Discovery of genetic modifiers of PTEN-ASD severity in a library of genetically diverse iPSC lines

ABSTRACT
It is increasingly apparent that both common and rare genetic variation influences the risk and severity of
syndromic autism spectrum disorders (ASD). Among patients with highly penetrant ASD associated mutations
there is often substantial heterogeneity in the severity of physical, behavioral, and cognitive deficits. However,
precisely which regions of the human genome affect disease outcomes in the context of any high confidence
ASD mutation are currently unknown. This critical gap in knowledge prevents the rational design of therapies
that target underlying molecular and cellular deficiencies.
Here, I will leverage genetically diverse iPSC lines to test the hypothesis that common genetic variation
shapes the severity of hyperproliferation phenotypes caused by mutations in PTEN, a highly penetrant ASD
associated gene. I will employ a novel pooled cell culture method, which allows rapid and efficient phenotyping
of dozens of distinct lines in the same culture dish, to quantify the variation in hyperproliferation induced by
PTEN haploinsufficiency. This will allow me to identify regions of the genome which modulate this ASD
relevant phenotype, and test for the presence of sex specific genetic effects. I will then mechanistically validate
associated loci with three distinct approaches. First, we will expand and validate our culture-based findings in
patients with 1) idiopathic autism with brain overgrowth with longitudinal MRI and neurocognitive profiling, from
whom these lines were generated, 2) ~600 deeply phenotyped patients with a variety of PTEN mutations and
clinical presentations. Second, we will correlate our findings with those from other genome wide association
studies to identify causal genes, and loci with shared genetic risk with other diseases. Third, we will validate
associated loci in isogenic PTEN(+/-) lines, and test hypotheses aimed at the mechanisms by which genetic
variants protect/exacerbate the effects of PTEN mutations. In all, the proposed studies will identify common
genetic modifiers of phenotypic severity and patient outcomes in a genetically defined ASD subtype.
To develop the expertise necessary for this cross-disciplinary project, I will undergo comprehensive training
in bioinformatics, statistical genetics, and molecular neurodevelopment under the guidance of my primary
mentor Jason Stein. I will also undergo supplemental training from my advisors in iPSC differentiation methods
(Beltran), MRI image analysis (Piven/Styner), ASD pathogenesis (Piven/Zylka/Eng), and approaches to
correlate genetic and clinical data (Stein/Piven/Eng). They will train me in the methods and principles required
to successfully complete this project. This training will facilitate a successfully transition into my independent
scientific career, where I will study genetic modifiers of neurodevelopmental disorders.