Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA229490 | ENA |
REPOSITORIES: ENA
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Project description:To screen candidate methylation markers for early detection of breast cancer, we performed methylated-CpG island recovery assay combined with CpG island array on 61982 CpG sites across 4162 genes in 10 breast tumor tissues and 10 non-tumor breast tissues. We detected 70 significantly hypermethylated genes in breast tumor tissues, including many novel hypermethylated genes such as ITGA4, NFIX, OTX2 and FGF12. Direct bisulfite sequencing showed widespread methylations occurred in intragenic regions of WT1, PAX6 and ITGA4 genes and promoter region of OTX2 in breast cancer tissue. COBRA assay in independent tumor and non-tumor samples confirmed that WT1, OTX2 and PAX6 genes were hypermethylated in breast cancer tissues. To explore the relationship between methylation and gene expression, gene expression profiling analysis was performed in 8 breast tumor tissues and 8 non-tumor breast tissues. We found that some hypermethylated genes in breast cancer were not expressed in breast tissues. RT-PCR assay showed that WT1 and PITX2 were only weakly expressed in the breast tumor tissues and weren’t expressed in most non-tumor breast tissues. OTX2 and PAX6 weren’t expressed in both breast tumor tissues and non-tumor tissues. Unpaired experiments, breast cancer tissue vs. normal cancer tissue. Biological replicates: 10 breast cancer tissue replicates, 10 normal breast tissue replicates.
2011-11-11 | E-GEOD-33445 | biostudies-arrayexpress
Project description:To screen candidate methylation markers for early detection of breast cancer, we performed methylated-CpG island recovery assay combined with CpG island array on 61982 CpG sites across 4162 genes in 10 breast tumor tissues and 10 non-tumor breast tissues. We detected 70 significantly hypermethylated genes in breast tumor tissues, including many novel hypermethylated genes such as ITGA4, NFIX, OTX2 and FGF12. Direct bisulfite sequencing showed widespread methylations occurred in intragenic regions of WT1, PAX6 and ITGA4 genes and promoter region of OTX2 in breast cancer tissue. COBRA assay in independent tumor and non-tumor samples confirmed that WT1, OTX2 and PAX6 genes were hypermethylated in breast cancer tissues. To explore the relationship between methylation and gene expression, gene expression profiling analysis was performed in 8 breast tumor tissues and 8 non-tumor breast tissues. We found that some hypermethylated genes in breast cancer were not expressed in breast tissues. RT-PCR assay showed that WT1 and PITX2 were only weakly expressed in the breast tumor tissues and weren’t expressed in most non-tumor breast tissues. OTX2 and PAX6 weren’t expressed in both breast tumor tissues and non-tumor tissues. Unpaired experiments, breast tumor tissues vs. breast non-tumor tissues. Biological replicates: 8 breast cancer tissue replicates, 8 breast non-tumor tissue replicates.
2011-11-11 | E-GEOD-33447 | biostudies-arrayexpress
Project description:The ability to consistently detect cell-free tumor-specific DNA in peripheral blood of patients with metastatic breast cancer provides the opportunity to detect changes in tumor burden and to monitor response to treatment. We developed cMethDNA, a quantitative multiplexed methylation specific PCR assay for a panel of ten genes, discovered through whole genome methylation array analysis of serum DNA. Cancer-specific methylated DNA was detected in training and test sets of recurrent Stage 4 patient sera with a sensitivity of >90% and a specificity of >96%. A core methylation signature was retained in serum, primary and metastatic tissues throughout the course of the disease, and the cMethDNA assay levels reflected patient response to chemotherapy. Together, our data suggest that the cMethDNA assay can provide a sensitive tool to detect minute levels of tumor DNA present in a vast excess of normal DNA in serum. Samples used: 11 cancer sera,,4 pools of normal leukocytes (5 donors per pool), 6 normal breast tissues microdissected, adjacent to tumor, 15 normal breast tissues, organoid preparations
2014-03-01 | E-GEOD-52621 | biostudies-arrayexpress
Project description:To screen candidate methylation markers for early detection of breast cancer, we performed methylated-CpG island recovery assay combined with CpG island array on 61982 CpG sites across 4162 genes in 10 breast tumor tissues and 10 non-tumor breast tissues. We detected 70 significantly hypermethylated genes in breast tumor tissues, including many novel hypermethylated genes such as ITGA4, NFIX, OTX2 and FGF12. Direct bisulfite sequencing showed widespread methylations occurred in intragenic regions of WT1, PAX6 and ITGA4 genes and promoter region of OTX2 in breast cancer tissue. COBRA assay in independent tumor and non-tumor samples confirmed that WT1, OTX2 and PAX6 genes were hypermethylated in breast cancer tissues. To explore the relationship between methylation and gene expression, gene expression profiling analysis was performed in 8 breast tumor tissues and 8 non-tumor breast tissues. We found that some hypermethylated genes in breast cancer were not expressed in breast tissues. RT-PCR assay showed that WT1 and PITX2 were only weakly expressed in the breast tumor tissues and weren’t expressed in most non-tumor breast tissues. OTX2 and PAX6 weren’t expressed in both breast tumor tissues and non-tumor tissues.
2011-11-11 | GSE33447 | GEO
Project description:To screen candidate methylation markers for early detection of breast cancer, we performed methylated-CpG island recovery assay combined with CpG island array on 61982 CpG sites across 4162 genes in 10 breast tumor tissues and 10 non-tumor breast tissues. We detected 70 significantly hypermethylated genes in breast tumor tissues, including many novel hypermethylated genes such as ITGA4, NFIX, OTX2 and FGF12. Direct bisulfite sequencing showed widespread methylations occurred in intragenic regions of WT1, PAX6 and ITGA4 genes and promoter region of OTX2 in breast cancer tissue. COBRA assay in independent tumor and non-tumor samples confirmed that WT1, OTX2 and PAX6 genes were hypermethylated in breast cancer tissues. To explore the relationship between methylation and gene expression, gene expression profiling analysis was performed in 8 breast tumor tissues and 8 non-tumor breast tissues. We found that some hypermethylated genes in breast cancer were not expressed in breast tissues. RT-PCR assay showed that WT1 and PITX2 were only weakly expressed in the breast tumor tissues and weren’t expressed in most non-tumor breast tissues. OTX2 and PAX6 weren’t expressed in both breast tumor tissues and non-tumor tissues.
2011-11-11 | GSE33445 | GEO
Project description:The ability to consistently detect cell-free tumor-specific DNA in peripheral blood of patients with metastatic breast cancer provides the opportunity to detect changes in tumor burden and to monitor response to treatment. We developed cMethDNA, a quantitative multiplexed methylation specific PCR assay for a panel of ten genes, discovered through whole genome methylation array analysis of serum DNA. Cancer-specific methylated DNA was detected in training and test sets of recurrent Stage 4 patient sera with a sensitivity of >90% and a specificity of >96%. A core methylation signature was retained in serum, primary and metastatic tissues throughout the course of the disease, and the cMethDNA assay levels reflected patient response to chemotherapy. Together, our data suggest that the cMethDNA assay can provide a sensitive tool to detect minute levels of tumor DNA present in a vast excess of normal DNA in serum.
2014-03-01 | GSE52621 | GEO
Project description:Circulating microRNAs (c-miRNAs) have emerged as measurable biomarkers (liquid biopsies) for cancer detection. The goal of our study was to identify novel biomarkers to predict long-term breast cancer risk in cancer-free women. We evaluated the ability of c-miRNAs to identify women most likely to develop breast cancer by profiling miRNA from serum obtained long before diagnosis. 24 breast cancer cases and controls (matched for risk and age) were identified from women enrolled in the High-Risk Breast Program at the UVM Cancer Center. We used Affymetrix miRNA v4 microarrays to interrogate miRNAs (miRBase v20) in the serum of cancer-free women at high-risk for breast cancer. The 24 cases developed breast cancer at least 6 months (average of 3.2 years) and the 24 controls remain cancer-free.
2018-01-22 | GSE98181 | GEO
Project description:Purpose: There is a quest for novel non-invasive diagnostic markers for the detection of breast cancer. The goal of this study is to identify circulating microRNA signatures using a cohort of Asian Chinese breast cancer patients, and to compare microRNA profiles between tumour and serum samples. Experimental design: MicroRNAs from paired breast cancer tumours, normal tissue and serum samples derived from 32 patients were comprehensively profiled using microarrays (1300 microRNAs against tumour and normal tissues) or LNA RT-PCR panels (742 microRNAs against serum samples). Serum samples from healthy individuals (n=22) were also employed as normal controls. Significant serum microRNAs, identified by logistic regression, were validated in an independent set of serum samples from patients (n=82) and healthy controls (n=53). Results: The 20 most significant microRNAs differentially expressed in breast cancer tumours included miR-21, miR-10b, and miR-145, previously shown to be dysregulated in breast cancer. Interestingly, 16 of the 20 most significant microRNAs differentially expressed in serum samples were novel. MiR-1, miR-92a, miR-133a and miR-133b were identified as the most important diagnostic markers, and were successfully validated; receiver operating characteristic curves derived from combinations of these microRNAs exhibited areas under the curves of 0.944-0.946. Only seven microRNAs were overexpressed in both tumours and serum, suggesting that microRNAs may be released into the serum selectively. Conclusion: The clinical employment of microRNA signatures as a non-invasive diagnostic strategy is promising, but should be further validated for different subtypes of breast cancers. "_A" and "_B" are two tissue sections of the same sample; "_1" and "_2" represents 2 runs of the same sample; na = not available All tissue samples were histologically confirmed by a pathologist using hematoxylin and eosin staining of cryosectioned specimens. One tumour sample was rejected due to failure to detect any tumour cells. Except for two samples (with 30% and 40% tumour cells), all tumour tissues employed had a minimum of 60% tumour cells, as estimated microscopically. Overall, the breast cancer tumour samples had an average of 71% tumour cells. The criteria for adjacent normal tissue were absence of tumour cells and presence of epithelial cells. Hence, after histological confirmation, 31 breast cancer tumours and 23 matched normal tissues were employed for microRNA extraction and profiling using microarray.
2013-09-06 | E-GEOD-42072 | biostudies-arrayexpress
Project description:Background MicroRNA expression is frequently dysregulated in cancer and it could be used potentially as a disease classifier and a prognostic tool in cancer. It has been reported that the cancer associated specific microRNAs were stably detected in blood. The objective of this study was to discover a panel of circulating microRNAs as potential ER+/HER2- breast cancer biomarkers. Methods We compared levels of circulating microRNAs in blood samples from 11 ER+/HER2- advanced breast cancer patients with age-matched 5 control subjects by using microarray-based expression profiling. We validated the level of microRNAs by real-time quantitative polymerase cycle reaction (RT-qPCR) in 40 control subjects, 180 early breast cancer patients (EBC), and 52 metastatic breast cancer patients (MBC). Then, we assessed the association between the levels of microRNA and clinical outcomes of ER+/HER2- metastatic breast cancer. Background MicroRNA expression is frequently dysregulated in cancer and it could be used potentially as a disease classifier and a prognostic tool in cancer. It has been reported that the cancer associated specific microRNAs were stably detected in blood. The objective of this study was to discover a panel of circulating microRNAs as potential ER+/HER2- breast cancer biomarkers. Methods We compared levels of circulating microRNAs in blood samples from 11 ER+/HER2- advanced breast cancer patients with age-matched 5 control subjects by using microarray-based expression profiling. We validated the level of microRNAs by real-time quantitative polymerase cycle reaction (RT-qPCR) in 40 control subjects, 180 early breast cancer patients (EBC), and 52 metastatic breast cancer patients (MBC). Then, we assessed the association between the levels of microRNA and clinical outcomes of ER+/HER2- metastatic breast cancer. Controls: 5 cases; ER +/HER2- breast cancer patients : 11 cases
2013-12-12 | E-GEOD-53179 | biostudies-arrayexpress
Project description:Analyses of circulating tumor cells (CTC) cultured from blood of patients with cancer may allow individualized testing for susceptibility to therapeutic regimens. We established ex vivo cultures of CTCs from six patients with metastatic estrogen receptor-positive breast cancer and performed RNA-Seq on those cultures. One sample each from six metastatic estrogen receptor positive breast cancer patients
2014-07-11 | E-GEOD-55807 | biostudies-arrayexpress