Investigation of the regulatory role of CBX2 in breast cancer via in silico transcriptomic analysis and in vitro cistromic analysis

Kalsi, Shannon Cartay

Abstract

Chromobox 2 (CBX2) is a component of Polycomb repressive protein complex 1 (PRC1), which is an epigenetic regulatory complex that downregulates the expression of target genes. CBX2 has been linked to cancer progression and development in several cancer types, with evidence showing it may play a role in a particularly aggressive form of breast cancer called triple-negative breast cancer (TNBC). TNBC is highly metastatic, has a poor prognosis and suffers from a lack of targeted therapeutics.

This study aimed to identify oncogenic processes regulated by CBX2 in breast cancer to aid further understanding of its potential role in this disease. Oncogenic pathways putatively regulated by CBX2 were determined via bioinformatic analysis of publicly available patient datasets using Gene Set Enrichment Analysis(GSEA) and analysis of RNA-sequencing data from a TNBC cell line (MDA-MB-231).

In silico analysis showed that CBX2 was upregulated in TNBC compared to normal breast tissue and elevated levels of CBX2 expression were associated with a decrease in overall survival (OS) and disease-free survival (DFS) in breast cancer. Our research identified that CBX2 was associated with upregulation of E2F and mTORC1 signalling pathways. Analysis of RNA sequencing data from MDAMB-231 cells, which were depleted of CBX2, showed upregulation of genes that code for inhibitors of E2F (RBL2) and mTORC1 (TSC1, TSC2 and PRKAA2) signalling, indicating that CBX2 represses the expression of these putative tumour suppressor genes in TNBC. Chromatin immunoprecipitation and CUTandRUN analysis in MDA-MB-231 cells indicated that CBX2 was bound to the promotor regions of RBL2, TSC1 and PRKAA2, indicating that CBX2 may directly regulate the expression of these genes.

Overall, this analysis identified oncogenic processes regulated by CBX2 in TNBC, and for the first time identified the potential mechanism by which CBX2 promotes these pathways. This knowledge is crucial to understand the specific role of CBX2 in TNBC and to aid investigations of CBX2 as a potentially novel therapeutic target.

Citation

Kalsi, S. C. Investigation of the regulatory role of CBX2 in breast cancer via in silico transcriptomic analysis and in vitro cistromic analysis. (Thesis). University of Hull. https://hull-repository.worktribe.com/output/4224331

• Thesis Type: Thesis
• Deposit Date: Oct 6, 2022
• Publicly Available Date: Feb 24, 2023
• Keywords: Biomedical sciences
• Public URL: https://hull-repository.worktribe.com/output/4224331
• Additional Information: Department of Biomedical Sciences, The University of Hull
• Award Date: Sep 1, 2021