10.4: Transient gene expression and short RNAs

There are scenarios where changing the gene expression of a cell temporarily instead of permanently is desirable. The most obvious example of this is vaccination – cells temporarily expressing an antigen “trains” the immune system to detect that antigen. There are two primary methods to transiently express a transgene. The first, as we’ve discussed, is to deliver it packaged in an adenovirus instead of a retrovirus. The transgene hangs out in the nucleus where it’s transcribed and translated, but it doesn’t change the cells’ genome and is eventually lost.

And the second way isn’t to deliver DNA, but rather messenger RNA. Now, it doesn’t need to get into the nucleus – simply delivering it to the cytosol with, say, lipid nanoparticles is enough to get the transgene expressed. This was the approach of the Pfizer and Moderna COVID vaccines – the third that was approved in the US was from Johnson and Johnson, which used an adenovirus called Ad26.

And while vaccines are an obvious use for transiently expressed transgenes, they’re not the only ones. For example, many cancers have mutations that help them escape the immune system. Using mRNA to train the immune system to recognize a tumor-specific antigen has huge potential as a therapeutic, particularly because a single treatment could encode multiple antigens and epitopes. mRNA also has potential to replace absent or defective proteins in patients with monogenic diseases – while it’s not going to be a permanent fix like you would get with a genomic modification, it is also easier to control and less risky than previous retroviral strategies have been. And of course the base-editors that we talked about earlier CAUSE a permanent change, but if you want to deliver these therapies as nucleic acids instead of packaged proteins – which is definitely easier – you don’t want cells making the base editors forever.

Finally, for the record, I consider these transient therapies to be gene therapies – delivery of nucleic acids that change gene expression. I know there’s some debate. No, they aren’t changing the cells’ genomic DNA – but they are nucleic acids, delivered to cells, for therapeutic benefit.

Short RNAs

Thus far, we’ve looked at gene therapies that contain and deliver actual genes. However, those aren’t the only nucleic acids that have biological function! Short interfering RNAs, or siRNAs, can be used to decrease the expression of a gene, and there are four that are FDA-approved. All four target enzymes that are overactive in metabolic diseases. And interestingly, none of them are packaged with lipids – instead, they’re chemically modified so that they’ll be taken up by their target cells, then infused directly into the patient’s blood stream.

Another disease that has been successfully treated with short RNAs is spinal muscular atrophy, or SMA. SMA is caused by a loss-of-function mutation in the SMN1 gene. However, a drug called Nusinersen is made of an RNA oligonucleotide that modulates the alternative splicing of SMN2. Injected directly into a patient’s cerebrospinal fluid, the oligonucleotide changes the splicing of SMN2 to produce a protein that has the same sequence of SMN1.