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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE331356 | GEO | 2026/09/17

REPOSITORIES: GEO

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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.

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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)

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

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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)

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

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

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