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Ciucci G, Braga L, Zacchigna S. Discovery platforms for RNA therapeutics. Br J Pharmacol 2024. [PMID: 38760893 DOI: 10.1111/bph.16424] [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: 11/29/2023] [Revised: 04/14/2024] [Accepted: 04/19/2024] [Indexed: 05/20/2024] Open
Abstract
RNA therapeutics are emerging as a unique opportunity to drug currently "undruggable" molecules and diseases. While their advantages over conventional, small molecule drugs, their therapeutic implications and the tools for their effective in vivo delivery have been extensively reviewed, little attention has been so far paid to the technological platforms exploited for the discovery of RNA therapeutics. Here, we provide an overview of the existing platforms and ex vivo assays for RNA discovery, their advantages and disadvantages, as well as their main fields of application, with specific focus on RNA therapies that have reached either phase 3 or market approval.
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Affiliation(s)
- Giulio Ciucci
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Luca Braga
- Functional Cell Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Serena Zacchigna
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
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2
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Leal AF, Herreno-Pachón AM, Benincore-Flórez E, Karunathilaka A, Tomatsu S. Current Strategies for Increasing Knock-In Efficiency in CRISPR/Cas9-Based Approaches. Int J Mol Sci 2024; 25:2456. [PMID: 38473704 PMCID: PMC10931195 DOI: 10.3390/ijms25052456] [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: 01/27/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
Since its discovery in 2012, the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) system has supposed a promising panorama for developing novel and highly precise genome editing-based gene therapy (GT) alternatives, leading to overcoming the challenges associated with classical GT. Classical GT aims to deliver transgenes to the cells via their random integration in the genome or episomal persistence into the nucleus through lentivirus (LV) or adeno-associated virus (AAV), respectively. Although high transgene expression efficiency is achieved by using either LV or AAV, their nature can result in severe side effects in humans. For instance, an LV (NCT03852498)- and AAV9 (NCT05514249)-based GT clinical trials for treating X-linked adrenoleukodystrophy and Duchenne Muscular Dystrophy showed the development of myelodysplastic syndrome and patient's death, respectively. In contrast with classical GT, the CRISPR/Cas9-based genome editing requires the homologous direct repair (HDR) machinery of the cells for inserting the transgene in specific regions of the genome. This sophisticated and well-regulated process is limited in the cell cycle of mammalian cells, and in turn, the nonhomologous end-joining (NHEJ) predominates. Consequently, seeking approaches to increase HDR efficiency over NHEJ is crucial. This manuscript comprehensively reviews the current alternatives for improving the HDR for CRISPR/Cas9-based GTs.
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Affiliation(s)
- Andrés Felipe Leal
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Angelica María Herreno-Pachón
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Faculty of Arts and Sciences, University of Delaware, Newark, DE 19716, USA
| | - Eliana Benincore-Flórez
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
| | - Amali Karunathilaka
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Faculty of Arts and Sciences, University of Delaware, Newark, DE 19716, USA
| | - Shunji Tomatsu
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Faculty of Arts and Sciences, University of Delaware, Newark, DE 19716, USA
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu 501-1194, Japan
- Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA 19144, USA
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3
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Yang C, Lei Y, Ren T, Yao M. The Current Situation and Development Prospect of Whole-Genome Screening. Int J Mol Sci 2024; 25:658. [PMID: 38203828 PMCID: PMC10779205 DOI: 10.3390/ijms25010658] [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: 11/21/2023] [Revised: 12/22/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
High-throughput genetic screening is useful for discovering critical genes or gene sequences that trigger specific cell functions and/or phenotypes. Loss-of-function genetic screening is mainly achieved through RNA interference (RNAi), CRISPR knock-out (CRISPRko), and CRISPR interference (CRISPRi) technologies. Gain-of-function genetic screening mainly depends on the overexpression of a cDNA library and CRISPR activation (CRISPRa). Base editing can perform both gain- and loss-of-function genetic screening. This review discusses genetic screening techniques based on Cas9 nuclease, including Cas9-mediated genome knock-out and dCas9-based gene activation and interference. We compare these methods with previous genetic screening techniques based on RNAi and cDNA library overexpression and propose future prospects and applications for CRISPR screening.
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Affiliation(s)
| | | | | | - Mingze Yao
- Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education and Institute of Biomedical Sciences, Shanxi University, Taiyuan 030006, China; (C.Y.); (Y.L.); (T.R.)
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4
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El-Ashmawy NE, Khedr EG, Abo-Saif MA, Hamouda SM. Long noncoding RNAs as regulators of epithelial mesenchymal transition in breast cancer: A recent review. Life Sci 2024; 336:122339. [PMID: 38097110 DOI: 10.1016/j.lfs.2023.122339] [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: 07/28/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
AIMS Breast cancer (BC) is the most frequently occurring cancer in women worldwide. BC patients are often diagnosed at advanced stages which are characterized by low survival rates. Distant metastasis is considered a leading cause of mortalities among BC patients. Epithelial-to-mesenchymal transition (EMT) is a transdifferentiation program that is necessary for cancer cells to acquire metastatic potential. In the last decade, long noncoding RNAs (lncRNAs) proved their significant contribution to different hallmarks of cancer, including EMT and metastasis. The primary aim of our review is to analyze recent studies concerning the molecular mechanisms of lncRNAs implicated in EMT regulation in BC. MATERIALS AND METHODS We adopted a comprehensive search on databases of PubMed, Web of Science, and Google Scholar using the following keywords: lncRNAs, EMT, breast cancer, and therapeutic targeting. KEY FINDINGS The different roles of lncRNAs in the mechanisms and signaling pathways governing EMT in BC were summarized. LncRNAs could induce or inhibit EMT through WNT/β-catenin, transforming growth factor-β (TGF-β), Notch, phosphoinositide 3-kinase/protein kinase B (PI3K/AKT), signal transducer and activator of transcription 3 (STAT3), and nuclear factor kappa B (NF-κB) pathways as well as via their interaction with histone modifying complexes and miRNAs. SIGNIFICANCE LncRNAs are key regulators of EMT and BC metastasis, presenting potential targets for therapeutic interventions. Further research is necessary to investigate the practical application of lncRNAs in clinical therapeutics.
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Affiliation(s)
- Nahla E El-Ashmawy
- Faculty of Pharmacy, Tanta University, Al-Geish Street, Tanta, El-Gharbia, Egypt.
| | - Eman G Khedr
- Faculty of Pharmacy, Tanta University, Al-Geish Street, Tanta, El-Gharbia, Egypt.
| | - Mariam A Abo-Saif
- Faculty of Pharmacy, Tanta University, Al-Geish Street, Tanta, El-Gharbia, Egypt.
| | - Sara M Hamouda
- Faculty of Pharmacy, Tanta University, Al-Geish Street, Tanta, El-Gharbia, Egypt.
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5
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Deng B, Xue J. HIV infection detection using CRISPR/Cas systems: Present and future prospects. Comput Struct Biotechnol J 2023; 21:4409-4423. [PMID: 37711183 PMCID: PMC10498128 DOI: 10.1016/j.csbj.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection poses substantial medical risks to global public health. An essential strategy to combat the HIV epidemic is timely and effective virus testing. CRISPR-based assays combine the highly compatible CRISPR system with different elements, yielding portability, digitization capabilities, low economic burden and low operational thresholds. The application of CRISPR-based assays has demonstrated rapid, accurate, and accessible means of pathogen testing, suggesting great potential as point-of-care (POC) assays. This review outlines the different types of CRISPR/Cas systems based on Cas proteins and their applications for the detection of HIV. Additionally, we also offer an overview of future perspectives on CRISPR-based methods for HIV detection, including advances in nucleic acid amplification-free testing, improved personal testing, and refined testing for HIV genotypes and drug-resistant strains.
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Affiliation(s)
- Bingpeng Deng
- Beijing Key Laboratory for Animal Models of Emerging and Re-Emerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, China
- NHC Key Laboratory of Human Disease Comparative Medicine, Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China
| | - Jing Xue
- Beijing Key Laboratory for Animal Models of Emerging and Re-Emerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, China
- NHC Key Laboratory of Human Disease Comparative Medicine, Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China
- Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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Reddy D, Wickman JR, Ajit SK. Epigenetic regulation in opioid induced hyperalgesia. NEUROBIOLOGY OF PAIN (CAMBRIDGE, MASS.) 2023; 14:100146. [PMID: 38099284 PMCID: PMC10719581 DOI: 10.1016/j.ynpai.2023.100146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/14/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
About 25 million American adults experience pain daily and one of the most commonly prescribed drugs to treat pain are opioids. Prolonged opioid usage and dose escalations can cause a paradoxical response where patients experience enhanced pain sensitivity. This opioid induced hyperalgesia (OIH) is a major hurdle when treating pain in the clinic because its underlying mechanisms are still not fully understood. OIH is also commonly overlooked and lacks guidelines to prevent its onset. Research on pain disorders and opioid usage have recognized potential epigenetic drivers of disease including DNA methylation, histone modifications, miRNA regulation, but their involvement in OIH has not been well studied. This article discusses epigenetic changes that may contribute to pathogenesis, with an emphasis on miRNA alterations in OIH. There is a crucial gap in knowledge including how multiple epigenetic modulators contribute to OIH. Elucidating the epigenetic changes underlying OIH and the crosstalk among these mechanisms could lead to the development of novel targets for the prevention and treatment of this painful phenomena.
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Affiliation(s)
- Deepa Reddy
- Department of Pharmacology & Physiology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102, USA
| | - Jason R. Wickman
- Department of Pharmacology & Physiology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102, USA
| | - Seena K. Ajit
- Department of Pharmacology & Physiology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102, USA
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Heidersbach AJ, Dorighi KM, Gomez JA, Jacobi AM, Haley B. A versatile, high-efficiency platform for CRISPR-based gene activation. Nat Commun 2023; 14:902. [PMID: 36804928 PMCID: PMC9938141 DOI: 10.1038/s41467-023-36452-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
CRISPR-mediated transcriptional activation (CRISPRa) is a powerful technology for inducing gene expression from endogenous loci with exciting applications in high throughput gain-of-function genomic screens and the engineering of cell-based models. However, current strategies for generating potent, stable, CRISPRa-competent cell lines present limitations for the broad utility of this approach. Here, we provide a high-efficiency, self-selecting CRISPRa enrichment strategy, which combined with piggyBac transposon technology enables rapid production of CRISPRa-ready cell populations compatible with a variety of downstream assays. We complement this with an optimized guide RNA scaffold that significantly enhances CRISPRa functionality. Finally, we describe a synthetic guide RNA tool set that enables transient, population-wide gene activation when used with the self-selecting CRISPRa system. Taken together, this versatile platform greatly enhances the potential for CRISPRa across a wide variety of cellular contexts.
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Affiliation(s)
- Amy J Heidersbach
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA, USA.
| | - Kristel M Dorighi
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA, USA
| | | | | | - Benjamin Haley
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA, USA.
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Boti MA, Athanasopoulou K, Adamopoulos PG, Sideris DC, Scorilas A. Recent Advances in Genome-Engineering Strategies. Genes (Basel) 2023; 14:129. [PMID: 36672870 PMCID: PMC9859587 DOI: 10.3390/genes14010129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/25/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023] Open
Abstract
In October 2020, the chemistry Nobel Prize was awarded to Emmanuelle Charpentier and Jennifer A. Doudna for the discovery of a new promising genome-editing tool: the genetic scissors of CRISPR-Cas9. The identification of CRISPR arrays and the subsequent identification of cas genes, which together represent an adaptive immunological system that exists not only in bacteria but also in archaea, led to the development of diverse strategies used for precise DNA editing, providing new insights in basic research and in clinical practice. Due to their advantageous features, the CRISPR-Cas systems are already employed in several biological and medical research fields as the most suitable technique for genome engineering. In this review, we aim to describe the CRISPR-Cas systems that have been identified among prokaryotic organisms and engineered for genome manipulation studies. Furthermore, a comprehensive comparison between the innovative CRISPR-Cas methodology and the previously utilized ZFN and TALEN editing nucleases is also discussed. Ultimately, we highlight the contribution of CRISPR-Cas methodology in modern biomedicine and the current plethora of available applications for gene KO, repression and/or overexpression, as well as their potential implementation in therapeutical strategies that aim to improve patients' quality of life.
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Affiliation(s)
| | | | - Panagiotis G. Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
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Madhi ZS, Shallan MA, Almaamuri AM, Alhussainy AA, AL- Salih SSS, Raheem AK, Alwan HJ, Jalil AT. Lipids and lipid derivatives for delivery of the CRISPR/Cas9 system. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Chen K, Shen Z, Wang G, Gu W, Zhao S, Lin Z, Liu W, Cai Y, Mushtaq G, Jia J, Wan C(C, Yan T. Research progress of CRISPR-based biosensors and bioassays for molecular diagnosis. Front Bioeng Biotechnol 2022; 10:986233. [PMID: 36185462 PMCID: PMC9524266 DOI: 10.3389/fbioe.2022.986233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR/Cas technology originated from the immune mechanism of archaea and bacteria and was awarded the Nobel Prize in Chemistry in 2020 for its success in gene editing. Molecular diagnostics is highly valued globally for its development as a new generation of diagnostic technology. An increasing number of studies have shown that CRISPR/Cas technology can be integrated with biosensors and bioassays for molecular diagnostics. CRISPR-based detection has attracted much attention as highly specific and sensitive sensors with easily programmable and device-independent capabilities. The nucleic acid-based detection approach is one of the most sensitive and specific diagnostic methods. With further research, it holds promise for detecting other biomarkers such as small molecules and proteins. Therefore, it is worthwhile to explore the prospects of CRISPR technology in biosensing and summarize its application strategies in molecular diagnostics. This review provides a synopsis of CRISPR biosensing strategies and recent advances from nucleic acids to other non-nucleic small molecules or analytes such as proteins and presents the challenges and perspectives of CRISPR biosensors and bioassays.
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Affiliation(s)
- Kun Chen
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Ziyi Shen
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Guanzhen Wang
- School of Life Sciences, Shanghai University, Shanghai, China
- University and College Key Lab of Natural Product Chemistry and Application in Xinjiang, School of Chemistry and Environmental Science, Yili Normal University, Yining, China
| | - Wei Gu
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Shengchao Zhao
- School of Life Sciences, Shanghai University, Shanghai, China
- University and College Key Lab of Natural Product Chemistry and Application in Xinjiang, School of Chemistry and Environmental Science, Yili Normal University, Yining, China
| | - Zihan Lin
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Wei Liu
- University and College Key Lab of Natural Product Chemistry and Application in Xinjiang, School of Chemistry and Environmental Science, Yili Normal University, Yining, China
| | - Yi Cai
- Key Laboratory of Molecular Target & Clinical Pharmacology and The State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Gohar Mushtaq
- Center for Scientific Research, Faculty of Medicine, Idlib University, Idlib, Syria
| | - Jia Jia
- School of Life Sciences, Shanghai University, Shanghai, China
- *Correspondence: Jia Jia, ; Chunpeng (Craig) Wan, ; Tingdong Yan,
| | - Chunpeng (Craig) Wan
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- *Correspondence: Jia Jia, ; Chunpeng (Craig) Wan, ; Tingdong Yan,
| | - Tingdong Yan
- School of Life Sciences, Shanghai University, Shanghai, China
- *Correspondence: Jia Jia, ; Chunpeng (Craig) Wan, ; Tingdong Yan,
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