CRISPR-Cas9 gene editing causes lots of mutations
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One of my favorite George Church quotes: "CRISPR: some call it genome editing. I call it genome vandalism".
Base Editors can actually edit DNA, but only single bases at a time. http://www.sciencemag.org/news/2017/10/novel-crispr-derived-...
There's a big prize waiting for the person who can harness DNA repair pathways in conjunction with Cas9 to make precise, multi-base DNA edits. Lots of folks are working on that now.
To simulate an entire human body is computationally mindboggling. The number of cells are in the tens of trillions and we'd need to simulate their responses, not just to the drugs we care about, but doing so while "operating" (feeding, sleeping, etc.) the simulated body.
And at a certain point couldn't you just feed the simulation DNA and watch it grow?
Our genomes are ~1.2B to 3.5B (sexual reproduction and life at all, respectively) years old.
Now imagine trying to patch that codebase in production...
The reality is so much more complicated, though, that even good analogies don't provide us with any path forward in terms of actual changes to make.
In simple terms, at least.
The complicated bit comes in knowing what to change. There are some diseases in which the entire disease is caused by a single mutation and changing that one mutation in the germ line would be sufficient to correct for the disease. However, most situations involve complex interactions with many genes in a way that making a single or small simple change would have many side effects, or cause other serious problems.
The root cause here is the DNA double-strand break induced by Cas9, and the ensuing DNA repair processes that occassionally produces large deletions (the paper reports two thirds or 32/48 were less than 50 bp and 21% or 10/48 were greater than 250 bp). This has been largely known by the DNA repair community for 20+ years.
Currently, our most powerful genome editing techniques rely on CRISPR's ability to induce double-strand breaks, such as HDR (for inserting designed sequences, used in gene drives for instance) and NHEJ (for knocking out genes, used in all current early-phase therapies under development). However, a double-strand break is among the most traumatic experiences a cell's genome can experience. We're currently taking advantage of the cell's freak-out attempts to repair its DNA for genome editing purposes, but the process is noisy and produces highly variable and stochastic outcomes. HDR, for instance, has a baseline efficiency of less than 20% in many cell types and conditions of therapeutic interest. Many papers have shown dramatically increased HDR rates at the expense of altering the cell's DNA repair pathways, but these were never going to be humanity's dominant therapeutic approach -- messing with DNA repair is dangerous and closely linked to cancer.
The holy grail is a genome-editing tool that is highly precise, with no off-target effects (edits only exactly in the genome where we want) and highly precise on-target effects (results in the same change everytime we apply it) and flexilbe (many designable changes). The messiness of cellular DNA repair is a major challenge to the second goal. The scientific community has recognized this and has been working on CRISPR-related genome-editing technologies that rely less or not at all on inducing double-strand breaks, thereby skipping the messiest part of the genome-editing process.
One example is base editing, where the endonuclease domains of Cas9 are disabled (called dCas9, sometimes explained as "dead" Cas9), and alternative enzymes that transform nucleotides (such as C->T) are attached to dCas9. In this setup, dCas9 provides the "homing" targeting while the attached enzyme enacts the editing without inducing a DSB. As it stands now, base editing is very exciting, but further work remains to develop base editors for all possible nucleotide transformations (a -> b for all a != b in {A, C, G, T}); it's not as flexible as HDR.
I do want to note another therapeutic domain of ex vivo therapies, where the messiness of DSB-associated genome editing strategies is much less of an issue, since cells can be screened after editing in vitro to control which genotypes we're inserting back into the patient.
Only one, but you might also get inflammation, organ failure, virus infection, cancer or autoimmune disease.
If this is so easy then why is it not standard practice? From the paper:
>"Results reported here also illustrate a need to thoroughly examine the genome when editing is conducted ex vivo. As genetic damage is frequent, extensive and undetectable by the short-range PCR assays that are commonly used, comprehensive genomic analysis is warranted to identify cells with normal genomes before patient administration." https://www.nature.com/articles/Nbt.4192
How much more expensive and time consuming will this procedure become if you require "comprehensive genomic analysis"? The merit of crispr/cas9 over other techniques was supposed to be how cheap and quick it was.
In all seriousness, how likely will the gene mutations from people self experimenting lead to a contagion? There are many CRISPR kits that people can buy to do their own experimentation.
This is still a very controversial statement, and far from definitively proven. Yes, even with a nature paper.
I also take issues with the phrase "lots". So far this effect has been observed only locally.
I believe the result, and I think it needs broader investigation but a summary like "gene-editing causes lots of mutations" is not accurate.
You may be interested in my comment from the last time this journal article was posted to HN.
It should be noted that "controversial" scientifically means something different than in the general public. What I mean is that we see and believe the current observations but are still waiting to fully understand the extent and reproducibility.
I'm also a biologist.
I guess I don't understand where your concern arises. I and others I know have used CRISPR-Cas9 to introduce arbitrary DNA mutations at loci of interest. We see many different types of lesions, ranging in size.
But anyway, I was just relating what I've heard from colleagues and my dis-taste for the articles definitive title.
This is why it is controversial.
I am taking issue with the articles title "CRISPR-Cas9 gene editing causes lots of mutations"
From the current literature, there have been bad and good examples of this, but it is still a field in flux. We do not know conclusively what the effect is, how large, and how local. This makes blanket statements like "CRISPR-Cas9 gene editing causes lots of mutations" controversial.