Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways

Abstract

Amyotrophic lateral sclerosis (ALS) is a devastating neurological disease with no effective treatment. We report the results of a moderate-scale sequencing study aimed at increasing the number of genes known to contribute to predisposition for ALS. We performed whole-exome sequencing of 2869 ALS patients and 6405 controls. Several known ALS genes were found to be associated, and TBK1 (the gene encoding TANK-binding kinase 1) was identified as an ALS gene. TBK1 is known to bind to and phosphorylate a number of proteins involved in innate immunity and autophagy, including optineurin (OPTN) and p62 (SQSTM1/sequestosome), both of which have also been implicated in ALS. These observations reveal a key role of the autophagic pathway in ALS and suggest specific targets for therapeutic intervention.

Copyright © 2015, American Association for the Advancement of Science.

Figures

Fig. 1. QQ plot of discovery results for dominant coding model

The results for the analysis of 2,874 case and 6,405 control exomes are shown. 16,491 covered genes passed QC with more than one case or control carrier for this test. The genes with the top 10 associations are labeled. The genomic inflation factor, lambda (λ), is 1.061. The association with SOD1 passed correction for multiple tests.

Fig. 2. Variants in TARDBP and VCP

Dominant coding variants are shown in TARDBP and VCP (discovery dataset). Case variants are enriched at the 3′ end of the gene in TARDBP and near the cell division protein 48 domain 2 region in VCP. LoF variants are filled in red, non-synonymous variants are filled in blue, and splice variants are filled in purple. Case variants are shown with red lines, control variants are shown with blue lines, and variants found in both cases and controls are shown with dashed lines.

Fig. 3. A diagram showing the genes and pathways implicated in ALS disease progression

Genes known to have sequence variants that cause or are associated with ALS are indicated in red. These mutations can lead to the formation of protein, or protein-RNA aggregates that appear as inclusion bodies in postmortem samples from both familial and sporadic ALS patients. Some of the mutant proteins adopt “prion-like” structures (see text for more detail). The misfolded proteins activate the ubiquitin/proteasome autophagy pathways to remove the misfolded proteins. Ubiquilin2 functions in both the Ub-proteosome and autophagy pathways. TBK-1 (boxed) lies at the interface between autophagy and inflammation and associates with and phosphorylates both optineurin and p62, which can, in turn, enhance inflammation. ISG15 is induced by type I interferons (α & β) and interacts with p62 and HDAC6 in the autophagosome.

Fig. 4. Variants in TBK1 and OPTN

Dominant not benign variants are shown in TBK1 and OPTN (combined datasets). LoF variants are filled in red, non-synonymous variants are filled in blue, and splice variants are filled in purple. Case variants are shown with red lines, control variants are shown with blue lines, and variants found in both cases and controls are shown with dashed lines.