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Expression data from breast tumors in different age-specific cohorts and for different sequentional disease stages

ABSTRACT: Compared transccriptome of breast cancer in young women to those arising in two mature groups to characterize the underlying biological mechanisms of the breast cancer in Middle Eastern young women. Also, compared the gene expression profile characteristic of the sequential disease stages (ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC)) of breast cancer to elucidate the molecular mechanisms of breast cancer progression in young women.

ORGANISM(S): Homo sapiens

PROVIDER: GSE29044 | GEO | 2014/08/01

SECONDARY ACCESSION(S): PRJNA140219

REPOSITORIES: GEO

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Expression data from breast tumors in different age-specific cohorts and for different sequentional disease stages

Project description:Compared transccriptome of breast cancer in young women to those arising in two mature groups to characterize the underlying biological mechanisms of the breast cancer in Middle Eastern young women. Also, compared the gene expression profile characteristic of the sequential disease stages (ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC)) of breast cancer to elucidate the molecular mechanisms of breast cancer progression in young women. Analyzed the whole-genome mRNA expression profile from tumor (n=73) and adjacent disease free tissues (n=36) using Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays.

2014-08-01 | E-GEOD-29044 | biostudies-arrayexpress

Transcriptome analysis reveals differences in cell cycle, growth and migration related genes that distinguish fibroblasts derived from pre-invasive and invasive breast cancer.

Project description:As the most common form of pre-invasive breast cancer, ductal carcinoma in situ (DCIS) affects over 50,000 women in the US annually. Despite standardized treatment involving lumpectomy and radiation therapy, up to 25 % of patients with DCIS experience disease recurrence often with invasive ductal carcinoma (IDC), indicating that a subset of patients may be under-treated. As most DCIS cases will not progress to invasion, many patients may experience over-treatment. By understanding the underlying processes associated with DCIS to IDC progression, we can identify new biomarkers to determine which DCIS cases may become invasive and improve treatment for patients. Accumulation of fibroblasts in IDC is associated with disease progression and reduced survival. While fibroblasts have been detected in DCIS, little is understood about their role in DCIS progression.We sought to determine whether DCIS fibroblasts were similar or distinct from normal and IDC fibroblasts at the transcriptome level, fibroblasts underwent transcriptome profilingthrough bulk RNA seq and pathway analysis. DCIS fibroblasts are phenotypically distinct from normal breast and IDC fibroblasts, and play an important role in breast cancer growth, invasion, and recruitment of myeloid cells. These studies provide novel insight into the role of DCIS fibroblasts in breast cancer progression and identify some key biomarkers associated with DCIS progression to IDC, with important clinical implications.

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Whole genome DASL analysis of tumour epithelial and stromal compartments during breast cancer progression

Project description:Analysis of gene expression changes in tumour epithelium (DCIS and invasive breast cancer) and stroma both immediately surrounding the lesions and more distantly. Total RNA obtained from Formalin Fixed Paraffin Embedded archival material and the individual compartments (stroma and epithelium) compared independently across the samples. Sample abbreviation key: BC = breast cancer DCIS = ductal carcinoma in situ IDC = invasive ductal carcinoma RM = remote metastasis S = stroma NS = near stroma.

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Single-Cell Transcriptome Profiling Reveals Intratumoral Heterogeneity and Molecular Features in Breast Cancer

Project description:Ductal carcinoma in situ (DCIS) is a nonobligate precursor of invasive breast cancer. Its biological features, particularly its intratumoral heterogeneity, remain obscure. Moreover, mechanism of lymph node metastasis is unclear. To address this deficiency, we performed single-cell transcriptome profiling of DCIS, invasive ductal carcinoma (IDC) and lymph node metastasis. Single-cell transcriptome analysis revealed that breast cancer exhibits intratumoral heterogeneity at the transcriptional level, defining specific functions, and that DCIS has similar heterogeneity to IDC.

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Analysis of DCIS using Clariom D transcriptomics array

Project description:Experiment description to give context to the data set: Ductal carcinoma in situ (DCIS), the most common type of pre-invasive lesion of breast, is being detected with increasing frequency with the advent of mammographic screening. Surgery is the mainstay for the treatment of DCIS. Based on the clinic-pathological features of DCIS, this may be followed by radiotherapy and/or endocrine therapy. The qualitative assessment of histological grade, expression of single protein biomarkers and more recently, mRNA analysis (DCIS Score) have been used to make these decisions. However, these factors do not fully predict the likelihood of development of invasive breast cancer treated with breast-conserving surgery. A majority of women with ductal carcinoma in situ (DCIS) receive breast-conserving surgery (BCS) but then face a risk of development of invasive breast cancer. Using Human Clariom D Pico Assay, we aim to compare the transcriptome profiles of DCIS in relation to development of invasive breast cancer (INV-BC) versus Non-INV-BC cases. Experimental Methods Clariom D Pico Human Transcriptome Array were performed according to Applied Biosystems/Thermo Fisher Scientific’s instructions. Experimental protocols are summarized in detail in Supplementary Methods (Supplementary Data). Sample annotation We compared the relative gene expression in development of invasive breast cancer (INV-BC) versus Non-INV-BC cases in Singapore cohort-59 cases (discovery cohort) and Italian cohort-50 cases (validation cohort). Microplate Plate and Well IDs are also provided as Clariom D ID list per cohort. Author information Dr. Sunil Badve is the Principal Investigator. Raw Data Probe Cell Intensity (CELL) and .ARR files which contain the design information for this study are provided (Human Clariom D Pico Assay).

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Molecular signatures of in-situ to invasive progression for basal-like breast cancers: An integrated mouse model and human tumor study [CGH]

Project description:This study identifies progression in breast ductal carcinoma in situ (DCIS) as it progresses towards triple negative invasive breast cancer (TNBC). Bulk DNA arrayCGH was performed on the C3Tag genetically engineered mouse model that forms human breast-like DCIS and TNBC.

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Array-based genome-wide transcriptome analysis of Ductal carcinoma in situ (DCIS)

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Gene Expression Signature of Microcalcification among Taiwanese Breast Cancer

Project description:Microcalcification is one of the most common radiological and pathological features of breast ductal carcinoma in situ (DCIS), and to a lesser extent, invasive ductal carcinoma. We evaluated transcriptional profiles associated with ectopic mammary mineralization. We evaluated the transcriptional profiles associated with breast cancer microcalcification for Taiwanese breast cancer and a gene expression signature was derived.

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