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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of breast cancer tumors of ductal and lobular types

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

SUBMITTER: Janos Demeter

PROVIDER: E-SMDB-3962 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Disease-specific genomic analysis: identifying the signature of pathologic biology.

Nicolau Monica M Tibshirani Robert R Børresen-Dale Anne-Lise AL Jeffrey Stefanie S SS

Bioinformatics (Oxford, England) 20070203 8

<h4>Motivation</h4>Genomic high-throughput technology generates massive data, providing opportunities to understand countless facets of the functioning genome. It also raises profound issues in identifying data relevant to the biology being studied.<h4>Results</h4>We introduce a method for the analysis of pathologic biology that unravels the disease characteristics of high dimensional data. The method, disease-specific genomic analysis (DSGA), is intended to precede standard techniques like clus ...[more]

PMID: 17277331

Similar Datasets

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.

2007-03-09 | E-SMDB-3963 | biostudies-arrayexpress

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 -80ÂºC 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.

2007-11-01 | E-GEOD-5764 | biostudies-arrayexpress

Analysis of microdissected invasive lobular and ductal breast carcinomas in relation to normal ductal and lobular cells

2007-03-16 | GSE5764 | GEO

Characterisation of gene expression of cancer-associated and normal fibroblasts from lobular and ductal breast cancer patients

Project description:The purpose of this study was to characterise gene expression differences between cultured human cancer-associated fibroblasts and normal fibroblasts from lobular and ductal breast cancer patients.

2021-12-31 | GSE148156 | GEO

Transcription profiling of human invasive breast cancer carcinomas with different histological types and invasive lobular carcinoma

Project description:Gene expression array analysis on a series of ten different histological special types of invasive breast carcinomas (tubular, micropapillary, mucinous A, mucinous B, endocrine, apocrine, metaplastic, medullary, adenoid cystic, invasive ductal carcinoma with osteoclastic giant cells) and invasive lobular carcinoma.<br><br>Note: this experiment was reloaded into ArrayExpress in August 2010 to include mappings between raw and processed data files. It now includes additional dye-swap combined normalized data files.

2010-08-20 | E-NCMF-3 | biostudies-arrayexpress

Single cell transcriptomic heterogeneity in invasive ductal and lobular breast cancer cells

Project description:Single cell transcriptomic heterogeneity in invasive ductal and lobular breast cancer cells

| PRJNA603358 | ENA

Epigenome analysis of normal ductal breast samples and infiltrating ductal breast cancer (BC) classified by tumour subtype

Project description:Genome wide DNA methylation profiling of non-tumoral and infiltrating ductal breast cancer (tumoral) samples. The HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across approximately 450,000 CpG in non-tumoral and tumoral samples. Non-tumoral samples included six frozen non-neoplastic breast tissues from reduction mammoplasties and tumoral samples included eight frozen tumors from each BC subtype, i.e. luminal A (LA), luminal B (LB), luminal-HER2 (LH), HER2 (H) and triple-negative (TN) (Total: 40 tumors).

2020-02-17 | GSE141338 | GEO

Single cell transcriptomic heterogeneity in invasive ductal and lobular breast cancer cells

Project description:Invasive lobular breast carcinoma (ILC), one of the major breast cancer histological subtypes, exhibits unique clinical and molecular features compared to the other well-studied ductal cancer subtype (IDC). The pathognomonic feature of ILC is loss of E-cadherin, mainly due to inactivating mutations within the CDH1 gene, but the extent of contribution of this genetic alteration to ILC-specific molecular characteristics remains largely understudied. To profile these features transcriptionally, we conducted single cell RNA sequencing on a panel of IDC and ILC cell lines, as well as an IDC cell line (T47D) with CRISPR-mediated knock out (KO) of CDH1. Inspection of intra-cell line heterogeneity illustrated genetically and transcriptionally distinct subpopulations in multiple cell lines and highlighted rare populations of cells with long latency and an apoptosis-related signature indicative of dormancy. Investigation of CDH1 KO-induced alterations showed transcriptomic membranous systems remodeling, elevated regulon activation resemblance of T47D CDH1 KO cells to ILCs, and suggests IRF1 as a major regulator of the pro-apoptotic and anti-proliferative feature of ILCs.

2020-11-05 | GSE144320 | GEO

Intra-Lesion Heterogeneity and Clonality of Lobular Carcinomas In Situ

Project description:<p>This study comprises prospectively accrued, microdissected fresh frozen samples of multifocal lobular carcinoma <i>in situ</i> (LCIS), ductal carcinoma <i>in situ</i> (DCIS), invasive lobular carcinoma and invasive ductal carcinoma from patients undergoing prophylactic or therapeutic mastectomies after a diagnosis on LCIS diagnosed and managed at Memorial Sloan Kettering Cancer Center (MSKCC). Microdissected samples were subjected to paired-end whole exome sequencing on an Illumina HiSeq 2000. The data generated were used to define the landscape of somatic genetic alterations of LCIS, DCIS, invasive lobular carcinoma and invasive ductal carcinoma, to define clonal relatedness of these lesions and to investigate the clonal shifts in the progression from <i>in situ</i> to invasive breast cancer.</p>

| phs001006 | dbGaP

Novel bio-marker discovery for stratification and prognosis of breast cancer patients

Project description:The study entails novel bio-marker discovery of Tumor Aggressive Grade signature (TAGs) genes and their role in recurrence free survival of breast cancer (BC) patients. Current BC dataset was used for co-expression analysis of TAGs genes and their role in BC progression. Additionally, recent findings have suggested an importance of structural organization of sense-antisense gene pairs (SAGPs) for transcription, post-transcriptional and post-translational events and their associations with cancer and disease. We studied SAGPs in which both gene partners are protein encoding genes (coding-coding SAGPs, ccSAGPs), their role in human BC development and demonstrated their potential for BC stratification and prognosis. Based on gene expression and correlation analyses we identified the robust set of breast cancer-relevant ccSAGPs (BCR-ccSAGPs). We isolated and characterized the sense-antisense gene classifier (SAGC) and evaluated its prognostic potential in various gene expression datasets comprising 1161 BC patients. The methods used included the Cox proportional survival analysis, statistical analysis of clinicopathologic parameters and differential gene expression.The SAGC was effective in identification of BC patients with the most aggressive disease. Independently, we validated the SAGC using 58 RNA samples of breast cancer tumors purchased from OriGene Technologies (Rockville, MD). Sixty two total RNA samples from breast tumors and normal breast epithelium have been purchased from OriGene Technologies in March, 2011. Four RNA samples were obtained from normal individuals. Among 58 breast tumors (58 patients) 56 were diagnosed as ductal breast adenocarcinoma, 1 - as lobular breast adenocarcinoma and 1 - as squamous cell carcinoma. Gene expression data for all the samples were quantified by using whole-genome RNA microarrays (HG-U133 plus 2.0, Affymetrix).

2015-05-10 | E-GEOD-61304 | biostudies-arrayexpress

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