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

Genome Aggregation Database Production Team; Genome Aggregation Database Consortium; 23andMe Research Team; Nicola Whiffin; Aaron Kleinman; Jamie L. Marshall; Eric V. Minikel; Julia K. Goodrich; Nicholas M. Quaife; Joanne B. Cole; Qingbo Wang; Konrad J. Karczewski; Beryl Cummings; Laurent Francioli; Kristen M. Laricchia; Anna Guan; Babak Alipanahi; Peter Morrison; Marco A.S. Baptista; Kalpana M. Merchant; Jessica Alföldi; Irina M. Armean; Eric Banks; Louis Bergelson; Kristian Cibulskis; Ryan L. Collins; Kristen M. Connolly; Miguel Covarrubias; Mark J. Daly; Stacey Donnelly; Yossi Farjoun; Steven Ferriera; Stacey Gabriel; Laura D. Gauthier; Jeff Gentry; Namrata Gupta; Thibault Jeandet; Diane Kaplan; Christopher Llanwarne; Ruchi Munshi; Benjamin M. Neale; Sam Novod; Anne H. O’Donnell-Luria; Nikelle Petrillo; Terho Lehtimäki; Kari M. Mattila; Jaana Suvisaari

doi:10.1038/s41591-020-0893-5

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

Genome Aggregation Database Production Team
, Genome Aggregation Database Consortium
, 23andMe Research Team
, Nicola Whiffin
, Aaron Kleinman
, Jamie L. Marshall
, Eric V. Minikel
, Julia K. Goodrich
, Nicholas M. Quaife
, Joanne B. Cole
, Qingbo Wang
, Konrad J. Karczewski
, Beryl Cummings
, Laurent Francioli
, Kristen M. Laricchia
, Anna Guan
, Babak Alipanahi
, Peter Morrison
, Marco A.S. Baptista
, Kalpana M. Merchant

Jessica Alföldi, Irina M. Armean, Eric Banks, Louis Bergelson, Kristian Cibulskis, Ryan L. Collins, Kristen M. Connolly, Miguel Covarrubias, Mark J. Daly, Stacey Donnelly, Yossi Farjoun, Steven Ferriera, Stacey Gabriel, Laura D. Gauthier, Jeff Gentry, Namrata Gupta, Thibault Jeandet, Diane Kaplan, Christopher Llanwarne, Ruchi Munshi, Benjamin M. Neale, Sam Novod, Anne H. O’Donnell-Luria, Nikelle Petrillo, Terho Lehtimäki, Kari M. Mattila, Jaana Suvisaari

Department of Clinical Chemistry

Research output: Contribution to journal › Article › Scientific › peer-review

95 Citations (Scopus)

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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 genes^1,2. Gain-of-kinase-function variants in LRRK2 are known to significantly increase the risk of Parkinson’s disease^3,4, suggesting that inhibition of LRRK2 kinase activity is a promising therapeutic strategy. While preclinical studies in model organisms have raised some on-target toxicity concerns^5–8, 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 language	English
Pages (from-to)	869-877
Number of pages	9
Journal	Nature Medicine
Volume	26
Issue number	6
DOIs	https://doi.org/10.1038/s41591-020-0893-5
Publication status	Published - 1 Jun 2020
Publication type	A1 Journal article-refereed

Funding

We thank the research participants and employees of 23andMe, Inc. and the research participants in gnomAD and the UK Biobank, for making this work possible. N. Whiffin is supported by a Rosetrees and Stoneygate Imperial College Research Fellowship. E.V. Minikel is supported by National Institutes of Health F31 AI22592. K.J.K. was supported by NIGMS F32 GM115208. This work was supported by the Michael J. Fox Foundation for Parkinson’s Research grant 12868, NIDDK U54DK105566, NIGMS R01GM104371, Wellcome Trust (107469/Z/15/Z); Medical Research Council (UK); NIHR Royal Brompton Biomedical Research Unit; NIHR Imperial Biomedical Research Centre. T.E is supported by Estonian Research Council grant PUT1660. L.M. is supported by Estonian Research Council grant PRG184. This research has been conducted using the UK Biobank Resource (https://doi.org/10.1101/572347) under Application Number 42890. These antibodies were selected based on their use in other publications and validation through IF and WB by the companies providing the antibodies. Company provided information is as follows: LRRK2: Immunogen: Fusion protein amino acids 970-2527 (C-terminus) of human LRRK2 (also known as Leucine-rich repeat serine/threonine-protein kinase 2, Dardarin and PARK8, accession number Q5S007) Mouse: 89% identity (1393/1557 amino acids identical) Rat: 89% identity (1392/1557 amino acids identical) <30% identity with LRRK1 Epitope mapped to within amino acids 1836-1845 (EGDLLVNPDQ) by PEPperPRINT through work funded by The Michael J. Fox Foundation for Parkinson’s Research. Monoclonal antibody info: Mouse strain: Balb/C Myeloma cell: SP2/0 Mouse Ig Isotype: IgG2a NeuroMab Applications: Immunoblot, Immunocytochemistry, Immunohistochemistry and Immunoprecipitation Species Reactivity: human, rat, mouse MW: > 200 kDa Immunoblot versus crude membranes from adult rat brain (RBM) and wild-type (WT) and LRRK2 KO mouse brains probed with N241A/34 (left) and K89/41 (right) TC supe. Mouse brain samples provided by Xiaojie Li, Ted Dawson and Valina Dawson (Johns Hopkins University). Adult rat brain immunohistochemistry (with antigen retrieval via sodium citrate pretreatment).

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Publication forum classification

Publication forum level 3

ASJC Scopus subject areas

General Biochemistry,Genetics and Molecular Biology

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10.1038/s41591-020-0893-5

s41591-020-0893-5Final published version, 2.51 MBLicence: CC BY

http://urn.fi/URN:NBN:fi:tuni-202012178961Licence: CC BY

Cite this

Genome Aggregation Database Production Team, Genome Aggregation Database Consortium, 23andMe Research Team, Whiffin, N., Kleinman, A., Marshall, J. L., Minikel, E. V., Goodrich, J. K., Quaife, N. M., Cole, J. B., Wang, Q., Karczewski, K. J., Cummings, B., Francioli, L., Laricchia, K. M., Guan, A., Alipanahi, B., Morrison, P., Baptista, M. A. S., ... Suvisaari, J. (2020). The effect of LRRK2 loss-of-function variants in humans. Nature Medicine, 26(6), 869-877. https://doi.org/10.1038/s41591-020-0893-5

@article{6854f05933e64bc5a82130aa3faccf50,

title = "The effect of LRRK2 loss-of-function variants in humans",

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{\textquoteright}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.",

author = "\{Genome Aggregation Database Production Team\} and \{Genome Aggregation Database Consortium\} and \{23andMe Research Team\} and Nicola Whiffin and Aaron Kleinman and Marshall, \{Jamie L.\} and Minikel, \{Eric V.\} and Goodrich, \{Julia K.\} and Quaife, \{Nicholas M.\} and Cole, \{Joanne B.\} and Qingbo Wang and Karczewski, \{Konrad J.\} and Beryl Cummings and Laurent Francioli and Laricchia, \{Kristen M.\} and Anna Guan and Babak Alipanahi and Peter Morrison and Baptista, \{Marco A.S.\} and Merchant, \{Kalpana M.\} and Jessica Alf{\"o}ldi and Armean, \{Irina M.\} and Eric Banks and Louis Bergelson and Kristian Cibulskis and Collins, \{Ryan L.\} and Connolly, \{Kristen M.\} and Miguel Covarrubias and Daly, \{Mark J.\} and Stacey Donnelly and Yossi Farjoun and Steven Ferriera and Stacey Gabriel and Gauthier, \{Laura D.\} and Jeff Gentry and Namrata Gupta and Thibault Jeandet and Diane Kaplan and Christopher Llanwarne and Ruchi Munshi and Neale, \{Benjamin M.\} and Sam Novod and O{\textquoteright}Donnell-Luria, \{Anne H.\} and Nikelle Petrillo and Terho Lehtim{\"a}ki and Mattila, \{Kari M.\} and Jaana Suvisaari",

note = "Funding Information: We thank the research participants and employees of 23andMe, Inc. and the research participants in gnomAD and the UK Biobank, for making this work possible. N. Whiffin is supported by a Rosetrees and Stoneygate Imperial College Research Fellowship. E.V. Minikel is supported by National Institutes of Health F31 AI22592. K.J.K. was supported by NIGMS F32 GM115208. This work was supported by the Michael J. Fox Foundation for Parkinson{\textquoteright}s Research grant 12868, NIDDK U54DK105566, NIGMS R01GM104371, Wellcome Trust (107469/Z/15/Z); Medical Research Council (UK); NIHR Royal Brompton Biomedical Research Unit; NIHR Imperial Biomedical Research Centre. T.E is supported by Estonian Research Council grant PUT1660. L.M. is supported by Estonian Research Council grant PRG184. This research has been conducted using the UK Biobank Resource (https://doi.org/10.1101/572347) under Application Number 42890. Funding Information: These antibodies were selected based on their use in other publications and validation through IF and WB by the companies providing the antibodies. Company provided information is as follows: LRRK2: Immunogen: Fusion protein amino acids 970-2527 (C-terminus) of human LRRK2 (also known as Leucine-rich repeat serine/threonine-protein kinase 2, Dardarin and PARK8, accession number Q5S007) Mouse: 89\% identity (1393/1557 amino acids identical) Rat: 89\% identity (1392/1557 amino acids identical) <30\% identity with LRRK1 Epitope mapped to within amino acids 1836-1845 (EGDLLVNPDQ) by PEPperPRINT through work funded by The Michael J. Fox Foundation for Parkinson{\textquoteright}s Research. Monoclonal antibody info: Mouse strain: Balb/C Myeloma cell: SP2/0 Mouse Ig Isotype: IgG2a NeuroMab Applications: Immunoblot, Immunocytochemistry, Immunohistochemistry and Immunoprecipitation Species Reactivity: human, rat, mouse MW: > 200 kDa Immunoblot versus crude membranes from adult rat brain (RBM) and wild-type (WT) and LRRK2 KO mouse brains probed with N241A/34 (left) and K89/41 (right) TC supe. Mouse brain samples provided by Xiaojie Li, Ted Dawson and Valina Dawson (Johns Hopkins University). Adult rat brain immunohistochemistry (with antigen retrieval via sodium citrate pretreatment). Publisher Copyright: {\textcopyright} 2020, The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.",

year = "2020",

month = jun,

day = "1",

doi = "10.1038/s41591-020-0893-5",

language = "English",

volume = "26",

pages = "869--877",

journal = "Nature Medicine",

issn = "1078-8956",

publisher = "Nature Research",

number = "6",

}

Genome Aggregation Database Production Team, Genome Aggregation Database Consortium, 23andMe Research Team, Whiffin, N, Kleinman, A, Marshall, JL, Minikel, EV, Goodrich, JK, Quaife, NM, Cole, JB, Wang, Q, Karczewski, KJ, Cummings, B, Francioli, L, Laricchia, KM, Guan, A, Alipanahi, B, Morrison, P, Baptista, MAS, Merchant, KM, Alföldi, J, Armean, IM, Banks, E, Bergelson, L, Cibulskis, K, Collins, RL, Connolly, KM, Covarrubias, M, Daly, MJ, Donnelly, S, Farjoun, Y, Ferriera, S, Gabriel, S, Gauthier, LD, Gentry, J, Gupta, N, Jeandet, T, Kaplan, D, Llanwarne, C, Munshi, R, Neale, BM, Novod, S, O’Donnell-Luria, AH, Petrillo, N, Lehtimäki, T, Mattila, KM & Suvisaari, J 2020, 'The effect of LRRK2 loss-of-function variants in humans', Nature Medicine, vol. 26, no. 6, pp. 869-877. https://doi.org/10.1038/s41591-020-0893-5

TY - JOUR

T1 - The effect of LRRK2 loss-of-function variants in humans

AU - Genome Aggregation Database Production Team

AU - Genome Aggregation Database Consortium

AU - 23andMe Research Team

AU - Whiffin, Nicola

AU - Kleinman, Aaron

AU - Marshall, Jamie L.

AU - Minikel, Eric V.

AU - Goodrich, Julia K.

AU - Quaife, Nicholas M.

AU - Cole, Joanne B.

AU - Wang, Qingbo

AU - Karczewski, Konrad J.

AU - Cummings, Beryl

AU - Francioli, Laurent

AU - Laricchia, Kristen M.

AU - Guan, Anna

AU - Alipanahi, Babak

AU - Morrison, Peter

AU - Baptista, Marco A.S.

AU - Merchant, Kalpana M.

AU - Alföldi, Jessica

AU - Armean, Irina M.

AU - Banks, Eric

AU - Bergelson, Louis

AU - Cibulskis, Kristian

AU - Collins, Ryan L.

AU - Connolly, Kristen M.

AU - Covarrubias, Miguel

AU - Daly, Mark J.

AU - Donnelly, Stacey

AU - Farjoun, Yossi

AU - Ferriera, Steven

AU - Gabriel, Stacey

AU - Gauthier, Laura D.

AU - Gentry, Jeff

AU - Gupta, Namrata

AU - Jeandet, Thibault

AU - Kaplan, Diane

AU - Llanwarne, Christopher

AU - Munshi, Ruchi

AU - Neale, Benjamin M.

AU - Novod, Sam

AU - O’Donnell-Luria, Anne H.

AU - Petrillo, Nikelle

AU - Lehtimäki, Terho

AU - Mattila, Kari M.

AU - Suvisaari, Jaana

N1 - Funding Information: We thank the research participants and employees of 23andMe, Inc. and the research participants in gnomAD and the UK Biobank, for making this work possible. N. Whiffin is supported by a Rosetrees and Stoneygate Imperial College Research Fellowship. E.V. Minikel is supported by National Institutes of Health F31 AI22592. K.J.K. was supported by NIGMS F32 GM115208. This work was supported by the Michael J. Fox Foundation for Parkinson’s Research grant 12868, NIDDK U54DK105566, NIGMS R01GM104371, Wellcome Trust (107469/Z/15/Z); Medical Research Council (UK); NIHR Royal Brompton Biomedical Research Unit; NIHR Imperial Biomedical Research Centre. T.E is supported by Estonian Research Council grant PUT1660. L.M. is supported by Estonian Research Council grant PRG184. This research has been conducted using the UK Biobank Resource (https://doi.org/10.1101/572347) under Application Number 42890. Funding Information: These antibodies were selected based on their use in other publications and validation through IF and WB by the companies providing the antibodies. Company provided information is as follows: LRRK2: Immunogen: Fusion protein amino acids 970-2527 (C-terminus) of human LRRK2 (also known as Leucine-rich repeat serine/threonine-protein kinase 2, Dardarin and PARK8, accession number Q5S007) Mouse: 89% identity (1393/1557 amino acids identical) Rat: 89% identity (1392/1557 amino acids identical) <30% identity with LRRK1 Epitope mapped to within amino acids 1836-1845 (EGDLLVNPDQ) by PEPperPRINT through work funded by The Michael J. Fox Foundation for Parkinson’s Research. Monoclonal antibody info: Mouse strain: Balb/C Myeloma cell: SP2/0 Mouse Ig Isotype: IgG2a NeuroMab Applications: Immunoblot, Immunocytochemistry, Immunohistochemistry and Immunoprecipitation Species Reactivity: human, rat, mouse MW: > 200 kDa Immunoblot versus crude membranes from adult rat brain (RBM) and wild-type (WT) and LRRK2 KO mouse brains probed with N241A/34 (left) and K89/41 (right) TC supe. Mouse brain samples provided by Xiaojie Li, Ted Dawson and Valina Dawson (Johns Hopkins University). Adult rat brain immunohistochemistry (with antigen retrieval via sodium citrate pretreatment). Publisher Copyright: © 2020, The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

PY - 2020/6/1

Y1 - 2020/6/1

N2 - 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.

AB - 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.

U2 - 10.1038/s41591-020-0893-5

DO - 10.1038/s41591-020-0893-5

M3 - Article

C2 - 32461697

AN - SCOPUS:85085479654

SN - 1078-8956

VL - 26

SP - 869

EP - 877

JO - Nature Medicine

JF - Nature Medicine

IS - 6

ER -

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

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