Author ORCID Identifier

https://orcid.org/0000-0003-1042-503X

Date of Award

2026

Document Type

Thesis (Ph.D.)

Department or Program

Cancer Biology

First Advisor

Brock C. Christensen

Abstract

Epithelial-mesenchymal transition (EMT) is increasingly recognized as a dynamic spectrum of cellular programthat contributes to tumor progression, metastasis, and therapeutic resistance. Rather than existing as discrete epithelial or mesenchymal phenotypes, tumor cells undergo intermediate EMT states in which epithelial and mesenchymal features are partially and variably expressed. In this thesis, I studied EMT state heterogeneity through two complementary and integrated dimensions: tumor-immune interactions and the dynamic remodeling of epigenetic programs across the EMT spectrum. Using a clonal EMT model derived from the murine triple-negative 4T1 mammary carcinoma cell line, including epithelial, intermediate, and mesenchymal states that are stably maintained in vivo, I first demonstrate that EMT progression is associated with a graded suppression of tumor immunogenicity. Single-cell transcriptomic profiling of orthotopic tumors reveals progressive downregulation of antigen presentation pathways and a coordinated decline in CD8+ T cell and NK cell infiltration and function, alongside a shift in B cell composition. In parallel, genome-scale DNA methylation profiling across in vitro cell states, primary tumors, and spontaneous lung metastases reveals that EMT progression is accompanied by global hypomethylation and the acquisition of distinct, intermediate-state–specific methylation programs. These intermediate EMT methylation signatures are largely preserved during primary tumor growth and partially retained in metastatic lesions. Conserved hypomethylated CpGs in intermediate states are enriched at binding sites of chromatin regulators such as MBD2 and SMARCB1. To address the challenge of cellular heterogeneity in bulk epigenomic data, I further applied DNA methylation–based deconvolution approaches to mouse tumor samples, enabling estimation of tumor burden and immune composition in primary tumors and metastatic lesions. Together, these findings describe EMT-associated heterogeneity at both the transcriptomic and epigenetic levels, illustrating EMT as a spectrum characterized by graded transcriptional changes and distinct DNA methylation programs. This work provides a framework for understanding the connection between EMT progression, immune suppression, and epigenetic remodeling, with broader implications for the identification of EMT-related therapeutic targets in breast cancer and other epithelial malignancies.

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