Team:NUS Singapore-Sci/Overview

NUS Singapore Science: InterLab

Project
Overview

A small change in sequence, a big leap for mankind
Genome editing is a recent technique shown to be versatile in manipulating genomes of living organisms. The technique of genome editing is seen as one of the most promising methods in a wide range of fields such as the treatment of genetic diseases, improvement of food security and in diagnostics.

Genome editing technologies have provided scientists with the ability to rapidly and economically introduce sequence-specific modifications into the genomes of a broad spectrum of cell types and organisms. Compared to previous techniques of gene manipulation, gene editing targets specific sites in the genetic sequence to render a particular gene function “silenced” and offers a “permanent” silencing of the particular gene. One of the most popular and easy to use system is the CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 protein. In this system, any modification to the genome is carried out by Cas9, an enzyme that can be directed to a specific region of the genome by a guiding sequence and carry out cleavage of the DNA, resulting in a change in gene function.

Genetic diseases are hard to cure. However base editing, a type of genome editing technique, has resulted in a paradigm shift in novel disease treatments. Such a system allows the modification of specific DNA bases, without causing any cleavage or breaks in the DNA strand, thus potentially minimising any off-target effects. In 2016, a group of scientists from the University of California, Berkeley demonstrated treatment of sickle cell anemia in mice using the CRISPR-Cas9 system (Dewitt et al., 2016). Each year, about 250,000 newborns worldwide are diagnosed with sickle cell anemia, with symptoms such as clogged blood vessels and lowered oxygen delivery to tissues - resulting in excruciating pain (Ledford, 2016). For such inherited or acquired genetic diseases, the CRISPR-Cas9 system holds much potential for treatment via base editing, especially those with no current treatment available.

However, with the current technology, non-specific targeting of the CRISPR-Cas9 system is a huge barrier in using genomic editing. Recent work has shown that while the CRISPR-Cas9 system can target genomes to make specific edits, a high percentage of non-specific editing still exists (Q. Zhang et al., 2018; Zhang, Tee, Wang, Huang, & Yang, 2015). Since edits made to DNA are permanent, these non-specific edits on somatic cells will be passed on to daughter cells. This could lead to irreversible damage done to the genome which could potentially be fatal. While scientists currently do not have a way to eliminate or minimise off-target effects, an alternative method is to modify the genome without editing the DNA strands.

In this project, we propose to develop a genome editing system that can target RNA strands instead, as RNA strand editing is transient and reversible. Recent work has shown that another Cas family protein, Cas13, has the ability to target specific RNA strands and degrade RNA, effectively lowering target protein levels (Cox et al., 2017). The RNA-targeting Cas13 enzyme functions in a very similar manner to the aforementioned Cas9 enzyme where both carry out cleavage of nucleic acid strands with the help of unique guide RNAs (gRNAs).

In light of this new CRISPR-Cas13 system, a team from Broad Institute in Massachusetts Institute of Technology (MIT) successfully designed a CRISPR-Cas13 system that performs A-to-I editing (Cox et al., 2017). Our team therefore aims to utilise this CRISPR-Cas13 system to make another type of base edit to RNA strands, specifically the C-to-U edit, called RESCUE (RNA Editing System for C-to-U Editing). RESCUE comprises various components: RESCUE Editor, RESCUE Reporter and RESCUE Model. We hope that the development of this system can diversify the current repertoire of RNA editing methods and allow for transient treatment of genetic diseases as compared to direct genome editing.
References
Cox, D. B. T., Gootenberg, J. S., Abudayyeh, O. O., Franklin, B., Kellner, M. J., Joung, J., & Zhang, F. (2017). RNA Editing with CRISPR-Cas13 HHS Public Access. Science, 358(6366), 1019–1027. http://doi.org/10.1126/science.aaq0180

Dewitt, M. A., Magis, W., Bray, N. L., Wang, T., Berman, J. R., Urbinati, F., Heo, S.J., Mitros, T., Muñoz, D.P., Boffelli, D., Kohn, D.B., Walters, M.C., Carroll, D., Martin, D.I., Corn, J.E. (2016). Selection-free Genome Editing of the Sickle Mutation in Human Adult Hematopoietic Stem/Progenitor Cells HHS Public Access. Sci Transl Med, 8(360), 360–134. http://doi.org/10.1126/scitranslmed.aaf9336

Ledford, H. (2016, October 12). CRISPR deployed to combat sickle-cell anaemia. Retrieved from https://www.nature.com/news/crispr-deployed-to-combat-sickle-cell-anaemia-1.20782

Zhang, Q., Xing, H. L., Wang, Z. P., Zhang, H. Y., Yang, F., Wang, X. C., & Chen, Q. J. (2018). Potential high-frequency off-target mutagenesis induced by CRISPR/Cas9 in Arabidopsis and its prevention. Plant Molecular Biology, 96(4–5), 445–456. http://doi.org/10.1007/s11103-018-0709-x

Zhang, X. H., Tee, L. Y., Wang, X. G., Huang, Q. S., & Yang, S. H. (2015). Off-target effects in CRISPR/Cas9-mediated genome engineering. Molecular Therapy - Nucleic Acids, 4(11), e264. http://doi.org/10.1038/mtna.2015.37