The Rise of RNA: Translating Challenges into Opportunities
From diagnostic biomarkers to innovative therapies, RNA holds great potential in revolutionizing healthcare. However, we have a long way to go before we recognize RNA’s full potential. The main problem stopping us from recognizing RNA’s full potential: RNA is challenging to work with due to technical difficulties in handling and storage, but promising methods are emerging.
The central dogma of molecular biology states that genetic information flows in one direction: from DNA to RNA to proteins.
While DNA and protein have entered our everyday language, RNA has remained the neglected middle sibling until its recent emergence as a pivotal molecule in clinical settings due to its versatility.
From diagnostic biomarkers to innovative therapies, RNA holds great promise in revolutionizing healthcare. There are currently a few approved RNA drugs and a dozen more in phase III clinical trials, but we have a long way to go before we recognize RNA’s full potential [Zhu et al. 2022]. The main problem stopping us from recognizing RNA’s full potential: RNA is challenging to work with due to the technical difficulties in handling and storage.
Here, we delve into the clinical importance of RNA, the hurdles in working with it, some emerging solutions, and the rising significance of RNA in healthcare.
A Brief Refresher
First, a brief primer on RNA for those who haven’t worked with it before. If DNA is a cookbook, the letters in the cookbook are the As, Cs, Gs, and Ts of DNA that tell your body what to cook. You don’t need to read every recipe (gene) in the cookbook at every point in time. Some recipes are made only once, while others are made every day for your entire life.
Your body makes a recipe by reading the recipe (transcription) onto a temporary recipe card (RNA). The body then reads that temporary recipe card (translation) and usually makes the recipe (proteins). However, these recipe cards can do more than just instruct the body on how to make proteins; they can even silence recipes that are being made (small interfering RNA). We’ll now take a deeper look at how various types of RNA are key to helping us understand diseases and dysfunctions, and even develop therapeutics.
Importance of RNA in Clinical Settings
RNA’s significance in clinical applications stems from its diverse functions [Byron et al. 2016]. One of its key roles lies in gene expression regulation. Various RNA species, including messenger RNA (mRNA), microRNA (miRNA), and long non-coding RNA (lncRNA), orchestrate gene expression, influencing cellular processes crucial for health and disease. For instance, dysregulated miRNAs have been implicated in cancer progression [Hussen et al. 2021], while lncRNAs modulate immune responses and cellular differentiation [Peltier et al. 2022].
Moreover, RNA is a valuable source of biomarkers for disease diagnosis and prognosis. Detecting specific RNA signatures, such as circulating tumor RNA, can aid in early cancer detection and treatment response monitoring. Furthermore, RNA biomarkers offer insights into disease subtypes and progression, enabling personalized therapeutic interventions [Sasso et al. 2022]. As one recent example, just this month (May 2024), the FDA approved ColoSense, an mt-sRNA screening test for colorectal cancer, the second deadliest cancer in the United States. This is particularly significant because “millions of eligible Americans do not get screened due to a lack of access to or avoidance of invasive options like colonoscopies” [Geneoscopy Blog, May 2024].
However, RNA is more than just a biomarker; it can also be used as a treatment, further underscoring its clinical importance. RNA interference technology harnesses small interfering RNAs (siRNAs) to silence target genes implicated in disease [Chen et al. 2019]. Additionally, mRNA vaccines like the Moderna and Pfizer COVID-19 vaccines represent a groundbreaking approach in vaccine development, offering rapid and adaptable platforms for combating infectious diseases and even cancer [Vishweshwaraiah & Dokholyan 2022].
In short — RNA is an incredibly versatile molecule that not only allows us to gain insights into disease processes, but also is a tool we can harness to combat and even prevent disease.
Challenges and Solutions for Working with RNA
RNA molecules are inherently unstable, prone to degradation by (a) ribonucleases (RNases) found throughout the environment, and (b) physical degradation. By enabling a longer shelf-life of RNA, we can enable RNA to be used for future research and downstream applications.
RNases are constantly shed by the humans that work with RNA. Wearing sterile gloves and gowns may not protect samples from RNase contamination, for the RNase shed from your skin cells can land in a sample, destroying the RNA inside in short order [Vincent et al. 2009].
And even if a sample is free from RNases, it’s still less stable than DNA because of its single-backbone structure, compared to DNA’s double-backbone [Chheda et al. 2023].
To mitigate these risks of losing RNA integrity, researchers employ various strategies. Decontamination reagents like RNase AWAY™ are used to destroy RNases during the preparation and handling of RNA. There are a few options for preservation after RNA isolation. One of the easiest methods is to add a stabilizing agent like RNAlater, which destroys lingering RNases. RNAlater can preserve RNA in solution or while it’s still in tissues for up to a week at room temperature, up to a month in a refrigerator, or longer when frozen. Other preservation methods include Zymo’s RNA Shield, which promises ambient temperature preservation of RNA for at least one month, and RNAES [Hernandez et al. 2022] which demonstrates preservation of RNA for 35 days.
Others simply freeze the tissue or other specimen type that contains RNA and hope the RNA will still be there when they try to access the RNA, though this often doesn’t preserve the RNA very well, and reports show pronounced declines in RNA quality within 24 hours [Huang et al. 2017].
Alternatively, they try to extract RNA from a sample preserved with other methods, like fixed-formalin paraffin-embedded (FFPE) tissues held at room temperature. However, FFPE is notoriously bad at preserving nucleic acids long-term, often only adequately preserving small fragments of RNA for up to 8 years [Yi et al. 2020].
To address this, Cache DNA has developed an encapsulation chemistry that shields RNA from degradants, with preliminary data showing no measurable degradation over two months at room temperature and an anticipated half-life on the order of decades.
Summary
Despite the challenges, RNA is an incredibly promising biomolecule whose potential is still being realized. RNA-based therapies hold incredible promise in treating a myriad of diseases, from genetic disorders to infectious diseases and cancer. The approval of mRNA COVID-19 vaccines is just one example of the incredible potential of RNA-based interventions.
Furthermore, high-throughput sequencing and single-cell sequencing technologies have helped the field unravel the complexity of RNA regulation networks, and continue to reveal novel therapeutic targets and biomarkers.
To realize the full potential of RNA in healthcare, we will need to overcome challenges in working with and storing RNA effectively, and promising new preservation and analysis technologies may help us achieve that vision.
