Background

Background: Why do we need COAT?

The vast majority of drugs that have been approved for use in humans are targeted against proteins and in particular against proteins present at the surface of cells or proteins with enzymatic functions.  Because proteins are very diverse and can be located at all possible cellular locations, each new drug has to be developed from scratch. An alternative to development of conventional protein-targeted drugs is to use drugs targeted against the messenger RNA (mRNA) molecules that encode the proteins. mRNA molecules are much more similar to each other, which makes  RNA drug more simple to develop:

  1. An RNA drug design is in principle very simple: synthesize a reverse complementary oligonucleotide that can bind to the target RNA according the basepairing rules established by Watson and Crick.
  2. All known genes can be targeted, including non protein coding genes, and thus, the use of RNA-targeting drugs is the most direct application of genomics information for the development of new medicines.
  3. RNA drugs based on antisense oligonucleotides have fairly similar and predictable toxicology and pharmacokinetics profiles.

Although theoretically very appealing, challenges to RNA drug development obviously remain. Contrary to the linear messenger RNA molecule depicted in Biology textbooks, RNA molecules inside cells are highly structured and bound by proteins. This restricts the accessibility of the RNAs for endogenous regulatory RNAs, such as miRNAs and for RNA-targeted drugs, such as antisense oligonucleotides (ASOs) and siRNAs (see figure 1). This is well documented for siRNAs (Tafer et al., 2008), which can have highly variable efficacies against their target sequences, and the same is the case for other antisense technologies such as RNAseH-recruiting ASOs (gapmers) and oligonucleotides blocking translation, splicing etc. Another important challenge for the development of RNA drugs is to widen the therapeutic window (between the desired effect and unwanted side effects) by increasing in vivo tolerability. In 2010, at the Third DIA meeting on Oligonucleotide Therapeutics, the industry/regulatory-subcommittee on off-target effects concluded that tolerability is the major issue that needs to be solved before the large potential of RNA drugs can be realized. At the cellular level low tolerability can be caused by two mechanisms: 1) hybridization of the oligonucleotide-drug to unwanted RNA targets or 2) interaction between the drug and intracellular or extracellular proteins. The first is an off-target or specificity issue and is highly dependent on the sequence and the accessibility. The second can be thought of as class or chemistry-determined effects, although it is likely that sequence motifs are associated with the risk of toxic effects. Because RNA drug efficacy and specificity is dependent on complementary base-pairing between the drug and the target and off-targets genome-wide, RNA drug development is particular likely to benefit immensely from a close collaboration between experimental biology and computer science that focus on sequencing based genome-wide experiments and computational analysis and modeling of the results.

RNA accessibility is limited by protein binding and RNA structure. This has important consequences for the efficiency and specificity of RNA drugs and posttranscriptional gene regulation.

Importantly, the work proposed in this project is not only interesting from an RNA drug perspective, but has broad implications for many central issues in modern biology. Inside cells the folding of RNA molecules and association with RNA-binding proteins (RNA-BPs) have important consequences for most cellular functions, including transcription, RNA processing, RNA export, RNA localization, translation and RNA stability. Thus, RNA structure and the RNA-protein interactome can be viewed as an important layer in gene expression that remains largely unmapped. The data produced by COAT will help fill in this gap in our knowledge and will be an important step in the functional annotation of the human genome. In the long term, this will facilitate the understanding and treatment of human diseases caused by defects in posttranscriptional regulation.