Epigenetics, copy number variation, and other molecular mechanisms underlying neurodevelopmental disabilities: New insights and diagnostic approaches

Journal of Developmental and Behavioral Pediatrics

Volumn 31, Issue 7, 2010, Pages 582-591

  Gropman, Andrea L ^a,b   Batshaw, Mark L ^a,b  

^a CHILDREN S RESEARCH INSTITUTE   (United States)

^b GEORGE WASHINGTON UNIVERSITY SCHOOL OF MEDICINE AND HEALTH SCIENCES   (United States)

Author keywords

epigenetics; intellectual disability; molecular genetics

Indexed keywords

HISTONE;

ARTICLE; CHILD; DEVELOPMENTAL DISORDER; DNA METHYLATION; FRAGILE X SYNDROME; GENE REGULATORY NETWORK; GENETIC EPIGENESIS; GENETIC PREDISPOSITION; GENETIC VARIABILITY; GENETICS; HUMAN; MENTAL DEFICIENCY; NEUROLOGIC DISEASE; RETT SYNDROME;

CHILD; DEVELOPMENTAL DISABILITIES; DNA METHYLATION; EPIGENESIS, GENETIC; FRAGILE X SYNDROME; GENE REGULATORY NETWORKS; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; HISTONES; HUMANS; MENTAL RETARDATION; NERVOUS SYSTEM DISEASES; RETT SYNDROME;

EID: 77957364779     PISSN: 0196206X     EISSN: None     Source Type: Journal    
DOI: 10.1097/DBP.0b013e3181ee384e     Document Type: Article

References (88)

1. Shen Y, Dies KA, Holm IA, et al; Autism Consortium Clinical Genetics/DNA Diagnostics Collaboration. Clinical genetic testing for patients with autism spectrum disorders. Pediatrics. 2010;125:e727-e735.
2. Battaglia A, Bianchini E, Carey JC. Diagnostic yield of the comprehensive assessment of developmental delay/mental retardation in an institute of child neuropsychiatry. Am J Med Genet. 1991;82:60-66.
3. First LR, Palfrey JS. The infant or young child with developmental delay. N Engl J Med. 1994;330:478-483.
4. Majnemer A, Shevell MI. The diagnostic yield of the neurologic assessment of the developmentally delayed child. J Pediatr. 1995;127:193-199.
5. Flint J, Wilkie AO. The genetics of mental retardation. Br Med Bull. 1996;52:453-464.
6. Shevell MI, Majnemer A, Rosenbaum P, Abrahamowicz M. Etiologic yield of subspecialists' evaluation of young children with global developmental delay. J Pediatr. 2000;136:593-598.
7. Srour M, Mazer B, Shevell MI. Analysis of clinical features predicting etiologic yield in the assessment of global developmental delay. Pediatrics. 2006;118:139-145.
8. Curry CJ, Stevenson RE, Aughton D, et al. Evaluation of mental retardation: recommendations of a Consensus Conference: American College of Medical Genetics. Am J Med Genet. 1997;72:468-477.
9. Shevell MI, Bejjani BA, Srour M, Rorem EA, Hall N, Shaffer LG. Array comparative genomic hybridization in global developmental delay. Am J Med Genet B Neuropsychiatr Genet. 2008;147B:1101-1108.
10. [Deleted in text.]
11. Urdinguio RG, Sanchez-Mut JV, Esteller M. Epigenetic mechanisms in neurological diseases: genes, syndromes, and therapies. Lancet Neurol. 2009;8:1056-1072.
12. Wong ST. Emerging treatment combinations: integrating therapy into clinical practice. Am J Health Syst Pharm. 2009;66:S9-S14.
13. Holliday R, Grigg GW. DNA methylation and mutation. Mutat Res. 1993;285:61-67.
14. Delcuve GP, Rastegar M, Davie JR. Epigenetic control. J Cell Physiol. 2009;219:243-250.
15. Illingworth RS, Bird AP. CpG islands-'a rough guide'. FEBS Lett. 2009;583:1713-1720.
16. Zhang TY, Meaney MJ. Epigenetics and the environmental regulation of the genome and its function. Annu Rev Psychol. 2010;61:439-466; C1-3.
17. Chwang WB, O'Riordan KJ, Levenson JM, Sweatt JD. ERK/MAPK regulates hippocampal histone phosphorylation following contextual fear conditioning. Learn Mem. 2006;13:322-328.
18. Stipanovich A, Valjent E, Matamales M, et al. A phosphatase cascade by which rewarding stimuli control nucleosomal response. Nature. 2008;453:879-884.
19. Abel T, Zukin RS. Epigenetic targets of HDAC inhibition in neurodegenerative and psychiatric disorders. Curr Opin Pharmacol. 2008;8:57-64.
20. Ramaswamy G, Slack FJ. siRNA. A guide for RNA silencing. Chem Biol. 2002;9:1053-1055.
21. Carthew RW. RNA interference: the fragile X syndrome connection. Curr Biol. 2002;12:R852-R854.
22. Choi YB, Ko JK, Shin J. The transcriptional corepressor, PELP1, recruits HDAC2 and masks histones using two separate domains. Biol Chem. 2004;279:50930-50941.
23. Amir RE, Van den Veyver IB, Wan M, Tran CQ, Francke U, Zoghbi HY. Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat Genet. 1999;23:185-188.
24. Trappe R, Laccone F, Cobilanschi J, et al. MECP2 mutations in sporadic cases of Rett syndrome are almost exclusively of paternal origin. Am J Hum Genet. 2001;68:1093-1101.
25. Topcu M, Akyerli C, Sayi A, et al. Somatic mosaicism for a MECP2 mutation associated with classic Rett syndrome in a boy. Eur J Hum Genet. 2002;10:77-81.
26. Schanen C. Rethinking the fate of males with mutations in the gene that causes Rett syndrome. Brain Dev. 2001;23(Suppl 1):S144-S146.
27. Echenne B, Roubertie A, Lugtenberg D, et al. Neurologic aspects of MECP2 gene duplication in male patients. Pediatr Neurol. 2009;41:187-191.
28. Chahrour M, Zoghbi HY. The story of Rett syndrome: from clinic to neurobiology. Neuron. 2007;56:422-437.
29. D'Esposito M, Quaderi NA, Ciccodicola A, et al. Isolation, physical mapping, and northern analysis of the X-linked human gene encoding methyl CpG-binding protein, MECP2. Mamm Genome. 1996;7:533-535.
30. Tao J, Van Esch H, Hagedorn-Greiwe M, et al. Mutations in the X-linked cyclin-dependent kinase-like 5 (CDKL5/STK9) gene are associated with severe neurodevelopmental retardation. Am J Hum Genet. 2004;75:1149-1154.
31. Weaving LS, Christodoulou J, Williamson SL, et al. Mutations of CDKL5 cause a severe neurodevelopmental disorder with infantile spasms and mental retardation. Am J Hum Genet. 2004;75:1079-1093.
32. Mari F, Azimonti S, Bertani I, et al. CDKL5 belongs to the same molecular pathway of MeCP2 and it is responsible for the earlyonset seizure variant of Rett syndrome. Hum Mol Genet. 2005;14:1935-1946.
33. Roelfsema JH, White SJ, Ariyurek Y, et al. Genetic heterogeneity in Rubinstein-Taybi syndrome: mutations in both the CBP and EP300 genes cause disease. Am J Hum Genet. 2005;76:572-580.
34. Petrij F, Giles RH, Dauwerse HG, et al. Rubinstein-Taybi syndrome caused by mutations in the transcriptional co-activator CBP. Nature. 1995;376:348-351.
35. Field M, Tarpey P, Boyle J, et al. Mutations in the RSK2 (RPS6KA3) gene cause Coffin-Lowry syndrome and nonsyndromic X-linked mental retardation. Clin Genet. 2006;70:509-515. (Pubitemid 44741473)
36. Jacquot S, Merienne K, De Cesare D, et al. Mutation analysis of the RSK2 gene in Coffin-Lowry patients: extensive allelic heterogeneity and a high rate of de novo mutations. Am J Hum Genet. 1998;63:1631-1640.
37. Merienne K, Pannetier S, Harel-Bellan A, Sassone-Corsi P. Mitogen-regulated RSK2-CBP interaction controls their kinase and acetylase activities. Mol Cell Biol. 2001;21:7089-7096.
38. Nicholls RD. The impact of genomic imprinting for neurobehavioral and developmental disorders. J Clin Invest. 2000;105:413-418.
39. Dan B. Angelman syndrome: current understanding and research prospects. Epilepsia. 2009;50:2331-2339.
40. Cassidy SB, Driscoll DJ. Prader-Willi syndrome. Eur J Hum Genet. 2009;17:3-13.
41. Smith A, Egan J, Ridley G, et al. Birth prevalence of Prader-Willi syndrome in Australia. Arch Dis Child. 2003;88:263-264.
42. McCandless SE, Brunger JW, Cassidy SB. The burden of genetic disease on inpatient care in a children's hospital. Am J Hum Genet. 2004;74:121-127.
43. Clayton-Smith J, Laan L. Angelman syndrome: a review of the clinical and genetic aspects. J Med Genet. 2003;40:87-95.
44. Lossie AC, Whitney MM, Amidon D, et al. Distinct phenotypes distinguish the molecular classes of Angelman syndrome. J Med Genet. 2001;38:834-845.
45. Probst FJ, Roeder ER, Enciso VB, et al. Chromosomal microarray analysis (CMA) detects a large X chromosome deletion including FMR1, FMR2, and IDS in a female patient with mental retardation. Am J Med Genet A. 2007;143A:1358-1365.
46. Kubota T, Wakui K, Nakamura T, et al. The proportion of cells with functional X disomy is associated with the severity of mental retardation in mosaic ring X Turner syndrome females. Cytogenet Genome Res. 2002;99:276-284.
47. Stranger BE, Forrest MS, Dunning M, et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science. 2007;315:848-853.
48. Sebat J, Lakshmi B, Troge J, et al. Large-scale copy number polymorphism in the human genome. Science. 2004;305:525-528.
49. Sebat J, Lakshmi B, Malhotra D, et al. Strong association of de novo copy number mutations with autism. Science. 2007;316:445-449.
50. Nakahori Y, Knight SJ, Holland J, et al. Molecular heterogeneity of the fragile X syndrome. Nucleic Acids Res. 1991;19:4355-4359.
51. Tabolacci E, Moscato U, Zalfa F, Bagni C, Chiurazzi P, Neri G. Epigenetic analysis reveals a euchromatic configuration in the FMR1 unmethylated full mutations. Eur J Hum Genet. 2008;16:1487-1498.
52. Chen KS, Manian P, Koeuth T, et al. Homologous recombination of a flanking repeat gene cluster is a mechanism for a common contiguous gene deletion syndrome. Nat Genet. 1997;17:154-163.
53. Greenberg F, Lewis RA, Potocki L, et al. Multi-disciplinary clinical study of Smith-Magenis syndrome (deletion 17p11.2). Am J Med Genet. 1996;62:247-254.
54. Potocki L, Glaze D, Tan DX, et al. Circadian rhythm abnormalities of melatonin in Smith-Magenis syndrome. J Med Genet. 2000;37:428-433.
55. De Leersnyder H, de Blois MC, Vekemans M, et al. beta (1)-adrenergic antagonists improve sleep and behavioural disturbances in a circadian disorder, Smith-Magenis syndrome. J Med Genet. 2001;38:586-590.
56. Seranski P, Hoff C, Radelof U, et al. RAI1 is a novel polyglutamine encoding gene that is deleted in Smith-Magenis syndrome patients. Gene. 2001;270:69-76.
57. Slager RE, Newton TL, Vlangos CN, Finucane B, Elsea SH. Mutations in RAI1 associated with Smith-Magenis syndrome. Nat Genet. 2003;33:466-468.
58. Bearden CE, Woodin MF, Wang PP, et al. The neurocognitive phenotype of the 22q11.2 deletion syndrome: selective deficit in visual-spatial memory. J Clin Exp Neuropsychol. 2001;23:447-464.
59. Golding-Kushner KJ, Weller G, Shprintzen RJ. Velo-cardio-facial syndrome: language and psychological profiles. J Craniofac Genet Dev Biol. 1985;5:259-266.
60. Wang PP, Solot C, Moss EM, et al. Developmental presentation of 22q11.2 deletion (DiGeorge/velocardiofacial syndrome). J Dev Behav Pediatr. 1998;19:342-345.
61. Morris CA, Thomas IT, Greenberg F. Williams syndrome: autosomal dominant inheritance. Am J Med Genet. 1993;47:478-481.
62. Nickerson E, Greenberg F, Keating MT, McCaskill C, Shaffer LG. Deletions of the elastin gene at 7q11.23 occur in approximately 90% of patients with Williams syndrome. Am J Hum Genet. 1995;56:1156-1161.
63. Frangiskakis JM, Ewart AK, Morris CA, et al. LIM-kinase1 hemizygosity implicated in impaired visuospatial constructive cognition. Cell. 1996;86:59-69.
64. Donnai D, Karmiloff-Smith A. Williams syndrome: from genotype through to the cognitive phenotype. Am J Med Genet. 2000;97:164-171.
65. Shaw-Smith C, Redon R, Rickman L, et al. Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features. J Med Genet. 2004;41:241-248.
66. Schoumans J, Ruivenkamp C, Holmberg E, Kyllerman M, Anderlid BM, Nordenskjold M. Detection of chromosomal imbalances in children with idiopathic mental retardation by array based comparative genomic hybridisation (array-CGH). J Med Genet. 2005;42:699-705.
67. Nelson DL, Warren ST. Trinucleotide repeat instability: when and where? Nat Genet. 1993;4:107-108.
68. Northrop EL, Ren H, Bruno DL, et al. Detection of cryptic subtelomeric chromosome abnormalities and identification of anonymous chromatin using a quantitative multiplex ligationdependent probe amplification (MLPA) assay. Hum Mutat. 2005;26:477-486.
69. Kirchhoff M, Pedersen S, Kjeldsen E, et al. Chromosome aberrations in mentally retarded and dysmorphic patients with normal karyotypes. Ugeskr Laeger 2004;166:4482-4485.
70. Lu X-Y, Phung MT, Shaw CA, et al. Genomic imbalances in neonates with birth defects: high detection rates by using chromosomal microarray analysis. Pediatrics. 2008;122:1310-1318.
71. Shinawi M, Cheung SW. The array CGH and its clinical implications. Drug Discov Today. 2008;13:760-770.
72. Mefford HC, Sharp AJ, Baker C, et al. Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. N Engl J Med. 2008;359:1685-1699.
73. Sharp AJ, Selzer RR, Veltman JA, et al. Characterization of a recurrent 15q24 microdeletion syndrome. Hum Mol Genet. 2007;16:567-572.
74. Weiss LA, Shen Y, Korn JM, et al; Autism Consortium. Association between microdeletion and microduplication at 16p11.2 and autism. N Engl J Med. 2008;358:667-675.
75. Kumar RA, Christian SL. Genetics of autism spectrum disorders. Curr Neurol Neurosci Rep. 2009;9:188-197.
76. Koolen DA, Sharp AJ, Hurst JA, et al. Clinical and molecular delineation of the 17q21.31 microdeletion syndrome. J Med Genet. 2008;45:710-720.
77. Stankiewicz P, Beaudet AL. Use of array CGH in the evaluation of dysmorphology, malformations, developmental delay, and idiopathic mental retardation. Curr Opin Genet Dev. 2007;17:182-192.
78. Shaffer LG, Theisen A, Bejjani BA, et al. The discovery of microdeletion syndromes in the post-genomic era: review of the methodology and characterization of a new 1q41q42 microdeletion syndrome. Genet Med. 2007;9:607-616.
79. Lugtenberg D, Veltman JA, van Bokhoven H. High-resolution genomic microarrays for X-linked mental retardation. Genet Med. 2007;9:560-565.
80. Shen Y, Irons M, Miller DT, et al. Development of a focused oligonucleotide-array comparative genomic hybridization chip for clinical diagnosis of genomic imbalance. Clin Chem. 2007;53:2051-2059.
81. Friedman JM, Baross A, Delaney AD, et al. Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. Am J Hum Genet. 2006;79:500-513.
82. Mefford HC. Genotype to phenotype-discovery and characterization of novel genomic disorders in a "genotype-first" era. Genet Med. 2009;11:836-842.
83. Speicher MR, Carter NP. The new cytogenetics: blurring the boundaries with molecular biology. Nat Rev Genet. 2005;6:782-792.
84. Flint J, Wilkie AO, Buckle VJ, Winter RM, Holland AJ, McDermid HE. The detection of subtelomeric chromosomal rearrangements in idiopathic mental retardation. Nat Genet. 1995;9:132-140.
85. Shaffer LG, Beaudet AL, Brothman AR, et al; Working Group of the Laboratory Quality Assurance Committee of the American College of Medical Genetics. Microarray analysis for constitutional cytogenetic abnormalities. Genet Med. 2007;9:654-662.
86. Wang W, Law HY, Chong SS. Detection and discrimination between deletional and non-deletional Prader-Willi and Angelman syndromes by methylation-specific PCR and quantitative melting curve analysis. J Mol Diagn. 2009;11:446-449.
87. Vecsey CG, Hawk JD, Lattal KM, et al. Histone deacetylase inhibitors enhance memory and synaptic plasticity via CREB: CBP-dependent transcriptional activation. J Neurosci. 2007;27:6128-6140.
88. Vissers LELM, de Vries BPA, Veltman JA. Genomic microarrays in mental retardation: from CNV to gene, from research to diagnosis. J Med Genet. 2010;47:289-297.