Genetic Toolkit reaches a whole new level

kw: book reviews, nonfiction, science, biology, crispr, cas9, cas12, cas13, biographies, nobel prize

For those who are aware of CRISPR, the usual meme is CRISPR/Cas9. "Nine!", you might say, "Are there eight more?" Yes, a whole lot more than that. Reading The Code Breaker: Jennifer Doudna, Gene Editing, and the Future of the Human Race, by Walter Isaacson, I learned of several others. First, a bit of jargon and some overly-brief explanation.

• CRISPR refers to a bacterial anti-viral defense system, and is the acronym for "Clustered Regularly Interspaced Short Palindromic Repeats". From back to front:
• "Palindromic Repeats" are strings of DNA that read the same both ways, such as GTCACCTAATCCACTG.
• "Short" because they are just portions of a virus's DNA sequence, probably just long enough to reliably detect a specific virus.
• "Regularly Interspaced" because they aren't jammed end-to-end but are separated by sequences that serve as delimiters.
• "Clustered" because they occur all grouped together in a bacteria's DNA.
• Cas is short for CRISPR-associated, and refers to enzymes that work with the Repeats, to cut DNA where the Repeat latches on.
• Cas9 is the shortest of the first dozen or so Cas enzymes to be discovered. It is "easiest" (only by comparison!) to work with. It cuts DNA exactly where a specific Repeat attaches.
• Cas12 and Cas13 not only cuts where the Repeat attaches, but goes on to cut up all the DNA in the vicinity.

I have a mental image of CRISPR/Cas9 (CC9 hereafter) at "homing scissors". If you dump a solution containing it, having the sequence in its Palindromic Repeat set to match some DNA in a specific virus, and that virus is present, in pretty short order the DNA of every virus present will be cut at the specified location. 

Gene editing is using CC9 to cut, and some associated chemicals to insert "new stuff" and seal the cut. It can be done with precision.

By contrast, my mental image of CC13, in particular, is an axe murderer with a roomful of victims. Perhaps a more prosaic image is someone splitting logs, going through a wood pile and making "small logs out of big ones". This enzyme complex and related ones such as CC12 form the basis for virus detection; we'll come to that in a moment.

The book is a biography of Jennifer Doudna, primarily a career biography, with just enough of the rest of her life included to produce a feel for her as a person. The author portrays someone most of us would love to work with and for: personable, demanding but not overbearing, not a micromanager yet fully engaged, and a superb team leader.

There are two big turning points in the book. Firstly, well into a career of study and work with RNA, Dr. Doudna and her collaborators, and others in usually-friendly competition with them, sought to take the bacterial CRISPR/CasX system and modify it to work inside non-bacterial cells (specifically, human cells and those of other animals). These parallel efforts bore fruit almost simultaneously, and were reported in professional publications about eight years ago. The series of breakthroughs turned CC9 into a premier gene editing tool. As the author learned at the lab bench, the process is "easy", at least in comparison to earlier genetic engineering tools such as TALENs.

Secondly, the "whack and chop" nature of CC13 makes it useful for virus detection, thus: Put it in solution with nucleic acid that has a fluorescent protein attached. The protein is not fluorescent until the DNA it is connected to is lopped off. If viruses are present that match the Repeat in the CC13 complex, the enzyme first cuts the virus's DNA, then begins cutting everything else it can reach. Do this with a UV light on, and the solution will begin to glow. More recent work has coupled the CC13 (or maybe CC12; I wasn't sure) with a dye so you can use it like a pregnancy "dipstick test". This is the basis for rapid Covid-19 tests.

There is much in the book on the ethics of gene editing. We read of the evolving feelings of Dr. Doudna, beginning with a visceral reaction, "No germline editing!", to a more nuanced view. The views of everyone in the field were rocked by the revelation in 2018 that a Chinese researcher, He Jiankui, had edited a gene in twin embryos to give them resistance to HIV; they were then implanted and brought to term, and the babies were born by C-section. The researcher, who expected acclaim, was instead prosecuted. Should he have been? That's a question we all must now answer, because the horse is out of the barn.

Writers of science fiction have for decades written stories about various aspects of gene editing, from the utopian to the dystopian. The reality is likely to be more prosaic. I recall the novella Mr. Boy by James P. Kelly, in which people regularly get their genes "twanked", either to boost characteristics they want, or to experiment with living in a very different body. We're not just talking temporary sex changes here: the teenage protagonist's best friend spends time as an intelligent Stegosaurus. I reckon that took a lot of twanking! Step back a pace or two, and it isn't hard to imagine parents choosing to give birth to a nascent Barbie or Mr. T, or perhaps Einstein or Venus Williams; upon growing up, if full-body "twanking" has arrived, the Mr. T may decide to become a bicycle racer instead, for example. And skin color might become as variable as that of a squid; perhaps we can get squid skin! "I'm feeling rather orange today; I'm tired of being blue," could become quite literal.

That paragraph is all my own. The author muses on the possibility that germline editing will result in decreased diversity, as though standards of attractiveness were universal. I think there could be a dip early on, followed by a blossoming of imagination. But I do hope that we first work toward eliminating scads of genetic diseases such as Huntington's and Cystic Fibrosis.

When a Nobelist gets "the call" it happens at a time convenient to King Carl Gustaf, which meant before 3:00 am in Berkeley. As usual, the media knew before Jennifer Doudna did, because her pre-Three phone call was from a reporter. She and her dear friend and collaborator Emmanuelle Charpentier were the Nobelists in Chemistry in 2020.

That's enough from me. I note that my last review was two weeks ago. This big (530 page) book rewards thoughtful reading. I'm just a tiny bit sorry to anyone who follows this blog. Read the book!