Allelic Expression Imbalance Promoting a Mutant PEX6 Allele Causes Zellweger Spectrum Disorder

Abstract

Zellweger spectrum disorders (ZSDs) are autosomal-recessive disorders that are caused by defects in peroxisome biogenesis due to bi-allelic mutations in any of 13 different PEX genes. Here, we identified seven unrelated individuals affected with an apparent dominant ZSD in whom a heterozygous mutant PEX6 allele (c.2578C>T [p.Arg860Trp]) was overrepresented due to allelic expression imbalance (AEI). We demonstrated that AEI of PEX6 is a common phenomenon and is correlated with heterozygosity for a frequent variant in the 3' untranslated region (UTR) of the mutant allele, which disrupts the most distal of two polyadenylation sites. Asymptomatic parents, who were heterozygous for PEX c.2578C>T, did not show AEI and were homozygous for the 3' UTR variant. Overexpression models confirmed that the overrepresentation of the pathogenic PEX6 c.2578T variant compared to wild-type PEX6 c.2578C results in a peroxisome biogenesis defect and thus constitutes the cause of disease in the affected individuals. AEI promoting the overrepresentation of a mutant allele might also play a role in other autosomal-recessive disorders, in which only one heterozygous pathogenic variant is identified.

Keywords: PEX1; PEX6; dominant-negative; metabolic; peroxisomal disorder; peroxisome; peroxisome biogenesis disorder.

Figure 1

PEX6 Defect in Individuals with ZSD (A) Schematic presentation of the role of the PEX1-PEX6 complex in the import of peroxisomal matrix proteins into peroxisomes. The peroxisomal protein receptor PEX5 binds matrix proteins, such as catalase, in the cytosol and transports these to the peroxisome, where the receptor docks at PEX proteins in the peroxisomal membrane and releases the matrix proteins into the matrix. After this, PEX5 is exported back into the cytosol through the action of the hexameric PEX1-PEX6 complex, which is anchored to the peroxisome via interaction of PEX6 with PEX26. (B) Pedigrees of seven affected families with the PEX6 c.2578C>T variant (only relevant members depicted). Filled symbols represent individuals suffering from a ZSD, asterisks indicate individuals heterozygous for the PEX6 c.2578C>T variant, and arrows indicate family members from whom primary skin fibroblasts were available for functional studies. (C and D) Immunofluorescence microscopy assays to determine the subcellular localization of peroxisomal matrix protein catalase (green) and receptor PEX5 (red) together with peroxisomal membrane proteins ABCD3 (red) or ABCD1 (green), respectively. (C) Representative microscopy images of cells of individual P1 and a control individual. In control cells catalase is peroxisomal (left) and PEX5 cytosolic (right), but in the cells of the affected individuals catalase is mislocalized to the cytosol and PEX5 to peroxisomes, demonstrating a severe defect in the import of the peroxisomal matrix proteins and the export of PEX5 in the cells of affected individuals (see Figure S1 for images of cells from other individuals). (D) Relative subcellular localization of catalase and PEX5 in cells of individual P2 and his asymptomatic mother, demonstrating only a mild defect in cells of the asymptomatic mother of individual P2 (see also Figures S1 and S6 for additional images).

Figure 2

AEI of PEX6 in Affected Individuals and Control Individuals with the Heterozygous 3′ UTR Variant PEX6 c.^∗442_445delTAAA (A and B) Allelic expression of PEX6 mRNA in cells of affected individuals and the mother of affected individual 2. PEX6 cDNA and genomic DNA were Sanger sequenced and the peak height of both PEX6 alleles were used to determine the relative abundance of each allele (see representative sequence reads in A). Mean c.2578T allele peak ratios in the different cell lines (B), expressed as the ratio of the mutant allele peak height (c.2578T) over the total peak height (c.2578T+c.2578C) as described in Moncini et al., depicted as mean with standard deviation of 6–19 analyzed electropherograms per cell line (or gDNA group) using 2–3 different primer sets. While the PEX6 allele ratio is in balance in genomic DNA of the affected individuals and genomic DNA and cDNA of the mother of individual P2 (i.e., equal peak heights), the mutant allele ratio in cDNA of all affected individuals is significantly increased, demonstrating the AEI of PEX6. (C and D) PEX6 mRNA expression in fibroblasts of affected individuals and fibroblasts of 22 unrelated control individuals with different combinations of the PEX6 c.^∗442_445delTAAA allele (homozygous for the allele without the deletion [“TAAA / TAAA”], homozygous for the PEX6 c.^∗442_445delTAAA allele [“delTAAA / delTAAA”] or compound heterozygous [“TAAA / delTAAA”]). (C) Mean allele peak ratios for the PEX6 c.^∗442_445delTAAA allele in cDNA of cells of the affected individuals and control cells heterozygous and homozygous for this allele, confirming that the AEI of PEX6 occurs only in the heterozygous cells. Shown are the peak ratios of the c.2816A variant, which is a common polymorphism (MAF 0.39 [ExAc] / 0.33 [1000 Genomes]) that is in cis with PEX6 c.^∗442_445delTAAA (see also Table 3). The peak ratios were determined as described in (B) and Moncini et al. and are presented as mean with standard deviation based on analysis of 5–10 electropherograms from 4–7 different cell lines per allele combination. (D) Results of quantitative RT-PCR experiments, demonstrating an increased level of total PEX6 mRNA but no expression of longer PEX6 c.^∗1_462 mRNA in cells homozygous for the PEX6 c.^∗442_445delTAAA. Depicted are the PEX6 mRNA levels normalized to reference gene expression or as ratio PEX6 c.^∗1_462 over total PEX6, with “TAAA / TAAA” values set as 1, as mean with standard deviation determined in 4–13 cell lines per allele combination. Statistical analyses for (B) and (C) were performed using one-sample t tests with a theoretical mean of 0.5, and for (D) using Mann-Whitney U tests (^∗∗p ≤ 0.01, ^∗∗∗p ≤ 0.001, ^∗∗∗∗ p ≤ 0.0001, ns not significant).

Figure 3

Overexpression Models of Dominant-Negative PEX6-p.Arg860Trp in Presence of Wild-Type PEX6 (A and B) Peroxisome biogenesis inSV40 immortalized control cells overexpressing PEX p.Arg860Trp. (A) Representative sequence reads obtained by Sanger sequencing of PEX6 cDNA in SV40 cells and SV40 cells over-expressing PEX6 c.2578C>T. The mutant PEX6 c.2578T allele displays a similar overrepresentation when compared to the endogenous wild-type PEX6 allele as observed in cells of the affected individuals (compare Figure 2A). (B) Imunofluorescence microscopy images of cells, which were double labeled to determine the subcellular localizations of catalase (green) and ABCD3 (red), or PEX5 (red) and ABCD1 (green), demonstrating a defect in peroxisomal catalase import and PEX5 export in SV40 cells over-expressing PEX6 p.Arg860Trp (compare also Figure S10). (C) Co-expression of mutant and wild-type PEX6 in PEX6-deficient cells. PEX6-deficient cells were co-transfected with wild-type PEX6 cDNA and PEX6 variants PEX6 c.2578T (p.Arg860Trp) (dark grey) or PEX6 c.821T (p.Pro274Leu) (light grey) in different ratios, together with the peroxisomal matrix protein marker GFP-SKL, whereupon the degree of GFP-SKL import into peroxisomes was determined. GFP-SKL import after transfection with wild-type PEX6 only was set as 1. Increased relative expression of PEX6-p.Arg860Trp results in a decreased peroxisomal import of GFP-SKL, which was far more pronounced than observed with PEX6 p.Pro274Leu. Data are depicted as mean with standard deviation of three independent experiments counting 180–300 cells per condition, and statistical analyses were performed using unpaired t tests (^∗p < 0.05, ^∗∗p < 0.01, ^∗∗∗p < 0.001, while an absence of a p value indicates non-significance).