1
|
Yao R, Xie C, Xia X. Recent progress in mRNA cancer vaccines. Hum Vaccin Immunother 2024; 20:2307187. [PMID: 38282471 PMCID: PMC10826636 DOI: 10.1080/21645515.2024.2307187] [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: 09/28/2023] [Accepted: 01/16/2024] [Indexed: 01/30/2024] Open
Abstract
The research and development of messenger RNA (mRNA) cancer vaccines have gradually overcome numerous challenges through the application of personalized cancer antigens, structural optimization of mRNA, and the development of alternative RNA-based vectors and efficient targeted delivery vectors. Clinical trials are currently underway for various cancer vaccines that encode tumor-associated antigens (TAAs), tumor-specific antigens (TSAs), or immunomodulators. In this paper, we summarize the optimization of mRNA and the emergence of RNA-based expression vectors in cancer vaccines. We begin by reviewing the advancement and utilization of state-of-the-art targeted lipid nanoparticles (LNPs), followed by presenting the primary classifications and clinical applications of mRNA cancer vaccines. Collectively, mRNA vaccines are emerging as a central focus in cancer immunotherapy, offering the potential to address multiple challenges in cancer treatment, either as standalone therapies or in combination with current cancer treatments.
Collapse
Affiliation(s)
- Ruhui Yao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chunyuan Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaojun Xia
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| |
Collapse
|
2
|
Pardi N, Krammer F. mRNA vaccines for infectious diseases - advances, challenges and opportunities. Nat Rev Drug Discov 2024:10.1038/s41573-024-01042-y. [PMID: 39367276 DOI: 10.1038/s41573-024-01042-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2024] [Indexed: 10/06/2024]
Abstract
The concept of mRNA-based vaccines emerged more than three decades ago. Groundbreaking discoveries and technological advancements over the past 20 years have resolved the major roadblocks that initially delayed application of this new vaccine modality. The rapid development of nucleoside-modified COVID-19 mRNA vaccines demonstrated that this immunization platform is easy to develop, has an acceptable safety profile and can be produced at a large scale. The flexibility and ease of antigen design have enabled mRNA vaccines to enter development for a wide range of viruses as well as for various bacteria and parasites. However, gaps in our knowledge limit the development of next-generation mRNA vaccines with increased potency and safety. A deeper understanding of the mechanisms of action of mRNA vaccines, application of novel technologies enabling rational antigen design, and innovative vaccine delivery strategies and vaccination regimens will likely yield potent novel vaccines against a wide range of pathogens.
Collapse
Affiliation(s)
- Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Ignaz Semmelweis Institute, Interuniversity Institute for Infection Research, Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
3
|
Ye R, Zhao H, Wang X, Xue Y. Technological advancements in deciphering RNA-RNA interactions. Mol Cell 2024; 84:3722-3736. [PMID: 39047724 DOI: 10.1016/j.molcel.2024.06.036] [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: 04/15/2024] [Revised: 06/11/2024] [Accepted: 06/28/2024] [Indexed: 07/27/2024]
Abstract
RNA-RNA interactions (RRIs) can dictate RNA molecules to form intricate higher-order structures and bind their RNA substrates in diverse biological processes. To elucidate the function, binding specificity, and regulatory mechanisms of various RNA molecules, especially the vast repertoire of non-coding RNAs, advanced technologies and methods that globally map RRIs are extremely valuable. In the past decades, many state-of-the-art technologies have been developed for this purpose. This review focuses on those high-throughput technologies for the global mapping of RRIs. We summarize the key concepts and the pros and cons of different technologies. In addition, we highlight the novel biological insights uncovered by these RRI mapping methods and discuss the future challenges for appreciating the crucial roles of RRIs in gene regulation across bacteria, viruses, archaea, and mammals.
Collapse
Affiliation(s)
- Rong Ye
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hailian Zhao
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi Wang
- State Key Laboratory of Female Fertility Promotion, Clinical Stem Cell Research Center, Peking University Third Hospital, Beijing 100191, China
| | - Yuanchao Xue
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
4
|
Chen S, Liu Z, Cai J, Li H, Qiu M. N1-methylpseudouridine modification level correlates with protein expression, immunogenicity, and stability of mRNA. MedComm (Beijing) 2024; 5:e691. [PMID: 39290255 PMCID: PMC11406044 DOI: 10.1002/mco2.691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/17/2024] [Accepted: 07/23/2024] [Indexed: 09/19/2024] Open
Affiliation(s)
- Shaoyi Chen
- Department of Thoracic Surgery Thoracic Oncology Institute and Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer Peking University People's Hospital Beijing China
- Institute of Advanced Clinical Medicine Peking University Beijing China
| | - Zheng Liu
- Department of Thoracic Surgery Thoracic Oncology Institute and Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer Peking University People's Hospital Beijing China
- Institute of Advanced Clinical Medicine Peking University Beijing China
| | - Jingsheng Cai
- Department of Thoracic Surgery Thoracic Oncology Institute and Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer Peking University People's Hospital Beijing China
- Institute of Advanced Clinical Medicine Peking University Beijing China
| | - Haoran Li
- Department of Thoracic Surgery Thoracic Oncology Institute and Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer Peking University People's Hospital Beijing China
- Institute of Advanced Clinical Medicine Peking University Beijing China
| | - Mantang Qiu
- Department of Thoracic Surgery Thoracic Oncology Institute and Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer Peking University People's Hospital Beijing China
- Institute of Advanced Clinical Medicine Peking University Beijing China
| |
Collapse
|
5
|
Diwan R, Gaytan SL, Bhatt HN, Pena-Zacarias J, Nurunnabi M. Liver fibrosis pathologies and potentials of RNA based therapeutics modalities. Drug Deliv Transl Res 2024; 14:2743-2770. [PMID: 38446352 DOI: 10.1007/s13346-024-01551-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 03/07/2024]
Abstract
Liver fibrosis (LF) occurs when the liver tissue responds to injury or inflammation by producing excessive amounts of scar tissue, known as the extracellular matrix. This buildup stiffens the liver tissue, hinders blood flow, and ultimately impairs liver function. Various factors can trigger this process, including bloodborne pathogens, genetic predisposition, alcohol abuse, non-steroidal anti-inflammatory drugs, non-alcoholic steatohepatitis, and non-alcoholic fatty liver disease. While some existing small-molecule therapies offer limited benefits, there is a pressing need for more effective treatments that can truly cure LF. RNA therapeutics have emerged as a promising approach, as they can potentially downregulate cytokine levels in cells responsible for liver fibrosis. Researchers are actively exploring various RNA-based therapeutics, such as mRNA, siRNA, miRNA, lncRNA, and oligonucleotides, to assess their efficacy in animal models. Furthermore, targeted drug delivery systems hold immense potential in this field. By utilizing lipid nanoparticles, exosomes, nanocomplexes, micelles, and polymeric nanoparticles, researchers aim to deliver therapeutic agents directly to specific biomarkers or cytokines within the fibrotic liver, increasing their effectiveness and reducing side effects. In conclusion, this review highlights the complex nature of liver fibrosis, its underlying causes, and the promising potential of RNA-based therapeutics and targeted delivery systems. Continued research in these areas could lead to the development of more effective and personalized treatment options for LF patients.
Collapse
Affiliation(s)
- Rimpy Diwan
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Texas El Paso, El Paso, TX, 79902, USA
- Department of Biomedical Engineering, College of Engineering, The University of Texas El Paso, El Paso, TX, 79968, USA
| | - Samantha Lynn Gaytan
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Texas El Paso, El Paso, TX, 79902, USA
- Department of Interdisciplinary Health Sciences, College of Health Sciences, The University of Texas El Paso, El Paso, Texas, 79968, USA
| | - Himanshu Narendrakumar Bhatt
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Texas El Paso, El Paso, TX, 79902, USA
- Department of Biomedical Engineering, College of Engineering, The University of Texas El Paso, El Paso, TX, 79968, USA
| | - Jacqueline Pena-Zacarias
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Texas El Paso, El Paso, TX, 79902, USA
- Department of Biological Sciences, College of Science, The University of Texas El Paso, El Paso, Texas, 79968, USA
| | - Md Nurunnabi
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Texas El Paso, El Paso, TX, 79902, USA.
- Department of Biomedical Engineering, College of Engineering, The University of Texas El Paso, El Paso, TX, 79968, USA.
- Department of Interdisciplinary Health Sciences, College of Health Sciences, The University of Texas El Paso, El Paso, Texas, 79968, USA.
- Border Biomedical Research Center, The University of Texas El Paso, El Paso, TX, 79968, USA.
| |
Collapse
|
6
|
Cao X, Zhang Y, Ding Y, Wan Y. Identification of RNA structures and their roles in RNA functions. Nat Rev Mol Cell Biol 2024; 25:784-801. [PMID: 38926530 DOI: 10.1038/s41580-024-00748-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2024] [Indexed: 06/28/2024]
Abstract
The development of high-throughput RNA structure profiling methods in the past decade has greatly facilitated our ability to map and characterize different aspects of RNA structures transcriptome-wide in cell populations, single cells and single molecules. The resulting high-resolution data have provided insights into the static and dynamic nature of RNA structures, revealing their complexity as they perform their respective functions in the cell. In this Review, we discuss recent technical advances in the determination of RNA structures, and the roles of RNA structures in RNA biogenesis and functions, including in transcription, processing, translation, degradation, localization and RNA structure-dependent condensates. We also discuss the current understanding of how RNA structures could guide drug design for treating genetic diseases and battling pathogenic viruses, and highlight existing challenges and future directions in RNA structure research.
Collapse
Affiliation(s)
- Xinang Cao
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Yueying Zhang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK.
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| |
Collapse
|
7
|
Makhamreh A, Tavakoli S, Fallahi A, Kang X, Gamper H, Nabizadehmashhadtoroghi M, Jain M, Hou YM, Rouhanifard SH, Wanunu M. Nanopore signal deviations from pseudouridine modifications in RNA are sequence-specific: quantification requires dedicated synthetic controls. Sci Rep 2024; 14:22457. [PMID: 39341872 PMCID: PMC11438862 DOI: 10.1038/s41598-024-72994-9] [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: 07/15/2024] [Accepted: 09/11/2024] [Indexed: 10/01/2024] Open
Abstract
Chemical modifications to mRNA respond dynamically to environmental cues and are important modulators of gene expression. Nanopore direct RNA sequencing has been applied for assessing the presence of pseudouridine (ψ) modifications through basecalling errors and signal analysis. These approaches strongly depend on the sequence context around the modification, and the occupancies derived from these measurements are not quantitative. In this work, we combine direct RNA sequencing of synthetic RNAs bearing site-specific modifications and supervised machine learning models (ModQuant) to achieve near-analytical, site-specific ψ quantification. Our models demonstrate that the ionic current signal features important for accurate ψ classification are sequence dependent and encompass information extending beyond n + 2 and n - 2 nucleotides from the ψ site. This is contradictory to current models, which assume that accurate ψ classification can be achieved with signal information confined to the 5-nucleotide k-mer window (n + 2 and n - 2 nucleotides from the ψ site). We applied our models to quantitatively profile ψ occupancy in five mRNA sites in datasets from seven human cell lines, demonstrating conserved and variable sites. Our study motivates a wider pipeline that uses ground-truth RNA control sets with site-specific modifications for quantitative profiling of RNA modifications. The ModQuant pipeline and guide are freely available at https://github.com/wanunulab/ModQuant .
Collapse
Affiliation(s)
- Amr Makhamreh
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Sepideh Tavakoli
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Ali Fallahi
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Xinqi Kang
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Miten Jain
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Meni Wanunu
- Department of Bioengineering, Northeastern University, Boston, MA, USA.
- Department of Physics, Northeastern University, Boston, MA, USA.
| |
Collapse
|
8
|
Zhang Z, Cheng D, Luo W, Hu D, Yang T, Hu K, Liang L, Liu W, Hu J. Molecular Dynamics Simulation of Lipid Nanoparticles Encapsulating mRNA. Molecules 2024; 29:4409. [PMID: 39339404 PMCID: PMC11433737 DOI: 10.3390/molecules29184409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2024] [Revised: 09/14/2024] [Accepted: 09/15/2024] [Indexed: 09/30/2024] Open
Abstract
mRNA vaccines have shown great potential in responding to emerging infectious diseases, with their efficacy and stability largely dependent on the delivery vehicles-lipid nanoparticles (LNPs). This study aims to explore the mechanisms by which LNPs encapsulate mRNA, as well as the effects of different N/P ratios and acid types in nucleic acid solutions on the structure and properties of LNPs, using the ethanol solvent injection method as the encapsulation technique. Six systems were designed, based on the composition and proportions of the existing mRNA vaccine mRNA-1273, and molecular dynamics (MD) simulations were employed to investigate the self-assembly process of LNPs. Ethanol was used as a solvent instead of pure water to better mimic experimental conditions. The results indicate that lipid components self-assemble into nanoparticles under neutral conditions, with the ionizable lipid SM-102 predominantly concentrating in the core of the particles. Upon mixing with nucleic acids in acidic conditions, LNPs undergo disassembly, during which protonated SM-102 encapsulates mRNA through electrostatic interactions, forming stable hydrogen bonds. Cluster structure analysis revealed that the four lipid components of LNPs are distributed sequentially from the outside inwards as DMG-PEG 2000, DSPC, cholesterol, and protonated SM-102. Moreover, LNPs constructed under low pH or low N/P ratios using citric acid exhibited larger volumes and more uniform distribution. These findings provide a scientific basis for further designing and optimizing LNP components to enhance the efficacy of mRNA vaccine encapsulation.
Collapse
Affiliation(s)
- Zhigang Zhang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Dazhi Cheng
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Wenqin Luo
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Donling Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Tiantian Yang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Kaixuan Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Li Liang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Wei Liu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China
- School of Life Science, Leshan Normal University, Leshan 614004, China
| |
Collapse
|
9
|
Feng S, Chen T, Zhang Y, Lu C. mRNA Fragmentation Pattern Detected by SHAPE. Curr Issues Mol Biol 2024; 46:10249-10258. [PMID: 39329962 PMCID: PMC11431040 DOI: 10.3390/cimb46090610] [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: 08/13/2024] [Revised: 09/12/2024] [Accepted: 09/14/2024] [Indexed: 09/28/2024] Open
Abstract
The success of messenger RNA (mRNA) vaccines in controlling COVID-19 has warranted further developments in new technology. Currently, their quality control process largely relies on low-resolution electrophoresis for detecting chain breaks. Here, we present an approach using multi-primer reverse transcription sequencing (MPRT-seq) to identify degradation fragments in mRNA products. Using this in-house-made mRNA containing two antigens and untranslated regions (UTRs), we analyzed the mRNA completeness and degradation pattern at a nucleotide resolution. We then analyzed the sensitive base sequence and its correlation with the secondary structure. Our MPRT-seq mapping shows that certain sequences on the 5' of bulge-stem-loop structures can result in preferential chain breaks. Our results agree with commonly used capillary electrophoresis (CE) integrity analysis but at a much higher resolution, and can improve mRNA stability by providing information to remove sensitive structures or sequences in the mRNA sequence design.
Collapse
Affiliation(s)
| | | | | | - Changrui Lu
- College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China; (S.F.); (T.C.); (Y.Z.)
| |
Collapse
|
10
|
Zhang Y, Mastouri M, Zhang Y. Accelerating drug discovery, development, and clinical trials by artificial intelligence. MED 2024; 5:1050-1070. [PMID: 39173629 DOI: 10.1016/j.medj.2024.07.026] [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: 04/01/2024] [Revised: 05/21/2024] [Accepted: 07/25/2024] [Indexed: 08/24/2024]
Abstract
Artificial intelligence (AI) has profoundly advanced the field of biomedical research, which also demonstrates transformative capacity for innovation in drug development. This paper aims to deliver a comprehensive analysis of the progress in AI-assisted drug development, particularly focusing on small molecules, RNA, and antibodies. Moreover, this paper elucidates the current integration of AI methodologies within the industrial drug development framework. This encompasses a detailed examination of the industry-standard drug development process, supplemented by a review of medications presently undergoing clinical trials. Conclusively, the paper tackles a predominant obstacle within the AI pharmaceutical sector: the absence of AI-conceived drugs receiving approval. This paper also advocates for the adoption of large language models and diffusion models as a viable strategy to surmount this challenge. This review not only underscores the significant potential of AI in drug discovery but also deliberates on the challenges and prospects within this dynamically progressing field.
Collapse
Affiliation(s)
- Yilun Zhang
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China; School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong, China
| | - Mohamed Mastouri
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China
| | - Yang Zhang
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China.
| |
Collapse
|
11
|
Wang T, Yu T, Liu Q, Sung TC, Higuchi A. Lipid nanoparticle technology-mediated therapeutic gene manipulation in the eyes. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102236. [PMID: 39005878 PMCID: PMC11245926 DOI: 10.1016/j.omtn.2024.102236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Millions of people worldwide have hereditary genetic disorders, trauma, infectious diseases, or cancer of the eyes, and many of these eye diseases lead to irreversible blindness, which is a major public health burden. The eye is a relatively small and immune-privileged organ. The use of nucleic acid-based drugs to manipulate malfunctioning genes that target the root of ocular diseases is regarded as a therapeutic approach with great promise. However, there are still some challenges for utilizing nucleic acid therapeutics in vivo because of certain unfavorable characteristics, such as instability, biological carrier-dependent cellular uptake, short pharmacokinetic profiles in vivo (RNA), and on-target and off-target side effects (DNA). The development of lipid nanoparticles (LNPs) as gene vehicles is revolutionary progress that has contributed the clinical application of nucleic acid therapeutics. LNPs have the capability to entrap and transport various genetic materials such as small interfering RNA, mRNA, DNA, and gene editing complexes. This opens up avenues for addressing ocular diseases through the suppression of pathogenic genes, the expression of therapeutic proteins, or the correction of genetic defects. Here, we delve into the cutting-edge LNP technology for ocular gene therapy, encompassing formulation designs, preclinical development, and clinical translation.
Collapse
Affiliation(s)
- Ting Wang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, No. 270, Xueyuan Road, Wenzhou, Zhejiang 325027, China
| | - Tao Yu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, No. 270, Xueyuan Road, Wenzhou, Zhejiang 325027, China
| | - Qian Liu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, No. 270, Xueyuan Road, Wenzhou, Zhejiang 325027, China
| | - Tzu-Cheng Sung
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, No. 270, Xueyuan Road, Wenzhou, Zhejiang 325027, China
| | - Akon Higuchi
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, No. 270, Xueyuan Road, Wenzhou, Zhejiang 325027, China
- Department of Chemical and Materials Engineering, National Central University, No. 300, Jhongda RD, Jhongli, Taoyuan 32001, Taiwan
| |
Collapse
|
12
|
Lu RM, Hsu HE, Perez SJLP, Kumari M, Chen GH, Hong MH, Lin YS, Liu CH, Ko SH, Concio CAP, Su YJ, Chang YH, Li WS, Wu HC. Current landscape of mRNA technologies and delivery systems for new modality therapeutics. J Biomed Sci 2024; 31:89. [PMID: 39256822 PMCID: PMC11389359 DOI: 10.1186/s12929-024-01080-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 08/20/2024] [Indexed: 09/12/2024] Open
Abstract
Realizing the immense clinical potential of mRNA-based drugs will require continued development of methods to safely deliver the bioactive agents with high efficiency and without triggering side effects. In this regard, lipid nanoparticles have been successfully utilized to improve mRNA delivery and protect the cargo from extracellular degradation. Encapsulation in lipid nanoparticles was an essential factor in the successful clinical application of mRNA vaccines, which conclusively demonstrated the technology's potential to yield approved medicines. In this review, we begin by describing current advances in mRNA modifications, design of novel lipids and development of lipid nanoparticle components for mRNA-based drugs. Then, we summarize key points pertaining to preclinical and clinical development of mRNA therapeutics. Finally, we cover topics related to targeted delivery systems, including endosomal escape and targeting of immune cells, tumors and organs for use with mRNA vaccines and new treatment modalities for human diseases.
Collapse
Affiliation(s)
- Ruei-Min Lu
- Biomedical Translation Research Center, Academia Sinica, Taipei, 11571, Taiwan
| | - Hsiang-En Hsu
- Biomedical Translation Research Center, Academia Sinica, Taipei, 11571, Taiwan
| | | | - Monika Kumari
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Taipei, 11529, Taiwan
| | - Guan-Hong Chen
- Biomedical Translation Research Center, Academia Sinica, Taipei, 11571, Taiwan
| | - Ming-Hsiang Hong
- Biomedical Translation Research Center, Academia Sinica, Taipei, 11571, Taiwan
| | - Yin-Shiou Lin
- Biomedical Translation Research Center, Academia Sinica, Taipei, 11571, Taiwan
| | - Ching-Hang Liu
- Biomedical Translation Research Center, Academia Sinica, Taipei, 11571, Taiwan
| | - Shih-Han Ko
- Biomedical Translation Research Center, Academia Sinica, Taipei, 11571, Taiwan
| | | | - Yi-Jen Su
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Taipei, 11529, Taiwan
| | - Yi-Han Chang
- Biomedical Translation Research Center, Academia Sinica, Taipei, 11571, Taiwan
| | - Wen-Shan Li
- Biomedical Translation Research Center, Academia Sinica, Taipei, 11571, Taiwan.
- Institute of Chemistry, Academia Sinica, No. 128, Academia Road, Section 2, Taipei, 11529, Taiwan.
| | - Han-Chung Wu
- Biomedical Translation Research Center, Academia Sinica, Taipei, 11571, Taiwan.
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Taipei, 11529, Taiwan.
| |
Collapse
|
13
|
Xiao H, Zhang Y, Yang X, Yu S, Chen Z, Lu A, Zhang Z, Zhang G, Zhang BT. SMTRI: A deep learning-based web service for predicting small molecules that target miRNA-mRNA interactions. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102303. [PMID: 39281703 PMCID: PMC11401195 DOI: 10.1016/j.omtn.2024.102303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 08/12/2024] [Indexed: 09/18/2024]
Abstract
Mature microRNAs (miRNAs) are short, single-stranded RNAs that bind to target mRNAs and induce translational repression and gene silencing. Many miRNAs discovered in animals have been implicated in diseases and have recently been pursued as therapeutic targets. However, conventional pharmacological screening for candidate small-molecule drugs can be time-consuming and labor-intensive. Therefore, developing a computational program to assist mature miRNA-targeted drug discovery in silico is desirable. Our previous work (https://doi.org/10.1002/advs.201903451) revealed that the unique functional loops formed during Argonaute-mediated miRNA-mRNA interactions have stable structural characteristics and may serve as potential targets for small-molecule drug discovery. Developing drugs specifically targeting disease-related mature miRNAs and their target mRNAs would avoid affecting unrelated ones. Here, we present SMTRI, a convolutional neural network-based approach for efficiently predicting small molecules that target RNA secondary structural motifs formed by interactions between miRNAs and their target mRNAs. Measured on three additional testing sets, SMTRI outperformed state-of-the-art algorithms by 12.9%-30.3% in AUC and 2.0%-18.4% in accuracy. Moreover, four case studies on the published experimentally validated RNA-targeted small molecules also revealed the reliability of SMTRI.
Collapse
Affiliation(s)
- Huan Xiao
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Yihao Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Xin Yang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Sifan Yu
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Ziqi Chen
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Zongkang Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Bao-Ting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| |
Collapse
|
14
|
Zhang J, Xiong YW, Zhu HL, Tan LL, Zhou H, Zheng XM, Zhang YF, Chang W, Xu DX, Wei T, Guan SZ, Wang H. Adolescent co-exposure to environmental cadmium and high-fat diet induces cognitive decline via Larp7 m6A-mediated SIRT6 inhibition. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135159. [PMID: 39002485 DOI: 10.1016/j.jhazmat.2024.135159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 07/07/2024] [Accepted: 07/07/2024] [Indexed: 07/15/2024]
Abstract
The effects and underlying mechanisms of adolescent exposure to combined environmental hazards on cognitive function remain unclear. Here, using a combined exposure model, we found significant cognitive decline, hippocampal neuronal damage, and neuronal senescence in mice exposed to cadmium (Cd) and high-fat diet (HFD) during adolescence. Furthermore, we observed a significant downregulation of Sirtuin 6 (SIRT6) expression in the hippocampi of co-exposed mice. UBCS039, a specific SIRT6 activator, markedly reversed the above adverse effects. Further investigation revealed that co-exposure obviously reduced the levels of La ribonucleoprotein 7 (LARP7), disrupted the interaction between LARP7 and SIRT6, ultimately decreasing SIRT6 expression in mouse hippocampal neuronal cells. Overexpression of Larp7 reversed the combined exposure-induced SIRT6 decrease and senescence in mouse hippocampal neuronal cells. Additionally, the results showed notably elevated levels of Larp7 m6A and YTH domain family protein 2 (YTHDF2) in mouse hippocampal neuronal cells treated with the combined hazards. Ythdf2 short interfering RNA, RNA immunoprecipitation, and RNA stability assays further demonstrated that YTHDF2 mediated the degradation of Larp7 mRNA under combined exposure. Collectively, adolescent co-exposure to Cd and HFD causes hippocampal senescence and cognitive decline in mice by inhibiting LARP7-mediated SIRT6 expression in an m6A-dependent manner.
Collapse
Affiliation(s)
- Jin Zhang
- Department of Toxicology, School of Public Health, Center for Big Data and Population Health of IHM, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Yong-Wei Xiong
- Department of Toxicology, School of Public Health, Center for Big Data and Population Health of IHM, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, China
| | - Hua-Long Zhu
- Department of Toxicology, School of Public Health, Center for Big Data and Population Health of IHM, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, China
| | - Lu-Lu Tan
- Department of Toxicology, School of Public Health, Center for Big Data and Population Health of IHM, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Huan Zhou
- Department of Toxicology, School of Public Health, Center for Big Data and Population Health of IHM, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Xin-Mei Zheng
- Department of Toxicology, School of Public Health, Center for Big Data and Population Health of IHM, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Yu-Feng Zhang
- Department of Toxicology, School of Public Health, Center for Big Data and Population Health of IHM, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Wei Chang
- Department of Toxicology, School of Public Health, Center for Big Data and Population Health of IHM, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - De-Xiang Xu
- Department of Toxicology, School of Public Health, Center for Big Data and Population Health of IHM, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, China
| | - Tian Wei
- Department of Toxicology, School of Public Health, Center for Big Data and Population Health of IHM, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, China.
| | - Su-Zhen Guan
- School of Public Health, Ningxia Medical University, China.
| | - Hua Wang
- Department of Toxicology, School of Public Health, Center for Big Data and Population Health of IHM, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, China.
| |
Collapse
|
15
|
Shoja Doost J, Fazel F, Boodhoo N, Sharif S. mRNA Vaccination: An Outlook on Innate Sensing and Adaptive Immune Responses. Viruses 2024; 16:1404. [PMID: 39339880 PMCID: PMC11437395 DOI: 10.3390/v16091404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/30/2024] Open
Abstract
Vaccination has led to significant dismantling of infectious diseases worldwide. Since the dawn of the SARS-CoV-2 pandemic, there has been increased popularity in the usage and study of the mRNA vaccine platform. Here, we highlight fundamental knowledge on mRNA vaccine pharmacology, followed by the immunity conferred by innate sensing and adaptive responses resulting from exposure to the mRNA vaccine construct and encapsulation materials. A better understanding of these immune mechanisms will shed light on further improvements in mRNA vaccine design, aiming to improve efficiency and optimize immune responses upon inoculation.
Collapse
Affiliation(s)
| | | | | | - Shayan Sharif
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada; (J.S.D.); (F.F.); (N.B.)
| |
Collapse
|
16
|
Hulscher N, McCullough PA, Marotta DE. Strategic deactivation of mRNA COVID-19 vaccines: New applications for siRNA therapy and RIBOTACs. J Gene Med 2024; 26:e3733. [PMID: 39183706 DOI: 10.1002/jgm.3733] [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: 06/02/2024] [Revised: 07/19/2024] [Accepted: 08/13/2024] [Indexed: 08/27/2024] Open
Abstract
The rapid development and authorization of messenger ribonucleic acid (mRNA) vaccines by Pfizer-BioNTech (BNT162b2) and Moderna (mRNA-1273) in 2020 marked a significant milestone in human mRNA product application, overcoming previous obstacles such as mRNA instability and immunogenicity. This paper reviews the strategic modifications incorporated into these vaccines to enhance mRNA stability and translation efficiency, such as the inclusion of nucleoside modifications and optimized mRNA design elements including the 5' cap and poly(A) tail. We highlight emerging concerns regarding the wide systemic biodistribution of these mRNA vaccines leading to prolonged inflammatory responses and other safety concerns. The regulatory framework guiding the biodistribution studies is pivotal in assessing the safety profiles of new mRNA formulations in use today. The stability of mRNA vaccines, their pervasive distribution, and the longevity of the encapsulated mRNA along with unlimited production of the damaging and potentially lethal spike (S) protein call for strategies to mitigate potential adverse effects. Here, we explore the potential of small interfering RNA (siRNA) and ribonuclease targeting chimeras (RIBOTACs) as promising solutions to target, inactivate, and degrade residual and persistent vaccine mRNA, thereby potentially preventing uncontrolled S protein production and reducing toxicity. The targeted nature of siRNA and RIBOTACs allows for precise intervention, offering a path to prevent and mitigate adverse events of mRNA-based therapies. This review calls for further research into siRNA and RIBOTAC applications as antidotes and detoxication products for mRNA vaccine technology.
Collapse
|
17
|
Phan T, Fan D, Melstrom LG. Developing Vaccines in Pancreatic Adenocarcinoma: Trials and Tribulations. Curr Oncol 2024; 31:4855-4884. [PMID: 39329989 PMCID: PMC11430674 DOI: 10.3390/curroncol31090361] [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] [Revised: 08/13/2024] [Accepted: 08/21/2024] [Indexed: 09/28/2024] Open
Abstract
Pancreatic adenocarcinoma represents one of the most challenging malignancies to treat, with dismal survival rates despite advances in therapeutic modalities. Immunotherapy, particularly vaccines, has emerged as a promising strategy to harness the body's immune system in combating this aggressive cancer. This abstract reviews the trials and tribulations encountered in the development of vaccines targeting pancreatic adenocarcinoma. Key challenges include the immunosuppressive tumor microenvironment, the heterogeneity of tumor antigens, and a limited understanding of immune evasion mechanisms employed by pancreatic cancer cells. Various vaccine platforms, including peptide-based, dendritic cell-based, and viral vector-based vaccines, have been explored in preclinical and clinical settings. However, translating promising results from preclinical models to clinical efficacy has proven elusive. In recent years, mRNA vaccines have emerged as a promising immunotherapeutic strategy in the fight against various cancers, including pancreatic adenocarcinoma. We will discuss the potential applications, opportunities, and challenges associated with mRNA vaccines in pancreatic cancer treatment.
Collapse
Affiliation(s)
- Thuy Phan
- Department of Surgery, City of Hope National Medical Center, Duarte, CA 91010, USA;
| | - Darrell Fan
- Department of Surgical Oncology, City of Hope National Medical Center, Duarte, CA 91010, USA;
| | - Laleh G. Melstrom
- Department of Surgical Oncology, City of Hope National Medical Center, Duarte, CA 91010, USA;
| |
Collapse
|
18
|
Li S, Moayedpour S, Li R, Bailey M, Riahi S, Kogler-Anele L, Miladi M, Miner J, Pertuy F, Zheng D, Wang J, Balsubramani A, Tran K, Zacharia M, Wu M, Gu X, Clinton R, Asquith C, Skaleski J, Boeglin L, Chivukula S, Dias A, Strugnell T, Montoya FU, Agarwal V, Bar-Joseph Z, Jager S. CodonBERT large language model for mRNA vaccines. Genome Res 2024; 34:1027-1035. [PMID: 38951026 PMCID: PMC11368176 DOI: 10.1101/gr.278870.123] [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: 12/15/2023] [Accepted: 06/25/2024] [Indexed: 07/03/2024]
Abstract
mRNA-based vaccines and therapeutics are gaining popularity and usage across a wide range of conditions. One of the critical issues when designing such mRNAs is sequence optimization. Even small proteins or peptides can be encoded by an enormously large number of mRNAs. The actual mRNA sequence can have a large impact on several properties, including expression, stability, immunogenicity, and more. To enable the selection of an optimal sequence, we developed CodonBERT, a large language model (LLM) for mRNAs. Unlike prior models, CodonBERT uses codons as inputs, which enables it to learn better representations. CodonBERT was trained using more than 10 million mRNA sequences from a diverse set of organisms. The resulting model captures important biological concepts. CodonBERT can also be extended to perform prediction tasks for various mRNA properties. CodonBERT outperforms previous mRNA prediction methods, including on a new flu vaccine data set.
Collapse
Affiliation(s)
- Sizhen Li
- Digital R&D, Sanofi, Cambridge, Massachusetts 02141, USA
| | | | - Ruijiang Li
- Digital R&D, Sanofi, Cambridge, Massachusetts 02141, USA
| | - Michael Bailey
- Digital R&D, Sanofi, Cambridge, Massachusetts 02141, USA
| | - Saleh Riahi
- Digital R&D, Sanofi, Cambridge, Massachusetts 02141, USA
| | | | - Milad Miladi
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts 02451, USA
| | - Jacob Miner
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts 02451, USA
| | - Fabien Pertuy
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts 02451, USA
| | - Dinghai Zheng
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts 02451, USA
| | - Jun Wang
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts 02451, USA
| | | | - Khang Tran
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts 02451, USA
| | - Minnie Zacharia
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts 02451, USA
| | - Monica Wu
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts 02451, USA
| | - Xiaobo Gu
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts 02451, USA
| | - Ryan Clinton
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts 02451, USA
| | - Carla Asquith
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts 02451, USA
| | - Joseph Skaleski
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts 02451, USA
| | - Lianne Boeglin
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts 02451, USA
| | - Sudha Chivukula
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts 02451, USA
| | - Anusha Dias
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts 02451, USA
| | - Tod Strugnell
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts 02451, USA
| | | | - Vikram Agarwal
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts 02451, USA
| | - Ziv Bar-Joseph
- Digital R&D, Sanofi, Cambridge, Massachusetts 02141, USA;
| | - Sven Jager
- Digital R&D, Sanofi, Cambridge, Massachusetts 02141, USA
| |
Collapse
|
19
|
He Y, Johnston APR, Pouton CW. Therapeutic applications of cell engineering using mRNA technology. Trends Biotechnol 2024:S0167-7799(24)00191-4. [PMID: 39153909 DOI: 10.1016/j.tibtech.2024.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/16/2024] [Accepted: 07/20/2024] [Indexed: 08/19/2024]
Abstract
Engineering and reprogramming cells has significant therapeutic potential to treat a wide range of diseases, by replacing missing or defective proteins, to provide transcription factors (TFs) to reprogram cell phenotypes, or to provide enzymes such as RNA-guided Cas9 derivatives for CRISPR-based cell engineering. While viral vector-mediated gene transfer has played an important role in this field, the use of mRNA avoids safety concerns associated with the integration of DNA into the host cell genome, making mRNA particularly attractive for in vivo applications. Widespread application of mRNA for cell engineering is limited by its instability in the biological environment and challenges involved in the delivery of mRNA to its target site. In this review, we examine challenges that must be overcome to develop effective therapeutics.
Collapse
Affiliation(s)
- Yujia He
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
| | - Angus P R Johnston
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
| | - Colin W Pouton
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia.
| |
Collapse
|
20
|
Palm SM, Horton CA, Zhang X, Collins K. Structure and sequence at an RNA template 5' end influence insertion of transgenes by an R2 retrotransposon protein. RNA (NEW YORK, N.Y.) 2024; 30:1227-1245. [PMID: 38960642 PMCID: PMC11331408 DOI: 10.1261/rna.080031.124] [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: 03/23/2024] [Accepted: 06/17/2024] [Indexed: 07/05/2024]
Abstract
R2 non-long terminal repeat retrotransposons insert site-specifically into ribosomal RNA genes (rDNA) in a broad range of multicellular eukaryotes. R2-encoded proteins can be leveraged to mediate transgene insertion at 28S rDNA loci in cultured human cells. This strategy, precise RNA-mediated insertion of transgenes (PRINT), relies on the codelivery of an mRNA encoding R2 protein and an RNA template encoding a transgene cassette of choice. Here, we demonstrate that the PRINT RNA template 5' module, which as a complementary DNA 3' end will generate the transgene 5' junction with rDNA, influences the efficiency and mechanism of gene insertion. Iterative design and testing identified optimal 5' modules consisting of a hepatitis delta virus-like ribozyme fold with high thermodynamic stability, suggesting that RNA template degradation from its 5' end may limit transgene insertion efficiency. We also demonstrate that transgene 5' junction formation can be either precise, formed by annealing the 3' end of first-strand complementary DNA with the upstream target site, or imprecise, by end-joining, but this difference in junction formation mechanism is not a major determinant of insertion efficiency. Sequence characterization of imprecise end-joining events indicates surprisingly minimal reliance on microhomology. Our findings expand the current understanding of the role of R2 retrotransposon transcript sequence and structure, and especially the 5' ribozyme fold, for retrotransposon mobility and RNA-templated gene synthesis in cells.
Collapse
Affiliation(s)
- Sarah M Palm
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - Connor A Horton
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - Xiaozhu Zhang
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
| |
Collapse
|
21
|
Zheng D, Wang J, Persyn L, Liu Y, Montoya FU, Cenik C, Agarwal V. Predicting the translation efficiency of messenger RNA in mammalian cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.11.607362. [PMID: 39149337 PMCID: PMC11326250 DOI: 10.1101/2024.08.11.607362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The degree to which translational control is specified by mRNA sequence is poorly understood in mammalian cells. Here, we constructed and leveraged a compendium of 3,819 ribosomal profiling datasets, distilling them into a transcriptome-wide atlas of translation efficiency (TE) measurements encompassing >140 human and mouse cell types. We subsequently developed RiboNN, a multitask deep convolutional neural network, and classic machine learning models to predict TEs in hundreds of cell types from sequence-encoded mRNA features, achieving state-of-the-art performance (r=0.79 in human and r=0.78 in mouse for mean TE across cell types). While the majority of earlier models solely considered 5' UTR sequence, RiboNN integrates contributions from the full-length mRNA sequence, learning that the 5' UTR, CDS, and 3' UTR respectively possess ~67%, 31%, and 2% per-nucleotide information density in the specification of mammalian TEs. Interpretation of RiboNN revealed that the spatial positioning of low-level di- and tri-nucleotide features (i.e., including codons) largely explain model performance, capturing mechanistic principles such as how ribosomal processivity and tRNA abundance control translational output. RiboNN is predictive of the translational behavior of base-modified therapeutic RNA, and can explain evolutionary selection pressures in human 5' UTRs. Finally, it detects a common language governing mRNA regulatory control and highlights the interconnectedness of mRNA translation, stability, and localization in mammalian organisms.
Collapse
Affiliation(s)
- Dinghai Zheng
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Jun Wang
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Logan Persyn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Yue Liu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | | | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Vikram Agarwal
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| |
Collapse
|
22
|
Tkaczyk C, Newton M, Patnaik MM, Thom G, Strain M, Gamson A, Daramola O, Murthy A, Douthwaite J, Stepanov O, Boger E, Yang H, Esser MT, Lidwell A, DiGiandomenico A, Santos L, Sellman BR. In vivo mRNA expression of a multi-mechanistic mAb combination protects against Staphylococcus aureus infection. Mol Ther 2024; 32:2505-2518. [PMID: 38822525 PMCID: PMC11405172 DOI: 10.1016/j.ymthe.2024.05.036] [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: 12/04/2023] [Revised: 04/30/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024] Open
Abstract
Single monoclonal antibodies (mAbs) can be expressed in vivo through gene delivery of their mRNA formulated with lipid nanoparticles (LNPs). However, delivery of a mAb combination could be challenging due to the risk of heavy and light variable chain mispairing. We evaluated the pharmacokinetics of a three mAb combination against Staphylococcus aureus first in single chain variable fragment scFv-Fc and then in immunoglobulin G 1 (IgG1) format in mice. Intravenous delivery of each mRNA/LNP or the trio (1 mg/kg each) induced functional antibody expression after 24 h (10-100 μg/mL) with 64%-78% cognate-chain paired IgG expression after 3 days, and an absence of non-cognate chain pairing for scFv-Fc. We did not observe reduced neutralizing activity for each mAb compared with the level of expression of chain-paired mAbs. Delivery of the trio mRNA protected mice in an S. aureus-induced dermonecrosis model. Intravenous administration of the three mRNA in non-human primates achieved peak serum IgG levels ranging between 2.9 and 13.7 μg/mL with a half-life of 11.8-15.4 days. These results suggest nucleic acid delivery of mAb combinations holds promise and may be a viable option to streamline the development of therapeutic antibodies.
Collapse
Affiliation(s)
- Christine Tkaczyk
- AstraZeneca, Early Vaccines & Immune Therapies, Gaithersburg, MD 20878, USA.
| | - Michael Newton
- AstraZeneca, BioPharmaceutical Development, BioPharmaceuticals R&D, Gaithersburg, MD 20878, USA
| | - Mun Mun Patnaik
- AstraZeneca, Early Vaccines & Immune Therapies, Gaithersburg, MD 20878, USA
| | - George Thom
- AstraZeneca, Discovery Sciences, BioPharmaceuticals R&D, Cambridge CB21 6GH, UK
| | - Martin Strain
- AstraZeneca, Biologics Engineering, BioPharmaceuticals R&D, Cambridge CB216GH, UK
| | - Adam Gamson
- AstraZeneca, Early Vaccines & Immune Therapies, Gaithersburg, MD 20878, USA
| | - Olalekan Daramola
- AstraZeneca, BioPharmaceutical Development, BioPharmaceuticals R&D, Cambridge CB21 6GH, UK
| | - Andal Murthy
- AstraZeneca, BioPharmaceutical Development, BioPharmaceuticals R&D, Cambridge CB21 6GH, UK
| | - Julie Douthwaite
- AstraZeneca, Discovery Sciences, BioPharmaceuticals R&D, Cambridge CB21 6GH, UK
| | - Oleg Stepanov
- Clinical Pharmacology and Pharmacometrics, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 8PA, UK
| | - Elin Boger
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Respirator & immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Haitao Yang
- Clinical Pharmacology and Pharmacometrics, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Mark T Esser
- AstraZeneca, Early Vaccines & Immune Therapies, Gaithersburg, MD 20878, USA
| | - Ashley Lidwell
- AstraZeneca, Early Vaccines & Immune Therapies, Gaithersburg, MD 20878, USA
| | | | - Luis Santos
- AstraZeneca, BioPharmaceutical Development, BioPharmaceuticals R&D, Gaithersburg, MD 20878, USA
| | - Bret R Sellman
- AstraZeneca, Early Vaccines & Immune Therapies, Gaithersburg, MD 20878, USA
| |
Collapse
|
23
|
Cao D, Zhao Y, Wang Y, Wei D, Yan M, Su S, Pan H, Wang Q. Effects of sleep deprivation on anxiety-depressive-like behavior and neuroinflammation. Brain Res 2024; 1836:148916. [PMID: 38609030 DOI: 10.1016/j.brainres.2024.148916] [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: 03/13/2024] [Revised: 03/31/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
BACKGROUND Depression is defined by a persistent low mood and disruptions in sleep patterns, with the WHO forecasting that major depression will rank as the third most prevalent contributor to the global burden of disease by the year 2030. Sleep deprivation serves as a stressor that triggers inflammation within the central nervous system, a process known as neuroinflammation. This inflammatory response plays a crucial role in the development of depression by upregulating the expression of inflammatory mediators that contribute to symptoms such as anxiety, hopelessness, and loss of pleasure. METHODS In this study, sleep deprivation was utilized as a method to induce anxiety and depressive-like behaviors in mice. The behavioral changes in the mice were then evaluated using the EZM, EPM, TST, FST, and SPT. H&E staining and Nissl staining was used to detect morphological changes in the medial prefrontal cortical (mPFC) regions. Elisa to assess serum CORT levels. Detection of mRNA levels and protein expression of clock genes, high mobility genome box-1 (Hmgb1), silent message regulator 6 (Sirt6), and pro-inflammatory factors by RT-qPCR, Western blotting, and immunofluorescence techniques. RESULTS Sleep deprivation resulted in decreased exploration of unfamiliar territory, increased time spent in a state of despair, and lower sucrose water intake in mice. Additionally, sleep deprivation led to increased secretion of serum CORT and upregulation of clock genes, IL6, IL1β, TNFα, Cox-2, iNOS, Sirt6, and Hmgb1. Sleep. CONCLUSIONS Sleep deprivation induces anxiety-depressive-like behaviors and neuroinflammation in the brain. Transcription of clock genes and activation of the Sirt6/Hmgb1 pathway may contribute to inflammatory responses in the mPFC.
Collapse
Affiliation(s)
- Dandan Cao
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangdong, Guangzhou, China; Medical College of Acupuncture-Moxibustion and Rehabilitation, Guangzhou University of Chinese Medicine, Guangdong, Guangzhou, China
| | - Yi Zhao
- The Affiliated TCM Hospital of Guangzhou Medical University, Guangdong, Guangzhou, China
| | - Yuting Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangdong, Guangzhou, China
| | - Dongyun Wei
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangdong, Guangzhou, China
| | - Minhao Yan
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangdong, Guangzhou, China
| | - Shijie Su
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangdong, Guangzhou, China
| | - Huashan Pan
- Guangdong Chaozhou Health Vocational College, Guangdong, Chaozhou, China
| | - Qi Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangdong, Guangzhou, China.
| |
Collapse
|
24
|
Miyazato P, Noguchi T, Ogawa F, Sugimoto T, Fauzyah Y, Sasaki R, Ebina H. 1mΨ influences the performance of various positive-stranded RNA virus-based replicons. Sci Rep 2024; 14:17634. [PMID: 39085360 PMCID: PMC11292005 DOI: 10.1038/s41598-024-68617-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 07/25/2024] [Indexed: 08/02/2024] Open
Abstract
Self-amplifying RNAs (saRNAs) are versatile vaccine platforms that take advantage of a viral RNA-dependent RNA polymerase (RdRp) to amplify the messenger RNA (mRNA) of an antigen of interest encoded within the backbone of the viral genome once inside the target cell. In recent years, more saRNA vaccines have been clinically tested with the hope of reducing the vaccination dose compared to the conventional mRNA approach. The use of N1-methyl-pseudouridine (1mΨ), which enhances RNA stability and reduces the innate immune response triggered by RNAs, is among the improvements included in the current mRNA vaccines. In the present study, we evaluated the effects of this modified nucleoside on various saRNA platforms based on different viruses. The results showed that different stages of the replication process were affected depending on the backbone virus. For TNCL, an insect virus of the Alphanodavirus genus, replication was impaired by poor recognition of viral RNA by RdRp. In contrast, the translation step was severely abrogated in coxsackievirus B3 (CVB3), a member of the Picornaviridae family. Finally, the effects of 1mΨ on Semliki forest virus (SFV), were not detrimental in in vitro studies, but no advantages were observed when immunogenicity was tested in vivo.
Collapse
Affiliation(s)
- Paola Miyazato
- The Research Foundation for Microbial Diseases of Osaka University (BIKEN), Suita, Osaka, Japan
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
| | - Takafumi Noguchi
- The Research Foundation for Microbial Diseases of Osaka University (BIKEN), Suita, Osaka, Japan
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
| | - Fumiyo Ogawa
- The Research Foundation for Microbial Diseases of Osaka University (BIKEN), Suita, Osaka, Japan
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
| | - Takeshi Sugimoto
- The Research Foundation for Microbial Diseases of Osaka University (BIKEN), Suita, Osaka, Japan
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
| | - Yuzy Fauzyah
- The Research Foundation for Microbial Diseases of Osaka University (BIKEN), Suita, Osaka, Japan
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
| | - Ryo Sasaki
- The Research Foundation for Microbial Diseases of Osaka University (BIKEN), Suita, Osaka, Japan
| | - Hirotaka Ebina
- The Research Foundation for Microbial Diseases of Osaka University (BIKEN), Suita, Osaka, Japan.
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan.
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan.
- Center for Advanced Modalities and DDS (CAMaD), Osaka University, Suita, Osaka, Japan.
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan.
| |
Collapse
|
25
|
Lungu CN, Mangalagiu II, Gurau G, Mehedinti MC. Variations of VEGFR2 Chemical Space: Stimulator and Inhibitory Peptides. Int J Mol Sci 2024; 25:7787. [PMID: 39063029 PMCID: PMC11276785 DOI: 10.3390/ijms25147787] [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: 06/06/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The kinase pathway plays a crucial role in blood vessel function. Particular attention is paid to VEGFR type 2 angiogenesis and vascular morphogenesis as the tyrosine kinase pathway is preferentially activated. In silico studies were performed on several peptides that affect VEGFR2 in both stimulating and inhibitory ways. This investigation aims to examine the molecular properties of VEGFR2, a molecule primarily involved in the processes of vasculogenesis and angiogenesis. These relationships were defined by the interactions between Vascular Endothelial Growth Factor receptor 2 (VEGFR2) and the structural features of the systems. The chemical space of the inhibitory peptides and stimulators was described using topological and energetic properties. Furthermore, chimeric models of stimulating and inhibitory proteins (for VEGFR2) were computed using the protein system structures. The interaction between the chimeric proteins and VEGFR was computed. The chemical space was further characterized using complex manifolds and high-dimensional data visualization. The results show that a slightly similar chemical area is shared by VEGFR2 and stimulating and inhibitory proteins. On the other hand, the stimulator peptides and the inhibitors have distinct chemical spaces.
Collapse
Affiliation(s)
- Claudiu N. Lungu
- Department of Functional and Morphological Science, Faculty of Medicine and Pharmacy, Dunarea de Jos University, 800010 Galati, Romania; (G.G.); (M.C.M.)
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol 1st Bvd, 700506 Iasi, Romania
| | - Ionel I. Mangalagiu
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol 1st Bvd, 700506 Iasi, Romania
| | - Gabriela Gurau
- Department of Functional and Morphological Science, Faculty of Medicine and Pharmacy, Dunarea de Jos University, 800010 Galati, Romania; (G.G.); (M.C.M.)
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol 1st Bvd, 700506 Iasi, Romania
| | - Mihaela Cezarina Mehedinti
- Department of Functional and Morphological Science, Faculty of Medicine and Pharmacy, Dunarea de Jos University, 800010 Galati, Romania; (G.G.); (M.C.M.)
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol 1st Bvd, 700506 Iasi, Romania
| |
Collapse
|
26
|
Carlero D, Fukuda S, Bocanegra R, Ando T, Martin-Benito J, Ibarra B. Conformational Dynamics of Influenza A Virus Ribonucleoprotein Complexes during RNA Synthesis. ACS NANO 2024; 18. [PMID: 39013014 PMCID: PMC11295199 DOI: 10.1021/acsnano.4c01362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/13/2024] [Accepted: 05/22/2024] [Indexed: 07/18/2024]
Abstract
Viral ribonucleoproteins (vRNPs) are the cornerstones of viral proliferation, as they form the macromolecular complexes that are responsible for the transcription and replication of most single-stranded RNA viruses. The influenza A virus (IAV) polymerase catalyzes RNA synthesis within the context of vRNPs where genomic viral RNA (vRNA) is packaged by the viral nucleoprotein (NP). We used high-speed atomic force microscopy and electron microscopy to study the conformational dynamics of individual IAV recombinant RNPs (rRNPs) during RNA synthesis. The rRNPs present an annular organization that allows for the real-time tracking of conformational changes in the NP-vRNA template caused by the advancing polymerase. We demonstrate that the rRNPs undergo a well-defined conformational cycle during RNA synthesis, which can be interpreted in light of previous transcription models. We also present initial estimations of the average RNA synthesis rate in the rRNP and its dependence on the nucleotide concentration and stability of the nascent RNA secondary structures. Furthermore, we provide evidence that rRNPs can perform consecutive cycles of RNA synthesis, accounting for their ability to recycle and generate multiple copies of RNA.
Collapse
Affiliation(s)
- Diego Carlero
- Centro
Nacional de Biotecnología Campus de Cantoblanco, 28049, Madrid, Spain
| | - Shingo Fukuda
- WPI
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Rebeca Bocanegra
- Instituto
Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, 28049, Madrid, Spain
- IMDEA
Nanociencia & CNB-CSIC-IMDEA Nanociencia Associated Unit “Unidad
de Nanobiotecnología”, 28049, Madrid, Spain
| | - Toshio Ando
- WPI
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Jaime Martin-Benito
- IMDEA
Nanociencia & CNB-CSIC-IMDEA Nanociencia Associated Unit “Unidad
de Nanobiotecnología”, 28049, Madrid, Spain
| | - Borja Ibarra
- Instituto
Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, 28049, Madrid, Spain
- IMDEA
Nanociencia & CNB-CSIC-IMDEA Nanociencia Associated Unit “Unidad
de Nanobiotecnología”, 28049, Madrid, Spain
| |
Collapse
|
27
|
Lin TY, Kleemann L, Jeżowski J, Dobosz D, Rawski M, Indyka P, Ważny G, Mehta R, Chramiec-Głąbik A, Koziej Ł, Ranff T, Fufezan C, Wawro M, Kochan J, Bereta J, Leidel SA, Glatt S. The molecular basis of tRNA selectivity by human pseudouridine synthase 3. Mol Cell 2024; 84:2472-2489.e8. [PMID: 38996458 PMCID: PMC11258540 DOI: 10.1016/j.molcel.2024.06.013] [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: 04/25/2023] [Revised: 03/14/2024] [Accepted: 06/13/2024] [Indexed: 07/14/2024]
Abstract
Pseudouridine (Ψ), the isomer of uridine, is ubiquitously found in RNA, including tRNA, rRNA, and mRNA. Human pseudouridine synthase 3 (PUS3) catalyzes pseudouridylation of position 38/39 in tRNAs. However, the molecular mechanisms by which it recognizes its RNA targets and achieves site specificity remain elusive. Here, we determine single-particle cryo-EM structures of PUS3 in its apo form and bound to three tRNAs, showing how the symmetric PUS3 homodimer recognizes tRNAs and positions the target uridine next to its active site. Structure-guided and patient-derived mutations validate our structural findings in complementary biochemical assays. Furthermore, we deleted PUS1 and PUS3 in HEK293 cells and mapped transcriptome-wide Ψ sites by Pseudo-seq. Although PUS1-dependent sites were detectable in tRNA and mRNA, we found no evidence that human PUS3 modifies mRNAs. Our work provides the molecular basis for PUS3-mediated tRNA modification in humans and explains how its tRNA modification activity is linked to intellectual disabilities.
Collapse
Affiliation(s)
- Ting-Yu Lin
- Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland.
| | - Leon Kleemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Jakub Jeżowski
- Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Dominika Dobosz
- Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Michał Rawski
- Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, 30-392 Kraków, Poland
| | - Paulina Indyka
- Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, 30-392 Kraków, Poland
| | - Grzegorz Ważny
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, 30-392 Kraków, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, 30-348 Kraków, Poland
| | - Rahul Mehta
- Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, 30-348 Kraków, Poland
| | | | - Łukasz Koziej
- Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Tristan Ranff
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Germany
| | - Christian Fufezan
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Germany
| | - Mateusz Wawro
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Jakub Kochan
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Joanna Bereta
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Sebastian A Leidel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland.
| | - Sebastian Glatt
- Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland.
| |
Collapse
|
28
|
Moradian H, Schwestka M, Roch T, Gossen M. Deconvolution of synthetic mRNA expression: Nucleoside chemistry alters translatability. Bioeng Transl Med 2024; 9:e10622. [PMID: 39036083 PMCID: PMC11256140 DOI: 10.1002/btm2.10622] [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: 06/12/2023] [Revised: 10/21/2023] [Accepted: 11/09/2023] [Indexed: 07/23/2024] Open
Abstract
Recent technological advances in the production of in vitro transcribed messenger RNA (IVT-mRNA) facilitate its clinical use as well as its application in basic research. In this regard, numerous chemical modifications, which are not naturally observed in endogenous mRNA, have been implemented primarily to address the issue of immunogenicity and improve its biological performance. However, recent findings suggested pronounced differences between expression levels of IVT-mRNAs with different nucleoside modifications in transfected cells. Given the multistep process of IVT-mRNA delivery and subsequent intracellular expression, it is unclear which step is influenced by IVT-mRNA chemistry. Here, we deconvolute this process and show that the nucleoside modification does not interfere with complexation of carriers, their physicochemical properties, and extracellular stability, as exemplified by selected modifications. The immediate effect of mRNA chemistry on the efficiency of ribosomal protein synthesis as a contributor to differences in expression was quantified by in vitro cell-free translation. Our results demonstrate that for the nucleoside modifications tested, translatability was the decisive step in determining overall protein production. Also of special importance for future work on rational selection of tailored synthetic mRNA chemistries, our findings set a workflow to identify potentially limiting, modification-dependent steps in the complex delivery process.
Collapse
Affiliation(s)
- Hanieh Moradian
- Institute of Active Polymers, Helmholtz‐Zentrum HereonTeltowGermany
- Berlin Institute of Health Center for Regenerative Therapies (BCRT)BerlinGermany
| | - Marko Schwestka
- Institute of Active Polymers, Helmholtz‐Zentrum HereonTeltowGermany
- Berlin Institute of Health Center for Regenerative Therapies (BCRT)BerlinGermany
| | - Toralf Roch
- Berlin Institute of Health Center for Regenerative Therapies (BCRT)BerlinGermany
- CheckImmune GmbH, Campus Virchow KlinikumBerlinGermany
| | - Manfred Gossen
- Institute of Active Polymers, Helmholtz‐Zentrum HereonTeltowGermany
- Berlin Institute of Health Center for Regenerative Therapies (BCRT)BerlinGermany
| |
Collapse
|
29
|
Wang C, Yuan F. A comprehensive comparison of DNA and RNA vaccines. Adv Drug Deliv Rev 2024; 210:115340. [PMID: 38810703 PMCID: PMC11181159 DOI: 10.1016/j.addr.2024.115340] [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: 03/28/2024] [Revised: 05/06/2024] [Accepted: 05/18/2024] [Indexed: 05/31/2024]
Abstract
Nucleic acid technology has revolutionized vaccine development, enabling rapid design and production of RNA and DNA vaccines for prevention and treatment of diseases. The successful deployment of mRNA and plasmid DNA vaccines against COVID-19 has further validated the technology. At present, mRNA platform is prevailing due to its higher efficacy, while DNA platform is undergoing rapid evolution because it possesses unique advantages that can potentially overcome the problems associated with the mRNA platform. To help understand the recent performances of the two vaccine platforms and recognize their clinical potentials in the future, this review compares the advantages and drawbacks of mRNA and DNA vaccines that are currently known in the literature, in terms of development timeline, financial cost, ease of distribution, efficacy, safety, and regulatory approval of products. Additionally, the review discusses the ongoing clinical trials, strategies for improvement, and alternative designs of RNA and DNA platforms for vaccination.
Collapse
Affiliation(s)
- Chunxi Wang
- Department of Biomedical Engineering, Duke University, Durham, NC 27705, United States
| | - Fan Yuan
- Department of Biomedical Engineering, Duke University, Durham, NC 27705, United States.
| |
Collapse
|
30
|
Wang Z, Xia A, Wang Q, Cui Z, Lu M, Ye Y, Wang Y, He Y. Natural polymorphisms in ZMET2 encoding a DNA methyltransferase modulate the number of husk layers in maize. PLANT PHYSIOLOGY 2024; 195:2129-2142. [PMID: 38431291 PMCID: PMC11213254 DOI: 10.1093/plphys/kiae113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/30/2024] [Accepted: 02/08/2024] [Indexed: 03/05/2024]
Abstract
DNA methylation affects agronomic traits and the environmental adaptability of crops, but the natural polymorphisms in DNA methylation-related genes and their contributions to phenotypic variation in maize (Zea mays) remain elusive. Here, we show that a polymorphic 10-bp insertion/deletion variant in the 3'UTR of Zea methyltransferase2 (ZMET2) alters its transcript level and accounts for variation in the number of maize husk layers. ZMET2 encodes a chromomethylase and is required for maintaining genome-wide DNA methylation in the CHG sequence context. Disruption of ZMET2 increased the number of husk layers and resulted in thousands of differentially methylated regions, a proportion of which were also distinguishable in natural ZMET2 alleles. Population genetic analyses indicated that ZMET2 was a target of selection and might play a role in the spread of maize from tropical to temperate regions. Our results provide important insights into the natural variation of ZMET2 that confers both global and locus-specific effects on DNA methylation, which contribute to phenotypic diversity in maize.
Collapse
Affiliation(s)
- Zi Wang
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Aiai Xia
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Qi Wang
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Zhenhai Cui
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang 110866, China
| | - Ming Lu
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Yusheng Ye
- Maize Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110065, China
| | - Yanbo Wang
- Maize Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110065, China
| | - Yan He
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| |
Collapse
|
31
|
Rouse WB, Tompkins VS, O’Leary CA, Moss WN. The RNA secondary structure of androgen receptor-FL and V7 transcripts reveals novel regulatory regions. Nucleic Acids Res 2024; 52:6596-6613. [PMID: 38554103 PMCID: PMC11194067 DOI: 10.1093/nar/gkae220] [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: 11/21/2023] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
The androgen receptor (AR) is a ligand-dependent nuclear transcription factor belonging to the steroid hormone nuclear receptor family. Due to its roles in regulating cell proliferation and differentiation, AR is tightly regulated to maintain proper levels of itself and the many genes it controls. AR dysregulation is a driver of many human diseases including prostate cancer. Though this dysregulation often occurs at the RNA level, there are many unknowns surrounding post-transcriptional regulation of AR mRNA, particularly the role that RNA secondary structure plays. Thus, a comprehensive analysis of AR transcript secondary structure is needed. We address this through the computational and experimental analyses of two key isoforms, full length (AR-FL) and truncated (AR-V7). Here, a combination of in-cell RNA secondary structure probing experiments (targeted DMS-MaPseq) and computational predictions were used to characterize the static structural landscape and conformational dynamics of both isoforms. Additionally, in-cell assays were used to identify functionally relevant structures in the 5' and 3' UTRs of AR-FL. A notable example is a conserved stem loop structure in the 5'UTR of AR-FL that can bind to Poly(RC) Binding Protein 2 (PCBP2). Taken together, our results reveal novel features that regulate AR expression.
Collapse
Affiliation(s)
- Warren B Rouse
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Van S Tompkins
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Collin A O’Leary
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Current Address: Departments of Biology and Chemistry, Cornell College, Mount Vernon, IA 52314, USA
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| |
Collapse
|
32
|
Potera K, Tomala K. Using yeasts for the studies of nonfunctional factors in protein evolution. Yeast 2024. [PMID: 38895906 DOI: 10.1002/yea.3970] [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: 01/31/2024] [Revised: 05/08/2024] [Accepted: 06/06/2024] [Indexed: 06/21/2024] Open
Abstract
The evolution of protein sequence is driven not only by factors directly related to protein function and shape but also by nonfunctional factors. Such factors in protein evolution might be categorized as those connected to energetic costs, synthesis efficiency, and avoidance of misfolding and toxicity. A common approach to studying them is correlational analysis contrasting them with some characteristics of the protein, like amino acid composition, but these features are interdependent. To avoid possible bias, empirical studies are needed, and not enough work has been done to date. In this review, we describe the role of nonfunctional factors in protein evolution and present an experimental approach using yeast as a suitable model organism. The focus of the proposed approach is on the potential negative impact on the fitness of mutations that change protein properties not related to function and the frequency of mutations that change these properties. Experimental results of testing the misfolding avoidance hypothesis as an explanation for why highly expressed proteins evolve slowly are inconsistent with correlational research results. Therefore, more efforts should be made to empirically test the effects of nonfunctional factors in protein evolution and to contrast these results with the results of the correlational analysis approach.
Collapse
Affiliation(s)
- Katarzyna Potera
- Faculty of Biology, Institute of Environmental Sciences, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Katarzyna Tomala
- Faculty of Biology, Institute of Environmental Sciences, Jagiellonian University, Krakow, Poland
| |
Collapse
|
33
|
Parveen A, Elkordy AA. Brief Insights into mRNA Vaccines: Their Successful Production and Nanoformulation for Effective Response against COVID-19 and Their Potential Success for Influenza A and B. Pathogens 2024; 13:500. [PMID: 38921798 PMCID: PMC11206352 DOI: 10.3390/pathogens13060500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/27/2024] Open
Abstract
A mRNA vaccine is a type of vaccine that induces an immune response. Antigen-encoding mRNA is delivered via vaccine carriers into the immune cells, which are produced because of antigen-encoding mRNA translation, a protein. For example, COVID-19 mRNA vaccines produce the spike protein of the COVID-19 virus, whereas for influenza virus, mRNA vaccines target the haemagglutinin protein to treat the flu, and it requires modifications depending on the pandemic or seasonal viruses as it is capable of adapting the immune response, which makes the development of vaccines arduous. The protein molecule promotes an adaptive immune response that eliminates and terminates the corresponding virus or pathogen. There are many challenges to delivering an mRNA vaccine into the body; hence, the encapsulation of the mRNA (usually within lipid nanoparticles) is necessary to protect the mRNA from the body's surrounding environment. In this review article, we focus mainly on the production, formulation, and stabilization of mRNA vaccines in general, elaborating more on and focusing more on SARS-CoV-2, or COVID-19, and influenza viruses, which have become a major concern as these viruses have turned into life-threatening diseases.
Collapse
Affiliation(s)
| | - Amal Ali Elkordy
- School of Pharmacy and Pharmaceutical Sciences, Faculty of Health Sciences and Wellbeing, University of Sunderland, Sunderland SR1 3SD, UK;
| |
Collapse
|
34
|
Niazi SK, Magoola M, Mariam Z. Innovative Therapeutic Strategies in Alzheimer's Disease: A Synergistic Approach to Neurodegenerative Disorders. Pharmaceuticals (Basel) 2024; 17:741. [PMID: 38931409 PMCID: PMC11206655 DOI: 10.3390/ph17060741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Alzheimer's disease (AD) remains a significant challenge in the field of neurodegenerative disorders, even nearly a century after its discovery, due to the elusive nature of its causes. The development of drugs that target multiple aspects of the disease has emerged as a promising strategy to address the complexities of AD and related conditions. The immune system's role, particularly in AD, has gained considerable interest, with nanobodies representing a new frontier in biomedical research. Advances in targeting antibodies against amyloid-β (Aβ) and using messenger RNA for genetic translation have revolutionized the production of antibodies and drug development, opening new possibilities for treatment. Despite these advancements, conventional therapies for AD, such as Cognex, Exelon, Razadyne, and Aricept, often have limited long-term effectiveness, underscoring the need for innovative solutions. This necessity has led to the incorporation advanced technologies like artificial intelligence and machine learning into the drug discovery process for neurodegenerative diseases. These technologies help identify therapeutic targets and optimize lead compounds, offering a more effective approach to addressing the challenges of AD and similar conditions.
Collapse
Affiliation(s)
| | | | - Zamara Mariam
- Centre for Health and Life Sciences, Coventry University, Coventry CV1 5FB, UK
| |
Collapse
|
35
|
Sioud M, Juzeniene A, Sæbøe-Larssen S. Exploring the Impact of mRNA Modifications on Translation Efficiency and Immune Tolerance to Self-Antigens. Vaccines (Basel) 2024; 12:624. [PMID: 38932353 PMCID: PMC11209393 DOI: 10.3390/vaccines12060624] [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: 05/06/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Therapeutic modified mRNAs are being developed for a broad range of human diseases. However, the impact of potential miscoding of modified mRNAs on self-tolerance remains unknown. Additionally, more studies are needed to explore the effects of nucleoside alkylation on translation. While all six tested modifications are tolerated as substrates by T7 RNA polymerase and inhibited mRNA immunogenicity, the translation efficiency varied significantly depending on the type of modification. In contrast to methylation, ethylation at the N1 position of pseudouridine (Ψ) hindered translation, suggesting that the C5-C1' glycosidic bond alone is not a critical element for high translation. Inhibition of mRNA translation was also observed with 5-methoxyuridine modification. However, this inhibition was partially alleviated through the optimization of mRNA coding sequences. BALB/c mice immunized with syngeneic ψ-modified mRNA encoding for Wilms' tumor antigen-1 (WT1) developed a low but significant level of anti-WT1 IgG antibodies compared to those immunized with either unmodified or N1-methyl ψ-modified mRNA. Overall, the data indicate that adding a simple ethyl group (-CH2CH3) at the N1 position of ψ has a major negative effect on translation despite its reduced immunogenicity. Additionally, mRNA containing Ψ may alter translation fidelity at certain codons, which could lead to a breakdown of immune tolerance to self-antigens. This concern should be taken into account during gene replacement therapies, although it could benefit mRNA-based vaccines by generating a diverse repertoire of antigens.
Collapse
Affiliation(s)
- Mouldy Sioud
- Department of Cancer Immunology, Oslo University Hospital, Radiumhospitalet, Ullernchausseen 70, 0379 Oslo, Norway
| | - Asta Juzeniene
- Department of Radiation Biology, Oslo University Hospital, Radiumhospitalet, Ullernchausseen 70, 0379 Oslo, Norway;
| | - Stein Sæbøe-Larssen
- Department of cellular Therapy, Oslo University Hospital, Radiumhospitalet, Ullernchausseen 70, 0379 Oslo, Norway;
| |
Collapse
|
36
|
Androsavich JR. Frameworks for transformational breakthroughs in RNA-based medicines. Nat Rev Drug Discov 2024; 23:421-444. [PMID: 38740953 DOI: 10.1038/s41573-024-00943-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2024] [Indexed: 05/16/2024]
Abstract
RNA has sparked a revolution in modern medicine, with the potential to transform the way we treat diseases. Recent regulatory approvals, hundreds of new clinical trials, the emergence of CRISPR gene editing, and the effectiveness of mRNA vaccines in dramatic response to the COVID-19 pandemic have converged to create tremendous momentum and expectation. However, challenges with this relatively new class of drugs persist and require specialized knowledge and expertise to overcome. This Review explores shared strategies for developing RNA drug platforms, including layering technologies, addressing common biases and identifying gaps in understanding. It discusses the potential of RNA-based therapeutics to transform medicine, as well as the challenges associated with improving applicability, efficacy and safety profiles. Insights gained from RNA modalities such as antisense oligonucleotides (ASOs) and small interfering RNAs are used to identify important next steps for mRNA and gene editing technologies.
Collapse
Affiliation(s)
- John R Androsavich
- RNA Accelerator, Pfizer Inc, Cambridge, MA, USA.
- Ginkgo Bioworks, Boston, MA, USA.
| |
Collapse
|
37
|
Curry E, Muir G, Qu J, Kis Z, Hulley M, Brown A. Engineering an Escherichia coli based in vivo mRNA manufacturing platform. Biotechnol Bioeng 2024; 121:1912-1926. [PMID: 38419526 DOI: 10.1002/bit.28684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/31/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
Synthetic mRNA is currently produced in standardized in vitro transcription systems. However, this one-size-fits-all approach has associated drawbacks in supply chain shortages, high reagent costs, complex product-related impurity profiles, and limited design options for molecule-specific optimization of product yield and quality. Herein, we describe for the first time development of an in vivo mRNA manufacturing platform, utilizing an Escherichia coli cell chassis. Coordinated mRNA, DNA, cell and media engineering, primarily focussed on disrupting interactions between synthetic mRNA molecules and host cell RNA degradation machinery, increased product yields >40-fold compared to standard "unengineered" E. coli expression systems. Mechanistic dissection of cell factory performance showed that product mRNA accumulation levels approached theoretical limits, accounting for ~30% of intracellular total RNA mass, and that this was achieved via host-cell's reallocating biosynthetic capacity away from endogenous RNA and cell biomass generation activities. We demonstrate that varying sized functional mRNA molecules can be produced in this system and subsequently purified. Accordingly, this study introduces a new mRNA production technology, expanding the solution space available for mRNA manufacturing.
Collapse
Affiliation(s)
- Edward Curry
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - George Muir
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Jixin Qu
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Zoltán Kis
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | | | - Adam Brown
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| |
Collapse
|
38
|
Aubé F, Fontrodona N, Guiguettaz L, Vallin E, Fabbri L, Lapendry A, Vagner S, Ricci EP, Auboeuf D. Metabolism-dependent secondary effect of anti-MAPK cancer therapy on DNA repair. NAR Cancer 2024; 6:zcae019. [PMID: 38690580 PMCID: PMC11059277 DOI: 10.1093/narcan/zcae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/08/2024] [Accepted: 04/29/2024] [Indexed: 05/02/2024] Open
Abstract
Amino acid bioavailability impacts mRNA translation in a codon-dependent manner. Here, we report that the anti-cancer MAPK inhibitors (MAPKi) decrease the intracellular concentration of aspartate and glutamate in melanoma cells. This coincides with the accumulation of ribosomes on codons corresponding to these amino acids and triggers the translation-dependent degradation of mRNAs encoding aspartate- and glutamate-rich proteins, involved in DNA metabolism such as DNA replication and repair. Consequently, cells that survive MAPKi degrade aspartate and glutamate likely to generate energy, which simultaneously decreases their requirement for amino acids due to the downregulation of aspartate- and glutamate-rich proteins involved in cell proliferation. Concomitantly, the downregulation of aspartate- and glutamate-rich proteins involved in DNA repair increases DNA damage loads. Thus, DNA repair defects, and therefore mutations, are at least in part a secondary effect of the metabolic adaptation of cells exposed to MAPKi.
Collapse
Affiliation(s)
- Fabien Aubé
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, LBMC, ENS, Lyon, France
| | - Nicolas Fontrodona
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, LBMC, ENS, Lyon, France
| | - Laura Guiguettaz
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
| | - Elodie Vallin
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
| | - Lucilla Fabbri
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France
- Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France
- Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Audrey Lapendry
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, LBMC, ENS, Lyon, France
| | - Stephan Vagner
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France
- Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France
- Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Emiliano P Ricci
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
| | - Didier Auboeuf
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, LBMC, ENS, Lyon, France
| |
Collapse
|
39
|
Wilkinson P, Jackson B, Fermor H, Davies R. A new mRNA structure prediction based approach to identifying improved signal peptides for bone morphogenetic protein 2. BMC Biotechnol 2024; 24:34. [PMID: 38783306 PMCID: PMC11112908 DOI: 10.1186/s12896-024-00858-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Signal peptide (SP) engineering has proven able to improve production of many proteins yet is a laborious process that still relies on trial and error. mRNA structure around the translational start site is important in translation initiation and has rarely been considered in this context, with recent improvements in in silico mRNA structure potentially rendering it a useful predictive tool for SP selection. Here we attempt to create a method to systematically screen candidate signal peptide sequences in silico based on both their nucleotide and amino acid sequences. Several recently released computational tools were used to predict signal peptide activity (SignalP), localization target (DeepLoc) and predicted mRNA structure (MXFold2). The method was tested with Bone Morphogenetic Protein 2 (BMP2), an osteogenic growth factor used clinically for bone regeneration. It was hoped more effective BMP2 SPs could improve BMP2-based gene therapies and reduce the cost of recombinant BMP2 production. RESULTS Amino acid sequence analysis indicated 2,611 SPs from the TGF-β superfamily were predicted to function when attached to BMP2. mRNA structure prediction indicated structures at the translational start site were likely highly variable. The five sequences with the most accessible translational start sites, a codon optimized BMP2 SP variant and the well-established hIL2 SP sequence were taken forward to in vitro testing. The top five candidates showed non-significant improvements in BMP2 secretion in HEK293T cells. All showed reductions in secretion versus the native sequence in C2C12 cells, with several showing large and significant decreases. None of the tested sequences were able to increase alkaline phosphatase activity above background in C2C12s. The codon optimized control sequence and hIL2 SP showed reasonable activity in HEK293T but very poor activity in C2C12. CONCLUSIONS These results support the use of peptide sequence based in silico tools for basic predictions around signal peptide activity in a synthetic biology context. However, mRNA structure prediction requires improvement before it can produce reliable predictions for this application. The poor activity of the codon optimized BMP2 SP variant in C2C12 emphasizes the importance of codon choice, mRNA structure, and cellular context for SP activity.
Collapse
Affiliation(s)
- Piers Wilkinson
- Department of Mechanical Engineering, Institute of Medical and Biological Engineering, University of Leeds, Leeds, UK.
| | - Brian Jackson
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Hazel Fermor
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Robert Davies
- Oral Biology, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| |
Collapse
|
40
|
Wang TT, Zhu HL, Ouyang KW, Wang H, Luo YX, Zheng XM, Ling Q, Wang KW, Zhang J, Chang W, Lu Q, Zhang YF, Yuan Z, Li H, Xiong YW, Wei T, Wang H. Environmental cadmium inhibits testicular testosterone synthesis via Parkin-dependent MFN1 degradation. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134142. [PMID: 38555669 DOI: 10.1016/j.jhazmat.2024.134142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
Low testosterone (T) levels are associated with many common diseases, such as obesity, male infertility, depression, and cardiovascular disease. It is well known that environmental cadmium (Cd) exposure can induce T decline, but the exact mechanism remains unclear. We established a murine model in which Cd exposure induced testicular T decline. Based on the model, we found Cd caused mitochondrial fusion disorder and Parkin mitochondrial translocation in mouse testes. MFN1 overexpression confirmed that MFN1-dependent mitochondrial fusion disorder mediated the Cd-induced T synthesis suppression in Leydig cells. Further data confirmed Cd induced the decrease of MFN1 protein by increasing ubiquitin degradation. Testicular specific Parkin knockdown confirmed Cd induced the ubiquitin-dependent degradation of MFN1 protein through promoting Parkin mitochondrial translocation in mouse testes. Expectedly, testicular specific Parkin knockdown also mitigated testicular T decline. Mito-TEMPO, a targeted inhibitor for mitochondrial reactive oxygen species (mtROS), alleviated Cd-caused Parkin mitochondrial translocation and mitochondrial fusion disorder. As above, Parkin mitochondrial translocation induced mitochondrial fusion disorder and the following T synthesis repression in Cd-exposed Leydig cells. Collectively, our study elucidates a novel mechanism through which Cd induces T decline and provides a new treatment strategy for patients with androgen disorders.
Collapse
Affiliation(s)
- Tian-Tian Wang
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Hua-Long Zhu
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Kong-Wen Ouyang
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Hua Wang
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China; Department of Respiratory Medicine, Anhui Provincial Children's Hospital, Hefei, Anhui 230000, China
| | - Ye-Xin Luo
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Xin-Mei Zheng
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Qing Ling
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Kai-Wen Wang
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Jin Zhang
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Wei Chang
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Qi Lu
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Yu-Feng Zhang
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Zhi Yuan
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Hao Li
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Yong-Wei Xiong
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Tian Wei
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Hua Wang
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China.
| |
Collapse
|
41
|
Park JK, Lee EB, Winthrop KL. What rheumatologists need to know about mRNA vaccines: current status and future of mRNA vaccines in autoimmune inflammatory rheumatic diseases. Ann Rheum Dis 2024; 83:687-695. [PMID: 38413167 DOI: 10.1136/ard-2024-225492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 02/14/2024] [Indexed: 02/29/2024]
Abstract
Messenger RNA (mRNA) vaccines as a novel vaccine platform offer new tools to effectively combat both emerging and existing pathogens which were previously not possible. The 'plug and play' feature of mRNA vaccines enables swift design and production of vaccines targeting complex antigens and rapid incorporation of new vaccine constituents as needed. This feature makes them likely to be adopted for widespread clinical use in the future.Currently approved mRNA vaccines include only those against SARS-CoV-2 virus. These vaccines demonstrate robust immunogenicity and offer substantial protection against severe disease. Numerous mRNA vaccines against viral pathogens are in the early to late phase of development. Several mRNA vaccines for influenza are tested in clinical trials, with some already in phase 3 studies. Other vaccines in the early and late phases of development include those targeting Cytomegalovirus, varicella zoster virus, respiratory syncytial virus and Epstein-Barr virus. Many of these vaccines will likely be indicated for immunosuppressed populations including those with autoimmune inflammatory rheumatic diseases (AIIRD). This review focuses on the mechanism, safety and efficacy of mRNA in general and summarises the status of mRNA vaccines in development for common infectious diseases of particular interest for patients with AIIRD.
Collapse
Affiliation(s)
- Jin Kyun Park
- Rheumatology, Seoul National University College of Medicine, Jongno-gu, Seoul, Korea (the Republic of)
| | - Eun Bong Lee
- Internal Medicine, Seoul National University College of Medicine, Jongno-gu, Seoul, Korea (the Republic of)
| | - Kevin L Winthrop
- School of Public Health, Oregon Health & Science University, Portland, Oregon, USA
| |
Collapse
|
42
|
Wang Q, Bu C, Dai Q, Chen J, Zhang R, Zheng X, Ren H, Xin X, Li X. Recent Progress in Nucleic Acid Pulmonary Delivery toward Overcoming Physiological Barriers and Improving Transfection Efficiency. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309748. [PMID: 38460157 PMCID: PMC11095210 DOI: 10.1002/advs.202309748] [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: 12/12/2023] [Revised: 02/04/2024] [Indexed: 03/11/2024]
Abstract
Pulmonary delivery of therapeutic agents has been considered the desirable administration route for local lung disease treatment. As the latest generation of therapeutic agents, nucleic acid has been gradually developed as gene therapy for local diseases such as asthma, chronic obstructive pulmonary diseases, and lung fibrosis. The features of nucleic acid, specific physiological structure, and pathophysiological barriers of the respiratory tract have strongly affected the delivery efficiency and pulmonary bioavailability of nucleic acid, directly related to the treatment outcomes. The development of pharmaceutics and material science provides the potential for highly effective pulmonary medicine delivery. In this review, the key factors and barriers are first introduced that affect the pulmonary delivery and bioavailability of nucleic acids. The advanced inhaled materials for nucleic acid delivery are further summarized. The recent progress of platform designs for improving the pulmonary delivery efficiency of nucleic acids and their therapeutic outcomes have been systematically analyzed, with the application and the perspectives of advanced vectors for pulmonary gene delivery.
Collapse
Affiliation(s)
- Qiyue Wang
- School of Pharmaceutical ScienceNanjing Tech UniversityNanjing211816China
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparation and ExcipientsNanjing210009China
| | - Chaozhi Bu
- Wuxi Maternity and Child Health Care HospitalAffiliated Women's Hospital of Jiangnan UniversityWuxi214002China
| | - Qihao Dai
- School of Pharmaceutical ScienceNanjing Tech UniversityNanjing211816China
| | - Jinhua Chen
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparation and ExcipientsNanjing210009China
- Center for Research Development and Evaluation of Pharmaceutical Excipients and Generic Drugs, Department of PharmaceuticsChina Pharmaceutical UniversityNanjing210009China
| | - Ruitao Zhang
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparation and ExcipientsNanjing210009China
- Center for Research Development and Evaluation of Pharmaceutical Excipients and Generic Drugs, Department of PharmaceuticsChina Pharmaceutical UniversityNanjing210009China
| | - Xiaomin Zheng
- Wuxi Maternity and Child Health Care HospitalAffiliated Women's Hospital of Jiangnan UniversityWuxi214002China
| | - Hao Ren
- School of Pharmaceutical ScienceNanjing Tech UniversityNanjing211816China
| | - Xiaofei Xin
- Center for Research Development and Evaluation of Pharmaceutical Excipients and Generic Drugs, Department of PharmaceuticsChina Pharmaceutical UniversityNanjing210009China
| | - Xueming Li
- School of Pharmaceutical ScienceNanjing Tech UniversityNanjing211816China
| |
Collapse
|
43
|
Hoskins I, Rao S, Tante C, Cenik C. Integrated multiplexed assays of variant effect reveal determinants of catechol-O-methyltransferase gene expression. Mol Syst Biol 2024; 20:481-505. [PMID: 38355921 PMCID: PMC11066095 DOI: 10.1038/s44320-024-00018-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
Multiplexed assays of variant effect are powerful methods to profile the consequences of rare variants on gene expression and organismal fitness. Yet, few studies have integrated several multiplexed assays to map variant effects on gene expression in coding sequences. Here, we pioneered a multiplexed assay based on polysome profiling to measure variant effects on translation at scale, uncovering single-nucleotide variants that increase or decrease ribosome load. By combining high-throughput ribosome load data with multiplexed mRNA and protein abundance readouts, we mapped the cis-regulatory landscape of thousands of catechol-O-methyltransferase (COMT) variants from RNA to protein and found numerous coding variants that alter COMT expression. Finally, we trained machine learning models to map signatures of variant effects on COMT gene expression and uncovered both directional and divergent impacts across expression layers. Our analyses reveal expression phenotypes for thousands of variants in COMT and highlight variant effects on both single and multiple layers of expression. Our findings prompt future studies that integrate several multiplexed assays for the readout of gene expression.
Collapse
Affiliation(s)
- Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Charisma Tante
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
| |
Collapse
|
44
|
Mercier BC, Labaronne E, Cluet D, Guiguettaz L, Fontrodona N, Bicknell A, Corbin A, Wencker M, Aube F, Modolo L, Jouravleva K, Auboeuf D, Moore MJ, Ricci EP. Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation. Genome Res 2024; 34:394-409. [PMID: 38508694 PMCID: PMC11067875 DOI: 10.1101/gr.277863.123] [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: 03/07/2023] [Accepted: 03/09/2024] [Indexed: 03/22/2024]
Abstract
mRNA translation and decay are tightly interconnected processes both in the context of mRNA quality-control pathways and for the degradation of functional mRNAs. Cotranslational mRNA degradation through codon usage, ribosome collisions, and the recruitment of specific proteins to ribosomes is an important determinant of mRNA turnover. However, the extent to which translation-dependent mRNA decay (TDD) and translation-independent mRNA decay (TID) pathways participate in the degradation of mRNAs has not been studied yet. Here we describe a comprehensive analysis of basal and signal-induced TDD and TID in mouse primary CD4+ T cells. Our results indicate that most cellular transcripts are decayed to some extent in a translation-dependent manner. Our analysis further identifies the length of untranslated regions, the density of ribosomes, and GC3 content as important determinants of TDD magnitude. Consistently, all transcripts that undergo changes in ribosome density within their coding sequence upon T cell activation display a corresponding change in their TDD level. Moreover, we reveal a dynamic modulation in the relationship between GC3 content and TDD upon T cell activation, with a reversal in the impact of GC3- and AU3-rich codons. Altogether, our data show a strong and dynamic interconnection between mRNA translation and decay in mammalian primary cells.
Collapse
Affiliation(s)
- Blandine C Mercier
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Emmanuel Labaronne
- Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, 69007 Lyon, France
- ADLIN Science, 9100 Evry-Courcouronnes, France
| | - David Cluet
- Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, 69007 Lyon, France
| | - Laura Guiguettaz
- Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, 69007 Lyon, France
| | - Nicolas Fontrodona
- Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, 69007 Lyon, France
| | - Alicia Bicknell
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Antoine Corbin
- Centre International de Recherche en Infectiologie Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Mélanie Wencker
- Centre International de Recherche en Infectiologie Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Fabien Aube
- Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, 69007 Lyon, France
| | - Laurent Modolo
- Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, 69007 Lyon, France
| | - Karina Jouravleva
- Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, 69007 Lyon, France
| | - Didier Auboeuf
- Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, 69007 Lyon, France
| | - Melissa J Moore
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA;
| | - Emiliano P Ricci
- Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, 69007 Lyon, France;
| |
Collapse
|
45
|
Bicknell AA, Reid DW, Licata MC, Jones AK, Cheng YM, Li M, Hsiao CJ, Pepin CS, Metkar M, Levdansky Y, Fritz BR, Andrianova EA, Jain R, Valkov E, Köhrer C, Moore MJ. Attenuating ribosome load improves protein output from mRNA by limiting translation-dependent mRNA decay. Cell Rep 2024; 43:114098. [PMID: 38625793 DOI: 10.1016/j.celrep.2024.114098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/24/2024] [Accepted: 03/27/2024] [Indexed: 04/18/2024] Open
Abstract
Developing an effective mRNA therapeutic often requires maximizing protein output per delivered mRNA molecule. We previously found that coding sequence (CDS) design can substantially affect protein output, with mRNA variants containing more optimal codons and higher secondary structure yielding the highest protein outputs due to their slow rates of mRNA decay. Here, we demonstrate that CDS-dependent differences in translation initiation and elongation rates lead to differences in translation- and deadenylation-dependent mRNA decay rates, thus explaining the effect of CDS on mRNA half-life. Surprisingly, the most stable and highest-expressing mRNAs in our test set have modest initiation/elongation rates and ribosome loads, leading to minimal translation-dependent mRNA decay. These findings are of potential interest for optimization of protein output from therapeutic mRNAs, which may be achieved by attenuating rather than maximizing ribosome load.
Collapse
Affiliation(s)
| | - David W Reid
- Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
| | | | | | - Yi Min Cheng
- Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
| | - Mengying Li
- Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
| | | | | | - Mihir Metkar
- Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
| | - Yevgen Levdansky
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Brian R Fritz
- Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
| | | | - Ruchi Jain
- Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
| | - Eugene Valkov
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | | | | |
Collapse
|
46
|
Nievergelt P, Berliat F, McAuley KE, Dorgan CR, van Well RM, Thorn A, Spingler B. RNA oligomers at atomic resolution containing 1-methylpseudouridine, an essential building block of mRNA vaccines. ChemMedChem 2024; 19:e202300600. [PMID: 38235959 DOI: 10.1002/cmdc.202300600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/19/2024]
Abstract
All widely used mRNA vaccines against COVID-19 contain in their sequence 1-methylpseudouridine (m1Ψ) instead of uridine. In this publication, we report two high resolution crystal structures (at up to 1.01 and 1.32 Å, respectively) of one such double-stranded 12-mer RNA sequence crystallized in two crystal forms. The structures are compared with similar structures which do not contain this modification. Additionally, the X-ray structure of 1-methyl-pseudouridine itself was determined.
Collapse
Affiliation(s)
- Philipp Nievergelt
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Florian Berliat
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | | | - Colin R Dorgan
- Biosynth Limited, Compton, Berkshire, RG20 6NE, United Kingdom
| | | | - Andrea Thorn
- Institut für Nanostruktur und Festkörperphysik, Universität Hamburg, 22761, Hamburg, Germany
| | - Bernhard Spingler
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| |
Collapse
|
47
|
Wongsodirdjo P, Caruso AC, Yong AK, Lester MA, Vella LJ, Hung YH, Nisbet RM. Messenger RNA-encoded antibody approach for targeting extracellular and intracellular tau. Brain Commun 2024; 6:fcae100. [PMID: 38585667 PMCID: PMC10996922 DOI: 10.1093/braincomms/fcae100] [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: 10/25/2023] [Revised: 02/19/2024] [Accepted: 03/21/2024] [Indexed: 04/09/2024] Open
Abstract
Monoclonal antibodies have emerged as a leading therapeutic agent for the treatment of disease, including Alzheimer's disease. In the last year, two anti-amyloid monoclonal antibodies, lecanemab and aducanumab, have been approved in the USA for the treatment of Alzheimer's disease, whilst several tau-targeting monoclonal antibodies are currently in clinical trials. Such antibodies, however, are expensive and timely to produce and require frequent dosing regimens to ensure disease-modifying effects. Synthetic in vitro-transcribed messenger RNA encoding antibodies for endogenous protein expression holds the potential to overcome many of the limitations associated with protein antibody production. Here, we have generated synthetic in vitro-transcribed messenger RNA encoding a tau-specific antibody as a full-sized immunoglobulin and as a single-chain variable fragment. In vitro transfection of human neuroblastoma SH-SY5Y cells demonstrated the ability of the synthetic messenger RNA to be translated into a functional tau-specific antibody. Furthermore, we show that the translation of the tau-specific single-chain variable fragment as an intrabody results in the specific engagement of intracellular tau. This work highlights the utility of messenger RNA for the delivery of antibody therapeutics, including intrabodies, for the targeting of tau in Alzheimer's disease and other tauopathies.
Collapse
Affiliation(s)
- Patricia Wongsodirdjo
- The Florey Institute, Parkville, Victoria 3052, Australia
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Alayna C Caruso
- The Florey Institute, Parkville, Victoria 3052, Australia
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Alicia K Yong
- The Florey Institute, Parkville, Victoria 3052, Australia
| | - Madeleine A Lester
- The Florey Institute, Parkville, Victoria 3052, Australia
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Laura J Vella
- The Florey Institute, Parkville, Victoria 3052, Australia
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Ya Hui Hung
- The Florey Institute, Parkville, Victoria 3052, Australia
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Rebecca M Nisbet
- The Florey Institute, Parkville, Victoria 3052, Australia
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3052, Australia
| |
Collapse
|
48
|
Parhiz H, Atochina-Vasserman EN, Weissman D. mRNA-based therapeutics: looking beyond COVID-19 vaccines. Lancet 2024; 403:1192-1204. [PMID: 38461842 DOI: 10.1016/s0140-6736(23)02444-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 07/06/2023] [Accepted: 10/30/2023] [Indexed: 03/12/2024]
Abstract
Recent advances in mRNA technology and its delivery have enabled mRNA-based therapeutics to enter a new era in medicine. The rapid, potent, and transient nature of mRNA-encoded proteins, without the need to enter the nucleus or the risk of genomic integration, makes them desirable tools for treatment of a range of diseases, from infectious diseases to cancer and monogenic disorders. The rapid pace and ease of mass-scale manufacturability of mRNA-based therapeutics supported the global response to the COVID-19 pandemic. Nonetheless, challenges remain with regards to mRNA stability, duration of expression, delivery efficiency, and targetability, to broaden the applicability of mRNA therapeutics beyond COVID-19 vaccines. By learning from the rapidly expanding preclinical and clinical studies, we can optimise the mRNA platform to meet the clinical needs of each disease. Here, we will summarise the recent advances in mRNA technology; its use in vaccines, immunotherapeutics, protein replacement therapy, and genomic editing; and its delivery to desired specific cell types and organs for development of a new generation of targeted mRNA-based therapeutics.
Collapse
Affiliation(s)
- Hamideh Parhiz
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Drew Weissman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
49
|
Bhatt U, Cucchiarini A, Luo Y, Evans CW, Mergny JL, Iyer KS, Smith NM. Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA. Genome Res 2024; 34:217-230. [PMID: 38355305 PMCID: PMC10984386 DOI: 10.1101/gr.278236.123] [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: 06/30/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
Secondary structure is a principal determinant of lncRNA function, predominantly regarding scaffold formation and interfaces with target molecules. Noncanonical secondary structures that form in nucleic acids have known roles in regulating gene expression and include G-quadruplexes (G4s), intercalated motifs (iMs), and R-loops (RLs). In this paper, we used the computational tools G4-iM Grinder and QmRLFS-finder to predict the formation of each of these structures throughout the lncRNA transcriptome in comparison to protein-coding transcripts. The importance of the predicted structures in lncRNAs in biological contexts was assessed by combining our results with publicly available lncRNA tissue expression data followed by pathway analysis. The formation of predicted G4 (pG4) and iM (piM) structures in select lncRNA sequences was confirmed in vitro using biophysical experiments under near-physiological conditions. We find that the majority of the tested pG4s form highly stable G4 structures, and identify many previously unreported G4s in biologically important lncRNAs. In contrast, none of the piM sequences are able to form iM structures, consistent with the idea that RNA is unable to form stable iMs. Unexpectedly, these C-rich sequences instead form Z-RNA structures, which have not been previously observed in regions containing cytosine repeats and represent an interesting and underexplored target for protein-RNA interactions. Our results highlight the prevalence and potential structure-associated functions of noncanonical secondary structures in lncRNAs, and show G4 and Z-RNA structure formation in many lncRNA sequences for the first time, furthering the understanding of the structure-function relationship in lncRNAs.
Collapse
Affiliation(s)
- Uditi Bhatt
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Anne Cucchiarini
- Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Yu Luo
- Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Cameron W Evans
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - K Swaminathan Iyer
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Nicole M Smith
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia;
| |
Collapse
|
50
|
Weissenboeck F, Klöcker N, Špaček P, Hüwel S, Rentmeister A. Stabilized 5' Cap Analogue for Optochemical Activation of mRNA Translation. ACS OMEGA 2024; 9:12810-12816. [PMID: 38524462 PMCID: PMC10955689 DOI: 10.1021/acsomega.3c08505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/02/2024] [Accepted: 01/19/2024] [Indexed: 03/26/2024]
Abstract
The 5' cap is a distinguishing feature of transcripts made by polymerase II and characterized by an N7-methylated guanosine (m7G) linked to the first transcribed nucleotide by a 5'-5' triphosphate bridge. It stabilizes eukaryotic mRNAs and plays a crucial role in translation initiation. Its importance in mRNA processing, translation, and turnover makes the 5' cap a privileged structure for engineering by non-natural modifications. A photocleavable group at the 5' cap of guanosine was recently used to mute translation of exogenous mRNAs. Its removal by light enabled direct control of protein production at the posttranscriptional level. Modifications in the triphosphate bridge impede degradation by specific decapping enzymes and maintain translation. Here, we combined 5' cap modifications at different positions and investigated how they impact 5' cap-dependent processes in distinct manners. We synthesized 5' cap analogues with a photocleavable group at the N2-position of m7G in addition to a medronate in the triphosphate bridge to obtain a photoactivatable 5' cap analogue featuring a methylene group between the β and γ phosphates. The resulting Medronate-FlashCap transiently or permanently impeded distinct crucial interactions of the 5' cap required for translation and degradation. We show that the Medronate-FlashCap is compatible with in vitro transcription to generate muted mRNA and that light can be used to activate translation in cells. After light-induced removal of the photocleavable group, the Medronate-FlashCap remained stable against degradation by the decapping enzyme DcpS. The additional methylene group renders the 5' cap resistant to DcpS, while maintaining the interaction with cap-binding proteins.
Collapse
Affiliation(s)
| | - Nils Klöcker
- Institute of Biochemistry, University of Münster, Münster 48149, Germany
| | - Petr Špaček
- Institute of Biochemistry, University of Münster, Münster 48149, Germany
| | - Sabine Hüwel
- Institute of Biochemistry, University of Münster, Münster 48149, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, University of Münster, Münster 48149, Germany
| |
Collapse
|