Oncogenic mutation BRAF V600E changes phenotypic behavior of THLE-2 liver cells through alteration of gene expression
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ABSTRACT:
PROVIDER: PRJNA800581 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17754577.fastq.gz | Fastqsanger.gz | |||
| SRR17754578.fastq.gz | Fastqsanger.gz | |||
| SRR17754579.fastq.gz | Fastqsanger.gz | |||
| SRR17754580.fastq.gz | Fastqsanger.gz | |||
| SRR17754581.fastq.gz | Fastqsanger.gz |
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Project description:The accumulation of mutations in cancer driver genes such as tumor suppressors or pro-to-oncogenes affects cellular homeostasis. Disturbances in the mechanism controlling prolifera-tion causes significant augmentation of cell growth and division due to the loss of sensitivity to the regulatory signals. Nowadays, an increasing number of cases of liver cancer are observed worldwide. Data provided by the International Cancer Genome Consortium (ICGC) have indi-cated many alterations within gene sequences, whose roles in tumor development are not well understood. A comprehensive analysis of liver cancer (hepatocellular carcinoma-virus associated) samples has identified new and rare mutations in B-Raf proto-oncogene (BRAF) in Japanese HCC patients, as well as BRAF V600E mutations in French HCC patients. However, their function on liver cancer has never been investigated. Here, using tests for functional analysis and next gen-eration sequencing we demonstrate the tumorigenic effect of BRAF V600E on hepatocytes (THLE-2 cell line). Moreover, we identified genes such as BMP6, CXCL11, IL1B, TBX21, RSAD2, MMP10, SERPIND1, which are possibly regulated by BRAF V600E-mediated mitogen-activated protein kinases/extracellular signal-regulated kinases (MAPK/ERK) signaling pathway. Through several functional assays, we demonstrated that BRAF L537M, D594A, and E648G mutations by its own are not pathogenic in liver cancer. The investigation of genome mutations and the de-termination of their impact on cellular processes and functions are crucial to unraveling the mo-lecular mechanisms of liver cancer development.
2022-01-28 | GSE194425 | GEO
Project description:Goals of the study was to compare transcripional and phenotypic response of mouse intestinal organoid cultures to the KRAS(G12V) or BRAF(V600E)oncogenes.
2018-06-02 | GSE115234 | GEO
Project description:BRAF(V600E) is a frequent mutation in colon cancer. We have analysed transcriptional effects of BRAF(V600E) in the intestinal epithelium of transgenic mice that harbour an inducible BRAF(V600E) transgene. Mice used in this experiment were compound transgenic for a stem-cell specific Lgr5-EGFP Reporter and either an inducible TdTomato-2A-BRAF(V600E) transgene or an inducibe TdTomato-luciferase transgene. Transgenes were induced by doxycycline (4mg/ml) treatment provided in a 1% sucrose solution in the drinking water of transgenic mice for 24h. Intestinal crypts were isolated by filtering (70um) following a PBS/EDTA incubation step. Single cell suspensions were made by digestion of crypts in 500ug/ml trypsine and 0.8u/ml DNAseI for approx. 20min at RT. Cell populations for profiling were isolated by FACS, using an Aria SOPR (BD), equipped with a 70um nozzle.
2013-12-31 | E-GEOD-50678 | biostudies-arrayexpress
Project description:This study used microarray expression analysis to identify global changes in transcript alteration in response to MEK inhibition. Genes under ERK control were identified in a panel of V600E BRAF and RTK-activated tumor cells and xenografts, using short-term inhibition of ERK activity using the MEK inhibitor PD0325901 (Pfizer). This SuperSeries is composed of the SubSeries listed below.
2009-02-11 | GSE10086 | GEO
Project description:In the human EGFR mutant adenocarcinoma cell line PC9 pBabe empty vector (EV) or BRAF V600E were overexpressed. RNA was extracted from EV, BRAF V600E overexpressing or osimertinib-resistant BRAF V600E expressing cells after 48h treatment with osimertinib, trametinib, a combination of both or vehicle controls. RNA was subjected to 3' UTR RNA sequencing.
2021-10-20 | E-MTAB-11004 | biostudies-arrayexpress
Project description:This study used microarray expression analysis to identify global changes in transcript alteration in response to MEK inhibition. Genes under ERK control were identified in a panel of V600E BRAF and RTK-activated tumor cells and xenografts, using short-term inhibition of ERK activity using the MEK inhibitor PD0325901 (Pfizer). Experiment Overall Design: Cell lines growing in culture (n=12) and murine xenografts (n=2) were treated with the MEK inhibitor PD0325901 or vehicle alone as control. Paired analysis of MEK inhibited to control samples was performed for two groups of tumor cells, V600E BRAF and RTK. Time course analysis was performed on one representative cell line in order to first determine the optimal time point to detect changes in all cell lines.
2009-02-20 | E-GEOD-10086 | biostudies-arrayexpress
Project description:The purpose of this study was to investigate the presence of a gene expression signature in BRAF V600E melanomas compared to wild type ones, all derived from sun-exposed sites. Microdissected tissues from excisional biopsies of 18 cutaneous melanomas were analyzed to detect the presence of BRAF and NRAS mutations and to profile whole genome expression by means of oligonucleotide microarrays. Class comparison methods were used to select differentially expressed genes between wild type and mutated lesions. Real Time RT-PCR and immunohistochemistry were applied to validate differences at the mRNA and protein levels on an independent cohort of samples. BRAF mutations were evidenced in 67% of melanomas. All of them consisted of the oncogenic change V600E (and the mutation event was independent of Clark's level). Data indicate that in V600E melanomas there is an over-expression of cancer stem cell markers and an upregulation of important oncogenes, like KRAS. This, together with the downregulation of genes involved in oxidative UV stress response and immuno system defense, confers an advantage to V600E melanomas compared to wt lesions. Moreover, the downregulation of topoisomerase I and CDKN2A results in an increased replicative potential associated with a decrease in senescence markers and a diminished DNA damage response. As far as the wild-type lesions, we interestingly pointed out the overexpression of PML, PIK3CA and the downregulation of two tumour suppressor genes (BRCA1 and TP73) relevant to DNA repair.
2024-12-31 | GSE22838 | GEO
Project description:To mimic the naturally occurring BRAF V600E mutation in lung cancer, a BRAF V600E knock-in BEAS-2B cell model was established using CRISPR/Cas9. The proteomics analysis was carried out to evaluate the underlying changes at the proteome level. Proteomics analysis revealed significant changes in the proteins involved in the biological processes including epithelial-mesenchymal transition (EMT), extracellular matrix (ECM)-receptor interaction, cell adhesion, focal adhesion, and cell metabolism upon BRAF V600E mutation.
2025-04-22 | PXD058027 | Pride
Project description:Background Main drawback of BRAF/MEK inhibitors (BRAF/MEKi)-based targeted therapy in the management of BRAF- mutated cutaneous metastatic melanoma (MM) is the development of therapeutic resistance. We aimed to define in this context the specific role of mTORC2, a signaling complex defined by the presence of the essential RICTOR subunit and regarded as an oncogenic driver in several tumor types, including MM. Methods After analyzing the TCGA MM patients’ database to explore both overall survival and molecular signatures as a function of intra-tumor RICTOR levels, we investigated the effects of RICTOR downregulation in BRAF V600E MM cell lines on their response to BRAF/MEKi in vitro. We performed a proteomic screening to identify proteins modulated by changes in RICTOR expression and Seahorse analysis to evaluate the effects of RICTOR depletion on mitochondrial respiration. The combination of BRAFi with drugs targeting proteins and processes emerged in the proteomic screening was carried out on RICTOR-deficient cells in vitro and in a xenograft setting in vivo. Results We found that low RICTOR levels in MM correlate with an overall worse clinical outcome. GSEA of low- RICTOR tumors revealed a gene expression signature suggestive of activation of the mitochondrial Electron Transport Chain (ETC) energy producing pathway. RICTOR-deficient BRAF V600E cells are intrinsically tolerant to BRAFi/MEKi and anticipate the onset of resistance to BRAFi upon prolonged drug exposure. In RICTOR- depleted cells, both mitochondrial respiration and expression of nicotinamide phosphoribosyltransferase (NAMPT) are enhanced, while their pharmacological inhibition restores sensitivity to BRAFi. Conclusions Our work unveils a novel tumor suppressing role for mTORC2 in the responses of BRAF V600E melanoma cells to targeted therapy and identifies the NAMPT-ETC axis as a potential therapeutic vulnerability of low- RICTOR tumors. Importantly, our findings support the concept that the evaluation of intra-tumor RICTOR levels in MM has a prognostic value, and may help predicting the response of patients to targeted therapy.
2024-06-22 | PXD050614 | Pride
Project description:Langerhans Cell Histiocytosis (LCH) is an inflammatory disease characterized by abnormal dendritic cells (DCs) with hyperactive ERK signaling, called “LCH cells”. Since DCs rely on ERK signaling to produce inflammatory signaling molecules in response to pathogenic cues, we hypothesized that hyperactive ERK will enhance DC inflammatory responses. We utilized the BRAF-V600E fl/+: CD11c-Cre mouse model of LCH which hyperactivates MAPK/ERK signaling in DCs. We cultured bone-marrow derived dendritic cells (BMDCs) from LCH and control mice (BRAF-V600E fl/+: Cre0) and stimulated them with LPS with or without a specific BRAF-V600E inhibitor. Polysome Profiling revealed a large and irreversible increase in levels of polysome bound RNA in the LCH-BMDCs compared to WT. We defined the LCH translatome by analyzing total and polysome-bound RNA from BMDCs using the Anota2seq program, which revealed a BRAF-V600E-mediated selective increase in LPS-induced inflammatory proteins.
2022-05-01 | GSE193610 | GEO