View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Liverpool Repository RESEARCH ARTICLE The Endocytic Membrane Trafficking Pathway Plays a Major Role in the Risk of Parkinson’s Disease Sara Bandres-Ciga, PhD,1,2 Sara Saez-Atienzar, PhD,3 Luis Bonet-Ponce, PhD,4 Kimberley Billingsley, MSc,1,5,6 Dan Vitale, MSc,7 Cornelis Blauwendraat, PhD,1 Jesse Raphael Gibbs, PhD,7 Lasse Pihlstrøm, MD, PhD,8 Ziv Gan-Or, MD, PhD,9,10 The International Parkinson’s Disease Genomics Consortium (IPDGC), Mark R. Cookson, PhD,4 Mike A. Nalls, PhD,1,11 and Andrew B. Singleton, PhD1* 1Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain 3Transgenics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 4Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 5Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom 6Department of Pathophysiology, University of Tartu, Tartu, Estonia 7Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 8Department of Neurology, Oslo University Hospital, Oslo, Norway 9Department of Neurology and Neurosurgery, Department of Human Genetics, McGill University, Montréal, Quebec, Canada 10Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada 11Data Tecnica International, Glen Echo, Maryland, USA ABSTRACT studies, summary-data based Mendelian randomization Background: PD is a complex polygenic disorder. In analyses were applied to explore possible functional recent years, several genes from the endocytic genomic associations with expression or methylation membrane-trafficking pathway have been suggested to quantitative trait loci. contribute to disease etiology. However, a systematic Results: The heritability estimate attributed to endocytic analysis of pathway-specific genetic risk factors is yet to membrane-trafficking pathway was 3.58% (standard be performed. error = 1.17). Excluding previously nominated PD endo- Objectives: To comprehensively study the role of the cytic membrane-trafficking pathway genes, the missing endocytic membrane-trafficking pathway in the risk of PD. heritability was 2.21% (standard error = 0.42). Random Methods: Linkage disequilibrium score regression was heritability simulations were estimated to be 1.44% used to estimate PD heritability explained by 252 genes (standard deviation = 0.54), indicating that the unbiased involved in the endocytic membrane-trafficking pathway total heritability explained by the endocytic membrane- including genome-wide association studies data from trafficking pathway was 2.14%. Polygenic risk score 18,869 cases and 22,452 controls. We used pathway- based on endocytic membrane-trafficking pathway specific single-nucleotide polymorphisms to construct a showed a 1.25 times increase of PD risk per standard polygenic risk score reflecting the cumulative risk of com- deviation of genetic risk. Finally, Mendelian randomiza- mon variants. To prioritize genes for follow-up functional tion identified 11 endocytic membrane-trafficking ----------------------------------------------------------------------------------------------------------------------- *Correspondence to: Dr. Andrew Singleton, Porter Neuroscience Relevant conflicts of interest/financial disclosures: Mike A. Nalls’ Center, 35 Convent Drive, Bethesda, MD 20892, USA; participation is supported by a consulting contract between Data Tec- E-mail: [email protected] nica International and the National Institute on Aging, NIH, Bethesda, fl Dr. Bandres-Ciga, Dr. Saez-Atienzar, and Dr. Bonet-Ponce contributed MD, USA, as a possible con ict of interest. Dr. Nalls also consults for equally to the work. SK Therapeutics Inc, Lysosomal Therapeutics Inc, the Michael J. Fox Foundation, and Vivid Genomics, among others. Funding agencies: This research was supported, in part, by the fi Intramural Research Program of the National Institutes of Health Full nancial disclosures and author roles may be found in the (National Institute on Aging, National Institute of Neurological Disor- online version of this article. ders and Stroke; project numbers: project numbers 1ZIA- Received: 3 October 2018; Revised: 5 December 2018; Accepted: 23 NS003154, Z01-AG000949-02, and Z01-ES101986). In addition, December 2018 this work was supported by the Department of Defense (award W81XWH-09-2-0128) and The Michael J. Fox Foundation for Published online 00 Month 2018 in Wiley Online Library Parkinson’s Research. (wileyonlinelibrary.com). DOI: 10.1002/mds.27614 Movement Disorders, 2019 1 BANDRES-CIGA ET AL pathway genes showing functional consequence associ- made to identify potential avenues within this biological ated to PD risk. process suitable for therapeutic interventions. © 2019 Conclusions: We provide compelling genetic evidence International Parkinson and Movement Disorder Society that the endocytic membrane-trafficking pathway plays a relevant role in disease etiology. Further research on this Key Words: endocytosis; genetic risk; heritability; pathway is warranted given that critical effort should be Parkinson’s disease; polygenic risk score Parkinson’s disease (PD) is a progressive neurodegen- cargo can be retained in early endosomes that will eventu- erative disorder clinically characterized by the manifes- ally mature into late endosomes and fuse with lysosomes tation of motor disturbances such as bradykinesia, to ensure cargo degradation. In parallel, proteins can also rigidity, tremor, and a wide range of nonmotor symp- traffic between endosomes and the Golgi apparatus (for a toms. Disease is caused by the death of the dopaminer- review, see a previous work9). A substantial amount of gic neurons in the SN with the consequent deficit of genetic variation in PD and parkinsonism previously striatal dopamine.1 The etiology of PD is complex, nominated genes has been associated with vesicle traffick- including genetic, epigenetic, and environmental fac- ing by endosomal gene alterations,10 including monogenic tors. Familial PD accounts for less than 10% of the genes (VPS35,11 DNAJC613,18) and GWAS-nominated total cases, mostly attributed to monogenic forms with genes (RAB7L1,12,13 SH3GL2,14 GAK,15,16 and autosomal-dominant (including SNCA, LRRK2, and CHMP2B15,17). In addition, other well-known PD genes, VPS35) or autosomal-recessive pattern of inheritance, such as LRRK212,13 and PLA2G6, 18 seem to be linked such as PARKIN, PINK1, and DJ-1, among others.2,3 to the aforementioned pathway through their biological However, the vast majority of the disease is considered interaction with EMPT genes. LRRK2 binds to to be sporadic, likely caused by the cumulative effect of RAB7L112,13 andPLA2G6interactswithVPS35and multiple common or rare variants of small or moderate VPS26, although a clear role of these genes in the EMTP effect sizes in addition to other unknown environmental is yet to be elucidated. The genes involved in the EMTP and stochastic factors. play different roles within the pathway. For instance, Over the last two decades, extensive work in genetics DNAJC6, SYNJ1, GAK,andSH3GL2 are linked to has uncovered up to 92 common risk loci associated clathrin-coated vesicles whereas VPS35, DNAJC13,or with idiopathic PD.4 As expected from complex diseases, RAB7L1 participate in recycling components from the the PD-related signals identified to date only account for endosomes to the Golgi. Hence, it seems plausible that a small proportion of the total phenotypic variation, other genes in that pathway could be involved in PD risk defined as heritability.5 It is estimated that only around and therefore account for the nonreported heritability. 10% to 15% of the overall heritable risk of PD is Based on these premises, we aimed to benefit from a cel- explained by current genome-wide association studies lular perspective to systematically explore the genetic con- (GWAS).4 The most plausible explanation for the “miss- tribution of 252 endosomal membrane-trafficking–related ing heritability” might be small effect sizes of the yet to genes on the susceptibility for PD. We set out to study to be discovered risk loci which do not reach GWAS signifi- what extent common variation in these genes might play a cance, as well as structural genomic and rare variation role on the genetic architecture of PD by performing poorly covered by current technology.6 Undoubtedly, genome-wide heritability estimations and polygenic risk the estimated heritability in PD suggests that a significant versus disease status and age at onset in the International amount of risk has not been uncovered yet. Parkinson’s Disease Genomics Consortium (IPDGC) Aligned with the genetic discoveries, a big effort has GWAS data set. We also applied Mendelian randomization been made to identify how those genes interact within to attempt to investigate possible functional genomic asso- biological pathways to elucidate the cellular and molecu- ciations between nominated variants of interest within this lar processes that could explain the neurodegenerative pathway versus expression and methylation