Diagnosing COL6-related disorders and methods for treating same
Inventors
BONNEMANN, Carsten G. • BOLDUC, Veronique • Muntoni, Francesco • WILTON, Steve • MACARTHUR, Daniel • LEK, Monkol • CUMMINGS, Beryl
Assignees
Murdoch University • Uclb • General Hospital Corp • Harvard University • US Department of Health and Human Services
Publication Number
US-11655470-B2
Publication Date
2023-05-23
Expiration Date
2037-07-05
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Abstract
A single nucleotide polymorphism (SNP) that results in development of a Type VI collagen, alpha 1 chain-related disorder, and the use of the SNP to identify individuals at risk for developing COL6-related disorders (COL6-RD). Also provided are antisense oligomers for treating individuals at risk for developing COL6-RD, as well as methods for screening compounds for their potential as therapeutic agents.
Core Innovation
The invention is a diagnostic and therapeutic method related to a newly discovered single nucleotide polymorphism (SNP) in intron 11 of the COL6A1 gene, which results in aberrant splicing of COL6A1 pre-mRNA. This mutation introduces a new 5′ splice donor site that leads to the insertion of a 72-base pair pseudo-exon in the mature mRNA, producing an aberrant alpha 1 chain of Type VI collagen protein and causing neuromuscular disorders including collagen VI-related disorders (COL6-RD) such as Ullrich muscular dystrophy. The detection of this SNP can be used to identify individuals at risk for developing these disorders.
Currently, collagen VI-related disorders are diagnosed through biochemical and genetic testing but a substantial number of patients meeting clinical criteria remain without a confirmed mutation. Furthermore, existing treatments focus on managing symptoms rather than curing the disease. The invention addresses the problem of insufficient diagnosis and treatment by identifying a frequent intronic mutation that had previously been undetected and providing antisense oligomers which modulate the splicing process to exclude the aberrantly included pseudo-exon, restoring production of the normal protein.
Specifically, antisense oligomers targeted to sequences in intron 11 of COL6A1 pre-mRNA hybridize to the mutant pre-mRNA, block the newly created splice donor site, and thereby restore normal splicing between exon 11 and exon 12. This results in mature mRNA encoding a wild-type alpha 1 chain. The invention also includes expression vectors encoding such antisense oligomers, methods of administering them for treatment, methods of diagnosing the presence of the mutation by detecting the T allele, and screening methods for compounds that modulate this splicing event.
Claims Coverage
The patent contains one independent claim directed to a synthetic antisense oligomer and related methods, expression vectors, and kits. The main inventive features involve the specific sequences of antisense oligomers that modulate COL6A1 pre-mRNA splicing, chemical modifications to the oligomers, and their functional effect on normalizing splicing.
Synthetic antisense oligomer sequences for splicing modulation
An antisense oligomer that comprises sequences selected from a group of specified SEQ ID NOs, or sequences closely related by length variations, targeted to intron 11 of COL6A1 pre-mRNA to modulate aberrant splicing caused by a non-native splice donor site.
Chemical modifications to antisense oligomers
The antisense oligomers are chemically modified to increase affinity for target RNA, increase nuclease resistance, and/or alter pharmacokinetics. Modifications include substitutions of sugars, internucleoside linkages, nucleobases, or combinations thereof, including morpholino oligomers.
Method of modulating COL6A1 pre-mRNA splicing
A method of modulating splicing of COL6A1 pre-mRNA having a non-native splice donor or acceptor site by contacting a cell expressing said mutated pre-mRNA with the antisense oligomer that causes restoration to normal splicing.
Expression vectors encoding antisense oligomers
An expression vector from plasmids, bacteriophages, yeast or viruses encoding the antisense oligomers capable of modulating COL6A1 pre-mRNA splicing.
Kits comprising the synthetic antisense oligomer
Kits comprising the synthetic antisense oligomer sequences, optionally with instructions for use.
The claims focus on the design and chemical modification of antisense oligomers targeted to intron 11 of COL6A1 pre-mRNA to restore normal splicing disrupted by a specific intronic mutation. Additional claims relate to methods of administering these oligomers to modulate splicing, vectors encoding them, and kits for therapeutic or diagnostic use.
Stated Advantages
Provides improved diagnostic capability by enabling detection of a previously unidentified common intronic mutation causing collagen VI-related disorders.
Offers a therapeutic approach that restores normal COL6A1 splicing, potentially curing or ameliorating COL6-RD rather than only slowing disease progression.
Enables targeted antisense oligomer treatment to prevent inclusion of a pathogenic pseudo-exon in COL6A1 mRNA.
Supports screening for compounds modulating COL6A1 splicing, facilitating drug development.
Documented Applications
Diagnosing individuals at risk for COL6-related disorders, especially Ullrich muscular dystrophy, by detecting presence of the T allele at the intron 11 locus of COL6A1 gene.
Treating individuals having the intron 11 mutation in COL6A1 with antisense oligomers or expression vectors encoding antisense oligomers to restore normal splicing and produce functional alpha 1(VI) chain protein.
Screening compounds for their ability to modulate COL6A1 pre-mRNA splicing using recombinant nucleic acid constructs comprising mutated intron 11 flanked by exons 11 and 12.
Use of kits comprising antisense oligomers and reagents for predictive diagnosis and treatment of COL6-related neuromuscular disorders.
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