ABSTRACT
Connecting a genotype with a phenotype can provide immediate advantages in the context of modern medicine. Especially useful would be an algorithm for predicting the impact of nonsynonymous single-nucleotide polymorphisms in the gene for PTEN, a protein that is implicated in most human cancers and connected to germline disorders that include autism. We have developed a protein impact predictor, PTENpred, that integrates data from multiple analyses using a support vector machine algorithm. PTENpred can predict phenotypes related to a human PTEN mutation with high accuracy. The output of PTENpred is designed for use by biologists, clinicians, and laymen, and features an interactive display of the three-dimensional structure of PTEN. Using knowledge about the structure of proteins, in general, and the PTEN protein, in particular, enables the prediction of consequences from damage to the human PTEN gene. This algorithm, which can be accessed online, could facilitate the implementation of effective therapeutic regimens for cancer and other diseases.
Subject(s)
Algorithms , Autistic Disorder/pathology , Neoplasms/pathology , PTEN Phosphohydrolase/genetics , Polymorphism, Single Nucleotide , Software , Autistic Disorder/genetics , Humans , Mutation , Neoplasms/genetics , PTEN Phosphohydrolase/metabolism , Phenotype , Predictive Value of Tests , Support Vector MachineABSTRACT
Phosphoinositides are membrane components that play critical regulatory roles in mammalian cells. The enzyme PTEN, which catalyzes the dephosphorylation of the phosphoinositide PIP3, is damaged in most sporadic tumors. Mutations in the PTEN gene have also been linked to autism spectrum disorders and other forms of delayed development. Here, human PTEN is shown to be on the cusp of unfolding under physiological conditions. Variants of human PTEN linked to somatic cancers and disorders on the autism spectrum are shown to be impaired in their conformational stability, catalytic activity, or both. Those variants linked only to autism have activity higher than the activity of those linked to cancers. PTEN-L, which is a secreted trans-active isoform, has conformational stability greater than that of the wild-type enzyme. These data indicate that PTEN is a fragile enzyme cast in a crucial role in cellular metabolism and suggest that PTEN-L is a repository for a critical catalytic activity.
Subject(s)
Autistic Disorder/genetics , Genetic Variation , Neoplasms/genetics , PTEN Phosphohydrolase/chemistry , PTEN Phosphohydrolase/genetics , Autistic Disorder/metabolism , Humans , Models, Molecular , Neoplasms/metabolism , PTEN Phosphohydrolase/metabolism , Protein Conformation , Protein Stability , Protein UnfoldingABSTRACT
Phosphatase and tensin homologue deleted from chromosome ten (PTEN) is a lipid phosphatase tumor suppressor that is lost or inactivated in most human tumors. The enzyme catalyzes the hydrolysis of phosphatidylinositol-(3,4,5)-trisphosphate (PIP3) to form phosphatidylinositol-(4,5)-bisphosphate (PIP2) and inorganic phosphate. Here, we report on the first continuous assay for the catalytic activity of PTEN. Using this assay, we demonstrate that human PTEN is activated by the reaction product PIP2, as well as in solutions of low salt concentration. This activation is abrogated in the K13A variant, which has a disruption in a putative binding site for PIP2. We also demonstrate that PTEN-L, which derives from alternative translation of the PTEN mRNA, is activated constitutively. These findings have implications for catalysis by PTEN in physiological environments and could expedite the development of PTEN-based chemotherapeutic agents.
