1
|
Zhang L, Lou W, Wang J. Advances in nucleic acid therapeutics: structures, delivery systems, and future perspectives in cancer treatment. Clin Exp Med 2024; 24:200. [PMID: 39196428 PMCID: PMC11358240 DOI: 10.1007/s10238-024-01463-4] [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: 06/19/2024] [Accepted: 08/08/2024] [Indexed: 08/29/2024]
Abstract
Cancer has emerged as a significant threat to human health. Nucleic acid therapeutics regulate the gene expression process by introducing exogenous nucleic acid fragments, offering new possibilities for tumor remission and even cure. Their mechanism of action and high specificity demonstrate great potential in cancer treatment. However, nucleic acid drugs face challenges such as low stability and limited ability to cross physiological barriers in vivo. To address these issues, various nucleic acid delivery vectors have been developed to enhance the stability and facilitate precise targeted delivery of nucleic acid drugs within the body. In this review article, we primarily introduce the structures and principles of nucleic acid drugs commonly used in cancer therapy, as well as their cellular uptake and intracellular transportation processes. We focus on the various vectors commonly employed in nucleic acid drug delivery, highlighting their research progress and applications in recent years. Furthermore, we propose potential trends and prospects of nucleic acid drugs and their carriers in the future.
Collapse
Affiliation(s)
- Leqi Zhang
- Department of Surgery, The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, 322000, China
| | - Wenting Lou
- Department of Surgery, The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, 322000, China
| | - Jianwei Wang
- Department of Surgery, The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, 322000, China.
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, 2nd Affiliated Hospital, Zhejiang University School of Medicine, Jiefang Road 88th, Hangzhou, 310009, China.
| |
Collapse
|
2
|
Romano R, Bucci C. Antisense therapy: a potential breakthrough in the treatment of neurodegenerative diseases. Neural Regen Res 2024; 19:1027-1035. [PMID: 37862205 PMCID: PMC10749614 DOI: 10.4103/1673-5374.385285] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/13/2023] [Accepted: 07/21/2023] [Indexed: 10/22/2023] Open
Abstract
Neurodegenerative diseases are a group of disorders characterized by the progressive degeneration of neurons in the central or peripheral nervous system. Currently, there is no cure for neurodegenerative diseases and this means a heavy burden for patients and the health system worldwide. Therefore, it is necessary to find new therapeutic approaches, and antisense therapies offer this possibility, having the great advantage of not modifying cellular genome and potentially being safer. Many preclinical and clinical studies aim to test the safety and effectiveness of antisense therapies in the treatment of neurodegenerative diseases. The objective of this review is to summarize the recent advances in the development of these new technologies to treat the most common neurodegenerative diseases, with a focus on those antisense therapies that have already received the approval of the U.S. Food and Drug Administration.
Collapse
Affiliation(s)
- Roberta Romano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Cecilia Bucci
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| |
Collapse
|
3
|
Berdecka D, De Smedt SC, De Vos WH, Braeckmans K. Non-viral delivery of RNA for therapeutic T cell engineering. Adv Drug Deliv Rev 2024; 208:115215. [PMID: 38401848 DOI: 10.1016/j.addr.2024.115215] [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: 11/21/2023] [Revised: 02/07/2024] [Accepted: 02/14/2024] [Indexed: 02/26/2024]
Abstract
Adoptive T cell transfer has shown great success in treating blood cancers, resulting in a growing number of FDA-approved therapies using chimeric antigen receptor (CAR)-engineered T cells. However, the effectiveness of this treatment for solid tumors is still not satisfactory, emphasizing the need for improved T cell engineering strategies and combination approaches. Currently, CAR T cells are mainly manufactured using gammaretroviral and lentiviral vectors due to their high transduction efficiency. However, there are concerns about their safety, the high cost of producing them in compliance with current Good Manufacturing Practices (cGMP), regulatory obstacles, and limited cargo capacity, which limit the broader use of engineered T cell therapies. To overcome these limitations, researchers have explored non-viral approaches, such as membrane permeabilization and carrier-mediated methods, as more versatile and sustainable alternatives for next-generation T cell engineering. Non-viral delivery methods can be designed to transport a wide range of molecules, including RNA, which allows for more controlled and safe modulation of T cell phenotype and function. In this review, we provide an overview of non-viral RNA delivery in adoptive T cell therapy. We first define the different types of RNA therapeutics, highlighting recent advancements in manufacturing for their therapeutic use. We then discuss the challenges associated with achieving effective RNA delivery in T cells. Next, we provide an overview of current and emerging technologies for delivering RNA into T cells. Finally, we discuss ongoing preclinical and clinical studies involving RNA-modified T cells.
Collapse
Affiliation(s)
- Dominika Berdecka
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Stefaan C De Smedt
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Winnok H De Vos
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Kevin Braeckmans
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| |
Collapse
|
4
|
Ma S, Howden SA, Keane SC. Use of steric blocking antisense oligonucleotides for the targeted inhibition of junction containing precursor microRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588531. [PMID: 38645194 PMCID: PMC11030329 DOI: 10.1101/2024.04.08.588531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Antisense oligonucleotides (ASOs) are widely used as therapeutics for neurodegenerative diseases, cancers, and virus infections. One class of ASOs functions to enhance protein expression by sequestering the mature microRNA (miRNA) in a double-stranded structure within the RNA-induced silencing complex (RISC). An alternative approach for the targeted control of gene expression is to use ASOs that bind to the pre-elements of miRNAs (pre-miRNAs) and modulate their enzymatic processing. Here, we demonstrate that ASOs can be used to disrupt a specific structural feature, "junction," within pre-miR-31 that is important in directing efficient processing by the Dicer/TRBP complex. Furthermore, we extend and validate this strategy to pre-miR-144, which has a similar junction-dependent structure-function relationship. We found that a significant number of human pre-miRNAs are predicted to contain junctions, and validated our ASO approach on several members of this group. Importantly, we also verified the application of junction-targeting ASOs for the specific inhibition of pre-miRNA processing in cell . Our study reemphasizes the important roles of RNA structure in regulating Dicer/TRBP processing of pre-miRNAs and provides the framework to develop structure-informed ASOs that serve to inhibit miRNA production.
Collapse
|
5
|
Hsia T, Chen Y. RNA-encapsulating lipid nanoparticles in cancer immunotherapy: From pre-clinical studies to clinical trials. Eur J Pharm Biopharm 2024; 197:114234. [PMID: 38401743 DOI: 10.1016/j.ejpb.2024.114234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/29/2024] [Accepted: 02/14/2024] [Indexed: 02/26/2024]
Abstract
Nanoparticle-based delivery systems such as RNA-encapsulating lipid nanoparticles (RNA LNPs) have dramatically advanced in function and capacity over the last few decades. RNA LNPs boast of a diverse array of external and core configurations that enhance targeted delivery and prolong circulatory retention, advancing therapeutic outcomes. Particularly within the realm of cancer immunotherapies, RNA LNPs are increasingly gaining prominence. Pre-clinical in vitro and in vivo studies have laid a robust foundation for new and ongoing clinical trials that are actively enrolling patients for RNA LNP cancer immunotherapy. This review explores RNA LNPs, starting from their core composition to their external membrane formulation, set against a backdrop of recent clinical breakthroughs. We further elucidate the LNP delivery avenues, broach the prevailing challenges, and contemplate the future perspectives of RNA LNP-mediated immunotherapy.
Collapse
Affiliation(s)
- Tiffaney Hsia
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yunching Chen
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan; Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan.
| |
Collapse
|
6
|
Song J, Luo N, Dong L, Peng J, Yi C. RNA base editors: The emerging approach of RNA therapeutics. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1844. [PMID: 38576085 DOI: 10.1002/wrna.1844] [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: 08/29/2023] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024]
Abstract
RNA-based therapeutics offer a flexible and reversible approach for treating genetic disorders, such as antisense oligonucleotides, RNA interference, aptamers, mRNA vaccines, and RNA editing. In recent years, significant advancements have been made in RNA base editing to correct disease-relevant point mutations. These achievements have significantly influenced the fields of biotechnology, biomedical research and therapeutics development. In this article, we provide a comprehensive overview of the design and performance of contemporary RNA base editors, including A-to-I, C-to-U, A-to-m6A, and U-to-Ψ. We compare recent innovative developments and highlight their applications in disease-relevant contexts. Lastly, we discuss the limitations and future prospects of utilizing RNA base editing for therapeutic purposes. This article is categorized under: RNA Processing > RNA Editing and Modification RNA in Disease and Development > RNA in Development.
Collapse
Affiliation(s)
- Jinghui Song
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Nan Luo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Liting Dong
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing Advanced Center of RNA Biology (BEACON), Peking University, Beijing, China
| |
Collapse
|
7
|
Bose R, Saleem I, Mustoe AM. Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states. Cell Chem Biol 2024; 31:17-35. [PMID: 38199037 PMCID: PMC10842484 DOI: 10.1016/j.chembiol.2023.12.010] [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: 09/11/2023] [Revised: 11/21/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
RNA secondary structure plays essential roles in encoding RNA regulatory fate and function. Most RNAs populate ensembles of alternatively paired states and are continually unfolded and refolded by cellular processes. Measuring these structural ensembles and their contributions to cellular function has traditionally posed major challenges, but new methods and conceptual frameworks are beginning to fill this void. In this review, we provide a mechanism- and function-centric compendium of the roles of RNA secondary structural ensembles and minority states in regulating the RNA life cycle, from transcription to degradation. We further explore how dysregulation of RNA structural ensembles contributes to human disease and discuss the potential of drugging alternative RNA states to therapeutically modulate RNA activity. The emerging paradigm of RNA structural ensembles as central to RNA function provides a foundation for a deeper understanding of RNA biology and new therapeutic possibilities.
Collapse
Affiliation(s)
- Ritwika Bose
- Therapeutic Innovation Center (THINC), Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Irfana Saleem
- Therapeutic Innovation Center (THINC), Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony M Mustoe
- Therapeutic Innovation Center (THINC), Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
8
|
Rehman SU, Ullah N, Zhang Z, Zhen Y, Din AU, Cui H, Wang M. Recent insights into the functions and mechanisms of antisense RNA: emerging applications in cancer therapy and precision medicine. Front Chem 2024; 11:1335330. [PMID: 38274897 PMCID: PMC10809404 DOI: 10.3389/fchem.2023.1335330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
The antisense RNA molecule is a unique DNA transcript consisting of 19-23 nucleotides, characterized by its complementary nature to mRNA. These antisense RNAs play a crucial role in regulating gene expression at various stages, including replication, transcription, and translation. Additionally, artificial antisense RNAs have demonstrated their ability to effectively modulate gene expression in host cells. Consequently, there has been a substantial increase in research dedicated to investigating the roles of antisense RNAs. These molecules have been found to be influential in various cellular processes, such as X-chromosome inactivation and imprinted silencing in healthy cells. However, it is important to recognize that in cancer cells; aberrantly expressed antisense RNAs can trigger the epigenetic silencing of tumor suppressor genes. Moreover, the presence of deletion-induced aberrant antisense RNAs can lead to the development of diseases through epigenetic silencing. One area of drug development worth mentioning is antisense oligonucleotides (ASOs), and a prime example of an oncogenic trans-acting long noncoding RNA (lncRNA) is HOTAIR (HOX transcript antisense RNA). NATs (noncoding antisense transcripts) are dysregulated in many cancers, and researchers are just beginning to unravel their roles as crucial regulators of cancer's hallmarks, as well as their potential for cancer therapy. In this review, we summarize the emerging roles and mechanisms of antisense RNA and explore their application in cancer therapy.
Collapse
Affiliation(s)
- Shahab Ur Rehman
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
| | - Numan Ullah
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
| | - Zhenbin Zhang
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
| | - Yongkang Zhen
- College of Animals Nutrition Yangzhou University, Yangzhou, China
| | - Aziz-Ud Din
- Department of Human Genetics, Hazara University Mansehra, Mansehra, Pakistan
| | - Hengmi Cui
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
- Institute of Epigenetics and Epigenomics Yangzhou University, College of Animal Nutrition Yangzhou University, Yangzhou, China
| | - Mengzhi Wang
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
- College of Animals Nutrition Yangzhou University, Yangzhou, China
| |
Collapse
|
9
|
Lauffer MC, van Roon-Mom W, Aartsma-Rus A. Possibilities and limitations of antisense oligonucleotide therapies for the treatment of monogenic disorders. COMMUNICATIONS MEDICINE 2024; 4:6. [PMID: 38182878 PMCID: PMC10770028 DOI: 10.1038/s43856-023-00419-1] [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: 05/10/2023] [Accepted: 11/27/2023] [Indexed: 01/07/2024] Open
Abstract
Antisense oligonucleotides (ASOs) are incredibly versatile molecules that can be designed to specifically target and modify RNA transcripts to slow down or halt rare genetic disease progression. They offer the potential to target groups of patients or can be tailored for individual cases. Nonetheless, not all genetic variants and disorders are amenable to ASO-based treatments, and hence, it is important to consider several factors before embarking on the drug development journey. Here, we discuss which genetic disorders have the potential to benefit from a specific type of ASO approach, based on the pathophysiology of the disease and pathogenic variant type, as well as those disorders that might not be suitable for ASO therapies. We further explore additional aspects, such as the target tissues, intervention time points, and potential clinical benefits, which need to be considered before developing a compound. Overall, we provide an overview of the current potentials and limitations of ASO-based therapeutics for the treatment of monogenic disorders.
Collapse
Affiliation(s)
- Marlen C Lauffer
- Dutch Center for RNA Therapeutics, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Willeke van Roon-Mom
- Dutch Center for RNA Therapeutics, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Annemieke Aartsma-Rus
- Dutch Center for RNA Therapeutics, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
| |
Collapse
|
10
|
Wong DCS, Harvey JP, Jurkute N, Thomasy SM, Moosajee M, Yu-Wai-Man P, Gilhooley MJ. OPA1 Dominant Optic Atrophy: Pathogenesis and Therapeutic Targets. J Neuroophthalmol 2023; 43:464-474. [PMID: 37974363 PMCID: PMC10645107 DOI: 10.1097/wno.0000000000001830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Affiliation(s)
- David C. S. Wong
- Department of Clinical Neurosciences (DCSW, PY-W-M), John van Geest Center for Brain Repair, University of Cambridge, Cambridge, United Kingdom; Cambridge Eye Unit (DCSW, PY-W-M), Addenbrooke's Hospital, Cambridge, United Kingdom; UCL Institute of Ophthalmology (JPH, NJ, MM, PY-W-M, MJG), London, United Kingdom; Moorfields Eye Hospital NHS Foundation Trust (JPH, NJ, MM, PY-W-M, MJG), London, United Kingdom; Department of Ophthalmology and Vision Science (SMT), School of Medicine, U.C. Davis, Sacramento, California; Department of Surgical and Radiological Sciences (SMT), School of Veterinary Medicine, U.C. Davis, California; Great Ormond Street Hospital (MM), London, United Kingdom; and The Francis Crick Institute (MM), London, United Kingdom
| | - Joshua P. Harvey
- Department of Clinical Neurosciences (DCSW, PY-W-M), John van Geest Center for Brain Repair, University of Cambridge, Cambridge, United Kingdom; Cambridge Eye Unit (DCSW, PY-W-M), Addenbrooke's Hospital, Cambridge, United Kingdom; UCL Institute of Ophthalmology (JPH, NJ, MM, PY-W-M, MJG), London, United Kingdom; Moorfields Eye Hospital NHS Foundation Trust (JPH, NJ, MM, PY-W-M, MJG), London, United Kingdom; Department of Ophthalmology and Vision Science (SMT), School of Medicine, U.C. Davis, Sacramento, California; Department of Surgical and Radiological Sciences (SMT), School of Veterinary Medicine, U.C. Davis, California; Great Ormond Street Hospital (MM), London, United Kingdom; and The Francis Crick Institute (MM), London, United Kingdom
| | - Neringa Jurkute
- Department of Clinical Neurosciences (DCSW, PY-W-M), John van Geest Center for Brain Repair, University of Cambridge, Cambridge, United Kingdom; Cambridge Eye Unit (DCSW, PY-W-M), Addenbrooke's Hospital, Cambridge, United Kingdom; UCL Institute of Ophthalmology (JPH, NJ, MM, PY-W-M, MJG), London, United Kingdom; Moorfields Eye Hospital NHS Foundation Trust (JPH, NJ, MM, PY-W-M, MJG), London, United Kingdom; Department of Ophthalmology and Vision Science (SMT), School of Medicine, U.C. Davis, Sacramento, California; Department of Surgical and Radiological Sciences (SMT), School of Veterinary Medicine, U.C. Davis, California; Great Ormond Street Hospital (MM), London, United Kingdom; and The Francis Crick Institute (MM), London, United Kingdom
| | - Sara M. Thomasy
- Department of Clinical Neurosciences (DCSW, PY-W-M), John van Geest Center for Brain Repair, University of Cambridge, Cambridge, United Kingdom; Cambridge Eye Unit (DCSW, PY-W-M), Addenbrooke's Hospital, Cambridge, United Kingdom; UCL Institute of Ophthalmology (JPH, NJ, MM, PY-W-M, MJG), London, United Kingdom; Moorfields Eye Hospital NHS Foundation Trust (JPH, NJ, MM, PY-W-M, MJG), London, United Kingdom; Department of Ophthalmology and Vision Science (SMT), School of Medicine, U.C. Davis, Sacramento, California; Department of Surgical and Radiological Sciences (SMT), School of Veterinary Medicine, U.C. Davis, California; Great Ormond Street Hospital (MM), London, United Kingdom; and The Francis Crick Institute (MM), London, United Kingdom
| | - Mariya Moosajee
- Department of Clinical Neurosciences (DCSW, PY-W-M), John van Geest Center for Brain Repair, University of Cambridge, Cambridge, United Kingdom; Cambridge Eye Unit (DCSW, PY-W-M), Addenbrooke's Hospital, Cambridge, United Kingdom; UCL Institute of Ophthalmology (JPH, NJ, MM, PY-W-M, MJG), London, United Kingdom; Moorfields Eye Hospital NHS Foundation Trust (JPH, NJ, MM, PY-W-M, MJG), London, United Kingdom; Department of Ophthalmology and Vision Science (SMT), School of Medicine, U.C. Davis, Sacramento, California; Department of Surgical and Radiological Sciences (SMT), School of Veterinary Medicine, U.C. Davis, California; Great Ormond Street Hospital (MM), London, United Kingdom; and The Francis Crick Institute (MM), London, United Kingdom
| | - Patrick Yu-Wai-Man
- Department of Clinical Neurosciences (DCSW, PY-W-M), John van Geest Center for Brain Repair, University of Cambridge, Cambridge, United Kingdom; Cambridge Eye Unit (DCSW, PY-W-M), Addenbrooke's Hospital, Cambridge, United Kingdom; UCL Institute of Ophthalmology (JPH, NJ, MM, PY-W-M, MJG), London, United Kingdom; Moorfields Eye Hospital NHS Foundation Trust (JPH, NJ, MM, PY-W-M, MJG), London, United Kingdom; Department of Ophthalmology and Vision Science (SMT), School of Medicine, U.C. Davis, Sacramento, California; Department of Surgical and Radiological Sciences (SMT), School of Veterinary Medicine, U.C. Davis, California; Great Ormond Street Hospital (MM), London, United Kingdom; and The Francis Crick Institute (MM), London, United Kingdom
| | - Michael J. Gilhooley
- Department of Clinical Neurosciences (DCSW, PY-W-M), John van Geest Center for Brain Repair, University of Cambridge, Cambridge, United Kingdom; Cambridge Eye Unit (DCSW, PY-W-M), Addenbrooke's Hospital, Cambridge, United Kingdom; UCL Institute of Ophthalmology (JPH, NJ, MM, PY-W-M, MJG), London, United Kingdom; Moorfields Eye Hospital NHS Foundation Trust (JPH, NJ, MM, PY-W-M, MJG), London, United Kingdom; Department of Ophthalmology and Vision Science (SMT), School of Medicine, U.C. Davis, Sacramento, California; Department of Surgical and Radiological Sciences (SMT), School of Veterinary Medicine, U.C. Davis, California; Great Ormond Street Hospital (MM), London, United Kingdom; and The Francis Crick Institute (MM), London, United Kingdom
| |
Collapse
|
11
|
Aggarwal G, Banerjee S, Jones SA, Benchaar Y, Bélanger J, Sévigny M, Smith DM, Niehoff ML, Pavlack M, de Vera IMS, Petkau TL, Leavitt BR, Ling K, Jafar-Nejad P, Rigo F, Morley JE, Farr SA, Dutchak PA, Sephton CF, Nguyen AD. Antisense oligonucleotides targeting the miR-29b binding site in the GRN mRNA increase progranulin translation. J Biol Chem 2023; 299:105475. [PMID: 37981208 PMCID: PMC10755782 DOI: 10.1016/j.jbc.2023.105475] [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: 09/18/2023] [Revised: 10/13/2023] [Accepted: 11/07/2023] [Indexed: 11/21/2023] Open
Abstract
Heterozygous GRN (progranulin) mutations cause frontotemporal dementia (FTD) due to haploinsufficiency, and increasing progranulin levels is a major therapeutic goal. Several microRNAs, including miR-29b, negatively regulate progranulin protein levels. Antisense oligonucleotides (ASOs) are emerging as a promising therapeutic modality for neurological diseases, but strategies for increasing target protein levels are limited. Here, we tested the efficacy of ASOs as enhancers of progranulin expression by sterically blocking the miR-29b binding site in the 3' UTR of the human GRN mRNA. We found 16 ASOs that increase progranulin protein in a dose-dependent manner in neuroglioma cells. A subset of these ASOs also increased progranulin protein in iPSC-derived neurons and in a humanized GRN mouse model. In FRET-based assays, the ASOs effectively competed for miR-29b from binding to the GRN 3' UTR RNA. The ASOs increased levels of newly synthesized progranulin protein by increasing its translation, as revealed by polysome profiling. Together, our results demonstrate that ASOs can be used to effectively increase target protein levels by partially blocking miR binding sites. This ASO strategy may be therapeutically feasible for progranulin-deficient FTD as well as other conditions of haploinsufficiency.
Collapse
Affiliation(s)
- Geetika Aggarwal
- Division of Geriatric Medicine, Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, Missouri, USA; Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St Louis, Missouri, USA; Institute for Translational Neuroscience, Saint Louis University, St Louis, Missouri, USA
| | - Subhashis Banerjee
- Division of Geriatric Medicine, Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, Missouri, USA; Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St Louis, Missouri, USA; Institute for Translational Neuroscience, Saint Louis University, St Louis, Missouri, USA
| | - Spencer A Jones
- Division of Geriatric Medicine, Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, Missouri, USA; Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St Louis, Missouri, USA; Institute for Translational Neuroscience, Saint Louis University, St Louis, Missouri, USA
| | - Yousri Benchaar
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Jasmine Bélanger
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Myriam Sévigny
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Denise M Smith
- Division of Geriatric Medicine, Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, Missouri, USA; Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St Louis, Missouri, USA; Institute for Translational Neuroscience, Saint Louis University, St Louis, Missouri, USA
| | - Michael L Niehoff
- Division of Geriatric Medicine, Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, Missouri, USA; Veterans Affairs Medical Center, St Louis, Missouri, USA
| | - Monica Pavlack
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St Louis, Missouri, USA; Institute for Translational Neuroscience, Saint Louis University, St Louis, Missouri, USA
| | - Ian Mitchelle S de Vera
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St Louis, Missouri, USA; Institute for Translational Neuroscience, Saint Louis University, St Louis, Missouri, USA
| | - Terri L Petkau
- Department of Medical Genetics, Centre for Molecular Medicine & Therapeutics, B.C. Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Blair R Leavitt
- Department of Medical Genetics, Centre for Molecular Medicine & Therapeutics, B.C. Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada; Division of Neurology, Department of Medicine, University of British Columbia Hospital, Vancouver, British Columbia, Canada; Center for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Karen Ling
- Ionis Pharmaceuticals, Carlsbad, California, USA
| | | | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, California, USA
| | - John E Morley
- Division of Geriatric Medicine, Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, Missouri, USA
| | - Susan A Farr
- Division of Geriatric Medicine, Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, Missouri, USA; Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St Louis, Missouri, USA; Institute for Translational Neuroscience, Saint Louis University, St Louis, Missouri, USA; Veterans Affairs Medical Center, St Louis, Missouri, USA
| | - Paul A Dutchak
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Chantelle F Sephton
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Andrew D Nguyen
- Division of Geriatric Medicine, Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, Missouri, USA; Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St Louis, Missouri, USA; Institute for Translational Neuroscience, Saint Louis University, St Louis, Missouri, USA.
| |
Collapse
|
12
|
Ang Z, Paruzzo L, Hayer KE, Schmidt C, Torres Diz M, Xu F, Zankharia U, Zhang Y, Soldan S, Zheng S, Falkenstein CD, Loftus JP, Yang SY, Asnani M, King Sainos P, Pillai V, Chong E, Li MM, Tasian SK, Barash Y, Lieberman PM, Ruella M, Schuster SJ, Thomas-Tikhonenko A. Alternative splicing of its 5'-UTR limits CD20 mRNA translation and enables resistance to CD20-directed immunotherapies. Blood 2023; 142:1724-1739. [PMID: 37683180 PMCID: PMC10667349 DOI: 10.1182/blood.2023020400] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 08/04/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023] Open
Abstract
Aberrant skipping of coding exons in CD19 and CD22 compromises the response to immunotherapy in B-cell malignancies. Here, we showed that the MS4A1 gene encoding human CD20 also produces several messenger RNA (mRNA) isoforms with distinct 5' untranslated regions. Four variants (V1-4) were detected using RNA sequencing (RNA-seq) at distinct stages of normal B-cell differentiation and B-lymphoid malignancies, with V1 and V3 being the most abundant. During B-cell activation and Epstein-Barr virus infection, redirection of splicing from V1 to V3 coincided with increased CD20 positivity. Similarly, in diffuse large B-cell lymphoma, only V3, but not V1, correlated with CD20 protein levels, suggesting that V1 might be translation-deficient. Indeed, the longer V1 isoform contained upstream open reading frames and a stem-loop structure, which cooperatively inhibited polysome recruitment. By modulating CD20 isoforms with splice-switching morpholino oligomers, we enhanced CD20 expression and anti-CD20 antibody rituximab-mediated cytotoxicity in a panel of B-cell lines. Furthermore, reconstitution of CD20-knockout cells with V3 mRNA led to the recovery of CD20 positivity, whereas V1-reconstituted cells had undetectable levels of CD20 protein. Surprisingly, in vitro CD20-directed chimeric antigen receptor T cells were able to kill both V3- and V1-expressing cells, but the bispecific T-cell engager mosunetuzumab was only effective against V3-expressing cells. To determine whether CD20 splicing is involved in immunotherapy resistance, we performed RNA-seq on 4 postmosunetuzumab follicular lymphoma relapses and discovered that in 2 of them, the downregulation of CD20 was accompanied by a V3-to-V1 shift. Thus, splicing-mediated mechanisms of epitope loss extend to CD20-directed immunotherapies.
Collapse
Affiliation(s)
- Zhiwei Ang
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Luca Paruzzo
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Katharina E. Hayer
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Carolin Schmidt
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Manuel Torres Diz
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Feng Xu
- Division of Genomic Diagnostic, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Urvi Zankharia
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA
| | - Yunlin Zhang
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Samantha Soldan
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA
| | - Sisi Zheng
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Joseph P. Loftus
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Scarlett Y. Yang
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Mukta Asnani
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Vinodh Pillai
- Division of Hematopathology, Children's Hospital of Philadelphia, Philadelphia, PA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Emeline Chong
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
| | - Marilyn M. Li
- Division of Genomic Diagnostic, Children's Hospital of Philadelphia, Philadelphia, PA
- Division of Hematopathology, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Sarah K. Tasian
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Paul M. Lieberman
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA
| | - Marco Ruella
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Stephen J. Schuster
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| |
Collapse
|
13
|
Sparmann A, Vogel J. RNA-based medicine: from molecular mechanisms to therapy. EMBO J 2023; 42:e114760. [PMID: 37728251 PMCID: PMC10620767 DOI: 10.15252/embj.2023114760] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
RNA-based therapeutics have the potential to revolutionize the treatment and prevention of human diseases. While early research faced setbacks, it established the basis for breakthroughs in RNA-based drug design that culminated in the extraordinarily fast development of mRNA vaccines to combat the COVID-19 pandemic. We have now reached a pivotal moment where RNA medicines are poised to make a broad impact in the clinic. In this review, we present an overview of different RNA-based strategies to generate novel therapeutics, including antisense and RNAi-based mechanisms, mRNA-based approaches, and CRISPR-Cas-mediated genome editing. Using three rare genetic diseases as examples, we highlight the opportunities, but also the challenges to wide-ranging applications of this class of drugs.
Collapse
Affiliation(s)
- Anke Sparmann
- Helmholtz Institute for RNA‐based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI)WürzburgGermany
| | - Jörg Vogel
- Helmholtz Institute for RNA‐based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI)WürzburgGermany
- Institute of Molecular Infection Biology (IMIB)University of WürzburgWürzburgGermany
| |
Collapse
|
14
|
Ruggiero V, Fagioli C, de Pretis S, Di Carlo V, Landsberger N, Zacchetti D. Complex CDKL5 translational regulation and its potential role in CDKL5 deficiency disorder. Front Cell Neurosci 2023; 17:1231493. [PMID: 37964795 PMCID: PMC10642286 DOI: 10.3389/fncel.2023.1231493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/10/2023] [Indexed: 11/16/2023] Open
Abstract
CDKL5 is a kinase with relevant functions in correct neuronal development and in the shaping of synapses. A decrease in its expression or activity leads to a severe neurodevelopmental condition known as CDKL5 deficiency disorder (CDD). CDD arises from CDKL5 mutations that lie in the coding region of the gene. However, the identification of a SNP in the CDKL5 5'UTR in a patient with symptoms consistent with CDD, together with the complexity of the CDKL5 transcript leader, points toward a relevant translational regulation of CDKL5 expression with important consequences in physiological processes as well as in the pathogenesis of CDD. We performed a bioinformatics and molecular analysis of the 5'UTR of CDKL5 to identify translational regulatory features. We propose an important role for structural cis-acting elements, with the involvement of the eukaryotic translational initiation factor eIF4B. By evaluating both cap-dependent and cap-independent translation initiation, we suggest the presence of an IRES supporting the translation of CDKL5 mRNA and propose a pathogenic effect of the C>T -189 SNP in decreasing the translation of the downstream protein.
Collapse
Affiliation(s)
- Valeria Ruggiero
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Claudio Fagioli
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stefano de Pretis
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Valerio Di Carlo
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
| | - Nicoletta Landsberger
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
| | - Daniele Zacchetti
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| |
Collapse
|
15
|
Cao Y, Liu H, Lu SS, Jones KA, Govind AP, Jeyifous O, Simmons CQ, Tabatabaei N, Green WN, Holder JL, Tahmasebi S, George AL, Dickinson BC. RNA-based translation activators for targeted gene upregulation. Nat Commun 2023; 14:6827. [PMID: 37884512 PMCID: PMC10603104 DOI: 10.1038/s41467-023-42252-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023] Open
Abstract
Technologies capable of programmable translation activation offer strategies to develop therapeutics for diseases caused by insufficient gene expression. Here, we present "translation-activating RNAs" (taRNAs), a bifunctional RNA-based molecular technology that binds to a specific mRNA of interest and directly upregulates its translation. taRNAs are constructed from a variety of viral or mammalian RNA internal ribosome entry sites (IRESs) and upregulate translation for a suite of target mRNAs. We minimize the taRNA scaffold to 94 nucleotides, identify two translation initiation factor proteins responsible for taRNA activity, and validate the technology by amplifying SYNGAP1 expression, a haploinsufficiency disease target, in patient-derived cells. Finally, taRNAs are suitable for delivery as RNA molecules by lipid nanoparticles (LNPs) to cell lines, primary neurons, and mouse liver in vivo. taRNAs provide a general and compact nucleic acid-based technology to upregulate protein production from endogenous mRNAs, and may open up possibilities for therapeutic RNA research.
Collapse
Affiliation(s)
- Yang Cao
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Huachun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Shannon S Lu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Krysten A Jones
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Anitha P Govind
- Department of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Okunola Jeyifous
- Department of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Christine Q Simmons
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Negar Tabatabaei
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - William N Green
- Department of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Jimmy L Holder
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Soroush Tahmasebi
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
| |
Collapse
|
16
|
Hedaya OM, Venkata Subbaiah KC, Jiang F, Xie LH, Wu J, Khor ES, Zhu M, Mathews DH, Proschel C, Yao P. Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy. Nat Commun 2023; 14:6166. [PMID: 37789015 PMCID: PMC10547706 DOI: 10.1038/s41467-023-41799-1] [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: 10/17/2022] [Accepted: 09/19/2023] [Indexed: 10/05/2023] Open
Abstract
Translation of upstream open reading frames (uORFs) typically abrogates translation of main (m)ORFs. The molecular mechanism of uORF regulation in cells is not well understood. Here, we data-mined human and mouse heart ribosome profiling analyses and identified a double-stranded RNA (dsRNA) structure within the GATA4 uORF that cooperates with the start codon to augment uORF translation and inhibits mORF translation. A trans-acting RNA helicase DDX3X inhibits the GATA4 uORF-dsRNA activity and modulates the translational balance of uORF and mORF. Antisense oligonucleotides (ASOs) that disrupt this dsRNA structure promote mORF translation, while ASOs that base-pair immediately downstream (i.e., forming a bimolecular double-stranded region) of either the uORF or mORF start codon enhance uORF or mORF translation, respectively. Human cardiomyocytes and mice treated with a uORF-enhancing ASO showed reduced cardiac GATA4 protein levels and increased resistance to cardiomyocyte hypertrophy. We further show the broad utility of uORF-dsRNA- or mORF-targeting ASO to regulate mORF translation for other mRNAs. This work demonstrates that the uORF-dsRNA element regulates the translation of multiple mRNAs as a generalizable translational control mechanism. Moreover, we develop a valuable strategy to alter protein expression and cellular phenotypes by targeting or generating dsRNA downstream of a uORF or mORF start codon.
Collapse
Affiliation(s)
- Omar M Hedaya
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Kadiam C Venkata Subbaiah
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Feng Jiang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Li Huitong Xie
- Department of Biomedical Genetics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Jiangbin Wu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Eng-Soon Khor
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Mingyi Zhu
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Chris Proschel
- Department of Biomedical Genetics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA.
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA.
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA.
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA.
| |
Collapse
|
17
|
Buthelezi LA, Pillay S, Ntuli NN, Gcanga L, Guler R. Antisense Therapy for Infectious Diseases. Cells 2023; 12:2119. [PMID: 37626929 PMCID: PMC10453568 DOI: 10.3390/cells12162119] [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: 06/29/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Infectious diseases, particularly Tuberculosis (TB) caused by Mycobacterium tuberculosis, pose a significant global health challenge, with 1.6 million reported deaths in 2021, making it the most fatal disease caused by a single infectious agent. The rise of drug-resistant infectious diseases adds to the urgency of finding effective and safe intervention therapies. Antisense therapy uses antisense oligonucleotides (ASOs) that are short, chemically modified, single-stranded deoxyribonucleotide molecules complementary to their mRNA target. Due to their designed target specificity and inhibition of a disease-causing gene at the mRNA level, antisense therapy has gained interest as a potential therapeutic approach. This type of therapy is currently utilized in numerous diseases, such as cancer and genetic disorders. Currently, there are limited but steadily increasing studies available that report on the use of ASOs as treatment for infectious diseases. This review explores the sustainability of FDA-approved and preclinically tested ASOs as a treatment for infectious diseases and the adaptability of ASOs for chemical modifications resulting in reduced side effects with improved drug delivery; thus, highlighting the potential therapeutic uses of ASOs for treating infectious diseases.
Collapse
Affiliation(s)
- Lwanda Abonga Buthelezi
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa; (L.A.B.); (S.P.); (N.N.N.); (L.G.)
- Department of Pathology, Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Shandre Pillay
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa; (L.A.B.); (S.P.); (N.N.N.); (L.G.)
- Department of Pathology, Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Noxolo Nokukhanya Ntuli
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa; (L.A.B.); (S.P.); (N.N.N.); (L.G.)
- Department of Pathology, Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lorna Gcanga
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa; (L.A.B.); (S.P.); (N.N.N.); (L.G.)
- Department of Pathology, Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa; (L.A.B.); (S.P.); (N.N.N.); (L.G.)
- Department of Pathology, Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- Faculty of Health Sciences, Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| |
Collapse
|
18
|
Ang Z, Paruzzo L, Hayer KE, Schmidt C, Torres Diz M, Xu F, Zankharia U, Zhang Y, Soldan S, Zheng S, Falkenstein CD, Loftus JP, Yang SY, Asnani M, King Sainos P, Pillai V, Chong E, Li MM, Tasian SK, Barash Y, Lieberman PM, Ruella M, Schuster SJ, Thomas-Tikhonenko A. Alternative splicing of its 5'-UTR limits CD20 mRNA translation and enables resistance to CD20-directed immunotherapies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.19.529123. [PMID: 37645778 PMCID: PMC10461923 DOI: 10.1101/2023.02.19.529123] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Aberrant skipping of coding exons in CD19 and CD22 compromises responses to immunotherapy for B-cell malignancies. Here, we show that the MS4A1 gene encoding human CD20 also produces several mRNA isoforms with distinct 5' untranslated regions (5'-UTR). Four variants (V1-4) were detectable by RNA-seq in distinct stages of normal B-cell differentiation and B-lymphoid malignancies, with V1 and V3 being the most abundant by far. During B-cell activation and Epstein-Barr virus infection, redirection of splicing from V1 to V3 coincided with increased CD20 positivity. Similarly, in diffuse large B-cell lymphoma only V3, but not V1, correlated with CD20 protein levels, suggesting that V1 might be translation-deficient. Indeed, the longer V1 isoform was found to contain upstream open reading frames (uORFs) and a stem-loop structure, which cooperatively inhibited polysome recruitment. By modulating CD20 isoforms with splice-switching Morpholino oligomers, we enhanced CD20 expression and anti-CD20 antibody rituximab-mediated cytotoxicity in a panel of B-cell lines. Furthermore, reconstitution of CD20-knockout cells with V3 mRNA led to the recovery of CD20 positivity, while V1-reconstituted cells had undetectable levels of CD20 protein. Surprisingly, in vitro CD20-directed CAR T cells were able to kill both V3- and V1-expressing cells, but the bispecific T cell engager mosunetuzumab was only effective against V3-expressing cells. To determine whether CD20 splicing is involved in immunotherapy resistance, we performed RNA-seq on four post-mosunetuzumab follicular lymphoma relapses and discovered that in two of them downregulation of CD20 was accompanied by the V3-to-V1 shift. Thus, splicing-mediated mechanisms of epitope loss extend to CD20-directed immunotherapies. Key Points In normal & malignant human B cells, CD20 mRNA is alternatively spliced into four 5'-UTR isoforms, some of which are translation-deficient.The balance between translation-deficient and -competent isoforms modulates CD20 protein levels & responses to CD20-directed immunotherapies. Explanation of Novelty We discovered that in normal and malignant B-cells, CD20 mRNA is alternatively spliced to generate four distinct 5'-UTRs, including the longer translation-deficient V1 variant. Cells predominantly expressing V1 were still sensitive to CD20-targeting chimeric antigen receptor T-cells. However, they were resistant to the bispecific anti-CD3/CD20 antibody mosunetuzumab, and the shift to V1 were observed in CD20-negative post-mosunetuzumab relapses of follicular lymphoma.
Collapse
|
19
|
Papaioannou I, Owen JS, Yáñez‐Muñoz RJ. Clinical applications of gene therapy for rare diseases: A review. Int J Exp Pathol 2023; 104:154-176. [PMID: 37177842 PMCID: PMC10349259 DOI: 10.1111/iep.12478] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 03/08/2023] [Accepted: 04/16/2023] [Indexed: 05/15/2023] Open
Abstract
Rare diseases collectively exact a high toll on society due to their sheer number and overall prevalence. Their heterogeneity, diversity, and nature pose daunting clinical challenges for both management and treatment. In this review, we discuss recent advances in clinical applications of gene therapy for rare diseases, focusing on a variety of viral and non-viral strategies. The use of adeno-associated virus (AAV) vectors is discussed in the context of Luxturna, licenced for the treatment of RPE65 deficiency in the retinal epithelium. Imlygic, a herpes virus vector licenced for the treatment of refractory metastatic melanoma, will be an example of oncolytic vectors developed against rare cancers. Yescarta and Kymriah will showcase the use of retrovirus and lentivirus vectors in the autologous ex vivo production of chimeric antigen receptor T cells (CAR-T), licenced for the treatment of refractory leukaemias and lymphomas. Similar retroviral and lentiviral technology can be applied to autologous haematopoietic stem cells, exemplified by Strimvelis and Zynteglo, licenced treatments for adenosine deaminase-severe combined immunodeficiency (ADA-SCID) and β-thalassaemia respectively. Antisense oligonucleotide technologies will be highlighted through Onpattro and Tegsedi, RNA interference drugs licenced for familial transthyretin (TTR) amyloidosis, and Spinraza, a splice-switching treatment for spinal muscular atrophy (SMA). An initial comparison of the effectiveness of AAV and oligonucleotide therapies in SMA is possible with Zolgensma, an AAV serotype 9 vector, and Spinraza. Through these examples of marketed gene therapies and gene cell therapies, we will discuss the expanding applications of such novel technologies to previously intractable rare diseases.
Collapse
Affiliation(s)
| | - James S. Owen
- Division of MedicineUniversity College LondonLondonUK
| | - Rafael J. Yáñez‐Muñoz
- AGCTlab.orgCentre of Gene and Cell TherapyCentre for Biomedical SciencesDepartment of Biological SciencesSchool of Life Sciences and the EnvironmentRoyal Holloway University of LondonEghamUK
| |
Collapse
|
20
|
Khorkova O, Stahl J, Joji A, Volmar CH, Wahlestedt C. Amplifying gene expression with RNA-targeted therapeutics. Nat Rev Drug Discov 2023; 22:539-561. [PMID: 37253858 PMCID: PMC10227815 DOI: 10.1038/s41573-023-00704-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2023] [Indexed: 06/01/2023]
Abstract
Many diseases are caused by insufficient expression of mutated genes and would benefit from increased expression of the corresponding protein. However, in drug development, it has been historically easier to develop drugs with inhibitory or antagonistic effects. Protein replacement and gene therapy can achieve the goal of increased protein expression but have limitations. Recent discoveries of the extensive regulatory networks formed by non-coding RNAs offer alternative targets and strategies to amplify the production of a specific protein. In addition to RNA-targeting small molecules, new nucleic acid-based therapeutic modalities that allow highly specific modulation of RNA-based regulatory networks are being developed. Such approaches can directly target the stability of mRNAs or modulate non-coding RNA-mediated regulation of transcription and translation. This Review highlights emerging RNA-targeted therapeutics for gene activation, focusing on opportunities and challenges for translation to the clinic.
Collapse
Affiliation(s)
- Olga Khorkova
- OPKO Health, Miami, FL, USA
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
| | - Jack Stahl
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Aswathy Joji
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Chemistry, University of Miami, Miami, FL, USA
| | - Claude-Henry Volmar
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA.
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA.
- Department of Chemistry, University of Miami, Miami, FL, USA.
| |
Collapse
|
21
|
Dong X, Zhang K, Xun C, Chu T, Liang S, Zeng Y, Liu Z. Small Open Reading Frame-Encoded Micro-Peptides: An Emerging Protein World. Int J Mol Sci 2023; 24:10562. [PMID: 37445739 DOI: 10.3390/ijms241310562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Small open reading frames (sORFs) are often overlooked features in genomes. In the past, they were labeled as noncoding or "transcriptional noise". However, accumulating evidence from recent years suggests that sORFs may be transcribed and translated to produce sORF-encoded polypeptides (SEPs) with less than 100 amino acids. The vigorous development of computational algorithms, ribosome profiling, and peptidome has facilitated the prediction and identification of many new SEPs. These SEPs were revealed to be involved in a wide range of basic biological processes, such as gene expression regulation, embryonic development, cellular metabolism, inflammation, and even carcinogenesis. To effectively understand the potential biological functions of SEPs, we discuss the history and development of the newly emerging research on sORFs and SEPs. In particular, we review a range of recently discovered bioinformatics tools for identifying, predicting, and validating SEPs as well as a variety of biochemical experiments for characterizing SEP functions. Lastly, this review underlines the challenges and future directions in identifying and validating sORFs and their encoded micropeptides, providing a significant reference for upcoming research on sORF-encoded peptides.
Collapse
Affiliation(s)
- Xiaoping Dong
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| | - Kun Zhang
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Chengfeng Xun
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| | - Tianqi Chu
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| | - Songping Liang
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| | - Yong Zeng
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Zhonghua Liu
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| |
Collapse
|
22
|
Hedaya OM, Subbaiah KCV, Jiang F, Xie LH, Wu J, Khor E, Zhu M, Mathews DH, Proschel C, Yao P. Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.15.545153. [PMID: 37397986 PMCID: PMC10312771 DOI: 10.1101/2023.06.15.545153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Translation of upstream open reading frames (uORFs) typically abrogates translation of main (m)ORFs. The molecular mechanism of uORF regulation in cells is not well understood. Here, we identified a double-stranded RNA (dsRNA) structure residing within the GATA4 uORF that augments uORF translation and inhibits mORF translation. Antisense oligonucleotides (ASOs) that disrupt this dsRNA structure promote mORF translation, while ASOs that base-pair immediately downstream (i.e., forming a bimolecular double-stranded region) of either the uORF or mORF start codon enhance uORF or mORF translation, respectively. Human cardiomyocytes and mice treated with a uORF-enhancing ASO showed reduced cardiac GATA4 protein levels and increased resistance to cardiomyocyte hypertrophy. We further show the general utility of uORF-dsRNA- or mORF- targeting ASO to regulate mORF translation for other mRNAs. Our work demonstrates a regulatory paradigm that controls translational efficiency and a useful strategy to alter protein expression and cellular phenotypes by targeting or generating dsRNA downstream of a uORF or mORF start codon. Bullet points for discoveries dsRNA within GATA4 uORF activates uORF translation and inhibits mORF translation. ASOs that target the dsRNA can either inhibit or enhance GATA4 mORF translation. ASOs can be used to impede hypertrophy in human cardiomyocytes and mouse hearts.uORF- and mORF-targeting ASOs can be used to control translation of multiple mRNAs.
Collapse
Affiliation(s)
- Omar M. Hedaya
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Kadiam C. Venkata Subbaiah
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Feng Jiang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Li Huitong Xie
- Department of Biomedical Genetics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Jiangbin Wu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - EngSoon Khor
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Mingyi Zhu
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - David H. Mathews
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Chris Proschel
- Department of Biomedical Genetics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| |
Collapse
|
23
|
Booth BJ, Nourreddine S, Katrekar D, Savva Y, Bose D, Long TJ, Huss DJ, Mali P. RNA editing: Expanding the potential of RNA therapeutics. Mol Ther 2023; 31:1533-1549. [PMID: 36620962 PMCID: PMC9824937 DOI: 10.1016/j.ymthe.2023.01.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/06/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
RNA therapeutics have had a tremendous impact on medicine, recently exemplified by the rapid development and deployment of mRNA vaccines to combat the COVID-19 pandemic. In addition, RNA-targeting drugs have been developed for diseases with significant unmet medical needs through selective mRNA knockdown or modulation of pre-mRNA splicing. Recently, RNA editing, particularly antisense RNA-guided adenosine deaminase acting on RNA (ADAR)-based programmable A-to-I editing, has emerged as a powerful tool to manipulate RNA to enable correction of disease-causing mutations and modulate gene expression and protein function. Beyond correcting pathogenic mutations, the technology is particularly well suited for therapeutic applications that require a transient pharmacodynamic effect, such as the treatment of acute pain, obesity, viral infection, and inflammation, where it would be undesirable to introduce permanent alterations to the genome. Furthermore, transient modulation of protein function, such as altering the active sites of enzymes or the interface of protein-protein interactions, opens the door to therapeutic avenues ranging from regenerative medicine to oncology. These emerging RNA-editing-based toolsets are poised to broadly impact biotechnology and therapeutic applications. Here, we review the emerging field of therapeutic RNA editing, highlight recent laboratory advancements, and discuss the key challenges on the path to clinical development.
Collapse
Affiliation(s)
| | - Sami Nourreddine
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | | | | | | | | | | | - Prashant Mali
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
24
|
Krasnodębski C, Sawuła A, Kaźmierczak U, Żuk M. Oligo-Not Only for Silencing: Overlooked Potential for Multidirectional Action in Plants. Int J Mol Sci 2023; 24:ijms24054466. [PMID: 36901895 PMCID: PMC10002457 DOI: 10.3390/ijms24054466] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
Oligo technology is a low-cost and easy-to-implement method for direct manipulation of gene activity. The major advantage of this method is that gene expression can be changed without requiring stable transformation. Oligo technology is mainly used for animal cells. However, the use of oligos in plants seems to be even easier. The oligo effect could be similar to that induced by endogenous miRNAs. In general, the action of exogenously introduced nucleic acids (Oligo) can be divided into a direct interaction with nucleic acids (genomic DNA, hnRNA, transcript) and an indirect interaction via the induction of processes regulating gene expression (at the transcriptional and translational levels) involving regulatory proteins using endogenous cellular mechanisms. Presumed mechanisms of oligonucleotides' action in plant cells (including differences from animal cells) are described in this review. Basic principles of oligo action in plants that allow bidirectional changes in gene activity and even those that lead to heritable epigenetic changes in gene expression are presented. The effect of oligos is related to the target sequence at which they are directed. This paper also compares different delivery methods and provides a quick guide to using IT tools to help design oligonucleotides.
Collapse
Affiliation(s)
- Cezary Krasnodębski
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - Agnieszka Sawuła
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - Urszula Kaźmierczak
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14A, 50-383 Wroclaw, Poland
| | - Magdalena Żuk
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
- Correspondence:
| |
Collapse
|
25
|
Kidwell A, Yadav SPS, Maier B, Zollman A, Ni K, Halim A, Janosevic D, Myslinski J, Syed F, Zeng L, Waffo AB, Banno K, Xuei X, Doud EH, Dagher PC, Hato T. Translation Rescue by Targeting Ppp1r15a through Its Upstream Open Reading Frame in Sepsis-Induced Acute Kidney Injury in a Murine Model. J Am Soc Nephrol 2023; 34:220-240. [PMID: 36283811 PMCID: PMC10103092 DOI: 10.1681/asn.2022060644] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/23/2022] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Translation shutdown is a hallmark of late-phase, sepsis-induced kidney injury. Methods for controlling protein synthesis in the kidney are limited. Reversing translation shutdown requires dephosphorylation of the eukaryotic initiation factor 2 (eIF2) subunit eIF2 α ; this is mediated by a key regulatory molecule, protein phosphatase 1 regulatory subunit 15A (Ppp1r15a), also known as GADD34. METHODS To study protein synthesis in the kidney in a murine endotoxemia model and investigate the feasibility of translation control in vivo by boosting the protein expression of Ppp1r15a, we combined multiple tools, including ribosome profiling (Ribo-seq), proteomics, polyribosome profiling, and antisense oligonucleotides, and a newly generated Ppp1r15a knock-in mouse model and multiple mutant cell lines. RESULTS We report that translation shutdown in established sepsis-induced kidney injury is brought about by excessive eIF2 α phosphorylation and sustained by blunted expression of the counter-regulatory phosphatase Ppp1r15a. We determined the blunted Ppp1r15a expression persists because of the presence of an upstream open reading frame (uORF). Overcoming this barrier with genetic and antisense oligonucleotide approaches enabled the overexpression of Ppp1r15a, which salvaged translation and improved kidney function in an endotoxemia model. Loss of this uORF also had broad effects on the composition and phosphorylation status of the immunopeptidome-peptides associated with the MHC-that extended beyond the eIF2 α axis. CONCLUSIONS We found Ppp1r15a is translationally repressed during late-phase sepsis because of the existence of an uORF, which is a prime therapeutic candidate for this strategic rescue of translation in late-phase sepsis. The ability to accurately control translation dynamics during sepsis may offer new paths for the development of therapies at codon-level precision. PODCAST This article contains a podcast at.
Collapse
Affiliation(s)
- Ashley Kidwell
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | | | - Bernhard Maier
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Amy Zollman
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Kevin Ni
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Arvin Halim
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Danielle Janosevic
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jered Myslinski
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Farooq Syed
- Department of Pediatrics and the Herman B. Wells Center, Indiana University School of Medicine, Indianapolis, Indiana
| | - Lifan Zeng
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Alain Bopda Waffo
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Kimihiko Banno
- Department of Physiology, Nara Medical University, Kashihara, Japan
| | - Xiaoling Xuei
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Emma H. Doud
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Pierre C. Dagher
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Takashi Hato
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
- Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, Indiana
| |
Collapse
|
26
|
Goyenvalle A, Jimenez-Mallebrera C, van Roon W, Sewing S, Krieg AM, Arechavala-Gomeza V, Andersson P. Considerations in the Preclinical Assessment of the Safety of Antisense Oligonucleotides. Nucleic Acid Ther 2023; 33:1-16. [PMID: 36579950 PMCID: PMC9940817 DOI: 10.1089/nat.2022.0061] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The nucleic acid therapeutics field has made tremendous progress in the past decades. Continuous advances in chemistry and design have led to many successful clinical applications, eliciting even more interest from researchers including both academic groups and drug development companies. Many preclinical studies in the field focus on improving the delivery of antisense oligonucleotide drugs (ONDs) and/or assessing their efficacy in target tissues, often neglecting the evaluation of toxicity, at least in early phases of development. A series of consensus recommendations regarding regulatory considerations and expectations have been generated by the Oligonucleotide Safety Working Group and the Japanese Research Working Group for the International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use S6 and Related Issues (WGS6) in several white papers. However, safety aspects should also be kept in sight in earlier phases while screening and designing OND to avoid subsequent failure in the development phase. Experts and members of the network "DARTER," a COST Action funded by the Cooperation in Science and Technology of the EU, have utilized their collective experience working with OND, as well as their insights into OND-mediated toxicities, to generate a series of consensus recommendations to assess OND toxicity in early stages of preclinical research. In the past few years, several publications have described predictive assays, which can be used to assess OND-mediated toxicity in vitro or ex vivo to filter out potential toxic candidates before moving to in vivo phases of preclinical development, that is, animal toxicity studies. These assays also have the potential to provide translational insight since they allow a safety evaluation in human in vitro systems. Yet, small preliminary in vivo studies should also be considered to complement this early assessment. In this study, we summarize the state of the art and provide guidelines and recommendations on the different tests available for these early stage preclinical assessments.
Collapse
Affiliation(s)
- Aurélie Goyenvalle
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, Versailles, France.,Address correspondence to: Aurélie Goyenvalle, PhD, Université Paris-Saclay, UVSQ, Inserm, END-ICAP, Versailles 78000, France
| | - Cecilia Jimenez-Mallebrera
- Laboratorio de Investigación Aplicada en Enfermedades Neuromusculares, Unidad de Patología Neuromuscular, Servicio de Neuropediatría, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain.,Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Departamento de Genética, Microbiología y Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Willeke van Roon
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sabine Sewing
- Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Arthur M. Krieg
- RNA Therapeutics Institute, University of Massachusetts, Worcester, Massachusetts, USA
| | - Virginia Arechavala-Gomeza
- Neuromuscular Disorders, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Patrik Andersson
- Safety Innovation, Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden.,Address correspondence to: Patrik Andersson, PhD, Safety Innovation, Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Pepparedsleden 1, Mölndal, Gothenburg 431 83, Sweden
| |
Collapse
|
27
|
Amanat M, Nemeth CL, Fine AS, Leung DG, Fatemi A. Antisense Oligonucleotide Therapy for the Nervous System: From Bench to Bedside with Emphasis on Pediatric Neurology. Pharmaceutics 2022; 14:2389. [PMID: 36365206 PMCID: PMC9695718 DOI: 10.3390/pharmaceutics14112389] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 09/05/2023] Open
Abstract
Antisense oligonucleotides (ASOs) are disease-modifying agents affecting protein-coding and noncoding ribonucleic acids. Depending on the chemical modification and the location of hybridization, ASOs are able to reduce the level of toxic proteins, increase the level of functional protein, or modify the structure of impaired protein to improve function. There are multiple challenges in delivering ASOs to their site of action. Chemical modifications in the phosphodiester bond, nucleotide sugar, and nucleobase can increase structural thermodynamic stability and prevent ASO degradation. Furthermore, different particles, including viral vectors, conjugated peptides, conjugated antibodies, and nanocarriers, may improve ASO delivery. To date, six ASOs have been approved by the US Food and Drug Administration (FDA) in three neurological disorders: spinal muscular atrophy, Duchenne muscular dystrophy, and polyneuropathy caused by hereditary transthyretin amyloidosis. Ongoing preclinical and clinical studies are assessing the safety and efficacy of ASOs in multiple genetic and acquired neurological conditions. The current review provides an update on underlying mechanisms, design, chemical modifications, and delivery of ASOs. The administration of FDA-approved ASOs in neurological disorders is described, and current evidence on the safety and efficacy of ASOs in other neurological conditions, including pediatric neurological disorders, is reviewed.
Collapse
Affiliation(s)
- Man Amanat
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christina L. Nemeth
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Amena Smith Fine
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Doris G. Leung
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Genetic Muscle Disorders, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Ali Fatemi
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| |
Collapse
|
28
|
Mittal S, Tang I, Gleeson JG. Evaluating human mutation databases for “treatability” using patient-customized therapy. MED 2022; 3:740-759. [DOI: 10.1016/j.medj.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 08/04/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022]
|
29
|
Mollica L, Cupaioli FA, Rossetti G, Chiappori F. An overview of structural approaches to study therapeutic RNAs. Front Mol Biosci 2022; 9:1044126. [PMID: 36387283 PMCID: PMC9649582 DOI: 10.3389/fmolb.2022.1044126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2023] Open
Abstract
RNAs provide considerable opportunities as therapeutic agent to expand the plethora of classical therapeutic targets, from extracellular and surface proteins to intracellular nucleic acids and its regulators, in a wide range of diseases. RNA versatility can be exploited to recognize cell types, perform cell therapy, and develop new vaccine classes. Therapeutic RNAs (aptamers, antisense nucleotides, siRNA, miRNA, mRNA and CRISPR-Cas9) can modulate or induce protein expression, inhibit molecular interactions, achieve genome editing as well as exon-skipping. A common RNA thread, which makes it very promising for therapeutic applications, is its structure, flexibility, and binding specificity. Moreover, RNA displays peculiar structural plasticity compared to proteins as well as to DNA. Here we summarize the recent advances and applications of therapeutic RNAs, and the experimental and computational methods to analyze their structure, by biophysical techniques (liquid-state NMR, scattering, reactivity, and computational simulations), with a focus on dynamic and flexibility aspects and to binding analysis. This will provide insights on the currently available RNA therapeutic applications and on the best techniques to evaluate its dynamics and reactivity.
Collapse
Affiliation(s)
- Luca Mollica
- Department of Medical Biotechnologies and Translational Medicine, L.I.T.A/University of Milan, Milan, Italy
| | | | | | - Federica Chiappori
- National Research Council—Institute for Biomedical Technologies, Milan, Italy
| |
Collapse
|
30
|
Huang S, Hao XY, Li YJ, Wu JY, Xiang DX, Luo S. Nonviral delivery systems for antisense oligonucleotide therapeutics. Biomater Res 2022; 26:49. [PMID: 36180936 PMCID: PMC9523189 DOI: 10.1186/s40824-022-00292-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/30/2022] [Indexed: 11/10/2022] Open
Abstract
Antisense oligonucleotides (ASOs) are an important tool for the treatment of many genetic disorders. However, similar to other gene drugs, vectors are often required to protect them from degradation and clearance, and to accomplish their transport in vivo. Compared with viral vectors, artificial nonviral nanoparticles have a variety of design, synthesis, and formulation possibilities that can be selected to accomplish protection and delivery for specific applications, and they have served critical therapeutic purposes in animal model research and clinical applications, allowing safe and efficient gene delivery processes into the target cells. We believe that as new ASO drugs develop, the exploration for corresponding nonviral vectors is inevitable. Intensive development of nonviral vectors with improved delivery strategies based on specific targets can continue to expand the value of ASO therapeutic approaches. Here, we provide an overview of current nonviral delivery strategies, including ASOs modifications, action mechanisms, and multi-carrier methods, which aim to address the irreplaceable role of nonviral vectors in the progressive development of ASOs delivery.
Collapse
Affiliation(s)
- Si Huang
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China.,Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, 410011, People's Republic of China.,Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Xin-Yan Hao
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China.,Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, 410011, People's Republic of China.,Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Yong-Jiang Li
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China.,Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, 410011, People's Republic of China.,Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Jun-Yong Wu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China.,Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, 410011, People's Republic of China.,Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Da-Xiong Xiang
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China.,Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, 410011, People's Republic of China.,Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Shilin Luo
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China. .,Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, 410011, People's Republic of China. .,Institute of Clinical Pharmacy, Central South University, Changsha, China.
| |
Collapse
|
31
|
Internal Ribosome Entry Site (IRES)-Mediated Translation and Its Potential for Novel mRNA-Based Therapy Development. Biomedicines 2022; 10:biomedicines10081865. [PMID: 36009412 PMCID: PMC9405587 DOI: 10.3390/biomedicines10081865] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 11/17/2022] Open
Abstract
Many conditions can benefit from RNA-based therapies, namely, those targeting internal ribosome entry sites (IRESs) and their regulatory proteins, the IRES trans-acting factors (ITAFs). IRES-mediated translation is an alternative mechanism of translation initiation, known for maintaining protein synthesis when canonical translation is impaired. During a stress response, it contributes to cell reprogramming and adaptation to the new environment. The relationship between IRESs and ITAFs with tumorigenesis and resistance to therapy has been studied in recent years, proposing new therapeutic targets and treatments. In addition, IRES-dependent translation initiation dysregulation is also related to neurological and cardiovascular diseases, muscular atrophies, or other syndromes. The participation of these structures in the development of such pathologies has been studied, yet to a far lesser extent than in cancer. Strategies involving the disruption of IRES–ITAF interactions or the modification of ITAF expression levels may be used with great impact in the development of new therapeutics. In this review, we aim to comprehend the current data on groups of human pathologies associated with IRES and/or ITAF dysregulation and their application in the designing of new therapeutic approaches using them as targets or tools. Thus, we wish to summarise the evidence in the field hoping to open new promising lines of investigation toward personalised treatments.
Collapse
|
32
|
Zhu Y, Zhu L, Wang X, Jin H. RNA-based therapeutics: an overview and prospectus. Cell Death Dis 2022; 13:644. [PMID: 35871216 PMCID: PMC9308039 DOI: 10.1038/s41419-022-05075-2] [Citation(s) in RCA: 172] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 01/21/2023]
Abstract
The growing understanding of RNA functions and their crucial roles in diseases promotes the application of various RNAs to selectively function on hitherto "undruggable" proteins, transcripts and genes, thus potentially broadening the therapeutic targets. Several RNA-based medications have been approved for clinical use, while others are still under investigation or preclinical trials. Various techniques have been explored to promote RNA intracellular trafficking and metabolic stability, despite significant challenges in developing RNA-based therapeutics. In this review, the mechanisms of action, challenges, solutions, and clinical application of RNA-based therapeutics have been comprehensively summarized.
Collapse
Affiliation(s)
- Yiran Zhu
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Liyuan Zhu
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Xian Wang
- grid.13402.340000 0004 1759 700XDepartment of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Hongchuan Jin
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| |
Collapse
|
33
|
Zhang L, Bernardo KD, Vickers TA, Tian J, Liang XH, Crooke ST. NAT10 and DDX21 Proteins Interact with RNase H1 and Affect the Performance of Phosphorothioate Oligonucleotides. Nucleic Acid Ther 2022; 32:280-299. [PMID: 35852833 PMCID: PMC9416547 DOI: 10.1089/nat.2021.0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
RNase H1-dependent phosphorothioate oligonucleotides (PS-ASOs) have been developed to treat various diseases through specific degradation of target RNAs. Although many factors or features of RNA and PS-ASOs have been demonstrated to affect antisense activity of PS-ASOs, little is known regarding the roles of RNase H1-associated proteins in PS-ASO performance. In this study, we report that two nucleolar proteins, NAT10 and DDX21, interact with RNase H1 and affect the potency and safety of PS-ASOs. The interactions of these two proteins with RNase H1 were determined using BioID proximity labeling in cells and confirmed biochemically. Reduction of NAT10 and DDX21 decreased PS-ASO activity in cells, and purified NAT10 and DDX21 proteins enhanced RNase H1 cleavage rates, indicating that these two proteins facilitate RNase H1 endoribonuclease activity. Consistently, reduction of these proteins increased the levels of R-loops, and impaired pre-rRNA processing. In addition, reduction of the two proteins increased the cytotoxicity of toxic PS-ASOs, and treatment of toxic PS-ASOs also altered the localization of these proteins. Together, this study shows for the first time that NAT10 and DDX21 interact with RNase H1 protein and enhance its enzymatic activity, contributing to the potency and safety of PS-ASOs.
Collapse
Affiliation(s)
- Lingdi Zhang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Karla D. Bernardo
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Timothy A. Vickers
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Jun Tian
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Xue-hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Stanley T. Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| |
Collapse
|
34
|
Curreri A, Sankholkar D, Mitragotri S, Zhao Z. RNA therapeutics in the clinic. Bioeng Transl Med 2022; 8:e10374. [PMID: 36684099 PMCID: PMC9842029 DOI: 10.1002/btm2.10374] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/08/2022] [Indexed: 01/25/2023] Open
Abstract
Ribonucleic acid (RNA) therapeutics are being actively researched as a therapeutic modality in preclinical and clinical studies. They have become one of the most ubiquitously known and discussed therapeutics in recent years in part due to the ongoing coronavirus pandemic. Since the first approval in 1998, research on RNA therapeutics has progressed to discovering new therapeutic targets and delivery strategies to enhance their safety and efficacy. Here, we provide an overview of the current clinically relevant RNA therapeutics, mechanistic basis of their function, and strategies to improve their clinical use. We discuss the 17 approved RNA therapeutics and perform an in-depth analysis of the 222 ongoing clinical trials, with an emphasis on their respective mechanisms and disease areas. We also provide perspectives on the challenges for clinical translation of RNA therapeutics and suggest potential strategies to address these challenges.
Collapse
Affiliation(s)
- Alexander Curreri
- John A. Paulson School of Engineering and Applied SciencesHarvard UniversityCambridgeMassachusettsUSA,Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMassachusettsUSA
| | | | - Samir Mitragotri
- John A. Paulson School of Engineering and Applied SciencesHarvard UniversityCambridgeMassachusettsUSA,Wyss Institute for Biologically Inspired Engineering at Harvard UniversityBostonMassachusettsUSA
| | - Zongmin Zhao
- Department of Pharmaceutical Sciences, College of PharmacyUniversity of Illinois at ChicagoChicagoIllinoisUSA,University of Illinois Cancer CenterChicagoIllinoisUSA
| |
Collapse
|
35
|
RNA modifications can affect RNase H1-mediated PS-ASO activity. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:814-828. [PMID: 35664704 PMCID: PMC9136273 DOI: 10.1016/j.omtn.2022.05.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/07/2022] [Indexed: 11/21/2022]
|
36
|
Zhou X, Rao S, Wrightstone E, Sun T, Lui ACW, Welsch R, Li L. Phytoene Synthase: The Key Rate-Limiting Enzyme of Carotenoid Biosynthesis in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:884720. [PMID: 35498681 PMCID: PMC9039723 DOI: 10.3389/fpls.2022.884720] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 03/16/2022] [Indexed: 05/27/2023]
Abstract
Phytoene synthase (PSY) catalyzes the first committed step in the carotenoid biosynthesis pathway and is a major rate-limiting enzyme of carotenogenesis. PSY is highly regulated by various regulators and factors to modulate carotenoid biosynthesis in response to diverse developmental and environmental cues. Because of its critical role in controlling the total amount of synthesized carotenoids, PSY has been extensively investigated and engineered in plant species. However, much remains to be learned on its multifaceted regulatory control and its catalytic efficiency for carotenoid enrichment in crops. Here, we present current knowledge on the basic biology, the functional evolution, the dynamic regulation, and the metabolic engineering of PSY. We also discuss the open questions and gaps to stimulate additional research on this most studied gene/enzyme in the carotenogenic pathway.
Collapse
Affiliation(s)
- Xuesong Zhou
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, United States
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Sombir Rao
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, United States
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Emalee Wrightstone
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, United States
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Tianhu Sun
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, United States
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Andy Cheuk Woon Lui
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, United States
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | | | - Li Li
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, United States
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| |
Collapse
|
37
|
Pandey PR, Young KH, Kumar D, Jain N. RNA-mediated immunotherapy regulating tumor immune microenvironment: next wave of cancer therapeutics. Mol Cancer 2022; 21:58. [PMID: 35189921 PMCID: PMC8860277 DOI: 10.1186/s12943-022-01528-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/31/2022] [Indexed: 12/16/2022] Open
Abstract
AbstractAccumulating research suggests that the tumor immune microenvironment (TIME) plays an essential role in regulation of tumor growth and metastasis. The cellular and molecular nature of the TIME influences cancer progression and metastasis by altering the ratio of immune- suppressive versus cytotoxic responses in the vicinity of the tumor. Targeting or activating the TIME components show a promising therapeutic avenue to combat cancer. The success of immunotherapy is both astounding and unsatisfactory in the clinic. Advancements in RNA-based technology have improved understanding of the complexity and diversity of the TIME and its effects on therapy. TIME-related RNA or RNA regulators could be promising targets for anticancer immunotherapy. In this review, we discuss the available RNA-based cancer immunotherapies targeting the TIME. More importantly, we summarize the potential of various RNA-based therapeutics clinically available for cancer treatment. RNA-dependent targeting of the TIME, as monotherapy or combined with other evolving therapeutics, might be beneficial for cancer patients’ treatment in the near future.
Collapse
|
38
|
Hui RWH, Mak LY, Seto WK, Yuen MF. RNA interference as a novel treatment strategy for chronic hepatitis B infection. Clin Mol Hepatol 2022; 28:408-424. [PMID: 35172540 PMCID: PMC9293617 DOI: 10.3350/cmh.2022.0012] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 11/26/2022] Open
Abstract
Chronic hepatitis B (CHB) is a major cause of liver-related morbidity and mortality. Functional cure of CHB, defined as sustainable hepatitis B surface antigen (HBsAg) seroclearance, is associated with improved clinical outcomes. However, functional cure is rarely attainable by current treatment modalities. RNA interference (RNAi) by small-interfering RNA (siRNA) and anti-sense oligonucleotide (ASO) has been studied as a novel treatment strategy for CHB. RNAi targets post-transcriptional messenger RNAs and pregenomic RNAs to reduce hepatitis B virus (HBV) antigen production and viral replication. By reducing viral antigens, host immune reconstitution against HBV may also be attained. Phase I/II trials on siRNAs have demonstrated them to be safe and well-tolerated. siRNA is effective when given in monthly doses with different total number of doses according to different trial design, and can lead to sustainable dose-dependent mean HBsAg reduction by 2–2.5 log. Incidences of HBsAg seroclearance after siRNA therapy have also been reported. ASOs have also been studied in early phase trials, and a phase Ib study using frequent dosing regimen within 4 weeks could achieve similar HBsAg reduction of 2 log from baseline. Given the established efficacy and safety of nucleos(t) ide analogues (NAs), future RNAi regimens will likely include NA backbone. While the current evidence on RNAi appears promising, it remains undetermined whether the potent HBsAg reduction by RNAi can result in a high rate of HBsAg seroclearance with durability. Data on RNAi from phase IIb/III trials are keenly anticipated.
Collapse
Affiliation(s)
- Rex Wan-Hin Hui
- Department of Medicine, The University of Hong Kong, Hong Kong
| | - Lung-Yi Mak
- Department of Medicine, The University of Hong Kong, Hong Kong.,State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Wai-Kay Seto
- Department of Medicine, The University of Hong Kong, Hong Kong.,State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Man-Fung Yuen
- Department of Medicine, The University of Hong Kong, Hong Kong.,State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| |
Collapse
|
39
|
Van de Vyver T, De Smedt SC, Raemdonck K. Modulating intracellular pathways to improve non-viral delivery of RNA therapeutics. Adv Drug Deliv Rev 2022; 181:114041. [PMID: 34763002 DOI: 10.1016/j.addr.2021.114041] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/12/2021] [Accepted: 11/02/2021] [Indexed: 12/12/2022]
Abstract
RNA therapeutics (e.g. siRNA, oligonucleotides, mRNA, etc.) show great potential for the treatment of a myriad of diseases. However, to reach their site of action in the cytosol or nucleus of target cells, multiple intra- and extracellular barriers have to be surmounted. Several non-viral delivery systems, such as nanoparticles and conjugates, have been successfully developed to meet this requirement. Unfortunately, despite these clear advances, state-of-the-art delivery agents still suffer from relatively low intracellular delivery efficiencies. Notably, our current understanding of the intracellular delivery process is largely oversimplified. Gaining mechanistic insight into how RNA formulations are processed by cells will fuel rational design of the next generation of delivery carriers. In addition, identifying which intracellular pathways contribute to productive RNA delivery could provide opportunities to boost the delivery performance of existing nanoformulations. In this review, we discuss both established as well as emerging techniques that can be used to assess the impact of different intracellular barriers on RNA transfection performance. Next, we highlight how several modulators, including small molecules but also genetic perturbation technologies, can boost RNA delivery by intervening at differing stages of the intracellular delivery process, such as cellular uptake, intracellular trafficking, endosomal escape, autophagy and exocytosis.
Collapse
Affiliation(s)
- Thijs Van de Vyver
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Stefaan C De Smedt
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Koen Raemdonck
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| |
Collapse
|
40
|
Quemener AM, Centomo ML, Sax SL, Panella R. Small Drugs, Huge Impact: The Extraordinary Impact of Antisense Oligonucleotides in Research and Drug Development. Molecules 2022; 27:536. [PMID: 35056851 PMCID: PMC8781596 DOI: 10.3390/molecules27020536] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/15/2021] [Accepted: 12/18/2021] [Indexed: 01/27/2023] Open
Abstract
Antisense oligonucleotides (ASOs) are an increasingly represented class of drugs. These small sequences of nucleotides are designed to precisely target other oligonucleotides, usually RNA species, and are modified to protect them from degradation by nucleases. Their specificity is due to their sequence, so it is possible to target any RNA sequence that is already known. These molecules are very versatile and adaptable given that their sequence and chemistry can be custom manufactured. Based on the chemistry being used, their activity may significantly change and their effects on cell function and phenotypes can differ dramatically. While some will cause the target RNA to decay, others will only bind to the target and act as a steric blocker. Their incredible versatility is the key to manipulating several aspects of nucleic acid function as well as their process, and alter the transcriptome profile of a specific cell type or tissue. For example, they can be used to modify splicing or mask specific sites on a target. The entire design rather than just the sequence is essential to ensuring the specificity of the ASO to its target. Thus, it is vitally important to ensure that the complete process of drug design and testing is taken into account. ASOs' adaptability is a considerable advantage, and over the past decades has allowed multiple new drugs to be approved. This, in turn, has had a significant and positive impact on patient lives. Given current challenges presented by the COVID-19 pandemic, it is necessary to find new therapeutic strategies that would complement the vaccination efforts being used across the globe. ASOs may be a very powerful tool that can be used to target the virus RNA and provide a therapeutic paradigm. The proof of the efficacy of ASOs as an anti-viral agent is long-standing, yet no molecule currently has FDA approval. The emergence and widespread use of RNA vaccines during this health crisis might provide an ideal opportunity to develop the first anti-viral ASOs on the market. In this review, we describe the story of ASOs, the different characteristics of their chemistry, and how their characteristics translate into research and as a clinical tool.
Collapse
Affiliation(s)
- Anais M. Quemener
- University Rennes, CNRS, IGDR (Institute of Genetics and Development of Rennes)-UMR 6290, F-35000 Rennes, France;
| | - Maria Laura Centomo
- Department of Oncology, University of Turin, 10124 Turin, Italy;
- Center for Genomic Medicine, Desert Research Institute, Reno, NV 89512, USA;
| | - Scott L. Sax
- Center for Genomic Medicine, Desert Research Institute, Reno, NV 89512, USA;
| | - Riccardo Panella
- Center for Genomic Medicine, Desert Research Institute, Reno, NV 89512, USA;
| |
Collapse
|
41
|
Crooke ST. Meeting the needs of patients with ultrarare diseases. Trends Mol Med 2022; 28:87-96. [PMID: 35000835 DOI: 10.1016/j.molmed.2021.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/19/2021] [Accepted: 12/02/2021] [Indexed: 12/16/2022]
Abstract
Patients with ultrarare diseases present unique challenges to the health care systems of developed economies that demand novel approaches, beginning with achieving a diagnosis and concluding with long-term treatment. The challenges derive from numbers. On the one hand, the rarity of the disease phenotypes means that the vast majority of ultrarare patients are never diagnosed, and for the fortunate few who are diagnosed, the journey to a genetic diagnosis is long and perilous. On the other hand, as more human genomes are sequenced, the number of these patients identified is growing logarithmically. Once patients are diagnosed, personalized medicines must be rapidly developed and delivered. Here I define the problems and propose a nonprofit model to meet the needs of some of these patients.
Collapse
|
42
|
Crooke ST. Progress in molecular biology and translational science addressing the needs of nano-rare patients. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 190:127-146. [DOI: 10.1016/bs.pmbts.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
43
|
Li M, Jancovski N, Jafar-Nejad P, Burbano LE, Rollo B, Richards K, Drew L, Sedo A, Heighway J, Pachernegg S, Soriano A, Jia L, Blackburn T, Roberts B, Nemiroff A, Dalby K, Maljevic S, Reid CA, Rigo F, Petrou S. Antisense oligonucleotide therapy reduces seizures and extends life span in an SCN2A gain-of-function epilepsy model. J Clin Invest 2021; 131:152079. [PMID: 34850743 DOI: 10.1172/jci152079] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/01/2021] [Indexed: 01/21/2023] Open
Abstract
De novo variation in SCN2A can give rise to severe childhood disorders. Biophysical gain of function in SCN2A is seen in some patients with early seizure onset developmental and epileptic encephalopathy (DEE). In these cases, targeted reduction in SCN2A expression could substantially improve clinical outcomes. We tested this theory by central administration of a gapmer antisense oligonucleotide (ASO) targeting Scn2a mRNA in a mouse model of Scn2a early seizure onset DEE (Q/+ mice). Untreated Q/+ mice presented with spontaneous seizures at P1 and did not survive beyond P30. Administration of the ASO to Q/+ mice reduced spontaneous seizures and significantly extended life span. Across a range of behavioral tests, Scn2a ASO-treated Q/+ mice were largely indistinguishable from WT mice, suggesting treatment is well tolerated. A human SCN2A gapmer ASO could likewise impact the lives of patients with SCN2A gain-of-function DEE.
Collapse
Affiliation(s)
- Melody Li
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Nikola Jancovski
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | | | - Lisseth E Burbano
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Ben Rollo
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Kay Richards
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Lisa Drew
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Alicia Sedo
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Jacqueline Heighway
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Svenja Pachernegg
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | | | - Linghan Jia
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Todd Blackburn
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia.,RogCon Biosciences, Miami Beach, Florida, USA
| | - Blaine Roberts
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Alex Nemiroff
- RogCon Biosciences, Miami Beach, Florida, USA.,Praxis Precision Medicines, Boston, Massachusetts, USA
| | - Kelley Dalby
- RogCon Biosciences, Miami Beach, Florida, USA.,Praxis Precision Medicines, Boston, Massachusetts, USA
| | - Snezana Maljevic
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Christopher A Reid
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Steven Petrou
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia.,RogCon Biosciences, Miami Beach, Florida, USA.,Praxis Precision Medicines, Boston, Massachusetts, USA
| |
Collapse
|
44
|
Wdowikowska A, Janicka M. Antisense oligonucleotide technology as a research tool in plant biology. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 49:1-12. [PMID: 34794541 DOI: 10.1071/fp21194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
An antisense oligonucleotide (ASO) is a short single-stranded deoxyribonucleotide complementary to the sense strand of a selected nucleic acid. As a result, an ASO can modulate gene expression through several mechanisms. The technology based on ASO has already been applied in studies on gene function in mammalian cells and selective therapeutic strategies for many diseases. The conceptual simplicity and low cost of this method, and the developments in the field of plant genome sequencing observed in the last decades, have paved the way for the ASO method also in plant biology. It is applied in gene function analysis as well as the development of non-invasive plant production technology involving gene modifications without transgenesis. Therefore, the first part of this review provides a comprehensive overview of the structure, mechanism of action and delivery methods of ASOs in plants and shows the most important features essential for the proper design of individual experiments. We also discuss potential issues and difficulties that may arise during practical ASO implementation. The second part of this article contains an analysis of ASO applications in various studies in the field of plant biology. We presented for the first time that ASOs were also successfully applied in cucumber.
Collapse
Affiliation(s)
- Anna Wdowikowska
- Department of Plant Molecular Physiology, Faculty of Biological Sciences, University of Wroclaw, Kanonia 6/8, 50-328 Wroclaw, Poland
| | - Malgorzata Janicka
- Department of Plant Molecular Physiology, Faculty of Biological Sciences, University of Wroclaw, Kanonia 6/8, 50-328 Wroclaw, Poland
| |
Collapse
|
45
|
Li Y, Li J, Wang J, Lynch D, Shen X, R. Corey D, Parekh D, Bhat B, Woo C, Cherry J, Napierala J, Napierala M. Targeting 3' and 5' untranslated regions with antisense oligonucleotides to stabilize frataxin mRNA and increase protein expression. Nucleic Acids Res 2021; 49:11560-11574. [PMID: 34718736 PMCID: PMC8599914 DOI: 10.1093/nar/gkab954] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/26/2022] Open
Abstract
Friedreich's ataxia (FRDA) is a severe multisystem disease caused by transcriptional repression induced by expanded GAA repeats located in intron 1 of the Frataxin (FXN) gene encoding frataxin. FRDA results from decreased levels of frataxin; thus, stabilization of the FXN mRNA already present in patient cells represents an attractive and unexplored therapeutic avenue. In this work, we pursued a novel approach based on oligonucleotide-mediated targeting of FXN mRNA ends to extend its half-life and availability as a template for translation. We demonstrated that oligonucleotides designed to bind to FXN 5' or 3' noncoding regions can increase FXN mRNA and protein levels. Simultaneous delivery of oligonucleotides targeting both ends increases efficacy of the treatment. The approach was confirmed in several FRDA fibroblast and induced pluripotent stem cell-derived neuronal progenitor lines. RNA sequencing and single-cell expression analyses confirmed oligonucleotide-mediated FXN mRNA upregulation. Mechanistically, a significant elongation of the FXN mRNA half-life without any changes in chromatin status at the FXN gene was observed upon treatment with end-targeting oligonucleotides, indicating that transcript stabilization is responsible for frataxin upregulation. These results identify a novel approach toward upregulation of steady-state mRNA levels via oligonucleotide-mediated end targeting that may be of significance to any condition resulting from transcription downregulation.
Collapse
Affiliation(s)
- Yanjie Li
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA
| | - Jixue Li
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA
| | - Jun Wang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA
| | - David R Lynch
- Division of Neurology and Pediatrics, Children’s Hospital of Philadelphia, Abramson Research Center, Room 502, Philadelphia, PA 19104, USA
| | - Xiulong Shen
- Department of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David R. Corey
- Department of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Darshan Parekh
- Translate Bio, 29 Hartwell Avenue, Lexington, MA 02421, USA
| | | | - Caroline Woo
- Translate Bio, 29 Hartwell Avenue, Lexington, MA 02421, USA
| | | | - Jill S Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA
| | - Marek Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA
| |
Collapse
|
46
|
Carvill GL, Matheny T, Hesselberth J, Demarest S. Haploinsufficiency, Dominant Negative, and Gain-of-Function Mechanisms in Epilepsy: Matching Therapeutic Approach to the Pathophysiology. Neurotherapeutics 2021; 18:1500-1514. [PMID: 34648141 PMCID: PMC8608973 DOI: 10.1007/s13311-021-01137-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2021] [Indexed: 02/04/2023] Open
Abstract
This review summarizes the pathogenic mechanisms that underpin the monogenic epilepsies and discusses the potential of novel precision therapeutics to treat these disorders. Pathogenic mechanisms of epilepsy include recessive (null alleles), haploinsufficiency, imprinting, gain-of-function, and dominant negative effects. Understanding which pathogenic mechanism(s) that underlie each genetic epilepsy is pivotal to design precision therapies that are most likely to be beneficial for the patient. Novel therapeutics discussed include gene therapy, gene editing, antisense oligonucleotides, and protein replacement. Discussions are illustrated and reinforced with examples from the literature.
Collapse
Affiliation(s)
- Gemma L Carvill
- Departments of Neurology, Pharmacology and Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Tyler Matheny
- Department Biochemistry and Molecular Genetics, School of Medicine, RNA Bioscience Initiative, University of Colorado, PO Box 6511, Aurora, CO, USA
| | - Jay Hesselberth
- Department Biochemistry and Molecular Genetics, School of Medicine, RNA Bioscience Initiative, University of Colorado, PO Box 6511, Aurora, CO, USA
| | - Scott Demarest
- Departments of Pediatrics and Neurology, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA.
| |
Collapse
|
47
|
Lenaers G, Neutzner A, Le Dantec Y, Jüschke C, Xiao T, Decembrini S, Swirski S, Kieninger S, Agca C, Kim US, Reynier P, Yu-Wai-Man P, Neidhardt J, Wissinger B. Dominant optic atrophy: Culprit mitochondria in the optic nerve. Prog Retin Eye Res 2021; 83:100935. [PMID: 33340656 DOI: 10.1016/j.preteyeres.2020.100935] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/05/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022]
Abstract
Dominant optic atrophy (DOA) is an inherited mitochondrial disease leading to specific degeneration of retinal ganglion cells (RGCs), thus compromising transmission of visual information from the retina to the brain. Usually, DOA starts during childhood and evolves to poor vision or legal blindness, affecting the central vision, whilst sparing the peripheral visual field. In 20% of cases, DOA presents as syndromic disorder, with secondary symptoms affecting neuronal and muscular functions. Twenty years ago, we demonstrated that heterozygous mutations in OPA1 are the most frequent molecular cause of DOA. Since then, variants in additional genes, whose functions in many instances converge with those of OPA1, have been identified by next generation sequencing. OPA1 encodes a dynamin-related GTPase imported into mitochondria and located to the inner membrane and intermembrane space. The many OPA1 isoforms, resulting from alternative splicing of three exons, form complex homopolymers that structure mitochondrial cristae, and contribute to fusion of the outer membrane, thus shaping the whole mitochondrial network. Moreover, OPA1 is required for oxidative phosphorylation, maintenance of mitochondrial genome, calcium homeostasis and regulation of apoptosis, thus making OPA1 the Swiss army-knife of mitochondria. Understanding DOA pathophysiology requires the understanding of RGC peculiarities with respect to OPA1 functions. Besides the tremendous energy requirements of RGCs to relay visual information from the eye to the brain, these neurons present unique features related to their differential environments in the retina, and to the anatomical transition occurring at the lamina cribrosa, which parallel major adaptations of mitochondrial physiology and shape, in the pre- and post-laminar segments of the optic nerve. Three DOA mouse models, with different Opa1 mutations, have been generated to study intrinsic mechanisms responsible for RGC degeneration, and these have further revealed secondary symptoms related to mitochondrial dysfunctions, mirroring the more severe syndromic phenotypes seen in a subgroup of patients. Metabolomics analyses of cells, mouse organs and patient plasma mutated for OPA1 revealed new unexpected pathophysiological mechanisms related to mitochondrial dysfunction, and biomarkers correlated quantitatively to the severity of the disease. Here, we review and synthesize these data, and propose different approaches for embracing possible therapies to fulfil the unmet clinical needs of this disease, and provide hope to affected DOA patients.
Collapse
Affiliation(s)
- Guy Lenaers
- MitoLab Team, UMR CNRS 6015 - INSERM U1083, Institut MitoVasc, Angers University and Hospital, Angers, France.
| | - Albert Neutzner
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland; Department of Ophthalmology University Hospital Basel, University of Basel, Basel, Switzerland.
| | - Yannick Le Dantec
- MitoLab Team, UMR CNRS 6015 - INSERM U1083, Institut MitoVasc, Angers University and Hospital, Angers, France
| | - Christoph Jüschke
- Human Genetics, Faculty VI - School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
| | - Ting Xiao
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Sarah Decembrini
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland; Department of Ophthalmology University Hospital Basel, University of Basel, Basel, Switzerland
| | - Sebastian Swirski
- Human Genetics, Faculty VI - School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
| | - Sinja Kieninger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Cavit Agca
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, Istanbul, Turkey; Nanotechnology Research and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
| | - Ungsoo S Kim
- Kim's Eye Hospital, Seoul, South Korea; Cambridge Centre for Brain Repair and MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK; Cambridge Eye Unit, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK; Moorfields Eye Hospital, London, UK
| | - Pascal Reynier
- MitoLab Team, UMR CNRS 6015 - INSERM U1083, Institut MitoVasc, Angers University and Hospital, Angers, France; Department of Biochemistry, University Hospital of Angers, Angers, France
| | - Patrick Yu-Wai-Man
- Cambridge Centre for Brain Repair and MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK; Cambridge Eye Unit, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK; Moorfields Eye Hospital, London, UK; UCL Institute of Ophthalmology, University College London, London, UK
| | - John Neidhardt
- Human Genetics, Faculty VI - School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany; Research Center Neurosensory Science, University Oldenburg, Oldenburg, Germany.
| | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany.
| |
Collapse
|
48
|
Kulkarni JA, Witzigmann D, Thomson SB, Chen S, Leavitt BR, Cullis PR, van der Meel R. The current landscape of nucleic acid therapeutics. NATURE NANOTECHNOLOGY 2021; 16:630-643. [PMID: 34059811 DOI: 10.1038/s41565-021-00898-0] [Citation(s) in RCA: 566] [Impact Index Per Article: 188.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 03/11/2021] [Indexed: 05/20/2023]
Abstract
The increasing number of approved nucleic acid therapeutics demonstrates the potential to treat diseases by targeting their genetic blueprints in vivo. Conventional treatments generally induce therapeutic effects that are transient because they target proteins rather than underlying causes. In contrast, nucleic acid therapeutics can achieve long-lasting or even curative effects via gene inhibition, addition, replacement or editing. Their clinical translation, however, depends on delivery technologies that improve stability, facilitate internalization and increase target affinity. Here, we review four platform technologies that have enabled the clinical translation of nucleic acid therapeutics: antisense oligonucleotides, ligand-modified small interfering RNA conjugates, lipid nanoparticles and adeno-associated virus vectors. For each platform, we discuss the current state-of-the-art clinical approaches, explain the rationale behind its development, highlight technological aspects that facilitated clinical translation and provide an example of a clinically relevant genetic drug. In addition, we discuss how these technologies enable the development of cutting-edge genetic drugs, such as tissue-specific nucleic acid bioconjugates, messenger RNA and gene-editing therapeutics.
Collapse
Affiliation(s)
- Jayesh A Kulkarni
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
- NanoMedicines Innovation Network, Vancouver, British Columbia, Canada
- NanoVation Therapeutics, Vancouver, British Columbia, Canada
| | - Dominik Witzigmann
- NanoMedicines Innovation Network, Vancouver, British Columbia, Canada
- NanoVation Therapeutics, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sarah B Thomson
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sam Chen
- Integrated Nanotherapeutics, Vancouver, British Columbia, Canada
| | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pieter R Cullis
- NanoMedicines Innovation Network, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Roy van der Meel
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
| |
Collapse
|
49
|
Thavarajah W, Hertz LM, Bushhouse DZ, Archuleta CM, Lucks JB. RNA Engineering for Public Health: Innovations in RNA-Based Diagnostics and Therapeutics. Annu Rev Chem Biomol Eng 2021; 12:263-286. [PMID: 33900805 PMCID: PMC9714562 DOI: 10.1146/annurev-chembioeng-101420-014055] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA is essential for cellular function: From sensing intra- and extracellular signals to controlling gene expression, RNA mediates a diverse and expansive list of molecular processes. A long-standing goal of synthetic biology has been to develop RNA engineering principles that can be used to harness and reprogram these RNA-mediated processes to engineer biological systems to solve pressing global challenges. Recent advances in the field of RNA engineering are bringing this to fruition, enabling the creation of RNA-based tools to combat some of the most urgent public health crises. Specifically, new diagnostics using engineered RNAs are able to detect both pathogens and chemicals while generating an easily detectable fluorescent signal as an indicator. New classes of vaccines and therapeutics are also using engineered RNAs to target a wide range of genetic and pathogenic diseases. Here, we discuss the recent breakthroughs in RNA engineering enabling these innovations and examine how advances in RNA design promise to accelerate the impact of engineered RNA systems.
Collapse
Affiliation(s)
- Walter Thavarajah
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA; .,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Center for Water Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Laura M Hertz
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
| | - David Z Bushhouse
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
| | - Chloé M Archuleta
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA; .,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Center for Water Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA; .,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Center for Water Research, Northwestern University, Evanston, Illinois 60208, USA.,Center for Engineering Sustainability and Resilience, Northwestern University, Evanston, Illinois 60208, USA
| |
Collapse
|
50
|
Pereira-Castro I, Moreira A. On the function and relevance of alternative 3'-UTRs in gene expression regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1653. [PMID: 33843145 DOI: 10.1002/wrna.1653] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022]
Abstract
Messanger RNA (mRNA) isoforms with alternative 3'-untranslated regions (3'-UTRs) are produced by alternative polyadenylation (APA), which occurs during transcription in most eukaryotic genes. APA fine-tunes gene expression in a cell-type- and cellular state-dependent manner. Selection of an APA site entails the binding of core cleavage and polyadenylation factors to a particular polyadenylation site localized in the pre-mRNA and is controlled by multiple regulatory determinants, including transcription, pre-mRNA cis-regulatory sequences, and protein factors. Alternative 3'-UTRs serve as platforms for specific RNA binding proteins and microRNAs, which regulate gene expression in a coordinated manner by controlling mRNA fate and function in the cell. Genome-wide studies illustrated the full extent of APA prevalence and revealed that specific 3'-UTR profiles are associated with particular cellular states and diseases. Generally, short 3'-UTRs are associated with proliferative and cancer cells, and long 3'-UTRs are mostly found in polarized and differentiated cells. Fundamental new insights on the physiological consequences of this widespread event and the molecular mechanisms involved have been revealed through single-cell studies. Publicly available comprehensive databases that cover all APA mRNA isoforms identified in many cellular states and diseases reveal specific APA signatures. Therapies tackling APA mRNA isoforms or APA regulators may be regarded as innovative and attractive tools for diagnostics or treatment of several pathologies. We highlight the function of APA and alternative 3'-UTRs in gene expression regulation, the control of these mechanisms, their physiological consequences, and their potential use as new biomarkers and therapeutic tools. This article is categorized under: RNA Processing > 3' End Processing RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.
Collapse
Affiliation(s)
- Isabel Pereira-Castro
- Gene Regulation, i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Alexandra Moreira
- Gene Regulation, i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| |
Collapse
|