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MUSCLE DISEASE Gene editing restores dystrophin expression in a canine model of Duchenne muscular dystrophy Leonela Amoasii 1,2 , John C. W. Hildyard 3 , Hui Li 1 , Efrain Sanchez-Ortiz 1 , Alex Mireault 1 , Daniel Caballero 1 , Rachel Harron 3 , Thaleia-Rengina Stathopoulou 4 , Claire Massey 3 , John M. Shelton 5 , Rhonda Bassel-Duby 1 , Richard J. Piercy 3 , Eric N. Olson 1 * Mutations in the gene encoding dystrophin, a protein that maintains muscle integrity and function, cause Duchenne muscular dystrophy (DMD). The deltaE50-MD dog model of DMD harbors a mutation corresponding to a mutational hotspotin the human DMD gene. We used adeno-associated viruses to deliver CRISPR gene editing components to four dogs and examined dystrophin protein expression 6 weeks after intramuscular delivery (n = 2) or 8 weeks after systemic delivery (n = 2). After systemic delivery in skeletal muscle, dystrophin was restored to levels ranging from 3 to 90% of normal, depending on muscle type. In cardiac muscle, dystrophin levels in the dog receiving the highest dose reached 92% of normal. The treated dogs also showed improved muscle histology. These large-animal data support the concept that, with further development, gene editing approaches may prove clinically useful for the treatment of DMD. T he persistent contraction and relaxation of cardiac and skeletal muscles necessitates mechanisms that maintain the integrity of muscle membranes (1, 2). Dystrophin is a large scaffolding protein that supports mus- cle structure and function by linking the cyto- skeleton with the sarcolemma of muscle tissue (1, 3, 4). Mutations in the dystrophin gene cause Duchenne muscular dystrophy (DMD), a disorder primarily affecting boys that is characterized by progressive muscle degeneration and atrophy, leading to premature death from cardiomyopathy and respiratory collapse (5). Thousands of muta- tions have been identified in the dystrophin gene, which spans ~2.5 megabases of DNA and contains 79 exons. Many of these mutations cluster into hotspots,most commonly in a region that spans exons 45 to 50, typically placing exon 51 out of frame with preceding exons and preventing ex- pression of functional dystrophin protein (6, 7). Therapies that induce skippingof exon 51 re- store the reading frame and in principle could benefit ~13% of DMD patients (8). An oligo- nucleotide that allows skipping of exon 51 can restore dystrophin expression to 0.22 to 0.32% of normal levels after 1 year of treatment and has been approved for DMD patients (913). CRISPR-Cas9 gene editing can target DMD mutations and restore dystrophin expression in mice and muscle cells derived from human induced pluripotent stem cells (iPSCs) (1422). An essential step toward clinical translation of gene editing as a therapeutic strategy for DMD is the demonstration of efficacy and safety of this approach in large mammals. The mutation carried by the deltaE50-MD ca- nine model of DMD leads to loss of exon 50 and moreover can be corrected by skipping of exon 51, making this a valuable model for translational studies. First identified as a naturally occurring, spontaneous mutation in Cavalier King Charles Spaniels (23) and now maintained on a beagle background, this model (in contrast to mice) exhibits many of the clinical and pathological RESEARCH Amoasii et al., Science 362, 8691 (2018) 5 October 2018 1 of 5 1 Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA. 2 Exonics Therapeutics, 75 Kneeland Street, Boston, MA 02111, USA. 3 Department of Clinical Science and Services, Comparative Neuromuscular Diseases Laboratory, Royal Veterinary College, London NW1 0TU, UK. 4 Section of Anaesthesia and Analgesia, Royal Veterinary College, London NW1 0TU, UK. 5 Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA. *Corresponding author. Email: [email protected] Fig. 1. Single-cut CRISPR editing of canine exon 50 in vivo and in vitro. (A) Scheme showing the CRISPR-Cas9mediated genome editing approach to correct the reading frame in DEx50 dogs by reframing and skipping of exon 51. Gray exons are out of frame. (B) Illustration of sgRNA binding position and sequence for sgRNA-ex51. PAM sequence for sgRNA is indicated in red. Black arrowhead indicates the cleavage site. (C) Sequence of the RT-PCR products of the DEx50-51 lower band confirmed that exon 49 spliced directly to exon 52, excluding exon 51. Sequence of RT-PCR products of DEx50 reframed (DEx50-RF). (D) Cranial tibialis muscles of DEx50 dogs were injected with AAV9s encoding sgRNA-51 and Cas9 and analyzed 6 weeks later. Dystrophin immunohistochemistry staining of cranial tibialis muscle of wild-type (WT) dog untreated, DEx50 dog untreated, DEx50 dogs contralateral (uninjected) muscle, and DEx50 dogs injected with AAV9-Cas9 and AAV9-sgRNA-51 (referred to as DEx50-#1A-AAV9s and DEx50-#1B-AAV9s). Scale bar: 50 mm. on January 3, 2019 http://science.sciencemag.org/ Downloaded from

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Page 1: MUSCLE DISEASE Gene editing restores dystrophin expression in … · 2020-04-13 · MUSCLE DISEASE Gene editing restores dystrophin expression in a canine model of Duchenne muscular

MUSCLE DISEASE

Gene editing restores dystrophinexpression in a canine model ofDuchenne muscular dystrophyLeonela Amoasii1,2, John C. W. Hildyard3, Hui Li1, Efrain Sanchez-Ortiz1,Alex Mireault1, Daniel Caballero1, Rachel Harron3, Thaleia-Rengina Stathopoulou4,Claire Massey3, John M. Shelton5, Rhonda Bassel-Duby1,Richard J. Piercy3, Eric N. Olson1*

Mutations in the gene encoding dystrophin, a protein that maintains muscle integrityand function, cause Duchenne muscular dystrophy (DMD). The deltaE50-MD dogmodel of DMD harbors a mutation corresponding to a mutational “hotspot” in thehuman DMD gene. We used adeno-associated viruses to deliver CRISPR gene editingcomponents to four dogs and examined dystrophin protein expression 6 weeksafter intramuscular delivery (n = 2) or 8 weeks after systemic delivery (n = 2). Aftersystemic delivery in skeletal muscle, dystrophin was restored to levels rangingfrom 3 to 90% of normal, depending on muscle type. In cardiac muscle, dystrophinlevels in the dog receiving the highest dose reached 92% of normal. The treateddogs also showed improved muscle histology. These large-animal data support theconcept that, with further development, gene editing approaches may prove clinicallyuseful for the treatment of DMD.

The persistent contraction and relaxation ofcardiac and skeletal muscles necessitatesmechanisms thatmaintain the integrity ofmuscle membranes (1, 2). Dystrophin is alarge scaffolding protein that supportsmus-

cle structure and function by linking the cyto-skeleton with the sarcolemma of muscle tissue(1, 3, 4). Mutations in the dystrophin gene causeDuchennemuscular dystrophy (DMD), a disorder

primarily affecting boys that is characterized byprogressive muscle degeneration and atrophy,leading to premature death fromcardiomyopathyand respiratory collapse (5). Thousands of muta-tions have been identified in the dystrophin gene,which spans ~2.5megabases of DNAand contains79 exons. Many of these mutations cluster into“hotspots,”most commonly in a region that spansexons 45 to 50, typically placing exon 51 out of

frame with preceding exons and preventing ex-pression of functional dystrophin protein (6, 7).Therapies that induce “skipping” of exon 51 re-store the reading frame and in principle couldbenefit ~13% of DMD patients (8). An oligo-nucleotide that allows skipping of exon 51 canrestore dystrophin expression to 0.22 to 0.32%of normal levels after 1 year of treatment and hasbeen approved for DMD patients (9–13).CRISPR-Cas9 gene editing can target DMD

mutations and restore dystrophin expressionin mice and muscle cells derived from humaninduced pluripotent stem cells (iPSCs) (14–22).An essential step toward clinical translation ofgene editing as a therapeutic strategy for DMDis the demonstration of efficacy and safety of thisapproach in large mammals.The mutation carried by the deltaE50-MD ca-

nine model of DMD leads to loss of exon 50 andmoreover can be corrected by skipping of exon 51,making this a valuable model for translationalstudies. First identified as a naturally occurring,spontaneous mutation in Cavalier King CharlesSpaniels (23) and now maintained on a beaglebackground, this model (in contrast to mice)exhibits many of the clinical and pathological

RESEARCH

Amoasii et al., Science 362, 86–91 (2018) 5 October 2018 1 of 5

1Department of Molecular Biology, Hamon Center forRegenerative Science and Medicine, Sen. Paul D. WellstoneMuscular Dystrophy Cooperative Research Center, Universityof Texas Southwestern Medical Center, 5323 Harry HinesBoulevard, Dallas, TX 75390, USA. 2Exonics Therapeutics,75 Kneeland Street, Boston, MA 02111, USA. 3Department ofClinical Science and Services, Comparative NeuromuscularDiseases Laboratory, Royal Veterinary College, LondonNW1 0TU, UK. 4Section of Anaesthesia and Analgesia, RoyalVeterinary College, London NW1 0TU, UK. 5Department ofInternal Medicine, University of Texas Southwestern MedicalCenter, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.*Corresponding author. Email: [email protected]

Fig. 1. Single-cut CRISPR editing of canine exon 50 in vivo andin vitro. (A) Scheme showing the CRISPR-Cas9–mediated genomeediting approach to correct the reading frame in DEx50 dogs byreframing and skipping of exon 51. Gray exons are out of frame.(B) Illustration of sgRNA binding position and sequence for sgRNA-ex51.PAM sequence for sgRNA is indicated in red. Black arrowhead indicatesthe cleavage site. (C) Sequence of the RT-PCR products of the DEx50-51lower band confirmed that exon 49 spliced directly to exon 52, excluding

exon 51. Sequence of RT-PCR products of DEx50 reframed (DEx50-RF).(D) Cranial tibialis muscles of DEx50 dogs were injected with AAV9sencoding sgRNA-51 and Cas9 and analyzed 6 weeks later. Dystrophinimmunohistochemistry staining of cranial tibialis muscle of wild-type(WT) dog untreated, DEx50 dog untreated, DEx50 dogs contralateral(uninjected) muscle, and DEx50 dogs injected with AAV9-Cas9and AAV9-sgRNA-51 (referred to as DEx50-#1A-AAV9s andDEx50-#1B-AAV9s). Scale bar: 50 mm.

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"Large animal models" describes non-rodent animals used for research including dogs and pigs. Mice and rats play very important roles in research, but for many diseases, large animal models more closely represent the human symptoms and response to therapies.
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Experiments in mice and cell culture are relatively rapid, high-throughput and cost-efficient compared to large animals. Therefore, potential therapies are usually first tested and developed in these systems before moving onto large animals.
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The defect in this dog model is similar to the defects found in a significant proportion of human DMD patients. This means that therapies tested with this model have the potential to help as many patients as possible.
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This oligonucleotide therapy has quite a modest effect on dystrophin levels. Compare these numbers to the improvement in dystrophin levels reported in this paper (3-90% of normal).
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This sentence makes it clear that the work here is exciting and promising for future therapies, but that there is still much work done before a treatment like this can help human patients.
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Repairing dystrophin expression in cardiac muscle is particularly important for a DMD treatment, since cardiomyopathy is a major cause of death of DMD patients.
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This strategy uses a single cut to cause reframing of the gene. This is in contrast to some other strategies that were reported slightly before this paper, which used multiple sgRNAs at once to generate two cuts in the gene. This results in excision of a larger piece of the gene.
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The dogs were only injected with the virus on one side of their body, allowing the researchers to compare the injected side and uninjected side of the same dog.
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Figure panels A and C summarize the main ways that the dystrophin reading frame was restored after introducing a DSB into the specified site of exon 51.
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This sentence summarizes the major goal of the study, as a step along the path towards therapeutic gene editing.
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The huge size of the dystrophin gene is an important consideration for therapies. For some diseases, patients can see improvement by introducing a "good" copy of the gene. However, the large size of the dystrophin gene makes delivering a good copy very challenging. Therefore, DMD therapies in general try to modify the existing dystrophin gene to correct the defect.
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This was an international effort, coordinated between researchers in the US and the UK.
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features of the human disease, such as muscleweakness, atrophy, and fibrosis (24).To correct the dystrophin reading frame in the

deltaE50-MD caninemodel (henceforth referredto as DEx50) (Fig. 1A), we used Streptococcuspyogenes Cas9 coupled with a single guide RNA(sgRNA) to target a region adjacent to the exon51 splice acceptor site (referred to as sgRNA-51)(Fig. 1B). The sgRNA-51 corresponded to a highlyconserved sequence that differs by only one nu-cleotide between the human and dog genomes(fig. S1A). Cas9 coupledwith each of these sgRNA-51 sequences introduced a genomic cut only inDNA of the respective species (fig. S1B).For the in vivo delivery of Cas9 and sgRNA-

51 to skeletalmuscle and heart tissue in dogs, weused recombinant adeno-associated virus sero-type 9 (referred to as AAV9), which displays pre-ferential tropism for these tissues (25, 26). Amuscle-specific creatine kinase (CK) regulatorycassette was used to drive expression of Cas9;three RNA polymerase III promoters (U6, H1,and 7SK) directed expression of the sgRNA, asdescribed previously inmice (fig. S2) (18). AAV9-Cas9 and AAV9-sgRNA-51 were initially intro-duced into the cranial tibialis muscles of two1-month-old dogs by intramuscular injectionwith 1.2 × 1013 AAV9 viral genomes (vg) of eachvirus. Muscles were analyzed 6 weeks after in-jection. In vivo targeting efficiency was esti-mated within muscle biopsy samples by reversetranscription–polymerase chain reaction (RT-PCR) with primers for sequences in exons 48and 53, and genomic PCR amplification pro-ducts spanning the target site were subjectedto amplicon deep sequencing. The latter indicatedthat a mean of 9.96% of total reads containedchanges at the targeted genomic site, includinginsertions, deletions, and substitutions (fig. S3).Themost commonly identifiedmutations witha mean of 2.35% contained an adenosine (A) in-sertion immediately 3′ to the Cas9 genomic cut-ting site (Fig. 1C). The deletions identified withthis method encompassed a highly predictedexonic splicing enhancer (ESE) site for exon 51(18, 27, 28) (fig. S3A). However, this method doesnot identify larger deletions that might occurbeyond the annealing sites of the primers usedfor PCR. Because these tissue samples containa mixture of muscle and nonmuscle cells, themethod likely underestimates the efficiency ofgene editing within muscle cells.Sequencing of RT-PCR products of RNA from

muscle of DEx50 dogs injected intramuscularlywith AAV9-Cas9 and AAV9-sgRNA-51 showedthat deletion of exon 51 (DEx50-51) allowedsplicing from exon 49 to 52, which restores thedystrophin open reading frame (fig. S3B). Ongels, the PCR product with the A insertion wasindistinguishable in size from non-edited cDNAproducts, so we performed deep-sequencing anal-ysis to quantify its abundance compared to othersmall insertions. Deep sequencing of the upperband containing the non-edited cDNA productand reframed cDNA products indicated that amean of 73.19% of total reads contained reframedcDNA products with an A insertion, a mean of

26.81% contained non-edited cDNAproduct, andthe rest contained small deletions and insertions(fig. S3C). However, nonsense-mediated decaymight affect the abundance of non-edited cDNAproducts. These data indicate that the two DEx50dogs injectedwith AAV9-Cas9 andAAV9-sgRNA-51 had a high frequency of reframing events(with cDNA products containing an A insertionin the sequence of exon 51) and exon 51 skippingevents resulting from deletion of the highly con-served ESE region.To evaluate the specificity of our gene edit-

ing approach, we analyzed predicted off-targetgenomic sites for possible promiscuous editing.A total of three potential genome-wide off-targetsites (OT1 to OT3) (fig. S4) were predicted in cod-ing exons and four in noncoding regions (fig. S4)by theCRISPRdesign tool (http://crispr.mit.edu/).We performed deep sequencing at the top pre-dicted off-target sites within protein-codingexons. None of these sites revealed notablymore sequence alterations than the backgroundanalysis performed with other regions of theamplicons (fig. S5).To evaluate dystrophin correction at the pro-

tein level, we performed histological analysis ofAAV9-injected cranial tibialis muscles 6 weeksafter AAV9 injection. Dystrophin immunohisto-

chemistry of muscle from DEx50 dogs injectedwith AAV9-Cas9 and AAV9-sgRNA-51 revealedwidespread expression: The majority of fiberswithin the injected muscles expressed sarcolem-mal dystrophin, albeit to varying levels (Fig. 1D).Western blot analysis confirmed the restorationof dystrophin expression in skeletalmuscle (Fig. 2,A and B) to ~60% of wild-type (WT) levels. Onaverage, 2% of WT levels of dystrophin weredetected in the uninjected contralateral muscles,far more than could be attributed to rare rever-tant events, which typically represent fewer than0.001% of fibers and are undetectable byWesternblot in DEx50 muscle. We attribute expression inuninjected contralateral muscles to leakage ofAAV9 into circulation. As assessed byhematoxylinand eosin (H&E) staining, the injected musclesappeared to be normalized relative to muscles ofuntreated animals, with fewer hypercontractedor necrotic fibers, reduced edema and fibrosis,and fewer regions of inflammatory cellular in-filtration (Fig. 2C). Immunohistochemistry fordevelopmental myosin heavy chain (dMHC), amarker of regenerating fibers, revealed amarkedreduction in dMHC-positive fibers within in-jected muscles (fig. S6).Dystrophin nucleates a series of proteins into

the dystrophin-associated glycoprotein complex

Amoasii et al., Science 362, 86–91 (2018) 5 October 2018 2 of 5

Fig. 2. Dystrophin correction after intramuscular delivery of AAV9-encoded gene editingcomponents. (A) Western blot analysis of dystrophin (DMD) and vinculin (VCL) expression in cranialtibialis muscles 6 weeks after intramuscular injection in 2 dogs (#1A and #1B). (B) Quantificationof dystrophin expression from blots after normalization to vinculin. (C) Histochemistry by H&Estaining of cranial tibialis muscle from a WTdog, DEx50 dog untreated, DEx50 contralateral uninjected,and DEx50 dogs injected intramuscularly with AAV9-Cas9 and AAV9-sgRNA-51 (referred to asDEx50-Dog-#1A-AAV9s and DEx50-Dog-#1B-AAV9s). Scale bar: 50 mm.

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This experiment shows that the cutting is very specific - even a single nucleotide mismatch between the sgRNA sequence and the genome sequence stops Cas9 from cutting the sequence.
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Adeno-associated viruses are currently the most common viruses for developing gene therapies. Normally the virus is a capsid containing viral DNA, but the capsid can be made without the viral DNA (called recombinant AAV). This essentially provides a shell for delivering DNA cargo into cells.
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These authors had previous developed and tested many aspects of this strategy in a mouse model. In their earlier work, they had introduced a double-strand break by CRISPR/Cas9 at the same site in the mouse gene as they are introducing here in the dog gene. For this paper, they also checked that the sgRNAs worked in cultured dog cells before building the AAV vector.
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This strategy doesn't introduce a repair template, so the DSB is repaired by NHEJ, which introduces a variety of mutations.
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The fact that the most common mutation is an insertion of a single nucleotide is a lucky break! This mutation restores the reading frame in exon 51. In their earlier work, the authors found that introduction of a single adenosine was also very common after CRISPR/Cas9 cutting in mice as well as mouse and human cells. It is not clear why this preference exists, but there is some evidence that A is preferentially inserted at DSBs, a phenomenon known as the "A rule."
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One way to restore the reading frame of the dystrophin gene is to leave out exon 51 entirely, and skip from exon 49 over to 52 (remember that exon 50 is already missing in this model). This region of exon 51 was chosen as the target for CRISPR/Cas9 cutting in the original mouse study because it contained a region that signals that exon 51 should be included when the gene is spliced (called an exonic splicing enhancer, ESE). The goal was to make mutations in this sequence, so that exon 51 is no longer included when the gene is spliced. In the mouse study, the authors found the adenosine insertion as a common alternative outcome of this strategy that also restores dystrophin expression.
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Overall, using this sgRNA the authors found two common categories of mutation that can put the dystrophin gene back in frame: either a single nucleotide (A) insertion, or mutations that cause exon 51 to be left out when the gene is spliced. These are shown in Figure 1.
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As one way to see if their strategy worked, the authors look at the size of part of the mRNA of the dystrophin gene (via RT-PCR). If exon 51 is skipped (for example because NHEJ introduced a mutation into the exonic splicing enhancer), the mRNA will be smaller, and will therefore run at a lower position on a gel.
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A significant concern for gene editing therapies is whether the therapy cuts at sites other than the intended targets. These off-target cuts could result in deleterious mutations. Computational tools allow researchers to predict where the most likely off-target events would occurs, so they can check if these sites were edited. However, these experiments do not survey the whole genome, so cannot totally rule out the possibility of some off-target editing somewhere else in the genome.
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There are two common ways to see if a protein is present: either to look for it directly in intact cells (immunohistochemistry), or to break the cells open, run their contents on a gel, and then probe for the protein (Western blot). Both have advantages. Immunohistochemistry tells you if the protein is in the right place in the cell. Western blot can tell you if the protein is the right size (remember that some mutations can abnormally shorten the protein). Here, the authors find that the protein produced by DMD dogs that have had their dystrophin genes repaired is in the same place and the same size as the protein from dogs without DMD mutations.
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The authors see that some cells are repaired on the uninjected side of the dog. They conclude that some of the AAV can get into the bloodstream, allowing it to move away from the injection site. The same effect was seen in mice.
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In addition to seeing that the dystrophin protein is being produced, the authors also see a reduction in DMD defects in the muscles.
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Cas9 is a relatively large gene, so Cas9 and the sgRNA cannot both fit into a single viral capsid. Therefore, they are packaged into separate viruses and injected together.
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The intensity (essentially the thickness and darkness) of a band on a Western blot can tell you how much of your protein is in your sample. When comparing the intensity of a particular protein band between samples, you want to ensure that samples you compare are otherwise identical (for example, they contain essentially the same number of cells). To do this, researchers also probe for a second protein that is expected to be the same between the two samples - in this paper, vinculin (VCL).
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RT-PCR converts mRNA back into DNA (then referred for as a cDNA), and amplifies the product so that it can be easily detected. It is a sensitive and quantitative strategy to detect even low abundance mRNAs. The resulting cDNA can also be used for sequencing.
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(DGC) to link the cytoskeleton and extracellularmatrix (3, 4). In DEx50 mice, dogs, and DMDpatients, these proteins are destabilized and donot localize to the subsarcolemmal region (4).Muscles injected with AAV9-Cas9 and AAV9-sgRNA-51 showed recovery of the DGC proteinb-dystroglycan compared to contralateral unin-jected muscles (fig. S7). We conclude that—atleast in a short time frame of 6 weeks—single-cut genomic editing usingAAV9-Cas9 andAAV9-sgRNA-51 can efficiently restore dystrophinexpression and assembly of the DGC in dys-trophic muscles. Immunohistochemistry usingcanine-specific CD4 and CD8 T cell markers(fig. S8) showed no evidence of enhanced mono-nuclear cellular infiltration or relevant hema-tological abnormalities in the treated animalscompared to untreated controls or referenceranges (fig. S9).Based on the high dystrophin-correction effi-

ciency observed after intramuscular injection ofAAV9-Cas9 and AAV9-sgRNA-51, we tested forrescue of dystrophin expression in two DEx50dogs after systemic delivery of gene editingcomponents. The dogs at 1 month of age wereinjected intravenously with the viruses andanalyzed 8 weeks later. We tested two doses(2 × 1013 vg/kg and 1 × 1014 vg/kg) of each of thetwo viruses (AAV9-Cas9 and AAV9-sgRNA-51).To avoid a possible immune reaction,we includeda transient regimen of immune suppression withthe high dose. Systemic delivery of 2 × 1013 vg/kgof each virus (total virus 4 × 1013 vg/kg) in DEx50-Dog-#2A resulted in expression of virus in pe-ripheral skeletalmuscle samples and, to a lowerextent, in heart samples, as shown by quan-titative PCR (qPCR) analysis (fig. S10A). Thedelivery of 1 × 1014 vg/kg of each virus (totalvirus 2 × 1014 vg/kg) in DEx50-Dog-#2B (viainfusion) allowed more widespread expressionof viral constructs in the peripheral skeletalmuscle samples and in heart samples (fig. S10B).Systemic delivery of AAV9-Cas9 and AAV9-sgRNA-51 led to dystrophin expression in a broadrange of muscles, including the heart, in gene-edited DEx50 dogs at 8 weeks after injection—and to a markedly greater extent than thatachieved with the lower dose (Fig. 3).To investigate the proportions of various in-

sertions and deletions (indels) generated by sys-temic delivery of AAV9-Cas9 andAAV9-sgRNA-51,we performed amplicon deep-sequencing analysisof the genomic DNA from heart, triceps, andbiceps muscles. The genomic deep-sequencinganalysis revealed an increased percentage of readscontaining changes at the targeted genomic site,especially of the 1A insertion mutation in the sam-ples from Dog-#2B compared to Dog-#2A (fig. S11).Additionally, we performed tracking indels

by decomposition (TIDE) (30) analysis at thegenomic and cDNA levels, which showed anincrease in numbers of indels in the samples fromDog-#2B compared to the samples from Dog-#2A(fig. S12). Testes analysis andWestern blot analy-sis showed no activity of Cas9 and confirmedmuscle-specific expression of gene editing machin-ery (fig. S13). Western blot analysis confirmed

Amoasii et al., Science 362, 86–91 (2018) 5 October 2018 3 of 5

Fig. 3. Immunostaining of dystrophin after intravenous delivery of AAV9-encoded geneediting components. Dystrophin immunohistochemistry staining of cranial tibialis, semitendinosus,biceps, triceps, diaphragm, heart, and tongue muscles of WT dog, untreated DEx50 dog, andDEx50 dogs injected systemically with AAV9-Cas9 and AAV9-sgRNA-51 at 2 × 1013vg/kg (total virus4 × 1013 vg/kg, referred to as DEx50-Dog #2A-AAV9s) and 1 × 1014 vg/kg (total virus 2 × 1014 vg/kg,referred to as DEx50-Dog #2B-AAV9s) for each virus.

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These experiments show that the dystrophin protein from the repaired gene can also interact with the normal binding partners of dystrophin, and direct them to the right places.
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After determining that their strategy worked when locally targeting a muscle by direct injection, they next wanted to know if they could broadly repair muscles throughout the body by introducing the viruses into the bloodstream. Since the Cas9 is expressed under a muscle-specific promoter, it will still only introduce DSBs into muscle cells.
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Determining the dose of a treatment that gives a maximal effect with minimal side-effects is a critical part of testing a therapy.
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A higher dose of virus is required to give a strong restoration of dystrophin expression in muscles throughout the body. The heart in particular showed very limited improvement at the lower dose.
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the restoration of dystrophin expression in skel-etal muscle (Fig. 4, A and B) to ~50, 20, and 3% ofWT levels for the cranial tibialis, triceps, andbiceps, respectively, after systemic delivery of2 × 1013 vg/kg of each virus (total virus 4 ×1013 vg/kg). For Dog-#2B, which received 1 ×1014 vg/kg of each virus (total virus 2 × 1014 vg/kg),Western blot analysis showed restoration ofdystrophin expression (Fig. 4, C and D, and fig.S14) to ~70, 25, 64, 58, 92, and 5% of WT levelsfor the cranial tibialis, triceps, biceps, diaphragm,heart, and tongue muscles, respectively. Similarto what was seen after intramuscular injection,muscles appeared normalized via H&E stain-ing (Fig. 4E). Immunostaining ofmuscle sectionsfrom treated DEx50 dogs also showed recoveryof b-dystroglycan expression (fig. S15) and wide-spread reduction in dMHC (fig. S16).To determine hematological and biochemical

parameters of the treated dogs compared to thecontrols, we collected blood samples the day be-fore injection and then at 1, 2, 4, 6, and 8 weeksafter injection. The blood samples from all fourdogs [healthy untreated, DEx50 untreated, andDEx50 dogs receiving 2 × 1013 vg/kg of eachvirus (total virus 4 × 1013 vg/kg) and 1 × 1014 vg/kgof each virus (total virus 2 × 1014 vg/kg)] beforeand after injection were unremarkable (fig. S17).Hematology counts, serum electrolytes, and kid-ney and liver function parameters remainedwith-in the normal ranges in all dogs. Additionally,blood samples were collected weekly for CK as-sessment:We observed amodest decline in serumCK activity in Dog-#2B treated with 1 × 1014 vg/kgof each virus (total virus 2 × 1014 vg/kg) (fig. S18)compared to the DEx50 untreated dog.To evaluate the targeting efficiency of a human

DMDmutation, we used a DMD iPSC line carry-ing a deletion from exon 48 to 50. Deletion ofexons 48 to 50 leads to a frameshift mutationand appearance of a premature stop codon inexon 51. To correct the dystrophin reading frame,we introduced two concentrations of Cas9 andsgRNA-51 (26 ng/ml, referred to as high, and13 ng/ml, referred to as low). Indel analysis showed55.8 and 31.9% of indels for the high and low con-centrations, respectively (fig. S19). Genomic deep-sequencing analysis revealed that 27.94% ofmutations contained a single A insertion 3′ to theprotospacer adjacent motif (PAM) sequence forthe high concentration condition and 19.03% forthe low concentration condition (fig. S20A), asobserved in mouse and dog cells with a similarsgRNA directed against the same genomic locus.DMD iPSCs treated with Cas9 and sgRNA-51 andinduced to form cardiomyocytes (iCMs) showedrestoration of dystrophin immunostaining (fig.S20B) and expression of dystrophin protein to 67to 100% of the levels of WT cardiomyocytes, asmeasured by Western blot (fig. S20, C and D).It has been estimated that even 15% of normal

levels of dystrophin would provide substantialtherapeutic benefits for DMD patients (30–32).Our results demonstrate the efficacy of single-cutgenome editing for restoration of dystrophin ex-pression in a large-animal model of DMD, reach-ing up to ~80% of WT levels in some muscles

Amoasii et al., Science 362, 86–91 (2018) 5 October 2018 4 of 5

Fig. 4. Western blot of dystrophin and muscle histology after intravenous delivery ofAAV9-encoded gene editing components. (A) Western blot analysis of dystrophin (DMD)and vinculin (VCL) of cranial tibialis, triceps, and biceps muscles of WT, untreated DEx50, andDEx50 injected with AAV9-Cas9 and AAV9-sgRNA-51 at 2 × 1013 vg/kg for each virus (totalvirus 4 × 1013 vg/kg, referred to as DEx50-Dog #2A-AAV9s). (B) Quantification of dystrophinexpression from blots after normalization to vinculin. (C) Western blot analysis of DMD andVCL of cranial tibialis, triceps, biceps, diaphragm, heart, and tongue muscles of WT, untreatedDEx50, and DEx50 injected with AAV9-Cas9 and AAV9-sgRNA-51 at 1 × 1014 vg/kg (totalvirus 2 × 1014 vg/kg, referred to as DEx50-Dog #2B-AAV9s). (D) Quantification of dystrophinexpression from blots after normalization to vinculin. (E) H&E staining of cranial tibialis,diaphragm, and biceps muscles of WT, untreated DEx50, and DEx50 injected with AAV9-Cas9and AAV9-sgRNA-51 at 2 × 1013 vg/kg for each virus (total virus 4 × 1013 vg/kg) and1 × 1014vg/kg for each virus (total virus 2 × 1014 vg/kg). Scale bar: 50 mm.

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In general, the authors see very similar effects of systemic treatment with the viruses as they saw with injection directly into the muscle, particularly in the dog that received the higher dose.
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These experiments suggest that there aren't significant side effects of systemic administration of the virus on the overall health of the dog.
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Induced pluripotent stem cells (iPSCs) provide a valuable strategy to test the feasibility of applying certain treatments in humans. They can be induced to convert into specific cell types, to model the effects of the mutation or treatment on function of particular tissues. They can be generated from patients with specific mutations, or generated from healthy people and the mutations inserted by genome editing. These iPSCs can then used to study therapeutic strategies.
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after 8 weeks. Longer-term studies are requiredto establish whether the expression of dystro-phin and the maintenance of muscle integritythat we observed are sustained.This study, while encouraging, is preliminary

and has several limitations, including the rela-tively small number of animals analyzed and theshort duration of the analysis (6 to 8 weeks).The possibility of off-target effects of in vivo geneediting is a further potential safety concern. Al-though our initial deep-sequencing analysis ofthe top predicted off-target sites revealed nospecific off-target gene editing above backgroundlevels in treated animals, it will be important tofurther assess possible off-target mutagenesisin longer-term studies with greater numbers ofanimals. Recent studies reported large deletionsand complex genomic rearrangements at targetsites of CRISPR-Cas9 in mouse embryonic cells,hematopoietic progenitors, and human immor-talized epithelial cells (33). However, these cellsare highly proliferative, are more genomicallyunstable in culture, and use different DNA repairpathways than somatic postmitotic cells (such asmuscle and heart cells) (34). Future studies willbe required to investigate the long-term genomicstability of gene-edited muscle tissues in vivo.Another potential concern with CRISPR-Cas9–mediated gene editing in vivo is immunogenicityof Cas9, particularly as expression persists afterinitial treatment. In this short-term study, we didnot observe CD4- or CD8-positive cell infiltrationof treated muscle, but longer-term studies withmore sensitive assays must be performed. Addi-tionally, although production of large quantitiesof AAV9 poses a challenge, doses of 2 × 1014vg/kghave been successfully used in human gene ther-apy trials (35).Finally, although gene editing and exon-skipping

oligonucleotides can both restore production of

internally deleted dystrophin proteins, similarto those expressed in Becker muscular dystro-phy, there are key distinctions between theseapproaches. Most notably, CRISPR gene editingmay be permanent and not require redelivery,whereas oligonucleotides require continuoustreatment. A corollary of this is that CRISPRtreatment may be difficult to terminate if safetyconcerns arise.

REFERENCES AND NOTES

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3. K. P. Campbell, S. D. Kahl, Nature 338, 259–262 (1989).4. J. M. Ervasti, K. Ohlendieck, S. D. Kahl, M. G. Gaver,

K. P. Campbell, Nature 345, 315–319 (1990).5. F. Muntoni, S. Torelli, A. Ferlini, Lancet Neurol. 2, 731–740 (2003).6. C. L. Bladen et al., Hum. Mutat. 36, 395–402 (2015).7. Y. Li et al., J. Int. Med. Res. 44, 99–108 (2016).8. A. Aartsma-Rus et al., Hum. Mutat. 30, 293–299 (2009).9. Y. Shimizu-Motohashi, S. Miyatake, H. Komaki, S. Takeda,

Y. Aoki, Am. J. Transl. Res. 8, 2471–2489 (2016).10. C. A. Stein, Mol. Ther. 24, 1884–1885 (2016).11. A. Aartsma-Rus, A. M. Krieg, Nucleic Acid Ther. 27, 1–3 (2017).12. J. J. Dowling, Nat. Rev. Neurol. 12, 675–676 (2016).13. J. R. Mendell et al., Ann. Neurol. 79, 257–271 (2016).14. C. Long et al., Science 351, 400–403 (2016).15. M. Tabebordbar et al., Science 351, 407–411 (2016).16. C. E. Nelson et al., Science 351, 403–407 (2016).17. C. Long et al., Sci. Adv. 4, p9004 (2018).18. L. Amoasii et al., Sci. Transl. Med. 9, eaan8081 (2017).19. N. E. Bengtsson et al., Nat. Commun. 8, 14454 (2017).20. J. P. Tremblay, J.-P. Iyombe-Engembe, B. Duchêne,

D. L. Ouellet, Mol. Ther. 24, 1888–1889 (2016).21. C. S. Young et al., Cell Stem Cell 18, 533–540 (2016).22. D. G. Ousterout et al., Nat. Commun. 6, 6244 (2015).23. G. L. Walmsley et al., PLOS ONE 5, e8647 (2010).24. J. Hildyard et al., Neuromuscul. Disord. 28, S18 (2018).25. Y. Yue et al., Hum. Mol. Genet. 24, 5880–5890 (2015).26. C. Zincarelli, S. Soltys, G. Rengo, J. E. Rabinowitz, Mol. Ther. 16,

1073–1080 (2008).27. P. J. Smith et al., Hum. Mol. Genet. 15, 2490–2508 (2006).28. L. Cartegni, J. Wang, Z. Zhu, M. Q. Zhang, A. R. Krainer,

Nucleic Acids Res. 31, 3568–3571 (2003).

29. E. K. Brinkman, T. Chen, M. Amendola, B. van Steensel,Nucleic Acids Res. 42, e168 (2014).

30. C. Godfrey et al., Hum. Mol. Genet. 24, 4225–4237 (2015).31. M. van Putten et al., J. Mol. Cell. Cardiol. 69, 17–23 (2014).32. A. H. Beggs et al., Am. J. Hum. Genet. 49, 54–67 (1991).33. M. Kosicki, K. Tomberg, A. Bradley, Nat. Biotechnol. 36,

765–771 (2018).34. E. D. Tichy et al., Stem Cells Dev. 19, 1699–1711 (2010).35. J. R. Mendell et al., N. Engl. J. Med. 377, 1713–1722 (2017).

ACKNOWLEDGMENTS

We thank V. Malladi (UT Southwestern Department of ClinicalSciences) for bioinformatics analysis; D. Church, S. Niessen,and D. Wells (RVC) for helpful research and clinical advice;staff and veterinarians within the RVC Biological Sciences Unitfor technical assistance and animal care; C. Rodriguez forassistance; and J. Cabrera for graphics. We are grateful toS. Hauschka (University of Washington) for the CK8 promoter.Funding: This work was supported by grants from the NIH(HL130253 and AR-067294), a Senator Paul D. Wellstone MuscularDystrophy Cooperative Research Center grant (U54 HD 087351),the Robert A. Welch Foundation (grant 1-0025 to E.N.O.), CureDuchenne, and Exonics Therapeutics. The RVC dog colonyprogram was established and/or is supported by grants fromthe Wellcome Trust (101550/Z/13/Z), Muscular Dystrophy UK(RA3/3077), Joining Jack, and Duchenne Ireland. Authorcontributions: L.A., J.C.W.H., C.M., T.-R.S., R.H., and R.J.P.performed the animal procedures; L.A., J.C.W.H., H.L., J.M.S.,and E.S.-O. performed the experiments; A.M. and D.C performedtissues pulverization; R.H. and C.M. assisted in the animal careand procedure. Competing interests: L.A., R.B.-D., R.J.P., andE.N.O. are consultants for Exonics Therapeutics. L.A. and E.N.O.are co-inventors on a patent application (provisional filingnumber 62/442,606) related to the strategy presented in thisstudy. The other authors declare no competing interests. Dataand materials availability: All data needed to evaluate theconclusions in the paper are present in the paper andsupplementary materials.

SUPPLEMENTARY MATERIALS

www.sciencemag.org/content/362/6410/86/suppl/DC1Materials and MethodsFigs. S1 to S20Table S1

11 May 2018; accepted 17 August 2018Published online 30 August 201810.1126/science.aau1549

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It will be important to know how long after treatment the beneficial effects persist. In principle, the gene edit is permanent and protein function will remain as long as the edited cell persists. However, these cells may eventually die and be replaced by descendants of un-edited cells.
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Therapeutic studies are exciting, and can give hope for patients and their families. Here, the authors provide reasons for caution.
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Since Cas9 is a bacterial protein, there are some concerns that patients who have had a prior exposure to the bacteria from which the Cas9 is derived will have a pre-existing immunity to Cas9. This could decrease efficacy of a treatment, or cause a dangerous immune reaction.
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Here, the authors compare their strategy with oligonucleotides that skip exon 51, which have shown efficacy in clinical trials and been FDA-approved as DMD treatments.
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Duchenne muscular dystrophy arises from mutations that cause frameshifts in the dystrophin gene. Becker muscular dystrophy mutations maintain the reading frame but remove a middle part of the protein. In general, patients with BMD have milder symptoms than DMD patients.
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dystrophyGene editing restores dystrophin expression in a canine model of Duchenne muscular

Thaleia-Rengina Stathopoulou, Claire Massey, John M. Shelton, Rhonda Bassel-Duby, Richard J. Piercy and Eric N. OlsonLeonela Amoasii, John C. W. Hildyard, Hui Li, Efrain Sanchez-Ortiz, Alex Mireault, Daniel Caballero, Rachel Harron,

originally published online August 30, 2018DOI: 10.1126/science.aau1549 (6410), 86-91.362Science 

, this issue p. 86ScienceRestoration of dystrophin expression was accompanied by improved muscle histology.editing components resulted in a substantial increase in dystrophin protein levels in skeletal and heart muscle.dog model of DMD that exhibits many features of the human disease. Intramuscular or systemic delivery of the gene

tested this strategy in aet al.yielded promising results in mouse models of DMD. In a small, short-term study, Amoasii hasin skeletal and heart muscle. The gene editing technology CRISPR-Cas9 can correct disease-causing mutations and

proteinspan. The disease is caused by mutations that reduce or prevent expression of dystrophin, an essential structural Duchenne muscular dystrophy (DMD) is characterized by progressive muscle weakness and a shortened life

Gene editing and muscular dystrophy

ARTICLE TOOLS http://science.sciencemag.org/content/362/6410/86

MATERIALSSUPPLEMENTARY http://science.sciencemag.org/content/suppl/2018/08/29/science.aau1549.DC1

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