Exon-Skipping Shows Potential to Treat Nonsense Mutations in CF

Marisa Wexler MS avatar

by Marisa Wexler MS |

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A team of scientists in New York has created small molecules called antisense oligonucleotides that could be used to “skip over” the mutated part of the CFTR gene to treat cystic fibrosis (CF) patients with a specific “nonsense” mutation and no available therapies.

Findings were published in the study, “Exon-skipping antisense oligonucleotides for cystic fibrosis therapy,” published in the journal PNAS.

CF is caused by mutations in the CFTR gene, which provides instructions for making the CFTR protein. This protein is important for regulating the movement of water and salts in and out of cells.

In recent years, a class of medications called CFTR modulators — such as the triple-combo therapy Trikafta, by Vertex Pharmaceuticals — has become widely available to treat CF. These medicines can increase the activity of the CFTR protein, but they only work in people with certain disease-causing mutations.

“Many mutations in the CFTR gene are not responsive to drugs used to treat CF,” Young Jin Kim, a doctoral student at Stony Brook University and the study’s first author, said in a press release.

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In particular, CFTR modulators do not work as treatments of nonsense mutations. A nonsense mutation is a change in the genetic code that results in a “stop” signal halfway through a gene — kind of like putting a period in the middle of a sentence.

“There is a significant unmet therapeutic need for patients with this type of mutation,” Kim said.

A nonsense mutation called W1282X is the sixth most common CF-causing mutation. It’s present in about 1.2% of patients and tends to be associated with more severe disease.

Within a cell’s DNA, genes are divided into sections called exons. When a gene gets “read,” all the exons are strung together in the messenger RNA (mRNA) sent to the cell’s protein-making machinery (ribosomes).

The W1282X mutation is located in exon 23 of the CFTR gene. Here, researchers tested if “skipping over” this exon might allow cells to produce a shorter, but still functional, version of the CFTR protein. Similar approaches have been successfully developed to treat disorders such as Duchenne muscular dystrophy.

In initial proof-of-concept experiments, the researchers illustrated that a shortened CFTR protein, made without exon 23, is biologically active. Based on measures of salt movement in and out of cells, the shortened protein was roughly half as active as the unmutated protein when treated with Trikafta.

“As low as 10% of normal CFTR function would provide a significant therapeutic benefit for CF patients who have a near-complete loss of CFTR function, as is the case for the W1282X mutation,” the scientists wrote, noting their findings support this overall treatment approach.

Researchers then designed antisense oligonucleotides, or ASOs, which are basically short pieces of genetic code that can modulate the genetic activity of the cell. Two ASOs that could promote skipping of exon 23 were identified

The team showed that treatment with the two ASOs, plus the two CFTR modulators present in Orkambi (ivacaftor/lumacaftor), could increase CFTR activity in cells carrying the W1282X mutation. (Orkambi is approved to treat patients with the common F508del mutation in both CFTR gene copies.)

CFTR activity in these treated cells is likely less than 10% what it is in cells with no mutation, the scientists said. “We anticipate that combining the ASO cocktail with Trikafta may further increase the CFTR activity,” they wrote.

These researchers are now hoping to progress their approach toward clinical trials.

“Our results thus provide an avenue for developing a therapeutic strategy based on [exon-skipping] ASO, in the era of CFTR-modulator therapy,” they concluded.