Browsing by Author "Afshar, Ulduz Sobhi."

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    Genome-wide localisation analysis for IRF4 target gene identification in melanoma cell lines
    (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2015., 2015.) Afshar, Ulduz Sobhi.; Emre, Tolga.
    Interferon Regulatory Factor 4 (IRF4) is a key transcription factor in development and function of immune cells. Also it has been shown that elevated IRF4 expression is a key factor for survival in some myeloid and lymphoid cancers. Recently, studies have shown IRF4 expression also in non-immune cells and malignancies such as melanocytes and melanoma. Studies from our lab and elsewhere demonstrated elevated expression levels of IRF4 is critical for melanocytes and melanoma cell lines. There is lack of knowledge about IRF4 regulated genes in melanoma, so we aimed at identi cation of its localization genome-wide using high-throughput sequencing of immunoprecipitated chromatin (ChIP-seq). First, we established and optimized ChIPqPCR (Chromatin immunoprecipitation coupled with quantitative polymerase chain reaction) experiments in our lab and con rmed several IRF4 binding regions in di erent loci such as Tyrosinase, a key developmental gene in melanocytes. Then, we performed ChIP-seq to identify IRF4 target genes genome-wide in a melanoma cell line. We set up a bioinformatics pipeline and analysed the ChIP-seq data to nd putative IRF4 binding regions and their associated genes. Afterwards, we characterized DNA motifs, associated genes, pathways and biological processes. Our results integrated with previous RNA-seq data suggests that IRF4 is regulating genes related to cell cycle and proliferation, and in cellular transport system.
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    IRF4-driven epigenetic changes in melanoma cells : understanding downstream effects for targeted therapy
    (Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2023., 2023) Afshar, Ulduz Sobhi.; Emre, Tolga.
    Despite recent advances in melanoma treatment, mortality rates for metastatic melanoma remain high, which indicates the need to identify new melanoma-critical genes and novel targeted therapies. Melanoma, like other cancers, is driven by driver mutations and the deregulation of epigenome and signaling pathways. Transcription factor IRF4 has been identified as a pivotal player in the development and maintenance of different cells, such as immune cells and melanocytes. Studies showed that IRF4 is an essential component of the survival and maintenance of hematopoietic cancers such as multiple myeloma. Different GWAS studies indicate a strong link between a variation in the IRF4 intronic region with pigmentation in melanocytes and predisposition to melanoma. In this thesis, analysis of patient data from The Cancer Genome Atlas and the integration of RNA-seq and ChIP-seq approaches have led to the identification of IRF4-regulated genes and pathways. Our data demonstrate that IRF4 is a modulator of epigenetic silencing in melanoma. Furthermore, we report that IRF4 is a key modulator of DNA methylation machinery and polycomb repressive complex, which subsequently results in global changes in the epigenetic suppressive marks in the cells. Also, we identify a subset of tumor suppressor genes (TSG) silenced through IRF4-mediated changes of these epigenetic marks. These TSGs are regulators of the cell cycle, PI3K-AKT pathway, and ciliogenesis in melanoma. Moreover, with CRISPR knockout screening, we set out to discover IRF4 synthetic lethal partners. Consistent with our findings, the screening results suggest a critical role for IRF4 as a regulator of the cell cycle and homeostasis pathways in melanoma cells.