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RNA-sequencing of treatment-naive, Lapatinib-resistant, and resistant-reversal SUM149 IBC cells

ABSTRACT: RNA-sequencing of treatment-naive, Lapatinib-resistant, and resistant-reversal SUM149 IBC cells

PROVIDER: PRJEB74062 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR12766503_1.fastq.gz	Fastqsanger.gz
	ERR12766503_2.fastq.gz	Fastqsanger.gz
	ERR12766504_1.fastq.gz	Fastqsanger.gz
	ERR12766504_2.fastq.gz	Fastqsanger.gz
	ERR12766505_1.fastq.gz	Fastqsanger.gz

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RNA-sequencing of treatment-naive, Lapatinib-resistant, and resistant-reversal SUM149 IBC cells

Project description:In this experiment, SUM149 IBC cells were cultured using baseline medium (N=3), and in baseline medium supplemented with increasing concentration of Lapatinib to induce resistance (N=3; rSUM149). Resistant reversal SUM149 cells (rrSUM149) were then generated by culturing in rSUM149 cells in baseline medium. Gene expression data were generated to identify differentially expressed genes, as well as differentially activated proteins and pathways during Lapatinib resistance and resistance reversal. Gene expression were also integrated with proteome expression data generated under the same conditions.

2024-04-05 | E-MTAB-13929 | biostudies-arrayexpress

Transcriptomic analysis of A3250 inflammatory breast cancer (IBC) cells, SUM149 IBC and MDA-MB-231 non-IBC cells

Project description:Purpose: Transcriptome profiling (RNA-seq) of a novel human Inflammatory Breast Cancer cell line A3250 in comparison to SUM149 and MDA-MB-231 Inflammatory Breast Cancer (IBC) is the most aggressive form of breast cancer with distinct clinical and histopathological features, but understanding of the unique aspects of IBC biology lags far behind that of other breast cancers. We describe a novel triple-negative IBC cell line, A3250, that recapitulates key features of human IBC in a mouse xenograft model.The purpose of this study was to compare differences in gene expression between A3250 IBC, MDA-MB-231 non-IBC and SUM149 IBC that does not present with typical clinical sympotms of IBC in a mouse model, with the goal of identifying unique molecular features for this unique type of breast cancer Results: RNA-Seq analysis identified expression profile characteristic for the novel A3250 IBC cell line, compared to SUM149 IBC and MDA-MB-231 non-IBC.

2021-10-01 | GSE180788 | GEO

Transcriptomic analysis of A3250 inflammatory breast cancer (IBC) cells, SUM149 IBC and MDA-MB-231 non-IBC cells

Project description:Transcriptomic analysis of A3250 inflammatory breast cancer (IBC) cells, SUM149 IBC and MDA-MB-231 non-IBC cells

| PRJNA749567 | ENA

RNA-seq analysis of SUM149 inflammatory breast cancer cells treated with computationally predicted drug combinations

Project description:Drug repurposing is a promising strategy for identifying new therapeutic approaches for inflammatory breast cancer (IBC), an aggressive breast cancer subtype with limited treatment options. This RNA-seq study was performed to evaluate transcriptional changes in SUM149 IBC cells after treatment with computationally predicted drug combinations derived from Gene Reversal Rate (GRR) analysis. SUM149 cells were treated for 24 hours with DMSO vehicle control or one of three dual-drug combinations: BMS-536924 plus AKT inhibitor IV, BMS-536924 plus tyrphostin AG1478, or temsirolimus plus AKT inhibitor IV, with three biological replicates per group. RNA-seq was used to assess global differential gene expression changes and to determine whether these drug combinations reversed genes associated with the IBC gene expression signature. The dataset includes raw sequencing files and processed gene expression/count matrices for all 12 samples.

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Differential gene expression profiles between SUM149 cells transfected with control siRNA and SUM149 cells transfected with siRNA targeting tarzarotene-induced gene 1 (TIG1)

2013-12-03 | GSE30543 | GEO

Expression data from SUM149 inflammatory breast cancer cells cultured in monolayer or Matrigel

Project description:Inflammatory breast cancer (IBC) is a rare type of breast cancer but accounts for up to 10% of breast cancer-related deaths. Plasticity between epithelial and mesenchymal feature is reported to be crucial in metastasis of IBC. Using Matigel culture, we induced epithelial to mesenchymal transition (EMT) in epithelial-like SUM149 IBC cells and identified overexpressed genes in this EMT process.

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Human breast cancer cells: parental v.s lapatinib-resistant clone

Project description:Transcriptional profiling of human HER2-positive BT474 breast cancer cells comparing control untreated cancer cells with lapatinib-resistant clone established by chronic treatment with lapatinib

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Differential gene expression profiles between SUM149 cells transfected with control siRNA and SUM149 cells transfected with siRNA targeting tarzarotene-induced gene 1 (TIG1)

Project description:We identified tazarotene-induced gene 1 (TIG1) as a potential tumorigenic gene in IBC. To investigate the underlying mechanism by which TIG1 promotes tumor growth and invasiveness of IBC cells, we first sought to identify TIG1 functional partners by using DNA microarray analysis to compare gene expression profiles between SUM149 cells transfected with control siRNA and SUM149 cells transfected with siRNA targeting TIG1. We identified receptor tyrosine kinase Axl as a functional partner of TIG1. SUM149 cells transiently transfected with control siRNA or siRNA targeting TIG1 were used. Total RNA was extracted and purified using RNeasy mini kit (Qiagen, Inc.) according to the manufacturer’s instructions. The integrity of the obtained RNA was assessed using an Agilent 2100 BioAnalyzer (Agilent Technologies). The Affymetrix HGU133 plus platform was used for hybridization, staining, and imaging of the arrays by following the manufacturer’s instructions. Gene expression analysis was performed in triplicate.

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