Loss of nucleoporin Nup50 is a risk factor for amyotrophic lateral sclerosis

Abstract

The genetic basis of amyotrophic lateral sclerosis (ALS) is still incompletely understood. Using two independent genetic strategies, we show here that a large part of ALS heritability lies in genes expressed in inhibitory and excitatory neurons, especially at splicing sites regulated by a defined set of RNA binding proteins including TDP-43 and FUS. We conducted a transcriptome wide association study (TWAS) and identified 59 loci associated with ALS, including 14 previously identified genes, some of them not previously reaching significance in genome wide association studies. Among the 45 novel genes, several genes are involved in pathways known to be affected in ALS such as mitochondrial metabolism (including ATP5H, ATP5D, BCS1L), proteostasis (including COPS7A, G2E3, TMEM175, USP35) or gene expression and RNA metabolism (including ARID1B, ATXN3, PTBP2, TAF10). Interestingly, decreased expression of NUP50, a constrained gene encoding a nuclear pore basket protein, was associated with ALS in TWAS (Zscore = -4, FDR = 0.034). 11 potentially pathogenic variants (CADD score > 20) in 23 patients were identified in the NUP50 gene, most of them in the region of the protein mediating interaction with Importin alpha, and including 2 frameshift mutations. In cells from two patients carrying NUP50 variants, we showed decreased levels of NUP50 protein. Importantly, knocking down Nup50 led to increased neuronal death associated with p62 and nucleoporin inclusions in cultured neurons, and motor defects in Drosophila and zebrafish models. In all, our study identifies alterations in splicing in neurons as a critical pathogenic process in ALS, uncovers several new loci potentially contributing to ALS missing heritability, and provides genetic evidence linking nuclear pore defects to ALS.

Causal Inference of Genetic Variants and Genes in Amyotrophic Lateral Sclerosis

“…This finding is an important supplement to previous findings suggesting microglia (Clarke and Patani, 2020), astrocytes (Do-Ha et al, 2018;Saez-Atienzar et al, 2021), and glutamatergic neurons Cronin et al (2008) as the key cell types functionally involved in the development of ALS. Our finding on inhibitory neurons is highly consistent with a recent study, which showed that genetic variants associated with ALS were mostly located in genes expressed in neurons, particularly in inhibitory neurons, and ALS risk loci were significantly enriched in excitatory and inhibitory neurons using single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) profiles (Megat et al, 2021). It is known that inhibitory neurons release the neurotransmitter gammaaminobutyric acid (GABA) to regulate the initiation of excitatory neurons, ensuring our brain functions smoothly and accident-free (Foerster et al, 2013;Ramirez-Jarquin and Tapia, 2018).…”

“…We compared the identified loci with the published TWASs and GWASs ( Supplementary Table S1 , p threshold < 5 × 10 −8 ), which was visualized with the R package “VennDiagram” ( Chen and Boutros, 2011 ). However, the latest TWAS ( Megat et al, 2021 ) was unavailable in the medRxiv and not included in the comparison.…”

In Silico Exploration of Metabolically Active Peptides as Potential Therapeutic Agents against Amyotrophic Lateral Sclerosis

“…Other genes including CHRNA3, DAO, GLT8D1, SARM1, ARID1B, G2E3, TMEM175, USP35, PTPRN2, SLC9A8, and MAPKAPK3 seem to be peripheral and less relevant in ALS. It has been reported that some ALS genes are involved in proteostasis (including COPS7A, USP35, TMEM175, and G2E3), mitochondrial metabolism (including ATP5D, ATP5H, and BCS1L) or gene expression and RNA metabolism (including ATXN3, ARID1B, TAF10, and PTBP2), and that decreased expression of NUP50 (a constrained gene encoding a nuclear pore basket protein) was connected with ALS in a transcriptome-wide association study [ 32 ]. A recent study of the existing ALS-causing genes has highlighted the role of structural variants in ALS pathogenesis and shown that genomic structural variants in valosin-containing protein (VCP), C9orf72, and Erb-B4 receptor tyrosine kinase 4 (ERBB4) genes impacted the risk of developing ALS, its progression and survival, the site of onset as well as the age of incidence [ 33 ].…”

“…The genes implicated in ALS in humans and animal models were adapted from the literature without duplication, yielding a total of 76 genes. Forty eight genes ( ATXN2, ANXA11, ALS2, ATXN3, ANG, C9orf72, CHMP2B, CHRNA3, CHCHD10, DCTN1, DNAJC7, DAOEWSR1, ERBB4, FUS, FIG4, GLT8D1, GLE1, hnRNPA2B1, hnRNPA1, KIF5A, MATR3, NEK1, NIPA1, NEFH, OPTN, PON1, PON2, PON3, PFN1, PRPH, SOD1, SETX, SQSTM1, SARM1, SPG11, SIGMAR1, TARDBP, TBK1, TUBA4A, TIA1, TAF15, UNC13A, UBQLN2, VCP, VAPB, VEGF, and WDR7 ) were collected from Smukowski et al [ 8 ], 11 genes ( ARID1B, ATP5H, ATP5D, BCS1L, COPS7A, G2E3, NUP50, PTBP2, TAF10, TMEM175, and USP35 ) from Megat et al [ 32 ], 11 genes ( CFAP410 , COG3 , ERGIC1 , GPX3, TNIP1 , HLA, MOBP, RPSA , PTPRN2 , SLC9A8, and SPATA2 ) from van Rheenen et al [ 112 ], and 6 genes ( ACSL5 , ATG16L2 , MAPKAPK3 , MAP1LC3A , SCFD12 , and PLXNB ) from Saez-Atienzar et al [ 1 ].…”

Brain Catalog: a comprehensive resource for the genetic landscape of brain-related traits

“…By using three TWAS methods (S-PrediXcan, UTMOST and JTI), we identified a total of 102 genes significantly associated with ALS by at least two methods (FDR < 0.05), of which 19 were reported in recent GWAS and post-GWAS studies ( 46 , 50 , 51 ) ( Supplementary Table S4 ), leaving a large number of newly identified candidate genes for ALS. By using the SMR analysis, we tested the exposure measurements from six types of cis-xQTLs and identified a total of 84 genes with significant evidence that likely mediated the genetic associations (FDR < 0.05 and HEIDI > 0.05).…”