Gapmers represent an advancement in molecular biology, offering a precise method to influence gene expression. These synthetic molecules interact with specific genetic instructions within cells, providing a valuable tool for fundamental research and new treatments. Their ability to selectively silence genes holds promise for understanding biological processes and addressing various health conditions.
What Are Gapmers?
A gapmer is an antisense oligonucleotide (ASO) with a chimeric structure. It consists of a central “gap” region of DNA-like nucleotides, flanked by modified RNA-like nucleotides. These flanking modifications often include 2′-O-methoxyethyl (2′-MOE), 2′-fluoro (2′-F) groups, or locked nucleic acids (LNA), which are RNA analogues “locked” into an optimal base pairing conformation. This design provides stability and binding affinity to their target RNA molecules.
The DNA gap is composed of 8 to 10 DNA nucleotides, with flanking regions of 2 to 5 modified nucleotides on each end. This arrangement allows the gapmer to maintain affinity for its target messenger RNA (mRNA) and resist degradation by nucleases, enzymes that break down nucleic acids. Gapmers can also incorporate phosphorothioate (PS) groups in their backbone, which improves cellular uptake and provides resistance to degradation.
How Gapmers Work
Gapmers work by activating a naturally occurring cellular enzyme called RNase H. The DNA “gap” region forms a hybrid duplex with a complementary target messenger RNA (mRNA) sequence. This DNA/RNA hybrid structure serves as a recognition signal for RNase H.
Once RNase H binds to this gapmer-mRNA duplex, it cleaves the RNA strand of the hybrid. This cleavage leads to the degradation of the target mRNA, preventing the cell from translating that mRNA into a protein. The resulting RNA fragments, which lack protective caps and tails, are then rapidly broken down by other enzymes in the cell, ensuring an efficient and sustained gene silencing effect. The sequence-specific interaction between the gapmer and its target allows for precise control over gene expression.
The gapmer remains intact after cleavage, allowing it to participate in multiple rounds of binding and degradation of target mRNA molecules. This catalytic action means a single gapmer molecule can degrade many mRNA copies, enhancing its potency. This specific interaction ensures only the intended mRNA is targeted, minimizing off-target effects or toxicity.
Therapeutic Applications of Gapmers
Gapmers show potential in therapeutic applications, particularly for diseases rooted in genetic dysregulation. Their ability to precisely silence genes makes them suitable for conditions where the overproduction of a harmful protein or a mutated gene contributes to disease pathology. Several gapmer-based therapies have received regulatory approval, with many more undergoing clinical trials.
For instance, mipomersen (Kynamro) is an approved gapmer therapy used for familial hypercholesterolemia, a genetic disorder characterized by very high cholesterol levels. Inotersen (Tegsedi) is another approved gapmer, used to treat hereditary transthyretin amyloidosis, a neurological condition. Additionally, volanesorsen has been conditionally approved in some regions for familial chylomicronemia syndrome, a rare genetic disorder affecting lipid metabolism.
Gapmers are also being investigated for other conditions, including cancers, Huntington’s disease, myotonic dystrophy, and infectious diseases like Japanese encephalitis virus. By reducing the production of specific proteins or restoring normal protein levels through targeted mRNA degradation, gapmers offer an approach to address the underlying causes of disease.
Distinguishing Gapmers from Other Genetic Therapies
Gapmers differ from other genetic therapies due to their mechanism of action, particularly their reliance on RNase H. While other nucleic acid-based drugs like small interfering RNAs (siRNAs) also lead to mRNA degradation, they do so through different cellular pathways. SiRNAs are double-stranded RNA molecules incorporated into the RNA-induced silencing complex (RISC), which then cleaves the target mRNA.
Other antisense oligonucleotides (ASOs) do not activate RNase H. These ASOs might work by physically blocking the ribosome to prevent protein production (steric blocking) or by altering how messenger RNA is processed (splicing modulation), without degrading the target mRNA. The DNA gap region in gapmers recruits RNase H. This direct enzymatic degradation of the target mRNA by RNase H provides an effective method for gene silencing, offering advantages compared to mechanisms that block translation or modify splicing.