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Genome-wide profiling of the DNA methylation landscape in primary and matastatic breast cancer types [468LN and 468PT]

ABSTRACT: Whole genome bisulphite sequencing of 2 human breast cancer cell lines representing a breast primary tumor and a matched lymph node metastasis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE56763 | GEO | 2014/09/03

SECONDARY ACCESSION(S): PRJNA244499

REPOSITORIES: GEO

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Genome-wide profiling of the DNA methylation landscape in primary and matastatic breast cancer types [468LN and 468PT]

Project description:Whole genome bisulphite sequencing of 2 human breast cancer cell lines representing a breast primary tumor and a matched lymph node metastasis. Sequencing of bisulfite converted DNA of cancer cell line samples.

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Plasma proteomic profiling of small size HER2-positive breast cancer

Project description:Lymph node status is a crucial predictor for the overall survival of invasive breast cancer. However, lymph node involvement is only detected in about half of HER2 positive patients. Currently, there are no biomarkers available for distinguishing small size HER2-positive breast cancers with different lymph node statuses. Thus, in the present study, we applied label-free quantitative proteomic strategy to construct plasma proteomic profiles of ten patients with small size HER2-positive breast cancers (5 patients with lymph node metastasis versus 5 patients with lymph node metastasis).

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Transcriptomic survey of lymph node-positive vs. - negative ductal breast cancer

Project description:Lymph node involvement is a major prognostic variable in breast cancer. Whether the molecular mechanisms that drive breast cancer cells to colonize lymph nodes are shared with their capacity to form distant metastases is yet to be established. In a transcriptomic survey aimed at identifying molecular factors associated with lymph node involvement of ductal breast cancer, we found that luminal differentiation, assessed by the expression of estrogen receptor (ER) and/or progesterone receptor (PR) and GATA3, was only infrequently lost in node-positive primary tumors and in matched lymph node metastases. The transcription factor GATA3 critically determines luminal lineage specification of mammary epithelium and is widely considered a tumor and metastasis suppressor in breast cancer. Strong expression of GATA3 and ER in a majority of primary node-positive ductal breast cancer was corroborated by quantitative RT-PCR and immunohistochemistry in the initial sample set, and by immunohistochemistry in an additional set from 167 patients diagnosed of node-negative and positive primary infiltrating ductal breast cancer, including 102 samples from loco-regional lymph node metastases matched to their primary tumors, as well as 37 distant metastases. These observations suggest that loss of luminal differentiation is not a major factor driving the ability of breast cancer cells to colonize regional lymph nodes. The transcriptomic study comprises 16 samples from Lymph node metastasis from infiltrating ductal breast carcinoma, 18 samples from Primary node-positive infiltrating ductal,7 samples from Primary node-negative infiltrating ductal and 3 samples from Unaffected lymph node were included. Their RNA was isolated and prepared for hybridization to human Affymetrix GeneChip arrays.

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single-cell RNA sequencing reveals the mechanism of human breast cancer metastasis

Project description:To obtain more information about the lymph node metastasis of breast cancer cells, we selected the matched primary breast cancer (PC), positive lymph nodes (PL), and negative lymph nodes (NL) of the same patient to perform integrated analysis. The PC, PL, NL samples were analysed with single-cell RNA sequencing.

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Single-cell RNA sequencing reveals the mechanism of human breast cancer metastasis

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