Discovery and Analysis of New Alternatively Spliced Isoforms of Autism Candidate Genes

Thursday, May 17, 2012
Sheraton Hall (Sheraton Centre Toronto)
11:00 AM
S. Kang1, X. Yang2,3, G. N. Lin1, R. Corominas1, Y. Shen2,3, S. A. Wanamaker2,3, S. Tam2,3, M. Rodriguez2,3, M. Broly2,3, J. Sebat1, K. Salehi-Ashtiani2,3, D. E. Hill2,3, M. Vidal2,3, T. Hao2,3 and L. M. Iakoucheva1, (1)Department of Psychiatry, University of California San Diego, La Jolla, CA, (2)Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, (3)Department of Genetics, Harvard Medical School, Boston, MA

Autism is a neurodevelopmental disorder involving a large number of functionally diverse genes. Currently, it is not completely understood how these genes interact with each other and with a majority of other human genes on a protein level. Even less is known about the influence of alternative splicing (AS) on protein-protein interactions.


Here, we aim at discovering new splice variants of autism candidate genes and at investigating their interaction patterns in the context of an autism protein-protein interaction network (i.e. autism interactome).


Our isoform discovery pipeline includes four major steps: (1) Cloning of AS isoforms of 191 autism candidate genes from normal adult and fetal human brain samples; (2) High throughput 454 sequencing of the cloned transcripts; (3) yeast two-hybrid screening to detect interactions of AS isoforms with ~15,000 human ORFs; (4) Analysis of the autism isoform network.


We have successfully cloned 373 AS isoforms from 124 out of the 191 autism candidate genes (an average of 3.0 isoforms per gene); 226/373 isoforms are newly discovered, i.e. are not present in the public databases. This corresponds to an average of 1.82 new isoforms per gene. By cloning novel isoforms, we were able to increase the isoform space of the autism candidate genes by 29%.

Next, we have built autism candidate genes-centred interactome using a high-throughput yeast two-hybrid system. We have tested 124 autism candidate genes and their 373 isoforms for interactions against ~15,000 human ORFs. We have identified 492 gene-level interactions, which correspond to 638 isoform-level interactions, between 75 autism candidate genes and 272 human proteins. By incorporating isoform interactions into the autism network, we were able to expand the interactome by 50%. The comparison between isoform networks from fetal and adult human brain tissues has demonstrated 45% overlap of interactions, indicating that different patterns of interactions may exist in the developing and adult human brains. In addition, out of 10 hub genes with more than 10 interacting partners, 8 had less than 20% partners shared between the isoforms with the most and the least numbers of interacting partners. This demonstrates the strong influence of alternative splicing on protein-protein interactions.


Our isoform discovery study has largely increased the isoform space of the autism candidate genes. The biological role of these AS isoforms was systematically investigated by detecting their interaction partners within the autism interactome framework. The splicing interactome demonstrates that interaction partners between different splice isoforms of the same gene are only partially shared, thereby illustrating the immense level of complexity of human interaction networks. 

See more of: Genetics and Genomics
See more of: Genetics
See more of: Biological Mechanisms
| More