Ribo-Club Encore

A deeper dive into specific scientific talks and few more observations

As I discussed in a previous substack, I attended an RNA conference in October and presented a poster of various issues of concerns with vaccine manufacturing. You can read about it here and my poster is here.

I thought I would write about some of the interesting and alarming individual presentations I attended. Of note, is that I brought along a notebook and wrote notes as the presenter talked. I noted quite a few young and older researchers doing the same. I commented to one sitting beside me and he said, yes he’s gone back to writing notes rather than using the computer because in the act of writing it down, you remember better. He had notes galore with drawing etc. This realization that computers are only a tool and useful for some tasks and not others gave me some hope that this initial enthusiasm for all things RNA will be tempered in the same way. I include a talk on this very thing in this post.

Deep in mind this post will be a bit scientific. Apologies in advance

Anna Blakely, UBC, Self-amplifying RNA vectors

Young, blond and ambitious, Anna Blakely gave a talk on saRNA, mostly restricted to the types of vectors used.

She emphasized that saRNA vectors in a vaccine context are dose-sparing compared to conventional mRNA vaccines. She said that the amount of RNA is directly correlated to frequency and severity of adverse events, so by decreasing the dose will hopefully decrease side effects. saRNA engages the ribosomes and thousands of copies are made so we can use 100X less of a dose. With respect to dose saRNA<circular RNA<modRNA. She claimes modRNA had protein expression for 5 days, circular RNA for 2 weeks and saRNA

-a whopping 40 days

Thus we can dose once monthly. Aint that grand? Useful for rare diseases and autoimmune diseases. She also looked at the different kinds of alphaviruses as a vector and found the genotype greatly impacts the immunogenicity of these vaccines. She believes vector engeenering will “open a new chapter of saRNA design” for more efficacious vaccines and therapies.

I don’t know where to go with this talk. Because saRNA is not codon-optimized and doesn’t use N-1-methylpseudouridine, she likely thinks it will be safe for autoimmune disease as you’ll avoid the frameshifting. Potential risks were not discussed. This was primarily a technical talk of how she designed these vectors. But, she also included this reference which is VERY interesting, and a very well done study.

Delivery vehicle and route of administration influences self-amplifying RNA biodistribution, expression kinetics, and reactogenicity

Here you can see the effect of route of administration impacting biodistribution AND then also if an LNP is used vs a polymer. Of note, the LNP used DID NOT INCLUDE DSPC (the helper lipid), it was ALC-0315:DOPE:Cholesterol:DMG-PEG-2000 and used DOPE a cationic lipid along with the ionizable lipid ALC-0315. This is because YOU NEED A DIFFERENT LNP TO TRANSFECT THE saRNA VACCINE. This saRNA stuff is a big rabbit hole.

John Bell, University of Ottawa, Oncolytic viruses (RNA based viral vectors for cancer therapy)

John Bell has been around for a long time and is well respected in the field of oncolytic virus research.

Many viruses package miRNAs into exosomes which then deliver their cargo to adjacent uninfected cells so that any anti-viral activity by the cell can be blocked. So they used this natural virus behaviour to enhance their oncolytic viral vectors. This means they developed miRNAs that were active within tumor cells (but not normal cells) which made the oncolytic virus grow more. They used this miRNA in combination with a drug to kill tumor cells. But what makes this really interesting is that these oncolytic viruses can reprogram exosomes making the tumor “act as a virus.” These exosomes contain all kinds of genetic material so that packaging the miRNA can modify the tumor cells. He said the development of amplifying pseudo-virus particles in exosomes can deliver therapeutic payloads.

His goal is to “design therapeutic strategies that turn viruses from stealth pathogens to finely tuned ‘viroceuticals’ that initiate both viral-mediated and immune mediated attacks against cancer.”

What could go wrong? Like these exosomes carrying miRNA? Do the vaccines act similarily? Do these patients isolate for “shedding?” after getting these products?

John Mattick, UNSW Sydney- Enhancers are Genes

Say what? His talk was beyond me but he said it is estimated that there are hundreds to thousands of enhancers in the human genome, sometimes clustered as “super enhancers.” Enhancers are genetic loci that control or enhance target genes which can be huncreds of kilobases away. The recognition that enhancers are genes explains this g-value enigma among other stuff.

AI tells me

The G-value paradox is a biological puzzle that describes the disconnect between the number of protein-coding genes in an organism and its biological complexity. For example, the nematode Caenorhabditis elegans has a similar number of genes to a human, even though it's made up of only a thousand cells.

So enhancers as genes could also explain cell-specific expression, genome wide incidence of transcription start sites and other stuff I don’t understand, lol. Which brings me to the SV40 promoter/enhancer. Gulp. If it doesn’t promote cancer, what other stuff is it doing?

Mattick is a big name in RNA biology. He has worked to

elucidate the hidden role played by non-coding RNA. He showed that regulatory information scales non-linearly with function in integrated complex systems and that the vast tracts of intronic and intergenic sequences in the genomes of humans and other complex organisms, previously thought to be junk, are transcribed in a developmentally regulated manner. His insights have led to the emerging realization that the majority of the human genome specifies a sophisticated internal RNA regulatory network that directs the trajectories of differentiation and development.

I think we have only scratched the surface with the possible actions of a SV40 enhancer/promoter in our cells.

He included a recent article on SYNTHETIC BIOLOGY

Building better mRNA for therapeutics

What does that mean?

1. branched poly-A tails (and I though the segmented one was bad enough)

2. different kinds of 5’ caps including a ‘branched cap’ and other changes to the mRNA backbone

Here is a nifty and horrifying graphic describing this

Totally synthetic mRNA. Like making a totally synthetic drug based on an herb or natural chemical. Only this is nucleic acid.And I thought he was the most reasonable of all the big names.

Steve Whyard, University of Manitoba, RNAi to control pest insects

So this prof has been using RNAi (like small interfering RNA that is in Onpattro) to control important agricultural pests. It is a NEW FRONTIER IN AGRICULTURE.

Hmmm, it was pretty interesting and the least scary of many of the talks. It is very species specific since these RNAi are very very small. About 20 nucleotides. They are looking at its effects on other non-targeted species like bacteria, soil insects and even birds. So far so good. But it needs long term study imho.

The issues are application. No LNPs here, they dont need to get into the leaves. Just spray it on for the insects to eat. But timing is critical. They don’t last long and get easily washed off. Plus the insects multiply too fast and get resistance pretty fast. Not sure this is going to work, but it bears keepin an eye out for this. Also, this is not mRNA so no protein is being made. The RNAi just interferes with critical gene expression. Very much like some pesticides.

There was also this guy from Bayer US, Dr William Moar who introduced

SMARTSTAX PRO which is already approved and in use in the US

So RNAi technology is already being used in the environment.

Dan Herschlag, Stanford University, Current-day lessons (cautionary tale)

This talk was the only one where it was pointed out that “scientists tend to maintain enourmours optimism for the future, perhaps paradoxical with respect to the skepticism inherent in the scientific method.“ Ya think?

He reminded the attendees that euphoria at using ribozymes to target proteins didn’t work out and led to marginal drug products. A post mortem analysis is required on this research so it can be used now as pre-mortem analysis to help direct scientific initiatives.

He recommended standards and roadmaps FIRST to balance current optimism in the medical applications of RNA and scepticism needed to carry out effective research.

Life is complex. Genomics is dominating now which gives cellular information while biochemistry is quantitative. A bridge between the two is required in his opinion. Basically he said you need binding affinities, and binding concepts. Uh like kinetics?? And dynamics?

This was music to this pharmacist’s ears. BIOCHEMISTRY, PHARMACOLOGY and KINETICS, LOL.

Unsurprisingly, there were no questions.

He directed all of use to read THIS paper. From 1964

This is Platt’s warning. True today as it was 60 years ago

Are RNA scientists willing to work at thinking? Or are they just methodologists?

THere were many other very interesting talks. On internal ribosome entry sites. Aptamers. Etc.

Thanks for reading, and pray the rosary.