Microarray-based gene expression data from BPLER tumor explants.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE48444 | GEO | 2013/07/02
SECONDARY ACCESSION(S): PRJNA210145
REPOSITORIES: GEO
Similar Datasets
Project description:The gene expression of 6 different mouse xenografts initiated by BPLER cells analyzed by microarray. Basal-like triple negative breast cancers (TNBC) have poor prognosis. To study the basal-like transcriptional profile of tumors transformed by defined genetic elements, the human breast epithelial cell line BPLER was injected into NOD/SCID mice. The resulting tumors were excised for expression analysis. Keywords: breast cancer, BPLER, metastasis, tumor stem cells, tumor initiating cells, breast adenocarcinoma BPLER cells were derived from human primary breast epithelial cells propagated in WIT medium (Ince et al, Cancer Cell, 2007). These cells were transformed with hTERT, SV40 early region and hRASV12 by retroviral transduction. BPLER have a TNBC-like phenotype in vitro and are highly enriched for tumor-initiating cells. To define the phenotype of BPLER-derived tumors in vivo, BPLER cells were injected in the mammary fat-pad of 6 NOD/SCID mice. Once tumors were palpable, mice were sacrificed and tumors excised. Total RNA was extracted using Trizol. The gene expression profile of each tumor was assessed by mRNA microarray analysis. Based on histology and principal component analysis of microarray data, BPLER tumors were remarkably similar to human primary TNBC encountered in the clinic (Petrocca et al, Cancer Cell, 2013).
2013-07-02 | E-GEOD-48444 | biostudies-arrayexpress
Project description:Triple negative breast cancer (TNBC) is an aggressive subtype that lack targeted clinical therapies. In addition, TNBC is heterogeneous and was recently further sub-classified into seven TNBC subtypes that displayed unique gene expression patterns. To develop therapeutic treatment regimens, we established seven patient-derived xenograft models from TNBC tumors. These xenograft models not only retained the histology and clinical markers of the corresponding patient tumors, but also bearing the same mutations and deletions identified in the patient tumors. Moreover, as part of evaluation of these models, we performed microarrays on the xenograft tumors to assess their TNBC subtypes. After obtaining IRB-approved informed written patient consent, breast cancer tissues were obtained fresh from Stanford Hospital and transplanted into the number 2 mammary fat pads of female NOD SCID mice (NOD.CB17-Prkdcscid/J, Jackson Laboratory West, Sacramento, CA, USA). Mice were maintained in pathogen-free animal housing. The established xenografts were subsequently passaged from mouse to mouse. Xenograft tumor tissues were frozen on dry ice for RNA isolation and microarray analysis.
2014-03-21 | E-GEOD-47079 | biostudies-arrayexpress
Project description:A bank of human breast tumor xenografts was established by serial passage of primary breast tumor fragments in the cleared mammary fat pads of immuno-compromised NOD-SCID-IL2Rgammac-/- mice. The expression profiles from four different tumors (23T, 315T, 50T and 838T) were classified using diagonal discriminant analysis. The training data set consisted of 1992 samples from Curtis et al. (2012, PMID: 22522925); class labels were based on tumor subtype information provided (Basal-like, Luminal A, Luminal B, HER2-enriched and Normal breast-like). Total RNA obtained from xenograft tumors from different patients have been profiled on the Illumina HT-12 BeadChip platform.
2013-06-09 | E-GEOD-47369 | biostudies-arrayexpress
Project description:A bank of human breast tumor xenografts was established by serial passage of primary breast tumor fragments in the cleared mammary fat pads of immuno-compromised NOD-SCID-IL2Rgammac-/- mice. The expression profiles from four different tumors (23T, 315T, 50T and 838T) were classified using diagonal discriminant analysis. The training data set consisted of 1992 samples from Curtis et al. (2012, PMID: 22522925); class labels were based on tumor subtype information provided (Basal-like, Luminal A, Luminal B, HER2-enriched and Normal breast-like).
2013-06-09 | GSE47369 | GEO
Project description:A bank of human breast tumor xenografts was established by serial passage of primary breast tumor fragments in the cleared mammary fat pads of immuno-compromised NOD-SCID-IL2Rgammac–/– mice. The 15 expression profiles from five different tumors were classified using the ClaNC method [1]. The training data set consisted of 94 samples from Herschkowitz et al. [2]; class labels were based on tumor subtype (Basal-like, Luminal A, Luminal B, Claudin-low, HER2+/ER- and Normal breast-like). [1] Dabney AR (2005) Classification of microarrays to nearest centroids. Bioinformatics 21:4148-4154. [2] Herschkowitz JI, et al. (2007) Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biol 8:R76.
2011-07-07 | GSE28570 | GEO
Project description:A bank of human breast tumor xenografts was established by serial passage of primary breast tumor fragments in the cleared mammary fat pads of immuno-compromised NOD-SCID-IL2Rgammac–/– mice. The 15 expression profiles from five different tumors were classified using the ClaNC method [1]. The training data set consisted of 94 samples from Herschkowitz et al. [2]; class labels were based on tumor subtype (Basal-like, Luminal A, Luminal B, Claudin-low, HER2+/ER- and Normal breast-like). [1] Dabney AR (2005) Classification of microarrays to nearest centroids. Bioinformatics 21:4148-4154. [2] Herschkowitz JI, et al. (2007) Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biol 8:R76. Total RNA obtained from xenograft tumors from 5 different patients have been profiled in triplicate on the Illumina HT-12 BeadChip platform.
2011-07-07 | E-GEOD-28570 | biostudies-arrayexpress
Project description:We report the single-cell transcriptome of breast cancer stem cells (BCSCs) from solid tumors taken from NOD/SCID mice.
2019-10-25 | GSE124888 | GEO
Project description:We recently found that Ubc13 controls breast cancer metastasis. However, the underlying molecular mechanisms remain elusive. In order to gain a better understanding of the signaling pathways controlled by Ubc13 in metastasis, we performed a gene array analysis on xenografts derived from orthotopically implanted MDA-MB-231 LM2 cells, which preferentially metastazize to lung in NOD/SCID mice. MDA-MB-231 LM2 cells were infected with lentivial shRNA constructs targeting either GFP (Control) or Ubc13 (ubc13). The resulting Control or Ubc13-silenced cells were implanted into fat pads of six weeks old female virgin NOD/SCID mice. After eight weeks, tumors were excised, followed by collagenase/hyaluronidase digestion to establish single cell suspension, from which epithelial cells were enriched by depleting mouse cells of hematopoietic, endothelial, and fibroblast origin (CD45, TER119, CD31 and BP-1). The enrihced epithelial cells (three Control and three Ubc13-KD cells) were lysed in TRIZOL to extract RNA, which were then used to run microarray.
2014-08-18 | E-GEOD-55649 | biostudies-arrayexpress
Project description:Breast cancer is a heterogeneous disease comprised of four molecular subtypes defined by whether the tumor-originating cells are luminal or basal epithelial cells. Breast cancers arising from the luminal mammary duct often express estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth receptor 2 (HER2). Tumors expressing ER and/or PR are treated with anti-hormonal therapies, while tumors overexpressing HER2 are targeted with monoclonal antibodies. Immunohistochemical detection of ER, PR, and HER2 receptors/proteins is a critical step in breast cancer diagnosis and guided treatment. Breast tumors that do not express these proteins are known as “triple negative breast cancer” (TNBC) and are typically basal-like. TNBCs are the most aggressive subtype, with the highest mortality rates and no targeted therapy, so there is a pressing need to identify important TNBC tumor regulators. The signal transducer and activator of transcription 3 (STAT3) transcription factor has been previously implicated as a constitutively active oncogene in TNBC. However, its direct regulatory gene targets and tumorigenic properties have not been well characterized. By integrating RNA-seq and ChIP-seq data from 2 TNBC tumors and 4 cell lines, we discovered novel gene signatures directly regulated by STAT3 that were enriched for processes involving inflammation, immunity, and invasion in TNBC. Functional analysis revealed that STAT3 has a key role regulating invasion and metastasis, a characteristic often associated with TNBC. Our findings suggest therapies targeting STAT3 may be important for preventing TNBC metastasis.
2017-06-10 | GSE85579 | GEO
Project description:Radioresistance of tumors is not completely understood. Our previous studies have shown that MCF-7 breast cancer cell line exposed to 6 Gy and allowed to recover for 7 days (D7-6G) developed radio-resistance. In this study, we have tested the ability of these cells to form tumors in SCID mice and characterized these tumors by proteomic analyses. Untreated (MCF-C) and D7-6G cells (MCF-R) were injected s.c. in SCID mice and tumor growth monitored. On day 18, the mice were sacrificed and proteins were extracted from tumor tissues label free proteomic analyses was carried out by LC-MS.
2021-01-04 | PXD022506 | Pride