CRISPR-Pass: Gene Rescue of Nonsense Mutations Using Adenine Base Editors

Abstract

A nonsense mutation is a substitutive mutation in a DNA sequence that causes a premature termination during translation and produces stalled proteins, resulting in dysfunction of a gene. Although it usually induces severe genetic disorders, there are no definite methods for inducing read through of premature termination codons (PTCs). Here, we present a targeted tool for bypassing PTCs, named CRISPR-pass, that uses CRISPR-mediated adenine base editors. CRISPR-pass, which should be applicable to 95.5% of clinically significant nonsense mutations in the ClinVar database, rescues protein synthesis in patient-derived fibroblasts, suggesting potential clinical utility.

Keywords: CRISPR-Cas9; base editing; nonsense mutation; premature termination codon; stop codon read through.

Graphical abstract

Figure 1

CRISPR-Pass for Restoring Abbreviated Gene Expression (A) Schematic of ABE-mediated CRISPR-pass. Targetable adenines are located in the coding or noncoding strand depending on the PAM’s orientation. All possible PTCs are shown in the upper boxes (coding strand targeting-TAA, TAG, TGA; noncoding strand targeting-TAA, TAG, TGA). The orange-colored shapes represent adenosine deaminase. (B) The percentages of different types of mutations causing pathological phenotypes in the ClinVar database. (C) The percentages of PTCs that are targetable by CRISPR-pass with various PAMs of variant ABEs and the recoverable rate of intact amino acids and bypassing alternative amino acids are depicted.

Figure 2

Restoring the Function of EGFP Gene Expression in Six KI HeLa Cell Lines Carrying Various Types of PTCs (A) Scheme for restoration of EGFP expression by CRISPR-pass. The first set of PTCs, which can be converted by targeting the coding strand, affect a residue that is located on a loop between the third and fourth beta strands; the second set of PTCs, which can be converted by targeting the noncoding strand, affect a residue that is located on a loop between the 10th and 11th beta strands. c-PTC, coding strand PTC; nc-PTC, noncoding strand PTC. GFP structures were originated from Wikimedia Commons created by Zephyris. (B) Schematic of NHEJ-mediated KI of the EGFP-PTC constructs into the AAVS1 site. Mutated EGFP KI cell lines were established for the three types of PTCs (TAA, TAG, and TGA). EGFP-PTC constructs were inserted into the AAVS1 site by NHEJ-mediated KI methods. The hygromysin B-resistant gene was also inserted for cell selection. (C) Fluorescence image of rescued EGFP expression in the c-TAA cell line after CRISPR-pass treatment. Three different versions of ABEs (ABE7.10, xABE, and ABEmax) were used for bypassing the PTCs in the EGFP gene. All scale bars are 100 μm. (D) Flow cytometry data after the different versions of ABEs (ABE7.10, xABE, and ABEmax) were treated in the c-TAA cell line. (E) Targeted deep-sequencing data showing the percentages of each of the four nucleotides at each position in the target DNA sequences as a substitution table, which was obtained from the c-TAA cell line after the ABEmax treatment. Bar graphs showing recovered EGFP expression levels as determined by flow cytometry (F) and showing A-to-G substitution rates at PTC sites as determined by targeted deep sequencing (G) for each EGFP-PTC KI cell line, after treatment with ABEs (ABE7.10, xABE, or ABEmax). Each dot represents the three independent experiments. Error bars represent SEM.

Figure 3

Restoring Abbreviated XPC Gene Expression in Patient-Derived Fibroblasts (A) Scheme for ABE-induced read through of an XPC-associated PTC. (B) Targeted deep-sequencing data showing the A-to-G substitution rate induced by ABEmax treatment at the PTC site in the XPC gene. (C) Expression level of the XPC protein in XPC mutant cells rescued by treatment with ABEs (ABEmax or xABE), compared with the expression level in untreated cells and cells treated with ataluren or gentamicin for 48 h. (D) Cell viability of WT skin fibroblasts (BJ-5ta), XPC mutant cells (GM14867), and XPC mutant cells treated with ABEs (ABEmax or xABE), ataluren, or gentamicin at 3 days after exposure to 254 nm ultraviolet radiation at a dose of 25 J/m². p values were calculated by one-way ANOVA with post-hoc Bonferroni’s multiple comparison tests (n = 6). p value indicators from a comparison with GM14867 cell viability are shown above each treatment group. NS, not significant (p > 0.05); *p < 0.05; ***p < 0.001. (E) Prolonged expression of the XPC protein after CRISPR-pass treatment. Significant and stable XPC protein expression was observed until at least 4 weeks after ABEmax treatment. However, XPC protein expression declined after removal of ataluren and gentamycin. Proteins were also prepared from ABEmax-treated XPC mutant cells at 2 and 4 weeks (subculturing twice per week) for comparison. Blue and red arrowheads indicate the positions of XPC protein.