
CRISPR-Cas9 gene editing causes lots of mutations - pmoriarty
https://www.dw.com/en/getting-real-crispr-cas9-gene-editing-causes-lots-of-mutations/a-44742022
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bru
Actual source: [https://www.sanger.ac.uk/news/view/genome-damage-
crisprcas9-...](https://www.sanger.ac.uk/news/view/genome-damage-
crisprcas9-gene-editing-higher-thought)

Paper:
[https://www.nature.com/articles/Nbt.4192](https://www.nature.com/articles/Nbt.4192)

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zfrenchee
Cas9 does not edit DNA, it cleaves DNA. What happens afterwards is up to the
cell. The hype machine has ignored this fact.

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-...](http://www.sciencemag.org/news/2017/10/novel-crispr-derived-base-
editors-surgically-alter-dna-or-rna-offering-new-ways-fix)

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.

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21
Does it cleave a whole segment off (two point cut), or just a single cut?

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distant_hat
Single cut.

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caio1982
Sometimes I think these gene editing techniques are more like having a
fantastic hex editor... but with a 5GB binary.

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throwaway5752
I think that if you wanted to reframe it this way, it's more like like editing
a 800MB binary with sed/regexes (with some degree of random side effects
injected sometimes)

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zip1234
And no way to really test it without just running it in production!

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d0lph
Really curious how far are we from being able to simulate the human body's
response to drugs/modification.

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tyre
We are so ridiculously far that it's not really worth thinking about. We're
still at the stage of simulating how molecules interact with each other. To
work our way up even to the single-cell organism level would be a historic
human achievement.

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.

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d0lph
I have no experience in this area, but. Once you get the molecules and their
interactions down wouldn't that make all other types of cells easier to
produce?

And at a certain point couldn't you just feed the simulation DNA and watch it
grow?

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infinite8s
It takes supercomputers days to simulate milliseconds of interactions between
a million atoms using classical mechanics (ie Newton's Laws, basically a ball
and spring model so not even accounting for quantum effects except through
very rough approximations in the spring constants). We don't even have an
accurate model for water yet.

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dandigangi
Not entirely unexpected to see stuff like this come up. We're still in the
early days of what gene editing is and will become. Keeping my fingers crossed
for its future.

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mxwsn
tl;dr: (1) The paper's main finding has been known by the DNA repair
community, (2) relying on DNA double-strand breaks for genome editing has been
known to be non-ideal in the long-term, and (3) current ex vivo therapies are
unaffected since we can screen cells after editing.

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.

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DividableMiddle
As a software engineer super interested in genome editing, are there any
software out there that will educate me through the process?

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mxwsn
Nearly all the software are tools for designing CRISPR gRNAs, not really
educational software. There are videos and books for learning more about the
whole thing though.

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jackgavigan
Every time I read about gene editing, I think of the short story _Sisters_ by
Greg Bear:
[https://www.baen.com/Chapters/ERBAEN0036/ERBAEN0036___1.htm](https://www.baen.com/Chapters/ERBAEN0036/ERBAEN0036___1.htm)

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LinuxBender
Isn't this the basis for the movie "I Am Legend"?

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.

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proaralyst
I suspect you're much more likely to give yourself cancer than cause an I am
Legend-style mutation.

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LinuxBender
Probably so, but I don't have any statistical data to form an opinion. Does
anyone track genetic incidents / blunders at a global scale?

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searine
>CRISPR-Cas9 gene editing causes lots of mutations

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.

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ejstronge
I don't think this is a controversial statement at all. Any CRISPR-Cas9 paper
published will at least discuss the prospect of undesired mutations; this is a
well-known concern.

You may be interested in my comment from the last time this journal article
was posted to HN.

[https://news.ycombinator.com/item?id=17544250](https://news.ycombinator.com/item?id=17544250)

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searine
Speaking as a biologist. Among my colleagues, it is still very controversial.

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.

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ejstronge
> Speaking as a biologist. Among my colleagues, it is still very
> controversial.

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.

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searine
I shouldn't have brought credentials into this, its bad form on my part.

But anyway, I was just relating what I've heard from colleagues and my dis-
taste for the articles definitive title.

