Editing Genomes with the Bacterial Immune System

Gene editing has been making the news recently, and it's not surprising. Editing our genomes would offer us the potential to cure any genetic disorder, and the field is advancing at a remarkable pace. Intriguingly, stage 2 clinical trials are in progress for an HIV/AIDS treatment that relies on genome editing. Altering the sequence of the CCR5 receptor, which HIV uses to enter and take over cells, appears to render it invulnerable to HIV.

What's more, emerging technologies are poised to make advances in genome editing treatments come far easier than we could have predicted. Among them are TALENs, or Transcription Activator-Like Effector Nucleases, derived from parasite proteins that re-program gene expression in plant hosts, called TALEs.

More recently, a system used by bacteria to fend off their own pathogens has been re-worked for editing our own genomes. It's called CRISPR (pronounced "crisper"). When a bacterial cell is invaded by a new virus, a Cas (CRISPR-associated) protein takes a sample of the foreign DNA and inserts it into the CRISPR locus. The foreign DNA, now called a "spacer," is housed between two repeat sequences in a long array of many such repeat-spacer-repeat triplets, each of which came from a different invader. Each time the cell divides, it relays this information to its daughter cells.

This system confers adaptive immunity on the bacterium, since the CRISPR sequences inserted into the genome are transcribed into RNA. Each spacer is cut free from its neighbors, and the repeat sequences cause it to fold into a loop structure that is recognized by other Cas proteins. If an invader injects DNA into the cell recognized by the CRISPR RNAs, Cas proteins are directed to chop up the invading DNA.

It must have come as a surprise to discover that humble bacteria have acquired immunity, but it turns out to be the case. We place the mammalian immune system on a pedestal because its remarkable complexity, with a confusing multitude of specialized cell types, is what allows us a fighting chance in the daily war against pathogens and invaders. Undeniably it does a better job than CRISPR, but what's intriguing about CRISPR is that we are just now learning how to turn it to our own benefit, by using it to edit genomes.

The key is that CRISPR works by cutting DNA using a CRISPR RNA as a guide. It is incredibly easy to produce RNA that binds to a given DNA sequence, since DNA and RNA share the same nucleic acid language: G pairs with C, and A pairs with T and U. It is in contrast very hard to produce a protein that binds to a given DNA sequence, since proteins have a completely different language than DNA. Our best tools are zinc fingers (which are in clinical trials for HIV) and TALENs. Zinc fingers do not have any sort of "code," where zinc finger units correspond to DNA units. TALENs, on the other hand, do, but it isn't perfect. Plus, the large size of TALEN proteins might turn out to be a liability.

A recent paper² demonstrates that CRISPR RNA-guided targeting of DNA can create double-strand breaks. These breaks, which are common also to the zinc finger and TALEN approach, are used to force the cell to repair the DNA with an introduced template. In gene therapy, the template is a correct gene sequence introduced in a viral genome. The cell uses the similarity between the chopped DNA and the template to repair the break, unknowingly correcting the genetic defect in the process. This paper showed that the CRISPR method can cause not one, but two, such repairs at once. Even more intriguing, CRISPR appears to be more efficient than TALENs in a head-to-head comparison of repair efficiency.

The elegance and simplicity of the CRISPR approach makes it an intriguing tool for gene therapy and genetic modification in general. Be on the lookout for more developments in this hot area, as the technology will almost certainly be tested in animal models for the first time this year.

References:

1. Horvath, P. & Barrangou, R. CRISPR/Cas, the Immune System of Bacteria and Archaea. Science 327, 167-170 (2010).

2. Cong, L. & Ran, F. A. et al. Multiplex Genome Engineering Using CRISPR/Cas Systems. Science. Published online January 3, 2013.