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New gene-editing 'pencils' rewrite DNA to erase disease

Harvard and MIT scientists develop new tools to fix genetic mutations among the most likely to cause disorders from genetic deafness to cystic fibrosis.

A pair of new gene-editing tools could be used to treat numerous diseases caused by mutations in human DNA, researchers say. 

Scientists at Harvard and MIT developed a gene-editing system called the Adenine Base Editor, or ABE, that uses a modified form of the well-known Crispr-Cas9 gene-editing tool and a new lab-developed enzyme to reverse disease-causing genetic mutations by rewriting the genetic code that makes up our DNA.

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The double helix of DNA is now subject to human revision using new gene-editing tools. 

Video screenshot by Eric Mack/CNET

The new technology works differently than Crispr-Cas9, which is often described as being like a pair of chemical scissors that can precisely cut and insert sequences of DNA into our genome. 

Harvard chemistry professor David Liu, who led research published in the journal Nature Wednesday, explained on a conference call with journalists that ABE is more like a pencil that can rewrite the letters that make up each strand of DNA so they're arranged properly into the sentences that make up our genomes.

The pencil metaphor is apt because the nucleotide molecules that predominantly make up DNA are abbreviated with the single letters A,C,G and T. A (for adenine) binds with T (thymine) to form one strand of the familiar double helix structure of DNA, while G (guanine) pairs with C (cytosine) to form the other. 

In the case of genetic mutations, though, the letters are switched around, causing disorders like genetic blindness and cystic fibrosis. ABE makes it possible to reverse one specific mutation by putting those letters in the right order so they pair up correctly to form the right genetic "words" or "sentences." This eliminates the genetic disorders that come from jumbled letters.  

The mutation ABE addresses is the most common disease-causing genetic mutation, according to Liu.

"We developed a new base editor -- a molecular machine -- that in a programmable, irreversible, efficient, and clean manner can correct these mutations in the genome of living cells," he explained in a statement. 

Liu and colleagues detail in the research paper how they used ABE to correct a mutation that causes hereditary hemochromatosis (HHC) in human cells. HHC is a disorder that causes the body to take on too much iron. 

He says the new tool is also among the most clean and accurate of existing gene-editing systems, leaving almost no unintentional random insertions, deletions or other unwanted edits in the genetic code.  

Dr. Derya Unutmaz, a professor at the Jackson Laboratory for Genomic Medicine in Connecticut, took to Twitter to call ABE "a very important advance in gene editing ... (that) may lead treatment for thousands of diseases."

At the same time, a different lab at MIT and Harvard's Broad Institute have developed a new Crispr-based system to edit the RNA in human cells. RNA is like the messenger between DNA and other parts of cells, so editing RNA results in temporary changes whereas changes to DNA are permanent.

The tool, called "Repair" for "RNA Editing for Programmable A to I Replacement" can reverse disease-causing genetic mutations at the RNA level. Like ABE, Repair also has the DNA-cutting function of Crispr disabled, acting more like a pencil than a pair of scissors. 

"Repair can fix mutations without tampering with the genome, and because RNA naturally degrades, it's a potentially reversible fix," David Cox said in a statement. Cox is a graduate student in Feng Zhang's lab at Broad and a co-author on a new paper published Wednesday in Science.  

For example, Repair might be a better a tool to treat something temporary like acute inflammation via RNA, according to Liu, because permanently removing the inflammatory response in DNA would likely have long-term health consequences.

Both new tools have proven successful in fixing disease-causing mutations in human cells, but are still a long way off from being used on actual humans. 

"For example, one has to develop a good delivery approach to getting the machine into the right tissues into the right cells at the right stage of the patient's life," Liu says of ABE. "A tremendous amount of work is still needed before these molecular machines can be used to treat human disease in patients ... but having a machine is an important starting point."  

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