CRISPR-Cas9, Base Editing, Investing, and More!

Hor ki chalda,

"Mandeep, what's that gibberish?" That's Punjabi for "Hi, how are you?" I thought I'd inject a little bit of my culture into these posts. 😊

Today, I thought I'd take a brief break from personal finance to talk about scientific developments, specifically CRISPR-Cas9.

CRISPR-Cas9 is a gene-editing tool that has gained significant attention in recent years. 2023 marks the first year a medication (Casgevy) using this technology was approved. 

I remember first hearing about CRISPR in the 2010s when I was in college at UC Davis. Watching this go from discovery to bedside has been nothing short of spectacular. In simple terms, CRISPR-Cas9 is a pair of molecular scissors that can be used to edit the genetic code of living organisms, including humans.

Consider it a rudimentary form of Microsoft Word for your DNA.

First, let's start off by describing what CRISPR is not. It's not a device used to give your french fries a delicious, crispy exterior. That would be an air-fryer =P

Here's how it works:

CRISPR stands for "Clustered Regularly Interspaced Short Palindromic Repeats," which are short, repeating sequences of DNA that were originally discovered in bacteria as a way to mount an immune response against foreign invaders like viruses. When attacked by a foreign threat like a virus, bacteria break off a piece of viral DNA (called protospacer DNA) and integrate it into its own DNA (spacer DNA). Bacteria then use this to slice-and-dice viral DNA if it ever reappears - somewhat similar to how we use antibodies to fight off infections.

Let’s break down CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) into simpler terms. "Clustered" means the sequence of DNA exists together in a cluster or group. "Regularly interspaced" means that the spacer DNA is regularly separated by palindromic repeats. Again, the spacer DNA is foreign DNA that bacteria have integrated into their genome as a defense mechanism. “Short palindromic repeats” refers to CRISPR DNA. There are short repeats of DNA that are “palindromic” which means they read the same backwards and forwards (5' to 3' - pronounced five prime to three prime) like the word racecar.

Cas9 refers to an enzyme that acts like a pair of molecular scissors. There are many different Cas proteins that are able to cut DNA - for example, Cas1, Cas2, etc. Cas gets its name from being associated with CRISPR (CRISPR-associated endonuclease) - the "C" from "CRISPR" and the "as" from "associated."

The pharmaceutical application of the CRISPR-Cas9 system works in three main steps:

Targeting: Scientists design a small, synthetic piece of RNA that acts as a guide. In natural biological systems, this is crRNA (CRISPR RNA). This single guide RNA (sgRNA) can "find" a specific part of the DNA sequence within a cell's genetic material.

Technically, the crRNA is held together on Cas9 with scaffolding RNA called tracrRNA, which, in aggregate, is called sgRNA. But let's not draw too much attention to this for clarity's sake, or we'll get lost in terminology and technicalities.

Cutting: Once the guide RNA locates its target DNA sequence, the Cas9 enzyme cuts the DNA at that location. When it cuts DNA, it cuts both strands causing what's called a double-strand break (DSB).

Editing: After the DNA is cut, the cell's natural repair mechanisms come into play. Specific changes to the DNA can be introduced during the repair process - like inserting new genetic material. In the case of Casgevy, there is no new gene inserted. Instead, expression of a gene called BCL11A is reduced, and fetal hemoglobin expression increases.

Casgevy isn't injected into a patient's body. A patient's stem cells are collected and edited ex vivo with CRISPR-Cas9, and then administered as a stem cell transplant. Needless to say, this process will likely only take place at an academic hospital, hematology center-of-excellence where this sensitive process can be carried out by trained professionals.

CRISPR-Cas9 isn't perfect.

One of the challenges of using CRISPR-Cas9 is the risk of off-target effects. This means that the gene-editing process could inadvertently affect other parts of the genome, potentially leading to unintended and harmful changes. This risk is listed in Casgevy's FDA labeled prescribing information in Section 5.4.

Base editing is a newer genome editing approach that uses components from CRISPR systems together with other enzymes to directly instill point mutations (changing individual bases) without making DSBs.

So how exactly does base editing work?

Base editing uses many of the components of CRISPR-Cas9. We still have a guide RNA and a Cas9 protein (albeit, modified) to cut DNA. The Cas9 protein is changed/impaired (specifically, called a nickase), so it doesn't cause DSBs. Instead, it causes a single-strand break/nick.

Now you know why it's called a "nickase."

Then, a base editor (a deaminase enzyme) is used to change a single base pair. This allows for fewer errors than traditional CRISPR-Cas9. However, it doesn't allow for large-scale changes like CRISPR-Cas9.

Aside: While I just said base editing doesn't cause DSBs - it USUALLY doesn't do so. In rare circumstances, you can get a DSB even with base editing. I'm just explaining the general steps and terminology without going through every exception because that would just make this post exceptionally complicated (no pun intended).

Prime editing is yet another way to insert changes that has some benefits compared to base editing. It utilizes a prime editing guide RNA (pegRNA) and an impaired Cas9 so it doesn't cause a DSB similar to base editing. The pegRNA allows for a DNA "find" and "replace" much like you might use in Microsoft Word, so you can make lots of changes and lots of types of changes.

Traditional CRISPR-Cas9, in my opinion, is just the beginning of gene-editing technology. Base editing may be more promising for genetic diseases with single point mutations. Prime editing has it's own pros and cons. More pros than cons, in my opinion...

There is also PASTE (programmable addition via site-specific targeting elements), which was developed by the lovely folks at MIT (study published in 2022) to deliver large DNA payloads using elements of CRISPR-Cas9. However, they haven't tried DNA payloads larger than 36 kb (kilobases) because of their adenoviral construct delivery mechanism. Maybe one day, they can deliver payloads that approach 100 kb.

Mandeep, how do I invest in CRISPR-Cas9/base editing/prime editing/PASTE?

Before we go there, let’s talk a bit about the wonderful people that discovered this technology.

Emmanuelle Charpentier (University of Vienna) and Jennifer Doudna (UC Berkeley) share a Nobel Prize in Chemistry for discovering CRISPR-Cas9. However, the patent to CRISPR-Cas9 is jointly held by Harvard and MIT. CRISPR Therapeutics doesn’t own the patent; it licenses the patent from Emmanuelle Charpentier, who happens to be the company’s scientific founder.

I don't hold any individual stocks, and while this technology is exciting, I personally won't be investing in it or any other emerging technologies (including AI). Promise isn't the same thing as efficacy, and efficacy means little without formulary access and favorable utilization management criteria.

My portfolio is and always will be 100% index funds, and this will not change no matter how much more or less knowledgeable I become about a particular domain. Stock picking isn't a game worth playing IMO. If you have some beer money you wouldn't mind going up in smoke, feel free to take a gamble. However, acknowledge it is a gamble and not a strategy. 95% of the experts on Wall Street working 100 hour weeks don't outperform the S&P 500 over long time horizons. I'm not willing to bet that I'll outperform them. It doesn't matter how smart one might think they are, the efficient market hypothesis reigns supreme.

If you're a stock picker, it would be wise to read up on the efficient market hypothesis and the paper on "efficient capital markets," which has been cited about 39,000 times (no exaggeration). The guy that wrote it is Eugene Fama, a Nobel prize winner, and is known as the "father of modern finance." I think he's a bit more credible than your room-temperature IQ TikToker trying to sell you their super-secret, stock market trading algorithms that return 1,209% per year, which they're willing to conveniently share with you for a one time payment of $99... I've interacted with used car salesmen that I trust more, but I digress.

It's a fascinating time to be alive, and I'm looking forward to the amazing advancements in science and technology that are just around the corner. Maybe, the best play is to grab a bag of chips, and enjoy the ride. We're in for an exciting journey :)

It goes without saying, none of this is investing or medical advice, and everything here is only my opinion. It doesn't reflect the views of any employers, past or present. I'm only writing about this because I love science. I hope you enjoyed this too! If you are a PhD molecular biologist (or a domain level expert), and you have identified any errors above, please kindly message me. Thanks!

The image for this article was generated courtesy of DALL-E 3.

If you liked this post, you might also like my post on the origins of vaccination, which you can find here.

Is there anything you found useful or that I missed above? If so, please leave a comment in the comment box below.

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