Autosomal-dominant adult neuronal ceroid lipofuscinosis caused by duplication in DNAJC5 initially missed by Sanger and whole-exome sequencing
Language English Country Great Britain, England Media print-electronic
Document type Journal Article, Research Support, Non-U.S. Gov't
PubMed
31919451
PubMed Central
PMC7253421
DOI
10.1038/s41431-019-0567-2
PII: 10.1038/s41431-019-0567-2
Knihovny.cz E-resources
- MeSH
- Cell Line MeSH
- Adult MeSH
- Gene Duplication * MeSH
- False Negative Reactions MeSH
- Genetic Testing standards MeSH
- Middle Aged MeSH
- Humans MeSH
- Membrane Proteins genetics metabolism MeSH
- Mice MeSH
- Neuronal Ceroid-Lipofuscinoses genetics pathology MeSH
- Neurons metabolism MeSH
- Protein Processing, Post-Translational MeSH
- HSP40 Heat-Shock Proteins genetics metabolism MeSH
- Whole Genome Sequencing standards MeSH
- Protein Transport MeSH
- Animals MeSH
- Check Tag
- Adult MeSH
- Middle Aged MeSH
- Humans MeSH
- Male MeSH
- Mice MeSH
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- cysteine string protein MeSH Browser
- Membrane Proteins MeSH
- HSP40 Heat-Shock Proteins MeSH
Adult-onset neuronal ceroid lipofuscinoses (ANCL, Kufs disease) are rare hereditary neuropsychiatric disorders characterized by intralysosomal accumulation of ceroid in tissues. The ceroid accumulation primarily affects the brain, leading to neuronal loss and progressive neurodegeneration. Although several causative genes have been identified (DNAJC5, CLN6, CTSF, GRN, CLN1, CLN5, ATP13A2), the genetic underpinnings of ANCL in some families remain unknown. Here we report one family with autosomal dominant (AD) Kufs disease caused by a 30 bp in-frame duplication in DNAJC5, encoding the cysteine-string protein alpha (CSPα). This variant leads to a duplication of the central core motif of the cysteine-string domain of CSPα and affects palmitoylation-dependent CSPα sorting in cultured neuronal cells similarly to two previously described CSPα variants, p.(Leu115Arg) and p.(Leu116del). Interestingly, the duplication was not detected initially by standard Sanger sequencing due to a preferential PCR amplification of the shorter wild-type allele and allelic dropout of the mutated DNAJC5 allele. It was also missed by subsequent whole-exome sequencing (WES). Its identification was facilitated by reanalysis of original WES data and modification of the PCR and Sanger sequencing protocols. Independently occurring variants in the genomic sequence of DNAJC5 encoding the cysteine-string domain of CSPα suggest that this region may be more prone to DNA replication errors and that insertions or duplications within this domain should be considered in unsolved ANCL cases.
Center for Pediatric Genomic Medicine Children's Mercy Hospital Kansas City MO USA
Centre Hospitalier de L´Universite de Montréal Montréal QC Canada
Montreal Neurological Hospital and Institute McGill University Montreal QC Canada
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Noskova L, Stranecky V, Hartmannova H, Pristoupilova A, Baresova V, Ivanek R, et al. Mutations in DNAJC5, encoding cysteine-string protein alpha, cause autosomal-dominant adult-onset neuronal ceroid lipofuscinosis. Am J Hum Genet. 2011;89:241–52. doi: 10.1016/j.ajhg.2011.07.003. PubMed DOI PMC
Arsov T, Smith KR, Damiano J, Franceschetti S, Canafoglia L, Bromhead CJ, et al. Kufs disease, the major adult form of neuronal ceroid lipofuscinosis, caused by mutations in CLN6. Am J Hum Genet. 2011;88:566–73. doi: 10.1016/j.ajhg.2011.04.004. PubMed DOI PMC
Smith KR, Dahl HH, Canafoglia L, Andermann E, Damiano J, Morbin M, et al. Cathepsin F mutations cause Type B Kufs disease, an adult-onset neuronal ceroid lipofuscinosis. Hum Mol Genet. 2013;22:1417–23. doi: 10.1093/hmg/dds558. PubMed DOI PMC
Smith KR, Damiano J, Franceschetti S, Carpenter S, Canafoglia L, Morbin M, et al. Strikingly different clinicopathological phenotypes determined by progranulin-mutation dosage. Am J Hum Genet. 2012;90:1102–7. doi: 10.1016/j.ajhg.2012.04.021. PubMed DOI PMC
van Diggelen OP, Thobois S, Tilikete C, Zabot MT, Keulemans JL, van Bunderen PA, et al. Adult neuronal ceroid lipofuscinosis with palmitoyl-protein thioesterase deficiency: first adult-onset patients of a childhood disease. Ann Neurol. 2001;50:269–72. doi: 10.1002/ana.1103. PubMed DOI
Xin W, Mullen TE, Kiely R, Min J, Feng X, Cao Y, et al. CLN5 mutations are frequent in juvenile and late-onset non-Finnish patients with NCL. Neurology. 2010;74:565–71. doi: 10.1212/WNL.0b013e3181cff70d. PubMed DOI
Bras J, Verloes A, Schneider SA, Mole SE, Guerreiro RJ. Mutation of the parkinsonism gene ATP13A2 causes neuronal ceroid-lipofuscinosis. Hum Mol Genet. 2012;21:2646–50.. doi: 10.1093/hmg/dds089. PubMed DOI PMC
Cotman SL, Karaa A, Staropoli JF, Sims KB. Neuronal ceroid lipofuscinosis: impact of recent genetic advances and expansion of the clinicopathologic spectrum. Curr Neurol Neurosci Rep. 2013;13:366. doi: 10.1007/s11910-013-0366-z. PubMed DOI PMC
Kmoch S, Stranecky V, Emes RD, Mitchison HM. Bioinformatic perspectives in the neuronal ceroid lipofuscinoses. Biochim Biophys Acta. 2013;1832:1831–41. doi: 10.1016/j.bbadis.2012.12.010. PubMed DOI
Berkovic SF, Staropoli JF, Carpenter S, Oliver KL, Kmoch S, Anderson GW, et al. Diagnosis and misdiagnosis of adult neuronal ceroid lipofuscinosis (Kufs disease) Neurology. 2016;87:579–84. PubMed PMC
Ehling R, Noskova L, Stranecky V, Hartmannova H, Pristoupilova A, Hodanova K, et al. Cerebellar dysfunction in a family harboring the PSEN1 mutation co-segregating with a cathepsin D variant p.A58V. J Neurol Sci. 2013;326:75–82. doi: 10.1016/j.jns.2013.01.017. PubMed DOI
van den Ameele J, Jedlickova I, Pristoupilova A, Sieben A, Van Mossevelde S, Ceuterick-de Groote C, et al. Teenage-onset progressive myoclonic epilepsy due to a familial C9orf72 repeat expansion. Neurology. 2018;90:e658–e663. doi: 10.1212/WNL.0000000000004999. PubMed DOI
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Bioinformatics. 2013;00:1–2.
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–303. doi: 10.1101/gr.107524.110. PubMed DOI PMC
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491–8. doi: 10.1038/ng.806. PubMed DOI PMC
Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinform. 2013;43:11 10 1–33. doi: 10.1002/0471250953.bi1110s43. PubMed DOI PMC
Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012;6:80–92. doi: 10.4161/fly.19695. PubMed DOI PMC
Paila U, Chapman BA, Kirchner R, Quinlan AR. GEMINI: integrative exploration of genetic variation and genome annotations. PLoS Comput Biol. 2013;9:e1003153. doi: 10.1371/journal.pcbi.1003153. PubMed DOI PMC
Landmann L. Deconvolution improves colocalization analysis of multiple fluorochromes in 3D confocal data sets more than filtering techniques. J Microsc. 2002;208(Pt 2):134–47. doi: 10.1046/j.1365-2818.2002.01068.x. PubMed DOI
Manders EMM, Verbeek FJ, Aten JA. Measurement of colocalization of objects in dual-color confocal images. J Microsc. 1993;169:375–82. doi: 10.1111/j.1365-2818.1993.tb03313.x. PubMed DOI
Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016;536:285–91. doi: 10.1038/nature19057. PubMed DOI PMC
Mole SE, Gardener E. Mutation and patient database for human NCL genes. 2019. https://www.ucl.ac.uk/ncl-disease/mutation-and-patient-database/mutation-and-patient-datasheets-human-ncl-genes. Accessed 22 Oct 2019.
Diez-Ardanuy C, Greaves J, Munro KR, Tomkinson NC, Chamberlain LH. A cluster of palmitoylated cysteines are essential for aggregation of cysteine-string protein mutants that cause neuronal ceroid lipofuscinosis. Sci Rep. 2017;7:10. doi: 10.1038/s41598-017-00036-8. PubMed DOI PMC
Burgoyne RD, Morgan A. Cysteine string protein (CSP) and its role in preventing neurodegeneration. Semin Cell Dev Biol. 2015;40:153–9. doi: 10.1016/j.semcdb.2015.03.008. PubMed DOI PMC
Gorenberg EL, Chandra SS. The role of co-chaperones in synaptic proteostasis and neurodegenerative disease. Front Neurosci. 2017;11:248. doi: 10.3389/fnins.2017.00248. PubMed DOI PMC
Fogel BL. Genetic and genomic testing for neurologic disease in clinical practice. Handb Clin Neurol. 2018;147:11–22. doi: 10.1016/B978-0-444-63233-3.00002-6. PubMed DOI