Genetic repair via CRISPR can inadvertently introduce other defects

A lot of the graphics that explain how CRISPR work show this very careful snipping of a strand of DNA. Tiny little scissors making pinpoint accuracy revisions. I think that's lead to a deep misunderstanding for most people (including myself) on how this technology actually works.

CRISPR is amazing, but it's still a fairly blunt tool. The article talks about one way: guide RNA can often bind to sequences that are very similar to the intended sequence, but not exactly, meaning it's probable that for every intended cut you're making several unintended ones. The "scissor" action itself, Cas9 protein, is less like a scissor cut and more like a jagged tear, which can damage surrounding DNA.

The repair pathways themselves are also imperfect. It's not a copy/paste like infographics show, it's more like emergency duct taping broken ends together.

All of that stuff combined...Again, amazing technology, but I get extremely nervous when I hear people talk about introducing CRISPR-based gene editing into the human gene pool. The generational effects there are still entirely unpredictable at this stage, could be disastrous, and any actual paths to trying to roll things back would be deeply ethically fraught.

Let's say you have a running program on a computer, and you figure out a way to swap out parts of its instructions / state in RAM while it is running. What are the odds of your swap causing problems? Now, what if the program is 100 - 1000x more complex than anything you have ever managed to create.

Consider a scenario where you're editing a function:

  function foo() { return a*2.1^2+0.52/2 }

So you do a find-all regex "1.*5" and delete all matching occurrences (à la CRISPER) to get:

  function foo() { return a*2.2/2 }

But unbeknownst to you, the code is littered with a bunch of commented out versions of the same function you're trying to edit:

  /* function foo() { return a*1.5/2.1 } */
  /* function foo() { return a*1.95/2.4 } */

And now those commented out versions now become:

  /* function foo() { return a*/2.1 } */
  /* function foo() { return a*/2.4 } */

And now the whole program doesn't compile anymore--or your patients get Leukemia. Oops.

There were some numbnuts that were calling themselves "Bio Hackers" and freely injecting themselves with random CRISPR injections. I wonder what's going to happen to them.

We should steer clear of modifying DNA directly until our understanding of biology is much much better.

For now, I think targeting RNA as an intermediate solution is the right approach.

Of course editing genes with CRISPR can introduce other defects! Genetic sequences can serve multiple purposes, alternative splicing, polygenic traits etc. It's an exciting discovery with interesting repurpose applications but DNAs application is not just a linear read

I once got into a debate with a classmate in undergrad. He had seen a Ted Talk and was very worried that CRISPR was going to create a new race of designer babies. I tried to explain that even CRISPR wasn't there yet, but he was under the common misconception that CRISPR is just a text editor for the genome [1].

If we want to take the computer code analogy, CRISPR is not vim/emacs/nano/ect., it is sed -i 's///g' with greedy options on.

The 'g' option is what got the researchers here. I hypothesize that a future problem will be CRISPR targeting previous CRISPR edits since the targets are relatively conserved.

[1]: https://xkcd.com/1823/

ScholarlyArticle: "Gene editing of NCF1 loci is associated with homologous recombination and chromosomal rearrangements" (2024) https://www.nature.com/articles/s42003-024-06959-z

I wonder if there's a pattern to genes that are adjacent to the target ones, which is not typically found adjacent to the pseudo ones. In other words, can the "search term" be expanded to make it more selective and then take action on the target region within it.

We do this because reversing what caused the defect is way out of our league, just like how most advanced drugs work. The point is you take it anyway because you likely have 2 choice.

I see a whole bunch of comments here where people have misunderstood the issue.

The problem here is not that unanticipated outcomes arose from our intended fix.

The problem that the exact edit we planned isn't happening in the first place, because the search-replace tools aren't yet specific and reliable enough.

Does it matter which CRISPR or CRISPR-like method is applied; or is there in general a dynamic response to gene editing in DNA/RNA?

In mice?

Changing code you don't understand can have effects you did not intend.

Who would have expected that?

No shit.

I would personally love to get a gene theraphy for an inherited auto-immune disease, but mankind just doesn't have 'the full picture' - yet. So i'll stick with known treatments.

I upvoted this because it's perhaps the most important research being conducted currently. But the seriousness of the issue is misleading.

CRISPR is revolutionary technology. Any side effects of its use require evolutionary improvements. The two are not the same.

With the decades of experience we have dealing with code and information, as well as the arrival of AI, I wish that people would stop obsessing about the difficulty of solving problems. The difficulty is gone. All problems are solvable now, it's just a matter of time, effort, and a tiny fraction of the money that used to be required.

But FUD seems to dominate these discussions. That's probably my biggest disappointment with, say, the rich and powerful who gatekeep funding and the media. It's even easier for them to solve these problems, or encourage healthy debate. But they seem to go out of their way to do the opposite. Like, if it weren't for wealth inequality, we could have been working on this stuff, and found the answers potentially years ago. I'll just never understand the so-called realists and how they hold us back in these times out of fear, which leads to false equivalence and generalization.