The last decade has seen human destiny quietly but irrevocably redirected. From blind victims of genetic-molecular chance, we have taken our first steps towards becoming purposed actors in our biological fates. Thanks to a new gene editing technology called CRISPR-Cas9 crafted by a small crew of unassuming biochemists who have been since vaulted into rockstar status, a whole litany of diseases that used to strike our species with remorseless regularity is now within a decade of becoming a roll call of Diseases That Were.
Duchenne Muscular Dystrophy, a genetic disease caused by a mutation at locus Xp21, strikes 1 in 5000 males, and causes muscles to waste away at an alarming rate. Victims are no longer able to walk by age 12, and typically die by 26.
Huntington’s Disease, the result of an excessive number of repetitions in gene HTT, strikes around 1 in 10,000 of European descent, and causes a breakdown in physical coordination that prevents its victims from speaking and mental symptoms that tumble towards dementia.
Sickle Cell Anemia, which affects over four million people worldwide, arises from a single mutation in the Beta-Globin gene, a T that should have been an A. One lone letter among billions, with resulting frequent bouts of pain, increased susceptibility to bacterial infection and stroke, and a life span averaging out around fifty years.
What all these share in common is their root in the messiness of genetic events. Over the course of our lives, our genes are subject to all manner of stresses and strains. Some of those are intentional, like the break-neck pace of genetic reorganization necessary to create a plethora of diverse antibodies to recognize the horde of infectious organisms that threaten our health. Others are the result of exposure to chemicals or radiation that break apart our DNA, and which our cells are pretty good, but not perfect, at repairing. And others still are created in the name of genetic diversity, as when our chromosomes swap genetic material during meiosis in order to create sex cells with a mixture of paternal and maternal traits.
That’s a lot of motion and chaos calling for minute molecular management. Usually, all goes well, but sometimes mistakes are made, a letter in the genetic code gets changed, or a sequence gets duplicated or deleted, and the result can be a disease that gets passed along through the generations, maiming and killing humans in the thousands and millions for no other reason than, essentially, a clerical error.
If there is one statement that should be non-controversial, it is that the fixing of those errors, and the relieving of the suffering they bring, is a desirable thing. Unfortunately, in spite of all our cleverness in genetic engineering throughout the late 20th century, we never got quite good enough at it to have a real chance at reliably curing human genetic disease. Designing and precisely delivering healthy genes was time consuming, expensive, and frustratingly inefficient.
But that’s when a few researchers studying different bacteria noticed something, a suspicious repeated sequence that showed up in the DNA of strains of bacteria of wildly different types in widely different environments. Closer scrutiny revealed that, stuck in between the common repetitive bits were slices and scraps of DNA that came from bacteriophages, viruses that make their living attacking and replicating within bacteria. Could this sequence of DNA be the bacteria’s form of an immune system, and if so, could its mysteries be unlocked and eventually harnessed by humans?
Enter our first hero: Jennifer Doudna. Doudna was a biochemist with an impressive list of achievements behind her when, in 2005, she was approached by geomicrobiologist Jillian Banfield. Banfield had a slim stack of papers relating to this section of repetitive DNA, and had a feeling that RNA had something to do with the functioning of the so-called crispr gene. They were both researchers at Berkeley, and Doudna was certainly the person to go to with questions about RNA. She had done important work on ribozymes, strands of RNA that are capable of acting as enzymes and even of editing themselves in ways that are important for origin-of-life research. Using X-Ray Crystallography (a method we talked about in Dorothy Hodgkin’s episode, which you can find here), she had been the first to determine the three dimensional structure of a ribozyme, including the position of its elusive magnesium ions.
Banfield’s question was how RNA might be employed by bacteria as part of an anti-virus immune system. Doudna’s lab took up the challenge and, within the space of seven years, had discovered not only how bacteria protect themselves from viruses, but created a gene editing tool of such precision, cost-effectiveness, and ease-of-use that it made the wildest dreams of gene therapy tangibly real.
But to do that they needed the insights and research experience of one other player: Emmanuelle Charpentier. Quiet, resourceful, and brilliant, Charpentier started her career intrigued by the question of how pathogens rearrange their genetic material to produce antibiotic resistance. The discovery that some bacteria had stretches of DNA seemingly tailor made to provide immunity to viruses was irresistible, and she set herself the task of mapping and determining the purpose of the RNA produced by CRISPR and its neighboring genes.
As it turned out, Doudna and Charpentier were studying two different, but related, CRISPR systems. Doudna’s, called Type I, used RNA and a whole fleet of accompanying enzymes to form a unit that, presented with viral DNA, would chew it up and utterly destroy it. Charpentier’s, Type II, was a much more civilized system that used two RNA strands to guide an enzyme called Cas9 to viral DNA, where it would make precise double-strand cuts.
In 2011, Charpentier approached Doudna and suggested they combine their resources and abilities to discover exactly how CRISPR-Cas9 did what it did, which would be the first step into, perhaps, harnessing that system for the purpose of gene editing.
Where previous gene editing methods suffered from imprecision, cost, and difficulty of use, the Charpentier-Doudna system was cheap and efficient, and their 2012 paper announcing their results launched a rush of experimentation.
How it works is this: the bacterium has stored on it a small stretch of viral DNA. Part of the CRISPR system is an RNA copy of that DNA which can sniff out and link up with its counterpart in any viral DNA floating about in the cell. That RNA copy of viral DNA, combined with another section of RNA discovered by Charpentier called tracrRNA, forms a complex that guides Cas9 directly to the viral DNA it is supposed to slice. It is a simple, highly specific, and beautifully effective defense against viral attack.
The next question, logically, was, could we replace the viral RNA with something else, say, a sequence of plant RNA or even human RNA, which would allow the CRISPR-Cas9 system to target a part of some eukaryotic organism’s genetic code and make a surgical cut? Charpentier and Doudna’s labs worked on perfecting such a system, creating a streamlined CRISPR-Cas9 complex that could be precisely tuned to make a slice at exactly one location in an organism’s sprawling genetic code. Where previous gene editing methods suffered from imprecision, cost, and difficulty of use, the Charpentier-Doudna system was cheap and efficient, and their 2012 paper announcing their results launched a rush of experimentation.
The last half decade has witnessed people coming up with uses of CRISPR-Cas9 to solve a whole slew of global problems. Doudna, from being the tallish blonde girl who grew up a bookish outsider among the native population of Hawaii and Charpentier, the quiet, efficient Parisian, were vaulted to superstar status even as they knuckled down to the onerous and thankless task of defending their patents.
While lawyers battle out the question of who will have the patent rights to the potential hundred-million dollar industry represented by CRISPR-Cas9 techniques, Doudna and Charpentier continue their research. Charpentier has discovered a protein, Cpf1, that can stand in for both the Cas9 enzyme and the tracrRNA, which could even further reduce the complexity of the gene editing mechanism. Meanwhile, Doudna is researching how other CRISPR systems function beyond types I and II and has stepped beyond the lab to become science’s most visible educator on the subject of gene editing, its limitations and vast promise.
And the world is taking their ideas and running, finding ways not only to fix the genetic clerical errors crippling millions of people the world over (tens of millions if you count the types of cancer that are genetic in origin), but harnessing CRISPR to dramatically lessen the pollution poured out by the meat industry, to solve the massive problem of organ donation shortages, to protect the world’s food supply from developing pathogens, and to halt the spread of infectious disease by modifying its carriers. The childhood of humanity, when we allowed ourselves to be buffeted about by chance and circumstance because we had no choice, is coming to a close. What adulthood will bring nobody can possibly say, but it will be a time of less pain, when our sorrows will be those we bring upon ourselves rather than those foisted upon us by the statistical vagaries of biochemistry and the mundane cunning of mutation gone amok.
FURTHER READING: There are two books about CRISPR-Cas9 to consider. One of them, A Crack in Creation (2017) by Jennifer Doudna herself (with Samuel Sternberg), is a brisk retelling of her lab’s work in unlocking the structure and function of CRISPR-Cas9 and the history of gene editing, with an extended section considering the ethical implications and practical promise of the technology. It is eminently readable, clear, and exciting. The illustrations are somewhat the opposite of illuminating, but Doudna and Sternberg’s prose is so clear you don’t actually need them to understand what’s going on. The other book is Modern Prometheus (2016) by Jim Kozubek which has more details on the legal battle between UC Berkeley and the Broad Institute over the CRISPR patent, but holyyyyyy crap does this dude like to talk about himself. If you want to get into the academic nitty-gritty it’s necessary but if you’re just looking for an introduction to the history of CRISPR-Cas9, you want Doudna. Nature also has a neat article on Charpentier you can find here.