Mutations in TUBG1, DYNC1H1, KIF5C and KIF2A cause malformations of cortical development and microcephaly

The genetic causes of malformations of cortical development (MCD) remain largely unknown. Here we report the discovery of multiple pathogenic missense mutations in TUBG1, DYNC1H1 and KIF2A, as well as a single germline mosaic mutation in KIF5C, in subjects with MCD. We found a frequent recurrence of mutations in DYNC1H1, implying that this gene is a major locus for unexplained MCD. We further show that the mutations in KIF5C, KIF2A and DYNC1H1 affect ATP hydrolysis, productive protein folding and microtubule binding, respectively. In addition, we show that suppression of mouse Tubg1 expression in vivo interferes with proper neuronal migration, whereas expression of altered γ-tubulin proteins in Saccharomyces cerevisiae disrupts normal microtubule behavior. Our data reinforce the importance of centrosomal and microtubule-related proteins in cortical development and strongly suggest that microtubule-dependent mitotic and postmitotic processes are major contributors to the pathogenesis of MCD.

[1]  Christopher A Walsh,et al.  What disorders of cortical development tell us about the cortex: one plus one does not always make two. , 2011, Current opinion in genetics & development.

[2]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[3]  C. Cantor,et al.  Microtubule assembly in the absence of added nucleotides. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[4]  N. Cowan,et al.  Chaperonin-mediated Folding of Vertebrate Actin-Related Protein and-Tubulin , 2002 .

[5]  N. Hirokawa,et al.  Golgi Vesiculation and Lysosome Dispersion in Cells Lacking Cytoplasmic Dynein , 1998, The Journal of cell biology.

[6]  R. Cross,et al.  Differential trafficking of Kif5c on tyrosinated and detyrosinated microtubules in live cells , 2008, Journal of Cell Science.

[7]  A. Boronat,et al.  A colorimetric assay for the determination of 4-diphosphocytidyl-2-C-methyl-D-erythritol 4-phosphate synthase activity. , 2005, Analytical biochemistry.

[8]  W. Tap,et al.  Specificity in chaperonin-mediated protein folding , 1995, Nature.

[9]  A. Represa,et al.  Mutations in the β-tubulin gene TUBB2B result in asymmetrical polymicrogyria , 2009, Nature Genetics.

[10]  P. Rakic,et al.  Cortical development: View from neurological mutants two decades later , 1995, Neuron.

[11]  HighWire Press The journal of neuroscience : the official journal of the Society for Neuroscience. , 1981 .

[12]  Kenneth H Downing,et al.  An atomic-level mechanism for activation of the kinesin molecular motors , 2010, Proceedings of the National Academy of Sciences.

[13]  Ralf Krahe,et al.  The γ-tubulin gene family in humans , 2000 .

[14]  Mohan L Gupta,et al.  Phenotypic spectrum of the tubulin-related disorders and functional implications of disease-causing mutations. , 2011, Current opinion in genetics & development.

[15]  A. Wynshaw-Boris,et al.  Lissencephaly: mechanistic insights from animal models and potential therapeutic strategies. , 2010, Seminars in cell & developmental biology.

[16]  D. Keays,et al.  Large spectrum of lissencephaly and pachygyria phenotypes resulting from de novo missense mutations in tubulin alpha 1A (TUBA1A) , 2007, Human mutation.

[17]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[18]  Stephan J Sanders,et al.  Whole exome sequencing identifies recessive WDR62 mutations in severe brain malformations , 2010, Nature.

[19]  K. Johnson An Update. , 1984, Journal of food protection.

[20]  R. Krahe,et al.  The gamma-tubulin gene family in humans. , 2000, Genomics.

[21]  N. Hirokawa,et al.  Kinesin superfamily motor proteins and intracellular transport , 2009, Nature Reviews Molecular Cell Biology.

[22]  B. V. van Bon,et al.  Diagnostic exome sequencing in persons with severe intellectual disability. , 2012, The New England journal of medicine.

[23]  D. Ledbetter,et al.  Differences in the gyral pattern distinguish chromosome 17–linked and X-linked lissencephaly , 1999, Neurology.

[24]  N. Cowan,et al.  Chaperonin-mediated folding of vertebrate actin-related protein and gamma-tubulin , 1993, The Journal of cell biology.

[25]  H. Shiraishi,et al.  A DYNC1H1 mutation causes a dominant spinal muscular atrophy with lower extremity predominance , 2012, neurogenetics.

[26]  John O. Thomas,et al.  A cytoplasmic chaperonin that catalyzes β-actin folding , 1992, Cell.

[27]  J. Chelly,et al.  Tubulin-related cortical dysgeneses: microtubule dysfunction underlying neuronal migration defects. , 2009, Trends in genetics : TIG.

[28]  A. Pestronk,et al.  Mutations in the tail domain of DYNC1H1 cause dominant spinal muscular atrophy , 2012, Neurology.

[29]  J. Veltman,et al.  De novo mutations in human genetic disease , 2012, Nature Reviews Genetics.

[30]  Samara L. Reck-Peterson,et al.  The Affinity of the Dynein Microtubule-binding Domain Is Modulated by the Conformation of Its Coiled-coil Stalk*[boxs] , 2005, Journal of Biological Chemistry.

[31]  B. V. van Bon,et al.  Mutations in DYNC1H1 cause severe intellectual disability with neuronal migration defects , 2012, Journal of Medical Genetics.

[32]  M. Weedon,et al.  Exome sequencing identifies a DYNC1H1 mutation in a large pedigree with dominant axonal Charcot-Marie-Tooth disease. , 2011, American journal of human genetics.

[33]  M. Simpson,et al.  Mutations in KIF11 cause autosomal-dominant microcephaly variably associated with congenital lymphedema and chorioretinopathy. , 2012, American journal of human genetics.

[34]  V. Caviness,et al.  Numbers, time and neocortical neuronogenesis: a general developmental and evolutionary model , 1995, Trends in Neurosciences.

[35]  P. Bork,et al.  Human non-synonymous SNPs: server and survey. , 2002, Nucleic acids research.

[36]  F. Studier,et al.  Use of T7 RNA polymerase to direct expression of cloned genes. , 1990, Methods in enzymology.

[37]  Martin W. Breuss,et al.  Mutations in the β-Tubulin Gene TUBB5 Cause Microcephaly with Structural Brain Abnormalities , 2012, Cell reports.

[38]  J. Gleeson,et al.  The centrosome in neuronal development , 2007, Trends in Neurosciences.

[39]  D. Agard,et al.  Microtubule nucleation by γ-tubulin complexes , 2011, Nature Reviews Molecular Cell Biology.

[40]  R. Kuzniecky,et al.  A developmental and genetic classification for malformations of cortical development: update 2012 , 2012, Brain : a journal of neurology.

[41]  Jamel Chelly,et al.  Human disorders of cortical development: from past to present , 2006, The European journal of neuroscience.

[42]  Huanming Yang,et al.  Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants , 2010, Nature Genetics.

[43]  N. Hirokawa,et al.  Point mutation of adenosine triphosphate-binding motif generated rigor kinesin that selectively blocks anterograde lysosome membrane transport , 1995, The Journal of cell biology.

[44]  N. Boddaert,et al.  Expanding the spectrum of TUBA1A-related cortical dysgenesis to Polymicrogyria , 2012, European Journal of Human Genetics.

[45]  Christian Gilissen,et al.  A de novo paradigm for mental retardation , 2010, Nature Genetics.

[46]  Gautier Koscielny,et al.  Ensembl 2012 , 2011, Nucleic Acids Res..

[47]  C. Fallet-Bianco,et al.  Mutations in the neuronal ß-tubulin subunit TUBB3 result in malformation of cortical development and neuronal migration defects. , 2010, Human molecular genetics.

[48]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[49]  S. Varambally,et al.  Structure and Functional Role of Dynein's Microtubule-Binding Domain , 2008, Science.

[50]  R. Vallee,et al.  Neuronal migration defects in the Loa dynein mutant mouse , 2011, Neural Development.

[51]  S. Henikoff,et al.  Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm , 2009, Nature Protocols.

[52]  S. Basit,et al.  Mutations in WDR62 gene in Pakistani families with autosomal recessive primary microcephaly , 2011, BMC neurology.

[53]  Yasushi Hiraoka,et al.  Mutations in Dynein Link Motor Neuron Degeneration to Defects in Retrograde Transport , 2003, Science.

[54]  R. Erickson Somatic gene mutation and human disease other than cancer: an update. , 2010, Mutation research.

[55]  A. Barkovich,et al.  Abnormal development of the human cerebral cortex: genetics, functional consequences and treatment options , 2008, Trends in Neurosciences.

[56]  Steve D. M. Brown,et al.  Mutations in α-Tubulin Cause Abnormal Neuronal Migration in Mice and Lissencephaly in Humans , 2007, Cell.

[57]  N. Cowan,et al.  A cytoplasmic chaperonin that catalyzes beta-actin folding. , 1992, Cell.

[58]  L. Tsai,et al.  Ndel1 Operates in a Common Pathway with LIS1 and Cytoplasmic Dynein to Regulate Cortical Neuronal Positioning , 2004, Neuron.

[59]  N. Hirokawa,et al.  Kinesin Superfamily Protein 2A (KIF2A) Functions in Suppression of Collateral Branch Extension , 2003, Cell.

[60]  N. Hirokawa,et al.  KIF5C, a novel neuronal kinesin enriched in motor neurons. , 2000, The Journal of neuroscience : the official journal of the Society for Neuroscience.