The effect of LRRK2 loss-of-function variants in humans.

Nat Med
Authors
Abstract

Human genetic variants predicted to cause loss-of-function of protein-coding genes (pLoF variants) provide natural in vivo models of human gene inactivation and can be valuable indicators of gene function and the potential toxicity of therapeutic inhibitors targeting these genes. Gain-of-kinase-function variants in LRRK2 are known to significantly increase the risk of Parkinson's disease, suggesting that inhibition of LRRK2 kinase activity is a promising therapeutic strategy. While preclinical studies in model organisms have raised some on-target toxicity concerns, the biological consequences of LRRK2 inhibition have not been well characterized in humans. Here, we systematically analyze pLoF variants in LRRK2 observed across 141,456 individuals sequenced in the Genome Aggregation Database (gnomAD), 49,960 exome-sequenced individuals from the UK Biobank and over 4 million participants in the 23andMe genotyped dataset. After stringent variant curation, we identify 1,455 individuals with high-confidence pLoF variants in LRRK2. Experimental validation of three variants, combined with previous work, confirmed reduced protein levels in 82.5% of our cohort. We show that heterozygous pLoF variants in LRRK2 reduce LRRK2 protein levels but that these are not strongly associated with any specific phenotype or disease state. Our results demonstrate the value of large-scale genomic databases and phenotyping of human loss-of-function carriers for target validation in drug discovery.

Year of Publication
2020
Journal
Nat Med
Date Published
2020 May 27
ISSN
1546-170X
DOI
10.1038/s41591-020-0893-5
PubMed ID
32461697
Links
Grant list
M735 / Rosetrees Trust
AI22592 / U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
GM115208 / U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
R01GM104371 / U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
12868 / Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)
107469/Z/15/Z / Wellcome Trust (Wellcome)
PUT1660 / Eesti Teadusagentuur (Estonian Research Council)
PRG184 / Eesti Teadusagentuur (Estonian Research Council)