Analysis of Selected mTOR Pathway Genes in ASD Families Reveals a Deletion Event in PTEN

Background: The co-occurrence of Autism Spectrum Disorders (ASD) and Tuberous Sclerosis Complex (TSC) has been recognized for many years. TSC involves two genes, TSC1 and TSC2, which function together to inhibit mammalian Target of Rapamycin (mTOR) signaling.  mTOR signaling plays an essential role in neural plasticity, and activation of mTOR signaling is known to result in rapid synthesis of a diverse array of neuronal proteins which may have implications for synapse strength. Therefore, aberrant regulation of mTOR signaling in neurons is a potential common cause for deficits associated with TSC as well as ASD.

Objectives: To investigate whether inherited variations in mTOR pathway genes may also be associated with genetic risk for ASD, we chose a candidate gene approach focusing on 7 genes known or suspected to be involved in aberrant regulation of mTOR signaling: TSC1, TSC2, FKBP1A, NF1, PTEN, RHEB and MYCBP2.

Methods: The association study included 3006 individuals from 743 Autism Genetic Resource Exchange (AGRE) families comprising 1177 ASD affected cases, as well as 1385 parents and 444 siblings who were either unaffected or had no phenotypic information. A total of 140 single-nucleotide polymorphisms (SNPs) spanning the candidate genes (including 7 rare variants in PTEN) were chosen using pairwise tagging and an R² threshold of 0.8 in HAPMAP. SNPs were genotyped with Sequenom, and Transmission Disequilibrium Test (TDT) was carried out using PLINK.  The deletion event in PTEN was initially detected by specific Mendelian errors in neighboring SNPs, and was later confirmed by real-time quantitative PCR, cloning and sequencing.

Results: Association analysis revealed no significant association of the 7 candidate mTOR pathway genes with ASD. However, an anomalous allele pattern of two adjacent SNPs in intron 1 of PTEN was identified in 21 AGRE families, which could be explained with the hypothetical occurrence of a deletion event. Direct sequencing of the two PTEN SNPs excluded the possibility of simple genotyping error, and quantitative PCR detected a ~50% decreased allele dosage, further strengthening evidence for the PTEN deletion. This is finally confirmed with cloning and sequencing. The PTEN deletion spans 898 bp in intron1, ending at 59 bp upstream of exon2.

Conclusions: An identical deletion of 898 bp in intron 1 of PTEN was found in a subset of ASD families. There was no record in these families of Cowden’s Syndrome, characterized by hamartomatous growths, or a variety of other cancers in which mutations in the PTEN tumor suppressor are implicated. However exclusion of some clinical records in the dataset cannot be ruled out. In addition to a role as a key regulator of the mTOR signaling pathway, PTEN has been implicated in ASD or autistic-like phenotypes in both humans and mouse models. As a next step, it is critical to investigate whether this deletion is associated with ASD, and whether it affects PTEN mRNA expression or processing. If confirmed, these results will break new ground for understanding the pathogenesis of a subset of ASD.