CRISPR - a molecular smart bomb

Fear the CRISPR!

Fear the CRISPR!

It looks like texting shorthand for the drawer in your fridge, or maybe a superhero that makes the air feel like a cool, refreshing winter morning, but it's really one of the most powerful tools in molecular biology. CRISPR has made lots of news headlines in the past two years for its potential to revolutionize molecular genetics and insert or otherwise change the genomes of many organisms quickly, efficiently and cheaply. But first, a little history.

CRISPR is really just a fancy pair of molecular scissors, although calling it "CRISPR" is not really accurate (it's much more accurate to call it CRISPR/Cas, as I'll talk about below). It was first discovered decades ago, but it wasn't until the past few years that its significance was recognized (by my old MCB professor at Berkeley, Jennifer Doudna). CRISPR stands for Clustered Regularly Interspersed Short Palindromic Repeats. Obviously, calling it "CRISPR" is way cooler. Like all of the previous "molecular scissors" that have been discovered, CRISPR is actually a tool used by bacteria to fend off bacteriophages (a type of virus that infects bacteria).

The way it works is this: when a bacteriophage injects its foreign genetic material into a bacterial cell, there are proteins in the cell that pick up bits of the foreign material and insert it into the host cell's DNA. The cell does this for every virus it gets infected with, so over time these bits build up and form a kind of library of foreign genetic material. "CRISPR" refers to this chain of DNA that contains the blueprints of all the different viruses the bacterial cell has encountered. 

And just like most pieces of DNA, these little fragments of foreign genetic material are constantly being transcribed into little snippets of RNA that then float around the cell. At the same time, the cell has these molecular scissors called Cas (CRISPR-associated proteins). Cas is like a ninja patrolling a neighborhood, but without direction as to whom they are looking for. But when these bits of foreign RNA hook up with Cas, it's like giving that ninja a mugshot of an assassination target. It then floats around the cell looking for viral genetic material that matches the RNA it has, and when it finds it, it snips (thereby protecting the bacterial cell against invaders).

So... what's so impressive about that? This is just one more endonuclease (a class of genetic scissors that cleaves DNA somewhere in the middle). We've known about endonucleases for quite some time and have been using them for a while (I myself used EcoR1 in lab experiments in college). Why then is CRISPR different? It's partly because it's interchangeable. Previous genetic scissors that we've used (like TALEN) had to be re-engineered for each different target in order to "program" them to cut at a particular place. That made this an expensive and time-intensive prospect to make a novel protein every time you wanted to point it at a different target. To extend the metaphor above, if CRISPR is a versatile ninja that is capable of seeking out and precisely cutting any target, then TALEN is like a specialized gun that only works against a particular enemy. Each time you have a new target, you need to first make a whole new gun.

The CRISPR Ninja

The CRISPR Ninja

So what makes CRISPR/Cas special is this versatility. The actual molecular scissors (Cas) don't change. It just uses bits of RNA floating around to guide it to its target (kind of like a ribosome). This makes the programming a lot easier and faster. Now instead of needing to engineer a new protein each time, you can just inject the ready-made Cas protein into a cell along with the strip of RNA (called guide-RNA, or gRNA for short) that you'd like it to use as your mugshot. In fact, if you inject multiple different pieces of gRNAs into a cell with the Cas protein, they've shown in studies that Cas will happily and efficiently go around and make cuts at all of the different gRNA sites with high specificity. That makes the system really easy to use and much cheaper.

Since the Cas protein is so easily programmable with gRNAs and the Cas protein itself is not very complicated, numerous labs have been making further tweaks to alter the Cas functionality. By making adjustments to Cas's anatomy, they've been able to not just cut out old DNA, but then insert new stuff. They've been able to change it to only nick one side of the DNA instead of both, and (more recently) they have even been able to make single base-pair changes (target a single G and turn it into a T, for example).

This opens the door for nearly endless bioengineering applications. From a medical perspective, this promises to be an incredibly powerful tool for correcting genetic diseases. But this has also, understandably, sparked a new debate about the bioethics of changing someone's genetic code, which is unfortunate. There seem to be a lot of people out there that are whole-heartedly against changing someone's genetic code for any reason. They use the slippery slope argument: "Well, what is a 'genetic illness'? What if someone says that being short has impacted their job prospects, so they want to be taller? If you're fixing dwarfism, then this is just a small step away, right?" I would argue, no, that's wrong.

There are many disease states out there that are the direct result of a single faulty gene. Take sickle cell anemia, for example. A change to a single base pair yields a hydrophobic amino acid that should have been hydrophilic. This results in the hemoglobin molecules being just a little too sticky with each other when the sickle hemoglobin (HbS) isn't carrying oxygen. These sticky hemoglobin molecules then chain together to form long, inflexible protein rods within red blood cells. That then results in misshapen sickle-like red blood cells that are more fragile and break more easily and also get stuck in vessels, causing vessel damage. This causes incredible amounts of pain and suffering to the patient. And all because of a single wrong base pair.

Warning, I'm about to get very opinionated. There are many, many more examples in medicine just like this. I think that it is naive and backward to shy away from such a useful therapy because it may be misused, or because you think there is something special or different about altering someone's genes. If we don't give a patient antibiotics, they could die. We've fundamentally altered the course of their lives by giving them an artificial compound. A baby with a severe heart defect can have their heart completely rearranged by surgery or an adult can have a pig valve inserted in their aorta. To CRISPR's detractors, how are these not fundamentally changing the nature of a person, but altering a single base pair out of billions is?

I'm not arguing for unfettered genetic engineering. I do believe there need to be limits and real discussions about which changes are acceptable and which aren't. But we need to get over ourselves and not let the specter of eugenics keep us from exploring and utilizing such a promising therapy that could help millions.