Inovio Pharm that also develops a COVID-19 vaccine. It’s technology is based on delievering DNA based.
I noticed that I feel more worried about DNA-based vaccines than mRNA based vaccines. I probably should try to articulate some of why.
After doing some preliminary skimming and examining my pre-existing knowledge around this… I’m now kind of conflicted and confused?
(Exploring this turned into a giant sprawl. It would be multiple research projects for me to fully dissolve my confusion here. I’ll leave the majority of my thoughts as a comment on this, but it may be so biology-dense that it mostly serves for my own reference.)
mRNA practically degrades itself. If an mRNA enters the cytoplasm, it might get diced by DICER but it otherwise is probably only good for a limited number of protein-producing ribosome-reads before it gets degraded or digested into unreadability.
DNA is a more robust molecule, befitting the archive-storage of the cell. In eukaryotes, almost all of it is permanently locked up in the nucleus, both for access and regulation reasons and as a protection against UV and other mutagens. DNA outside of the nucleus in a eukaryotic cell usually only comes up only in the context of viruses, cancer, GMOs, or ongoing problems or oddities with that cell.
(But apparently bits of it exist naturally, but have probably been understudied? That’s something that I didn’t fully realize until today. Pathology and pathogen-imitating GMOs are literally the only context where I have ever heard this come up before.)
How can this possibly happen non-pathologically in humans? What really confuses me is… getting DNA outside the nucleus in the first place as a non-freak occurrence requires at least one of:
Generation of loose DNA partial-transcripts while trying not to generate extra confusion during cell replication
If it’s handled as ssDNA, that actually would leave it in a form pretty distinct from the usual dsDNA storage. And even as dsDNA, there are epigentic tags you could use to see that it’s handled correctly.
This does have the benefit of being an “out” channel from the nucleus, not a security-vulnerability “in” channel.
I think I’ve reasoned myself to thinking this is the most likely explanation? I’ll have to do more research to confirm/negate this guess.
DNA cut-outs that permanently leave the nucleus, never to return (resulting in its absence in the next replication cycle)
You could come up with a clever working version made from frequently-duplicated genes with extra copies (ex: transposons), but… I’ve never heard of this. And it’s a little evolutionarily-fragile.
This does have the benefit of being an “out” channel from the nucleus, not a security-vulnerability “in” channel.
Reverse-Transcriptase (the most insidious of all viral proteins, that thing that crafts DNA from RNA)
Humans do have a special RT for extending telomeres, but it’s rarely expressed, and if a random cell is expressing it that’s a cancer waiting to happen.
There are retrotransposons that copy-paste themselves around the genome. But like… that’s basically a nasty virus that got lazy and whose deck is short a few cards.
Cytoplasmic replication
I am under the impression that this is not happening
In eukaryotes, I get the impression that DNA is usually not getting replicated out there in the cytoplasm, at least? DNA viruses usually have to do at least one of two things:
Get themselves into the nucleus somehow (via small size and/or transport proteins)
Carry their own replication proteins around with them in the virion, to produce those initial RNA transcripts that produce enough replication proteins for them to get by.
If the treatment involves entering the nucleus of fully-intact undamaged cells, or replicating itself (so really, either of these methods), the alarm bells in my head would be blaring.
But if it’s just circles of extracellular DNA… I’m now kind of conflicted and confused? How virus-like do you have to be to make that a viable thing to do?
Some other lingering points of confusion/research:
Plants use ambient restriction-enzymes to make being a random cytoplasmic DNA a hazardous game (on the assumption that ambient cytoplasmic DNA is usually viruses, and the non-viruses will have co-evolved with the particular restriction enzymes to make this system work). I don’t actually know that animals do, though. And you could always species-tailor it...
I also have no idea how efficient or inefficient extracellular transcriptase would be for producing mRNA transcripts. If it’s inefficient, you might have to use a pretty strong primer, and I find myself a tiny bit concerned about that in a long-lived human therapeutic.
In our previous related thread of related conversation, you mentioned:
I noticed that I feel more worried about DNA-based vaccines than mRNA based vaccines. I probably should try to articulate some of why.
After doing some preliminary skimming and examining my pre-existing knowledge around this… I’m now kind of conflicted and confused?
(Exploring this turned into a giant sprawl. It would be multiple research projects for me to fully dissolve my confusion here. I’ll leave the majority of my thoughts as a comment on this, but it may be so biology-dense that it mostly serves for my own reference.)
mRNA practically degrades itself. If an mRNA enters the cytoplasm, it might get diced by DICER but it otherwise is probably only good for a limited number of protein-producing ribosome-reads before it gets degraded or digested into unreadability.
DNA is a more robust molecule, befitting the archive-storage of the cell. In eukaryotes, almost all of it is permanently locked up in the nucleus, both for access and regulation reasons and as a protection against UV and other mutagens. DNA outside of the nucleus in a eukaryotic cell usually only comes up only in the context of viruses, cancer, GMOs, or ongoing problems or oddities with that cell.
(But apparently bits of it exist naturally, but have probably been understudied? That’s something that I didn’t fully realize until today. Pathology and pathogen-imitating GMOs are literally the only context where I have ever heard this come up before.)
How can this possibly happen non-pathologically in humans? What really confuses me is… getting DNA outside the nucleus in the first place as a non-freak occurrence requires at least one of:
Generation of loose DNA partial-transcripts while trying not to generate extra confusion during cell replication
If it’s handled as ssDNA, that actually would leave it in a form pretty distinct from the usual dsDNA storage. And even as dsDNA, there are epigentic tags you could use to see that it’s handled correctly.
This does have the benefit of being an “out” channel from the nucleus, not a security-vulnerability “in” channel.
I think I’ve reasoned myself to thinking this is the most likely explanation? I’ll have to do more research to confirm/negate this guess.
DNA cut-outs that permanently leave the nucleus, never to return (resulting in its absence in the next replication cycle)
You could come up with a clever working version made from frequently-duplicated genes with extra copies (ex: transposons), but… I’ve never heard of this. And it’s a little evolutionarily-fragile.
This does have the benefit of being an “out” channel from the nucleus, not a security-vulnerability “in” channel.
Reverse-Transcriptase (the most insidious of all viral proteins, that thing that crafts DNA from RNA)
Humans do have a special RT for extending telomeres, but it’s rarely expressed, and if a random cell is expressing it that’s a cancer waiting to happen.
There are retrotransposons that copy-paste themselves around the genome. But like… that’s basically a nasty virus that got lazy and whose deck is short a few cards.
Cytoplasmic replication
I am under the impression that this is not happening
In eukaryotes, I get the impression that DNA is usually not getting replicated out there in the cytoplasm, at least? DNA viruses usually have to do at least one of two things:
Get themselves into the nucleus somehow (via small size and/or transport proteins)
Carry their own replication proteins around with them in the virion, to produce those initial RNA transcripts that produce enough replication proteins for them to get by.
If the treatment involves entering the nucleus of fully-intact undamaged cells, or replicating itself (so really, either of these methods), the alarm bells in my head would be blaring.
But if it’s just circles of extracellular DNA… I’m now kind of conflicted and confused? How virus-like do you have to be to make that a viable thing to do?
Some other lingering points of confusion/research:
Plants use ambient restriction-enzymes to make being a random cytoplasmic DNA a hazardous game (on the assumption that ambient cytoplasmic DNA is usually viruses, and the non-viruses will have co-evolved with the particular restriction enzymes to make this system work). I don’t actually know that animals do, though. And you could always species-tailor it...
I also have no idea how efficient or inefficient extracellular transcriptase would be for producing mRNA transcripts. If it’s inefficient, you might have to use a pretty strong primer, and I find myself a tiny bit concerned about that in a long-lived human therapeutic.