Neurodegenerative Diseases pp 479-489 | Cite as
Gene Linkage and Systems Biology
Abstract
In the past two decades it has become increasingly clear that the risk for many neurodegenerative disorders is at least partially genetic. Assignment of causality for a given gene depends on showing that a particular variant shows either segregation within a family or association with disease across a population. In terms of lifetime risk of disease, the former generally show strong effects compared to the latter. In rare, but interesting, circumstances there are genetic loci that contain different variants that encode either highly penetrant Mendelian disease but also that contribute to risk of sporadic disease. Here, we will discuss the current efforts to complete our understanding of the genetic architecture of neurodegenerative diseases of aging with a particular focus on Parkinson’s disease. We will also briefly outline attempts to use systematic approaches to infer relationships between genes associated with the same diseases, which likely demonstrate that in each case there are a relatively small number of underlying biological pathways or processes that may explain pathogenesis.
Keywords
Genome-wide association studies Parkinson’s disease Alzheimer’s disease Amyotrophic lateral sclerosisAbbreviations
- AD
Alzheimer’s disease
- ALS
Amyotrophic lateral sclerosis
- ApoE
Apolipoprotein E
- eQTL
Expression quantitative trait loci
- GWAS
Genome-wide association study
- HD
Huntington’s disease
- LRRK2
Leucine-rich repeat kinase 2
- PD
Parkinson’s disease
- SNP
Single nucleotide polymorphism
Notes
Acknowledgments
This research was supported entirely by the Intramural Research Program of the NIH, National Institute on Aging.
References
- 1.The Huntington’s Disease Collaborative Research Group (1993) A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington’s disease chromosomes. Cell 72:971–983CrossRefGoogle Scholar
- 2.Banfi S, Servadio A, Chung MY et al (1994) Identification and characterization of the gene causing type 1 spinocerebellar ataxia. Nat Genet 7:513–520CrossRefPubMedGoogle Scholar
- 3.La Spada AR, Wilson EM, Lubahn DB et al (1991) Androgen receptor gene mutations in X-linked spinal and bulbar muscular atrophy. Nature 352:77–79CrossRefPubMedGoogle Scholar
- 4.Goate A, Chartier-Harlin MC, Mullan M et al (1991) Segregation of a missense mutation in the amyloid precursor protein gene with familial Alzheimer’s disease. Nature 349:704–706CrossRefPubMedGoogle Scholar
- 5.Rosen DR, Siddique T, Patterson D et al (1993) Mutations in Cu/Zn superoxide dismutase gene are associated with familial amyotrophic lateral sclerosis. Nature 362:59–62CrossRefPubMedGoogle Scholar
- 6.Polymeropoulos MH, Lavedan C, Leroy E et al (1997) Mutation in the alpha-synuclein gene identified in families with Parkinson’s disease. Science 276:2045–2047CrossRefPubMedGoogle Scholar
- 7.Funayama M, Hasegawa K, Ohta E et al (2005) An LRRK2 mutation as a cause for the parkinsonism in the original PARK8 family. Ann Neurol 57:918–921CrossRefPubMedGoogle Scholar
- 8.Paisán-Ruíz C, Jain S, Evans EW et al (2004) Cloning of the gene containing mutations that cause PARK8-linked Parkinson’s disease. Neuron 44:595–600CrossRefPubMedGoogle Scholar
- 9.Zimprich A, Biskup S, Leitner P et al (2004) Mutations in LRRK2 cause autosomal-dominant parkinsonism with pleomorphic pathology. Neuron 44:601–607CrossRefPubMedGoogle Scholar
- 10.Benamer HTS, de Silva R (2010) LRRK2 G2019S in the North African population: a review. Eur Neurol 63:321–325CrossRefPubMedGoogle Scholar
- 11.DeJesus-Hernandez M, Mackenzie IR, Boeve BF et al (2011) Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron 72:245–256CrossRefPubMedPubMedCentralGoogle Scholar
- 12.Renton AE, Majounie E, Waite A et al (2011) A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD. Neuron 72:257–268CrossRefPubMedPubMedCentralGoogle Scholar
- 13.Rohrer JD, Isaacs AM, Mizielinska S et al (2015) C9orf72 expansions in frontotemporal dementia and amyotrophic lateral sclerosis. Lancet Neurol 14:291–301CrossRefPubMedGoogle Scholar
- 14.Kay DM, Kramer P, Higgins D et al (2005) Escaping Parkinson’s disease: a neurologically healthy octogenarian with the LRRK2 G2019S mutation. Mov Disord 20:1077–1078CrossRefPubMedGoogle Scholar
- 15.Bardien S, Lesage S, Brice A, Carr J (2011) Genetic characteristics of leucine-rich repeat kinase 2 (LRRK2) associated Parkinson’s disease. Parkinsonism Relat Disord 17:501–508CrossRefPubMedGoogle Scholar
- 16.Gwinn-Hardy K, Chen JY, Liu HC et al (2000) Spinocerebellar ataxia type 2 with parkinsonism in ethnic Chinese. Neurology 55:800–805CrossRefPubMedGoogle Scholar
- 17.Puschmann A (2013) Monogenic Parkinson’s disease and parkinsonism: clinical phenotypes and frequencies of known mutations. Parkinsonism Relat Disord 19:407–415CrossRefPubMedGoogle Scholar
- 18.Langston JW, Schüle B, Rees L et al (2015) Multisystem Lewy body disease and the other parkinsonian disorders. Nat Genet 47:1378–1384CrossRefPubMedGoogle Scholar
- 19.Leroy E, Boyer R, Auburger G et al (1998) The ubiquitin pathway in Parkinson’s disease. Nature 395:451–452CrossRefPubMedGoogle Scholar
- 20.Lord J, AJ L, Cruchaga C (2014) Identification of rare variants in Alzheimer’s disease. Front Genet 5:369CrossRefPubMedPubMedCentralGoogle Scholar
- 21.Zimprich A, Benet-Pagès A, Struhal W et al (2011) A mutation in VPS35, encoding a subunit of the Retromer complex, causes late-onset Parkinson disease. Am J Hum Genet 89:168–175CrossRefPubMedPubMedCentralGoogle Scholar
- 22.Cirulli ET, Lasseigne BN, Petrovski S et al (2015) Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways. Science 347:1436–1441CrossRefPubMedPubMedCentralGoogle Scholar
- 23.Sharma M, Ioannidis JPA, Aasly JO et al (2012) A multi-centre clinico-genetic analysis of the VPS35 gene in Parkinson disease indicates reduced penetrance for disease-associated variants. J Med Genet 49:721–726CrossRefPubMedPubMedCentralGoogle Scholar
- 24.Freischmidt A, Wieland T, Richter B et al (2015) Haploinsufficiency of TBK1 causes familial ALS and fronto-temporal dementia. Nat Neurosci 18:631–636CrossRefPubMedGoogle Scholar
- 25.Chartier-Harlin M-C, Dachsel JC, Vilariño-Güell C et al (2011) Translation initiator EIF4G1 mutations in familial Parkinson disease. Am J Hum Genet 89:398–406CrossRefPubMedPubMedCentralGoogle Scholar
- 26.Nichols N, Bras JM, Hernandez DG et al (2015) EIF4G1 mutations do not cause Parkinson’s disease. Neurobiol Aging 36:2444.e1–2444.e4CrossRefGoogle Scholar
- 27.Manolio TA, Collins FS, Cox NJ et al (2009) Finding the missing heritability of complex diseases. Nature 461:747–753CrossRefPubMedPubMedCentralGoogle Scholar
- 28.Strittmatter WJ, Saunders AM, Schmechel D et al (1993) Apolipoprotein E: high-avidity binding to beta-amyloid and increased frequency of type 4 allele in late-onset familial Alzheimer disease. Proc Natl Acad Sci U S A 90:1977–1981CrossRefPubMedPubMedCentralGoogle Scholar
- 29.Pihlstrøm L, Toft M (2011) Genetic variability in SNCA and Parkinson’s disease. Neurogenetics 12:283–293CrossRefPubMedGoogle Scholar
- 30.Pittman AM, Fung H-C, de Silva R (2006) Untangling the tau gene association with neurodegenerative disorders. Hum Mol Genet 2:R188–R195CrossRefGoogle Scholar
- 31.JPA I (2008) Why most discovered true associations are inflated. Epidemiology 19:640–648CrossRefGoogle Scholar
- 32.Lambert JC, Ibrahim-Verbaas CA, Harold D et al (2013) Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer’s disease. Nat Genet 45:1452–1458CrossRefPubMedPubMedCentralGoogle Scholar
- 33.Naj AC, Jun G, Reitz C et al (2014) Effects of multiple genetic loci on age at onset in late-onset Alzheimer disease: a genome-wide association study. JAMA Neurol 71:1394–1404CrossRefPubMedPubMedCentralGoogle Scholar
- 34.Nalls MA, Pankratz N, Lill CM et al (2014) Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson’s disease. Nat Genet 46:989–993CrossRefPubMedPubMedCentralGoogle Scholar
- 35.Nalls MA, McLean CY, Rick J et al (2015) Diagnosis of Parkinson’s disease on the basis of clinical and genetic classification: a population-based modelling study. Lancet Neurol 14:1002–1009CrossRefPubMedPubMedCentralGoogle Scholar
- 36.MacArthur DG, Manolio TA, Dimmock DP et al (2014) Guidelines for investigating causality of sequence variants in human disease. Nature 508:469–476CrossRefPubMedPubMedCentralGoogle Scholar
- 37.Tan E-K (2007) The role of common genetic risk variants in Parkinson disease. Clin Genet 72:387–393CrossRefPubMedGoogle Scholar
- 38.Singleton A, Hardy J (2011) A generalizable hypothesis for the genetic architecture of disease: pleomorphic risk loci. Hum Mol Genet 20:R158–R162CrossRefPubMedPubMedCentralGoogle Scholar
- 39.Singleton AB, Farrer M, Johnson J et al (2003) Alpha-Synuclein locus triplication causes Parkinson’s disease. Science 302:841CrossRefPubMedGoogle Scholar
- 40.Gibbs JR, van der Brug MP, Hernandez DG et al (2010) Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet 6:e1000952CrossRefPubMedPubMedCentralGoogle Scholar
- 41.Villegas-Llerena C, Phillips A, Garcia-Reitboeck P et al (2015) Microglial genes regulating neuroinflammation in the progression of Alzheimer’s disease. Curr Opin Neurobiol 36:74–81CrossRefPubMedGoogle Scholar
- 42.Wood WG, Li L, Müller WE, Eckert GP (2014) Cholesterol as a causative factor in Alzheimer’s disease: a debatable hypothesis. J Neurochem 129:559–572CrossRefPubMedPubMedCentralGoogle Scholar
- 43.Guerreiro R, Wojtas A, Bras J et al (2013) TREM2 variants in Alzheimer’s disease. N Engl J Med 368:117–127CrossRefPubMedGoogle Scholar
- 44.Jonsson T, Stefansson H, Steinberg S et al (2013) Variant of TREM2 associated with the risk of Alzheimer’s disease. N Engl J Med 368:107–116CrossRefPubMedGoogle Scholar
- 45.Novarino G, Fenstermaker AG, Zaki MS et al (2014) Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science 343:506–511CrossRefPubMedPubMedCentralGoogle Scholar
- 46.Esteves T, Durr A, Mundwiller E et al (2014) Loss of association of REEP2 with membranes leads to hereditary spastic paraplegia. Am J Hum Genet 94:268–277CrossRefPubMedPubMedCentralGoogle Scholar
- 47.Beilina A, Rudenko IN, Kaganovich A et al (2014) Unbiased screen for interactors of leucine-rich repeat kinase 2 supports a common pathway for sporadic and familial Parkinson disease. Proc Natl Acad Sci U S A 111(7):2626–2631CrossRefPubMedPubMedCentralGoogle Scholar
- 48.MacLeod DA, Rhinn H, Kuwahara T et al (2013) RAB7L1 interacts with LRRK2 to modify intraneuronal protein sorting and Parkinson’s disease risk. Neuron 77:425–439CrossRefPubMedPubMedCentralGoogle Scholar