Epidemiological, clinical and biochemical characterization of the p.(Ala359Asp) SMPD1 variant causing Niemann-Pick disease type B

Abstract

Niemann-Pick disease type B (NPDB) is a rare, inherited lysosomal storage disorder that occurs due to variants in the sphingomyelin phosphodiesterase 1 (SMPD1) gene and the resultant deficiency of acid sphingomyelinase (ASM) activity. While numerous variants causing NPDB have been described, only a small number have been studied in any detail. Herein, we describe the frequency of the p.(Ala359Asp) variant in the healthy Chilean population, and determine the haplotype background of homozygous patients to establish if this variant originated from a common founder. Genomic DNA samples from 1691 healthy individuals were analyzed for the p.(Ala359Asp) variant. The frequency of p.(Ala359Asp) was found to be 1/105.7, predicting a disease incidence of 1/44 960 in Chile, higher than the incidence estimated by the number of confirmed NPDB cases. We also describe the clinical characteristics of 13 patients homozygous for p.(Ala359Asp) and all of them had moderate to severe NPDB disease. In addition, a conserved haplotype and shared 280 Kb region around the SMPD1 gene was observed in the patients analyzed, indicating that the variant originated from a common ancestor. The haplotype frequency and mitochondrial DNA analysis suggest an Amerindian origin for the variant. To assess the effect of the p.(Ala359Asp) variant, we transfected cells with the ASM-p.(Ala359Asp) cDNA and the activity was only 4.2% compared with the wild-type cDNA, definitively demonstrating the causative effect of the variant on ASM function. Information on common variants such as p.(Ala359Asp) is essential to guide the successful implementation for future therapies and benefit to patients.

Figure 1

Haplotypes of the six homozygous p.(Ala359Asp) NPDB Chilean patients. The colors indicate the common haplotypes for each patient's chromosomes: pink for p.(Ala359Asp) variant; green for common haplotypes and yellow for non conserved markers. H1 and H2 refer to the constructed haplotypes for each patient.

Figure 2

Population origin of the SMPD1 p.(Ala359Asp) variant. Graphical depictions of the patients' haplotypes constructed from eight SNPs within the SMPD1 gene region, with haplotype frequencies derived from the 1000 Genomes Project: African (AFR; n=88); Han Chinese in Beijing, China (CHB; n=97); Utah residents with Northern and Western European ancestry from the CEPH collection (CEU; n=82); Mexican ancestry from Los Angeles, USA (MXL; n=60); and from our data (HUI; n=11). ^aSignificantly different to HUI; ^bSignificantly different to CHB; ^cSignificantly different to MXL; ^dSignificantlyy different to CEU; ^eSignificantly different to AFR. P<0.05, χ²-test. SMPD1, sphingomyelin phosphodiesterase 1; SNP, single nucleotide polymorphism.

Figure 3

Functional characterization of the SMPD1 p.(Ala359Asp) variant. COS-7 cells transiently expressing the ASM wild-type (WT) and the p.(Ala359Asp) variants were generated and an ASM activity assay was performed on cell lysates (a). Data represents the mean±SE of three to five experiments as a percent of the ASM activity induced by wild-type ASM. *P<0.0001. (b) The levels of expression of endogenous, WT and p.(Ala359Asp) ASM protein in cells were assessed by Western immunoblotting. About 10 μg of total cell lysate protein was loaded into each lane. ASM, acid sphingomyelinase; SMPD1, sphingomyelin phosphodiesterase 1.