Tumor-promoting roles of the chromatin-associated DEK oncogene in metastatic melanoma

As a multifunctional, conserved yet unique non-histone chromatin-architectural factor, the DEK oncoprotein is known to be involved in multiple nuclear processes, including chromatin remodeling, transcriptional regulation, and DNA damage response. Although aberrant DEK expression has been identified in various cancers, its precise mechanistic contribution to tumorigenesis remains incompletely understood. This includes its genome-wide chromatin binding patterns in cancer cells and how this affects chromatin structure and cellular functions. Therefore, the aim of this thesis is to investigate the chromatin binding landscape and functional role of DEK in chromatin organization and transcriptional regulation with a particular focus on phosphorylation-dependent modulation by the casein kinase 2 (CK2) in cancer cells, particularly melanoma cell lines. Using chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq), we first mapped the genome-wide DEK occupancy in HeLa S3 cells and identified DEK binding sites enriched at transcriptionally active genomic regions. Integrative analyses using gene expression microarray and ATAC-seq data sets revealed that DEK knockout led to extensive chromatin accessibility changes and transcriptional reprogramming, including the upregulation of genes involved in melanogenesis and tumor suppression. Notably, DEK functions both as a transcriptional repressor and activator in a context-dependent manner, modulating gene expression through direct promoter binding and distal chromatin interactions. Further comparative profiling in primary melanocytes and several melanoma cell lines revealed distinct cell-type-specific DEK binding patterns between non-tumorigenic and malignant cells, suggesting a role in oncogenic chromatin reprogramming. In addition, epigenomic characterization showed that melanoma subtypes with different mutations exhibited divergent histone modification landscapes, particularly in the distribution of the active enhancer mark H3K27ac. To explore the role of phosphorylation in regulating DEK, the CK2 inhibitor CX-4945 (Silmitasertib) was used in SK-Mel-103 melanoma cells. Combined ChIP-seq and LC-MS/MS analyses showed that CX-4945 reduced overall cellular phosphorylation level, and specifically, sites mapped to serine 287 / 288 in DEK in SK-Mel-103 cells. DEK binding was redistributed across chromatin, with altered gene expression patterns and increased association at regions marked by the repressive histone modification H3K9me3. These changes correlated with elevated chromatin compaction and increased nuclear and cytoplasmic DEK accumulation. These effects were further validated through DEK knockdown experiments, which attenuated CX-4945-induced chromatin compaction and transcriptional repression. Collectively, these findings highlight DEK as a dynamic chromatin architectural protein regulated by phosphorylation and cellular context. By delineating its role in chromatin remodeling, gene regulation, and melanoma progression, this work provides new insights into the mechanisms by which DEK contributes to chromatin regulation and melanoma progression and establishes a foundation for potential therapeutic targeting of the DEK-CK2 regulatory pathway in cancer.