Gene-editing instrument will get its inevitable Nobel

Enlarge /. Emmanuelle Charpentier reminds everyone of pandemic safety at the start of a press conference following the announcement of her Nobel Prize.

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On Wednesday, the Nobel Prize Committee awarded the Nobel Prize in Chemistry to Emmanuelle Charpentier and Jennifer Doudna, who made important contributions to the development of the CRISPR gene editing system, which was used to create the first gene-edited humans. This award could cause some controversy, as many other contributions were made to the development of CRISPR (enough to ensure a fierce patent battle), and Charpentier and Doudna's work covered the biology of chemistry widely. But no one will argue that gene editing wasn't earmarked for a Nobel Prize.

Basic research

The story of CRISPR gene editing is a classic science story: a group of people working in a not particularly cutting edge area of ​​science found something weird. The "something" in this case was a curiosity in the genome sequences of a number of bacteria. Though very distantly related, all species had a section of the genome in which a number of DNA sequences were repeated with a short spacer in between. The sequences took the name CRISPR for "Clustered Regular Interspaced Short Palindromic Repeats," but no one knew what they were doing there.

The fact that they could be important became apparent when the researchers realized that bacteria with CRISPR sequences invariably also had a small set of genes. Since bacteria tended to quickly lose genes and repeat sequences that did not serve useful functions, this obviously implied some kind of utility. However, it took 18 years before anyone noticed that the repeated sequences matched those in the genome of viruses that infected the bacteria.

A key experiment came two years later in 2007 when researchers exposed bacteria to a virus and then removed those that resisted infection. Without exception, they found that the resistant strains had taken up copies of CRISPR that matched the sequences of the virus. CRISPR acted like a bacterial immune system, allowing them to remember and deactivate pathogens to which they were previously exposed.

It's worth noting that studying the defenses of bacteria against viruses is not an obvious route to a revolution in biotechnology, and it's kind of very basic research that would never industry funded. However, this is the second time, and the first time the restriction enzymes that made recombinant DNA possible were discovered, which won the 1978 Nobel Prize.

How does this work?

However, all of this left many questions unanswered. We knew there were sequences of DNA and we knew there were genes, but we didn't know how they worked. Over time, people found that many of the genes were responsible for identifying foreign DNA and turning it into CRISPR repeats. And it became clear that near the repeats, the DNA caused it to be transcribed into RNA. Charpentier and Doudna made important contributions to the assembly.

Around 2010, Emmanuelle Charpentier led a team that found that the CRISPR repeats were transcribed from both strands of DNA in the double helix. This meant that the two RNA populations could also form a two-stranded double helix. The team confirmed that these two strands of RNA are essential for the system to function.

It was then that Charpentier began working with Doudna to understand what the double-stranded RNA could do. They eventually identified that it was cut into smaller pieces that were combined with one of the CRISPR-associated genes, CAS-9. CAS-9 then used the RNA to identify matching DNA sequences in a virus that it would cut. Cutting the DNA of a virus is enough to inactivate it and protect the bacteria.

But Charpentier and Doudna quickly realized that this was a potential tool. When the RNA tells the system which sequences to cut, replacing the RNA with another RNA could redirect it to cut another sequence completely. And there are many possible uses of a programmable DNA cutting enzyme, as it is possible to use the cut to inactivate a gene, or even replace it in another version of the gene.

To show that this is possible, Charpentier and Doudna made two important developments. They showed that CAS-9 didn't require the complicated process of making matching RNAs, which were then cut into smaller pieces. A shorter RNA engineered to loop back on itself and form a double helix would work just as well, simplifying the system a lot. They went on to show that changing the sequence of this RNA to match something other than a virus was enough to realign it to something that wasn't a virus. The CRISPR-CAS-9 system could be reprogrammed to cut any sequence desired.

The two knew exactly what they had developed. The last sentence of the abstract of their main paper states that their work "highlights the potential of using the system for RNA-programmable genome editing".

A revolution

The world was listening. Only six years after these words were published we had the birth of the first genetically edited children.

There is also a lot going on that does not include ethically challenged and scientifically questionable research on humans. Despite a long dispute over who owns the patents for various aspects of CRISPR technology, it has already found widespread use as a tool to manipulate research organisms such as the mouse. People have developed CRISPR-based tests for SARS-CoV-2 that work quickly and at room temperature. And well-regulated human trials have already taken place.

Therefore, many people were involved in applying Charpentier and Doudna's findings to different projects. Others have further developed the actual system themselves and adapted it in order to process individual bases or to cut with higher specificity. And the story we outlined above makes it clear that Charpentier and Doudna went well into the CRISPR story after some of the basics were worked out. There are invariably complaints about people excluded from Nobel Prizes.

Another thing that could cause some controversy is the fact that this award is placed in the Chemistry category. Some of the studies on CRISPR systems involved a high level of chemistry, such as figuring out the details of the actual cutting mechanisms and base pair interactions required to make it work. However, the Charpentier and Doudna key paper shows only a series of gels that reveal the presence of various DNA and RNA molecules. In other words, the work is way beyond the end of molecular biology and is closely related to regular biology. Chemists who are sensitive to such things will have many reasons to complain.

But you will likely have a hard time finding someone who believes that the development of CRISPR gene editing does not deserve a Nobel Prize, or that Charpentier and Doudna did not make a significant contribution to the development of the tool it has become.