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Genetics and genomics of Parkinson’s disease Lin, Michelle K; Farrer, Matthew J Jun 30, 2014

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REVIEWGenetics and genomics of Parkinson’s diseaseMichelle K Lin and Matthew J Farrer*AbstractParkinson’s disease (PD) is a progressively debilitating neurodegenerative syndrome. Although best described as amovement disorder, the condition has prominent autonomic, cognitive, psychiatric, sensory and sleep components.Striatal dopaminergic innervation and nigral neurons are progressively lost, with associated Lewy pathology readilyapparent on autopsy. Nevertheless, knowledge of the molecular events leading to this pathophysiology is limited.Current therapies offer symptomatic benefit but they fail to slow progression and patients continue to deteriorate.Recent discoveries in sporadic, Mendelian and more complex forms of parkinsonism provide novel insight intodisease etiology; 28 genes, including those encoding alpha-synuclein (SNCA), leucine-rich repeat kinase 2 (LRRK2)and microtubule-associated protein tau (MAPT), have been linked and/or associated with PD. A consensus regardingthe affected biological pathways and molecular processes has also started to emerge. In early-onset and more atypical PD, deficits in mitophagy pathways and lysosomal function appear to be prominent. By contrast, in moretypical late-onset PD, chronic, albeit subtle, dysfunction in synaptic transmission, early endosomal trafficking andreceptor recycling, as well as chaperone-mediated autophagy, provide a unifying synthesis of the molecular pathwaysinvolved. Disease-modification (neuroprotection) is no longer such an elusive goal given the unparalleled opportunityfor diagnosis, translational neuroscience and therapeutic development provided by genetic discovery.Clinical features, main treatments and challengesParkinson’s disease (PD) is a progressively debilitatingneurodegenerative disease that becomes increasinglychallenging to manage. Until recently, the underlyingmolecular cause(s) have remained elusive, as have hopesof disease-modification (neuroprotection). The need foradvances in understanding and treating the disease isgreat as PD is the second most common neurodegenera-tive disorder after Alzheimer’s disease. The estimatedworldwide prevalence is 1% in the population >60 yearsof age, increasing to 4% at 80 years of age [1]. Themedian age of onset is about 70 years but about 4% ofpatients manifest early-onset disease (before they reach50 years of age).In PD, the clinical heterogeneity, disease course andresponse to medication vary widely [2]. Motor symptomsare associated with profound neuronal loss in the sub-stantia nigra pars compacta (SN), depleting the striatumof dopaminergic inhibition. Hence, restorative dopamin-ergic therapies are the main treatment. Monoamine oxi-dase inhibitors are initially used to prevent endogenousdopamine catabolism; alternatively, L-DOPA, the meta-bolic precursor of dopamine, and/or dopamine agonistsare used. In selected patients, deep brain stimulation(DBS) of striatal output pathways has also proven effect-ive [3]. There are, however, several non-motor symp-toms, of which many are non-dopaminergic and withoutremedy [4]. For example, 30% of patients develop mild-cognitive impairment within 5 years of motor symptomsand many develop dementia [5]. PD is clinically and/orpathologically distinct from other forms of parkinsonism(Box 1). A definitive diagnosis of PD requires the pres-ence of Lewy bodies and Lewy neurites (proteinaceousintracellular inclusions) in the brain stem (midbrain), al-though these lesions are often more widespread [6,7].Here, we review recent genetic and genomic findings instudies of PD, we provide some integration and synthesisof the molecular pathways involved, and we discuss thetranslational implications.Early linkage and candidate gene studiesClassical linkage analysis has proven a powerful approachfor the identification of specific disease-associatedgenes and mutations in families with multi-incidentparkinsonism [8]. Genome-wide association and twinstudies further demonstrate that even idiopathic sporadic* Correspondence: mfarrer@can.ubc.caDjavad Mowafaghian Centre for Brain Health, Centre for AppliedNeurogenetics, Department of Medical Genetics, University of BritishColumbia, Vancouver, BC V6T 1Z3, Canada© 2014 Lin and Farrer; licensee BioMed Central Ltd. The licensee has exclusive rights to distribute this article, in any medium, for12 months following its publication. After this time, the article is available under the terms of the Creative CommonsAttribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproductionin any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Lin and Farrer Genome Medicine 2014, 6:48http://genomemedicine.com/content/6/6/48PD has a significant genetic component [9,10]. Mutantgene discovery by linkage with association provides an un-equivocal burden of proof, and is the foundation requiredfor translational neuroscience. Nevertheless, geneticallydefined carriers may have variable expressivity and pene-trance and may never ‘phenoconvert’ to symptomatic dis-ease. Age remains an important determinant, even infamilies with dominant, recessive or X-linked patterns ofsegregation. Not surprisingly, in vivo modeling in mam-malian systems is challenging if the expectation is to re-capitulate the human phenotype. Gene discovery efforts inPD have been expertly reviewed and we provide some his-torical context in Box 2. In this review, we focus on moretypical, late-onset PD with Lewy body pathology, the dis-ease type suffered by the majority of patients, and suggesthow recent discoveries might unify existing ideas to sug-gest novel pathways and therapeutic targets.In this context of genomic discovery, genes at three loci -alpha-synuclein (SNCA), leucine-rich repeat kinase 2(LRRK2) and microtubule-associated protein tau (MAPT) -deserve special mention, although the molecular relation-ship between them has yet to be elucidated. Both SNCAand LRRK2 assignments were originally implicated by thediscovery (by linkage analysis) of pathogenic mutationsthat segregate within families, and these observations wereextended into idiopathic PD by candidate gene studies.Combined pooled analysis by the Genetic Epidemiologyof Parkinson’s disease Consortium (www.geopd.org), litera-ture meta-analysis (www.pdgene.org) and more recentgenome-wide association studies (GWAS) have providedcompelling support for the involvement of these loci.Missense and multiplication mutations (duplication andtriplication) in SNCA lead to PD, subsequent dementiaand fulminant diffuse Lewy body disease on autopsy [11].Levels of gene expression are inversely correlated with ageat symptom onset. In rodents, SNCA overexpression mayrecapitulate many of the features of PD, whereas knockoutmice are viable and fertile and appear to have little sign ofdisease [12]. The alpha-synuclein protein promotes pre-synaptic SNARE complex assembly, synaptic vesicle exo-cytosis and reciprocal plasmalemma endocytosis [13].Alpha-synuclein protein aggregates, however, may also be-have pathologically as prion proteins [14]. Transplants offetal tissue into the striatum of human patients have beenobserved to develop Lewy-body pathology [15]. Similarly,iatrogenic inoculation of alpha-synuclein oligomers intomouse brain leads to widespread Lewy-like pathology,albeit requiring endogenous alpha-synuclein for trans-mission [16]. Hence, down-regulation or suppression ofSNCA may represent one mechanism to slow diseaseprogression [17]. Similarly, therapies that enhance theclearance of Lewy aggregates, including immunotherapiestargeting potentially toxic forms of alpha-synuclein, mightbe neuroprotective [18].LRRK2 parkinsonism is clinically indistinguishablefrom idiopathic PD. The age of onset and age-dependentcumulative incidence is similarly broad, although diseaseprogression in carriers of LRRK2 mutations is morehomogeneous [19]. A founder haplotype has been notedfor LRRK2 p.G2019S in most populations. Penetranceappears to be ethnic-specific with a lifetime cumulativeBox 1. Parkinsonism and Parkinson’s diseaseParkinsonism is used as an adjective to describe a movementdisorder generally consisting of one of more features of tremor,bradykinesia and rigidity. The most common forms are drug-induced(for example, as a side-effect of antipsychotic neuroleptics), orvascular resulting from a stroke. When used as an adjective,the term parkinsonism does not imply that the symptoms areprogressive or neurodegenerative, or that they are associatedwith a specific neuropathology. Parkinsonism may not respondto levodopa therapy. PD itself has the same core triad of symptoms,but it begins asymmetrically, one side of the body being moreprofoundly affected than the other, and postural instability istypically a feature. In PD, symptoms respond well to levodopareplacement therapy, and typically worsen with disease durationdespite medication. Symptoms become bilateral in advanced PD,and dopaminergic imaging, using modalities such as DaTscan,highlights the same pattern of progression.PD, but not parkinsonism, is often associated with a variety ofautonomic problems (constipation, bowel and bladderincontinence, drooling), cognitive dysfunctions (from mildimpairments in executive function to dementia), motorproblems (from dystonia to dyskinesia), neuropsychiatricsymptoms (mood disorders, such as depression to impulsecontrol), sensory problems (from unexplained pain syndromesto hyposmia or anosmia) and sleep disorders (daytimesleepiness to REM sleep behavior disorder). Several of theseproblems, including dyskinesia, mood disorders and daytimesleepiness, may be associated with levodopa therapy or theuse of dopamine agonists.A definite diagnosis of PD is reserved for patients with Lewybody pathology and neuronal loss in the midbrain, which isoften more widely distributed to involve the myentericplexus, vagus and olfactory bulb. By contrast, parkinsonismmay be associated with a variety of pathologies, includingneurofibrillary tangles (such as in progressive supranuclear palsy,corticobasal ganglionic degeneration, or parkinsonism-dementiacomplex of Guam), to the predominant oligodendroglialalpha-synuclein pathology of multiple system atrophy, orpredominant cortical Lewy pathology associated with dementiawith Lewy bodies.Lin and Farrer Genome Medicine 2014, 6:48 Page 2 of 16http://genomemedicine.com/content/6/6/48Box 2. Genetic insights and evolving neuroscience1997 A missense substitution, p.A53T, is discovered in the gene encoding alpha-synuclein (SNCA) in a family from Contursi, Italy whosemembers were susceptible to autosomal dominant, late-onset parkinsonism [56]. Alpha-synuclein, then known as ‘Non-amyloid componentof plaques’ (NACP), provides a link between PD and Alzheimer’s disease. Whether alpha-synuclein monomers, oligomers or fibrils are the toxicspecies becomes a topic for debate. Physiologically, the Zebra Finch homolog of SNCA is found to be required for song learning, pre-synapticplasticity, and vesicle trafficking in neurotransmission.Alpha-synuclein immunohistochemistry reveals much more occult Lewy pathology than had been visualized previously by hematoxylinand eosin (H&E) staining, and replaced the use of PGP9.5 (an antibody for Ubiquitin C-terminal hydrolase1 (UCHL1)) [136]. It is arguedthat familial and idiopathic forms of parkinsonism are the same disease, with similar ontology. Nevertheless, epidemiologists claim thatthe etiology of late-onset PD is environmental, rather than due to a genetic predisposition, supported by the results of twin studies.Further debate centers on whether ubiqinated Lewy body ‘aggresomes’ are pathologic or protective.1998 Homozygous parkin deletions are linked to recessively inherited juvenile and early-onset parkinsonism, albeit without documentedLewy pathology [109]. Parkin mutations soon explain around 15% of all early-onset parkinsonism (in those younger than 45 years) [137]. Asthe parkin mutations affect a ubiquitin E3 ligase, the field focuses on proteasome inhibition, attempting to identify parkin’s substrates and tonominate the toxic species. Patients with parkin mutations and Lewy or tau pathology have subsequently been described [138,139]. Thecrystal structure of the ubiquitin ligase reveals how its activity is regulated [116].1999-2001 Candidate gene studies of polymorphic variability in SNCA and microtubule-associated protein tau (MAPT) highlight theroles of these genes in idiopathic, late-onset PD [57,140,141]. MAPT is implicated in progressive supranuclear palsy, in part because ofthe discovery of splicing mutations in another 4R-tauopathy, frontotemporal dementia with parkinsonism linked to chromosome 17(FTDP-17) [44]. Large-scale GWAS provide further confirmation [9,52,55,142].2003 DJ-1 mutations that were discovered in early-onset parkinsonism [123] highlight a role for oxidative stress in PD. The findingshelp to justify the use of toxin-based models using 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) as an analog of the herbicideparaquat or the pesticide rotenone.2003-2004 SNCA triplication and duplication mutations demonstrate a dose-dependent relationship between expression and pathogenicity[58,143-146] that is now supported by several mouse models. Lowering SNCA RNA and/or SNCA protein expression is nominated as atherapeutic target, supported by in vivo studies.2004 Recessively inherited mutations are identified in the Pten-induced kinase 1 gene (PINK1) in early-onset parkinsonism [147]. By2006, PINK1 was found to regulate Parkin recruitment and mitophagy [114,115]. FBXO7 is within the same pathway, pointing to mitochondrialmaintenance as a therapeutic opportunity [68]. Hexokinase is identified through interaction screens as an upstream component of thepathway [119]. PINK1 is shown to phosphorylate ubiquitin to activate parkin [117].2004-2005 Dominantly inherited mutations are identified in the LRRK2 gene in late-onset PD [32]. In 2005, LRRK2 p.G2019S was linkedto PD in Norwegian families [148], and found to be the major determinant of sporadic PD in Ashkenazi Jews and North-African Berbers.Kinase inhibition is nominated as a therapeutic strategy. Pleomorphic alpha-synuclein, 4R-tau or ubiquitin pathologies in affected carrierssuggest that Lewy pathology should not be required for a definite diagnosis of PD [32]. LRRK2 is implicated in protein sorting or traffickingand in autophagy. Polymorphic variants in LRRK2 are found to lower or increase the risk of sporadic PD [34].2006 ATP13A2 recessive mutations are identified in juvenile and early-onset parkinsonism [102]. Several lysosome-associated proteinshave subsequently been linked to rare and rather atypical forms, including ATP1A3 in rapid-onset parkinsonism-dystonia, and mostrecently ATP6AP2 [71]. Polymorphic variants in the glucocerebrosidase gene GBA1 are reproducibly associated with late-onset PD,highlighting a role for endosomal trafficking and lysosomal function [98].2009 GWAS studies in PD confirm associations with SNCA and MAPT, and find evidence for additional loci [50-52].2011 VPS35 D620N is linked to dominant late-onset PD [63]. Many families have the same, albeit de novo, substitution that supportspathogenicity. By contrast, mutations in EIF4G1 R1205H require further genetic and functional support for their assignment [149].2013-2014 Mutations in DNAJC13, along with VPS35, in late-onset Lewy-body PD further highlight involvement of the retromer-WASHcomplex, endosomal protein sorting and trafficking [63,64,93].2014 Further meta-analysis of GWAS supports known and novel loci. Nevertheless, for most loci the precise gene and underlyingvariability remain elusive.Lin and Farrer Genome Medicine 2014, 6:48 Page 3 of 16http://genomemedicine.com/content/6/6/48risk of parkinsonism in p.G2019S carriers being 22% forAshkenazi Jews (living in the US), 45% for Norwegiansand 80% for Arab-Berbers [20-22], which is an import-ant consideration for genetic counseling. For AshkenaziJews in Israel and Arab-Berbers in Tunisia the pene-trance of disease is similar. In these countries, the fre-quency of LRRK2 p.G2019S carriers in healthy controlsis relatively high at 1 to 2% [23,24]. While genetic driftmay be sufficient explanation for the high frequency ofLRRK2 p.G2019S carriers in healthy controls, positiveselection may also contribute; LRRK2 is associated withintestinal inflammatory disorders, immune response andkidney function, which if compromised may be mostdeleterious in hot climates [25-27]. Overall, only a smallproportion (approximately 1%) of familial and sporadicPD is likely explained by LRRK2 p.G2019S; other vari-ability, such as the p.G2385R mutation, which is fre-quent throughout Asia, most significantly contributes topopulation-attributable risk [28] (Table 1).At post-mortem, the majority of patients with pathogenicLRRK2 mutations have Lewy-body disease [29]. However,even within families with the same mutation, pleomorphicpathologies have been observed. These include neurofibril-lary tangles and tufted astrocytes (4R-tauopathies, as in-clusion of MAPT exon 10 leads to the production oftau protein with four microtubule-binding domains), TarDNA-binding protein 43 and ubiquitin immune-positiveaggregates, or simply nigral neuronal loss with gliosis[30-32]. The variable penetrance and alternative end-stagepathologies most likely reflect genetic and/or environmen-tal modifiers and stochastic factors, and have yet to be de-fined. Nevertheless, genetically defined cohorts of patientswith parkinsonism such as LRRK2 p.G2019S parkinsonismmight allow the identification of biomarkers of disease pro-gression and inform clinical trials [19].As the most common genetic cause of PD, LRRK2 andits protein interactions are a logical place to search fornovel therapeutic targets. The domains of LRRK2 in-clude armadillo and ankyrin repeat regions, leucine-richrepeat (LRR), Ras of complex GTPase (Roc), C-terminalof Ras (COR), kinase and WD40. LRRK2 is a ROCO pro-tein, with a Ras GTPase and a kinase in one molecule;these activities have established roles in other organisms orcell types in dynamically modifying the actin cytoskeleton[33]. Pathogenic LRRK2 mutations are primarily found inthe GTPase Roc domain (p.R1437H, p.R1441C/G/H),the kinase domain (p.G2019S, p.I2020T) and interveningC-terminal of Roc (p.Y1699C), whereas susceptibility vari-ants may also be found in protein-protein interaction do-mains (WD40 p.G2385R) [34]. Competitive inhibition ofLRRK2 kinase is presently considered as one therapeutictarget given that the p.G2019S mutation activates kinaseactivity, autophosphorylation and/or phosphorylation ofsubstrates [35]. However, data on the first identified sub-strate, moesin, which is a filamentous actin tether, havenot been recapitulated ex or in vivo [36]. LRRK2 proteinlevels also diminish with aging, with knock-in of LRRK2pathogenic mutations into the mouse genome [26] andwith kinase inhibition [37,38]. LRRK2 probably functionsas a dimer or higher molecular weight scaffold, with manyprotein-protein interactions. The activities of the Roc,COR and kinase domains are interconnected [39], and themany physiologic functions of the protein complex haveyet to be fully elucidated.Table 1 Genomic loci implicated in Parkinson’s disease by genome-wide association analysesGene Chr AssociatedSNP/locus Genes within locusa Odds ratio[95% CI] P-valueGBA 1q21 N370S TRIM46, MUC1, MIR92B, THBS3, GBAP1-GBA-FAM189B, SCAMP3,CLK2, HCN3, PKLR3.37[2.67-4.29] 1.11E-24SYT11/RAB25 1q21 chr1:154105678 MIR7851, UBQLN4, LAMTOR2-RAB25-MEX3A, LMNA 1.67[1.41-1.98] 5.70E-09PM20D1 1q32 rs11240572 NUCK1-RAB7L1-SLC41A1, PM20D1 0.74[0.69-0.80] 1.01E-14STK39 2q24 rs2102808 STK39 1.28[1.19-1.38] 1.54E-11MCCC1/LAMP3 3q27 rs11711441 MCCC1-LAMP3-MCF2L2 0.84[0.80-0.89] 8.72E-12BST1 4p15 rs4698412 FAM200B-BST1 0.87[0.83-0.91] 2.28E-10GAK/DGKQ 4p16 rs1564282 CPLX1-GAK-TMEM175-DGKQ-SLC26A1, IDUA, FGFRL1 1.29[1.20-1.38] 6.54E-13SNCA 4q21 rs356220 SNCA-MMRN1 1.30[1.25-1.34] 3.06E-49HLA-DRB5 6p21 rs2395163 HLA-DRB5-HLA-DRB1, HLA-DRB6 0.75[0.68-0.84] 2.90E-07GPNMB 7p15 rs156429 GPNMB-MALSU1-IGF2BP3 0.89[0.86-0.93] 2.69E-10LRRK2 12q12 rs34778348 SLC2A13-LRRK2-MUC19, CNTN1 2.23[1.89-2.63] 2.97E-21CCDC62/HIP1R 12q24 rs12817488 DENR-HIP1R-VPS37B, ABCB9, OGFOD2, 1.17[1.09-1.25] 2.99E-06MAPT/STH 17q21 H1H2, 900kb inversion ARHGAP27, PLEKHM1, CRHR1, SPPL2C-MAPT-STH, KANSL1,LRRC37A, NSFP1, ARL17A/B0.78[0.75-0.80] 3.54E-52Chr, chromosomal band; CI, confidence interval. aGenes within 100 kb of the most significantly associated SNP annotated from the UCSC genome browser (hg19).Odds ratios and P-values are the most significant findings from the PDGene database [150].Lin and Farrer Genome Medicine 2014, 6:48 Page 4 of 16http://genomemedicine.com/content/6/6/48An association between PD and MAPT and the sur-rounding 17q21 locus results from an ancient paracentricinversion and was robustly implicated in clinical PD andin autopsy-confirmed series of PD in Caucasian popula-tions [40-42]. Of note, similar variability in the MAPTlocus has been unequivocally implicated in progressivesupranuclear palsy, but not in Alzheimer’s disease, al-though tau is a major component of the neurofibrillarytangle pathology in both conditions [43]. Splice and mis-sense mutations were first described in frontotemporal de-mentia [44] and the inversion region was subsequentlyimplicated in 17q21.31 microdeletion syndromes [45], butneither pathologic mutations nor tau pathology are foundin PD. Thus, genetic variability in neighboring genes,within or flanking the MAPT inversion, may contribute.Some examples of additional genes and pathogenic muta-tions discovered through family-based linkage analysis ofparkinsonism are summarized in Table 2.Genome-wide association studiesWhile there are several genetic models for disease suscep-tibility, the ‘rare variant common disease’ model largelyexplains Mendelian heritability (one allele of major effectsegregating with familial disease) whereas the ‘commonvariant common disease’ model (or multiple rare variantson common ancestral haplotypes) forms the theoreticalbasis of GWAS [46]. Built upon large, multi-institutionalconsortia, GWAS have dominated the search for novelgenes in human traits in recent years. Collectively, morethan 2,600 genomic regions (loci) of modest effect size(odds ratio <1.5) have been associated with >350 complextraits and have implicated underlying genes that play arole in disease causality or susceptibility [47]. Genome-wide genotyping, with approximately 0.5 to 1 millionmarkers, is used to assess frequency differences in case-control designs, and is able to capture common geneticcontributions to disease in linkage disequilibrium.The first GWAS for PD were small and underpowered,showing little overlap in results [48,49]. Subsequently,there was an appreciation that larger numbers of markersand subjects are required for meaningful discovery andreplication. Past North American and European effortsincluded analysis of familial parkinsonism [50] and ofunrelated case-control series [51-54]. A web-based‘direct- to-consumer’ effort, which is based on self reportrather than clinical exam, is by far the largest study to date[9]. However, genomic imputation of single nucleotidepolymorphisms (SNPs) in linkage disequilibrium allowsdatasets to be combined. In 2011, the InternationalParkinson Disease Genomics Consortium conducted ameta-analysis from five GWAS datasets [55]. Over 7million SNPs based on approximately 1 million geno-types per individual were imputed in silico: the datawere collected from 5,333 cases and 12,019 controls inthe discovery phase, followed by 7,053 cases and 9,007controls in the replication phase. Six loci previouslyassociated with idiopathic PD were replicated and fivenew loci were identified (Table 1). Data from the latestmega-meta-GWAS, including over 13,000 patients withPD and 80,000 control subjects, are eagerly awaited.Table 2 Mendelian mutations in familial parkinsonismGene Mutation(s) OMIM Reference(s)Dominantly inherited, late onset parkinsonism with Lewy pathologySNCA Locus multiplication and missense mutations: A30P, E46K, H50Q, G51N, A53T 168601, 605543 [56,58]LRRK2 R1437H, R1441H, R1441G, R1441C, Y1699C, G2019S, I2020T 607060 [20,31,32]VPS35 D620N 614203 [63,64]EIF4G1 R1205H 614251 [149]DNAJC13 N855S 614334 [93]Recessively inherited, early-onset or X-linked atypical parkinsonismPARK2 (Parkin) Numerous exon deletions, duplications and missense mutations 600116 [109]PINK1 Rare locus and exon deletions. Numerous missense mutations, including E129X, Q129fsX157, P196L,G309N W437X, G440E, Q456X605909 [147,151]DJ-1 Deletions and missense: dup168-185, A39S, E64D, D149A, Q163L, L166P, M261I. 606324 [123]DNAJC6 Splice site c.801 -2 A > G and truncating mutation Q734X 615528 [70]ATP13A2 Missense: L552fsX788, M810R, G877R, G1019fsX1021. Small insertions and deletions: 1103insGA, del2742TT 606693 [102]FBXO7 T22M, R378G, R498X 260300 [68]PLA2G6 D331Y, R635Q,R741Q, R747W 612953 [152]ATP6AP2 Splice site mutations [71]SYNJ1 Homozygous missense: R258Q 615530 [72]OMIM, Online Mendelian Inheritance in Man, a database that catalogs all the known diseases with a genetic component.Lin and Farrer Genome Medicine 2014, 6:48 Page 5 of 16http://genomemedicine.com/content/6/6/48Nevertheless, in the same Caucasian populations, the gen-etic variance explained is unlikely to increase in propor-tion to the sample size and investment. While additionalloci may be nominated, these assignments are likely to beof smaller effect and will require independent validation.Overall, the most significant GWAS associations are atchromosomal bands 4q22 and 17q21 and support SNCAand MAPT assignments, which were first identified in link-age and candidate gene studies [41,56-58]. Nevertheless,GWAS illustrates that the etiology of PD is genetically het-erogeneous and novel loci may yet be identified, especiallywithin under-represented non-Caucasian populations; forexample, PARK16, BST1 and SYT11 were identified in aJapanese study [52]. Although a risk allele identified in onepopulation should be a risk allele for all (the genotypic-attributable risk), their frequencies may be ethnically spe-cific and lead to widely divergent population-attributablerisks. For example, Caucasians have two major haplotypes(H1 and H2) for the MAPT locus; only H1 is present inAsian populations whereas the frequency of H2 is about20% in Caucasians. The MAPT locus is significantly asso-ciated with PD in Caucasian studies but does not appearin a Japanese GWAS [51,52]. Conversely, the PM20D1locus was most clearly associated with PD in JapaneseGWAS (5 to 8% differences between cases and controls)[52], whereas PM20D1 allele frequencies in Caucasian stud-ies were similar in cases and controls (1% difference) [51].It is important to note that genomic loci are not dis-ease genes per se. Within each genomic locus, there maybe numerous genes of which one or all may be candi-dates contributing to disease risk. An illustration is theGAK-DGKQ locus that is significantly associated withPD [9,50,55]. GAK and DGKQ are in complete linkagedisequilibrium and both proteins have important roles inclathrin-mediated vesicular trafficking [59,60]. Further-more, no coding mutations have been identified in anyGWAS locus or gene except for those previously identifiedthrough linkage studies in families (that is, LRRK2 andSNCA). Rather, these associations are ascribed to subtledifferences in wild-type gene expression, for which RNAsilencing and overexpression models may be informative.Common variants of modest effect, on common haplo-types, may lead to modest transcriptional or functionalchanges. Directly genotyping a ‘causal variant’ will providethe greatest odds ratio for disease association and providesthe rationale for locus-specific sequencing and furtherassociation testing. For some disease-associated loci, mul-tiple rare variants of major effect may be responsible, inaggregate, although they will have occurred on the mostfrequent haplotypes.Next-generation sequencing for PDMost of the genetic variants in the human genome are aconsequence of mutation with recent populationexpansion and are present at very low frequencies(<0.5%) [61]. Collectively, rare variants are more com-mon than frequent variants in any given population andeach individual has many unique de novo point muta-tions. If these cluster within specific genomic loci in pa-tients with a disease such as PD, they highlight genes ormutational hotspots likely to confer disease susceptibil-ity. To Sanger sequence gene-by-gene in search of acausative variant for PD is a time-consuming and cost-limited effort. Nevertheless, the detection of rare andunique variants via direct sequencing has become moreaffordable with the advancement of next-generationmethods.Within families, whole-exome sequencing (WES) hasproven to be effective in uncovering rare causal mutationsof major effect in small sample sizes, and is considerablyless expensive than whole-genome sequencing. The firstproof-of-concept work discovered pathogenic variants inFreeman-Sheldon syndrome in just four unrelated affectedindividuals [62]. The first WES study of parkinsonism re-vealed the p.D620N mutation in VPS35 (the vacuolar sort-ing protein 35 gene) by sequencing affected cousin-pairsin autosomal dominant kindreds with late-onset disease[63,64]. These findings have been confirmed worldwide,suggesting that VPS35 contributes to approximately 1% offamilial parkinsonism and 0.2% of sporadic PD [65-67].WES has become the fastest method for the identifica-tion of novel genes in parkinsonism, contributing tothe discoveries of FBXO7, WRD45, DNAJC6, DNAJC13,ATP6AP2 and SYNJ1 in recent years [68-72].Variants in non-coding and highly conserved genomicregions may also contribute to risk, and might explain the‘missing heritability’ underlying complex trait disorders.Whole-genome sequencing (WGS) now enables the se-quencing of untranslated regions (UTRs), including genepromoters, enhancers, introns, and 5′ and 3′ UTRs. Thesecontribute to the regulation of gene expression directlythrough transcription-factor binding, via microRNA andnoncoding RNA mechanisms and through alternativeexon splicing, and can influence the phenotypic varianceof some traits. Two examples relevant to parkinsonism in-clude 5′ UTR expansions in FMR1 in Fragile X-associatedtremor-ataxia syndrome [73] and non-coding mutationsin ATP6AP2 that contribute to aberrant alternativesplicing [71].Next-generation DNA-sequencing panels can be usedfor novel mutation discovery in a locus-centric approach.In genome-wide family-based studies, when seeking toidentify novel genes, it is prudent to examine and excludethose genes already implicated in parkinsonism (includingdevelopmental and aging syndromes as described earlier).Unique probes or amplicons can cover exonic regions orspan entire loci, and target DNA can be barcoded and se-quenced in parallel for multiple individuals. Such panelsLin and Farrer Genome Medicine 2014, 6:48 Page 6 of 16http://genomemedicine.com/content/6/6/48have many benefits: first, they provide affordable and rapidgenetic diagnoses to better inform patient treatment, with-out problems arising from incidental findings [74]; second,they allow the discovery of as-yet-unknown mutations ingenes known to be related to PD; and third, in aggregate,the results nominate genetic variants that may further ex-plain the heterogeneity of clinical and pathologic presenta-tions. Similar bioinformatic filters might be applied toWES or WGS in silico. In a gene-centric approach, with alimited number of genes studied per assay relative to WESor WGS, the interpretation is simplified. Nevertheless,custom capture or amplification methods can produce ar-tifacts as oligomers may not be perfectly complementaryto the human genome being interrogated, and this mayintroduce some allelic bias.Another pitfall of next-generation sequencing (NGS)methods is the inability to sequence repetitive regionsand structural variations. For example, SNCA multiplica-tions, the GBA loci versus its pseudogene, or indeed anyrepetitive regions may confound sequence analysis; mostsequence read lengths are relatively short (approximately100 to 200 bp) and may be misaligned as a consequence.Almost half of the human genome consists of repeats thatplay an active role in genome evolution, although largestructural rearrangements may result in disease [75]. Inad-equate sequence read-depth may also lead to annotationerrors. Most publically shared WGS has been performed atrelatively low read depths; for example, the 1000 Genomeseffort achieved 2x to 6x coverage (www.1000genomes.org).For WES, >100x coverage is considered necessary for diag-nostic testing [76]. Nevertheless, specific NGS resultsshould be validated by Sanger sequencing to prevent falsepositives. Higher-coverage sequencing, longer read lengthsand innovative bioinformatic approaches continue to offersignificant improvements.In studies involving WES or WGS of familial PD, rarevariants can be prioritized for validation and replicationin additional samples by looking at the intersection ofthose shared by affected family members and not sharedby elderly unaffected relatives. Typically, in approximately58 Mb of exome sequencing approximately 80,000 singlenucleotide variants are observed per individual, of whichapproximately 250 encode substitutions not annotated inpublic databases. To further reduce this number, a power-ful approach has been to compare affected cousin-pairs, incontrast to affected sibling-pairs, to reduce the number ofalleles shared by descent (from approximately 125 to ap-proximately 31 variants). In ‘pair-wise sharing analysis’non-synonymous missense mutations that have a fre-quency less than the incidence of PD (<0.003), which areevolutionarily conserved and predicted as damaging, areprioritized as good candidates for follow-up. However,caution is warranted in comparative analyses: the pheno-copy rate of late-onset PD is approximately 18% infamilies in which a monogenic cause of disease is alreadydefined [77]. The strategy may also exclude causal or riskvariants. For example, SNCA p.A53T was the first muta-tion identified in PD but is neither evolutionarily con-served nor predicted to be deleterious [56].Molecular pathways in PDMany genetic components now appear to contribute tothe pathogenesis of parkinsonism. It is largely unknownwhether the proteins involved function in overlappingbiological pathways, whose dysfunction results in theprogressive loss of striatal dopaminergic innervation anddeath of midbrain nigral neurons. Nevertheless, some re-lationships, involving the perturbation of relatively fewcellular systems, are apparent (Figure 1). The affectedsystems include synaptic transmission, endosomal traf-ficking, lysosomal-autophagy and energy metabolism ormitophagy.Synaptic transmissionAlpha-synuclein protein is found abundantly at the pre-synaptic terminals of neurons and is involved in synapticrelease [13] (Figure 1). Monomeric forms of alpha-synuclein may contribute to endophilin-A1-relatedmembrane curvature, facilitating both synaptic vesicleexo- and endocytosis [78]. A tetrameric conformationhas been proposed for alpha-synuclein and this might pro-vide a parsimonious explanation of how amino-terminalpoint mutations lead to the same functional deficits[79,80]. The conformation of alpha-synuclein has previ-ously revealed physiologic interactions with mitochondria[81] and with presynaptic tubulovesicular or endosomalstructures when alpha-synuclein is overexpressed in trans-genic mice [82].At the synapse, LRRK2 levels regulate glutamate trans-mission, dopamine-dependent plasticity and striatal signaltransduction [83,84]. LRRK2 protein levels and mutant-specific phenotypes have long been observed in neuriticoutgrowth (affecting branching and length) in primarycultures [85,86] and in neurogenesis in vivo [87]. InDrosophila, LRRK2 kinase has been shown to regulate theEndoA phosphorylation cycle, and pathogenic mutationsappear to impede synaptic endocytosis [88] (Figure 1).LRRK2 protein is also reported to interact with thedynamin superfamily of GTPases, which mediate bothmembrane scission in clathrin-induced endocytosis andmitochondrial fission and fusion [89]. In Caenorhabditiselegans, knockout of LRK-1 (the single homolog ofmammalian LRRK1 and LRRK2) leads to impairmentin presynaptic protein sorting and axonal trafficking[90]. Several important functions have also been as-cribed to the LRRK2 protein complex in non-neuronalcells, including kidney cells [26,91], and in innateimmunity [92].Lin and Farrer Genome Medicine 2014, 6:48 Page 7 of 16http://genomemedicine.com/content/6/6/48Axon terminalAutophagosomeDamagedmitochondrionMultivesicularbodySynaptic vesicle Peroxisome GlutamateGlutamatereceptorDopamineDopaminereceptorGolgi apparatusEndosomeLysosomeMisfolded oraggregated proteinActinClathrin-coatedmembraneMicrotubulesSomaNucleusCortex orthalamusPresynapticglutamatergic axon(excitatory)(a)(a)(b)(d)Dentritic spine ofmedium spiny neuronEarlyendosomePresynapticdopaminergic axon(inhibitory)SNCALRRK2SNCASNCALRRK2DNAJC6SYNJ1ParkinPINK1VPS35GBAATP13A2ATP6AP2GBAGBAVPS35DNAJC13(c)MAPTMAPTParkinLRRK2VPS35DNAJC13DNAJC6SYNJ1DCTN1(e)VPS35(f)Figure 1 (See legend on next page.)Lin and Farrer Genome Medicine 2014, 6:48 Page 8 of 16http://genomemedicine.com/content/6/6/48Recessively inherited mutations in DNAJC6 have recentlybeen identified in juvenile parkinsonism [70]. DNAJC6encodes auxilin, a homolog of cyclin-G associated kin-ase (GAK; Table 1), which is preferentially expressedin neurons and involved in clathrin uncoating and syn-aptic vesicle recycling. Similarly, recessively inheritedmutations in SYNJ1, encoding synaptojamin, that com-plexes with Hsc70 and auxilin, have been implicated indisease [72].Endosomal traffickingEndosomal trafficking is a highly complex and dynamiccellular process whereby vesicles or cargos that are inter-nalized at the plasma membrane are subsequentlyrecycled, directly or via the trans-Golgi network, andtargeted for degradation by lysosomal autophagy. Muta-tions in VPS35 and RME-8 (receptor-mediated endo-cytosis 8, also known as DNAJC13) were recently linkedto late-onset Lewy body parkinsonism and directly im-plicate endosomal trafficking in disease pathogenesis[63,93]. Neurons have a critical need to recycle membranereceptors. This can be accomplished through the clathrin-independent retromer system, a tubulovesicular tripartitecomplex of VPS26 (vacuolar sorting protein 26), VPS29and VPS35 that relies on sorting nexins to stipulate thedestinations of specific cargos, such as neurotransmitter re-ceptors. Multiple VPS35 subunits coalesce about FAM21, asubunit of the WASH (Wiskott-Aldrich syndrome proteinand scar homolog) complex, to mediate dynamic actin re-modeling [94]. RME-8 also binds sorting nexins andFAM21 to influence WASH and cargo trafficking [95].VPS35 may also physically interact with LRRK2 andRab7L1 (within the PM20D1 locus; Table 1) to influencethese processes [96].Lysosomal autophagyLysosomes have an essential function in maintainingprotein and organelle integrity within cells and impairedlysosomal function may play an important role in thepathogenesis of PD. Aggregated alpha-synuclein, in theform of Lewy neuritic or Lewy body inclusions, that failsto be degraded by proteosomal or lysosomal systems isthe pathologic hallmark of PD. It is presently unknownwhether the intracellular protein aggregation observedin most late-onset neurodegenerative diseases is a causeor consequence of dysfunction in these pathways [97].The formation of intracellular aggregated alpha-synucleinor tau inclusions, albeit not a primary pathology, is alsofound in several ceroid lipofuscinosis disorders. These in-clude glycolipid storage diseases such as Gaucher diseaseand Niemann-Pick type C that are most prevalent in Ash-kenazi Jewish communities. Although the GBA (glucocer-ebrosidase gene) mutations are recessively inherited inGaucher disease, heterozygote carriers have an increasedprevalence of PD and dementia with Lewy bodies (Table 1)[98]. A lysosomal pathway for parkinsonism centeredaround ceramide metabolism has been hypothesized [99].Loss of GBA activity increases intracellular glucosylcera-mide accumulation, resulting in decreased lysosomal deg-radation and subsequent accumulation of alpha-synuclein[100]. Whether the latter reflects impaired GBA traffickingfrom the endoplasmic reticulum and Golgi to lysosomesor whether it results directly from lysosomal dysfunctionis unclear. In genetically engineered mice, GBA mutationspromote alpha-synuclein accumulation in a dose- andtime-dependent manner, with the animals developingLewy-like pathology in the brain and associated motorand cognitive phenotypes. By contrast, loss of GBA ac-tivity results in neuronal ubiquitinopathy and formation(See figure on previous page.)Figure 1 Cellular processes implicated in familial late-onset, Lewy body parkinsonism. In late onset parkinsonism, which is mostreminiscent of Lewy body PD, a novel synthesis is emerging whereby regulatory steps in synaptic neurotransmission, receptor recycling,endosomal trafficking and lysosomal degradation are controlled by relatively few proteins. Studies in neurons and brain are limited but manyreciprocal connections are apparent [8]. For example, (a) SNCA functions with heat shock chaperone Hsc70 and SNAP25 to promote membraneSNARE complex assembly and exocytosis in neurotransmission. (b) In mammalian cells, LRRK2 may also regulate cleavage of invaginatedendocytic membrane through interaction with dynamin. Several other genes, including DNAJC6 (with homology to GAK) and SYNJ1, encodeproteins important in clathrin uncoating. In Drosophila, LRK1 (the homolog of mammalian LRRK1 and LRRK2) phosphorylates endophilin A todirectly regulate endocytosis. In the mammalian striatum the expression levels of SNCA and endophilin A are reciprocally related. (c) In the endosome,VPS35 and the retromer cargo-selective-complex (CSC; comprising VPS35-VPS26 and VPS29) play an important role in membrane protein cargosorting. The CSC is best described in endosome to trans-Golgi network retrieval in the soma, most specifically in recycling cation-independentmannose-6-phosphate receptor that traffics acidic hydrolases (including GBA) to the lysosome. However, recent studies in neurons have revealed thatVPS35 and WASH are also crucial in protein recycling (d) of specific synaptic receptors from early endosome to plasma membrane, and (e) inthe V-ATPase required for lysosomal acidification. Importantly, CSC trafficking can be mediated by sorting nexin interaction with dynactinp150Glued (DCTN1), dynein, tau (MAPT) and microtubules, or via the WASH complex, DNAJC13 and actin polymerization. DNAJC13 was firstdescribed in endocytosis in C. elegans, rather than in post-endocytic trafficking, and like SNCA requires Hsc70 to function. LRRK2 has also beenshown to interact with VPS35 and microtubules, and like SNCA may be intrinsically targeted to lysosomal membranes by protein motifs forchaperone-mediated autophagy. Clearance of insoluble SNCA aggregates is also mediated by the endosomal system and lysosomal degradation [153].Several other lysosomal proteins, including ATP13A2 and ATP6AP2, have been implicated in atypical parkinsonism. EIF4G1, through mTOR regulationof protein translation, serves to balance autophagic activity and metabolism or ATP levels, whereas (f) PINK1 and Parkin are intrinsically involved inmitochondrial quality control in early onset parknsonism.Lin and Farrer Genome Medicine 2014, 6:48 Page 9 of 16http://genomemedicine.com/content/6/6/48of axonal spheroids, a phenotype that is shared withother lysosomal storage disorders prior to increasedalpha-synuclein concentrations [101].Two juvenile or early-onset forms of atypical parkin-sonism result directly from mutations in lysosomalproteins. X-linked parkinsonism, with onset in malesbetween 14 and 50 years of age and associated withpost-mortem tau pathology, is a consequence of spli-cing or protein isoform deficits in ATP6AP2 (encodingATPase, H+ transporting, lysosomal accessory protein2) [71]. Recessively inherited pathogenic mutations inATP13A2 (ATPase type 13A2 gene) also result in im-paired lysosomal proteolysis, leading to Kufor-Rakebsyndrome [102]. Patients and knock-out mice developceroid lipofuscin neuronal pathology, and the mice showconcomitant upregulation of alpha-synuclein protein inthe hippocampus [103]. Many genes are implicated inneurodegeneration with brain iron accumulation, includ-ing ATP13A2, PLA2G6, PANK2, C19orf12, FA2H, WDR45,FTL, CP, and DCAF17 [104].Mitochondrial metabolismThe earliest link between mitochondrial dysfunction andparkinsonism was observed in illicit drug users. MPTP(1-methyi-4-phenyl-1,2,3,6-tetrahydropyridine) is specif-ically transported into dopamine neurons via the dopa-mine transporter and is then oxidized into toxic MPP+, anon-competitive complex inhibitor of the electron trans-port chain [105]. Deficits of mitochondrial complex I havebeen noted in idiopathic PD [106], although evidence fromdirect sequencing studies of normal brain has provenequivocal. Mitochondrial mutations in humans lead toseveral neuromuscular disorders [107]. While the majorityare not associated with parkinsonism, similar movementdisorders with or without chronic progressive ophthalmo-plegia can be caused by mutations in mitochondrial DNApolymerase γ (POLG), a proofreading enzyme. Mousemodels with defective POLG exhibit premature ageingwhereas older homozygous, but not heterozygous, POLGmice show significant reductions in striatal dopaminergicterminals as well as deficits in motor function [108].The importance of mitochondria in parkinsonism ishighlighted by the identification of mutations in severalgenes within a common pathway for mitophagy. Muta-tions in the PARK2 (parkin) gene result in a recessiveform of early-onset parkinsonism [109]. Parkin proteinwas first described as a proteosomal E3 ubiquitin ligase re-sponsible for K48 substrate polyubiquination (targeting tothe proteosome) and K63 monoubiquination (for signaling)[110]. In addition, parkin may have several physiologicalroles in neurons - for example, in Eps15 monoubiquination[111] and in the regulation of neuronal apoptosis as part ofa SCF-like complex [112]. Most highlighted is the roleof parkin in regulating the degradation of depolarized oruncoupled mitochondria, in concert with PINK1 (Pten-induced kinase 1) and FBXO7 (F-box domain-containingprotein), which are also genes implicated in recessive early-onset parkinsonism [68,113]. Drosophila parkin and PINK1knockout models exhibit similar mitochondrial and wingphenotypes, and a series of elegant experiments has dem-onstrated that PINK1 is required for the recruitment ofparkin to mitochondria [114,115]. The crystal structure ofparkin has now been solved [116] and PINK1 has beenshown to phosphorylate ubiquitin required for parkin’s ac-tivation [117]. Two recent RNA interference screens haveidentified upstream regulators of mitophagy, albeit withlimited overlap [118,119]. These include TOMM7, essentialfor stabilizing PINK1 on the outer mitochondrial mem-brane; HSPA1L and BAG4, which may help to regulateparkin translocation to mitochondria; and SIAH3, which islocalized to mitochondria and inhibits PINK1 after mito-chondrial damage, thereby reducing parkin translocation.Hexokinase activity, occurring downstream of Akt but up-stream of PINK1, may also be required in the recruitmentof parkin to depolarized mitochondria [119]. STOML2,mitofusin1/2, GRP75, HSP60, LRPPRC, and TUFM havebeen nominated as downstream targets of the PINK1/parkin pathway [120-122]. DJ-1 mutations, which resultin early-onset parkinsonism [123], may also regulatePINK1-dependent parkin translocation to depolarizedmitochondria [124]. DJ-1 deficiency leads to alteredmitochondrial morphology and increased levels of react-ive oxygen species (ROS) [124]. Traditionally, knock-out mouse models of parkin, PINK1 or DJ-1 result inmitochondrial dysfunction [125] but do not develop thelocomotor phenotype of parkinsonism, nigral neuronalloss or Lewy-body pathology; rather they have elevateddopaminergic tone due to deficits in D2 presynapticregulation of release [126,127]. However, a recent condi-tional parkin knockout mouse model demonstrated pro-gressive loss of dopamine neurons in a PARIS-dependentpathway [128]. Thus, protein components of the parkin/PINK1 mitochondrial pathways remain plausible thera-peutic targets for human carriers of these mutations andpotentially for idiopathic PD.While mitochondrial mutations and proteins involved inmitophagy have been directly implicated in parkinsonism,there is accumulating albeit indirect evidence that mito-chondrial function is central to disease pathogenesis and/orprogression. For example, alpha-synuclein overexpressionmay impair mitochondrial activity, thereby accumulatingmitochondrial DNA damage and degeneration, ultimatelyresulting in neuronal death [129]. For LRRK2, mitochon-drial pathology was observed in human dopaminergic neu-rons derived from inducible pluripotent cell lines of LRRK2p.G2019S carriers [130] and in aging p.G2019S transgenicmice [131]. In primary cortical neurons, overexpressionof wild-type LRRK2 and of pathogenic mutant LRRK2Lin and Farrer Genome Medicine 2014, 6:48 Page 10 of 16http://genomemedicine.com/content/6/6/48proteins both increased recruitment of mitochondrialdynamin-like protein to fragmenting mitochondria [132].Conclusions and future directionsIdiopathic PD, albeit a sporadic disorder with low herit-ability, now appears to have a significant genetic compo-nent. Many genes have been identified and several morewill probably emerge from a variety of complementary ap-proaches. Most immediately, targeted genomic sequencingmight identify functional variants in GWAS-associatedloci, whereas additional GWAS in non-Caucasian popula-tions might identify novel loci. WES in families with par-kinsonism is also a pragmatic step to identify more genesusing a concordant ‘pairwise’ approach. Ultimately, collab-orative pooled analysis of exome data might facilitate asso-ciation analysis; power estimates suggest that as few as 50exomes may be sufficient to identify a novel locus for re-cessive disease, although 10,000 are likely to be requiredto identify a novel dominant gene mutation [133]. Never-theless, segregation of rare mutations with disease and/orfunctional studies will be needed. Inevitably, with lesspenetrant variants, the results from these approaches willbecome increasingly difficult to interpret. Hence, ratherthan focusing on PD as the trait, more investment maybe warranted on longitudinal studies. In addition, bettercharacterization of trait components, such as cognition inPD, symptom progression and response to medication,would enable further genetic variability to be identified.Similar analyses in more genetically homogeneous popula-tions (employing linkage, association and genome sequen-cing) and in sample series or pedigrees of sufficient sizeand structure may enable the joint contribution of genesand environment to be assessed meaningfully. We suggestthat a genetic predisposition to PD should not be consid-ered ‘causal’, rather disease reflects chronic molecular dys-function and the failure of age-associated compensation.To date, four biological pathways have been impli-cated in familial parkinsonism: synaptic neurotransmis-sion, endosomal trafficking, lysosomal autophagy andmitochondrial metabolism. Direct interactions betweengenetic components and these pathways are emerging,whether VPS35 and RME-8 in late onset PD, or parkinand PINK1 in mitophagy in early onset parkinsonism.Although the processes highlighted may be viewedseparately, several employ the same protein machineryand may be temporally and functionally related. For ex-ample, synaptic dysfunction, resulting from or leadingto alpha-synucleinopathy, impairs the balance of exo-and endocytosis, neurotransmission and early endosomalreceptor recycling. These changes will alter flux throughthe endosomal pathway and ultimately place demand onautophagy and lysosomal fusion with multivesicular bod-ies. Many of the same proteins are involved in more thanone of the four pathways; for example, VPS35 directlyaffects both early-endosome receptor recycling in den-dritic spines and lysosomal ATPase recycling from multi-vesicular bodies [134]. Similarly, LRRK2 appears to becentrally involved in neurite outgrowth and in membraneprotein cargo sorting and trafficking, interacts with dyna-min GTPases, and may regulate endophilin phosphoryl-ation, membrane scission and endocytosis. VPS35, RME-8and potentially LRRK2 coordinate the WASH complex inspecific actin networks underlying membrane deform-ation, tubulation and cargo trafficking. The caveat is thatmany of the biological insights may be model specific, orhave yet to be performed in vertebrate systems in post-mitotic neurons or in brain.In conclusion, genomic and genetic investigations shouldcontinue to be a main priority for future research. Know-ledge of the pathogenic pathways underlying the etiologyand ontology of PD clearly facilitates an understanding ofcommon protein components and central processes thatare crucial for therapeutic development. Our understand-ing of the normal physiology of the brain, of specific neur-onal populations, protein pathways and the function ofindividual proteins, is rudimentary. When it comes to for-mulating a molecular synthesis of the pathways involved inparkinsonism, genetic insights may be unbiased and un-equivocal but those insights must be carefully weighted.Genetic association is far from causation and much work isrequired to understand the specific contribution of GWAS,let alone to translate the information from such studiesinto novel treatments to slow or halt the progression ofidiopathic PD. In interpreting linkage and exome studies,the phenotypes of patients and families must be care-fully considered. The heterogeneity of parkinsonism isconsiderable and there are many forms that may not beetiologically related. Arguably, findings from familiallate-onset Lewy-body parkinsonism may be more rele-vant to idiopathic PD than those from atypical and/orearly-onset forms. Brain pathology, long required for adefinite diagnosis, appears increasingly pleomorphic ingenetically defined disease, even for the same mutationin the same family. Such alternative pathologic outcomesbecome more intriguing as specific molecular deficits inmembrane protein sorting and cargo trafficking arerevealed. That aggregate alpha-synuclein and tau path-ologies may be seeded and transmissible throughout thecerebrum presents an attractive means to explore Braakstaging (a regional and temporal scheme for the progres-sion of these inclusion body pathologies) and vulnerablecell populations in specific genetic backgrounds. Muchneuroscience in PD was derived from model systemsbased on toxin administration, and may not accuratelyreflect the human condition. Why the substantia nigrapars compacta is selectively lost in PD remains enig-matic, but through human genetics we now have rele-vant molecular targets and tools to investigate this.Lin and Farrer Genome Medicine 2014, 6:48 Page 11 of 16http://genomemedicine.com/content/6/6/48With such advances, therapeutic prospects for diseasemodification (neuroprotection) should be viewed withmore optimism [135].AbbreviationsATP13A2: ATPase type 13A2 gene; ATP6AP2: ATPase, H+ transporting,lysosomal accessory protein 2; CSC: cargo-selective-complex; DBS: deep brainstimulation; EIF4G1: elongation initiation factor 4 gamma 1; FBXO7: F-boxdomain-containing protein 7; FTDP-17: frontotemporal dementia withparkinsonism linked to chromosome 17; GAK: cyclin-G associated kinase;GBA: glucocerebrosidease gene; GWAS: genome-wide association study; H&Estaining: hematoxylin and eosin staining; LRRK2: leucine-rich repeat kinase 2protein; MAPT: microtubule-associated protein tau; MPTP: 1-methyi-4-phenyl-1,2,3,6-tetrahydropyridine; NACP: non-amyloid component of plaques;NGS: next-generation sequencing; OMIM: Online Mendelian Inheritance inMan; PD: Parkinson’s disease; POLG: DNA polymerase γ; RME-8: receptor-mediatedendocytosis 8; ROS: reactive oxygen species; SN: substantial nigra parscompacta; SNCA: alpha-synuclein gene; SNP: single nucleotidepolymorphism; UCHL1: Ubiquitin C-terminal hydrolase1; UTR: untranslatedregion; VPS35: vacuolar sorting protein 35; WASH: Wiskott-Aldrichsyndrome protein and scar homolog; WES: whole-exome sequencing;WGS: whole-genome sequencing.Competing interestsThe authors declare that they have no competing interests.AcknowledgementsWe are indebted to the Canada Excellence Research Chairs program and theDr Donald Rix BC Leadership Chair in Genetic Medicine for ongoing supportof the Centre of Applied Neurogenetics and Translational Neuroscience.Published: 30 June 2014References1. de Lau LM, Breteler MM: Epidemiology of Parkinson’s disease. 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