What if instead of editing a harmful gene, or blocking the protein it produces, you could simply switch it off?
If you want a picture of biomedical research, imagine a boot stamping on a biologist’s face – for decades. The boot is labeled ‘medicinal chemistry’. This should not be taken as an insult to medicinal chemists, who heroically navigate maybe the hardest field in biomedicine. Rather, what I mean is this. A biologist might have a clear hypothesis about how to stop a disease, such as: blocking a particular protein will lower blood cholesterol and reduce the risk of heart disease. Naturally enough, the biologist would like to test that hypothesis. But there is no magic button to switch off this protein; something physical has to do the blocking. Usually, that thing is a small chemical carefully designed to be administered into the body, bind to the protein, block it – and do nothing else. In practice, this almost never goes as planned, which is a major reason most drugs fail in clinical trials.
It’s worse than this: medicinal chemists struggle to come up with ways to interact with most proteins at all. The majority of human proteins are considered ‘undruggable’, meaning that none of the small molecules we can currently synthesize can effectively bind to them, either because those proteins lack a convenient pocket for drugs to attach to or because they are ‘intrinsically disordered’, with little coherent structure. Drug discovery ends up focusing on the minority of targets that are druggable, like the proverbial drunk searching for his keys under the streetlamp because that’s where the light shines.
Even for those targets, success is far from guaranteed. A drug that works in the lab might be broken down in the body before it reaches its target protein, interfere with other proteins and cause toxic side effects, or fail to be absorbed and distributed to the right tissues. Our ability to predict what small molecule drugs will do in the body is so poor that even if the drug works, it might be for a different reason than originally hypothesized!
But what if, instead of spending years optimizing small molecule chemistry to treat just one disease, and all that work merely delivering a sharp reminder that no plan survives first contact with the enemy, there really was a magic button to switch off any gene we chose? In that case, we could treat not just high cholesterol but dozens of deadly diseases, from Alzheimer’s to diabetes to Huntington’s disease.
Welcome to the world of siRNA therapy.
Silencing genes
The story of siRNA begins in 1990, when the scientists at the DNA Plant Technology Corporation in California were trying to figure out why their petunias turned white. They had actually been trying to make their petunias darker, by adding an extra copy of the gene for an enzyme that produces pigment. Presumably, adding an extra copy of a gene for an enzyme would mean more enzyme and therefore more pigment. But somehow, the extra copy eliminated the enzyme’s production, rather than boosting it. They named this baffling effect ‘cosuppression’. Subsequent work by other researchers revealed its cause: a special kind of RNA molecule, siRNA, had interfered with the enzyme’s production. Andrew Fire and Craig Mello later won a Nobel prize for this discovery.
Biologists had already known about RNA for several decades. Similar to DNA, RNA is a complex molecule built from a chain of smaller building blocks that encode genetic information. But the two differ in one important detail: the building blocks of RNA have one extra oxygen atom compared to DNA (hence its name, ribonucleic acid, as opposed to DNA’s ‘deoxy’-ribonucleic acid). This oxygen is prone to chemical reactions that can break RNA molecules. DNA is stabler and is therefore used to store genetic information in all multicellular life. RNA molecules tend to be short-lived, and take many different forms within cells, carrying instructions, helping to assemble proteins, regulating genes, and catalyzing reactions. And while DNA is ‘double-stranded’, with two linked strands of building blocks twisting into its famous helix shape, RNA often exists as just one strand.
DNA contains the instructions for making proteins, from the enzymes that digest food to the keratin and collagen that form our hair and skin. But to get from DNA to protein, the genetic code is first transcribed into an intermediate RNA molecule, called ‘messenger RNA’ or mRNA, which is then translated into protein. If the mRNA is destroyed, the protein won’t be built.
That’s exactly what siRNA, or ‘small interfering RNA’, does: it’s a short strand of RNA that interferes with the production of protein by destroying mRNA. An siRNA molecule binds to a piece of mRNA with a matching sequence, like a kind of barcode, and targets it for destruction by the cell’s gene-silencing machinery, which cuts the mRNA into pieces.
siRNA also explains what happened in the petunias. Adding an extra copy of the pigment-producing gene triggered the petunias to develop siRNA targeting that sequence, and because the newly introduced gene and the original gene shared the same sequence, both were silenced, the flowers lost their pigment and turned white. This is a naturally occurring process: siRNA is used to ‘silence’ unwanted genes, such as those of viruses that have entered the cell. But we can also use it to artificially block the production of proteins that cause disease.
by Jacob Witten, Works in Progress | Read more:
Image: uncredited
by Jacob Witten, Works in Progress | Read more:
Image: uncredited
