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  • Information from Lay-Language Summaries is Embargoed Until the Conclusion of the Scientific Presentation

    692—Genetic Correlates of Autism

    Wednesday, November 13, 2013, 8:00 am - 11:15 am

    692.01: Contribution of the long noncoding RNA MSNP1AS to autism risk

    Location: 32B

    1Psychiatry, 2USC, Los Angeles, CA

    Abstract Body: Genetic factors contribute to autism spectrum disorder (ASD) risk. However, the genetics of ASD have proven to be complex. Genome-wide association studies (GWASs) are designed to identify novel genes and pathways that contribute to complex disorder risk. Application of GWAS techniques to ASD identified genetic markers with genome-wide significant association on chromosomes 5p14.1, 5p15.2, and 20p12.1. The chromosome 5p14.1 marker rs4307059 was also associated with social communication phenotypes in a general population sample, providing additional evidence that this chromosome 5p14.1 genetic signal contributes to autism-related phenotypes. Although widely interpreted as implicating the nearest protein-coding genes, CDH9 and CDH10, the original GWAS publication reported a lack of correlation between rs4307059 genotype and brain expression of these genes. We discovered a long noncoding RNA that is transcribed directly at the chromosome 5p14.1 GWAS site. Northern hybridization confirmed expression of the ~4 kb noncoding RNA, MSNP1AS (moesin pseudogene 1, antisense), and indicated that MSNP1AS binds the transcript of the X chromosome protein-coding gene moesin (MSN). Quantitative PCR was used to determine expression levels of MSNP1AS, MSN, CDH9 and CDH10 in 10 pairs of autism-control postmortem temporal cortex samples. Expression of the MSNP1AS noncoding RNA was correlated with rs4307059 genotype and increased 12-fold in individuals with ASD compared to controls. Consistent with previous reports, expression levels of CDH9 and CDH10 were not correlated with either ASD diagnosis or rs4307059 genotype. Expression of MSN was increased 2.4-fold in ASD samples. Despite the significantly increased MSN RNA, moesin protein levels were not increased in postmortem temporal cortex of individuals with ASD, suggesting that the noncoding RNA MSNP1AS may play a role in reducing moesin protein. To test this hypothesis, we over-expressed MSNP1AS in a human neuronal cell line. Western blot analysis indicated a significant 40% decrease in moesin protein, establishing that MSNP1AS negatively regulates moesin protein expression. MPSNP1AS represents an ASD candidate gene with genome-wide significant association, functional correlation with the ASD-associated genetic allele, and a large increase in expression in postmortem ASD temporal cortex. MSNP1AS binds MSN, and over-expression of MSNP1AS causes a decrease in moesin protein. This ongoing work represents the post-GWAS translation of genetic findings to an understanding of their biological consequences and highlights the potential contributions of noncoding RNAs to ASD risk.

    Lay Language Summary: Our work identified an unexpected type of gene that contributes to autism, opening a new avenue for studying the causes of the disorder. A highly significant genetic association signal for autism pointed to the MSNP1AS gene. However, the MSNP1AS gene does not code for a protein. Instead, MSNP1AS is a long non-coding RNA that regulates expression of a protein that is known to influence brain development and immune function. More than half the long RNAs in the human brain are non-coding, but their functions are often unknown. The discovery of a functional, autism-associated non-coding RNA provides a new channel to study the causes of autism, for which there currently is no cure.
    Autism spectrum disorder (ASD) is a lifelong neurodevelopmental disability characterized by problems with social interaction, communication and repetitive behaviors. The Centers for Disease Control and Prevention estimates that 1 in 88 children in the United States have an ASD. ASD is highly heritable, suggesting that genetics are an important contributing factor, but many questions about its causes remain.
    A 2009 study published in Nature found genome-wide significant association of genetic risk factors underlying ASD on chromosome 5. Expression of the nearest protein-coding genes (CDH9 and CDH10), however, were not influenced by the genetic factors.In a 2012 Science Translational Medicine paper, we hypothesized that a previously undetected genetic component might lie closer to the markers. Using bioinformatics techniques, we discovered that a new gene, MSNP1AS, was located directly at the ASD-associated genetic markers. We also found that expression levels of the genewere 12 times higher in brain samples from ASD patients than in samples from healthy individuals. The brain expression of MSNP1AS was correlated with the ASD-associated genetic markers. Finally, we showed that over-expression of MSNP1AS caused a decrease in moesin protein in human cell lines. Previous studies showed that moesin RNA is central to a network of genes with altered expression in postmortem brain samples from people with ASD. Like the previous studies, we found that moesin RNA levels were increased in those brain samples, while actual moesin protein levels were not. These results suggest the MSNP1AS may play a role in suppressing moesin protein expression, which may increase the risk for autism.
    The next step for this research is to determine the impact of MSNP1AS over-expression in the developing brain and immune system. Ongoing experiments also will examine the mechanisms by which MSNP1AS and other non-coding RNAs influence brain development.
    Prior to completion of the Human Genome Project, it was estimated that human DNA would produce about 100,000 protein-coding genes. This was a reasonable estimate based on the size of the human genome and the complexity of human development compared to yeast and fruit flies. Surprisingly, the Human Genome Project revealed that humans have only about 21,000 protein-coding genes, slightly more than a mouse and slightly less than a grape. How does something as complex as the human brain result from so few protein-coding genes? The genes that encode proteins comprise less than 2 percent of the human genome. In recent years, we have learned that most of the remaining 98 percent of human DNA also has a function. One of those functions is to produce long non-coding RNAs, like MSNP1AS. New RNA-Seq technologies indicate that the percentage of long RNAs that are non-coding increases with the developmental complexity of the organism, and the majority of long RNAs in human brain are non-coding. Some of these non-coding RNAs are likely to impact brain development.