RNA-seq analysis of murine Sox4+/+ versus Sox4-/- 4T1 TNBC cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA602502 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10919463.fastq.gz | Fastqsanger.gz | |||
| SRR10919464.fastq.gz | Fastqsanger.gz | |||
| SRR10919465.fastq.gz | Fastqsanger.gz | |||
| SRR10919466.fastq.gz | Fastqsanger.gz | |||
| SRR10919467.fastq.gz | Fastqsanger.gz |
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Project description:We identified the SOX4 transcription factor and integrin alpha V encoded by the ITGAV gene as important resistance mechanisms to T cell-mediated cytotoxicity of TNBC cells. Here, we performed RNA seq. analysis of SOX4 and ITGAV deficient (CRISPR knockout) BT549 human and 4T1 murine TNBC cells as compared to control edited counterparts. Additionally, we performed SOX4 specific ChIP-seq studies in BT549 human TNBC cells. The objective of the study was to identify the molecular regulators and signaling pathways that mediate resistance to T cell mediated immunity. GSEA analysis of RNA-seq data showed that the 'interferon response' represented one of the top pathways for genes upregulated in SOX4 or ITGAV edited compared to control TNBC cells. In contrast, gene sets associated with TGF beta and TNF alpha/NF kappa b were negatively enriched in both Sox4 and Itgav edited TNBC cells. Further analysis of RNA-seq data showed that SOX4 or ITGAV edited TNBC cells contained higher mRNA levels of many interferon-stimulated genes (ISGs), including genes associated with important innate immune pathways such as RIG-I/MDA-5, cGAS - STING and the AIM2 inflammasome
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Project description:Differential expression levels of mRNAs in control 4T1 versus M2 macrophages co-cultured 4T1 murine breast cancer cells
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