Poster #67 - Colette Trouillot

Multiomics Analysis of Impact of Increased FOXD3 Expression in BRAF-Mutant Melanoma

Colette E. Trouillot, M.S.[1,2]; Will Madden, B.S.[1]; Glenn Mersky, M.S.[1]; Dan A. Erkes, PhD [1]; Scott Varney, PhD [1]; Timothy J. Purwin, PhD [1]; and Andrew E. Aplin [1,3] 1Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19017, USA 2 School of Biomedical Engineering, Science & Health Systems, Drexel University, Philadelphia, PA 19104, USA. 3 Sidney Kimmel Comprehensive Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.

Despite advances in immune checkpoint and mitogen activated protein kinase (MAPK) pathway inhibitor therapies for cutaneous melanoma patients, resistance and relapse still occur. Roughly 50% of melanomas have activating mutations in v-Raf murine sarcoma viral oncogene homolog B (BRAF), but additional mutations that can impact treatment efficacy occur such as phosphatase and tensin homolog (PTEN), tumor protein 53 (p53) and protein kinase B (AKT1, AKT2, and AKT3). MAPK inhibitor (MAPKi) treatment is FDA-approved for treating BRAF V600E mutant melanomas. The neural crest transcription factor forkhead box D3 (FOXD3), typically lowly expressed in melanoma cell lines, increases during MAPKi treatment, but how FOXD3 upregulation promotes resistance is still unknown. While some genes regulated by FOXD3 have been determined, the full breadth of genes and their downstream effects remain to be determined. We used RNA-sequencing (RNA-seq) data from inducibly expressed FOXD3 melanoma cell lines to identify activated and repressed gene signatures for FOXD3. Enrichment analysis confirmed the repressed gene signature in bulk and single cell RNA-seq data. Gene signature scoring of additional publicly available RNA-seq data confirmed that regardless of the existence of these additional mutations, FOXD3 expression increases with MAPKi treatment. This expression diverges as the cells become resistant to MAPKi treatment. This effect was seen not only in cell line data, but also patient data when comparing tumors that remain responsive to drug versus those that become resistant. Furthermore, we also observed diverging behavior of FOXD3 within a cell line as it becomes resistant. Additional analyses suggest that hyperactivation of MAPK pathway leads to decreased FOXD3 expression in resistant cell lines. Previous research suggests mutations driving MAPKi resistance occur not only between different cell lines but also within an individual cell line; therefore, we will perform variant analysis to understand the interplay of variants and FOXD3 in melanoma resistance.