. Notably, they have demonstrated abundance, dynamic expression, back-splicing events, and spatiotemporally regulation in the human brain. Accordingly, they are expected to be involved in brain functions and related diseases. Studies in animals and human brain have revealed differential expression of circRNAs in brain compartments. Interestingly, contributing roles of circRNAs in the regulation of central nervous system (CNS) development have been demonstrated in a number of studies. It has been proposed that circRNAs play role in substantial neurological functions like neurotransmitter-associated tasks, neural cells maturation, and functions of synapses. Furthermore, 3 main pathways have been identified in association with circRNAs's host genes including axon guidance, Wnt signaling, and transforming growth factor beta (TGF-β) signaling pathways, which are known to be involved in substantial functions like migration and differentiation of neurons and specification of axons, and thus play role in brain development. In this review, we have an overview to the biogenesis, biological functions of circRNAs, and particularly their roles in human brain development and the pathogenesis of neurodegenerative diseases including Alzheimer's diseases, multiple sclerosis, Parkinson's disease and brain tumors.
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Integrating Analysis to Identify Differential circRNAs Involved in Goat Endometrial Receptivity. Int J Mol Sci 2023; 24:ijms24021531. [PMID: 36675045 PMCID: PMC9865150 DOI: 10.3390/ijms24021531] [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: 10/31/2022] [Revised: 12/27/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Endometrial receptivity is one of the main factors underlying a successful pregnancy, with reports substantiating the fact that suboptimal endometrial receptivity accounts for two-thirds of early implantation event failures. The association between circRNAs and endometrial receptivity in the goat remains unclear. This study aims to identify potential circRNAs and regulatory mechanisms related to goat endometrial receptivity. Therefore, the endometrial samples on day 16 of pregnancy and day 16 of the estrous cycle were analyzed using high-throughput RNA-seq and bioinformatics. The results show that 4666 circRNAs were identified, including 7 downregulated and 11 upregulated differentially expressed circRNAs (DE-circRNAs). Back-splicing and RNase R resistance verified the identified circRNAs. We predicted the competing endogenous RNA (ceRNA) regulatory mechanism and potential target genes of DE-circRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of these predicted target genes suggest that DE-circRNAs were significantly involved in establishing endometrial receptivity. Furthermore, Sanger sequencing, qPCR, correlation analysis and Fluorescence in Situ Hybridization (FISH) show that circ_MYRF derived from the host gene myelin regulatory factor (MYRF) might regulate the expression of interferon stimulating gene 15 (ISG15), thereby promoting the formation of endometrial receptivity. These novel findings may contribute to a better understanding of the molecular mechanisms regulating endometrial receptivity and promoting the maternal recognition of pregnancy (MRP).
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Guo C, Lv H, Bai Y, Guo M, Li P, Tong S, He K. Circular RNAs in extracellular vesicles: Promising candidate biomarkers for schizophrenia. Front Genet 2023; 13:997322. [PMID: 36685830 PMCID: PMC9852742 DOI: 10.3389/fgene.2022.997322] [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: 07/18/2022] [Accepted: 12/05/2022] [Indexed: 01/09/2023] Open
Abstract
As one of common and severe mental illnesses, schizophrenia is difficult to be diagnosed exactly. Both its pathogenesis and the causes of its development are still uncertain because of its etiology complexity. At present, the diagnosis of schizophrenia is mainly based on the patient's symptoms and signs, lacking reliable biomarkers that can be used for diagnosis. Circular RNAs in extracellular vesicles (EV circRNAs) can be used as promising candidate biomarkers for schizophrenia and other diseases, for they are not only high stability and disease specificity, but also are rich in contents and easy to be detected. The review is to focus on the research progress of the correlation between circRNAs and schizophrenia, and then to explores the possibility of EV circRNAs as new biomarkers for the schizophrenia diagnosis.
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Affiliation(s)
- Chuang Guo
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
| | - Haibing Lv
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
| | - Yulong Bai
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
| | - Meng Guo
- Network Center, Inner Mongolia Minzu University, Tongliao, China
| | - Pengfei Li
- Affiliated Hospital of Inner Mongolia Minzu University, Tongliao, China
| | - Shuping Tong
- Affiliated Hospital of Inner Mongolia Minzu University, Tongliao, China
| | - Kuanjun He
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China,*Correspondence: Kuanjun He,
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Wang Z, Deng H, Jin Y, Luo M, Huang J, Wang J, Zhang K, Wang L, Zhou J. Circular RNAs: biology and clinical significance of breast cancer. RNA Biol 2023; 20:859-874. [PMID: 37882644 PMCID: PMC10730165 DOI: 10.1080/15476286.2023.2272468] [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] [Accepted: 10/08/2023] [Indexed: 10/27/2023] Open
Abstract
Circular RNAs (circRNAs) are novel noncoding RNAs with covalently closed-loop structures that can regulate eukaryotic gene expression. Due to their stable structure, circRNAs are widely distributed in the cytoplasm and have important biological functions, including as microRNA sponges, RNA-binding protein conjugates, transcription regulators, and translation templates. Breast cancer is among the most common malignant cancers diagnosed in women worldwide. Despite the development of comprehensive treatments, breast cancer still has high mortality rates. Recent studies have unmasked critical roles for circRNAs in breast cancer as regulators of tumour initiation, progression, and metastasis. Further, research has revealed that some circRNAs have the potential for use as diagnostic and prognostic biomarkers in clinical practice. Herein, we review the biogenesis and biological functions of circRNAs, as well as their roles in different breast cancer subtypes. Moreover, we provide a comprehensive summary of the clinical significance of circRNAs in breast cancer. CircRNAs are believed to be a hot focus in basic and clinical research of breast cancer, and innovative future research directions of circRNAs could be used as biomarkers, therapeutic targets, or novel drugs.Abbreviations: CeRNA: Competitive endogenous RNA; ciRNA: Circular intronic RNA; circRNA: Circular RNA; EIciRNA: Exon-intron circRNA; EMT: Epithelial-mesenchymal transition; IRES: Internal ribosome entry site; lncRNA: Long non-coding RNA; miRNA: MicroRNA; MRE: MiRNA response element; ncRNA: Non-coding RNA; RBP: RNA-binding protein; RNA-seq: RNA sequencing; RT-PCR: Reverse transcription-polymerase chain reaction.
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Affiliation(s)
- Zhanwei Wang
- Department of Breast Surgery, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Hao Deng
- The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
- Department of Breast Surgery and Oncology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yao Jin
- The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
- Department of Breast Surgery and Oncology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Meng Luo
- The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
- Department of Breast Surgery and Oncology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jia Huang
- The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
- Department of Breast Surgery and Oncology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jing Wang
- The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
- Department of Breast Surgery and Oncology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kun Zhang
- The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
- Department of Breast Surgery and Oncology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Li Wang
- Department of Emergency, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiaojiao Zhou
- The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
- Department of Breast Surgery and Oncology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Liao J, Zhang Q, Huang J, He H, Lei J, Shen Y, Wang J, Xiao Y. The emerging role of circular RNAs in Parkinson's disease. Front Neurosci 2023; 17:1137363. [PMID: 36925739 PMCID: PMC10012279 DOI: 10.3389/fnins.2023.1137363] [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: 01/04/2023] [Accepted: 02/03/2023] [Indexed: 02/18/2023] Open
Abstract
Parkinson's disease (PD) is the second most prevalent neurodegenerative disease and the most common movement disorder. It involves a gradual loss of dopaminergic neurons in the substantia nigra. Although many studies have been conducted, the underlying molecular pathways of PD remain largely unknown. Circular RNAs (circRNAs), a novel class of non-coding RNAs with a covalently closed loop structure, are common in the brain. They are stable, conserved molecules that are widely expressed in eukaryotes in tissue-, cell-, and development-specific patterns. Many circRNAs have recently been identified in nervous system diseases, and some circRNA expression profiles have been linked to PD. Given that recent research has indicated the essential roles of various circRNAs in the development and progression of neurodegenerative diseases, the identification of individual circRNAs may be a promising strategy for finding new treatment targets for PD. Moreover, the search for circRNAs with high specificity and sensitivity will open up new avenues for the early diagnosis and treatment of PD. Herein, we address the biogenesis, properties, and roles of circRNAs and review their potential utility as biomarkers and therapeutic targets in PD.
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Affiliation(s)
- Jiajia Liao
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Department of Rehabilitation Medicine, Jiangbin Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qinxin Zhang
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jinjun Huang
- Department of Rehabilitation, Guiping People's Hospital, Guiping, China
| | - Honghu He
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jiang Lei
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yuefei Shen
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jin Wang
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yousheng Xiao
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Cheng Z, Qin W, Li S, Shao S, Liu B. Emerging roles of circular RNAs in cancer therapy-induced cardiotoxicity. Front Cardiovasc Med 2023; 10:1152436. [PMID: 37020518 PMCID: PMC10067915 DOI: 10.3389/fcvm.2023.1152436] [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: 01/27/2023] [Accepted: 03/06/2023] [Indexed: 04/07/2023] Open
Abstract
Cancer therapy-induced cardiotoxicity (CTIC) is an important cause of death in cancer survivors which often results in the withdrawal or discontinuation of drugs. The underlying mechanisms of CTIC remain unclear. Circular RNAs (circRNAs) are a class of non-coding regulatory RNA molecules which have emerged in recent years. They are generated by back splicing and have powerful biological functions, including transcription and splicing, isolating or building macromolecular scaffolds to interfere with microRNA activity and signaling pathways, and acting as templates for translation. Moreover, circRNAs demonstrate high abundance and significant stability. CircRNAs can be used as novel biomarkers because they often function in a cell-type and tissue-specific manner. CircRNAs have attracted increasing attention in cardiovascular disease research, and recent studies exploring the role of circRNAs in CTIC have had promising results. This review will summarize the current understanding of circRNAs' biogenesis, regulation and function. Their clinical potential as biomarkers, therapeutic agents and drug targets will also be explored.
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Affiliation(s)
- Ziji Cheng
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wanting Qin
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shaoling Li
- Department of Pathology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shuijin Shao
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Baonian Liu
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Correspondence: Baonian Liu
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Liu Y, Chen Q, Bao J, Pu Y, Han J, Zhao H, Ma Y, Zhao Q. Genome-Wide Analysis of Circular RNAs Reveals circCHRNG Regulates Sheep Myoblast Proliferation via miR-133/SRF and MEF2A Axis. Int J Mol Sci 2022; 23:ijms232416065. [PMID: 36555706 PMCID: PMC9781509 DOI: 10.3390/ijms232416065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
As relatively new members of the non-coding RNA family, circRNAs play important roles in a variety of biological processes. However, the temporal expression pattern and the function of circRNAs during sheep skeletal muscle development remains unclear. This study aimed to identify circRNAs related to sheep skeletal muscle development and explore their roles in myoblast proliferation. The circRNA expression profiles of longissimus dorsi of sheep from F90, L30, and A3Y were obtained by the RNA-seq method. The function and mechanisms of the novel circCHRNG in muscle satellite cell proliferation were explored using CCK-8 assay, Western blot, qPCR, and dual-luciferase reporter assay. We identified 12,375 circRNAs, including 476, 133, and 233 DEcircRNAs found among three comparative groups. KEGG results showed that DEcircRNAs were enriched in muscle contraction, the regulation of cell proliferation, and the AMPK, insulin, and PI3K-Akt signaling pathways. Notably, a novel circRNA, termed circRNA CHRNG, acts as a miR-133 sponge to promote skeletal muscle satellite cell proliferation. Our study provides a systematic description of circRNAs of ovine skeletal muscle across fetal, lamb, and adult stages. GO and KEGG analyses showed that DEcircRNAs were enriched in multiple pathways associated with muscle development, such as the PI3K-Akt and AMPK signaling pathways. In addition, we propose that circCHRNG acts as a miR-133 sponge to upregulate the expression levels of SRF and MEF2A, thereby promoting myoblast proliferation.
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Affiliation(s)
- Yue Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qian Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jingjing Bao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yabin Pu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Huijing Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuehui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qianjun Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence:
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Abstract
Bone is a connective tissue that has important functions in the human body. Cells and the extracellular matrix (ECM) are key components of bone and are closely related to bone-related diseases. However, the outcomes of conventional treatments for bone-related diseases are not promising, and hence it is necessary to elucidate the exact regulatory mechanisms of bone-related diseases and identify novel biomarkers for diagnosis and therapy. Circular RNAs (circRNAs) are single-stranded RNAs that form closed circular structures without a 5' cap or 3' tail and polycyclic adenylate tails. Due to their high stability, circRNAs have the potential to be typical biomarkers. Accumulating evidence suggests that circRNAs are involved in bone-related diseases, including osteoarthritis, osteoporosis, osteosarcoma, multiple myeloma, intervertebral disc degeneration, and rheumatoid arthritis. Herein, we summarize the recent research progress on the characteristics and functions of circRNAs, and highlight the regulatory mechanism of circRNAs in bone-related diseases.
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Affiliation(s)
- Linghui HU
- School of Exercise and Health, Shanghai University of Sport, Shanghai200438, China
| | - Wei WU
- School of Exercise and Health, Shanghai University of Sport, Shanghai200438, China
| | - Jun ZOU
- School of Exercise and Health, Shanghai University of Sport, Shanghai200438, China,Jun ZOU,
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47
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Zhu B, Gao J, Zhang Y, Liao B, Zhu S, Li C, Liao J, Liu J, Jiang C, Zeng J. CircRNA/miRNA/mRNA axis participates in the progression of partial bladder outlet obstruction. BMC Urol 2022; 22:191. [PMID: 36434693 PMCID: PMC9700926 DOI: 10.1186/s12894-022-01132-2] [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: 07/02/2022] [Accepted: 10/25/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND More and more evidence showed that circRNA/miRNA/mRNA axis played a vital role in the pathogenesis of some diseases. However, the role of circRNA/miRNA/mRNA axis in partial bladder outlet obstruction (pBOO) remains unknown. Our study aimed to explore the complex regulatory mechanism of circRNA/miRNA/mRNA axis in pBOO. METHODS The pBOO rat model was established, and the bladder tissues were collected for mRNA sequencing. The differentially expressed mRNAs were analyzed by high-throughput sequencing, and the GO and KEGG analysis of the differentially expressed mRNAs were performed. Competing endogenous RNAs (ceRNAs) analysis identified the potential regulation function of circRNA/miRNA/mRNA axis in pBOO. qRT-PCR detected the expression of circRNA/miRNA/mRNA. miRanda software was performed to predict the relationship between circRNA and miRNA, miRNA and mRNA. RESULTS Compared with the sham group, a total of 571 mRNAs were differentially expressed in the pBOO group, of which 286 were up-regulated and 285 were down-regulated. GO analysis showed that the mRNAs were mainly involved in cellular process, single-organism process, and cell, etc. KEGG analysis showed that the enriched signaling pathways were metabolic pathways, cell adhesion molecules (CAMs), and HTLV-I infection, etc. Based on the previous transcriptome data and differentially expressed circRNAs, we drew the ceRNA network regulation diagram. qRT-PCR results confirmed that chr3:113195876|113197193/rno-miR-30c-1-3p/Gata4, chr1:126188351|126195625/rno-miR-153-5p/Diaph3, and chr9:81258380|81275269/rno-miR-135b-5p/Pigr axis may have ceRNA function. miRanda confirmed there have the binding sites of circRNA/miRNA/mRNA axis. CONCLUSIONS CircRNA/miRNA/mRNA axis was involved in the progression of pBOO. Our research on the circRNA/miRNA/mRNA axis revealed new pathogenesis and treatment strategies for pBOO.
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Affiliation(s)
- Baoyi Zhu
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Jun Gao
- grid.410737.60000 0000 8653 1072Department of Basic Medical Research, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, 511518 Guangdong People’s Republic of China
| | - Yuying Zhang
- Department of Child Health Care, Shenzhen Longhua Maternity and Child Health Care Hospital, Shenzhen, 518000 Guangdong People’s Republic of China
| | - Baojian Liao
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China ,grid.9227.e0000000119573309Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510700 Guangdong People’s Republic of China
| | - Sihua Zhu
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Chunling Li
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Junhao Liao
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Jianjia Liu
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Chonghe Jiang
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Jianwen Zeng
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
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Li Q, Wang L, Xing K, Yang Y, Abiola Adetula A, Liu Y, Yi G, Zhang H, Sweeney T, Tang Z. Identification of circRNAs Associated with Adipogenesis Based on RNA-Seq Data in Pigs. Genes (Basel) 2022; 13:2062. [PMID: 36360299 PMCID: PMC9689998 DOI: 10.3390/genes13112062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024] Open
Abstract
Adipocytes or fat cells play a vital role in the storage and release of energy in pigs, and many circular RNAs (circRNAs) have emerged as important regulators in various tissues and cell types in pigs. However, the spatio-temporal expression pattern of circRNAs between different adipose deposition breeds remains elusive. In this study, RNA sequencing (RNA-seq) produced transcriptome profiles of Western Landrace (lean-type) and Chinese Songliao black pigs (obese-type) with different thicknesses of subcutaneous fat tissues and were used to identify circRNAs involved in the regulation of adipogenesis. Gene expression analysis revealed 883 circRNAs, among which 26 and 11 circRNAs were differentially expressed between Landrace vs. Songliao pigs and high- vs. low-thickness groups, respectively. We also analyzed the interaction between circRNAs and microRNAs (miRNAs) and constructed their interaction network in adipogenesis; gene ontology classification and pathway analysis revealed two vital circRNAs, with the majority of their target genes enriched in biological functions such as fatty acids biosynthesis, fatty acid metabolism, and Wnt/TGF-β signaling pathways. These candidate circRNAs can be taken as potential targets for further experimental studies. Our results show that circRNAs are dynamically expressed and provide a valuable basis for understanding the molecular mechanism of circRNAs in pig adipose biology.
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49
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Ferguson LB, Mayfield RD, Messing RO. RNA biomarkers for alcohol use disorder. Front Mol Neurosci 2022; 15:1032362. [PMID: 36407766 PMCID: PMC9673015 DOI: 10.3389/fnmol.2022.1032362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Alcohol use disorder (AUD) is highly prevalent and one of the leading causes of disability in the US and around the world. There are some molecular biomarkers of heavy alcohol use and liver damage which can suggest AUD, but these are lacking in sensitivity and specificity. AUD treatment involves psychosocial interventions and medications for managing alcohol withdrawal, assisting in abstinence and reduced drinking (naltrexone, acamprosate, disulfiram, and some off-label medications), and treating comorbid psychiatric conditions (e.g., depression and anxiety). It has been suggested that various patient groups within the heterogeneous AUD population would respond more favorably to specific treatment approaches. For example, there is some evidence that so-called reward-drinkers respond better to naltrexone than acamprosate. However, there are currently no objective molecular markers to separate patients into optimal treatment groups or any markers of treatment response. Objective molecular biomarkers could aid in AUD diagnosis and patient stratification, which could personalize treatment and improve outcomes through more targeted interventions. Biomarkers of treatment response could also improve AUD management and treatment development. Systems biology considers complex diseases and emergent behaviors as the outcome of interactions and crosstalk between biomolecular networks. A systems approach that uses transcriptomic (or other -omic data, e.g., methylome, proteome, metabolome) can capture genetic and environmental factors associated with AUD and potentially provide sensitive, specific, and objective biomarkers to guide patient stratification, prognosis of treatment response or relapse, and predict optimal treatments. This Review describes and highlights state-of-the-art research on employing transcriptomic data and artificial intelligence (AI) methods to serve as molecular biomarkers with the goal of improving the clinical management of AUD. Considerations about future directions are also discussed.
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Affiliation(s)
- Laura B. Ferguson
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX, United States,Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, TX, United States,Department of Neuroscience, University of Texas at Austin, Austin, TX, United States,*Correspondence: Laura B. Ferguson,
| | - R. Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX, United States,Department of Neuroscience, University of Texas at Austin, Austin, TX, United States
| | - Robert O. Messing
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX, United States,Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, TX, United States,Department of Neuroscience, University of Texas at Austin, Austin, TX, United States
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50
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Josipovic N, Ebbesen KK, Zirkel A, Danieli-Mackay A, Dieterich C, Kurian L, Hansen TB, Papantonis A. circRAB3IP modulates cell proliferation by reorganizing gene expression and mRNA processing in a paracrine manner. RNA (NEW YORK, N.Y.) 2022; 28:1481-1495. [PMID: 35973723 PMCID: PMC9745835 DOI: 10.1261/rna.079195.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/01/2022] [Indexed: 05/18/2023]
Abstract
Circular RNAs are an endogenous long-lived and abundant noncoding species. Despite their prevalence, only a few circRNAs have been dissected mechanistically to date. Here, we cataloged nascent RNA-enriched circRNAs from primary human cells and functionally assigned a role to circRAB3IP in sustaining cellular homeostasis. We combined "omics" and functional experiments to show how circRAB3IP depletion deregulates hundreds of genes, suppresses cell cycle progression, and induces senescence-associated gene expression changes. Conversely, excess circRAB3IP delivered to endothelial cells via extracellular vesicles suffices for accelerating their division. We attribute these effects to an interplay between circRAB3IP and the general splicing factor SF3B1, which can affect transcript variant expression levels of cell cycle-related genes. Together, our findings link the maintenance of cell homeostasis to the presence of a single circRNA.
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Affiliation(s)
- Natasa Josipovic
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Karoline K Ebbesen
- Department of Molecular Biology and Genetics (MBG), Aarhus University, 8000 Aarhus, Denmark
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus, Denmark
| | - Anne Zirkel
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Adi Danieli-Mackay
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Christoph Dieterich
- Bioinformatics and Systems Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Leo Kurian
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Institute of Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Thomas B Hansen
- Department of Molecular Biology and Genetics (MBG), Aarhus University, 8000 Aarhus, Denmark
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
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