1
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Wang H, Wang EZR, Feng B, Chakrabarti S. CircRNA_012164/MicroRNA-9-5p axis mediates cardiac fibrosis in diabetic cardiomyopathy. PLoS One 2024; 19:e0302772. [PMID: 39042659 PMCID: PMC11265710 DOI: 10.1371/journal.pone.0302772] [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: 04/11/2024] [Accepted: 06/11/2024] [Indexed: 07/25/2024] Open
Abstract
Noncoding RNAs play a part in many chronic diseases and interact with each other to regulate gene expression. MicroRNA-9-5p (miR9) has been thought to be a potential inhibitor of diabetic cardiomyopathy. Here we examined the role of miR9 in regulating cardiac fibrosis in the context of diabetic cardiomyopathy. We further expanded our studies through investigation of a regulatory circularRNA, circRNA_012164, on the action of miR9. We showed at both the in vivo and in vitro level that glucose induced downregulation of miR9 and upregulation of circRNA_012164 resulted in the subsequent upregulation of downstream fibrotic genes. Further, knockdown of circRNA_012164 shows protective effects in cardiac endothelial cells and reverses increased transcription of genes associated with fibrosis and fibroblast proliferation through a regulatory axis with miR9. This study presents a novel regulatory axis involving noncoding RNA that is evidently important in the development of cardiac fibrosis in diabetic cardiomyopathy.
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Affiliation(s)
- Honglin Wang
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - Eric Zi Rui Wang
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - Biao Feng
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - Subrata Chakrabarti
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
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2
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Choi SW, Nam JW. Optimal design of synthetic circular RNAs. Exp Mol Med 2024; 56:1281-1292. [PMID: 38871815 PMCID: PMC11263348 DOI: 10.1038/s12276-024-01251-w] [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: 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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3
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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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4
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Jauregui-Lozano J, McGovern SE, Bakhle KM, Hagins AC, Weake VM. Establishing the contribution of active histone methylation marks to the aging transcriptional landscape of Drosophila photoreceptors. Sci Rep 2023; 13:5105. [PMID: 36991154 PMCID: PMC10060402 DOI: 10.1038/s41598-023-32273-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
Studies in multiple organisms have shown that aging is accompanied by several molecular phenotypes that include dysregulation of chromatin. Since chromatin regulates DNA-based processes such as transcription, alterations in chromatin modifications could impact the transcriptome and function of aging cells. In flies, as in mammals, the aging eye undergoes changes in gene expression that correlate with declining visual function and increased risk of retinal degeneration. However, the causes of these transcriptome changes are poorly understood. Here, we profiled chromatin marks associated with active transcription in the aging Drosophila eye to understand how chromatin modulates transcriptional outputs. We found that both H3K4me3 and H3K36me3 globally decrease across all actively expressed genes with age. However, we found no correlation with changes in differential gene expression. Downregulation of the H3K36me3 methyltransferase Set2 in young photoreceptors revealed significant changes in splicing events that overlapped significantly with those observed in aging photoreceptors. These overlapping splicing events impacted multiple genes involved in phototransduction and neuronal function. Since proper splicing is essential for visual behavior, and because aging Drosophila undergo a decrease in visual function, our data suggest that H3K36me3 could play a role in maintaining visual function in the aging eye through regulating alternative splicing.
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Affiliation(s)
- Juan Jauregui-Lozano
- Department of Biochemistry, Purdue University, 175 S. University Street, West Lafayette, IN, 47907, USA
- University of California San Diego, San Diego, CA, 92093, USA
| | - Sarah E McGovern
- Department of Biochemistry, Purdue University, 175 S. University Street, West Lafayette, IN, 47907, USA
| | - Kimaya M Bakhle
- Department of Biochemistry, Purdue University, 175 S. University Street, West Lafayette, IN, 47907, USA
| | - Arrianna C Hagins
- Department of Biochemistry, Purdue University, 175 S. University Street, West Lafayette, IN, 47907, USA
| | - Vikki M Weake
- Department of Biochemistry, Purdue University, 175 S. University Street, West Lafayette, IN, 47907, USA.
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA.
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5
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Fatema K, Larson Z, Barrott J. Navigating the genomic instability mine field of osteosarcoma to better understand implications of non-coding RNAs. BIOCELL 2022; 46:2177-2193. [PMID: 35755302 PMCID: PMC9224338 DOI: 10.32604/biocell.2022.020141] [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] [Indexed: 11/19/2022]
Abstract
Osteosarcoma is one of the most genomically complex cancers and as result, it has been difficult to assign genomic aberrations that contribute to disease progression and patient outcome consistently across samples. One potential source for correlating osteosarcoma and genomic biomarkers is within the non-coding regions of RNA that are differentially expressed. However, it is unsurprising that a cancer classification that is fraught with genomic instability is likely to have numerous studies correlating non-coding RNA expression and function have been published on the subject. This review undertakes the formidable task of evaluating the published literature of noncoding RNAs in osteosarcoma. This is not the first review on this topic and will certainly not be the last. The review is organized with an introduction into osteosarcoma and the epigenetic control of gene expression before reviewing the molecular function and expression of long non-coding RNAs, circular RNAs, and short non-coding RNAs such as microRNAs, piwi RNAs, and short-interfering RNAs. The review concludes with a review of the literature and how the biology of non-coding RNAs can be used therapeutically to treat cancers, especially osteosarcoma. We conclude that non-coding RNA expression and function in osteosarcoma is equally complex to understanding the expression differences and function of coding RNA and proteins; however, with the added lens of both coding and non-coding genomic sequence, researchers can begin to identify the patterns that consistently associate with aggressive osteosarcoma.
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Affiliation(s)
- Kaniz Fatema
- Biomedical and Pharmaceutical Science, Idaho State University, Pocatello, 83209, USA
| | - Zachary Larson
- Biomedical and Pharmaceutical Science, Idaho State University, Pocatello, 83209, USA
| | - Jared Barrott
- Biomedical and Pharmaceutical Science, Idaho State University, Pocatello, 83209, USA
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6
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De Palma FDE, Salvatore F, Pol JG, Kroemer G, Maiuri MC. Circular RNAs as Potential Biomarkers in Breast Cancer. Biomedicines 2022; 10:725. [PMID: 35327527 PMCID: PMC8945016 DOI: 10.3390/biomedicines10030725] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 02/06/2023] Open
Abstract
Due to the high heterogeneity and initially asymptomatic nature of breast cancer (BC), the management of this disease depends on imaging together with immunohistochemical and molecular evaluations. These tests allow early detection of BC and patient stratification as they guide clinicians in prognostication and treatment decision-making. Circular RNAs (circRNAs) represent a class of newly identified long non-coding RNAs. These molecules have been described as key regulators of breast carcinogenesis and progression. Moreover, circRNAs play a role in drug resistance and are associated with clinicopathological features in BC. Accumulating evidence reveals a clinical interest in deregulated circRNAs as diagnostic, prognostic and predictive biomarkers. Furthermore, due to their covalently closed structure, circRNAs are highly stable and easily detectable in body fluids, making them ideal candidates for use as non-invasive biomarkers. Herein, we provide an overview of the biogenesis and pleiotropic functions of circRNAs, and report on their clinical relevance in BC.
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Affiliation(s)
- Fatima Domenica Elisa De Palma
- Equipe 11 Labellisée Par La Ligue Nationale Contre Le Cancer, Centre de Recherche Des Cordeliers, Inserm U1138, Université de Paris Cité, Sorbonne Université, 75006 Paris, France; (J.G.P.); (G.K.)
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94800 Villejuif, France
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy;
- CEINGE-Biotecnologie Avanzate, 80145 Naples, Italy
| | - Francesco Salvatore
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy;
- CEINGE-Biotecnologie Avanzate, 80145 Naples, Italy
- Inter-University Center for multifactorial and multi genetic chronic human diseases, “Federico II”-Naples, Tor Vergata-Roma II, and Chieti-Pescara Universities, 80131 Naples, Italy
| | - Jonathan G. Pol
- Equipe 11 Labellisée Par La Ligue Nationale Contre Le Cancer, Centre de Recherche Des Cordeliers, Inserm U1138, Université de Paris Cité, Sorbonne Université, 75006 Paris, France; (J.G.P.); (G.K.)
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94800 Villejuif, France
| | - Guido Kroemer
- Equipe 11 Labellisée Par La Ligue Nationale Contre Le Cancer, Centre de Recherche Des Cordeliers, Inserm U1138, Université de Paris Cité, Sorbonne Université, 75006 Paris, France; (J.G.P.); (G.K.)
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94800 Villejuif, France
- Institut Universitaire de France, 75005 Paris, France
- Department of Biology, Institut du Cancer Paris CARPEM, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France
| | - Maria Chiara Maiuri
- Equipe 11 Labellisée Par La Ligue Nationale Contre Le Cancer, Centre de Recherche Des Cordeliers, Inserm U1138, Université de Paris Cité, Sorbonne Université, 75006 Paris, France; (J.G.P.); (G.K.)
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94800 Villejuif, France
- Department of Pharmacy, University of Naples “Federico II”, 80131 Naples, Italy
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7
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Huang HB, Luo HT, Wei NN, Liu ML, He F, Yang W, Dong J, Yang XF, Li FR. Integrative analysis reveals a lineage-specific circular RNA landscape for adipo-osteogenesis of human mesenchymal stem cells. Stem Cell Res Ther 2022; 13:106. [PMID: 35279206 PMCID: PMC8917624 DOI: 10.1186/s13287-022-02792-5] [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: 09/22/2021] [Accepted: 02/28/2022] [Indexed: 12/03/2022] Open
Abstract
Background The balance between osteogenesis and adipogenesis of mesenchymal stem cells (MSCs) is critical to skeletal development and diseases. As a research hotspot, circular RNAs (circRNAs) have expanded our understanding of a hidden layer of the transcriptome. Yet, their roles during adipo-osteogenesis remain poorly described. Methods The identity of human MSCs derived from bone marrow and adipose were first determined by flow cytometry, cellular staining, and quantitative polymerase chain reaction (qPCR). Multi-strategic RNA-sequencing was performed using Poly A, RiboMinus and RiboMinus/RNase R methods. Integrative analysis was performed to identify lineage-specific expressed circRNAs. The structural and expressional characteristics were identified by Sanger sequencing and qPCR, respectively. The regulatory effects of adipogenesis-specific circ-CRLF1 were confirmed using siRNA transcfection and qPCR. Results We generated a whole transcriptome map during adipo-osteogenesis based on 10 Poly A, 20 RiboMinus and 20 RiboMinus/ RNase R datasets. A total of 31,326 circRNAs were identified and quantified from ~ 3.4 billion paired-end reads. Furthermore, the integrative analysis revealed that 1166 circRNA genes exhibited strong lineage-specific expression patterns. Their host genes were enriched in distinct biological functions, such as cell adhesion, cytokine signaling, and cell division. We randomly selected and validated the back-spliced junction sites and expression patterns of 12 lineage-specific circRNAs. Functional analysis indicated that circ-CRLF1 negatively regulated adipogenesis. Conclusions Our integrative analysis reveals an accurate and generally applicable lineage-specific circRNA landscape for adipo-osteogenesis of MSCs and provides a potential therapeutic target, circ-CRLF1, for the treatment of skeleton-related disease. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02792-5.
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Affiliation(s)
- Hai-Bo Huang
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), ShenzhenGuangdong, 518020, China.,Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, 518020, Guangdong, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, 510632, Guangdong, China.,Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Hai-Tao Luo
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), ShenzhenGuangdong, 518020, China.,Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, 518020, Guangdong, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Na-Na Wei
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), ShenzhenGuangdong, 518020, China.,Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, 518020, Guangdong, China.,Kunpeng Institute of Modern Agriculture at Foshan, Foshan, 528200, China
| | - Miao-Ling Liu
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), ShenzhenGuangdong, 518020, China.,Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, 518020, Guangdong, China
| | - Fei He
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), ShenzhenGuangdong, 518020, China.,Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, 518020, Guangdong, China
| | - Wei Yang
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), ShenzhenGuangdong, 518020, China.,Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, 518020, Guangdong, China
| | - Jun Dong
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, 510632, Guangdong, China. .,Department of Pathophysiology, Key Laboratory of the State Administration of Traditional Chinese Medicine, Jinan University, Guangzhou, 510632, Guangdong, China.
| | - Xiao-Fei Yang
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), ShenzhenGuangdong, 518020, China. .,Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, 518020, Guangdong, China.
| | - Fu-Rong Li
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), ShenzhenGuangdong, 518020, China. .,Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, 518020, Guangdong, China. .,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, 510632, Guangdong, China.
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8
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Babin L, Andraos E, Fuchs S, Pyronnet S, Brunet E, Meggetto F. From circRNAs to fusion circRNAs in hematological malignancies. JCI Insight 2021; 6:151513. [PMID: 34747369 PMCID: PMC8663548 DOI: 10.1172/jci.insight.151513] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Circular RNAs (circRNAs) represent a type of endogenous noncoding RNA generated by back-splicing events. Unlike the majority of RNAs, circRNAs are covalently closed, without a 5' end or a 3' poly(A) tail. A few circRNAs can be associated with polysomes, suggesting a protein-coding potential. CircRNAs are not degraded by RNA exonucleases or ribonuclease R and are enriched in exosomes. Recent developments in experimental methods coupled with evolving bioinformatic approaches have accelerated functional investigation of circRNAs, which exhibit a stable structure, a long half-life, and tumor specificity and can be extracted from body fluids and used as potential biological markers for tumors. Moreover, circRNAs may regulate the occurrence and development of cancers and contribute to drug resistance through a variety of molecular mechanisms. Despite the identification of a growing number of circRNAs, their effects in hematological cancers remain largely unknown. Recent studies indicate that circRNAs could also originate from fusion genes (fusion circRNAs, f-circRNAs) next to chromosomal translocations, which are considered the primary cause of various cancers, notably hematological malignancies. This Review will focus on circRNAs and f-circRNAs in hematological cancers.
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Affiliation(s)
- Loelia Babin
- CRCT INSERM, UMR1037, Toulouse, France.,Toulouse III University-Paul Sabatier, UMR1037 INSERM, UMR5071 CNRS, Toulouse, France.,The Toulouse Cancer Laboratory of Excellence (TOUCAN), Toulouse, France
| | - Elissa Andraos
- CRCT INSERM, UMR1037, Toulouse, France.,Toulouse III University-Paul Sabatier, UMR1037 INSERM, UMR5071 CNRS, Toulouse, France.,The Toulouse Cancer Laboratory of Excellence (TOUCAN), Toulouse, France
| | - Steffen Fuchs
- CRCT INSERM, UMR1037, Toulouse, France.,Toulouse III University-Paul Sabatier, UMR1037 INSERM, UMR5071 CNRS, Toulouse, France.,The Toulouse Cancer Laboratory of Excellence (TOUCAN), Toulouse, France.,Department of Pediatric Oncology, Charité University Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stéphane Pyronnet
- CRCT INSERM, UMR1037, Toulouse, France.,Toulouse III University-Paul Sabatier, UMR1037 INSERM, UMR5071 CNRS, Toulouse, France.,The Toulouse Cancer Laboratory of Excellence (TOUCAN), Toulouse, France
| | - Erika Brunet
- Imagine Institute INSERM Joint Research Unit 1163, Laboratory of Genome Dynamics in the Immune System, Paris, France.,Paris Descartes-Sorbonne University, Imagine Institute, Paris, France
| | - Fabienne Meggetto
- CRCT INSERM, UMR1037, Toulouse, France.,Toulouse III University-Paul Sabatier, UMR1037 INSERM, UMR5071 CNRS, Toulouse, France.,The Toulouse Cancer Laboratory of Excellence (TOUCAN), Toulouse, France
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9
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Razpotnik R, Nassib P, Kunej T, Rozman D, Režen T. Identification of Novel RNA Binding Proteins Influencing Circular RNA Expression in Hepatocellular Carcinoma. Int J Mol Sci 2021; 22:7477. [PMID: 34299096 PMCID: PMC8307310 DOI: 10.3390/ijms22147477] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 12/24/2022] Open
Abstract
Circular RNAs (circRNAs) are increasingly recognized as having a role in cancer development. Their expression is modified in numerous cancers, including hepatocellular carcinoma (HCC); however, little is known about the mechanisms of their regulation. The aim of this study was to identify regulators of circRNAome expression in HCC. Using publicly available datasets, we identified RNA binding proteins (RBPs) with enriched motifs around the splice sites of differentially expressed circRNAs in HCC. We confirmed the binding of some of the candidate RBPs using ChIP-seq and eCLIP datasets in the ENCODE database. Several of the identified RBPs were found to be differentially expressed in HCC and/or correlated with the overall survival of HCC patients. According to our bioinformatics analyses and published evidence, we propose that NONO, PCPB2, PCPB1, ESRP2, and HNRNPK are candidate regulators of circRNA expression in HCC. We confirmed that the knocking down the epithelial splicing regulatory protein 2 (ESRP2), known to be involved in the maintenance of the adult liver phenotype, significantly changed the expression of candidate circRNAs in a model HCC cell line. By understanding the systemic changes in transcriptome splicing, we can identify new proteins involved in the molecular pathways leading to HCC development and progression.
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Affiliation(s)
- Rok Razpotnik
- Centre for Functional Genomics and Bio-Chips, Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, 1000 Ljubljana, Slovenia; (R.R.); (P.N.); (D.R.)
| | - Petra Nassib
- Centre for Functional Genomics and Bio-Chips, Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, 1000 Ljubljana, Slovenia; (R.R.); (P.N.); (D.R.)
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, 1230 Domžale, Slovenia;
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chips, Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, 1000 Ljubljana, Slovenia; (R.R.); (P.N.); (D.R.)
| | - Tadeja Režen
- Centre for Functional Genomics and Bio-Chips, Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, 1000 Ljubljana, Slovenia; (R.R.); (P.N.); (D.R.)
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