How do antisense oligonucleotide (ASO) gene therapy drugs work?

In summary

ASOs are short fragments of RNA that bind to nascent mRNA strands so ribosomes can’t bind to the nascent mRNA strand and create proteins. The key to this therapy is to remember that ribosomes need a single stranded mRNA molecule, and ASO therapies bind to the mRNA molecule, making it double stranded in some places. ASO therapies are gene therapy because they target defective genes to prevent the “bad” protein from being generated.

In depth

ASO therapies are an up-and-coming type of drug class that uses fragments of RNA to prevent defective proteins from being formed. Since mRNA is the template that ribosomes use to create proteins, a defective copy of mRNA can generate defective protein.

Nascent mRNA strands exist freely in the cytoplasm while they wait for a ribosome to bind to them and generate the protein—the perfect time for the nascent mRNA to become “deactivated.” An ASO has the reverse complement sequence to the target mRNA, so ASO molecule deactivates a nascent mRNA strand by base pairing to that target sequence. Since the ribosome can only bind to single stranded mRNA, and the ASO is binding where the ribosome wants to bind, the ribosome won’t interact with the mRNA to create the specific protein for which that mRNA molecule encodes.

Among gene therapy modalities, ASOs are advantageous because the concept is relatively simple. Once the ASO sequence is finalized, the molecule can be generated like any other oligonucleotide sequence with a bunch of organic chemistry reactions. Unlike a more technically complicated modality like CRISPR-Cas9, where we’re asking the drug to perform numerous steps, we’re just asking an ASO to stick to the mRNA strand like Velcro so the ribosomes bounce off. Additionally, unlike CRISPR-Cas9, the drug formulation doesn’t include a bunch of different drug components that need to magically come together and work in a cell. In traditional ASO therapies, no matter what kind of delivery mechanism you’re using, those short fragments are the only therapeutically active ingredient.

Given these benefits though, an ASO is a band aid, because it doesn’t actually solve the root cause of the genetic defect. Unlike CRISPR-Cas9, ASOs won’t fix the DNA that encodes for these defective mRNA strands. The cell will create these defective mRNA molecules into perpetuity and will need to be treated by long term ASO therapy. With ASOs, you’re not actually editing the genome—you’re negating the products of the defective genome. For nonessential proteins, the absence of having the protein at all probably beats having a defective copy. However, if the protein is essential, using a drug that completely inhibits its production is probably a bad idea.

In literature

These are some of my favorite papers to help you learn more about ASOs!

https://pubmed.ncbi.nlm.nih.gov/32964539/

https://pubmed.ncbi.nlm.nih.gov/30691367/

https://pubmed.ncbi.nlm.nih.gov/33762737/

Next month, let’s talk about a similarly functioning modality, siRNA.