Genome-wide Analyses Identify KIF5A as a Novel ALS Gene

To identify novel genes associated with ALS, we undertook two lines of investigation. We carried out a genome-wide association study comparing 20,806 ALS cases and 59,804 controls. Independently, we performed a rare variant burden analysis comparing 1,138 index familial ALS cases and 19,494 controls. Through both approaches, we identified kinesin family member 5A (KIF5A) as a novel gene associated with ALS. Interestingly, mutations predominantly in the N-terminal motor domain of KIF5A are causative for two neurodegenerative diseases: hereditary spastic paraplegia (SPG10) and Charcot-Marie-Tooth type 2 (CMT2). In contrast, ALS-associated mutations are primarily located at the C-terminal cargo-binding tail domain and patients harboring loss-of-function mutations displayed an extended survival relative to typical ALS cases. Taken together, these results broaden the phenotype spectrum resulting from mutations in KIF5A and strengthen the role of cytoskeletal defects in the pathogenesis of ALS.Peer reviewe

Targeted Exon Capture and Sequencing in Sporadic Amyotrophic Lateral Sclerosis

<div><p>Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease that results in progressive degeneration of motor neurons, ultimately leading to paralysis and death. Approximately 10% of ALS cases are familial, with the remaining 90% of cases being sporadic. Genetic studies in familial cases of ALS have been extremely informative in determining the causative mutations behind ALS, especially as the same mutations identified in familial ALS can also cause sporadic disease. However, the cause of ALS in approximately 30% of familial cases and in the majority of sporadic cases remains unknown. Sporadic ALS cases represent an underutilized resource for genetic information about ALS; therefore, we undertook a targeted sequencing approach of 169 known and candidate ALS disease genes in 242 sporadic ALS cases and 129 matched controls to try to identify novel variants linked to ALS. We found a significant enrichment in novel and rare variants in cases versus controls, indicating that we are likely identifying disease associated mutations. This study highlights the utility of next generation sequencing techniques combined with functional studies and rare variant analysis tools to provide insight into the genetic etiology of a heterogeneous sporadic disease.</p></div

Sequenced genes and hits category repartitions.

<p>All genes fall into the four following categories: known ALS disease genes (Known ALS), genes potentially associated with ALS (Associated), candidate genes from a previously published analysis of ALS trios (Trios) and genes containing RNA Recognition Motifs (RRM) bearing high prion scores or are very toxic when expressed in yeast. A) Pie chart showing the four categories of genes sequenced. B) Bar graph showing the number of rare or novel variants found in cases in controls for the genes in which the most variants were found. The number of variants found in controls was adjusted for a control cohort of the same size than the ALS cohort. C) Localization of novel variants (in red) identified in this study for some of the top hits. Position of some selected variants already linked with ALS, or other diseases (Floating-Harbor syndrome, SRCAP), are indicated in orange (or in orange heat map, SOD1).</p

ALS variants prevalence among different genetic backgrounds.

<p>Prevalence of ANG, FUS, OPTN and SOD1 variants in ALS between our American cohort and Irish, Italian and Korean populations <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004704#pgen.1004704-Kenna2" target="_blank">[35]</a>–<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004704#pgen.1004704-Chi2" target="_blank">[38]</a>.</p><p>ALS variants prevalence among different genetic backgrounds.</p

Predicted effects of new TAF15 variant on aggregation and conservation.

<p>A) ZipperDB prediction of the increase of the TAF15 p.R150K variant fibrilization propensity versus the wild type. B) TAF15 p.R150 residue is highly conserved within mammals.</p

Functional characterization of newly identified p.Y526C FUS variant.

<p>V5-tagged wild type FUS, ALS causative P525L and newly identified Y526C variants were transfected into N2A mouse neuroblastoma cells and their localization was determined by fluorescence microscopy. As previously reported wild type FUS localized in the nucleus while P525L and Y526C FUS were mislocalized to the cytoplasm. Scale bar is 30µm.</p

Comparison with Irish population.

<p>Genes are sorted into two categories, depending on whether they where implicated in the Mendelian form of the disease (equivalent to the “known ALS” category in this paper) or are low penetrance/tentative ALS genes (“associated”), as used in the original publication <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004704#pgen.1004704-Kenna2" target="_blank">[35]</a>.</p><p>Comparison with Irish population.</p

SNPs previously associated with ALS.

<p>Number of variants in ALS and control samples for fourteen SNPs in ten genes (<i>ALAD, ANG, APEX1, APOE, HFE, OGG1, PON1, PON2, PVR</i> and <i>SOD2</i>) previously linked with ALS <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004704#pgen.1004704-Wang1" target="_blank">[54]</a>–<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004704#pgen.1004704-Greenway2" target="_blank">[86]</a>.</p><p>SNPs previously associated with ALS.</p