Genetics of Autism

1. Genetics of Autism A Bioinformatics Analysis of Suspected Genes and Products Teresa LuPone BIO 283

2. What is Autism? • Defined by a spectrum of disorders containing varying degrees of the following three basic symptomologies • Social Impairment • Inattention, delayed or non-responsiveness, inability to respond to social cues. • Communication Difficulties • Delayed speech development, difficulties with self expression, conversational difficulties. • Repetitive and Stereotyped behaviors • Repetitive words, phrases or motor movements, obsessive focus on interests. (National Institute of Mental Health)

3. More on Autism • Prevalence • 1992: 1 in 150 affected • 2008: 1 in 88 affected • Boys 5 times more likely. • Evidence to date: • Ruling out of some environmental factors • Vaccines: 2004 findings did not support the rumor that vaccines contributed to incidence of autism (CDC) • Emerging evidence for genetic causation and possible correlation with other diseases. • Immunity abnormalities has a significant number of ASD affected individuals with immune problems. • Cytogenetic studies, Oxidative stress. • Suspected genes (short list) • FOXP2 • UBE3A • MECP-2 • RELN

4. The Genetic Component • FOXP2: multivariantgene involved in regulation of other genes. • Important roles: speech and language center development in brain. (RefSeq 2010). Located on Chromosome 7 • FOXP2 Map: http://tinyurl.com/cxbxdaf • Sequence: http://www.ncbi.nlm.nih.gov/nuccore/21322221 • MECP-2: Located on the X chromosome. • Females with Rett syndrome found similar abnormalities to ASD expression. (Persico et. al.) • MECP-2 Map: http://tinyurl.com/btr9nec • Sequence: http://www.ncbi.nlm.nih.gov/nuccore/22830571 • UBE3A: a gene involved in ubiquitin ligase, essential to ubiquitin activation. • Mutations cause severe diseases characterized by: severe motor and intellectual retardation, ataxia, hypotonia, epilepsy, and absence of speech. • UBE3A Map: http://tinyurl.com/d2clzcf • Sequence: http://www.ncbi.nlm.nih.gov/nuccore/21306876 • RELN: large ECM protein that is believed to control cell-cell interactions and neuronal migration that is essential in brain development. Mutations of this gene are associated with autosomal recessive lissencephaly with cerebellar hypoplasia (RefSeq, 2008). • RELN Map: http://tinyurl.com/blrc8c2 • Sequence: http://www.ncbi.nlm.nih.gov/nuccore/1809222

5. Purpose • The goal of this project is to analyze the emerging evidence for the genetic basis of autism, using bioinformatics computational tools for similarities to support the following claim. Genes that may have a role within autism must have some similarity in their gene products, which may have some influence over the spectrum disorders of autism..

6. Materials & Methods • Software/Databases Employed: • NCBI: ORF Finder, Gene, Nucleotide, RefSeq, Conserved Domain, MeSH, PubMed and BLASTp • EMBL-EBI protein tools not employed but used as reference. • Cn3D used for protein visualization. • Suspected Genes are run through the ORF finder in NCBI. • Largest ORF’s chosen due to the strong likelihood of a functional protein. • Resulting proposed protein sequences were run through a BLASTp • Analyzed for conserved domains. • Conserved domains or similar protein structures if any were visualized with Cn3d protein visualization tool.

7. Results

8. FOXP2 Results BLAST results pictogram for FOXP2

9. FOXP2 Results Above: Sequence alignment of proposed protein with putative p150 protein. Left: ORF with translated protein.

10. MECP-2 Results BLAST results pictogram for MECP-2

11. MECP-2 Results Above: ORF with translated protein. Right: Sequence alignment of proposed protein with putative p150 protein. Top right: methyl CpG binding protein visualization, extremely similar to proposed protein.

12. UBE3A Results BLAST results pictogram for UBE3A

13. UBE3A Results Above: Sequence alignment of proposed protein with hCG1777785 protein. Left: ORF with translated protein.

14. RELN Results BLAST results pictogram for RELN

15. RELN Results Above: Sequence alignment of proposed protein with putative p150 protein. Left: ORF with translated protein.

16. Conserved Domain of FOXP2, UBE3A and RELN Results Above: Phylogram of protein families within this conserved domain. Left: Virtual proposed protein of the conserved domain.

17. Evaluations • Some structural similarity. Three shared a conserved domain in their longest ORF gene product. • No evidence has been found yet in their causal roles in autism, future wet lab work is suggested. • Partial support for the claim: • Genes that may have a role within autism must have some similarity in their gene products, which may have some influence over the spectrum disorders of autism.

18. References • Ameis, S. H., & Szatmari, P. (2012). Imaging-genetics in autism spectrum disorder: Advances, translational impact, and future directions. Frontiers in Psychiatry, 3(46), 16. Retrieved from www.frontiersin.org. • Klei, L., Sanders, S. J., Murtha, M. T., & ET AL (2012). Common genetics variants, acting additively, are a major source of risk for autism. Molecular Autism, 3(9), 28. doi:10.1186/2040-2392-2-9. • Muhle, R., Trentacoste, S. V., & Rapin, I. (2004, May). The Genetics of Autism.Pediatrics. Retrieved October 10, 2012, from http://www.pediatrics.org/cgi/content/full/113/e472 • NIMH. (2011, October 26). A parent's guide to autism. website: http://www.nimh.nih.gov/health/publications/a-parents-guide-to-autism-spectrum-disorder/what-is-autism-spectrum-disorder-asd.shtml • (n.d.). Autism spectrum disorders. website: http://www.cdc.gov/ncbddd/autism/index.html • Perisco, A. M., Van de Water, J., & Pardo, C. A. (2012). Autism: Where Genetics Meets the Immune System. Autism Research and Treatment, 2012. doi:10.1155/2012/486359.

19. Questions? A special thank you to Erin Ramirez for her help in experimental design and our professor Dr. Dash!