The initial excitement surrounding RNA
drugs stemmed from the simplicity of the concept. “It’s really easy in principle to design an RNA drug that targets mRNA,” states Krogh. “In a disease in which a gene is over-expressed, you can in theory synthesise an oligonucleotide (oligo) that turns this gene off. All that is required is an oligo that reverse complements a gene’s mRNA to enable binding. It’s easy on paper, but in reality it’s proven a lot harder to find oligos with all the right drug properties.” The structured nature of mRNA is, quite
literally, an obstacle to RNA drugs. Not only do oligos need to be complementary to the target mRNA, but they also need to target regions that are accessible. “mRNA fold into what we call a ‘secondary structure’, so it can fold into structures much like proteins can,” explains Krogh, “If they are structured
other genes with coincidentally similar sequences. These ‘off-target’ effects can cause significant
problems in the
development of a drug. In order to study these effects, the team at COAT has been developing a method that can experimentally map all the binding sites of an oligo. Beginning with tens of thousands, the method reduces the number by selecting oligo sequences with the minimal amount of close sequence matches to unintended RNA targets. One of the centre’s most exciting
discoveries concerns the problem that many oligos are poorly tolerated. This was of very practical importance to COAT’s industrial member at Roche Innovation Center Copenhagen, where Morten Lindow has been struggling to find ways to identify and get rid of oligos with low
AT A GLANCE Project Information
Project Title: Centre for Computational and Applied Transcriptomics
Project Objective: The main objective of COAT is to facilitate the design of efficient and safe RNA drugs in part by investigating how RNA structure and RNA-protein interactions affect gene expression
Project Duration and Timing: Duration 5 years, ending July 2016.
Project Funding: The Innovation Foundation, formerly Danish Strategic Research Council
“People were expecting that it would be more complex to discern and would involve all kinds of investigations, but it was quite simple”
then the oligo can’t bind to the target.” A further encumbrance to RNA access is if a protein binds the target site. The advances in DNA sequencing that
have occurred in the last ten years allow the team at COAT to investigate how these oligos target mRNA with a particular view to the accessibility of RNA drugs. The ability to perform transcriptome-wide sequencing and the like provide the tools for analysing the binding sites of the huge amounts of short RNA sequences involved. For instance, the centre was recently able to report significant improvements in the methods for probing RNA accessibility. Using a massive parallel-sequencing-based method called hydroxyl radical footprinting (HRF), COAT have arrived at a way to discern the structure of mRNAs to an unprecedented degree. “Although not completely accurate, our method for probing combined with computational methods for prediction gives us very good estimates of mRNA structure and hence accessibility to RNA drugs,” Krogh remarks. Although drugs are designed with specific
mRNA targets in mind, there can be a tendency to stray off target and include other genes in their effects. In essence, the drug will manage to suppress the gene it is meant to but then reduce the expression of
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tolerability. The fact that an oligo has low tolerability (essentially meaning it is poisonous) may not emerge until toxicity is evident in murine models, quite some way along the road of drug development. However, Lindow and his colleagues were surprised to find that from sequence alone it is possible to predict toxicity. “People were expecting that it would be more complex to discern and would involve all kinds of investigations” says Lindow, “but it was quite simple.” It’s not yet possible to make
predictions that are a hundred
percent accurate, but it has already radically reduced the amount of experiments that are usually necessary. If a drug is predicted to be very toxic, RICC doesn’t even begin to test it. Established in 2011, the COAT has
achieved a considerable amount of success in its short life. Naturally, Krogh expects the
research carried out between the
partners to continue in academia, but it’s hoped that COAT will be able to carry on the relationship that’s been built with RICC beyond the current 2016 timeline for the centre. As more is learnt about the structure of human RNA and protein-RNA interactions, it’s a relationship that could see the future of RNA drug development realise its potential at last.
★ 25
Project Partners: The University of Copenhagen, Denmark The University of California, Santa Cruz, U.S.A. Aarhus University, Denmark. Roche Innovation Center, Denmark
MAIN CONTACT
Professor Anders Krogh Professor Anders Krogh is the director of the COAT centre and the Head of Section for Computational and RNA biology, Department of Biology, University of Copenhagen. He leads an independent 2-year Master’s programme in bioinformatics which graduates 25 candidates per year.
Contact: Tel: +45 51827056 Email:
Krogh@binf.ku.dk Web:
www1.bio.ku.dk/binf
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