#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

Human Intellectual Disability Genes Form Conserved Functional Modules in


Intellectual Disability (ID) disorders, defined by an IQ below 70, are genetically and phenotypically highly heterogeneous. Identification of common molecular pathways underlying these disorders is crucial for understanding the molecular basis of cognition and for the development of therapeutic intervention strategies. To systematically establish their functional connectivity, we used transgenic RNAi to target 270 ID gene orthologs in the Drosophila eye. Assessment of neuronal function in behavioral and electrophysiological assays and multiparametric morphological analysis identified phenotypes associated with knockdown of 180 ID gene orthologs. Most of these genotype-phenotype associations were novel. For example, we uncovered 16 genes that are required for basal neurotransmission and have not previously been implicated in this process in any system or organism. ID gene orthologs with morphological eye phenotypes, in contrast to genes without phenotypes, are relatively highly expressed in the human nervous system and are enriched for neuronal functions, suggesting that eye phenotyping can distinguish different classes of ID genes. Indeed, grouping genes by Drosophila phenotype uncovered 26 connected functional modules. Novel links between ID genes successfully predicted that MYCN, PIGV and UPF3B regulate synapse development. Drosophila phenotype groups show, in addition to ID, significant phenotypic similarity also in humans, indicating that functional modules are conserved. The combined data indicate that ID disorders, despite their extreme genetic diversity, are caused by disruption of a limited number of highly connected functional modules.


Vyšlo v časopise: Human Intellectual Disability Genes Form Conserved Functional Modules in. PLoS Genet 9(10): e32767. doi:10.1371/journal.pgen.1003911
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003911

Souhrn

Intellectual Disability (ID) disorders, defined by an IQ below 70, are genetically and phenotypically highly heterogeneous. Identification of common molecular pathways underlying these disorders is crucial for understanding the molecular basis of cognition and for the development of therapeutic intervention strategies. To systematically establish their functional connectivity, we used transgenic RNAi to target 270 ID gene orthologs in the Drosophila eye. Assessment of neuronal function in behavioral and electrophysiological assays and multiparametric morphological analysis identified phenotypes associated with knockdown of 180 ID gene orthologs. Most of these genotype-phenotype associations were novel. For example, we uncovered 16 genes that are required for basal neurotransmission and have not previously been implicated in this process in any system or organism. ID gene orthologs with morphological eye phenotypes, in contrast to genes without phenotypes, are relatively highly expressed in the human nervous system and are enriched for neuronal functions, suggesting that eye phenotyping can distinguish different classes of ID genes. Indeed, grouping genes by Drosophila phenotype uncovered 26 connected functional modules. Novel links between ID genes successfully predicted that MYCN, PIGV and UPF3B regulate synapse development. Drosophila phenotype groups show, in addition to ID, significant phenotypic similarity also in humans, indicating that functional modules are conserved. The combined data indicate that ID disorders, despite their extreme genetic diversity, are caused by disruption of a limited number of highly connected functional modules.


Zdroje

1. RopersHH (2010) Genetics of early onset cognitive impairment. Annu Rev Genomics Hum Genet 11: 161–187.

2. van BokhovenH (2011) Genetic and Epigenetic Networks in Intellectual Disabilities. Annual Review of Genetics 45: 81–104.

3. Nadif KasriN, Van AelstL (2008) Rho-linked genes and neurological disorders. Pflugers Arch 455: 787–797.

4. KrabLC, GoordenSM, ElgersmaY (2008) Oncogenes on my mind: ERK and MTOR signaling in cognitive diseases. Trends Genet 24: 498–510.

5. NajmabadiH, HuH, GarshasbiM, ZemojtelT, AbediniSS, et al. (2011) Deep sequencing reveals 50 novel genes for recessive cognitive disorders. Nature 478: 57–63.

6. PavlowskyA, ChellyJ, BilluartP (2012) Emerging major synaptic signaling pathways involved in intellectual disability. Mol Psychiatry 17: 682–693.

7. GilmanSR, IossifovI, LevyD, RonemusM, WiglerM, et al. (2011) Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses. Neuron 70: 898–907.

8. EhningerD, LiW, FoxK, StrykerMP, SilvaAJ (2008) Reversing neurodevelopmental disorders in adults. Neuron 60: 950–960.

9. BellenHJ, TongC, TsudaH (2010) 100 years of Drosophila research and its impact on vertebrate neuroscience: a history lesson for the future. Nat Rev Neurosci 11: 514–522.

10. GattoCL, BroadieK (2011) Drosophila modeling of heritable neurodevelopmental disorders. Curr Opin Neurobiol 21: 834–841.

11. KruegerDD, BearMF (2011) Toward fulfilling the promise of molecular medicine in fragile X syndrome. Annu Rev Med 62: 411–429.

12. DietzlG, ChenD, SchnorrerF, SuKC, BarinovaY, et al. (2007) A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila. Nature 448: 151–156.

13. MatthewsKA, KaufmanTC, GelbartWM (2005) Research resources for Drosophila: the expanding universe. Nat Rev Genet 6: 179–193.

14. SchnorrerF, SchonbauerC, LangerCCH, DietzlG, NovatchkovaM, et al. (2010) Systematic genetic analysis of muscle morphogenesis and function in Drosophila. Nature 464: 287–291.

15. Neumüller RalphA, RichterC, FischerA, NovatchkovaM, Neumüller KlausG, et al. (2011) Genome-Wide Analysis of Self-Renewal in Drosophila Neural Stem Cells by Transgenic RNAi. Cell Stem Cell 8: 580–593.

16. BenzerS (1967) Behavioural mutants of Drosophila isolated by countercurrent distribution. Proc Natl Acad Sci U S A 58: 1112–1119.

17. LuY, WangF, LiY, FerrisJ, LeeJA, et al. (2009) The Drosophila homologue of the Angelman syndrome ubiquitin ligase regulates the formation of terminal dendritic branches. Hum Mol Genet 18: 454–462.

18. CadiganKM, JouAD, NusseR (2002) Wingless blocks bristle formation and morphogenetic furrow progression in the eye through repression of Daughterless. Development 129: 3393–3402.

19. FreemanM (1996) Reiterative use of the EGF receptor triggers differentiation of all cell types in the Drosophila eye. Cell 87: 651–660.

20. LiWZ, LiSL, ZhengHY, ZhangSP, XueL (2012) A broad expression profile of the GMR-GAL4 driver in Drosophila melanogaster. Genet Mol Res 11: 1997–2002.

21. HiesingerPR, FayyazuddinA, MehtaSQ, RosenmundT, SchulzeKL, et al. (2005) The v-ATPase V0 subunit a1 is required for a late step in synaptic vesicle exocytosis in Drosophila. Cell 121: 607–620.

22. Pak (2010) Why Drosophila to study phototransduction? J Neurogenet 24: 55–66.

23. GalyA, SchenckA, SahinHB, QurashiA, SahelJA, et al. (2011) CYFIP dependent actin remodeling controls specific aspects of Drosophila eye morphogenesis. Dev Biol 359: 37–46.

24. SchenckA, BardoniB, LangmannC, HardenN, MandelJL, et al. (2003) CYFIP/Sra-1 Controls Neuronal Connectivity in Drosophila and Links the Rac1 GTPase Pathway to the Fragile X Protein. Neuron 38: 887–898.

25. BayesA, van de LagemaatLN, CollinsMO, CroningMDR, WhittleIR, et al. (2011) Characterization of the proteome, diseases and evolution of the human postsynaptic density. Nat Neurosci 14: 19–21.

26. SamaIE, HuynenMA (2010) Measuring the physical cohesiveness of proteins using physical interaction enrichment. Bioinformatics 26: 2737–2743.

27. JonesRG, ThompsonCB (2009) Tumor suppressors and cell metabolism: a recipe for cancer growth. Genes Dev 23: 537–548.

28. ChoYY, YaoK, KimHG, KangBS, ZhengD, et al. (2007) Ribosomal S6 kinase 2 is a key regulator in tumor promoter induced cell transformation. Cancer Res 67: 8104–8112.

29. LanL, HanH, ZuoH, ChenZ, DuY, et al. (2010) Upregulation of myosin Va by Snail is involved in cancer cell migration and metastasis. Int J Cancer 126: 53–64.

30. TakagishiY, MurataY (2006) Myosin Va mutation in rats is an animal model for the human hereditary neurological disease, Griscelli syndrome type 1. Ann N Y Acad Sci 1086: 66–80.

31. PilgramGS, PotikanondS, BainesRA, FradkinLG, NoordermeerJN (2010) The roles of the dystrophin-associated glycoprotein complex at the synapse. Mol Neurobiol 41: 1–21.

32. SchmidtWM, UddinMH, DysekS, Moser-ThierK, PirkerC, et al. (2011) DNA damage, somatic aneuploidy, and malignant sarcoma susceptibility in muscular dystrophies. PLoS Genet 7: e1002042.

33. GlassDJ (2005) A signaling role for dystrophin: inhibiting skeletal muscle atrophy pathways. Cancer Cell 8: 351–352.

34. NguyenLS, JollyL, ShoubridgeC, ChanWK, HuangL, et al. (2011) Transcriptome profiling of UPF3B/NMD-deficient lymphoblastoid cells from patients with various forms of intellectual disability. Mol Psychiatry 17: 1103–15.

35. WuG, GuoZ, ChatterjeeA, HuangX, RubinE, et al. (2006) Overexpression of glycosylphosphatidylinositol (GPI) transamidase subunits phosphatidylinositol glycan class T and/or GPI anchor attachment 1 induces tumorigenesis and contributes to invasion in human breast cancer. Cancer Res 66: 9829–9836.

36. RobinsonPN, KöhlerS, BauerS, SeelowD, HornD, et al. (2008) The Human Phenotype Ontology: A Tool for Annotating and Analyzing Human Hereditary Disease. The American Journal of Human Genetics 83: 610–615.

37. OtiM, HuynenMA, BrunnerHG (2009) The biological coherence of human phenome databases. Am J Hum Genet 85: 801–808.

38. OtiM, HuynenMA, BrunnerHG (2008) Phenome connections. Trends Genet 24: 103–106.

39. van BonBWM, OortveldMAW, NijtmansLG, FenckovaM, NijhofB, et al. (2013) CEP89 is required for mitochondrial metabolism and neuronal function in man and fly. Hum Mol Genet 22: 3138–3151.

40. WillemsenMH, NijhofB, FenckovaM, NillesenWM, BongersEMHF, et al. (2013) GATAD2B loss-of-function mutations cause a recognisable syndrome with intellectual disability and are associated with learning deficits and synaptic undergrowth in Drosophila. J Med Genet 50: 507–514.

41. MukhopadhyayA, KramerJ, MerkxG, LugtenbergD, SmeetsD, et al. (2010) CDK19 is disrupted in a female patient with bilateral congenital retinal folds, microcephaly and mild mental retardation. Hum Genet 128: 281–291.

42. CliffeST, KramerJM, HussainK, RobbenJH, de JongEK, et al. (2009) SLC29A3 gene is mutated in pigmented hypertrichosis with insulin-dependent diabetes mellitus syndrome and interacts with the insulin signaling pathway. Hum Mol Genet 18: 2257–2265.

43. Mummery-WidmerJL, YamazakiM, StoegerT, NovatchkovaM, BhaleraoS, et al. (2009) Genome-wide analysis of Notch signalling in Drosophila by transgenic RNAi. Nature 458: 987–992.

44. StoweIB, MercadoEL, StoweTR, BellEL, Oses-PrietoJA, et al. (2012) A shared molecular mechanism underlies the human rasopathies Legius syndrome and Neurofibromatosis-1. Genes Dev 26: 1421–1426.

45. WaterhamHR, EbberinkMS (2012) Genetics and molecular basis of human peroxisome biogenesis disorders. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease 1822: 1430–1441.

46. MolinariF, FoulquierF, TarpeyPS, MorelleW, BoisselS, et al. (2008) Oligosaccharyltransferase-subunit mutations in nonsyndromic mental retardation. Am J Hum Genet 82: 1150–1157.

47. ZhouH, ClaphamDE (2009) Mammalian MagT1 and TUSC3 are required for cellular magnesium uptake and vertebrate embryonic development. Proc Natl Acad Sci U S A 106: 15750–15755.

48. HouleD, GovindarajuDR, OmholtS (2010) Phenomics: the next challenge. Nat Rev Genet 11: 855–866.

49. BilderRM, SabbFW, CannonTD, LondonED, JentschJD, et al. (2009) Phenomics: the systematic study of phenotypes on a genome-wide scale. Neuroscience 164: 30–42.

50. BolducFV, TullyT (2009) Fruit flies and intellectual disability. Fly (Austin) 3: 91–104.

51. ZoghbiHY, BearMF (2012) Synaptic dysfunction in neurodevelopmental disorders associated with autism and intellectual disabilities. Cold Spring Harb Perspect Biol 4: pii: a009886.

52. McGaryKL, ParkTJ, WoodsJO, ChaHJ, WallingfordJB, et al. (2010) Systematic discovery of nonobvious human disease models through orthologous phenotypes. Proc Natl Acad Sci U S A 107: 6544–6549.

53. MouriK, HoriuchiSY, UemuraT (2012) Cohesin controls planar cell polarity by regulating the level of the seven-pass transmembrane cadherin Flamingo. Genes Cells 17: 509–524.

54. GrayRS, RoszkoI, Solnica-KrezelL (2011) Planar cell polarity: coordinating morphogenetic cell behaviors with embryonic polarity. Dev Cell 21: 120–133.

55. HigginbothamH, EomTY, MarianiLE, BachledaA, HirtJ, et al. (2012) Arl13b in primary cilia regulates the migration and placement of interneurons in the developing cerebral cortex. Dev Cell 23: 925–938.

56. LiaoTS, CallGB, GuptanP, CespedesA, MarshallJ, et al. (2006) An efficient genetic screen in Drosophila to identify nuclear-encoded genes with mitochondrial function. Genetics 174: 525–533.

57. BeveJ, HuGZ, MyersLC, BalciunasD, WerngrenO, et al. (2005) The structural and functional role of Med5 in the yeast Mediator tail module. J Biol Chem 280: 41366–41372.

58. RoyS, ErnstJ, KharchenkoPV, KheradpourP, NegreN, et al. (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330: 1787–1797.

59. ErwinDH, LaflammeM, TweedtSM, SperlingEA, PisaniD, et al. (2011) The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science 334: 1091–1097.

60. SilvaAJ, EhningerD (2009) Adult reversal of cognitive phenotypes in neurodevelopmental disorders. J Neurodev Disord 1: 150–157.

61. KramerJM, KochinkeK, OortveldMA, MarksH, KramerD, et al. (2011) Epigenetic regulation of learning and memory by Drosophila EHMT/G9a. PLoS Biol 9: e1000569.

62. DangVT, KassahnKS, MarcosAE, RaganMA (2008) Identification of human haploinsufficient genes and their genomic proximity to segmental duplications. Eur J Hum Genet 16: 1350–1357.

63. BrandAH, PerrimonN (1993) Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118: 401–415.

64. KramerJM, StaveleyBE (2003) GAL4 causes developmental defects and apoptosis when expressed in the developing eye of Drosophila melanogaster. Genet Mol Res 2: 43–47.

65. VerstrekenP, KohT-W, SchulzeKL, ZhaiRG, HiesingerPR, et al. (2003) Synaptojanin Is Recruited by Endophilin to Promote Synaptic Vesicle Uncoating. Neuron 40: 733–748.

66. TweedieS, AshburnerM, FallsK, LeylandP, McQuiltonP, et al. (2009) FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Research 37: D555–D559.

67. BoguskiMS, SchulerGD (1995) ESTablishing a human transcript map. Nat Genet 10: 369–371.

68. HuangDW, ShermanBT, LempickiRA (2008) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protocols 4: 44–57.

69. HuangDW, ShermanBT, LempickiRA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research 37: 1–13.

70. Keshava PrasadTS, GoelR, KandasamyK, KeerthikumarS, KumarS, et al. (2009) Human Protein Reference Database–2009 update. Nucleic Acids Research 37: D767–D772.

71. WilesAM, DodererM, RuanJ, GuTT, RaviD, et al. (2010) Building and analyzing protein interactome networks by cross-species comparisons. BMC Syst Biol 4: 36.

72. GuruharshaKG, RualJ-F, ZhaiB, MintserisJ, VaidyaP, et al. (2011) A Protein Complex Network of Drosophila melanogaster. Cell 147: 690–703.

73. MuraliT, PacificoS, YuJ, GuestS, RobertsGG (2010) DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. Nucleic Acids Res 39: D736–743.

74. YuJ, PacificoS, LiuG, FinleyRLJr (2008) DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. BMC Genomics 9: 461.

75. KrzywinskiM, ScheinJ, BirolI, ConnorsJ, GascoyneR, et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19: 1639–1645.

76. SmootME, OnoK, RuscheinskiJ, WangP-L, IdekerT (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431–432.

77. WarsowG, GreberB, FalkS, HarderC, SiatkowskiM, et al. (2010) ExprEssence - Revealing the essence of differential experimental data in the context of an interaction/regulation net-work. BMC Systems Biology 4: 164.

78. van DrielMA, BruggemanJ, VriendG, BrunnerHG, LeunissenJAM (2006) A text-mining analysis of the human phenome. Eur J Hum Genet 14: 535–542.

79. MelicharekDJ, RamirezLC, SinghS, ThompsonR, MarendaDR (2010) Kismet/CHD7 regulates axon morphology, memory and locomotion in a Drosophila model of CHARGE syndrome. Hum Mol Genet 19: 4253–4264.

80. NewsomeTP, SchmidtS, DietzlG, KelemanK, ÅslingB, et al. (2000) Trio Combines with Dock to Regulate Pak Activity during Photoreceptor Axon Pathfinding in Drosophila. Cell 101: 283–294.

81. Ben-ZviA, Ben-GigiL, YagilZ, LermanO, BeharO (2008) Semaphorin3A regulates axon growth independently of growth cone repulsion via modulation of TrkA signaling. Cellular Signalling 20: 467–479.

82. KipreosET, LanderLE, WingJP, HeWW, HedgecockEM (1996) cul-1 Is Required for Cell Cycle Exit in C. elegans and Identifies a Novel Gene Family. Cell 85: 829–839.

83. Endoh-YamagamiS, KarkarKM, MaySR, CobosI, ThwinMT, et al. (2010) A mutation in the pericentrin gene causes abnormal interneuron migration to the olfactory bulb in mice. Dev Biol 340: 41–53.

84. JaglinXH, ChellyJ (2009) Tubulin-related cortical dysgeneses: microtubule dysfunction underlying neuronal migration defects. Trends in Genetics 25: 555–566.

85. RosenbergerG, GalA, KutscheK (2005) αPIX Associates with Calpain 4, the Small Subunit of Calpain, and Has a Dual Role in Integrin-mediated Cell Spreading. Journal of Biological Chemistry 280: 6879–6889.

86. EggertA, HoR, IkegakiN, LiuX-g, BrodeurGM (2000) Different effects of TrkA expression in neuroblastoma cell lines with or without MYCN amplification. Medical and Pediatric Oncology 35: 623–627.

87. IraciN, DiolaitiD, PapaA, PorroA, ValliE, et al. (2011) A SP1/MIZ1/MYCN Repression Complex Recruits HDAC1 at the TRKA and p75NTR Promoters and Affects Neuroblastoma Malignancy by Inhibiting the Cell Response to NGF. Cancer Res 71: 404–412.

88. GlassDJ (2005) A signaling role for dystrophin: Inhibiting skeletal muscle atrophy pathways. Cancer Cell 8: 351–352.

89. MouriK, HoriuchiS-y, UemuraT (2012) Cohesin controls planar cell polarity by regulating the level of the seven-pass transmembrane cadherin Flamingo. Genes to Cells 17: 509–524.

90. Gray RyanS, RoszkoI, Solnica-KrezelL (2011) Planar Cell Polarity: Coordinating Morphogenetic Cell Behaviors with Embryonic Polarity. Developmental Cell 21: 120–133.

91. Garcia-GonzaloFR, CorbitKC, Sirerol-PiquerMS, RamaswamiG, OttoEA, et al. (2011) A transition zone complex regulates mammalian ciliogenesis and ciliary membrane composition. Nat Genet 43: 776–784.

92. GordenNT, ArtsHH, ParisiMA, CoeneKLM, LetteboerSJF, et al. (2008) CC2D2A Is Mutated in Joubert Syndrome and Interacts with the Ciliopathy-Associated Basal Body Protein CEP290. The American Journal of Human Genetics 83: 559–571.

93. ChangB, KhannaH, HawesN, JimenoD, HeS, et al. (2006) In-frame deletion in a novel centrosomal/ciliary protein CEP290/NPHP6 perturbs its interaction with RPGR and results in early-onset retinal degeneration in the rd16 mouse. Hum Mol Genet 15: 1847–1857.

94. ConsortiumTm, RoyS, ErnstJ, KharchenkoPV, KheradpourP, et al. (2010) Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE. Science 330: 1787–1797.

Štítky
Genetika Reprodukčná medicína

Článok vyšiel v časopise

PLOS Genetics


2013 Číslo 10
Najčítanejšie tento týždeň
Najčítanejšie v tomto čísle
Kurzy

Zvýšte si kvalifikáciu online z pohodlia domova

Aktuální možnosti diagnostiky a léčby litiáz
nový kurz
Autori: MUDr. Tomáš Ürge, PhD.

Všetky kurzy
Prihlásenie
Zabudnuté heslo

Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.

Prihlásenie

Nemáte účet?  Registrujte sa

#ADS_BOTTOM_SCRIPTS#