The peptide nucleic acid-based technique offers an alternative to CRISPR-Cas9

A research team from Carnegie Mellon University and Yale University will advance their innovative, synthetic nucleic acid-based gene editing technique under a new grant from the National Institutes of Health’s (NIH’s) Somatic Cell Genome Editing (SCGE) Program.

“Our PNA technique offers a promising avenue for treating — and possibly curing — a wide range of genetic diseases in a safer, less invasive way than other gene editing methods,” said Danith Ly, professor of chemistry and director of the Institute for Biomolecular Design and Discovery at Carnegie Mellon. “Support from the NIH’s SCGE program will allow us to further develop our technology and help us move toward clinical use.”

NIH created the SCGE Program in 2018 to improve genome-editing technologies and make genome-editing therapies more widely available. The program awarded 24 grants this year.

“Genome editing has extraordinary potential to alter the treatment landscape for common and rare diseases,” said Christopher P. Austin, National Center for Advancing Translational Sciences (NCATS) director and SCGE Program Working Group chair. “The field is still in its infancy, and these newly funded projects promise to improve strategies to address a number of challenges, such as how best to deliver the right genes to the correct places in the genome efficiently and effectively. Together, the projects will help advance the translation of genome-editing technologies into patient care.”

Carnegie Mellon’s Ly, with Yale Professor of Therapeutic Radiology and Genetics Peter Glazer and Yale Professor of Biomedical Engineering, Chemical and Environmental Engineering and Physiology Mark Saltzman, have developed a novel system for gene editing that intravenously delivers a peptide nucleic acid (PNA) molecule paired with a donor strand of DNA to a malfunctioning gene using FDA-approved nanoparticles.

PNAs, a synthetic nucleic acid technology pioneered by Ly at Carnegie Mellon’s Mellon College of Science, contain a protein-like backbone that can be programmed with the same nucleobases found in DNA and RNA. For gene editing, Ly programmed a PNA to open a double-stranded DNA molecule at the site of a targeted mutation. The donor strand of DNA binds to the faulty DNA, triggering the DNA’s innate repair mechanisms. In previous studies, the Carnegie Mellon and Yale team used this gene editing technique to cure beta thalassemia in adult mice and in fetal mice in utero.

Since PNA-based gene editing harnesses the DNA repair pathway, it is much less likely to modify off-target genes than methods that cut DNA using an enzyme, including CRISPR-Cas9. In fact, in earlier studies the researchers were unable to find evidence of any erroneous offsite repairs caused by the PNA therapy.

The new grant will allow the Carnegie Mellon and Yale researchers to continue to advance their gene therapy technique in an effort to move the technique closer to clinical therapeutic applications. Specifically, they will scale up production of PNAs, improve the PNAs’ DNA binding properties, develop new nanoparticle formulations for enhanced in vivo editing, and develop new strategies to enhance the efficiency of their technique.

Ly’s work has been made possible by the support of the DSF Charitable Foundation, who has donated $7 million to Carnegie Mellon’s Center for Nucleic Acids Science and Technology (CNAST), enabling the center to engage in fundamental research aimed at developing synthetic chemistry solutions for the diagnosis and treatment of disease.

The SCGE program is supported by the NIH Common Fund and led by NCATS.