Thursday, November 5, 2020

Gene Silencing vs. Gene Editing


CRISPR and Gene Editing are grabbing the headlines, but Gene Silencing and RNAi continue to keep investors interested.


Recent Nobel Prize awards for CRISPR pioneers Jennifer Doudna and Emmanuelle Charpentier have brought a renewed round of interest in the gene editing technology.  In addition to CRISPR-designed plants, trees, and therapeutics, gene editing is even being evaluated as a way to diagnose and test for COVID-19.


But editing genes is just one way to use genetic information to treat disease.  Gene silencing often doesn’t get the press that CRISPR or even gene therapy does, but its first FDA-approved product hit the market in 2018, a second one did so late last year.  Additionally Takeda and Arrowhead Pharmaceuticals recently announced a deal worth up to $1 billion to use the technology to treat a rare liver disease, RNAi developer Siranomics has completed  a $105 million D round, and leading RNAi supplier Alnylam’s two FDA approved RNAi therapies are on course to surpass $300 million in annual revenue this year, and the company could have its third therapeutic approved by the FDA by early next year.


Gene silencing, also known as RNA interference, or RNAi, leaves the existing DNA in the cell nuclei in place.  Rather than editing DNA like CRISPR or replacing it like gene therapy, it works by breaking up the messenger RNA carrying DNA instructions on its way to the cell’s ribosomes where it would otherwise produce proteins.  This could be particularly helpful in stopping cancer cells or other harmful cells from producing proteins and ultimately stopping their growth.


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                                                           RNA "sliced and diced" in a cell, Source: NIH



It should be noted that RNAi is very different than mRNA therapies like the one Moderna is trialing for COVID-19.  These produce healthy proteins, rather than inhibiting the transmission of disease-causing ones. 


One of the main benefits of RNAi is that there’s no potential health risk from changing the DNA.  The messenger RNA is intercepted and destroyed post-transcription, but pre-translation, so the impact is not permanent.   


RNAi is more of a defensive technique against disease while CRISPR can be seen as an offensive one.  It binds to the messenger RNA (mRNA) traveling through the cell in order to break it up.  But like a linebacker tackling a much smaller quarterback, RNA is fragile, and can come apart easily.  This has both benefits and drawbacks in how effective it can be preventing the unwanted effects of a particular gene expression.


RNAi depends on two variants of the nucleic acid: single stranded micro interfering RNA, or miRNA, and double stranded small interfering RNA, or siRNA.   siRNA works by attacking the target mRNA and triggering a RNA-induced silencing complex, or RISC.  This includes cleaving off a single strand sequence that is complementary to the messenger RNA and halts is progression.  miRNA, unlike siRNA, only has to be partially complementary to the messenger RNA, which also means it can reach a wider range of targets. A third variant, shRNA, or short hairpin RNA, functions similarly to siRNA, but has the added benefit of permanently altering the nucleus to produce the interfering RNA, allowing for more than a one time treatment.  The “hairpin” refers to its structure, which connects the ends of the sequence with a semicircular structure, not unlike the end of a paper clip.


With RNA being much more fragile than DNA, delivering RNAi therapies has proven to be far more challenging than simply encapsulating them in viral vectors as is typically done with DNA therapies.  Additionally, mRNAs need a shell that can penetrate a cell membrane in spite of both being negatively charged.   As a result, drug developers are increasingly looking to LNPs, or lipid nanoparticles, that can maintain efficacy and structure of RNA and offer lower overall risk than injecting viruses into the body.   


             mRNA Overview, Source: NIH


LNPs are tiny lipid bubbles that can encapsulate nucleic acids and other proteins.  Their main drawback traditionally has been their interactions with immune cells and their small size makes them easy to be swept out of the body by an immune attack.  However, the body does not develop antibodies against them as it does traditional viral vectors.  Moreover, their use was validated after Alnylam’s Onpattro (Patisiran) became the first FDA-approved RNAi therapeutic in 2018.  


While LNPs can be used to package DNA as well, interest in using them to deliver both RNAi and RNA therapies like Moderna’s COVID-19 vaccine has been growing dramatically since Onpattro was approved.  Moderna recently fought and lost an important patent battle against Arbutus over the LNP it could have been using in its COVID vaccine that is currently in Phase III trials.  Moderna has since said it has advanced its LNP technology beyond what it licensed from Arbutus, but the key point is that the delivery mechanism is a major economic and therapeutic component of the vaccine, not just the mRNA sequence.


The LNP research going into mRNA COVID vaccines could ultimately stimulate further advancements in its use for RNAi.  Delivery, which has traditionally been a challenge for RNAi is actually turning into a strength as more drug producers have started to look at LNPs as a safer alternative for encapsulating DNA than viral vectors. 


Existing RNAi therapies have been targeted at rare diseases, but advances in LNP vectors could help open up RNAi to wider scale uses not just in COVID vaccines, but oncology and other areas where delivery has been uncertain and less tested.  While gene editing might continue to grab the headlines, there’s a promising future developing for gene silencing.


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