Gene expression of Tamoxifen induced control (TC), dormancy-like (TD) or relapse (TR) cell samples
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE280971 | GEO | 2024/11/08
REPOSITORIES: GEO
Similar Datasets
Project description:To generate a dormancy state in vivo, ovariectomized female BALB/c athymic mice (simulating the post-menopausal state) with ER+MC cell (MCF7) derived xenografts were treated with Fulvestrant (FUL). Throughout the treatment period, no significant differences in the body weight of the FUL-treated groups (FD and FR) compared to the vehicle-treated groups (FC) were observed. Whereas xenografts in the vehicle-treated group (as control group: FC) continued to increase in volume, the xenograft volumes of the FUL-treated group regressed 20%-30% in the first week and then remained stable during the four-week administration of FUL. Thereafter, half of the xenografts in FUL-treated mice were resected at random and designated as a dormancy-like group (FD). For the remaining FUL treated xenografts, treatment was discontinued and xenograft volume was observed to gradually increase. This group was defined as the relapse group (FR) and would mimic relapses observed after discontinuation of anti-estrogen therapy in patients.
2024-11-08 | GSE280970 | GEO
Project description:GOAL: Identification of genes and/or pathways involved in the pathogenesis of animal models of Rheumatoid Arthritis (RA). Total RNA samples were extracted from synovial fibroblast ex vivo cultures or whole joints (J), isolated from arthritic mice (197, DARE) and their corresponding normal (F1, wt) littermates. Fluorescent-labeled cRNA probes were utilized to hybridize (in duplicates for 197, indicated by "new") the Affymetrix Mu11K oligonucleotide DNA chipset (A+B). In detail the samples are:<br> <table> <tr> <td> <u>Animal model</u> </td> <td> <u>Sample source</u> </td> <td> <u>Sample name</u> </td> </tr> <tr> <td> Tg197 </td> <td> Tg197 ex-vivo cultured synoviocyte populations </td> <td> 197 </td> </tr> <tr> <td> Tg197 </td> <td> Tg197 ex-vivo cultured synoviocyte populations </td> <td> 197new </td> </tr> <tr> <td> Tg197 </td> <td> wt ex-vivo cultured synoviocyte populations </td> <td> F1 </td> </tr> <tr> <td> Tg197 </td> <td> wt ex-vivo cultured synoviocyte populations </td> <td> F1new </td> </tr> <tr> </tr> <tr> <td> Tg197 </td> <td> Tg197 whole joints </td> <td> 197J </td> </tr> <tr> <td> Tg197 </td> <td> Tg197 whole joints </td> <td> 197Jnew </td> </tr> <tr> <td> Tg197 </td> <td> wt whole joints </td> <td> F1J </td> </tr> <tr> <td> Tg197 </td> <td> wt whole joints </td> <td> F1Jnew </td> </tr> <tr> </tr> <tr> <td> DARE </td> <td> DARE ex-vivo cultured synoviocyte populations </td> <td> DARE </td> </tr> <tr> <td> DARE </td> <td> wt ex-vivo cultured synoviocyte populations </td> <td> wt </td> </tr> <tr> <td> DARE </td> <td> DARE whole joints </td> <td> DAREJ </td> </tr> <tr> <td> DARE </td> <td> wt whole joints </td> <td> wtJ </td> </tr> </table> <br> Submitted files carry the extension A or B, corresponding to the subArrays of chipset Mu11K. Arthritic samples were always compared with the corresponding wt sample and not to a common reference chip.
2005-06-30 | E-MEXP-255 | biostudies-arrayexpress
Project description:Gene expression of Tamoxifen induced control (TC), dormancy-like (TD) or relapse (TR) cell samples
| PRJNA1181567 | ENA
Project description:<p><u>Description of Cohort</u>: The California Pacific Medical Center (CPMC) Breast Health Cohort is a cohort study based at CPMC and is linked to the San Francisco Mammography Registry, one of the sites of the NCI-funded Breast Cancer Screening Consortium (U01CA063740). CPMC is a community hospital in San Francisco, which has one of the highest volumes for mammography in San Francisco. Between September 2004 and June 2007, >90,000 mammograms were performed at CPMC. The CPMC breast health cohort collects demographic and risk factor data on women receiving mammography through participation in the San Francisco Mammography Registry, as part of the Breast Cancer Screening Consortium (U01CA063740). The SFMR database collects information from all sources, including a questionnaire on demographic and risk factor information, the clinical results of the breast examination, the measures of breast density by Dr. John Shepherd and the women who agreed to donate a blood sample. By merging these various sources of information we have very efficiently developed a large sample of women who have donated blood and have had a measure of mamographic density.</p> <p><i>Blood Collection</i>: Dr. Steve Cummings is leading an effort to collect and archive blood samples from women who are receiving mammography screening. All women who are sent for a screening mammogram at CPMC are considered eligible. Since the cohort began collecting blood samples in July 2004 until June 2007, samples have been collected from over 11,000 women.</p> <p><i>Measurement of Breast Density</i>: Dr. John Shepherd is currently measuring breast density in a large fraction of the cohort using an automated approach with single X-ray absorptiometry. Dr. Shepherd has established a link with the CPMC mammography center that allows him to collect routine digital mammography information. Using the data from the mammogram, Dr. Shepherd and his group have developed the single X-ray absorptiometry (SXA) technique for measuring density which is described in more detail below.</p> <p>The table demonstrates the distribution of demographic variables and some breast cancer risk factors of women who donated blood and had a breast density measurement in the CPMC breast health cohort. Nearly 80% of the participants are Caucasian and most of the women are post-menopausal with a median age of ~52. Since it will be difficult to accrue a large enough sample from each ethnic group, our study will focus only on Caucasian women.</p> <p><b>Table</b>: Demographic variables, reproductive history and family history of breast cancer among 2962 women participating in the CPMC cohort study who contributed blood samples between 1994-1997. <table border="1"> <tr> <th>Variable</th> <th>Median/Percentage</th> </tr> <tr> <td>Age (Median/IQR)</td> <td align="center">52 (46-59)</td> </tr> <tr> <td>Ethnicity</td> <td></td> </tr> <tr> <td align="right">Caucasian/White</td> <td align="center">0.76</td> </tr> <tr> <td align="right">Asian/Pacific Islander</td> <td align="center">0.141</td> </tr> <tr> <td align="right">Hispanic</td> <td align="center">0.029</td> </tr> <tr> <td align="right">Mixed Race/Ethnicity</td> <td align="center">0.039</td> </tr> <tr> <td align="right">African American/Black</td> <td align="center">0.022</td> </tr> <tr> <td align="right">American Indian</td> <td align="center">0.001</td> </tr> <tr> <td align="right">Other</td> <td align="center">0.009</td> </tr> <tr> <td>First degree relative with breast cancer</td> <td align="center">0.17</td> </tr> <tr> <td>Age at first birth</td> <td></td> </tr> <tr> <td>Nulliparous</td> <td align="center">0.39</td> </tr> <tr> <td align="right">Age<20</td> <td align="center">0.043</td> </tr> <tr> <td align="right">Age>40</td> <td align="center">0.032</td> </tr> <tr> <td align="right">Age<30, ≥20</td> <td align="center">0.251</td> </tr> <tr> <td align="right">Age>30, ≤40</td> <td align="center">0.282</td> </tr> </table> </p> <p><u>Measurement of Breast Density in Cohort</u>: Measurement of breast density is accomplished using an automated technique for all mammograms obtained by Dr. Shepherd using Single X-Ray absorptiometry (SXA). SXA measurement of breast density is done on approximately 30% of all screening mammograms. Below we describe the method for measurement of breast density by SXA by Dr. Shepherd's group and its validation and association with breast cancer. As we demonstrate below, breast density, as measured by SXA, is an automated, highly reproducible measure of the density of breast tissue and is associated with breast cancer risk.</p> <p><i>SXA for Quantifying Breast Density</i>: Single x-ray absorptiometry (SXA) was initially developed for measuring bone density. SXA can determine the fraction of each of two densities simultaneously using the fact the sample is a constant thickness, the thickness in known, and the total attenuation is known. In applying this technique to breast density, we assume a two compartment model: fat and non-fatty (fibroglandular tissue). We use a reference material composed of various concentrations of two materials: one which is the same density as fat and another which is the same density as fibroglandular tissue. The reference material (phantom) is placed in the X-ray field with each mammogram. We have been able to implement this in a way that is unintrusive to the patient and technologist at CPMC.</p> <p>Assuming this two-compartment model and a constant known breast thickness, we can then calculate the percent density at any region of the breast based on the assumption that % pixel grey-scale is proportion to the mass fractions of breast fat and lean tissue. If reference materials (a phantom) of fat and fibroglandular tissue are imaged with the patient's breast and the reference materials have the same thickness as the patient's breast, then the breast's grey-scale values can be converted to fat/fibroglandular mass fractions by interpolating between those two references. The total percent density is found by averaging the volume fraction over all breast pixels.</p> <p>The phantom being used for breast density assessment at CPMC began to be used in September 2004. The phantom does not have to be manipulated by the technologist and stays attached on the mammography device during standard craniocaudal (CC) views. Thus it creates minimal to no interference with the clinical mammogram.</p> <p><i>Reproducibility of breast density measures</i>: Traditional measures of mammographic density require some human interpretation. A human reader outlines the area perceived to be dense and a computer then calculates the percent area outlined as a percent of the entire image. Thus, while traditional mammographic density is associated with breast cancer risk, it has some limitations. In a study by Drs. Shepherd, Kerlikowske, et al., the correlation coefficient (Pearson's R) between different readers was 0.8-0.9.</p> <p>In contrast to the traditional mammographic density measurement, the SXA measurement is fully automated and, therefore, the reproducibility of the measurement is higher. Dr. Shepherd and colleagues have performed a replication study of SXA as a measurement of breast density. They have estimated the correlation coefficient of the SXA measurement of breast density to be >0.98. Thus, as expected for an automated measure, SXA is a highly reproducible measure of mammographic breast density.</p> <p>Drs. Shepherd and Kerlikowske have recently analyzed the association between breast cancer risk and breast density as measured by SXA (Shepherd et al., Cancer Epi Biomarkers and Prev, 2011, PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/21610220" target="_blank">21610220</a>). They found that women in the highest quintile of % volumetric density had an odds ratio of 4.1 (95% CI: 2.3 - 7.2) for breast cancer risk compared to women in the lowest quintile of volumetric density. Thus volumetric density appears to be a highly reproducible, automated measure of breast cancer.</p>
| phs000395.v1.p1 | EGA
Project description:Interventions: <tr>
<td>An eHealth assessment and education tool for evaluating and educating FIT positive participants who are referred for colonoscopy, ‘the Digital Intake Tool’.</td>
</tr>
Primary outcome(s): The primary outcome of this study is an adequate bowel preparation defined as a Boston bowel preparation score of 6 or higher.
Study Design: N/A: single arm study, Open (masking not used), Historical, single, Other
| 2443799 | ecrin-mdr-crc
Project description:Expression data from vehicle tumor associated macrophages (TAM) VS PLX3397 treated-TAM.
| PRJNA377074 | ENA
Project description:Immunodeficient RAG1-/- mice bearing MDA-MB231-LUC+ tumors of 50-70 mm3 were daily administrated by gavage with vehicle (containing, 0.5% carboxymethylcellulose, 1.8 % NaCl, 0.4 % Tween-80, 0.9 %. benzyl alcohol, and ultrapure water adjusted to pH 6.0) or sunitinib (40mg/kg/day) for 30 days followed by treatment withdrawal for 3-4 weeks to allow the tumor regrowth until reaching the same volume as that of the vehicle treated group. Mice were sacrificed when tumor reached the volume of 350-400 mm3 and RNAs of two tumors from two different mice treated with sunitinib or vehicle were extracted.
2014-08-24 | GSE50795 | GEO
Project description:To investigate molecular mechanisms of resistance, we used two different in vivo xenograft models of estrogen receptor-positive (ER+) breast cancer, with or without HER2 over-expression (MCF7/HER2-18 and MCF7 wt, respectively). Mice with established tumors were assigned to the following treatment groups: continued estrogen supplementation (E2), estrogen deprivation (ED), ED plus tamoxifen (Tam), all with or without the EGFR tyrosine kinase inhibitor gefinitinib (G). Another group received ED plus the antiestrogen fulvestrant (MCF7 wt only). Tumors with acquired or de novo resistance to these endocrine therapies were profiled for mRNA expression using Affymetrix Genechip arrays. This SuperSeries is composed of the following subset Series:; GSE8139: Expression data from MCF7/HER2-18 xenografts; GSE8140: Expression data from MCF7 wt xenografts Experiment Overall Design: MCF7 xenografts were established in ovariectomized five to six week-old nu/nu athymic nude mice supplemented with 0.25 mg 21 day release estrogen pellets by inoculating subcutaneously (s.c.) 5E-6 cells. When tumors reached the size of 150-200 mm3 (3-5 weeks), the animals were randomly allocated to continued estrogen (E2), continued estrogen with gefitinib (E2+G; 100mg/kg, 5 days/week), estrogen withdrawal alone (ED; by removal of the estrogen pellets), and estrogen withdrawal plus tamoxifen citrate (Tam; 500 microg/animal s.c. in peanut oil, 5 days/week), with either gefitinib (Tam+G; 100mg/kg, 5 days/week) or vehicle (1% Tween 80) administered via gavage, as well as estrogen withdrawal plus fulvestrant (ICI 182,780) in the MCF7 wt model (Fulv; 5mg/mouse s.c. once weekly), and estrogen withdrawal with gefitinib (ED+G). Tumors were harvested for molecular studies when they became resistant to treatment and reached the size of 1000 mm3 (n=7). Experiment Overall Design: Refer to individual Series
2008-12-05 | E-GEOD-8141 | biostudies-arrayexpress
Project description:Four vehicle-treated and four HhAntag-treated pancreatic xenograft tumors were profiled for gene expression changes using Affymetrix U133 Plus 2.0 and Affymetrix Mouse Genome 430 2.0 arrays. Keywords: comparative gene expression, hedgehog, hh A primary human pancreatic tumor xenograft (1051178-A) was established by direct implantation of surgical material into female CD1 nu/nu mice of 6-8 weeks of age. Tumors were serially passaged into larger cohorts of mice for efficacy testing and subsequently distributed into tumor volume-matched cohorts upon tumors reaching between 200 to 350 mm3. HhAntag was resuspended in 0.5% methyl-cellulose, 0.2% Tween-80 (MCT) and administered orally twice daily at 75 mg/kg from a 10 mg/ml suspension. MCT alone served as vehicle control. Tumor xenografts (4/group) were excised following 21 days of dosing and RNA was extracted. Preparation of complementary RNA, Human Genome U133 Plus 2.0 array and Mouse Genome 430 2.0 array hybridizations, and subsequent data analysis were carried out using Affymetrix protocols, with signal intensities being determined by the MAS5.0 algorithm.
2008-09-12 | E-GEOD-11981 | biostudies-arrayexpress
Project description:Immunodeficient RAG1-/- mice bearing MDA-MB231-LUC+ tumors of 50-70 mm3 were daily administrated by gavage with vehicle (containing, 0.5% carboxymethylcellulose, 1.8 % NaCl, 0.4 % Tween-80, 0.9 %. benzyl alcohol, and ultrapure water adjusted to pH 6.0) or sunitinib (40mg/kg/day) for 30 days followed by treatment withdrawal for 3-4 weeks to allow the tumor regrowth until reaching the same volume as that of the vehicle treated group. Mice were sacrificed when tumor reached the volume of 350-400 mm3 and RNAs of two tumors from two different mice treated with sunitinib or vehicle were extracted. One color experiment with 2 experimental conditions: Sunitinib vs Vehicle (n=2), corresponding to a total of 4 samples.
2014-08-24 | E-GEOD-50795 | biostudies-arrayexpress