Decoding breast cancer tissue-stroma interactions using species-specific sequencing
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ABSTRACT:
PROVIDER: PRJNA277852 | ENA |
REPOSITORIES: ENA
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Project description:Decoding genome-wide effects of experimental tissue-tissue or cell-cell interactions is important, for example, to better understand tumor-stroma interactions after transplantation (xenografting). Transcriptome analysis of intermixed human and mouse cells has frequently relied on the need to separate the two cell populations prior to transcriptome analysis, which introduces confounding effects on gene expression. To circumvent this problem, we perform a bioinformatics-based genome-wide transcriptome analysis technique separating the mouse and human transcriptome part of a dataset, which allows a mixed mouse and human cell population to be sequenced without prior cell sorting. We use the new technology – which we call S3 (“S-cube” for Species-specific sequencing) technology – to provide new insights into the Notch downstream response following Notch ligand-stimulation and to explore transcriptional changes following transplantation of luminal (MCF7) and basal-type (MDA-MB-231) human breast cancer cells into mammary fat pad tissue in mice. Analysis of Notch response to ligand in three settings: co-culture, immobilized ligand and xenografted tumors
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Project description:Decoding genome-wide effects of experimental tissue-tissue or cell-cell interactions is important, for example, to better understand tumor-stroma interactions after transplantation (xenografting). Transcriptome analysis of intermixed human and mouse cells has frequently relied on the need to separate the two cell populations prior to transcriptome analysis, which introduces confounding effects on gene expression. To circumvent this problem, we perform a bioinformatics-based genome-wide transcriptome analysis technique separating the mouse and human transcriptome part of a dataset, which allows a mixed mouse and human cell population to be sequenced without prior cell sorting. We use the new technology – which we call S3 (“S-cube” for Species-specific sequencing) technology – to provide new insights into the Notch downstream response following Notch ligand-stimulation and to explore transcriptional changes following transplantation of luminal (MCF7) and basal-type (MDA-MB-231) human breast cancer cells into mammary fat pad tissue in mice.
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Project description:Breast cancers display a high degree of diversity between and within tumors due to variations in both tumor cells and non-malignant cells of the tumor microenvironment (TME). While most studies on the TME have focused on stroma located within the tumor mass, few studies have examined the peri-tumoral microenvironment, which extends beyond the tumor margins and includes the surrounding, benign-appearing tissues. Here, we examined the heterogeneity in tumors and peri-tumoral stroma from 10 ER+PR+HER2- invasive breast carcinomas, through multi-region transcriptomic profiling. Tumor samples were obtained from the center, superior, inferior, medial, and lateral (C, S, Inf, M, L) regions of each tumor. Peritumoral samples were obtained from four radial directions corresponding to the regions the tumor samples were collected from (S, Inf, M, L) and from three zones of increasing distances from the tumor margins (Zone 1: 1-3 cm, Zone 2: 3-5 cm, Zone 3: 5-7 cm). To represent the normal breast transcriptomic state, 5 non-directional samples were each obtained from 3 non-tumor bearing breasts (NTB) - 1 patient had undergone cosmetic reduction mammoplasty and 2 patients were germline BRCA2-mutation carriers who had undergone risk-reducing mammoplasties. Total RNA was isolated and microarray was performed using the human Clariom™ S Assay (ThermoFisher Scientific). In total, 144 transcriptomic profiles (47 Tumor, 82 peri-tumoral stroma, 15 NTB) were analyzed. Heterogeneity was observed both within and between the tumor samples, highlighting that unlike the histological classification, an individual tumor is often comprised of several molecular sub-types. Similarly, the peri-tumoral stroma was also heterogeneous, albeit independent of the tumor heterogeneity. Four distinct stromal clusters were noted, which differed in their molecular pathways and cell type composition. Among these, the adipose-enriched stroma that had inflammatory cancer-associated fibroblasts and innate immune cells was significantly associated with poorer overall survival, in contrast to the myofibroblast-enriched stroma. These data together suggest that the peri-tumoral heterogeneity may be an important determinant of the evolution and treatment of breast cancers.
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