Abstract
Functional variomics provides the foundation for personalized medicine by linking genetic variation to disease expression, outcome and treatment, yet its utility is dependent on appropriate assays to evaluate mutation impact on protein function. To fully assess the effects of 106 missense and nonsense variants of PTEN associated with autism spectrum disorder, somatic cancer and PTEN hamartoma syndrome (PHTS), we take a deep phenotypic profiling approach using 18 assays in 5 model systems spanning diverse cellular environments ranging from molecular function to neuronal morphogenesis and behavior. Variants inducing instability occur across the protein, resulting in partial-to-complete loss-of-function (LoF), which is well correlated across models. However, assays are selectively sensitive to variants located in substrate binding and catalytic domains, which exhibit complete LoF or dominant negativity independent of effects on stability. Our results indicate that full characterization of variant impact requires assays sensitive to instability and a range of protein functions.
Highlights
Functional variomics provides the foundation for personalized medicine by linking genetic variation to disease expression, outcome and treatment, yet its utility is dependent on appropriate assays to evaluate mutation impact on protein function
Confidence of gene association to Autism spectrum disorder (ASD) is enhanced by identification of de novo, likely gene disrupting (LGD) mutations; the most common de novo mutations identified in individuals with ASD are missense (MS) variants of unknown significance (VUS)[2,7]
We selected PTEN MS and nonsense (NS) mutations identified in individuals with ASD, intellectual disability (ID), developmental delay (DD), somatic cancer and PTEN hamartoma syndrome (PHTS), as well as variants found among the general population (Fig. 1a, Supplementary Data 1)
Summary
Functional variomics provides the foundation for personalized medicine by linking genetic variation to disease expression, outcome and treatment, yet its utility is dependent on appropriate assays to evaluate mutation impact on protein function. To fully assess the effects of 106 missense and nonsense variants of PTEN associated with autism spectrum disorder, somatic cancer and PTEN hamartoma syndrome (PHTS), we take a deep phenotypic profiling approach using 18 assays in 5 model systems spanning diverse cellular environments ranging from molecular function to neuronal morphogenesis and behavior. In order to probe the molecular mechanisms causing variant dysfunction in these assays, we perform flow cytometry analysis of human embryonic kidney (HEK293) cells overexpressing PTEN variants to parse effects on protein stability and catalytic activity These multi-model results provide robust validation of measures of variant function in highly diverse cellular environments to uncover complexities of the contribution of single-nucleotide mutations to protein dysfunction and pathophysiology
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