Modeling the functional genomics of autism using human neurons (original) (raw)
Bucan M, Abrahams BS, Wang K, Glessner JT, Herman EI, Sonnenblick LI et al. Genome-wide analyses of exonic copy number variants in a family-based study point to novel autism susceptibility genes. PLoS Genet 2009; 5: e1000536. ArticlePubMedPubMed Central Google Scholar
Glessner JT, Wang K, Cai G, Korvatska O, Kim CE, Wood S et al. Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature 2009; 459: 569–573. ArticleCASPubMedPubMed Central Google Scholar
Ma D, Salyakina D, Jaworski JM, Konidari I, Whitehead PL, Andersen AN et al. A genome-wide association study of autism reveals a common novel risk locus at 5p14.1. Ann Hum Genet 2009; 73 (Part 3): 263–273. ArticleCASPubMedPubMed Central Google Scholar
Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R et al. Functional impact of global rare copy number variation in autism spectrum disorders. Nature 2010; 466: 368–372. ArticleCASPubMedPubMed Central Google Scholar
Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, Walsh T et al. Strong association of de novo copy number mutations with autism. Science 2007; 316: 445–449. ArticleCASPubMedPubMed Central Google Scholar
Wang K, Zhang H, Ma D, Bucan M, Glessner JT, Abrahams BS et al. Common genetic variants on 5p14.1 associate with autism spectrum disorders. Nature 2009; 459: 528–533. ArticleCASPubMedPubMed Central Google Scholar
Weiss LA, Arking DE, Daly MJ, Chakravarti A . A genome-wide linkage and association scan reveals novel loci for autism. Nature 2009; 461: 802–808. ArticleCASPubMedPubMed Central Google Scholar
Bill BR, Geschwind DH . Genetic advances in autism: heterogeneity and convergence on shared pathways. Curr Opin Genet Dev 2009; 19: 271–278. ArticleCASPubMedPubMed Central Google Scholar
Silverman JL, Yang M, Lord C, Crawley JN . Behavioural phenotyping assays for mouse models of autism. Nat Rev Neurosci 2010; 11: 490–502. ArticleCASPubMedPubMed Central Google Scholar
Nakatani J, Tamada K, Hatanaka F, Ise S, Ohta H, Inoue K et al. Abnormal behavior in a chromosome-engineered mouse model for human 15q11-13 duplication seen in autism. Cell 2009; 137: 1235–1246. ArticlePubMedPubMed Central Google Scholar
Flint J, Shifman S . Animal models of psychiatric disease. Curr Opin Genet Dev 2008; 18: 235–240. ArticleCASPubMed Google Scholar
Kabashi E, Champagne N, Brustein E, Drapeau P . In the swim of things: recent insights to neurogenetic disorders from zebrafish. Trends Genet 2010; 26: 373–381. ArticleCASPubMed Google Scholar
Miller JA, Horvath S, Geschwind DH . Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways. Proc Natl Acad Sci USA 2010; 107: 12698–12703. ArticleCASPubMedPubMed Central Google Scholar
Konopka G, Bomar JM, Winden K, Coppola G, Jonsson ZO, Gao F et al. Human-specific transcriptional regulation of CNS development genes by FOXP2. Nature 2009; 462: 213–217. ArticleCASPubMedPubMed Central Google Scholar
Oldham MC, Konopka G, Iwamoto K, Langfelder P, Kato T, Horvath S et al. Functional organization of the transcriptome in human brain. Nat Neurosci 2008; 11: 1271–1282. ArticleCASPubMedPubMed Central Google Scholar
Plaisier CL, Horvath S, Huertas-Vazquez A, Cruz-Bautista I, Herrera MF, Tusie-Luna T et al. A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia. PLoS Genet 2009; 5: e1000642. ArticlePubMedPubMed Central Google Scholar
Winden KD, Oldham MC, Mirnics K, Ebert PJ, Swan CH, Levitt P et al. The organization of the transcriptional network in specific neuronal classes. Mol Syst Biol 2009; 5: 291. ArticlePubMedPubMed Central Google Scholar
Chen Y, Zhu J, Lum PY, Yang X, Pinto S, MacNeil DJ et al. Variations in DNA elucidate molecular networks that cause disease. Nature 2008; 452: 429–435. ArticleCASPubMedPubMed Central Google Scholar
Horvath S, Zhang B, Carlson M, Lu KV, Zhu S, Felciano RM et al. Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target. Proc Natl Acad Sci USA 2006; 103: 17402–17407. ArticleCASPubMedPubMed Central Google Scholar
Marchetto MC, Carromeu C, Acab A, Yu D, Yeo GW, Mu Y et al. A model for neural development and treatment of Rett syndrome using human induced pluripotent stem cells. Cell 2010; 143: 527–539. ArticleCASPubMedPubMed Central Google Scholar
Hu BY, Weick JP, Yu J, Ma LX, Zhang XQ, Thomson JA et al. Neural differentiation of human induced pluripotent stem cells follows developmental principles but with variable potency. Proc Natl Acad Sci USA 2010; 107: 4335–4340. ArticleCASPubMedPubMed Central Google Scholar
Bauman ML, Kemper TL . Neuroanatomic observations of the brain in autism: a review and future directions. Int J Dev Neurosci 2005; 23: 183–187. ArticlePubMed Google Scholar
Geschwind DH, Levitt P . Autism spectrum disorders: developmental disconnection syndromes. Curr Opin Neurobiol 2007; 17: 103–111. ArticleCASPubMed Google Scholar
Wexler EM, Paucer A, Kornblum HI, Palmer TD, Geschwind DH . Endogenous Wnt signaling maintains neural progenitor cell potency. Stem Cells 2009; 27: 1130–1141. ArticleCASPubMedPubMed Central Google Scholar
Svendsen CN, ter Borg MG, Armstrong RJ, Rosser AE, Chandran S, Ostenfeld T et al. A new method for the rapid and long term growth of human neural precursor cells. J Neurosci Methods 1998; 85: 141–152. ArticleCASPubMed Google Scholar
Palmer TD, Schwartz PH, Taupin P, Kaspar B, Stein SA, Gage FH . Cell culture. Progenitor cells from human brain after death. Nature 2001; 411: 42–43. ArticleCASPubMed Google Scholar
Esquenet M, Swinnen JV, Heyns W, Verhoeven G . LNCaP prostatic adenocarcinoma cells derived from low and high passage numbers display divergent responses not only to androgens but also to retinoids. J Steroid Biochem Mol Biol 1997; 62: 391–399. ArticleCASPubMed Google Scholar
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81: 559–575. ArticleCASPubMedPubMed Central Google Scholar
Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF et al. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res 2007; 17: 1665–1674. ArticleCASPubMedPubMed Central Google Scholar
Abu-Khalil A, Fu L, Grove EA, Zecevic N, Geschwind DH . Wnt genes define distinct boundaries in the developing human brain: implications for human forebrain patterning. J Comp Neurol 2004; 474: 276–288. ArticleCASPubMed Google Scholar
Dahlstrand J, Lardelli M, Lendahl U . Nestin mRNA expression correlates with the central nervous system progenitor cell state in many, but not all, regions of developing central nervous system. Brain Res Dev Brain Res 1995; 84: 109–129. ArticleCASPubMed Google Scholar
Lee MK, Tuttle JB, Rebhun LI, Cleveland DW, Frankfurter A . The expression and posttranslational modification of a neuron-specific beta-tubulin isotype during chick embryogenesis. Cell Motil Cytoskeleton 1990; 17: 118–132. ArticleCASPubMed Google Scholar
Izant JG, McIntosh JR . Microtubule-associated proteins: a monoclonal antibody to MAP2 binds to differentiated neurons. Proc Natl Acad Sci USA 1980; 77: 4741–4745. ArticleCASPubMedPubMed Central Google Scholar
Eng LF . Glial fibrillary acidic protein (GFAP): the major protein of glial intermediate filaments in differentiated astrocytes. J Neuroimmunol 1985; 8: 203–214. ArticleCASPubMed Google Scholar
Scales TM, Lin S, Kraus M, Goold RG, Gordon-Weeks PR . Nonprimed and DYRK1A-primed GSK3 beta-phosphorylation sites on MAP1B regulate microtubule dynamics in growing axons. J Cell Sci 2009; 122 (Part 14): 2424–2435. ArticleCASPubMedPubMed Central Google Scholar
Heins N, Malatesta P, Cecconi F, Nakafuku M, Tucker KL, Hack MA et al. Glial cells generate neurons: the role of the transcription factor Pax6. Nat Neurosci 2002; 5: 308–315. ArticleCASPubMed Google Scholar
Bailey JA, Lahiri DK . Neuronal differentiation is accompanied by increased levels of SNAP-25 protein in fetal rat primary cortical neurons: implications in neuronal plasticity and Alzheimer's disease. Ann N Y Acad Sci 2006; 1086: 54–65. ArticleCASPubMed Google Scholar
Flanagan JG, Vanderhaeghen P . The ephrins and Eph receptors in neural development. Annu Rev Neurosci 1998; 21: 309–345. ArticleCASPubMed Google Scholar
Pasterkamp RJ, Kolodkin AL . Semaphorin junction: making tracks toward neural connectivity. Curr Opin Neurobiol 2003; 13: 79–89. ArticleCASPubMed Google Scholar
Gaspard N, Gaillard A, Vanderhaeghen P . Making cortex in a dish: in vitro corticopoiesis from embryonic stem cells. Cell Cycle 2009; 8: 2491–2496. ArticleCASPubMed Google Scholar
Johnson MB, Kawasawa YI, Mason CE, Krsnik Z, Coppola G, Bogdanovic D et al. Functional and evolutionary insights into human brain development through global transcriptome analysis. Neuron 2009; 62: 494–509. ArticleCASPubMedPubMed Central Google Scholar
Uemura T, Lee SJ, Yasumura M, Takeuchi T, Yoshida T, Ra M et al. Trans-synaptic interaction of GluRdelta2 and Neurexin through Cbln1 mediates synapse formation in the cerebellum. Cell 2010; 141: 1068–1079. ArticleCASPubMed Google Scholar
Fairless R, Masius H, Rohlmann A, Heupel K, Ahmad M, Reissner C et al. Polarized targeting of neurexins to synapses is regulated by their C-terminal sequences. J Neurosci 2008; 28: 12969–12981. ArticleCASPubMedPubMed Central Google Scholar
Zhang B, Horvath S . A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 2005; 4: Article17. ArticlePubMed Google Scholar
Mars WM, Zarnegar R, Michalopoulos GK . Activation of hepatocyte growth factor by the plasminogen activators uPA and tPA. Am J Pathol 1993; 143: 949–958. CASPubMedPubMed Central Google Scholar
Cook Jr EH, Scherer SW . Copy-number variations associated with neuropsychiatric conditions. Nature 2008; 455: 919–923. ArticleCASPubMed Google Scholar
Crespi B, Badcock C . Psychosis and autism as diametrical disorders of the social brain. Behav Brain Sci 2008; 31: 241–261; discussion 261–320. PubMed Google Scholar
Crespi B, Stead P, Elliot M . Evolution in health and medicine Sackler colloquium: Comparative genomics of autism and schizophrenia. Proc Natl Acad Sci USA 2009; 107 (Suppl 1): 1736–1741. PubMed Google Scholar
Purcell SM, Wray NR, Stone JL, Visscher PM, O’Donovan MC, Sullivan PF et al. Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature 2009; 460: 748–752. CASPubMed Google Scholar
Konopka G . Functional genomics of the brain: uncovering networks in the CNS using a systems approach. Wiley Interdiscip Rev Syst Biol Med 2010; 3: doi: 10.1002/wsbm.139. PubMed Google Scholar
Toro R, Konyukh M, Delorme R, Leblond C, Chaste P, Fauchereau F et al. Key role for gene dosage and synaptic homeostasis in autism spectrum disorders. Trends Genet 2010; 26: 363–372. ArticleCASPubMed Google Scholar
Scott-Van Zeeland AA, Abrahams BS, Alvarez-Retuerto AI, Sonnenblick LI, Rudie JD, Ghahremani D et al. Altered functional connectivity in frontal lobe circuits is associated with variation in the autism risk gene CNTNAP2. Sci Transl Med 2010; 2: 56ra80. ArticlePubMedPubMed Central Google Scholar
Melillo R, Leisman G . Autistic spectrum disorders as functional disconnection syndrome. Rev Neurosci 2009; 20: 111–131. ArticlePubMed Google Scholar
Betancur C, Sakurai T, Buxbaum JD . The emerging role of synaptic cell-adhesion pathways in the pathogenesis of autism spectrum disorders. Trends Neurosci 2009; 32: 402–412. ArticleCASPubMed Google Scholar
Spence SJ, Schneider MT . The role of epilepsy and epileptiform EEGs in autism spectrum disorders. Pediatr Res 2009; 65: 599–606. ArticlePubMedPubMed Central Google Scholar
van Bon BWM, Mefford HC, de Vries BBA . 15q13.3 Microdeletion. In: Pagon RA, Bird TD, Dolan CR, Stephens K (eds). GeneReviews [Internet]. Seattle (WA): University of Washington, Seattle; 1993–2010, December 23.
Hamdan FF, Daoud H, Piton A, Gauthier J, Dobrzeniecka S, Krebs MO et al. De Novo SYNGAP1 mutations in nonsyndromic intellectual disability and autism. Biol Psychiatry 2011; 69: 898–901. ArticleCASPubMed Google Scholar
Walsh CA, Engle EC . Allelic diversity in human developmental neurogenetics: insights into biology and disease. Neuron 2010; 68: 245–253. ArticleCASPubMedPubMed Central Google Scholar
Brooks-Kayal A . Epilepsy and autism spectrum disorders: are there common developmental mechanisms? Brain Dev 2010; 32: 731–738. ArticlePubMed Google Scholar
Strauss KA, Puffenberger EG, Huentelman MJ, Gottlieb S, Dobrin SE, Parod JM et al. Recessive symptomatic focal epilepsy and mutant contactin-associated protein-like 2. N Engl J Med 2006; 354: 1370–1377. ArticleCASPubMed Google Scholar
Chu TT, Liu Y . An integrated genomic analysis of gene-function correlation on schizophrenia susceptibility genes. J Hum Genet 2010; 55: 285–292. ArticleCASPubMed Google Scholar
Lesch KP, Timmesfeld N, Renner TJ, Halperin R, Roser C, Nguyen TT et al. Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies. J Neural Transm 2008; 115: 1573–1585. ArticleCASPubMed Google Scholar
Kim HG, Kishikawa S, Higgins AW, Seong IS, Donovan DJ, Shen Y et al. Disruption of neurexin 1 associated with autism spectrum disorder. Am J Hum Genet 2008; 82: 199–207. ArticleCASPubMedPubMed Central Google Scholar
Kumar RA, Sudi J, Babatz TD, Brune CW, Oswald D, Yen M et al. A de novo 1p34.2 microdeletion identifies the synaptic vesicle gene RIMS3 as a novel candidate for autism. J Med Genet 2010; 47: 81–90. ArticleCASPubMed Google Scholar
Garbern JY, Neumann M, Trojanowski JQ, Lee VM, Feldman G, Norris JW et al. A mutation affecting the sodium/proton exchanger, SLC9A6, causes mental retardation with tau deposition. Brain 2010; 133 (Part 5): 1391–1402. ArticlePubMedPubMed Central Google Scholar
Egea J, Klein R . Bidirectional Eph-ephrin signaling during axon guidance. Trends Cell Biol 2007; 17: 230–238. ArticleCASPubMed Google Scholar
Roffers-Agarwal J, Gammill LS . Neuropilin receptors guide distinct phases of sensory and motor neuronal segmentation. Development 2009; 136: 1879–1888. ArticleCASPubMedPubMed Central Google Scholar
Hilario JD, Rodino-Klapac LR, Wang C, Beattie CE . Semaphorin 5A is a bifunctional axon guidance cue for axial motoneurons in vivo. Dev Biol 2009; 326: 190–200. ArticleCASPubMed Google Scholar
Barbaric I, Gokhale PJ, Andrews PW . High-content screening of small compounds on human embryonic stem cells. Biochem Soc Trans 2010; 38: 1046–1050. ArticleCASPubMed Google Scholar