Encoding therapies: RNA-based drugs reshaping healthcare

RNA-based therapeutic drugs have been recently advancing clinical trials and into the healthcare industry. RNA, or ribonucleic acid, is a fundamental biomolecule essential for the expression of genes encoded in the genome. In the recent years, RNA-based drugs have gained considerable attention because when introduced into cells it is possible to direct them to produce specific proteins with therapeutic activity. For the purposes of this article, RNA-based drugs are those that are strictly composed of the nucleoside sequences found in natural RNA that once administered can either be translated into a therapeutic peptide, as is the case of messenger RNA (mRNA), or remain untranslated to interact with cellular processes. Of note, while the RNA therapeutics field also considers antisense oligonucleotides (ASOs), these are composed of nucleosides found in DNA as opposed to just in RNA, and are thus beyond the scope of this article and to be addressed in a separate article. In brief, the following insight article explores the key aspects of RNA-based therapeutics, including its mechanisms, applications, challenges, market trends, and future directions. 

RNA-based therapeutics have the potential to treat a wide range of diseases, including infectious diseases, cancer, and genetic disorders that were previously considered untreatable. The use of RNA as a cell therapy involves designing synthetic RNA molecules that mimic the structure and function of natural intra-cellular RNA molecules. Specifically, messenger RNA (mRNA) molecules encoding specific proteins can be used as a vaccine or to restore cellular function associated with genetic diseases. For example, mRNA-based vaccines can be designed to encode peptides that function as antigens, which stimulate the immune system to produce a specific immune response against a virus or bacteria. Additionally, mRNA-based therapeutics can be designed to encode functional proteins capable of restoring cellular functions disrupted in disease due to missing or dysfunctional proteins. This approach to protein-replacement therapy has shown promising results in the treatment of genetic disorders such as cystic fibrosis and muscular dystrophy, in which patients lack functional proteins due to indels and point-mutations. Alternatively, other types of RNA-therapeutics can be designed to bind to specific intra-cellular mRNA sequences, leading to the degradation of the mRNA and reduction of the expression of the corresponding protein. Finally, RNA-therapeutics can also be designed to target non-coding RNA molecules, such as microRNAs, which play a crucial role in regulating gene expression and are involved in various diseases and cancer.

Considerable amount of work has been performed to enhance the biocompatibility of RNA-based therapeutics manufactured by pharmaceutical corporations. RNA administered by itself is highly immune-stimulatory due to surveillance pathways intrinsic to the cell meant to detect the presence of viruses¹. The identification of exogenous nucleic acids in the cell is accomplished by receptors that are part of the innate immune system, such as the endosomal membrane-bound Toll-like receptors (TLRs)². Therapeutic RNA is typically synthesized with polymerases through a method termed in-vitro transcription (IVT). In 2010, two research groups working independently found that inserting pseudouridine into RNA molecules facilitated evasion of the typical degradation machinery of exogenous RNAs in mammalian cells^3,4, thereby increasing translational efficiency of the encoded peptide. Pseudouridine is one of the many RNA modifications that naturally exist so that the cell can differentiate intra-cellular RNA from exogenous viral RNA. In 2017, a collaborative group working with Moderna $MRNA, a leading biopharmaceutical corporation focused on mRNA-based therapeutics, demonstrated that incorporating N1-methylpseudouridine (m1Ψ) further increased the stability and translational efficiency of mRNA molecules⁵. Moderna has since incorporated m1Ψ modifications into all of its mRNA-based therapeutics, including its COVID-19 vaccine, elasomeran, also known as mRNA-1273 and commercially known as Spikevax. The promising results of using m1Ψ in mRNA vaccines has led to further exploration of additional naturally-occurring nucleoside modifications (e.g. 5-methylcytidine or 5mC) that could in combination enhance the biocompatibility of all RNA therapeutics. This biocompatibility is of particular importance for those RNA therapeutics that may require repeat dosing, because immune memory could limit the effectiveness of the drug product.

RNA-based drugs face several additional challenges, with one of the biggest being the delivery of RNA molecules to target cells. RNA is a large, easily degradable, and negatively charged molecule that makes it difficult for them to cross the cell membrane. To overcome this challenge, various molecular tools have been developed over the past 20 years, such as lipid nanoparticles (LNPs) and viral vectors. Currently, LNPs represent the most suitable system to date for RNA-based drug delivery⁶. Considerable amount of work has been performed to optimize encapsulation efficiency of the RNA-LNP synthesis process, which is easily scalable and can be designed to be targeted at desired cell types by conjugating ligands of cell-surface receptors. However, it is worth noting that components of current LNP formulations are known to be immunogenic, thus inducing systematic inflammation^7,8. While inflammation induced by LNPs is thought to contribute to the efficacy of mRNA-based prophylactic vaccines by acting as an adjuvant, it further poses a problem with modalities intended for other types of RNA-based therapeutics, specially those that require multiple doses. Finally, another challenge imposed by the immune system towards the use of RNA-based therapeutics is the presence of double-stranded RNA molecules (dsRNA), which are impurities resulting from the IVT manufacturing process. Similar to the immunogenic effect of unmodified RNA, the presence of dsRNA impurities activate TLR surveillance pathways meant to detect viral genomes during infections⁹. Overall, the causes for immunogenicity stemming from the various aspects of currently manufactured RNA-based therapeutics still pose challenges to the industry.

While these challenges must be addressed to ensure the safety and efficacy of RNA-based therapeutics, several biopharmaceutical companies around the world, both large and small, are currently involved in developing them in their portfolios. To recall, back in 2018, Alnylam Pharmaceuticals successfully commercialized patisiran, the first FDA-approved RNA-based therapeutic. It is worth noting that this approval came after Alnylam’s blockbuster failure with siRNA drug revusiran, which caused more deaths in the therapeutic arm, suggested to have been caused by toxicities mediated by non-specific TLR activation^10,11. Thus, the first wave of RNA-based drugs mostly failed clinical trials due to the TLR-mediated toxicity problems described earlier in this article. However, the development and commercialization of mRNA-based prophylactic vaccines used for mitigating the coronavirus pandemic has recently reigned investor confidence and paved the way for wider industry acceptance of RNA-based therapies. As of 2023, there are more than 90 biopharmaceutical companies between the public and private markets developing RNA-based therapeutics. Most therapeutics are currently between preclinical development and phase 1 trials, and only a handful, exactly seven drugs, have made it to the approval stage (Table 1). Of these seven drugs, four are interfering RNAs (i.e. siRNAs), and only two are mRNA-based drugs, both the mRNA drugs being the prophylactic vaccines for SARS-COV-2.

Table 1: Approved RNA-based drugs up to date

Overall, the advancements made in the understanding of RNA biology and the development of novel delivery mechanisms have opened up a new frontier in drug discovery and commercialization. These advances as well as several setbacks have enabled the industry to pursue strategic engineering of RNA molecules to ensure their efficacy and safety. As a result, the RNA-based drug industry is expected to play a significant role in reshaping healthcare in the coming years, potentially leading to the development of new treatments for a range of diseases and conditions which were previously thought to be untreatable.

References

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