SMPD1 expression profile and mutation landscape help decipher genotype-phenotype association and precision diagnosis for acid sphingomyelinase deficiency

Abstract

Background: Acid sphingomyelinase deficiency (ASMD) disorder, also known as Niemann-Pick disease (NPD) is a rare genetic disease caused by mutations in SMPD1 gene, which encodes sphingomyelin phosphodiesterase (ASM). Except for liver and spleen enlargement and lung disease, two subtypes (Type A and B) of NDP have different onset times, survival times, ASM activities, and neurological abnormalities. To comprehensively explore NPD's genotype-phenotype association and pathophysiological characteristics, we collected 144 NPD cases with strict quality control through literature mining.

Results: The difference in ASM activity can differentiate NPD type A from other subtypes, with the ratio of ASM activity to the reference values being lower in type A (threshold 0.045 (4.45%)). Severe variations, such as deletion and insertion, can cause complete loss of ASM function, leading to type A, whereas relatively mild missense mutations generally result in type B. Among reported mutations, the p.Arg3AlafsX76 mutation is highly prevalent in the Chinese population, and the p.R608del mutation is common in Mediterranean countries. The expression profiles of SMPD1 from GTEx and single-cell RNA sequencing data of multiple fetal tissues showed that high expressions of SMPD1 can be observed in the liver, spleen, and brain tissues of adults and hepatoblasts, hematopoietic stem cells, STC2_TLX1-positive cells, mesothelial cells of the spleen, vascular endothelial cells of the cerebellum and the cerebrum of fetuses, indicating that SMPD1 dysfunction is highly likely to have a significant effect on the function of those cell types during development and the clinicians need pay attention to these organs or tissues as well during diagnosis. In addition, we also predicted 21 new pathogenic mutations in the SMPD1 gene that potentially cause the NPD, signifying that more rare cases will be detected with those mutations in SMPD1. Finally, we also analysed the function of the NPD type A cells following the extracellular milieu.

Conclusions: Our study is the first to elucidate the effects of SMPD1 mutation on cell types and at the tissue level, which provides new insights into the genotype-phenotype association and can help in the precise diagnosis of NPD.

Keywords: Acid sphingomyelinase deficiency; Genotype; Niemann-pick disease type a and B; Novel target for the subtypes; Phenotype.

Fig. 1

A novel threshold for determining NPD subtypes. A ASM levels in clinical cases are collected. B ROC curve for the predictability of the threshold. ASM ratio, the ratio of the activity of acid sphingomyelin phosphodiesterase of the patients to the reference value; NPA, Niemann–Pick disease type A; NPB, Niemann–Pick disease type B; ROC, receiver operating characteristic curve; AUC, area under the curve

Fig. 2

Statistics of the mutation sites on the SMPD1 gene. A Distribution of the patients by onset age. F, female. M, male. B Country of origin of the patients: Mediterranean countries, including Italy, Algeria, Spain, Turkey, Maghreb, Jordan, and North Africa; Asian countries, such as China and Japan; European countries, such as Caucasian (documented by the research), Poland, Gypsy (documented by the research), and the Netherlands; Middle East countries including Iran and Palestine. C Amino acid mutation frequency in all collected cases. D SMPD1 mutation types (do not include all mutations). Severe mutations include deletions, insertions, and nonsense. E SMPD1 mutation distribution in domains of ASM domains in each subtype of NPD. A, NPA. AB, intermediate NPD subtype. B, NPB. F Distribution of missense mutations on the conserved domain of the human ASM protein. Each point represents one reported mutation in the collected cases. Points are coloured according to the domains. G The landscape of SMPD1 mutations and 21 novel pathogenic variants prediction based on the databases of ClinVar, ANNOVAR and the EVE model. Purple squares, novel predicted pathogenic variants. Orange triangles, pathogenic/likely pathogenic variants from the ClinVar. Domains were annotated by NCBI. Please note: in A, E panels, A, NPA. AB, intermediate. B, NPB. In D, F, and G, domains were retrieved from the NCBI (NP_000534.3), namely, saposin (B) (smart00741, Location: 89 → 161), metallophosphatase domain (cd00842, Location: 202 → 497) and Calcineurin-like phosphoesterase domain (Metallophos for short, pfam00149, Location: 255 → 462)

Fig. 3

Pathogenic variants allele distribution. A Top 20 pathogenic variants in gnomAD. B Frequency of the pathogenic/likely pathogenic variants with population specificity in gnomAD. AAA, African/African American. AJ, Ashkenazi Jewish. EA, East Asian. ENF, European (non-Finnish). FIN, Finnish. LAA, Latino/Admixed American. SA, South Asian. C SMPD1 mutation allele frequency in two data sources. Huabiao, the public project database of whole exomes of the Chinese Han. EA, data from east Asia of the gnomAD

Fig. 4

SMPD1 gene expression in all tissues. Expression profiles of the SMPD1 gene in different organs based on the GSE156793

Fig. 5

Expression profiles of the SMPD1 gene based on GTEx data

Fig. 6

Expression profile of the SMPD1 protein with the help of the public datasets. A SMPD1 protein expression in Wang et al. B SMPD1 protein expression in the study of Carlyle et al. C SMPD1 protein expression in the study of Kushner et al. D Correlation analysis between the ASM expression at both protein and gene level by spearman. Tissues studied were the consensus with GTEx and ProteomicsDB

Fig. 7

Pathways involved in NPA fibroblasts cells in response to sphingomyelin treatment. A DEGs illustrated with a volcano plot. B CASP7, PRKCD and SMPD1 expression following the SM treatment. *, p < 0.05. C Enrichment analysis of Gene Ontology (GO) terms withtop 50 DEGS. Oxidoreductase activity 1, oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen. Oxidoreductase activity 2, oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water. BP, biological process. CC, cellular component. MF, molecular function