Fibroblasts from XP-F patients still retain relatively high repair activities which are reflected predominantly in the mild phenotype due to residual repair capabilities in full-length alleles with point mutations (reviewed in Matsumura et al., 1998). The aim was to create an XPF KO cell line from immortalized fetal lung fibroblasts (MRC5Vi), already used in DNA repair
studies (Ogi et al., 2010; Sertic et al., 2011), by employing the CRISPR/Cas9 nuclease system targeting one of the first exons (one-three) of XPF. The feasibility for a complete XPF KO in human fibroblasts was assumed based on a previously established Xpf-deficient mouse model (Tian et al., 2004).
A transient transfection approach with a puromycin resistance cassette containing a plasmid for selection of positive clones was applied to circumvent long-term expression of artificial nucleases in the cells in order to minimize off-target effects (see 3.1.4.9 and 3.3.1.4).
Different guide RNAs were analyzed in respect to on and off-target effects to identify suitable target sequences in exon two of XPF. Single clone expansion was followed by amplifying and sequencing exon two to verify the successful KO (see 3.1.4.7). At this point, cells were sensitive to puromycin again. Figure 17A shows a part of the XPF exon two sequencing results from a positive clone, visualizing the generation of a compound heterozygous, complete, and still viable XPF KO cell line. In this section, the binding of the guide RNA (black arrow) in XPF exon two is indicated. As expected the Cas9 nuclease induces a DSB
~3bp upstream of the PAM sequence (Ran et al., 2013). Part of the guide sequence was deleted during the NHEJ process. One allele contains a seven nt deletion resulting in a premature stop codon nine nts downstream. In addition to this, the second allele shows an insertion of three nts and a premature stop after twelve nts, respectively. This is probably a result of a second cutting event by the Cas9 nuclease at the same position. Complete sequencing of the XPF gene did not reveal any additional mutations.
Furthermore, the XPF KO clone containing the mutation, was subject to standard enzyme mismatch cleavage experiments (EML), the T7EI and surveyor nuclease assay (see 3.1.4.8).
For the T7E1 assay, PCR products were generated from genomic DNA of WT and XPF KO MRC5Vi cells, using primers for XPF exon two as described above (see 3.1.4.1) (see Table 7). Subsequently, PCR products were denatured, followed by re-annealing, leading to a population of double strand fragments, of which some contained mismatches due to the afore mentioned compound heterozygous nature of the KO. These mismatches could be detected by T7EI and visualized on an agarose gel (see 3.1.3.4). WT cells did not yield amplicons susceptible to site-specific cleavage by T7EI (see Figure 17B), while XPF KO cells showed efficient cleavage of the endogenous chromosomal target sequence, evidenced by T7EI digestion products (arrows). This confirmed the presence of indels at the locus.
Surprisingly, there was an additional cleavage product, also in the WT cells (arrow head) that can be explained by a physiologically appearing already described three nt deletion in exon
two (polymorphism rs771203473 (NCBI), deletion AGA/-, chromosome 16:13922057-13922059). PCR amplicons from mutant (KO) and WT DNA were likewise prepared for the surveyor nuclease assay. Afterwards, equal amounts of KO and WT DNA were mixed and hybridized by heating and cooling the mixture to form hetero- and homoduplexes (see 3.1.4.8). In accordance with the T7EI assay, the WT cells did not show cleavage products, whereas in the WT+KO mixture, as well as in the KO alone, cleavage products could be detected. This was in concurrence with the compound heterozygous state of the KO (see Figure 17C, arrows). As observed in the assay before, an additional cleavage product was detected (arrow head).
Figure 17: Structural analyses of XPF CRISPR/Cas9 KO and WT MRC5Vi cells
(A) Sanger sequencing of XPF exon two from WT (upper panel) and KO (middle and lower panel) cells. The start of the guide RNA binding sequence is illustrated by a black arrow, while the dashed line marks the start of the sequence alterations in the XPF KO cells. The green sequence represents the deletion in the KO cells, while the blue nts are inserted. Red nts indicate the continuation of the WT sequence after the CRISPR event up until the stop codon (underlined), resulting from the frameshift. Two different alleles of the KO cells originating from the CRISPR/Cas9 genome editing are depicted in the middle and lower panel. (B) XPF exon two was PCR amplified from genomic DNA of WT and KO cells, denaturated, reannealed and T7EI-digested or (C) subject to a surveyor nuclease assay. The positions of digested DNA are illustrated by black arrows, while the arrow head marks an additional digestion product that can be seen in the WT cells as well (polymorphism). (D) Horizontal SDS-PAGE followed by western blot analyses was used to assess protein expression. Therefore, equal amounts of cytosolic and nuclear extracts of WT and KO cells were loaded onto ready-to-use SDS-gels and stained with an anti-XPF or anti-ERCC1 antibody. The membrane was stripped and reprobed for anti-β-actin to serve as loading control. Representatively, one of three independent experiments is shown. (E) Subsequent to complementation of the XPF KO cells with a plasmid coding for XPF cDNA, the same procedure was performed. Adapted from (Lehmann et al., 2017).
Moreover, generation of a complete XPF KO on protein level was confirmed. Therefor, cytosolic and nuclear protein fractions of WT and KO cells were isolated (see 3.4.1). Full-length XPF molecular weight is predicted to be 112kDa. The KO induced a premature stop codon after 86/87 aa, resulting in a theoretic molecular weight of approximately 10kDa.
Protein expression was assessed using horizontal SDS-Page followed by western blotting as described in 3.4.3, 3.4.4, and 3.4.5. WT cells showed an accumulation of nuclear XPF (13.88), while in XPF KO cells XPF was below limits of detection in the cytosol as well as in the nucleus, verifying the total lack of the protein (see Figure 17D). This was also true for lower sections of the gel, where a 10kDa protein would be visible (section of the gel not shown). After overexpression of a plasmid containing XPF cDNA (see 3.3.1.4), XPF protein expression could be restored in the cytosol (3.20) as well as in the nucleus (18.32) of XPF KO cells (see Figure 17E). In addition, protein expression of ERCC1, XPF’s functional heterodimer partner necessary for the catalytic activity in DNA repair, was assessed. In the cytosol, ERCC1 presented as a double band at 38kDa, which is probably caused by post-translational modifications (Nowotny & Gaur, 2016; Perez-Oliva et al., 2015). While WT cells displayed an accumulation of the modified form of ERCC1 in the nucleus (8.82) (Figure 17D), ERCC1 could not be detected in the nucleus of XPF KO cells. This suggests an inability of ERCC1 to enter the nucleus without its binding partner XPF. Transfection of XPF KO cells with a plasmid containing XPF cDNA (see 3.3.1.4) rescued nuclear localization of ERCC1 (see Figure 17E).
Quantitative real-time PCR was applied to analyze differences in XPF mRNA expression between WT and KO cells (see 3.1.3.2 and 3.1.4.2). Interestingly, there was a reduction of about 50% in the KO cells (WT XPF normalized to GAPDH 100 ± 4.71%, KO 54.76 ± 13.32%), probably due to nonsense-mediated messenger decay (see Figure 18) (reviewed in Chang et al., 2007).
Figure 18: Decrease in XPF expression in XPF KO cells assessed by quantitative real-time PCR
Comparison of XPF mRNA expression levels from MRC5Vi WT and XPF KO cells. Expression levels are shown as relative values and GAPDH was used as the internal control gene to normalize the expression of the target gene. Results represent mean values from three independent experiments in duplicates. Data are presented as mean ± SEM. Statistical significances were calculated by applying the one-tailed, unpaired student's t-test (* P < 0.05).