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Gnanamony M, Demirkhanyan L, Ge L, Sojitra P, Bapana S, Norton JA, Gondi CS. Circular dumbbell miR-34a-3p and -5p suppresses pancreatic tumor cell-induced angiogenesis and activates macrophages. Oncol Lett 2021; 21:75. [PMID: 33365086 PMCID: PMC7716711 DOI: 10.3892/ol.2020.12336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 10/02/2020] [Indexed: 12/18/2022] Open
Abstract
Angiogenesis is a tightly regulated biological process by which new blood vessels are formed from pre-existing blood vessels. This process is also critical in diseases such as cancer. Therefore, angiogenesis has been explored as a drug target for cancer therapy. The future of effective anti-angiogenic therapy lies in the intelligent combination of multiple targeting agents with novel modes of delivery to maximize therapeutic effects. Therefore, a novel approach is proposed that utilizes dumbbell RNA (dbRNA) to target pathological angiogenesis by simultaneously targeting multiple molecules and processes that contribute to angiogenesis. In the present study, a plasmid expressing miR-34a-3p and -5p dbRNA (db34a) was constructed using the permuted intron-exon method. A simple protocol to purify dbRNA from bacterial culture with high purity was also developed by modification of the RNASwift method. To test the efficacy of db34a, pancreatic cancer cell lines PANC-1 and MIA PaCa-2 were used. Functional validation of the effect of db34a on angiogenesis was performed on human umbilical vein endothelial cells using a tube formation assay, in which cells transfected with db34a exhibited a significant reduction in tube formation compared with cells transfected with scrambled dbRNA. These results were further validated in vivo using a zebrafish angiogenesis model. In conclusion, the present study demonstrates an approach for blocking angiogenesis using db34a. The data also show that this approach may be used to targeting multiple molecules and pathways.
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Affiliation(s)
- Manu Gnanamony
- Department of Pediatrics, University of Illinois College of Medicine Peoria, Peoria, IL 61605, USA
| | - Lusine Demirkhanyan
- Department of Internal Medicine, University of Illinois College of Medicine Peoria, Peoria, IL 61605, USA
| | - Liang Ge
- University of Pittsburgh Medical Center, Presbyterian University Hospital, Pittsburgh, PA 15213, USA
| | - Paresh Sojitra
- Sanford Center for Digestive Health, Sioux Falls, SD 57105, USA
| | - Sneha Bapana
- Department of Internal Medicine, University of Illinois College of Medicine Peoria, Peoria, IL 61605, USA
| | - Joseph A. Norton
- Department of Internal Medicine, University of Illinois College of Medicine Peoria, Peoria, IL 61605, USA
| | - Christopher S. Gondi
- Department of Internal Medicine, University of Illinois College of Medicine Peoria, Peoria, IL 61605, USA
- Department of Surgery, University of Illinois College of Medicine Peoria, Peoria, IL 61605, USA
- Department of Pathology, University of Illinois College of Medicine Peoria, Peoria, IL 61605, USA
- Correspondence to: Dr Christopher S. Gondi, Department of Internal Medicine, University of Illinois College of Medicine Peoria, 1 Illini Drive, Peoria, IL 61605, USA, E-mail:
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Kikuchi Y, Umekage S. Extracellular nucleic acids of the marine bacterium Rhodovulum sulfidophilum and recombinant RNA production technology using bacteria. FEMS Microbiol Lett 2019; 365:4705897. [PMID: 29228187 DOI: 10.1093/femsle/fnx268] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/05/2017] [Indexed: 12/21/2022] Open
Abstract
Extracellular nucleic acids of high molecular weight are detected ubiquitously in seawater. Recent studies have indicated that these nucleic acids are, at least in part, derived from active production by some bacteria. The marine bacterium Rhodovulum sulfidophilum is one of those bacteria. Rhodovulumsulfidophilum is a non-sulfur phototrophic marine bacterium that is known to form structured communities of cells called flocs, and to produce extracellular nucleic acids in culture media. Recently, it has been revealed that this bacterium produces gene transfer agent-like particles and that this particle production may be related to the extracellular nucleic acid production mechanism. This review provides a summary of recent physiological and genetic studies of these phenomena and also introduces a new method for extracellular production of artificial and biologically functional RNAs using this bacterium. In addition, artificial RNA production using Escherichia coli, which is related to this topic, will also be described.
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Affiliation(s)
- Yo Kikuchi
- Department of Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - So Umekage
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
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Balke D, Hieronymus R, Müller S. Challenges and Perspectives in Nucleic Acid Enzyme Engineering. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 170:21-35. [DOI: 10.1007/10_2017_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Zhao ZJ, Shen J. Circular RNA participates in the carcinogenesis and the malignant behavior of cancer. RNA Biol 2017; 14:514-521. [PMID: 26649774 PMCID: PMC5449088 DOI: 10.1080/15476286.2015.1122162] [Citation(s) in RCA: 330] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 11/02/2015] [Accepted: 11/16/2015] [Indexed: 01/01/2023] Open
Abstract
Circular RNAs (circRNAs) are long, non-coding RNAs that result from the non-canonical splicing of linear pre-mRNAs. However, the characteristics and the critical role of circRNA in co-/post-transcriptional regulation were not well recognized until the "microRNA sponge" function of circRNA is discovered. Recent studies have mainly been devoted to the function of the circular RNA sponge for miR-7 (ciRS-7) and sex-determining region Y (SRY) by targeting microRNA-7 (miR-7) and microRNA-138 (miR-138), respectively. In this review, we illustrate the specific role of circRNAs in a wide variety of cancers and in regulating the biological behavior of cancers via miR-7 or miR-138 regulation. Furthermore, circRNA, together with its gene silencing ability, also shows its potential in RNA interference (RNAi) therapy by binding to target RNAs, which provides a novel perspective in cancer treatment. Thus, this review concerns the biogenesis, biological function, oncogenesis, progression and possible therapies for cancer involving circRNAs.
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Affiliation(s)
- Zhen-Jun Zhao
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Jun Shen
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
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Abstract
Over the past 2 decades, different types of circular RNAs have been discovered in all kingdoms of life, and apparently, those circular species are more abundant than previously thought. Apart from circRNAs in viroids and viruses, circular transcripts have been discovered in rodents more than 20 y ago and recently have been reported to be abundant in many organisms including humans. Their exact function remains still unknown, although one may expect extensive functional studies to follow the currently dominant research into identification and discovery of circRNA by sophisticated sequencing techniques and bioinformatics. Functional studies require models and as such methods for preparation of circRNA in vitro. Here, we will review current protocols for RNA circularization and discuss future prospects in the field.
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Affiliation(s)
- Sabine Müller
- a Universität Greifswald, Institut für Biochemie , Greifswald , Germany
| | - Bettina Appel
- a Universität Greifswald, Institut für Biochemie , Greifswald , Germany
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Petkovic S, Müller S. RNA circularization strategies in vivo and in vitro. Nucleic Acids Res 2015; 43:2454-65. [PMID: 25662225 PMCID: PMC4344496 DOI: 10.1093/nar/gkv045] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 01/07/2015] [Accepted: 01/12/2015] [Indexed: 12/30/2022] Open
Abstract
In the plenitude of naturally occurring RNAs, circular RNAs (circRNAs) and their biological role were underestimated for years. However, circRNAs are ubiquitous in all domains of life, including eukaryotes, archaea, bacteria and viruses, where they can fulfill diverse biological functions. Some of those functions, as for example playing a role in the life cycle of viral and viroid genomes or in the maturation of tRNA genes, have been elucidated; other putative functions still remain elusive. Due to the resistance to exonucleases, circRNAs are promising tools for in vivo application as aptamers, trans-cleaving ribozymes or siRNAs. How are circRNAs generated in vivo and what approaches do exist to produce ring-shaped RNAs in vitro? In this review we illustrate the occurrence and mechanisms of RNA circularization in vivo, survey methods for the generation of circRNA in vitro and provide appropriate protocols.
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Affiliation(s)
- Sonja Petkovic
- Institut für Biochemie, Ernst Moritz Arndt Universität Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Sabine Müller
- Institut für Biochemie, Ernst Moritz Arndt Universität Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
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RETRACTED: Construction of circular miRNA sponges targeting miR-21 or miR-221 and demonstration of their excellent anticancer effects on malignant melanoma cells. Int J Biochem Cell Biol 2013; 45:2643-50. [DOI: 10.1016/j.biocel.2013.09.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 08/31/2013] [Accepted: 09/02/2013] [Indexed: 11/19/2022]
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Ponchon L, Catala M, Seijo B, El Khouri M, Dardel F, Nonin-Lecomte S, Tisné C. Co-expression of RNA-protein complexes in Escherichia coli and applications to RNA biology. Nucleic Acids Res 2013; 41:e150. [PMID: 23804766 PMCID: PMC3753655 DOI: 10.1093/nar/gkt576] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
RNA has emerged as a major player in many cellular processes. Understanding these processes at the molecular level requires homogeneous RNA samples for structural, biochemical and pharmacological studies. We previously devised a generic approach that allows efficient in vivo expression of recombinant RNA in Escherichia coli. In this work, we have extended this method to RNA/protein co-expression. We have engineered several plasmids that allow overexpression of RNA–protein complexes in E. coli. We have investigated the potential of these tools in many applications, including the production of nuclease-sensitive RNAs encapsulated in viral protein pseudo-particles, the co-production of non-coding RNAs with chaperone proteins, the incorporation of a post-transcriptional RNA modification by co-production with the appropriate modifying enzyme and finally the production and purification of an RNA–His-tagged protein complex by nickel affinity chromatography. We show that this last application easily provides pure material for crystallographic studies. The new tools we report will pave the way to large-scale structural and molecular investigations of RNA function and interactions with proteins.
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Affiliation(s)
- Luc Ponchon
- CNRS, UMR 8015, Laboratoire de Cristallographie et RMN biologiques, 4 avenue de l'Observatoire, 75006 Paris, France and Université Paris Descartes, Sorbonne Paris Cité, UMR 8015, Laboratoire de Cristallographie et RMN biologiques, 4 avenue de l'Observatoire, 75006 Paris, France
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