Gene Expression Profiling of PTEN Knockout Embryonic Cultured Neuron Shows Differential Expressed Genes Overlapping with Human Autism Candidate Genes Converging to Common Pathological Pathways

Background:  Patients with PTEN Hamartoma Tumor Syndrome (PHTS) harboring germ line PTEN mutations are known to be associated with autism spectrum disorders (ASDs). Studies in PTEN knockout mice demonstrated defects in different social interaction behaviors and the critical role of the phosphatidylinositol 3-kinase (PI3-K) signaling pathway. Neuromorphological studies showed that PTEN loss could lead to macrocephaly, enlarged neuronal cell bodies with hypertrophic dendrites and axonal tracts with increased number of synapses. Microarray and transcriptomic studies of neurospheres and neural tissues with PTEN loss were reported, respectively. However, the spectrum of downstream genetic elements which govern these neuromorphological and behavioral changes are still not fully characterized.

Objectives:  We sought to determine the gene expression profile of PTEN knockout neurons in order to delineate possible molecular mechanisms underlying the neuropathological changes which lead to ASDs.

Methods:  Primary neurons from E15.5 frontal cortices of wild-type and nestin-positive neural progenitor specific PTEN knockout mice were obtained and cultured for 5 days or 14 days. RNA samples were harvested from three control and three PTEN knockout neurons from littermate mice and analyzed by HiSeq transcriptome sequencing. In order to identify functional pathways affected by PTEN deletion, differential expressed genes (DEGs) were analyzed by gene ontology and pathways enrichment. To further investigate ASDs related pathway dysfunctions, DEGs with q-value <0.05 were compared with ASDs associated genes from the SFARI repository. Common genes from both lists were further analyzed by pathways enrichment.

Results: Over four hundred upregulated and around one hundred downregulated DEGs were identified comparing primary neurons with or without PTEN. Comparing all genes with q<0.05 and ASDs associated genes from the SFARI repository, almost two hundreds common genes were identified. Amongst these, thirty-one DEGs (including both up- and down-regulated) with fold change >2 were identified. Both gene lists converged at common functional pathways – focal adhesion and extracellular matrix-receptor interaction – which are also the top two enriched pathways within individual gene lists.

Conclusions:  Our results show genes and related functional pathways that are perturbed with PTEN deletion in neuron. The comparison with ASDs associated genes helps us to focus on pathways that are commonly shared and affected in ASDs. Furthermore, these results can allow us to focus on genes and molecular pathways that may be responsible for the neuropathological changes. Their further functional characterization may generate novel targets for treating this neurodevelopmental disorder.