CRISPR For Dummies

[Alfalfa Bill]

There are many science news stories about the wonderful new technology CRISPR which appears to change DNA sequences and alter genes. It is said to have many great potential applications. I read Wiki but still don't understand.

In a simple way, could you explain how CRISPR works?

Specifically, what are some of the many great potential applications for CRISPR?

[art...@yahoo.com]

Crispr allows you to readily change a DNA sequence. You could correct a genetic defect or see what happens when you change a DNA sequence. It can be done in most if not all organisms. In one controversial experiment, some human embryos were altered via CRISPR. However, the embryos that were chosen to do the experiments were cases in which an egg was fertilized by two sperm (these do not usually survive) and the fertilized eggs were not implanted.

[bill van]

In article <e5c38681-68b2-496e...@googlegroups.com>,

Here's a story that seems fairly clear to me:

<http://news.sciencemag.org/biology/2015/12/crispr-helps-heal-mice-muscul
ar-dystrophy>

It seems they have been "editing" gene sequences to remove defective
bits of genes that cause or allow serious diseases to develop. That's in
mice, but it seems they're ready to do it with people.

All great, but when they did the same thing with fruits and vegetables,
we got genetically modified foods, and a lot of people got scared
shitless of "Frankenfoods" etc, without any evidence that I've seen of
harmful consequences.

I expect that as soon as the same people get wind of this, there will be
hell to pay. Throw in a few religious groups that oppose mucking around
with the human body, and I think there's a big fight brewing.
--
bill

[Alfalfa Bill]

I see how you can gene engineer a zygote but how practically can you gene engineer an animal with millions and millions of cells?

[Les Albert]

Here is an animated youtube about how it works:
https://www.youtube.com/watch?v=0dRT7slyGhs

Les

[Alfalfa Bill]

Thanks Les and Bill. I understand in a basic way how CRISPR works.

Let me ask about the applications.

Jack Horner said some day people will take a chicken egg and reverse engineer it to hatch as a dinosaur. I can see how CRISPR would be great for that. But I read predictions that CRISPR will cure cancer. How would that work? Wouldn't we have to have a test tube baby to do a genetic analysis and CRISPR it right away to fix mutations?

Is there any application for CRISPR to treat an adult with cancer?

[art...@yahoo.com]

If you can target the tumor crispr could treat it.

[art...@yahoo.com]

There are always stem cells. If you need to get into a lot of cells. You need some luck
..

[Howard]

bill van <bil...@delete.shaw.ca> wrote

> All great, but when they did the same thing with fruits and
> vegetables, we got genetically modified foods, and a lot of people got
> scared shitless of "Frankenfoods" etc, without any evidence that I've
> seen of harmful consequences.
>
> I expect that as soon as the same people get wind of this, there will
> be hell to pay. Throw in a few religious groups that oppose mucking
> around with the human body, and I think there's a big fight brewing.

I think GMOs have generally been benign, but I'm sympathetic to people
who fear that the controls are pretty heavily weighted toward an honor
system, and that's not a good way to handle things.

I think the issue is less persuasive on human health, since I think
we're generally capable of screening out a harmful variety of chicken or
strawberries if necessary. Natural invasive pests are bad enough, and
I'm not convinced some random corporate exec won't decide to override
sound scientific opinions about the crosspollination abilities of some
new variety of plant and end up causing the rise of a horribly invasive
weed, for example, or will rush the introduction of a new variety of
fish that screws up a major ecosystem.

There's an argument that this can happen with traditional hybrids, and
this is true, but that argument is also trying obscure the fact that
GMOs can be developed much faster in general than normal hybrids and can
include vastly wider new traits.

[Bob]

On Sunday, January 3, 2016 at 8:54:27 PM UTC-5, art...@yahoo.com wrote:

> If you can target the tumor crispr could treat it.

I would think that if you had a tumor-specific sequence, there'd be easier ways.

[bill van]

In article <XnsA584D8B8AE...@46.165.242.75>,

I'm not that concerned about real threats in this context. I'm quite
concerned that once the news stories, especially on the TV news, get the
right combination of scary and easy to understand, there will be a huge
backlash and the anti-GMO crowd will go apeshit and hold back some
important medical progress.
--
bill

[Les Albert]

On Sun, 3 Jan 2016 17:23:24 -0800 (PST), Alfalfa Bill

<tedth...@aol.com> wrote:
>On Sunday, January 3, 2016 at 6:55:37 PM UTC-6, Les wrote:
>> On Sun, 3 Jan 2016 15:35:19 -0800 (PST), Alfalfa Bill
>> <tedth...@aol.com> wrote:

>> >There are many science news stories about the wonderful new technology CRISPR
>> >which appears to change DNA sequences and alter genes. It is said to have many great potential applications.
>> >I read Wiki but still don't understand.
>> >In a simple way, could you explain how CRISPR works?
>> >Specifically, what are some of the many great potential applications for CRISPR?

>> Here is an animated youtube about how it works:
>> https://www.youtube.com/watch?v=0dRT7slyGhs

>Thanks Les and Bill. I understand in a basic way how CRISPR works.
>Let me ask about the applications.
>Jack Horner said some day people will take a chicken egg and reverse engineer it to hatch as a dinosaur.

> can see how CRISPR would be great for that. But I read predictions that CRISPR will cure cancer.

>ow would that work? Wouldn't we have to have a test tube baby to do a genetic analysis and CRISPR

>t right away to fix mutations?
>Is there any application for CRISPR to treat an adult with cancer?

CRISPR is a gene editing research tool; it is not a specific treatment
or cure for cancer. CRISPR technology makes it easier and faster to
study mutations identified by The Cancer Genome Atlas and test new
cancer drug targets. Here is a recent article from the National
Cancer Institute at NIH that explains the uses of CRISPR in cancer
research:
http://www.cancer.gov/about-cancer/causes-prevention/research/crispr#3

Les

[Snidely]

Howard noted that:

> bill van <bil...@delete.shaw.ca> wrote
>
>> All great, but when they did the same thing with fruits and
>> vegetables, we got genetically modified foods, and a lot of people got
>> scared shitless of "Frankenfoods" etc, without any evidence that I've
>> seen of harmful consequences.
>>
>> I expect that as soon as the same people get wind of this, there will
>> be hell to pay. Throw in a few religious groups that oppose mucking
>> around with the human body, and I think there's a big fight brewing.
>
> I think GMOs have generally been benign, but I'm sympathetic to people
> who fear that the controls are pretty heavily weighted toward an honor
> system, and that's not a good way to handle things.

And one of the uses of CRISPR that's in discussion is an "OFF" switch
to incorporate in GMOs.

>
> I think the issue is less persuasive on human health, since I think
> we're generally capable of screening out a harmful variety of chicken or
> strawberries if necessary. Natural invasive pests are bad enough, and
> I'm not convinced some random corporate exec won't decide to override
> sound scientific opinions about the crosspollination abilities of some
> new variety of plant and end up causing the rise of a horribly invasive
> weed, for example, or will rush the introduction of a new variety of
> fish that screws up a major ecosystem.
>
> There's an argument that this can happen with traditional hybrids, and
> this is true, but that argument is also trying obscure the fact that
> GMOs can be developed much faster in general than normal hybrids and can
> include vastly wider new traits.

--
Trust, but verify.

[Snidely]

On Sunday or thereabouts, Alfalfa Bill asked ...

Yes. Just like existing gene modification via viruses has application
for treating an adult with cancer. Currently there are (AIUI) to
techniques available: take the patients cells (of some particular type
where the genetic error is important), modify them in a test tube, and
return them to the patient's body. The other technique is to prep a
virus to carry the DNA into target cells, introduce that into the
patient, where the virus modifies the cells. Either process would be
more efficient with CRISPR doing the gene modification rather than the
older, less precise editing techniques.

CRISPR may also allow you to easily modify cancer cells to correct
their disabled self-destruct genes, or to turn off genes that allow
cancer cells to grab resources. These techniques are still in the
future, though.

/dps




--
Who, me? And what lacuna?

[Snidely]

On Sunday, Bob yelped out that:

Depends on what you try to do with the tumor. If you just want to kill
it, immunotherapy seems to be the way to go ... with the caveat that
the great challenge there is the tumor's ability to hide from the
immune system. So there are advantages to using immunotherapy along
with some way to turn off the "cloaking" genes. It may also be nice to
turn re-enable the self-destruct genes like P51 that have been shut
down in a tumor, or to limit their ability to promote blood vessel
growth. There is even the possibility (in a more distant future) of
being able to turn the tumor back into healthy tissue.

/dps

--
There's nothing inherently wrong with Big Data. What matters, as it
does for Arnold Lund in California or Richard Rothman in Baltimore, are
the questions -- old and new, good and bad -- this newest tool lets us
ask. (R. Lerhman, CSMonitor.com)

[Howard]

bill van <bil...@delete.shaw.ca> wrote in
news:billvan-ED70D4...@shawnews.vc.shawcable.net:

I'm sympathetic to that point of view. On a somewhat related note, the NY
Times had an interesting article yesterday about a key regulator of cancer
treatments and issues about the pace of approvals.

http://nyti.ms/1Jl8Xh0

It's obviously very easy for treatments to get bogged down in the approval
process.

I think this is a good couple of pieces by Michael Specter from
newyorker.com on some of the issues --

http://tinyurl.com/pk3d6ou

http://tinyurl.com/p9anb4j

I'm not saying the research should be banned, but we really don't have a
good regulatory framework in place for handling it. And just as it's easy
to demogogue against genetic research, it's also extremely to do the same
thing for it.

The first article describes one possible approach to eliminating Lyme
Disease by rewriting the genes of wild mice to eliminate their ability to
act as hosts. It includes a telling sentence:

Esvelt [the researcher] stressed that such an approach would
become possible only after much more research and a
lengthy series of public discussions on the risks and benefits
of the process.

The first part of that sentence is true -- much more work is needed. But
the second is not -- there is little forcing public discussions on risks
and benefits, and it would be fairly trivial for agribusiness lobbyists to
gain extremely relaxed standards if a Republican was elected president, and
it could also happen under a Democrat, though somewhat less likely.

That need for public discussion is the point of the second Michael Specter
piece. Monsanto did early GMO work largely in secret and acted with a
great lack of transparency, and to this day sees the issue through the lens
of PR and trade secrecy rather than science. That lack of open discussion
is a major reason for the backlash, but I see little sign that future
agricultural or medical business interests will act very differently.

We also don't have a good legal framework for handling related IP issues,
and I think it's worth wondering what happens if key developments get
walled off by patent owners -- we may well end up with a sympathetic
government structure enforcing private regulation of cancer treatments, for
example. As the Martin Shkreli case shows, it's pretty easy for companies
to game the current system to control the supply of essential drugs, and in
the US the courts, patent system and Congress have been extremely bad at
figuring out current IP issues, which isn't encouraging for what they'll do
with CRISPR-related research.

[Howard]

Snidely <snide...@gmail.com> wrote :

> Howard noted that:
>> bill van <bil...@delete.shaw.ca> wrote
>>
>>> All great, but when they did the same thing with fruits and
>>> vegetables, we got genetically modified foods, and a lot of people
>>> got scared shitless of "Frankenfoods" etc, without any evidence that
>>> I've seen of harmful consequences.
>>>
>>> I expect that as soon as the same people get wind of this, there
>>> will be hell to pay. Throw in a few religious groups that oppose
>>> mucking around with the human body, and I think there's a big fight
>>> brewing.
>>
>> I think GMOs have generally been benign, but I'm sympathetic to
>> people who fear that the controls are pretty heavily weighted toward
>> an honor system, and that's not a good way to handle things.
>
> And one of the uses of CRISPR that's in discussion is an "OFF" switch
> to incorporate in GMOs.

One of the challenges is how good the knowledge of switches there is right
now (or in the near future). My understanding is that genetics is
increasingly being seen as less and less an issue of Gene X controls Trait
Y and more and more about the role of a gene in a system and network. So
for instance altering a gene so that it turns off a certain property when
an organism reaches maturity may not end the effect of the gene in other
ways.

That may not be a problem if we had a full, or even strong understanding of
what we're up to, but my sense is that the ability to change genes is
outstripping our ability to understand what happens both in the immediately
modified organism and in future generations.

[Alfalfa Bill]

So the new genes created by CRISPR have an ability to kill the cancer cells and they kill cancer cells quicker than new cancer cells are created. Is that right?

[art...@yahoo.com]

Resistance could be a problem

[Snidely]

Howard blurted out:

> Snidely <snide...@gmail.com> wrote :
>
>> Howard noted that:
>>> bill van <bil...@delete.shaw.ca> wrote
>>>
>>>> All great, but when they did the same thing with fruits and
>>>> vegetables, we got genetically modified foods, and a lot of people
>>>> got scared shitless of "Frankenfoods" etc, without any evidence that
>>>> I've seen of harmful consequences.
>>>>
>>>> I expect that as soon as the same people get wind of this, there
>>>> will be hell to pay. Throw in a few religious groups that oppose
>>>> mucking around with the human body, and I think there's a big fight
>>>> brewing.
>>>
>>> I think GMOs have generally been benign, but I'm sympathetic to
>>> people who fear that the controls are pretty heavily weighted toward
>>> an honor system, and that's not a good way to handle things.
>>
>> And one of the uses of CRISPR that's in discussion is an "OFF" switch
>> to incorporate in GMOs.
>
> One of the challenges is how good the knowledge of switches there is right
> now (or in the near future). My understanding is that genetics is
> increasingly being seen as less and less an issue of Gene X controls Trait
> Y and more and more about the role of a gene in a system and network. So
> for instance altering a gene so that it turns off a certain property when
> an organism reaches maturity may not end the effect of the gene in other
> ways.

My understanding, based only on preliminary reading, is that the goal
is to turn the /organism/ off (for genetically engineered bacteria).

For crops, rendering the pollen impotent except when grown with certain
nutrients would work, and I think is in the range of accessible
solutions.

>
> That may not be a problem if we had a full, or even strong understanding of
> what we're up to, but my sense is that the ability to change genes is
> outstripping our ability to understand what happens both in the immediately
> modified organism and in future generations.

A big part of what gene editing is being used for is to determine the
impact of different genes, and CRISPR is likely to accelerate that.

/dps

--
Trust, but verify.

[Snidely]

On Monday, art...@yahoo.com snipped a lot, some restored here;
> Alfalfa Bill noted that:

> > So the new genes created by CRISPR have an ability to kill the cancer cells
> > and they kill cancer cells quicker than new cancer cells are created. Is
> > that right?

CRISPR doesn't create genes. It cuts DNA at specific targets, to
either elide existing genes or to allow the insertion of other genes.

The effects of the editing will depend on what the editing is. The
goal of using CRISPR to fight cancer is, AIUI,
- to make tumors less aggressive
- to make it easier to target cancers with other treatments
(immunotherapy, for instance)
- to target tumors directly
Different gene editing choices support the different goals.

> Resistance could be a problem

I'm not sure what you're seeing resistance to (other than public
acceptance of research and treatments). CRISPR is basically the same
machinery the cell uses for normal operation. Except for single-cell
embryos, I think it is currently done outside the body, and the edited
cells re-introduced to the body. Those would generally be the patients
cells. Updating genes inside the body will probably involve some
heavily engineered viruses (which is how non-CRISPR DNA repairs are
done), and the ability to customize the viral shell for an individual's
immune system will be relatively easy (HIV has taught us a lot in this
area).

[bill van]

In article <mn.25347e014a8d0e32.127094@snitoo>,

The resistance I see is precisely in the form of public hostility, just
as soon as some of the anti-GMO folks figure out what CRISPR is about
and start whipping up fear among the unclear of thinking.
--
bill

[Bill Turlock]

On Mon, 04 Jan 2016 23:01:35 -0800, bill van <bil...@delete.shaw.ca>
wrote:

>The resistance I see is precisely in the form of public hostility, just
>as soon as some of the anti-GMO folks figure out what CRISPR is about
>and start whipping up fear among the unclear of thinking.

http://imgur.com/gallery/GO6oFzv

[Snidely]

After serious thinking bill van wrote :

And then some prominent person's child will be saved by gene editing
and all of sudden it will be fashionable.

Or it will take place overseas and the US opinion will become
irrelevant.

/dps

--
"This is all very fine, but let us not be carried away be excitement,
but ask calmly, how does this person feel about in in his cooler
moments next day, with six or seven thousand feet of snow and stuff on
top of him?"
_Roughing It_, Mark Twain.

[Howard]

bill van <bil...@delete.shaw.ca> wrote

>>
> The resistance I see is precisely in the form of public hostility,
> just as soon as some of the anti-GMO folks figure out what CRISPR is
> about and start whipping up fear among the unclear of thinking.

From a political standpoint, the biggest risk is from anti-abortion types.
In any political calculation, they've been vastly more effective than the
anti-GMOs.

In the US, which will probably be the biggest initial location of medical
research, anything involving fetal cells and human embryos is an explosive
topic, and it's fairly easy for opponents to cut off funding in areas they
view as crossing their lines. Some GMO opponents may have tried to stop
federal funding, but they have been ineffective, while stem cell research
has been blocked and deeply curtailed due to opposition from abortion
opponents. In just one recent example, the Planned Parenthood fight has
centered around the false claim that PP sells fetal tissue for research,
and it's a clear shot at the research in general.

[Howard]

I think the concern in this case is that there may well be other things
happening -- the pollen may be impotent except when when grown with certain
nutrients, but the change may also affect something else in an unrelated
area for the plant due to incomplete understanding of the functions of the
gene. Or, over time in practical usage, the On switch conditions change
and the pollen becomes viable not only in limited circumstances but in
larger areas.

When you're talking about fairly limited changes -- say an increase in
Vitamin C production in a vegetable -- the issues with modification are
very low risk. But when you start getting into uses like toxicity to
insects, you run much greater risks.

>> That may not be a problem if we had a full, or even strong
>> understanding of what we're up to, but my sense is that the ability
>> to change genes is outstripping our ability to understand what
>> happens both in the immediately modified organism and in future
>> generations.
>
> A big part of what gene editing is being used for is to determine the
> impact of different genes, and CRISPR is likely to accelerate that.

That's definitely true, and one big hope is that CRISPR will result in a
virtuous cycle where large scale testing is easy enough to enable the kind
of verification that makes more CRISPR research viable.

[art...@yahoo.com]

On Tuesday, January 5, 2016 at 1:12:14 AM UTC-5, Snidely wrote:
> On Monday, art...@yahoo.com snipped a lot, some restored here;
> > Alfalfa Bill noted that:
>
> > > So the new genes created by CRISPR have an ability to kill the cancer cells
> > > and they kill cancer cells quicker than new cancer cells are created. Is
> > > that right?
>
> CRISPR doesn't create genes. It cuts DNA at specific targets, to
> either elide existing genes or to allow the insertion of other genes.
>
> The effects of the editing will depend on what the editing is. The
> goal of using CRISPR to fight cancer is, AIUI,
> - to make tumors less aggressive
> - to make it easier to target cancers with other treatments
> (immunotherapy, for instance)
> - to target tumors directly
> Different gene editing choices support the different goals.
>
> > Resistance could be a problem
>
> I'm not sure what you're seeing resistance to (other than public
> acceptance of research and treatments). CRISPR is basically the same
> machinery the cell uses for normal operation. Except for single-cell
> embryos, I think it is currently done outside the body, and the edited
> cells re-introduced to the body. Those would generally be the patients
> cells.

If you are trying to treat cancer, then you need to get the agents into all of the cancer cells. Some cells might be resistant to the vector used or may have mutations that make the therapy worthless. For example many mutant (about 1/2) cancer cells lack a gene called p53 which causes abnormal cells to kill themselves. Introduction of the normal p53 (by Crispr or other methods) could be useful, but the cancer cell cells could develop other mutations preventing P53 from functioning. The nature of cancer cells is that they are highly genetically variable increasing the problem of resistance.

[Snidely]

art...@yahoo.com submitted this idea :

And my point is that customizing the vector will get much easier, even
though that's typically virus technology (for the surface proteins)
rather than CRISPR (which would be used for the DNA load).

We already understand enough about that that a much better flu vaccine
is just around the corner (not 2016, but good chance before 2020, I
hear).