Base editing: advances and therapeutic opportunities

Abstract

Base editing — the introduction of single-nucleotide variants (SNVs) into DNA or RNA in living cells — is one of the most recent advances in the field of genome editing. As around half of known pathogenic genetic variants are due to SNVs, base editing holds great potential for the treatment of numerous genetic diseases, through either temporary RNA or permanent DNA base alterations. Recent advances in the specificity, efficiency, precision and delivery of DNA and RNA base editors are revealing exciting therapeutic opportunities for these technologies. We expect the correction of single point mutations will be a major focus of future precision medicine.

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Fig. 1: General overview of DNA base editing technologies.
Fig. 2: General overview of RNA base editing technologies.
Fig. 3: DNA base editor and protospacer design scheme.
Fig. 4: Base editor delivery strategies.

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Acknowledgements

E.M.P. is supported by the Molecular Biophysics Training Grant, National Institutes of Health (NIH) Grant T32 GM008326. A.C.K. is partially funded by NIH grant R21 GM135736. G.W.Y. is partially funded by NIH grants EY029166 and NS103172. The authors gratefully acknowledge M. Singh, G. Ciaramella and N. Gaudelli for helpful discussions.

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E.M.P. conceptualized, wrote and edited the manuscript and designed the figures. A.C.K. conceptualized, wrote and edited the manuscript. I.M.S. and G.W.Y. contributed substantially to the content and further reviewed and edited the manuscript.

Corresponding author

Correspondence to Alexis C. Komor.

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Competing interests

A.C.K. is a member of the scientific advisory board (SAB) of Pairwise Plants, and is an equity holder for Pairwise Plants and Beam Therapeutics. I.M.S. is an employee and shareholder of Beam Therapeutics. G.W.Y. is co-founder, member of the Board of Directors, on the SAB, equity holder and paid consultant for Locana and Eclipse BioInnovations. G.W.Y. is a visiting professor at the National University of Singapore. A.C.K.’s and G.W.Y.’s interests have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. The authors declare no other competing financial interests.

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Glossary

Precision medicine

The development of disease prevention and treatment strategies based on a patient’s individual characteristics (that is, genomic sequence).

Single-nucleotide variants

(SNVs). Major cause of genetic diseases, targetable with base editors.

Guide RNA

(gRNA). A short sequence of RNA that recognizes the target DNA region of interest and directs the Cas enzyme to bind for editing to occur (also known as the spacer and single guide RNA).

Cas9

(CRISPR-associated protein 9). The enzyme responsible for DNA double-stranded cutting (wtCas9), single-stranded cutting or nicking (Cas9n), or no DNA cutting (wherein Cas9 is catalytically inactive, dCas9) activity. All three Cas9 variants maintain DNA binding ability.

Base editors

Genome editing tools that allow for the direct, irreversible conversion of target cytosine or adenine bases at a specific genomic locus without relying on double-stranded DNA breaks.

Protospacer

A DNA locus of interest targeted with genome editing agent; base pairs with the guide RNA.

IUPAC nucleotide codes

N = adenine/cytosine/guanine/thymine, R = adenine/guanine, Y = cytosine/thymine, V = adenine/cytosine/guanine (in order of appearance).

Protospacer adjacent motif

(PAM). A variable region on the 5′ or 3′ end of the protospacer, required for Cas protein binding to the target locus. PAM requirements vary among different Cas enzymes (the most widely used Streptococcus pyogenes Cas9 requires an NGG PAM).

R-loop

A tripartite structure consisting of unpaired DNA and a paired DNA:RNA hybrid. Following R-loop formation, the unpaired or single-stranded DNA is accessible for base editing.

Antisense oligonucleotides

(ASOs). Small pieces of DNA or RNA that bind to specific molecules of RNA.

ADARDD

(Deaminase domain of adenosine deaminase acting on RNA enzyme). The first reported case explored for A-to-I RNA base editing.

Activity window

A defined region of single-stranded DNA accessible for base editing activity. Activity windows vary among different base editor variations.

Ribonucleoprotein complexes

(RNPs). Macromolecular structures containing both Cas9 protein and guide RNA molecules.

IUPAC amino acid codes

V = valine, W = tryptophan, R = arginine, A = alanine, K = lysine, G = glycine, Y = tyrosine, E = glutamic acid, P = proline (in order of appearance).

Prime editing

A recently developed genome editing technology that, like base editing, does not rely on double-stranded breaks.

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Porto, E.M., Komor, A.C., Slaymaker, I.M. et al. Base editing: advances and therapeutic opportunities. Nat Rev Drug Discov (2020). https://doi.org/10.1038/s41573-020-0084-6

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