1
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Gao J, Gunasekar S, Xia ZJ, Shalin K, Jiang C, Chen H, Lee D, Lee S, Pisal ND, Luo JN, Griciuc A, Karp JM, Tanzi R, Joshi N. Gene therapy for CNS disorders: modalities, delivery and translational challenges. Nat Rev Neurosci 2024; 25:553-572. [PMID: 38898231 DOI: 10.1038/s41583-024-00829-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
Gene therapy is emerging as a powerful tool to modulate abnormal gene expression, a hallmark of most CNS disorders. The transformative potentials of recently approved gene therapies for the treatment of spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS) and active cerebral adrenoleukodystrophy are encouraging further development of this approach. However, most attempts to translate gene therapy to the clinic have failed to make it to market. There is an urgent need not only to tailor the genes that are targeted to the pathology of interest but to also address delivery challenges and thereby maximize the utility of genetic tools. In this Review, we provide an overview of gene therapy modalities for CNS diseases, emphasizing the interconnectedness of different delivery strategies and routes of administration. Important gaps in understanding that could accelerate the clinical translatability of CNS genetic interventions are addressed, and we present lessons learned from failed clinical trials that may guide the future development of gene therapies for the treatment and management of CNS disorders.
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Affiliation(s)
- Jingjing Gao
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA.
- Center for Bioactive Delivery, Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, USA.
| | - Swetharajan Gunasekar
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ziting Judy Xia
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kiruba Shalin
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA
| | - Christopher Jiang
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Hao Chen
- Marine College, Shandong University, Weihai, China
| | - Dongtak Lee
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sohyung Lee
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Nishkal D Pisal
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA
| | - James N Luo
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Ana Griciuc
- Harvard Medical School, Boston, MA, USA.
- Genetics and Aging Research Unit, McCance Center for Brain Health, Mass General Institute for Neurodegenerative Disease and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
| | - Jeffrey M Karp
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Harvard-MIT Program in Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Rudolph Tanzi
- Harvard Medical School, Boston, MA, USA.
- Genetics and Aging Research Unit, McCance Center for Brain Health, Mass General Institute for Neurodegenerative Disease and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
| | - Nitin Joshi
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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2
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Assa G, Kalter N, Rosenberg M, Beck A, Markovich O, Gontmakher T, Hendel A, Yakhini Z. Quantifying allele-specific CRISPR editing activity with CRISPECTOR2.0. Nucleic Acids Res 2024:gkae651. [PMID: 39077930 DOI: 10.1093/nar/gkae651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 06/24/2024] [Accepted: 07/18/2024] [Indexed: 07/31/2024] Open
Abstract
Off-target effects present a significant impediment to the safe and efficient use of CRISPR-Cas genome editing. Since off-target activity is influenced by the genomic sequence, the presence of sequence variants leads to varying on- and off-target profiles among different alleles or individuals. However, a reliable tool that quantifies genome editing activity in an allelic context is not available. Here, we introduce CRISPECTOR2.0, an extended version of our previously published software tool CRISPECTOR, with an allele-specific editing activity quantification option. CRISPECTOR2.0 enables reference-free, allele-aware, precise quantification of on- and off-target activity, by using de novo sample-specific single nucleotide variant (SNV) detection and statistical-based allele-calling algorithms. We demonstrate CRISPECTOR2.0 efficacy in analyzing samples containing multiple alleles and quantifying allele-specific editing activity, using data from diverse cell types, including primary human cells, plants, and an original extensive human cell line database. We identified instances where an SNV induced changes in the protospacer adjacent motif sequence, resulting in allele-specific editing. Intriguingly, differential allelic editing was also observed in regions carrying distal SNVs, hinting at the involvement of additional epigenetic factors. Our findings highlight the importance of allele-specific editing measurement as a milestone in the adaptation of efficient, accurate, and safe personalized genome editing.
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Affiliation(s)
- Guy Assa
- Arazi School of Computer Science, Reichman University, Herzliya 4610101, Israel
| | - Nechama Kalter
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Michael Rosenberg
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Avigail Beck
- Arazi School of Computer Science, Reichman University, Herzliya 4610101, Israel
| | - Oshry Markovich
- Rahan Meristem (1998) Ltd. Kibbutz Rosh-Hanikra, Western Galilee 2282500, Israel
| | - Tanya Gontmakher
- Rahan Meristem (1998) Ltd. Kibbutz Rosh-Hanikra, Western Galilee 2282500, Israel
| | - Ayal Hendel
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Zohar Yakhini
- Arazi School of Computer Science, Reichman University, Herzliya 4610101, Israel
- The Henry & Marilyn Taub Faculty of Computer Science, Technion - Israel Institute of Technology, Haifa 3200003, Israel
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3
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Carufe KEW, Economos NG, Glazer PM. Peptide Nucleic Acid-Mediated Regulation of CRISPR-Cas9 Specificity. Nucleic Acid Ther 2024. [PMID: 39037032 DOI: 10.1089/nat.2024.0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024] Open
Abstract
Although CRISPR-Cas9 gene therapies have proven to be a powerful tool across many applications, improvements are necessary to increase the specificity of this technology. Cas9 cutting in off-target sites remains an issue that limits CRISPR's application in human-based therapies. Treatment of autosomal dominant diseases also remains a challenge when mutant alleles differ from the wild-type sequence by only one base pair. Here, we utilize synthetic peptide nucleic acids (PNAs) that bind selected spacer sequences in the guide RNA (gRNA) to increase Cas9 specificity up to 10-fold. We interrogate variations in PNA length, binding position, and degree of homology with the gRNA. Our findings reveal that PNAs bound in the region distal to the protospacer adjacent motif (PAM) site effectively enhance specificity in both on-target/off-target and allele-specific scenarios. In addition, we demonstrate that introducing deliberate mismatches between PNAs bound in the PAM-proximal region of the gRNA can modulate Cas9 activity in an allele-specific manner. These advancements hold promise for addressing current limitations and expanding the therapeutic potential of CRISPR technology.
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Affiliation(s)
- Kelly E W Carufe
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Nicholas G Economos
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
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Rosignoli S, Lustrino E, Conci A, Fabrizi A, Rinaldo S, Latella M, Enzo E, Prosseda G, De Rosa L, De Luca M, Paiardini A. AlPaCas: allele-specific CRISPR gene editing through a protospacer-adjacent-motif (PAM) approach. Nucleic Acids Res 2024; 52:W29-W38. [PMID: 38795068 PMCID: PMC11223865 DOI: 10.1093/nar/gkae419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/23/2024] [Accepted: 05/07/2024] [Indexed: 05/27/2024] Open
Abstract
Gene therapy of dominantly inherited genetic diseases requires either the selective disruption of the mutant allele or the editing of the specific mutation. The CRISPR-Cas system holds great potential for the genetic correction of single nucleotide variants (SNVs), including dominant mutations. However, distinguishing between single-nucleotide variations in a pathogenic genomic context remains challenging. The presence of a PAM in the disease-causing allele can guide its precise targeting, preserving the functionality of the wild-type allele. The AlPaCas (Aligning Patients to Cas) webserver is an automated pipeline for sequence-based identification and structural analysis of SNV-derived PAMs that satisfy this demand. When provided with a gene/SNV input, AlPaCas can: (i) identify SNV-derived PAMs; (ii) provide a list of available Cas enzymes recognizing the SNV (s); (iii) propose mutational Cas-engineering to enhance the selectivity towards the SNV-derived PAM. With its ability to identify allele-specific genetic variants that can be targeted using already available or engineered Cas enzymes, AlPaCas is at the forefront of advancements in genome editing. AlPaCas is open to all users without a login requirement and is freely available at https://schubert.bio.uniroma1.it/alpacas.
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Affiliation(s)
- Serena Rosignoli
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome 00185, Italy
| | - Elisa Lustrino
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome 00185, Italy
| | - Alessio Conci
- Centre for Regenerative Medicine “Stefano Ferrari”, Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Alessandra Fabrizi
- Centre for Regenerative Medicine “Stefano Ferrari”, Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Serena Rinaldo
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome 00185, Italy
| | | | - Elena Enzo
- Centre for Regenerative Medicine “Stefano Ferrari”, Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Gianni Prosseda
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Laura De Rosa
- Centre for Regenerative Medicine “Stefano Ferrari”, Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Michele De Luca
- Centre for Regenerative Medicine “Stefano Ferrari”, Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome 00185, Italy
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5
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Milovanova E, Gomon S, Rocha G. Classic lattice corneal dystrophy: a brief review and summary of treatment modalities. Graefes Arch Clin Exp Ophthalmol 2024; 262:1667-1681. [PMID: 37934291 DOI: 10.1007/s00417-023-06297-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 10/10/2023] [Accepted: 10/26/2023] [Indexed: 11/08/2023] Open
Abstract
PURPOSE To provide a brief summary and comparison of the most recent literature on available and theorized treatment modalities for classic lattice corneal dystrophy (LCD). This paper aims to support practitioners in their management of this disease. METHODS A search was carried out on available literature through PubMed and Google Scholar of English language articles up to January 2023 that relate to the treatment of LCD. Due to scarcity of literature regarding specific novel therapies for LCD, results from other corneal pathologies (granular corneal dystrophy, corneal scarring) are sometimes included for contrast, which is clearly denoted. RESULTS LCD is a slowly progressive disease that leads to recurrent epithelial corneal erosions, stromal haze, corneal opacification, substantial discomfort, and visual impairment. Due to its autosomal-dominant inheritance pattern, this disease can persist throughout ancestral lines and requires consistent treatment and follow-up. An optimal management plan is necessary to (1) prolong years of life with best achievable visual acuity; (2) treat painful recurrent corneal erosions as they occur; (3) ensure proper follow-up throughout the life of a patient, as well as monitor at-risk offspring; and (4) monitor efficacy of treatment. CONCLUSIONS This paper addresses (1) treatment for early disease including corneal epithelial debridement, photo therapeutic keratectomy (PTK), femtosecond laser-assisted lamellar keratectomy (FLK), and others; (2) treatment for late disease including full thickness keratoplasties and anterior lamellar keratoplasties; and (3) potential future treatment considerations including a wide variety of topical/systemic, genetic, and regenerative approaches.
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Affiliation(s)
- Ekaterina Milovanova
- Department of Ophthalmology, University of Manitoba, Winnipeg, Manitoba, Canada.
| | - Stanislav Gomon
- Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Guillermo Rocha
- Department of Ophthalmology & Visual Sciences, McGill University, Montréal, Canada
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6
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Bolduc V, Sizov K, Brull A, Esposito E, Chen GS, Uapinyoying P, Sarathy A, Johnson K, Bönnemann CG. Allele-specific CRISPR/Cas9 editing inactivates a single nucleotide variant associated with collagen VI muscular dystrophy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586265. [PMID: 38585815 PMCID: PMC10996683 DOI: 10.1101/2024.03.22.586265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The application of allele-specific gene editing tools can expand the therapeutic options for dominant genetic conditions, either via gene correction or via allelic gene inactivation in situations where haploinsufficiency is tolerated. Here, we used allele-targeted CRISPR/Cas9 guide RNAs (gRNAs) to introduce inactivating frameshifting indels at a single nucleotide variant in the COL6A1 gene (c.868G>A; G290R), a variant that acts as dominant negative and that is associated with a severe form of congenital muscular dystrophy. We expressed spCas9 along with allele-targeted gRNAs, without providing a repair template, in primary fibroblasts derived from four patients and one control subject. Amplicon deep-sequencing for two gRNAs tested showed that single nucleotide deletions accounted for the majority of indels introduced. While activity of the two gRNAs was greater at the G290R allele, both gRNAs were also active at the wild-type allele. To enhance allele-selectivity, we introduced deliberate additional mismatches to one gRNA. One of these optimized gRNAs showed minimal activity at the WT allele, while generating productive edits and improving collagen VI matrix in cultured patient fibroblasts. This study strengthens the potential of gene editing to treat dominant-negative disorders, but also underscores the challenges in achieving allele selectivity with gRNAs.
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Affiliation(s)
- Véronique Bolduc
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Katherine Sizov
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Astrid Brull
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Eric Esposito
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Grace S Chen
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Prech Uapinyoying
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Center for Genetic Medicine Research, Children's National Research and Innovation Campus, Children's National Hospital, Washington, DC, 20012, USA
| | - Apurva Sarathy
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Kory Johnson
- Bioinformatics Core, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Carsten G Bönnemann
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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7
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Park CS, Habib O, Lee Y, Hur JK. Applications of CRISPR technologies to the development of gene and cell therapy. BMB Rep 2024; 57:2-11. [PMID: 38178651 PMCID: PMC10828430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/14/2023] [Accepted: 12/26/2023] [Indexed: 01/06/2024] Open
Abstract
Advancements in gene and cell therapy have resulted in novel therapeutics for diseases previously considered incurable or challenging to treat. Among the various contributing technologies, genome editing stands out as one of the most crucial for the progress in gene and cell therapy. The discovery of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and the subsequent evolution of genetic engineering technology have markedly expanded the field of target-specific gene editing. Originally studied in the immune systems of bacteria and archaea, the CRISPR system has demonstrated wide applicability to effective genome editing of various biological systems including human cells. The development of CRISPR-based base editing has enabled directional cytosine-tothymine and adenine-to-guanine substitutions of select DNA bases at the target locus. Subsequent advances in prime editing further elevated the flexibility of the edit multiple consecutive bases to desired sequences. The recent CRISPR technologies also have been actively utilized for the development of in vivo and ex vivo gene and cell therapies. We anticipate that the medical applications of CRISPR will rapidly progress to provide unprecedented possibilities to develop novel therapeutics towards various diseases. [BMB Reports 2024; 57(1): 2-11].
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Affiliation(s)
- Chul-Sung Park
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea
| | - Omer Habib
- Division of R&D, RedGene Inc., Seoul 08790, Korea
| | - Younsu Lee
- Division of R&D, RedGene Inc., Seoul 08790, Korea
| | - Junho K. Hur
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea
- Department of Genetics, College of Medicine, Hanyang University, Seoul 04763, Korea
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul 04763, Korea
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8
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Wu J, Tao Y, Deng D, Meng Z, Zhao Y. The applications of CRISPR/Cas-mediated genome editing in genetic hearing loss. Cell Biosci 2023; 13:93. [PMID: 37210555 DOI: 10.1186/s13578-023-01021-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/25/2023] [Indexed: 05/22/2023] Open
Abstract
Hearing loss (HL) can be caused by a number of different genetic factors. Non-syndromic HL refers that HL occurs as an isolated symptom in an individual, whereas syndromic HL refers that HL is associated with other symptoms or abnormalities. To date, more than 140 genes have been identified as being associated with non-syndromic HL, and approximately 400 genetic syndromes can include HL as one of the clinical symptoms. However, no gene therapeutic approaches are currently available to restore or improve hearing. Therefore, there is an urgent necessity to elucidate the possible pathogenesis of specific mutations in HL-associated genes and to investigate the promising therapeutic strategies for genetic HL. The development of the CRISPR/Cas system has revolutionized the field of genome engineering, which has become an efficacious and cost-effective tool to foster genetic HL research. Moreover, several in vivo studies have demonstrated the therapeutic efficacy of the CRISPR/Cas-mediated treatments for specific genetic HL. In this review, we briefly introduce the progress in CRISPR/Cas technique as well as the understanding of genetic HL, and then we detail the recent achievements of CRISPR/Cas technique in disease modeling and therapeutic strategies for genetic HL. Furthermore, we discuss the challenges for the application of CRISPR/Cas technique in future clinical treatments.
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Affiliation(s)
- Junhao Wu
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital of Sichuan University, Chengdu, 610041, China
- Department of Audiology and Speech Language Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Yong Tao
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital of Sichuan University, Chengdu, 610041, China
- Department of Audiology and Speech Language Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Di Deng
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital of Sichuan University, Chengdu, 610041, China
- Department of Audiology and Speech Language Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Zhaoli Meng
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital of Sichuan University, Chengdu, 610041, China.
- Department of Audiology and Speech Language Pathology, West China Hospital of Sichuan University, Chengdu, China.
| | - Yu Zhao
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital of Sichuan University, Chengdu, 610041, China.
- Department of Audiology and Speech Language Pathology, West China Hospital of Sichuan University, Chengdu, China.
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9
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Seo SY, Min S, Lee S, Seo JH, Park J, Kim HK, Song M, Baek D, Cho SR, Kim HH. Massively parallel evaluation and computational prediction of the activities and specificities of 17 small Cas9s. Nat Methods 2023:10.1038/s41592-023-01875-2. [PMID: 37188955 DOI: 10.1038/s41592-023-01875-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 04/10/2023] [Indexed: 05/17/2023]
Abstract
Recently, various small Cas9 orthologs and variants have been reported for use in in vivo delivery applications. Although small Cas9s are particularly suited for this purpose, selecting the most optimal small Cas9 for use at a specific target sequence continues to be challenging. Here, to this end, we have systematically compared the activities of 17 small Cas9s for thousands of target sequences. For each small Cas9, we have characterized the protospacer adjacent motif and determined optimal single guide RNA expression formats and scaffold sequence. High-throughput comparative analyses revealed distinct high- and low-activity groups of small Cas9s. We also developed DeepSmallCas9, a set of computational models predicting the activities of the small Cas9s at matched and mismatched target sequences. Together, this analysis and these computational models provide a useful guide for researchers to select the most suitable small Cas9 for specific applications.
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Affiliation(s)
- Sang-Yeon Seo
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | | | - Sungtae Lee
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung Hwa Seo
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jinman Park
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hui Kwon Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Myungjae Song
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Dawoon Baek
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Rehabilitation Medicine, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Sung-Rae Cho
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Graduate Program of Biomedical Engineering, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyongbum Henry Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea.
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Republic of Korea.
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10
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Nguyen K, Malik TN, Chaput JC. Chemical evolution of an autonomous DNAzyme with allele-specific gene silencing activity. Nat Commun 2023; 14:2413. [PMID: 37105964 PMCID: PMC10140269 DOI: 10.1038/s41467-023-38100-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Low activity has been the primary obstacle impeding the use of DNA enzymes (DNAzymes) as gene silencing agents in clinical applications. Here we describe the chemical evolution of a DNAzyme with strong catalytic activity under near physiological conditions. The enzyme achieves ~65 turnovers in 30 minutes, a feat only previously witnessed by the unmodified parent sequence under forcing conditions of elevated Mg2+ and pH. Structural constraints imposed by the chemical modifications drive catalysis toward a highly preferred UGUD motif (cut site underlined) that was validated by positive and negative predictions. Biochemical assays support an autonomous RNA cleavage mechanism independent of RNase H1 engagement. Consistent with its strong catalytic activity, the enzyme exhibits persistent allele-specific knock-down of an endogenous mRNA encoding an undruggable oncogenic KRAS target. Together, these results demonstrate that chemical evolution offers a powerful approach for discovering new chemotype combinations that can imbue DNAzymes with the physicochemical properties necessary to support therapeutic applications.
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Affiliation(s)
- Kim Nguyen
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697-3958, USA
| | - Turnee N Malik
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697-3958, USA
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697-3958, USA.
- Department of Chemistry, University of California, Irvine, CA, 92697-3958, USA.
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697-3958, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, 92697-3958, USA.
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11
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Wang Y, Qi T, Liu J, Yang Y, Wang Z, Wang Y, Wang T, Li M, Li M, Lu D, Chang ACY, Yang L, Gao S, Wang Y, Lan F. A highly specific CRISPR-Cas12j nuclease enables allele-specific genome editing. SCIENCE ADVANCES 2023; 9:eabo6405. [PMID: 36763662 PMCID: PMC9917002 DOI: 10.1126/sciadv.abo6405] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
The CRISPR-Cas system can treat autosomal dominant diseases by nonhomologous end joining (NHEJ) gene disruption of mutant alleles. However, many single-nucleotide mutations cannot be discriminated from wild-type alleles by current CRISPR-Cas systems. Here, we functionally screened six Cas12j nucleases and determined Cas12j-8 as an ideal genome editor with a hypercompact size. Cas12j-8 displayed comparable activity to AsCas12a and Un1Cas12f1. Cas12j-8 is a highly specific nuclease sensitive to single-nucleotide mismatches in the protospacer adjacent motif (PAM)-proximal region. We experimentally proved that Cas12j-8 enabled allele-specific disruption of genes with a single-nucleotide polymorphism (SNP). Cas12j-8 recognizes a simple TTN PAM that provides for high target site density. In silico analysis reveals that Cas12j-8 enables allele-specific disruption of 25,931 clinically relevant variants in the ClinVar database, and 485,130,147 SNPs in the dbSNP database. Therefore, Cas12j-8 would be particularly suitable for therapeutic applications.
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Affiliation(s)
- Yao Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Tao Qi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Jingtong Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Yuan Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Ziwen Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Ying Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Tianyi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Miaomiao Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Mingqing Li
- Laboratory for Reproductive Immunology, NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Hospital of Obstetrics and Gynecology, Shanghai Medical School, Fudan University, Shanghai 200080, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning, Science and Technology Research Institute, Chongqing 400020, China
| | - Alex Chia Yu Chang
- Department of Cardiology and Shanghai Institute Precision Medicine, Ninth People’s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200125, China
| | - Li Yang
- Center for Molecular Medicine, Children’s Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yongming Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
| | - Feng Lan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
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12
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Tomihara K, Andolfatto P, Kiuchi T. Allele-specific knockouts reveal a role for apontic-like in the evolutionary loss of larval melanin pigmentation in the domesticated silkworm, Bombyx mori. INSECT MOLECULAR BIOLOGY 2022; 31:701-710. [PMID: 35752945 PMCID: PMC9633403 DOI: 10.1111/imb.12797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 06/22/2022] [Indexed: 05/25/2023]
Abstract
The domesticated silkworm, Bombyx mori, and its wild progenitor, B. mandarina, are extensively studied as a model case of the evolutionary process of domestication. A conspicuous difference between these species is the dramatic reduction in melanin pigmentation in both larval and adult B. mori. Here we evaluate the efficiency of CRISPR/Cas9-targeted knockouts of pigment-related genes as a tool to understand their potential contributions to domestication-associated melanin pigmentation loss in B. mori. To demonstrate the efficacy of targeted knockouts in B. mandarina, we generated a homozygous CRISPR/Cas9-targeted knockout of yellow-y. In yellow-y knockout mutants, black body colour became lighter throughout the larval, pupal and adult stages, confirming a role for this gene in melanin pigment formation. Further, we performed allele-specific CRISPR/Cas9-targeted knockouts of the pigment-related transcription factor, apontic-like (apt-like) in B. mori × B. mandarina F1 hybrid individuals which exhibit B. mandarina-like larval pigmentation. Knockout of the B. mandarina allele of apt-like in F1 embryos results in white patches on the dorsal integument of larvae, whereas corresponding knockouts of the B. mori allele consistently exhibit normal F1 larval pigmentation. These results demonstrate a contribution of apt-like to the evolution of reduced melanin pigmentation in B. mori. Together, our results demonstrate the feasibility of CRISPR/Cas9-targeted knockouts as a tool for understanding the genetic basis of traits associated with B. mori domestication.
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Affiliation(s)
- Kenta Tomihara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY 10026, USA
| | - Takashi Kiuchi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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13
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Weiss JS, Willoughby CE, Abad-Morales V, Turunen JA, Lisch W. Update on the Corneal Dystrophies-Genetic Testing and Therapy. Cornea 2022; 41:1337-1344. [PMID: 36219210 DOI: 10.1097/ico.0000000000002857] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/07/2021] [Indexed: 11/26/2022]
Abstract
ABSTRACT One major purpose of the IC3D Corneal Dystrophy Nomenclature Revision was to include genetic information with a goal of facilitating investigation into the pathogenesis, treatment, and perhaps even prevention of the corneal dystrophies, an ambitious goal. Over a decade has passed since the first publication of the IC3D Corneal Dystrophy Nomenclature Revision. Gene therapy is available for an early-onset form of inherited retinal degeneration called Leber congenital amaurosis, but not yet for corneal degenerations. We review the current state of affairs regarding our original ambitious goal. We discuss genetic testing, gene therapy [RNA interference (RNAi) and genome editing], and ocular delivery of corneal gene therapy for the corneal dystrophies. Why have gene therapy techniques not yet been introduced for the corneal dystrophies?
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Affiliation(s)
- Jayne S Weiss
- Department of Ophthalmology, Pathology and Pharmacology, Louisiana State University School of Medicine, New Orleans, LA
| | - Colin E Willoughby
- Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Víctor Abad-Morales
- Fundació de Recerca de l'Institut de Microcirurgia Ocular, Barcelona, Spain
- Department of Genetics, Institut de Microcirurgia Ocular (IMO), Barcelona, Spain; Dr. Abad-Morales is now with the SpliceBio, Barcelona, Spain, Barcelona, Spain
| | - Joni A Turunen
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland; and
| | - Walter Lisch
- Department of Ophthalmology, University Medical Center of the Johannes Gutenberg, University Mainz, Mainz, Germany
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14
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Li R, Wang Q, She K, Lu F, Yang Y. CRISPR/Cas systems usher in a new era of disease treatment and diagnosis. MOLECULAR BIOMEDICINE 2022; 3:31. [PMID: 36239875 PMCID: PMC9560888 DOI: 10.1186/s43556-022-00095-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/27/2022] [Indexed: 11/21/2022] Open
Abstract
The discovery and development of the CRISPR/Cas system is a milestone in precise medicine. CRISPR/Cas nucleases, base-editing (BE) and prime-editing (PE) are three genome editing technologies derived from CRISPR/Cas. In recent years, CRISPR-based genome editing technologies have created immense therapeutic potential with safe and efficient viral or non-viral delivery systems. Significant progress has been made in applying genome editing strategies to modify T cells and hematopoietic stem cells (HSCs) ex vivo and to treat a wide variety of diseases and disorders in vivo. Nevertheless, the clinical translation of this unique technology still faces many challenges, especially targeting, safety and delivery issues, which require further improvement and optimization. In addition, with the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), CRISPR-based molecular diagnosis has attracted extensive attention. Growing from the specific set of molecular biological discoveries to several active clinical trials, CRISPR/Cas systems offer the opportunity to create a cost-effective, portable and point-of-care diagnosis through nucleic acid screening of diseases. In this review, we describe the development, mechanisms and delivery systems of CRISPR-based genome editing and focus on clinical and preclinical studies of therapeutic CRISPR genome editing in disease treatment as well as its application prospects in therapeutics and molecular detection.
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Affiliation(s)
- Ruiting Li
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Ke-yuan Road 4, No. 1, Gao-peng Street, Chengdu, 610041 Sichuan China
| | - Qin Wang
- grid.412723.10000 0004 0604 889XSchool of Pharmacy, Southwest Minzu University, Chengdu, 610225 Sichuan China
| | - Kaiqin She
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Ke-yuan Road 4, No. 1, Gao-peng Street, Chengdu, 610041 Sichuan China ,grid.412901.f0000 0004 1770 1022Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Fang Lu
- grid.412901.f0000 0004 1770 1022Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yang Yang
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Ke-yuan Road 4, No. 1, Gao-peng Street, Chengdu, 610041 Sichuan China ,grid.412901.f0000 0004 1770 1022Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan China
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15
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Mirjalili Mohanna SZ, Djaksigulova D, Hill AM, Wagner PK, Simpson EM, Leavitt BR. LNP-mediated delivery of CRISPR RNP for wide-spread in vivo genome editing in mouse cornea. J Control Release 2022; 350:401-413. [PMID: 36029893 DOI: 10.1016/j.jconrel.2022.08.042] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 01/02/2023]
Abstract
CRISPR/Cas9-based genome-editing therapies are poised to change the clinical outcome for many diseases with validated therapeutic targets awaiting an appropriate delivery system. Recent advances in lipid nanoparticle (LNP) technology make them an attractive platform for the delivery of various forms of CRISPR/Cas9, including the efficient and transient Cas9/gRNA ribonucleoprotein (RNP) complexes. In this study, we initially tested our novel LNP platform by delivering pre-complexed RNPs and template DNA to cultured mouse cortical neurons, and obtained successful ex vivo genome editing. We then directly injected LNP-packaged RNPs and DNA template into the mouse cornea to evaluate in vivo delivery. For the first time, we demonstrated wide-spread genome editing in the cornea using our LNP-RNPs. The ability of our LNPs to transfect the cornea highlights the potential of our novel delivery platform to be used in CRISPR/Cas9-based genome editing therapies of corneal diseases.
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Affiliation(s)
- Seyedeh Zeinab Mirjalili Mohanna
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC, Canada; Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Diana Djaksigulova
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC, Canada
| | | | | | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC, Canada; Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada.
| | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC, Canada; Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada; Incisive Genetics Inc., Vancouver, BC, Canada
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16
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Bchetnia M, Dionne Gagné R, Powell J, Morin C, McCuaig C, Dupérée A, Germain L, Tremblay JP, Laprise C. Allele-Specific Inactivation of an Autosomal Dominant Epidermolysis Bullosa Simplex Mutation Using CRISPR-Cas9. CRISPR J 2022; 5:586-597. [PMID: 35862015 DOI: 10.1089/crispr.2021.0132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Epidermolysis bullosa simplex (EBS) is a rare mechanobullous disease caused by dominant-negative mutations in either keratin 5 (KRT5) or keratin 14 (KRT14) genes. Until now, there is no cure for EBS and the care is primarily palliative. The discovery of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 system raised hope for the treatment of EBS and many other autosomal dominant diseases by mutant allele-specific gene disruption. In this study, we aim to disrupt the mutant allele for the heterozygous EBS pathogenic variation c.449T>C (p.Leu150Pro) within KRT5. This mutation generates, naturally, a novel protospacer-adjacent motif for the endonuclease Streptococcus pyogenes Cas9. Thus, we designed a single-guide RNA that guides the Cas9 to introduce a DNA cleavage of the mutant allele in patient's keratinocytes. Then, transfected cells were single-cell cloned and analyzed by deep sequencing. The expression of KRT5 and KRT14 was quantified, and the keratin intermediate filament stability was assessed. Results showed successful stringent mutant allele-specific knockout. An absence of synthesis of mutant transcript was further confirmed indicating permanent mutant allele-specific inactivation. Edited EBS patient keratinocytes produced a lower amount of K5 and K14 proteins compared with nonedited EBS cells, and no disturbance of cellular properties was observed.
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Affiliation(s)
- Mbarka Bchetnia
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi (UQAC), Saguenay, Canada.,Centre intersectoriel en santé durable (CISD), Université du Québec à Chicoutimi (UQAC), Saguenay, Canada
| | - Rebecca Dionne Gagné
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi (UQAC), Saguenay, Canada
| | - Julie Powell
- Service de Dermatologie, CHU Sainte-Justine, Montréal, Canada
| | - Charles Morin
- Centre Intégré Universitaire de Santé et de Services Sociaux du Saguenay-Lac-Saint-Jean, Hôpital Universitaire de Chicoutimi, Saguenay, Canada
| | | | - Audrey Dupérée
- Centre Intégré Universitaire de Santé et de Services Sociaux du Saguenay-Lac-Saint-Jean, Hôpital Universitaire de Chicoutimi, Saguenay, Canada
| | - Lucie Germain
- Département de chirurgie, Faculté de médecine, Centre de Recherche en Organogénèse Expérimentale de l'Université Laval/LOEX, Université Laval, Québec, Canada.,Centre de recherche du CHU de Québec, Université Laval, Québec, Canada
| | | | - Catherine Laprise
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi (UQAC), Saguenay, Canada.,Centre intersectoriel en santé durable (CISD), Université du Québec à Chicoutimi (UQAC), Saguenay, Canada
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17
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Salman M, Verma A, Singh VK, Jaffet J, Chaurasia S, Sahel DK, Ramappa M, Singh V. New Frontier in the Management of Corneal Dystrophies: Basics, Development, and Challenges in Corneal Gene Therapy and Gene Editing. Asia Pac J Ophthalmol (Phila) 2022; 11:346-359. [PMID: 36041149 DOI: 10.1097/apo.0000000000000443] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/26/2021] [Indexed: 12/13/2022] Open
Abstract
ABSTRACT Corneal dystrophies represent a group of heterogeneous hereditary disorders causing progressive corneal opacification and blindness. Current corneal transplant management for corneal dystrophies faces the challenges of repeated treatments, complex surgical procedures, shortage of appropriate donor cornea, and, more importantly, graft rejection. Genetic medicine could be an alternative treatment regime to overcome such challenges. Cornea carries promising scope for a gene-based therapy involving gene supplementation, gene silencing, and gene editing in both ex vivo and in vivo platforms. In the cornea, ex vivo gene therapeutic strategies were attempted for corneal graft survival, and in vivo gene augmentation therapies aimed to prevent herpes stromal keratitis, neovascularization, corneal clouding, and wound healing. However, none of these studies followed a clinical trial-based successful outcome. CRISPR/Cas system offers a broad scope of gene editing and engineering to correct underlying genetic causes in corneal dystrophies. Corneal tissue--specific gene correction in vitro with minimal off-target effects and optimal gene correction efficiency followed by their successful surgical implantation, or in vivo CRISPR administration targeting pathogenic genes finds a way to explore therapeutic intervention for corneal dystrophies. However, there are many limitations associated with such CRISPR-based corneal treatment management. This review will look into the development of corneal gene therapy and CRISPR-based study in corneal dystrophies, associated challenges, potential approaches, and future directions.
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Affiliation(s)
- Mohd Salman
- Prof. Brien Holden Eye Research Center, Champalimaud Translational Centre for Eye Research L.V. Prasad Eye Institute, Hyderabad, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Anshuman Verma
- Prof. Brien Holden Eye Research Center, Champalimaud Translational Centre for Eye Research L.V. Prasad Eye Institute, Hyderabad, India
- MNR Foundation for Research and Innovations, MNR Medical College, MNR Nagar, Sangareddy, Telangana, India
| | - Vijay Kumar Singh
- Prof. Brien Holden Eye Research Center, Champalimaud Translational Centre for Eye Research L.V. Prasad Eye Institute, Hyderabad, India
| | - Jilu Jaffet
- Prof. Brien Holden Eye Research Center, Champalimaud Translational Centre for Eye Research L.V. Prasad Eye Institute, Hyderabad, India
| | - Sunita Chaurasia
- The Centre of Excellence for Rare Eye Diseases, L. V. Prasad Eye Institute, Hyderabad, India
| | - Deepak Kumar Sahel
- Department of Pharmacy, Birla Institute of Technology and Science - Pilani Campus. Vidya Vihar, Pilani, Rajasthan, India and
| | - Muralidhar Ramappa
- Cornea and Anterior Segment Services, L.V. Prasad Eye Institute, Kallam Anji Reddy Campus, L.V. Prasad Marg, Hyderabad, Telangana, India
| | - Vivek Singh
- Prof. Brien Holden Eye Research Center, Champalimaud Translational Centre for Eye Research L.V. Prasad Eye Institute, Hyderabad, India
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18
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Guide RNAs containing universal bases enable Cas9/Cas12a recognition of polymorphic sequences. Nat Commun 2022; 13:1617. [PMID: 35338140 PMCID: PMC8956631 DOI: 10.1038/s41467-022-29202-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 03/03/2022] [Indexed: 12/15/2022] Open
Abstract
CRISPR/Cas complexes enable precise gene editing in a wide variety of organisms. While the rigid identification of DNA sequences by these systems minimizes the potential for off-target effects, it consequently poses a problem for the recognition of sequences containing naturally occurring polymorphisms. The presence of genetic variance such as single nucleotide polymorphisms (SNPs) in a gene sequence can compromise the on-target activity of CRISPR systems. Thus, when attempting to target multiple variants of a human gene, or evolved variants of a pathogen gene using a single guide RNA, more flexibility is desirable. Here, we demonstrate that Cas9 can tolerate the inclusion of universal bases in individual guide RNAs, enabling simultaneous targeting of polymorphic sequences. Crucially, we find that specificity is selectively degenerate at the site of universal base incorporation, and remains otherwise preserved. We demonstrate the applicability of this technology to targeting multiple naturally occurring human SNPs with individual guide RNAs and to the design of Cas12a/Cpf1-based DETECTR probes capable of identifying multiple evolved variants of the HIV protease gene. Our findings extend the targeting capabilities of CRISPR/Cas systems beyond their canonical spacer sequences and highlight a use of natural and synthetic universal bases.
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19
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Fu R, He W, Dou J, Villarreal OD, Bedford E, Wang H, Hou C, Zhang L, Wang Y, Ma D, Chen Y, Gao X, Depken M, Xu H. Systematic decomposition of sequence determinants governing CRISPR/Cas9 specificity. Nat Commun 2022; 13:474. [PMID: 35078987 PMCID: PMC8789861 DOI: 10.1038/s41467-022-28028-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 01/04/2022] [Indexed: 12/20/2022] Open
Abstract
The specificity of CRISPR/Cas9 genome editing is largely determined by the sequences of guide RNA (gRNA) and the targeted DNA, yet the sequence-dependent rules underlying off-target effects are not fully understood. To systematically explore the sequence determinants governing CRISPR/Cas9 specificity, here we describe a dual-target system to measure the relative cleavage rate between off- and on-target sequences (off-on ratios) of 1902 gRNAs on 13,314 synthetic target sequences, and reveal a set of sequence rules involving 2 factors in off-targeting: 1) a guide-intrinsic mismatch tolerance (GMT) independent of the mismatch context; 2) an "epistasis-like" combinatorial effect of multiple mismatches, which are associated with the free-energy landscape in R-loop formation and are explainable by a multi-state kinetic model. These sequence rules lead to the development of MOFF, a model-based predictor of Cas9-mediated off-target effects. Moreover, the "epistasis-like" combinatorial effect suggests a strategy of allele-specific genome editing using mismatched guides. With the aid of MOFF prediction, this strategy significantly improves the selectivity and expands the application domain of Cas9-based allele-specific editing, as tested in a high-throughput allele-editing screen on 18 cancer hotspot mutations.
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Affiliation(s)
- Rongjie Fu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Wei He
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Jinzhuang Dou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Oscar D Villarreal
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Ella Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Helen Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Connie Hou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Liang Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Yalong Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Dacheng Ma
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, USA
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, USA
- Department of Chemistry, Rice University, Houston, TX, 77005, USA
- Department of Bioengineering, Rice University, Houston, TX, 77005, USA
| | - Martin Depken
- Kavli Institute of NanoScience and Department of BionanoScience, Delft University of Technology, Delft, 2629HZ, the Netherlands
| | - Han Xu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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20
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Szarka G, Balogh M, Tengölics ÁJ, Ganczer A, Völgyi B, Kovács-Öller T. The role of gap junctions in cell death and neuromodulation in the retina. Neural Regen Res 2021; 16:1911-1920. [PMID: 33642359 PMCID: PMC8343308 DOI: 10.4103/1673-5374.308069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/14/2020] [Accepted: 01/11/2021] [Indexed: 12/26/2022] Open
Abstract
Vision altering diseases, such as glaucoma, diabetic retinopathy, age-related macular degeneration, myopia, retinal vascular disease, traumatic brain injuries and others cripple many lives and are projected to continue to cause anguish in the foreseeable future. Gap junctions serve as an emerging target for neuromodulation and possible regeneration as they directly connect healthy and/or diseased cells, thereby playing a crucial role in pathophysiology. Since they are permeable for macromolecules, able to cross the cellular barriers, they show duality in illness as a cause and as a therapeutic target. In this review, we take recent advancements in gap junction neuromodulation (pharmacological blockade, gene therapy, electrical and light stimulation) into account, to show the gap junction's role in neuronal cell death and the possible routes of rescuing neuronal and glial cells in the retina succeeding illness or injury.
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Affiliation(s)
- Gergely Szarka
- János Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Retinal Electrical Synapses Research Group, National Brain Research Program (NAP 2.0), Hungarian Academy of Sciences, Budapest, Hungary
- Department of Experimental Zoology and Neurobiology, University of Pécs, Pécs, Hungary
| | - Márton Balogh
- János Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Retinal Electrical Synapses Research Group, National Brain Research Program (NAP 2.0), Hungarian Academy of Sciences, Budapest, Hungary
- Department of Experimental Zoology and Neurobiology, University of Pécs, Pécs, Hungary
| | - Ádám J. Tengölics
- János Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Retinal Electrical Synapses Research Group, National Brain Research Program (NAP 2.0), Hungarian Academy of Sciences, Budapest, Hungary
- Department of Experimental Zoology and Neurobiology, University of Pécs, Pécs, Hungary
| | - Alma Ganczer
- János Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Retinal Electrical Synapses Research Group, National Brain Research Program (NAP 2.0), Hungarian Academy of Sciences, Budapest, Hungary
- Department of Experimental Zoology and Neurobiology, University of Pécs, Pécs, Hungary
| | - Béla Völgyi
- János Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Retinal Electrical Synapses Research Group, National Brain Research Program (NAP 2.0), Hungarian Academy of Sciences, Budapest, Hungary
- Department of Experimental Zoology and Neurobiology, University of Pécs, Pécs, Hungary
- Medical School, University of Pécs, Pécs, Hungary
| | - Tamás Kovács-Öller
- János Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Retinal Electrical Synapses Research Group, National Brain Research Program (NAP 2.0), Hungarian Academy of Sciences, Budapest, Hungary
- Medical School, University of Pécs, Pécs, Hungary
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21
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Donohoue PD, Pacesa M, Lau E, Vidal B, Irby MJ, Nyer DB, Rotstein T, Banh L, Toh MS, Gibson J, Kohrs B, Baek K, Owen ALG, Slorach EM, van Overbeek M, Fuller CK, May AP, Jinek M, Cameron P. Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells. Mol Cell 2021; 81:3637-3649.e5. [PMID: 34478654 DOI: 10.1016/j.molcel.2021.07.035] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/28/2021] [Accepted: 07/28/2021] [Indexed: 12/26/2022]
Abstract
The off-target activity of the CRISPR-associated nuclease Cas9 is a potential concern for therapeutic genome editing applications. Although high-fidelity Cas9 variants have been engineered, they exhibit varying efficiencies and have residual off-target effects, limiting their applicability. Here, we show that CRISPR hybrid RNA-DNA (chRDNA) guides provide an effective approach to increase Cas9 specificity while preserving on-target editing activity. Across multiple genomic targets in primary human T cells, we show that 2'-deoxynucleotide (dnt) positioning affects guide activity and specificity in a target-dependent manner and that this can be used to engineer chRDNA guides with substantially reduced off-target effects. Crystal structures of DNA-bound Cas9-chRDNA complexes reveal distorted guide-target duplex geometry and allosteric modulation of Cas9 conformation. These structural effects increase specificity by perturbing DNA hybridization and modulating Cas9 activation kinetics to disfavor binding and cleavage of off-target substrates. Overall, these results pave the way for utilizing customized chRDNAs in clinical applications.
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Affiliation(s)
- Paul D Donohoue
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA.
| | - Martin Pacesa
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Elaine Lau
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Bastien Vidal
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Matthew J Irby
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - David B Nyer
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Tomer Rotstein
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Lynda Banh
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Mckenzi S Toh
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Jason Gibson
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Bryan Kohrs
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Kevin Baek
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Arthur L G Owen
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Euan M Slorach
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Megan van Overbeek
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Christopher K Fuller
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Andrew P May
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA.
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| | - Peter Cameron
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA.
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22
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Nowińska A, Chlasta-Twardzik E, Dembski M, Wróblewska-Czajka E, Ulfik-Dembska K, Wylęgała E. Detailed corneal and genetic characteristics of a pediatric patient with macular corneal dystrophy - case report. BMC Ophthalmol 2021; 21:285. [PMID: 34301210 PMCID: PMC8299585 DOI: 10.1186/s12886-021-02041-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/07/2021] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Corneal dystrophies are a group of rare, inherited disorders that are usually bilateral, symmetric, slowly progressive, and not related to environmental or systemic factors. The majority of publications present the advanced form of the disease with a typical clinical demonstration. The initial signs and symptoms of different epithelial and stromal corneal dystrophies are not specific; therefore, it is very important to establish the early characteristic corneal features of these disorders that could guide the diagnostic process. CASE PRESENTATION The main purpose of this study was to report the differential diagnosis of a pediatric patient with bilateral anterior corneal involvement suspected of corneal dystrophy. An 8-year-old male patient presented with asymptomatic, persistent, superficial, bilateral, diffuse, anterior corneal opacities. Slit lamp examination results were not specific. Despite the lack of visible stromal involvement on the slit lamp examination, corneal analysis based on confocal microscopy and optical coherence tomography revealed characteristic features of macular corneal dystrophy (MCD). The diagnosis of MCD was confirmed by CHST6 gene sequencing. The early corneal characteristic features of MCD, established based on the findings of this case report, include corneal astigmatism (not specific), diffuse corneal thinning without a pattern of corneal ectasia (specific), and characteristic features on confocal microscopy (specific), including multiple, dark, oriented striae at different corneal depths. CONCLUSIONS The clinical examination should be complemented with corneal imaging techniques, such as confocal microscopy and optical coherence tomography. In patients suspected of corneal dystrophy, genetic testing plays an important role in establishing the final diagnosis.
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Affiliation(s)
- Anna Nowińska
- Chair and Clinical Department of Ophthalmology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, ul. Panewnicka 65, 40-760, Katowice, Poland.
- Ophthalmology Department, Railway Hospital in Katowice, Katowice, Poland.
| | - Edyta Chlasta-Twardzik
- Chair and Clinical Department of Ophthalmology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, ul. Panewnicka 65, 40-760, Katowice, Poland
- Ophthalmology Department, Railway Hospital in Katowice, Katowice, Poland
| | - Michał Dembski
- Chair and Clinical Department of Ophthalmology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, ul. Panewnicka 65, 40-760, Katowice, Poland
- Ophthalmology Department, Railway Hospital in Katowice, Katowice, Poland
| | - Ewa Wróblewska-Czajka
- Chair and Clinical Department of Ophthalmology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, ul. Panewnicka 65, 40-760, Katowice, Poland
- Ophthalmology Department, Railway Hospital in Katowice, Katowice, Poland
| | - Klaudia Ulfik-Dembska
- Chair and Clinical Department of Ophthalmology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, ul. Panewnicka 65, 40-760, Katowice, Poland
- Ophthalmology Department, Railway Hospital in Katowice, Katowice, Poland
| | - Edward Wylęgała
- Chair and Clinical Department of Ophthalmology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, ul. Panewnicka 65, 40-760, Katowice, Poland
- Ophthalmology Department, Railway Hospital in Katowice, Katowice, Poland
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23
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Carpenter JC, Lignani G. Gene Editing and Modulation: the Holy Grail for the Genetic Epilepsies? Neurotherapeutics 2021; 18:1515-1523. [PMID: 34235638 PMCID: PMC8608979 DOI: 10.1007/s13311-021-01081-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2021] [Indexed: 02/04/2023] Open
Abstract
Epilepsy is a complex neurological disorder for which there are a large number of monogenic subtypes. Monogenic epilepsies are often severe and disabling, featuring drug-resistant seizures and significant developmental comorbidities. These disorders are potentially amenable to a precision medicine approach, of which genome editing using CRISPR/Cas represents the holy grail. Here we consider mutations in some of the most 'common' rare epilepsy genes and discuss the different CRISPR/Cas approaches that could be taken to cure these disorders. We consider scenarios where CRISPR-mediated gene modulation could serve as an effective therapeutic strategy and discuss whether a single gene corrective approach could hold therapeutic potential in the context of homeostatic compensation in the developing, highly dynamic brain. Despite an incomplete understanding of the mechanisms of the genetic epilepsies and current limitations of gene editing tools, CRISPR-mediated approaches have game-changing potential in the treatment of genetic epilepsy over the next decade.
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Affiliation(s)
- Jenna C Carpenter
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, Queen Square House, London, WC1N 3BG, UK
| | - Gabriele Lignani
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, Queen Square House, London, WC1N 3BG, UK.
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24
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Amador C, Shah R, Ghiam S, Kramerov AA, Ljubimov AV. Gene therapy in the anterior eye segment. Curr Gene Ther 2021; 22:104-131. [PMID: 33902406 DOI: 10.2174/1566523221666210423084233] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/14/2021] [Accepted: 04/04/2021] [Indexed: 11/22/2022]
Abstract
This review provides comprehensive information about the advances in gene therapy in the anterior segment of the eye including cornea, conjunctiva, lacrimal gland, and trabecular meshwork. We discuss gene delivery systems including viral and non-viral vectors as well as gene editing techniques, mainly CRISPR-Cas9, and epigenetic treatments including antisense and siRNA therapeutics. We also provide a detailed analysis of various anterior segment diseases where gene therapy has been tested with corresponding outcomes. Disease conditions include corneal and conjunctival fibrosis and scarring, corneal epithelial wound healing, corneal graft survival, corneal neovascularization, genetic corneal dystrophies, herpetic keratitis, glaucoma, dry eye disease, and other ocular surface diseases. Although most of the analyzed results on the use and validity of gene therapy at the ocular surface have been obtained in vitro or using animal models, we also discuss the available human studies. Gene therapy approaches are currently considered very promising as emerging future treatments of various diseases, and this field is rapidly expanding.
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Affiliation(s)
- Cynthia Amador
- Eye Program, Board of Governors Regenerative Medicine Institute and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Ruchi Shah
- Eye Program, Board of Governors Regenerative Medicine Institute and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Sean Ghiam
- Sackler School of Medicine, New York State/American Program of Tel Aviv University, Tel Aviv, Israel
| | - Andrei A Kramerov
- Eye Program, Board of Governors Regenerative Medicine Institute and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Alexander V Ljubimov
- Eye Program, Board of Governors Regenerative Medicine Institute and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States
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25
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Nguyen K, Wang Y, England WE, Chaput JC, Spitale RC. Allele-Specific RNA Knockdown with a Biologically Stable and Catalytically Efficient XNAzyme. J Am Chem Soc 2021; 143:4519-4523. [PMID: 33750115 DOI: 10.1021/jacs.0c11353] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Therapeutic targeting of allele-specific single nucleotide mutations in RNA is a major challenge in biology and medicine. Herein, we describe the utility of the XNAzyme X10-23 to knock down allele-specific mRNA sequences in cells. We demonstrate the value of this approach by targeting the "undruggable" mutation G12V in oncogenic KRAS. Our results demonstrate how catalytic XNAs could be employed to suppress the expression of mRNAs carrying disease-causing mutations that are difficult to target at the protein level with small molecule therapeutics.
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26
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Compound heterozygous mutations in TGFBI cause a severe phenotype of granular corneal dystrophy type 2. Sci Rep 2021; 11:6986. [PMID: 33772078 PMCID: PMC7997986 DOI: 10.1038/s41598-021-86414-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/10/2021] [Indexed: 12/28/2022] Open
Abstract
We investigated the clinical and genetic features of patients with severe phenotype of granular corneal dystrophy type 2 (GCD2) associated with compound heterozygosity in the transforming growth factor-β-induced (TGFBI) gene. Patients with severe GCD2 underwent ophthalmic examination (best-corrected visual acuity test, intraocular pressure measurement, slit-lamp examination, and slit-lamp photograph analysis) and direct Sanger sequencing of whole-TGFBI. The patient’s family was tested to determine the pedigrees. Five novel mutations (p.(His174Asp), p.(Ile247Asn), p.(Tyr88Cys), p.(Arg257Pro), and p.(Tyr468*)) and two known mutations (p.(Asn544Ser) and p.(Arg179*)) in TGFBI were identified, along with p.(Arg124His), in the patients. Trans-phase of TGFBI second mutations was confirmed by pedigree analysis. Multiple, extensive discoid granular, and increased linear deposits were observed in the probands carrying p.(Arg124His) and other nonsense mutations. Some patients who had undergone phototherapeutic keratectomy experienced rapid recurrence (p.(Ile247Asn) and p.(Asn544Ser)); however, the cornea was well-maintained in a patient who underwent deep anterior lamellar keratoplasty (p.(Ile247Asn)). Thus, compound heterozygosity of TGFBI is associated with the phenotypic variability of TGFBI corneal dystrophies, suggesting that identifying TGFBI second mutations may be vital in patients with extraordinarily severe phenotypes. Our findings indicate the necessity for a more precise observation of genotype–phenotype correlation and additional care when treating TGFBI corneal dystrophies.
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27
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Wang Y, Nguyen K, Spitale RC, Chaput JC. A biologically stable DNAzyme that efficiently silences gene expression in cells. Nat Chem 2021; 13:319-326. [DOI: 10.1038/s41557-021-00645-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/26/2021] [Indexed: 11/09/2022]
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28
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Rabinowitz R, Offen D. Single-Base Resolution: Increasing the Specificity of the CRISPR-Cas System in Gene Editing. Mol Ther 2021; 29:937-948. [PMID: 33248248 PMCID: PMC7938333 DOI: 10.1016/j.ymthe.2020.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 12/26/2022] Open
Abstract
The CRISPR-Cas system holds great promise in the treatment of diseases caused by genetic variations. The Cas protein, an RNA-guided programmable nuclease, generates a double-strand break at precise genomic loci. However, the use of the clustered regularly interspersed short palindromic repeats (CRISPR)-Cas system to distinguish between single-nucleotide variations is challenging. The promiscuity of the guide RNA (gRNA) and its mismatch tolerance make allele-specific targeting an elusive goal. This review presents a meta-analysis of previous studies reporting position-dependent mismatch tolerance within the gRNA. We also examine the conservativity of the seed sequence, a region within the gRNA with stringent sequence dependency, and propose the existence of a subregion within the seed sequence with a higher degree of specificity. In addition, we summarize the reports on high-fidelity Cas nucleases with improved specificity and compare the standard gRNA design methodology to the single-nucleotide polymorphism (SNP)-derived protospacer adjacent motif (PAM) approach, an alternative method for allele-specific targeting. The combination of the two methods may be advantageous in designing CRISPR-based therapeutics and diagnostics for heterozygous patients.
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Affiliation(s)
- Roy Rabinowitz
- Department of Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Felsenstein Medical Research Center, Tel Aviv University, Tel Aviv, Israel.
| | - Daniel Offen
- Department of Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Felsenstein Medical Research Center, Tel Aviv University, Tel Aviv, Israel.
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29
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Goldberg GW, Spencer JM, Giganti DO, Camellato BR, Agmon N, Ichikawa DM, Boeke JD, Noyes MB. Engineered dual selection for directed evolution of SpCas9 PAM specificity. Nat Commun 2021; 12:349. [PMID: 33441553 PMCID: PMC7807044 DOI: 10.1038/s41467-020-20650-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/18/2020] [Indexed: 12/26/2022] Open
Abstract
The widely used Streptococcus pyogenes Cas9 (SpCas9) nuclease derives its DNA targeting specificity from protein-DNA contacts with protospacer adjacent motif (PAM) sequences, in addition to base-pairing interactions between its guide RNA and target DNA. Previous reports have established that the PAM specificity of SpCas9 can be altered via positive selection procedures for directed evolution or other protein engineering strategies. Here we exploit in vivo directed evolution systems that incorporate simultaneous positive and negative selection to evolve SpCas9 variants with commensurate or improved activity on NAG PAMs relative to wild type and reduced activity on NGG PAMs, particularly YGG PAMs. We also show that the PAM preferences of available evolutionary intermediates effectively determine whether similar counterselection PAMs elicit different selection stringencies, and demonstrate that negative selection can be specifically increased in a yeast selection system through the fusion of compensatory zinc fingers to SpCas9.
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Affiliation(s)
- Gregory W Goldberg
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA.
| | - Jeffrey M Spencer
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
| | - David O Giganti
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
| | - Brendan R Camellato
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
| | - Neta Agmon
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
- Neochromosome, Inc., Alexandria Center for Life Science, New York, NY, 10016, USA
| | - David M Ichikawa
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, 11201, USA
| | - Marcus B Noyes
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA.
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30
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Ocular delivery of CRISPR/Cas genome editing components for treatment of eye diseases. Adv Drug Deliv Rev 2021; 168:181-195. [PMID: 32603815 DOI: 10.1016/j.addr.2020.06.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 06/02/2020] [Accepted: 06/12/2020] [Indexed: 12/26/2022]
Abstract
A variety of inherited or multifactorial ocular diseases call for novel treatment paradigms. The newly developed genome editing technology, CRISPR, has shown great promise in treating these diseases, but delivery of the CRISPR/Cas components to target ocular tissues and cells requires appropriate use of vectors and routes of administration to ensure safety, efficacy and specificity. Although adeno-associated viral (AAV) vectors are thus far the most commonly used tool for ocular gene delivery, sustained expression of CRISPR/Cas components may cause immune reactions and an increased risk of off-target editing. In this review, we summarize the ocular administration routes and discuss the advantages and disadvantages of viral and non-viral vectors for delivery of CRISPR/Cas components to the eye. We review the existing studies of CRISPR/Cas genome editing for ocular diseases and discuss the major challenges of the technology in ocular applications. We also discuss the most recently developed CRISPR tools such as base editing and prime editing which may be used for future ocular applications.
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31
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Zhao G, Li J, Tang Y. AsCRISPR: A Web Server for Allele-Specific Single Guide RNA Design in Precision Medicine. CRISPR J 2020; 3:512-522. [PMID: 33346704 DOI: 10.1089/crispr.2020.0071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Allele-specific genomic targeting by CRISPR is a versatile strategy that has been increasingly exploited not only in treating inherited dominant diseases and mutation-driven cancers, but also in other important fields such as genome imprinting, haploinsufficiency, and genome loci imaging. Despite its tremendous utilities, few bioinformatic tools have been implemented for the allele-specific purpose of CRISPR. We thus developed AsCRISPR (Allele-specific CRISPR), a comprehensive web tool to aid the design of short-guide RNA (sgRNA) sequences that can discriminate between alleles. AsCRISPR allows users to analyze both their own identified variants and heterozygous single nucleotide polymorphisms and, importantly, output the candidate sgRNAs and their quality control information. To facilitate targeting dominant diseases, AsCRISPR analyzed dominant single nucleotide variants (SNVs) retrieved from ClinVar and OMIM databases, and generated a dominant database of candidate-discriminating sgRNAs that may specifically target the alternative allele for each dominant SNV site. Moreover, a validated database was established, which manually curated the discriminating sgRNAs that were experimentally validated in the mounting literature for multiple allele-specific purposes.
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Affiliation(s)
- Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Yu Tang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, P.R. China
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32
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Chen AC, Niruthisard D, Chung DD, Chuephanich P, Aldave AJ. Identification of A Novel TGFBI Gene Mutation (p.Serine524Cystine) Associated with Late Onset Recurrent Epithelial Erosions and Bowman Layer Opacities. Ophthalmic Genet 2020; 41:639-644. [PMID: 32880217 DOI: 10.1080/13816810.2020.1814345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/01/2020] [Accepted: 08/19/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Most transforming growth factor beta-induced (TGFBI) corneal dystrophies are associated with a characteristic phenotype, clinical course, and a conserved mutation in the TGFBI gene. However, we report a novel TGFBI missense mutation associated with a late-onset, variant Bowman layer dystrophy. METHODS Participants underwent slit-lamp examination and multimodal imaging. Polymerase chain reaction amplification and Sanger sequencing were performed on saliva-derived genomic DNA to screen TGFBI exons 4 and 12 as well as COL17A1 exon 46. PolyPhen-2 and SIFT were used to predict the functional impact of any identified variants. RESULTS A 56-year-old Thai woman reported a four-year history of decreased vision and intermittent eye irritation, suggestive of recurrent epithelial erosions, in both eyes. Slit-lamp exam revealed bilateral, irregular, limbal-sparing Bowman layer opacities, which were also noted on anterior segment optical coherence tomography. Phototherapeutic keratectomy was performed in the right eye, improving the best-corrected visual acuity from 20/50 to 20/30. Sequencing of the TGFBI gene revealed a novel heterozygous, missense mutation in exon 12 (c.1571 C > G; p.Ser524Cys), which was present in an affected son and absent in an unaffected son, and was predicted to be damaging by PolyPhen-2 and SIFT. The patient was diagnosed with a variant Bowman layer dystrophy given the late onset of an atypical phenotype and the identification of a novel TGFBI mutation. CONCLUSIONS A novel TGFBI missense mutation is associated with a late-onset Bowman layer dystrophy. Given the atypical clinical appearance and course, molecular genetic analysis was utilized to establish a definitive diagnosis.
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Affiliation(s)
- Angela C Chen
- Stein Eye Institute, David Geffen School of Medicine at UCLA , Los Angeles, CA, USA
| | - Duangratn Niruthisard
- Stein Eye Institute, David Geffen School of Medicine at UCLA , Los Angeles, CA, USA
- Department of Ophthalmology, Banphaeo General Hospital (Public Organization) , Samutsakhon, Thailand
| | - Doug D Chung
- Stein Eye Institute, David Geffen School of Medicine at UCLA , Los Angeles, CA, USA
| | - Pichaya Chuephanich
- Department of Ophthalmology, Phramongkutklao Hospital, Phramongkutklao College of Medicine , Bangkok, Thailand
| | - Anthony J Aldave
- Stein Eye Institute, David Geffen School of Medicine at UCLA , Los Angeles, CA, USA
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33
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Rabinowitz R, Almog S, Darnell R, Offen D. CrisPam: SNP-Derived PAM Analysis Tool for Allele-Specific Targeting of Genetic Variants Using CRISPR-Cas Systems. Front Genet 2020; 11:851. [PMID: 33014011 PMCID: PMC7461778 DOI: 10.3389/fgene.2020.00851] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/13/2020] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) is a promising novel technology that holds the potential of treating genetic diseases. Safety and specificity of the treatment are to be further studied and developed prior to implementation of the technology into the clinic. The guide-RNA (gRNA) allows precise position-specific DNA targeting, although it may tolerate small changes such as point mutations. The permissive nature of the CRISPR-Cas system makes allele-specific targeting a challenging goal. Hence, an allele-specific targeting approach is in need for future treatments of heterozygous patients suffering from diseases caused by dominant negative mutations. The single-nucleotide polymorphism (SNP)-derived protospacer adjacent motif (PAM) approach allows highly allele-specific DNA cleavage due to the existence of a novel PAM sequence only at the target allele. Here, we present CrisPam, a computational tool that detects PAMs within the variant allele for allele-specific targeting by CRISPR-Cas systems. The algorithm scans the sequences and attempts to identify the generation of multiple PAMs for a given reference sequence and its variations. A successful result is such that at least a single PAM is generated by the variation nucleotide. Since the PAM is present within the variant allele only, the Cas enzyme will bind the variant allele exclusively. Analyzing a dataset of human pathogenic point mutations revealed that 90% of the analyzed mutations generated at least a single PAM. Thus, the SNP-derived PAM approach is ideal for targeting most of the point mutations in an allele-specific manner. CrisPam simplifies the gRNAs design process to specifically target the allele of interest and scans a wide range of 26 unique PAMs derived from 23 Cas enzymes. CrisPam is freely available at https://www.danioffenlab.com/crispam.
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Affiliation(s)
- Roy Rabinowitz
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Shiri Almog
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Roy Darnell
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Daniel Offen
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Tel Aviv University, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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34
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Normal peripheral blood neutrophil numbers accompanying ELANE whole gene deletion mutation. Blood Adv 2020; 3:2470-2473. [PMID: 31427279 DOI: 10.1182/bloodadvances.2019000498] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/21/2019] [Indexed: 01/14/2023] Open
Abstract
Key Points
The patient reported here, along with collective observations in the literature, suggest that ELANE deletion does not cause neutropenia. Potential therapeutic genome editing involving knockout of the mutant ELANE allele is therefore not expected to produce neutropenia.
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35
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Bastola P, Song L, Gilger BC, Hirsch ML. Adeno-Associated Virus Mediated Gene Therapy for Corneal Diseases. Pharmaceutics 2020; 12:pharmaceutics12080767. [PMID: 32823625 PMCID: PMC7464341 DOI: 10.3390/pharmaceutics12080767] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 12/14/2022] Open
Abstract
According to the World Health Organization, corneal diseases are the fourth leading cause of blindness worldwide accounting for 5.1% of all ocular deficiencies. Current therapies for corneal diseases, which include eye drops, oral medications, corrective surgeries, and corneal transplantation are largely inadequate, have undesirable side effects including blindness, and can require life-long applications. Adeno-associated virus (AAV) mediated gene therapy is an optimistic strategy that involves the delivery of genetic material to target human diseases through gene augmentation, gene deletion, and/or gene editing. With two therapies already approved by the United States Food and Drug Administration and 200 ongoing clinical trials, recombinant AAV (rAAV) has emerged as the in vivo viral vector-of-choice to deliver genetic material to target human diseases. Likewise, the relative ease of applications through targeted delivery and its compartmental nature makes the cornea an enticing tissue for AAV mediated gene therapy applications. This current review seeks to summarize the development of AAV gene therapy, highlight preclinical efficacy studies, and discuss potential applications and challenges of this technology for targeting corneal diseases.
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Affiliation(s)
- Prabhakar Bastola
- Ophthalmology, University of North Carolina, Chapel Hill, NC 27599, USA; (P.B.); (L.S.); (B.C.G.)
- Gene Therapy Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Liujiang Song
- Ophthalmology, University of North Carolina, Chapel Hill, NC 27599, USA; (P.B.); (L.S.); (B.C.G.)
- Gene Therapy Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Brian C. Gilger
- Ophthalmology, University of North Carolina, Chapel Hill, NC 27599, USA; (P.B.); (L.S.); (B.C.G.)
- Clinical Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Matthew L. Hirsch
- Ophthalmology, University of North Carolina, Chapel Hill, NC 27599, USA; (P.B.); (L.S.); (B.C.G.)
- Gene Therapy Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Correspondence: ; Tel.: +1-919-966-0696
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36
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Christie KA, Robertson LJ, Conway C, Blighe K, DeDionisio LA, Chao-Shern C, Kowalczyk AM, Marshall J, Turnbull D, Nesbit MA, Moore CBT. Mutation-Independent Allele-Specific Editing by CRISPR-Cas9, a Novel Approach to Treat Autosomal Dominant Disease. Mol Ther 2020; 28:1846-1857. [PMID: 32416058 PMCID: PMC7403340 DOI: 10.1016/j.ymthe.2020.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 02/14/2020] [Accepted: 05/01/2020] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas9 provides a tool to treat autosomal dominant disease by non-homologous end joining (NHEJ) gene disruption of the mutant allele. In order to discriminate between wild-type and mutant alleles, Streptococcus pyogenes Cas9 (SpCas9) must be able to detect a single nucleotide change. Allele-specific editing can be achieved by using either a guide-specific approach, in which the missense mutation is found within the guide sequence, or a protospacer-adjacent motif (PAM)-specific approach, in which the missense mutation generates a novel PAM. While both approaches have been shown to offer allele specificity in certain contexts, in cases where numerous missense mutations are associated with a particular disease, such as TGFBI (transforming growth factor β-induced) corneal dystrophies, it is neither possible nor realistic to target each mutation individually. In this study, we demonstrate allele-specific CRISPR gene editing independent of the disease-causing mutation that is capable of achieving complete allele discrimination, and we propose it as a targeting approach for autosomal dominant disease. Our approach utilizes natural variants in the target region that contain a PAM on one allele that lies in cis with the causative mutation, removing the constraints of a mutation-dependent approach. Our innovative patient-specific guide design approach takes into account the patient's individual genetic make-up, allowing on- and off-target activity to be assessed in a personalized manner.
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Affiliation(s)
- Kathleen A Christie
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK
| | - Louise J Robertson
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK
| | - Caroline Conway
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK
| | - Kevin Blighe
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK
| | | | - Connie Chao-Shern
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK; Avellino Laboratories, Menlo Park, CA 94025, USA
| | - Amanda M Kowalczyk
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK
| | - John Marshall
- Department of Genetics, UCL Institute of Ophthalmology, London EC1V 9EL, UK
| | - Doug Turnbull
- Genomics and Cell Characterization Core Facility, University of Oregon, OR 97403, USA
| | - M Andrew Nesbit
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK
| | - C B Tara Moore
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK; Avellino Laboratories, Menlo Park, CA 94025, USA.
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Baran-Rachwalska P, Torabi-Pour N, Sutera FM, Ahmed M, Thomas K, Nesbit MA, Welsh M, Moore CBT, Saffie-Siebert SR. Topical siRNA delivery to the cornea and anterior eye by hybrid silicon-lipid nanoparticles. J Control Release 2020; 326:192-202. [PMID: 32653503 DOI: 10.1016/j.jconrel.2020.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/03/2020] [Accepted: 07/05/2020] [Indexed: 12/18/2022]
Abstract
The major unmet need and crucial challenge hampering the exciting potential of RNAi therapeutics in ophthalmology is to find an effective, safe and non-invasive means of delivering siRNA to the cornea. Although all tissues of the eye are accessible by injection, topical application is preferable for the frequent treatment regimen that would be necessary for siRNA-induced gene silencing. However, the ocular surface is one of the more complex biological barriers for drug delivery due to the combined effect of short contact time, tear dilution and poor corneal cell penetration. Using nanotechnology to overcome the challenges, we developed a unique silicon-based delivery platform for ocular delivery of siRNA. This biocompatible hybrid of porous silicon nanoparticles and lipids has demonstrated an ability to bind nucleic acid and deliver functional siRNA to corneal cells both in vitro and in vivo. Potent transfection of human corneal epithelial cells with siRNA-ProSilic® formulation was followed by a successful downregulation of reporter protein expression. Moreover, siRNA complexed with this silicon-based hybrid and applied in vivo topically to mice eyes penetrated across all cornea layers and resulted in a significant reduction of the targeted protein expression in corneal epithelium. In terms of siRNA loading capacity, system versatility, and potency of action, ProSilic provides unique attributes as a biodegradable delivery platform for therapeutic oligonucleotides.
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Affiliation(s)
- Paulina Baran-Rachwalska
- SiSaf Ltd, Surrey Research Park, Guildford GU2 7RE, United Kingdom; Biomedical Sciences Research Institute, University of Ulster, Coleraine BT52 1SA, United Kingdom
| | | | | | - Mukhtar Ahmed
- SiSaf Ltd, Surrey Research Park, Guildford GU2 7RE, United Kingdom
| | - Keith Thomas
- Biomedical Sciences Research Institute, University of Ulster, Coleraine BT52 1SA, United Kingdom
| | - M Andrew Nesbit
- Biomedical Sciences Research Institute, University of Ulster, Coleraine BT52 1SA, United Kingdom
| | - Michael Welsh
- SiSaf Ltd, Surrey Research Park, Guildford GU2 7RE, United Kingdom
| | - C B Tara Moore
- SiSaf Ltd, Surrey Research Park, Guildford GU2 7RE, United Kingdom; Biomedical Sciences Research Institute, University of Ulster, Coleraine BT52 1SA, United Kingdom.
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38
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Nielsen NS, Poulsen ET, Lukassen MV, Chao Shern C, Mogensen EH, Weberskov CE, DeDionisio L, Schauser L, Moore TC, Otzen DE, Hjortdal J, Enghild JJ. Biochemical mechanisms of aggregation in TGFBI-linked corneal dystrophies. Prog Retin Eye Res 2020; 77:100843. [DOI: 10.1016/j.preteyeres.2020.100843] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/17/2020] [Accepted: 01/23/2020] [Indexed: 12/22/2022]
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Lukassen MV, Poulsen ET, Donaghy J, Mogensen EH, Christie KA, Roshanravan H, DeDioniso L, Nesbit MA, Moore T, Enghild JJ. Protein Analysis of the TGFBI R124H Mouse Model Gives Insight into Phenotype Development of Granular Corneal Dystrophy. Proteomics Clin Appl 2020; 14:e1900072. [PMID: 32558206 DOI: 10.1002/prca.201900072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 05/14/2020] [Indexed: 01/20/2023]
Abstract
PURPOSE Mutations in the transforming growth factor β-induced protein (TGFBIp) are associated with TGFBI-linked corneal dystrophies, which manifests as protein deposits in the cornea. A total of 70 different disease-causing mutations have been reported so far including the common R124H substitution, which is associated with granular corneal dystrophy type 2 (GCD2). The disease mechanism of GCD2 is not known and the current treatments only offer temporary relief due to the reoccurrence of deposits. EXPERIMENTAL DESIGN The corneal protein profiles of the three genotypes (wild-type (WT), heterozygotes, and homozygotes) of a GCD2 mouse model are compared using label-free quantitative LC-MS/MS. RESULTS The mice do not display corneal protein deposits and the global protein expression between the three genotypes is highly similar. However, the expression of mutated TGFBIp is 41% of that of the WT protein. CONCLUSIONS AND CLINICAL RELEVANCE It is proposed that the lowered expression level of mutant TGFBIp protein relative to WT protein is the direct cause of the missing development of corneal deposits in the mouse. The overall protein profiles of the corneas are not impacted by the reduced amount of TGFBIp. Altogether, this supports a partial reduction in mutated TGFBIp as a potential treatment strategy for GCD2.
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Affiliation(s)
- Marie V Lukassen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000, Denmark.,Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, 8000, Denmark
| | - Ebbe T Poulsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000, Denmark
| | - Jack Donaghy
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, BT52 1SA, UK
| | - Emilie H Mogensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000, Denmark
| | - Kathleen A Christie
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, BT52 1SA, UK
| | | | - Larry DeDioniso
- Avellino Labs USA, Menlo Park, San Francisco, CA, 94025, USA
| | - M Andrew Nesbit
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, BT52 1SA, UK
| | - Tara Moore
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, BT52 1SA, UK.,Avellino Labs USA, Menlo Park, San Francisco, CA, 94025, USA
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000, Denmark.,Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, 8000, Denmark
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40
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Soh YQ, Kocaba V, Weiss JS, Jurkunas UV, Kinoshita S, Aldave AJ, Mehta JS. Corneal dystrophies. Nat Rev Dis Primers 2020; 6:46. [PMID: 32528047 DOI: 10.1038/s41572-020-0178-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/24/2020] [Indexed: 12/21/2022]
Abstract
Corneal dystrophies are broadly defined as inherited disorders that affect any layer of the cornea and are usually progressive, bilateral conditions that do not have systemic effects. The 2015 International Classification of Corneal Dystrophies classifies corneal dystrophies into four classes: epithelial and subepithelial dystrophies, epithelial-stromal TGFBI dystrophies, stromal dystrophies and endothelial dystrophies. Whereas some corneal dystrophies may result in few or mild symptoms and morbidity throughout a patient's lifetime, others may progress and eventually result in substantial visual and ocular disturbances that require medical or surgical intervention. Corneal transplantation, either with full-thickness or partial-thickness donor tissue, may be indicated for patients with advanced corneal dystrophies. Although corneal transplantation techniques have improved considerably over the past two decades, these surgeries are still associated with postoperative risks of disease recurrence, graft failure and other complications that may result in blindness. In addition, a global shortage of cadaveric corneal graft tissue critically limits accessibility to corneal transplantation in some parts of the world. Ongoing advances in gene therapy, regenerative therapy and cell augmentation therapy may eventually result in the development of alternative, novel treatments for corneal dystrophies, which may substantially improve the quality of life of patients with these disorders.
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Affiliation(s)
- Yu Qiang Soh
- Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore, Singapore.,Singapore National Eye Centre, Singapore, Singapore.,Ophthalmology Academic Clinical Program, Duke-NUS Graduate Medical School, Singapore, Singapore.,Department of Clinical Sciences, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Viridiana Kocaba
- Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore, Singapore.,Netherlands Institute for Innovative Ocular Surgery, Rotterdam, Netherlands
| | - Jayne S Weiss
- Department of Ophthalmology, Pathology and Pharmacology, Louisiana State University, School of Medicine, New Orleans, USA
| | - Ula V Jurkunas
- Cornea and Refractive Surgery Service, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA.,Schepens Eye Research Institute, Boston, Massachusetts, USA.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Shigeru Kinoshita
- Department of Frontier Medical Science and Technology for Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Anthony J Aldave
- Stein Eye Institute, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Jodhbir S Mehta
- Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore, Singapore. .,Singapore National Eye Centre, Singapore, Singapore. .,Ophthalmology Academic Clinical Program, Duke-NUS Graduate Medical School, Singapore, Singapore. .,Department of Clinical Sciences, Duke-NUS Graduate Medical School, Singapore, Singapore.
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41
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Yu J, Xiang X, Huang J, Liang X, Pan X, Dong Z, Petersen TS, Qu K, Yang L, Zhao X, Li S, Zheng T, Xu Z, Liu C, Han P, Xu F, Yang H, Liu X, Zhang X, Bolund L, Luo Y, Lin L. Haplotyping by CRISPR-mediated DNA circularization (CRISPR-hapC) broadens allele-specific gene editing. Nucleic Acids Res 2020; 48:e25. [PMID: 31943080 PMCID: PMC7049710 DOI: 10.1093/nar/gkz1233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 12/19/2019] [Accepted: 12/24/2019] [Indexed: 12/15/2022] Open
Abstract
Allele-specific protospacer adjacent motif (asPAM)-positioning SNPs and CRISPRs are valuable resources for gene therapy of dominant disorders. However, one technical hurdle is to identify the haplotype comprising the disease-causing allele and the distal asPAM SNPs. Here, we describe a novel CRISPR-based method (CRISPR-hapC) for haplotyping. Based on the generation (with a pair of CRISPRs) of extrachromosomal circular DNA in cells, the CRISPR-hapC can map haplotypes from a few hundred bases to over 200 Mb. To streamline and demonstrate the applicability of the CRISPR-hapC and asPAM CRISPR for allele-specific gene editing, we reanalyzed the 1000 human pan-genome and generated a high frequency asPAM SNP and CRISPR database (www.crispratlas.com/knockout) for four CRISPR systems (SaCas9, SpCas9, xCas9 and Cas12a). Using the huntingtin (HTT) CAG expansion and transthyretin (TTR) exon 2 mutation as examples, we showed that the asPAM CRISPRs can specifically discriminate active and dead PAMs for all 23 loci tested. Combination of the CRISPR-hapC and asPAM CRISPRs further demonstrated the capability for achieving highly accurate and haplotype-specific deletion of the HTT CAG expansion allele and TTR exon 2 mutation in human cells. Taken together, our study provides a new approach and an important resource for genome research and allele-specific (haplotype-specific) gene therapy.
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Affiliation(s)
- Jiaying Yu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Xi Xiang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - Jinrong Huang
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
- Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Xue Liang
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Xiaoguang Pan
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Zhanying Dong
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | | | - Kunli Qu
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Ling Yang
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaoying Zhao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Siyuan Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Tianyu Zheng
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Zhe Xu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Chengxun Liu
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Peng Han
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Fengping Xu
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Xin Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Lars Bolund
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus 8200, Denmark
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Mirjalili Mohanna SZ, Hickmott JW, Lam SL, Chiu NY, Lengyell TC, Tam BM, Moritz OL, Simpson EM. Germline CRISPR/Cas9-Mediated Gene Editing Prevents Vision Loss in a Novel Mouse Model of Aniridia. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:478-490. [PMID: 32258211 PMCID: PMC7114625 DOI: 10.1016/j.omtm.2020.03.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 03/09/2020] [Indexed: 12/18/2022]
Abstract
Aniridia is a rare eye disorder, which is caused by mutations in the paired box 6 (PAX6) gene and results in vision loss due to the lack of a long-term vision-saving therapy. One potential approach to treating aniridia is targeted CRISPR-based genome editing. To enable the Pax6 small eye (Sey) mouse model of aniridia, which carries the same mutation found in patients, for preclinical testing of CRISPR-based therapeutic approaches, we endogenously tagged the Sey allele, allowing for the differential detection of protein from each allele. We optimized a correction strategy in vitro then tested it in vivo in the germline of our new mouse to validate the causality of the Sey mutation. The genomic manipulations were analyzed by PCR, as well as by Sanger and next-generation sequencing. The mice were studied by slit lamp imaging, immunohistochemistry, and western blot analyses. We successfully achieved both in vitro and in vivo germline correction of the Sey mutation, with the former resulting in an average 34.8% ± 4.6% SD correction, and the latter in restoration of 3xFLAG-tagged PAX6 expression and normal eyes. Hence, in this study we have created a novel mouse model for aniridia, demonstrated that germline correction of the Sey mutation alone rescues the mutant phenotype, and developed an allele-distinguishing CRISPR-based strategy for aniridia.
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Affiliation(s)
- Seyedeh Zeinab Mirjalili Mohanna
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC V5Z 4H4, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Jack W Hickmott
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC V5Z 4H4, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Siu Ling Lam
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Nina Y Chiu
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC V5Z 4H4, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Tess C Lengyell
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Beatrice M Tam
- Department of Ophthalmology and Visual Sciences and Centre for Macular Research, The University of British Columbia, Vancouver, BC, Canada
| | - Orson L Moritz
- Department of Ophthalmology and Visual Sciences and Centre for Macular Research, The University of British Columbia, Vancouver, BC, Canada
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC V5Z 4H4, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
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43
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Wu J, Tang B, Tang Y. Allele-specific genome targeting in the development of precision medicine. Theranostics 2020; 10:3118-3137. [PMID: 32194858 PMCID: PMC7053192 DOI: 10.7150/thno.43298] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 01/18/2020] [Indexed: 12/11/2022] Open
Abstract
The CRISPR-based genome editing holds immense potential to fix disease-causing mutations, however, must also handle substantial natural genetic variations between individuals. Previous studies have shown that mismatches between the single guide RNA (sgRNA) and genomic DNA may negatively impact sgRNA efficiencies and lead to imprecise specificity prediction. Hence, the genetic variations bring about a great challenge for designing platinum sgRNAs in large human populations. However, they also provide a promising entry for designing allele-specific sgRNAs for the treatment of each individual. The CRISPR system is rather specific, with the potential ability to discriminate between similar alleles, even based on a single nucleotide difference. Genetic variants contribute to the discrimination capabilities, once they generate a novel protospacer adjacent motif (PAM) site or locate in the seed region near an available PAM. Therefore, it can be leveraged to establish allele-specific targeting in numerous dominant human disorders, by selectively ablating the deleterious alleles. So far, allele-specific CRISPR has been increasingly implemented not only in treating dominantly inherited diseases, but also in research areas such as genome imprinting, haploinsufficiency, spatiotemporal loci imaging and immunocompatible manipulations. In this review, we will describe the working principles of allele-specific genome manipulations by virtue of expanding engineering tools of CRISPR. And then we will review new advances in the versatile applications of allele-specific CRISPR targeting in treating human genetic diseases, as well as in a series of other interesting research areas. Lastly, we will discuss their potential therapeutic utilities and considerations in the era of precision medicine.
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Affiliation(s)
- Junjiao Wu
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Beisha Tang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan 410008, China
| | - Yu Tang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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Moore T, Chao-Shern C, DeDionisio L, Christie KA, Nesbit MA. Gene Editing for Corneal Stromal Regeneration. Methods Mol Biol 2020; 2145:59-75. [PMID: 32542601 DOI: 10.1007/978-1-0716-0599-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
CRISPR/Cas9 gene editing holds the promise of sequence-specific alteration of the genome to achieve therapeutic benefit in the treated tissue. Cas9 is an RNA-guided nuclease in which the sequence of the RNA can be altered to match the desired target. However, care must be taken in target choice and RNA guide design to ensure both maximum on-target and minimum off-target activity. The cornea is an ideal tissue for gene therapy due to its small surface area, accessibility, immune privilege, avascularity, and ease of visualization. Herein, we describe the design, testing, and delivery of Cas9 and guide RNAs to target genes expressed in the cornea.
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Affiliation(s)
- Tara Moore
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, UK.
- Avellino Lab USA, Inc., Menlo Park, CA, USA.
| | - Connie Chao-Shern
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, UK
- Avellino Lab USA, Inc., Menlo Park, CA, USA
| | | | - Kathleen A Christie
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, UK
| | - M Andrew Nesbit
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, UK
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CRISPR Diagnosis and Therapeutics with Single Base Pair Precision. Trends Mol Med 2019; 26:337-350. [PMID: 31791730 DOI: 10.1016/j.molmed.2019.09.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/25/2019] [Accepted: 09/25/2019] [Indexed: 12/11/2022]
Abstract
Clustered regularly interspaced short palindromic repeats, or CRISPR, has been widely accepted as a versatile genome editing tool with significant potential for medical application. Reliable allele specificity is one of the most critical elements for successful application of this technology to develop high-precision therapeutics and diagnostics. CRISPR-based genome editing tools achieve high-fidelity distinction of single-base differences in target genomic loci by structural identification of CRISPR-associated (Cas) proteins and sequences of the guide RNAs. In this review, we describe the structural features of ribonucleoprotein complex formation by CRISPR proteins and guide RNAs that eventually recognize target DNA sequences. This structural understanding provides the basis for the recent applications of enhanced single-base precision genome editing technologies for effective distinction of specific alleles.
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Keough KC, Lyalina S, Olvera MP, Whalen S, Conklin BR, Pollard KS. AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design. Genome Biol 2019; 20:167. [PMID: 31416467 PMCID: PMC6694686 DOI: 10.1186/s13059-019-1783-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/03/2019] [Indexed: 12/26/2022] Open
Abstract
The CRISPR/Cas system is a highly specific genome editing tool capable of distinguishing alleles differing by even a single base pair. Target sites might carry genetic variations that are not distinguishable by sgRNA designing tools based on one reference genome. AlleleAnalyzer is an open-source software that incorporates single-nucleotide variants and short insertions and deletions to design sgRNAs for precisely editing 1 or multiple haplotypes of a sequenced genome, currently supporting 11 Cas proteins. It also leverages patterns of shared genetic variation to optimize sgRNA design for different human populations. AlleleAnalyzer is available at https://github.com/keoughkath/AlleleAnalyzer .
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Affiliation(s)
- Kathleen C Keough
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, CA, USA
- Gladstone Institutes, San Francisco, CA, USA
| | - Svetlana Lyalina
- Gladstone Institutes, San Francisco, CA, USA
- Bioinformatics Graduate Program, University of California, San Francisco, CA, USA
| | | | - Sean Whalen
- Gladstone Institutes, San Francisco, CA, USA
| | - Bruce R Conklin
- Gladstone Institutes, San Francisco, CA, USA.
- Departments of Biostatistics, Medicine, Ophthalmology and Pharmacology, University of California, San Francisco, CA, USA.
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA.
- Department of Epidemiology & Biostatistics, Institute for Human Genetics, Quantitative Biology Institute, and Institute for Computational Health Sciences, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, California, USA.
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Mills EM, Barlow VL, Luk LYP, Tsai YH. Applying switchable Cas9 variants to in vivo gene editing for therapeutic applications. Cell Biol Toxicol 2019; 36:17-29. [PMID: 31418127 PMCID: PMC7051928 DOI: 10.1007/s10565-019-09488-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/29/2019] [Indexed: 12/20/2022]
Abstract
Progress in targeted gene editing by programmable endonucleases has paved the way for their use in gene therapy. Particularly, Cas9 is an endonuclease with high activity and flexibility, rendering it an attractive option for therapeutic applications in clinical settings. Many disease-causing mutations could potentially be corrected by this versatile new technology. In addition, recently developed switchable Cas9 variants, whose activity can be controlled by an external stimulus, provide an extra level of spatiotemporal control on gene editing and are particularly desirable for certain applications. Here, we discuss the considerations and difficulties for implementing Cas9 to in vivo gene therapy. We put particular emphasis on how switchable Cas9 variants may resolve some of these barriers and advance gene therapy in the clinical setting.
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Affiliation(s)
- Emily M Mills
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | | | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK.
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The future of keratoplasty: cell-based therapy, regenerative medicine, bioengineering keratoplasty, gene therapy. Curr Opin Ophthalmol 2019; 30:286-291. [PMID: 31045881 DOI: 10.1097/icu.0000000000000573] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW To provide an update on the state of development of novel therapeutic modalities for the treatment of corneal diseases. RECENT FINDINGS Novel corneal therapeutics may be broadly classified as cell therapy, regenerative medicine, bioengineered corneal grafts and gene therapy. Cell therapy encompasses cultivation of cells, such as corneal endothelial cells (CECs) and keratocytes to replenish the depleted native cell population. Regenerative medicine is mainly applicable to the corneal endothelium, and is dependent on the ability of native, healthy CECs to restore the corneal endothelium following trauma or descemetorhexis; this approach may be effective for the treatment of Peter's anomaly and Fuchs endothelial corneal dystrophy (FECD). Bioengineered corneal grafts are synthetic constructs designed to replace cadaveric corneal grafts; tissue-engineered endothelial-keratoplasty grafts and bioengineered stromal grafts have been experimented in animal models with favourable results. Gene therapy with antisense oligonucleotide and CRISPR endonucleases, including deactivated Cas9, may potentially be used to treat FECD and TGFBI-related corneal dystrophies. SUMMARY These novel therapeutic modalities may potentially supersede keratoplasty as the standard of care in the future.
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Fuchs endothelial corneal dystrophy and corneal endothelial diseases: East meets West. Eye (Lond) 2019; 34:427-441. [PMID: 31267087 DOI: 10.1038/s41433-019-0497-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 04/21/2019] [Accepted: 04/27/2019] [Indexed: 12/13/2022] Open
Abstract
Fuchs endothelial corneal dystrophy (FECD) is amongst one of the most common indications for endothelial keratoplasty worldwide. Despite being originally described among Caucasians, it is now known to be prevalent among a large number of populations, including Asians. While the FECD phenotype is classically described as that of central guttate and pigment deposits associated with corneal endothelial dysfunction, there are subtle yet important differences in how FECD and its phenocopies may present in Caucasians vs Asians. Such differences are paralled by genotypic variations and disease management preferences which appear to be geographically and ethnically delineated. This article provides a succinct review of such differences, with a focus on diagnostic and management issues which may be encountered by ophthalmologists practicing in the different geographic regions, when evaluating a patient with FECD.
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Sun D, Sun Z, Jiang H, Vaidya AM, Xin R, Ayat NR, Schilb AL, Qiao PL, Han Z, Naderi A, Lu ZR. Synthesis and Evaluation of pH-Sensitive Multifunctional Lipids for Efficient Delivery of CRISPR/Cas9 in Gene Editing. Bioconjug Chem 2019; 30:667-678. [PMID: 30582790 PMCID: PMC6429435 DOI: 10.1021/acs.bioconjchem.8b00856] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/20/2018] [Indexed: 01/06/2023]
Abstract
CRISPR/Cas9 system is a promising approach for gene editing in gene therapy. Effective gene editing requires safe and efficient delivery of CRISPR/Cas9 system in target cells. Several new multifunctional pH-sensitive amino lipids were designed and synthesized with modification of the amino head groups for intracellular delivery of CRISPR/Cas9 system. These multifunctional pH-sensitive amino lipids exhibited structurally dependent formulation of stable nanoparticles with the DNA plasmids of CRISPR/Cas9 system with the sizes ranging from 100 to 200 nm. The amino lipid plasmid DNA nanoparticles showed pH-sensitive hemolysis with minimal hemolytic activity at pH 7.4 and increased hemolysis at acidic pH (pH = 5.5, 6.5). The nanoparticles exhibited low cytotoxicity at an N/P ratio of 10. Expression of both Cas9 and sgRNA of the CRISPR/Cas9 system was in the range from 4.4% to 33%, dependent on the lipid structure in NIH3T3-GFP cells. The amino lipids that formed stable nanoparticles with high expression of both Cas9 and sgRNA mediated high gene editing efficiency. ECO and iECO mediated more efficient gene editing than other tested lipids. ECO mediated up to 50% GFP suppression based on observations with confocal microscopy and nearly 80% reduction of GFP mRNA based on RT-PCR measurement in NIH3T3-GFP cells. The multifunctional pH-sensitive amino lipids have the potential for efficient intracellular delivery of CRISPR/Cas9 for effective gene editing.
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Affiliation(s)
| | | | - Hongfa Jiang
- Department
of Biomedical
Engineering, School of Engineering, Case
Western Reserve University, Cleveland, Ohio 44106, United States
| | - Amita M. Vaidya
- Department
of Biomedical
Engineering, School of Engineering, Case
Western Reserve University, Cleveland, Ohio 44106, United States
| | - Rui Xin
- Department
of Biomedical
Engineering, School of Engineering, Case
Western Reserve University, Cleveland, Ohio 44106, United States
| | - Nadia R. Ayat
- Department
of Biomedical
Engineering, School of Engineering, Case
Western Reserve University, Cleveland, Ohio 44106, United States
| | - Andrew L. Schilb
- Department
of Biomedical
Engineering, School of Engineering, Case
Western Reserve University, Cleveland, Ohio 44106, United States
| | - Peter L. Qiao
- Department
of Biomedical
Engineering, School of Engineering, Case
Western Reserve University, Cleveland, Ohio 44106, United States
| | - Zheng Han
- Department
of Biomedical
Engineering, School of Engineering, Case
Western Reserve University, Cleveland, Ohio 44106, United States
| | - Amirreza Naderi
- Department
of Biomedical
Engineering, School of Engineering, Case
Western Reserve University, Cleveland, Ohio 44106, United States
| | - Zheng-Rong Lu
- Department
of Biomedical
Engineering, School of Engineering, Case
Western Reserve University, Cleveland, Ohio 44106, United States
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