Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomics profiling of some commonly used cell lines at the base-line culture condition

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE137391 | GEO | 2019/10/16

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Proteomic profiling of exosomes isolated from invasive and proliferative melanoma cell lines and correlation with exosomes from plasma of human melanoma patients pre- and post-checkpoint inhibitor treatment

Project description:Over the last decades, exosomes have received increasing attention due to their involvement in numerous pathologies including cancer. Tumor-derived exosomes and exosomes derived from the tumor microenvironment are implicated in multiple mechanisms that support disease progression such as the escape of malignant cells from immunosurveillance, tumor cell growth, tumor angiogenesis, preparation of a pre-metastatic niche and remodeling of the extracellular matrix, thereby promoting dissemination and metastasis. Here, we performed protein expression phenotyping of exosomes derived from different invasive and proliferative melanoma cell lines (n=8) to provide a solid framework of gene expression programs, which - in a clinical setting - would be useful for prognosis and may also predict treatment response. Cell line characteristics have been published previously (Wenzina et al.,2020). Having identified a set of differentially expressed proteins in proliferative and invasive melanoma cell lines, we correlated them to the protein composition of plasma exosomes from melanoma patients pre and post immunotherapy treatment (n=7) as well as healthy controls (n=5).

2022-07-14 | PXD025475 | Pride

ZEB1 controls a lineage-specific transcriptional program essential for melanoma cell state transitions [RNA-seq]

Project description:Cell plasticity sustains intra-tumor heterogeneity and treatment resistance in melanoma. Deciphering the transcriptional mechanisms governing reversible phenotypic transitions between proliferative/differentiated and invasive/stem-like states is required. Expression of the ZEB1 transcription factor is frequently activated in melanoma, where it fosters adaptive resistance to targeted therapies. Here, we performed a genome-wide characterization of ZEB1 transcriptional targets, by combining ChIP-sequencing and RNA-sequencing, upon phenotype switching in melanoma models. We identified and validated ZEB1 binding peaks in the promoter of key lineage-specific genes crucial for melanoma cell identity. Mechanistically, ZEB1 negatively regulates SOX10-MITF dependent proliferative/melanocytic programs and positively regulates AP-1 driven invasive and stem-like programs. Comparative analyses with breast carcinoma cells revealed lineage-specific ZEB1 binding, leading to the design of a more reliable melanoma-specific ZEB1 regulon. We then developed single-cell spatial multiplexed analyses to characterize melanoma cell states intra-tumoral heterogeneity in human melanoma samples. Combined with scRNA-Seq analyses, our findings confirmed increased ZEB1 expression in Neural-Crest-like cells and mesenchymal cells, underscoring its significance in vivo in both populations. Overall, our results define ZEB1 as a major transcriptional regulator of cell states transitions and provide a better understanding of lineage-specific transcriptional programs sustaining intra-tumor heterogeneity in melanoma.

2024-03-26 | GSE246603 | GEO

ZEB1 controls a lineage-specific transcriptional program essential for melanoma cell state transitions [ChIP-seq]

2024-03-26 | GSE246672 | GEO

MITF controls the TCA cycle to modulate the melanoma hypoxia response

Project description:In response to the dynamic intra-tumor microenvironment, melanoma cells adopt different phenotypic states possessing distinct biological properties associated with differential expression of the microphthalmia-associated transcription factor (MITF). The response to hypoxia, a major microenvironmental cue, is underpinned by expression of hypoxia-inducible transcription factors (HIFs) that reprogram metabolism and promote pro-angiogenic VEGF expression. HIF1 indirectly represses MITF via the transcription factor bHLHE40/DEC1, and MITF can activate HIF1 expression. Although HIF and MITF share a highly related DNA-binding specificity, it is unclear whether they share a subset of target genes. Moreover, the genome-wide impact of hypoxia on melanoma, which genes are direct HIF targets, and whether melanoma cell lines representing different phenotypic states exhibit distinct hypoxic responses is unknown. Here we show, that three different melanoma cell lines exhibit widely different hypoxia responses with only a core 23 genes regulated in common after 12 h in hypoxia. Surprisingly, under hypoxia MITF is transiently up-regulated by HIF1 and co-regulates a subset of HIF targets including VEGFA. Significantly, we also show that MITF represses itself and also regulates SDHB to control the TCA cycle and suppress pseudo-hypoxia. Our results reveal a previously unsuspected role for MITF in metabolism and the network of factors underpinning the hypoxic response in melanoma.

2019-06-13 | GSE132624 | GEO

PREDICT: untargeted metabolomic profiling in a Brassica napus (canola) breeding population by GC-MS

Project description:Genome-wide association studies (GWAS) identified thousands of genetic loci associated with complex plant traits, including many traits of agronomical importance. However, functional interpretation of GWAS results remains challenging because of large candidate regions due to linkage disequilibrium. High-throughput omics technologies, such as genomics, transcriptomics, proteomics, and metabolomics open new avenues for integrative systems biological analyses and help to nominate systems information supported (prime) candidate genes. In the present study, we capitalize on a diverse canola population with spring-type 477 lines which was previously analysed by high-throughput phenotyping (Knoch et al., 2020), and by RNA sequencing and metabolite profiling for multi-omics-based hybrid performance prediction (Knoch et al., 2021). We deepened the phenotypic data analysis, now providing 123 time-resolved image-based traits, to gain insight into the complex relations during early vegetative growth and re-analysed the transcriptome data based on the latest Darmor-bzh v10 genome assembly (Rousseau-Gueutin et al., 2020). Genome-wide association testing revealed 61,298 robust quantitative trait loci (QTL) including 187 metabolite-QTL, 56,814 expression-QTL, and 4,297 phenotypic QTL, many clustered in pronounced hotspots. Combining information about QTL colocalisation across omics layers and correlations between omics features allowed us to discover prime candidate genes for metabolic and vegetative growth variation. Prioritized candidate genes for early biomass accumulation include A06p05760.1_BnaDAR (PIAL1), A10p16280.1_BnaDAR, C07p48260.1_BnaDAR (PRL1), and C07p48510.1_BnaDAR (CLPR4). Moreover, we observed unequal effects of the Brassica A and C subgenomes on early biomass production.

2023-11-20 | MTBLS8056 | MetaboLights

SeaIce, Espegrend, Microscosm, Mnemi

Project description:454 dataset for Hosia, et al. Torstensson et al. Dinasquet et al.

| PRJEB7907 | ENA

Identification of functional interactions through integration and systems analysis of matched gene and microRNA expression data across the Ludwig-Melbourne Melanoma (LM-MEL) Cell Line Panel

Project description:MicroRNAs contribute to metastatic progression in many cancers by modulation of phenotypic reprogramming processes such as epithelial-mesenchymal plasticity. However, it remains challenging to identify microRNA-mRNA interactions of functional significance at endogenous expression levels. The LM-MEL cell line panel comprises a large set of unique melanoma cell lines derived from largely metastatic melanoma tumours, as described in Behren et al, PCMR 2013 26(4):597-600 (PMID 23527996). For this study, 57 of the cell lines underwent matched gene expression (Illumina HT12v4 microarray) and small RNASeq (Illumina HiSeq) profiling in unperturbed conditions, generating a large dataset of matched gene and microRNA abundance data which was integrated with available phenotypic annotations covering several conditions of biological interest. We developed a novel systems analysis workflow to identify putative regulatory interactions suitable for subsequent validation.

2016-11-03 | GSE89438 | GEO

Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state.

Project description:Understanding the molecular processes underlying intra-tumor heterogeneity is of critical importance to improve the efficiency of therapy and overcome drug resistance. In malignant melanoma, heterogeneity is though to arise -at least partly- through epigenetic rather than genetic reprogramming of proliferating cells, leading to the appearance within the primary tumors of a phenotypically distinct invasive cell subpopulation. The invasive melanoma cells are at the origin of metastatic spread and are thought to provide a reservoir of therapeutically resistant cells. To decipher the gene regulatory networks that underlie the proliferative and invasive cellular states we integrated publicly available gene expression and DNA methylation data from tumor biopsies with a newly generated compendium of open chromatin and histone modification profiling of melanoma cultures that are dominant in either of the two subpopulations. Extensive in silico analyses identified SOX10 and MITF, and AP-1 and TEADs as key upstream regulators of the proliferative and invasive transcriptomes, respectively. Knock-down experiments confirmed the implication of TEADs in the invasive gene network and, more importantly, established a causative link between activation of these transcription factors and melanoma cell invasion and sensitivity to MAPK inhibitors.

2015-03-05 | GSE60665 | GEO

Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state.

2015-03-05 | GSE60663 | GEO

Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state.

2015-03-05 | GSE60664 | GEO