Ontology highlight
ABSTRACT:
PROVIDER: PRJNA148437 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE28335: Melanoma cell culture phenotypes I GSE33727: Melanoma cell culture phenotypes II Refer to individual Series
2011-11-17 | E-GEOD-33728 | biostudies-arrayexpress
Project description:Despite the availabilty of imaging-based and mass-spectrometry-based methods for spatial proteomics, a key challenge remains connecting images with single-cell-resolution protein abundance measurements. Here we introduce Deep Visual Proteomics (DVP), which combines artificial-intelligence-driven image analysis of cellular phenotypes with automated single-cell or single-nucleus laser microdissection and ultra-high-sensitivity mass spectrometry. DVP links protein abundance to complex cellular or subcellular phenotypes while preserving spatial context. By individually excising nuclei from cell culture, we classified distinct cell states with proteomic profiles defined by known and uncharacterized proteins. In an archived primary melanoma tissue, DVP identified spatially resolved proteome changes as normal melanocytes transition to fully invasive melanoma, revealing pathways that change in a spatial manner as cancer progresses, such as mRNA splicing dysregulation in metastatic vertical growth that coincides with reduced interferon signaling and antigen presentation. The ability of DVP to retain precise spatial proteomic information in the tissue context has implications for the molecular profiling of clinical samples.
2022-04-27 | PXD023904 | Pride
Project description:In vivo, melanoma cells transition though distinct phenotypic states in response to a changing microenvironment, and most notably can switch between invasive and proliferative phenotypes characterized by high and low levels of MITF activity (Hoek and Goding, 2010; Hoek et al., 2008). Since melanoma cell lines isolated from human tumors tend also to fall into either proliferative or invasive, slow-growing phenotypes (Hoek et al., 2006), it seems likely that established lines reflect specific phenotypic states within tumors, including those detected using single cell RNA-seq, that are then fixed and maintained under nutrient–rich culture conditions where the microenvironmental stresses encountered in vivo are absent. Indeed, it has been shown that melanoma cell lines presenting distinct phenotypic states exhibit very different responses to microenvironmental cues such as hypoxia (Louphrasitthiphol et al., 2019). The aim of this study is to characterise some of the commonly use cell lines and assign each with a phenotypic state base on its transcriptomics.
2019-10-16 | GSE137391 | GEO
Project description:SOX9 manipulation in human melanoma cell culture
| PRJNA843328 | ENA
Project description:It is generally accepted that human cancers derive from a mutated single cell. However, the genetic steps characterizing various stages of progression remain unclear. Studying a unique case of metastatic melanoma, we observed that cell lines derived from metachronous metastases arising over a decade retained a central core of genetic stability in spite of divergent phenotypes. In the present study we expanded our previous observations comparing these autologous cell lines of clonal derivation with heterologous ones and correlated array Comparative Genomic Hybridization (aCGH) with gene expression profiling to determine their relative contribution to the dynamics of disease progression. aCGH and gene expression profiling were performed on autologous cell lines and heterologous melanoma cell lines originated from other patients. A striking correlation existed between total extent of genetic imbalances, global transcriptional patterns and cellular phenotypes; they did not follow a strict temporal progression but stemmed independently at various time points from a central core of genetic stability best explained according to the cancer stem cell hypothesis; although their contribution was intertwined, genomic imbalances detectable by aCGH contributed only 25% of the transcriptional traits determining autologous tumors distinctiveness. Our study provides important insights about the dynamics of cancer progression and supports the development of targeted anti-cancer therapies against stable genetic factors determining the individuality of each patientâs disease that are maintained throughout the end stage of disease. Keywords: genetic modification design PBMC from a female donor were Ficoll gradient separated and used throughout the study as reference.. Validation of array CGH accuracy was done by obtaining six additional PBMC from female donors and six PBMC from male donors to confirm stability of gene representation in autosomes and sex-determined imbalances within the X and Y chromosome regions. Five melanoma cell lines were generated from distinct cutaneous melanoma metastases that progressively appeared in patient 888. Other melanoma cell lines were generated from cutaneous melanoma metastases from other patients. The melanoma cell line A375 was purchased from the American Type Culture Collection. For each cell line arrayCGh has been performed.
2010-05-25 | E-GEOD-8777 | biostudies-arrayexpress
Project description:Human low passage melanoma cell lines were compared after 24h culture alone or in presence of melanoma-specific CD8+ T cell clones
2016-08-30 | GSE79991 | GEO
Project description:Transcriptomic analysis of short term melanoma cell culture
| PRJNA1128029 | ENA
Project description:The use of patient-derived primary cell cultures in cancer preclinical assays, including drug screens and genotoxic studies, has increased in recent years. However, their translational value is constrained by several limitations, including variability that can be caused by the culture conditions. Here, we show that the medium composition commonly used to propagate primary melanoma cultures has limited their representability of their tumor of origin, their cellular plasticity and modified their sensitivity to therapy. We established and compared cultures from different melanoma patients propagated in parallel in low-tyrosine (Ham’s F10) or, in high-tyrosine (Ham’s F10 supplemented with tyrosine, RPMI/DMEM) media. Tyrosine is the precursor of melanin biosynthesis, a process particularly active in differentiated melanocytes and melanoma cells. Unexpectedly, we found that the high tyrosine concentrations promoted an early phenotypic drift towards either a mesenchymal-like or senescence-like phenotype, and prevented the establishment of cultures of melanoma cells harboring differentiated features, which we show are frequently present in human clinical biopsies. Moreover, the invasive phenotype emerging in these culture conditions appeared irreversible and, as expected, associated with intrinsic resistance to MAPKi. In sharp contrast, differentiated melanoma cell cultures retained their phenotypes upon propagation in low-tyrosine medium, and importantly their phenotypic plasticity, a key hallmark of melanoma cells. Our findings underline the importance of culturing melanoma cells in low-tyrosine-containing medium in order to preserve their phenotypic identity of origin and cellular plasticity.
2021-11-03 | GSE171456 | GEO