Gene interference technology used in FSH muscular dystrophy

Proof-of-principle study is the first to use CRISPR technology on the “repeat genome,” as well as its first successful use in primary human muscle cells

BOSTON – (November 3, 2015) – The FSH Society, the award-winning non-profit and global leader in the quest to cure Facioscapulohumeral Muscular Dystrophy (FSHD), announced that an FSH Society-funded research team led by Peter Jones, PhD, at the University of Massachusetts Medical School (UMMS) has successfully used a derivation of the CRISPR-based gene-editing method known as dCas9 to target and silence the DNA sequence implicated in FSHD. This genetic condition, which affects an estimated 1 in 8,000 people, is among the most common forms of muscular dystrophy.

The work represents two firsts. “While CRISPR technology has been used successfully in early studies of genome editing, this is the first report in which a CRISPR-based system has been used to ameliorate pathogenic gene expression in FSHD,” writes the paper’s lead author Charis Himeda, PhD. “This is also, to our knowledge, the first time the technique has been used successfully in primary human muscle cells.”

The CRISPR/Cas9 system originated from the discovery of a mechanism that bacteria employ to purge their genomes of foreign genes, somewhat like a primal immune system. Molecular biologists have figured out how to harness this natural system to specifically target genomic sequences.

Typically, the CRISPR/Cas9 technology is used to cut the DNA to change or remove specific sequences. However, the potential off-target effects of introducing non-specific cuts to the genome are a serious concern. As an alternative, the CRISPR/dCas9 system does not cut the DNA, instead altering the expression status of the targeted gene by recruiting either gene activation or repression proteins. In theory, CRISPR/Cas9 could be used to treat classic genetic disorders by editing gene sequences while CRISPR/dCas9 could be used to silence mutant disease-causing genes or activate beneficial genes.

In FSHD, muscle degeneration results not from a misspelled gene but rather from a different type of genetic error. The most common form of the condition, FSHD1, is caused by a shortening of a variable tandem repeat region of so-called “junk” DNA on chromosome 4. This repeat genome region consists of numerous repetitive units called “D4Z4.” Normally, humans have between 11 to over 100 D4Z4 units in this location, but in individuals with FSHD1, there are only between one and 10 units.

This repeat region harbors a gene called DUX4. Normally, this gene is repressed. But in FSHD, the reduced number of repeats, together with loss of methyl groups in the region, causes changes in the structure of the chromatin (the complex of molecules that form the chromosome). The result is that DUX4, and possibly a number of noncoding RNAs, become prone to being expressed, triggering chemical events that lead to muscle destruction.

Several research groups, including ones funded by FSH Society grants, are using CRISPR/Cas9 to edit the DUX4 gene in an effort to render it non-functional. The UMMS group, however, decided to more broadly target several regions of the D4Z4 repeats. “The D4Z4 repeats encode multiple coding and noncoding RNAs, which have the potential to play downstream pathogenic roles in FSHD. Thus, targeting the FSHD locus to return the chromatin to its non-pathogenic, more repressed state might be more therapeutically beneficial than simply targeting DUX4,” the authors explain. The methods developed and demonstrated by this study “should pave the way for more effective and stable correction of FSHD and other epigenetic diseases.”

The work may have powerful implications beyond the relatively rare incidence of FSHD. “With increasing evidence that the repeat genome (comprising nearly half the human genome) plays important roles in gene regulation, additional diseases will likely be found associated with aberrant repetitive genomic sequences,” the authors said. “We have provided the first evidence that the repeat genome can be targeted via the CRISPR system, which is likely to prove useful as this hitherto overlooked portion of the genome is decoded.”

The newly published work was supported by the National Institute of Arthritis, Musculoskeletal, and Skin Diseases grant #1R01AR062587 and the Association Française contre les Myopathies grant #AFM15700. The FSH Society funded work in the Jones lab that laid the foundations for the current study and supported development of the UMMS Wellstone Center FSHD cell and DNA repository used in this research.

Reference
Charis L. Himeda, Takako I. Jones, and Peter L. Jones. CRISPR/dCas9-mediated transcriptional inhibition ameliorates the epigenetic dysregulation at D4Z4 and represses DUX4-fl in FSH muscular dystrophy. Molecular Therapy, accepted article preview online 03 November 2015; doi:10.1038/mt.2015.200. View on PubMed.

See press coverage of this story:

• How CRISPR could lead to a cure for muscular dystrophy (Washington Post)

• How Controversial Gene Editing Could Lead To Groundbreaking Cures (Huffington Post)