Gene Expression Associated with Acute myeloid leukemia using Gene Enrichment Analysis (GSEA)

Yohana Alemseged

Mentors: Dr. Laura Harris, Harris Interdisciplinary Research 

Date/Time: August 23rd, 2022 at 2:00pm.

Abstract: Gene expression is a powerful process which uses the information encoded in a gene to make an RNA molecule that codes proteins that serve many functions in the cell. In this study I selected Acute myeloid leukemia (AML), which is the most severe form of Cancer a heterogeneous clonal disorder of hematopoietic Stem/progenitor cells featured by excessive proliferation and subsequent accumulation of immature myeloid blasts, followed by impaired hematopoiesis in the bone marrow. The Data GSE 122917 was taken from National Cancer Biotechnology Information (NCBI). The study was to compare the mRNA expression profile of bone marrow mesenchymal stromal cells from newly diagnosed to the relapsed patient to identify the gene that are under expressed and over expressed. A python script was used which is Computational Meta-analysis approaches to examine differential gene expression pathways activity changes associated with altered states of cellular physiology. The healthy donor was used as a control whereas the AML and the relapsed patient samples were experimental.  Z-score first obtained to get the T-score. The python script gives an output of gene signature, leading edges for each signature. GSEA revealed that 126 genes are over-expressed, For the most under-expressed gene were 119 genes most surprisingly most of the genes are related to AML. Database for Annotation Visualization and Integrated Discovery (DAVID) was used to investigate the biological function of each gene compared to a large list of genes. The genes that are over-expressed are related more to the genes in lysosomes. Whereas the majority of the genes in the under-expressed correlated to the genes in the nucleus. Overall, the main goal of the study is to increase the treatment response rate and put AML into a complete remission.