Monday, July 25, 2016


CRISPR -- clustered regularly interspaced short palindromic repeats -- is a potent genetic-editing tool. It's called this because each CRISPR unit is made of repeated DNA base-pair sequences that can be read the same way forward or in reverse and are separated by "spacer" pairs. Think of it like an organic Morse code palindrome.

With CRISPR we can now edit any genetic code -- including our own. In the three years since its advent, researchers have used CRISPR to investigate everything from sickle-cell anemia and muscular dystrophy to cystic fibrosis and cataracts. One group has even used it to snip off the cellular receptors that HIV exploits in order to infect the human immune system. If the disease is caused by your genetics -- doesn't matter if it's due to a single malformed gene, as is the case with Huntington's or sickle cell, or if it's the byproduct of hundreds mutations like diabetes and Alzheimer's -- CRISPR can conceivably fix it…

These CRISPR units can easily slice through DNA and replace nucleotide bases with others, but they aren't accurate enough to consistently aim at specific locations. For that, each CRISPR needs an RNA-based "guide," called a Cas (CRISPR associated) gene. These guides search for a specific set of nucleotides, usually a 20-pair sequence, and bind to the site once they locate it. That's a pretty impressive feat, given that the human genome contains around 20,000 genes. Working in unison, a CRISPR/Cas system can target and silence the expression of single genes anywhere along a given strand of DNA about as easily as you can edit a Word document. It's basically "find-and-replace" for genetics…

The biological mechanism behind CRISPR is actually quite ancient. See, scientists used to think that bacteria were equipped only with innate immunity -- the lowest, most budget form of biological defense around. Since a microbe's restriction enzymes will blindly attack and destroy any unprotected DNA they come in contact with, scientists figured that it was just automatic, a simple reflex. Multicellular organisms, conversely, enjoy acquired immunity, which enables them to mount specific counters to different threats. It wasn't until they discovered CRISPR that researchers figured out bacteria and archaea have been leaning on acquired immunity for eons. They'd been using it as a rudimentary adaptive immune system against viruses…

"I would bet that within 20 years, somebody is going to make a unicorn," Hank Greely, director of Stanford University's Center for Law and the Biosciences, told me during a recent phone call. "Some Silicon Valley billionaire with a 12-year-old daughter will get her a unicorn for her birthday. It will involve taking genes that grow horns and moving them into a horse."…

In 2014, a team of geneticists in China managed to give wheat full immunity against powdery mildew -- one of the most common and widespread plant pathogens on the planet -- by cutting just three genes out of its DNA. Similarly, researchers at the King Abdullah University of Science and Technology's Center for Desert Agriculture have used CRISPR technology to "immunize" tomatoes against the yellow leaf curl virus while a team from the National Institute for Biotechnology and Genetic Engineering (NIBGE) in Pakistan has done the same for cotton leaf curl. And just last year a Japanese team drastically increased the shelf life of tomatoes by editing the gene that controls the rate of their ripening…

What you will see is an explosion of novel uses for the technology. Gene editing is quickly moving from the realm of pure academia and into the hands of the general public and private enterprise. This transition resembles that of another transformative technology: personal computers. Computers went from being, essentially, toys for adults to a keystone of the modern era. CRISPR has the potential to do the same but for biology.

Take Ethan Perlstein for example. "I initially wanted to be a professor," he explains. "Like a lot of people who get trained in graduate school, especially in biomedical sciences, are thinking we're going to be professors ... that's how you can be a scientist professionally." However, the nation's glut of postgraduates has long outpaced the supply of available professorships. "My goal was academia; reality suggested that I take another path. And actually through my explorations on Twitter, I learned about rare diseases." His subsequent interactions with the social media communities that spring up around these rare diseases led him to found Perlstein Lab.

This San Francisco-based biotech startup is using CRISPR technology to drastically accelerate research into some of humanity's least-studied diseases. "There are about 4,000 inherited diseases that are caused by a single broken gene," Perlstein said, with roughly 5 percent of those manifesting during childhood and nearly all of which have no known pharmaceutical treatment. Specifically, Perlstein's team is working on drugs that can treat Niemann-Pick Type C, a lysosomal storage disorder that causes a buildup of toxic material within cells; and N-glycanase 1 Deficiency, a congenital glycosylation disorder that causes a whole host of issues, from cognitive impairment to joint deformities. Both of these devastating illnesses are caused by a single recessive gene, potentially by just one incorrect base pairing.

"These rare diseases, especially the ones that are caused by a single broken gene, tend to involve pathways and networks within the cell that are very ancient," Perlstein explained. What's more, those primal genes are disproportionately more likely to "break" than, say, the relatively new genes that control your autoimmune system. Their ancient nature enables the lab to effectively model them in simple animals -- specifically, fruit flies, zebrafish and yeasts.

"In the past, there have been technologies available with which to make disease models but that would essentially require taking a sledgehammer to the genome," Perlstein said. "CRISPR changes the situation as it allows for very elegant and precise changes to happen -- down to a single letter change." So once researchers identify the genetic source of the disease, they're able to "program" that same fault into their animal models and measure the effect of the disease in them.

By using CRISPR to break a test animal's genes in the exact same place and the exact same way as in the patient, Perlstein's researchers are able to create a perfectly customized model. Plus they can do so far more quickly than traditional methods would allow. "Depending on the kind of mutation you're trying to create [using CRISPR], it can be quite fast," Perlstein said. "You're only really limited by the breeding time of the animal."

Since the diseases that Perlstein's team research are recessive, the lab can't introduce these gene breaks directly into the models and then immediately study them. Instead, the team introduces these breaks into an organism and then breeds a second generation. Those organisms are then screened those that possess both copies of the recessive gene. Once a sufficient population of models that carry the gene defect has been bred, the lab leverages an automated system to expose them to thousands of chemicals and compounds to see if they have any positive effect -- reversing, or at least reducing the disease's symptoms.


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