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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of human tumor and stroma from breast catured by LCM of inflammatory and non inflammatory breast cancers

ABSTRACT: Tumor epithelium and surrounding stromal cells were isolated using laser capture microdissection of human breast cancer to examine differences in gene expression based on tissue types from inflammatory and non-inflammatory breast cancer Experiment Overall Design: We applied LCM to obtain samples enriched in tumor epithelium and stroma from 15 IBC and 35 non-IBC cases to study the relative contribution of each component to the IBC phenotype and to patient survival.

ORGANISM(S): Homo sapiens

SUBMITTER: Stefan Ambs

PROVIDER: E-GEOD-5847 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A stromal gene signature associated with inflammatory breast cancer.

Boersma Brenda J BJ Reimers Mark M Yi Ming M Ludwig Joseph A JA Luke Brian T BT Stephens Robert M RM Yfantis Harry G HG Lee Dong H DH Weinstein John N JN Ambs Stefan S

International journal of cancer 20080301 6

The factors that determine whether a breast carcinoma will develop into inflammatory breast cancer (IBC) remain poorly understood. Recent evidence indicates that the tumor stroma influences cancer phenotypes. We tested the hypotheses that the gene expression signature of the tumor stroma is a distinctive feature of IBC. We used laser capture microdissection to obtain enriched populations of tumor epithelial cells and adjacent stromal cells from 15 patients with IBC and 35 patients with invasive, ...[more]

PMID: 17999412

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Tumor and stroma from breast by LCM

Project description:Tumor epithelium and surrounding stromal cells were isolated using laser capture microdissection of human breast cancer to examine differences in gene expression based on tissue types from inflammatory and non-inflammatory breast cancer Keywords: LCM

2007-09-30 | GSE5847 | GEO

Genomic Analysis of Microdissected Inflammatory Breast Cancer

Project description:Inflammatory breast cancer (IBC) is a unique clinical entity characterized by rapid onset of erythema and swelling of the breast often without an obvious breast mass. Many studies have examined and compared gene expression between IBC and non-IBC (nIBC), repeatedly finding clusters associated with receptor subtype, but no consistent gene signature associated with IBC has been validated. Here we examined microdissected IBC tumor cells compared to microdissected nIBC tumor cells matched based on estrogen and HER-2/neu receptor status. Genomic profiling of 20 inflammatory breast cancer (IBC), 20 non-IBC and 5 normal was studied.

2013-03-29 | E-GEOD-45582 | biostudies-arrayexpress

Expression Analysis of Microdissected Inflammatory Breast Cancer

Project description:Inflammatory breast cancer (IBC) is a unique clinical entity characterized by rapid onset of erythema and swelling of the breast often without an obvious breast mass. Many studies have examined and compared gene expression between IBC and non-IBC (nIBC), repeatedly finding clusters associated with receptor subtype, but no consistent gene signature associated with IBC has been validated. Here we examined microdissected IBC tumor cells compared to microdissected nIBC tumor cells matched based on estrogen and HER-2/neu receptor status. Gene expression profiling of 20 inflammatory breast cancer (IBC), 20 non-IBC and 5 normal was studied.

2013-03-29 | E-GEOD-45581 | biostudies-arrayexpress

Genomic Analysis of Microdissected Inflammatory Breast Cancer

2013-03-29 | GSE45582 | GEO

Expression Analysis of Microdissected Inflammatory Breast Cancer

2013-03-29 | GSE45581 | GEO

Inflammatory versus non-inflammatory breast cancers

Project description:Inflammatory Breast Cancer (IBC) is the most aggressive form of breast carcinoma characterized by the rapid onset of inflammatory signs. The molecular fingerprint for this rare, severe and unique clinical entity is still not elucidated. The goal of the present work was to detect both gene expression levels and alternate RNA splice variants specific to IBC. Experimental Design: In order to identify differentially expressed genes and splicing events, we performed splice-sensitive array profiling using Affymetrix Exon Array and quantitative RT-PCR analyses in a large series of 177 IBC compared to 183 non-IBC. We also assessed the prognostic value of the identified candidate genes and splice variants. Results: A 5-splice signature (HSPA8, RPL10, RPL4, DIDO1 and EVL) was able to distinguish IBC from non-IBC tumors (p<10-7). This splice signature was associated with poor metastasis-free survival (MFS) in hormone receptor-negative non-IBC (p=0.02), whereas it had no prognostic value in IBC patients. A PAM analysis of deregulated genes in IBC compared to non-IBC identified a 10-gene signature highly predictive of IBC phenotype and conferring a poor prognosis in non-IBC. The most up-regulated genes in IBC were 3 hemoglobin genes able to highly discriminate IBC from non IBC (p<10-4). In epithelial breast tumor cells, Hb protein expression was confirmed by immunohistochemistry. Conclusions: IBC has a specific spliced transcript profile that deserves further functional studies. Above all, IBC is characterized by hemoglobin genes overexpression, a fact that may lead to increased tumor progression. If confirmed, hemoglobins may serve as therapeutic targets.

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Progression of ductal carcinoma in situ to invasive breast cancer

Project description:Ductal carcinoma in situ (DCIS) is a precursor lesion that can give rise to invasive breast cancer (IBC). It has been proposed that both the nature of the lesion and the tumor microenvironment play key roles in progression to IBC. Here, laser capture microdissected tissue samples from epithelium and stroma in normal breast, pure DCIS, and pure IBC were employed to define key gene expression profiles associated with disease progression. Tumor and matching stroma were profiled for 9 DCIS patients, 10 IBC patients, and 3 normal breast. Differential gene expression was evaluated for paired normal stroma versus normal epitelium samples, paired DCIS stroma versus DCIS epitelium samples, paired IBC stroma versus IBC epitelium, IBC stroma versus DCIS stroma, and IBC epithelium versus DCIS epithelium.

2012-03-31 | E-GEOD-33692 | biostudies-arrayexpress

Comparison of human Inflammatory and non-Inflammatory breast cancer samples

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2012-02-23 | E-MTAB-1006 | biostudies-arrayexpress

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Project description:Inflammatory breast cancer (IBC) is a rare and understudied disease, with 40% of cases presenting with HER2-positive IBC. Within a cohort of newly diagnosed patients with HER2-positive IBC, we sought to (i) assess the pathologic complete response (pCR) rate of short-term neoadjuvant dual-HER2-blockade and paclitaxel, (ii) define baseline and on-treatment transcriptional profiles of tumor biopsies that are associated with pCR, and (iii) identify biologic pathways that may explain the effect of neoadjuvant therapy on pathologic tumor response.

2022-09-01 | GSE207248 | GEO

Microarray data for inflammatory breast cancer cases

Project description:Inflammatory breast cancer (IBC) is a rare and aggressive type of breast cancer (BC) whose molecular basis is poorly understood. We performed a comprehensive molecular analysis of 24 fresh frozen IBC biopsies naïve of treatment, using a high-resolution microarray platform The most common genes covered by copy number alterations included gains of MYC and MDM4, and losses affecting TP53 and RB1. MYC and MDM4 genes have been related to IBC aggressiveness, and MDM4 might also represent a new therapeutic target in IBC. Thirteen IBC cases presented copy-neutral of heterozygosity (cnLOH) or losses covering CHL1, which gives additional evidence of its role as a tumor suppressor. Functional enrichment analysis with the most common alterations revealed genes associated with inflammatory regulation and immune response. Particularly, IL6R and IL7 could represent therapeutic targets for IBC treatment. Chromothripsis patterns were identified in nine cases and chromosomal instability in 50% of cases. High homologous recombination (HR) deficiency scores were observed in triple-negative IBC and those with metastasis. High telomeric allelic imbalance (TAI) score was detected in patients having worse overall survival (OS). TAI score could also be useful to predict deficiency in homologous recombination (HR) genes and to identify patients for platinum or PARP inhibitor therapy. Our study describes the most common genomic alterations in IBC and their association with clinical findings, providing a framework for improved diagnosis and therapeutic opportunities for this aggressive tumor type.

2020-01-24 | GSE144015 | GEO

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