51
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Sachdev S, Potočnik T, Rems L, Miklavčič D. Revisiting the role of pulsed electric fields in overcoming the barriers to in vivo gene electrotransfer. Bioelectrochemistry 2022; 144:107994. [PMID: 34930678 DOI: 10.1016/j.bioelechem.2021.107994] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/15/2021] [Accepted: 11/02/2021] [Indexed: 12/21/2022]
Abstract
Gene therapies are revolutionizing medicine by providing a way to cure hitherto incurable diseases. The scientific and technological advances have enabled the first gene therapies to become clinically approved. In addition, with the ongoing COVID-19 pandemic, we are witnessing record speeds in the development and distribution of gene-based vaccines. For gene therapy to take effect, the therapeutic nucleic acids (RNA or DNA) need to overcome several barriers before they can execute their function of producing a protein or silencing a defective or overexpressing gene. This includes the barriers of the interstitium, the cell membrane, the cytoplasmic barriers and (in case of DNA) the nuclear envelope. Gene electrotransfer (GET), i.e., transfection by means of pulsed electric fields, is a non-viral technique that can overcome these barriers in a safe and effective manner. GET has reached the clinical stage of investigations where it is currently being evaluated for its therapeutic benefits across a wide variety of indications. In this review, we formalize our current understanding of GET from a biophysical perspective and critically discuss the mechanisms by which electric field can aid in overcoming the barriers. We also identify the gaps in knowledge that are hindering optimization of GET in vivo.
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Affiliation(s)
- Shaurya Sachdev
- University of Ljubljana, Faculty of Electrical Engineering, Tržaška cesta 25, 1000 Ljubljana, Slovenia
| | - Tjaša Potočnik
- University of Ljubljana, Faculty of Electrical Engineering, Tržaška cesta 25, 1000 Ljubljana, Slovenia
| | - Lea Rems
- University of Ljubljana, Faculty of Electrical Engineering, Tržaška cesta 25, 1000 Ljubljana, Slovenia
| | - Damijan Miklavčič
- University of Ljubljana, Faculty of Electrical Engineering, Tržaška cesta 25, 1000 Ljubljana, Slovenia.
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52
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Borna S, Lee E, Sato Y, Bacchetta R. Towards gene therapy for IPEX syndrome. Eur J Immunol 2022; 52:705-716. [PMID: 35355253 PMCID: PMC9322407 DOI: 10.1002/eji.202149210] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/29/2022] [Accepted: 03/29/2022] [Indexed: 11/30/2022]
Abstract
Immune dysregulation polyendocrinopathy enteropathy X linked (IPEX) syndrome is an uncurable disease of the immune system, with immune dysregulation that is caused by mutations in FOXP3. Current treatment options, such as pharmacological immune suppression and allogeneic hematopoietic stem cell transplantation, have been beneficial but present limitations, and their life‐long consequences are ill‐defined. Other similar blood monogenic diseases have been successfully treated using gene transfer in autologous patient cells, thus providing an effective and less invasive therapeutic. Development of gene therapy for patients with IPEX is particularly challenging because successful strategies must restore the complex expression profile of the transcription factor FOXP3, ensuring it is tightly regulated and its cell subset‐specific roles are maintained. This review summarizes current efforts toward achieving gene therapy to treat immune dysregulation in IPEX patients.
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Affiliation(s)
- Simon Borna
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Esmond Lee
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Yohei Sato
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Rosa Bacchetta
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Center for Definitive and Curative Medicine, Stanford University School of Medicine, Stanford, CA, USA
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53
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Ravendran S, Hernández SS, König S, Bak RO. CRISPR/Cas-Based Gene Editing Strategies for DOCK8 Immunodeficiency Syndrome. Front Genome Ed 2022; 4:793010. [PMID: 35373187 PMCID: PMC8969908 DOI: 10.3389/fgeed.2022.793010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/14/2022] [Indexed: 12/17/2022] Open
Abstract
Defects in the DOCK8 gene causes combined immunodeficiency termed DOCK8 immunodeficiency syndrome (DIDS). DIDS previously belonged to the disease category of autosomal recessive hyper IgE syndrome (AR-HIES) but is now classified as a combined immunodeficiency (CID). This genetic disorder induces early onset of susceptibility to severe recurrent viral and bacterial infections, atopic diseases and malignancy resulting in high morbidity and mortality. This pathological state arises from impairment of actin polymerization and cytoskeletal rearrangement, which induces improper immune cell migration-, survival-, and effector functions. Owing to the severity of the disease, early allogenic hematopoietic stem cell transplantation is recommended even though it is associated with risk of unintended adverse effects, the need for compatible donors, and high expenses. So far, no alternative therapies have been developed, but the monogenic recessive nature of the disease suggests that gene therapy may be applied. The advent of the CRISPR/Cas gene editing system heralds a new era of possibilities in precision gene therapy, and positive results from clinical trials have already suggested that the tool may provide definitive cures for several genetic disorders. Here, we discuss the potential application of different CRISPR/Cas-mediated genetic therapies to correct the DOCK8 gene. Our findings encourage the pursuit of CRISPR/Cas-based gene editing approaches, which may constitute more precise, affordable, and low-risk definitive treatment options for DOCK8 deficiency.
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Affiliation(s)
| | | | | | - Rasmus O. Bak
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
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54
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Augmented lipid-nanoparticle-mediated in vivo genome editing in the lungs and spleen by disrupting Cas9 activity in the liver. Nat Biomed Eng 2022; 6:157-167. [DOI: 10.1038/s41551-022-00847-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 01/11/2022] [Indexed: 12/14/2022]
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55
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The EHA Research Roadmap: Hematopoietic Stem Cell Gene Therapy. Hemasphere 2022; 6:e671. [PMID: 35198856 PMCID: PMC8855740 DOI: 10.1097/hs9.0000000000000671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/14/2021] [Indexed: 11/26/2022] Open
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56
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Mitochondrial Genome Editing to Treat Human Osteoarthritis-A Narrative Review. Int J Mol Sci 2022; 23:ijms23031467. [PMID: 35163384 PMCID: PMC8835930 DOI: 10.3390/ijms23031467] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 12/27/2022] Open
Abstract
Osteoarthritis (OA) is a severe, common chronic orthopaedic disorder characterised by a degradation of the articular cartilage with an incidence that increases over years. Despite the availability of various clinical options, none can stop the irreversible progression of the disease to definitely cure OA. Various mutations have been evidenced in the mitochondrial DNA (mtDNA) of cartilage cells (chondrocytes) in OA, leading to a dysfunction of the mitochondrial oxidative phosphorylation processes that significantly contributes to OA cartilage degeneration. The mitochondrial genome, therefore, represents a central, attractive target for therapy in OA, especially using genome editing procedures. In this narrative review article, we present and discuss the current advances and breakthroughs in mitochondrial genome editing as a potential, novel treatment to overcome mtDNA-related disorders such as OA. While still in its infancy and despite a number of challenges that need to be addressed (barriers to effective and site-specific mtDNA editing and repair), such a strategy has strong value to treat human OA in the future, especially using the groundbreaking clustered regularly interspaced short palindromic repeats (CRIPSR)/CRISPR-associated 9 (CRISPR/Cas9) technology and mitochondrial transplantation approaches.
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57
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Nambiar TS, Baudrier L, Billon P, Ciccia A. CRISPR-based genome editing through the lens of DNA repair. Mol Cell 2022; 82:348-388. [PMID: 35063100 PMCID: PMC8887926 DOI: 10.1016/j.molcel.2021.12.026] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 01/22/2023]
Abstract
Genome editing technologies operate by inducing site-specific DNA perturbations that are resolved by cellular DNA repair pathways. Products of genome editors include DNA breaks generated by CRISPR-associated nucleases, base modifications induced by base editors, DNA flaps created by prime editors, and integration intermediates formed by site-specific recombinases and transposases associated with CRISPR systems. Here, we discuss the cellular processes that repair CRISPR-generated DNA lesions and describe strategies to obtain desirable genomic changes through modulation of DNA repair pathways. Advances in our understanding of the DNA repair circuitry, in conjunction with the rapid development of innovative genome editing technologies, promise to greatly enhance our ability to improve food production, combat environmental pollution, develop cell-based therapies, and cure genetic and infectious diseases.
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Affiliation(s)
- Tarun S Nambiar
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lou Baudrier
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta T2N 4N1, Canada
| | - Pierre Billon
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta T2N 4N1, Canada.
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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58
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Vaidyanathan S, Baik R, Chen L, Bravo DT, Suarez CJ, Abazari SM, Salahudeen AA, Dudek AM, Teran CA, Davis TH, Lee CM, Bao G, Randell SH, Artandi SE, Wine JJ, Kuo CJ, Desai TJ, Nayak JV, Sellers ZM, Porteus MH. Targeted replacement of full-length CFTR in human airway stem cells by CRISPR-Cas9 for pan-mutation correction in the endogenous locus. Mol Ther 2022; 30:223-237. [PMID: 33794364 PMCID: PMC8753290 DOI: 10.1016/j.ymthe.2021.03.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/23/2021] [Accepted: 03/25/2021] [Indexed: 01/07/2023] Open
Abstract
Cystic fibrosis (CF) is a monogenic disease caused by impaired production and/or function of the CF transmembrane conductance regulator (CFTR) protein. Although we have previously shown correction of the most common pathogenic mutation, there are many other pathogenic mutations throughout the CF gene. An autologous airway stem cell therapy in which the CFTR cDNA is precisely inserted into the CFTR locus may enable the development of a durable cure for almost all CF patients, irrespective of the causal mutation. Here, we use CRISPR-Cas9 and two adeno-associated viruses (AAVs) carrying the two halves of the CFTR cDNA to sequentially insert the full CFTR cDNA along with a truncated CD19 (tCD19) enrichment tag in upper airway basal stem cells (UABCs) and human bronchial epithelial cells (HBECs). The modified cells were enriched to obtain 60%-80% tCD19+ UABCs and HBECs from 11 different CF donors with a variety of mutations. Differentiated epithelial monolayers cultured at air-liquid interface showed restored CFTR function that was >70% of the CFTR function in non-CF controls. Thus, our study enables the development of a therapy for almost all CF patients, including patients who cannot be treated using recently approved modulator therapies.
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Affiliation(s)
| | - Ron Baik
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Lu Chen
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dawn T Bravo
- Department of Otolaryngology-Head and Neck Surgery, Stanford, CA 94305, USA
| | - Carlos J Suarez
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Shayda M Abazari
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Ameen A Salahudeen
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA
| | - Amanda M Dudek
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Timothy H Davis
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Ciaran M Lee
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Scott H Randell
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Steven E Artandi
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jeffrey J Wine
- Department of Psychology, Stanford University, Stanford, CA 94305, USA
| | - Calvin J Kuo
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA
| | - Tushar J Desai
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jayakar V Nayak
- Department of Otolaryngology-Head and Neck Surgery, Stanford, CA 94305, USA
| | - Zachary M Sellers
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
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59
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Jiang L, Ingelshed K, Shen Y, Boddul SV, Iyer VS, Kasza Z, Sedimbi S, Lane DP, Wermeling F. CRISPR/Cas9-Induced DNA Damage Enriches for Mutations in a p53-Linked Interactome: Implications for CRISPR-Based Therapies. Cancer Res 2022; 82:36-45. [PMID: 34750099 PMCID: PMC9397613 DOI: 10.1158/0008-5472.can-21-1692] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/08/2021] [Accepted: 10/20/2021] [Indexed: 01/07/2023]
Abstract
Inactivating p53 mutations are the most abundant genetic alterations found in cancer. Here we show that CRISPR/Cas9-induced double-stranded DNA breaks enrich for cells deficient in p53 and in genes of a core CRISPR-p53 tumor suppressor interactome. Such enrichment could predispose to cancer development and thus pose a challenge for clinical CRISPR use. Transient p53 inhibition could suppress the enrichment of cells with these mutations. The level of DNA damage response induced by an sgRNA influenced the enrichment of p53-deficient cells and could be a relevant parameter in sgRNA design to limit cellular enrichment. Furthermore, a dataset of >800 human cancer cell lines identified additional factors influencing the enrichment of p53-mutated cells, including strong baseline CDKN1A expression as a predictor for an active CRISPR-p53 axis. Taken together, these data provide details about p53 biology in the context of CRISPR-induced DNA damage and identify strategies to enable safer CRISPR use. SIGNIFICANCE: CRISPR-mediated DNA damage enriches for cells with escape mutations in a core CRISPR-p53 interactome, which can be suppressed by transient inhibition of p53.
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Affiliation(s)
- Long Jiang
- Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Katrine Ingelshed
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Yunbing Shen
- Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Sanjaykumar V. Boddul
- Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Vaishnavi Srinivasan Iyer
- Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden.,School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Zsolt Kasza
- Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Saikiran Sedimbi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - David P. Lane
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,p53 Laboratory (p53Lab), Agency for Science, Technology, and Research (A*STAR), Singapore
| | - Fredrik Wermeling
- Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden.,Corresponding Author: Fredrik Wermeling, Department of Medicine, Solna, Karolinska Institutet, Stockholm 17176, Sweden. E-mail:
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60
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Yin H, Sun L, Pu Y, Yu J, Feng W, Dong C, Zhou B, Du D, Zhang Y, Chen Y, Xu H. Ultrasound-Controlled CRISPR/Cas9 System Augments Sonodynamic Therapy of Hepatocellular Carcinoma. ACS CENTRAL SCIENCE 2021; 7:2049-2062. [PMID: 34963897 PMCID: PMC8704033 DOI: 10.1021/acscentsci.1c01143] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Indexed: 05/02/2023]
Abstract
Sonodynamic therapy (SDT), relying on the generation of reactive oxygen species (ROS), is a promising clinical therapeutic modality for the treatment of hepatocellular carcinoma (HCC) due to its noninvasiveness and high tissue-penetration depth, whereas the oxidative stress and antioxidative defense system in cancer cells significantly restrict the prevalence of SDT. Herein, we initially identified that NFE2L2 was immediately activated during SDT, which further inhibited SDT efficacy. To address this intractable issue, an ultrasound remote control of the cluster regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) release system (HMME@Lip-Cas9) was meticulously designed and constructed, which precisely knocks down NFE2L2 to alleviate the adverse effects and augment the therapeutic efficiency of SDT. The hematoporphyrin monomethyl ether (HMME) in this system yielded abundant ROS to damage cancer cells under ultrasound irradiation, and meanwhile the generated ROS could induce lysosomal rupture to release Cas9/single guide RNA ribonucleoprotein (RNP) and destroy the oxidative stress-defensing system, significantly promoting tumor cell apoptosis. This study provides a new paradigm for HCC management and lays the foundation for the widespread application of CRISPR/Cas9 with promising clinical translation, meanwhile developing a synergistic therapeutic modality in the combination of SDT with gene editing.
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Affiliation(s)
- Haohao Yin
- Center
of Minimally Invasive Treatment for Tumor, Department of Medical Ultrasound,
Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200072, P. R. China
- Ultrasound
Research and Education Institute, Clinical Research Center for Interventional
Medicine, School of Medicine, Tongji University, Shanghai 200072, P. R. China
- Shanghai
Engineering Research Center of Ultrasound Diagnosis and Treatment, Shanghai 200072, P. R. China
- National
Clinical Research Center for Interventional Medicine, Shanghai 200072, P. R. China
| | - Liping Sun
- Center
of Minimally Invasive Treatment for Tumor, Department of Medical Ultrasound,
Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200072, P. R. China
- Ultrasound
Research and Education Institute, Clinical Research Center for Interventional
Medicine, School of Medicine, Tongji University, Shanghai 200072, P. R. China
- Shanghai
Engineering Research Center of Ultrasound Diagnosis and Treatment, Shanghai 200072, P. R. China
- National
Clinical Research Center for Interventional Medicine, Shanghai 200072, P. R. China
| | - Yinying Pu
- Center
of Minimally Invasive Treatment for Tumor, Department of Medical Ultrasound,
Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200072, P. R. China
- Ultrasound
Research and Education Institute, Clinical Research Center for Interventional
Medicine, School of Medicine, Tongji University, Shanghai 200072, P. R. China
- Shanghai
Engineering Research Center of Ultrasound Diagnosis and Treatment, Shanghai 200072, P. R. China
- National
Clinical Research Center for Interventional Medicine, Shanghai 200072, P. R. China
| | - Jifeng Yu
- Center
of Minimally Invasive Treatment for Tumor, Department of Medical Ultrasound,
Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200072, P. R. China
- Ultrasound
Research and Education Institute, Clinical Research Center for Interventional
Medicine, School of Medicine, Tongji University, Shanghai 200072, P. R. China
- Shanghai
Engineering Research Center of Ultrasound Diagnosis and Treatment, Shanghai 200072, P. R. China
- National
Clinical Research Center for Interventional Medicine, Shanghai 200072, P. R. China
| | - Wei Feng
- Shanghai
Engineering Research Center of Organ Repair, Materdicine Lab, School
of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
- (W.F.)
| | - Caihong Dong
- Department
of Ultrasound, Zhongshan Hospital, Fudan
University, Shanghai 200032, P. R. China
| | - Bangguo Zhou
- Center
of Minimally Invasive Treatment for Tumor, Department of Medical Ultrasound,
Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200072, P. R. China
- Ultrasound
Research and Education Institute, Clinical Research Center for Interventional
Medicine, School of Medicine, Tongji University, Shanghai 200072, P. R. China
- Shanghai
Engineering Research Center of Ultrasound Diagnosis and Treatment, Shanghai 200072, P. R. China
- National
Clinical Research Center for Interventional Medicine, Shanghai 200072, P. R. China
| | - Dou Du
- Center
of Minimally Invasive Treatment for Tumor, Department of Medical Ultrasound,
Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200072, P. R. China
- Ultrasound
Research and Education Institute, Clinical Research Center for Interventional
Medicine, School of Medicine, Tongji University, Shanghai 200072, P. R. China
- Shanghai
Engineering Research Center of Ultrasound Diagnosis and Treatment, Shanghai 200072, P. R. China
- National
Clinical Research Center for Interventional Medicine, Shanghai 200072, P. R. China
| | - Yan Zhang
- Center
of Minimally Invasive Treatment for Tumor, Department of Medical Ultrasound,
Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200072, P. R. China
- Ultrasound
Research and Education Institute, Clinical Research Center for Interventional
Medicine, School of Medicine, Tongji University, Shanghai 200072, P. R. China
- Shanghai
Engineering Research Center of Ultrasound Diagnosis and Treatment, Shanghai 200072, P. R. China
- National
Clinical Research Center for Interventional Medicine, Shanghai 200072, P. R. China
| | - Yu Chen
- Shanghai
Engineering Research Center of Organ Repair, Materdicine Lab, School
of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
- E-mail: (Y.C.)
| | - Huixiong Xu
- Center
of Minimally Invasive Treatment for Tumor, Department of Medical Ultrasound,
Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200072, P. R. China
- Ultrasound
Research and Education Institute, Clinical Research Center for Interventional
Medicine, School of Medicine, Tongji University, Shanghai 200072, P. R. China
- Shanghai
Engineering Research Center of Ultrasound Diagnosis and Treatment, Shanghai 200072, P. R. China
- National
Clinical Research Center for Interventional Medicine, Shanghai 200072, P. R. China
- E-mail: (H.X.X.)
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61
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Hamann MV, Beschorner N, Vu XK, Hauber I, Lange UC, Traenkle B, Kaiser PD, Foth D, Schneider C, Büning H, Rothbauer U, Hauber J. Improved targeting of human CD4+ T cells by nanobody-modified AAV2 gene therapy vectors. PLoS One 2021; 16:e0261269. [PMID: 34928979 PMCID: PMC8687595 DOI: 10.1371/journal.pone.0261269] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/26/2021] [Indexed: 12/12/2022] Open
Abstract
Adeno-associated viruses (AAV) are considered non-pathogenic in humans, and thus have been developed into powerful vector platforms for in vivo gene therapy. Although the various AAV serotypes display broad tropism, frequently infecting multiple tissues and cell types, vectors for specific and efficient targeting of human CD4+ T lymphocytes are largely missing. In fact, a substantial translational bottleneck exists in the field of therapeutic gene transfer that would require in vivo delivery into peripheral disease-related lymphocytes for subsequent genome editing. To solve this issue, capsid modification for retargeting AAV tropism, and in turn improving vector potency, is considered a promising strategy. Here, we genetically modified the minor AAV2 capsid proteins, VP1 and VP2, with a set of novel nanobodies with high-affinity for the human CD4 receptor. These novel vector variants demonstrated improved targeting of human CD4+ cells, including primary human peripheral blood mononuclear cells (PBMC) and purified human CD4+ T lymphocytes. Thus, the technical approach presented here provides a promising strategy for developing specific gene therapy vectors, particularly targeting disease-related peripheral blood CD4+ leukocytes.
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Affiliation(s)
- Martin V. Hamann
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg – Lübeck – Borstel – Riems, Hamburg, Germany
| | - Niklas Beschorner
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg – Lübeck – Borstel – Riems, Hamburg, Germany
| | - Xuan-Khang Vu
- Institute of Experimental Haematology, Hannover Medical School, Hannover, Germany
| | - Ilona Hauber
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
| | - Ulrike C. Lange
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg – Lübeck – Borstel – Riems, Hamburg, Germany
- Department of Anaesthesiology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Bjoern Traenkle
- Natural and Medical Science Institute at the University Tübingen (NMI), Reutlingen, Germany
| | - Philipp D. Kaiser
- Natural and Medical Science Institute at the University Tübingen (NMI), Reutlingen, Germany
| | - Daniel Foth
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
| | - Carola Schneider
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
| | - Hildegard Büning
- German Center for Infection Research (DZIF), Partner Site Hamburg – Lübeck – Borstel – Riems, Hamburg, Germany
- Institute of Experimental Haematology, Hannover Medical School, Hannover, Germany
| | - Ulrich Rothbauer
- Natural and Medical Science Institute at the University Tübingen (NMI), Reutlingen, Germany
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Reutlingen, Germany
| | - Joachim Hauber
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg – Lübeck – Borstel – Riems, Hamburg, Germany
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Angius A, Scanu AM, Arru C, Muroni MR, Carru C, Porcu A, Cossu-Rocca P, De Miglio MR. A Portrait of Intratumoral Genomic and Transcriptomic Heterogeneity at Single-Cell Level in Colorectal Cancer. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:1257. [PMID: 34833475 PMCID: PMC8624593 DOI: 10.3390/medicina57111257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 12/24/2022]
Abstract
In the study of cancer, omics technologies are supporting the transition from traditional clinical approaches to precision medicine. Intra-tumoral heterogeneity (ITH) is detectable within a single tumor in which cancer cell subpopulations with different genome features coexist in a patient in different tumor areas or may evolve/differ over time. Colorectal carcinoma (CRC) is characterized by heterogeneous features involving genomic, epigenomic, and transcriptomic alterations. The study of ITH is a promising new frontier to lay the foundation towards successful CRC diagnosis and treatment. Genome and transcriptome sequencing together with editing technologies are revolutionizing biomedical research, representing the most promising tools for overcoming unmet clinical and research challenges. Rapid advances in both bulk and single-cell next-generation sequencing (NGS) are identifying primary and metastatic intratumoral genomic and transcriptional heterogeneity. They provide critical insight in the origin and spatiotemporal evolution of genomic clones responsible for early and late therapeutic resistance and relapse. Single-cell technologies can be used to define subpopulations within a known cell type by searching for differential gene expression within the cell population of interest and/or effectively isolating signal from rare cell populations that would not be detectable by other methods. Each single-cell sequencing analysis is driven by clustering of cells based on their differentially expressed genes. Genes that drive clustering can be used as unique markers for a specific cell population. In this review we analyzed, starting from published data, the possible achievement of a transition from clinical CRC research to precision medicine with an emphasis on new single-cell based techniques; at the same time, we focused on all approaches and issues related to this promising technology. This transition might enable noninvasive screening for early diagnosis, individualized prediction of therapeutic response, and discovery of additional novel drug targets.
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Affiliation(s)
- Andrea Angius
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Cittadella Universitaria di Cagliari, 09042 Monserrato, Italy
| | - Antonio Mario Scanu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
| | - Caterina Arru
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.A.); (C.C.)
| | - Maria Rosaria Muroni
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
| | - Ciriaco Carru
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.A.); (C.C.)
| | - Alberto Porcu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
| | - Paolo Cossu-Rocca
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
| | - Maria Rosaria De Miglio
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
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Lai M, Maori E, Quaranta P, Matteoli G, Maggi F, Sgarbanti M, Crucitta S, Pacini S, Turriziani O, Antonelli G, Heeney JL, Freer G, Pistello M. CRISPR/Cas9 Ablation of Integrated HIV-1 Accumulates Proviral DNA Circles with Reformed Long Terminal Repeats. J Virol 2021; 95:e0135821. [PMID: 34549986 PMCID: PMC8577360 DOI: 10.1128/jvi.01358-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/12/2021] [Indexed: 12/03/2022] Open
Abstract
Gene editing may be used to excise the human immunodeficiency virus type 1 (HIV-1) provirus from the host cell genome, possibly eradicating the infection. Here, using cells acutely or latently infected by HIV-1 and treated with long terminal repeat (LTR)-targeting CRISPR/Cas9, we show that the excised HIV-1 provirus persists for a few weeks and may rearrange in circular molecules. Although circular proviral DNA is naturally formed during HIV-1 replication, we observed that gene editing might increase proviral DNA circles with restored LTRs. These extrachromosomal elements were recovered and probed for residual activity through their transfection in uninfected cells. We discovered that they can be transcriptionally active in the presence of Tat and Rev. Although confirming that gene editing is a powerful tool to eradicate HIV-1 infection, this work highlights that, to achieve this goal, the LTRs must be cleaved in several pieces to avoid residual activity and minimize the risk of reintegration in the context of genomic instability, possibly caused by the off-target activity of Cas9. IMPORTANCE The excision of HIV-1 provirus from the host cell genome has proven feasible in vitro and, to some extent, in vivo. Among the different approaches, CRISPR/Cas9 is the most promising tool for gene editing. The present study underlines the remarkable effectiveness of CRISPR/Cas9 in removing the HIV-1 provirus from infected cells and investigates the fate of the excised HIV-1 genome. This study demonstrates that the free provirus may persist in the cell after editing and in appropriate circumstances may reactivate. As an episome, it might be transcriptionally active, especially in the presence of Tat and Rev. The persistence of the HIV-1 episome was strongly decreased by gene editing with multiple targets. Although gene editing has the potential to eradicate HIV-1 infection, this work highlights a potential issue that warrants further investigation.
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Affiliation(s)
- Michele Lai
- Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Eyal Maori
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paola Quaranta
- Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Giulia Matteoli
- Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
- Virology Unit, Pisa University Hospital, Pisa, Italy
| | | | - Stefania Crucitta
- Pharmacology Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Simone Pacini
- Hematology Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Ombretta Turriziani
- Laboratory of Virology, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Guido Antonelli
- Laboratory of Virology, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Jonathan L. Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Giulia Freer
- Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Mauro Pistello
- Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
- Virology Unit, Pisa University Hospital, Pisa, Italy
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64
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Murty T, Mackall CL. Gene editing to enhance the efficacy of cancer cell therapies. Mol Ther 2021; 29:3153-3162. [PMID: 34673274 PMCID: PMC8571170 DOI: 10.1016/j.ymthe.2021.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 12/18/2022] Open
Abstract
Adoptive T cell therapies have shown impressive signals of activity, but their clinical impact could be enhanced by technologies to increase T cell potency and diminish the cost and labor involved in manufacturing these products. Gene editing platforms are under study in this arena to (1) enhance immune cell potency by knocking out molecules that inhibit immune responses; (2) deliver genetic payloads into precise genomic locations and thereby enhance safety and/or improve the gene expression profile by leveraging physiologic promoters, enhancers, and repressors; and (3) enable off-the-shelf therapies by preventing alloreactivity and immune rejection. This review discusses gene editing approaches that have been the best studied in the context of human T cells and adoptive T cell therapies, summarizing their current status and near-term potential for translation.
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Affiliation(s)
- Tara Murty
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA; Program in Biophysics, Stanford University, Stanford, CA, USA; Medical Scientist Training Program, Stanford University, Stanford, CA, USA
| | - Crystal L Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Kocher T, Bischof J, Haas SA, March OP, Liemberger B, Hainzl S, Illmer J, Hoog A, Muigg K, Binder HM, Klausegger A, Strunk D, Bauer JW, Cathomen T, Koller U. A non-viral and selection-free COL7A1 HDR approach with improved safety profile for dystrophic epidermolysis bullosa. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:237-250. [PMID: 34458008 PMCID: PMC8368800 DOI: 10.1016/j.omtn.2021.05.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/25/2021] [Indexed: 12/26/2022]
Abstract
Gene editing via homology-directed repair (HDR) currently comprises the best strategy to obtain perfect corrections for pathogenic mutations of monogenic diseases, such as the severe recessive dystrophic form of the blistering skin disease epidermolysis bullosa (RDEB). Limitations of this strategy, in particular low efficiencies and off-target effects, hinder progress toward clinical applications. However, the severity of RDEB necessitates the development of efficient and safe gene-editing therapies based on perfect repair. To this end, we sought to assess the corrective efficiencies following optimal Cas9 nuclease and nickase-based COL7A1-targeting strategies in combination with single- or double-stranded donor templates for HDR at the COL7A1 mutation site. We achieved HDR-mediated correction efficiencies of up to 21% and 10% in primary RDEB keratinocytes and fibroblasts, respectively, as analyzed by next-generation sequencing, leading to full-length type VII collagen restoration and accurate deposition within engineered three-dimensional (3D) skin equivalents (SEs). Extensive on- and off-target analyses confirmed that the combined treatment of paired nicking and single-stranded oligonucleotides constituted a highly efficient COL7A1-editing strategy, associated with a significantly improved safety profile. Our findings, therefore, represent a further advancement in the field of traceless genome editing for genodermatoses.
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Affiliation(s)
- Thomas Kocher
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Johannes Bischof
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Simone Alexandra Haas
- Institute for Transfusion Medicine and Gene Therapy, Medical Center – University of Freiburg, 79106 Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center – University of Freiburg, 79106 Freiburg, Germany
| | - Oliver Patrick March
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Bernadette Liemberger
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Stefan Hainzl
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Julia Illmer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Anna Hoog
- Cell Therapy Institute, SCI-TReCS, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Katharina Muigg
- Cell Therapy Institute, SCI-TReCS, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Heide-Marie Binder
- Cell Therapy Institute, SCI-TReCS, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Alfred Klausegger
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Dirk Strunk
- Cell Therapy Institute, SCI-TReCS, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Johann Wolfgang Bauer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center – University of Freiburg, 79106 Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center – University of Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Ulrich Koller
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
- Corresponding author Ulrich Koller, EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, Strubergasse 22, 5020 Salzburg, Austria.
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66
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Aquino-Jarquin G. Current advances in overcoming obstacles of CRISPR/Cas9 off-target genome editing. Mol Genet Metab 2021; 134:77-86. [PMID: 34391646 DOI: 10.1016/j.ymgme.2021.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/03/2021] [Accepted: 08/03/2021] [Indexed: 12/14/2022]
Abstract
CRISPR/Cas9-based technology has revolutionized biomedical research by providing a high-fidelity gene-editing method, foreshadowing a significant impact on the therapeutics of many human genetic disorders previously considered untreatable. However, off-target events represent a critical hurdle before genome editing can be fully established in clinical practice. This mini-review recapitulates some recent advances for detecting and overcoming off-target effects mediated by the CRISPR/Cas9 system that could increase the likelihood of clinical success of the CRISPR-based approaches.
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Affiliation(s)
- Guillermo Aquino-Jarquin
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Hospital Infantil de México, Federico Gómez, Ciudad de México, Mexico; Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, Mexico.
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67
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Wagner DL, Peter L, Schmueck-Henneresse M. Cas9-directed immune tolerance in humans-a model to evaluate regulatory T cells in gene therapy? Gene Ther 2021; 28:549-559. [PMID: 33574580 PMCID: PMC8455332 DOI: 10.1038/s41434-021-00232-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 01/20/2021] [Indexed: 01/31/2023]
Abstract
The dichotomic nature of the adaptive immune response governs the outcome of clinical gene therapy. On the one hand, neutralizing antibodies and cytotoxic T cells can have a dramatic impact on the efficacy and safety of human gene therapies. On the other hand, regulatory T cells (Treg) can promote tolerance toward transgenes thereby enabling long-term benefits of in vivo gene therapy after a single administration. Pre-existing antibodies and T cell immunity has been a major obstacle for in vivo gene therapies with viral vectors. As CRISPR-Cas9 gene editing advances toward the clinics, the technology's inherent immunogenicity must be addressed in order to guide clinical treatment decisions. This review summarizes the recent evidence on Cas9-specific immunity in humans-including early results from clinical trials-and discusses the risks for in vivo gene therapies. Finally, we focus on solutions and highlight the potential role of Cas9-specific Treg cells to promote immune tolerance. As a "beneficial alliance" beyond Cas9-immunity, antigen-specific Treg cells may serve as a living and targeted immunosuppressant to increase safety and efficacy of gene therapy.
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Affiliation(s)
- Dimitrios Laurin Wagner
- Berlin Institute of Health (BIH)-Center for Regenerative Therapies (B-CRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Center for Advanced Therapies (BeCAT), Charité-Universitätsmedizin Berlin, Berlin, Germany
- Institute of Transfusion Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lena Peter
- Berlin Institute of Health (BIH)-Center for Regenerative Therapies (B-CRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
- Einstein Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Michael Schmueck-Henneresse
- Berlin Institute of Health (BIH)-Center for Regenerative Therapies (B-CRT), Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Berlin Center for Advanced Therapies (BeCAT), Charité-Universitätsmedizin Berlin, Berlin, Germany.
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68
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Shen Y, Verboon JM, Zhang Y, Liu N, Kim YJ, Marglous S, Nandakumar SK, Voit RA, Fiorini C, Ejaz A, Basak A, Orkin SH, Xu J, Sankaran VG. A unified model of human hemoglobin switching through single-cell genome editing. Nat Commun 2021; 12:4991. [PMID: 34404810 PMCID: PMC8371164 DOI: 10.1038/s41467-021-25298-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/02/2021] [Indexed: 12/17/2022] Open
Abstract
Key mechanisms of fetal hemoglobin (HbF) regulation and switching have been elucidated through studies of human genetic variation, including mutations in the HBG1/2 promoters, deletions in the β-globin locus, and variation impacting BCL11A. While this has led to substantial insights, there has not been a unified understanding of how these distinct genetically-nominated elements, as well as other key transcription factors such as ZBTB7A, collectively interact to regulate HbF. A key limitation has been the inability to model specific genetic changes in primary isogenic human hematopoietic cells to uncover how each of these act individually and in aggregate. Here, we describe a single-cell genome editing functional assay that enables specific mutations to be recapitulated individually and in combination, providing insights into how multiple mutation-harboring functional elements collectively contribute to HbF expression. In conjunction with quantitative modeling and chromatin capture analyses, we illustrate how these genetic findings enable a comprehensive understanding of how distinct regulatory mechanisms can synergistically modulate HbF expression. Genetic mechanisms underlying fetal hemoglobin (HbF) regulation and switching are not fully understood. Here, the authors develop a single-cell genome editing functional assay to model how effects of mutation-harbouring functional elements contribute to HbF expression.
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Affiliation(s)
- Yong Shen
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeffrey M Verboon
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nan Liu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yoon Jung Kim
- Children's Medical Center Research Institute, Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Samantha Marglous
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Satish K Nandakumar
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard A Voit
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Claudia Fiorini
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ayesha Ejaz
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anindita Basak
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Howard Hughes Medical Institute, Boston, MA, USA
| | - Jian Xu
- Children's Medical Center Research Institute, Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. .,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Harvard Stem Cell Institute, Cambridge, MA, USA.
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69
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Feliciano CM, Wu K, Watry HL, Marley CBE, Ramadoss GN, Ghanim HY, Liu AZ, Zholudeva LV, McDevitt TC, Saporta MA, Conklin BR, Judge LM. Allele-Specific Gene Editing Rescues Pathology in a Human Model of Charcot-Marie-Tooth Disease Type 2E. Front Cell Dev Biol 2021; 9:723023. [PMID: 34485306 PMCID: PMC8415563 DOI: 10.3389/fcell.2021.723023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/22/2021] [Indexed: 12/26/2022] Open
Abstract
Many neuromuscular disorders are caused by dominant missense mutations that lead to dominant-negative or gain-of-function pathology. This category of disease is challenging to address via drug treatment or gene augmentation therapy because these strategies may not eliminate the effects of the mutant protein or RNA. Thus, effective treatments are severely lacking for these dominant diseases, which often cause severe disability or death. The targeted inactivation of dominant disease alleles by gene editing is a promising approach with the potential to completely remove the cause of pathology with a single treatment. Here, we demonstrate that allele-specific CRISPR gene editing in a human model of axonal Charcot-Marie-Tooth (CMT) disease rescues pathology caused by a dominant missense mutation in the neurofilament light chain gene (NEFL, CMT type 2E). We utilized a rapid and efficient method for generating spinal motor neurons from human induced pluripotent stem cells (iPSCs) derived from a patient with CMT2E. Diseased motor neurons recapitulated known pathologic phenotypes at early time points of differentiation, including aberrant accumulation of neurofilament light chain protein in neuronal cell bodies. We selectively inactivated the disease NEFL allele in patient iPSCs using Cas9 enzymes to introduce a frameshift at the pathogenic N98S mutation. Motor neurons carrying this allele-specific frameshift demonstrated an amelioration of the disease phenotype comparable to that seen in an isogenic control with precise correction of the mutation. Our results validate allele-specific gene editing as a therapeutic approach for CMT2E and as a promising strategy to silence dominant mutations in any gene for which heterozygous loss-of-function is well tolerated. This highlights the potential for gene editing as a therapy for currently untreatable dominant neurologic diseases.
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Affiliation(s)
- Carissa M. Feliciano
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
- Gladstone Institutes, San Francisco, CA, United States
| | - Kenneth Wu
- Gladstone Institutes, San Francisco, CA, United States
| | | | - Chiara B. E. Marley
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
- Gladstone Institutes, San Francisco, CA, United States
| | - Gokul N. Ramadoss
- Gladstone Institutes, San Francisco, CA, United States
- Biomedical Sciences Ph.D. Program, University of California, San Francisco, San Francisco, CA, United States
| | | | - Angela Z. Liu
- Gladstone Institutes, San Francisco, CA, United States
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, United States
| | | | - Todd C. McDevitt
- Gladstone Institutes, San Francisco, CA, United States
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Mario A. Saporta
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Bruce R. Conklin
- Gladstone Institutes, San Francisco, CA, United States
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, United States
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
- Innovative Genomics Institute, Berkeley, CA, United States
| | - Luke M. Judge
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
- Gladstone Institutes, San Francisco, CA, United States
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Cortijo-Gutiérrez M, Sánchez-Hernández S, Tristán-Manzano M, Maldonado-Pérez N, Lopez-Onieva L, Real PJ, Herrera C, Marchal JA, Martin F, Benabdellah K. Improved Functionality of Integration-Deficient Lentiviral Vectors (IDLVs) by the Inclusion of IS 2 Protein Docks. Pharmaceutics 2021; 13:pharmaceutics13081217. [PMID: 34452178 PMCID: PMC8401568 DOI: 10.3390/pharmaceutics13081217] [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: 07/09/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Integration-deficient lentiviral vectors (IDLVs) have recently generated increasing interest, not only as a tool for transient gene delivery, but also as a technique for detecting off-target cleavage in gene-editing methodologies which rely on customized endonucleases (ENs). Despite their broad potential applications, the efficacy of IDLVs has historically been limited by low transgene expression and by the reduced sensitivity to detect low-frequency off-target events. We have previously reported that the incorporation of the chimeric sequence element IS2 into the long terminal repeat (LTR) of IDLVs increases gene expression levels, while also reducing the episome yield inside transduced cells. Our study demonstrates that the effectiveness of IDLVs relies on the balance between two parameters which can be modulated by the inclusion of IS2 sequences. In the present study, we explore new IDLV configurations harboring several elements based on IS2 modifications engineered to mediate more efficient transgene expression without affecting the targeted cell load. Of all the insulators and configurations analysed, the insertion of the IS2 into the 3′LTR produced the best results. After demonstrating a DAPI-low nuclear gene repositioning of IS2-containing episomes, we determined whether, in addition to a positive effect on transcription, the IS2 could improve the capture of IDLVs on double strand breaks (DSBs). Thus, DSBs were randomly generated, using the etoposide or locus-specific CRISPR-Cas9. Our results show that the IS2 element improved the efficacy of IDLV DSB detection. Altogether, our data indicate that the insertion of IS2 into the LTR of IDLVs improved, not only their transgene expression levels, but also their ability to be inserted into existing DSBs. This could have significant implications for the development of an unbiased detection tool for off-target cleavage sites from different specific nucleases.
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Affiliation(s)
- Marina Cortijo-Gutiérrez
- GENYO, Centre for Genomics and Oncological Research, Genomic Medicine Department, Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Av. de la Illustration 114, 18016 Granada, Spain; (M.C.-G.); (S.S.-H.); (M.T.-M.); (N.M.-P.); (F.M.)
| | - Sabina Sánchez-Hernández
- GENYO, Centre for Genomics and Oncological Research, Genomic Medicine Department, Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Av. de la Illustration 114, 18016 Granada, Spain; (M.C.-G.); (S.S.-H.); (M.T.-M.); (N.M.-P.); (F.M.)
| | - María Tristán-Manzano
- GENYO, Centre for Genomics and Oncological Research, Genomic Medicine Department, Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Av. de la Illustration 114, 18016 Granada, Spain; (M.C.-G.); (S.S.-H.); (M.T.-M.); (N.M.-P.); (F.M.)
| | - Noelia Maldonado-Pérez
- GENYO, Centre for Genomics and Oncological Research, Genomic Medicine Department, Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Av. de la Illustration 114, 18016 Granada, Spain; (M.C.-G.); (S.S.-H.); (M.T.-M.); (N.M.-P.); (F.M.)
| | - Lourdes Lopez-Onieva
- GENYO, Centre for Genomics and Oncological Research, Molecular Oncology Department, Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Av. de la Illustration 114, 18016 Granada, Spain; (L.L.-O.); (P.J.R.)
- Department of Biochemistry and Molecular Biology I, Faculty of Science, University of Granada, Avenida Fuentenueva s/n, 18071 Granada, Spain
| | - Pedro J. Real
- GENYO, Centre for Genomics and Oncological Research, Molecular Oncology Department, Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Av. de la Illustration 114, 18016 Granada, Spain; (L.L.-O.); (P.J.R.)
- Department of Biochemistry and Molecular Biology I, Faculty of Science, University of Granada, Avenida Fuentenueva s/n, 18071 Granada, Spain
- Personalized Oncology Group, Bio-Health Research Institute (ibs Granada), 18016 Granada, Spain
| | - Concha Herrera
- Maimonides Institute of Biomedical Research in Cordoba (IMIBIC), 14004 Cordoba, Spain;
- Department of Haematology, Reina Sofía University Hospital, 14004 Cordoba, Spain
| | - Juan Antonio Marchal
- Biomedical Research Institute (ibs. Granada), 18012 Granada, Spain;
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, 18016 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
- Excellence Research Unit: Modeling Nature (MNat), University of Granada, 18016 Granada, Spain
| | - Francisco Martin
- GENYO, Centre for Genomics and Oncological Research, Genomic Medicine Department, Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Av. de la Illustration 114, 18016 Granada, Spain; (M.C.-G.); (S.S.-H.); (M.T.-M.); (N.M.-P.); (F.M.)
| | - Karim Benabdellah
- GENYO, Centre for Genomics and Oncological Research, Genomic Medicine Department, Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Av. de la Illustration 114, 18016 Granada, Spain; (M.C.-G.); (S.S.-H.); (M.T.-M.); (N.M.-P.); (F.M.)
- Correspondence: ; Tel.: +34-958-715-500
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72
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Lattanzi A, Camarena J, Lahiri P, Segal H, Srifa W, Vakulskas CA, Frock RL, Kenrick J, Lee C, Talbott N, Skowronski J, Cromer MK, Charlesworth CT, Bak RO, Mantri S, Bao G, DiGiusto D, Tisdale J, Wright JF, Bhatia N, Roncarolo MG, Dever DP, Porteus MH. Development of β-globin gene correction in human hematopoietic stem cells as a potential durable treatment for sickle cell disease. Sci Transl Med 2021; 13:13/598/eabf2444. [PMID: 34135108 DOI: 10.1126/scitranslmed.abf2444] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 05/25/2021] [Indexed: 12/11/2022]
Abstract
Sickle cell disease (SCD) is the most common serious monogenic disease with 300,000 births annually worldwide. SCD is an autosomal recessive disease resulting from a single point mutation in codon six of the β-globin gene (HBB). Ex vivo β-globin gene correction in autologous patient-derived hematopoietic stem and progenitor cells (HSPCs) may potentially provide a curative treatment for SCD. We previously developed a CRISPR-Cas9 gene targeting strategy that uses high-fidelity Cas9 precomplexed with chemically modified guide RNAs to induce recombinant adeno-associated virus serotype 6 (rAAV6)-mediated HBB gene correction of the SCD-causing mutation in HSPCs. Here, we demonstrate the preclinical feasibility, efficacy, and toxicology of HBB gene correction in plerixafor-mobilized CD34+ cells from healthy and SCD patient donors (gcHBB-SCD). We achieved up to 60% HBB allelic correction in clinical-scale gcHBB-SCD manufacturing. After transplant into immunodeficient NSG mice, 20% gene correction was achieved with multilineage engraftment. The long-term safety, tumorigenicity, and toxicology study demonstrated no evidence of abnormal hematopoiesis, genotoxicity, or tumorigenicity from the engrafted gcHBB-SCD drug product. Together, these preclinical data support the safety, efficacy, and reproducibility of this gene correction strategy for initiation of a phase 1/2 clinical trial in patients with SCD.
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Affiliation(s)
- Annalisa Lattanzi
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.,Center for Definitive and Curative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Joab Camarena
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Premanjali Lahiri
- Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - Helen Segal
- Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - Waracharee Srifa
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Richard L Frock
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Josefin Kenrick
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Ciaran Lee
- APC Microbiome Ireland, University College Cork, T12 YN60 Cork, Ireland
| | - Narae Talbott
- Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - Jason Skowronski
- Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - M Kyle Cromer
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, DK-8000 Aarhus, Denmark.,Aarhus Institute of Advanced Studies (AIAS), Aarhus University, DK-8000 Aarhus, Denmark
| | - Sruthi Mantri
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77006, USA
| | - David DiGiusto
- Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - John Tisdale
- Molecular and Clinical Hematology Branch, NHLBI, Bethesda, MD 20814, USA
| | - J Fraser Wright
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.,Center for Definitive and Curative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Neehar Bhatia
- Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA.,Deceased
| | - Maria Grazia Roncarolo
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.,Center for Definitive and Curative Medicine, Stanford University, Stanford, CA 94305, USA.,Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Daniel P Dever
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA. .,Center for Definitive and Curative Medicine, Stanford University, Stanford, CA 94305, USA.,Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
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73
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Abstract
Therapeutic gene editing with the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system offers significant improvements in specificity and programmability compared with previous methods. CRISPR editing strategies can be used ex vivo and in vivo with many theoretic disease applications. Off-target effects of CRISPR-mediated gene editing are an important outcome to be aware of, minimize, and detect. The current methods of regulatory approval for personalized therapies are complex and may be proved inefficient as these therapies are implemented more widely. The role of pathologists and laboratory medicine practitioners is vital to the clinical implementation of therapeutic gene editing.
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Affiliation(s)
- Elan Hahn
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, Room 6231, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
| | - Matthew Hiemenz
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California 90027, USA; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California 90033, USA
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74
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Kurgan G, Turk R, Li H, Roberts N, Rettig GR, Jacobi AM, Tso L, Sturgeon M, Mertens M, Noten R, Florus K, Behlke MA, Wang Y, McNeill MS. CRISPAltRations: a validated cloud-based approach for interrogation of double-strand break repair mediated by CRISPR genome editing. Mol Ther Methods Clin Dev 2021; 21:478-491. [PMID: 33981780 PMCID: PMC8082044 DOI: 10.1016/j.omtm.2021.03.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/29/2021] [Indexed: 12/26/2022]
Abstract
CRISPR systems enable targeted genome editing in a wide variety of organisms by introducing single- or double-strand DNA breaks, which are repaired using endogenous molecular pathways. Characterization of on- and off-target editing events from CRISPR proteins can be evaluated using targeted genome resequencing. We characterized DNA repair fingerprints that result from non-homologous end joining (NHEJ) after double-stranded breaks (DSBs) were introduced by Cas9 or Cas12a for >500 paired treatment/control experiments. We found that building biological understanding of the repair into a novel analysis tool (CRISPAltRations) improved the quality of the results. We validated our software using simulated, targeted amplicon sequencing data (11 guide RNAs [gRNAs] and 603 on- and off-target locations) and demonstrated that CRISPAltRations outperforms other publicly available software tools in accurately annotating CRISPR-associated indels and homology-directed repair (HDR) events. We enable non-bioinformaticians to use CRISPAltRations by developing a web-accessible, cloud-hosted deployment, which allows rapid batch processing of samples in a graphical user interface (GUI) and complies with HIPAA security standards. By ensuring that our software is thoroughly tested, version controlled, and supported with a user interface (UI), we enable resequencing analysis of CRISPR genome editing experiments to researchers no matter their skill in bioinformatics.
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Affiliation(s)
- Gavin Kurgan
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | - Rolf Turk
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215
| | | | | | | | - Lauren Tso
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | | | | | | | | | | | - Yu Wang
- Integrated DNA Technologies, Coralville, IA 52241, USA
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75
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Targeted delivery of CRISPR-Cas9 and transgenes enables complex immune cell engineering. Cell Rep 2021; 35:109207. [PMID: 34077734 PMCID: PMC8236216 DOI: 10.1016/j.celrep.2021.109207] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/09/2021] [Accepted: 05/11/2021] [Indexed: 01/04/2023] Open
Abstract
As genome engineering advances cell-based therapies, a versatile approach to introducing both CRISPR-Cas9 ribonucleoproteins (RNPs) and therapeutic transgenes into specific cells would be transformative. Autologous T cells expressing a chimeric antigen receptor (CAR) manufactured by viral transduction are approved to treat multiple blood cancers, but additional genetic modifications to alter cell programs will likely be required to treat solid tumors and for allogeneic cellular therapies. We have developed a one-step strategy using engineered lentiviral particles to introduce Cas9 RNPs and a CAR transgene into primary human T cells without electroporation. Furthermore, programming particle tropism allows us to target a specific cell type within a mixed cell population. As a proof-of-concept, we show that HIV-1 envelope targeted particles to edit CD4+ cells while sparing co-cultured CD8+ cells. This adaptable approach to immune cell engineering ex vivo provides a strategy applicable to the genetic modification of targeted somatic cells in vivo.
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76
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Amit I, Iancu O, Levy-Jurgenson A, Kurgan G, McNeill MS, Rettig GR, Allen D, Breier D, Ben Haim N, Wang Y, Anavy L, Hendel A, Yakhini Z. CRISPECTOR provides accurate estimation of genome editing translocation and off-target activity from comparative NGS data. Nat Commun 2021; 12:3042. [PMID: 34031394 PMCID: PMC8144550 DOI: 10.1038/s41467-021-22417-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/04/2021] [Indexed: 12/26/2022] Open
Abstract
Controlling off-target editing activity is one of the central challenges in making CRISPR technology accurate and applicable in medical practice. Current algorithms for analyzing off-target activity do not provide statistical quantification, are not sufficiently sensitive in separating signal from noise in experiments with low editing rates, and do not address the detection of translocations. Here we present CRISPECTOR, a software tool that supports the detection and quantification of on- and off-target genome-editing activity from NGS data using paired treatment/control CRISPR experiments. In particular, CRISPECTOR facilitates the statistical analysis of NGS data from multiplex-PCR comparative experiments to detect and quantify adverse translocation events. We validate the observed results and show independent evidence of the occurrence of translocations in human cell lines, after genome editing. Our methodology is based on a statistical model comparison approach leading to better false-negative rates in sites with weak yet significant off-target activity.
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Affiliation(s)
- Ido Amit
- Arazi School of Computer Science, Interdisciplinary Center, Herzliya, Israel
| | - Ortal Iancu
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Alona Levy-Jurgenson
- Department of Computer Science, Technion-Israel Institute of Technology, Haifa, Israel
| | - Gavin Kurgan
- Integrated DNA Technologies Inc., Coralville, IA, USA
| | | | | | - Daniel Allen
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Dor Breier
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Nimrod Ben Haim
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Yu Wang
- Integrated DNA Technologies Inc., Coralville, IA, USA
| | - Leon Anavy
- Arazi School of Computer Science, Interdisciplinary Center, Herzliya, Israel
| | - Ayal Hendel
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
| | - Zohar Yakhini
- Arazi School of Computer Science, Interdisciplinary Center, Herzliya, Israel.
- Department of Computer Science, Technion-Israel Institute of Technology, Haifa, Israel.
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77
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Miura K, Ogura A, Kobatake K, Honda H, Kaminuma O. Progress of genome editing technology and developmental biology useful for radiation research. JOURNAL OF RADIATION RESEARCH 2021; 62:i53-i63. [PMID: 33978171 PMCID: PMC8114227 DOI: 10.1093/jrr/rraa127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/26/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Following the development of genome editing technology, it has become more feasible to create genetically modified animals such as knockout (KO), knock-in, and point-mutated animals. The genome-edited animals are useful to investigate the roles of various functional genes in many fields of biological science including radiation research. Nevertheless, some researchers may experience difficulty in generating genome-edited animals, probably due to the requirement for equipment and techniques for embryo manipulation and handling. Furthermore, after obtaining F0 generation, genome-edited animals generally need to be expanded and maintained for analyzing the target gene function. To investigate genes essential for normal birth and growth, the generation of conditional KO (cKO) animals in which a tissue- or stage-specific gene mutation can be introduced is often required. Here, we describe the basic principle and application of genome editing technology including zinc-finger nuclease, transcription-activator-like effector nuclease, and clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR associated protein (Cas) systems. Recently advanced developmental biology methods have enabled application of the technology, especially CRISPR/Cas, to zygotes, leading to the prompt production of genome-edited animals. For pre-implantation embryos, genome editing via oviductal nucleic acid delivery has been developed as an embryo manipulation- or handling-free method. Examining the gene function at F0 generation is becoming possible by employing triple-target CRISPR technology. This technology, in combination with a blastocyst complementation method enables investigation of even birth- and growth-responsible genes without establishing cKO strains. We hope that this review is helpful for understanding and expanding genome editing-related technology and for progressing radiation research.
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Affiliation(s)
- Kento Miura
- Department of Disease Model, Research Institute of Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
- RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Atsuo Ogura
- RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
- RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Kohei Kobatake
- Department of Disease Model, Research Institute of Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
- Department of Urology, Hiroshima University, Hiroshima 734-8553, Japan
| | - Hiroaki Honda
- Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Osamu Kaminuma
- Department of Disease Model, Research Institute of Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
- RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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78
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Cai W, Luo T, Mao L, Wang M. Spatiotemporal Delivery of CRISPR/Cas9 Genome Editing Machinery Using Stimuli‐Responsive Vehicles. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202005644] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Weiqi Cai
- Beijing National Laboratory for Molecular Science CAS Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry Chinese Academy of Sciences (ICCAS) No. 2, North first street Zhongguancun Beijing 100190 China
- University of Chinese Academy of Sciences No.19 (A) Yuquan Road Shijingshan District China
| | - Tianli Luo
- Beijing National Laboratory for Molecular Science CAS Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry Chinese Academy of Sciences (ICCAS) No. 2, North first street Zhongguancun Beijing 100190 China
- University of Chinese Academy of Sciences No.19 (A) Yuquan Road Shijingshan District China
| | - Lanqun Mao
- Beijing National Laboratory for Molecular Science CAS Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry Chinese Academy of Sciences (ICCAS) No. 2, North first street Zhongguancun Beijing 100190 China
- University of Chinese Academy of Sciences No.19 (A) Yuquan Road Shijingshan District China
| | - Ming Wang
- Beijing National Laboratory for Molecular Science CAS Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry Chinese Academy of Sciences (ICCAS) No. 2, North first street Zhongguancun Beijing 100190 China
- University of Chinese Academy of Sciences No.19 (A) Yuquan Road Shijingshan District China
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79
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Liu P, Liang SQ, Zheng C, Mintzer E, Zhao YG, Ponnienselvan K, Mir A, Sontheimer EJ, Gao G, Flotte TR, Wolfe SA, Xue W. Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice. Nat Commun 2021; 12:2121. [PMID: 33837189 PMCID: PMC8035190 DOI: 10.1038/s41467-021-22295-w] [Citation(s) in RCA: 146] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/08/2021] [Indexed: 12/26/2022] Open
Abstract
Prime editors (PEs) mediate genome modification without utilizing double-stranded DNA breaks or exogenous donor DNA as a template. PEs facilitate nucleotide substitutions or local insertions or deletions within the genome based on the template sequence encoded within the prime editing guide RNA (pegRNA). However, the efficacy of prime editing in adult mice has not been established. Here we report an NLS-optimized SpCas9-based prime editor that improves genome editing efficiency in both fluorescent reporter cells and at endogenous loci in cultured cell lines. Using this genome modification system, we could also seed tumor formation through somatic cell editing in the adult mouse. Finally, we successfully utilize dual adeno-associated virus (AAVs) for the delivery of a split-intein prime editor and demonstrate that this system enables the correction of a pathogenic mutation in the mouse liver. Our findings further establish the broad potential of this genome editing technology for the directed installation of sequence modifications in vivo, with important implications for disease modeling and correction.
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Affiliation(s)
- Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shun-Qing Liang
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Chunwei Zheng
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Esther Mintzer
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Yan G Zhao
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Karthikeyan Ponnienselvan
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Aamir Mir
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Terence R Flotte
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
- Departments of Pediatrics and Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.
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80
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Abstract
The move from reading to writing the human genome offers new opportunities to improve human health. The United States National Institutes of Health (NIH) Somatic Cell Genome Editing (SCGE) Consortium aims to accelerate the development of safer and more-effective methods to edit the genomes of disease-relevant somatic cells in patients, even in tissues that are difficult to reach. Here we discuss the consortium's plans to develop and benchmark approaches to induce and measure genome modifications, and to define downstream functional consequences of genome editing within human cells. Central to this effort is a rigorous and innovative approach that requires validation of the technology through third-party testing in small and large animals. New genome editors, delivery technologies and methods for tracking edited cells in vivo, as well as newly developed animal models and human biological systems, will be assembled-along with validated datasets-into an SCGE Toolkit, which will be disseminated widely to the biomedical research community. We visualize this toolkit-and the knowledge generated by its applications-as a means to accelerate the clinical development of new therapies for a wide range of conditions.
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81
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Abstract
Genetic diseases cause numerous complex and intractable pathologies. DNA sequences encoding each human's complexity and many disease risks are contained in the mitochondrial genome, nuclear genome, and microbial metagenome. Diagnosis of these diseases has unified around applications of next-generation DNA sequencing. However, translating specific genetic diagnoses into targeted genetic therapies remains a central goal. To date, genetic therapies have fallen into three broad categories: bulk replacement of affected genetic compartments with a new exogenous genome, nontargeted addition of exogenous genetic material to compensate for genetic errors, and most recently, direct correction of causative genetic alterations using gene editing. Generalized methods of diagnosis, therapy, and reagent delivery into each genetic compartment will accelerate the next generations of curative genetic therapies. We discuss the structure and variability of the mitochondrial, nuclear, and microbial metagenomic compartments, as well as the historical development and current practice of genetic diagnostics and gene therapies targeting each compartment.
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Affiliation(s)
- Theodore L Roth
- Medical Scientist Training Program, University of California, San Francisco, California 94143, USA; .,Department of Microbiology and Immunology and Diabetes Center, University of California, San Francisco, California 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California 94720, USA.,Gladstone Institutes, San Francisco, California 94158, USA
| | - Alexander Marson
- Department of Microbiology and Immunology and Diabetes Center, University of California, San Francisco, California 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California 94720, USA.,Gladstone Institutes, San Francisco, California 94158, USA.,Department of Medicine, University of California, San Francisco, California 94143, USA.,Parker Institute for Cancer Immunotherapy, San Francisco, California 94129, USA.,Chan Zuckerberg Biohub, San Francisco, California 94158, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, USA
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82
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Policarpi C, Dabin J, Hackett JA. Epigenetic editing: Dissecting chromatin function in context. Bioessays 2021; 43:e2000316. [PMID: 33724509 DOI: 10.1002/bies.202000316] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/06/2021] [Accepted: 02/11/2021] [Indexed: 12/11/2022]
Abstract
How epigenetic mechanisms regulate genome output and response to stimuli is a fundamental question in development and disease. Past decades have made tremendous progress in deciphering the regulatory relationships involved by correlating aggregated (epi)genomics profiles with global perturbations. However, the recent development of epigenetic editing technologies now enables researchers to move beyond inferred conclusions, towards explicit causal reasoning, through 'programing' precise chromatin perturbations in single cells. Here, we first discuss the major unresolved questions in the epigenetics field that can be addressed by programable epigenome editing, including the context-dependent function and memory of chromatin states. We then describe the epigenetic editing toolkit focusing on CRISPR-based technologies, and highlight its achievements, drawbacks and promise. Finally, we consider the potential future application of epigenetic editing to the study and treatment of specific disease conditions.
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Affiliation(s)
- Cristina Policarpi
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Juliette Dabin
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Jamie A Hackett
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
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83
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Miura H, Imafuku J, Kurosaki A, Sato M, Ma Y, Zhang G, Mizutani A, Kamimura K, Gurumurthy CB, Liu D, Ohtsuka M. Novel reporter mouse models useful for evaluating in vivo gene editing and for optimization of methods of delivering genome editing tools. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:325-336. [PMID: 33850636 PMCID: PMC8020343 DOI: 10.1016/j.omtn.2021.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 03/02/2021] [Indexed: 11/15/2022]
Abstract
The clustered regularly interspersed palindromic repeats (CRISPR) system is a powerful genome-editing tool to modify genomes, virtually in any species. The CRISPR tool has now been utilized in many areas of medical research, including gene therapy. Although several proof-of-concept studies show the feasibility of in vivo gene therapy applications for correcting disease-causing mutations, and new and improved tools are constantly being developed, there are not many choices of suitable reporter models to evaluate genome editor tools and their delivery methods. Here, we developed and validated reporter mouse models containing a single copy of disrupted EGFP (ΔEGFP) via frameshift mutations. We tested several delivery methods for validation of the reporters, and we demonstrated their utility to assess both non-homologous end-joining (NHEJ) and via homology-directed repair (HDR) processes in embryos and in somatic tissues. With the use of the reporters, we also show that hydrodynamic delivery of ribonucleoprotein (RNP) with Streptococcus pyogenes (Sp)Cas9 protein mixed with synthetic guide RNA (gRNA) elicits better genome-editing efficiencies than the plasmid vector-based system in mouse liver. The reporters can also be used for assessing HDR efficiencies of the Acidaminococcus sp. (As)Cas12a nuclease. The results suggest that the ΔEGFP mouse models serve as valuable tools for evaluation of in vivo genome editing.
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Affiliation(s)
- Hiromi Miura
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Kanagawa, Japan.,Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Kanagawa, Japan
| | - Jurai Imafuku
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Kanagawa, Japan
| | - Aki Kurosaki
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Kanagawa, Japan
| | - Masahiro Sato
- Section of Gene Expression Regulation, Frontier Science Research Center, Kagoshima University, Kagoshima, Japan
| | - Yongjie Ma
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Guisheng Zhang
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Akiko Mizutani
- Faculty of Health and Medical Science, Teikyo Heisei University, Tokyo, Japan
| | - Kenya Kamimura
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.,Department of General Medicine, Niigata University School of Medicine, Niigata, JAPAN
| | - Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, University of Nebraska Medical Center, Omaha, NE, USA.,Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Dexi Liu
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Kanagawa, Japan.,Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Kanagawa, Japan.,Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
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84
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Sharma G, Sharma AR, Bhattacharya M, Lee SS, Chakraborty C. CRISPR-Cas9: A Preclinical and Clinical Perspective for the Treatment of Human Diseases. Mol Ther 2021; 29:571-586. [PMID: 33238136 PMCID: PMC7854284 DOI: 10.1016/j.ymthe.2020.09.028] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/12/2020] [Accepted: 09/16/2020] [Indexed: 12/21/2022] Open
Abstract
At present, the idea of genome modification has revolutionized the modern therapeutic research era. Genome modification studies have traveled a long way from gene modifications in primary cells to genetic modifications in animals. The targeted genetic modification may result in the modulation (i.e., either upregulation or downregulation) of the predefined gene expression. Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated nuclease 9 (Cas9) is a promising genome-editing tool that has therapeutic potential against incurable genetic disorders by modifying their DNA sequences. In comparison with other genome-editing techniques, CRISPR-Cas9 is simple, efficient, and very specific. This enabled CRISPR-Cas9 genome-editing technology to enter into clinical trials against cancer. Besides therapeutic potential, the CRISPR-Cas9 tool can also be applied to generate genetically inhibited animal models for drug discovery and development. This comprehensive review paper discusses the origin of CRISPR-Cas9 systems and their therapeutic potential against various genetic disorders, including cancer, allergy, immunological disorders, Duchenne muscular dystrophy, cardiovascular disorders, neurological disorders, liver-related disorders, cystic fibrosis, blood-related disorders, eye-related disorders, and viral infection. Finally, we discuss the different challenges, safety concerns, and strategies that can be applied to overcome the obstacles during CRISPR-Cas9-mediated therapeutic approaches.
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Affiliation(s)
- Garima Sharma
- Neuropsychopharmacology and Toxicology Program, College of Pharmacy, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do 24252, Republic of Korea
| | - Manojit Bhattacharya
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do 24252, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do 24252, Republic of Korea.
| | - Chiranjib Chakraborty
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do 24252, Republic of Korea; Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal 700126, India.
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85
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Advances and Obstacles in Homology-Mediated Gene Editing of Hematopoietic Stem Cells. J Clin Med 2021; 10:jcm10030513. [PMID: 33535527 PMCID: PMC7867106 DOI: 10.3390/jcm10030513] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 12/14/2022] Open
Abstract
Homology-directed gene editing of hematopoietic stem and progenitor cells (HSPCs) is a promising strategy for the treatment of inherited blood disorders, obviating many of the limitations associated with viral vector-mediated gene therapies. The use of CRISPR/Cas9 or other programmable nucleases and improved methods of homology template delivery have enabled precise ex vivo gene editing. These transformative advances have also highlighted technical challenges to achieve high-efficiency gene editing in HSPCs for therapeutic applications. In this review, we discuss recent pre-clinical investigations utilizing homology-mediated gene editing in HSPCs and highlight various strategies to improve editing efficiency in these cells.
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86
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Klaver-Flores S, Zittersteijn HA, Canté-Barrett K, Lankester A, Hoeben RC, Gonçalves MAFV, Pike-Overzet K, Staal FJT. Genomic Engineering in Human Hematopoietic Stem Cells: Hype or Hope? Front Genome Ed 2021; 2:615619. [PMID: 34713237 PMCID: PMC8525357 DOI: 10.3389/fgeed.2020.615619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
Many gene editing techniques are developed and tested, yet, most of these are optimized for transformed cell lines, which differ from their primary cell counterparts in terms of transfectability, cell death propensity, differentiation capability, and chromatin accessibility to gene editing tools. Researchers are working to overcome the challenges associated with gene editing of primary cells, namely, at the level of improving the gene editing tool components, e.g., the use of modified single guide RNAs, more efficient delivery of Cas9 and RNA in the ribonucleoprotein of these cells. Despite these efforts, the low efficiency of proper gene editing in true primary cells is an obstacle that needs to be overcome in order to generate sufficiently high numbers of corrected cells for therapeutic use. In addition, many of the therapeutic candidate genes for gene editing are expressed in more mature blood cell lineages but not in the hematopoietic stem cells (HSCs), where they are tightly packed in heterochromatin, making them less accessible to gene editing enzymes. Bringing HSCs in proliferation is sometimes seen as a solution to overcome lack of chromatin access, but the induction of proliferation in HSCs often is associated with loss of stemness. The documented occurrences of off-target effects and, importantly, on-target side effects also raise important safety issues. In conclusion, many obstacles still remain to be overcome before gene editing in HSCs for gene correction purposes can be applied clinically. In this review, in a perspective way, we will discuss the challenges of researching and developing a novel genetic engineering therapy for monogenic blood and immune system disorders.
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Affiliation(s)
| | - Hidde A. Zittersteijn
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Arjan Lankester
- Department of Pediatrics, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Rob C. Hoeben
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Karin Pike-Overzet
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
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87
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Sharma R, Dever DP, Lee CM, Azizi A, Pan Y, Camarena J, Köhnke T, Bao G, Porteus MH, Majeti R. The TRACE-Seq method tracks recombination alleles and identifies clonal reconstitution dynamics of gene targeted human hematopoietic stem cells. Nat Commun 2021; 12:472. [PMID: 33473139 PMCID: PMC7817666 DOI: 10.1038/s41467-020-20792-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
Targeted DNA correction of disease-causing mutations in hematopoietic stem and progenitor cells (HSPCs) may enable the treatment of genetic diseases of the blood and immune system. It is now possible to correct mutations at high frequencies in HSPCs by combining CRISPR/Cas9 with homologous DNA donors. Because of the precision of gene correction, these approaches preclude clonal tracking of gene-targeted HSPCs. Here, we describe Tracking Recombination Alleles in Clonal Engraftment using sequencing (TRACE-Seq), a methodology that utilizes barcoded AAV6 donor template libraries, carrying in-frame silent mutations or semi-randomized nucleotides outside the coding region, to track the in vivo lineage contribution of gene-targeted HSPC clones. By targeting the HBB gene with an AAV6 donor template library consisting of ~20,000 possible unique exon 1 in-frame silent mutations, we track the hematopoietic reconstitution of HBB targeted myeloid-skewed, lymphoid-skewed, and balanced multi-lineage repopulating human HSPC clones in mice. We anticipate this methodology could potentially be used for HSPC clonal tracking of Cas9 RNP and AAV6-mediated gene targeting outcomes in translational and basic research settings.
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Affiliation(s)
- Rajiv Sharma
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Daniel P Dever
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - Ciaran M Lee
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Armon Azizi
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Yidan Pan
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Joab Camarena
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - Thomas Köhnke
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA.
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA.
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA.
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88
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Kocher T, Koller U. Advances in gene editing strategies for epidermolysis bullosa. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 182:81-109. [PMID: 34175052 DOI: 10.1016/bs.pmbts.2020.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Epidermolysis bullosa represents a monogenetic disease comprising a variety of heterogeneous mutations in at least 16 genes encoding structural proteins crucial for skin integrity. Due to well-defined mutations but still lacking causal treatment options for the disease, epidermolysis bullosa represents an ideal candidate for gene therapeutic interventions. Recent developments and improvements in the genome editing field have paved the way for the translation of various gene repair strategies into the clinic. With the ability to accurately predict and monitor targeting events within the human genome, the translation might soon be possible. Here, we describe current advancements in the genome editing field for epidermolysis bullosa, along with a discussion of aspects and strategies for precise and personalized gene editing-based medicine, in order to develop efficient and safe ex vivo as well as in vivo genome editing therapies for epidermolysis bullosa patients in the future.
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Affiliation(s)
- Thomas Kocher
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Ulrich Koller
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, Salzburg, Austria.
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89
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Della Mina E, Guérin A, Tangye SG. Molecular requirements for human lymphopoiesis as defined by inborn errors of immunity. Stem Cells 2021; 39:389-402. [PMID: 33400834 DOI: 10.1002/stem.3327] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/07/2020] [Indexed: 12/19/2022]
Abstract
Hematopoietic stem cells (HSCs) are the progenitor cells that give rise to the diverse repertoire of all immune cells. As they differentiate, HSCs yield a series of cell states that undergo gradual commitment to become mature blood cells. Studies of hematopoiesis in murine models have provided critical insights about the lineage relationships among stem cells, progenitors, and mature cells, and these have guided investigations of the molecular basis for these distinct developmental stages. Primary immune deficiencies are caused by inborn errors of immunity that result in immune dysfunction and subsequent susceptibility to severe and recurrent infection(s). Over the last decade there has been a dramatic increase in the number and depth of the molecular, cellular, and clinical characterization of such genetically defined causes of immune dysfunction. Patients harboring inborn errors of immunity thus represent a unique resource to improve our understanding of the multilayered and complex mechanisms underlying lymphocyte development in humans. These breakthrough discoveries not only enable significant advances in the diagnosis of such rare and complex conditions but also provide substantial improvement in the development of personalized treatments. Here, we will discuss the clinical, cellular, and molecular phenotypes, and treatments of selected inborn errors of immunity that impede, either intrinsically or extrinsically, the development of B- or T-cells at different stages.
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Affiliation(s)
- Erika Della Mina
- Immunology and Immunodeficiency Laboratory, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St. Vincent's Clinical School, University of New South Wales, Darlinghurst, New South Wales, Australia
| | - Antoine Guérin
- Immunology and Immunodeficiency Laboratory, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St. Vincent's Clinical School, University of New South Wales, Darlinghurst, New South Wales, Australia
| | - Stuart G Tangye
- Immunology and Immunodeficiency Laboratory, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St. Vincent's Clinical School, University of New South Wales, Darlinghurst, New South Wales, Australia
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90
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Abstract
Notch (Notch1 through 4) are transmembrane receptors that determine cell differentiation and function, and are activated following interactions with ligands of the Jagged and Delta-like families. Notch has been established as a signaling pathway that plays a critical role in the differentiation and function of cells of the osteoblast and osteoclast lineages as well as in skeletal development and bone remodeling. Pathogenic variants of Notch receptors and their ligands are associated with a variety of genetic disorders presenting with significant craniofacial and skeletal manifestations. Lateral Meningocele Syndrome (LMS) is a rare genetic disorder characterized by neurological manifestations, meningoceles, skeletal developmental abnormalities and bone loss. LMS is associated with NOTCH3 gain-of-function pathogenic variants. Experimental mouse models of LMS revealed that the bone loss is secondary to increased osteoclastogenesis due to enhanced expression of receptor activator of nuclear factor kappa B ligand by cells of the osteoblast lineage. There are no effective therapies for LMS. Antisense oligonucleotides targeting Notch3 and antibodies that prevent the activation of NOTCH3 are being tested in preclinical models of the disease. In conclusion, LMS is a serious genetic disorder associated with NOTCH3 pathogenic variants. Novel experimental models have offered insight on mechanisms responsible and ways to correct the disease.
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Affiliation(s)
- Ernesto Canalis
- Department of Orthopaedic Surgery and Medicine, UConn Musculoskeletal Institute, UConn Health, Farmington, CT, United States
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91
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Song X, Liu C, Wang N, Huang H, He S, Gong C, Wei Y. Delivery of CRISPR/Cas systems for cancer gene therapy and immunotherapy. Adv Drug Deliv Rev 2021; 168:158-180. [PMID: 32360576 DOI: 10.1016/j.addr.2020.04.010] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 04/19/2020] [Accepted: 04/27/2020] [Indexed: 02/07/2023]
Abstract
The clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems are efficient and versatile gene editing tools, which offer enormous potential to treat cancer by editing genome, transcriptome or epigenome of tumor cells and/or immune cells. A large body of works have been done with CRISPR/Cas systems for genetic modification, and 16 clinical trials were conducted to treat cancer by ex vivo or in vivo gene editing approaches. Now, promising preclinical works have begun using CRISPR/Cas systems in vivo. However, efficient and safe delivery of CRISPR/Cas systems in vivo is still a critical challenge for their clinical applications. This article summarizes delivery of CRISPR/Cas systems by physical methods, viral vectors and non-viral vectors for cancer gene therapy and immunotherapy. The prospects for the development of physical methods, viral vectors and non-viral vectors for delivery of CRISPR/Cas systems are reviewed, and promising advances in cancer treatment using CRISPR/Cas systems are discussed.
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Affiliation(s)
- Xiangrong Song
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Chao Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Ning Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Hai Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Siyan He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Changyang Gong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China.
| | - Yuquan Wei
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China.
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92
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Houghton BC, Booth C. Gene Therapy for Primary Immunodeficiency. Hemasphere 2021; 5:e509. [PMID: 33403354 PMCID: PMC7773329 DOI: 10.1097/hs9.0000000000000509] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/21/2020] [Indexed: 12/27/2022] Open
Abstract
Over the past 3 decades, there has been significant progress in refining gene therapy technologies and procedures. Transduction of hematopoietic stem cells ex vivo using lentiviral vectors can now create a highly effective therapeutic product, capable of reconstituting many different immune system dysfunctions when reinfused into patients. Here, we review the key developments in the gene therapy landscape for primary immune deficiency, from an experimental therapy where clinical efficacy was marred by adverse events, to a commercialized product with enhanced safety and efficacy. We also discuss progress being made in preclinical studies for challenging disease targets and emerging gene editing technologies that are showing promising results, particularly for conditions where gene regulation is important for efficacy.
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Affiliation(s)
- Benjamin C. Houghton
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Claire Booth
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- Department of Paediatric Immunology, Great Ormond Street NHS Foundation Trust, London, United Kingdom
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93
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Danner E, Lebedin M, de la Rosa K, Kühn R. A homology independent sequence replacement strategy in human cells using a CRISPR nuclease. Open Biol 2021; 11:200283. [PMID: 33499763 PMCID: PMC7881171 DOI: 10.1098/rsob.200283] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/30/2020] [Indexed: 01/01/2023] Open
Abstract
Precision genomic alterations largely rely on homology directed repair (HDR), but targeting without homology using the non-homologous end-joining (NHEJ) pathway has gained attention as a promising alternative. Previous studies demonstrated precise insertions formed by the ligation of donor DNA into a targeted genomic double-strand break in both dividing and non-dividing cells. Here, we demonstrate the use of NHEJ repair to replace genomic segments with donor sequences; we name this method 'Replace' editing (Rational end-joining protocol delivering a targeted sequence exchange). Using CRISPR/Cas9, we create two genomic breaks and ligate a donor sequence in-between. This exchange of a genomic for a donor sequence uses neither microhomology nor homology arms. We target four loci in cell lines and show successful exchange of exons in 16-54% of human cells. Using linear amplification methods and deep sequencing, we quantify the diversity of outcomes following Replace editing and profile the ligated interfaces. The ability to replace exons or other genomic sequences in cells not efficiently modified by HDR holds promise for both basic research and medicine.
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Affiliation(s)
- Eric Danner
- Max Delbrück Center for Molecular Medicine of the Helmholtz Association, Berlin, Germany
| | | | | | - Ralf Kühn
- Max Delbrück Center for Molecular Medicine of the Helmholtz Association, Berlin, Germany
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94
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Abstract
Primary immunodeficiencies (PIDs) are a group of rare inherited disorders of the immune system. Many PIDs are devastating and require a definitive therapy to prevent progressive morbidity and premature mortality. Allogeneic haematopoietic stem cell transplantation (alloHSCT) is curative for many PIDs, and while advances have resulted in improved outcomes, the procedure still carries a risk of mortality and morbidity from graft failure or graft-versus-host disease (GvHD). Autologous haematopoietic stem cell gene therapy (HSC GT) has the potential to correct genetic defects across haematopoietic lineages without the complications of an allogeneic approach. HSC GT for PID has been in development for the last two decades and the first licensed HSC-GT product for adenosine deaminase-deficient severe combined immunodeficiency (ADA-SCID) is now available. New gene editing technologies have the potential to circumvent some of the problems associated with viral gene-addition. HSC GT for PID shows great promise, but requires a unique approach for each disease and carries risks, notably insertional mutagenesis from gamma-retroviral gene addition approaches and possible off-target toxicities from gene-editing techniques. In this review, we discuss the development of HSC GT for PID and outline the current state of clinical development before discussing future developments in the field.
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Affiliation(s)
- Thomas A Fox
- University College London (UCL) Institute of Immunity and Transplantation, UCL, London, UK.,Department of Clinical Haematology, UCL Hospitals NHS Foundation Trust, London, UK.,Molecular and Cellular Immunology Section, UCL Great Ormond Street (GOS) Institute of Child Health, London, UK
| | - Claire Booth
- Molecular and Cellular Immunology Section, UCL Great Ormond Street (GOS) Institute of Child Health, London, UK.,Department of Paediatric Immunology, GOS Hospital for Sick Children NHS Foundation Trust, London, UK
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95
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Genome-Wide Analysis of Off-Target CRISPR/Cas9 Activity in Single-Cell-Derived Human Hematopoietic Stem and Progenitor Cell Clones. Genes (Basel) 2020; 11:genes11121501. [PMID: 33322084 PMCID: PMC7762975 DOI: 10.3390/genes11121501] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 11/28/2020] [Accepted: 12/11/2020] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9)-mediated genome editing holds remarkable promise for the treatment of human genetic diseases. However, the possibility of off-target Cas9 activity remains a concern. To address this issue using clinically relevant target cells, we electroporated Cas9 ribonucleoprotein (RNP) complexes (independently targeted to two different genomic loci, the CXCR4 locus on chromosome 2 and the AAVS1 locus on chromosome 19) into human mobilized peripheral blood-derived hematopoietic stem and progenitor cells (HSPCs) and assessed the acquisition of somatic mutations in an unbiased, genome-wide manner via whole genome sequencing (WGS) of single-cell-derived HSPC clones. Bioinformatic analysis identified >20,000 total somatic variants (indels, single nucleotide variants, and structural variants) distributed among Cas9-treated and non-Cas9-treated control HSPC clones. Statistical analysis revealed no significant difference in the number of novel non-targeted indels among the samples. Moreover, data analysis showed no evidence of Cas9-mediated indel formation at 623 predicted off-target sites. The median number of novel single nucleotide variants was slightly elevated in Cas9 RNP-recipient sample groups compared to baseline, but did not reach statistical significance. Structural variants were rare and demonstrated no clear causal connection to Cas9-mediated gene editing procedures. We find that the collective somatic mutational burden observed within Cas9 RNP-edited human HSPC clones is indistinguishable from naturally occurring levels of background genetic heterogeneity.
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96
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Baltagiannis EG, Ziogas DE, Cho WC, Mitsis M, Roukos DH. Tumor heterogeneity-driven individualized therapy. Future Oncol 2020; 17:235-240. [PMID: 33305621 DOI: 10.2217/fon-2020-0915] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Evangelos G Baltagiannis
- Centre for Biosystems & Genome Network Medicine, Ioannina University, Ioannina, 45110, Greece.,Department of Surgery, University Hospital of Ioannina, Ioannina, 45500, Greece
| | - Demosthenis E Ziogas
- Centre for Biosystems & Genome Network Medicine, Ioannina University, Ioannina, 45110, Greece.,Department of Surgery, General Hospital of Ioannina, Ioannina, 45445, Greece
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong, 999077, China
| | - Michail Mitsis
- Department of Surgery, University Hospital of Ioannina, Ioannina, 45500, Greece.,Cancer Biobank Centre, Ioannina University, Ioannina, 45110, Greece
| | - Dimitrios H Roukos
- Centre for Biosystems & Genome Network Medicine, Ioannina University, Ioannina, 45110, Greece.,Department of Surgery, University Hospital of Ioannina, Ioannina, 45500, Greece.,Department of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, 11527, Greece
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97
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Abstract
Haematopoietic stem and progenitor cell (HSPC) gene therapy has emerged as an effective treatment modality for monogenic disorders of the blood system such as primary immunodeficiencies and β-thalassaemia. Medicinal products based on autologous HSPCs corrected using lentiviral and gammaretroviral vectors have now been approved for clinical use, and the site-specific genome modification of HSPCs using gene editing techniques such as CRISPR-Cas9 has shown great clinical promise. Preclinical studies have shown engineered HSPCs could also be used to cross-correct non-haematopoietic cells in neurodegenerative metabolic diseases. Here, we review the most recent advances in HSPC gene therapy and discuss emerging strategies for using HSPC gene therapy for a range of diseases.
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98
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Bennett EP, Petersen BL, Johansen IE, Niu Y, Yang Z, Chamberlain CA, Met Ö, Wandall HH, Frödin M. INDEL detection, the 'Achilles heel' of precise genome editing: a survey of methods for accurate profiling of gene editing induced indels. Nucleic Acids Res 2020; 48:11958-11981. [PMID: 33170255 PMCID: PMC7708060 DOI: 10.1093/nar/gkaa975] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 10/05/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022] Open
Abstract
Advances in genome editing technologies have enabled manipulation of genomes at the single base level. These technologies are based on programmable nucleases (PNs) that include meganucleases, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated 9 (Cas9) nucleases and have given researchers the ability to delete, insert or replace genomic DNA in cells, tissues and whole organisms. The great flexibility in re-designing the genomic target specificity of PNs has vastly expanded the scope of gene editing applications in life science, and shows great promise for development of the next generation gene therapies. PN technologies share the principle of inducing a DNA double-strand break (DSB) at a user-specified site in the genome, followed by cellular repair of the induced DSB. PN-elicited DSBs are mainly repaired by the non-homologous end joining (NHEJ) and the microhomology-mediated end joining (MMEJ) pathways, which can elicit a variety of small insertion or deletion (indel) mutations. If indels are elicited in a protein coding sequence and shift the reading frame, targeted gene knock out (KO) can readily be achieved using either of the available PNs. Despite the ease by which gene inactivation in principle can be achieved, in practice, successful KO is not only determined by the efficiency of NHEJ and MMEJ repair; it also depends on the design and properties of the PN utilized, delivery format chosen, the preferred indel repair outcomes at the targeted site, the chromatin state of the target site and the relative activities of the repair pathways in the edited cells. These variables preclude accurate prediction of the nature and frequency of PN induced indels. A key step of any gene KO experiment therefore becomes the detection, characterization and quantification of the indel(s) induced at the targeted genomic site in cells, tissues or whole organisms. In this survey, we briefly review naturally occurring indels and their detection. Next, we review the methods that have been developed for detection of PN-induced indels. We briefly outline the experimental steps and describe the pros and cons of the various methods to help users decide a suitable method for their editing application. We highlight recent advances that enable accurate and sensitive quantification of indel events in cells regardless of their genome complexity, turning a complex pool of different indel events into informative indel profiles. Finally, we review what has been learned about PN-elicited indel formation through the use of the new methods and how this insight is helping to further advance the genome editing field.
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Affiliation(s)
- Eric Paul Bennett
- Copenhagen Center for Glycomics, Department of Odontology and Molecular and Cellular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Bent Larsen Petersen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Ida Elisabeth Johansen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Yiyuan Niu
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, China
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Odontology and Molecular and Cellular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | | | - Özcan Met
- Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Department of Odontology and Molecular and Cellular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Morten Frödin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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99
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Xie M, Viviani M, Fussenegger M. Engineering precision therapies: lessons and motivations from the clinic. Synth Biol (Oxf) 2020; 6:ysaa024. [PMID: 33817342 PMCID: PMC7998714 DOI: 10.1093/synbio/ysaa024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/18/2022] Open
Abstract
In the past decade, gene- and cell-based therapies have been at the forefront of the biomedical revolution. Synthetic biology, the engineering discipline of building sophisticated 'genetic software' to enable precise regulation of gene activities in living cells, has been a decisive success factor of these new therapies. Here, we discuss the core technologies and treatment strategies that have already gained approval for therapeutic applications in humans. We also review promising preclinical work that could either enhance the efficacy of existing treatment strategies or pave the way for new precision medicines to treat currently intractable human conditions.
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Affiliation(s)
- Mingqi Xie
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zheijang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zheijang, China
| | - Mirta Viviani
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zheijang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zheijang, China
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
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100
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Kotowski M, Sharma S. CRISPR-Based Editing Techniques for Genetic Manipulation of Primary T Cells. Methods Protoc 2020; 3:mps3040079. [PMID: 33217926 PMCID: PMC7720142 DOI: 10.3390/mps3040079] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/15/2022] Open
Abstract
While clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing techniques have been widely adapted for use in immortalised immune cells, efficient manipulation of primary T cells has proved to be more challenging. Nonetheless, the rapid expansion of the CRISPR toolbox accompanied by the development of techniques for delivery of CRISPR components into primary T cells now affords the possibility to genetically manipulate primary T cells both with precision and at scale. Here, we review the key features of the techniques for primary T cell editing and discuss how the new generation of CRISPR-based tools may advance genetic engineering of these immune cells. This improved ability to genetically manipulate primary T cells will further enhance our fundamental understanding of cellular signalling and transcriptional networks in T cells and more importantly has the potential to revolutionise T cell-based therapies.
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