An antisense oligonucleotide to rescue multiple splicing mutations in hotspot exons
Overview
Research by William Fairbrother at Brown University centers around a therapeutic use of ASOs to enhance splicing for various mutations using a single ASO. This can allow for the expansion of treatment options for a broader range of patients with the same underlying genetic disorder without the need for multiple ASO development. Fairbrother’s “one-size-fits-many” therapeutic solution could be more cost effective for treating rare diseases.
Technology
The research demonstrates that multiple splice-disrupting mutations within these hotspot exons can be corrected by a single Antisense Oligonucleotide (ASO). The strategy involves targeting the splice sites of either the upstream or downstream flanking exons to promote inclusion and reverse exon skipping caused by mutations.
Novel ASOs were designed and generated for the experiments. They were designed to target specific splice sites (5'ss or 3'ss) of the flanking exons surrounding a targeted hotspot exon. The purpose was to promote or inhibit exon inclusion and rescue splicing mutations. The paper also lists the sequences of some of these specifically designed ASOs (e.g., for LDLR exon 11 and PTEN exon 4).
1,733 splice-disrupting mutations were studied. These are not uniformly distributed but are concentrated in approximately 8% of exons most susceptible to splicing mutations, termed "hotspot exons". These hotspot exons were found to be enriched for SDVs, with 83 identified in actionable genes. Variants causing severe splicing defects (extreme SDVs or eSDVs) were strongly associated with pathogenicity and rarity in the population.The study validated the “one-size-fits-many” concept by showing that ASOs could reverse exon skipping induced by a splicing inhibitor (Pladienolide B) and, crucially, by specific splice-disrupting variants in genes like TSC1 and MLH1.
Application
Fairbrother focused on mutations found in 71 clinically actionable disease genes. A few examples where defects in these genes are associated with particular conditions include:
● Long QT syndrome (associated with SCN3B gene defects)
● Lynch syndrome (associated with MLH1 gene defects)
● Breast and ovarian cancers (associated with BRCA1 gene defects)
The ASO rescue strategy was also demonstrated on specific variants in TSC1 exon 14 and MLH1 exon 9. Furthermore, they mention that their analysis identified BRCA2 exon 13 as a hotspot exon, with cancer-associated mutations likely causing exon skipping.
The study leveraged data from ClinVar and Geisinger MyCode, which contain information on variants associated with various human diseases. The broader aim is to address diseases where splicing mutations play a significant role.
Startup Opportunity: Brown has filed IP around the composition of matter of the ASOs and their application in turning off genes. We are interested in exploring startup opportunities around this technology. Dr. Fairbrother has had previous startups and patents.
References:
Principal Investigator
William Fairbrother
Professor of Biology
Molecular Biology, Cell Biology and Biochemistry
Brown University
william_fairbrother@brown.edu
https://vivo.brown.edu/display/wfairbro
Contact
Melissa Simon
Business Development Director
Brown Technology Innovations
Melissa_j_simon@brown.edu
Brown Tech ID 3514