October 25, 2017

expert reaction to study looking at CRISPR for RNA editing

Publishing in Science, researchers report a new version of the genome editing tool CRISPR – using Cas13 – which can target and edit RNA.

Dr Helen O’Neill, Programme Director, Reproductive Science and Women’s Health, UCL, said:

“A second paper this week [the other being the Nature paper on base editing] has also used adenosine deaminases fused with CRISPR/Cas machinery, but to target and edit RNA, instead of DNA.  Ribonucleic acid (RNA) is a single-stranded nucleic acid which plays a central role in the pathway from DNA to proteins.  Mutations in our DNA can result in the inability of RNA to carry out essential roles in protein synthesis which are needed for most biological processes.  Manipulating RNA potentially poses fewer ethical concerns than editing DNA as the effects would not necessarily be permanent.

“This paper first assessed a range of Cas13 enzymes to determine their ability to knockdown RNA in mammalian cells.  They then fused an inactive form of the most efficient enzyme tested to an adenosine deaminase (capable of altering specific bases) and were able to show efficient RNA editing.  The technique, aptly named REPAIR (RNA editing for programmable A to I (G) replacement) paves the way for selectable and time specific modulation of a gene’s output.

“This is an exciting week for genetic research – these papers highlight the fast pace of the field and the continuous improvements being made in genome editing, bringing it closer and closer to the clinic.”

Prof. Darren Griffin, Professor of Genetics, University of Kent, said:

“This is a very novel innovation in the latest gene editing technology, providing a much needed research tool and a possible future route for targeted therapy.  By targeting the message (RNA) rather than the DNA itself, this means that effects on genes can be modified for a short amount of time, and at particular crucial stages.  Importantly, the effects of the manipulation are transient and can thus be removed when no longer needed.  Possible future routes to therapy may include trying this method on cancer cells or neuronal cells, however we are a long way off that at the moment.”

Dr Ben Davies, Head of Transgenic Group, Wellcome Centre for Human Genetics, University of Oxford, said:

“Feng Zhang adds to his already impressive series of papers applying Cas13, a CRISPR-associated RNA-guided RNAse, for achieving targeted manipulation of RNA within the mammalian cell (in this case a human embryonic kidney cell line, Hek293 cells).  This class of enzyme can be directed to the mRNA produced from a specific target gene, by a readily programmable guide-RNA.

“Previous editing systems have adapted the RNA-guided DNA-cleaving enzyme Cas9 to direct the activity of nucleotide-changing enzymes to actual DNA.  What’s interesting about this study is that a repair can be made to an RNA molecule which leaves the DNA completely intact – thus editing of RNA can be achieved without any changes made to the underlying DNA.  This might make the method safer with respect to the off-target changes which have been reported for CRISPR/Cas based systems, as lasting damage or change to the underlying DNA sequence is avoided.  In addition the REPAIR system is a lot more flexible with respect to target choice than the existing DNA base editing systems.

“However, the REPAIR system is also associated with off-target activity.  These effects are reduced using structure-based mutagenesis to make the REPAIR system more specific, but off-target RNA edits are still ultimately detectable.  Further work may be necessary before these REPAIR system can be applied therapeutically.

“The fact that the system addresses RNA, also means that any therapeutic application would have to involve a permanent activity of the REPAIR system, to effectively edit all the transcripts generated from a mutant gene.  The transience of the REPAIR activity may limit the application of this RNA system in gene therapy approaches.  However, in basic biomedical research, the added temporal control of perturbing RNA molecules is particularly exciting and could be used to great effect in interrogating the role of specific genes and their transcripts in biological processes.  One could conceivably assay function before, during and after a manipulation of a target transcript.  It could thus provide an excellent alternative to the widely used RNA-interference approach, a method which also transiently reduces target transcript levels.  Indeed it’s fascinating to see that in this manuscript the reported specificity of the REPAIR system is over one hundred times higher than a conventional RNA-interference approach.”

* ‘RNA editing with CRISPR-Cas13’ by David B.T. Cox et al. published in Science on Wednesday 25 October 2017.

Declared interests

Dr Helen O’Neill: “I have nothing to declare/no conflicts of interests.”

None received.