Extended Data Fig. 7: Functional characterisation of NPHP4 and its S862N variant during VZV infection.
(a) The percentage of nucleotide insertion/deletion (indel) within the sgRNA-targeted region of the NPHP4 gene in the NPHP4-KO cells as compared to NTC. (b) The abundance of NPHP4 protein was assessed by western blot analysis (exact band indicated by an arrow). (c) Resazurin viability assay of the NTC and NPHP4 knockout cell line. Mean and standard error to the mean are indicated (n = 3 independent experiments) (d) Western blot analysis of the expression level of the HA-NPHP4 and -NPHP4-S862N constructs in NTC and NPHP4-knockout (KO) cells. (e) Volcano plot of differentially regulated transcripts in SK-N-BE2 cells infected with VZV, as compared to mock cells. Significant host protein changes (two-sided adjusted p-value ≤ 5.10−2, |median log2 fold change| ≥ 1, n = 3 independent experiments) are represented with black dots. (Supplementary Table 5) (f) Comparison of differentially regulated transcripts (log2 fold change) following VZV infection in NTC and NPHP4 knockout (KO) SK-N-BE2 cells. (n = 3 independent experiments) (Supplementary Table 5) (g, h) Normalized transcript counts of the WNT target genes FOSL1 and ZEB2 in SK-N-BE2 cells NTC or NPHP4-KO following VZV-infection as displayed in (f) (two-sided Wald test unadjusted p-value are indicated; n = 3 independent experiments) (i) Interactomes of HA-NPHP4 wild-type generated by affinity-purification coupled to mass-spectrometry in neuroblastoma SK-N-BE2 cells. Significant host protein association are marked in black (two-sided Welch t-test, permutation-based FDR ≤ 1.10−2, S0 = 4, n = 4 independent experiments) (Supplementary Table 5). Associated cilia basal body proteins (Reactome 267965) are indicated in light blue, including the NPHP1-NPHP4-NPHP8(RPGRIP1L) complex which is labelled. Associated 14-3-3 proteins are indicated in dark blue.
