Healing muscular dystrophy with CRISPR

This article first appeared in Science magazine and is by Jocelyn Kaiser, staff writer

The red-hot genome editing tool known as CRISPR has scored another achievement — researchers have used it to treat a severe form of muscular dystrophy in mice.

Three groups report in Science that they wielded CRISPR to snip out part of a defective gene in mice with Duchenne muscular dystrophy (DMD), allowing the animals to make an essential muscle protein. The approach is the first time CRISPR has been successfully delivered throughout the body to treat grown animals with a genetic disease.

DMD, which mainly affects boys, stems from defects in the gene coding for dystrophin, a protein that helps strengthen and protect muscle fibers. Without dystrophin, skeletal and heart muscles degenerate; people with DMD typically end up in a wheelchair, then on a respirator, and die around age 25. The rare disease usually results from missing DNA or other defects in the 79 exons, or stretches of protein-coding DNA, that make up the long dystrophin gene.

Researchers haven’t yet found an effective treatment for the DMD disorder. It has proven difficult to deliver enough muscle-building stem cells into the right tissues to stop the disease. Conventional gene therapy uses a virus to carry a good version of a broken gene into cells, but can’t replace the full dystrophin gene as it is too large.

Some gene therapists are hoping to give people with DMD a “micro” dystrophin gene that would result in a short but working version of the protein and reduce the severity of the disease. Companies have also developed compounds that cause the cell’s DNA-reading machinery to bypass a defective exon in the dystrophin gene and produce a short but functional form of the crucial protein. But these so-called exon-skipping drugs haven’t yet won over regulators because they have side effects and only modestly improved muscle performance in clinical trials.

Now, CRISPR has entered the picture. The technology, which Science dubbed 2015’s Breakthrough of the Year, relies on a strand of RNA to guide an enzyme called Cas9 to a precise spot in the genome, where the enzyme snips the DNA. Cells then repair the gap either by rejoining the broken strands or by using a provided DNA template to create a new sequence.

Scientists have already used CRISPR to correct certain genetic disorders in cells taken from animals or people and to treat a liver disease in adult mice. Last year, researchers showed CRISPR could repair flawed dystrophin genes in mouse embryos.

But using CRISPR to treat people who already have DMD seemed impractical, because mature muscle cells in adults don’t typically divide and therefore don’t have the necessary DNA repair machinery turned on for adding or correcting genes. CRISPR could, however, be used to snip out a faulty exon so that the cell’s gene reading machinery would make a shortened version of dystrophin—similar to the exon-skipping and microgene approaches.

Now, three teams have done just this in young mice with DMD. Graduate student Chengzu Long and others in Eric Olson’s group at University of Texas Southwestern Medical Center in Dallas used a harmless adeno-associated virus to carry DNA encoding CRISPR’s guide RNA and Cas9 into the mice’s muscle cells and cut out the faulty exon  — Science1. In the treated mice, which had CRISPR-ferrying viruses injected directly into muscles or into their bloodstream, heart and skeletal muscle cells made a truncated form of dystrophin, and the rodents performed better on tests of muscle strength than untreated DMD mice.

Teams led by biomedical engineer Charles Gersbach of Duke University in Durham, North Carolina, and Harvard stem cell researcher Amy Wagers, both collaborating with CRISPR pioneer Feng Zhang of Harvard and the Broad Institute in Cambridge, Massachusetts, report similar results — Science2.

CRISPR’s accuracy was also reassuring. None of the teams found much evidence of off-target effects — unintended or potentially harmful cuts to other parts of the genome.

The Wagers team also showed that the dystrophin gene was repaired in muscle stem cells, which replenish mature muscle tissue. That is “very important,” Wagers says, because the therapeutic effects of CRISPR may otherwise fade, as mature muscle cells degrade over time.

The treatment wasn’t a cure: The mice receiving CRISPR didn’t do as well on muscle tests as normal mice. However, “there’s a ton of room for optimization of these approaches,” Gersbach says. And as many as 80% of people with DMD could benefit from having a faulty exon removed, Olson notes. However, he adds, researchers are years away from clinical trials. His group now plans to show CRISPR performs equally well in mice with other dystrophin gene mutations found in people, then establish that the strategy is safe and effective in larger animals.

Other muscular dystrophy researchers are encouraged.

“Collectively the approach looks very promising for clinical translation,” says Jerry Mendell of Nationwide Children’s Hospital in Columbus.

Adds Ronald Cohn of the Hospital for Sick Children in Toronto, Canada: “The question we all had is whether CRISPR gene editing can occur in vivo in skeletal muscle.” The new studies, he says, are “an incredibly exciting step forward.”

Abstract 1: In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy
Duchenne muscular dystrophy (DMD) is a devastating disease affecting about 1 out of 5000 male births and caused by mutations in the dystrophin gene. Genome editing has the potential to restore expression of a modified dystrophin gene from the native locus to modulate disease progression. In this study, adeno-associated virus was used to deliver the CRISPR/Cas9 system to the mdx mouse model of DMD to remove the mutated exon 23 from the dystrophin gene. This includes local and systemic delivery to adult mice and systemic delivery to neonatal mice. Exon 23 deletion by CRISPR/Cas9 resulted in expression of the modified dystrophin gene, partial recovery of functional dystrophin protein in skeletal myofibers and cardiac muscle, improvement of muscle biochemistry, and significant enhancement of muscle force. This work establishes CRISPR/Cas9-based genome editing as a potential therapy to treat DMD.

Abstract 2: Rationally engineered Cas9 nucleases with improved specificity
The RNA-guided endonuclease Cas9 is a versatile genome-editing tool with a broad range of applications from therapeutics to functional annotation of genes. Cas9 creates double-strand breaks (DSBs) at targeted genomic loci complementary to a short RNA guide. However, Cas9 can cleave off-target sites that are not fully complementary to the guide, which poses a major challenge for genome editing. Here, we use structure-guided protein engineering to improve the specificity of Streptococcus pyogenes Cas9 (SpCas9). Using targeted deep sequencing and unbiased whole-genome off-target analysis to assess Cas9-mediated DNA cleavage in human cells, we demonstrate that “enhanced specificity” SpCas9 (eSpCas9) variants reduce off-target effects and maintain robust on-target cleavage. Thus, eSpCas9 could be broadly useful for genome-editing applications requiring a high level of specificity.

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Dystrophin (light green) is abundant in (left) cardiac muscle from normal mice,
missing in mice with Duchenne muscular dystrophy or DMD (center),
and partially restored in Duchenne mice treated with CRISPR/Cas9 (right).

Image Credit: C. E. Nelson et al.