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Wang Q, Rao GS, Marsic T, Aman R, Mahfouz M. Fusion of FokI and catalytically inactive prokaryotic Argonautes enables site-specific programmable DNA cleavage. J Biol Chem 2024:107720. [PMID: 39214308 DOI: 10.1016/j.jbc.2024.107720] [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: 04/26/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
Site-specific nucleases are crucial for genome engineering applications in medicine and agriculture. The ideal site-specific nucleases are easily reprogrammable, highly specific in target site recognition, robust in nuclease activities. Prokaryotic Argonaute (pAgo) proteins have received much attention as biotechnological tools due to their ability to recognize specific target sequences without a protospacer adjacent motif (PAM), but their lack of intrinsic double-stranded DNA (dsDNA) unwinding activity limits their utility in key applications such as gene editing. Recently, we developed a pAgo-based system for site-specific DNA cleavage at physiological temperatures independently of the DNA form, using peptide nucleic acids (PNAs) to facilitate unwinding dsDNA targets. Here, we fused catalytically dead pAgos with the nuclease domain of the restriction endonuclease FokI and named this modified platform PNA-assisted FokI-(d)pAgo (PNFP) editors. In the PNFP system, catalytically inactive pAgo recognizes and binds to a specific target DNA sequence based on a programmable guide DNA sequence; upon binding to the target site, the FokI domains dimerize and introduce precise dsDNA breaks. We explored key parameters of the PNFP system including the requirements of PNA and guide DNAs, the specificity of PNA and guide DNA on target cleavage, the optimal concentration of different components, reaction time for invasion and cleavage and ideal temperature and reaction buffer, to ensure efficient DNA editing in vitro. The results demonstrated robust site-specific target cleavage by PNFP system at optimal conditions in vitro. We envision that the PNFP system will provide higher editing efficiency and specificity with fewer off-target effects in vivo.
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Affiliation(s)
- Qiaochu Wang
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Gundra Sivakrishna Rao
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Tin Marsic
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Rashid Aman
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
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2
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Polak A, Machnik G, Bułdak Ł, Ruczyński J, Prochera K, Bujak O, Mucha P, Rekowski P, Okopień B. The Application of Peptide Nucleic Acids (PNA) in the Inhibition of Proprotein Convertase Subtilisin/Kexin 9 ( PCSK9) Gene Expression in a Cell-Free Transcription/Translation System. Int J Mol Sci 2024; 25:1463. [PMID: 38338741 PMCID: PMC10855603 DOI: 10.3390/ijms25031463] [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: 11/19/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Proprotein convertase subtilisin/kexin 9 (PCSK9) is a protein that plays a key role in the metabolism of low-density lipoprotein (LDL) cholesterol. The gain-of-function mutations of the PCSK9 gene lead to a reduced number of surface LDL receptors by binding to them, eventually leading to endosomal degradation. This, in turn, is the culprit of hypercholesterolemia, resulting in accelerated atherogenesis. The modern treatment for hypercholesterolemia encompasses the use of biological drugs against PCSK9, like monoclonal antibodies and gene expression modulators such as inclisiran-a short, interfering RNA (siRNA). Peptide nucleic acid (PNA) is a synthetic analog of nucleic acid that possesses a synthetic peptide skeleton instead of a phosphate-sugar one. This different structure determines the unique properties of PNA (e.g., neutral charge, enzymatic resistance, and an enormously high affinity with complementary DNA and RNA). Therefore, it might be possible to use PNA against PCSK9 in the treatment of hypercholesterolemia. We sought to explore the impact of three selected PNA oligomers on PCSK9 gene expression. Using a cell-free transcription/translation system, we showed that one of the tested PNA strands was able to reduce the PCSK9 gene expression down to 74%, 64%, and 68%, as measured by RT-real-time PCR, Western blot, and HPLC, respectively. This preliminary study shows the high applicability of a cell-free enzymatic environment as an efficient tool in the initial evaluation of biologically active PNA molecules in the field of hypercholesterolemia research. This cell-free approach allows for the omission of the hurdles associated with transmembrane PNA transportation at the early stage of PNA selection.
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Affiliation(s)
- Agnieszka Polak
- Department of Internal Medicine and Clinical Pharmacology, Faculty of Medical Science in Katowice, Medical University of Silesia, Medykow 18, 40-752 Katowice, Poland
| | - Grzegorz Machnik
- Department of Internal Medicine and Clinical Pharmacology, Faculty of Medical Science in Katowice, Medical University of Silesia, Medykow 18, 40-752 Katowice, Poland
| | - Łukasz Bułdak
- Department of Internal Medicine and Clinical Pharmacology, Faculty of Medical Science in Katowice, Medical University of Silesia, Medykow 18, 40-752 Katowice, Poland
| | - Jarosław Ruczyński
- Laboratory of Chemistry of Biologically Active Compounds, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (J.R.); (K.P.)
| | - Katarzyna Prochera
- Laboratory of Chemistry of Biologically Active Compounds, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (J.R.); (K.P.)
| | - Oliwia Bujak
- Laboratory of Chemistry of Biologically Active Compounds, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (J.R.); (K.P.)
| | - Piotr Mucha
- Laboratory of Chemistry of Biologically Active Compounds, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (J.R.); (K.P.)
| | - Piotr Rekowski
- Laboratory of Chemistry of Biologically Active Compounds, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (J.R.); (K.P.)
| | - Bogusław Okopień
- Department of Internal Medicine and Clinical Pharmacology, Faculty of Medical Science in Katowice, Medical University of Silesia, Medykow 18, 40-752 Katowice, Poland
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3
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Wang H, Su Y, Chen D, Li Q, Shi S, Huang X, Fang M, Yang M. Advances in the mechanisms and applications of inhibitory oligodeoxynucleotides against immune-mediated inflammatory diseases. Front Pharmacol 2023; 14:1119431. [PMID: 36825156 PMCID: PMC9941346 DOI: 10.3389/fphar.2023.1119431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/26/2023] [Indexed: 02/09/2023] Open
Abstract
Inhibitory oligodeoxynucleotides (ODNs) are short single-stranded DNA, which capable of folding into complex structures, enabling them to bind to a large variety of targets. With appropriate modifications, the inhibitory oligodeoxynucleotides exhibited many features of long half-life time, simple production, low toxicity and immunogenicity. In recent years, inhibitory oligodeoxynucleotides have received considerable attention for their potential therapeutic applications in immune-mediated inflammatory diseases (IMIDs). Inhibitory oligodeoxynucleotides could be divided into three categories according to its mechanisms and targets, including antisense ODNs (AS-ODNs), DNA aptamers and immunosuppressive ODNs (iSup ODNs). As a synthetic tool with immunomodulatory activity, it can target RNAs or proteins in a specific way, resulting in the reduction, increase or recovery of protein expression, and then regulate the state of immune activation. More importantly, inhibitory oligodeoxynucleotides have been used to treat immune-mediated inflammatory diseases, including inflammatory disorders and autoimmune diseases. Several inhibitory oligodeoxynucleotide drugs have been developed and approved on the market already. These drugs vary in their chemical structures, action mechanisms and cellular targets, but all of them could be capable of inhibiting excessive inflammatory responses. This review summarized their chemical modifications, action mechanisms and applications of the three kinds of inhibitory oligodeoxynucleotidesin the precise treatment of immune-mediated inflammatory diseases.
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Affiliation(s)
- Hongrui Wang
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Yingying Su
- Department of Anatomy, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Duoduo Chen
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Qi Li
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Shuyou Shi
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Xin Huang
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Mingli Fang
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China,*Correspondence: Mingli Fang, ; Ming Yang,
| | - Ming Yang
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China,*Correspondence: Mingli Fang, ; Ming Yang,
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Li C, Zhou Z, Ren C, Deng Y, Peng F, Wang Q, Zhang H, Jiang Y. Triplex-forming oligonucleotides as an anti-gene technique for cancer therapy. Front Pharmacol 2022; 13:1007723. [PMID: 36618947 PMCID: PMC9811266 DOI: 10.3389/fphar.2022.1007723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Triplex-forming oligonucleotides (TFOs) can bind to the major groove of double-stranded DNA with high specificity and affinity and inhibit gene expression. Triplex-forming oligonucleotides have gained prominence because of their potential applications in antigene therapy. In particular, the target specificity of triplex-forming oligonucleotides combined with their ability to suppress oncogene expression has driven their development as anti-cancer agents. So far, triplex-forming oligonucleotides have not been used for clinical treatment and seem to be gradually snubbed in recent years. But triplex-forming oligonucleotides still represent an approach to down-regulate the expression of the target gene and a carrier of active substances. Therefore, in the present review, we will introduce the characteristics of triplex-forming oligonucleotides and their anti-cancer research progress. Then, we will discuss the challenges in their application.
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Affiliation(s)
- Chun Li
- Department of Rehabilitation Medicine, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Zunzhen Zhou
- Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Chao Ren
- Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Yi Deng
- Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Feng Peng
- Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Qiongfen Wang
- Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Hong Zhang
- Department of Rehabilitation Medicine, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai, China,*Correspondence: Hong Zhang, ; Yuan Jiang,
| | - Yuan Jiang
- Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China,*Correspondence: Hong Zhang, ; Yuan Jiang,
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5
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Luks VL, Mandl H, DiRito J, Barone C, Freedman-Weiss MR, Ricciardi AS, Tietjen GG, Egan ME, Saltzman WM, Stitelman DH. Surface conjugation of antibodies improves nanoparticle uptake in bronchial epithelial cells. PLoS One 2022; 17:e0266218. [PMID: 35385514 PMCID: PMC8986008 DOI: 10.1371/journal.pone.0266218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/16/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Advances in Molecular Therapy have made gene editing through systemic or topical administration of reagents a feasible strategy to treat genetic diseases in a rational manner. Encapsulation of therapeutic agents in nanoparticles can improve intracellular delivery of therapeutic agents, provided that the nanoparticles are efficiently taken up within the target cells. In prior work we had established proof-of-principle that nanoparticles carrying gene editing reagents can mediate site-specific gene editing in fetal and adult animals in vivo that results in functional disease improvement in rodent models of β-thalassemia and cystic fibrosis. Modification of the surface of nanoparticles to include targeting molecules (e.g. antibodies) holds the promise of improving cellular uptake and specific cellular binding. METHODS AND FINDINGS To improve particle uptake for diseases of the airway, like cystic fibrosis, our group tested the impact of nanoparticle surface modification with cell surface marker antibodies on uptake in human bronchial epithelial cells in vitro. Binding kinetics of antibodies (Podoplanin, Muc 1, Surfactant Protein C, and Intracellular Adhesion Molecule-1 (ICAM)) were determined to select appropriate antibodies for cellular targeting. The best target-specific antibody among those screened was ICAM antibody. Surface conjugation of nanoparticles with antibodies against ICAM improved cellular uptake in bronchial epithelial cells up to 24-fold. CONCLUSIONS This is a first demonstration of improved nanoparticle uptake in epithelial cells using conjugation of target specific antibodies. Improved binding, uptake or specificity of particles delivered systemically or to the luminal surface of the airway would potentially improve efficacy, reduce the necessary dose and thus safety of administered therapeutic agents. Incremental improvement in the efficacy and safety of particle-based therapeutic strategies may allow genetic diseases such as cystic fibrosis to be cured on a fundamental genetic level before birth or shortly after birth.
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Affiliation(s)
- Valerie L. Luks
- Department of Surgery, Yale University, New Haven, CT, United States of America
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Hanna Mandl
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States of America
| | - Jenna DiRito
- Department of Surgery, Yale University, New Haven, CT, United States of America
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States of America
| | - Christina Barone
- Department of Pediatrics, Yale University, New Haven, CT, United States of America
| | | | - Adele S. Ricciardi
- Department of Surgery, Yale University, New Haven, CT, United States of America
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Gregory G. Tietjen
- Department of Surgery, Yale University, New Haven, CT, United States of America
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States of America
| | - Marie E. Egan
- Department of Pediatrics, Yale University, New Haven, CT, United States of America
| | - W. Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, CT, United States of America
| | - David H. Stitelman
- Department of Surgery, Yale University, New Haven, CT, United States of America
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6
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Direct targeting of amplified gene loci for proapoptotic anticancer therapy. Nat Biotechnol 2021; 40:325-334. [PMID: 34711990 PMCID: PMC8930417 DOI: 10.1038/s41587-021-01057-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 08/05/2021] [Indexed: 12/16/2022]
Abstract
Gene amplification drives oncogenesis in a broad spectrum of cancers. A number of drugs have been developed to inhibit the protein products of amplified driver genes, but their clinical efficacy is often hampered by drug resistance. Here, we introduce a therapeutic strategy for targeting cancer-associated gene amplifications by activating the DNA damage response with triplex-forming oligonucleotides (TFOs), which drives induction of apoptosis in tumors, whereas cells without amplifications process lower levels of DNA damage. Focusing on cancers driven by HER2-amplification, we find that TFOs targeting HER2 induce copy number-dependent DNA double strand breaks and activate p53-independent apoptosis in HER2-positive cancer cells and human tumor xenografts via a mechanism that is independent of HER2 cellular function. This strategy has demonstrated in vivo efficacy comparable with current precision medicines and provided a feasible alternative to combat drug resistance in HER-positive breast and ovarian cancer models. These findings offer a general strategy for targeting tumors with amplified genomic loci.
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7
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Cosenza LC, Gasparello J, Romanini N, Zurlo M, Zuccato C, Gambari R, Finotti A. Efficient CRISPR-Cas9-based genome editing of β-globin gene on erythroid cells from homozygous β 039-thalassemia patients. Mol Ther Methods Clin Dev 2021; 21:507-523. [PMID: 33997100 PMCID: PMC8091488 DOI: 10.1016/j.omtm.2021.03.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/30/2021] [Indexed: 12/13/2022]
Abstract
Gene editing by the CRISPR-Cas9 nuclease system technology can be considered among the most promising strategies to correct hereditary mutations in a variety of monogenic diseases. In this paper, we present for the first time the correction, by CRISPR-Cas9 gene editing, of the β039-thalassemia mutation, one of the most frequent in the Mediterranean area. The results obtained demonstrated the presence of normal β-globin genes after CRISPR-Cas9 correction of the β039-thalassemia mutation performed on erythroid precursor cells from homozygous β039-thalassemia patients. This was demonstrated by allele-specific PCR and sequencing. Accumulation of corrected β-globin mRNA and relevant "de novo" production of β-globin and adult hemoglobin (HbA) were found with high efficiency. The CRISPR-Cas9-forced HbA production levels were associated with a significant reduction of the excess of free α-globin chains. Genomic toxicity of the editing procedure (low indels and no off-targeting) was analyzed. The protocol might be the starting point for the development of an efficient editing of CD34+ cells derived from β039 patients and for the design of combined treatments using, together with the CRISPR-Cas9 editing of the β-globin gene, other therapeutic approaches, such as, for instance, induction of HbA and/or fetal hemoglobin (HbF) using chemical inducers.
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Affiliation(s)
- Lucia Carmela Cosenza
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, Ferrara University, Ferrara, Italy
| | - Jessica Gasparello
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, Ferrara University, Ferrara, Italy
| | - Nicola Romanini
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, Ferrara University, Ferrara, Italy
| | - Matteo Zurlo
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, Ferrara University, Ferrara, Italy
| | - Cristina Zuccato
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, Ferrara University, Ferrara, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, Ferrara University, Ferrara, Italy
- Interuniversity Consortium for Biotechnology (CIB), Trieste, Italy
- Biotechnology Center, University of Ferrara, 44100 Ferrara, Italy
| | - Alessia Finotti
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, Ferrara University, Ferrara, Italy
- Interuniversity Consortium for Biotechnology (CIB), Trieste, Italy
- Biotechnology Center, University of Ferrara, 44100 Ferrara, Italy
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8
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Moscoso CG, Steer CJ. Liver targeted gene therapy: Insights into emerging therapies. DRUG DISCOVERY TODAY. TECHNOLOGIES 2020; 34:9-19. [PMID: 33357766 DOI: 10.1016/j.ddtec.2020.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 10/23/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022]
Abstract
The large number of monogenic metabolic disorders originating in the liver poses a unique opportunity for development of gene therapy modalities to pursue curative approaches. Various disorders have been successfully treated via liver-directed gene therapy, though most of the advances have been in animal models, with only limited success in clinical trials. Pre-clinical data in animals using non-viral approaches, including the Sleeping Beauty transposon system, are discussed. The various advances with viral vectors for liver-directed gene therapy are also a focus of this review, including retroviral, adenoviral, recombinant adeno-associated viral, and SV40 vectors. Genome editing techniques, including zinc finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeats (CRISPR), are also described. Further, the various controversies in the field with regards to somatic vs. germline editing using CRISPR in humans are explored, while also highlighting the myriad of preclinical advances. Lastly, newer technologies are reviewed, including base editing and prime editing, which use CRISPR with exciting adjunctive properties to avoid double-stranded breaks and thus the recruitment of endogenous repair mechanisms. While encouraging results have been achieved recently, there are still significant challenges to overcome prior to the broad use of vector-based and genome editing techniques in the clinical arena. As these technologies mature, the promise of a cure for many disabling inherited metabolic disorders is within reach, and urgently needed.
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Affiliation(s)
- Carlos G Moscoso
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA.
| | - Clifford J Steer
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA; Department of Genetics, Cell Biology and Development, University of Minnesota Medical School, Minneapolis, Minnesota 55455 USA.
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9
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Pavlovic K, Tristán-Manzano M, Maldonado-Pérez N, Cortijo-Gutierrez M, Sánchez-Hernández S, Justicia-Lirio P, Carmona MD, Herrera C, Martin F, Benabdellah K. Using Gene Editing Approaches to Fine-Tune the Immune System. Front Immunol 2020; 11:570672. [PMID: 33117361 PMCID: PMC7553077 DOI: 10.3389/fimmu.2020.570672] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/20/2020] [Indexed: 12/26/2022] Open
Abstract
Genome editing technologies not only provide unprecedented opportunities to study basic cellular system functionality but also improve the outcomes of several clinical applications. In this review, we analyze various gene editing techniques used to fine-tune immune systems from a basic research and clinical perspective. We discuss recent advances in the development of programmable nucleases, such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas-associated nucleases. We also discuss the use of programmable nucleases and their derivative reagents such as base editing tools to engineer immune cells via gene disruption, insertion, and rewriting of T cells and other immune components, such natural killers (NKs) and hematopoietic stem and progenitor cells (HSPCs). In addition, with regard to chimeric antigen receptors (CARs), we describe how different gene editing tools enable healthy donor cells to be used in CAR T therapy instead of autologous cells without risking graft-versus-host disease or rejection, leading to reduced adoptive cell therapy costs and instant treatment availability for patients. We pay particular attention to the delivery of therapeutic transgenes, such as CARs, to endogenous loci which prevents collateral damage and increases therapeutic effectiveness. Finally, we review creative innovations, including immune system repurposing, that facilitate safe and efficient genome surgery within the framework of clinical cancer immunotherapies.
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Affiliation(s)
- Kristina Pavlovic
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
- Maimonides Institute of Biomedical Research in Cordoba (IMIBIC), Cellular Therapy Unit, Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
| | - María Tristán-Manzano
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
| | - Noelia Maldonado-Pérez
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
| | - Marina Cortijo-Gutierrez
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
| | - Sabina Sánchez-Hernández
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
| | - Pedro Justicia-Lirio
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
- LentiStem Biotech, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
| | - M. Dolores Carmona
- Maimonides Institute of Biomedical Research in Cordoba (IMIBIC), Cellular Therapy Unit, Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
| | - Concha Herrera
- Maimonides Institute of Biomedical Research in Cordoba (IMIBIC), Cellular Therapy Unit, Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
- Department of Hematology, Reina Sofía University Hospital, Córdoba, Spain
| | - Francisco Martin
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
| | - Karim Benabdellah
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
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10
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Muangkaew P, Vilaivan T. Modulation of DNA and RNA by PNA. Bioorg Med Chem Lett 2020; 30:127064. [PMID: 32147357 DOI: 10.1016/j.bmcl.2020.127064] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 02/22/2020] [Accepted: 02/24/2020] [Indexed: 02/08/2023]
Abstract
Peptide nucleic acid (PNA), a synthetic DNA mimic that is devoid of the (deoxy)ribose-phosphate backbone yet still perfectly retains the ability to recognize natural nucleic acids in a sequence-specific fashion, can be employed as a tool to modulate gene expressions via several different mechanisms. The unique strength of PNA compared to other oligonucleotide analogs is its ability to bind to nucleic acid targets with secondary structures such as double-stranded and quadruplex DNA as well as RNA. This digest aims to introduce general readers to the advancement in the area of modulation of DNA/RNA functions by PNA, its current status and future research opportunities, with emphasis on recent progress in new targeting modes of structured DNA/RNA by PNA and PNA-mediated gene editing.
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Affiliation(s)
- Penthip Muangkaew
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
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11
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Indumathi K, Abiram A, Praveena G. Effect of peptidic backbone on the nucleic acid dimeric strands. Mol Phys 2020. [DOI: 10.1080/00268976.2019.1584682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- K. Indumathi
- Department of Physics, PSGR Krishnammal College for Women, Coimbatore, India
| | - A. Abiram
- Department of Physics, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - G. Praveena
- Department of Physics, PSGR Krishnammal College for Women, Coimbatore, India
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12
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Ricciardi AS, Bahal R, Farrelly JS, Quijano E, Bianchi AH, Luks VL, Putman R, López-Giráldez F, Coşkun S, Song E, Liu Y, Hsieh WC, Ly DH, Stitelman DH, Glazer PM, Saltzman WM. In utero nanoparticle delivery for site-specific genome editing. Nat Commun 2018; 9:2481. [PMID: 29946143 PMCID: PMC6018676 DOI: 10.1038/s41467-018-04894-2] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 05/30/2018] [Indexed: 01/16/2023] Open
Abstract
Genetic diseases can be diagnosed early during pregnancy, but many monogenic disorders continue to cause considerable neonatal and pediatric morbidity and mortality. Early intervention through intrauterine gene editing, however, could correct the genetic defect, potentially allowing for normal organ development, functional disease improvement, or cure. Here we demonstrate safe intravenous and intra-amniotic administration of polymeric nanoparticles to fetal mouse tissues at selected gestational ages with no effect on survival or postnatal growth. In utero introduction of nanoparticles containing peptide nucleic acids (PNAs) and donor DNAs corrects a disease-causing mutation in the β-globin gene in a mouse model of human β-thalassemia, yielding sustained postnatal elevation of blood hemoglobin levels into the normal range, reduced reticulocyte counts, reversal of splenomegaly, and improved survival, with no detected off-target mutations in partially homologous loci. This work may provide the basis for a safe and versatile method of fetal gene editing for human monogenic disorders.
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Affiliation(s)
- Adele S Ricciardi
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA
- Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA
- Department of Surgery, Yale University, New Haven, CT, 06520, USA
| | - Raman Bahal
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA
- Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, 06269, USA
| | - James S Farrelly
- Department of Surgery, Yale University, New Haven, CT, 06520, USA
| | - Elias Quijano
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA
- Department of Genetics, Yale University, New Haven, CT, 06520, USA
| | - Anthony H Bianchi
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA
| | - Valerie L Luks
- Department of Surgery, Yale University, New Haven, CT, 06520, USA
| | - Rachael Putman
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA
- Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA
| | - Francesc López-Giráldez
- Department of Genetics, Yale University, New Haven, CT, 06520, USA
- Yale Center for Genome Analysis (YCGA), Yale University, New Haven, CT, 06477, USA
| | - Süleyman Coşkun
- Department of Neurosurgery, Yale University, New Haven, CT, 06520, USA
| | - Eric Song
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA
| | - Yanfeng Liu
- Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA
| | - Wei-Che Hsieh
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, Pittsburgh, Pennsylvania, 15213, USA
| | - Danith H Ly
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, Pittsburgh, Pennsylvania, 15213, USA
| | | | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA.
- Department of Genetics, Yale University, New Haven, CT, 06520, USA.
| | - W Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA.
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Abstract
Peptide nucleic acids (PNAs) can bind duplex DNA in a sequence-targeted manner, forming a triplex structure capable of inducing DNA repair and producing specific genome modifications. Since the first description of PNA-mediated gene editing in cell free extracts, PNAs have been used to successfully correct human disease-causing mutations in cell culture and in vivo in preclinical mouse models. Gene correction via PNAs has resulted in clinically-relevant functional protein restoration and disease improvement, with low off-target genome effects, indicating a strong therapeutic potential for PNAs in the treatment or cure of genetic disorders. This review discusses the progress that has been made in developing PNAs as an effective, targeted agent for gene editing, with an emphasis on recent in vivo, nanoparticle-based strategies.
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14
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Aravalli RN, Steer CJ. CRISPR/Cas9 therapeutics for liver diseases. J Cell Biochem 2018; 119:4265-4278. [PMID: 29266637 DOI: 10.1002/jcb.26627] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/18/2017] [Indexed: 12/20/2022]
Abstract
The development of innovative genome editing techniques in recent years has revolutionized the field of biomedicine. Among the novel approaches, the clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas9) technology has become the most popular, in part due to its matchless ability to carry out gene editing at the target site with great precision. With considerable successes in animal and preclinical studies, CRISPR/Cas9-mediated gene editing has paved the way for its use in human trials, including patients with a variety of liver diseases. Gene editing is a logical therapeutic approach for liver diseases because many metabolic and acquired disorders are caused by mutations within a single gene. In this review, we provide an overview on current and emerging therapeutic strategies for the treatment of liver diseases using the CRISPR/Cas9 technology.
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Affiliation(s)
- Rajagopal N Aravalli
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Clifford J Steer
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota.,Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
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15
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Quijano E, Bahal R, Ricciardi A, Saltzman WM, Glazer PM. Therapeutic Peptide Nucleic Acids: Principles, Limitations, and Opportunities. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2017; 90:583-598. [PMID: 29259523 PMCID: PMC5733847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Since their invention in 1991, peptide nucleic acids (PNAs) have been used in a myriad of chemical and biological assays. More recently, peptide nucleic acids have also been demonstrated to hold great potential as therapeutic agents because of their physiological stability, affinity for target nucleic acids, and versatility. While recent modifications in their design have further improved their potency, their preclinical development has reached new heights due to their combination with recent advancements in drug delivery. This review focuses on recent advances in PNA therapeutic applications, in which chemical modifications are made to improve PNA function and nanoparticles are used to enhance PNA delivery.
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Affiliation(s)
- Elias Quijano
- Department of Genetics, Yale University, New Haven, CT
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT
| | - Adele Ricciardi
- Department of Biomedical Engineering, Yale University, New Haven, CT
| | - W. Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, CT
| | - Peter M. Glazer
- Department of Therapeutic Radiology, Yale University, New Haven, CT
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16
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Aravalli RN, Steer CJ. Gene editing technology as an approach to the treatment of liver diseases. Expert Opin Biol Ther 2016; 16:595-608. [DOI: 10.1517/14712598.2016.1158808] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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17
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Aravalli RN, Belcher JD, Steer CJ. Liver-targeted gene therapy: Approaches and challenges. Liver Transpl 2015; 21:718-37. [PMID: 25824605 PMCID: PMC9353592 DOI: 10.1002/lt.24122] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 03/06/2015] [Accepted: 03/14/2015] [Indexed: 12/15/2022]
Abstract
The liver plays a major role in many inherited and acquired genetic disorders. It is also the site for the treatment of certain inborn errors of metabolism that do not directly cause injury to the liver. The advancement of nucleic acid-based therapies for liver maladies has been severely limited because of the myriad untoward side effects and methodological limitations. To address these issues, research efforts in recent years have been intensified toward the development of targeted gene approaches using novel genetic tools, such as zinc-finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats as well as various nonviral vectors such as Sleeping Beauty transposons, PiggyBac transposons, and PhiC31 integrase. Although each of these methods uses a distinct mechanism of gene modification, all of them are dependent on the efficient delivery of DNA and RNA molecules into the cell. This review provides an overview of current and emerging therapeutic strategies for liver-targeted gene therapy and gene repair.
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Affiliation(s)
- Rajagopal N. Aravalli
- Department of Radiology, University of Minnesota Medical School, Minneapolis, MN 54455
| | - John D. Belcher
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 54455
| | - Clifford J. Steer
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 54455,Genetics, Cell Biology and Development, University of Minnesota Medical School, Minneapolis, MN 54455
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