Micro-RNA expression signatures in breast cancer progression
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Vilde Haakensen
PROVIDER: E-MTAB-3759 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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2011-03-01 | E-MTAB-471 | biostudies-arrayexpress
Project description:Gene expression studies on breast cancer have generally been performed on tissue obtained at the time of surgery. Overexpression of several genes may be a result of surgical trauma or preoperative manipulation, and may not reflect any biological impact of the disease. This study compares the expression profiles in preoperative tissue while tumor is still in its normal milieu to postoperative tissue from the same tumor obtained during surgery.
2011-03-01 | E-MTAB-469 | biostudies-arrayexpress
Project description:A total of 79 breast tumors (71 malignant tumors, 6 fibroadenomas, and 2 DCIS) were studied and compared to the reduction mammoplastic specimens of 12 healthy women as well as adjacent cancer-free tissue for 23 of the malignant tumors. Polycomb Group (PcG) proteins Bmi-1 and Mel-18 were then studied more closely first on mRNA expression level using microarray data from two of our ongoing projects and then on protein expression level using immunohistochemistry.
2010-07-01 | E-MTAB-271 | biostudies-arrayexpress
Project description:Gene expression studies on breast cancer have generally been performed on tissue obtained at the time of surgery. Overexpression of several genes may be a result of surgical trauma or preoperative manipulation, and may not reflect any biological impact of the disease. This study compares the expression profiles in preoperative tissue while tumor is still in its normal milieu to postoperative tissue from the same tumor obtained during surgery.
2011-03-01 | E-MTAB-470 | biostudies-arrayexpress
Project description:Detection of breast cancer (BC) in young women is challenging because mammography, the most common tool for detecting BC, is not effective on the dense breast tissue characteristic of young women. In addition to the limited means for detecting their BC, young women face a transient increased risk of pregnancy-associated BC. As a consequence, reproductively active women could benefit significantly from a tool that provides them with accurate risk assessment and early detection of BC. One potential method for detection of BC is biochemical monitoring of proteins and other molecules in bodily fluids such as serum, nipple aspirate, ductal lavage, tear, urine, saliva and breast milk. Of all these fluids, only breast milk provides access to a large volume of breast tissue, in the form of exfoliated epithelial cells, and to the local breast environment, in the form of molecules in the milk. Thus, analysis of breast milk is a non-invasive method with significant potential for assessing BC risk. Here we analyzed human breast milk by mass spectrometry (MS)-based proteomics to build a biomarker signature for early detection of BC. Ten milk samples from 8 women provided 5 paired-groups (cancer versus control) for analysis of differentially expressed proteins: 2 within woman comparisons (milk from a diseased breast versus a healthy breast of the same woman) and 3 across women comparisons (milk from a woman with cancer versus a woman without cancer). Despite a wide range in the time between milk donation and cancer diagnosis (cancer diagnosis occurred from 1 month before to 24 months after milk donation), the levels of some proteins differed significantly between cancer and control in several of the 5 comparison groups. These pilot data are supportive of the idea that molecular analysis of breast milk will identify proteins informative for early detection and accurate assessment of BC risk, and warrant further research.
2017-12-18 | PXD007066 | Pride
Project description:Whole transcriptome sequencing was performed on tumors collected from patients before and after hydroxyprogesterone exposure and controls. By comparing the gene expression patterns in exposed and unexposed groups, we aim to understand the molecular basis of action of hydroxyprogesterone on primary breast tumors in peri-operative setting.
2024-02-10 | E-MTAB-11412 | biostudies-arrayexpress
Project description:Analysis of breast cancer tumors following fulvestrant treatment for 4 weeks. Fulvestrant is a highly specific ER antagonist used to treat postmenopausal women with breast cancer. Data provide insight into the molecular mechanism of action of fulvestrant on whole genome expression.
2014-07-22 | E-MTAB-887 | biostudies-arrayexpress
Project description:Introduction: microRNAs (miRNAs) are short non-coding RNAs that negatively regulate gene expression and may play a causal role in invasive breast cancer. Since many genetic aberrations of invasive disease are detectable in earlier stages, we hypothesized that miRNA expression dysregulation and the predicted changes in gene expression would also be found in early breast neoplasias. Methods: Expression profiling of 365 miRNAs by RT-qPCR was combined with laser-capture microdissection to obtain an epithelial specific miRNA expression signature of normal breast epithelium (n=9) and of paired samples of histologically normal epithelium (HN) and ductal carcinoma in situ (DCIS) (n=16). To determine how miRNAs may control the expression of co-dysregulated mRNAs we also performed gene expression microarray analysis in the same paired HN and DCIS samples and integrated this with miRNA-target prediction. We further validated several target pairs by modulating the expression levels of miRNAs in MCF7 cells and measured the expression of target mRNAs and proteins. Results: Thirty-five miRNAs were aberrantly expressed between RM, HN and DCIS. Twenty-nine miRNAs and 420 mRNAs were aberrantly expressed between HN and DCIS. Combining these two datasets with miRNA-target prediction we identified two established target pairs (miR-195:CCND1 and miR-21:NFIB) and tested several novel miRNA:mRNA target pairs. Over-expression of the putative tumor-suppressor miR-125b, under-expressed in DCIS, repressed the expression of MEMO1, which is required for ErbB2-driven cell motility (also a target of miR-125b); and NRIP1/RIP140, which modulates the transcriptional activity of the estrogen receptor. Knockdown of the putative oncogenic miRNAs miR-182 and miR-183, both highly over-expressed in DCIS, increased the expression of CBX7 (which regulates E-cadherin expression), DOK4, NMT2, and EGR1. Augmentation of CBX7 by knockdown of miR-182 expression, in turn, positively regulated the expression of E-cadherin, a key protein involved in maintaining normal epithelial cell morphology which is commonly lost during neoplastic progression. Conclusions: These data provide the first miRNA expression profile of normal breast epithelium and of pre-invasive breast carcinoma. Further, we demonstrate that altered miRNA expression can modulate gene expression changes that characterize these early cancers. We conclude that miRNA dysregulation likely plays a substantial role in early breast cancer development. The expression of 365 microRNAs were measured in 19 total samples via multiplex reverse transcription PCR using the TaqMan Human MicroRNA Low Density Array. Patients age ranged from 42-75. Equal amounts of total RNA from 9 reduction mammoplasty samples (age range 42-75) were combined into a pooled RM control (PRM), this sample was run in triplicate. Remaining 16 samples consist of matched samples of ductal carcinoma in situ and adjacent histologically normal breast epithelium, these are identified by case number and histologic lesion.
2011-02-17 | E-GEOD-24508 | biostudies-arrayexpress
Project description:Expression of adipocytokines and glucocorticoid related genes are associated with down regulation of E-cadherin mRNA in colorectal carcinomas
2012-03-30 | E-MTAB-833 | biostudies-arrayexpress
Project description:Experiment description to give context to the data set: Ductal carcinoma in situ (DCIS), the most common type of pre-invasive lesion of breast, is being detected with increasing frequency with the advent of mammographic screening. Surgery is the mainstay for the treatment of DCIS. Based on the clinic-pathological features of DCIS, this may be followed by radiotherapy and/or endocrine therapy. The qualitative assessment of histological grade, expression of single protein biomarkers and more recently, mRNA analysis (DCIS Score) have been used to make these decisions. However, these factors do not fully predict the likelihood of development of invasive breast cancer treated with breast-conserving surgery. A majority of women with ductal carcinoma in situ (DCIS) receive breast-conserving surgery (BCS) but then face a risk of development of invasive breast cancer. Using Human Clariom D Pico Assay, we aim to compare the transcriptome profiles of DCIS in relation to development of invasive breast cancer (INV-BC) versus Non-INV-BC cases. Experimental Methods Clariom D Pico Human Transcriptome Array were performed according to Applied Biosystems/Thermo Fisher Scientific’s instructions. Experimental protocols are summarized in detail in Supplementary Methods (Supplementary Data). Sample annotation We compared the relative gene expression in development of invasive breast cancer (INV-BC) versus Non-INV-BC cases in Singapore cohort-59 cases (discovery cohort) and Italian cohort-50 cases (validation cohort). Microplate Plate and Well IDs are also provided as Clariom D ID list per cohort. Author information Dr. Sunil Badve is the Principal Investigator. Raw Data Probe Cell Intensity (CELL) and .ARR files which contain the design information for this study are provided (Human Clariom D Pico Assay).
2022-06-02 | E-MTAB-9856 | biostudies-arrayexpress