Discipline: Biological Sciences
Subcategory: Genetics
Session: 1
Room: Exhibit Hall A
Ceveta E. Sieh - Clark Atlanta University
Co-Author(s): Andrea Chaney, Clark Atlanta University, Atlanta, GA; Alira Danaher, Clark Atlanta University, Atlanta, GA; Nathan J. Bowen, Clark Atlanta University, Atlanta, GA
The transcription of Zic family member 2 (ZIC2) is aberrantly increased in many types of cancer cells relative to the epithelial cells found in matched healthy tissue. We hypothesize that aberrant increased ZIC2 expression contributes to cancer initiation and progression. Currently, we are investigating ZIC2 expression in E006AA cells. E006AA cells are reported to be prostate cancer cells derived from an African American man. However, some reports have questioned both the prostate and African American origins of these cells. The ZIC2 locus was edited by CRISPR-Cas9 gene editing in E006AA resulting in a deletion of the translation start site of ZIC2. The loss of ZIC2 protein expression was verified by immunoblotting analysis. The ZIC2 edited cells were shown to replicate significantly slower than the unedited parental cells. In order to further explain how the loss of ZIC2 contributed to these altered phenotypes, we performed RNA-sequencing on the ZIC2 edited cells. We intersected the RNA-seq results with publicly available chromatin immunoprecipitation sequencing (ChIP-Seq) data from ZIC2 knockout HCT116 colon cancer cells to identify genes that are putative direct transcriptional targets of ZIC2 in E006AA cells. Gene Set Enrichment Analysis of the differentially expressed genes revealed that pathways involved in mitochondrial activity and cholesterol synthesis were altered in the absence of ZIC2. We also compared the RNA-Seq gene expression profile from E006AA to RNA-Seq profiles from other cancer cell lines in order to identify the most likely tissue of origin of the E006AA cells. In an attempt to compare the geographic ancestry of the E006AA cells to previously published reports, we performed genotype analysis on the RNA-Seq data that we produced on E006AA. The E006AA genotype was analyzed for similarity to known populations worldwide. Here, we present our analyses and discuss their implications for research based on the E006AA cell line. Research in the Bowen lab is supported by NSF Grant #1623287, NIH/NIMHD/RCMI Grant #5 G12 MD007590 and NIH/NIMHD/P20 Grant #2P20MD002285.
Funder Acknowledgement(s): NSF Grant #1623287; NIH/NIMHD/RCMI Grant #5 G12 MD007590; NIH/NIMHD/P20 Grant #2P20MD002285
Faculty Advisor: Nathan J Bowen, nbowen@cau.edu
Role: I analyzed the transcriptome of E006AA using computational methods to identify similarity to other cell transcriptomes and to identify genotype similarity to world populations.