During my research internship in Bosnakovski Lab in the Department of Pediatrics at the University of Minnesota, I focused on investigating genes encoding surface proteins related to CIC-DUX4 sarcoma (CDS), a rare and aggressive pediatric cancer with a median survival of less than two years.
Throughout my research, I conducted Differential Experssion analysis on generated cell lines and tumor samples using DESeq2 and texima packages. This analytical approach enabled the identification of genes exhibiting altered expression levels. The multiple test correction was undertaken using the Benjamini and Hochberg method, with a stringent criterion of adjusted p-value < 0.05. I also crafted impactful visual aids, including heatmaps, volcano plots, and waterfall plots. These tools played a pivotal role in conveying the intricacies of gene expression patterns, making the research findings accessible and comprehensible to a broader audience. One of the highlights of this research endeavor was the identification of a subset of 19 genes, characterized by their dual attributes: inclusion in the surfaceome gene repertoire and consistent differential expression across cell lines following iP300w treatment. These genes represent a promising next step for further exploration and potential antibody development to CDS.
I was honored to present this study at the Masonic Cancer Center Research Symposium 2023 and 2024 Joint Mathematics Meetings (JMM). Here is my poster.
