CTC-ITB-01
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB37968 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4084610.fastq.gz | Fastqsanger.gz | |||
| ERR4084640.fastq.gz | Fastqsanger.gz | |||
| ERR4084780.fastq.gz | Fastqsanger.gz | |||
| ERR4084611.fastq.gz | Fastqsanger.gz | |||
| ERR4084641.fastq.gz | Fastqsanger.gz |
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Project description:The CTC-iChip microfluidic device [PMID: 23552373 ] enables isolation of rare viable circulating tumor cells (CTCs) directly from whole blood specimens of patients with cancer. Reanalysis of freshly isolated CTC from 31 women with hormone receptor positive metastatic breast cancer.
2023-06-20 | GSE215886 | GEO
Project description:To characterize the most frequent genomic alterations in circulating tumor cells in breast cancer using a paired tumor-normal approach. Each normal sample was obtained from the white blood cell fraction of a patient's blood from which corresponding circulating tumor cells were isolated.
2014-02-03 | E-MTAB-2136 | biostudies-arrayexpress
Project description:Metastatic cancer cells, originating from cancer stem cells with metastatic capacity, utilize nutrient flexibility to overcome the hurdles of metastatic cascade. However, the nutrient supply for maintaining the stemness potentials of metastatic cancer cells remains unknown. Here, we revealed that metastatic breast cancer cells maintain stemness and initiate metastasis upon detachment via uptaking and oxidating lactate. In detached metastasizing breast cancer cells, lactate was incorporated into tricarboxylic acid cycle and boosted oxidative phosphorylation, and then promoted the stemness potentials via α-KG-DNMT3B-mediated SOX2 hypomethylation. Moreover, lactate was uptake and oxidated in mitochondria by CD147/MCT1/LDHB complex, whose existence correlates to the stemness potentials and tumor metastasis in breast cancer patients. An intracellularly expressed single chain variable fragment targeting mitochondrial CD147 (mito-CD147 scFv) effectively disrupted mitochondrial CD147/MCT1/LDHB complex, inhibited lactate-induced stemness potentials, depleted circulating breast cancer cells and reduced metastatic burden, suggesting a promising clinical application in reducing lactate-fueled metastasis.
2025-01-09 | PXD059617 |
Project description:In many patients with solid tumors circulating tumor cells (CTCs), that form metastases, can be identified in peripheral blood. Detection and characterization of CTCs in cancer patients provide a unique opportunity to predict patient survival, select and monitor the efficacy of treatment as well as to gain insights into the cascade of metastatic events. Here, we describe a novel approach to identify CTC-specific molecular markers. Using an integrated platform for immunomagnetic enrichment and immunofluorescent identification of CTCs, blood samples with large numbers of CTCs were identified from patients with colorectal, prostate and breast cancers. Despite enrichment, CTCs are still outnumbered by "nonspecifically" captured leukocytes. In order to determine gene expression profile for CTCs, "background" gene expression signature of white blood cells must be taken into account. To this end, following enrichment for CTCs, RNA was also extracted from the remaining CTC-depleted blood samples. The following samples were used to generate the global expression profiles for CTCs:<br><br> 1a) SAMPLE170711SUB735: CTC-enriched blood sample from a patient with breast cancer). 3700 CTCs were identified per 7.5 ml of peripheral blood in this patient.<br> 1b) SAMPLE170712SUB735: Corresponding CTC-depleted blood sample for the above patient with breast cancer.<br> 2a) SAMPLE170829SUB750: CTC-enriched blood sample from a patient with prostate cancer. 647 CTCs were identified per 7.5 ml of peripheral blood in this patient.<br> 2b) SAMPLE170830SUB750: Corresponding CTC-depleted blood sample for the above patient with prostate cancer.<br> 3a) SAMPLE170831SUB751: CTC-enriched sample from a patient with colorectal cancer. 180 CTCs were identified per 7.5 ml of peripheral blood in this patient.<br> 3b) SAMPLE170832SUB751: Corresponding CTC-depleted blood sample for the above patient with colorectal cancer.
2005-06-30 | E-MEXP-136 | biostudies-arrayexpress
Project description:The study of breast cancer pathogenesis relies heavily on the use of established cell lines often derived from metastatic lesions, which while having significantly contributed to the knowledge of breast cancer biology may inadvertently limit the understanding of the mechanisms governing the metastatic process. Our goal was to establish primary cultures from dissociation of breast tumors in order to provide cellular models that may better recapitulate breast cancer pathogenesis and the metastatic process. These cellular models differ from recently developed patient derived xenograft models (PDX) in that they can be used for both in vitro and in vivo studies. Here we report the characterization of six cellular models derived from the dissociation of primary breast tumor specimens, referred to as “dissociated tumor (DT) cells”. Among the DT cells are those that are tumorigenic and metastatic in immunosuppressed mice, and a group of cancer-associated fibroblasts (CAFs). In vitro, DT cells were characterized by proliferation assays, colony formation assays, protein and gene expression profiling, including PAM50 predictor analysis. The latter showed DT cultures similar to their paired primary tumor and as belonging to the basal and Her2-enriched subtypes, offering novel cellular models of these ER-negative breast cancer subtypes. In vivo, three DT cultures are tumorigenic in NOD/SCID and NSG mice, and one of these is metastatic to lymph nodes and lung after orthotopic inoculation into the mammary fat pad, without excision of the primary tumor. DT cultures comprised of CAFs were isolated from luminal-A, Her2-enriched and basal primary tumors, providing subtype-specific components of the tumor microenvironment. Altogether, these DT cultures provide closer-to-primary cellular models for the study of breast cancer pathogenesis, metastasis and tumor microenvironment. reference x sample
2014-08-22 | E-GEOD-55070 | biostudies-arrayexpress
Project description:Increased numbers of endothelial cells are observed in peripheral blood of cancer patients. These circulating endothelial cells (CECs) may contribute to the formation of blood vessels in the tumor or reflect vascular damage caused by treatment or tumor growth. Characterization of these cells may aid in the understanding of the angiogenic process and may provide biomarkers for treatment efficacy of angiogenesis inhibitors. To identify markers typical for CECs in cancer patients we assessed global gene expression profiles of CD146 immunomagnetically enriched CECs from healthy donors and patients with metastatic breast, colorectal, prostate, lung and renal cancer.
2006-11-08 | E-MEXP-476 | biostudies-arrayexpress
Project description:Unraveling the yet unknown molecular mechanisms regulating the biology of metastasis-competent Circulating Tumor Cells (CTCs) is important for better understanding metastatic growth and disease relapses in patients with colon cancer. We investigated and compared the transcriptome profiles of the CTC line and of a cell line derived from a primary colon cancer to get some insight into the specific molecular mechanism of metastasis-competent CTCs. We used microarrays to establish the molecular portrait of the metastasis-competent CTC and of HT-29 cells
2019-06-02 | GSE82198 | GEO
Project description:Analyses of circulating tumor cells (CTC) cultured from blood of patients with cancer may allow individualized testing for susceptibility to therapeutic regimens. We established ex vivo cultures of CTCs from six patients with metastatic estrogen receptor-positive breast cancer and performed RNA-Seq on those cultures. One sample each from six metastatic estrogen receptor positive breast cancer patients
2014-07-11 | E-GEOD-55807 | biostudies-arrayexpress
Project description:The study of breast cancer pathogenesis relies heavily on the use of established cell lines often derived from metastatic lesions, which while having significantly contributed to the knowledge of breast cancer biology may inadvertently limit the understanding of the mechanisms governing the metastatic process. Our goal was to establish primary cultures from dissociation of breast tumors in order to provide cellular models that may better recapitulate breast cancer pathogenesis and the metastatic process. These cellular models differ from recently developed patient derived xenograft models (PDX) in that they can be used for both in vitro and in vivo studies. Here we report the characterization of six cellular models derived from the dissociation of primary breast tumor specimens, referred to as “dissociated tumor (DT) cells”. Among the DT cells are those that are tumorigenic and metastatic in immunosuppressed mice, and a group of cancer-associated fibroblasts (CAFs). In vitro, DT cells were characterized by proliferation assays, colony formation assays, protein and gene expression profiling, including PAM50 predictor analysis. The latter showed DT cultures similar to their paired primary tumor and as belonging to the basal and Her2-enriched subtypes, offering novel cellular models of these ER-negative breast cancer subtypes. In vivo, three DT cultures are tumorigenic in NOD/SCID and NSG mice, and one of these is metastatic to lymph nodes and lung after orthotopic inoculation into the mammary fat pad, without excision of the primary tumor. DT cultures comprised of CAFs were isolated from luminal-A, Her2-enriched and basal primary tumors, providing subtype-specific components of the tumor microenvironment. Altogether, these DT cultures provide closer-to-primary cellular models for the study of breast cancer pathogenesis, metastasis and tumor microenvironment.
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Project description:Background MicroRNA expression is frequently dysregulated in cancer and it could be used potentially as a disease classifier and a prognostic tool in cancer. It has been reported that the cancer associated specific microRNAs were stably detected in blood. The objective of this study was to discover a panel of circulating microRNAs as potential ER+/HER2- breast cancer biomarkers. Methods We compared levels of circulating microRNAs in blood samples from 11 ER+/HER2- advanced breast cancer patients with age-matched 5 control subjects by using microarray-based expression profiling. We validated the level of microRNAs by real-time quantitative polymerase cycle reaction (RT-qPCR) in 40 control subjects, 180 early breast cancer patients (EBC), and 52 metastatic breast cancer patients (MBC). Then, we assessed the association between the levels of microRNA and clinical outcomes of ER+/HER2- metastatic breast cancer. Background MicroRNA expression is frequently dysregulated in cancer and it could be used potentially as a disease classifier and a prognostic tool in cancer. It has been reported that the cancer associated specific microRNAs were stably detected in blood. The objective of this study was to discover a panel of circulating microRNAs as potential ER+/HER2- breast cancer biomarkers. Methods We compared levels of circulating microRNAs in blood samples from 11 ER+/HER2- advanced breast cancer patients with age-matched 5 control subjects by using microarray-based expression profiling. We validated the level of microRNAs by real-time quantitative polymerase cycle reaction (RT-qPCR) in 40 control subjects, 180 early breast cancer patients (EBC), and 52 metastatic breast cancer patients (MBC). Then, we assessed the association between the levels of microRNA and clinical outcomes of ER+/HER2- metastatic breast cancer. Controls: 5 cases; ER +/HER2- breast cancer patients : 11 cases
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