Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome profiling of the microdissected breast tissue compartments

ABSTRACT: In addition to the accumulation of pro-oncogenic mutations in the epithelial cells, the tumorigenic process involves the dysregulation of the interactions between the epithelial cells and their microenvironment, as well as alterations within the microenvironment itself. Therefore, investigating the causes of the loss of the normal tissue homeostasis in the earliest stages of breast cancer carcinogenesis is the necessary underpinning of an effective breast cancer prevention strategy. In order to comprehensively capture the transcriptomic alterations occurring in the breast in a precancerous stage, we examined a unique resource present in our institute including breast tissue biopsies donated by women two to six years prior to the clinical manifestation of breast cancer (labeled “susceptible normal tissue”) as well as specimens from healthy women. Donors in the two cohorts were at a premenopausal status and were matched according to age, racial background and menstrual phase. Both the susceptible and healthy breast tissues appear histologically normal. Upon microdissection of the three breast tissue compartments including epithelial, stromal and adipose tissue, transcriptomic analysis was performed. Upregulation of genes involved in lipid metabolism and fatty acid transport was observed also in the susceptible stroma and adipose tissue compartments, respectively.

ORGANISM(S): Homo sapiens

PROVIDER: GSE141828 | GEO | 2019/12/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Whole transcriptome analysis of breast tissues prior to breast cancer diagnosis [RNA-seq]

Project description:The Susan G. Komen Tissue Bank at Indiana University Simon Cancer Center (KTB) is the only repository of normal breast tissues donated by healthy women. As expected, a relatively small number of KTB donors (≈5%) diagnosed with breast cancer a few years post-donation. The specimens originally donated by these women (here labeled “susceptible normal tissue”) provide a window into the earliest phases of breast cancer development. Here, we investigated the transcriptomic changes in the histologically normal breast tissues donated by women 2-8 years prior to their diagnosis of breast cancer (mostly DCIS), as compared with breasts from age-matched healthy subjects.

2021-09-30 | GSE166044 | GEO

Whole methylome analysis of breast tissues prior to breast cancer diagnosis [methyl-capture]

Project description:The Susan G. Komen Tissue Bank at Indiana University Simon Cancer Center (KTB) is the only repository of normal breast tissues donated by healthy women. As expected, a relatively small number of KTB donors (≈5%) diagnosed with breast cancer a few years post-donation. The specimens originally donated by these women (here labeled “susceptible normal tissue”) provide a window into the earliest phases of breast cancer development. Here, we investigated the DNA metylation changes in the histologically normal breast tissues donated by women 2-8 years prior to their diagnosis of breast cancer (mostly DCIS), as compared with breasts from age-matched healthy subjects.

2021-09-30 | GSE166045 | GEO

Transcription profiling of human tumor microenvironment during breast cancer progression

Project description:To better understand the role of tumor microenvironment in breast cancer progression, we combined laser capture microdissection and microarray analysis to provide a comprehensive catalog of gene expression changes in both tumor and tumor-associated stroma. Experiment Overall Design: We used LCM to isolate the epithelial and stroma compartments separately from each of 14 fresh frozen primary breast cancer biopsies. In the epithelial compartment, we captured normal (N) and malignant (DCIS or IDC or both where available) epithelium from each tissue slide. In the stroma compartment, we captured both normal stroma away from the malignant lesion (NSS) and the DCIS-associated stroma (ISS) and/or IDC-associated stroma (INVS) whenever possible.

2009-02-26 | E-GEOD-14548 | biostudies-arrayexpress

A spatially resolved single cell genomic atlas of the adult human breast [scRNA_cells]

Project description:The adult human breast comprises an intricate network of epithelial ducts and lobules that are embedded in connective and adipose tissue. While most previous studies have focused on the breast epithelial system, many of the non-epithelial cell types remain understudied. Here, we constructed a comprehensive Human Breast Cell Atlas (HBCA) at single-cell and spatial resolution. Our single-cell transcriptomics data profiled 714,331 cells from 126 women, and 120,024 nuclei from 20 women, identifying 12 major cell types and 58 biological cell states. These data revealed abundant pericyte, endothelial and immune cell populations, and highly diverse luminal epithelial cell states. Spatial mapping using four different technologies revealed an unexpectedly rich ecosystem of tissue-resident immune cells, as well as distinct molecular differences between ductal and lobular regions. Collectively, these data provide an unprecedented reference of the adult normal breast tissue for studying mammary biology and diseases such as breast cancer.

2023-06-29 | GSE235326 | GEO

A spatially resolved single cell genomic atlas of the adult human breast [snRNA_nuclei]

2023-06-29 | GSE234817 | GEO

A spatially resolved single cell genomic atlas of the adult human breast [visium]

2023-06-29 | GSE234814 | GEO

Co-exposure to preadipocytes and Dioxin increase breast cancer cells aggressiveness through the generation of polynuclear giants cells.

Project description:Breast cancer (BC) is an important disease with high incidence as well as mortality among women, and critical socio-economic impacts. In the past 50 years, it has become a major health problem for women worldwide with over 2 million new cases diagnosed in 2018. This represents about 12% of all new cancer cases, 25% of all cancers in women and more than 600.000 cases of deaths worldwide in 2018 (Bray et al, 2018). If the cancer is located only in the breast, the 5-year relative survival rate of people with BC is 99% but this rate decreases if it is spread to lymph nodes (85%) and more dramatically if diagnosed with distant metastasis (26%) (Howlader et al, 2019; Siegel et al, 2017). Metastatic process, or the spread of tumor cells throughout the body, is responsible for about 90% of cancer patient deaths (Chaffer et al, 2011) and represents the central clinical challenge of solid tumor oncology. The development and progression of BC are complex processes that involve hormonal factors as well as numerous genetic and epigenetic alterations. During the past 10 years, many studies have focused on the role of the tumor microenvironment and the peritumoral stromal fraction, composed of adipose tissue, cancer-associated fibroblasts, endothelial cells and immune cells as macrophages and leukocytes. During tumor progression, cancer cells will deeply modify their microenvironment which in return will promote the growth and dissemination of the tumor (Allen et al, 2011; Polanska et al, 2013). Adipose tissue, consisting of mainly mature adipocytes and progenitors (preadipocytes and adipose-derived stem cells (ADSCs), is the most abundant component surrounding BC cells. Adipose tissue exerts a major endocrine and secretory role, and represents then an essential actor in the inflammatory, angiogenic or remodeling responses of the extracellular matrix, which influences tumor behavior.

2021-02-09 | PXD014328 | Pride

Normal breast tissue of obese women is enriched for macrophage markers and macrophage-associated gene expression

Project description:Activation of inflammatory pathways is one plausible mechanism underlying the association between obesity and increased breast cancer risk. However, macrophage infiltration and local biomarkers of inflammation in breast adipose tissue have seldom been studied in association with obesity. Gene expression profiles of normal breast tissue from reduction mammoplasty patients were evaluated by whole genome microarrays to identify patterns associated with obesity status (normal-weight, body mass index (BMI) <25; overweight, BMI 25-29.9; obese, BMI > or equal to 30). The presence of macrophage-enriched inflammatory loci with immunopositivity for CD68 protein was evaluated by immunohistochemistry (IHC). After adjusting for confounding by age, 760 genes were differentially expressed (203 up and 557 down; FDR = 0.026) between normal-weight and obese women. Gene ontology analysis suggested significant enrichment for pathways involving IL-6, IL-8, CCR5 signaling in macrophages and RXRalpha and PPARalpha activation, consistent with a pro-inflammatory state and suggestive of macrophage infiltration. Gene set enrichment analysis also demonstrated that the genomic signatures of monocytes and macrophages were over-represented in the obese group with FDR of 0.08 and 0.13, respectively. Increased macrophage infiltration was confirmed by IHC, which showed that the breast adipose tissue of obese women had higher average macrophage counts (mean = 8.96 vs. 3.56 in normal-weight women) and inflammatory foci counts (mean = 4.91 vs. 2.67 in normal-weight women). Obesity is associated with local inflammation and macrophage infiltration in normal human breast adipose tissues. Given the role of macrophages in carcinogenesis, these findings have important implications for breast cancer etiology and progression. 72 normal breast tissue samples from patients undergoing reduction mammoplasty. Reference design.

2011-11-08 | E-GEOD-33526 | biostudies-arrayexpress

Metabolic Microenvironments in Normal Breast and Breast Cancer (MS analysis)

Project description:The purpose of this study was to understand the metabolomic changes in a breast tissue microenvironment at various stages of cancer development and progression (i.e. normal breast, DCIS, and invasive cancer). The goal of this metabolomics pilot and feasibility study was to apply a broad spectrum GC-MS metabolomics method to determine whether changes in normal tissue of women with cancer correlate with progression and or the subtype of the disease.

2014-04-30 | ST000054 | MetabolomicsWorkbench

Normal breast tissue of obese women is enriched for macrophage markers and macrophage-associated gene expression

2011-11-08 | GSE33526 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data