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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Wen K, Chen X, Gu J, Chen Z, Wang Z. Beyond traditional translation: ncRNA derived peptides as modulators of tumor behaviors. J Biomed Sci 2024; 31:63. [PMID: 38877495 PMCID: PMC11177406 DOI: 10.1186/s12929-024-01047-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 05/24/2024] [Indexed: 06/16/2024] Open
Abstract
Within the intricate tapestry of molecular research, noncoding RNAs (ncRNAs) were historically overshadowed by a pervasive presumption of their inability to encode proteins or peptides. However, groundbreaking revelations have challenged this notion, unveiling select ncRNAs that surprisingly encode peptides specifically those nearing a succinct 100 amino acids. At the forefront of this epiphany stand lncRNAs and circRNAs, distinctively characterized by their embedded small open reading frames (sORFs). Increasing evidence has revealed different functions and mechanisms of peptides/proteins encoded by ncRNAs in cancer, including promotion or inhibition of cancer cell proliferation, cellular metabolism (glucose metabolism and lipid metabolism), and promotion or concerted metastasis of cancer cells. The discoveries not only accentuate the depth of ncRNA functionality but also open novel avenues for oncological research and therapeutic innovations. The main difficulties in the study of these ncRNA-derived peptides hinge crucially on precise peptide detection and sORFs identification. Here, we illuminate cutting-edge methodologies, essential instrumentation, and dedicated databases tailored for unearthing sORFs and peptides. In addition, we also conclude the potential of clinical applications in cancer therapy.
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Affiliation(s)
- Kang Wen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China
| | - Xin Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China
| | - Jingyao Gu
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China
| | - Zhenyao Chen
- Department of Respiratory Endoscopy, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P.R. China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Zhaoxia Wang
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China.
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3
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Choi SW, Nam JW. Optimal design of synthetic circular RNAs. Exp Mol Med 2024:10.1038/s12276-024-01251-w. [PMID: 38871815 DOI: 10.1038/s12276-024-01251-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 06/15/2024] Open
Abstract
Circular RNAs are an unusual class of single-stranded RNAs whose ends are covalently linked via back-splicing. Due to their versatility, the need to express circular RNAs in vivo and in vitro has increased. Efforts have been made to efficiently and precisely synthesize circular RNAs. However, a review on the optimization of the processes of circular RNA design, synthesis, and delivery is lacking. Our review highlights the multifaceted aspects considered when producing optimal circular RNAs and summarizes the available options for each step of exogenous circular RNA design and synthesis, including circularization strategies. Additionally, this review describes several potential applications of circular RNAs.
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Affiliation(s)
- Seo-Won Choi
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
- Bio-BigData Center, Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, 04763, Republic of Korea.
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
- Hanyang Institute of Advanced BioConvergence, Hanyang University, Seoul, 04763, Republic of Korea.
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4
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Lee K, Ku J, Ku D, Kim Y. Inverted Alu repeats: friends or foes in the human transcriptome. Exp Mol Med 2024:10.1038/s12276-024-01177-3. [PMID: 38871814 DOI: 10.1038/s12276-024-01177-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 06/15/2024] Open
Abstract
Alu elements are highly abundant primate-specific short interspersed nuclear elements that account for ~10% of the human genome. Due to their preferential location in gene-rich regions, especially in introns and 3' UTRs, Alu elements can exert regulatory effects on the expression of both host and neighboring genes. When two Alu elements with inverse orientations are positioned in close proximity, their transcription results in the generation of distinct double-stranded RNAs (dsRNAs), known as inverted Alu repeats (IRAlus). IRAlus are key immunogenic self-dsRNAs and post-transcriptional cis-regulatory elements that play a role in circular RNA biogenesis, as well as RNA transport and stability. Recently, IRAlus dsRNAs have emerged as regulators of transcription and activators of Z-DNA-binding proteins. The formation and activity of IRAlus can be modulated through RNA editing and interactions with RNA-binding proteins, and misregulation of IRAlus has been implicated in several immune-associated disorders. In this review, we summarize the emerging functions of IRAlus dsRNAs, the regulatory mechanisms governing IRAlus activity, and their relevance in the pathogenesis of human diseases.
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Affiliation(s)
- Keonyong Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jayoung Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Doyeong Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Yoosik Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Graduate School of Engineering Biology, KAIST, Daejeon, 34141, Republic of Korea.
- KAIST Institute for BioCentury (KIB), Daejeon, 34141, Republic of Korea.
- KAIST Institute for Health Science and Technology (KIHST), Daejeon, 34141, Republic of Korea.
- BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.
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5
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Hwang HJ, Kim YK. Molecular mechanisms of circular RNA translation. Exp Mol Med 2024:10.1038/s12276-024-01220-3. [PMID: 38871818 DOI: 10.1038/s12276-024-01220-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 06/15/2024] Open
Abstract
Circular RNAs (circRNAs) are covalently closed single-stranded RNAs without a 5' cap structure and a 3' poly(A) tail typically present in linear mRNAs of eukaryotic cells. CircRNAs are predominantly generated through a back-splicing process within the nucleus. CircRNAs have long been considered non-coding RNAs seemingly devoid of protein-coding potential. However, many recent studies have challenged this idea and have provided substantial evidence that a subset of circRNAs can associate with polysomes and indeed be translated. Therefore, in this review, we primarily highlight the 5' cap-independent internal initiation of translation that occurs on circular RNAs. Several molecular features of circRNAs, including the internal ribosome entry site, N6-methyladenosine modification, and the exon junction complex deposited around the back-splicing junction after back-splicing event, play pivotal roles in their efficient internal translation. We also propose a possible relationship between the translatability of circRNAs and their stability, with a focus on nonsense-mediated mRNA decay and nonstop decay, both of which are well-characterized mRNA surveillance mechanisms. An in-depth understanding of circRNA translation will reshape and expand our current knowledge of proteomics.
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Affiliation(s)
- Hyun Jung Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yoon Ki Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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6
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Chen M, Chen Y, Wang K, Deng X, Chen J. Non‐m 6A RNA modifications in haematological malignancies. Clin Transl Med 2024; 14:e1666. [PMID: 38880983 PMCID: PMC11180698 DOI: 10.1002/ctm2.1666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 06/18/2024] Open
Abstract
Dysregulated RNA modifications, stemming from the aberrant expression and/or malfunction of RNA modification regulators operating through various pathways, play pivotal roles in driving the progression of haematological malignancies. Among RNA modifications, N6-methyladenosine (m6A) RNA modification, the most abundant internal mRNA modification, stands out as the most extensively studied modification. This prominence underscores the crucial role of the layer of epitranscriptomic regulation in controlling haematopoietic cell fate and therefore the development of haematological malignancies. Additionally, other RNA modifications (non-m6A RNA modifications) have gained increasing attention for their essential roles in haematological malignancies. Although the roles of the m6A modification machinery in haematopoietic malignancies have been well reviewed thus far, such reviews are lacking for non-m6A RNA modifications. In this review, we mainly focus on the roles and implications of non-m6A RNA modifications, including N4-acetylcytidine, pseudouridylation, 5-methylcytosine, adenosine to inosine editing, 2'-O-methylation, N1-methyladenosine and N7-methylguanosine in haematopoietic malignancies. We summarise the regulatory enzymes and cellular functions of non-m6A RNA modifications, followed by the discussions of the recent studies on the biological roles and underlying mechanisms of non-m6A RNA modifications in haematological malignancies. We also highlight the potential of therapeutically targeting dysregulated non-m6A modifiers in blood cancer.
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Affiliation(s)
- Meiling Chen
- Department of HematologyFujian Institute of HematologyFujian Provincial Key Laboratory on HematologyFujian Medical University Union HospitalFuzhouChina
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
| | - Yuanzhong Chen
- Department of HematologyFujian Institute of HematologyFujian Provincial Key Laboratory on HematologyFujian Medical University Union HospitalFuzhouChina
| | - Kitty Wang
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
| | - Xiaolan Deng
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
| | - Jianjun Chen
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
- Gehr Family Center for Leukemia ResearchCity of Hope Medical Center and Comprehensive Cancer CenterDuarteCaliforniaUSA
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7
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Shi Y, Shen F, Chen X, Sun M, Zhang P. Current understanding of circular RNAs in preeclampsia. Hypertens Res 2024; 47:1607-1619. [PMID: 38605141 DOI: 10.1038/s41440-024-01675-x] [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: 11/17/2023] [Revised: 02/28/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024]
Abstract
Preeclampsia (PE) is a multiple organ and system disease that seriously threatens the safety of the mother and infant during pregnancy, and has a profound impact on the morbidity and mortality of the mother and new babies. Presently, there are no remedies for cure of PE as to the mechanisms of PE are still unclear, and the only way to eliminate the symptoms is to deliver the placenta. Thus, new therapeutic targets for PE are urgently needed. Approximately 95% of human transcripts are thought to be non-coding RNAs, and the roles of them are to be increasingly recognized of great importance in various biological processes. Circular RNAs (circRNAs) are a class of non-coding RNAs, with no 5' caps and 3' polyadenylated tails, commonly produced by back-splicing of exons. The structure of circRNAs makes them more stable than their counterparts. Increasing evidence shows that circRNAs are involved in the pathogenesis of PE, but the biogenesis, functions, and mechanisms of circRNAs in PE are poorly understood. In the present review, we mainly summarize the biogenesis, functions, and possible mechanisms of circRNAs in the development and progression of PE, as well as opportunities and challenges in the treatment and prevention of PE.
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Affiliation(s)
- Yajun Shi
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Fangrong Shen
- Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xionghui Chen
- Department of Emergency Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China.
- Institute of Trauma Medicine, Soochow University, Suzhou, China.
- Jiangsu Provincial Medical Innovation Center of Trauma Medicine, Suzhou, China.
| | - Miao Sun
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, China.
| | - Pengjie Zhang
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, China.
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8
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Digby B, Finn S, Ó Broin P. Computational approaches and challenges in the analysis of circRNA data. BMC Genomics 2024; 25:527. [PMID: 38807085 PMCID: PMC11134749 DOI: 10.1186/s12864-024-10420-0] [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: 02/13/2024] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Circular RNAs (circRNA) are a class of non-coding RNA, forming a single-stranded covalently closed loop structure generated via back-splicing. Advancements in sequencing methods and technologies in conjunction with algorithmic developments of bioinformatics tools have enabled researchers to characterise the origin and function of circRNAs, with practical applications as a biomarker of diseases becoming increasingly relevant. Computational methods developed for circRNA analysis are predicated on detecting the chimeric back-splice junction of circRNAs whilst mitigating false-positive sequencing artefacts. In this review, we discuss in detail the computational strategies developed for circRNA identification, highlighting a selection of tool strengths, weaknesses and assumptions. In addition to circRNA identification tools, we describe methods for characterising the role of circRNAs within the competing endogenous RNA (ceRNA) network, their interactions with RNA-binding proteins, and publicly available databases for rich circRNA annotation.
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Affiliation(s)
- Barry Digby
- School of Mathematical and Statistical Sciences, University of Galway, Galway, Ireland.
| | - Stephen Finn
- Discipline of Histopathology, School of Medicine, Trinity College Dublin and Cancer Molecular Diagnostic Laboratory, Dublin, Ireland
| | - Pilib Ó Broin
- School of Mathematical and Statistical Sciences, University of Galway, Galway, Ireland
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9
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Eshraghi R, Shafie D, Raisi A, Goleij P, Mirzaei H. Circular RNAs: a small piece in the heart failure puzzle. Funct Integr Genomics 2024; 24:102. [PMID: 38760573 DOI: 10.1007/s10142-024-01386-z] [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: 01/28/2024] [Revised: 04/15/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
Cardiovascular disease, specifically heart failure (HF), remains a significant concern in the realm of healthcare, necessitating the development of new treatments and biomarkers. The RNA family consists of various subgroups, including microRNAs, PIWI-interacting RNAs (piRAN) and long non-coding RNAs, which have shown potential in advancing personalized healthcare for HF patients. Recent research suggests that circular RNAs, a lesser-known subgroup of RNAs, may offer a novel set of targets and biomarkers for HF. This review will discuss the biogenesis of circular RNAs, their unique characteristics relevant to HF, their role in heart function, and their potential use as biomarkers in the bloodstream. Furthermore, future research directions in this field will be outlined. The stability of exosomal circRNAs makes them suitable as biomarkers, pathogenic regulators, and potential treatments for cardiovascular diseases such as atherosclerosis, acute coronary syndrome, ischemia/reperfusion injury, HF, and peripheral artery disease. Herein, we summarized the role of circular RNAs and their exosomal forms in HF diseases.
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Affiliation(s)
- Reza Eshraghi
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Davood Shafie
- Heart Failure Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Arash Raisi
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Pouya Goleij
- Department of Genetics, Faculty of Biology, Sana Institute of Higher Education, Sari, Iran.
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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10
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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.
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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
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11
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Sun X, Zhao X, Xu Y, Yan Y, Han L, Wei M, He M. Potential therapeutic strategy for cancer: Multi-dimensional cross-talk between circRNAs and parental genes. Cancer Lett 2024; 588:216794. [PMID: 38453043 DOI: 10.1016/j.canlet.2024.216794] [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: 01/09/2024] [Revised: 02/27/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
In many ways, circular RNAs (circRNAs) have been demonstrated to be crucial in the onset and advancement of cancer throughout the last ten years and have become a new focus of intense research in the field of RNAs. Accumulating studies have demonstrated that circRNAs can regulate parental gene expression via a variety of biological pathways. Furthermore, research into the complex interactions between circRNAs and their parental genes will shed light on their biological roles and open up new avenues for circRNAs' potential clinical translational uses. However, to date, multi-dimensional cross-talk between circRNAs and parental genes have not been systematically elucidated. Particularly intriguing is circRNA's exploration of tumor targeting, and potential therapeutic uses based on the parental gene regulation perspective. Here, we discuss their biogenesis, take a fresh look at the molecular mechanisms through which circRNAs control the expression of their parental genes in cancer. We further highlight We further highlight the latest circRNA clinical translational applications, including prognostic diagnostic markers, cancer vaccines, gDNA, and so on. Demonstrating the potential benefits and future applications of circRNA therapy.
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Affiliation(s)
- Xiaoyu Sun
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Xinyi Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Yan Xu
- Department of Urology, The First Hospital of China Medical University, Shenyang, China.
| | - Yuanyuan Yan
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Li Han
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China; Liaoning Medical Diagnosis and Treatment Center, Liaoning Province, China.
| | - Miao He
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
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12
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Wei Z, Zhang C, Song Y, Han D, Liu J, Song X, Chao F, Wang S, Xu G, Chen G. CircUBE3A(2,3,4,5) promotes adenylate-uridylate-rich binding factor 1 nuclear translocation to suppress prostate cancer metastasis. Cancer Lett 2024; 588:216743. [PMID: 38423246 DOI: 10.1016/j.canlet.2024.216743] [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: 11/13/2023] [Revised: 02/07/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024]
Abstract
Metastatic progression is the primary cause of mortality in prostate cancer (PCa) patients. Although circular RNAs (circRNAs) have been implicated in cancer progression and metastasis, our current understanding of their role in PCa metastasis remains limited. In this study, we identified that circUBE3A(2,3,4,5), which originated from exons 2, 3, 4 and 5 of the human ubiquitin-protein ligase E3A (UBE3A) gene, was specifically downregulated in PCa tissues and correlated with the Gleason score, bone metastasis, and D'Amico risk classification. Through the in vitro and in vivo experiments, we demonstrated that overexpression of circUBE3A(2,3,4,5) inhibited PCa cell migration, invasion, metastasis, and proliferation. Mechanistically, circUBE3A(2,3,4,5) was found to bind to adenylate-uridylate-rich binding factor 1 (AUF1), promoting the translocation of AUF1 into the nucleus. This led to decreased AUF1 in the cytoplasm, resulting in methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) mRNA instability and a subsequent reduction at the protein level. The downregulation of MTHFD2 further inhibited vimentin expression, thereby suppressing PCa cell epithelial-mesenchymal transition. Additionally, two pairs of the short-inverted repeats (TSIRs) in flanking introns were identified to synergistically facilitate the generation of circUBE3A(2,3,4,5) and other circRNAs. In summary, TSIRs-induced circUBE3A(2,3,4,5) acts as a suppressor of PCa metastasis by enhancing AUF1 nuclear translocation, reducing MTHFD2, and subsequently inhibiting vimentin expression. This study characterizes circUBE3A(2,3,4,5) as a functional circRNA and proposes it as a highly promising target for preventing PCa metastasis.
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Affiliation(s)
- Ziwei Wei
- Department of Urology, Jinshan Hospital, Fudan University, 201508, Shanghai, China
| | - Cong Zhang
- Department of Urology, Jinshan Hospital, Fudan University, 201508, Shanghai, China; Department of Urology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Yufeng Song
- Department of Urology, Jinshan Hospital, Fudan University, 201508, Shanghai, China
| | - Dunsheng Han
- Department of Urology, Jinshan Hospital, Fudan University, 201508, Shanghai, China
| | - Jinke Liu
- Department of Urology, Jinshan Hospital, Fudan University, 201508, Shanghai, China
| | - Xiaoming Song
- Department of Urology, Jinshan Hospital, Fudan University, 201508, Shanghai, China
| | - Fan Chao
- Department of Urology, Zhongshan Hospital, Fudan University (Xiamen Branch), Xiamen, 361015, Fujian, China
| | - Shiyu Wang
- Research Center for Clinical Medicine, Jinshan Hospital, Fudan University, 201508, Shanghai, China.
| | - Guoxiong Xu
- Research Center for Clinical Medicine, Jinshan Hospital, Fudan University, 201508, Shanghai, China.
| | - Gang Chen
- Department of Urology, Jinshan Hospital, Fudan University, 201508, Shanghai, China.
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13
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Ma A, Yang Y, Lu L, Zhang Y, Zhang X, Zheng J, Zheng X. Emerging roles of circular RNAs in nasopharyngeal carcinoma: functions and implications. Cell Death Discov 2024; 10:192. [PMID: 38664370 PMCID: PMC11045839 DOI: 10.1038/s41420-024-01964-x] [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: 02/05/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a distinct malignancy primarily prevalent in Southern China and Southeast Asia. Circular RNAs (circRNAs), a class of non-coding RNAs, are evolutionarily conserved and exhibit remarkable stability. Their dysregulation has been observed in various cancers, including NPC. In this review, we investigate the pivotal role of circRNAs in NPC, focusing specifically on their involvement in tumor proliferation, apoptosis, metastasis, angiogenesis, stemness, metabolism, and the tumor microenvironment. We highlight the diagnostic and prognostic potential of circRNAs in NPC, emphasizing their utility as biomarkers for early detection, disease monitoring, and prediction of treatment outcomes. Additionally, we explore the therapeutic implications of circRNAs in NPC, highlighting their potential for targeted therapies.
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Affiliation(s)
- Aiyu Ma
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Yuzhong Yang
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Lu Lu
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Yan Zhang
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Xuemei Zhang
- Department of Pathology, Liuzhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
| | - Jinhua Zheng
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China.
| | - Xiang Zheng
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China.
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14
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Zhou Z, Zhang J, Zheng X, Pan Z, Zhao F, Gao Y. CIRI-Deep Enables Single-Cell and Spatial Transcriptomic Analysis of Circular RNAs with Deep Learning. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308115. [PMID: 38308181 PMCID: PMC11005702 DOI: 10.1002/advs.202308115] [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: 10/25/2023] [Revised: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Circular RNAs (circRNAs) are a crucial yet relatively unexplored class of transcripts known for their tissue- and cell-type-specific expression patterns. Despite the advances in single-cell and spatial transcriptomics, these technologies face difficulties in effectively profiling circRNAs due to inherent limitations in circRNA sequencing efficiency. To address this gap, a deep learning model, CIRI-deep, is presented for comprehensive prediction of circRNA regulation on diverse types of RNA-seq data. CIRI-deep is trained on an extensive dataset of 25 million high-confidence circRNA regulation events and achieved high performances on both test and leave-out data, ensuring its accuracy in inferring differential events from RNA-seq data. It is demonstrated that CIRI-deep and its adapted version enable various circRNA analyses, including cluster- or region-specific circRNA detection, BSJ ratio map visualization, and trans and cis feature importance evaluation. Collectively, CIRI-deep's adaptability extends to all major types of RNA-seq datasets including single-cell and spatial transcriptomic data, which will undoubtedly broaden the horizons of circRNA research.
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Affiliation(s)
- Zihan Zhou
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
| | - Jinyang Zhang
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
| | - Xin Zheng
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
| | - Zhicheng Pan
- Center for Computational Biology Flatiron InstituteNew York10010USA
| | - Fangqing Zhao
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
| | - Yuan Gao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
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15
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Suciu TS, Feștilă D, Berindan-Neagoe I, Nutu A, Armencea G, Aghiorghiesei AI, Vulcan T, Băciuț M. Circular RNA-Mediated Regulation of Oral Tissue-Derived Stem Cell Differentiation: Implications for Oral Medicine and Orthodontic Applications. Stem Cell Rev Rep 2024; 20:656-671. [PMID: 38279054 PMCID: PMC10984898 DOI: 10.1007/s12015-024-10683-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] [Accepted: 01/16/2024] [Indexed: 01/28/2024]
Abstract
Circular RNAs (circRNAs) are a novel class of endogenous non-coding RNAs (ncRNAs) which unlike linear RNAs, have a covalently closed continuous loop structure. circRNAs are found abundantly in human cells and their biology is complex. They feature unique expression to different types of cells, tissues, and developmental stages. To the present, the functional roles of circular RNAs are not fully understood. They reportedly act as microRNA (miRNA) sponges, therefore having key regulatory functions in diverse physiological and pathological processes. As for dentistry field, lines of evidence indicate that circRNAs play vital roles in the odontogenic and osteogenic differentiation of dental pulp stem cells (DPSCs) and periodontal ligament stem cells (PDLSCs). Abnormal expression of circRNAs have been found in other areas of pathology frequently reflected also in the oral environment, such as inflammation or bone and soft tissue loss. Therefore, circRNAs could be of significant importance in various fields in dentistry, especially in bone and soft tissue engineering and regeneration. Understanding the molecular mechanisms occurring during the regulation of oral biological and tissue remodeling processes could augment the discovery of novel diagnostic biomarkers and therapeutic strategies that will improve orthodontic and other oral therapeutic protocols.
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Affiliation(s)
- Tudor-Sergiu Suciu
- Department of Orthodontics and Dentofacial Orthopedics, Iuliu Hațieganu University of Medicine and Pharmacy, 400083, Cluj-Napoca, Romania
| | - Dana Feștilă
- Department of Orthodontics and Dentofacial Orthopedics, Iuliu Hațieganu University of Medicine and Pharmacy, 400083, Cluj-Napoca, Romania.
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hațieganu University of Medicine and Pharmacy, 400337, Cluj-Napoca, Romania
| | - Andreea Nutu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hațieganu University of Medicine and Pharmacy, 400337, Cluj-Napoca, Romania
| | - Gabriel Armencea
- Department of Maxillofacial Surgery and Implantology, Iuliu Hațieganu University of Medicine and Pharmacy, 400029, Cluj-Napoca, Romania
| | - Alexandra Iulia Aghiorghiesei
- Department of Prosthodontics and Dental Materials, Iuliu Hațieganu University of Medicine and Pharmacy, 400006, Cluj-Napoca, Romania
| | - Talida Vulcan
- Department of Dermatology, Iuliu Hațieganu University of Medicine and Pharmacy, 400006, Cluj-Napoca, Romania
| | - Mihaela Băciuț
- Department of Maxillofacial Surgery and Implantology, Iuliu Hațieganu University of Medicine and Pharmacy, 400029, Cluj-Napoca, Romania
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16
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Teng M, Xia ZJ, Lo N, Daud K, He HH. Assembling the RNA therapeutics toolbox. MEDICAL REVIEW (2021) 2024; 4:110-128. [PMID: 38680684 PMCID: PMC11046573 DOI: 10.1515/mr-2023-0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/29/2024] [Indexed: 05/01/2024]
Abstract
From the approval of COVID-19 mRNA vaccines to the 2023 Nobel Prize awarded for nucleoside base modifications, RNA therapeutics have entered the spotlight and are transforming drug development. While the term "RNA therapeutics" has been used in various contexts, this review focuses on treatments that utilize RNA as a component or target RNA for therapeutic effects. We summarize the latest advances in RNA-targeting tools and RNA-based technologies, including but not limited to mRNA, antisense oligos, siRNAs, small molecules and RNA editors. We focus on the mechanisms of current FDA-approved therapeutics but also provide a discussion on the upcoming workforces. The clinical utility of RNA-based therapeutics is enabled not only by the advances in RNA technologies but in conjunction with the significant improvements in chemical modifications and delivery platforms, which are also briefly discussed in the review. We summarize the latest RNA therapeutics based on their mechanisms and therapeutic effects, which include expressing proteins for vaccination and protein replacement therapies, degrading deleterious RNA, modulating transcription and translation efficiency, targeting noncoding RNAs, binding and modulating protein activity and editing RNA sequences and modifications. This review emphasizes the concept of an RNA therapeutic toolbox, pinpointing the readers to all the tools available for their desired research and clinical goals. As the field advances, the catalog of RNA therapeutic tools continues to grow, further allowing researchers to combine appropriate RNA technologies with suitable chemical modifications and delivery platforms to develop therapeutics tailored to their specific clinical challenges.
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Affiliation(s)
- Mona Teng
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ziting Judy Xia
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Nicholas Lo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Kashif Daud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Housheng Hansen He
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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17
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Zhang L, Liu H, Xiong W, He H, Fu T, Long X, Li X, Liang J, Ding H, Xu Y, Liu Y, Dai X. CircFOXO3 mediates hypoxia-induced autophagy of endometrial stromal cells in endometriosis. FASEB J 2024; 38:e23515. [PMID: 38470367 DOI: 10.1096/fj.202301654rr] [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: 08/15/2023] [Revised: 02/02/2024] [Accepted: 02/12/2024] [Indexed: 03/13/2024]
Abstract
Endometriosis is a benign gynecological disease that shares some common features of malignancy. Autophagy plays vital roles in endometriosis and influences endometrial cell metastasis, and hypoxia was identified as the initiator of this pathological process through hypoxia inducible factor 1 alpha (HIF-1α). A newly discovered circular RNA FOXO3 (circFOXO3) is critical in cell autophagy, migration, and invasion of various diseases and is reported to be related to hypoxia, although its role in endometriosis remains to be elucidated up to now. In this study, a lower circFOXO3 expression in ectopic endometrium was investigated. Furthermore, we verified that circFOXO3 could regulate autophagy by downregulating the level of p53 protein to mediate the migration and invasion of human endometrial stromal cells (T HESCs). Additionally, the effects of HIF-1α on circFOXO3 and autophagy were examined in T HESCs. Notably, overexpression of HIF-1α could induce autophagy and inhibit circFOXO3 expression, whereas overexpressing of circFOXO3 under hypoxia significantly inhibited hypoxia-induced autophagy. Mechanistically, the direct combination between HIF-1α and HIF-1α-binding site on adenosine deaminase 1 acting on RNA (ADAR1) promoter increased the level of ADAR1 protein, which bind directly with circFOXO3 pre-mRNA to block the cyclization of circFOXO3. All these results support that hypoxia-mediated ADAR1 elevation inhibited the expression of circFOXO3, and then autophagy was induced upon loss of circFOXO3 via inhibition of p53 degradation, participating in the development of endometriosis.
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Affiliation(s)
- Ling Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Shandong Key Laboratory of Reproductive Medicine, Department of Obstetrics and Gynecology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Hengwei Liu
- Department of Obstetrics and Gynecology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, China
| | - Wenqian Xiong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Haitang He
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tian Fu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xuefeng Long
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoou Li
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jiaxin Liang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hui Ding
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ying Xu
- Department of Reproductive Medicine, Wuhan No.1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yi Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xin Dai
- Shandong Key Laboratory of Reproductive Medicine, Department of Obstetrics and Gynecology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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18
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Ferreira HJ, Stevenson BJ, Pak H, Yu F, Almeida Oliveira J, Huber F, Taillandier-Coindard M, Michaux J, Ricart-Altimiras E, Kraemer AI, Kandalaft LE, Speiser DE, Nesvizhskii AI, Müller M, Bassani-Sternberg M. Immunopeptidomics-based identification of naturally presented non-canonical circRNA-derived peptides. Nat Commun 2024; 15:2357. [PMID: 38490980 PMCID: PMC10943130 DOI: 10.1038/s41467-024-46408-3] [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: 07/21/2023] [Accepted: 02/16/2024] [Indexed: 03/18/2024] Open
Abstract
Circular RNAs (circRNAs) are covalently closed non-coding RNAs lacking the 5' cap and the poly-A tail. Nevertheless, it has been demonstrated that certain circRNAs can undergo active translation. Therefore, aberrantly expressed circRNAs in human cancers could be an unexplored source of tumor-specific antigens, potentially mediating anti-tumor T cell responses. This study presents an immunopeptidomics workflow with a specific focus on generating a circRNA-specific protein fasta reference. The main goal of this workflow is to streamline the process of identifying and validating human leukocyte antigen (HLA) bound peptides potentially originating from circRNAs. We increase the analytical stringency of our workflow by retaining peptides identified independently by two mass spectrometry search engines and/or by applying a group-specific FDR for canonical-derived and circRNA-derived peptides. A subset of circRNA-derived peptides specifically encoded by the region spanning the back-splice junction (BSJ) are validated with targeted MS, and with direct Sanger sequencing of the respective source transcripts. Our workflow identifies 54 unique BSJ-spanning circRNA-derived peptides in the immunopeptidome of melanoma and lung cancer samples. Our approach enlarges the catalog of source proteins that can be explored for immunotherapy.
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Affiliation(s)
- Humberto J Ferreira
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
| | - Brian J Stevenson
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - HuiSong Pak
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jessica Almeida Oliveira
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
| | - Florian Huber
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
| | - Marie Taillandier-Coindard
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
| | - Justine Michaux
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
| | - Emma Ricart-Altimiras
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
| | - Anne I Kraemer
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
| | - Lana E Kandalaft
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Daniel E Speiser
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Markus Müller
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
- Agora Cancer Research Centre, Lausanne, Switzerland.
- Center of Experimental Therapeutics, Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
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19
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Karagianni K, Bibi A, Madé A, Acharya S, Parkkonen M, Barbalata T, Srivastava PK, de Gonzalo-Calvo D, Emanueli C, Martelli F, Devaux Y, Dafou D, Nossent AY. Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102085. [PMID: 38192612 PMCID: PMC10772297 DOI: 10.1016/j.omtn.2023.102085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
RNA editing, a common and potentially highly functional form of RNA modification, encompasses two different RNA modifications, namely adenosine to inosine (A-to-I) and cytidine to uridine (C-to-U) editing. As inosines are interpreted as guanosines by the cellular machinery, both A-to-I and C-to-U editing change the nucleotide sequence of the RNA. Editing events in coding sequences have the potential to change the amino acid sequence of proteins, whereas editing events in noncoding RNAs can, for example, affect microRNA target binding. With advancing RNA sequencing technology, more RNA editing events are being discovered, studied, and reported. However, RNA editing events are still often overlooked or discarded as sequence read quality defects. With this position paper, we aim to provide guidelines and recommendations for the detection, validation, and follow-up experiments to study RNA editing, taking examples from the fields of cardiovascular and brain disease. We discuss all steps, from sample collection, storage, and preparation, to different strategies for RNA sequencing and editing-sensitive data analysis strategies, to validation and follow-up experiments, as well as potential pitfalls and gaps in the available technologies. This paper may be used as an experimental guideline for RNA editing studies in any disease context.
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Affiliation(s)
- Korina Karagianni
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Alessia Bibi
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Alisia Madé
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, Italy
| | - Shubhra Acharya
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-alzette, Luxembourg
| | - Mikko Parkkonen
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - Teodora Barbalata
- Lipidomics Department, Institute of Cellular Biology and Pathology “Nicolae Simionescu” of the Romanian Academy, 8, B. P. Hasdeu Street, 050568 Bucharest, Romania
| | | | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | | | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, Italy
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Dimitra Dafou
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - A. Yaël Nossent
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
- Department of Nutrition, Exercise and Sports (NEXS), University of Copenhagen, Copenhagen, Denmark
| | - on behalf of EU-CardioRNA COST Action CA17129
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-alzette, Luxembourg
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
- Lipidomics Department, Institute of Cellular Biology and Pathology “Nicolae Simionescu” of the Romanian Academy, 8, B. P. Hasdeu Street, 050568 Bucharest, Romania
- National Heart & Lung Institute, Imperial College London, London, UK
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
- Department of Nutrition, Exercise and Sports (NEXS), University of Copenhagen, Copenhagen, Denmark
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20
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Ding W, Ding L, Lu Y, Sun W, Wang Y, Wang J, Gao Y, Li M. Circular RNA-circLRP6 protects cardiomyocyte from hypoxia-induced apoptosis by facilitating hnRNPM-mediated expression of FGF-9. FEBS J 2024; 291:1246-1263. [PMID: 38105623 DOI: 10.1111/febs.17038] [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: 04/18/2023] [Revised: 09/30/2023] [Accepted: 12/15/2023] [Indexed: 12/19/2023]
Abstract
Coronary atherosclerosis-induced myocardial ischemia leads to cardiomyocyte apoptosis. The regulatory mechanisms for cardiomyocyte apoptosis have not been fully understood. Circular RNAs are non-coding RNAs which play important roles in heart function maintenance and progression of heart diseases by regulating gene transcription and protein translation. Here, we reported a conserved cardiac circular RNA, which is generated from the second exon of LRP6 and named circLRP62-2 . CircLRP62-2 can protect cardiomyocyte from hypoxia-induced apoptosis. The expression of circLRP62-2 in cardiomyocytes was down-regulated under hypoxia, while forced expression of circLRP62-2 inhibited cell apoptosis. Normally, circLRP62-2 was mainly localized in the nucleus. Under hypoxia, circLRP62-2 is associated with heterogeneous nuclear ribonucleoprotein M (hnRNPM) to be translocated into the cytoplasm. It recruited hnRNPM to fibroblast growth factor 9 (FGF9) mRNA to enhance the expression of FGF9 protein, promoting hypoxia-adaption and viability of cardiomyocytes. In summary, this study uncovers a new inhibitor of apoptosis and reveals a novel anti-apoptotic pathway composed of circLRP62-2 , hnRNPM, and FGF9, which may provide therapeutic targets for coronary heart disease and ischemic myocardial injury.
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Affiliation(s)
- Wei Ding
- The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, China
| | - Lin Ding
- School of Basic Medical Sciences, Qingdao University, China
| | - Yijian Lu
- School of Basic Medical Sciences, Qingdao University, China
| | - Weihan Sun
- School of Basic Medical Sciences, Qingdao University, China
| | - Yu Wang
- School of Basic Medical Sciences, Qingdao University, China
| | - Jianxun Wang
- School of Basic Medical Sciences, Qingdao University, China
| | - Yufang Gao
- The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, China
| | - Mengyang Li
- School of Basic Medical Sciences, Qingdao University, China
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21
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Chen X, Cai D, Li H, Wei Q, Li X, Han Z, Liang J, Xie J, Ruan J, Liu J, Xiang Z, Dong W, Guo W. Exosomal U2AF2 derived from human bone marrow mesenchymal stem cells attenuates the intervertebral disc degeneration through circ_0036763/miR-583/ACAN axis. Regen Ther 2024; 25:344-354. [PMID: 38362337 PMCID: PMC10867602 DOI: 10.1016/j.reth.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/18/2024] [Accepted: 01/25/2024] [Indexed: 02/17/2024] Open
Abstract
Intervertebral disc degeneration (IDD) is one of the major leading causes of back pain affecting the patient's quality of life. However, the roles of circular RNA (circRNA) in IDD remains unclear. This study aimed to explore the function and underlying mechanism of circ_0036763 in IDD. In this study, expressions of circ_0036763, U2 small nuclear RNA auxiliary factor 2 (U2AF2), miR-583 and aggrecan (ACAN) in primary human nucleus pulposus cells (HNPCs) derived from IDD patients and healthy controls were detected by quantitative real-time reverse transcription-PCR (qRT-PCR) or Western blot (WB). The relationship between pre-circ_0036763 and U2AF2, circ_0036763 and miR-583, miR-583 and ACAN mRNA was determined by bioinformatic analysis, miRNA pull down or RNA immunoprecipitation (RIP) assay. The expressions of Collagen I and Collagen II were evaluated by WB. Co-culture of bone marrow mesenchymal stem cells (bMSCs) or bMSCs-derived exosomes and HNPCs were performed to identify the effect of U2AF2 on the mature of circ_0036763 and ACAN. Results indicated that circ_0036763, U2AF2 and ACAN were downregulated while miR-583 was upregulated in HNPCs derived from IDD patients compared with that in normal HNPCs. Besides, overexpression of circ_0036763 elevated the expressions of ACAN and Collagen II whereas reduced Collagen I expression in HNPCs. Moreover, U2AF2 promoted the mature of circ_0036763, and circ_0036763 positively regulated ACAN by directly sponging miR-583. Furthermore, exosomal U2AF2 derived from bMSCs could increase U2AF2 levels in HNPCs and subsequently regulate the expression of ACAN by circ_0036763/miR-583 axis. In summary, circ_0036763 modified by exosomal U2AF2 derived from bMSCs alleviated IDD through regulating miR-583/ACAN axis in HNPCs. Thus, this study might provide novel therapeutic targets for IDD.
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Affiliation(s)
- Xiaofeng Chen
- Department of Orthopedics, Panyu Hospital of Chinese Medicine, No.93 and 65 Qiaodong Road, Panyu District, Guangzhou 511400, China
| | - Dongling Cai
- Department of Orthopedics, Panyu Hospital of Chinese Medicine, No.93 and 65 Qiaodong Road, Panyu District, Guangzhou 511400, China
| | - Hao Li
- Department of Orthopedics, Panyu Hospital of Chinese Medicine, No.93 and 65 Qiaodong Road, Panyu District, Guangzhou 511400, China
| | - Qipeng Wei
- Department of Orthopedics, Panyu Hospital of Chinese Medicine, No.93 and 65 Qiaodong Road, Panyu District, Guangzhou 511400, China
| | - Xi Li
- Department of Dermatology, Panyu Hospital of Chinese Medicine, No.93 and 65 Qiaodong Road, Panyu District, Guangzhou 511400, China
- Guangzhou University of Chinese Medicine, No.12 Jichang Road, Baiyun Disitrct, Guangzhou 510405, China
| | - Zhuangxun Han
- Department of Orthopedics, Panyu Hospital of Chinese Medicine, No.93 and 65 Qiaodong Road, Panyu District, Guangzhou 511400, China
| | - Jinjun Liang
- Department of Orthopedics, Panyu Hospital of Chinese Medicine, No.93 and 65 Qiaodong Road, Panyu District, Guangzhou 511400, China
| | - Junxian Xie
- Department of Orthopedics, Panyu Hospital of Chinese Medicine, No.93 and 65 Qiaodong Road, Panyu District, Guangzhou 511400, China
| | - Jiajian Ruan
- Guangzhou University of Chinese Medicine, No.12 Jichang Road, Baiyun Disitrct, Guangzhou 510405, China
| | - Jincheng Liu
- Guangzhou University of Chinese Medicine, No.12 Jichang Road, Baiyun Disitrct, Guangzhou 510405, China
| | - Zhen Xiang
- Guangzhou University of Chinese Medicine, No.12 Jichang Road, Baiyun Disitrct, Guangzhou 510405, China
| | - Wenxuan Dong
- Guangzhou University of Chinese Medicine, No.12 Jichang Road, Baiyun Disitrct, Guangzhou 510405, China
| | - Weijun Guo
- Department of Orthopedics, Panyu Hospital of Chinese Medicine, No.93 and 65 Qiaodong Road, Panyu District, Guangzhou 511400, China
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22
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Son S, Jeong H, Lee G, Park JH, Yoo S. Biogenesis of circular RNAs in vitro and in vivo from the Drosophila Nk2.1 / scarecrow gene. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582126. [PMID: 38463984 PMCID: PMC10925093 DOI: 10.1101/2024.02.26.582126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
scarecrow ( scro ) encodes a fly homolog of mammalian Nkx2.1 that is vital for early fly development as well as for optic lobe development. Interestingly, scro was reported to produce a circular RNA (circRNA). In this study, we identified 12 different scro circRNAs, which are either mono- or multi-exonic forms. The most abundant forms are circE2 carrying the second exon only and bi-exonic circE3-E4. Levels of circE2 show an age-dependent increase in adult heads, supporting a general trend of high accumulation of circRNAs in aged fly brains. Aligning sequences of introns flanking exons uncovered two pairs of intronic complementary sequences (ICSs); one pair residing in introns 1 and 2 and the other in introns 2 and 4. The first pair was demonstrated to be essential for the circE2 production in cell-based assays; furthermore, deletion of the region including potential ICS components in the intron-2 reduced in vivo production of circE2 and circE3-E4 by 80%, indicating them to be essential for the biogenesis of these isoforms. Besides the ICS, the intron regions immediately abutting exons seemed to be responsible for a basal level of circRNA formation. Moreover, the replacement of scro -ICS with those derived from laccase2 was comparably effective in scro -circRNA production, buttressing the importance of the hairpin-loop structure formed by ICS for the biogenesis of circRNA. Lastly, overexpressed scro affected outcomes of both linear and circular RNAs from the endogenous scro locus, suggesting that Scro plays a direct or indirect role in regulating expression levels of either or both forms.
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23
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Saleem A, Khan MU, Zahid T, Khurram I, Ghani MU, Ullah I, Munir R, Calina D, Sharifi-Rad J. Biological role and regulation of circular RNA as an emerging biomarker and potential therapeutic target for cancer. Mol Biol Rep 2024; 51:296. [PMID: 38340202 DOI: 10.1007/s11033-024-09211-3] [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: 11/15/2023] [Accepted: 01/04/2024] [Indexed: 02/12/2024]
Abstract
Circular RNAs (circRNAs) are a unique family of endogenous RNAs devoid of 3' poly-A tails and 5' end caps. These single-stranded circRNAs, found in the cytoplasm, are synthesized via back-splicing mechanisms, merging introns, exons, or both, resulting in covalently closed circular loops. They are profusely expressed across the eukaryotic transcriptome and offer heightened stability against exonuclease RNase R compared to linear RNA counterparts. This review endeavors to provide a comprehensive overview of circRNAs' characteristics, biogenesis, and mechanisms of action. Furthermore, aimed to shed light on the potential of circRNAs as significant biomarkers in various cancer types. It has been performed an exhaustive literature review, drawing on recent studies and findings related to circRNA characteristics, synthesis, function, evaluation techniques, and their associations with oncogenesis. CircRNAs are intricately associated with tumor progression and development. Their multifaceted roles encompass gene regulation through the sponging of proteins and microRNAs, controlling transcription and splicing, interacting with RNA binding proteins (RBPs), and facilitating gene translation. Due to these varied roles, circRNAs have become a focal point in tumor pathology investigations, given their promising potential as both biomarkers and therapeutic agents. CircRNAs, due to their unique biogenesis and multifunctionality, hold immense promise in the realm of oncology. Their stability, widespread expression, and intricate involvement in gene regulation underscore their prospective utility as reliable biomarkers and therapeutic targets in cancer. As our understanding of circRNAs deepens, advanced techniques for their detection, evaluation, and manipulation will likely emerge. These advancements might catalyze the translation of circRNA-based diagnostics and therapeutics into clinical practice, potentially revolutionizing cancer care and prognosis.
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Affiliation(s)
- Ayman Saleem
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Umer Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan.
| | - Tazeen Zahid
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Iqra Khurram
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Usman Ghani
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Inam Ullah
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Rakhtasha Munir
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349, Craiova, Romania.
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24
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Surendran A, Huang C, Liu L. Circular RNAs and their roles in idiopathic pulmonary fibrosis. Respir Res 2024; 25:77. [PMID: 38321530 PMCID: PMC10848557 DOI: 10.1186/s12931-024-02716-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease with limited treatment options. Circular RNAs (circRNAs) have emerged as a novel class of non-coding RNAs with diverse functions in cellular processes. This review paper aims to explore the potential involvement of circRNAs in the pathogenesis of IPF and their diagnostic and therapeutic implications. We begin by providing an overview of the epidemiology and risk factors associated with IPF, followed by a discussion of the pathophysiology underlying this complex disease. Subsequently, we delve into the history, types, biogenesis, and functions of circRNAs and then emphasize their regulatory roles in the pathogenesis of IPF. Furthermore, we examine the current methodologies for detecting circRNAs and explore their diagnostic applications in IPF. Finally, we discuss the potential utility of circRNAs in the treatment of IPF. In conclusion, circRNAs hold great promise as novel biomarkers and therapeutic targets in the management of IPF.
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Affiliation(s)
- Akshaya Surendran
- The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Chaoqun Huang
- The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Lin Liu
- The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA.
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.
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25
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Zhou W, Li X, Li X, Liu Y, Song W, Yang Q. The role of circular RNA in preeclampsia: From pathophysiological mechanism to clinical application. Life Sci 2024; 338:122407. [PMID: 38184270 DOI: 10.1016/j.lfs.2023.122407] [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: 11/05/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/08/2024]
Abstract
Preeclampsia (PE) is a common pregnancy-induced hypertension disorder that poses a significant threat to the health of pregnant women and fetuses, and has become a leading cause of maternal, fetal, and neonatal mortality. Currently, the therapy strategy for PE is mainly prevention management and symptomatic treatment, and only delivery can completely terminate PE. Therefore, a deeper understanding of the pathogenesis of PE is needed to make treatment and prevention more effective and targeted. With the deepening of molecular etiology research, circular RNAs (circRNAs) have been found to be widely involved in various processes of PE pathogenesis. As a kind of RNA with a special "head to tail" loop structure, the characteristics of circRNAs enable them to play diverse roles in the pathophysiology of PE, and can also serve as ideal biomarkers for early prediction and monitoring progression of PE. In this review, we summarized the latest research on PE-related circRNAs, trying to elucidate the unique or shared roles of circRNAs in various pathophysiological mechanisms of PE, aiming to provide a whole picture of current research on PE-related circRNAs, and extend a new perspective for the precise screening and targeted therapy of PE.
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Affiliation(s)
- Wenjing Zhou
- Medical Research Center, The Second Hospital of Jilin University, Changchun, Jilin, China; Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Xiuying Li
- Medical Research Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China.
| | - Xin Li
- Medical College, Jilin Engineering Vocational College, Siping, Jilin, China.
| | - Yaojia Liu
- Medical Research Center, The Second Hospital of Jilin University, Changchun, Jilin, China.
| | - Wenling Song
- Department of Obstetrics, The First Hospital of Jilin University, Changchun, Jilin, China.
| | - Qiwei Yang
- Medical Research Center, The Second Hospital of Jilin University, Changchun, Jilin, China.
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26
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Roy A, Ghosh A. Epigenetic Restriction Factors (eRFs) in Virus Infection. Viruses 2024; 16:183. [PMID: 38399958 PMCID: PMC10892949 DOI: 10.3390/v16020183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The ongoing arms race between viruses and their hosts is constantly evolving. One of the ways in which cells defend themselves against invading viruses is by using restriction factors (RFs), which are cell-intrinsic antiviral mechanisms that block viral replication and transcription. Recent research has identified a specific group of RFs that belong to the cellular epigenetic machinery and are able to restrict the gene expression of certain viruses. These RFs can be referred to as epigenetic restriction factors or eRFs. In this review, eRFs have been classified into two categories. The first category includes eRFs that target viral chromatin. So far, the identified eRFs in this category include the PML-NBs, the KRAB/KAP1 complex, IFI16, and the HUSH complex. The second category includes eRFs that target viral RNA or, more specifically, the viral epitranscriptome. These epitranscriptomic eRFs have been further classified into two types: those that edit RNA bases-adenosine deaminase acting on RNA (ADAR) and pseudouridine synthases (PUS), and those that covalently modify viral RNA-the N6-methyladenosine (m6A) writers, readers, and erasers. We delve into the molecular machinery of eRFs, their role in limiting various viruses, and the mechanisms by which viruses have evolved to counteract them. We also examine the crosstalk between different eRFs, including the common effectors that connect them. Finally, we explore the potential for new discoveries in the realm of epigenetic networks that restrict viral gene expression, as well as the future research directions in this area.
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Affiliation(s)
- Arunava Roy
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
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27
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Mueller F, Witteveldt J, Macias S. Antiviral Defence Mechanisms during Early Mammalian Development. Viruses 2024; 16:173. [PMID: 38399949 PMCID: PMC10891733 DOI: 10.3390/v16020173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/11/2024] [Accepted: 01/20/2024] [Indexed: 02/25/2024] Open
Abstract
The type-I interferon (IFN) response constitutes the major innate immune pathway against viruses in mammals. Despite its critical importance for antiviral defence, this pathway is inactive during early embryonic development. There seems to be an incompatibility between the IFN response and pluripotency, the ability of embryonic cells to develop into any cell type of an adult organism. Instead, pluripotent cells employ alternative ways to defend against viruses that are typically associated with safeguard mechanisms against transposable elements. The absence of an inducible IFN response in pluripotent cells and the constitutive activation of the alternative antiviral pathways have led to the hypothesis that embryonic cells are highly resistant to viruses. However, some findings challenge this interpretation. We have performed a meta-analysis that suggests that the susceptibility of pluripotent cells to viruses is directly correlated with the presence of receptors or co-receptors for viral adhesion and entry. These results challenge the current view of pluripotent cells as intrinsically resistant to infections and raise the fundamental question of why these cells have sacrificed the major antiviral defence pathway if this renders them susceptible to viruses.
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Affiliation(s)
- Felix Mueller
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King’s Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; (F.M.); (J.W.)
- Centre for Virus Research, MRC-University of Glasgow, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Jeroen Witteveldt
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King’s Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; (F.M.); (J.W.)
| | - Sara Macias
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King’s Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; (F.M.); (J.W.)
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28
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Zhang Z, Gao Z, Fang H, Zhao Y, Xing R. Therapeutic importance and diagnostic function of circRNAs in urological cancers: from metastasis to drug resistance. Cancer Metastasis Rev 2024:10.1007/s10555-023-10152-9. [PMID: 38252399 DOI: 10.1007/s10555-023-10152-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 10/31/2023] [Indexed: 01/23/2024]
Abstract
Circular RNAs (circRNAs) are a member of non-coding RNAs with no ability in encoding proteins and their aberrant dysregulation is observed in cancers. Their closed-loop structure has increased their stability, and they are reliable biomarkers for cancer diagnosis. Urological cancers have been responsible for high mortality and morbidity worldwide, and developing new strategies in their treatment, especially based on gene therapy, is of importance since these malignant diseases do not respond to conventional therapies. In the current review, three important aims are followed. At the first step, the role of circRNAs in increasing or decreasing the progression of urological cancers is discussed, and the double-edged sword function of them is also highlighted. At the second step, the interaction of circRNAs with molecular targets responsible for urological cancer progression is discussed, and their impact on molecular processes such as apoptosis, autophagy, EMT, and MMPs is highlighted. Finally, the use of circRNAs as biomarkers in the diagnosis and prognosis of urological cancer patients is discussed to translate current findings in the clinic for better treatment of patients. Furthermore, since circRNAs can be transferred to tumor via exosomes and the interactions in tumor microenvironment provided by exosomes such as between macrophages and cancer cells is of importance in cancer progression, a separate section has been devoted to the role of exosomal circRNAs in urological tumors.
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Affiliation(s)
- Zhibin Zhang
- College of Traditional Chinese Medicine, Chengde Medical College, Chengde, 067000, Hebei, China.
| | - Zhixu Gao
- Chengde Medical College, Chengde, 067000, Hebei, China
| | - Huimin Fang
- Chengde Medical College, Chengde, 067000, Hebei, China
| | - Yutang Zhao
- Chengde Medical College, Chengde, 067000, Hebei, China
| | - Rong Xing
- Chengde Medical College, Chengde, 067000, Hebei, China
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29
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Whittle BJ, Izuogu OG, Lowes H, Deen D, Pyle A, Coxhead J, Lawson RA, Yarnall AJ, Jackson MS, Santibanez-Koref M, Hudson G. Early-stage idiopathic Parkinson's disease is associated with reduced circular RNA expression. NPJ Parkinsons Dis 2024; 10:25. [PMID: 38245550 PMCID: PMC10799891 DOI: 10.1038/s41531-024-00636-y] [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: 07/25/2023] [Accepted: 01/08/2024] [Indexed: 01/22/2024] Open
Abstract
Neurodegeneration in Parkinson's disease (PD) precedes diagnosis by years. Early neurodegeneration may be reflected in RNA levels and measurable as a biomarker. Here, we present the largest quantification of whole blood linear and circular RNAs (circRNA) in early-stage idiopathic PD, using RNA sequencing data from two cohorts (PPMI = 259 PD, 161 Controls; ICICLE-PD = 48 PD, 48 Controls). We identified a replicable increase in TMEM252 and LMNB1 gene expression in PD. We identified novel differences in the expression of circRNAs from ESYT2, BMS1P1 and CCDC9, and replicated trends of previously reported circRNAs. Overall, using circRNA as a diagnostic biomarker in PD did not show any clear improvement over linear RNA, minimising its potential clinical utility. More interestingly, we observed a general reduction in circRNA expression in both PD cohorts, accompanied by an increase in RNASEL expression. This imbalance implicates the activation of an innate antiviral immune response and suggests a previously unknown aspect of circRNA regulation in PD.
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Affiliation(s)
- Benjamin J Whittle
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Osagie G Izuogu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Hannah Lowes
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Dasha Deen
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Jon Coxhead
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Rachael A Lawson
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Alison J Yarnall
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Michael S Jackson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
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30
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Tan X, Zhang J, Dong J, Huang M, Zhou Z, Wang D. Novel Insights into the Circadian Rhythms Based on Long Noncoding and Circular RNA Profiling. Int J Mol Sci 2024; 25:1161. [PMID: 38256234 PMCID: PMC10816401 DOI: 10.3390/ijms25021161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/07/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Circadian rhythm disorders pose major risks to human health and animal production activity, and the hypothalamus is the center of circadian rhythm regulation. However, the epigenetic regulation of circadian rhythm based on farm animal models has been poorly investigated. We collected chicken hypothalamus samples at seven time points in one light/dark cycle and performed long noncoding RNA (lncRNA), circular RNA (circRNA), and mRNA sequencing to detect biomarkers associated with circadian rhythm. We enhanced the comprehensive expression profiling of ncRNAs and mRNAs in the hypothalamus and found two gene sets (circadian rhythm and retinal metabolism) associated with the light/dark cycle. Noncoding RNA networks with circadian expression patterns were identified by differential expression and circadian analysis was provided that included 38 lncRNAs, 15 circRNAs, and 200 candidate genes. Three lncRNAs (ENSGALT00000098661, ENSGALT00000100816, and MSTRG.16980.1) and one circRNA (novel_circ_010168) in the ncRNA-mRNA regulatory network were identified as key molecules influencing circadian rhythm by regulating AOX1 in retinal metabolism. These ncRNAs were predicted to be related to pernicious anemia, gonadal, eye disease and other disorders in humans. Together, the findings of this study provide insights into the epigenetic mechanisms of circadian rhythm and reveal AOX1 as a promising target of circadian rhythm regulation.
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Affiliation(s)
| | | | | | | | | | - Deqian Wang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.T.)
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31
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Mandal AK. Recent insights into crosstalk between genetic parasites and their host genome. Brief Funct Genomics 2024; 23:15-23. [PMID: 36307128 PMCID: PMC10799329 DOI: 10.1093/bfgp/elac032] [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: 08/04/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 01/21/2024] Open
Abstract
The bulk of higher order organismal genomes is comprised of transposable element (TE) copies, i.e. genetic parasites. The host-parasite relation is multi-faceted, varying across genomic region (genic versus intergenic), life-cycle stages, tissue-type and of course in health versus pathological state. The reach of functional genomics though, in investigating genotype-to-phenotype relations, has been limited when TEs are involved. The aim of this review is to highlight recent progress made in understanding how TE origin biochemical activity interacts with the central dogma stages of the host genome. Such interaction can also bring about modulation of the immune context and this could have important repercussions in disease state where immunity has a role to play. Thus, the review is to instigate ideas and action points around identifying evolutionary adaptations that the host genome and the genetic parasite have evolved and why they could be relevant.
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Affiliation(s)
- Amit K Mandal
- Corresponding author: A.K. Mandal, Nuffield Department of Surgical Sciences (NDS), University of Oxford, Old Road Campus Research building (ORCRB), Oxford OX3 7DQ, UK. Tel: +44 (0)1865 617123; Fax: +44 (0)1865 768876; E-mail:
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32
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Diallo LH, Mariette J, Laugero N, Touriol C, Morfoisse F, Prats AC, Garmy-Susini B, Lacazette E. Specific Circular RNA Signature of Endothelial Cells: Potential Implications in Vascular Pathophysiology. Int J Mol Sci 2024; 25:680. [PMID: 38203852 PMCID: PMC10779679 DOI: 10.3390/ijms25010680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/23/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Circular RNAs (circRNAs) are a recently characterized family of gene transcripts forming a covalently closed loop of single-stranded RNA. The extent of their potential for fine-tuning gene expression is still being discovered. Several studies have implicated certain circular RNAs in pathophysiological processes within vascular endothelial cells and cancer cells independently. However, to date, no comparative study of circular RNA expression in different types of endothelial cells has been performed and analysed through the lens of their central role in vascular physiology and pathology. In this work, we analysed publicly available and original RNA sequencing datasets from arterial, veinous, and lymphatic endothelial cells to identify common and distinct circRNA expression profiles. We identified 4713 distinct circRNAs in the compared endothelial cell types, 95% of which originated from exons. Interestingly, the results show that the expression profile of circular RNAs is much more specific to each cell type than linear RNAs, and therefore appears to be more suitable for distinguishing between them. As a result, we have discovered a specific circRNA signature for each given endothelial cell type. Furthermore, we identified a specific endothelial cell circRNA signature that is composed four circRNAs: circCARD6, circPLXNA2, circCASC15 and circEPHB4. These circular RNAs are produced by genes that are related to endothelial cell migration pathways and cancer progression. More detailed studies of their functions could lead to a better understanding of the mechanisms involved in physiological and pathological (lymph)angiogenesis and might open new ways to tackle tumour spread through the vascular system.
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Affiliation(s)
- Leïla Halidou Diallo
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Jérôme Mariette
- MIAT, University of Toulouse, INRAE, 31326 Castanet-Tolosan, France;
| | - Nathalie Laugero
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Christian Touriol
- UMR1037 INSERM, University of Toulouse, 2 Avenue Hubert Curien, 31100 Toulouse, France;
| | - Florent Morfoisse
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Anne-Catherine Prats
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Barbara Garmy-Susini
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Eric Lacazette
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
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Wei J, Li M, Chen S, Xue C, Zheng L, Duan Y, Deng H, Fan S, Xiong W, Zhou M. CircBRD7 attenuates tumor growth and metastasis in nasopharyngeal carcinoma via epigenetic activation of its host gene. Cancer Sci 2024; 115:139-154. [PMID: 37940358 PMCID: PMC10823269 DOI: 10.1111/cas.15998] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/01/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023] Open
Abstract
BRD7 was identified as a tumor suppressor in nasopharyngeal carcinoma (NPC). Circular RNAs (CircRNAs) are involved in the occurrence and development of NPC as oncogenes or tumor suppressors. However, the function and mechanism of the circular RNA forms derived from BRD7 in NPC are not well understood. In this study, we first identified that circBRD7 was a novel circRNA derived from BRD7 that inhibited cell proliferation, migration, invasion of NPC cells, as well as the xenograft tumor growth and metastasis in vivo. Mechanistically, circBRD7 promoted the transcriptional activation and expression of BRD7 by enhancing the enrichment of histone 3 lysine 27 acetylation (H3K27ac) in the promoter region of its host gene BRD7, and BRD7 promoted the formation of circBRD7. Therefore, circBRD7 formed a positive feedback loop with BRD7 to inhibit NPC development and progression. Moreover, restoration of BRD7 expression rescued the inhibitory effect of circBRD7 on the malignant progression of NPC. In addition, circBRD7 demonstrated low expression in NPC tissues, which was positively correlated with BRD7 expression and negatively correlated with the clinical stage of NPC patients. Taken together, circBRD7 attenuates the tumor growth and metastasis of NPC by forming a positive feedback loop with its host gene BRD7, and targeting the circBRD7/BRD7 axis is a promising strategy for the clinical diagnosis and treatment of NPC.
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Affiliation(s)
- Jianxia Wei
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaChina
- Cancer Research Institute and School of Basic Medical SciencesCentral South UniversityChangshaChina
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCentral South UniversityChangshaChina
| | - Mengna Li
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaChina
- Cancer Research Institute and School of Basic Medical SciencesCentral South UniversityChangshaChina
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCentral South UniversityChangshaChina
| | - Shipeng Chen
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaChina
- Cancer Research Institute and School of Basic Medical SciencesCentral South UniversityChangshaChina
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCentral South UniversityChangshaChina
| | - Changning Xue
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaChina
- Cancer Research Institute and School of Basic Medical SciencesCentral South UniversityChangshaChina
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCentral South UniversityChangshaChina
| | - Lemei Zheng
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaChina
- Cancer Research Institute and School of Basic Medical SciencesCentral South UniversityChangshaChina
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCentral South UniversityChangshaChina
| | - Yumei Duan
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaChina
- Cancer Research Institute and School of Basic Medical SciencesCentral South UniversityChangshaChina
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCentral South UniversityChangshaChina
| | - Hongyu Deng
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaChina
| | - Songqing Fan
- Department of Pathology, the Second Xiangya HospitalCentral South UniversityChangshaChina
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaChina
- Cancer Research Institute and School of Basic Medical SciencesCentral South UniversityChangshaChina
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCentral South UniversityChangshaChina
| | - Ming Zhou
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaChina
- Cancer Research Institute and School of Basic Medical SciencesCentral South UniversityChangshaChina
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCentral South UniversityChangshaChina
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Zeng Q, Liu CH, Ampuero J, Wu D, Jiang W, Zhou L, Li H, Bai L, Romero-Gómez M, Tang H. Circular RNAs in non-alcoholic fatty liver disease: Functions and clinical significance. RNA Biol 2024; 21:1-15. [PMID: 38113132 PMCID: PMC10761141 DOI: 10.1080/15476286.2023.2290769] [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: 07/11/2023] [Indexed: 12/21/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD), which affects approximately 25% of the global population, is an urgent health issue leading to various metabolic comorbidities. Circular RNAs (circRNAs), covalently closed RNA molecules, are characterized by ubiquity, diversity, stability, and conservatism. Indeed, they participate in various biological processes via distinct mechanisms that could modify the natural history of NAFLD. In this review, we briefly introduce the biogenesis, characteristics, and biological functions of circRNAs. Furthermore, we summarize circRNAs expression profiles in NAFLD by intersecting seven sequencing data sets and describe the cellular roles of circRNAs and their potential advantages as biomarkers of NAFLD. In addition, we emphatically discuss the exosomal non-coding RNA sorting mechanisms and possible functions in recipient cells. Finally, we extensively discuss the potential application of targeting disease-related circRNAs and competing endogenous RNA networks through gain-of-function and loss-of-function approaches in targeted therapy of NAFLD.
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Affiliation(s)
- Qingmin Zeng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Chang-Hai Liu
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Javier Ampuero
- Digestive Diseases Unit, Virgen del Rocío University Hospital. SeLiver group at Institute of Biomedicine of Seville (IBIS: HUVRocío/CSIC/US). University of Seville, Seville, Spain
| | - Dongbo Wu
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Disease, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Jiang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Disease, West China Hospital, Sichuan University, Chengdu, China
| | - Lingyun Zhou
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Disease, West China Hospital, Sichuan University, Chengdu, China
| | - Hong Li
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Disease, West China Hospital, Sichuan University, Chengdu, China
| | - Lang Bai
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Disease, West China Hospital, Sichuan University, Chengdu, China
| | - Manuel Romero-Gómez
- Digestive Diseases Unit, Virgen del Rocío University Hospital. SeLiver group at Institute of Biomedicine of Seville (IBIS: HUVRocío/CSIC/US). University of Seville, Seville, Spain
| | - Hong Tang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Disease, West China Hospital, Sichuan University, Chengdu, China
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Wu H, Chen LL. The Functional Circular RNA Screening via RfxCas13d/BSJ-gRNA System. Methods Mol Biol 2024; 2765:173-191. [PMID: 38381340 DOI: 10.1007/978-1-0716-3678-7_10] [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
Although discovered decades ago, functions of circular RNAs (circRNAs) produced from exon(s) back-splicing of pre-mRNAs have only been unveiled recently. As circRNAs share overlapping sequences with their cognate linear RNAs, except for the back-splicing junction sites, it is difficult to distinguish circRNAs from cognate mRNAs in functional studies. In this chapter, we describe a programmable method for the large-scale functional circRNA screening based on the RNA-guided, RNA-targeting CRISPR-Cas13 (RfxCas13d) system. This method can be applied both in vivo and in cell to explore highly expressed circRNAs that may influence cell growth, either under natural conditions or in response to environmental stimulation, without disturbing cognate linear mRNAs.
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Affiliation(s)
- Hao Wu
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Ling-Ling Chen
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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Baulina NM, Kiselev IS, Chumakova OS, Favorova OO. Circular RNAs: Biogenesis, Functions, and Role in Myocardial Hypertrophy. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S1-S13. [PMID: 38621741 DOI: 10.1134/s0006297924140013] [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: 05/30/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 04/17/2024]
Abstract
Circular RNAs (circRNAs) are a large class of endogenous single-stranded covalently closed RNA molecules. High-throughput RNA sequencing and bioinformatic algorithms have identified thousands of eukaryotic circRNAs characterized by high stability and tissue-specific expression pattern. Recent studies have shown that circRNAs play an important role in the regulation of physiological processes in the norm and in various diseases, including cardiovascular disorders. The review presents current concepts of circRNA biogenesis, structural features, and biological functions, describes the methods of circRNA analysis, and summarizes the results of studies on the role of circRNAs in the pathogenesis of hypertrophic cardiomyopathy, the most common inherited heart disease.
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Affiliation(s)
- Natalia M Baulina
- Chazov National Medical Research Centre of Cardiology, Ministry of Health of the Russian Federation, Moscow, 121552, Russia.
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Ivan S Kiselev
- Chazov National Medical Research Centre of Cardiology, Ministry of Health of the Russian Federation, Moscow, 121552, Russia
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Olga S Chumakova
- Chazov National Medical Research Centre of Cardiology, Ministry of Health of the Russian Federation, Moscow, 121552, Russia
| | - Olga O Favorova
- Chazov National Medical Research Centre of Cardiology, Ministry of Health of the Russian Federation, Moscow, 121552, Russia
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
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Hoque P, Romero B, Akins RE, Batish M. Exploring the Multifaceted Biologically Relevant Roles of circRNAs: From Regulation, Translation to Biomarkers. Cells 2023; 12:2813. [PMID: 38132133 PMCID: PMC10741722 DOI: 10.3390/cells12242813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
CircRNAs are a category of regulatory RNAs that have garnered significant attention in the field of regulatory RNA research due to their structural stability and tissue-specific expression. Their circular configuration, formed via back-splicing, results in a covalently closed structure that exhibits greater resistance to exonucleases compared to linear RNAs. The distinctive regulation of circRNAs is closely associated with several physiological processes, as well as the advancement of pathophysiological processes in several human diseases. Despite a good understanding of the biogenesis of circular RNA, details of their biological roles are still being explored. With the steady rise in the number of investigations being carried out regarding the involvement of circRNAs in various regulatory pathways, understanding the biological and clinical relevance of circRNA-mediated regulation has become challenging. Given the vast landscape of circRNA research in the development of the heart and vasculature, we evaluated cardiovascular system research as a model to critically review the state-of-the-art understanding of the biologically relevant functions of circRNAs. We conclude the review with a discussion of the limitations of current functional studies and provide potential solutions by which these limitations can be addressed to identify and validate the meaningful and impactful functions of circRNAs in different physiological processes and diseases.
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Affiliation(s)
- Parsa Hoque
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA;
| | - Brigette Romero
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA;
| | - Robert E Akins
- Nemours Children’s Research, Nemours Children’s Health System, Wilmington, DE 19803, USA;
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA;
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA;
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38
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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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Tang S, Cai L, Wang Z, Pan D, Wang Q, Shen Y, Zhou Y, Chen Q. Emerging roles of circular RNAs in the invasion and metastasis of head and neck cancer: Possible functions and mechanisms. CANCER INNOVATION 2023; 2:463-487. [PMID: 38125767 PMCID: PMC10730008 DOI: 10.1002/cai2.50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/27/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2023]
Abstract
Head and neck cancer (HNC) is the seventh most prevalent malignancy worldwide in 2020. Cancer metastasis is the main cause of poor prognosis in HNC patients. Recently, circular RNAs (circRNAs), initially thought to have no biological function, are attracting increasing attention, and their crucial roles in mediating HNC metastasis are being extensively investigated. Existing studies have shown that circRNAs primarily function through miRNA sponges, transcriptional regulation, interacting with RNA-binding proteins (RBPs) and as translation templates. Among these functions, the function of miRNA sponge is the most prominent. In this review, we summarized the reported circRNAs involved in HNC metastasis, aiming to elucidate the regulatory relationship between circRNAs and HNC metastasis. Furthermore, we summarized the latest advances in the epidemiological information of HNC metastasis and the tumor metastasis theories, the biogenesis, characterization and functional mechanisms of circRNAs, and their potential clinical applications. Although the research on circRNAs is still in its infancy, circRNAs are expected to serve as prognostic markers and effective therapeutic targets to inhibit HNC metastasis and significantly improve the prognosis of HNC patients.
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Affiliation(s)
- Shouyi Tang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Luyao Cai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Zhen Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Dan Pan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Qing Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Yingqiang Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Yu Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
- State Institute of Drug/Medical Device Clinical TrialWest China Hospital of StomatologyChengduChina
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
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Kong Z, Lu Y, Yang Y, Chang K, Lin Y, Huang Y, Wang C, Zhang L, Xu W, Zhao S, Li Y. m6A-Mediated Biogenesis of circDDIT4 Inhibits Prostate Cancer Progression by Sequestrating ELAVL1/HuR. Mol Cancer Res 2023; 21:1342-1355. [PMID: 37647111 PMCID: PMC10690048 DOI: 10.1158/1541-7786.mcr-22-0271] [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: 04/06/2022] [Revised: 08/11/2022] [Accepted: 08/28/2023] [Indexed: 09/01/2023]
Abstract
The pathologic significance of the circular RNA DDIT4 (circDDIT4), which is formed by backsplicing at the 3'-untranslated region (UTR) with a 5' splice acceptor site in exon 2 of linear DDIT4 mRNA, has yet to be determined. Our study found that circDDIT4 is downregulated in prostate cancer and functions as a tumor suppressor during prostate cancer progression. By competitively binding to ELAV-like RNA binding protein 1 (ELAVL1/HuR) through its 3'-UTR, circDDIT4 acts as a protein sponge to decrease the expression of prostate cancer-overexpressed anoctamin 7 (ANO7). This promotes prostate cancer cell apoptosis while inhibiting cell proliferation and metastasis. Furthermore, we discovered that N6-methyladenosine (m6A) modification facilitates the biogenesis of circDDIT4. The methyltransferase complex consisting of WTAP/METTL3/METTL14 increases the level of circDDIT4, while the RNA demethylase FTO decreases it. IMPLICATIONS These findings suggest that abnormal cotranscriptional modification of m6A promotes prostate cancer initiation and progression via a circular RNA-protein-cell signaling network.
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Affiliation(s)
- Zhe Kong
- Obstetrics and Gynecology Hospital of Fudan University, State Key Lab of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Key Laboratory of Reproduction Regulation of NPFPC (SIPPR, IRD), Fudan University, Shanghai, P.R. China
| | - Yali Lu
- Obstetrics and Gynecology Hospital of Fudan University, State Key Lab of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Key Laboratory of Reproduction Regulation of NPFPC (SIPPR, IRD), Fudan University, Shanghai, P.R. China
| | - Yue Yang
- Obstetrics and Gynecology Hospital of Fudan University, State Key Lab of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Key Laboratory of Reproduction Regulation of NPFPC (SIPPR, IRD), Fudan University, Shanghai, P.R. China
| | - Kun Chang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, P.R. China
| | - Yan Lin
- Institutes of Biomedical Sciences, Fudan University, Shanghai, P.R. China
| | - Yan Huang
- Obstetrics and Gynecology Hospital of Fudan University, State Key Lab of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Key Laboratory of Reproduction Regulation of NPFPC (SIPPR, IRD), Fudan University, Shanghai, P.R. China
| | - Chenji Wang
- Obstetrics and Gynecology Hospital of Fudan University, State Key Lab of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Key Laboratory of Reproduction Regulation of NPFPC (SIPPR, IRD), Fudan University, Shanghai, P.R. China
| | - Lu Zhang
- Obstetrics and Gynecology Hospital of Fudan University, State Key Lab of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Key Laboratory of Reproduction Regulation of NPFPC (SIPPR, IRD), Fudan University, Shanghai, P.R. China
| | - Wei Xu
- Institutes of Biomedical Sciences, Fudan University, Shanghai, P.R. China
| | - Shimin Zhao
- Obstetrics and Gynecology Hospital of Fudan University, State Key Lab of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Key Laboratory of Reproduction Regulation of NPFPC (SIPPR, IRD), Fudan University, Shanghai, P.R. China
- Institute of Metabolism and Integrative Biology (IMIB), Key Laboratory of Reproduction Regulation of NPFPC, Fudan University, Shanghai, P.R. China
| | - Yao Li
- Obstetrics and Gynecology Hospital of Fudan University, State Key Lab of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Key Laboratory of Reproduction Regulation of NPFPC (SIPPR, IRD), Fudan University, Shanghai, P.R. China
- Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai, P.R. China
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Ma XK, Zhai SN, Yang L. Approaches and challenges in genome-wide circular RNA identification and quantification. Trends Genet 2023; 39:897-907. [PMID: 37839990 DOI: 10.1016/j.tig.2023.09.006] [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: 07/18/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 10/17/2023]
Abstract
Numerous circular RNAs (circRNAs) produced from back-splicing of exon(s) have been recently revealed on a genome-wide scale across species. Although generally expressed at a low level, some relatively abundant circRNAs can play regulatory roles in various biological processes, prompting continuous profiling of circRNA in broader conditions. Over the past decade, distinct strategies have been applied in both transcriptome enrichment and bioinformatic tools for detecting and quantifying circRNAs. Understanding the scope and limitations of these strategies is crucial for the subsequent annotation and characterization of circRNAs, especially those with functional potential. Here, we provide an overview of different transcriptome enrichment, deep sequencing and computational approaches for genome-wide circRNA identification, and discuss strategies for accurate quantification and characterization of circRNA.
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Affiliation(s)
- Xu-Kai Ma
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| | - Si-Nan Zhai
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
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Zhang J, Li Y, Zhang J, Liu L, Chen Y, Yang X, Liao X, He M, Jia Z, Fan J, Bian JS, Nie X. ADAR1 regulates vascular remodeling in hypoxic pulmonary hypertension through N1-methyladenosine modification of circCDK17. Acta Pharm Sin B 2023; 13:4840-4855. [PMID: 38045055 PMCID: PMC10692360 DOI: 10.1016/j.apsb.2023.07.006] [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: 04/07/2023] [Revised: 06/13/2023] [Accepted: 07/05/2023] [Indexed: 12/05/2023] Open
Abstract
Pulmonary hypertension (PH) is an extremely malignant pulmonary vascular disease of unknown etiology. ADAR1 is an RNA editing enzyme that converts adenosine in RNA to inosine, thereby affecting RNA expression. However, the role of ADAR1 in PH development remains unclear. In the present study, we investigated the biological role and molecular mechanism of ADAR1 in PH pulmonary vascular remodeling. Overexpression of ADAR1 aggravated PH progression and promoted the proliferation of pulmonary artery smooth muscle cells (PASMCs). Conversely, inhibition of ADAR1 produced opposite effects. High-throughput whole transcriptome sequencing showed that ADAR1 was an important regulator of circRNAs in PH. CircCDK17 level was significantly lowered in the serum of PH patients. The effects of ADAR1 on cell cycle progression and proliferation were mediated by circCDK17. ADAR1 affects the stability of circCDK17 by mediating A-to-I modification at the A5 and A293 sites of circCDK17 to prevent it from m1A modification. We demonstrate for the first time that ADAR1 contributes to the PH development, at least partially, through m1A modification of circCDK17 and the subsequent PASMCs proliferation. Our study provides a novel therapeutic strategy for treatment of PH and the evidence for circCDK17 as a potential novel marker for the diagnosis of this disease.
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Affiliation(s)
- Junting Zhang
- Shenzhen Institute of Respiratory Disease, Shenzhen Key Laboratory of Respiratory Disease, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China; Post-Doctoral Scientific Research Station of Basic Medicine, Jinan University, Guangzhou 510632, China
| | - Yiying Li
- Shenzhen Institute of Respiratory Disease, Shenzhen Key Laboratory of Respiratory Disease, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China; Post-Doctoral Scientific Research Station of Basic Medicine, Jinan University, Guangzhou 510632, China
| | - Jianchao Zhang
- Shenzhen Institute of Respiratory Disease, Shenzhen Key Laboratory of Respiratory Disease, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China; Post-Doctoral Scientific Research Station of Basic Medicine, Jinan University, Guangzhou 510632, China
| | - Lu Liu
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuan Chen
- Lung Transplant Group, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi 211103, China
| | - Xusheng Yang
- Lung Transplant Group, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi 211103, China
| | - Xueyi Liao
- Shenzhen Institute of Respiratory Disease, Shenzhen Key Laboratory of Respiratory Disease, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China; Post-Doctoral Scientific Research Station of Basic Medicine, Jinan University, Guangzhou 510632, China
| | - Muhua He
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zihui Jia
- Lung Transplant Group, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi 211103, China
| | - Jun Fan
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou 510632, China
| | - Jin-Song Bian
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiaowei Nie
- Shenzhen Institute of Respiratory Disease, Shenzhen Key Laboratory of Respiratory Disease, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China; Post-Doctoral Scientific Research Station of Basic Medicine, Jinan University, Guangzhou 510632, China
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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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Wang R, Zhong J, Pan X, Su Z, Xu Y, Zhang M, Chen X, Chen N, Yu T, Zhou Q. A novel intronic circular RNA circFGFR1 int2 up-regulates FGFR1 by recruiting transcriptional activators P65/FUS and suppressing miR-4687-5p to promote prostate cancer progression. J Transl Med 2023; 21:840. [PMID: 37993879 PMCID: PMC10664560 DOI: 10.1186/s12967-023-04718-y] [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: 08/25/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023] Open
Abstract
Fibroblast growth factor receptor 1 (FGFR1) is a core component of the FGFs/FGFR pathway that activates multiple signalling pathways, including ERK1/2, PI3K/AKT, PLCγ, and NF-κB. Aberrant expression of FGFR1 due to gene amplification, chromosome rearrangement, point mutation, and epigenetic deregulations, have been reported in various cancers. FGFR1 overexpression has also been reported in prostate cancer (PCa), but the underlining mechanisms are not clear. Here we report a novel circular RNA, circFGFR1int2, derived from intron 2 of FGFR1 gene, which is overexpressed in PCa and associated with tumor progression. Importantly, we show that circFGFR1int2 facilitates FGFR1 transcription by recruiting transcription activators P65/FUS and by interacting with FGFR1 promoter. Moreover, we show that circFGFR1int2 suppresses post-transcriptional inhibitory effects of miR-4687-5p on FGFR1 mRNA. These mechanisms synergistically promote PCa cell growth, migration, and invasion. Overexpression of circFGFR1int2 is significantly correlated with higher tumor grade, Gleason score, and PSA level, and is a significant unfavorable prognosticator for CRPC-free survival (CFS) (RR = 3.277, 95% confidence interval: 1.192-9.009; P = 0.021). These findings unravelled novel mechanisms controlling FGFR1 gene expression by intronic circRNA and its potential clinicopathological utility as a diagnostic or therapeutic target.
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Affiliation(s)
- Ruyue Wang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jinjing Zhong
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiuyi Pan
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhengzheng Su
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yunyi Xu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Mengni Zhang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xueqin Chen
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ni Chen
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ting Yu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Qiao Zhou
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China.
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Sberna G, Maggi F, Amendola A. Virus-Encoded Circular RNAs: Role and Significance in Viral Infections. Int J Mol Sci 2023; 24:16547. [PMID: 38003737 PMCID: PMC10671809 DOI: 10.3390/ijms242216547] [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: 10/31/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 11/26/2023] Open
Abstract
Circular RNAs (circRNAs) have been the focus of intense scientific research to understand their biogenesis, mechanisms of action and regulatory functions. CircRNAs are single stranded, covalently closed RNA molecules lacking the 5'-terminal cap and the 3'-terminal polyadenine chain, characteristics that make them very stable and resistant. Synthesised by both cells and viruses, in the past circRNAs were considered to have no precise function. Today, increasing evidence shows that circRNAs are ubiquitous, some of them are tissue- and cell-specific, and critical in multiple regulatory processes (i.e., infections, inflammation, oncogenesis, gene expression). Moreover, circRNAs are emerging as important biomarkers of viral infection and disease progression. In this review, we provided an updated overview of current understanding of virus-encoded and cellular-encoded circRNAs and their involvement in cellular pathways during viral infection.
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Affiliation(s)
| | | | - Alessandra Amendola
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy; (G.S.)
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Li Z, Zhao F, Zhou T, Zhang J, Xu C. COL, a pipeline for identifying putatively functional back-splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566217. [PMID: 38014194 PMCID: PMC10680571 DOI: 10.1101/2023.11.08.566217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Circular RNAs (circRNAs) are a class of generally non-coding RNAs produced by back-splicing. Although the vast majority of circRNAs are likely to be products of splicing error and thereby confer no benefits to organisms, a small number of circRNAs have been found to be functional. Identifying other functional circRNAs from the sea of mostly non-functional circRNAs is an important but difficult task. Because available experimental methods for this purpose are of low throughput or versality and existing computational methods have limited reliability or applicability, new methods are needed. We hypothesize that functional back-splicing events that generate functional circRNAs (i) exhibit substantially higher back-splicing rates than expected from the total splicing amounts, (ii) have conserved splicing motifs, and (iii) show unusually high back-splicing levels. We confirm these features in back-splicing shared among human, macaque, and mouse, which should enrich functional back-splicing. Integrating the three features, we design a computational pipeline named COL for identifying putatively functional back-splicing. Using experimentally verified functional back-splicing as a benchmark, we find COL to outperform a commonly used computational method with a similar data requirement. We conclude that COL is an efficient and versatile method for rapid identification of putatively functional back-splicing and circRNAs that can be experimentally validated.
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Dhahri H, Fondufe-Mittendorf YN. Exploring the interplay between PARP1 and circRNA biogenesis and function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1823. [PMID: 37957925 PMCID: PMC11089078 DOI: 10.1002/wrna.1823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 11/15/2023]
Abstract
PARP1 (poly-ADP-ribose polymerase 1) is a multidomain protein with a flexible and self-folding structure that allows it to interact with a wide range of biomolecules, including nucleic acids and target proteins. PARP1 interacts with its target molecules either covalently via PARylation or non-covalently through its PAR moieties induced by auto-PARylation. These diverse interactions allow PARP1 to participate in complex regulatory circuits and cellular functions. Although the most studied PARP1-mediated functions are associated with DNA repair and cellular stress response, subsequent discoveries have revealed additional biological functions. Based on these findings, PARP1 is now recognized as a major modulator of gene expression. Several discoveries show that this multifunctional protein has been intimately connected to several steps of mRNA biogenesis, from transcription initiation to mRNA splicing, polyadenylation, export, and translation of mRNA to proteins. Nevertheless, our understanding of PARP1's involvement in the biogenesis of both coding and noncoding RNA, notably circular RNA (circRNA), remains restricted. In this review, we outline the possible roles of PARP1 in circRNA biogenesis. A full examination of the regulatory roles of PARP1 in nuclear processes with an emphasis on circRNA may reveal new avenues to control dysregulation implicated in the pathogenesis of several diseases such as neurodegenerative disorders and cancers. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Hejer Dhahri
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA
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Tan MH. Identification of Bona Fide RNA Editing Sites: History, Challenges, and Opportunities. Acc Chem Res 2023; 56:3033-3044. [PMID: 37827987 DOI: 10.1021/acs.accounts.3c00462] [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: 10/14/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by the adenosine deaminase acting on the RNA (ADAR) family of enzymes of which there are three members (ADAR1, ADAR2, and ADAR3), is a major gene regulatory mechanism that diversifies the transcriptome. It is widespread in many metazoans, including humans. As inosine is interpreted by cellular machineries mainly as guanosine, A-to-I editing effectively gives A-to-G nucleotide changes. Depending on its location, an editing event can generate new protein isoforms or influence other RNA processing pathways. Researchers have found that ADAR-mediated editing performs diverse functions. For example, it enables living organisms such as cephalopods to adapt rapidly to fluctuating environmental conditions such as water temperature. In development, the loss of ADAR1 is embryonically lethal partly because endogenous double-stranded RNAs (dsRNAs) are no longer marked by inosines, which signal "self", and thus cause the melanoma differentiation-associated protein 5 (MDA5) sensor to trigger a deleterious interferon response. Hence, ADAR1 plays a key role in preventing aberrant activation of the innate immune system. Furthermore, ADAR enzymes have been implicated in myriad human diseases. Intriguingly, some cancer cells are known to exploit ADAR1 activity to dodge immune responses. However, the exact identities of immunogenic RNAs in different biological contexts have remained elusive. Consequently, there is tremendous interest in identifying inosine-containing RNAs in the cell.The identification of A-to-I RNA editing sites is dependent on the sequencing of nucleic acids. Technological and algorithmic advancements over the past decades have revolutionized the way editing events are detected. At the beginning, the discovery of editing sites relies on Sanger sequencing, a first-generation technology. Both RNA, which is reverse transcribed into complementary DNA (cDNA), and genomic DNA (gDNA) from the same source are analyzed. After sequence alignment, one would require an adenosine to be present in the genome but a guanosine to be detected in the RNA sample for a position to be declared as an editing site. However, an issue with Sanger sequencing is its low throughput. Subsequently, Illumina sequencing, a second-generation technology, was invented. By permitting the simultaneous interrogation of millions of molecules, it enables many editing sites to be identified rapidly. However, a key challenge is that the Illumina platform produces short sequencing reads that can be difficult to map accurately. To tackle the challenge, we and others developed computational workflows with a series of filters to discard sites that are likely to be false positives. When Illumina sequencing data sets are properly analyzed, A-to-G variants should emerge as the most dominant mismatch type. Moreover, the quantitative nature of the data allows us to build a comprehensive atlas of editing-level measurements across different biological contexts, providing deep insights into the spatiotemporal dynamics of RNA editing. However, difficulties remain in identifying true A-to-I editing sites in short protein-coding exons or in organisms and diseases where DNA mutations and genomic polymorphisms are prevalent and mostly unknown. Nanopore sequencing, a third-generation technology, promises to address the difficulties, as it allows native RNAs to be sequenced without conversion to cDNA, preserving base modifications that can be directly detected through machine learning. We recently demonstrated that nanopore sequencing could be used to identify A-to-I editing sites in native RNA directly. Although further work is needed to enhance the detection accuracy in single molecules from fewer cells, the nanopore technology holds the potential to revolutionize epitranscriptomic studies.
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Affiliation(s)
- Meng How Tan
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637459, Singapore
- HP-NTU Digital Manufacturing Corporate Laboratory, Nanyang Technological University, Singapore 637460, Singapore
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Wang Y, Zhao J, Wu J, Liu J, Wang Y, Xu T, Zhang M, Zhuang M, Zou L, Sun W, Han P, Song X. Genome-wide perturbations of A-to-I RNA editing dysregulated circular RNAs promoting the development of cervical cancer. Comput Biol Med 2023; 166:107546. [PMID: 37826952 DOI: 10.1016/j.compbiomed.2023.107546] [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: 07/28/2023] [Revised: 09/11/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]
Abstract
Cervical cancer, the second most common female malignant tumor, seriously threatens women's health and lives. Despite the availability of the HPV vaccine, effective treatment options for cervical cancer are still lacking. New research perspectives now clarify that RNA editing dysregulation and changes in circRNA expression are jointly involved in disease pathogenesis, so molecular changes associated with circRNA and RNA editing may provide clues for the development of new therapeutic strategies for cervical cancer. In this study, we designed a series of pipelines to identify and analyze dysregulated RNA editing events in circRNAs. Our findings indicate a decrease in A-to-I RNA editing levels in cervical cancer compared to normal tissues, and editing may influence the back-splicing process of circRNAs through structural modifications of Alu elements. Moreover, our research reveals that RNA editing could modulate circRNA biogenesis by influencing RNA binding protein (RBP) binding on a transcriptome-wide scale, as well as influence the expression and coding potential of circRNAs. Importantly, we identified three RNA editing sites that could serve as potential biomarkers. In summary, our study presents a comprehensive landscape of RNA editing perturbations in circRNAs, providing new insights into the complex relationship between RNA editing and circRNA dysregulation in cervical cancer.
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Affiliation(s)
- Yulan Wang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Jian Zhao
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Jing Wu
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211166, China
| | - Jingjing Liu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Yixuan Wang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Tianyi Xu
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Meng Zhang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Minhui Zhuang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Lingxiao Zou
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Wei Sun
- Department of Gynecology and Obstetrics, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China.
| | - Ping Han
- Department of Gynecology and Obstetrics, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China.
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China.
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Xu L, Wang P, Li L, Li L, Huang Y, Zhang Y, Zheng X, Yi P, Zhang M, Xu M. circPSD3 is a promising inhibitor of uPA system to inhibit vascular invasion and metastasis in hepatocellular carcinoma. Mol Cancer 2023; 22:174. [PMID: 37884951 PMCID: PMC10601121 DOI: 10.1186/s12943-023-01882-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Vascular invasion is a major route for intrahepatic and distant metastasis in hepatocellular carcinoma (HCC) and is a strong negative prognostic factor. Circular RNAs (circRNAs) play important roles in tumorigenesis and metastasis. However, the regulatory functions and underlying mechanisms of circRNAs in the development of vascular invasion in HCC are largely unknown. METHODS High throughput sequencing was used to screen dysregulated circRNAs in portal vein tumor thrombosis (PVTT) tissues. The biological functions of candidate circRNAs in the migration, vascular invasion, and metastasis of HCC cells were examined in vitro and in vivo. To explore the underlying mechanisms, RNA sequencing, MS2-tagged RNA affinity purification, mass spectrometry, and RNA immunoprecipitation assays were performed. RESULTS circRNA sequencing followed by quantitative real-time PCR (qRT-PCR) revealed that circRNA pleckstrin and Sect. 7 domain containing 3 (circPSD3) was significantly downregulated in PVTT tissues. Decreased circPSD3 expression in HCC tissues was associated with unfavourable characteristics and predicted poor prognosis in HCC. TAR DNA-binding protein 43 (TDP43) inhibited the biogenesis of circPSD3 by interacting with the downstream intron of pre-PSD3. circPSD3 inhibited the intrahepatic vascular invasion and metastasis of HCC cells in vitro and in vivo. Serpin family B member 2 (SERPINB2), an endogenous bona fide inhibitor of the urokinase-type plasminogen activator (uPA) system, is the downstream target of circPSD3. Mechanistically, circPSD3 interacts with histone deacetylase 1 (HDAC1) to sequester it in the cytoplasm, attenuating the inhibitory effect of HDAC1 on the transcription of SERPINB2. In vitro and in vivo studies demonstrated that circPSD3 is a promising inhibitor of the uPA system. CONCLUSIONS circPSD3 is an essential regulator of vascular invasion and metastasis in HCC and may serve as a prognostic biomarker and therapeutic target.
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Affiliation(s)
- Liangliang Xu
- Division of Liver Surgery, Department of General Surgery, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu, Sichuan Province, 610041, China
| | - Peng Wang
- Division of Liver Surgery, Department of General Surgery, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu, Sichuan Province, 610041, China
| | - Li Li
- Institute of Clinical Pathology, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Lian Li
- Division of Liver Surgery, Department of General Surgery, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu, Sichuan Province, 610041, China
| | - Yang Huang
- Division of Liver Surgery, Department of General Surgery, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu, Sichuan Province, 610041, China
| | - Yanfang Zhang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, China
| | - Xiaobo Zheng
- Department of Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, China
| | - Pengsheng Yi
- Department of Hepato-biliary-pancrease, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan Province, 637000, China
| | - Ming Zhang
- Division of Liver Surgery, Department of General Surgery, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu, Sichuan Province, 610041, China.
| | - Mingqing Xu
- Division of Liver Surgery, Department of General Surgery, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu, Sichuan Province, 610041, China.
- Department of Hepatopancreatobiliary Surgery, Meishan City People's Hospital, Meishan Hospital of West China Hospital, Sichuan University, Meishan, 620000, China.
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