1
|
Drula R, Braicu C, Neagoe IB. Current advances in circular RNA detection and investigation methods: Are we running in circles? WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1850. [PMID: 38702943 DOI: 10.1002/wrna.1850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/30/2024] [Accepted: 04/01/2024] [Indexed: 05/06/2024]
Abstract
Circular RNAs (circRNAs), characterized by their closed-loop structure, have emerged as significant transcriptomic regulators, with roles spanning from microRNA sponging to modulation of gene expression and potential peptide coding. The discovery and functional analysis of circRNAs have been propelled by advancements in both experimental and bioinformatics tools, yet the field grapples with challenges related to their detection, isoform diversity, and accurate quantification. This review navigates through the evolution of circRNA research methodologies, from early detection techniques to current state-of-the-art approaches that offer comprehensive insights into circRNA biology. We examine the limitations of existing methods, particularly the difficulty in differentiating circRNA isoforms and distinguishing circRNAs from their linear counterparts. A critical evaluation of various bioinformatics tools and novel experimental strategies is presented, emphasizing the need for integrated approaches to enhance our understanding and interpretation of circRNA functions. Our insights underscore the dynamic and rapidly advancing nature of circRNA research, highlighting the ongoing development of analytical frameworks designed to address the complexity of circRNAs and facilitate the assessment of their clinical utility. As such, this comprehensive overview aims to catalyze further advancements in circRNA study, fostering a deeper understanding of their roles in cellular processes and potential implications in disease. This article is categorized under: RNA Methods > RNA Nanotechnology RNA Methods > RNA Analyses in Cells RNA Methods > RNA Analyses In Vitro and In Silico.
Collapse
Affiliation(s)
- Rareș Drula
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana-Berindan Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| |
Collapse
|
2
|
Ren W, Yuan Y, Peng J, Mutti L, Jiang X. The function and clinical implication of circular RNAs in lung cancer. Front Oncol 2022; 12:862602. [PMID: 36338714 PMCID: PMC9629004 DOI: 10.3389/fonc.2022.862602] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 08/26/2022] [Indexed: 12/02/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Despite the recent advent of promising new targeted therapies, lung cancer diagnostic strategies still have difficulty in identifying the disease at an early stage. Therefore, the characterizations of more sensible and specific cancer biomarkers have become an important goal for clinicians. Circular RNAs are covalently close, endogenous RNAs without 5' end caps or 3'poly (A) tails and have been characterized by high stability, abundance, and conservation as well as display cell/tissue/developmental stage-specific expressions. Numerous studies have confirmed that circRNAs act as microRNA (miRNA) sponges, RNA-binding protein, and transcriptional regulators; some circRNAs even act as translation templates that participate in multiple pathophysiological processes. Growing evidence have confirmed that circRNAs are involved in the pathogenesis of lung cancers through the regulation of proliferation and invasion, cell cycle, autophagy, apoptosis, stemness, tumor microenvironment, and chemotherapy resistance. Moreover, circRNAs have emerged as potential biomarkers for lung cancer diagnosis and prognosis and targets for developing new treatments. In this review, we will summarize recent progresses in identifying the biogenesis, biological functions, potential mechanisms, and clinical applications of these molecules for lung cancer diagnosis, prognosis, and targeted therapy.
Collapse
Affiliation(s)
- Wenjun Ren
- Department of Cardiovascular Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China
- Department of Thoracic Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yixiao Yuan
- Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jun Peng
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Luciano Mutti
- The Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, United States
| | - Xiulin Jiang
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
3
|
Rajcsanyi LS, Diebels I, Pastoors L, Kanber D, Peters T, Volckmar AL, Zheng Y, Grosse M, Dieterich C, Hebebrand J, Kaiser FJ, Horsthemke B, Hinney A. Evidence for correlations between BMI-associated SNPs and circRNAs. Sci Rep 2022; 12:12643. [PMID: 35879369 PMCID: PMC9314347 DOI: 10.1038/s41598-022-16495-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/11/2022] [Indexed: 11/25/2022] Open
Abstract
Circular RNAs (circRNAs) are regulators of processes like adipogenesis. Their expression can be modulated by SNPs. We analysed links between BMI-associated SNPs and circRNAs. First, we detected an enrichment of BMI-associated SNPs on circRNA genomic loci in comparison to non-significant variants. Analysis of sex-stratified GWAS data revealed that circRNA genomic loci encompassed more genome-wide significant BMI-SNPs in females than in males. To explore whether the enrichment is restricted to BMI, we investigated nine additional GWAS studies. We showed an enrichment of trait-associated SNPs in circRNAs for four analysed phenotypes (body height, chronic kidney disease, anorexia nervosa and autism spectrum disorder). To analyse the influence of BMI-affecting SNPs on circRNA levels in vitro, we examined rs4752856 located on hsa_circ_0022025. The analysis of heterozygous individuals revealed an increased level of circRNA derived from the BMI-increasing SNP allele. We conclude that genetic variation may affect the BMI partly through circRNAs.
Collapse
Affiliation(s)
- Luisa Sophie Rajcsanyi
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany. .,Center for Translational Neuro- and Behavioural Sciences, University Hospital Essen, Essen, Germany.
| | - Inga Diebels
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lydia Pastoors
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Deniz Kanber
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Triinu Peters
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Center for Translational Neuro- and Behavioural Sciences, University Hospital Essen, Essen, Germany
| | - Anna-Lena Volckmar
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Yiran Zheng
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Center for Translational Neuro- and Behavioural Sciences, University Hospital Essen, Essen, Germany
| | - Martin Grosse
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Christoph Dieterich
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Center for Translational Neuro- and Behavioural Sciences, University Hospital Essen, Essen, Germany
| | - Frank J Kaiser
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | | | - Anke Hinney
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany. .,Center for Translational Neuro- and Behavioural Sciences, University Hospital Essen, Essen, Germany.
| |
Collapse
|
4
|
Fan C, Lei X, Tie J, Zhang Y, Wu FX, Pan Y. CircR2Disease v2.0: An Updated Web Server for Experimentally Validated circRNA-disease Associations and Its Application. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:435-445. [PMID: 34856391 PMCID: PMC9801044 DOI: 10.1016/j.gpb.2021.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 10/24/2021] [Accepted: 11/24/2021] [Indexed: 01/26/2023]
Abstract
With accumulating dysregulated circular RNAs (circRNAs) in pathological processes, the regulatory functions of circRNAs, especially circRNAs as microRNA (miRNA) sponges and their interactions with RNA-binding proteins (RBPs), have been widely validated. However, the collected information on experimentally validated circRNA-disease associations is only preliminary. Therefore, an updated CircR2Disease database providing a comprehensive resource and web tool to clarify the relationships between circRNAs and diseases in diverse species is necessary. Here, we present an updated CircR2Disease v2.0 with the increased number of circRNA-disease associations and novel characteristics. CircR2Disease v2.0 provides more than 5-fold experimentally validated circRNA-disease associations compared to its previous version. This version includes 4201 entries between 3077 circRNAs and 312 disease subtypes. Secondly, the information of circRNA-miRNA, circRNA-miRNA-target, and circRNA-RBP interactions has been manually collected for various diseases. Thirdly, the gene symbols of circRNAs and disease name IDs can be linked with various nomenclature databases. Detailed descriptions such as samples and journals have also been integrated into the updated version. Thus, CircR2Disease v2.0 can serve as a platform for users to systematically investigate the roles of dysregulated circRNAs in various diseases and further explore the posttranscriptional regulatory function in diseases. Finally, we propose a computational method named circDis based on the graph convolutional network (GCN) and gradient boosting decision tree (GBDT) to illustrate the applications of the CircR2Disease v2.0 database. CircR2Disease v2.0 is available at http://bioinfo.snnu.edu.cn/CircR2Disease_v2.0 and https://github.com/bioinforlab/CircR2Disease-v2.0.
Collapse
Affiliation(s)
- Chunyan Fan
- School of Computer Science, Shaanxi Normal University, Xi’an 710119, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi’an 710119, China,Corresponding authors.
| | - Jiaojiao Tie
- School of Computer Science, Shaanxi Normal University, Xi’an 710119, China
| | - Yuchen Zhang
- School of Computer Science, Shaanxi Normal University, Xi’an 710119, China
| | - Fang-Xiang Wu
- Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada,Corresponding authors.
| | - Yi Pan
- Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA,Corresponding authors.
| |
Collapse
|
5
|
CircRNA Expression Profiles in Canine Mammary Tumours. Vet Sci 2022; 9:vetsci9050205. [PMID: 35622733 PMCID: PMC9145538 DOI: 10.3390/vetsci9050205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 02/06/2023] Open
Abstract
Numerous studies have shown that the occurrence and development of tumours are associated with the expression of circular RNAs (circRNAs). However, the expression profile and clinical significance of circRNAs in canine mammary tumours remain unclear. In this paper, we collected tissue samples from three dogs with canine mammary tumours and analysed the expression profiles of circRNAs in these samples using high-throughput sequencing technology. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses revealed 14 biological processes associated with these genes, and 11 of these genes were selected for qRT-PCR to verify their authenticity. CircRNAs have sponge adsorption to miRNAs, so we constructed a circRNA-miRNA network map using Cytoscape software. As a result, we identified a total of 14,851 circRNAs in canine mammary tumours and its adjacent normal tissues. Of these, 106 were differentially expressed (fold change ≥ 2, p ≤ 0.05), and 64 were upregulated and 42 were downregulated. The GO analysis revealed that the biological processes involved were mainly in the regulation of the secretory pathway, the regulation of neurotransmitter secretion and the positive regulation of phagocytosis. Most of these biological pathways were associated with the cGMP-PKG (cyclic guanosine monophosphate) signalling pathway, the cAMP (cyclic adenosine monophosphate) signalling pathway and the oxytocin signalling pathway. After screening, source genes closely associated with canine mammary tumours were found to include RYR2, PDE4D, ROCK2, CREB3L2 and UBA3, and associated circRNAs included chr27:26618544-26687235-, chr26:8194880-8201833+ and chr17:7960861-7967766-. In conclusion, we reveals the expression profile of circRNAs in canine mammary tumours. In addition, some circRNAs might be used as potential biomarkers for molecular diagnosis.
Collapse
|
6
|
Aishanjiang K, Wei XD, Fu Y, Lin X, Ma Y, Le J, Han Q, Wang X, Kong X, Gu J, Wu H. Circular RNAs and Hepatocellular Carcinoma: New Epigenetic Players With Diagnostic and Prognostic Roles. Front Oncol 2021; 11:653717. [PMID: 33959506 PMCID: PMC8093866 DOI: 10.3389/fonc.2021.653717] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/22/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death worldwide. Due to the lack of potent diagnosis and prognosis biomarkers and effective therapeutic targets, the overall prognosis of survival is poor in HCC patients. Circular RNAs (circRNAs) are a class of novel endogenous non-coding RNAs with covalently closed loop structures and implicated in diverse physiological processes and pathological diseases. Recent studies have demonstrated the involvement of circRNAs in HCC diagnosis, prognosis, development, and drug resistance, suggesting that circRNAs may be a class of novel targets for improving HCC diagnosis, prognosis, and treatments. In fact, some artificial circRNAs have been engineered and showed their therapeutic potential in treating HCV infection and gastric cancer. In this review, we introduce the potential of circRNAs as biomarkers for HCC diagnosis and prognosis, as therapeutic targets for HCC treatments and discuss the challenges in circRNA research and chances of circRNA application.
Collapse
Affiliation(s)
- Kedeerya Aishanjiang
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Department of Collaborative Innovation Center for Biomedicine, Shanghai, China.,Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xin-Dong Wei
- Department of General Surgery, The 81st Hospital Affiliated to Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Yi Fu
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Department of Collaborative Innovation Center for Biomedicine, Shanghai, China
| | - Xinjie Lin
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Department of Collaborative Innovation Center for Biomedicine, Shanghai, China
| | - Yujie Ma
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Department of Collaborative Innovation Center for Biomedicine, Shanghai, China
| | - Jiamei Le
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Department of Collaborative Innovation Center for Biomedicine, Shanghai, China
| | - Qiuqin Han
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Department of Collaborative Innovation Center for Biomedicine, Shanghai, China
| | - Xuan Wang
- Department of General Surgery, The 81st Hospital Affiliated to Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Xiaoni Kong
- Institute of Clinical Immunology, Department of Liver Diseases, Central Laboratory, ShuGuang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jinyang Gu
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hailong Wu
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Department of Collaborative Innovation Center for Biomedicine, Shanghai, China.,Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China.,Collaborative Innovation Center for Biomedicine, Shanghai University of Medicine & Health Sciences, Shanghai, China
| |
Collapse
|
7
|
Carter JM, Ang DA, Sim N, Budiman A, Li Y. Approaches to Identify and Characterise the Post-Transcriptional Roles of lncRNAs in Cancer. Noncoding RNA 2021; 7:19. [PMID: 33803328 PMCID: PMC8005986 DOI: 10.3390/ncrna7010019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/28/2021] [Accepted: 03/05/2021] [Indexed: 02/06/2023] Open
Abstract
It is becoming increasingly evident that the non-coding genome and transcriptome exert great influence over their coding counterparts through complex molecular interactions. Among non-coding RNAs (ncRNA), long non-coding RNAs (lncRNAs) in particular present increased potential to participate in dysregulation of post-transcriptional processes through both RNA and protein interactions. Since such processes can play key roles in contributing to cancer progression, it is desirable to continue expanding the search for lncRNAs impacting cancer through post-transcriptional mechanisms. The sheer diversity of mechanisms requires diverse resources and methods that have been developed and refined over the past decade. We provide an overview of computational resources as well as proven low-to-high throughput techniques to enable identification and characterisation of lncRNAs in their complex interactive contexts. As more cancer research strategies evolve to explore the non-coding genome and transcriptome, we anticipate this will provide a valuable primer and perspective of how these technologies have matured and will continue to evolve to assist researchers in elucidating post-transcriptional roles of lncRNAs in cancer.
Collapse
Affiliation(s)
- Jean-Michel Carter
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551, Singapore; (D.A.A.); (N.S.); (A.B.)
| | - Daniel Aron Ang
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551, Singapore; (D.A.A.); (N.S.); (A.B.)
| | - Nicholas Sim
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551, Singapore; (D.A.A.); (N.S.); (A.B.)
| | - Andrea Budiman
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551, Singapore; (D.A.A.); (N.S.); (A.B.)
| | - Yinghui Li
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551, Singapore; (D.A.A.); (N.S.); (A.B.)
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore 138673, Singapore
| |
Collapse
|
8
|
Elcheva IA, Spiegelman VS. The Role of cis- and trans-Acting RNA Regulatory Elements in Leukemia. Cancers (Basel) 2020; 12:E3854. [PMID: 33419342 PMCID: PMC7766907 DOI: 10.3390/cancers12123854] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023] Open
Abstract
RNA molecules are a source of phenotypic diversity and an operating system that connects multiple genetic and metabolic processes in the cell. A dysregulated RNA network is a common feature of cancer. Aberrant expression of long non-coding RNA (lncRNA), micro RNA (miRNA), and circular RNA (circRNA) in tumors compared to their normal counterparts, as well as the recurrent mutations in functional regulatory cis-acting RNA motifs have emerged as biomarkers of disease development and progression, opening avenues for the design of novel therapeutic approaches. This review looks at the progress, challenges and future prospects of targeting cis-acting and trans-acting RNA elements for leukemia diagnosis and treatment.
Collapse
Affiliation(s)
- Irina A. Elcheva
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, P.O. Box 850, MC H085, 500 University Drive, Hershey, PA 17033-0850, USA
| | - Vladimir S. Spiegelman
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, P.O. Box 850, MC H085, 500 University Drive, Hershey, PA 17033-0850, USA
| |
Collapse
|