DOI QR코드

DOI QR Code

Molecular genetic decoding of malformations of cortical development

  • Lim, Jae Seok (Graduate School of Medical Science and Engineering, KAIST) ;
  • Lee, Jeong Ho (Graduate School of Medical Science and Engineering, KAIST)
  • 투고 : 2014.12.16
  • 심사 : 2015.04.13
  • 발행 : 2015.06.30

초록

Malformations of cortical development (MCD) cover a broad spectrum of developmental disorders which cause the various clinical manifestations including epilepsy, developmental delay, and intellectual disability. MCD have been clinically classified based on the disruption of developmental processes such as proliferation, migration, and organization. Molecular genetic studies of MCD have improved our understanding of these disorders at a molecular level beyond the clinical classification. These recent advances are resulted from the development of massive parallel sequencing technology, also known as next-generation sequencing (NGS), which has allowed researchers to uncover novel molecular genetic pathways associated with inherited or de novo mutations. Although an increasing number of disease-related genes or genetic variations have been identified, genotype-phenotype correlation is hampered when the biological or pathological functions of identified genetic variations are not fully understood. To elucidate the causality of genetic variations, in vivo disease models that reflect these variations are required. In the current review, we review the use of NGS technology to identify genes involved in MCD, and discuss how the functions of these identified genes can be validated through in vivo disease modeling.

키워드

참고문헌

  1. Barkovich AJ, Guerrini R, Kuzniecky RI, Jackson GD, Dobyns WB. A developmental and genetic classification for malformations of cortical development: update 2012. Brain 2012;135:1348-69. https://doi.org/10.1093/brain/aws019
  2. Pang T, Atefy R, Sheen V. Malformations of cortical development. Neurologist 2008;14:181-91. https://doi.org/10.1097/NRL.0b013e31816606b9
  3. Guerrini R. Genetic malformations of the cerebral cortex and epilepsy. Epilepsia 2005;46(Suppl)1:32-7.
  4. Manzini MC, Walsh CA. What disorders of cortical development tell us about the cortex: one plus one does not always make two. Curr Opin Genet Dev 2011;21:333-9. https://doi.org/10.1016/j.gde.2011.01.006
  5. Bilguvar K, Ozturk AK, Louvi A, Kwan KY, Choi M, Tatli B, et al. Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations. Nature 2010;467:207-10. https://doi.org/10.1038/nature09327
  6. Hussain MS, Baig SM, Neumann S, Nurnberg G, Farooq M, Ahmad I, et al. A truncating mutation of CEP135 causes primary microcephaly and disturbed centrosomal function. Am J Hum Genet 2012;90:871-8. https://doi.org/10.1016/j.ajhg.2012.03.016
  7. Poirier K, Lebrun N, Broix L, Tian G, Saillour Y, Boscheron C, et al. Mutations in TUBG1, DYNC1H1, KIF5C and KIF2A cause malformations of cortical development and microcephaly. Nat Genet 2013;45:639-47. https://doi.org/10.1038/ng.2613
  8. Lee JH, Huynh M, Silhavy JL, Kim S, Dixon-Salazar T, Heiberg A, et al. De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly. Nat Genet 2012;44:941-5. https://doi.org/10.1038/ng.2329
  9. Riviere JB, Mirzaa GM, O'Roak BJ, Beddaoui M, Alcantara D, Conway RL, et al. De novo germline and postzygotic mutations in AKT3, PIK3R2 and PIK3CA cause a spectrum of related megalencephaly syndromes. Nat Genet 2012;44:934-40. https://doi.org/10.1038/ng.2331
  10. Yu TW, Mochida GH, Tischfield DJ, Sgaier SK, Flores-Sarnat L, Sergi CM, et al. Mutations in WDR62, encoding a centrosome-associated protein, cause microcephaly with simplified gyri and abnormal cortical architecture. Nat Genet 2010;42:1015-20. https://doi.org/10.1038/ng.683
  11. Bakircioglu M, Carvalho OP, Khurshid M, Cox JJ, Tuysuz B, Barak T, et al. The essential role of centrosomal NDE1 in human cerebral cortex neurogenesis. Am J Hum Genet 2011;88:523-35. https://doi.org/10.1016/j.ajhg.2011.03.019
  12. Boycott KM, Vanstone MR, Bulman DE, MacKenzie AE. Rare-disease genetics in the era of next-generation sequencing: discovery to translation. Nat Rev Genet 2013;14:681-91. https://doi.org/10.1038/nrg3555
  13. Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP. Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet 2014;15:121-32. https://doi.org/10.1038/nrg3642
  14. Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet 2011;12:745-55. https://doi.org/10.1038/nrg3031
  15. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010;20:1297-303. https://doi.org/10.1101/gr.107524.110
  16. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011;43:491-8. https://doi.org/10.1038/ng.806
  17. Bras J, Guerreiro R, Hardy J. Use of next-generation sequencing and other whole-genome strategies to dissect neurological disease. Nat Rev Neurosci 2012;13:453-64.
  18. Barak T, Kwan KY, Louvi A, Demirbilek V, Saygi S, Tuysuz B, et al. Recessive LAMC3 mutations cause malformations of occipital cortical development. Nat Genet 2011;43:590-4. https://doi.org/10.1038/ng.836
  19. Murdock DR, Clark GD, Bainbridge MN, Newsham I, Wu YQ, Muzny DM, et al. Whole-exome sequencing identifies compound heterozygous mutations in WDR62 in siblings with recurrent polymicrogyria. Am J Med Genet A 2011;155A:2071-7.
  20. Poduri A, Evrony GD, Cai X, Elhosary PC, Beroukhim R, Lehtinen MK, et al. Somatic activation of AKT3 causes hemispheric developmental brain malformations. Neuron 2012;74:41-8. https://doi.org/10.1016/j.neuron.2012.03.010
  21. Jamuar SS, Lam AT, Kircher M, D'Gama AM, Wang J, Barry BJ, et al. Somatic mutations in cerebral cortical malformations. N Engl J Med 2014;371:733-43. https://doi.org/10.1056/NEJMoa1314432
  22. Poduri A, Evrony GD, Cai X, Walsh CA. Somatic mutation, genomic variation, and neurological disease. Science 2013;341:1237758. https://doi.org/10.1126/science.1237758
  23. Ding L, Wendl MC, McMichael JF, Raphael BJ. Expanding the computational toolbox for mining cancer genomes. Nat Rev Genet 2014;15:556-70. https://doi.org/10.1038/nrg3767
  24. Kim SY, Speed TP. Comparing somatic mutation-callers: beyond Venn diagrams. BMC Bioinformatics 2013;14:189. https://doi.org/10.1186/1471-2105-14-189
  25. Goode DL, Hunter SM, Doyle MA, Ma T, Rowley SM, Choong D, et al. A simple consensus approach improves somatic mutation prediction accuracy. Genome Med 2013;5:90. https://doi.org/10.1186/gm494
  26. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods 2010;7:248-9. https://doi.org/10.1038/nmeth0410-248
  27. Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 2003;31:3812-4. https://doi.org/10.1093/nar/gkg509
  28. Reva B, Antipin Y, Sander C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res 2011;39:e118. https://doi.org/10.1093/nar/gkr407
  29. Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 2014;46:310-5. https://doi.org/10.1038/ng.2892
  30. Thomas KR, Capecchi MR. Site-directed mutagenesis by gene targeting in mouse embryo-derived stem cells. Cell 1987;51:503-12. https://doi.org/10.1016/0092-8674(87)90646-5
  31. Uhlmann EJ, Wong M, Baldwin RL, Bajenaru ML, Onda H, Kwiatkowski DJ, et al. Astrocyte-specific TSC1 conditional knockout mice exhibit abnormal neuronal organization and seizures. Ann Neurol 2002;52:285-96. https://doi.org/10.1002/ana.10283
  32. Way SW, McKenna J 3rd, Mietzsch U, Reith RM, Wu HC, Gambello MJ. Loss of Tsc2 in radial glia models the brain pathology of tuberous sclerosis complex in the mouse. Hum Mol Genet 2009;18:1252-65. https://doi.org/10.1093/hmg/ddp025
  33. Gu H, Marth JD, Orban PC, Mossmann H, Rajewsky K. Deletion of a DNA polymerase beta gene segment in T cells using cell type-specific gene targeting. Science 1994;265:103-6. https://doi.org/10.1126/science.8016642
  34. Bi W, Sapir T, Shchelochkov OA, Zhang F, Withers MA, Hunter JV, et al. Increased LIS1 expression affects human and mouse brain development. Nat Genet 2009;41:168-77. https://doi.org/10.1038/ng.302
  35. Wolfer DP, Crusio WE, Lipp HP. Knockout mice: simple solutions to the problems of genetic background and flanking genes. Trends Neurosci 2002;25:336-40. https://doi.org/10.1016/S0166-2236(02)02192-6
  36. Crusio WE. Flanking gene and genetic background problems in genetically manipulated mice. Biol Psychiatry 2004;56:381-5. https://doi.org/10.1016/j.biopsych.2003.12.026
  37. Papaioannou VE, Behringer RR. Early embryonic lethality in genetically engineered mice: diagnosis and phenotypic analysis. Vet Pathol 2012;49:64-70. https://doi.org/10.1177/0300985810395725
  38. Kratochwil CF, Rijli FM. The Cre/Lox system to assess the development of the mouse brain. Methods Mol Biol 2014;1082:295-313. https://doi.org/10.1007/978-1-62703-655-9_20
  39. LoTurco J, Manent JB, Sidiqi F. New and improved tools for in utero electroporation studies of developing cerebral cortex. Cereb Cortex 2009;19(Suppl 1):i120-5. https://doi.org/10.1093/cercor/bhp033
  40. dal Maschio M, Ghezzi D, Bony G, Alabastri A, Deidda G, Brondi M, et al. High-performance and site-directed in utero electroporation by a triple-electrode probe. Nat Commun 2012;3:960. https://doi.org/10.1038/ncomms1961
  41. Takahashi M, Sato K, Nomura T, Osumi N. Manipulating gene expressions by electroporation in the developing brain of mammalian embryos. Differentiation 2002;70:155-62. https://doi.org/10.1046/j.1432-0436.2002.700405.x
  42. Fukuchi-Shimogori T, Grove EA. Neocortex patterning by the secreted signaling molecule FGF8. Science 2001;294:1071-4. https://doi.org/10.1126/science.1064252
  43. Bai J, Ramos RL, Ackman JB, Thomas AM, Lee RV, LoTurco JJ. RNAi reveals doublecortin is required for radial migration in rat neocortex. Nat Neurosci 2003;6:1277-83. https://doi.org/10.1038/nn1153
  44. Feliciano DM, Su T, Lopez J, Platel JC, Bordey A. Single-cell Tsc1 knockout during corticogenesis generates tuber-like lesions and reduces seizure threshold in mice. J Clin Invest 2011;121:1596-607. https://doi.org/10.1172/JCI44909
  45. Shimogori T, Ogawa M. Gene application with in utero electroporation in mouse embryonic brain. Dev Growth Differ 2008;50:499-506. https://doi.org/10.1111/j.1440-169X.2008.01045.x
  46. Beaulieu CL, Samuels ME, Ekins S, McMaster CR, Edwards AM, Krainer AR, et al. A generalizable pre-clinical research approach for orphan disease therapy. Orphanet J Rare Dis 2012;7:39. https://doi.org/10.1186/1750-1172-7-39