Genetic reports abstractAssociation of NIPA1 repeat expansions with amyotrophic lateral sclerosis in a large international cohort
Introduction
Amyotrophic lateral sclerosis (ALS) is a rapidly progressive neurodegenerative disorder characterized by the loss of both upper and lower motor neurons leading to progressive weakness, spasticity, and ultimately respiratory failure (Hardiman et al., 2011, van Es et al., 2017). The complex genetic architecture of ALS is characterized by 5%–15% of patients with a positive family history, where it is assumed that there is a single causal mutation (Andersen and Al-Chalabi, 2011). However, even in most seemingly sporadic patients, a large genetic contribution is expected and causal mutations have been reported despite a negative family history (Al-Chalabi et al., 2017, McLaughlin et al., 2015). To date, mutations in more than 20 different genes have been implicated in ALS, one of the most prominent being an intronic repeat expansion in C9orf72 (Al-Chalabi et al., 2017).
In addition to C9orf72, repeat expansions in other genes have been reported in ALS, including ATXN2 and NIPA1 (Blauw et al., 2012, Elden et al., 2010). NIPA1 (nonimprinted in Prader-Willi/Angelman syndrome 1) mutations are known to cause hereditary spastic paraplegia (HSP) type 6, a neurodegenerative disease characterized by slowly progressive upper motor neuron signs (predominantly in the lower limbs) and is a condition that to some extent has phenotypic overlap with ALS (Rainier et al., 2003). Interestingly, a genomewide screen for copy number variants found an association with rare deletions in NIPA1 and ALS and subsequent genetic analyses revealed that long (or expanded) polyalanine repeats in NIPA1 confer increased disease susceptibility (Blauw et al., 2010, Blauw et al., 2012). In most people (98%), the 5′-end of NIPA1 (NCBI: NM_144599.4) encodes for a stretch of 12 or 13 alanine residues of which 7 or 8 are encoded by a (GCG)n trinucleotide repeat (TNR), although both shorter and longer GCG stretches have been reported in nonaffected individuals (Chai et al., 2003). In the previous study, an analysis of an international cohort of 2292 patients with ALS and 2777 controls showed that “long” repeats (>8) in NIPA1 were enriched in ALS cases compared with controls (5.5% versus 3.6%; OR 1.71; p = 1.6 × 10−4) (Blauw et al., 2012).
Although interesting and potentially relevant, only a small fraction of initially positive results from candidate gene studies (such as that performed on NIPA1) replicated consistently (Hirschhorn et al., 2002). Therefore, additional steps, such as replication of the findings and imposing a proper significance threshold (such as exome or genomewide significance), are required to make any claims of causality (MacArthur et al., 2014).
We therefore set out to perform a large-scale replication study to further investigate the role of NIPA1 polyalanine expansions with ALS, in which we characterized NIPA1 repeat size in a large international cohort of patients with ALS and unaffected controls and then meta-analyze our results with previous reports.
Section snippets
Subjects
All participants gave written informed consent and approval was obtained from the local, relevant ethical committees for medical research. Genotyping experiments were performed on 6231 samples comprising 3955 patients with ALS and 2276 healthy controls from 6 populations. All patients were diagnosed according to the revised El Escorial criteria. Control subjects were from ongoing population-based studies on risk factors in ALS. All related individuals were excluded from further analysis. The
Replication
We first tried to replicate the initial findings in an independent Dutch cohort comprising 1517 ALS cases and 1370 unaffected controls by genotyping the GCG repeat length in NIPA1 using repeat PCR and/or Sanger sequencing. As was reported previously, we found the most frequent alleles to consist of either 7 or 8 (GCG)n repeats (25% and 72%, respectively) (Fig. 1). Our analysis showed a similar allele frequency difference of expanded or “long” alleles (repeat length of 9 or longer) between
Discussion
In this study, we included a large international cohort and additionally meta-analyzed the NIPA1 expansion genotypes in a total of 6245 patients with ALS and 5051 controls. Given that we were able to replicate our previous results in an independent cohort and observed an increase in significance in the overall meta-analysis, our data add to the evidence that expanded NIPA1 repeats are a risk factor for sporadic ALS. Mutations in NIPA1 were already known to cause HSP type 6, a neurodegenerative
Disclosure statement
L.H. van den Berg serves on scientific advisory boards for the Prinses Beatrix Spierfonds, Thierry Latran Foundation, Biogen, and Cytokinetics; and serves on the editorial board of Amyotrophic Lateral Sclerosis And Frontotemporal Degeneration and the Journal of Neurology, Neurosurgery, and Psychiatry. O. Hardiman has received speaking honoraria from Novarits, Biogen Idec, Sanofi Aventis, and Merck-Serono; has been a member of advisory panels for Biogen Idec, Allergen, Ono Pharmaceuticals,
Acknowledgements
This study was supported by the ALS Foundation Netherlands, the Belgian ALS Liga and National Lottery, and Agency for Innovation by Science and Technology (IWT), and the MND Association (UK) (Project MinE, www.projectmine.com). Research leading to these results has received funding from the European Community's Health Seventh Framework Program (FP7/2007-2013). This study was supported by ZonMW under the frame of E-Rare-2, the ERA Net for Research on Rare Diseases (PYRAMID). This is an EU Joint
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2023, Neurobiology of AgingCitation Excerpt :DNA repeat expansions are an important part of the genetic architecture of ALS.; Intronic hexanucleotide repeats in C9orf72 are is the most frequent genetic cause of ALS. Additionally, CAA trinucleotide expansions in NIPA1 and CAG expansions in ATXN1 and ATXN2 have been associated with the disease (Blauw et al., 2012; DeJesus-Hernandez et al., 2011; Elden et al., 2010; Tazelaar et al., 2020; Tazelaar et al., 2019). Repetitive elements comprise a large part of the human genome, but despite recent advances, accurate repeat-length detection from WGS-data remains challenging (de Koning et al., 2011; Dolzhenko et al., 2020; Dolzhenko et al., 2019).
Repeats expansions in ATXN2, NOP56, NIPA1 and ATXN1 are not associated with ALS in Africans
2021, IBRO Neuroscience ReportsCitation Excerpt :In this study we found no difference between long alleles (≥9 GCG repeats) among South African ALS and controls; this contrasts with previous reports in northern Europeans in which the long alleles were >1.5x more likely in cases with ALS (Blauw et al., 2012; Tazelaar et al., 2019). However, our results are similar to a recent multicohort analysis from ProjectMinE, which included substantial numbers of cases with ALS (and controls) from the United Kingdom and the United States, and which found similar frequencies of NIPA1 long alleles between ALS cases and controls (4.7 vs 4.4%) (Tazelaar et al., 2019; van Blitterswijk et al., 2014). A modest association between ATXN1 intermediate REs 33–38 and ALS in Europeans has been reported (Tazelaar et al., 2020), but this was not replicated in this African sample.
The genetic architecture of ALS
2021, Neurobiology of DiseaseCitation Excerpt :Using next-generation sequencing data, these tools show high efficiency in detecting expanded alleles and can be used as accurate quantifiers of repeat expansions in the genome (Dolzhenko et al., 2017; Dolzhenko et al., 2020). Other repeats have also been investigated, including in NIPA1 (Tazelaar et al., 2019), and in other ataxia genes (Lattante et al., 2018; Hirano et al., 2018; Tazelaar et al., 2020). Using DNA pooling, a dinucleotide repeat in the ELP3 gene was found to be associated with ALS and the gene shown to be vital for normal neuronal function (Simpson et al., 2009).
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This article contains supplementary material available from the authors by request or via the Internet at https://doi.org/10.1016/j.neurobiolaging.2018.09.012.
- 1
These authors contributed equally.
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Members and affiliations of the Project MinE ALS Sequencing Consortium are listed in Supplementary Information.