The identities of the inventors of the hammer are lost to history, but we suspect that once they had their first working model, they quickly started bashing stuff. In 2016, biologist Shawn Liu felt the same way.
He and colleagues at the Whitehead Institute in Cambridge, Mass., had just invented a form of CRISPR-Cas9 that, unlike the original genome editing tool, leaves DNA’s “letters” alone but adds or removes genetic silencers — turning gene expression off or on. (A few other teams came up with the same idea for “epigenetic editing” almost simultaneously.)
Liu, a postdoctoral fellow in Rudolf Jaenisch’s lab, wanted something to sic his cool new tool on. What better than fragile X syndrome? The cruel genetic disease causes mental retardation (with symptoms usually worse in boys than girls) and is caused by the silencing of a gene called FMR1.
Liu decided to test whether his new tool, called DNA methylation editing, could unmute the devastating genetic silencing in both neuron-making human stem cells and mature neurons themselves, in lab dishes, and whether neurons with full-throated FMR1 could shake off the abnormalities that cause fragile X. In both cases the answer was yes, they and colleagues showed in a series of elegant experiments reported last year in Cell.
On Monday, STAT announced that the study was the Editors’ Pick in STAT Madness 2019.
The annual competition to identify the year’s best innovations in biomedicine started with a record 160 entries. They included a fast CRISPR-based test for viruses such as Zika and dengue, a device to treat the ringing in ears called tinnitus, a pill that mimics gastric bypass surgery, and the discoveries of the genetic mutations that drive children’s cancers and of neurons that connect the gut and the brain. We then selected 64 for NCAA-style brackets, based on the originality, scientific rigor, and potential impact of the work. Readers voted for a winner in each pairing until, after six rounds and 313,870 votes, the University of Michigan (the tinnitus research) beat the University of Utah (using evolutionary analyses to identify disease-related genes) in the finals.
STAT staffers meanwhile evaluated the 64 to come up with an Editors’ Pick — no easy task when comparing research as different as lab-grown lungs transplanted into pigs and the invention of a genetic barcode to track all the cells descended from one progenitor.
We are crowning the fragile X paper for two main reasons. It used a form of genome editing (an exciting field that has not previously won STAT Madness) that goes well beyond the original. And, although it is very preliminary (“only in mice,” as skeptics say), it suggested that genome editing might one day treat the most complicated of human diseases: those affecting the brain.
STAT is in good company in recognizing Liu’s work. He was a 2017 recipient of a competitive grant from the Damon Runyon Cancer Research Foundation. With his postdoc position winding down, he has received several job offers, a proud Jaenisch said.
In fragile X, which strikes 1 in 3,600 boys, FMR1 is silenced by the hypermethylation — off-switches galore — of a “promoter” region. In this region, the DNA letters CGG repeat themselves, about 20 times in healthy people but hundreds of times in boys with fragile X. Atop each CGG triplet sits a methyl group, a cluster of three atoms that act as genetic silencers. With its promoter silenced, “the whole FMR1 gene shuts down,” Jaenisch said, causing synapses to crackle with out-of-control electrical activity, resulting in the intellectual, social, and emotional dysfunction of fragile X.
Liu’s CRISPR tool therefore needed to remove hundreds of the off-switches to get the promoter to live up to its moniker.
Like classic CRISPR, the epigenetic version has a guide molecule, RNA, that makes a beeline for a particular DNA target. But where classic CRISPR pairs the guide with a DNA-cutting enzyme such as Cas9, this version uses “dead Cas9.” Instead of cutting DNA, it ferries enzymes that add or remove methyl groups. In human stem cells derived from boys with fragile X, a single guide RNA led CRISPR to the 450 methylated CGG repeats, and demethylated — unsilenced — them. That restored production of FMR1 in the stem cells to as much as 90 percent of normal.
Neurons that developed from the edited stem cells also produced near-normal amounts of FMR1 and, crucially, had normal electrophysiology, not the crazy firing of fragile X neurons. Liu also edited mature neurons, which are difficult to edit with CRISPR. “But you have to target them if you want to be successful” treating neurological disorders such as fragile X or Rett syndrome, he said. The edited neurons also started behaving normally.
“We were pretty lucky,” Liu said. “We got efficient editing and very few off-target effects,” meaning edits in regions of the genome they hadn’t aimed for.
For the crucial test, the scientists transplanted edited human neurons into the brains of mice. Despite their alien locale, just over half the neurons continued producing FMR1 and kept up their healthy firing patterns. “Production was stable for as long as we checked” — three months — Liu said.
The experiments showed that epigenetic editing can unsilence FMR1. And that, Jaenisch said, “suggests potential therapeutic strategies. We don’t know if fragile X can be reversed postnatally, and we don’t know the best way to introduce [CRISPR] into the brains of patients. This is a question of gene transfer, where there have been enormous advances — but which remains a very, very difficult problem.”
To treat fragile X, CRISPR would have to unsilence FMR1 in “a sufficient number” of brain neurons, Jaenisch said, and keep it unsilenced. “But Shawn’s work gives us some confidence that you can restore healthy levels of gene expression and, even more important, normal electrophysiology,” he said.
Correction: This story has been corrected to include that fragile X strikes both girls and boys, with worse symptoms in the latter.