Autism and related diseases, collectively known as autism spectrum disorders (ASD), are the fastest growing neurodevelopmental disorders in the U.S., affecting as many as one in 200 children. Very little is known about the causes of ASD, which appear to include both genetic and environmental factors. We propose to use induced pluripotent stem cell technology to compare the development of autistic, Fragile X (mental retardation), and normal neuronal cells in vitro in an effort to understand the underlying pathology that leads to the neurological dysfunction. We propose to generate iPSCs from affected individuals and controls, characterize them using high-throughput genetic and epigenetic methods for comparison with our large existing database of pluripotent and neural stem cell molecular profiles, and study their differentiation in vitro using a set of molecular and physiological tools. For the first (R21) phase, we will focus on discovery and the development of tools. We will obtain autistic fibroblasts from Dr. Philip Schwartz, a longtime collaborator who has recently launched an NIH- sponsored program to generate autism fibroblasts and iPSCs as a resource for the research community. We will perform pilot studies with a limited number of patient-specific lines, providing Dr. Schwartz with the iPSCs we generate using our established methods and new virus-free methods in development. We will follow their differentiation in vitro into a variety of neuronal cell types, characterizing selected subpopulations for global expression of mRNA and microRNAs, DNA methylation (epigenetic) profile, and copy number variation (SNP genotyping). Finally, we will systematically compare the properties of differentiated disease-specific and control iPSC-derived neurons using optical and electrophysiological methods. For the second (R33) phase, we will incorporate more cell lines (produced by our group and by Dr. Schwartz) and optimize the tools that are most promising. First we will expand the "Autism Stem Cell Matrix" database of molecular profiles and use bioinformatics tools to identify significant differences between disease-specific and control cultures. We will extend the functional studies by maturing the cells in vitro into three-dimensional cortex-like aggregates and characterizing their synaptic interactions in this model of early CNS development. Finally, we will combine a lineage tracing tool ("Brainbow") with cell type-specific gene expression methods to focus on molecular differences among neuronal subtypes. Our goal is to produce a comprehensive analysis comparing functional development of autistic, Fragile X, and normal neuronal cells in vitro. From this detailed study, we hope to provide clues to the developmental causes of autism.

Public Health Relevance

Autism is a disorder of neural development whose causes are virtually unknown;largely because of this lack of knowledge, there are no consistently successful treatments for this disease that is expected to affect 4 million children and their families in the US by the end of the next decade. The goal of this project is to shed light on the causes of autism by studying development of the nervous system in a controlled tissue culture environment using sophisticated molecular tools. We will obtain cells from the skin of autistic patients, using a virtually painless procedure, and turn them into induced pluripotent cells (iPSCs) that can develop into every cell type in the body. We will study the development of these cells into nerve cells in tissue culture, comparing them with cells from unaffected children. From this detailed study, we hope to learn what goes wrong during brain development in autistic children, and help develop a strategy for effective treatment.

Agency
National Institute of Health (NIH)
Institute
National Institute of Mental Health (NIMH)
Type
Exploratory/Developmental Grants Phase II (R33)
Project #
5R33MH087925-04
Application #
8326533
Study Section
Special Emphasis Panel (ZMH1-ERB-M (02))
Program Officer
Panchision, David M
Project Start
2009-09-30
Project End
2014-08-31
Budget Start
2012-09-01
Budget End
2014-08-31
Support Year
4
Fiscal Year
2012
Total Cost
$460,152
Indirect Cost
$199,163
Name
Scripps Research Institute
Department
Type
DUNS #
781613492
City
La Jolla
State
CA
Country
United States
Zip Code
92037
Bhutani, Kunal; Nazor, Kristopher L; Williams, Roy et al. (2016) Whole-genome mutational burden analysis of three pluripotency induction methods. Nat Commun 7:10536
Wang, Yu-Chieh; Lin, Victor; Loring, Jeanne F et al. (2015) The 'sweet' spot of cellular pluripotency: protein glycosylation in human pluripotent stem cells and its applications in regenerative medicine. Expert Opin Biol Ther 15:679-87
Garitaonandia, Ibon; Amir, Hadar; Boscolo, Francesca Sesillo et al. (2015) Increased risk of genetic and epigenetic instability in human embryonic stem cells associated with specific culture conditions. PLoS One 10:e0118307
Wang, Yu-Chieh; Stein, Jason W; Lynch, Candace L et al. (2015) Glycosyltransferase ST6GAL1 contributes to the regulation of pluripotency in human pluripotent stem cells. Sci Rep 5:13317
Boland, Michael J; Nazor, Kristopher L; Loring, Jeanne F (2014) Epigenetic regulation of pluripotency and differentiation. Circ Res 115:311-24
Peterson, Suzanne E; Loring, Jeanne F (2014) Genomic instability in pluripotent stem cells: implications for clinical applications. J Biol Chem 289:4578-84
Nazor, Kristopher L; Boland, Michael J; Bibikova, Marina et al. (2014) Application of a low cost array-based technique - TAB-Array - for quantifying and mapping both 5mC and 5hmC at single base resolution in human pluripotent stem cells. Genomics 104:358-67
Kurian, Leo; Sancho-Martinez, Ignacio; Nivet, Emmanuel et al. (2013) Conversion of human fibroblasts to angioblast-like progenitor cells. Nat Methods 10:77-83
Jones, Jennifer C; Sabatini, Karen; Liao, Xiaoyan et al. (2013) Melanocytes derived from transgene-free human induced pluripotent stem cells. J Invest Dermatol 133:2104-8
Ramsköld, Daniel; Luo, Shujun; Wang, Yu-Chieh et al. (2012) Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol 30:777-82

Showing the most recent 10 out of 15 publications