Project description:Gene expression profiles were established for Inflammatory breast cancer samples from patients treated at the Institut Paoli-Calmettes.
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).
Project description:Genome wide DNA methylation profiling of primary breast cancer tumors and their axillary metastasis and/or ipsilateral breast recurrence and/or contralateral breast recurrence. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included 20 primary breast tumors and their matched axillary metastasis, 17 primary breast tumors and their matched ipsilateral breast recurrence, and 11 primary breast tumors and their matched contralateral breast recurrence. Bisulphite converted DNA from the 96 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2 contributed by Institut Curie - Fabien Reyal
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). 1280 breast cancer serums (74 in training cohort, 1206 in test cohort), 54 benign breast diseases serums in test cohort, 2836 non-cancer control serums (1493 in training cohort, 1343 in test cohort), 514 non-breast benign diseases serums in training cohort. 150 of the non-cancer control serums in training cohort and 412 of the non-breast benign diseases serums in training cohort have been uploaded previously and are avaialable under GSE59856 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59856).
Project description:Gene expression profiling of breast cancer primary tumor was performed to identify gene expression that is related to the presence of sufficient tumor cells. These gene profile can be used for identification of tumor samples that are eligible for microarray diagnostics. A cohort of 403 early-stage primary breast cancer tumors was analyzed against a breast cancer reference pool
Project description:SNP Expression profiling of human breast cancer: 29 tumor samples, 4 pure normal breat samples and 8 lymphocytes samples Keywords: Human Cancer
Project description:Faratian2009 - Role of PTEN in Trastuzumab
resistance
This model is described in the article:
Systems biology
reveals new strategies for personalizing cancer medicine and
confirms the role of PTEN in resistance to trastuzumab.
Faratian D, Goltsov A, Lebedeva G,
Sorokin A, Moodie S, Mullen P, Kay C, Um IH, Langdon S, Goryanin
I, Harrison DJ.
Cancer Res. 2009 Aug; 69(16):
6713-6720
Abstract:
Resistance to targeted cancer therapies such as trastuzumab
is a frequent clinical problem not solely because of
insufficient expression of HER2 receptor but also because of
the overriding activation states of cell signaling pathways.
Systems biology approaches lend themselves to rapid in silico
testing of factors, which may confer resistance to targeted
therapies. Inthis study, we aimed to develop a new kinetic
model that could be interrogated to predict resistance to
receptor tyrosine kinase (RTK) inhibitor therapies and directly
test predictions in vitro and in clinical samples. The new
mathematical model included RTK inhibitor antibody binding,
HER2/HER3 dimerization and inhibition, AKT/mitogen-activated
protein kinase cross-talk, and the regulatory properties of
PTEN. The model was parameterized using quantitative
phosphoprotein expression data from cancer cell lines using
reverse-phase protein microarrays. Quantitative PTEN protein
expression was found to be the key determinant of resistance to
anti-HER2 therapy in silico, which was predictive of unseen
experiments in vitro using the PTEN inhibitor bp(V). When
measured in cancer cell lines, PTEN expression predicts
sensitivity to anti-HER2 therapy; furthermore, this
quantitative measurement is more predictive of response
(relative risk, 3.0; 95% confidence interval, 1.6-5.5; P <
0.0001) than other pathway components taken in isolation and
when tested by multivariate analysis in a cohort of 122 breast
cancers treated with trastuzumab. For the first time, a systems
biology approach has successfully been used to stratify
patients for personalized therapy in cancer and is further
compelling evidence that PTEN, appropriately measured in the
clinical setting, refines clinical decision making in patients
treated with anti-HER2 therapies.
This model is hosted on
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and identified by:
BIOMD0000000424.
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