Author ORCID Identifier

0000-0002-1440-7165

Date of Graduation

12-2025

Document Type

Dissertation (PhD)

Program Affiliation

Genetics and Epigenetics

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

Kunal Rai

Committee Member

Mark Bedford

Committee Member

Jeffrey Chang

Committee Member

Kyle Eagen

Committee Member

Nicholas Navin

Abstract

Functional states of the genome are dictated by chromosomal interactions through 3D genome folding. While its role in tumorigenesis is becoming clearer, its contribution to metastasis has yet to be explored. In this thesis, I investigate how chromatin architecture influences melanoma progression, given its aggressive metastatic behavior. The transition to metastasis requires cellular plasticity, including changes in cell state such as epithelial-to-mesenchymal transition, suggesting a role for epigenomic remodeling. However, whether chromosome looping directly influences metastatic cell fate decisions is unclear. Mammalian genomes are organized into Topologically Associating Domains (TADs), insulated regions maintained by CTCF and cohesin that regulate enhancer-promoter (E-P) interactions. Disruption of these domains and loops alters gene expression and contributes to cancer progression. Here, I identify significant alterations in chromatin looping between primary and metastatic melanoma, implicating 3D genome remodeling in metastatic potential.

One of the central discoveries of this thesis is the role of super-enhancer looping in mediating inflammatory signaling and immune evasion in disseminated tumor cells. The mechanisms underlying organotropic colonization during metastasis remain poorly understood. I demonstrate that reprogrammed three-dimensional chromatin structure of metastatic melanoma cells contributes to this process. Using a newly developed aggressive melanoma model, I establish that chromatin reorganization facilitates survival and growth of disseminated tumor cells within the lung metastatic niche, in part by promoting immune evasion. These adaptations involve chromatin hyperacetylation, AP-1 transcription factor enrichment, and promiscuous intrachromosomal interactions. Specifically, I identify two de novo long-range super-enhancer loops of clinical relevance that establish regulatory hubs encompassing interferon response and pro-survival genes. Epigenetic editing of a single super-enhancer anchor silences the metastatic-specific hub, resulting in coordinated downregulation of genes within the loop, increased susceptibility to CD8⁺ T cell cytotoxicity, attenuated lung metastasis, and improved host survival. While these findings support a role for these loops in immune modulation, they may also contribute to metastatic fitness through additional mechanisms such as survival and metabolic reprogramming. Collectively, this study reveals that tumor-intrinsic chromatin loop function via a novel action-at-a-distance super-enhancer model contributes to melanoma lung colonization, positioning 3D genome reorganization as a potential therapeutic vulnerability that may extend to other metastatic cancers.

To further define higher order chromatin organization in the context of melanoma progression, I performed an unbiased comparative analysis of loop domains across a cohort of patient-matched primary and metastatic melanomas. This resulted in identification of conserved metastatic TAD disruptions (splits) that epigenetically misregulated the expression of clustered protocadherins (cPCDH) via CTCF rewiring. Epigenetic silencing of these CTCF sites resulted in alterations in adhesion-migration dynamics of melanoma cells.

This thesis is the first to describe the contribution of chromosomal looping in the context of melanoma metastasis. By integrating chromatin conformation capture techniques with functional epigenetic perturbation studies, I show that spatial genome reorganization supports metastatic fitness through features such as immune evasion and transcriptional control. These findings provide a framework for understanding how chromatin architecture influences metastasis and illuminate alternative therapeutic modalities for metastatic melanoma.

Keywords

3D Genome, Epigenetic Editing, Metastatic Melanoma, Enhancer Biology, Fitness, Chromatin States, Transcriptional Hub, CTCF, Immune Evasion, Metastatic Fitness

Download

Available for download on Friday, May 08, 2026

Share

COinS