Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders

Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Science (Impact Factor: 33.61). 11/2012; 338(6114). DOI: 10.1126/science.1227764
Source: PubMed


Exome sequencing studies of autism spectrum disorders (ASDs) have identified many de novo mutations but few recurrently disrupted
genes. We therefore developed a modified molecular inversion probe method enabling ultra-low-cost candidate gene resequencing
in very large cohorts. To demonstrate the power of this approach, we captured and sequenced 44 candidate genes in 2446 ASD
probands. We discovered 27 de novo events in 16 genes, 59% of which are predicted to truncate proteins or disrupt splicing.
We estimate that recurrent disruptive mutations in six genes—CHD8, DYRK1A, GRIN2B, TBR1, PTEN, and TBL1XR1—may contribute to 1% of sporadic ASDs. Our data support associations between specific genes and reciprocal subphenotypes
(CHD8-macrocephaly and DYRK1A-microcephaly) and replicate the importance of a β-catenin–chromatin-remodeling network to ASD etiology.

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    • "Abnormalities in activity-regulated transcriptional pathways have been implicated in neurodevelopmental disorders (Pfeiffer et al., 2010; King et al., 2013), especially in autism spectrum disorders (ASDs), which are characterized by deficits in social interaction and communication, cognitive inflexibility, repetitive behaviors, and intellectual disability. Recent genetic studies have found recurrent mutations of T-brain-1 (TBR1), encoding a brain-specific T-box transcription factor (Bulfone et al., 1995), in ASD patients and identified Tbr1 as a causative gene in ASDs (Neale et al., 2012; O’Roak et al., 2012a; Huang et al., 2014). "
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    ABSTRACT: The activity-regulated gene expression of transcription factors is required for neural plasticity and function in response to neuronal stimulation. T-brain-1 (TBR1), a critical neuron-specific transcription factor for forebrain development, has been recognized as a high-confidence risk gene for autism spectrum disorders (ASDs). Here, we show that in addition to its role in brain development, Tbr1 responds to neuronal activation and further modulates the Grin2b expression in adult brains and mature neurons. The expression levels of Tbr1 were investigated using both immunostaining and quantitative RT-PCR analyses. We found that the mRNA and protein expression levels of Tbr1 are induced by excitatory synaptic transmission driven by bicuculline or glutamate treatment in cultured mature neurons. The upregulation of Tbr1 expression requires the activation of both AMPA and NMDA receptors. Furthermore, behavioral training triggers Tbr1 induction in the adult mouse brain. The elevation of Tbr1 expression is associated with Grin2b upregulation in both mature neurons and adult brains. Using Tbr1-deficient neurons, we further demonstrated that TBR1 is required for the induction of Grin2b upon neuronal activation. Taken together with the previous studies showing that TBR1 binds the Grin2b promoter and controls expression of luciferase reporter driven by Grin2b promoter, the evidence suggests that TBR1 directly controls Grin2b expression in mature neurons. We also found that the addition of the calcium-calmodulin kinase II (CaMKII) antagonist KN-93, but not the calcium-dependent phosphatase calcineurin antagonist cyclosporin A, to cultured mature neurons noticeably inhibited Tbr1 induction, indicating that neuronal activation upregulates Tbr1 expression in a CaMKII-dependent manner. In conclusion, our study suggests that Tbr1 plays an important role in adult mouse brains in response to neuronal activation to modulate the activity-regulated gene transcription required for neural p
    Frontiers in Cellular Neuroscience 09/2014; 8:280. DOI:10.3389/fncel.2014.00280 · 4.29 Impact Factor
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    • "For example, all of the members of the Shank protein family that indirectly link NMDAR and mGluR were identified as autism causative genes (Durand et al., 2007; Hung et al., 2008; Berkel et al., 2010; Pinto et al., 2010; Peca et al., 2011; Sato et al., 2012; Schmeisser et al., 2012; Won et al., 2012). Mutations in the NR2b gene were consistently identified in patients with autism (O’Roak et al., 2012). These observations support the current hypothesis that the intellectual disabilities associated with autism are caused by unbalanced synaptic activity. "
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    ABSTRACT: Innate immune responses have been shown to influence brain development and function. Dysregulation of innate immunity is significantly associated with psychiatric disorders such as autism spectrum disorders and schizophrenia, which are well-known neurodevelopmental disorders. Recent studies have revealed that critical players of the innate immune response are expressed in neuronal tissues and regulate neuronal function and activity. For example, Sarm1, a negative regulator that acts downstream of Toll-like receptor (TLR) 3 and 4, is predominantly expressed in neurons. We have previously shown that Sarm1 regulates neuronal morphogenesis and the expression of inflammatory cytokines in the brain, which then affects learning ability, cognitive flexibility, and social interaction. Because impaired neuronal morphogenesis and dysregulation of cytokine expression may disrupt neuronal activity, we investigated whether Sarm1 knockdown affects the synaptic responses of neurons. We here show that reduced Sarm1 expression impairs metabotropic glutamate receptor (mGluR)-dependent long-term depression (LTD) formation but enhances N-methyl-D-aspartate receptor (NMDAR)-dependent long-term potentiation production in hippocampal CA1 neurons. The expression levels of post-synaptic proteins, including NR2a, NR1, Shank1 and Shank3, are also altered in Sarm1 knockdown mice, suggesting a role for Sarm1 in the maintenance of synaptic homeostasis. The addition of a positive allosteric modulator of mGluR5, CDPPB, ameliorates the LTD defects in slice recording and the behavioral deficits in social interaction and associative memory. These results suggest an important role for mGluR5 signaling in the function of Sarm1. In conclusion, our study demonstrates a role for Sarm1 in the regulation of synaptic plasticity. Through these mechanisms, Sarm1 knockdown results in the impairment of associative memory and social interactions in mice.
    Frontiers in Cellular Neuroscience 04/2014; 8(1):87. DOI:10.3389/fncel.2014.00087 · 4.29 Impact Factor
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    • "PTEN dysregulation has been linked to disorders that include Lhermitte–Duclos disease (Liaw et al., 1997), Cowden syndrome (Goffin et al., 2001), Proteus syndrome (Zhou et al., 2001), and Bannayan–Riley–Ruvalcaba syndrome (Arch et al., 1997; Eng, 2003). Additionally, PTEN mutations have been associated with a number of neurological conditions, such as epilepsy, macrocephaly, mental retardation, and autism spectrum disorders (Marsh et al., 1999; Goffin et al., 2001; Zhou et al., 2003; Butler et al., 2005; Herman et al., 2007; O’Roak et al., 2012; Epi4K Consortium and Epilepsy Phenome/Genome Project, 2013). Dysregulation of either TSC1 or TSC2 leads to TSC, a disorder characterized by the widespread development of non-malignant tumors in multiple organ systems, including the brain, eyes, heart, skin, and lungs (for review, see Franz et al., 2010). "
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    ABSTRACT: The phosphatidylinositol-3-kinase/phosphatase and tensin homolog (PTEN)-mammalian target of rapamycin (mTOR) pathway regulates a variety of neuronal functions, including cell proliferation, survival, growth, and plasticity. Dysregulation of the pathway is implicated in the development of both genetic and acquired epilepsies. Indeed, several causal mutations have been identified in patients with epilepsy, the most prominent of these being mutations in PTEN and tuberous sclerosis complexes 1 and 2 (TSC1, TSC2). These genes act as negative regulators of mTOR signaling, and mutations lead to hyperactivation of the pathway. Animal models deleting PTEN, TSC1, and TSC2 consistently produce epilepsy phenotypes, demonstrating that increased mTOR signaling can provoke neuronal hyperexcitability. Given the broad range of changes induced by altered mTOR signaling, however, the mechanisms underlying seizure development in these animals remain uncertain. In transgenic mice, cell populations with hyperactive mTOR have many structural abnormalities that support recurrent circuit formation, including somatic and dendritic hypertrophy, aberrant basal dendrites, and enlargement of axon tracts. At the functional level, mTOR hyperactivation is commonly, but not always, associated with enhanced synaptic transmission and plasticity. Moreover, these populations of abnormal neurons can affect the larger network, inducing secondary changes that may explain paradoxical findings reported between cell and network functioning in different models or at different developmental time points. Here, we review the animal literature examining the link between mTOR hyperactivation and epileptogenesis, emphasizing the impact of enhanced mTOR signaling on neuronal form and function.
    Frontiers in Molecular Neuroscience 03/2014; 7:18. DOI:10.3389/fnmol.2014.00018 · 4.08 Impact Factor
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