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Klementieva NV, Lunev EA, Shmidt AA, Loseva EM, Savchenko IM, Svetlova EA, Galkin II, Polikarpova AV, Usachev EV, Vassilieva SG, Marina VI, Dzhenkova MA, Romanova AD, Agutin AV, Timakova AA, Reshetov DA, Egorova TV, Bardina MV. RNA Interference Effectors Selectively Silence the Pathogenic Variant GNAO1 c.607 G > A In Vitro. Nucleic Acid Ther 2024; 34:90-99. [PMID: 38215303 DOI: 10.1089/nat.2023.0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024] Open
Abstract
RNA interference (RNAi)-based therapeutics hold the potential for dominant genetic disorders, enabling sequence-specific inhibition of pathogenic gene products. We aimed to direct RNAi for the selective suppression of the heterozygous GNAO1 c.607 G > A variant causing GNAO1 encephalopathy. By screening short interfering RNA (siRNA), we showed that GNAO1 c.607G>A is a druggable target for RNAi. The si1488 candidate achieved at least twofold allelic discrimination and downregulated mutant protein to 35%. We created vectorized RNAi by incorporating the si1488 sequence into the short hairpin RNA (shRNA) in the adeno-associated virus (AAV) vector. The shRNA stem and loop were modified to improve the transcription, processing, and guide strand selection. All tested shRNA constructs demonstrated selectivity toward mutant GNAO1, while tweaking hairpin structure only marginally affected the silencing efficiency. The selectivity of shRNA-mediated silencing was confirmed in the context of AAV vector transduction. To conclude, RNAi effectors ranging from siRNA to AAV-RNAi achieve suppression of the pathogenic GNAO1 c.607G>A and discriminate alleles by the single-nucleotide substitution. For gene therapy development, it is crucial to demonstrate the benefit of these RNAi effectors in patient-specific neurons and animal models of the GNAO1 encephalopathy.
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Affiliation(s)
- Natalia V Klementieva
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Evgenii A Lunev
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna A Shmidt
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Irina M Savchenko
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A Svetlova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Ivan I Galkin
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna V Polikarpova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Evgeny V Usachev
- Laboratory of Translational Biomedicine, Gamaleya National Research Center for Epidemiology, Moscow, Russia
| | - Svetlana G Vassilieva
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | | | - Marina A Dzhenkova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Anna D Romanova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
| | - Anton V Agutin
- State Budgetary Healthcare Institution of Moscow Region "Balashikha Hospital," Balashikha, Russia
| | - Anna A Timakova
- Institute for Regenerative Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | | | - Tatiana V Egorova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Maryana V Bardina
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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Egorova TV, Polikarpova AV, Vassilieva SG, Dzhenkova MA, Savchenko IM, Velyaev OA, Shmidt AA, Soldatov VO, Pokrovskii MV, Deykin AV, Bardina MV. CRISPR-Cas9 correction in the DMD mouse model is accompanied by upregulation of Dp71f protein. Mol Ther Methods Clin Dev 2023; 30:161-180. [PMID: 37457303 PMCID: PMC10339130 DOI: 10.1016/j.omtm.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a severe hereditary disease caused by a deficiency in the dystrophin protein. The most frequent types of disease-causing mutations in the DMD gene are frameshift deletions of one or more exons. Precision genome editing systems such as CRISPR-Cas9 have shown potential to restore open reading frames in numerous animal studies. Here, we applied an AAV-CRISPR double-cut strategy to correct a mutation in the DMD mouse model with exon 8-34 deletion, encompassing the N-terminal actin-binding domain. We report successful excision of the 100-kb genomic sequence, which includes exons 6 and 7, and partial improvement in cardiorespiratory function. While corrected mRNA was abundant in muscle tissues, only a low level of truncated dystrophin was produced, possibly because of protein instability. Furthermore, CRISPR-Cas9-mediated genome editing upregulated the Dp71f dystrophin isoform on the sarcolemma. Given the previously reported Dp71-associated muscle pathology, our results question the applicability of genome editing strategies for some DMD patients with N-terminal mutations. The safety and efficacy of CRISPR-Cas9 constructs require rigorous investigation in patient-specific animal models.
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Affiliation(s)
- Tatiana V. Egorova
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Marlin Biotech LLC, Sochi 354340, Russia
| | - Anna V. Polikarpova
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Marlin Biotech LLC, Sochi 354340, Russia
| | - Svetlana G. Vassilieva
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Marina A. Dzhenkova
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Irina M. Savchenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Oleg A. Velyaev
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna A. Shmidt
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Vladislav O. Soldatov
- Research Institute of Living Systems Pharmacology, Belgorod National Research University, Belgorod 308007, Russia
| | - Mikhail V. Pokrovskii
- Research Institute of Living Systems Pharmacology, Belgorod National Research University, Belgorod 308007, Russia
| | - Alexey V. Deykin
- Marlin Biotech LLC, Sochi 354340, Russia
- Joint Center for Genetic Technologies, Laboratory of Genetic Technologies and Gene Editing for Biomedicine and Veterinary Medicine, Department of Pharmacology and Clinical Pharmacology, Belgorod National Research University, Belgorod 308015, Russia
| | - Maryana V. Bardina
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Marlin Biotech LLC, Sochi 354340, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
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Egorova TV, Galkin II, Velyaev OA, Vassilieva SG, Savchenko IM, Loginov VA, Dzhenkova MA, Korshunova DS, Kozlova OS, Ivankov DN, Polikarpova AV. In-Frame Deletion of Dystrophin Exons 8-50 Results in DMD Phenotype. Int J Mol Sci 2023; 24:ijms24119117. [PMID: 37298068 DOI: 10.3390/ijms24119117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/12/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
Mutations that prevent the production of proteins in the DMD gene cause Duchenne muscular dystrophy. Most frequently, these are deletions leading to reading-frame shift. The "reading-frame rule" states that deletions that preserve ORF result in a milder Becker muscular dystrophy. By removing several exons, new genome editing tools enable reading-frame restoration in DMD with the production of BMD-like dystrophins. However, not every truncated dystrophin with a significant internal loss functions properly. To determine the effectiveness of potential genome editing, each variant should be carefully studied in vitro or in vivo. In this study, we focused on the deletion of exons 8-50 as a potential reading-frame restoration option. Using the CRISPR-Cas9 tool, we created the novel mouse model DMDdel8-50, which has an in-frame deletion in the DMD gene. We compared DMDdel8-50 mice to C57Bl6/CBA background control mice and previously generated DMDdel8-34 KO mice. We discovered that the shortened protein was expressed and correctly localized on the sarcolemma. The truncated protein, on the other hand, was unable to function like a full-length dystrophin and prevent disease progression. On the basis of protein expression, histological examination, and physical assessment of the mice, we concluded that the deletion of exons 8-50 is an exception to the reading-frame rule.
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Affiliation(s)
- Tatiana V Egorova
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
- Marlin Biotech LLC, Sochi 354340, Russia
| | - Ivan I Galkin
- Marlin Biotech LLC, Sochi 354340, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Oleg A Velyaev
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Svetlana G Vassilieva
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Irina M Savchenko
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Vyacheslav A Loginov
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Marina A Dzhenkova
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Diana S Korshunova
- Core Facilities, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Olga S Kozlova
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Dmitry N Ivankov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Anna V Polikarpova
- Laboratory of Modeling and Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
- Marlin Biotech LLC, Sochi 354340, Russia
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Polikarpova AV, Egorova TV, Lunev EA, Tsitrina AA, Vassilieva SG, Savchenko IM, Silaeva YY, Deykin AV, Bardina MV. CRISPR/Cas9-generated mouse model with humanizing single-base substitution in the Gnao1 for safety studies of RNA therapeutics. Front Genome Ed 2023; 5:1034720. [PMID: 37077890 PMCID: PMC10106585 DOI: 10.3389/fgeed.2023.1034720] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
The development of personalized medicine for genetic diseases requires preclinical testing in the appropriate animal models. GNAO1 encephalopathy is a severe neurodevelopmental disorder caused by heterozygous de novo mutations in the GNAO1 gene. GNAO1 c.607 G>A is one of the most common pathogenic variants, and the mutant protein Gαo-G203R likely adversely affects neuronal signaling. As an innovative approach, sequence-specific RNA-based therapeutics such as antisense oligonucleotides or effectors of RNA interference are potentially applicable for selective suppression of the mutant GNAO1 transcript. While in vitro validation can be performed in patient-derived cells, a humanized mouse model to rule out the safety of RNA therapeutics is currently lacking. In the present work, we employed CRISPR/Cas9 technology to introduce a single-base substitution into exon 6 of the Gnao1 to replace the murine Gly203-coding triplet (GGG) with the codon used in the human gene (GGA). We verified that genome-editing did not interfere with the Gnao1 mRNA or Gαo protein synthesis and did not alter localization of the protein in the brain structures. The analysis of blastocysts revealed the off-target activity of the CRISPR/Cas9 complexes; however, no modifications of the predicted off-target sites were detected in the founder mouse. Histological staining confirmed the absence of abnormal changes in the brain of genome-edited mice. The created mouse model with the “humanized” fragment of the endogenous Gnao1 is suitable to rule out unintended targeting of the wild-type allele by RNA therapeutics directed at lowering GNAO1 c.607 G>A transcripts.
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Affiliation(s)
- Anna V. Polikarpova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech, Sochi, Russia
| | - Tatiana V. Egorova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech, Sochi, Russia
| | - Evgenii A. Lunev
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexandra A. Tsitrina
- Koltzov Institute of Developmental Biology Russian Academy of Sciences, Moscow, Russia
| | - Svetlana G. Vassilieva
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech, Sochi, Russia
| | - Irina M. Savchenko
- Marlin Biotech, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yuliya Y. Silaeva
- Core Facility Center, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
| | - Alexey V. Deykin
- Marlin Biotech, Sochi, Russia
- Core Facility Center, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Laboratory of Genetic Technologies and Genome Editing for Biomedicine and Animal Health, Joint Center for Genetic Technologies, Belgorod National Research University, Belgorod, Russia
| | - Maryana V. Bardina
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- *Correspondence: Maryana V. Bardina,
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Lunev EA, Shmidt AA, Vassilieva SG, Savchenko IM, Loginov VA, Marina VI, Egorova TV, Bardina MV. [Effective Viral Delivery of Genetic Constructs to Neuronal Culture for Modeling and Gene Therapy of GNAO1 Encephalopathy]. Mol Biol (Mosk) 2022; 56:604-618. [PMID: 35964317 DOI: 10.31857/s0026898422040061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/28/2022] [Indexed: 06/15/2023]
Abstract
GNAO1 encephalopathy is an orphan genetic disease associated with early infantile epilepsy, impaired motor control, and severe developmental delay. The disorder is caused by mutations in the GNAO1 gene, leading to dysfunction of the encoded protein Gao1. There is no cure for this disease, and symptomatic therapy is ineffective. Phenotypic heterogeneity highlights the need for a personalized approach for treating patients with a specific clinical variant of GNAO1 and requires the study of the disease mechanism in animal and cell models. Towards this aim, we developed an approach for modeling GNAO1 encephalopathy and testing gene therapy drugs in primary neurons derived from healthy mice. We optimized the delivery of transgenes to Gαo1-expressing neurons using recombinant adeno-associated viruses (rAAV). We assessed the tropism of five neurotropic AAV serotypes (1, 2, 6, 9, DJ) for Gαo1-positive neurons from the whole mouse brain. The DJ serotype showed the highest potential as a reporter delivery vehicle, infecting up to 66% of Gαo1-expressing cells without overt cytotoxicity. We demonstrated that AAV-DJ also provides efficient delivery and expression of genetic constructs encoding normal and mutant Gαo1, as well as short hairpin RNA (shRNA) to suppress endogenous Gnao1 in murine neurons. Our results will further simplify the study of the pathological mechanism for clinical variants of GNAO1, as well as optimize the testing of gene therapy approaches for GNAO1 encephalopathy in cell models.
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Affiliation(s)
- E A Lunev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
- Marlin Biotech LLC, Sochi, 354340 Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - A A Shmidt
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - S G Vassilieva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - I M Savchenko
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - V A Loginov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - V I Marina
- Marlin Biotech LLC, Sochi, 354340 Russia
| | - T V Egorova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - M V Bardina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
- Marlin Biotech LLC, Sochi, 354340 Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
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