Presented by Oyeyemi Ajayi Prashant Kuntala and Colin

Presented by: Oyeyemi Ajayi, Prashant Kuntala, and Colin Kruse

CRISPR/CAS 9 SYSTEM ØIn response to DSB, two DNA repair pathways: NHEJ and HDR are initiated. ØHDR competes with NHEJ during the resolution of DSBs. ØCurrent approach induces Indels from cellular response to ds. DNA breaks

This new approach enables the direct, irreversible conversion of one target DNA base into another in a programmable manner, without requiring ds. DNA backbone cleavage or a donor template.

A SIMPLISTIC BROAD OVERVIEW OF A NEW APPROACH TO BASE EDITING

Protein Engineering Of Base Editors ( three Generations )

Base Editor – generation 1 • Catalytically dead Cas 9 (d. Cas 9) fused with r. APOBEC 1 (Cytidine deaminase enzyme) to the N-terminus. • • Inactive nuclease activity (Asp 10 Ala mutation, His 840 Ala) Programmable conversion of C to U in DNA. Activity window is approx. 3 to 6 nt In vitro efficiency : 50 to 80% C to U conversion of substrate strands

Context dependence of BE 1 Ø BE 1 activity preference Ø APOBEC 1 prefer substrates with TC or CC Ø TC > CC > AC > GC Ø Max editing efficiency at position 7

Base Editor – generation 1 • Catalytically dead Cas 9 (d. Cas 9) fused with r. APOBEC 1 (Cytidine deaminase enzyme) to the N-terminus. • • Inactive nuclease activity (Asp 10 Ala and His 840 Ala mutations) Programmable conversion of C to U in DNA. Activity window is approx. 3 to 6 nt In vitro efficiency : 50 to 80% C to U conversion of substrate strands • But efficiency of C to T editing in Human cells was about 0. 8 to 7. 7% of total DNA.

Base Editor- generation 2 • Hypothesis: Base excision repair (BER) reverts U: G to C: G pair • BE 2 • Uracil DNA glycosylase inhibitor (UGI) fused to the C–terminus of BE 1. • Increased efficiency in human cells by 3 -fold, 20% of total DNA sequences. • Indel formation rates <= 0. 1% in both BE 1 and BE 2

Base Editor – generation 3 • To augment the base editing efficiency – manipulate cellular DNA repair further. • Hypothesis: By nicking the unedited strand, MMR will preferentially repair the unedited strand (G to A) • BE 3 • Restored the catalytic His residue in Cas 9 (BE 2) that nicks the nonedited strand, containing a G opposite of edited U.

Outcome of BE 3 • Nicking the non-edited strand augmented base editing efficiency in human cells 2 -6 fold relative to BE 2, resulting in up to 37% of total DNA sequences containing the targeted C to T.

The Pros and Cons of BE 3

BE 3 -Mediated Correction of Disease-Relevant Mutations Komor et al. set out to correct the two potent missense mutations that could be corrected by C to T (or G to A) base editing Øp 53 Tyr 163 Cys mutation: cancer associated. ØAPOE 4, Cys 158 Arg mutation: potent Alzheimer's risk factor

BE 3 -Mediated Induced Base Correction

The Potential of Base Editing

Questions?