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Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of human primary breast tumors and MDA-MB-231 subpopulations

ABSTRACT: Subpopulations of MDA-MB-231 that exhibit different metastatic tropisms when injected into immuno-deficient mice. Also, a cohort of primary breast cancers surgically resected at the Memorial Sloan-Kettering Cancer Center (MSKCC).

ORGANISM(S): Homo sapiens

SUBMITTER: Agnes Viale

PROVIDER: E-GEOD-2603 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genes that mediate breast cancer metastasis to lung.

Minn Andy J AJ Gupta Gaorav P GP Siegel Peter M PM Bos Paula D PD Shu Weiping W Giri Dilip D DD Viale Agnes A Olshen Adam B AB Gerald William L WL Massagué Joan J

Nature 20050701 7050

By means of in vivo selection, transcriptomic analysis, functional verification and clinical validation, here we identify a set of genes that marks and mediates breast cancer metastasis to the lungs. Some of these genes serve dual functions, providing growth advantages both in the primary tumour and in the lung microenvironment. Others contribute to aggressive growth selectively in the lung. Many encode extracellular proteins and are of previously unknown relevance to cancer metastasis. ...[more]

PMID: 16049480

Similar Datasets

Subpopulations of MDA-MB-231 and Primary Breast Cancers

Project description:Subpopulations of MDA-MB-231 that exhibit different metastatic tropisms when injected into immuno-deficient mice. Also, a cohort of primary breast cancers surgically resected at the Memorial Sloan-Kettering Cancer Center (MSKCC). Keywords = Breast cancer Keywords = lung metastasis Keywords: parallel sample

2005-07-28 | GSE2603 | GEO

RNA sequencing quantitative analysis of exosome miRNAs in plasma in Metastatic renal cell carcinoma (mRCC)

Project description:Purpose: Since clinical characteristics are often inaccurate and subjective, we evaluated the prognostic value of plasma exosomal miRNAs to predict survival in metastatic renal cell cancer (mRCC). Methods: RNA sequencing was performed to identify candidate exosomal miRNAs associated with overall survival in a screening cohort of 41 mRCC patients.Candidate miRNAs were further evaluated for prognosis by TaqMan quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) in a follow-up cohort of 65 mRCC patients. Results: RNA sequencing in screening cohort generated 3.75 million mappable reads per patient, of those with normalized read counts>8 RPM (reads per million), 93.8% were mapped to miRNAs for a total of 322 unique miRNAs. Cox regression analysis identified 20 miRNAs that were associated with overall survival (OS, FDR< 0.05). Among these 20 significant miRNAs, three were validated in a separate independent cohort of 65 patients with mRCC.Patients with lower expression of miR-26a1-3p, miR-let-7i-5p and miR-615-3p had a significantly poorer OS than those with higher expression. Multivariate model by combining miR-let-7i-5p and the Memorial Sloan-Kettering Cancer Center (MSKCC) score significantly improved survival prediction. Conclusions: Our study identifies multiple plasma exosomal miRNAs showing association with survival in mRCC stage patients. Multivariate model by combining miR-let-7i-5p and the Memorial Sloan-Kettering Cancer Center (MSKCC) score significantly improved survival prediction.

2017-10-31 | GSE93175 | GEO

Expression data from colorectal cancer patients

Project description:The study consist of patients who presented at Memorial Sloan-Kettering Cancer Center with a colonic neoplasm between 1992 and 2004. Biological specimens used in this study include primary colon adenocarcinomas, adenomas, metastasis and corresponding normal mucosae.

2012-10-02 | GSE41258 | GEO

Transcription profiling of human cisplatin based chemotherarpy adult male germ cell tumor patients - validation set for prediction of outcome

Project description:This series represents expression profiles of 34 non-seminoma germ cell tumors (NSGCTs) from patients who received cisplatin based chemotherarpy for treatment of their disease for whom full clinical follow-up information was available. These specimens were used as a validation set to test outcome prediction models using a subset of previously profiled GCT specimens (see GEO accession #GSE3218). Experiment Overall Design: Tumor tissues were collected under IRB-approved protocols at the Memorial Sloan-Kettering Cancer Center, New York, between 1987 and 2003. The tumor samples consist of 34 NSGCT specimens. RNA was isolated, labeled, and hybridized to Affymetrix U133A and U133B microarrays using standard protocols. Data were processed by the RMA method.

2008-10-26 | E-GEOD-10783 | biostudies-arrayexpress

Expression data from colorectal cancer patients

2012-10-02 | E-GEOD-41258 | biostudies-arrayexpress

Transcription profiling of human adult male germ cell tumours

Project description:Expression profiling of a panel of 101 adult male germ cell tumors and 5 normal testis specimens was performed on Affymetrix U133A and U133B microarrays. This data has been used to:; 1) generate a gene classifier that predicts histology (see PMID 15870693). 2) identify candidate target genes on 12p, a region that is gained in almost 100% of germ cell tumors (see PMID 16424014); 3) identify pluripotency associated genes through comparison of pluripotent embryonal carcinoma vs. undifferentiated seminoma. ONGOING:; 4) Identification of genes associated with patient outcome and cisplatin resistance. Experiment Overall Design: Tumor tissues were collected under IRB-approved protocols at the Memorial Sloan-Kettering Cancer Center, New York, between 1987 and 1999. The tumor samples consist of 17 seminomas, 15 pure EC, 15 pure T, 10 pure YS, 2 pure CC, and 42 NSGCT with mixed histologies. There were six patients who had each had two tumors per patient that were included in this study (designated with the same number but different letter- e.g. 155A and 155C are from same patient but represent two different tumors, one being the primary testicular lesion, the other being a liver metastasis). Five normal testis specimens (and one pooled sample consisting of equal amounts of the 5 normal testis specimens) from individual of similar ages were used as controls.

2008-06-12 | E-GEOD-3218 | biostudies-arrayexpress

Transcriptomal Diversity of Long-Term Glioblastoma Survivors

Project description:Glioblastoma (GBM) is a highly aggressive type of glioma with poor prognosis. However, a small number of patients live much longer than the median survival. A better understanding of these long-term survivors (LTS) may provide important insight into the biology of GBM. We identified 7 patients with GBM treated at Memorial Sloan-Kettering Cancer Center (MSKCC) with survival greater than 48 months. We characterized the transcriptome of each patient and determined rates of MGMT promoter methylation and IDH1 and IDH2 mutational status. We identified LTS in two independent cohorts (TCGA and REMBRANDT) and analyzed the transcriptomal characteristics of these LTS. The median overall survival of our cohort was 62.5 months. LTS were distributed between the proneural (n=2), neural (n=2), classical (n=2) and mesenchymal (n=1) subtypes. Similarly, LTS in the TCGA and REMBRANDT cohorts demonstrated diverse transcriptomal subclassification identity. The majority of the MSKCC LTS (71%) were found to have methylation of the MGMT promoter. None of the patients had an IDH1 or IDH2 mutations, and IDH mutation occurred in a minority of the TCGA LTS as well. A set of 42 genes was found to be differentially expressed in the MSKCC and TCGA LTS. While IDH mutant proneural tumors impart a better prognosis in the short-term, survival beyond 4 years does not require IDH mutation and is not dictated by a single transcriptional subclass. In contrast, MGMT methylation continues to have strong prognostic value for survival beyond 4 years. These findings have substantial impact for understanding GBM biology and progression.

2014-05-02 | GSE54077 | GEO

Analysis of changes in gene expression in epidermal stem cells upon loss of Polycomb silencing

Project description:Although in vitro studies of embryonic stem cells have identified Polycomb repressor complexes (PRCs) as key regulators of differentiation, it remains unclear as to how PRC-mediated mechanisms control fates of multipotent progenitors in developing tissues. Here, we show that an essential PRC component, Ezh2, is expressed in epidermal progenitors, but diminishes concomitant with embryonic differentiation and with postnatal decline in proliferative activity. We show that Ezh2 controls proliferative potential of basal progenitors by repressing the Ink4A-Ink4B locus, and tempers the developmental rate of differentiation by preventing premature recruitment of AP1 transcriptional activator to the structural genes that are required for epidermal differentiation. Together, our studies reveal that PRCs control epigenetic modifications temporally and spatially in tissue-restricted stem cells by maintaining their proliferative potential and globally repressing undesirable differentiation programs, while selectively establishing a specific terminal differentiation program in a step-wise fashion. RNAs from FACS-purified WT and Ezh2 cKO basal cells were provided to the Genomics Core Facility of the Memorial Sloan-Kettering Cancer Center (MSKCC) for quality control, quantification, reverse transcription, labeling and hybridization to MOE430A 2.0 microarray chips (Affymetrix). Arrays were scanned per the manufacturer’s specifications for the Affymetrix MOE430v2 chip.

2009-12-18 | E-GEOD-14045 | biostudies-arrayexpress

A unique pair of microarray datasets for microRNA profiling: data with careful design (Dataset A)

Project description:We set out to demonstrate the logistic feasibility of careful study design in microarray studies and the level of scientific benefits it can provide, in comparison with post-hoc data adjustment such as normalization, for preventing confounding handling effects and improving the accuracy and reproducibility of disease-relevant biomarker detection. Towards this end, we conducted a study of microRNA expression using endometroid endometrial cancer tumors (n=96) and serous ovarian cancer tumors (n=96) that were all primary, untreated, and collected in 2000-2012 at Memorial Sloan Kettering Cancer Center. The same set of tumor tissue samples were profiled twice using the Agilent microRNA microarrays with different study designs.

2018-01-08 | GSE108838 | GEO

Gene expression data from patients with pancreatic ductal adenocarcinoma

Project description:Pancreatic ductal adenocarcinoma (PDAC) is one of the most treatment-resistant malignancies in human. To perform transcriptomic profiling on PDAC, we collected primary PDAC tissues from surgically resected PDAC patients at the Memorial-Sloan Kettering Cancer Center (NY, USA). Morphogenesis of epithelial tissues relies on the precise developmental control of cell polarity and architecture. In the early Drosophila embryo, the primary epithelium forms during cellularisation, following a tightly controlled genetic programme where specific sets of genes are up-regulated. Some of them, for instance, control membrane invagination between the nuclei anchored at the apical surface of the syncytium. We used microarrays to detail transcritomic profiling of PDACs.

2021-09-23 | GSE184585 | GEO

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