Analysis of Kozak sequences variants of haploinsufficient genes

We conceived that the availability of base editors and the possible presence of suboptimal Kozak sequences in the human genome could provide an elegant approach to modulate translational efficiency for the molecular compensation of some haploinsufficient disorders. Moreover, such an approach would be independent of the type of alteration inactivating the defective allele and, therefore, highly suitable for gene therapy protocols. To find base conversions upregulating translational efficiency, we systematically screened 5261 (4621 unique) variants of Kozak sequences for translational strength. We designed these variants in the main AUG context of 230 previously annotated haploinsufficient genes. Analysis of our library of Kozak variants, bearing the conversions that base editors can reproduce, proved that weak Kozak sequences are present at about a 20% frequency in our gene sample. We validated the variants of five genes and base edited one of them in a cell model, providing proof of principle of the approach, which we called BOOST (Base editing cOrrection of haplOinSufficiency by Translational enhancement). HEK293T cells transduced independently with 2 Kozak variants libraries were sorted into 4 gates according to the EGFP/mCherry ratio as a measure of Kozak strength. After cell sorting, the Kozak sequences from the 4 subpopulations (gates) were amplified and sequenced, for a total of 8 samples: 4 gates with library A, 4 gates with library B (reduced synthesis error rate)