Delivering a New “Post-COVID” Generation of RNA Therapeutics

The COVID-19 pandemic has turned RNA into a household word, but what new innovations and changes will we see in the RNA therapeutics space going forward and how many will actually reach the clinic?

The last couple of years proved a turning point for biotech companies such as BioNTech and Moderna, with a focus on developing vaccines and therapeutics based on messenger (m)RNA. The rapid approval and rollout of the COVID vaccines saved hundreds of thousands of lives, generating enormous publicity and profits for the companies and their collaborators and the field in general.

Of course, while RNA is now much discussed, even among non-scientists, there is much more to the field than mRNA vaccines alone. RNA technology for use in medicine was also under development for a long time before the pandemic.

First considered a possibility in the 1960’s, it took until 1990 for the first RNA therapeutic proof of concept experiment to take place. Researchers demonstrated that mice injected with a certain mRNA resulted in the animals producing the protein encoded by the mRNA. This was the start of the journey to get RNA therapeutics to the clinic.

The 2006 Nobel Prize in Physiology or Medicine was awarded to Andrew Fire and Craig Mello “for their discovery of RNA interference – gene silencing by double-stranded RNA.” This opened the door to the development of RNA interference (RNAi) based therapies, although it was not an easy path to the market.

Alnylam, the first company to have an RNAi therapy approved (patisiran in 2017), had many setbacks before finally having their first product approved by the FDA. For example, an early RNAi candidate, revusiran, reached Phase III trials for treatment of the rare disease hereditary transthyretin-related amyloidosis (hATTR) but the company had to be scrapped after 18 patients died during the trials. However, they overcame these difficulties and now have a number of RNAi therapies on the market.

Driven perhaps by early successes of companies like Alnylam and certainly influenced by the pandemic, there has been a dramatic increase in the number of new RNA therapeutics companies founded in the last few years.

There are new types of RNA being used as therapeutics, such as circular, self-replicating, and transfer (t)RNA, but advances in delivery and targeting are also allowing researchers and companies to target new diseases and conditions such as pre-eclampsia. Geoff Nosrati, is chief business officer of one such company, Nutcracker Therapeutics. “It’s exciting to be at the cutting edge of mRNA, we’ve had this enormous worldwide experiment in mRNA vaccination, which turned out to be very, very successful,” he told Inside Precision Medicine.

“Now I think there’s a challenge on all of the RNA companies to figure out the many different ways RNA can be exploited therapeutically, not just in vaccines.”

The many types of RNA

A recent development in the RNA therapeutics field is an expansion on the different types of RNA being developed for therapeutic purposes.

Initially focused largely on RNAi, and subsequently mRNA, new startups are applying a combination of natural inspiration with genetic engineering technology.

Orna Therapeutics is one of several recently founded biotechs, including Laronde, focusing on circular RNA, mostly for treating cancer. The technology was created by Alex Wesselhoeft and colleagues during his PhD at MIT. “Circular RNA is something that occurs in all of our cells. And its function is a little bit mysterious. But the one thing that’s known about it is that it’s more stable than the linear RNA from which is derived,” explained CEO Tom Barnes.

The company specializes in developing fully engineered, circular RNA therapeutics, which Orna calls oRNAs. According to the company, these RNAs have several advantages including high levels of protein expression, simple and cost-effective manufacturing, and more efficient delivery to targets, as more of the circular RNA’s can be packaged into lipid nanoparticles than linear RNAs.

“Most of the challenge in making full length mRNA is the fact that it’s hard to separate from all the other junk,” Barnes told Inside Precision Medicine. Adding, “because of the way we make circles, there are no short species, all circles are obligately full length.”

Investors seem to believe in the potential of Orna’s technology, as last month the company announced a $221 million Series B financing and signed a big collaboration deal with Merck including an upfront payment of $150 million and up to $3.5 billion in development, regulatory, and sales milestones.

Another type of RNA being incorporated into therapeutic, as well as vaccine, pipelines is self-replicating or self-amplifying RNA. Again, a number of startup companies are working on developing this format, such as Arcturus Therapeutics, Chimeron Bio, and Replicate Bioscience.

“With conventional mRNA, you’re delivering an instruction manual to the cell that tells you how to produce a protein. With self-replicating (sr)RNAs, it’s like co-delivering a copy machine into the cell along with an instruction manual. You get that increased amount of protein that sticks around. So, it’s much easier to have a more durable therapeutic effect,” said Replicate CEO, Nathan Wang.

No srRNA therapies have yet reached the market, but the theoretical advantages are that lower initial dosing levels are needed, and that therapeutic effects could last for longer meaning fewer dosing sessions are needed overall.

“For the proteins we administer, some of them need to be administered daily; with this kind of long-lasting protein expression, you may be able to switch that to monthly, or quarterly,” says Wang.

Therapeutic transfer (t)RNA is a further addition to the ever-expanding pantheon of RNA technologies being using to create advanced therapeutics. One of the newer options on the RNA therapeutics scene, several startups have launched in this area over the last year including Alltrna, Shape Therapeutics, Tevard Biosciences, and hC Bioscience.

Serial entrepreneur Leslie Williams, now CEO of hC Bioscience, was on the look out for a new project and she was intrigued by a paper that came out in late 2019, describing the technology that is now the foundation of the company.

As much as 15% of all genetic disease can be accounted for by one type of mutation, known as a ‘nonsense’ mutation. These mutations create premature termination codons (PTCs). This means instead of a normal amino acid being added to a protein during translation, it stops being formed abnormally early and can result in protein dysfunction and disease.

hC Bioscience is aiming to target these mutations using tRNA in both cancer and rare diseases. “We target the proteome, not the genome,” says Williams. “Our lead platform is what we call Patch, with which we’re targeting PTCs, and we in essence restore protein function.”

The importance of delivery and targeting

All the experts agree that good delivery and more advanced targeting methods are crucial for future RNA therapeutics to succeed.

“Everybody realizes now that delivery is the thing that becomes rate limiting to everything you want to do,” emphasizes Barnes. “You can have the world’s best payload, but if you don’t have delivery, you don’t have anything, because a very large number multiplied by zero is still zero!”

Methods of delivery for RNA therapeutics vary depending on the type of RNA. For example, RNAi therapies, such as those developed by Alnylam, are small enough to not require transport in lipid nanoparticles (LNPs), a commonly used method of delivery. But they still need help to get to their target. Instead, N-acetylgalactosamine (GalNAc) small interfering (si)RNA conjugates are now widely used as a way of transporting RNAi therapies.

“From about 2006 until Moderna got going again, no one was doing LNPs really anymore, because no one was trying,” explained Barnes. However, in contrast to RNAi-based therapies, mRNA-based vaccines are bigger and do require encapsulation in LNPs or a similar delivery molecule to get to their target in one piece. All the approved COVID-19 mRNA vaccines use LNPs.

As the urgency of the pandemic has started to wane, various legal disputes have started to surface around use of LNP technology by the big RNA therapeutics companies, really highlighting how important having a good, patent protected delivery method is for this type of technology.

Some therapies, such as the mRNA-based cell reprogramming and gene editing technologies designed by Exacis Therapeutics, are designed in the lab, which can make the process easier.

“Delivery is really much more of an issue when you’re delivering it to a patient,” says Greg Fiore, Exacis CEO. “With the vaccines, or with the Alnylam products, that’s the real challenge, because all these therapies like to go to the liver preferentially. The blood supply from the GI tract passes through the liver first. So if you want to bypass the liver it’s not the easiest thing in the world.”

Suzanne Saffie-Siebert, CEO and founder of U.K.-based SiSaf, has worked on delivery methods for genetic therapies for a long time and has pioneered a special type of LNP including silicon. She explained that classic LNPs have their problems, as they are not always very stable and can spontaneously rupture or expand in size depending on environmental conditions.

“Inorganic material can be very good for delivery systems… the issue with this sort of inorganic material is safety,” says Saffie-Siebert. “Bioabsorbability is a key factor if we want to make these inorganic materials safe and potentially as good as LNP products in terms of the usability and FDA approval and safety for patients.”

SiSaf’s Bio-Courier system combines inorganic silicon with organic materials to make an optimized delivery particle that does not require ultra-cold storage and minimizes wastage during manufacturing.

“Normally, RNA encapsulation is during the process of vesicle formation. You introduce the RNA in the manufacturing part when you’re still processing the vesicles, which means up to 30% of your RNA is degraded through the process of heat and filtration. We do not have that process. RNA is introduced to the process at the end, not within our process.”

More diverse targeting is something that is also becoming easier, meaning that therapies do not necessarily have to go through the liver and more complex conditions can be treated. For example, siRNA biotech Comanche Biopharma is aiming to tackle the large unmet need of pre-eclampsia using RNA therapeutics.

“An siRNA is uniquely suited for this target,” explains Mike Young, co-founder and president of the company. “We’re going after sFlt1, that’s a soluble, anti-angiogenic factor. When the placenta experiences ischemia, it wants to remodel the vasculature and it produces Flt1. This angiogenic factor is inadvertently promoting the overexpression of sFlt1, which is antiangiogenic. The problem with that for a small molecule or antibody is their ability to discriminate between the two because they are virtually identical, other than one being membrane bound. It would knock out both, and that would be a very, very bad thing.”

Omega Therapeutics is taking a different approach to targeting and is using epigenetics to target DNA. “Our genome broadly is organized into roughly 15,000 or so insulated genomic domains, which contain essentially all of our genes and the regulatory elements that control them and act really as nature’s filing system for genes,” explained Thomas McCauley, chief scientific officer at the company.

McCauley and colleagues are designing what they call Omega Epigenomic Controllers, which are programmable mRNA medicines that have a DNA binding domain that targets these insulated genomic domains and an effector protein that makes very, very specific epigenetic marks.

Exploiting the silver lining

What does the future hold for RNA therapeutics? A silver lining of the COVID-19 pandemic is the positive impact it has had on the world of RNA vaccines and therapeutics. Many companies have sprung up over the last couple of years, doubtless hoping to capitalize on the current interest in RNA, but whether or not they manage to bring products to the market remains to be seen.

“Five years ago, mRNA was considered sort of an esoteric approach from a therapeutic perspective. And now, it’s a household word,” agrees McCauley.

“I think that being able to access those additional therapeutic areas, is really something that we’re going to be seeing a lot of in the next five to 10 years, with the way the technology is moving,” adds Wang. “Oncology, and immunology spaces, especially are going to be really ripe for disruption with this type of technology.”

New tools such as Orna’s circular RNA and Replicate’s self-amplifying RNA technology, as well as new approaches such as hC Bioscience’s tRNA technology, along with many others, seem certain to expand the number of therapeutic options available and also to improve other methods already in the clinic.

For example, Orna has ambitions to improve current cancer immunotherapy options using its circular RNA technology and a new version of CAR T-cell therapy with less patient side effects. Part of the research at the company has also revealed they can make full length dystrophin protein using the circular RNA, something the company is now exploring as a possible treatment for muscular dystrophy.

Williams advocates having a diverse team of experts to help get these advanced therapies to the clinic. “The computational side, the translational biology side, as well as the delivery have been the Achilles heel,” she emphasizes.

Certainly, with the current litigation around LNP use and the importance of getting the therapy to the right area in one piece, accurate and efficient delivery and targeting are crucial. But seemingly straightforward logistical factors can also hold things up if not taken into consideration.

“We have this fast-moving train of RNA companies, without probably the full infrastructure required around manufacturing and distribution,” says Nosrati.

“I’m not sure that all of the huge RNA factories that are well designed for massive scale COVID output are really well designed for the production of the tiny little batches you’ll need for clinical development. We’re going to find some bottlenecks, probably around just getting all of these new therapies into the clinic in terms of producing the GMP grade material. That’s kind of a boring unsexy problem. But it is a huge problem.”

Helen Albert is senior editor at Inside Precision Medicine and a freelance science journalist. Prior to going freelance, she was editor-in-chief at Labiotech, an English-language, digital publication based in Berlin focusing on the European biotech industry. Before moving to Germany, she worked at a range of different science and health-focused publications in London. She was editor of The Biochemist magazine and blog, but also worked as a senior reporter at Springer Nature’s medwireNews for a number of years, as well as freelancing for various international publications. She has written for New Scientist, Chemistry World, Biodesigned, The BMJ, Forbes, Science Business, Cosmos magazine, and GEN. Helen has academic degrees in genetics and anthropology, and also spent some time early in her career working at the Sanger Institute in Cambridge before deciding to move into journalism.