MiRNA expression profiling in early stage breast cancer
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE31309 | GEO | 2012/02/02
SECONDARY ACCESSION(S): PRJNA146101
REPOSITORIES: GEO
Similar Datasets
Project description:MiRNA profiling from whole blood (EDTA) was used to identify a miRNA profile applicable for early stage breast cancer detection In the study presented here, a consecutively collected, well-defined cohort of 48 patients with early stage breast cancer (invasive ductal carcinoma) at diagnosis was compared with a cohort of 57 healthy individuals for known homo sapiens miRNAs (mirbase 15).
2012-02-02 | E-GEOD-31309 | biostudies-arrayexpress
Project description:We have assayed differential miRNA expression between late stage (stage IV) metastatic Her2+ and Her2- breast cancer.
2010-04-29 | GSE20066 | GEO
Project description:Oxysterols, oxidized derivatives of cholesterol, act in breast cancer (BC) as selective estrogen receptor modulators and affect cholesterol homeostasis, drug transport, nuclear and cell receptors, and other signaling proteins. Using overlapping data from patients with early-stage estrogen receptor-positive BC—high-coverage targeted DNA sequencing (99 patients, 113 genes), mRNA sequencing (67 patients), and full miRNome by microarrays (123 patients)—we describe complex mRNA-miRNA and miRNA-miRNA interaction (correlation) networks, with validation in two carefully curated public datasets (n=538 in total) and 11 databases. The ESR1-CH25H-INSIG1-ABCA9 axis was the most prominent, being interconnected through hsa-miR-125b-5p, but also hsa-miR-99a-5p, hsa-miR-100-5p, hsa miR 143 3p, hsa-199b-5p, hsa-miR-376a-3p, and hsa-miR-376c-3p. Mutations in SC5D, CYP46A1, and its functionally linked gene set were associated with multiple differentially expressed genes. STARD5 was upregulated in patients with positive lymph node status. High expression of miR-19b-3p was weakly associated with poor survival in multiple datasets. This is the first detailed dedicated study of interactions between DNA variation and mRNA expression of oxysterol-related genes, the miRNA transcriptome, and clinical factors in BC.
2023-08-02 | GSE225292 | GEO
Project description:Copy number alteration profiling of human early-stage (stage I and II) breast cancers. We aimed to describe the commonly occurred chromosome alterations in early-stage breast cancer (stage I and II) and to explore the implications of the recurrently altered regions (RAR) on the patient prognosis. For this purpose, we analyzed the DNA copy number alterations (CNAs) across the whole genome using oligoarray-comparative genomic hybridization (CGH) in the discovery set of EBC patients.
2012-05-09 | GSE37839 | GEO
Project description:We have assayed differential miRNA expression between late stage (stage IV) metastatic Her2+ and Her2- breast cancer. 4 late stage metastatic Her2- samples were compared to 3 late stage metastatic Her2+ samples. There are 4 within array replicates for each sample.
2010-04-29 | E-GEOD-20066 | biostudies-arrayexpress
Project description:Pooled blood plasma hi-res MS/MS top-down dataset from early-stage breast cancer patients; LC 1 Part 3
2010-10-19 | PRD000185 | Pride
Project description:Copy number alteration profiling of human early-stage (stage I and II) breast cancers. We aimed to describe the commonly occurred chromosome alterations in early-stage breast cancer (stage I and II) and to explore the implications of the recurrently altered regions (RAR) on the patient prognosis. For this purpose, we analyzed the DNA copy number alterations (CNAs) across the whole genome using oligoarray-comparative genomic hybridization (CGH) in the discovery set of EBC patients. 48 cases of early-stage breast cancer were used in this study.
2012-05-08 | E-GEOD-37839 | biostudies-arrayexpress
Project description:MicroRNA (miRNA/miR) miR526b and miR655 overexpressed tumor cell-free secretions promote breast cancer phenotypes in the tumor microenvironment (TME). However, the mechanisms of miRNA regulating TME have never been investigated. With mass spectrometry analysis of MCF7-miRNA-overexpressed versus miRNA-low MCF7-Mock tumor cell secretomes, we identified 34 novel secretory proteins coded by eight genes YWHAB, TXNDC12, MYL6B, SFN, FN1, PSMB6, PRDX4, and PEA15 those are differentially regulated. We used bioinformatic tools and systems biology approaches to identify these markers’ role in breast cancer. Gene ontology analysis showed that the top functions are related to apoptosis, oxidative stress, membrane transport, and motility, supporting miRNA-induced phenotypes. These secretory markers expression is high in breast tumors, and a strong positive correlation exists between upregulated markers’ mRNA expressions with miRNA cluster expression in luminal A breast tumors. Gene expression of secretome markers is higher in tumor tissues compared to normal samples, and immunohistochemistry data supported gene expression data. Moreover, both up and downregulated marker expressions are associated with breast cancer patient survival. miRNA regulates these marker protein expressions by targeting transcription factors of these genes. Premature miRNA (pri-miR526b and pri-miR655) are established breast cancer blood biomarkers. Here we report novel secretory markers upregulated by miR526b and miR655 (YWHAB, MYL6B, PSMB6, and PEA15) are significantly upregulated in breast cancer patients’ plasma, and are potential breast cancer biomarkers.
2023-05-10 | PXD031771 | Pride
Project description:MicroRNAs (miRNAs), which are stably present in serum, have been reported to be potentially useful for detecting cancer. In the present study, we examined the expression profiles of serum miRNAs in large cohorts to identify the miRNAs that can be used to detect breast cancer in the early stage. We comprehensively evaluated serum miRNA expression profiles using highly sensitive microarray analysis. A total of 1,280 serum samples of breast cancer patients stored in the National Cancer Center Biobank were used. Additionally, 2,836 serum samples were obtained from non-cancer controls and 514 from patients with other types of cancers or benign diseases. The samples were divided to a training cohort including non-cancer controls, other cancers and breast cancer and a test cohort including non-cancer controls and breast cancer. The training cohort was used to identify a combination of miRNAs that detect breast cancer, and the test cohort was used to validate that combination. miRNA expression was compared between breast cancer and non-breast cancer serum , and a combination of five miRNAs (miR-1246, miR-1307-3p, miR-4634, miR-6861-5p, and miR-6875-5p) was found to detect breast cancer. This combination had a sensitivity of 97.3%, specificity of 82.9%, and accuracy of 89.7% for breast cancer in the test cohort Additionally, the combination could detect breast cancer in the early stage (sensitivity of 98.0% for T0).
2016-01-21 | GSE73002 | GEO
Project description:Introduction: Circulating microRNAs (miRNAs) exhibit remarkable stability and may serve as biomarkers in several clinical cancer settings. The aim of this study was to investigate changes in the levels of specific circulating miRNA following breast cancer surgery and evaluate whether these alterations were also observed in an independent data set. Methods: Global miRNA analysis was performed on prospectively collected serum samples from 24 post-menopausal women with estrogen receptor-positive early-stage breast cancer before surgery and 3 weeks after tumor resection using global LNA-based quantitative real-time PCR (qPCR). Results: Numbers of specific miRNAs detected in the samples ranged from 142 to 161, with 107 miRNAs detectable in all samples. After correction for multiple comparisons, 3 circulating miRNAs (miR-338-3p, miR-223 and miR-148a) exhibited significantly lower, and 1 miRNA (miR-107) higher levels in post-operative vs. pre-operative samples (p<0.05). No miRNAs were consistently undetectable in the post-operative samples compared to the pre-operative samples. Subsequently, our findings were compared to a dataset from a comparable patient population analyzed using similar study design and the same qPCR profiling platform, resulting in limited agreement. Conclusions: A panel of 4 circulating miRNAs exhibited significantly altered levels following radical resection of primary ER+ breast cancers in post-menopausal women. These specific miRNAs may be involved in tumorigenesis and could potentially be used to monitor whether all cancer cells have been removed at surgery and/or, subsequently, whether the patients develop recurrence. 48 serum samples were prospectively collected from 24 patients with early stage breast cancer before and after surgery at Odense University Hospital. Serum was prepared within one hour of sample collection after centrifugation (2000 x g; 10 min at 20 M-BM-:C) and immediately stored at -80 M-BM-:C.
2014-11-01 | E-GEOD-57661 | biostudies-arrayexpress