Phosphatase and tensin homolog (Pten) is a tumor suppressor gene that is knocked out or mutated in many cancers. Additionally, knocking out this gene in mice causes cataracts and other developmental issues with the lens. This project involves analyzing differential gene expression in the form of RNAseq data encompassing the entire transcriptome of the lens from mice with lens-specific knockout of Pten. From this we hope to answer the question of what are the actual molecular pathways Pten is regulating in lens development by determining its downstream effects. Elucidating the actual pathways that are responsible for Pten’s effect on lens development will be instrumental in future research that seeks to treat diseases that result in abnormally small or misshapen lenses such as microphakia and aphakia. In order to begin analysis of the transcriptome, significantly differentially expressed genes were determined using Excel after filtering out data based on parameters for significance, in order to compile a list of up or down regulated genes. They were then analyzed using gene ontology (GO) term analysis (Metascape) in order to determine GO terms that could give us insight into which molecular pathways are involved. The GO term analysis revealed that genes associated with the negative regulation of epithelial cell proliferation, as well as the Wnt signaling pathway were significantly downregulated. One of these genes, Gata3, has been implicated in recent literature to be involved in regulation of cyclin dependent kinase inhibitors that results in increased proliferation, so it is plausible that the absence of Pten is responsible for this change. However, the differential expression of these genes must be confirmed in future research using RT-qPCR. This work has been extremely valuable to my future career in medicine, in which I plan to do research that will likely involve the interpretation of bioinformatics data.
Author: David Dieker
Faculty Advisor: Dr. Michael Robinson, Biology
Graduate Student Advisor: Anil Upreti, Biology
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