The effect of LRRK2 loss-of-function variants in humans.
Adult
Aged
Aged, 80 and over
Biological Specimen Banks
Cell Line
Embryonic Stem Cells
/ metabolism
Female
Gain of Function Mutation
/ genetics
Heterozygote
Humans
Leucine-Rich Repeat Serine-Threonine Protein Kinase-2
/ antagonists & inhibitors
Longevity
/ genetics
Loss of Function Mutation
/ genetics
Lymphocytes
/ metabolism
Male
Middle Aged
Myocytes, Cardiac
/ metabolism
Parkinson Disease
/ drug therapy
Phenotype
Journal
Nature medicine
ISSN: 1546-170X
Titre abrégé: Nat Med
Pays: United States
ID NLM: 9502015
Informations de publication
Date de publication:
06 2020
06 2020
Historique:
received:
20
03
2020
accepted:
20
04
2020
pubmed:
29
5
2020
medline:
9
9
2020
entrez:
29
5
2020
Statut:
ppublish
Résumé
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
Identifiants
pubmed: 32461697
doi: 10.1038/s41591-020-0893-5
pii: 10.1038/s41591-020-0893-5
pmc: PMC7303015
doi:
Substances chimiques
LRRK2 protein, human
EC 2.7.11.1
Leucine-Rich Repeat Serine-Threonine Protein Kinase-2
EC 2.7.11.1
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
869-877Subventions
Organisme : Department of Health
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_UP_1102/20
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 107469/Z/15/Z
Pays : United Kingdom
Organisme : NIMH NIH HHS
ID : R01 MH085548
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH123451
Pays : United States
Organisme : NIDDK NIH HHS
ID : U54 DK105566
Pays : United States
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NIGMS NIH HHS
ID : R01 GM104371
Pays : United States
Organisme : NIGMS NIH HHS
ID : F32 GM115208
Pays : United States
Organisme : Medical Research Council
ID : MC_QA137853
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_PC_17228
Pays : United Kingdom
Organisme : British Heart Foundation
ID : RG/18/10/33842
Pays : United Kingdom
Organisme : NIMH NIH HHS
ID : R01 MH104964
Pays : United States
Organisme : British Heart Foundation
ID : CS/14/2/30841
Pays : United Kingdom
Investigateurs
Irina M Armean
(IM)
Eric Banks
(E)
Louis Bergelson
(L)
Kristian Cibulskis
(K)
Ryan L Collins
(RL)
Kristen M Connolly
(KM)
Miguel Covarrubias
(M)
Beryl Cummings
(B)
Mark J Daly
(MJ)
Stacey Donnelly
(S)
Yossi Farjoun
(Y)
Steven Ferriera
(S)
Stacey Gabriel
(S)
Laura D Gauthier
(LD)
Jeff Gentry
(J)
Namrata Gupta
(N)
Thibault Jeandet
(T)
Diane Kaplan
(D)
Kristen M Laricchia
(KM)
Christopher Llanwarne
(C)
Ruchi Munshi
(R)
Benjamin M Neale
(BM)
Sam Novod
(S)
Anne H O'Donnell-Luria
(AH)
Nikelle Petrillo
(N)
Timothy Poterba
(T)
David Roazen
(D)
Valentin Ruano-Rubio
(V)
Andrea Saltzman
(A)
Kaitlin E Samocha
(KE)
Molly Schleicher
(M)
Cotton Seed
(C)
Matthew Solomonson
(M)
Jose Soto
(J)
Grace Tiao
(G)
Kathleen Tibbetts
(K)
Charlotte Tolonen
(C)
Christopher Vittal
(C)
Gordon Wade
(G)
Arcturus Wang
(A)
Nicholas A Watts
(NA)
Ben Weisburd
(B)
Carlos A Aguilar-Salinas
(CA)
Tariq Ahmad
(T)
Christine M Albert
(CM)
Diego Ardissino
(D)
Gil Atzmon
(G)
John Barnard
(J)
Laurent Beaugerie
(L)
Emelia J Benjamin
(EJ)
Michael Boehnke
(M)
Lori L Bonnycastle
(LL)
Erwin P Bottinger
(EP)
Donald W Bowden
(DW)
Matthew J Bown
(MJ)
John C Chambers
(JC)
Juliana C Chan
(JC)
Daniel Chasman
(D)
Judy Cho
(J)
Mina K Chung
(MK)
Bruce Cohen
(B)
Adolfo Correa
(A)
Dana Dabelea
(D)
Dawood Darbar
(D)
Ravindranath Duggirala
(R)
Josée Dupuis
(J)
Patrick T Ellinor
(PT)
Roberto Elosua
(R)
Jeanette Erdmann
(J)
Martti Färkkilä
(M)
Jose Florez
(J)
Andre Franke
(A)
Gad Getz
(G)
Benjamin Glaser
(B)
Stephen J Glatt
(SJ)
David Goldstein
(D)
Clicerio Gonzalez
(C)
Leif Groop
(L)
Christopher Haiman
(C)
Craig Hanis
(C)
Matthew Harms
(M)
Mikko Hiltunen
(M)
Matti M Holi
(MM)
Christina M Hultman
(CM)
Mikko Kallela
(M)
Jaakko Kaprio
(J)
Sekar Kathiresan
(S)
Bong-Jo Kim
(BJ)
Young Jin Kim
(YJ)
George Kirov
(G)
Jaspal Kooner
(J)
Seppo Koskinen
(S)
Harlan M Krumholz
(HM)
Subra Kugathasan
(S)
Soo Heon Kwak
(SH)
Markku Laakso
(M)
Terho Lehtimäki
(T)
Ruth J F Loos
(RJF)
Steven A Lubitz
(SA)
Ronald C W Ma
(RCW)
Daniel G MacArthur
(DG)
Jaume Marrugat
(J)
Kari M Mattila
(KM)
Steven McCarroll
(S)
Mark I McCarthy
(MI)
Dermot McGovern
(D)
Ruth McPherson
(R)
James B Meigs
(JB)
Olle Melander
(O)
Andres Metspalu
(A)
Peter M Nilsson
(PM)
Michael C O'Donovan
(MC)
Dost Ongur
(D)
Lorena Orozco
(L)
Michael J Owen
(MJ)
Colin N A Palmer
(CNA)
Aarno Palotie
(A)
Kyong Soo Park
(KS)
Carlos Pato
(C)
Ann E Pulver
(AE)
Nazneen Rahman
(N)
Anne M Remes
(AM)
John D Riou
(JD)
Samuli Ripatti
(S)
Dan M Roden
(DM)
Danish Saleheen
(D)
Veikko Salomaa
(V)
Nilesh J Samani
(NJ)
Jeremiah Scharf
(J)
Heribert Schunkert
(H)
Moore B Shoemaker
(MB)
Pamela Sklar
(P)
Hilkka Soininen
(H)
Harry Sokol
(H)
Tim Spector
(T)
Patrick F Sullivan
(PF)
Jaana Suvisaari
(J)
E Shyong Tai
(ES)
Yik Ying Teo
(YY)
Tuomi Tiinamaija
(T)
Ming Tsuang
(M)
Dan Turner
(D)
Teresa Tusie-Luna
(T)
Erkki Vartiainen
(E)
Marquis P Vawter
(MP)
James S Ware
(JS)
Hugh Watkins
(H)
Rinse K Weersma
(RK)
Maija Wessman
(M)
James G Wilson
(JG)
Ramnik J Xavier
(RJ)
Michelle Agee
(M)
Adam Auton
(A)
Robert K Bell
(RK)
Katarzyna Bryc
(K)
Sarah L Elson
(SL)
Pierre Fontanillas
(P)
Nicholas A Furlotte
(NA)
Barry Hicks
(B)
David A Hinds
(DA)
Karen E Huber
(KE)
Ethan M Jewett
(EM)
Yunxuan Jiang
(Y)
Keng-Han Lin
(KH)
Nadia K Litterman
(NK)
Matthew H McIntyre
(MH)
Kimberly F McManus
(KF)
Joanna L Mountain
(JL)
Elizabeth S Noblin
(ES)
Carrie A M Northover
(CAM)
Steven J Pitts
(SJ)
G David Poznik
(GD)
J Fah Sathirapongsasuti
(JF)
Janie F Shelton
(JF)
Suyash Shringarpure
(S)
Chao Tian
(C)
Joyce Y Tung
(JY)
Vladimir Vacic
(V)
Xin Wang
(X)
Catherine H Wilson
(CH)
Commentaires et corrections
Type : CommentIn
Type : CommentIn
Type : ErratumIn
Références
Nelson, M. R. et al. The support of human genetic evidence for approved drug indications. Nat. Genet. 47, 856–860 (2015).
doi: 10.1038/ng.3314
pubmed: 26121088
Plenge, R. M., Scolnick, E. M. & Altshuler, D. Validating therapeutic targets through human genetics. Nat. Rev. Drug Discov. 12, 581–594 (2013).
pubmed: 23868113
doi: 10.1038/nrd4051
Greggio, E. et al. Kinase activity is required for the toxic effects of mutant LRRK2/dardarin. Neurobiol. Dis. 23, 329–341 (2006).
pubmed: 16750377
doi: 10.1016/j.nbd.2006.04.001
West, A. B. et al. Parkinson’s disease-associated mutations in leucine-rich repeat kinase 2 augment kinase activity. Proc. Natl Acad. Sci. USA 102, 16842–16847 (2005).
pubmed: 16269541
doi: 10.1073/pnas.0507360102
pmcid: 1283829
Andersen, M. A. et al. PFE-360-induced LRRK2 inhibition induces reversible, non-adverse renal changes in rats. Toxicology 395, 15–22 (2018).
pubmed: 29307545
doi: 10.1016/j.tox.2018.01.003
Fuji, R. N. et al. Effect of selective LRRK2 kinase inhibition on nonhuman primate lung. Sci. Transl. Med. 7, 273ra15 (2015).
pubmed: 25653221
doi: 10.1126/scitranslmed.aaa3634
Baptista, M. A. S. et al. Loss of leucine-rich repeat kinase 2 (LRRK2) in rats leads to progressive abnormal phenotypes in peripheral organs. PLoS ONE 8, e80705 (2013).
pubmed: 24244710
pmcid: 3828242
doi: 10.1371/journal.pone.0080705
Hinkle, K. M. et al. LRRK2 knockout mice have an intact dopaminergic system but display alterations in exploratory and motor co-ordination behaviors. Mol. Neurodegener. 7, 25 (2012).
pubmed: 22647713
pmcid: 3441373
doi: 10.1186/1750-1326-7-25
Karczewski, K. J. et al. Variation across 141,456 human exomes and genomes reveals the spectrum of loss-of-function intolerance across human protein-coding genes. Preprint at bioRxiv https://doi.org/10.1101/531210 (2019).
Blauwendraat, C. et al. Frequency of loss of function variants in LRRK2 in Parkinson disease. JAMA Neurol. 75, 1416–1422 (2018).
pubmed: 30039155
pmcid: 6248108
doi: 10.1001/jamaneurol.2018.1885
de Lau, L. M. L. & Breteler, M. M. B. Epidemiology of Parkinson’s disease. Lancet Neurol. 5, 525–535 (2006).
pubmed: 16713924
doi: 10.1016/S1474-4422(06)70471-9
Polymeropoulos, M. H. et al. Mapping of a gene for Parkinson’s disease to chromosome 4q21–q23. Science 274, 1197–1199 (1996).
pubmed: 8895469
doi: 10.1126/science.274.5290.1197
Klein, C. & Westenberger, A. Genetics of Parkinson’s disease. Cold Spring Harb. Perspect. Med. 2, a008888 (2012).
pubmed: 22315721
pmcid: 3253033
doi: 10.1101/cshperspect.a008888
Zimprich, A. et al. Mutations in LRRK2 cause autosomal-dominant parkinsonism with pleomorphic pathology. Neuron 44, 601–607 (2004).
pubmed: 15541309
doi: 10.1016/j.neuron.2004.11.005
Goldwurm, S. et al. Evaluation of LRRK2 G2019S penetrance: relevance for genetic counseling in Parkinson disease. Neurology 68, 1141–1143 (2007).
pubmed: 17215492
doi: 10.1212/01.wnl.0000254483.19854.ef
Do, C. B. et al. Web-based genome-wide association study identifies two novel loci and a substantial genetic component for Parkinson’s disease. PLoS Genet. 7, e1002141 (2011).
pubmed: 21738487
pmcid: 3121750
doi: 10.1371/journal.pgen.1002141
MacLeod, D. et al. The familial Parkinsonism gene LRRK2 regulates neurite process morphology. Neuron 52, 587–593 (2006).
pubmed: 17114044
doi: 10.1016/j.neuron.2006.10.008
West, A. B. et al. Parkinson’s disease-associated mutations in LRRK2 link enhanced GTP-binding and kinase activities to neuronal toxicity. Hum. Mol. Genet. 16, 223–232 (2007).
pubmed: 17200152
doi: 10.1093/hmg/ddl471
Steger, M. et al. Phosphoproteomics reveals that Parkinson’s disease kinase LRRK2 regulates a subset of Rab GTPases. eLife 5, e12813 (2016).
pubmed: 26824392
pmcid: 4769169
doi: 10.7554/eLife.12813
Roosen, D. A. & Cookson, M. R. LRRK2 at the interface of autophagosomes, endosomes and lysosomes. Mol. Neurodegener. 11, 73 (2016).
pubmed: 27927216
pmcid: 5142374
doi: 10.1186/s13024-016-0140-1
Di Maio, R. et al. LRRK2 activation in idiopathic Parkinson’s disease. Sci. Transl. Med. 10, eaar5429 (2018).
pubmed: 30045977
pmcid: 6344941
doi: 10.1126/scitranslmed.aar5429
Zhao, H. T. et al. LRRK2 antisense oligonucleotides ameliorate α-synuclein inclusion formation in a Parkinson’s disease mouse model. Mol. Ther. Nucleic Acids 8, 508–519 (2017).
pubmed: 28918051
pmcid: 5573879
doi: 10.1016/j.omtn.2017.08.002
Chen, Z. C. et al. Phosphorylation of amyloid precursor protein by mutant LRRK2 promotes AICD activity and neurotoxicity in Parkinson’s disease. Sci. Signal. 10, eaam6790 (2017).
pubmed: 28720718
doi: 10.1126/scisignal.aam6790
Chen, J., Chen, Y. & Pu, J. Leucine-rich repeat kinase 2 in Parkinson’s disease: updated from pathogenesis to potential therapeutic target. Eur. Neurol. 79, 256–265 (2018).
pubmed: 29705795
doi: 10.1159/000488938
Daniel, G. & Moore, D. J. in Behavioral Neurobiology of Huntington’s Disease and Parkinson’s Disease (eds Nguyen, H. H. P. & Cenci, M. A.) 331–368 (Springer Berlin Heidelberg, 2015).
Cohen, J. C., Boerwinkle, E., Mosley, T. H. Jr & Hobbs, H. H. Sequence variations in PCSK9, low LDL, and protection against coronary heart disease. N. Engl. J. Med 354, 1264–1272 (2006).
pubmed: 16554528
doi: 10.1056/NEJMoa054013
TG and HDL Working Group of the Exome Sequencing Project, National Heart, Lung and Blood Institute et al. Loss-of-function mutations in APOC3, triglycerides, and coronary disease. N. Engl. J. Med 371, 22–31 (2014).
doi: 10.1056/NEJMoa1307095
Myocardial Infarction Genetics Consortium Investigators et al. Inactivating mutations in NPC1L1 and protection from coronary heart disease. N. Engl. J. Med 371, 2072–2082 (2014).
doi: 10.1056/NEJMoa1405386
Minikel, E. V. et al. Quantifying prion disease penetrance using large population control cohorts. Sci. Transl. Med. 8, 322ra9 (2016).
pubmed: 26791950
pmcid: 4774245
Lek, M. et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291 (2016).
pubmed: 27535533
pmcid: 5018207
doi: 10.1038/nature19057
MacArthur, D. G. et al. A systematic survey of loss-of-function variants in human protein-coding genes. Science 335, 823–828 (2012).
pubmed: 22344438
pmcid: 3299548
doi: 10.1126/science.1215040
Minikel, E. V. et al. Evaluating potential drug targets through human loss-of-function genetic variation. Preprint at bioRxiv https://doi.org/10.1101/530881 (2019).
Van Hout, C. V. et al. Whole exome sequencing and characterization of coding variation in 49,960 individuals in the UK Biobank. Preprint at bioRxiv https://doi.org/10.1101/572347 (2019).
Mir, R. et al. The Parkinson’s disease VPS35[D620N] mutation enhances LRRK2-mediated Rab protein phosphorylation in mouse and human. Biochem. J. 475, 1861–1883 (2018).
pubmed: 29743203
doi: 10.1042/BCJ20180248
Berndsen, K. et al. PPM1H phosphatase counteracts LRRK2 signaling by selectively dephosphorylating Rab proteins. eLife 8, e50416 (2019).
pubmed: 31663853
pmcid: 6850886
doi: 10.7554/eLife.50416
Gupta, R. P. & Strachan, D. P. Ventilatory function as a predictor of mortality in lifelong non-smokers: evidence from large British cohort studies. BMJ Open 7, e015381 (2017).
pubmed: 28706094
pmcid: 5734388
doi: 10.1136/bmjopen-2016-015381
McLaren, W. et al. The Ensembl variant effect predictor. Genome Biol. 17, 122 (2016).
pubmed: 27268795
pmcid: 4893825
doi: 10.1186/s13059-016-0974-4
Cummings, B. B. et al. Transcript expression-aware annotation improves rare variant discovery and interpretation. Preprint at bioRxiv https://doi.org/10.1101/554444 (2019).
Pato, M. T. et al. The genomic psychiatry cohort: partners in discovery. Am. J. Med. Genet. B Neuropsychiatr. Genet. 162B, 306–312 (2013).
pubmed: 23650244
doi: 10.1002/ajmg.b.32160
Saleheen, D. et al. Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity. Nature 544, 235–239 (2017).
pubmed: 28406212
pmcid: 5600291
doi: 10.1038/nature22034
Ripke, S. et al. Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Nat. Genet. 45, 1150–1159 (2013).
pubmed: 23974872
pmcid: 3827979
doi: 10.1038/ng.2742
Bipolar Disorder and Schizophrenia Working Group of the Psychiatric Genomics Consortium. Genomic dissection of bipolar disorder and schizophrenia, including 28 subphenotypes. Cell 173, 1705–1715 (2018).
pmcid: 6432650
doi: 10.1016/j.cell.2018.05.046
Genovese, G. et al. Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia. Nat. Neurosci. 19, 1433–1441 (2016).
pubmed: 27694994
pmcid: 5104192
doi: 10.1038/nn.4402
Borodulin, K. et al. Cohort profile: the national FINRISK study. Int. J. Epidemiol. 47, 696 (2018).
pubmed: 29165699
doi: 10.1093/ije/dyx239
Leitsalu, L. et al. Cohort profile: Estonian biobank of the Estonian Genome Center, University of Tartu. Int. J. Epidemiol. 44, 1137–1147 (2015).
pubmed: 24518929
doi: 10.1093/ije/dyt268
1000 Genomes Project Consortium et al. A global reference for human genetic variation. Nature 526, 68–74 (2015).
doi: 10.1038/nature15393
Bellenguez, C. et al. A robust clustering algorithm for identifying problematic samples in genome-wide association studies. Bioinformatics 28, 134–135 (2012).
pubmed: 22057162
doi: 10.1093/bioinformatics/btr599
Levey, A. S. & Stevens, L. A. Estimating GFR using the CKD Epidemiology Collaboration (CKD-EPI) creatinine equation: more accurate GFR estimates, lower CKD prevalence estimates and better risk predictions. Am. J. Kidney Dis. 55, 622–627 (2010).
pubmed: 20338463
pmcid: 2846308
doi: 10.1053/j.ajkd.2010.02.337
UK10K Consortium et al. The UK10K project identifies rare variants in health and disease. Nature 526, 82–90 (2015).
doi: 10.1038/nature14962
Freidlin, B., Zheng, G., Li, Z. & Gastwirth, J. L. Trend tests for case-control studies of genetic markers: power, sample size and robustness. Hum. Hered. 53, 146–152 (2002).
pubmed: 12145550
doi: 10.1159/000064976
Lian, X. et al. Cozzarelli Prize Winner: robust cardiomyocyte differentiation from human pluripotent stem cells via temporal modulation of canonical Wnt signaling. Proc. Natl Acad. Sci. USA 109, E1848–E1857 (2012).
pubmed: 22645348
doi: 10.1073/pnas.1200250109
pmcid: 3390875
McKenna, A. et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
pubmed: 20644199
pmcid: 2928508
doi: 10.1101/gr.107524.110
Dale, R. K., Pedersen, B. S. & Quinlan, A. R. Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics 27, 3423–3424 (2011).
pubmed: 21949271
pmcid: 3232365
doi: 10.1093/bioinformatics/btr539
Naito, Y., Hino, K., Bono, H. & Ui-Tei, K. CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics 31, 1120–1123 (2015).
pubmed: 25414360
doi: 10.1093/bioinformatics/btu743