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Molecular cytogenetic analysis and resequencing of contactin associated protein-like 2 in autism spectrum disorders - PubMed

Molecular cytogenetic analysis and resequencing of contactin associated protein-like 2 in autism spectrum disorders

Betul Bakkaloglu et al. Am J Hum Genet. 2008 Jan.

Abstract

Autism spectrum disorders (ASD) are a group of related neurodevelopmental syndromes with complex genetic etiology. We identified a de novo chromosome 7q inversion disrupting Autism susceptibility candidate 2 (AUTS2) and Contactin Associated Protein-Like 2 (CNTNAP2) in a child with cognitive and social delay. We focused our initial analysis on CNTNAP2 based on our demonstration of disruption of Contactin 4 (CNTN4) in a patient with ASD; the recent finding of rare homozygous mutations in CNTNAP2 leading to intractable seizures and autism; and in situ and biochemical analyses reported herein that confirm expression in relevant brain regions and demonstrate the presence of CNTNAP2 in the synaptic plasma membrane fraction of rat forebrain lysates. We comprehensively resequenced CNTNAP2 in 635 patients and 942 controls. Among patients, we identified a total of 27 nonsynonymous changes; 13 were rare and unique to patients and 8 of these were predicted to be deleterious by bioinformatic approaches and/or altered residues conserved across all species. One variant at a highly conserved position, I869T, was inherited by four affected children in three unrelated families, but was not found in 4010 control chromosomes (p = 0.014). Overall, this resequencing data demonstrated a modest nonsignificant increase in the burden of rare variants in cases versus controls. Nonetheless, when viewed in light of two independent studies published in this issue of AJHG showing a relationship between ASD and common CNTNAP2 alleles, the cytogenetic and mutation screening data suggest that rare variants may also contribute to the pathophysiology of ASD, but place limits on the magnitude of this contribution.

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Figures

Figure 1
Figure 1

Mapping of a De Novo Inversion (inv(7)(q11.22;q35)) in a Child with Developmental Delay (A) Pedigree of a family with an affected male child with developmental delay. The parents, grandparents, and two older siblings are not affected with a neurodevelopmental disorder. (B) G-banded metaphase chromosomes and ideogram for normal (left) and inverted (right) chromosomes are presented. (C and D) FISH mapping of q35 (C) and q11.22 (D) breakpoints. Images show the two BACs that span the breaks. The experimental probe is seen at the expected positions on the normal (nml) chromosomes 7q35 and 7q11.22, respectively. Two fluorescence signals are visible on the inverted (inv) chromosomes indicating that the probes span the break points. Photographs were taken with a 100× objective lens. (E and F) Schematics showing the location of the spanning BACs relative to the disrupted genes. (E) The edges of the BAC RP11-1012D24 are 1314 kb and 821 kb away from the centromeric and telomeric ends of CNTNAP2. (F) The edges of the BAC RP11-709J20 are 926 kb and 110 kb away from the centromeric and telomeric ends of AUTS2.

Figure 2
Figure 2

Expression of Cntnap2 mRNA in Postnatal Mouse Brain Sections of P9 mouse brain were hybridized with a Cntnap2 antisense probe. We detected expression in the cortex (A–D), septum (A), basal ganglia (A and B), many thalamic (B–D) and hypothalamic (C–E) nuclei, with particularly high levels observed in the anterior nucleus and the habenula, part of the amygdala (C), the superior colliculus and the periaqueductal gray (F), pons, cerebellum, and medulla, again with particularly high levels seen in the inferior olive. All panels represent coronal sections and are shown in anterior to posterior order. Ctx, cortex; CPu, caudate putamen; Se, septum; GP, globus pallidus; Th, thalamus; Hip; hippocampal formation; A, amygdala; HTh, hypothalamus; SC, superior colliculus; PAG, periaqueductal gray; Pn, pontine nuclei.

Figure 3
Figure 3

Expression and Biochemical Analyses of CNTNAP2/Cntnap2 (A–C) Cortical expression of CNTNAP2/Cntnap2. Sections of human temporal cortex at 6 and 58 years of age (A and B) and P7 mouse cortex (C) were hybridized with corresponding antisense riboprobes. Expression is detected in cortical layers II–V in the human temporal lobe (A and B) and II–VI in the mouse neocortex (C). (D) Cofractionation of Cntn2/TAG-1 and Cntnap2 in synaptic plasma membranes. Rat forebrain homogenate (homog.) was subfractionated into postnuclear supernatant (S1), synaptosomal supernatant (S2), crude synaptosomes (P2), synaptosomal membranes (LP1), crude synaptic vesicles (LP2), synaptic plasma membranes (SPM), and mitochondria (mito.). The synaptic membrane protein N-cadherin and the synaptic vesicle protein synaptotagmin 1 served as markers for these respective fractions. Numbers on the left indicate positions of molecular weight markers. Protein concentrations were determined with the Pierce BCA assay and equal amounts of each fraction were analyzed. Monoclonal antibodies to Cntn2/TAG-1 (3.1C12, developed by Thomas Jessell, Columbia University) were obtained from the Developmental Studies Hybridoma Bank maintained by the University of Iowa, to synaptotagmin 1 (41.1) from Synaptic Systems (Göttingen, Germany), and to N-cadherin from BD Biosciences (# 610920). Polyclonal antibodies to Cntnap2 were obtained from Sigma (# C 8737).

Figure 4
Figure 4

Sequencing of CNTNAP2 Identifies Rare Unique Nonsynonymous Variants (A) Diagram of the CNTNAP2 protein highlighting the location of unique predicted deleterious variants (modified from SMART). The locations of patient variants are indicated. Variants in red are predicted to be deleterious or at conserved sites. Asterisk indicates variant was identified in three independent families; SP, signal peptide; FA58C, coagulation factor 5/8 C-terminal domain; LamG, Laminin G domain; EGF and EFG-L, epidermal growth factor-like domains; TM, transmembrane domain; 4.1M, putative band 4.1 homologs' binding motif; black vertical bar, C-terminal type II PDZ binding sequence. Figure is to scale. (B) Pedigrees for all families with variants predicted to be deleterious at conserved sites (I to XIII) or which all affected relatives carry the identified variant (IX–X). The individuals carrying the suspect allele are noted and are heterozygous. The brothers inheriting the D1129H variant are monozygotic twins. Affected status was calculated with the AGRE diagnosis algorithm, which is based on ADI-R scores. Blackened symbols represent an autism diagnosis, half-filled symbols indicate a not-quite-autism (NQA) diagnosis, and crosshatched individuals have a broad spectrum diagnosis.

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