The use of RNAi as a therapeutic approach has developed faster than anyone can imagine, but one challenge remains.
Progress in the life sciences over the last half-century seems eerily familiar to an Olympic track and field event, with molecular biology coming in first place in every race. As the most successful Olympiad over the last 50 years, molecular biology, as a discipline, has spawned many new fields including genomics, proteomics, bioinformatics, as well as an entire industry: biotechnology. Among the more groundbreaking discoveries in molecular biology over the last 20 years was that of RNA interference (RNAi), a biological mechanism for regulation of gene expression found in nearly every organism, and based on the biochemical activity of small interfering RNA (siRNA). The mechanism of RNAi is very well known and consists of the complementary base-pairing of a specific siRNA with a messenger RNA (mRNA) target. The science and mechanism of RNAi led to the awarding of the 2006 Nobel Prize in Medicine to Andrew Fire and Craig Mello. Of course, this mechanism has also been exploited as a therapeutic approach by the pharmaceutical and biotechnology industries.
RNAi has been used quite extensively to target genes associated with cancer, many of which have been identified as playing a role in tumorigenesis and in the survival or proliferation of cancer cells; these genes have also been referred to as cancer biomarkers. The use of RNAi to knock down expression of cancer biomarkers have legitimized this approach as a bona fide therapeutic weapon and has led to a push to identify novel tumor drug targets and the development of innovative siRNA modification and delivery strategies. siRNA delivery remains the only hurdle in the race to create the perfect therapeutic.
To modify, or not to modify
Life Technologies Corporation (Carlsbad, Calif.) is a big fan of modifying siRNA molecules, especially synthetic duplexes. Invitrogen, part of Life Technologies Corporation, produces two flavors of siRNA: unmodified and chemically-modified. The unmodified version consists of 19- to 21-mer duplexes with overhangs. “[The unmodified molecules] are out of favor because most people doing siRNA work want to use chemically-modified molecules,” says Christofer Cunning, PhD, senior manager, Market Development, Molecular Biology Reagents at Life Technologies Corporation. Chemically-modified siRNAs first became commercially available with Invitrogen’s Stealth siRNA products. With the acquisition of Ambion through the Applied Biosystems merger, Life Technologies Corporation has also added the Silencer Select siRNA product, which is also a chemically-modified siRNA. Researchers could use either product for in vitro and in vivo studies.
“With Silencer Select, the chemical modification is public information and that is an LNA-modified molecule. What is not released is the position of LNA on Silencer Select siRNAs,” says Cunning.
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Figure 1: Optimization for siRNA delivery among the cell lines. Real-time RT-PCR targeting of HPRT1 revealed the best electroporation conditions considering cell viability and siRNA delivery for each cell line. Conditions with the most significant knockdown were repeated three times. (Source: Jessica Alluin of City of Hope)
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So why is chemical modification of siRNA important? siRNA heteroduplexes are composed of a sense (passenger) strand and an antisense (guide) strand. Although one would rather the sense strand not interact with any transcript, it often does. “Chemical modification allows the preclusion of the sense strand from siRNA targeting. And you see more specificity because the antisense or guide strand is the only strand participating in knockdown,” says Cunning. In the case of Stealth RNAi siRNA, the chemical modification protects siRNA from destruction by nucleases.
Also, says Tod Woolf, PhD, president and chief executive officer, RXi Pharmaceuticals, Worcester, Mass.: “Two strands of unmodified RNA do not have very good pharmacology.” The history of chemical modification of siRNA actually began with initial academic work by Nobel laureate Craig Mello, followed by work performed by Mello and Woolf at Sequitur. Chemical modification of siRNA leads to a number of druggable properties. “Our latest self delivery RNAi technology has virtually all the properties that we would want in a compound,” says Woolf. Chief among these properties is serum stability of the compound, i.e., when the double stranded RNA is injected into an animal, it is not degraded by nucleases.
Chemical modification of double-stranded RNA is not a new concept, having its roots in the earlier antisense, ribozyme, and aptamer technologies that were rampant for RNAi technologies. “You can modify the RNA at every linkage with something called [2’-O-methyl] and the RNA would be stable as a rock, but it won’t turn off the gene at all. So somewhere between no modifications and modifying every one—you can use different modifications at different points—[is where we aim],” says Woolf. RXi’s expertise lies in designing an RNAi molecule that is stable and extremely active by selecting where to modify the molecule.
Special delivery
In contrast to unmodified siRNA, RXi’s self-delivering siRNA is easily taken up by target cells. To create these properties, RXi had to further enhance their proprietary RNA-modifying chemistry in order to change the configuration of the siRNA molecule. They make the compound smaller and add two different chemistries that allow it to be spontaneously taken up by target cells without the need for a transfection reagent. In addition, these modifications prevent the siRNA compound from being removed by the kidneys, thus enhancing their activity in vivo.
“As the field progresses, [RNAi] delivery [will be] accomplished tissue by tissue,” says Woolf.
In order to knock down cancer biomarkers with siRNA in vitro cell-based assays, there must first be a way to deliver the compound to the target cell. That’s where transfection technologies (electroporation, liposomes, viral delivery, etc.) come into play. BioRad (Hercules, Calif.) produces electroporation instrumentation for performing this critical step. “Electroporation is probably the most reliable form [of transfection] regardless of the cells you are working with,” says Michelle Collins, PhD, global product manager, Transfection Instrumentation, at BioRad. “The benefit [of electroporation] over lipids is that with electroporation you can explore the difficult-to-transfect cells, the primary cells, the stem cells.”
Targets
“There is a good understanding of molecular targets in oncology that we can exploit via RNAi and these drugs will complement current cancer therapies,” says Ian MacLachlan, PhD, executive vice president and chief scientific officer, Tekmira Pharmaceuticals Corp., Burnaby, British Columbia, Canada. Tekmira’s lead oncology product candidate is an siRNA-based drug targeting polo-like kinase 1 (PLK1). “PLK1 is over-expressed in many tumor types and knockdown of PLK1 via RNAi results in potent tumor cell killing without the side effects associated with traditional chemotherapy drugs.”
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Figure 2: Stealth RNAi siRNA is stabilized against nuclease degradation in serum. Unmodified 21-mer dsRNA sequence (left panel) and corresponding Stealth RNAi siRNA sequence (right panel) at 0, 4, 8, 24, 48, and 72 hours following incubation in 10% mouse serum. Following incubation samples were separated on a Novex 15% TBE-Urea polyacrylamide precast gel and stained with methylene blue. (Source: Life Technologies) |
Utilizing their proprietary SNALP (stable nucleic acid-lipid particles) technology, which is designed to deliver high concentrations of siRNA to cancerous cells, Tekmira developed the lead compound for which it will file an Investigational New Drug application in 2010. “In addition, Tekmira has also supported the advancement of ALN-VSP, our partner Alnylam Pharmaceuticals oncology product, which is currently being evaluated in a Phase 1 clinical trial for liver cancer and cancers with liver involvement,” says MacLachlan. “ALN-VSP targets two genes, [vascular endothelial growth factor (VEGF)] and [kinesin spindle protein (KSP)], and employs Tekmira’s SNALP delivery technology.”
“RNAi is gaining significant attention in oncology drug research as it is a novel mechanism of action that results in potent cell killing with a side effect profile amenable to combination therapy with current standard of care drugs,” says MacLachlan.
“Therapeutic RNAi provides the hope of selectively inhibiting any target protein by inhibiting its synthesis,” says David Heimbrook, PhD, vice president, Discovery Oncology, Roche, Nutley, N.J. “The concept has been thoroughly proven in cells—the great challenge with this approach is to effectively deliver the RNAi to the tumor in animals, and ultimately in people.” Focused on areas of oncology drug development such as angiogenesis, survival signaling, signal transduction, and harnessing the immune system to target cancer cells, Roche is playing its hand as a developer of RNAi-based therapeutics. The company intends to knock down targets that are essential to the survival of the cancer cells. Roche will monitor the effectiveness of potential therapeutics by measuring RNAi-induced reduction in target protein and biomarker expression. “The consequence of inhibiting the protein synthesis should lead to inhibition of tumor growth, which can also be assessed by other biomarkers” says Heimbrook, who adds that this is part of the overall “Personalized Healthcare Strategy,” which is applied to all of Roche’s development candidates in oncology.
“We can inhibit targets which we know are essential for the growth of tumor cells [but] that cannot be readily inhibited by any other approach,” says Heimbrook. Currently, all of Roche’s RNAi drug candidates in their oncology programs, as well as in other indications, are at the preclinical stage.”
Clearing the hurdle
RNAi has become one of the primary therapeutic approaches used by the pharmaceutical and biotechnology industries. Among the primary reasons for its success has been its exquisite specificity, which has enabled RNAi-based therapeutics to reach optimal efficacy with minimal associated adverse events. Chemical modification of siRNA molecules can be attributed to this successful specificity. Currently, RNAi-based therapeutics are being developed to target critical cancer biomarkers, such as PLK-1 and VEGF. The only remaining hurdle is delivery, but based on developments such as SNALP and self-delivering siRNA, it is not likely to remain a hurdle for much longer.
This article was published in Bioscience Technology magazine: Vol. 32, No. 11, November, 2008, pp. 1, 10-12.