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As I understand it, mRNA vaccines operate by taking a gene for some distinctive feature of the target virus and arranging for the cells of the vaccine recipient to manufacture the proteins that make up the distinctive feature and present them to the body of the host, which will then form an immune response to the feature.

My question is: how is this feature, assuming it has been manufactured, presented to the body? In other words, is the expectation that it would exist as a separate unit and that separate unit would exit the host cell somehow and be recognized?

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    $\begingroup$ Your cited example is the concept behind recombinant viral vaccines, like the ChAdOx1 by Astrazeneca. Nothing to do with mRNA one. $\endgroup$
    – Shred
    Oct 28, 2021 at 17:06
  • $\begingroup$ @Shred I edited the question to remove irrelevant comments about how the genomic material enters the cell. $\endgroup$
    – Imprisoned Rhesus
    Oct 28, 2021 at 22:48
  • $\begingroup$ I came here by accident looking for an answer on whether the cells contracting the mRNA get destroyed by the immune system. For instance, Dr. Mobeen Syed suggests that the material exits the cell only as: (1) exposed via MHC I, e.g. in case of a muscle cell, or (2) exposed via MHC II in case of antigen-presenting cell, or (3) debris when the cell self-destruction is triggered by a CD8 T cell. Such interpretation seems to be in conflict with the answers here suggesting that the spike material can exit an intact cell by itself. Video: youtu.be/9EfToFXwx98 $\endgroup$
    – Roman Riabenko
    Oct 31, 2021 at 10:40
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    $\begingroup$ @RomanRiabenko Well, you should read my comments below in the answers. Concerning cell destruction, when a cell undergoes apoptosis there is a protease cascade that destroys all the proteins in the cell before it disintegrates. Also, as I stated in my comments, a disembodied viral protein would not have the same folded shape by itself that it would have on an intact and complete virus, so it would be unlikely that a fragmentary viral protein would have a useful immunological pattern that could be acquired by a B cell. $\endgroup$
    – Imprisoned Rhesus
    Oct 31, 2021 at 10:46
  • $\begingroup$ @Shred: It's rather unclear, I admit, but I think the OP means SARS-CoV-2 by "vector virus". Still the Q could be edited for more clarity. $\endgroup$
    – Fizz
    Oct 31, 2021 at 10:46

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MHC presentation of cleaved spike protein is only part of the picture; afterall, the immunity conferred by vaccines is largely owed to neutralizing antibodies produced by B-cells, which do not recognize MHC-bound peptides but rather intact antigen. While MHC presentation is important for T-cell (and ultimately B-cell) activation, the fact is that the spike protein encoded by these mRNA vaccines is presented on the surface of transfected cells for B-cell recognition.

Here is a great review that not only discusses the mRNA vaccines but, as far as I can tell, all of the other vaccine strategies as well. It should answer your question in more detail than I would presume to.

Heinz FX, Stiasny K. 2021. Distinguishing features of current COVID-19 vaccines: knowns and unknowns of antigen presentation and modes of action. NPJ Vaccines 6(1):104

In the course of cellular SARS-CoV-2 infection (Fig. 1a), the S protein is synthesized from one of the viral subgenomic mRNAs and co-translationally transported into the lumen of the endoplasmic reticulum (ER) by the use of a signal sequence at its N-terminus, comprising residues 1 to 13 of its total 1273 amino acids... After completion of translation, the protein remains attached to the ER membrane through a C-terminal membrane anchor... When S is synthesized as an isolated protein (Fig. 1b) (as in mRNA and adenovirus vector vaccines as well as for production of recombinant subunit vaccines), the pathway of biosynthesis is very similar.

enter image description here

Fig. 1: a Infected cells: Subgenomic mRNAs for viral structural proteins are translated in association with the ER (S, M, and E) or in the cytoplasm (N), and virus assembly takes place in the ERGIC. Virus particles are transported through the TGN and released from the cells probably via lysosomes. During transport, S is cleaved into S1 and S2 by the cellular protease furin in the TGN. Some spike molecules, not assembled into virions, are also transported to the plasma membrane despite the presence of an ER retention signal15. b Transfected cells: Biosynthesis of S occurs in the absence of interactions with other viral proteins. Proteolytic cleavage into S1 and S2 occurs in the TGN similar to that in infected cells, but some shedding of cleaved S1 and conversion of S2 into its post-fusion structure (S2*) may occur in the absence of stabilizing mutations. ER—endoplasmic reticulum; ERGIC—endoplasmic reticulum Golgi intermediate compartment; TGN—Trans Golgi Network; RNP—Ribonucleoprotein; Viral proteins: S—spike, M—membrane; E—envelope; N—nucleoprotein.

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  • $\begingroup$ I think you may be misunderstanding the paper. The diagram you embed shows S1, a viral peptide pool, mounted on the exterior of plasma membrane. This can only be possible via presentation by MHC by my understanding. Also, the spike protein has something like 316 different peptides. I would expect these subunits to be presented, not the entire peptide pool all at once. When a proteasome cleaves a protein I don't think it is predictable what subset of peptide sequences are created. If you are suggesting that the entire protein or one of the pools gets excreted directly by the TGN (continued) $\endgroup$
    – Imprisoned Rhesus
    Oct 29, 2021 at 4:13
  • $\begingroup$ I think that would be an unproven assertion, because I believe there are range of conditions a protein has to fulfill before it can be transported this way and viral proteins would not, I expect, fulfill these conditions. Furthermore, even a viral protein was execreted directly, it would not have immunological benefit because T-cells can only analyze peptides mounted on MHC, not free-floating molecules. B cells on the other hand bind to structures on complete and folded pathogens. (continued) $\endgroup$
    – Imprisoned Rhesus
    Oct 29, 2021 at 4:28
  • $\begingroup$ It would seem to be unlikely that a disembodied S protein would fold properly without the presence of the rest of the virion, and if the protein is not properly folded, that would seem to make it unlikely that a BCR would bind to it successfully. $\endgroup$
    – Imprisoned Rhesus
    Oct 29, 2021 at 4:28
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    $\begingroup$ S1 is not a "viral peptide pool", it is a domain of the spike protein. You can see the structure of the complete spike protein, including S1 and membrane-bound S2 domains in Fig 2 of the review. It is this complete, folded protein (or at least the S2 domain) that is displayed on the cell surface. $\endgroup$
    – canadianer
    Oct 29, 2021 at 6:31
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    $\begingroup$ In concert with the cellular machinery, the spike protein has evolved to fold and enter the secretory pathway of infected cells naturally. It is not unreasonable to expect that it would follow the same pathway regardless of the absence of other viral proteins. Here is a paper which detects intact spike protein on the surface of HEK293T cells after transfection with either the wild-type spike protein mRNA or the mRNA of the Moderna vaccine. $\endgroup$
    – canadianer
    Oct 29, 2021 at 6:31
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Your assumption is wrong. A mRNA vaccine only contains a mRNA for the protein against which you want to vaccinate, encapsulated in a lipid membrane. These membrane vesicle fuses with the membrane of the target cell and releases the mRNA into the cell. There free ribosomes can bind to the mRNA and translate it into a protein. Part of this protein is presented on the cell surface by the MHC complex and thus presented to the immune system. The mRNA is degraded after some time (although it has been modified to slow down this process), no further copies are made or integrated into the genome.

Speaking of virus based vaccines (like Sputnik V or Astra Zeneca) rely on a virus to deliver a piece of DNA into the cell which contains the information on the protein against which you want to vaccinate. This is transcribed into mRNA and eventually translated into protein. From the virus DNA usually the genes which are responsible for replication are removed so you get no new generation of viruses. Also the virus cannot do anything on its own, since it is not alive and needs a target cell and its machinery.

This resource gives a nice overview over the different vaccine types.

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  • $\begingroup$ First of all, this does not answer the question. Secondly, your understanding is incorrect, if you actually read the link you put in your non-answer, you will see that in the section on mRNA vaccines, it explicitly shows a vector virus being used to insert the mRNA into the cell in steps 2 and 3. $\endgroup$
    – Imprisoned Rhesus
    Oct 28, 2021 at 16:58
  • $\begingroup$ @ImprisonedRhesus Chris's answer is correct. You are reading the wrong section of the link, the part about viral vector vaccines rather than the mRNA vaccine (the top row in the image is the mRNA vaccine; no viral vector there). The part of this answer that specifically addresses your title question is "Part of this protein is presented on the cell surface by the MHC complex and thus presented to the immune system" while the rest addresses other misconceptions in the question. $\endgroup$
    – Bryan Krause ♦
    Oct 28, 2021 at 17:07
  • $\begingroup$ @BryanKrause Huh, ok, so I stand corrected, but it is more or less irrelevant to the question how mRNA gets into the cell. I am asking about the presentation afterwards, so focusing on a minor and irrelevant part of my question that happens to be wrong seems like a comment, not an answer. $\endgroup$
    – Imprisoned Rhesus
    Oct 28, 2021 at 17:54
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    $\begingroup$ @ImprisonedRhesus The vast majority of the text in your question is centered around misconceptions of how things work and imagined solutions based on those misconceptions. I think an answer that failed to address those would be incomplete. $\endgroup$
    – Bryan Krause ♦
    Oct 28, 2021 at 17:58
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    $\begingroup$ @Chris I edited the question to remove irrelevant comments about how the genomic material enters the cell. You know this community would be a lot more useful if it spent more time answering questions and less time obsessing about minor errors in the question. The people who ask questions are typically those who don't understand the subject very well to begin with. If I was a PhD in immunology I would never have asked the question in the first place. $\endgroup$
    – Imprisoned Rhesus
    Oct 28, 2021 at 22:51
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How do mRNA vaccines work with respect to presentation of the antigen?

According to a DynaMed article, the egress mechanisms expected to play a role are 3:

enter image description here

(Note that this image may be somewhat misleading, in that [skeletal] muscle fibers [which are very long lived, multi-nucleated cells] don't normally express MHC-I according to a (peer-reviewed) article. I'm unsure if satellite stem cells in the muscle, which serve to repair the multi-nucleated fiber cells by supplying nuclei, have MHC-I.)

As you self-answered, in muscle cells, the MHC-I pathway exposes peptide fragments to "killer T-cells" (CD8)... but there's also release of proteins into extra-cellular space from where they are picked up by B cells, which produce antibodies.

Further MHC-II is engaged in APCs present in muscle and lymph nodes; we know at least from the reported side effects of mRNA vaccines that lymphadenopathy (swelling of lymph nodes) does happen often enough following mRNA vaccine administration.

I think however that the relative ratios of spike protein (following mRNA vaccine administration) reaching these 3 routes haven't been exactly quantified. (I've search a fair bit, but I could not find any papers on exactly that issue.)

Ultimately, both memory B cells and memory T cells (hopefully) give long-term immune memory against that kind of infection, which at least give the host a head-start in a race against a new infection.

It's worth noting that mRNA vaccines don't produce the same ratios of neutralizing to binding antibodies (to the spike) as a real SARS-CoV-2 infection.

vaccinees generate more non-neutralizing antibodies than COVID-19 survivors resulting in a lower ratio of neutralizing to binding antibodies. These data were already apparent in the early phase clinical trials but remained unrecognized at the time (Walter, 2020).

[...] the burning question of whether the abundant non-neutralizing antibodies do have a protective effect in vivo will need to be elucidated by follow-up studies

mRNA vaccines also produce a lot more (spike) neutralizing antibodies than a real infection (same paper), at least initially--there's apparently a fair bit of decay over time though. Both of these suggest that spikes produced by mRNA vaccines get a lot of B cell attention, which might indicate a lot of them spikes produced by mRNA vaccines egress into extra-cellular space.

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  • $\begingroup$ As I commented to a different answer, I don't really believe the "extra cellular protein" stuff, unless you give me much more specific info. First of all, B cells only recognize FOLDED and intact pathogens, like a complete virus. The idea that a B cell would successfully memoize a disembodied protein fragment seems unlikely to me. Also, the shape of this fragment would be different than what it would be on a complete virus, so even if it did so, there would be no immunological benefit. (continued) $\endgroup$
    – Imprisoned Rhesus
    Oct 31, 2021 at 10:16
  • $\begingroup$ Secondly, you have not shown how a disembodied viral protein can exit a human cell. Viruses use a complex envelopment mechanism to get out of cells which is only available to a complete virus, not viral fragments. Genuine cell self-product proteins only can leave the cell through the Golgi apparatus which requires specialized carriers that human-generated proteins are designed attach to. There is no evidence I know of that a viral fragment would be able to adopt these carriers and use the Golgi apparatus to escape the cell. $\endgroup$
    – Imprisoned Rhesus
    Oct 31, 2021 at 10:19
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    $\begingroup$ "The idea that a B cell would successfully memoize a disembodied protein fragment seems unlikely to me." Please ask that separately as it's a simpler issue to answer on that level, not related to mRNA vaccines. You could even ask it on Skeptics SE. The 2nd issue (protein egress) is more interesting/challenging to prove directly, I admit, but again it's better suited for a separate question. You've basically used this Q of yours to ask two different ones, related to your disbeliefs. (Your counter-theory that only MHC-I works still doesn't explain anti-bodies, I'll note, though.) $\endgroup$
    – Fizz
    Oct 31, 2021 at 10:32
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    $\begingroup$ "B cells only recognize FOLDED and intact pathogens" That is completely untrue. B cells will recognize foreign sequences or structures however they're presented to them, whether it's a protein fragment or an intact virion. $\endgroup$
    – MattDMo
    Oct 31, 2021 at 21:32
  • $\begingroup$ S.Seneff, G.Nigh suggested that muscle cell also presents MHC II. "Muscle cells do express MHC class II proteins (Cifuentes-Diaz et al., 1992). As contrasted with class I, class II MHC proteins specialize in transporting intact proteins to the surface as opposed to small peptide sequences derived from the partial breakdown of the proteins (Jiang et al., 2013)." dpbh.nv.gov/uploadedFiles/dpbhnvgov/content/Boards/BOH/Meetings/… $\endgroup$
    – Roman Riabenko
    Nov 1, 2021 at 8:11
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The way the antigenic material is presented is via a peptide MHC complex which appear on the surface of the cell. The various proteins present in a given cytoplasm are randomly selected and automatically chopped up by proteosomes and the resulting short peptide chains are then channeled through a special kind of cellular structure called a major histocompatibility complex and mounted on its surface exterior to the cell. If the target antigen protein is indeed being successfully manufactured inside the cell, then we can it expect that these products will be periodically cut up in the manner described and be exposed. The exposed peptide then serves as an example both for helper T-cells to stimulate immune response (such as antibody class switching), and also serves as the epitope to cytotoxic T-cells which can kill the infected cell. Below is a diagram illustrating the mechanism:

MHC mechanics illustration

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  • $\begingroup$ Downvotes with no comments. $\endgroup$
    – Imprisoned Rhesus
    Oct 30, 2021 at 22:42
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    $\begingroup$ This isn't incorrect, but it's incomplete in a major way to the point of being misleading; the vast majority of mRNA vaccine studies measure (neutralizing) antibodies, but how do you get [any] spike antibodies from this "cytotoxic T-cell"? $\endgroup$
    – Fizz
    Oct 31, 2021 at 8:18
  • $\begingroup$ @Fizz Helper T-cells (CD4+) can attach to MHC just the same way that cytotoxic T-cells (CD8+) attach. However, CD4+ cells stimulate an immune response that includes antibody signalling. I added a statement to that effect in my answer. $\endgroup$
    – Imprisoned Rhesus
    Oct 31, 2021 at 15:09
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    $\begingroup$ You're still missing direct B cell activation, which is a major part of the immune reaction. B cell receptors bind directly to antigen and cause B cell activation, which is then enhanced by $T_H$ cells, but not initiated by them. The MHC-I pathway is only part of the system. You're also completely missing the MHC-II pathway (which CD4s recognize, CD8s only do MHC-I) and the effect of professional APCs. $\endgroup$
    – MattDMo
    Oct 31, 2021 at 21:36
  • $\begingroup$ @MattDMo Let me know if this comment of mine got go be removed, as maybe it refers to some other question, which might exist at Stackexchange. Re "B cell receptors bind directly to antigen and cause B cell activation" . That should work without any uptake of antigen? Do B cells uptake whole virus? Or do they uptake "debris", see above, nothing left after "clean apoptosis"? And, what's more, if presentation on MHC2 needs incorporation, may contact and let go suffice in a situation of activation of memory B cells? $\endgroup$
    – Peter Bernhard
    Nov 5, 2021 at 19:16

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