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Transcription profiling of human ductal and lobular breast cancers with familial or Cowden disease history

ABSTRACT: A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | 74 samples on Affymetrix HG-U133 Plus 2.0 GeneChips arrays for 74 patients. 5 samples on CGH CIT v7 | Breast carcinoma is the main malignant tumor occurring in patients with Cowden disease, a cancer prone syndrome caused by germline mutation of the tumor suppressor gene PTEN. To better understand this disease, we have performed a transcriptomic study of three Cowden disease breast carcinomas included in a panel of 74 familial breast cancers. Unsupervised clustering of these 74 tumors followed the intrinsic gene classification of breast cancer except for a group of five tumors that included the three Cowden tumors. The gene expression profile of the Cowden tumors shows considerable overlap with that of a breast cancer subgroup known as molecular apocrine breast carcinoma, which is suspected to have increased androgenic signaling and shows frequent ERBB2 amplification. A histological and immunohistochemical study performed on 13 additional cases of Cowden disease breast carcinomas, for which RNA was not available, showed that they have apocrine histological features and express GGT1, a marker of molecular apocrine breast carcinoma. These data suggest that activation of the ERBB2-PI3K-AKT pathway by loss of PTEN at early stages of tumorigenesis promotes the formation of breast tumors with apocrine features. | Submitter : Renaud Schiappa schiappar@ligue-cancer.net | Project leader : Michel Longy longy@bergonie.org

ORGANISM(S): Homo sapiens

SUBMITTER: Fabien Petel

PROVIDER: S-ECPF-TABM-854 | biostudies-other |

REPOSITORIES: biostudies-other

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Transcription profiling of human ductal and lobular breast cancers with familial or Cowden disease history.

Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | 74 samples on Affymetrix HG-U133 Plus 2.0 GeneChips arrays for 74 patients. 5 samples on CGH CIT v7 | Breast carcinoma is the main malignant tumor occurring in patients with Cowden disease, a cancer prone syndrome caused by germline mutation of the tumor suppressor gene PTEN. To better understand this disease, we have performed a transcriptomic study of three Cowden disease breast carcinomas included in a panel of 74 familial breast cancers. Unsupervised clustering of these 74 tumors followed the intrinsic gene classification of breast cancer except for a group of five tumors that included the three Cowden tumors. The gene expression profile of the Cowden tumors shows considerable overlap with that of a breast cancer subgroup known as molecular apocrine breast carcinoma, which is suspected to have increased androgenic signaling and shows frequent ERBB2 amplification. A histological and immunohistochemical study performed on 13 additional cases of Cowden disease breast carcinomas, for which RNA was not available, showed that they have apocrine histological features and express GGT1, a marker of molecular apocrine breast carcinoma. These data suggest that activation of the ERBB2-PI3K-AKT pathway by loss of PTEN at early stages of tumorigenesis promotes the formation of breast tumors with apocrine features. | Submitter : Renaud Schiappa schiappar@ligue-cancer.net | Project leader : Michel Longy longy@bergonie.org

2010-07-29 | E-TABM-854 | biostudies-arrayexpress

Transcription profiling of breast cancer tumors of ductal and lobular types

Project description:Breast cancer tumors of ductal (D) and lobular (L) type. Not all lobular tumors are "classical lobular" tumors. Experiment "BC2_Jeffrey_minus_G50_1" was denoted as BC-D-002.

| S-ECPF-SMDB-3962 | biostudies-other

Transcription profiling of breast cancer tumors of ductal and classical lobular types

Project description:Breast cancer tumors: of ductal (D) and classical lobular (L) type. Experiment "BC2_Jeffrey_minus_G50_1" was denoted as BC-D-002.

| S-ECPF-SMDB-3963 | biostudies-other

Transcription profiling of human lobular and ductal invasive carcinomas vs normal breast tissue from the same patient to identify gene expression profiles of ductal and lobular carcinomas in relation to normal ductal and lobular cells

Project description:The aim of our study was to identify gene expression profiles of ductal and lobular carcinomas in relation to normal ductal and lobular cells. We examined ten mastectomy specimens from postmenopausal breast cancer patients. Ductal and lobular tumor and normal cells were microdissected from cryosections. Fifty nanograms of total RNA were amplified and labeled by PCR and in vitro transcription. GCOS pairwise comparison algorithm and rank products have identified multiple genes that are differentially expressed in comparisons between ductal and lobular tumor and normal cell types. The results suggest that these genes are involved in epithelial-mesenchymal transition, TGFbeta and Wnt signaling. These changes are present in both tumor types but appear to be more prominent in lobular carcinomas. Ten surgical specimens obtained by mastectomy from postmenopausal patients with invasive ductal (IDC) and lobular breast (ILC) carcinomas were investigated. Of these, 5 were IDCs and 5 were ILCs. Tumor and normal tissues from the same mammary gland were identified by an experienced pathologist, snap-frozen in liquid nitrogen and stored at -80ºC for further analysis. Microdissection, RNA isolation, amplification, labeling and microarray analysis are described in sample definitions. Samples from particular cell types (normal ductal, normal lobular, tumor ductal, tumor lobular - 10, 10, 5, 5 samples, respectively) were considered as biological replicates and were compared in between.

| S-ECPF-GEOD-5764 | biostudies-other

Transcription profiling of human breast cancers

Project description:Signatures of Oncogenic Pathway Deregulation in Human Cancers. The ability to define cancer subtypes, recurrence of disease, and response to specific therapies using DNA microarray-based gene expression signatures has been demonstrated in multiple studies. Such data is also of substantial importance to the analysis of cellular signaling pathways central to the oncogenic process. With this focus, we have developed a series of gene expression signatures that reliably reflect the activation status of several oncogenic pathways. When evaluated in several large collections of human cancers, these gene expression signatures identify patterns of pathway deregulation in tumors, and clinically relevant associations with disease outcomes. Combining signature-based predictions across several pathways identifies coordinated patterns of pathway deregulation that distinguish between specific cancers and tumor sub-types. Clustering tumors based on pathway signatures further defines prognosis in respective patient subsets, demonstrating that patterns of oncogenic pathway deregulation underlie the development of the oncogenic phenotype and reflect the biology and outcome of specific cancers. Furthermore, predictions of pathway deregulation in cancer cell lines are shown to coincide with sensitivity to therapeutic agents that target components of the pathway, underscoring the potential for such pathway prediction to guide the use of targeted therapeutics. Experiment Overall Design: RNA was extracted from frozen tissue of primary breast tumors for gene array analysis.

| S-ECPF-GEOD-3143 | biostudies-other

Germline mutations in CDH1 are infrequent in women with early-onset or familial lobular breast cancers.

Project description:Germline mutations in CDH1 are associated with hereditary diffuse gastric cancer; lobular breast cancer also occurs excessively in families with such condition.To determine if CDH1 is a susceptibility gene for lobular breast cancer in women without a family history of diffuse gastric cancer, germline DNA was analysed for the presence of CDH1 mutations in 318 women with lobular breast cancer who were diagnosed before the age of 45 years or had a family history of breast cancer and were not known, or known not, to be carriers of germline mutations in BRCA1 or BRCA2. Cases were ascertained through breast cancer registries and high-risk cancer genetic clinics (Breast Cancer Family Registry, the kConFab and a consortium of breast cancer genetics clinics in the United States and Spain). Additionally, Multiplex Ligation-dependent Probe Amplification was performed for 134 cases to detect large deletions.No truncating mutations and no large deletions were detected. Six non-synonymous variants were found in seven families. Four (4/318 or 1.3%) are considered to be potentially pathogenic through in vitro and in silico analysis.Potentially pathogenic germline CDH1 mutations in women with early-onset or familial lobular breast cancer are at most infrequent.

| S-EPMC3003879 | biostudies-literature

Transcription profiling of human breast cancers (30)

Project description:We used microarrays to profile 30 human primary breast tumors and determine global gene expression patterns and molecular subtypes Experiment Overall Design: RNA from SNAP frozen human tumor biopsies was analyzed on Affymetrix mircroarrays

| S-ECPF-GEOD-12763 | biostudies-other

Chromatin accessibility landscape and active transcription factors in primary human invasive lobular and ductal breast carcinomas.

Project description:BackgroundInvasive lobular breast carcinoma (ILC), the second most prevalent histological subtype of breast cancer, exhibits unique molecular features compared with the more common invasive ductal carcinoma (IDC). While genomic and transcriptomic features of ILC and IDC have been characterized, genome-wide chromatin accessibility pattern differences between ILC and IDC remain largely unexplored.MethodsHere, we characterized tumor-intrinsic chromatin accessibility differences between ILC and IDC using primary tumors from The Cancer Genome Atlas (TCGA) breast cancer assay for transposase-accessible chromatin with sequencing (ATAC-seq) dataset.ResultsWe identified distinct patterns of genome-wide chromatin accessibility in ILC and IDC. Inferred patient-specific transcription factor (TF) motif activities revealed regulatory differences between and within ILC and IDC tumors. EGR1, RUNX3, TP63, STAT6, SOX family, and TEAD family TFs were higher in ILC, while ATF4, PBX3, SPDEF, PITX family, and FOX family TFs were higher in IDC.ConclusionsThis study reveals the distinct epigenomic features of ILC and IDC and the active TFs driving cancer progression that may provide valuable information on patient prognosis.

| S-EPMC9338552 | biostudies-literature

Transcription profiling of human atypical ductal hyperplasia tissue from women with or without a history of breast cancer

Project description:Fresh Atypical ductal hyperplasia (ADH) tissue collected from breast of a women who either (1) had no prior history of breast cancer and had not developed breast cancer in five years after diagnosis, (2) had cancer before ADH, or had cancer at the time as ADH or developed cancer after ADH diagnosis

| S-ECPF-GEOD-2429 | biostudies-other

Germline E-cadherin mutations in familial lobular breast cancer.

Project description:BACKGROUND: The cell surface glycoprotein E-cadherin (CDH1) is a key regulator of adhesive properties in epithelial cells. Germline mutations in CDH1 are well established as the defects underlying hereditary diffuse gastric cancer (HDGC) syndrome, and an increased risk of lobular breast cancer (LBC) has been described in HDGC kindreds. However, germline CDH1 mutations have not been described in patients with LBC in non-HDGC families. This study aimed to investigate the frequency of germline CDH1 mutations in patients with LBC with early onset disease or family histories of breast cancer without DGC. METHODS: Germline DNA was analysed in 23 women with invasive lobular or mixed ductal and lobular breast cancers who had at least one close relative with breast cancer or had themselves been diagnosed before the age of 45 years, had tested negative for a germline BRCA1 or BRCA2 mutation, and reported no personal or family history of diffuse gastric cancer. The full coding sequence of CDH1 including splice junctions was amplified using PCR and screened for mutations using DHPLC and sequencing. RESULTS: A novel germline CDH1 truncating mutation in the extracellular portion of the protein (517insA) was identified in one woman who had LBC at the age of 42 years and a first degree relative with invasive LBC. CONCLUSIONS: Germline CDH1 mutations can be associated with invasive LBC in the absence of diffuse gastric cancer. The finding, if confirmed, may have implications for management of individuals at risk for this breast cancer subtype. Clarification of the cancer risks in the syndrome is essential.

| S-EPMC2752184 | biostudies-literature

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