Rare Variant Burden Analysis within Enhancers Identifies CAV1 as an ALS Risk Gene

Abstract

Summary Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disease. CAV1 and CAV2 organize membrane lipid rafts (MLRs) important for cell signaling and neuronal survival, and overexpression of CAV1 ameliorates ALS phenotypes in vivo . Genome-wide association studies localize a large proportion of ALS risk variants within the non-coding genome, but further characterization has been limited by lack of appropriate tools. By designing and applying a pipeline to identify pathogenic genetic variation within enhancer elements responsible for regulating gene expression, we identify disease-associated variation within CAV1/CAV2 enhancers, which replicate in an independent cohort. Discovered enhancer mutations reduce CAV1/CAV2 expression and disrupt MLRs in patient-derived cells, and CRISPR-Cas9 perturbation proximate to a patient mutation is sufficient to reduce CAV1/CAV2 expression in neurons. Additional enrichment of ALS-associated mutations within CAV1 exons positions CAV1 as an ALS risk gene. We propose CAV1/CAV2 overexpression as a personalized medicine target for ALS.

Synapsin-caveolin-1 gene therapy preserves neuronal and synaptic morphology and prevents neurodegeneration in a mouse model of AD

“…Others have detected decreased Cav-1 transcript in degenerating neurons in postmortem human brains, 12 and a recent study out of the University of Sheffield revealed reduced Cav-1 expression and disrupted MLR in human samples as an ALS-associated risk variant. 32 Proteomics also did not detect any difference in the total TrkB, which is similar to our IB results. We also did not find a significant difference in total TrkB expression since the highly expressed Trun-TrkB dilutes any detectable change in fl-TrkB (Trun-TrkB is abundantly expressed and serves as a dominant-negative receptor).…”

DGLinker: flexible knowledge-graph prediction of disease–gene associations

“…they were not yet present in the DG databases used in the experiment. These were ATXN1 ( 61 ), ATXN3 ( 62 ), SCFD1 ( 62 ), CAV1 ( 63 ) and SPTLC1 ( 64 ). Only ACSL5 ( 62 ) and GLT8D1 ( 65 ) were not present among the predicted genes.…”

Genome-wide Identification of the Genetic Basis of Amyotrophic Lateral Sclerosis

“…We filtered for rare, deleterious variants within KANK1 enhancer, promoter and coding regions based on evolutionary conservation, functional annotations and population frequency (Huang et al, 2017; Karczewski et al, 2020; Rentzsch et al, 2019; Ritchie et al, 2014) ( Methods ). Enhancer and promoter regions for KANK1 were defined as previously described (Cooper-Knock et al, 2020; Fishilevich et al, 2017). Enhancer and promoter regions were independently enriched with ALS-associated rare deleterious variants (P<0.05, SKAT; Fig.…”

“…ALS GWAS studies to date have lost power by considering genetic variants in isolation, whereas in reality, a biological system is the product of a large number of interacting partners (Li et al, 2019; Wang et al, 2011). Moreover, noncoding regulatory regions of the genome have been relatively neglected in efforts to pinpoint the genetic basis of ALS, despite their functional synergy with the coding sequence (Cooper-Knock et al, 2020; Wang et al, 2018). Indeed, GWAS studies have suggested that a significant proportion of missing heritability in ALS is distributed throughout noncoding chromosomal regions (Nicolas et al, 2018; van Rheenen et al, 2016).…”