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New variants in Spanish Niemann–Pick type c disease patients

Abstract

Niemann–Pick type C (NPC) disease is a rare inherited disease, with progressive neurodegeneration as the main symptom. It is a lysosomal storage disorder caused by mutations in NPC1 or NPC2 genes, leading to a lysosomal cholesterol trafficking impairment. Disease indicators are the clinical suspicion and biomarker levels. However, a genetic study is mandatory for the diagnosis, which is complicated due to the different variants with unknown significance. The aim of this work was to identify the variants responsible for NPC in our pediatric population. Twenty-two samples from non-related infants believed to have NPC disease were analyzed during the last 3 years. Surrogate biomarkers of the disease were evaluated whenever possible. Sanger sequencing for both genes is reported for all samples. Complementary genetic studies were performed when necessary. NPC disease was confirmed in 31.8% of subjects due to homozygous or compound heterozygous genetic variants in NPC1. The following four novel variants were identified: a gross deletion variant composed of the gene promoter and the first exon, NM_000271.3:c.385delT, NM_000271.3:c.1553+1342_1655-291del, and NM_000271.3:c.1757delA. None had functional activity and all resulted in important structural changes in the protein.

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Abbreviations

7-KC:

7-Ketocholesterol

ASMD:

Acid sphingomyelinase deficiency

CCL18/PARC:

Chemokine (C–C motif) ligand 18/pulmonary and activation-regulated chemokine

ChT:

Chitotriosidase

HGMD:

Human gene mutation database

lysoSM:

Lysosphingomielyne

LSD:

Lysosomal storage disease

MLPA:

Multiplex ligation-dependent probe amplification

NCBI:

National Center for Biotechnology Information

NPC:

Niemann–Pick type C

ORF:

Open reading frame

PDB:

Protein data bank

SSD:

Sterol-sensing domain

References

  1. 1.

    Lloyd-evans E, Morgan AJ, He X et al (2010) Niemann-Pick disease type C1 is a sphingosine storage disease that causes deregulation of lysosomal calcium. Nat Med 14:1247–1256. https://doi.org/10.1038/nm.1876

  2. 2.

    Vanier MT, Gissen P, Bauer P et al (2016) Diagnostic tests for Niemann-Pick disease type C (NP-C): a critical review. Mol Genet Metab 118:244–254. https://doi.org/10.1016/j.ymgme.2016.06.004

  3. 3.

    Sitarska D, Ługowska A (2019) Laboratory diagnosis of the Niemann–Pick type C disease: an inherited neurodegenerative disorder of cholesterol metabolism. Metab Brain Dis 34:1253–1260. https://doi.org/10.1007/s11011-019-00445-w

  4. 4.

    Vanier MT (2010) Niemann–Pick disease type C. Orphanet J Rare Dis 5:1–18. https://doi.org/10.1186/1750-1172-5-16

  5. 5.

    Hammond N, Munkacsi AB, Sturley SL (2019) The complexity of a monogenic neurodegenerative disease: more than two decades of therapeutic driven research into Niemann–Pick type C disease. Biochim Biophys Acta Mol Cell Biol Lipids 1864:1109–1123. https://doi.org/10.1016/j.bbalip.2019.04.002

  6. 6.

    Li X, Saha P, Li J et al (2016) Clues to the mechanism of cholesterol transfer from the structure of NPC1 middle lumenal domain bound to NPC2. Proc Natl Acad Sci USA 113:10079–10084. https://doi.org/10.1073/pnas.1611956113

  7. 7.

    Ioannou YA (2000) The structure and function of the Niemann–Pick C1 protein. Mol Genet Metab 181:175–181. https://doi.org/10.1006/mgme.2000.3061

  8. 8.

    Watari H, Blanchette-Mackie EJ, Dwyer NK et al (1999) Mutations in the leucine zipper motif and sterol-sensing domain inactivate the Niemann–Pick C1 glycoprotein. J Biol Chem 274:21861–21866. https://doi.org/10.1074/JBC.274.31.21861

  9. 9.

    Infante RE, Radhakrishnan A, Abi-Mosleh L et al (2008) Purified NPC1 protein II: Localization of sterol binding to a 240-amino acid soluble luminal loop. J Biol Chem 283:1064–1075. https://doi.org/10.1074/jbc.M707944200

  10. 10.

    Ko DC, Binkley J, Sidow A, Scott MP (2003) The integrity of a cholesterol-binding pocket in Niemann–Pick C2 protein is necessary to control lysosome cholesterol levels. Proc Natl Acad Sci USA 100:2518–2525. https://doi.org/10.1073/pnas.0530027100

  11. 11.

    Friedland N, Liou H-L, Lobel P, Stock AM (2003) Structure of a cholesterol-binding protein deficient in Niemann–Pick type C2 disease. Proc Natl Acad Sci USA 100:2512–2517. https://doi.org/10.1073/pnas.0437840100

  12. 12.

    Newton J, Milstien S, Spiegel S (2018) Niemann–Pick type C disease: the atypical sphingolipidosis. Adv Biol Regul 70:82–88. https://doi.org/10.1016/j.jbior.2018.08.001

  13. 13.

    Patterson MC, Clayton P, Gissen P et al (2017) Recommendations for the detection and diagnosis of Niemann–Pick disease type C: an update. Neurol Clin Pract 7:499–511. https://doi.org/10.1212/CPJ.0000000000000399

  14. 14.

    Barone R, Sotgiu S, Musumeci S (2007) Plasma chitotriosidase in health and pathology. Clin Lab 53:321–333

  15. 15.

    Boot RG, Verhoek M, De FM et al (2004) Marked elevation of the chemokine CCL18/PARC in Gaucher disease: a novel surrogate marker for assessing therapeutic intervention. Blood 103:33–40. https://doi.org/10.1182/blood-2003-05-1612.Reprints

  16. 16.

    Ries M, Schaefer E, Lührs T et al (2006) Critical assessment of chitotriosidase analysis in the rational laboratory diagnosis of children with Gaucher disease and Niemann–Pick disease type A/B and C. J Inherit Metab Dis 29:647–652. https://doi.org/10.1007/s10545-006-0363-3

  17. 17.

    De Castro-Orós I, Irún P, Cebolla JJ et al (2017) Assessment of plasma chitotriosidase activity, CCL18/PARC concentration and NP-C suspicion index in the diagnosis of Niemann–Pick disease type C: a prospective observational study. J Transl Med 15:43. https://doi.org/10.1186/s12967-017-1146-3

  18. 18.

    Hammerschmidt TG, de Oliveira Schmitt Ribas G, Saraiva-Pereira ML et al (2017) Molecular and biochemical biomarkers for diagnosis and therapy monitorization of Niemann–Pick type C patients. Int J Dev Neurosci 66:18–23. https://doi.org/10.1016/j.ijdevneu.2017.11.007

  19. 19.

    Zhang H, Wang Y, Lin N et al (2014) Diagnosis of Niemann–Pick disease type C with 7-ketocholesterol screening followed by NPC1/NPC2 gene mutation confirmation in Chinese patients. Orphanet J Rare Dis 9:82. https://doi.org/10.1186/1750-1172-9-82

  20. 20.

    Welford RWD, Garzotti M, Marques Lourenço C et al (2014) Plasma lysosphingomyelin demonstrates great potential as a diagnostic biomarker for Niemann–Pick disease type C in a Retrospective study. PLoS ONE 9:e114669. https://doi.org/10.1371/journal.pone.0114669

  21. 21.

    Giese A-K, Mascher H, Grittner U et al (2015) A novel, highly sensitive and specific biomarker for Niemann–Pick type C1 disease. Orphanet J Rare Dis 10:78. https://doi.org/10.1186/s13023-015-0274-1

  22. 22.

    Sidhu R, Mondjinou Y, Qian M et al (2019) N-acyl-O-phosphocholineserines: structures of a novel class of lipids that are biomarkers for Niemann–Pick C1 disease. J Lipid Res 60:1410–1424. https://doi.org/10.1194/jlr.RA119000157

  23. 23.

    Maekawa J, Matsumoto N et al (2019) Structural determination of lysosphingomyelin-509 and discovery of novel class lipids from patients with Niemann–Pick disease type C. Int J Mol Sci 20:5018. https://doi.org/10.3390/ijms20205018

  24. 24.

    Polo G, Burlina AP, Kolamunnage TB et al (2017) Diagnosis of sphingolipidoses: a new simultaneous measurement of lysosphingolipids by LC-MS/MS. Clin Chem Lab Med 55:403–414. https://doi.org/10.1515/cclm-2016-0340

  25. 25.

    Papandreou A, Gissen P (2016) Diagnostic workup and management of patients with suspected Niemann–Pick type C disease. Ther Adv Neurol Disord Ther Adv Neurol Disord 9:216–229

  26. 26.

    Jiang X, Sidhu R, Mydock-McGrane L et al (2016) Development of a bile acid–based newborn screen for Niemann–Pick disease type C. Sci Transl Med 8:337. https://doi.org/10.1126/scitranslmed.aaf2326

  27. 27.

    Geberhiwot T, Moro A, Dardis A et al (2018) Consensus clinical management guidelines for Niemann–Pick disease type C. Orphanet J Rare Dis 13:50. https://doi.org/10.1186/s13023-018-0785-7

  28. 28.

    Cooper D, Ball E, Stenson P, et al (2016) The human gene mutation database. https://www.hgmd.cf.ac.uk/ac/index.php

  29. 29.

    den Dunnen JT, White SJ (2006) MLPA and MAPH: sensitive detection of deletions and duplications. In: Arnette C (ed) Current protocols in human genetics. Wiley, Hoboken, pp 7.14.1–7.14.20

  30. 30.

    Anheim M, Lagha-Boukbiza O, Fleury-Lesaunier M-C et al (2014) Heterogeneity and frequency of movement disorders in juvenile and adult-onset Niemann–Pick C disease. J Neurol 261:174–179. https://doi.org/10.1007/s00415-013-7159-9

  31. 31.

    Vaz-Drago R, Custódio N, Carmo-Fonseca M (2017) Deep intronic mutations and human disease. Hum Genet 136:1093–1111. https://doi.org/10.1007/s00439-017-1809-4

  32. 32.

    Polese-Bonatto M, Bock H, Farias ACS et al (2019) Niemann–Pick disease type C: mutation spectrum and novel sequence variations in the human NPC1 gene. Mol Neurobiol 56:6426–6435. https://doi.org/10.1007/s12035-019-1528-z

  33. 33.

    Mahmoud IG, Elmonem MA, Elkhateeb NM et al (2019) Clinical, biomarker and genetic spectrum of Niemann–Pick type C in Egypt: the detection of nine novel NPC1 mutations. Clin Genet 95:537–539

  34. 34.

    Pineda M, Mengel E, Jahnová H et al (2016) A suspicion index to aid screening of early-onset Niemann–Pick disease type C (NP-C). BMC Pediatr 16:107. https://doi.org/10.1186/s12887-016-0641-7

  35. 35.

    Hollak CEM, van Weely S, van Oers MHJ, Aerts JMFG (1994) Marked elevation of plasma chitotriosidase activity. a novel hallmark of gaucher disease. J Clin Invest 93:1288–1292. https://doi.org/10.1172/JCI117084

  36. 36.

    Irún P, Alfonso P, Aznarez S et al (2013) Chitotriosidase variants in patients with Gaucher disease. Implications for diagnosis and therapeutic monitoring. Clin Biochem 46:1804–1807. https://doi.org/10.1016/j.clinbiochem.2013.09.006

  37. 37.

    Lin N, Zhang H, Qiu W et al (2014) Determination of 7-ketocholesterol in plasma by LC–MS for rapid diagnosis of acid SMase-deficient Niemann–Pick disease. J Lipid Res 55:338–343. https://doi.org/10.1194/jlr.D044024

  38. 38.

    Baila-Rueda L, Cenarro A, Barcelo-Batllori S et al (2013) Simultaneous determination of oxysterols, phytosterols and cholesterol precursors by high performance liquid chromatography tandem mass spectrometry in human serum. Anal methods 5:2249–2257. https://doi.org/10.1039/C3AY26395A

  39. 39.

    Giraldo P, Alfonso P, Irún P et al (2012) Mapping the genetic and clinical characteristics of Gaucher disease in the Iberian Peninsula. Orphanet J Rare Dis 7:17. https://doi.org/10.1186/1750-1172-7-17

  40. 40.

    Landrum MJ, Lee JM, Benson M et al (2016) ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res 44:D862–D868. https://doi.org/10.1093/nar/gkv1222

  41. 41.

    Sievers F, Higgins DG (2018) Clustal Omega for making accurate alignments of many protein sequences. Protein Sci 27:135–145. https://doi.org/10.1002/pro.3290

  42. 42.

    Berman HM, Westbrook J, Feng Z et al (2000) The protein data bank. Nucleic Acids Res 28:235–242. https://doi.org/10.1093/nar/28.1.235

  43. 43.

    Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-Pdb viewer: an environment for comparative protein modeling. Electrophoresis 18:2714–2723. https://doi.org/10.1002/elps.1150181505

  44. 44.

    Macías-Vidal J, Rodríguez-Pascau L, Sánchez-Ollé G et al (2011) Molecular analysis of 30 Niemann–Pick type C patients from Spain. Clin Genet 80:39–49. https://doi.org/10.1111/j.1399-0004.2010.01504.x

  45. 45.

    Millat G, Marçais C, Tomasetto C et al (2001) Niemann–Pick C1 disease: correlations between NPC1 mutations, levels of NPC1 protein, and phenotypes emphasize the functional significance of the putative sterol-sensing domain and of the cysteine-rich luminal loop. Am J Hum Genet 68:1373–1385. https://doi.org/10.1086/320606

  46. 46.

    Ribeiro I, Marcão A, Amaral O et al (2001) Niemann–Pick type C disease : NPC1 mutations associated with severe and mild cellular cholesterol trafficking alterations. Hum Genet. https://doi.org/10.1007/s004390100531

  47. 47.

    Greer WL, Riddell DC, Gillan TL et al (1998) The Nova Scotia (Type D) form of Niemann–Pick disease is caused by a G3097T transversion in NPC1. Am J Hum Genet 63:52–54. https://doi.org/10.1086/301931

  48. 48.

    Yamamoto T, Nanba E, Ninomiya H et al (1999) NPC1 gene mutations in Japanese patients with Niemann–Pick disease type C. Hum Genet 18:10–16. https://doi.org/10.1007/s004399900059

  49. 49.

    Fernández-Valero E, Ballart A, Iturriaga C et al (2005) Identification of 25 new mutations in 40 unrelated Spanish Niemann–Pick type C patients : genotype–phenotype correlations. Clin Genet 68:245–254. https://doi.org/10.1111/j.1399-0004.2005.00490.x

  50. 50.

    Dopazo J, Amadoz A, Bleda M et al (2016) 267 Spanish exomes reveal population-specific differences in disease-related genetic variation. Mol Biol Evol 33:1205. https://doi.org/10.1093/molbev/msw005

  51. 51.

    Yerushalmi B, Sokol RJ, Narkewicz MR et al (2002) Niemann–Pick disease type C in neonatal cholestasis at a North American Center. J Pediatr Gastroenterol Nutr 35:44–50. https://doi.org/10.1097/00005176-200207000-00011

  52. 52.

    Moreira-Silva H, Maio I, Bandeira A et al (2019) Metabolic liver diseases presenting with neonatal cholestasis: at the crossroad between old and new paradigms. Eur J Pediatr 178:515–523. https://doi.org/10.1007/s00431-019-03328-5

  53. 53.

    Miller JN, Pearce DA (2014) Nonsense-mediated decay in genetic disease: friend or foe? Mutat Res Rev Mutat Res. https://doi.org/10.1016/j.mrrev.2014.05.001

  54. 54.

    Slavoff SA, Mitchell AJ, Schwaid AG et al (2013) Peptidomic discovery of short open reading frame–encoded peptides in human cells. Nat Chem Biol 9:59–64. https://doi.org/10.1038/nchembio.1120

  55. 55.

    Menschaert G, Van Criekinge W, Notelaers T et al (2013) Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events. Mol Cell Proteomics 12:1780–1790. https://doi.org/10.1074/mcp.M113.027540

  56. 56.

    Rodríguez-Pascau L, Toma C, Macías-Vidal J et al (2012) Characterisation of two deletions involving NPC1 and flanking genes in Niemann–Pick type C disease patients. Mol Genet Metab 107:716–720. https://doi.org/10.1016/j.ymgme.2012.10.004

  57. 57.

    Stampfer M, Theiss S, Amraoui Y et al (2013) Niemann–Pick disease type C clinical database : cognitive and coordination deficits are early disease indicators. Orphanet J Rare Dis 8:1–11. https://doi.org/10.1186/1750-1172-8-35

  58. 58.

    Kaminski WE, Klünemann H-HH, Ibach B et al (2002) Identification of novel mutations in the NPC1 gene in German patients with Niemann–Pick C disease. J Inherit Metab Dis 25:385–389. https://doi.org/10.1023/a:1020151801060

  59. 59.

    López de Frutos L, Romero-Imbroda J, Rodríguez-Sureda V, Giraldo P (2017) New variant associated with Niemann–Pick disease type C: neurological manifestations and biochemical, molecular, and cellular characterisation. Neurologia. https://doi.org/10.1016/j.nrl.2017.07.010

  60. 60.

    Bountouvi E, Papadopoulou A, Vanier MT et al (2017) Novel NPC1 mutations with different segregation in two related Greek patients with Niemann–Pick type C disease: molecular study in the extended pedigree and clinical correlations. BMC Med Genet 18:51. https://doi.org/10.1186/s12881-017-0409-4

  61. 61.

    Khafizov K, Ivanov MV, Glazova OV, Kovalenko SP (2015) Computational approaches to study the effects of small genomic variations. J Mol Model 21:251. https://doi.org/10.1007/s00894-015-2794-y

  62. 62.

    Topçu M, Aktas D, Öztoprak M et al (2017) Prospective Turkish Cohort Study to investigate the frequency of Niemann–Pick disease type C mutations in consanguineous families with at least one homozygous family member. Mol Diagn Ther 21:643–651. https://doi.org/10.1007/s40291-017-0293-9

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Acknowledgements

The authors thank all the patients and physicians that provide us the samples.

Funding

There is no funding source.

Author information

LLF, Ph.D. designed, performed, and interpreted the Sanger sequencing studies, drafted the initial manuscript, and reviewed and revised the manuscript. JJC, Ph.D. performed part of the biomarker studies, performed and interpreted MLPA studies, and reviewed and revised the manuscript. LAE, M.D., Ph.D., SS, M.D., and AV, M.D., performed the clinical study and reviewed and revised the manuscript. CL coordinated and prepared sample matrices and reviewed and revised the manuscript. PI, Ph.D. performed the biomarker studies and critically reviewed the manuscript for important intellectual content. PG, Ph.D. performed clinical studies, confirmed and accepted the final reports, and reviewed and revised the manuscript. All authors approved of the final manuscript as submitted and agree to be accountable for all aspects of the work.

Correspondence to Laura López de Frutos.

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The study was conducted in accordance with the principles stated in the Declaration of Helsinki-Ethical Principles for Medical Research Involving Human Subjects, Helsinki, Finland, 1964, and as amended in Fortaleza, Brazil, 2013. The study design was approved by the institutional board of the FEETEG foundation.

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López de Frutos, L., Cebolla, J.J., Aldámiz-Echevarría, L. et al. New variants in Spanish Niemann–Pick type c disease patients. Mol Biol Rep (2020). https://doi.org/10.1007/s11033-020-05308-7

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Keywords

  • New variants
  • Niemann–pick type C
  • NPC1
  • Pathogenic variants