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Bb41305d-b461-4427-99e4-a3cf9b21c66d - samples

ABSTRACT: A set of 56 EpCAM-positive cells derived from bone marrow aspirates of breast cancer patients or patients without a cancererous disease (30 cells from 21 M0-stage and 11 cells from five M1-stage breast cancer patients, 15 cells from seven non-cancer patients serving as controls). EpCAM-positive cells from breast cancer patients were considered disseminated tumor cells as they harbored copy number alterations and showed high expression of the epithelial marker EpCAM and the mammary luminal progenitor marker KIT in comparison to EpCAM-positive bone marrow cells from non-cancer patients. Paired-end RNA-Sequencing of the samples was performed on Illumina NovaSeq6000, raw data are provided in the Fastq format.

PROVIDER: EGAD00001006359 | EGA |

REPOSITORIES: EGA

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Detection and isolation of circulating tumor cells from breast cancer patients using CUB domain-containing protein 1 (CDCP1) Detection and isolation of circulating tumor cells from breast cancer patients using CUB domain-containing protein 1 (CDCP1) Detection and isolation of circulating tumor cells from breast cancer patients using CUB domain-containing protein 1 (CDCP1)

Project description:Circulating tumor cells (CTCs) and disseminated tumour cells with mesenchymal traits are difficult to detect by epithelial marker proteins. Particularly, triple negative breast cancers (TNBC) that are prone to therapy failure release a subpopulation of circulating tumour cells (CTCs) with mesenchymal traits. To provide tools that support their detection and analysis, the cell line BC-M1 established from disseminated tumour cells in the bone marrow of a breast cancer patient and a bone metastasis subline of MDA-MB-231 were analysed. Mass spectrometry analysis revealed high levels of CUB domain-containing protein 1 (CDCP1) in BC-M1. CDCP1 was found in other carcinoma cell lines (MDA-MB-231, MDA-MB-468) and other DTC cell lines (LC-M1, PC-E1) as well. Peripheral blood mononuclear cells were virtually negative for CDCP1 by Western Blot and immunofluorescent staining. Presence of CDCP1 in CTCs was confirmed by CellSearch. Here, CDCP1 positive CTCs were detected in eight of 30 analysed breast cancer patients. For the isolation of CTCs from the blood of breast cancer patients, we established a sandwich magnetic-activated cell sorting (MACS). The extracellular domain of CDCP1 served for cell catching and the cytoplasmic domain of CDCP1 for immunofluorescent detection of CDCP1 in CTCs. We showed that the MACS approach is suitable for the isolation of EpCam/keratin negative breast cancer cells from the blood and isolated CDCP1 positive CTCs from breast cancer patients by MACS. Hence, our approach is particularly suited for the detection and isolation of CTCs from TNBC when low EpCam or keratin levels limit the application of conventional approaches.

2023-03-20 | PXD035203 | Pride

DNA profiling of EpCAM-positive cells in bone marrow of early breast cancer (EBC) patients

Project description:Parallel DNA and RNA profiling of EpCAM-positive cells in bone marrow and primary tumor tissue with positive disseminated tumor cell (DTC) count via immunomagnetic Enrichment/Flow Cytometry (IE/FC) of metastatic breast cancer (MBC) patients confirm their malignant nature We developed a novel approach to isolate tumor cells with high purity from bone marrow which was subjected to immunomagnetic enrichment using EpCAM beads followed by fluorescence activated cell sorting (IE/FACS) to isolate EpCAM-positive cells away from leukocytes (CD45+). For DNA profiling, sorted cells were subjected to BAC array comparative genomic hybridization analysis following whole genome amplification. For RNA profiling, QPCR analysis was performed on sixty four (64) cancer-related genes using Taqman® low density arrays. For non-tumor controls, RNA profiling was performed on matched leukocytes (CD45+) isolated from the same enriched bone marrow samples.

2019-04-04 | GSE112756 | GEO

microRNA expression profiles in bone marrow fractions from gastric cancer patients

Project description:Both disseminated tumor cells and noncancerous host cells contributed to cancer progression cooperatively in bone marrow. Bone marrow samples were obtained from 4 gastric cancer patients, and were separated into 3 fractions (CD45 positive, CD45 negative/EpCAM positive, and CD14 positive fractions) by the automagnetic-activated cell separation (AutoMACS) system using CD45, EpCAM, and CD14 microbeads (Miltenyi Biotec, Germany). microRNA expression profiles in each fractions were evaluated in order to identify candidate prognostic markers for gastric cancer patients. In 4 patients with gastric cancer, bone marrow samples (40 mL) were obtained from iliac bones. Nucleated cells were collected by gradient centrifugation using Ficoll-Paque PREMIUM (GE Healthcare Life Science, USA) and Leucosep (Greiner Bio-One, Germany) according to the manufacturer’s instructions. Next, we separated bone marrow cells into 3 fractions using MACS: CD45 positive (CD45+), CD45 negative/EpCAM positive (CD45-/EpCAM+), and CD14 positive (CD14+). microRNA expression levels of whole bone marrow cells and each fractions were measured by the miRCURY™ LNA array microarray (6th gen-hsa, mmu & rno#208402, Exiqon, Vedbaek, Denmark). The miRCURY™ LNA array microarray slides were scanned using the Agilent G2505C Microarray Scanner System (Agilent Technologies, Inc., USA) and the data analysis was carried out using the Feature Extraction 10.7.3.1 (Agilent Technologies, Inc., USA).

2013-08-23 | E-GEOD-40325 | biostudies-arrayexpress

microRNA expression profiles in bone marrow fractions from gastric cancer patients

2013-08-23 | GSE40325 | GEO

Microarray correpsonding to the paper manuscript titled: Targeted expression profiling of single disseminated cancer cells isolated from bone marrow of prostate cancer patients

Project description:Bone is the most frequent site of metastasis in prostate cancer (PCa) and patients with bone metastases are deemed incurable. Targeting prostate cancer cells that disseminated to the bone marrow (BM) prior to surgery and before metastatic outgrowth may therefore prevent lethal metastasis. This prompted us to directly analyse the transcriptome of disseminated cancer cells (DCC) isolated from non-metastatic (UICC stage M0) prostate cancer patients. We screened 105 BM samples of M0-stage prostate cancer patients and 18 BM samples of patients without malignancy for the presence of EpCAM+ single cells. In total we isolated 270 cells from both groups by micromanipulation and globally amplified their mRNA. We used targeted transcriptional profiling to unambiguously identify DCCs for subsequent in-depth analysis. Transcriptomes of all cells were examined for the expression of EPCAM, KRT8, KRT18, KRT19, KRT14, KRT6a, KRT5, KLK3 (PSA), MAGEA2, MAGEA4, PTPRC (CD45), CD33, CD34, CD19, GYPC, SCL4A1 (band 3), and HBA2. Using these transcripts we found it impossible to reliably identify true DCCs. We then applied combined genome and transcriptome analysis of single cells and found that EpCAM+ cells from controls expressed transcripts thought to be epithelial-specific, while true DCCs may express haematopoietic transcripts. These results point to an unexpected plasticity of epithelial cancer cells in bone marrow and question common transcriptional criteria to identify DCCs. Array-CGH was used to analyze EpCAM-positive single cells isolated from bone marrow of M0-stage prostate cancer patients, and individuals without cancer. The purpose was to demonstrate that cells with genomic aberrations are true tumour cells.

2014-10-20 | E-GEOD-59631 | biostudies-arrayexpress

DNA profiling of EpCAM-positive cells in bone marrow of early breast cancer (EBC) patients

Project description:DNA profiling of EpCAM-positive cells in bone marrow of early breast cancer (EBC) patients

| PRJNA448907 | ENA

RNA profiling of EpCAM-positive cells in bone marrow of early breast cancer (EBC) patients

Project description:RNA profiling of EpCAM-positive cells in bone marrow of early breast cancer (EBC) patients

| PRJNA448910 | ENA

EpCAM expressing Hs578T cells

2010-12-02 | GSE25743 | GEO

EpCAM expressing Hs578T cells

Project description:EpCAM is frequently overexpressed in human invasive breast cancer. We reported EpCAM overexpression to be an independent prognostic marker for poor overall survival in node-positive breast cancer. We used microarrays in order to investigate changes of the transcriptome on EpCAM gene overexpression in human breast cancer cells Hs578T cells were found to express only very little EpCAM mRNA and protein in comparison to established and well characterized breast cancer cell lines such as MCF-7 or SK-BR-3. Hs578T cells were stably transfected with the EpCAM cDNA containing construct pIRESpuro3_EpCAM and the respective empty vector control.

2010-12-02 | E-GEOD-25743 | biostudies-arrayexpress

RNA profiling of EpCAM-positive cells in bone marrow of early breast cancer (EBC) patients

Project description:We developed a novel approach to isolate tumor cells with high purity from bone marrow which was subjected to immunomagnetic enrichment using EpCAM beads followed by fluorescence activated cell sorting (IE/FACS) to isolate EpCAM-positive cells away from leukocytes (CD45+). For RNA profiling, QPCR analysis was performed on sixty four (64) cancer-related genes using Taqman® low density arrays. For non-tumor controls, RNA profiling was performed on matched leukocytes (CD45+) isolated from the same enriched bone marrow samples from 17 of the 30 patients.

2019-04-04 | GSE112757 | GEO

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