Human loss-of-function variants suggest that partial LRRK2 inhibition is a safe therapeutic strategy for Parkinson’s disease
Whiffin N., Armean IM., Kleinman A., Marshall JL., Minikel EV., Karczewski KJ., Cummings BB., Francioli L., Laricchia K., Wang Q., Guan A., Alipanahi B., Morrison P., Baptista MAS., Merchant KM., Ware JS., Havulinna AS., Iliadou B., Lee J-J., Nadkarni GN., Whiteman C., Daly M., Esko T., Hultman C., Loos RJF., Milani L., Palotie A., Pato C., Pato M., Saleheen D., Sullivan PF., Alföldi J., Cannon P., MacArthur DG.
<jats:title>Abstract</jats:title><jats:p>Human genetic variants causing loss-of-function (LoF) of protein-coding genes provide natural <jats:italic>in vivo</jats:italic> models of gene inactivation, which are powerful indicators of gene function and the potential toxicity of therapeutic inhibitors targeting these genes<jats:sup>1,2</jats:sup>. Gain-of-kinase-function variants in <jats:italic>LRRK2</jats:italic> are known to significantly increase the risk of Parkinson’s disease<jats:sup>3,4</jats:sup>, suggesting that inhibition of LRRK2 kinase activity is a promising therapeutic strategy. Whilst preclinical studies in model organisms have raised some on-target toxicity concerns<jats:sup>5–8</jats:sup>, the biological consequences of LRRK2 inhibition have not been well characterized in humans. Here we systematically analyse LoF variants in <jats:italic>LRRK2</jats:italic> observed across 141,456 individuals sequenced in the Genome Aggregation Database (gnomAD)<jats:sup>9</jats:sup> and over 4 million participants in the 23andMe genotyped dataset, to assess their impact at a molecular and phenotypic level. After thorough variant curation, we identify 1,358 individuals with high-confidence predicted LoF variants in <jats:italic>LRRK2</jats:italic>, several with experimental validation. We show that heterozygous LoF of <jats:italic>LRRK2</jats:italic> reduces LRRK2 protein level by ~50% but is not associated with reduced life expectancy, or with any specific phenotype or disease state. These data suggest that therapeutics that downregulate LRRK2 levels or kinase activity by up to 50% are unlikely to have major on-target safety liabilities. Our results demonstrate the value of large scale genomic databases and phenotyping of human LoF carriers for target validation in drug discovery.</jats:p>