CRISPR and Gene Drive technology

[Roderick_Femm]

From NPR article here:

I am not a scientist, but this scares the bejeezus out of me for the future of this planet.

“I regard a mosquito that transmits malaria as a pathogen — and as a pathogen we have the right to eliminate it,” Crisanti says. “We have eliminated viruses like smallpox. We are trying to eliminate polio. I don’t see a big difference.”

Gene drives could also be used to fight agricultural pests.

Gene drives are sequences of DNA that defy the usual rules of genetics. They can be passed along to future generation at a far greater rate than occurs naturally.

Everything I have ever read or heard about CRISPR is that it is relatively easy to use, especially compared with previous genetic engineering methods. It is not something that maybe only one or two very sophisticated laboratories could use, it sounds like any competent bio-geneticist (or whatever the appropriate term is) could learn to use it. Among that large an assortment of scientists, there are bound to be crackpots and nut cases. This Crisanti doesn’t sound far from that herself.

Leaving aside the sci-fi disaster movie scenarios, the article raises plenty of questions about how we don’t know the effects on wider ecological systems of wiping out a single species, no matter how pestiferous it is. Against that, we are asked to weigh the cost in human terms of a disease like malaria.

How the hell do you make that kind of calculation?

[JWT_Kottekoe]

I think this must be the article you were trying to link. CRISPR by itself doesn’t scare me as much as gene drive, which is truly frightening.

[tim314]

I don’t mean to minimize the thorny ethical issues here, but it’s worth keeping in mind just how terrible mosquitos are. When it comes to killing people, humans far outclass any other animal, except mosquitos who are substantially better at it than we are:

The deadliest animal in the world

If that number has held steady over time (which I don’t know), then it’s like a Holocaust every decade.

[Roderick_Femm]

However bad mosquitos are, we don’t know what the effects of their absence would be. Would something worse take over their ecological niche? And then what other unpleasant species will we decide to remove next?

And the scientist who doesn’t “see any difference” between bacteria, viruses, and animals like mosquitos. Mosquitos are not a pathogen, sometimes they carry pathogens, that seems to me like a huge difference.

JWT Kottekoe, thanks for correcting my link. I always check my links before posting, I guess I was too busy worrying this time.

The thing about CRISPR and gene drive together is that (if I understand correctly) CRISPR is what makes it possible to push gene drive relatively easily.

[mozchron]

I’ve been locked out of my account for a long tome but managed with board admin help to get back on for this. I’ll post a detailed post on this today or tomorrow. I know these guys, and saw this data presented at meetings over the last couple of years, and am very familiar with it.

Bottom line, don’t get too worried yet.

Also, Crisanti is a man, not a woman

[Snarky_Kong]

@Roderick_Femm

However bad mosquitos are, we don’t know what the effects of their absence would be. Would something worse take over their ecological niche? And then what other unpleasant species will we decide to remove next?

Is there any amount of death that mosquitos could cause that would make you support their destruction?

What percentage chance would you need to give catastrophic unforeseen effects to occur before they outweigh guaranteed deaths. Many species have gone extinct without killing tens of millions of people.

[Stranger_On_A_Train]

@Roderick_Femm

However bad mosquitos are, we don’t know what the effects of their absence would be. Would something worse take over their ecological niche? And then what other unpleasant species will we decide to remove next?

And the scientist who doesn’t “see any difference” between bacteria, viruses, and animals like mosquitos. Mosquitos are not a pathogen, sometimes they carry pathogens, that seems to me like a huge difference.

Mosquitos are incidental pollinators but they aren’t unique to any plant. The idea that there are specific, pre-determined ecological niches is not a correct view of evolution; species occupy ‘niches’ in the sense that they habe some native ability to exploit a resource but it isn’t as if you eliminated the platypus a wallaby would evolve a duckbill and flippers to replace it.

We’ve been eliminating “unpleasent species” of pathogens, predators, pests, and other threats since humanity started agriculture, and while it is true that this can sometimes result in undesired consequences, it is also a matter of protecting people from natural threats. In the case of mosquitos, they are a carrier of numerous pathogens which cause hundreds of millions of infections and over a million deaths a year; no rational person is going to argue that we are better off with them having free reign.

The concern about gene drive is real, not because it can target out a specific species but because of unintended consequences and specifically horizontal gene transfer which we still don’t know enough about to be assured that genetic changes can’t be conveyed ro other species unintentionally. Even though we are assured that modified genes cannot be transferred to people in any reasonable time frame, the potential for adverse genetic changes in more closely related species that could have far reaching impacts on obligate pollinators does require caution and careful investigation before releasing gene drive mechanisms into the wild, but the benefit in eliminating the prolific carrier of harmful pathogens makes it worth he effort, especially if mosquitos can be modified to be less harmful to humans than outright exterminated.

Stranger

[chappachula]

@Stranger_On_A_Train

Mosquitos aren’t unique to any plant… the benefit in eliminating the prolific carrier of harmful pathogens makes it worth the effort

What about the mosquito’s function in the food chain?

I hate mosquitos as much as everybody else.
But lots of other animals love them…They must taste pretty good, if you’re a bird, frog,bat, lizard, etc. Who in turn taste good to larger predators, etc…

It seems like we should be careful before we casually declare the benefits of eliminating all the 'skeeters.

[Stranger_On_A_Train]

Hence why I ended the post with “…especially if mosquitos can be modified to be less harmful to humans than outright exterminated.”

Stranger

[bump]

I’d think the bigger concern would be how the areas of the world most affected by mosquito-borne disease would adapt to not losing a million people a year to mosquito borne diseases.

That could seriously stress already fragile social structures and governments.

[mozchron]

OK, there are two issues here.

First is the “gene drive”. Second is what the gene drive is doing in this situation.

Gene drive isn’t a new concept. It’s been around as an idea since at least the 1940’s. It has gone through many iterations since that time (hybrid sterility, chromosomal translocations, transposable elements, homing endonucleases, and now CRISPR).

There is nothing special about CRISPR in concept; it’s uniqueness comes from execution. EVERYTHING we can do with CRISPR we were already able to do without it. CRISPR just makes it easier and faster.

All CRISPR does is allow one to make a cut in a DNA sequence at a specific sequence. When this happens, the cells DNA repair mechanism repairs the cut by one of 2 ways.

1. Jam the cut ends back together in a process known as “non-homologous end joining (NHEJ). NHEJ is error prone and tends to result in a few nucleotides being added or deleted, often resulting in a premature stop codon in the sequence and a non-functional gene. This is what we do when we use CRISPR to “knock out” a gene.

2. If a piece of DNA is provided containing a sequence that you want to insert flanked by sequences matching either end of the cut site (the “repair template”, instead of repairing the cut by NHEJ, the cut is repaired by splicing the repair template into the break. This is called “homology-directed repair “ (HDR). This is how we make specific changes to a DNA sequence at a specific site.

HDR is the key to CRISPR gene drive. In a diploid organism (that has chromosomes in pairs) if one chromosome is cut, the homologous sequence on the other chromosome can act as the repair template. If a CRISPR module is placed onto one chromosome and targets a site to cut on the other chromosome in the same place (i.e. it is inserted into its own cut site) it will cut the other chromosome, and when HDR repairs the cut, the CRISPR sequence will be copied onto the other chromosome. In this way, organisms that are heterozygous for the CRISPR sequence become homozygotes, and instead of transmitting the CRISPR sequence to 50% of their offspring, they will transmit it to 100% (assuming that the copying [or “homing”] efficiency is 100%). Each of the offspring will be heterozygous, become homozygous, and transmit to 100% of THEIR offspring. That’s your Gene Drive.

Again, this isn’t new. There is a naturally occurring gene called a Homing Endonuclease Gene (or “HEG”) that spread through populations by exactly this mechanism. It exists naturally in slime mold but has been artificially transferred to mosquitoes by this same laboratory group. This was done over ten years ago. The problem with HEGs as gene drive candidates is that the target sequence is very long and it’s difficult to change it, so you can’t use them to target any gene in the genome.

Once CRISPR was developed, it was very easy to take what we already knew from HEGs and extend to CRISPR.

OK. So that’s how gene drive works. What are the authors doing in this case? Previous work was to use gene drive to spread anti-malaria genes into populations. But that’s not what’s going on here.

In this case, the authors are targeting a mosquito sex determining gene called doublesex. Simplifying things a bit, when this gene is completely disrupted, female development gets screwed up (they get kind of intersex) and they can’t bite or reproduce. If they have one copy, they’re fine, of they have zero copies, they’re screwed.

So because of the drive aspect, this gene increases in frequency even though it is essentially lethal in the homozygous state. Ultimately this results in a population crash if the gene spreads to high enough frequency (no females left). They also did some experiments to show that in their lab cages, resistance to the gene did not develop.

All good. Very clever molecular biology building on a mountain of research by this group and others over the last 2 decades. Do I think this will work?

No I do not.

Here’s where we shift from the realm of data to the realm of opinion. But I’d say my opinion is an educated and experienced one. DISCLAIMER: I am know in the community as a skeptic of gene drive. But I have been working on various aspects of gene drive for 20 years, and only became a skeptic due to data. SO take that for what it’s worth.

I have no issues with the molecular biology presented in this paper. But to say that resistance won’t develop is a fantasy IMO (the authors toned this down in the final published version; I had seen an earlier draft version where this lack of resistance was highly touted in the title and abstract). You can’t trick evolution.

I would bet a large amount of money that if this was released into nature, resistance to the drive (probably mutations in the target site) would evolve and shut it down. This is an issue with any CRISPR-based gene drive system. This same group published a paper a few years ago where they used CRISPR to target an introduced gene for green fluorescent protein (meaning if the drive works the mosquitoes lose their green fluorescence over time). Resistance to that evolved in cage populations within 4 generations.

Resistance will evolve in response to fitness costs. There is no bigger fitness cost than death (or sterility, which from an evolutionary standpoint is the same thing). We see this in nature. In mosquitoes, there are naturally occurring genes called “meotic drive”, that often kill female offspring but not males. But if you take a random sample of mosquitoes and breed them, you never see the effect of these genes. Because resistance alleles (of a variety of sorts) evolve to suppress them. But if you take the mosquitoes and outcross them to distant populations you often then see the meiotic drive genes work (in the form of male-biased sex ratios) because the outcrossed population lacks the suppressor alleles.

If these traits would spread, they would have evolved by themselves already. But they haven’t. They won’t spread because the selection for resistance is so high.

If we want to get genes to spread in populations, we need to stop focusing on drive efficiency and start focusing on mitigating fitness costs (or engineering fitness benefits – surprisingly tricky!). I do not think that gene drives to crash populations will every work.

But I get in friendly arguments with these folks all the time. Time will tell who is correct…

[mozchron]

@bump

I’d think the bigger concern would be how the areas of the world most affected by mosquito-borne disease would adapt to not losing a million people a year to mosquito borne diseases.

That could seriously stress already fragile social structures and governments.

God, I hate this argument, which is always put forth by people living comfortable first world lives in developed countries. Sure, “millions of people dying prematurely is a GOOD thing, because those areas can’t adjust to the population expansion”. Funny how that only works when it’s anonymous brown people (mostly children) dying “over there”.

If it was happening in the USA, do you think that argument would hold water? Its disgusting.

[mozchron]

@Roderick_Femm

However bad mosquitos are, we don’t know what the effects of their absence would be. Would something worse take over their ecological niche? And then what other unpleasant species will we decide to remove next?

Remember, we’re not talking about eliminating all mosquitoes. There are thousands of species of mosquitoes, maybe 50 or a 100 are important for disease transmission. In most areas, if you eliminate one species, there are plenty more that are not epidemiologically important that can fulfill the food web requirements.

And also, in many areas the mosquitoes we are trying to eliminate are introduced invasive species anyway.

[jasg]

Thanks mozchron - interesting science and explained well. Far past my decades old biology degree but very understandable.

[Stranger_On_A_Train]

@bump

I’d think the bigger concern would be how the areas of the world most affected by mosquito-borne disease would adapt to not losing a million people a year to mosquito borne diseases.

That could seriously stress already fragile social structures and governments.

Nonsense. Not only is that increase a drop in the bucket of population growth, dealing with malaria and other mosquito-carried pathogenic disease is an enormous stress on care services and impairs productivity. If you are genuinely concerned about environmental and sociopolitical stress of population growth, the obvious answer is to expand and promote family planning and contraceptive services, as well as social support services so that people don’t have so many children to begin with.

Stranger

[Ruken]

Specifically, we’re talking about 450k deaths pet year globally, when Africa’s population is increasing by 30 million per year.

Never mind that the “concern” would still be abhorrent even if the numbers were different.

[Roderick_Femm]

@mozchron

… Crisanti is a man, not a woman

I saw the name was Andrea, and I know that can be a man’s name in Italian (or is it always a man’s name in Italian?) but I didn’t want to assume that it was a man.

[chappachula]

@mozchron

I’ve been locked out of my account for a long tome but managed to get back on for this.

Wow!–Your post was just what I needed—an explanation of Crispr gene tech that was clear, and didn’t scare me away.*
Thanks!

I dunno how somebody as smart as you got yourself locked out of your account --but welcome back!..And this time, please make sure you keep hanging around.

• (I almost failed biology in 8th grade, and have hated the subject ever since)

[mozchron]

@chappachula

Wow!–Your post was just what I needed—an explanation of Crispr gene tech that was clear, and didn’t scare me away.*
Thanks!

I dunno how somebody as smart as you got yourself locked out of your account --but welcome back!..And this time, please make sure you keep hanging around.

Smart and absent-minded often go together…

[bump]

@mozchron

God, I hate this argument, which is always put forth by people living comfortable first world lives in developed countries. Sure, “millions of people dying prematurely is a GOOD thing, because those areas can’t adjust to the population expansion”. Funny how that only works when it’s anonymous brown people (mostly children) dying “over there”.

If it was happening in the USA, do you think that argument would hold water? Its disgusting.

Oh, stuff it.

That wasn’t what I was saying, although I can see how you’d get that. I was saying that you don’t want to just do something like that in a vacuum without planning and preparing the countries affected for it. Otherwise you end up with a whole other set of tragic circumstances- famines, conflicts, etc…