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Single cell mapping of breast tumor stroma reveals dynamically evolving compositions of cancer-associated fibroblasts along tumor progression (bulk RNA-seq dataset)

ABSTRACT: Single cell mapping of breast tumor stroma reveals dynamically evolving compositions of cancer-associated fibroblasts along tumor progression (bulk RNA-seq dataset)

PROVIDER: PRJNA629493 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11652441_1.fastq.gz	Fastqsanger.gz
	SRR11652441_2.fastq.gz	Fastqsanger.gz
	SRR11652442_1.fastq.gz	Fastqsanger.gz
	SRR11652442_2.fastq.gz	Fastqsanger.gz
	SRR11652443_1.fastq.gz	Fastqsanger.gz

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Project description:Intrahepatic cholangiocarcinoma (ICC) is the second most common type of primary cancer in the liver. ICC is an aggressive cancer with poor prognosis and limited therapeutic strategies. The identification of new drug targets and prognostic biomarkers is an important clinical challenge for ICC. The presence of an abundant stroma is a histological hallmark of ICC. Given the well established role of the stromal compartment in the progression of cancer diseases, we hypothesized that relevant biomarkers could be identified by analyzing the stroma of ICC. By combining laser capture microdissection and gene expression profiling we demonstrated that ICC stromal cells exhibit dramatic genomic changes. We identified a signature of 1,073 non-redundant genes that significantly discriminate the tumor stroma from non tumor fibrous tissue. Functional analysis of differentially expressed genes demonstrated that up-regulated genes in the stroma of ICC were related to cell cycle, extracellular matrix and Transforming Growth Factor beta (TGFM-NM-2) pathways. Tissue microarray analysis using an independent cohort of 40 ICC patients validated at a protein level the increase expression of Collagen 4, Laminin, Osteopontin/SPP1, KIAA0101 and TGFM-NM-22 genes in the stroma of ICC. Statistical analysis of clinical and pathological features demonstrated that the expression of Osteopontin, TGFM-NM-22 and Laminin in the stroma of ICC was significantly correlated with patient overall survival. More importantly, multivariate analysis demonstrated that the stromal expression of Osteopontin was an independent prognostic marker for overall and disease-free survival. Conclusion: The study identifies clinically relevant genomic alterations in the stroma of ICC, including candidates biomarkers for prognosis, supporting the idea that tumor stroma is an important factor for ICC onset and progression. 20 RNA samples were analyzed, from 10 patients with ICC. For each patient, RNA were isolated from laser capture microdissected (LCM) stroma from tumor and non tumor areas.

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Single cell mapping of breast tumor stroma reveals dynamically evolving compositions of cancer-associated fibroblasts along tumor progression (bulk RNA-seq dataset)

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