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

Nicola Whiffin (Lead / Corresponding author), Irina M. Armean, Aaron Kleinman, Jamie L. Marshall, Eric V. Minikel, Julia K. Goodrich, Nicholas M. Quaife, Joanne B. Cole, Qingbo Wang, Konrad J. Karczewski, Beryl B. Cummings, Laurent Francioli, Kristen Laricchia, Anna Guan, Babak Alipanahi, Peter Morrison, Marco A. S. Baptista, Kalpana M. Merchant, , James S. Ware, Aki S. Havulinna, Bozenna Iliadou, Jung-Jin Lee, Girish N. Nadkarni, Cole Whiteman, 23andMe Research Team, Mark Daly, Tõnu Esko, Christina Hultman, Ruth J. F. Loos, Lili Milani, Aarno Palotie, Carlos Pato, Michele Pato, Danish Saleheen, Patrick F. Sullivan, Jessica Alföldi, Paul Cannon, Daniel G. MacArthur

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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 genes1,2. Gain-of-kinase-function variants in LRRK2 are known to significantly increase the risk of Parkinson’s disease3,4, suggesting that inhibition of LRRK2 kinase activity is a promising therapeutic strategy. While preclinical studies in model organisms have raised some on-target toxicity concerns5–8, 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)9, 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 work10, 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.

Original languageEnglish
Number of pages21
JournalNature Medicine
Early online date27 May 2020
DOIs
Publication statusE-pub ahead of print - 27 May 2020

Keywords

  • Genomics
  • Neurological disorders

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    Whiffin, N., Armean, I. M., Kleinman, A., Marshall, J. L., Minikel, E. V., Goodrich, J. K., Quaife, N. M., Cole, J. B., Wang, Q., Karczewski, K. J., Cummings, B. B., Francioli, L., Laricchia, K., Guan, A., Alipanahi, B., Morrison, P., Baptista, M. A. S., Merchant, K. M., ... MacArthur, D. G. (2020). The effect of LRRK2 loss-of-function variants in humans. Nature Medicine. https://doi.org/10.1038/s41591-020-0893-5