Sequential screening nominates the Parkinson’s disease associated kinase LRRK2 as a regulator of Clathrin-mediated endocytosis

Mutations in leucine-rich repeat kinase 2 (LRRK2) are an established cause of inherited Parkinson’s disease (PD). LRRK2 is expressed in both neurons and glia in the central nervous system, but its physiological function(s) in each of these cell types is uncertain. Through sequential screens, we report a functional interaction between LRRK2 and Clathrin adaptor protein complex 2 (AP2). Analysis of LRRK2 KO tissue revealed a significant dysregulation of AP2 complex components, suggesting LRRK2 may act upstream of AP2. In line with this hypothesis, expression of LRRK2 was found to modify recruitment and phosphorylation of AP2. Furthermore, expression of LRRK2 containing the R1441C pathogenic mutation resulted in impaired clathrin-mediated endocytosis (CME). A decrease in activity-dependent synaptic vesicle endocytosis was also observed in neurons harboring an endogenous R1441C LRRK2 mutation. Alongside LRRK2, several PD-associated genes intersect with membrane-trafficking pathways. To investigate the genetic association between Clathrin-trafficking and PD, we used polygenetic risk profiling from IPDGC genome wide association studies (GWAS) datasets. Clathrin-dependent endocytosis genes were found to be associated with PD across multiple cohorts, suggesting common variants at these loci represent a cumulative risk factor for disease. Taken together, these findings suggest CME is a LRRK2-mediated, PD relevant pathway.

[1]  Sonja W. Scholz,et al.  Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies , 2019, The Lancet Neurology.

[2]  Kejie Li,et al.  An integrated transcriptomics and proteomics analysis reveals functional endocytic dysregulation caused by mutations in LRRK2 , 2019, Neurobiology of Disease.

[3]  M. Nalls,et al.  The endocytic membrane trafficking pathway plays a major role in the risk of Parkinson's disease , 2019, Movement disorders : official journal of the Movement Disorder Society.

[4]  S. Hilfiker,et al.  The G2019S variant of leucine-rich repeat kinase 2 (LRRK2) alters endolysosomal trafficking by impairing the function of the GTPase RAB8A , 2019, The Journal of Biological Chemistry.

[5]  Sonja W. Scholz,et al.  Expanding Parkinson’s disease genetics: novel risk loci, genomic context, causal insights and heritable risk , 2018 .

[6]  Sonja W. Scholz,et al.  Parkinson’s disease genetics: identifying novel risk loci, providing causal insights and improving estimates of heritable risk , 2018, bioRxiv.

[7]  M. Cookson,et al.  Proteomic analysis reveals co-ordinated alterations in protein synthesis and degradation pathways in LRRK2 knockout mice , 2018, Human molecular genetics.

[8]  D. Krainc,et al.  LRRK2 phosphorylation of auxilin mediates synaptic defects in dopaminergic neurons from patients with Parkinson’s disease , 2018, Proceedings of the National Academy of Sciences.

[9]  M. Kaksonen,et al.  Mechanisms of clathrin-mediated endocytosis , 2018, Nature Reviews Molecular Cell Biology.

[10]  M. Cookson,et al.  LRRK2 phosphorylates membrane-bound Rabs and is activated by GTP-bound Rab7L1 to promote recruitment to the trans-Golgi network , 2018, Human molecular genetics.

[11]  S. Pfeffer,et al.  Rab29 activation of the Parkinson's disease‐associated LRRK2 kinase , 2017, The EMBO journal.

[12]  P. Hof,et al.  Parkinson's Disease-Associated LRRK2 Hyperactive Kinase Mutant Disrupts Synaptic Vesicle Trafficking in Ventral Midbrain Neurons , 2017, The Journal of Neuroscience.

[13]  Matthias Mann,et al.  Systematic proteomic analysis of LRRK2-mediated Rab GTPase phosphorylation establishes a connection to ciliogenesis , 2017, eLife.

[14]  David S. Lorberbaum,et al.  Genetic evidence that Nkx2.2 acts primarily downstream of Neurog3 in pancreatic endocrine lineage development , 2017, eLife.

[15]  M. Cookson,et al.  LRRK2 at the interface of autophagosomes, endosomes and lysosomes , 2016, Molecular Neurodegeneration.

[16]  M. Cecchini,et al.  Ultrastructural Characterization of the Lower Motor System in a Mouse Model of Krabbe Disease , 2016, Scientific Reports.

[17]  A. Gitler,et al.  Defects in trafficking bridge Parkinson's disease pathology and genetics , 2016, Nature.

[18]  V. D’Agati,et al.  LRRK2 and RAB7L1 coordinately regulate axonal morphology and lysosome integrity in diverse cellular contexts , 2016, Scientific Reports.

[19]  M. Ueffing,et al.  Structural model of the dimeric Parkinson’s protein LRRK2 reveals a compact architecture involving distant interdomain contacts , 2016, Proceedings of the National Academy of Sciences.

[20]  S. Schmid,et al.  Endocytic pathways and endosomal trafficking: a primer , 2016, Wiener Medizinische Wochenschrift.

[21]  Matthias Mann,et al.  Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases , 2016, eLife.

[22]  L. Bubacco,et al.  LRRK2 phosphorylates pre-synaptic N-ethylmaleimide sensitive fusion (NSF) protein enhancing its ATPase activity and SNARE complex disassembling rate , 2016, Molecular Neurodegeneration.

[23]  Elie Needle,et al.  Pathogenic LRRK2 mutations, through increased kinase activity, produce enlarged lysosomes with reduced degradative capacity and increase ATP13A2 expression. , 2015, Human molecular genetics.

[24]  Elie Needle,et al.  Leucine-rich Repeat Kinase 2 (LRRK2) Pharmacological Inhibition Abates α-Synuclein Gene-induced Neurodegeneration* , 2015, The Journal of Biological Chemistry.

[25]  W. Seol,et al.  An early endosome regulator, Rab5b, is an LRRK2 kinase substrate. , 2015, Journal of biochemistry.

[26]  Mark R Cookson,et al.  LRRK2 Pathways Leading to Neurodegeneration , 2015, Current Neurology and Neuroscience Reports.

[27]  Claudia Manzoni,et al.  Computational analysis of the LRRK2 interactome , 2015, PeerJ.

[28]  Amaia M. Arranz,et al.  LRRK2 functions in synaptic vesicle endocytosis through a kinase-dependent mechanism , 2015, Journal of Cell Science.

[29]  W. Ruan,et al.  LRRK2 localizes to endosomes and interacts with clathrin‐light chains to limit Rac1 activation , 2015, EMBO reports.

[30]  Jack Euesden,et al.  PRSice: Polygenic Risk Score software , 2014, Bioinform..

[31]  M. Nalls,et al.  Phosphorylation of LRRK2 by casein kinase 1α regulates trans-Golgi clustering via differential interaction with ARHGEF7 , 2014, Nature Communications.

[32]  I. Ferrer,et al.  LRRK2 delays degradative receptor trafficking by impeding late endosomal budding through decreasing Rab7 activity. , 2014, Human molecular genetics.

[33]  A. Kortholt,et al.  Structural biology of the LRRK2 GTPase and kinase domains: implications for regulation , 2014, Front. Mol. Neurosci..

[34]  Suneil K. Kalia,et al.  Unbiased screen for interactors of leucine-rich repeat kinase 2 supports a common pathway for sporadic and familial Parkinson disease , 2014, Proceedings of the National Academy of Sciences.

[35]  K. Marder,et al.  RAB7L1 Interacts with LRRK2 to Modify Intraneuronal Protein Sorting and Parkinson’s Disease Risk , 2013, Neuron.

[36]  Xiongwei Zhu,et al.  Kinase inhibitors arrest neurodegeneration in cell and C. elegans models of LRRK2 toxicity. , 2013, Human molecular genetics.

[37]  P. Verstreken,et al.  LRRK2 Controls an EndoA Phosphorylation Cycle in Synaptic Endocytosis , 2012, Neuron.

[38]  Pietro De Camilli,et al.  Synaptic vesicle endocytosis. , 2012, Cold Spring Harbor perspectives in biology.

[39]  W. Dauer,et al.  Leucine-rich repeat kinase 2 for beginners: six key questions. , 2012, Cold Spring Harbor perspectives in medicine.

[40]  John Hardy,et al.  A generalizable hypothesis for the genetic architecture of disease: pleomorphic risk loci. , 2011, Human molecular genetics.

[41]  Cosetta Minelli,et al.  The meta-analysis of genome-wide association studies , 2011, Briefings Bioinform..

[42]  W. Wurst,et al.  LRRK2 Controls Synaptic Vesicle Storage and Mobilization within the Recycling Pool , 2011, The Journal of Neuroscience.

[43]  Mark R. Cookson,et al.  The role of leucine-rich repeat kinase 2 (LRRK2) in Parkinson's disease , 2010, Nature Reviews Neuroscience.

[44]  E. Tan,et al.  Leucine-Rich Repeat Kinase 2-Linked Parkinson’s Disease: Clinical and Molecular Findings , 2010, Journal of movement disorders.

[45]  T. Kirchhausen,et al.  Roles of AP-2 in Clathrin-Mediated Endocytosis , 2010, PloS one.

[46]  R. J. Kelleher,et al.  Loss of leucine-rich repeat kinase 2 causes impairment of protein degradation pathways, accumulation of α-synuclein, and apoptotic cell death in aged mice , 2010, Proceedings of the National Academy of Sciences.

[47]  Sonja W. Scholz,et al.  Genome-Wide Association Study reveals genetic risk underlying Parkinson’s disease , 2009, Nature Genetics.

[48]  P. Lewis The function of ROCO proteins in health and disease , 2009, Biology of the cell.

[49]  John P A Ioannidis,et al.  Meta-analysis in genome-wide association studies. , 2009, Pharmacogenomics.

[50]  G. Schiavo,et al.  Coordinated regulation of AP2 uncoating from clathrin-coated vesicles by rab5 and hRME-6 , 2008, The Journal of cell biology.

[51]  N. Hattori,et al.  LRRK2 regulates synaptic vesicle endocytosis. , 2008, Experimental cell research.

[52]  V. Haucke,et al.  Clathrin‐Mediated Endocytosis at Synapses , 2007, Traffic.

[53]  M. Cookson,et al.  The R1441C mutation of LRRK2 disrupts GTP hydrolysis. , 2007, Biochemical and biophysical research communications.

[54]  David W. Miller,et al.  Kinase activity is required for the toxic effects of mutant LRRK2/dardarin , 2006, Neurobiology of Disease.

[55]  C. Ross,et al.  Parkinson's disease-associated mutations in leucine-rich repeat kinase 2 augment kinase activity. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[56]  J. Bonifacino,et al.  Clathrin Adaptor AP-2 Is Essential for Early Embryonal Development , 2005, Molecular and Cellular Biology.

[57]  David W. Miller,et al.  Mutations in PTEN-induced putative kinase 1 associated with recessive parkinsonism have differential effects on protein stability. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[58]  S. Schmid,et al.  Differential requirements for AP-2 in clathrin-mediated endocytosis , 2003, The Journal of cell biology.

[59]  Sandra L. Schmid,et al.  Phosphorylation of the AP2 μ subunit by AAK1 mediates high affinity binding to membrane protein sorting signals , 2002, The Journal of cell biology.

[60]  J. Swedlow,et al.  Phosphorylation of threonine 156 of the μ2 subunit of the AP2 complex is essential for endocytosis in vitro and in vivo , 2001, Current Biology.

[61]  K. von Figura,et al.  Binding of AP2 to Sorting Signals Is Modulated by AP2 Phosphorylation* , 2001, The Journal of Biological Chemistry.

[62]  D. Moore,et al.  Understanding the GTPase Activity of LRRK2: Regulation, Function, and Neurotoxicity. , 2017, Advances in neurobiology.

[63]  J. Trojanowski,et al.  Clinical correlations with Lewy body pathology in LRRK2-related Parkinson disease. , 2015, JAMA neurology.

[64]  S. Homma,et al.  Depletion of extracellular signal-regulated kinase 1 in mice with cardiomyopathy caused by lamin A/C gene mutation partially prevents pathology before isoenzyme activation. , 2014, Human molecular genetics.

[65]  I. Ferrer,et al.  LRRK 2 delays degradative receptor trafficking by impeding late endosomal budding through decreasing Rab 7 activity , 2014 .

[66]  W. Ruan,et al.  LRRK 2 localizes to endosomes and interacts with clathrin-light chains to limit Rac 1 activation , 2014 .

[67]  W. Betz,et al.  Imaging synaptic vesicle exocytosis and endocytosis with FM dyes , 2007, Nature Protocols.