Transcriptome-(Phospho)proteome Characterization of the Brain of a Constitutional Model of Cytoplasmic-predominant Pten Expression With Autism-Like Phenotypes

Abstract

BackgroundPTEN, a well-studied tumor suppressor, has one of the strongest Mendelian associations with autism spectrum disorder (ASD), representing a special case in autism’s complex genetic architecture. Animal modeling for constitutional Pten mutation creates an opportunity to study how disruption of Pten affects neurobiology, providing insights that may be generalizable or at least inform our understanding of ASD. Although the neural transcriptome has been well characterized in Pten models, little has been done concerning the proteome and phosphoproteome. This is a critical gap in knowledge given that these –omic landscapes are more proximal to the actively observed biology than the transcriptome.MethodsWe sought to comprehensively characterize the neural proteome and phosphoproteome of the Ptenm3m4/m3m4 mouse, which exhibits cytoplasmic-predominant Pten expression. Proteomic and phosphoproteomic scans of Ptenm3m4/m3m4 and wildtype mouse brain at two-weeks- (P14) and six-weeks-of-age (P40) were performed using liquid chromatography with tandem mass spectrometry technology. Following quantification of differentially expressed/phosphorylated proteins, we performed gene overlap, gene enrichment, pathway, and network analyses to identify the similarity across the various datasets and understand the affected biological landscape.ResultsWe identified numerous differentially expressed/phosphorylated proteins, finding that dysregulation was greater at P40, consistent with the prior neural transcriptome data. We found the affected biological pathways were largely related to PTEN function, neurological processes, or neuroinflammation. Although we found minimal overlap among differentially expressed transcriptome-proteome-phosphoproteome molecules between P14 and P40 brains, there was congruence amongst the affected pathways. Importantly, network analysis identified Pten and Psd-95 as predominant regulatory nodes in the proteome and phosphoproteome, respectively. Moreover, we found overlap between our differentially expressed/phosphorylated proteins and known ASD risk genes.ConclusionsDifferential expression/phosphorylation revealed by transcriptome-proteome/phosphoproteome analyses of a germline Pten mutation model point to ASD risk genes like Pten and Psd-95 as major hubs in the protein networks, highlighting their important regulatory influence. Our observations here suggest Pten and Psd-95, known interactors in biological networks in the brain, are critical to either initiation or maintenance of cellular and perhaps organismal phenotypes related to ASD. Future research should explore rescuing Pten and Psd-95 function in attempts to ameliorate neurological pathologies and behavioral abnormalities.