Project description:This SuperSeries is composed of the following subset Series: GSE17349: Expression data for melanoma short-term cultures and cell lines GSE17359: Affymetrix SNP array data for 3 melanoma short-term cultures and cell lines GSE20156: RNA-Seq of melanoma short-term cultures and cell lines Refer to individual Series
Project description:Uveal melanoma cell lines and short-term cultures of human uveal melanoma cells from biopsy samples were treated with 100 nM FR900359 or vehicle. RNA-seq was performed.
Project description:We profiled the gene expression levels from 8 melanoma short-term cultures and 1 melanoma cell line in order to compare to expression level estimates obtained by RNA-seq.
Project description:Brain metastasis is a significant cause of morbidity and mortality in multiple cancer types and represents an unmet clinical need. The mechanisms that mediate metastatic cancer growth in the brain parenchyma are largely unknown. Melanoma, which has the highest rate of brain metastasis among common cancer types, is an ideal model to study how cancer cells adapt to the brain parenchyma. We utilized pairs of brain metastasis-derived (BM) and non-brain metastasis-derived (NBM) melanoma short term cultures (STCs) obtained from the same patient. We performed TMT based multiplexed analysis of these cell lines using off-line fractionation to increase our proteomics coverage. Our unbiased proteomics analysis of these melanoma short-term cultures revealed that proteins implicated in neurodegenerative pathologies are differentially expressed in melanoma cells explanted from brain metastases compared to those derived from extracranial metastases. We showed that melanoma cells require amyloid beta for growth and survival in the brain parenchyma. Melanoma-secreted A beta activates surrounding astrocytes to a pro-metastatic, anti-inflammatory phenotype and prevents phagocytosis of melanoma by microglia. Finally, we demonstrate that pharmacological inhibition of Abeta decreases brain metastatic burden.
Project description:Investigation of expression differences induced by expression of the histone methyltransferase SETDB1 in human melanoma short-term culture WM451-Lu. A six-chip study using total RNA prepared from WM451-Lu melanoma short-term cultures infected with either a lentivirus encoding GFP (control) or SETDB1. Cells were allowed to grow for 2 days post-infection.
Project description:Histone post-translational modifications (PTMs) generate a complex combinatorial code that regulate gene expression and nuclear functions, and whose deregulation has been documented in different types of cancers. Therefore, the availability of relevant culture models that can be manipulated and that retain the epigenetic features of the tissue of origin is absolutely crucial for studying epigenetic mechanisms underlying cancer, as well as for testing epigenetic drugs and uncovering possible epigenetic biomarkers. In this study, we took advantage of quantitative mass spectrometry to comprehensively profile histone PTMss in patient tumor tissues, primary cultures and cell lines from two representative tumor models, breast cancer and glioblastoma, revealing a dramatic and systematic rewiring of histone marks in cell culture conditions, which include a decrease of H3K27me3, H3K79me1/me2 and H3K9ac/K14ac, and an increase of H3K36me1/me2. While some changes occurr in short-term primary cultures, most of them are instead time-dependent and appear only in long-term cultures. Remarkably, such change mostly revert in cell line- and primary cell-derived in vivo xenograft models. Our results support the use of short-term cultures and xenografts models as the most representative models of in vivo epigenetic processes, and suggest cautions when using cell lines and long-term primary cultures for epigenetic investigations.