Abstract
Melanoma, a neural crest-derived cancer, exemplifies the complex interplay of genetic and non-genetic factors driving tumor progression, therapeutic resistance, and phenotypic plasticity. Central to this adaptability is SOX10, a master regulator of neural crest development and melanocyte differentiation, whose expression is controlled by enhancer elements that are reactivated in melanoma. This work provides a comprehensive investigation into the regulatory landscape of SOX10, integrating insights from zebrafish models, human melanoma cell lines, and comparative genomics to uncover the mechanisms underlying SOX10 enhancer activity during development and cancer progression. Using zebrafish as a model system, we identified and validated multiple SOX10 enhancer elements through ATAC-seq, CRISPR-mediated deletions, and enhancer-reporter assays. These studies revealed the spatiotemporal roles of individual enhancers in neural crest development and their reactivation in melanoma. Functional characterization of these enhancers highlighted their critical contributions to SOX10 expression, melanoma cell identity, and the dynamic process of phenotype switching, where melanoma cells transition between drug-sensitive and drug-resistant states. In human melanoma cell lines, deletion of conserved SOX10 enhancer elements led to significant transcriptional and phenotypic shifts, driving cells toward a more invasive, mesenchymal-like state associated with increased drug resistance. RNA-seq and gene set enrichment analyses identified key regulatory networks and candidate genes, that mediate these transitions. Notably, NTRK1 emerged as a promising therapeutic target, with its inhibition restoring drug sensitivity in phenotype-switched, resistant cells. This study further demonstrated the translational potential of cross-species genomic approaches by identifying human SOX10 enhancer elements with conserved functionality in zebrafish. Leveraging CRISPR-based tools, we established a workflow for dissecting enhancer activity and modulating gene expression with precision, offering a scalable method to uncover regulatory mechanisms in development and disease. By elucidating the role of SOX10 enhancers in melanoma plasticity and phenotype switching, this work advances our understanding of the epigenetic regulation of melanoma progression. It provides a foundation for developing novel therapeutic strategies that target enhancer elements to modulate melanoma cell states, combat drug resistance, and improve patient outcomes. This integrative approach underscores the critical importance of regulatory elements in shaping cellular identity, offering new avenues for intervention in melanoma and other neural crest-derived cancers.
Committee Chair
Charles Kaufman
Committee Members
Kristen Kroll; Lavinia Sheets; Michael Meers; Thor Theunnissen
Degree
Doctor of Philosophy (PhD)
Author's Department
Biology & Biomedical Sciences (Molecular Cell Biology)
Document Type
Dissertation
Date of Award
5-8-2025
Language
English (en)
DOI
https://doi.org/10.7936/zq13-nf93
Author's ORCID
https://orcid.org/0000-0002-2558-4829
Recommended Citation
DeGeorgia, Sophia Noah, "Tank to Bedside: How insights from zebrafish inform our understanding of human melanoma drug resistance" (2025). Arts & Sciences Theses and Dissertations. 3552.
The definitive version is available at https://doi.org/10.7936/zq13-nf93