Studying the Oncogenic and Epigenetic Impact of CTCF Loss of Heterozygosity and Zinc-Finger 1 Mutation in Breast Cancer

• Main Author: Lebeau, Benjamin
• Format: Dissertation
• Language: English
• Published: ProQuest Dissertations & Theses 01-01-2022
• Subjects: Biochemistry; Biomarkers; Breast cancer; Chromosomes; DNA methylation; Epigenetics; Genetics; Mutation; Oncology
• ISBN: 9798380709392

While epigenetic processes are important drivers of tumor progression, the contribution of deregulated chromatin architecture, including topologically associated domains (TADs), to cancer progression remains ambiguous. CTCF is a central regulator of higher-order chromatin structure that undergoes copy number loss in over half of all breast cancers. Also, mutations of CTCF ZF1 are exclusive to breast cancer and are associated with metastasis and therapeutic resistance. The impact of these CTCF defects on epigenetic programming, chromatin architecture and cancer progression remain unclear. We find that under physiological conditions, CTCF organizes subTADs to limit the expression of oncogenic pathways, including PI3K and cell adhesion networks. Loss of a single CTCF allele potentiates cell invasion through compromised chromatin insulation, a reorganization of chromatin architecture and histone programming that facilitates de novo promoter-enhancer contacts within TADs. However, this change in the higher-order chromatin landscape leads to a vulnerability to inhibitors of mTOR. Next, we developed and employed a novel motif analysis software, MoMotif, to define the previously uncharacterized recognition motif of CTCF zinc-finger 1 (ZF1), and to characterize the impact of CTCF ZF1 mutation on its association with chromatin. Using MoMotif, we identified an extension of the CTCF core binding motif that is recognized by a functional CTCF ZF1. Using a combination of ChIP-Seq and RNA-Seq, we discover that the inability to bind this extended motif drives an altered transcriptional program, here again enriched within TADs, that mimics the harmful oncogenic phenotypes observed clinically. These data support a model whereby subTAD reorganization drives both the modification of histones at de novo enhancer promoter-contacts and transcriptional upregulation of oncogenic transcriptional networks.