WO2022047876A1 - 杜氏肌营养不良症相关的外显子剪接增强子、sgRNA、基因编辑工具及应用 - Google Patents
杜氏肌营养不良症相关的外显子剪接增强子、sgRNA、基因编辑工具及应用 Download PDFInfo
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Definitions
- the invention belongs to the field of gene therapy, and relates to a Duchenne muscular dystrophy-related exon splicing enhancer, sgRNA, and a gene editing tool in mammals (experimental animal models and human patients) targeting gene mutation type hereditary diseases. Mutational transformation therapy. In particular, it relates to the gene editing therapy of Duchenne muscular dystrophy DMD in mouse models and human patients.
- rare diseases are uncommon diseases in a certain area, with the number of patients accounting for 0.065% to 0.1% of the total population.
- the pathogenesis of these diseases is often difficult to find, and there is a lack of targeted treatment drugs, which brings great harm to the health of patients and brings a great burden to their families and society.
- the pathogenesis of rare diseases is often due to genetic mutations, resulting in complex and multiple clinical disease manifestations. Due to the limitations of diagnostic methods, patients are generally classified as a single disease after showing clinical symptoms in the early course of the disease, and only after long-term treatment does not improve, will they be further judged as difficult and undiagnosed diseases. Therefore, related research on difficult and undiagnosed diseases/rare diseases needs to be carried out urgently, including but not limited to: exploration of pathogenic mechanisms, optimization of diagnostic methods, tracking of disease progression, screening of drug targets, and combination of gene editing technology for targeted The development of genetic drugs, etc.; at the same time, the discovery and improvement of animal models of special rare diseases can also improve our comprehensive understanding of rare diseases and the innovation of targeted drugs.
- the present invention takes muscular dystrophy (Muscular Dystrophy), a rare disease that has been clinically discovered earlier but lacks effective treatment methods for a long time, as the breakthrough point, takes Duchenne Muscular Dystrophy (DMD) as the research object, and combines new
- Muscular Dystrophy DMD
- the mouse model was discovered, the gene therapy for the disease was developed and optimized, and the gene therapy was applied to the human genome sequence.
- Duchenne Muscular Dystrophy is an X-chromosome genetic disorder that can be detected in about 1 in 4,000 newborn males.
- DMD Duchenne Muscular Dystrophy
- myocardial tissue damage and dysfunction are the most deadly threats.
- the clinical treatments that can be given are limited to the relief of symptoms: for example, the use of angiotensin inhibitors to relieve the discomfort caused by the deterioration of myocardial function, such drugs Including Pandinopril, and a variety of Lol beta-blockers.
- interventional therapy also helps to relieve the symptoms of DMD patients, including cardiac circulatory assistance system and respiratory assistance system.
- Sarepta Therapeutics is a biotechnology company focused on developing precision gene therapy for rare diseases.
- the Golodirsen developed by it was approved by the U.S. FDA on December 12, 2019, for the treatment of DMD patients diagnosed with exon 53 skipping gene mutations. It is estimated that about 8% of people with DMD carry this mutation.
- Golodirsen is an antisense oligonucleotide that works by targeting the dystrophin sequence. Therefore, drugs designed for other mutation sites are still a huge gap at present. At present, on a global scale, including DMD-targeted drugs that have entered clinical trials, the competition is fierce, but the demand is still huge.
- the purpose of the present invention is to provide a Duchenne muscular dystrophy-related exon splicing enhancer, sgRNA, and gene editing tools for genetically mutated rare diseases, which can be used as medicines for mammals (disease animal models and human patients) ) in vivo gene editing therapy.
- the present invention provides a Duchenne muscular dystrophy-related exon splicing enhancer, the exon splicing enhancer is an exon splicing enhancer element targeting human DMD gene Exon51, and its nuclear
- the nucleotide sequence includes:
- the DMD gene Exon51 can be induced to skip reading, thereby realizing gene editing therapy in mammals.
- CRISPR nuclease which can disrupt the structure of ESE by introducing deletion inserts (Insertions and deletions, Indels) through DNA double-strand breaks; antisense oligonucleotide ASO, by targeting the corresponding element of pre-mRNA in cells position, preventing its retention in the final protein amino acid sequence.
- the present invention also provides a Duchenne muscular dystrophy-related single-stranded guide RNA (single-strand guide RNA, sgRNA) that can target a specific genome, and the sequence of the sgRNA includes:
- the nucleotide sequence of the sgRNA for the Dmd-E4 mouse mutation site is shown in SEQ ID No.4.
- sgRNA-1 of human DMD gene Exon51 its nucleotide sequence is shown in SEQ ID No.8.
- sgRNA-2 of human DMD gene Exon51 its nucleotide sequence is shown in SEQ ID No.9.
- sgRNA-3 of human DMD gene Exon51 its nucleotide sequence is shown in SEQ ID No.10.
- sgRNA-4 of human DMD gene Exon51 its nucleotide sequence is shown in SEQ ID No.11.
- sgRNA-5 of human DMD gene Exon51 its nucleotide sequence is shown in SEQ ID No.12.
- sgRNA-6 of human DMD gene Exon51 its nucleotide sequence is shown in SEQ ID No.13.
- sgRNA-7 of human DMD gene Exon51 its nucleotide sequence is shown in SEQ ID No.14.
- sgRNA-8 of human DMD gene Exon51 its nucleotide sequence is shown in SEQ ID No.15.
- sgRNA-9 of human DMD gene Exon51 its nucleotide sequence is shown in SEQ ID No.16.
- sgRNA-10 of human DMD gene Exon51 its nucleotide sequence is shown in SEQ ID No.17.
- sgRNA-11 of human DMD gene Exon51 its nucleotide sequence is shown in SEQ ID No.18.
- sgRNA-12 of human DMD gene Exon51 its nucleotide sequence is shown in SEQ ID No.19.
- sgRNA-13 of human DMD gene Exon51 its nucleotide sequence is shown in SEQ ID No.20.
- the sgRNA combined with the gene editing tool can be used in the preparation of a drug for treating Duchenne muscular dystrophy.
- the present invention also provides a Duchenne muscular dystrophy-related gene editing tool, comprising a fusion protein of cytosine deaminase and a Cas9 mutant, the sgRNA of claim 2 and a vector.
- the vectors are commonly used biological plasmids, such as AAV vector plasmids, pCDNA3.1 plasmids, and the like.
- cytosine deaminase can be AID, apobec etc., preferably, cytosine deaminase is AID, and the amino acid sequence and nucleic acid sequence of the fusion protein of AID and Cas9 mutant are respectively as SEQ ID NO.1 and SEQ ID NO.2 is shown.
- the gene editing tool is packaged by adeno-associated virus vector AAV.
- Adeno-associated virus AAV can deliver the nucleic acid sequence expressing AID-Cas9 fusion protein and sgRNA to target cells, so that it can express proteins with DNA editing function and sgRNA molecules with guiding function in cells, wherein sgRNA can guide AID-
- the Cas9 fusion protein is integrated into a specific genomic locus in target cells to induce and transform pathogenic mutations and inactivate them for the purpose of treating diseases.
- the promoter of the adeno-associated virus vector AAV is Syn100 promoter or a promoter designed based on ck8a, mhck7 and the like.
- nucleotide sequence of the adeno-associated virus vector AAV is shown in SEQ ID NO.3.
- the present invention also provides the application of the above-mentioned gene editing tool in preparing a medicine for treating Duchenne muscular dystrophy.
- the invention takes the DMD mouse model and the pathogenic mutation carried by human DMD patients as examples, through designing and constructing a gene editing tool, and using adeno-associated virus AAV to realize the treatment of the DMD mouse model in vivo; of pathogenic mutations, and designed a gene editing scheme to achieve the transformation of pathogenic mutations at the cellular level.
- the invention provides an innovative treatment method for gene mutation type hereditary rare diseases, and is expected to achieve a breakthrough therapeutic effect on many hereditary rare diseases.
- Figure 1 shows the composition of functional elements including gene editing tools, wherein A is a separate package of viruses, and B is a combined package of viruses;
- Figure 2 is a flow chart of the treatment for the new DMD mouse disease model Dmd-E4, wherein A is the preventive treatment for newborn mice, and B is the reparative treatment for adult mice;
- Figure 3 shows the partial sequencing results of the AAV plasmid
- Figure A is the sequencing comparison result of the Syn100 promoter
- Figure B is the sequencing comparison result of the fusion protein of AID and Cas9 mutant
- Figure C is the sequencing comparison result of the U6 promoter.
- Figure 4 AAV treatment successfully repaired the disease phenotype caused by defective Dystrophin expression in Dmd-E4 mice, in which: Panel A, reverse transcription PCR of RNA in the hearts of treated Dmd-E4 mice, The primers were designed in Exon3 and Exon5 to detect the occurrence of skipping in Exon4 carrying the mutation, Dmd is the gene encoding the dystrophin protein in mice, and Gapdh is the internal reference for PCR; Figure B, using the quantitative method of capillary electrophoresis, it was determined that Exon4 skipped reading.
- FIG. 5 AAV treatment successfully restored muscle function and prolonged survival in Dmd-E4 mice.
- Panel A the serum creatine kinase content of treated Dmd-E4 mice was measured, WT and untreated Dmd-E4 mouse samples were used as controls;
- Panel B using HE staining and Masson staining methods, Assess the degree of myocardial inflammatory cell infiltration and fibrosis in Dmd-E4 mice after treatment;
- Figure C according to the results of Masson staining, quantitative statistics on the recovery of myocardial fibrosis in Dmd-E4 mice after treatment;
- Figure D using the micro-CT method to detect the degree of spinal curvature in Dmd-E4 mice, with WT mice and untreated mice as controls;
- E the quantitative statistics of spinal curvature in D;
- F Using the tension device to detect the degradation of the maximum muscle tension of the whole body in the treated Dmd-E4 mice during the cyclic force;
- G graph the survival time statistics of W
- Figure 6 Gene editing tools can successfully induce corresponding modifications of the DMD gene in human cells.
- Picture A two sgRNAs were successfully screened in K562 cell line, which can induce Exon51 to skip reading. The picture shows the results of reverse transcription PCR after RNA extraction from edited K562 cells, showing that the combination of two sgRNAs can induce efficient induction K562 cells lacking Exon50 successfully skipped Exon51;
- Panel B Exon51 inducing DMD gene skipped in normal human iPS and DMDExon50-deficient cells;
- Panel C using immunofluorescence detection to determine the presence of Dystrophin protein in edited iPS cells The expression was restored in Figure D; the expression of Dystrophin protein was restored in the edited iPS cells by the method of western blot;
- Figure E the quantitative statistics of the restored expression of the protein in Figure D.
- the invention takes DMD mouse models and pathogenic mutations carried by human DMD patients as examples, and realizes the transformation of pathogenic mutations by designing and constructing gene editing tools.
- the present invention will be further described below in conjunction with specific embodiments and accompanying drawings:
- Example 1 AAV virus carrying gene editing tools
- the gene editing tool designed according to the present invention is shown in Figure 1. Taking AID as an example, we clone the corresponding sequence into the AAV plasmid, including the following steps:
- the pAAV2 backbone vector (purchased from addgene, but not limited to) was double-digested based on the restriction sites of XhoI and NotI.
- the amino acid sequences of AID and Cas9 fusion proteins in the gene editing tool were designed.
- the amino acid sequences and nucleic acid sequences are shown in SEQ ID NO.1 and SEQ ID NO.2, respectively.
- the double-stranded DNA fragment was directly synthesized, and the elements such as the Syn100 promoter and tailing signal were connected to the AAV backbone vector to obtain the AAV vector plasmid expressing the AID-Cas9 mutant fusion protein, the sequence of which is SEQ ID NO.3 shown.
- the sequences of U6 promoter, H1 promoter and 7SK promoter can be linked with sgRNAs that recognize the exon splicing site of pathogenic mutation, and the Syn100 promoter and tailing can be used at the same time.
- the U6 promoter was linked with the sgRNA targeting the exon splicing site of the pathogenic mutation to construct an AAV plasmid vector with a 4.9kbp insert sequence. Part of the results of the relevant plasmid cloning is shown in Figure 3 below.
- a novel DMD mouse disease model Dmd-E4 with abnormal cardiac function was selected, which can be purchased from Jiangsu Jicui Yaokang Biotechnology Co., Ltd., but is not limited thereto.
- Dmd-E4 showed cardiac hypertrophy, fibrosis and other phenotypes in the heart at 6-8 weeks, and showed severe degeneration of cardiac function at about 8 months. This process closely mimics the cardiac pathology of DMD patients.
- the expression of Dystrophin protein can be retained to the maximum extent and its biological function can be restored.
- Example 1 the method of Example 1 was used to construct a gene editing tool, wherein the designed sgRNA sequence for the Dmd-E4 mouse mutation site was shown in SEQ ID NO. 4, and the obtained expression was for the Dmd-E4 mouse mutation site
- the AAV vector plasmid of the sgRNA the sequence of which is shown in SEQ ID NO.5.
- the corresponding sequence comprising the AID-Cas9 fusion protein and the sgRNA against Dmd-E4 mice in the same AAV vector plasmid is shown in SEQ ID NO.6.
- the virus with the serotype AAV9 was selected to synthesize and purify, and the Dmd-E4 mice were treated according to the preventive treatment of newborn mice and the repair treatment of adult mice, as shown in Figure 2.
- Dmd-E4 mice were mated with KO male and female mice. After the female mice became pregnant, the male and female mice were separated into cages, and the pregnant female mice were observed every two days for production. After the birth of the newborn Dmd-E4 mice , observe the gender, select 3-5 male mice as the experimental group, and another 3-5 male mice as the negative control group;
- adeno-associated virus AAV (titer 10 13 vg/mL) carrying gene editing tools was administered by intraperitoneal injection or facial vein injection, and control mice were simultaneously given an equal volume of sterile PBS, Afterwards, they were reared normally with the female mice;
- mice When the mice grew to about 2 months, in addition to the experimental group and the control group, 3-5 WT male mice of the same age were taken, and the following treatments were performed at the same time: After the mice were anesthetized, the function of the tibialis anterior muscle was first performed. Test, echocardiography, etc., then collect cardiac arteriovenous blood to kill mice, centrifuge to separate serum and store at -80°C, and collect cardiac muscle, skeletal muscle, tibialis anterior muscle, back muscle, liver, brain, kidney at the same time and other tissues, and extract its protein, RNA, genomic DNA, and retain enough tissue for immunofluorescence staining, hematoxylin and eosin staining, etc.
- FIG. 4D-F is the immunization of the protein in the mouse heart Blot detection, in which, Figure 4D is the band map, Figure 3E is the quantitative statistics of the bands in the 3D figure, Figure 4F Dystrophin protein expression, the results show that treated Dmd-E4 significantly restored Dystrophin protein expression.
- small animal cardiac ultrasonography was used to investigate whether the changes of cardiac related physiological structures in Dmd-E4 mice were repaired after AAV treatment. The results are shown in Figure 4G, the results show that the heart-related physiological structures of Dmd-E4 mice were basically repaired after treatment.
- Figure 5A is the measurement result of creatine kinase content in the serum of mice. It can be seen from the figure that compared with WT and untreated Dmd-E4 mouse samples, the creatine kinase content of Dmd-E4 mice after treatment Decreased significantly.
- HE staining and Masson staining were used to evaluate the degree of myocardial inflammatory cell infiltration and fibrosis in the treated Dmd-E4 mice. At the same time, according to the results of Masson staining, the myocardial fibrosis in the treated Dmd-E4 mice was quantitatively counted.
- Figure 5H shows the molecular biological evidence of gene editing in Dmd-E4 mouse cardiomyocytes.
- the pre-mRNA of the corresponding cells was subjected to reverse transcription PCR, followed by high-throughput sequencing, and it was found that the expected sgRNA was near the target position.
- the mutation of Dmd-E4 mice is the molecular basis and basis for the treatment of cardiac disease phenotype in Dmd-E4 mice.
- adeno-associated virus AAV (titer 10 13 vg/mL) carrying gene editing tools was administered by tail vein injection or skeletal muscle in situ injection, and control mice were simultaneously given an equal volume of sterile PBS;
- mice were treated for about 2 months, in addition to the experimental group and the control group, 3-5 WT male mice of the same age were taken, and the following treatments were performed simultaneously: Functional tests, echocardiography, etc., then the cardiac arteriovenous blood was collected to kill the mice, and the serum was centrifuged and stored at -80°C.
- Example 3 Gene editing of the DMD model of human induced pluripotent stem cell iPSC successfully restored the expression of Dystrophin protein
- the present invention has successfully implemented the gene editing therapy of human cells.
- iPSCs induced pluripotent stem cells
- CRISPR-cas9 method to specifically delete the exon 50 of the Dystrophin-encoding gene DMD, Exon50, so that the dystrophin protein encoding
- the sequence produced a frameshift mutation, thereby constructing a mutation type that mimics a DMD patient, making it a good DMD disease model cell.
- sgRNA is sgRNA-12 as shown in SEQ ID No.19 and sgRNA-13 as shown in SEQ ID No.20, and sgRNA-12 mainly targets the outer surface as shown in SEQ ID No.21 and SEQ ID No.22.
- Exon splicing enhancers. sgRNA-13 mainly targets the exon splicing enhancer as shown in SEQ ID NO.24.
- the above two sgRNA-12s were screened in the human K562 cell line and could induce the skip reading of Exon51.
- Figure 6A the results of reverse transcription PCR after RNA extraction from the edited K562 cells showed that both sgRNAs could Induced mutation, combined use can efficiently induce K562 cells lacking Exon50 to successfully skip to Exon51.
- the open reading frame of Dystrophin protein in iPS cells lacking Exon50 can be restored, thereby rebuilding the expression of Dystrophin protein.
- the specific implementation is as follows:
- mTeSR1 medium was replaced with RPMI/B27-insulin medium containing 6uM CHIR99021, and cultured for 2 days;
- the medium was replaced with RPMI/B27-insulin medium containing 5 ⁇ M IWR1, and cultured for 2 days;
- IWR1 stimulation was removed, the medium was replaced with RPMI/B27-insulin medium, and cultured for 2 days;
- the cell culture medium was changed to RPMI/B27 medium, and then the medium was used for culturing, and the medium was changed every two days to obtain human pluripotent stem cells differentiated into cardiomyocytes.
- iPS cells differentiated into cardiomyocytes were digested with Accutase and plated in 6-well plates, and 4 ⁇ 10 5 cells were plated in each well;
- plasmid expressing AID and Cas9 mutant fusion protein such as Lenti-V2-AIDx-nSaCas9(KKH)-Ugi plasmid
- 500 ng of UGI expressing plasmid such as pCDNA3.1-Ugi
- 1.5 ⁇ g Mix the sgRNA plasmid in 150 ⁇ l opti-MEM, add 2.5 ⁇ l PLUS TM reagent, and mix gently;
- the remaining sgRNA-1 to sgRNA-11 shown in SEQ ID No.7-SEQ ID No.18 all target the corresponding exons shown in SEQ ID No.21-SEQ ID No.24 of the present invention
- the splicing enhancer when constructed as a gene editing tool, efficiently induces skipping Exon51, thereby enabling the treatment of human DMD.
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Abstract
Description
Claims (9)
- 一种杜氏肌营养不良症相关的外显子剪接增强子,其特征在于,所述外显子剪接增强子为靶向人类DMD基因Exon51的外显子剪接增强子元件,其核苷酸序列包括:1)如SEQ ID N0.21所示的序列及其反向互补序列;2)如SEQ ID N0.22所示的序列及其反向互补序列;3)如SEQ ID N0.23所示的序列及其反向互补序列;4)如SEQ ID N0.24所示的序列及其反向互补序列。
- 一种杜氏肌营养不良症相关的sgRNA,其特征在于,所述sgRNA的序列包括:针对Dmd-E4小鼠突变位点的sgRNA,其核苷酸序列如SEQ ID N0.4所示;针对人类DMD基因Exon50的sgRNA,其核苷酸序列如SEQ ID N0.7所示;针对人类DMD基因Exon51的sgRNA-1,其核苷酸序列如SEQ ID N0.8所示;针对人类DMD基因Exon51的sgRNA-2,其核苷酸序列如SEQ ID N0.9所示;针对人类DMD基因Exon51的sgRNA-3,其核苷酸序列如SEQ ID N0.10所示;针对人类DMD基因Exon51的sgRNA-4,其核苷酸序列如SEQ ID N0.11所示;针对人类DMD基因Exon51的sgRNA-5,其核苷酸序列如SEQ ID N0.12所示;针对人类DMD基因Exon51的sgRNA-6,其核苷酸序列如SEQ ID N0.13所示;针对人类DMD基因Exon51的sgRNA-7,其核苷酸序列如SEQ ID N0.14所示;针对人类DMD基因Exon51的sgRNA-8,其核苷酸序列如SEQ ID N0.15所示;针对人类DMD基因Exon51的sgRNA-9,其核苷酸序列如SEQ ID N0.16所示;针对人类DMD基因Exon51的sgRNA-10,其核苷酸序列如SEQ ID N0.17所示;针对人类DMD基因Exon51的sgRNA-11,其核苷酸序列如SEQ ID N0.18所示;针对人类DMD基因Exon51的sgRNA-12,其核苷酸序列如SEQ ID N0.19所示;针对人类DMD基因Exon51的sgRNA-13,其核苷酸序列如SEQ ID N0.20所示。
- 一种权利要求2所述sgRNA在制备治疗杜氏肌营养不良症的药物中的应用。
- 一种杜氏肌营养不良症相关的基因编辑工具,其特征在于,包括胞嘧啶脱氨酶和Cas9突变体的融合蛋白、权利要求2所述sgRNA和载体。
- 根据权利要求4所述的基因编辑工具,其特征在于,所述胞嘧啶脱氨酶为AID,AID和Cas9突变体的融合蛋白的氨基酸序列以及核酸序列分别如SEQ ID NO.1和SEQ ID NO.2所示。
- 根据权利要求4所述的基因编辑工具,其特征在于,所述基因编辑工具由腺相关病毒 载体AAV包装。
- 根据权利要求6所述的基因编辑工具,其特征在于,所述腺相关病毒载体AAV的启动子为Syn100启动子或基于ck8a、mhck7设计的启动子。
- 根据权利要求6所述的基因编辑工具,其特征在于,腺相关病毒载体AAV的核苷酸序列如SEQ ID NO.3所示。
- 一种权利要求4-8任一项所述基因编辑工具在制备治疗杜氏肌营养不良症的药物中的应用。
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WO2022204476A1 (en) * | 2021-03-26 | 2022-09-29 | The Board Of Regents Of The University Of Texas System | Nucleotide editing to reframe dmd transcripts by base editing and prime editing |
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