jujubeen66 said:
Okay this is getting better. Thanks Yggdrasil (love that moniker) for a more in depth explanation. I check out your links and I'm going to run my new understanding past you to see if I get it.
Well, I'm no
@Ygggdrasil, but I'm awake, so I might as well take a crack at it. NB--I have no idea what your level of expertise is, so this might be a little basic.
The true target of the mRNA structure is the dendritic cell because it is responsible for informing the core immune system of the antigen spike protein.
This isn't strictly true. Given a mode of transfection (in this case cationic liposome-based transfection), each cell type has a certain transfection efficiency. In (roughly) lay terms, what that means is that each cell type (dendritic, other immune, muscle cell, fat cell, etc.) will be transfected (i.e., mRNA from the liposome will make its way into a given cell's cytoplasm) with a certain efficiency--sometimes the transfection will succeed; sometimes it will fail. In vitro, a good optimized transfection efficiency may be on the order of 50-70%: 50-70% of cells will have non-native genetic information introduced into them. I don't know tons about in vivo transfection efficiency, but I imagine it'll be lower. Living things are complicated.
Exogenous mRNA is encased in a lipid molecule to hide it from the immune system initially which would assault it if it were recognized in a free state.
mRNA is encased in a liposome (think of it as a nanoscopic soap bubble made up of molecules that look a lot like the molecules that make up the membrane of your cells). This is less to hide it from the immune system and more to hide it from an enzyme called RNAse which is...just everywhere and a huge pain in the butt. RNAse's entire job is to chew up RNA into its monomeric pieces. It's very good at its job, and it's expressed both inside cells and outside of cells. In fact, RNA research labs have to take special pains to exclude the presence of RNAse in their experiments. The liposome in the vaccine has two functions: 1) it gives the mRNA some breathing room and a buffer against encountering RNAse, thus increasing the likelihood it'll find its way into a cell, and 2) the liposome itself, being cationic, will associate well with the anionic nucleic acid and, since its molecules share similiarities with your cell membranes, it can integrate more effectively with the cell and deposit its mRNA payload more efficiently into the cytoplasm of your cells.
Once in the cytoplasm, the mRNA strands find ribosome, pass on the protein code, and the ribosomes begin churning out the proteins.
This is all fine.
The cell actually does chew up some of the proteins produced, but displays the bulk of the production on its cell surface for the benefit of the immune system.
Am I solid so far?
Close enough.
it sounds like dendritic cells could be totally covered in this mess.
Maybe. The adaptive immune system is wildly complicated, so I'll let this be for the moment.
It says the mRNA is a copy of the DNA strands coding for the protein in the coronavirus- but there are lots of those I understand.
There are lots of proteins that make up SARS-CoV-2, and there has been some talk of using mRNA to code for multiple proteins so that variants (whose structural proteins tend to mutate more slowly than the spike protein) can be caught more easily with boosters.
Also, that piece says that non-dendritic cells can take up the mRNA as well and produce the spike protein, but what would they do with it, since muscle cells aren't immune cells?
All of the body's cells contain ribosomes.
@Ygggdrasil's point was that, ultimately, it's the immune cells that need to recognize foreign proteins to kickstart the process of adaptive immunity. But if muscle cells express antigens on their surfaces, the immune system will still find out about it eventually: immune cells constantly circulate throughout the body, bouncing off other cells and occasionally attaching to foreign invader-jerks (by recognizing antigens--foreigners--bound to a protein known as the major histocompatibility complex--non-foreigner--and signaling that something is amiss).
I would imagine that at the beyond microscopic level of circulation where veins and arteries are nearly one, it would be possible that mRNA vehicles could be taken up there as well.
Sure, why not?
That article also said mRNA cannot penetrate the nucleus, but it didn't say why not. If the lipid capsule shields the mRNA structure from detection by the immune system, what prevents it from tricking the endoplasmic reticulum ( did I get that right?)
The liposome that encases the mRNA becomes part of the lipid cell membrane when it deposits its mRNA payload into the cytoplasm. At that point, the mRNA is naked in the cytoplasm; there is no packaging that will send it through the nuclear membrane.
Also, the Stanford piece always used RNA and not mRNA, they are quite different correct? that was confusing, and even worse once I got to dsRNA!
There are lots of RNA's. It's admittedly confusing. mRNA is specifically what gets translated by the ribosome into proteins. The ribosome knows it's chewing on mRNA and not another version of RNA due to the presence of what's called a polyadenine (or polyA) tail. Basically, all native mRNA is post-transcriptionally modified (modified after being synthesized from DNA) by tagging it with a tail made of lots of adenines in a row. The ribosome recognizes this polyA tail, binding to it and beginning the translation of the mRNA into a protein. The vaccine takes advantage of this by sticking a polyA tail onto the mRNA.
The Nature article was a treasure trove but it will take more time to digest and I don't have the background to crunch it all but some material stood out quickly. IVT= in vivo transcription? I don't think it was decoded.
Not at work right now so I don't have journal access.
They explain that RNA is a copied DNA template and one assumes that the segment of the Covid virus that codes for the protein was copied. I understand though that RNA doesn't always copy completely and often leaves out material that it deems superfluous.
I'm not sure this is accurate the way you're thinking about it. The ribosome will translate whatever mRNA you give it. There are (rare) errors, but it would be helpful to know where you're getting this from.
The mRNA degrades quickly, although the lipid case does prolong its durability yes?
Yes
once it is gone, can/do the ribosomes continue to make the proteins or is the presence of the coded mRNA crucial?
The presence of the mRNA is crucial. The ribosome can't operate without mRNA in its binding pocket.
Can the dendritic cell ever be covered with too many proteins such that they might free float in interstitial fluid and actually attach to ACE2 receptor cells elsewhere? ( no one mentions this)
Haha, well I admit, I'd never thought of this before. But no, typically overexpression of a protein doesn't extend to this degree. I suppose it's possible, albeit extremely unlikely, that a spike protein may escape its host cell and attach to another ACE2 receptor somewhere. But at any rate, things attach to ACE2 receptors all the time (namely angiotensin, the A in ACE2). The problem with COVID is that it uses the ACE2 receptor to enter a cell and hijack its protein production machinery to produce more COVID.
If, in fact, the cell is covered in whole and protein fragments, isn't a certain level of fraying possible?
Not sure what this means.
The Nature article is very complex and I would love to have someone hold my hand through it sometime,
Will get to it at work at some point.
but until then I'll just ask for clarification on some vocab: what is a cap structure? when they say the cap measures 5' how long is that exactly?
I'll have to read the article. 5' and 3' usually refer to the (non-equivalent) ends of a nucleic acid strand (wiki to the rescue:
https://en.wikipedia.org/wiki/Directionality_(molecular_biology))
What is a poly A tail- I heard a podcast somewhere that claimed that this was a structure that limited the life of the mRNA strands, true?
See above.
Finally, the Nature article indicated that the accompanying adjuvants play a rather crucial role in ensuring that the proteins are expressed strongly and recognized by the immune system and that some of these could result in the production of Interferon. Isn't that a good immune response? It sounded negative in the article.
I'd have to read the article to see for myself.
You're all terrific for helping me out in understanding this. Thanks.
OK,
@Ygggdrasil I'm totally taking credit for this.
