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Goleij P, Babamohamadi M, Rezaee A, Sanaye PM, Tabari MAK, Sadreddini S, Arefnezhad R, Motedayyen H. Types of RNA therapeutics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:41-63. [PMID: 38360005 DOI: 10.1016/bs.pmbts.2023.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
RNA therapy is one of the new treatments using small RNA molecules to target and regulate gene expression. It involves the application of synthetic or modified RNA molecules to inhibit the expression of disease-causing genes specifically. In other words, it silences genes and suppresses the transcription process. The main theory behind RNA therapy is that RNA molecules can prevent the translation into proteins by binding to specific messenger RNA (mRNA) molecules. By targeting disease-related mRNA molecules, RNA therapy can effectively silence or reduce the development of harmful proteins. There are different types of RNA molecules used in therapy, including small interfering RNAs (siRNAs), microRNAs (miRNAs), aptamer, ribozyme, and antisense oligonucleotides (ASOs). These molecules are designed to complement specific mRNA sequences, allowing them to bind and degrade the targeted mRNA or prevent its translation into protein. Nanotechnology is also highlighted to increase the efficacy of RNA-based drugs. In this chapter, while examining various methods of RNA therapy, we discuss the advantages and challenges of each.
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Affiliation(s)
- Pouya Goleij
- Department of Genetics, Sana Institute of Higher Education, Sari, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mehregan Babamohamadi
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran; Department of Biology, School of Natural Sciences, University of Tabriz, Tabriz, Iran; Stem Cell and Regenerative Medicine Innovation Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Aryan Rezaee
- Student Research Committee, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Mohammad Amin Khazeei Tabari
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran; USERN Office, Mazandaran University of Medical Sciences, Sari, Iran
| | - Sarvin Sadreddini
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Arefnezhad
- Coenzyme R Research Institute, Tehran, Iran; Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Hossein Motedayyen
- Autoimmune Diseases Research Center, Kashan University of Medical Sciences, Kashan, Iran.
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Shi X, Won M, Tang C, Ding Q, Sharma A, Wang F, Kim JS. RNA splicing based on reporter genes system: Detection, imaging and applications. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Rational Design of an Activatable Reporter for Quantitative Imaging of RNA Aberrant Splicing In Vivo. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:904-911. [PMID: 32405512 PMCID: PMC7210378 DOI: 10.1016/j.omtm.2020.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 04/13/2020] [Indexed: 02/02/2023]
Abstract
Pre-mRNA splicing, the process of removing introns from pre-mRNA and the arrangement of exons to produce mature transcripts, is a crucial step in the expression of most eukaryote genes. However, the splicing kinetics remain poorly characterized in living cells, mainly because current methods cannot provide the dynamic information of splicing events. Here, we developed a genetically encoded bioluminescence reporter for real-time imaging of the pre-mRNA splicing process in living subjects. We showed that the bioluminescence reporter is able to visualize the pre-mRNA aberrant splicing process in living cells in a dose- and time-dependent manner. Moreover, this reporter could provide quantitative and longitudinal information of splicing activity in response to exogenous splicing inhibitors in living animals. Our data suggest that this activatable reporter could serve as a promising tool for the high-throughput screening of splicing modulators, which would facilitate the drug development for human diseases caused by the abnormal splicing of mRNA.
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Seo MJ, Park JH, Lee KC, Lee YJ, Lee TS, Choi TH, Lee SW, Kim KI, Kang JH. Small Animal PET Imaging of hTERT RNA-Targeted HSV1-tk Gene Expression with Trans-Splicing Ribozyme. Cancer Biother Radiopharm 2019; 35:26-32. [PMID: 31746630 DOI: 10.1089/cbr.2019.2839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background: Trans-splicing ribozymes (TSR) are useful anticancer agents targeting cancer-specific transcripts and replacing the RNA to induce anticancer gene expression specifically and selectively in cancer cells. Similar to other gene therapy methods, it is also important to evaluate the transgene expression for target specificity and ribozyme activity. Materials and Methods: In this study, the authors performed in vivo small animal positron emission tomography (PET) imaging and biodistribution assay to evaluate human telomerase reverse transcriptase (hTERT) RNA-targeting-specific TSR, which directs the expression of herpes simplex virus type 1 thymidine kinase (HSV1-tk) gene selectively in hTERT-positive tumors through targeted RNA replacement of the hTERT transcript. Results: The hTERT RNA-targeted HSV1-tk expression with TSR was monitored by PET imaging with 124I labeled 2'-fluoro-2'-deoxy-1-β-D-arabinofuranosyl-5-iodouracil, which is one of the thymidine derivatives acting as substrates for HSV1-tk, in hTERT-positive tumor-bearing mice. Conclusions: Imaging of hTERT RNA-targeted HSV1-tk expression by TSR could be used in the development of advanced gene therapy using tumor-specific TSR.
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Affiliation(s)
- Min-Jung Seo
- Division of Applied RI, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Ju Hui Park
- Division of Applied RI, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Kyo Chul Lee
- Division of Applied RI, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Yong Jin Lee
- Division of Applied RI, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Tae Sup Lee
- Division of Applied RI, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Tae Hyun Choi
- Division of Applied RI, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Seong-Wook Lee
- Department of Integrated Life Sciences, Research Institute of Advanced Omics, Dankook University, Yongin, Korea
| | - Kwang Il Kim
- Division of Applied RI, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Joo Hyun Kang
- Division of Applied RI, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
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Lee CH, Han SR, Lee SW. Group I Intron-Based Therapeutics Through Trans-Splicing Reaction. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 159:79-100. [PMID: 30340790 DOI: 10.1016/bs.pmbts.2018.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In 1982, the Cech group discovered that an intron structure in an rRNA precursor of Tetrahymena thermophila is sufficient to complete splicing without assistance from proteins. This was the first moment that scientists recognized RNAs can have catalytic activities derived from their own unique three-dimensional structures and thus play more various roles in biological processes than thought before. Several additional catalytic RNAs, called ribozymes, were subsequently identified in nature followed by intense studies to reveal their mechanisms of action and to engineer them for use in fields such as molecular cell biology, therapeutics, imaging, etc. Naturally occurring RNA-targeting ribozymes can be broadly classified into two categories by their abilities: Self-cleavage and self-splicing. Since ribozymes use base-pairing to recognize cleavage sites, identification of the catalytic center of naturally occurring ribozymes enables to engineer from "self" to "trans" acting ones which has accelerated to design and use ribozyme as valuable tools in gene therapy fields. Especially, group I intron-based trans-splicing ribozyme has unique property to use as a gene therapeutic agent. It can destroy and simultaneously repair (and/or reprogram) target RNAs to yield the desired therapeutic RNAs, maintaining endogenous spatial and temporal gene regulation of target RNAs. There have been progressive improvements in trans-splicing ribozymes and successful applications of these elements in gene therapy and molecular imaging approaches for various pathogenic conditions. In this chapter, current status of trans-splicing ribozyme therapeutics, focusing on Tetrahymena group I intron-based ribozymes, and their future prospects will be discussed.
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Affiliation(s)
- Chang Ho Lee
- Department of Integrated Life Sciences, Dankook University, Yongin, Republic of Korea
| | | | - Seong-Wook Lee
- Department of Integrated Life Sciences, Dankook University, Yongin, Republic of Korea; Rznomics Inc., Gwangju, Republic of Korea.
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Lee CH, Han SR, Lee SW. Therapeutic applications of group I intron-based trans-splicing ribozymes. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1466. [PMID: 29383855 DOI: 10.1002/wrna.1466] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 12/10/2017] [Accepted: 12/14/2017] [Indexed: 12/21/2022]
Abstract
Since the breakthrough discovery of catalytic RNAs (ribozymes) in the early 1980s, valuable ribozyme-based gene therapies have been developed for incurable diseases ranging from genetic disorders to viral infections and cancers. Ribozymes can be engineered and used to downregulate or repair pathogenic genes via RNA cleavage mediated by trans-cleaving ribozymes or repair and reprograming mediated by trans-splicing ribozymes, respectively. Uniquely, trans-splicing ribozymes can edit target RNAs via simultaneous destruction and repair (and/or reprograming) to yield the desired therapeutic RNAs, thus selectively inducing therapeutic gene activity in cells expressing the target RNAs. In contrast to traditional gene therapy approaches, such as simple addition of therapeutic transgenes or inhibition of disease-causing genes, the selective repair and/or reprograming abilities of trans-splicing ribozymes in target RNA-expressing cells facilitates the maintenance of endogenous spatial and temporal gene regulation and reduction of disease-associated transcript expression. In molecular imaging technologies, trans-splicing ribozymes can be used to reprogram specific RNAs in living cells and organisms by the 3'-tagging of reporter RNAs. The past two decades have seen progressive improvements in trans-splicing ribozymes and the successful application of these elements in gene therapy and molecular imaging approaches for various pathogenic conditions, such as genetic, infectious, and malignant disease. This review provides an overview of the current status of trans-splicing ribozyme therapeutics, focusing on Tetrahymena group I intron-based ribozymes, and their future prospects. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Chang Ho Lee
- Department of Integrated Life Sciences, Dankook University, Yongin, Republic of Korea
| | - Seung Ryul Han
- Department of Integrated Life Sciences, Dankook University, Yongin, Republic of Korea
| | - Seong-Wook Lee
- Department of Integrated Life Sciences, Dankook University, Yongin, Republic of Korea
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Kim YH, Moon JY, Kim EO, Lee SJ, Kang SH, Kim SK, Heo K, Lee Y, Kim H, Kim KT, Kim D, Song MS, Lee SW, Lee Y, Koh SS, Kim IH. Efficient targeting and tumor retardation effect of pancreatic adenocarcinoma up-regulated factor (PAUF)-specific RNA replacement in pancreatic cancer mouse model. Cancer Lett 2013; 344:223-31. [PMID: 24189457 DOI: 10.1016/j.canlet.2013.10.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 10/19/2013] [Accepted: 10/27/2013] [Indexed: 12/15/2022]
Abstract
The soluble protein pancreatic adenocarcinoma up-regulated factor (PAUF) plays an important role in pancreatic tumor progression and has begun to attract attention as a therapeutic target for pancreatic cancer. We herein present PAUF RNA-targeting gene therapy strategies with both targeting and therapeutic function using trans-splicing ribozyme (TSR) in pancreatic cancer. We developed adenoviral PAUF-targeting TSR (Rz) containing a PAUF-specific internal guide sequence (IGS) determined by library screening. This Rz harbors suicide gene, herpes simplex virus thymidine kinase (HSV-tk) or firefly luciferase (Luc) as a transgene for 3' exon replacement of PAUF RNAs. Ad-Rz-TK, Rz harboring the HSV-tk, showed significant inhibition of tumor growth in vivo as well as PAUF-dependent cell death in vitro via a successful trans-splicing reaction. Selective induction of Rz-controlled transgene in PAUF-expressing pancreatic cancer was confirmed through noninvasive in vivo imaging; a luminescence signal from Rz harboring Luc (Ad-Rz-Luc) was detectable only in pancreatic tumor sites, not in normal mice. In addition, a [(125)I] FIAU signal reflecting thymidine kinase expression through SPECT and ex vivo biodistribution was co-localized with the tumor sites when we treated with Ad-Rz-TK in orthotopic xenograft model. Taken together, these results imply that PAUF-targeting TSR can contribute to successful targeted gene therapy for pancreatic cancer.
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Affiliation(s)
- Yun-Hee Kim
- Research Institute & Hospital, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-769, Republic of Korea.
| | - Ju Young Moon
- Research Institute & Hospital, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-769, Republic of Korea
| | - Eun-Ok Kim
- Research Institute & Hospital, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-769, Republic of Korea
| | - Sang-Jin Lee
- Research Institute & Hospital, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-769, Republic of Korea
| | - Se Hun Kang
- Research Institute & Hospital, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-769, Republic of Korea
| | - Seok Ki Kim
- Research Institute & Hospital, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-769, Republic of Korea
| | - Kyun Heo
- Research Institute & Hospital, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-769, Republic of Korea
| | - Yusun Lee
- Research Institute & Hospital, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-769, Republic of Korea
| | - Hana Kim
- Research Institute & Hospital, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-769, Republic of Korea
| | - Kyung-Tae Kim
- Research Institute & Hospital, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-769, Republic of Korea
| | - Daehong Kim
- Research Institute & Hospital, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-769, Republic of Korea
| | - Min Sun Song
- Department of Molecular Biology, Institute of Nanosensor and Biotechnology, Dankook University, Suji-Gu, Yongin, Republic of Korea
| | - Seoung-Wook Lee
- Department of Molecular Biology, Institute of Nanosensor and Biotechnology, Dankook University, Suji-Gu, Yongin, Republic of Korea
| | - Yangsoon Lee
- Therapeutic Antibody Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Sang Seok Koh
- Therapeutic Antibody Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - In-Hoo Kim
- Research Institute & Hospital, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-769, Republic of Korea.
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Andou T, Endoh T, Mie M, Kobatake E. Direct detection of RNAs in living cells using peptide-inserted Renilla luciferase. Analyst 2011; 136:2446-9. [PMID: 21541389 DOI: 10.1039/c1an15130d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In this study, non-engineered RNAs were detected in living cells using bioluminescence. Two types of probe were utilized: a peptide inserted RLuc (PI-RLuc) probe and a split-RNA probe. Incorporation of the PI-RLuc and split-RNA probes enabled the direct detection of RNA introduced into living cells.
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Affiliation(s)
- Takashi Andou
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Japan
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Fiskaa T, Birgisdottir AB. RNA reprogramming and repair based on trans-splicing group I ribozymes. N Biotechnol 2010; 27:194-203. [PMID: 20219714 DOI: 10.1016/j.nbt.2010.02.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
While many traditional gene therapy strategies attempt to deliver new copies of wild-type genes back to cells harboring the defective genes, RNA-directed strategies offer a range of novel therapeutic applications. Revision or reprogramming of mRNA is a form of gene therapy that modifies mRNA without directly changing the transcriptional regulation or the genomic gene sequence. Group I ribozymes can be engineered to act in trans by recognizing a separate RNA molecule in a sequence-specific manner, and to covalently link a new RNA sequence to this separate RNA molecule. Group I ribozymes have been shown to repair defective transcripts that cause human genetic or malignant diseases, as well as to replace transcript sequences by foreign RNA resulting in new cellular functions. This review provides an overview of current strategies using trans-splicing group I ribozymes in RNA repair and reprogramming.
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Affiliation(s)
- Tonje Fiskaa
- RNA and Transcriptomics Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway.
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So MK, Gowrishankar G, Hasegawa S, Chung JK, Rao J. Imaging Target mRNA and siRNA-Mediated Gene Silencing In Vivo with Ribozyme-Based Reporters. Chembiochem 2008; 9:2682-91. [DOI: 10.1002/cbic.200800370] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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