mRNA's next challenge: Will it work as a drug?
science.sciencemag.org
science.sciencemag.org
https://sci-hub.se/downloads/2020-12-18/44/10.1126@science.3...
Or just:
curl --resolve sci-hub.se:443:186.2.163.219 --remote-name https://sci-hub.se/downloads/2020-12-18/44/10.1126@science.3...
https://sci-hub.tech/donation/
They accomplished one of Aaron Schwartz's dreams.
Ditto with archive.is and their domain struggles.
Are there any possible long term side effects of using such an mRNA drug that are yet unanticipated? All the short term side effects are known / will soon be. Anything beyond that, we haven't had enough experience to know?
There are people that this was tested on still hanging around with no lasting negative effects (to my knowledge).
I don't know anything about biochemistry, and I'm aware that the above is just remote speculation. It is meant as an example of food for thought. But I do wonder when a whole field of scientists state "there is no possibility of unexpected long-term side effects" to a therapeutic tool that has never been used at anything resembling this scale.
Would love to hear more experts discuss why this is considered sufficiently long-term safe to make the decision of vaccinating a billion people after nine months of testing. Am I missing something, or is it just a question of the precautionary principle in this case being considered too costly?
Edit: sorry, my comment may have sounded snarky, which was not my intention. World-wide vaccinations do carry a risk. It’s just that such a risk clearly pales in comparison to the very known downsides of the current situation. I am in no way a vaccine expert and cannot comment intelligently on why long-term risks are considered to be low.
That's not to say it isn't possible, but many things are possible but sufficiently unlikely that we take those risks. We eat, drink, and breathe many things every day that we don't fully understand the ingredients or impacts of.
For the analogy to be more accurate, the parts should explicitly not be bicycle parts.
From the responses you’d think I was talking about brain chips injected by Bill Gates, but I suppose this is the result when a layman attempts to explain something unfamiliar to other laymen.
FDA approvals aren't a black and white affair. Some drugs are approved as orphan drugs through trials designed to be much cheaper than Phase 1-3 trials when they treat diseases that wouldn't be profitable for pharma, for example, and there is a path for preliminary compassionate use approvals and accelerated development for stuff like chemo where the disease is terminal anyway. The FDA works with each company to tailor the process to their needs (although, obviously, they stick to a strict standard unless there's good justification).
Likewise, the vaccine rollout won't be all or nothing. We won't even have a billion doses for a long while and the focus will (likely) be on vaccinating those for whom the benefits outweigh the extra risk like front line medical staff and the immunocompromised or elderly. I don't expect the world to get vaccinated at gun point, although the rules for schools and other institutions will quickly accumulate to cover most of the population.
Personally, I'm not going to be taking the vaccine for a while since no one in my family is at risk and we're (mentally) preparing for several years of varying levels of isolation and other precautions. I have faith in the system for the most part since I've worked on an FDA application before (clinical diagnostics, not therapeutics), but the kind of geopolitical and economic pressure its under right now is unprecedented and should keep epidemiologists up at night (hell, it probably does). It's going to be up to each individual to balance their risks and obligations at least until we get more data.
These new vaccines have a 90% efficacy. It's probably a no-brainer to give them to someone in their 70s or 80s with a high likelihood of having an adverse covid case. But a 20-year-old?
Out of a purely selfish wish of having a more normal world, part of me wants to suppress these thoughts and think "I'm probably excessively cautious, it's a good thing that the economic pressures will probably ensure that most are vaccinated in a year or two". But I do worry that many healthy people don't have a complete view of the potential for unknown unknowns when they decide to take it.
The selfish part of me is thankful that someone else does the dirty job for ensuring that those thoughts aren's spread wider. I'm really hoping that the authorities know what they're doing, and I'd definitely be lying awake at night if I was in that role.
I probably won't take it myself - there, I said it - but rather wait and get more data, or maybe go as far as seeing when one of the protein-based vaccines are ready.
People only use the precautionary principle for things they don't want to do.
It's very good for that, since it always results in recommending not to do things.
I think, generally, it has been discussed. There's lots of research on mRNA vaccines going back decades at this point, though they haven't made it to market until now. I see people saying "it's not being discussed" often on this site, but really, anyone saying "no, this is safe" has the implicit support of all that research behind them.
"Suppose someone was infected with a retrovirus, could reverse transcriptase embed that rna into the dna? This could be especially worrisome if we're talking about a pregnant woman and fetus undergoes rapid cell division... etc.."
I would be surprised if I did not mangle up some terms & concepts in the paraphrasing above. Someone who knows more can correct me or just watch/read the fda hearing.
Another thing that was mentioned in the FDA hearing was that pfizer also tested it on HIV positive people. HIV is a retrovirus which also carries the reverse transcriptase enzyme. I don't want to draw any conclusions from this because I don't have any medical knowledge. Maybe someone here with more insight could comment.
> Moreover, mRNA vaccines induce transient antigen expression, while DNA vaccines provide a long-lasting expression, thus mimicking an acute viral infection. Although a transitory gene expression might be desirable as it minimizes potential risks of genetic transformation, this inevitably affects mRNA potency, thus necessitating a dose increase.
This means that mRNA reduce the risk of genetic transformation compared to DNA vaccines, but it comes as a price because you have to deliver a larger dose of mRNA.
This means that when circumstances say no you cant, biological entities find a work around.
as a cover your ass practice, even the smallest chance of occurence means non zero chance.
in this case an mRNA would have to be captured by a reverse transcription system most likely due to co-infection with a retro virus, that complex would have to be functional and would have to be transported into the nucleus.
this is a very remote chance but non zero, thus :
"minimizes potential risks of genetic transformation"
the RNA must interact with retroviral reverse transcriptase in a manner that makes a functional complex or it will just be snipped apart and decycled like garbage.
RNA will fold and produce 2' structure this has interesting consequence. catalytic RNA, structural RNA, stabilizing or protective RNA..
[0] https://www.youtube.com/watch?v=RYwVnzYf4V8
[1] https://pubmed.ncbi.nlm.nih.gov/20358252/
[2] https://sci-hub.st/https://doi.org/10.1007/s00018-010-0346-2 [PDF]
[3] https://www.researchgate.net/profile/Tania_Matamoros2/public... [PDF]
from the paper [3] above: "Reverse transcription initiates after binding of a cellular tRNA primer (in HIV-1, tRNA Lys,3 ), to the primer binding site (PBS). The PBS is a sequence of 18 nucleotides, located downstream of the 5’-end of the genomic RNA. The viral RNA that serves as template for reverse transcription is flanked by repeat (R) sequences at its 5 ́ and 3 ́ termini."
the vaccine mRNA does not meet these requirements.
retroviral RNA is configured to function with the reverse transcriptase. Promiscuity to include other RNA is exceptional not common.
virally infected cells also undergo changes that exclude further infection so they have the cell to themselves.
i would like to say zero chance, but life is in the business of sidestepping the rules to its advantage, however you have a much greater chance of being attacked by a shark while hiking the sahara dunes.
the situation was artificially created.
the retroviral Reverse Transcriptase must be present in the individual cells also infected with the covid virus.
Anti-vaxxers are generally tolerated until there's a critical mass of them, which start causing problems for everyone else.
At any rate, government tyranny has killed millions and millions more than viruses have. And I won't stand for it. Medical tyranny will never be tolerated. If YOU want the vaccine, you get it. That's how liberty works.
So, while I used to write comments like yours, myself, I don't bother anymore. I'd have to spend years toeing the line to build up enough karma to not get shadowbanned for it.
Anyway, I sign in here to say that I'm with you. I think it's important to show that this point of view is not the minority view in this country, and maybe even the world, despite all the media does to make it look like it is.
It looks like China's already started World War 3 in terms of "Unrestricted Warfare" (China's term, not mine): financial, biological, psychological, political. Just regarding COVID, they told the world COVID wasn't infectious between people, they held a 40,000-person potluck dinner in Wuhan while the virus was spreading and then let people travel out of the city, they threatened to turn ships around and withhold masks and medicine produced in China...how can anyone look at what China's done and not recognize their malicious intent? At the same time, they're building up their military around the world, indebting poor African nations, pushing their troops into Nepal and India (and actually killing Indian soldiers)...the list goes on and on. We have to wake up before it's too late.
[Of course, the 50 Cent Army is active on HN. Watch my comment fade away...]
Now, we have the (repeatedly) proven ability to avoid such a disaster, and you argue we should not? You really think protection from disease is not a basic human right?
We are not gods. At least with previous vaccines we just killed off the active parts and said “hey, go bull fight this” to our immune system.
Last bit: Leverage works in both ways
It depends on the function of the protein if this leads to a bad outcome.
This statement cuts both ways — if this recent pandemic was human made we need human solutions... only IF the virus is insurmountable.
As someone with direct experience with a large N, this virus is nothing to exponentially increase long term and second order risk with human “solutions” ... UNLESS the long term effects for asymptomatic cases are severe and under reported.
Again... too many variables outstanding to be certain, but highly cautious
https://www.reuters.com/article/uk-factcheck-hiv/fact-check-...
"This is a reference to trials of a vaccine being developed by the biotech company CSL and The University of Queensland which used a fragment of a HIV virus protein as a component to stabilise the vaccine (here). Production was halted after trials showed that antibodies generated in response to the protein fragment could lead to false positives on some HIV tests (here)."
I'm not sure but I strongly assume yes.
The MAIN reason for this skepticism is that if it was just possible to introduce RNA such that we could have a net positive benefit against coronavirus, a virus that has existed for almost as long as mammals have, we'd have naturally evolved this ability.
The reason we haven't is because it will introduce more problems than it solves down the line.
It could very well be that with a limited understanding of human immune system, we have stumbled upon a solution to a problem that has affected us for millions of years. So, I think some people should try it. But forcing it on the masses is a terrible idea.
Also, COVID-19 has not been around "for millions of years." Other coronaviruses, such as the common cold, have. The evolutionary benefits of defense against the common cold are fairly different than benefits against COVID-19. And immunity against one coronavirus doesn't grant immunity against all other coronaviruses.
That is true. Most of them don't work, not without creating worse problems down the line. Specially, if it's something as simple as creating some proteins that the body can already produce (which is what happens when mRNA vaccine is given). If the solution was as simple, evolution would have found ways to do that.
Currently, some deadly diseases do have some treatments that work... but that comes at HUGE expense i.e. a LOT of energy has to be spent for little gain. It is only possible because there is huge inequality among people and the rich class can afford to spend enormous energy and manpower to treat those diseases. If and when the world becomes more equal, this will no longer be possible (you'd think that "robot slaves" working off of "free energy" would solve that... I don't think that's going to happen but that's a different discussion).
>Also, COVID-19 has not been "around for millions of years."
We can't know that. It could very well be that COVID-19 had infected mammals before and we naturally god rid of it in a few generations. When infections come about, "weaker" individuals die and those with stronger immunity survive and reproduce and the species of COVID-19 might have died out. Some coronaviruses continue to live with us because they don't cause major problems... but there must have been many more which caused major problems and we had had to deal with them differently... and one of them could have been very similar to COVID-19.
But yeah, it could also be that this is the first time we're encountering it. So, let's go with that. My argument doesn't change.
>immunity against one coronavirus doesn't grant immunity against all other coronaviruses
True. However, in millions of years, our immune system has encountered many species and strains of coroviruses, and trained on that data and come up with a much more generalized and long term solution. I'd rather trust that than some random know it all people who think that have a better solution with very limited knowledge of what is going on.
Having said that, I'm not against testing new solutions. It's the scale that bothers me.
We'd have naturally evolved the ability to train our immune systems against specific things it hasn't seen before? How would that POSSIBLY work?
The novelty of this particular coronavirus is sort of the problem here, since people don't already have immunity, so your "millions of years" thing is completely off base.
You seem to be arguing against the possibility of a "universal vaccine" for all viruses but that's entirely not what this is. It's very specifically targeted and the idea that we'd evolve the ability to target things specifically without actually being exposed to them in the same way is plainly nonsense.
> How would that POSSIBLY work?
Through a process called V(D)J recombination [2]. Essentially, every lymphocyte gets a different receptor of random shape, and purely by chance there will be a few lymphocytes with a receptor that matches the shape of the invading viruses (in most cases).
But the poster I was responding to was claiming that our immune system should have evolved the ability to not respond to those threats, but anticipate their specific forms without seeing them. That vaccination as a concept is hogwash because if it was useful, we'd have done it through evolution. But that's plainly nonsensical - we wouldn't need a system that functioned by random variation if we evolved the ability to know what the real targets would be, but we couldn't do that without specific knowledge, which we can't get without being exposed to the things, by which time ... it's too late to have then already built the specific defenses.
See my response to another comment. We must have dealt with countless species and strains of coronaviruses already. So, our genes have a lot of training they need. Even if we haven't trained for this particular strain or species, we will most likely fare better than the solution that has never been tried ever.
What if the children of those vaccinated turn out to be much weaker against other common antigens start dropping dead? It will set humanity back by a lot.
These are not exaggerated hypotheticals. These are VERY REAL possibilities: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5607155/ https://www.ncbi.nlm.nih.gov/books/NBK233000/
>since people don't already have immunity, so your "millions of years" thing is completely off base.
We do. Most people are completely unaffeted by the virus. It's a relatively small percentage that has severe problems. To endanger EVERYONE because a small percentage is affected is downright retarded. Having said that, I'm not at all against trying different things out. The best way to roll it out would be to do it over a VERY LONG PERIOD, spanning generations. And most importantly, keeping significant number of people completely unvaccinated. This has not been a problem until now because big enough population chose to be unvaccinated. However, the scale of current problem might mean that this could change... which is terrifying.
>> The reason we haven't is because it will introduce more problems than it solves down the line.
This is just not sound reasoning, and it's a terrible argument against the vaccine. Have you ever taken antibiotics? Or have you ever benefited long-term from anything medical that we didn't "evolve" through natural selection? Because I sure as hell have. How does this not apply to other vaccines, which have clearly saved an astonishing number of lives, and have, almost without exception, not produced the kind of long-term existential threats to humanity you seem to be hinting at.
It does apply to all vaccines. Vaccines bias the immune system, which has evolved to be general enough to deal with problems that generally come our way. This bias caused by vaccines results in better performance against those specific viruses but comparatively worse performance against most of anything else. This can also result in auto immune disorders down the line:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5607155/
Generally, this bias also happens naturally when viruses infects populations. But the tradeoff is mostly worth it when the virus is still at large... and the natural population is optimized for wide variety of attacks because the immune systems are biased in many different ways in the first place, so even after a pandemic, the resulting population will still have a varied enough immune systems.
Large scale vaccinations bias the population in a very few particular ways. When vaccines for multiple viruses are given to everyone, the immune systems become more and more similar than it would ever happen naturally. So, mass vaccinations make us more fragile as a species against future pandemics, not to mention the autoimmune disorders that also happen as a result.
Given that vaccines have unintended consequences, you probably agree that targetted vaccinations are effective i.e. what if we could vaccinate exactly those who will get infected right before they get infected? That way, we could help them fight the infections better while not affecting anyone else. Right? That is how the immune system already works. It starts the fight right after it detects the infection.
Sometimes, the immune response is not appropriate and can cause more problems than it solves. The same can happen with vaccines.
Sometimes, the immune response may be appropriate but is not sufficent to save the host. The same can happen to vaccinated individuals. It can be argued that the headstart that one gets because of early vaccination might make it worth it... but you also have to consider how many will be vaccinated even though they never really get infected and how many will be missed anyway... and there is also a cost to determining these things. So, overall, it is highly unlikely to be worth it.
The doses have 30-100 ug. Assume 1)this is pure RNA, and 2)the molecules are about the same size as the spike protein sequence. With these assumptions, a dose gives you 10^10 RNA molecules. Average sputum samples show about 10^6 molecules/mL; max samples show 10^9/mL. I don't know how vaccines dilute when you inject it into somebody's shoulder, but it doesn't seem unreasonable to say the final conc will be between 10^6 and 10^9 RNA/mL.
So RNA is going to be in us, whether we want it or not. The question is, do you want the whole genome, or part of the genome. I'm picking the one that doesn't make more virus.
Is this way of injecting mRNA really any different from just injecting someone with a virus? Not in the sense that it makes you ill but in the sense that a virus would do the same thing just with more harmful mRNA.
If you inject with virus, presumably the virus would begin to replicate and attack your body.
You don't want the virus RNA, that would be presumably all that plus more!
The answer to your question is, it's a subset of the virus.
The mRNA is translated to a protein, which is the actual target your immune system then recognises as foreign, attacks, and remembers.
In a sense, it's a lot like a prodrug, which is a "traditional" small-molecule that is turned into the actual drug by some interaction with your body–your stomach acid, for example.
"mRNA" might sound scary. But it isn't going to change your genome or anything like that; it's strictly downstream from DNA. Any virus, bacteria, or salad you eat contains far more mRNA in addition to DNA or RNA, and the first of those really does come with mechanisms to insert itself into your cells' DNA and has evolved to defend itself against your defences, and to slowly take over your body in some way or other.
There are some short-term risks on the order of, say, eating lobster for the first time. Allergies, for example, which can be quite severe and even deadly. But those are exactly the risks the trials would have uncovered, and the people possibly at risks of such things would already know they are susceptible.
There is no known mechanism for any risk that would not manifest within the first day or two.
You have heard of mad cow disease? Also how misshaped proteins are pretty much impossible to destroy eh?
HOWEVER, knowing we as humans tried to replicate the exact “key card” into our cells that makes this virus so potent (aka the spikey bits with the ACE receptor end) worries me greatly. That’s not on evolutionary time scales or mutations... that sounds like IVF and diabetes.
If you think it's a risk, quantify and measure it, and compare it to the risk of not doing anything. People love to grouse about vaccines, bit they never seen keen on doing the math. (Because it consistently does not support such an argument.)
https://www.modernatx.com/pipeline/modernas-mrna-clinical-tr...
A handful of studies are currently recruiting for Phase 2, so that means there was a successful Phase 1 some years ago. So those people would, I believe, be the longest-surviving patients to have received an mRNA vaccine.
They might be followed closely for a long time; but it may only be a handful of people too.
For therapeutic proteins you usually work the other way around: You design the shape and try to get a sequence that folds as intended. In other words, the inverse folding problem.
While this is true, DeepFold’s algorithm is only applicable to extant proteins having enough evolutionary information, which is arguably a small fraction of the theoretical sequence space. Fortunately, machine-learning approaches for de novo protein design are being actively developed as we speak.
Didn't the challenge include predicting previously unseen/unsolved proteins? Based on that, I would wager that what DeepFold learned is an evolutionary "language" that maps out a large useful subset of the entire possibility space. Natural evolution tends build upon previous successes so it seems probable evolution has mapped out a fairly useful "language" of patterns for useful protein shapes. Especially given only a portion of the shape is critical to function for many proteins.
But agreed, de novo protein design based on DeepFold's successes probably will outperform a naive approach by orders of magnitude. But why wait if even a naive approach is already orders of magnitude better than current methods?
Either way, I'm excited to see who comes up with the first custom protein(s) to catalyze industrial processes! Get some yeast/bacteria to mass produce a protein based alternative to platinum catalyzer's for fuel cells using an active site with organically available (and cheap) metals. Design half of it to stick to a polymer so it coats nicely. Bam, no more trying to get some weird polymer/perovskite with the right properties. Not sure mRNA is needed at that point versus CRISPR, but maybe it's more effective.
All protein sequences in the competition lacked a published solved structure, but they had enough effective (remotely) homologous sequences to predict coevolution-derived interresidue distances and contacts. All those sequences were already present in databases and therefore within the known protein universe.
> Based on that, I would wager that what DeepFold learned is an evolutionary "language" that maps out a large useful subset of the entire possibility space.
This might be true, depending on how “foldable” the unexplored space is. A reverse DeepFold would give some clues on that.
> Natural evolution tends build upon previous successes so it seems probable evolution has mapped out a fairly useful "language" of patterns for useful protein shapes
This is already known. The structural and functional diversity we see in existing proteins originated from a relatively limited repertoire of conserved protein domain folds, or even subdomain-sized fragments in some cases.
> Either way, I'm excited to see who comes up with the first custom protein(s) to catalyze industrial processes!
Same here! Especially since the de novo design of enzymes has been progressing slowly but steadily.
Ah, I see what you're saying a bit better. Makes more sense to how the the possible "design" space for novel proteins could be limited. Designing novel active sites could be especially tricky, more than it'd seem at first glance. A folded structure that'd effectively transfer electrons from one target species to another in a catalyzer protein could likely be outside the explored "vocabulary" of extant proteins as it'd require specialized pathways and precise positioning. Chlorophyll is pretty unchanged in evolution as I understand it.Thanks, interesting background! I'll keep an eye out for the de novo design algorithms.
I still have questions about the mRNA vaccine concept. Maybe some well-informed HNer can shed light?
1. If the goal is to get the desired protein inside the patient's body, why is injecting mRNA that produces the protein more effective than simply introducing the protein itself?
2. How does the patient's immune system know to treat this protein as unwanted if it's being produced by the body's own cells?
3. How do vaccine developers avoid creating an over-active immune response in the patient (i.e. an allergy)?
So the trick really is to design the RNA and the delivery system so that it produces an immune response of the right magnitude. Too weak and it doesn't work, too strong and it's harmful.
Antibodies that bind to your own proteins are filtered in an earlier stage in antibody production. Real viral proteins are also produced by your own cells, so that is never a factor by which you could distinguish friend from foe.
2. The imune system knows all your protein already, t cells are evolved in the thymus gland, if they attack anything "self", they get destriyed.
Which one? I don't remember any vaccine that injects immortalized cells.
the cells are used to manufacture quantities of the virus in an extremely weakened form. This gives a chance for the immune systemto mount a response before the pathogen initiates systemic disease response.
the cells in question are not freshly harvested from a foetus, the progenitor cells are harvested and kept in continual culture for use. the reason immortalized cells are used is to escape the "expiry date" of a normal cell.
>>Some vaccines currently available were developed using cell strains cultured from two fetuses aborted for other purposes in the 1960s.[6]<<
i lifted this link from the wiki page provided:
So far, nobody has been able to provide a satisfying answer.
The other mechanism is that the immune system doesn't react only to foreign antigens, there also needs to be some general activation of the immune system in that area for a real response.
The full answer is that this is really, really complex like pretty much everything involving the immune system. And auto-immune diseases indicate that the immune system doesn't always get this right.
in very loose terms both keys must be presented while the immune system is in training, the instances where protiens are expressed with out cell surface recognition molecules in proximity are invalid thus foriegn, and memory immunity to this "failed login" is maintained. when both factors [protien plus recognition] are present constituitively over the course of development the immune response is squelched.
this is known as central tolerance.
The immune system can't know who produced a certain molecule.
2. Someone already said, but a protein has no marker saying "local produce". It is either allowed or not and the body reacts or not when detecting it.
3. They hope. Measure the dosage and adjust. As it was reported, some people getting the vaccine have an allergic reaction, but hopefully it will be rare and under control. So far there are only a few cases reported.
My intuition is that many cancers can start when proteins are mis-copied, and mRNA therapy seems to rely on copying to work very reliably. Does introduced mRNA increase the risk or impacts of mis-copying?
Is there an ELI5 intuition for why mRNA therapy is safe and won't lead to cells becoming cancerous?
Same as always: do a long-term clinical trial and look for any side effects.
The ELI5 version:
Think of the cell as a factory for proteins. The blueprints for all of the different kinds of proteins it can produce are encoded in DNA and stored in the foreman's office. When the cell wants to make a particular protein, the foreman copies the instructions from the blueprint onto slips of paper (mRNA), and sends them to the assembly line workers. This type of copying happens all the time, and is pretty reliable -- and even if it's not, the end result is just some wasted time and a junk part. The blueprints are unaffected. mRNA vaccines sneak some unauthorized instructions to the workers, who then run a ghost shift to produce the protein we want to cause an immune response to.
When we need to create a second factory, we need to photocopy all the blueprints for the new cell. This uses a totally different process (a photocopier assembled specifically for the job of copying whole blueprints onto more blueprint paper, and not the work-order slips sent to the assembly line). The photocopier is pretty reliable too, but occasionally it introduces artifacts, and eventually, enough of these errors can build up to create mistakes in the blueprints. The blueprints have instructions on how to deal with errors in a new factory (by blowing it up), but if enough of those failsafe instructions are obscured by copier artifacts, you now have a potentially cancerous cell.
The foreman's office doesn't usually make changes to the blueprints based on work order slips. It's possible with a special copy machine -- this is how HIV works, by sneaking that machine in -- but without a work order slip to blueprint copier, it doesn't matter how many fake work order slips we pass into the cell. They will only affect the production line, not the foreman's office.
The more detailed, and almost certainly wrong-in-the-details version:
There are three types of encoding for genetic material: in DNA, in RNA, and in proteins.
In order for the information encoded in genetic information to be active in a biological system, it has to be expressed as a protein -- a physical manifestation with binding sites and the ability to interact with other molecules. Ribosomes, a component of the cell, do the "assembly" part of transferring genetic information to a protein. This is called "translation".
DNA is the long-term storage of the information eventually expressed as proteins -- it's a collection of templates in long term storage. So there has to be a process to get information from the long-term storage of DNA, in the nucleus of the cell, to the ribosomes elsewhere in the cell.
Messenger RNA is the intermediary molecule which carries the genetic information from the DNA to the ribosomes. It's produced in the nucleus of the cell by a mechanism called "transcription", which copies a subset of a DNA molecule into a complementary RNA molecule encoding the same information. The DNA double-helix is "unzipped", a complementary RNA strand is assembled, and the double-helix reforms. The mRNA can then be transported to the ribosomes.
mRNA is a useful vaccine mechanism, because we're co-opting a late stage of the cell's protein production pipeline. We don't have to assemble the target protein by hand and figure out how to modify it make it stable for distribution -- a task that would need to be repeated for each protein we wanted to make. Instead, we can figure out how to synthesis mRNA, and we don't need to worry about either synthesis or stability for the end protein product.
When we talk about cancer and mis-copying, this is at a much earlier stage in the pipeline. When a cell splits into two cells through mitosis, we don't want a subset of the protein templates in the cell's genetic material; we want a complete copy. This is a separate biological pipeline, which involves the cell building up a mechanism to do the copying, dissolving the membrane of the nucleus, and ultimately producing and collating copies of all the DNA from the nucleus. This is an entirely separate process, and messenger RNA isn't involved at all.
There is a route for information to travel from RNA back to DNA, and this is the mechanism retroviruses use, and HIV is the most famous example. A complete retrovirus particle includes reverse transcriptase, an enzyme which allows them to transfer information from RNA back to DNA. This is the reverse of the normal DNA -> RNA pattern described above, hence the name _retro_virus. Without that enzyme or something like it, there isn't a pathway to convert RNA back to DNA, and human cells don't normally express an enzyme which has this function.
That said, I can imagine once we figure out how to deliver the mRNA to precisely the right targets, this would be a lot easier (eg engineering receptor ligands onto the mRNA lipid delivery particles).
I'm not trying to downplay the health issues or impact of COVID, just saying that it has the potential for one heck of a silver lining. Not least of which is that even if other mRNA uses aren't forthcoming, we're incredibly more prepared to fight another pandemic, especially other Corona strains, that could be more harmful.
(the first SARS certainly encouraged vaccine research)
The situation reminds me of research into serotonin's role in depression. Like mRNA in its field, ideas about serotonin and a little bit of research were bouncing around for a few decades. The drug that was ultimately branded Prozac was developed in the early 70's, but not brought to market until the mid 80's. Then, it's ground breaking efficacy compared to prior drugs & for people not helped by those other drugs acted as a catalyst for research that now forms the foundation for modern treatment of mood disorders-- certainly far from perfect, but also far better than 30-40 years ago.
For example, Prozac's minor role as a norepinephrine reuptake inhibitor sparked significant research into that neurotransmitter as well, leading to yet another generation of new drugs, SNRI's like Cymbalta that which are not only a useful for depression & anxiety, but also for the treatment of certain forms of chronic pain & as an aid for quitting smoking.
It's too early to tell for sure, but I see the potential for the moment in history to be a similarly catalyzing event for mRNA research & subsequent treatments.
(Unless of course the vaccine produces a zombie apocalypse, the relatively small trials by chance not having anyone impacted by that potential "side effect" of zombie-ism, in which case I'll feel pretty silly sitting here a few months from now having to eat my words. And brains, lots of brains.)
Might be able to guide mRNA too.
mRNAs are great as a vaccine to trigger an anti-cancer response, combined with checkpoint inhibitors. The big challenge is to choose a good personalized mix of peptides (encoded as mRNAs) in a way that scales to thousands of patients.
This is now industrialized. Print the mRNA, slap it in lipids, inject. https://www.idtdna.com/
https://www.healio.com/news/infectious-disease/20201209/uk-a...
here it says that UK authorities advise that people with a history of allergic reactions may not get the mRNA based vaccine, as they may get an anaphylactic event. Now wikipedia says that this is a potentially serious condition https://en.wikipedia.org/wiki/Anaphylaxis
Now I am confused, https://www.aafa.org/allergy-facts/ says that some 50 million people in the US suffer from some kind of allergies, does that imply that 15% of the population can't get the mRNA vaccine? Now would that figure have any implications on the effectiveness of vaccination? Should people with allergies get a different kind of vaccine? Many questions remain.
I don't see a public discussion of these issues.
I have hay-fever and Asthma and you won't be able to stop me getting the vaccine. I see far more risk from COVID than the vaccine.
I have to question your motivations here. Your post is disingenuous at best.
Sorry for asking questions.
[1] https://edition.cnn.com/2020/12/09/health/covid-vaccine-alle...
I think they should give some detailed clarifications on the issue to the public, as the producers of the vaccines can't be sued for damages, in the event that something goes wrong.
https://theintercept.com/2020/08/28/coronavirus-vaccine-prep... (for the US, don't have any information for GB on that issue) In the EU producers were also seeking exemptions https://www.berliner-zeitung.de/en/covid-19-vaccine-makers-w...
My main questions after watching: how long do the spike proteins attach to our cell membranes? Do they get cleaned up eventually?
Also, will it lead to damage to the cell in anyway?
there are many quotes regarding ~every Xmonths you are a new person.
The original gene therapies (early 2000s) were essentially RNA therapies (adenovirus). And their unethical rush and subsequent failures caused a bit of a 'gene therapy winter' [1]. We've since made enormous progress on both the ability to safely deliver genes, but also our ability to generate/design new useful genes.
[1] https://www.labiotech.eu/in-depth/gene-therapy-history/
> In 1972, a paper titled ‘Gene therapy for human genetic disease?’ was published in Science by US scientists Theodore Friedmann and Richard Roblin, who outlined the immense potential of incorporating DNA sequences into patients’ cells for treating people with genetic disorders. However, they urged caution in the development of the technology, pointing out several key bottlenecks in scientific understanding that still needed to be addressed.
Figuring out what sequence of mRNA will be the right one to get a cell to produce the right antibodies for the job, getting that sequence sliced out of the viral RNA, getting that all into a form where it can be absorbed by cells and not just instantly degrade are all nontrivial tasks.
The devil’s in the details: compare to the field of software or cpu engineering... seems straightforward enough to just have more instruction decoders, but due to complexities only ditching x86 has actually made it possible for Apple to do this.
I found this video (from 2013) in the other thread today about the vaccine Moderna Vaccine taking two days to make: https://news.ycombinator.com/item?id=25468959
https://en.wikipedia.org/wiki/Polymerase_chain_reaction
the emphasis in the wiki article is on DNA, the same basic principles apply with RNA.
for example you can start with RNA and use reverse trancriptase to produce a DNA sequence, amplify that sequence to a large copy number by repeatedly replicating it then transcribe the DNA to produce large quantities of RNA.
or you can start with the DNA [in large quantities of purity] then create many copies of the RNA by repeatedly transcribing the DNA.
The practice of artificial [in vitro] gene synthesis can create arbitrary sequences for input to the process[es].
https://en.wikipedia.org/wiki/Artificial_gene_synthesis
liposomes are manufactured via biochemical-mechanical process.
This is not my understanding. PCR works to produce DNA because the DNA polymerase enzyme creates DNA copies from DNA templates, and those copies become templates themselves, feeding back into the chain reaction.
I'm not aware of similar enzymes capable of making RNA copies from RNA templates (RNA polymerases use DNA templates AFAIK).
I was imagining the RNA vaccines would have used a fully synthetic oligo production method, to get the extreme purity required. But it might be that some sort of PCR-like amplification process is used. Would love to read more if someone has details.
to wit : https://chempedia.info/info/viral_rna_polymerase/
I was making reference to the process of cyclic amplification, in a manner palatable to non biology literate individuals
The same _basic_ principles
as can be read in the chempedia example the process of RNApol replication of RNA from RNA template is error prone, thus it is superior to create a large copy number of DNA template corresponding to the mRNA desired as DNA amplification is self correcting for the most part.
dependent upon experimental or procedural requirements it may be desirable to produce error prone replication variants of the RNA template, however it is quite possible to go from RNA template to RNA product with RNApol.
due to the fragile nature of RNA there must be some shielding or , a low cycle rate is used in conjunction with immediate harvest and stabilization of the product.
the sars-2 covid19 virus replicates by way of an RNA dependent RNApol [rdRNApol]
Producing RNA from DNA amplicons (PCR products) makes sense, I'm curious if that is the source of material from in the vaccines, or if it's artificially synthesized?
Would that be a trade secret?
when you have determined a sequence of RNA corresponding to a desired protien you may construct a DNA template with modification to suit your purpose.
the DNA polymerase used for DNA PCR is originally from a high tempurature tolerant organism, [thermophillic bcterium] and it is possible via searching high and low to find an organism that bears high temperature tolerant rdRNApol
https://www.sciencedirect.com/topics/biochemistry-genetics-a...
and BTW the original inventor of PCR [kary mullis]
was awake AF on LSD when he conceived of this technology while sitting on a park bench.
https://en.wikipedia.org/wiki/Kary_Mullis
i believe the original PCR was performed MANUALLY! with glassware and perfectionist tedium.
https://en.wikipedia.org/wiki/Kary_Mullis#Use_of_hallucinoge...
you may find this to be interesting:
Reading how Pfizer and Moderna worked on it together, they needed detailed gene sequencing to understand how to design a potential vaccine. Even then they were left with a lot of potential options they still had to whittle down. Finally even with all that work they’re left with a vaccine with complex storage requirements.
So it’s entirely possible that we just didn’t have the surrounding technical ability even if theoretically it was possible. The gene sequencing to sequence it quickly and share that across the entire world, the compute needed to do try different experiments at scale, the manufacturing capabilities, Moderna having invested in the space for the preceding 10 years, existing experience with developing a SARS vaccine, etc.
Moderna's vaccine is a great deal easier to store than the BioNTech/Pfizer vaccine (requires 'normal' freezers for storage, can be at refrigerator temperatures for a longer period).
There was quite a lot of development on basic techniques of working with RNA necessary before that could even in isolated circumstances be easier than, or even competitive with, “isolate the antigen, inject it, done”.
> The question is, how did this start just now?
It didn't.
Getting a treatment to market isn't the start of application of a new technique in medicine; its usually something that happens many years, often decades, into work using the technique.
1) Develop synthesis technique for large scale high purity mRNA without base errors or truncations.
2) Discover pseudouridine modification to decrease innate immune response.
3) Discover and optimize lipid nanoparticles for encapsulation of mRNA to prevent its degradation.
4) Optimize LNPs and miRNA sites in UTRs for localization to desired cell type and to prevent aggregation in undesired or dangerous cells/organs.
Poof, that's it!
Read the history section of the rna vaccine wiki: https://en.m.wikipedia.org/wiki/RNA_vaccine
You’re right, we’ve understood that this could be done for a long time. Not quite the 70s, but.. at least the 90s. But believing something is possible and knowing how to do it are different:
1989 - injected rna maybe goes into cells
1990 - proof injected rna creates proteins
1994 - proof injected rna creates immune responses
Then:
“2005 they published a joint paper that solved one of the key technical barriers by using modified nucleosides to get mRNA inside human cells without setting off the body's defense system”
That kicked off a ton of research, but:
“Up until 2020, these mRNA biotech companies had poor results testing mRNA drugs for cardiovascular, metabolic and renal diseases; selected targets for cancer; and rare diseases like Crigler–Najjar syndrome”
But why did they spend from 2005 to 2020 working on mRNA drugs and not vaccines? Capitalism. Vaccines are not generally profitable (take once, you’re done) - so vaccines are not an appealing target for a startup with investors wanting big returns. (Source: https://www.statnews.com/2017/01/10/moderna-trouble-mrna/)
Medical research needs to be driven by what can help people, not by what can make the most money.
If we had a different administration in the USA we may have been able to conquer that quickly with sheer cash and coordination since the knowledge how to build melt blown N95 machines is there. For whatever reason we just didn't.
The immune system is incredibly dangerous to its own host if mishandled. By stimulating response, you are trying to light a cigarette using a white phosphorus flamethrower, so to say.
It took a lot of time to find the optimal way of mRNA delivery that a) really does something but b) does not provoke a massive, counterproductive response. This is a very narrow rocky ledge with precipices on both sides to walk.
> It's ok to post stories from sites with paywalls that have workarounds. In comments, it's ok to ask how to read an article and to help other users do so. But please don't post complaints about paywalls. Those are off topic.
HIV, Ebola certain cancers, etc. What about using it to train our immune system for more complex diseases like Malaria or various bacteria? What about investigating if the general techniques can also somehow combat simpler diseases like prions which don’t even have RNA.
And bacteria aren't in general limited by immune response. The immune system has zero difficulty detecting a bacterial infection, but it happens at a wildly different scale and can't be fought with a fundamentally chemical means like our bodies do with virii.
And the point about prions seems to misunderstand this technique. The way an mRNA vaccine works is by transmitting blueprints for a viral protein (but not the rest of the virus) into the body's cells, where ribosomes then synthesize the disembodied proteins, which get detected as "foreign invaders" and produce a lasting immune response which would then be effective against the real virus.
Prions, remember, are just misfolded versions of your body's own proteins. They have the same sequence of amino acids as "correct" proteins and just an incorrect shape. mRNA only transmits the sequence, not the shape. And in any case your cell's DNA already has the sequence encoded, because you're not dead.
I was thinking more that research into biotech generally improves our knowledge. I don't know biology at all but I figured some evolution of technologies associated with CRISPR + mRNA + other things would be useful as a team in solving prion diseases. So maybe mRNA can become efficient enough that it's used to train the immune system to target the misfolded proteins themselves to try to limit damage while the treatment is ongoing. Futuristic now certainly, but is it definitely 100% impossible ever even as our knowledge & tech improves? Or maybe mRNA can exploit something in the prion process we don't yet understand. Maybe CRISPR could be part of the overall treatment therapy as you inoculate more of the body from whatever is propagating the bad code through your body which could be a time-consuming process (think vaccine at the genetic level - you potentially need to get it to every cell in the body).
Obviously this is all sci-fi stuff & some of it impossible & out there. I still like to imagine sci-fi is useful as potential roadmaps to brainstorm how we might solve impossible problems - even if we miss, we'll land somewhere useful.
- Mostly lay person view (some bioinformatics experience)
The latin plural of 'virus' does not exist. It is a nebulous, uncountable concept to ancient rome. Like 'malaise' or 'ocean' (we can pluralize oceans in english, but hopefully you can imagine that a language would treat it as a concept for which the concept of pluralization doesn't make sense).
You'd think: Hey, it's `-us`, I know that one, it pluralizes to `-i`, but, no. There is no plural. It's a rare form that also ends in -us but doesn't work like most of the words you know derived from latin that end in -us.
But there is `vir`, latin for 'man', and the plural of that is viri.
So, 'viri', as in 'the latin pluralized form of virus', is dead wrong.
There is no -ii ending in latin. At all.
The plural of 'virus' in english is 'viruses'. Any other form is stupid. Sometimes language does that, but surely you'd agree that something like 'irregardless', whilst somewhat common, sounds very unprofessional. virii is the same way.
Triarii?
(My knowledge of latin as a language comes primarily from Rome Total War).
Should you mean no -ii ending to "virus" at all, it would appear to be a reasonable assertion. However if by "at all", you mean of any word in Latin, that is demonstrably false.
http://latindictionary.wikidot.com/noun:filius
Nominative and vocative plural: filii
Usage example:
"... et nihilo minus amicum gravem virum aut fidelem libertum lateri filii sui adiungere, ..."
https://thelatinlibrary.com/quintilian/quintilian.institutio...
Also by referring to ancient Rome you treat Latin as some sort of a fixed, dead language, but English speakers do that irregular pluralisation to words borrowed from the modern languages descented from Latin too (see cappuccini), and so for example in Romanian plural of virus is virusuri, and in Neo-Latin it's vira. Personally I want to prefer virusuri just because it's the funniest one.
Somatic mutations can trigger the misfolding as well.
The reason we don't have an HIV vaccine is because HIV embedds itself in the DNA of some cells and some of those cells don't start producing virions right away, the immune system can't detect them, you clear the visible infection, but just weeks after, those hidden cells start producing the virus and the infection starts over. So the issue with HIV is the hidden reservoir of infected cells, afik.
> These drugs face the challenges of targeting mRNA to specific tissues and giving strong, lasting benefits without excessive side effects.
This innovation reminds me of Virginia Postrel's book The Fabric of Civilization: How Textiles Made the World [1]. Postrel describes several key technological innovations that propelled the manufacture of cloth from fiber farming to thread weaving to cloth weaving to cloth dying/decorating to distribution. Each innovation moved the bottleneck to a different layer in the value chain.
The mRNA platforms are ideal for vaccines but ultimately, the downstream safety/efficacy trials are the new bottleneck. There was a time when futurists obsessed about nanobots but these mRNA platforms are the ultimate nanobots, in my opinion. They can be configured to program biological cells to manufacture simple proteins in situ. This is a very powerful tool, but like the historical innovations in spinning and weaving, the technology can produced many orders of magnitude more potentially useful outputs than the rest of the value chain can use effectively (for now).
[1] https://www.basicbooks.com/titles/virginia-postrel/the-fabri...