Author ORCID Identifier
Date of Graduation
8-2023
Document Type
Thesis (MS)
Program Affiliation
Quantitative Sciences
Degree Name
Masters of Science (MS)
Advisor/Committee Chair
Wenbo Li
Committee Member
Ken Chen
Committee Member
Peter Van Loo
Committee Member
Nidhi Sahni
Committee Member
Krishna Bhat
Abstract
Recent advances in cancer genetics found that strong oncogene transcription can occur on a form of non-chromosome DNAs that is often amplified to tens or hundreds of copies, and that can exist in more than half of cancer types. This type of genetic material was termed extrachromosomal DNA (ecDNA). ecDNA appears to be epigenetically highly accessible and transcriptionally active compared with chromosomal DNA, which may partially underlie their critical roles in driving oncogene overexpression and cancer evolution. However, the full molecular mechanisms and regulators that confer the exceptional transcriptional activity of ecDNA-associated genes are incompletely understood.
Enhancers are key genetic elements that drive tissue-specific and sometimes cancer-type-specific gene expression programs. How enhancers mechanistically achieve so remains an active area of research. Transcriptome analysis found that active enhancers often generate ncRNAs that are termed enhancer RNAs (eRNAs). Emerging studies illustrated that at least some eRNAs can recruit transcriptional regulatory proteins and promote enhancer-promoter interaction to enhance the transcription of the target genes. In cancers, the dysregulation of eRNAs is associated with tumorigenesis and cancer progression.
Given the special biological features of ecDNA in cancer and important roles of some eRNAs, we aim to dissect the landscape and functions of ecDNA-derived enhancer RNA in glioblastoma (GBM). GBM is a devastating cancer type that requires mechanistic knowledge of its development and progression. Understanding ecDNA and eRNA related mechanisms in GBM gene regulation will provide new knowledge and potentially new diagnostic or therapeutic targets. Our analysis of whole genome sequencing (WGS) of GBM tumors revealed tens of ecDNAs that exist in specific GBMs, including one dominant ecDNA that harbors EGFR gene and its associated noncoding regions (referred to as ecEGFR). Further analysis coupled with RNA-seq identified an enhancer RNA frequently co-amplified with ecEGFR, termed as EGFRe. Moreover, EGFRe showed significant overexpression and elevated transcriptional activity in ecEGFR-positive samples. To deepen the understanding of the expression patterns of EGFRe at higher resolution, our single cell analysis based on 150,223 cells confirmed that EGFRe were uniquely overexpressed by tumor cells from ecEGFR+ samples. Additionally, we observed strong correlation between EGFRe overexpression and astrocyte-like cell state, as well as cell cycle pathways. Lastly, we conducted expression quantification of eRNAs in glioblastoma stem cell (GSC) models using qPCR and TT-seq, confirming the existence of EGFRe.
Keywords
ecDNA, cancer genomics, non-coding RNA