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Loss of δ-catenin function in severe autism.

Turner TN, Sharma K, Oh EC, Liu YP, Collins RL, Sosa MX, Auer DR, Brand H, Sanders SJ, Moreno-De-Luca D, Pihur V, Plona T, Pike K, Soppet DR, Smith MW, Cheung SW, Martin CL, State MW, Talkowski ME, Cook E, Huganir R, Katsanis N, Chakravarti A - Nature (2015)

Bottom Line: Autism is a multifactorial neurodevelopmental disorder affecting more males than females; consequently, under a multifactorial genetic hypothesis, females are affected only when they cross a higher biological threshold.Here we show the use of this strategy by identifying missense and dosage sequence variants in the gene encoding the adhesive junction-associated δ-catenin protein (CTNND2) in female-enriched multiplex families and demonstrating their loss-of-function effect by functional analyses in zebrafish embryos and cultured hippocampal neurons from wild-type and Ctnnd2 mouse embryos.Finally, through gene expression and network analyses, we highlight a critical role for CTNND2 in neuronal development and an intimate connection to chromatin biology.

View Article: PubMed Central - PubMed

Affiliation: 1] Center for Complex Disease Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [2] Predoctoral Training Program in Human Genetics and Molecular Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [3] National Institute of Mental Health (NIMH) Autism Centers of Excellence (ACE) Genetics Consortium at the University of California, Los Angeles, Los Angeles, California 90095, USA.

ABSTRACT
Autism is a multifactorial neurodevelopmental disorder affecting more males than females; consequently, under a multifactorial genetic hypothesis, females are affected only when they cross a higher biological threshold. We hypothesize that deleterious variants at conserved residues are enriched in severely affected patients arising from female-enriched multiplex families with severe disease, enhancing the detection of key autism genes in modest numbers of cases. Here we show the use of this strategy by identifying missense and dosage sequence variants in the gene encoding the adhesive junction-associated δ-catenin protein (CTNND2) in female-enriched multiplex families and demonstrating their loss-of-function effect by functional analyses in zebrafish embryos and cultured hippocampal neurons from wild-type and Ctnnd2 mouse embryos. Finally, through gene expression and network analyses, we highlight a critical role for CTNND2 in neuronal development and an intimate connection to chromatin biology. Our data contribute to the understanding of the genetic architecture of autism and suggest that genetic analyses of phenotypic extremes, such as female-enriched multiplex families, are of innate value in multifactorial disorders.

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Read and Amplicon Metrics in CTNND2 Sequencing. (a) Histogram of Reads per Sample; (b) Average quality scores across the read across all samples with each sample represented by a separate line; (c) Boxplot of Coverage per Amplicon.
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Figure 9: Read and Amplicon Metrics in CTNND2 Sequencing. (a) Histogram of Reads per Sample; (b) Average quality scores across the read across all samples with each sample represented by a separate line; (c) Boxplot of Coverage per Amplicon.

Mentions: CTNND2 harbored two deleterious variants, G34S and R713C both of which were absent in 3,889 European controls (1000G and Exome Variant Server (EVS)); G34S was present at a frequency of 5.3x10−4 in 1,869 African ancestry samples (EVS) and in one Luhyan sample (NA19020) (Extended Data Figure 2). To estimate their frequency, we genotyped 10,782 samples from the HapMap and autism collections: the only additional individuals with G34S were an affected female and her mother (SSC02696, SSC03276) from the Simons Simplex Collection (SSC). Principal component analysis on polymorphism data from G34S individuals found that our autism cases were not of African ancestry, identifying a new ancestral origin for G34S (Extended Data Figure 3). For R713C, only our FEMF samples were heterozygous. Next-generation CTNND2 sequencing in 362 additional autism females (Extended Data Figures 4) identified a total of seven variants (G34S, R713C and five new variants: P189L, P224L, G275C, R454H, T862M) of which four (G34S, G275C, R713C, T862M) were conserved to zebrafish (Figure 2a, Supplementary Table S4). We also identified Q507P in an autistic male from 170 SSC probands. An identical analysis of 379 European ancestry control samples (1000G) yielded three variants after validation (R330H,D465N,A482T), one conserved to zebrafish. On aggregate, variants at these conserved CTNND2 residues are significantly more frequent in autism than in controls (P=0.04 vs. 1000G; P=7.8x10−4 vs. EVS).


Loss of δ-catenin function in severe autism.

Turner TN, Sharma K, Oh EC, Liu YP, Collins RL, Sosa MX, Auer DR, Brand H, Sanders SJ, Moreno-De-Luca D, Pihur V, Plona T, Pike K, Soppet DR, Smith MW, Cheung SW, Martin CL, State MW, Talkowski ME, Cook E, Huganir R, Katsanis N, Chakravarti A - Nature (2015)

Read and Amplicon Metrics in CTNND2 Sequencing. (a) Histogram of Reads per Sample; (b) Average quality scores across the read across all samples with each sample represented by a separate line; (c) Boxplot of Coverage per Amplicon.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383723&req=5

Figure 9: Read and Amplicon Metrics in CTNND2 Sequencing. (a) Histogram of Reads per Sample; (b) Average quality scores across the read across all samples with each sample represented by a separate line; (c) Boxplot of Coverage per Amplicon.
Mentions: CTNND2 harbored two deleterious variants, G34S and R713C both of which were absent in 3,889 European controls (1000G and Exome Variant Server (EVS)); G34S was present at a frequency of 5.3x10−4 in 1,869 African ancestry samples (EVS) and in one Luhyan sample (NA19020) (Extended Data Figure 2). To estimate their frequency, we genotyped 10,782 samples from the HapMap and autism collections: the only additional individuals with G34S were an affected female and her mother (SSC02696, SSC03276) from the Simons Simplex Collection (SSC). Principal component analysis on polymorphism data from G34S individuals found that our autism cases were not of African ancestry, identifying a new ancestral origin for G34S (Extended Data Figure 3). For R713C, only our FEMF samples were heterozygous. Next-generation CTNND2 sequencing in 362 additional autism females (Extended Data Figures 4) identified a total of seven variants (G34S, R713C and five new variants: P189L, P224L, G275C, R454H, T862M) of which four (G34S, G275C, R713C, T862M) were conserved to zebrafish (Figure 2a, Supplementary Table S4). We also identified Q507P in an autistic male from 170 SSC probands. An identical analysis of 379 European ancestry control samples (1000G) yielded three variants after validation (R330H,D465N,A482T), one conserved to zebrafish. On aggregate, variants at these conserved CTNND2 residues are significantly more frequent in autism than in controls (P=0.04 vs. 1000G; P=7.8x10−4 vs. EVS).

Bottom Line: Autism is a multifactorial neurodevelopmental disorder affecting more males than females; consequently, under a multifactorial genetic hypothesis, females are affected only when they cross a higher biological threshold.Here we show the use of this strategy by identifying missense and dosage sequence variants in the gene encoding the adhesive junction-associated δ-catenin protein (CTNND2) in female-enriched multiplex families and demonstrating their loss-of-function effect by functional analyses in zebrafish embryos and cultured hippocampal neurons from wild-type and Ctnnd2 mouse embryos.Finally, through gene expression and network analyses, we highlight a critical role for CTNND2 in neuronal development and an intimate connection to chromatin biology.

View Article: PubMed Central - PubMed

Affiliation: 1] Center for Complex Disease Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [2] Predoctoral Training Program in Human Genetics and Molecular Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [3] National Institute of Mental Health (NIMH) Autism Centers of Excellence (ACE) Genetics Consortium at the University of California, Los Angeles, Los Angeles, California 90095, USA.

ABSTRACT
Autism is a multifactorial neurodevelopmental disorder affecting more males than females; consequently, under a multifactorial genetic hypothesis, females are affected only when they cross a higher biological threshold. We hypothesize that deleterious variants at conserved residues are enriched in severely affected patients arising from female-enriched multiplex families with severe disease, enhancing the detection of key autism genes in modest numbers of cases. Here we show the use of this strategy by identifying missense and dosage sequence variants in the gene encoding the adhesive junction-associated δ-catenin protein (CTNND2) in female-enriched multiplex families and demonstrating their loss-of-function effect by functional analyses in zebrafish embryos and cultured hippocampal neurons from wild-type and Ctnnd2 mouse embryos. Finally, through gene expression and network analyses, we highlight a critical role for CTNND2 in neuronal development and an intimate connection to chromatin biology. Our data contribute to the understanding of the genetic architecture of autism and suggest that genetic analyses of phenotypic extremes, such as female-enriched multiplex families, are of innate value in multifactorial disorders.

Show MeSH
Related in: MedlinePlus