Breast Cancer Cell Density: Imaging assay of the density- and context-dependence of small molecule perturbagen response in breast cancer cell lines. Dataset 2 of 3: Mean cell count and mean normalized growth rate inhibition values across all replicates.
Ontology highlight
ABSTRACT:
SUBMITTER: Marc Hafner, Mario Niepel
PROVIDER: LDS-1262 | LINCS | 2017-03-14
REPOSITORIES: LINCS
Dataset's files
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| HMS_LINCS&file=LDS-1262.tar.gz | Other |
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2017-03-14 | LDS-1263 | LINCS
Project description:In previous studies, we identified a distantly related rhomboid homologue gene known as RHBDD2 (Rhomboid domain containing 2) to be markedly overexpressed in the advanced stages of the breast and colorectal cancer diseases. In order to identify RHBDD2 modulated pathways, we analyzed two breast cancer cell lines (MCF7 and T47D) from control and RHBDD2-siRNA transient gene silencing followed by gene expression profiling analysis using the whole genome Toray 3D-GeneTM Human Oligo Chip. Statistical analysis of the Toray's 3D gene expression profiling data identified 566 commonly differentially expressed genes in association to the RHBDD2 knockdown in both breast cancer cell lines. Among the statistically significant over-represented biological process, we found the apoptosis, cell cycle and response to DNA damage process related genes. In addition, categories of genes found in the ubiquitin-proteasome and oxidative phosphorylation were also highly enriched related genes in the commonly deregulated gene list. We further used a lentivirus-based system (shRNA-pLKO.1) for stable silencing of RHBDD2 mRNA in the T47D breast cancer cell line. Using a staurosporine-induced apoptosis model, we demonstrate that RHBDD2 abrogation resulted in an apoptosis-resistant phenotype of T47D breast cancer cell line. These data are in line with a recent study, suggesting that RHBDD2 expression could be up-modulated in response to 5FU-induced apoptosis in colorectal cancer cells. Taken together, these data suggest that RHBDD2 could be involved in the modulation of the programmed cell death in cancer cells. In order to analyze differential gene expression profiling of RHBDD2 silencing and control cells, total RNA was isolated from replicate experiments from two breast cancer cell lines (MCF7 and T47D) derived from the negative control-siRNA and the RHBDD2-siRNA treatments in duplicate experiments.
2013-04-10 | E-GEOD-43015 | biostudies-arrayexpress
Project description:PurposeCell size is a fundamental characteristic of all tissues, and changes in cell size in cancer reflect tumor status and response to treatments, such as apoptosis and cell-cycle arrest. Unfortunately, cell size can currently be obtained only by pathological evaluation of tumor tissue samples obtained invasively. Previous imaging approaches are limited to preclinical MRI scanners or require relatively long acquisition times that are impractical for clinical imaging. There is a need to develop cell-size imaging for clinical applications.MethodsWe propose a clinically feasible IMPULSED (imaging microstructural parameters using limited spectrally edited diffusion) approach that can characterize mean cell sizes in solid tumors. We report the use of a combination of pulse sequences, using different gradient waveforms implemented on clinical MRI scanners and analytical equations based on these waveforms to analyze diffusion-weighted MRI signals and derive specific microstructural parameters such as cell size. We also describe comprehensive validations of this approach using computer simulations, cell experiments in vitro, and animal experiments in vivo and demonstrate applications in preoperative breast cancer patients.ResultsWith fast acquisitions (~7 minutes), IMPULSED can provide high-resolution (1.3 mm in-plane) mapping of mean cell size of human tumors in vivo on clinical 3T MRI scanners. All validations suggest that IMPULSED provides accurate and reliable measurements of mean cell size.ConclusionThe proposed IMPULSED method can assess cell-size variations in tumors of breast cancer patients, which may have the potential to assess early response to neoadjuvant therapy.
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Project description:Molecular mechanisms of cell cycle exit are poorly understood. A group of genes required for cell cycle exit and maintenance of cell quiescence in human fibroblasts following serum deprivation has been recently identified. Studies on lymphocytes following growth factor deprivation-induced cell cycle exit have predominantly focused on the initiation of apoptosis. A set of genes involved in lymphocyte quiescence have also been identified among genes highly expressed in resting lymphocytes and down-regulated after cell activation. In our study, proliferating IL-2-dependent human T cells were forced to exit cell cycle by growth factor withdrawal, and their gene expression profiles were examined. The differential gene expression analysis was performed in primary and immortalized IL-2-dependent T lymphocytes. Cell samples were collected directly from the IL-2-containing cultures and 8-hrs following IL-2 withdrawal, before apoptosis could be evidenced by the Annexin-V staining. The three primary T lymphoblast cell populations were obtained from the peripheral blood mononuclear cells (PBMC) stimulated for 24h by wheat germ agglutinin and cultured in the presence of IL-2 up to 4-8 population doublings. As shown by the cell surface analysis, these populations were composed of T cells exclusively. Samples of these cell populations were subsequently analyzed as biological replicates. Two spontaneously immortalized IL-2-dependent T cell lines were derived from normal spleen and from PBMC derived from Nijmegen Breakage Syndrome patient. Gene expression was assessed by the Affymetrix microarray HG-U133 2.0 Plus that detects 38,500 genes. The expression of a selected number of genes was verified by the qRT-PCR method. We have identified a set of 53 genes that we called a â??T lymphocyte cell cycle exit signatureâ??, comprised of 13 up-regulated and 40 down-regulated genes. Genes linked to transcription, cell cycle, cell growth, proliferation and differentiation, cell adhesion and immune functions were found to be overrepresented among the differentially expressed, before and after IL-2 deprivation. Among those, PIM1, BCL2, IL-8, HBEGF, DUSP6, OSM, CISH, SOCS2, SOCS3, LIF and IL13 were down-regulated and RPS24, SQSTM1, TMEM1, LRRC8D, ECOP, YY1AP1, C1orf63, ASAH1, SLC25A46 and MIA3 were up-regulated. Identification of genes involved in cell cycle exit and quiescence, may provide new insights into the mechanisms of tissue repair and regeneration as well as of cancer development. Experiment Overall Design: Cell sources and cell sample preparation. Experiment Overall Design: Samples of three primary, IL-2-dependent T lymphoblast cell lines, derived from three healthy donors (j, 43, 6) were collected from IL-2-containing culture and 8-hrs following IL-2 withdrawal (three pairs, each sample was analyzed once = 6 samples). Experiment Overall Design: The two spontaneously immortalized IL-2-dependent T cell lines were derived from normal spleen (line5) and from PBMC derived from a Nijmegen Breakage Syndrome patient (S9). Samples of the two immortalized cell lines were collected in three biological replicates each, from the cultures with and without IL-2 (2 x 2 x 3 = 12 samples).
2009-08-23 | E-GEOD-13909 | biostudies-arrayexpress
Project description:The failure rate of randomized phase III oncology clinical trials is extremely high, even when preceded by encouraging preclinical studies and phase II trial results of the same therapy. Thus, there is considerable effort being made to improve the predictive clinical potential of preclinical models, in addition to improving phase II trial design. With respect to the former, preclinical models have historically relied heavily on treatment of primary spontaneous or transplanted tumors rather than the more common and therapeutically challenging clinical trial circumstance of advanced metastatic disease. Here, we show that the oral antiangiogenic tyrosine kinase inhibitor (TKI), sunitinib, which failed to meet primary or secondary survival endpoints in 4 separate phase III metastatic breast cancer (MBC) trials, either alone or with chemotherapy, similarly failed to show monotherapy or combination chemotherapy efficacy in a model of postsurgical advanced MBC using a metastatic variant of the MDA-MB-231 triple-negative human breast cancer. In contrast, the drug was effective when used to treat established orthotopic primary tumors. Similar results were obtained with pazopanib monotherapy, another antiangiogenic oral TKI. However, when an antibody targeting the VEGF pathway (DC101) was tested, it showed a trend in modestly improving the efficacy of paclitaxel therapy, thus resembling to a degree prior phase III clinical results of bevacizumab plus paclitaxel in MBC. Our results suggest the potential value of treating postsurgical advanced metastatic disease as a possible strategy to improve preclinical models for predicting outcomes in patients with metastatic disease.
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Project description:CD44 is a transmembrane glycoprotein playing a key role in cel adhesion to the extracellular matrix. CD44 expression is upregulated in various cancer cells and recognized as a molecular marker for tumor-initiating cancer cells. However, the intricate correlation between CD44 and underlying biological functions is yet to be fully disclosed at molecular levels. Here, we discovererd global proteome changes induced by CD44 knockdown in the four different breast cancer cell lines by TMT based quantitative proteomics.
2021-06-10 | PXD015171 | Pride
Project description:MicroRNAs (miRNAs) have been recently detected in the circulation of cancer patients, where they are associated with clinical parameters. Discovery profiling of circulating small RNAs has not been previously reported in breast cancer (BC), and was carried out in this study to identify blood-based small RNA markers of BC clinical outcome. The pre-treatment sera of 42 stage II–III locally advanced and inflammatory BC patients who received neoadjuvant chemotherapy (NCT) followed by surgical tumor resection were analyzed for marker identification by deep sequencing all circulating small RNAs.
2013-07-20 | E-GEOD-49035 | biostudies-arrayexpress
Project description:Triple negative breast cancer (TNBC) is a highly heterogeneous disease representing the most aggressive breast cancer (BC) subtype. Lack of Estrogen Receptor alpha (ERα), progesterone receptor (PR) and epidermal growth factor receptor 2 (HER2/neu) expression makes TNBC immune to common therapies, significantly limiting the treatment options and suggesting the need to identify novel therapeutic targets. It was previously reported that Estrogen Receptor beta (ERβ) is expressed in a fraction of TNBC patients, where its presence correlates with improved patient outcome. Recently, we demonstrated an oncosuppressive ERβ effect in TNBC cell models expressing exogenous ERβ. On the other hand, it was shown that ERβ is involved in miRNA-mediated gene regulation in hormone-responsive BC cells, suggesting similar effect also in TNBC. To verify this hypothesis, we performed small non-coding RNA (sncRNA) sequencing on three engineered cell lines belonging to different TNBC molecular subtypes. ERβ-specific changes of sncRNA profile revealed that the major part of deregulated molecules are subtype specific, with only few commonly regulated ones. In order to validate the obtained results, we performed sncRNA profiling of 12 ERβ positive and 32 ERβ negative TNBC tissues, whose receptor status was assessed by immunohistochemistry in our previous research. Also here, ERβ-specific group of deregulated sncRNAs was identified. Interestingly, comparison of obtained in vitro and in vivo results revealed 2 differentially expressed miRNAs, displaying the same behavior in all three analyzed cell lines and tissues. In concordance with our previous results, IPA signaling pathway analysis performed on genes targeted by deregulated miRNAs highlighted downregulation of cholesterol biosynthesis pathway and upregulation of several signaling processes. Taken together, these findings suggest that ERβ is able to exert its oncosuppressive role in TNBC through miRNA-mediated regulation of gene expression.
2020-04-04 | E-MTAB-8807 | biostudies-arrayexpress
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