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Role of Ubc13 in Breast Cancer Metastasis

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE55649 | GEO | 2014/08/18

SECONDARY ACCESSION(S): PRJNA241030

REPOSITORIES: GEO

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Role of Ubc13 in Breast Cancer Metastasis

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

Profiling protease and protease inhibitor gene expression in tumors and their microenvironment

2008-07-21 | GSE6413 | GEO

Genome-wide profiles of multiple histone modifications in MDA-MB-231 and LM2-4175 cell lines

Project description:LM2-4175 cell line was originally selected from MDA-MB-231,but has more aggressive characteristics in invasion, migration and metastasis. In addition, LM2 cell line specifically metastasizes to lung. To understand the regulatory mechanisms of lung metastasis in breast cancer, we analyzed the chromatin structure of MDA-MB-231 and LM2-4175 cell lines.

2019-07-31 | GSE124379 | GEO

Next generation sequencing analysis of transcriptomes in MDA-MB-231 and LM2-4175 cell lines

Project description:LM2-4175 cell line was originally selected from MDA-MB-231,but has more aggressive characteristics in invasion, migration and metastasis. In addition, LM2 cell line specifically metastasizes to lung. To understand the melecular mechanisms of lung metastasis in breast cancer,we analyzed the RNA-seq data of MDA-MB-231 and LM2-4175 cell lines.

2019-07-31 | GSE124380 | GEO

Profiling protease and protease inhibitor gene expression in tumors and their microenvironment

Project description:To assist in the identification of proteases, their endogenous inhibitors, and proteins that interact with proteases or proteolytic pathways in biological tissues, a dual species oligonucleotide microarray has been developed in conjunction with Affymetrix, Inc. To investigate the performance of the array, gene expression profiles were analyzed in pure mouse and human samples and orthotopically implanted xenografts of human A549 lung and MDA-MB-231 breast carcinomas. The Hu/Mu ProtIn array is a valuable discovery tool for the identification of components of human and murine proteolytic pathways in health and disease, and has particular utility in the determination of cellular origins of proteases and protease inhibitors in xenograft models of human cancer. Keywords: gene expression profiles were analyzed in pure mouse and human samples and orthotopically implanted xenografts of human A549 lung and MDA-MB-231 breast carcinomas Commercial pan human and mouse total RNA replicate samples (n=3) were profiled. In addition, human ductal stage II or III breast carcinoma biopsies (n=18) were compared to normal human breast biopsies (n=13). Spontaneous spontaneous murine mammary carcinomas from MMTV-PyMT+(FVB/n) (n=8) and MMTV-PyMT+/uPARAP-/-(FVB/n) (n=2) transgenic mice were compared to normal mouse mammary fat pads (n=4; female Rag-1 tm1Mom retired breeders at >6 weeks post lactation). In vitro cultures of MDA-MB-231 human breast carcinoma cells (n=3) and MDA-MB-231 orthotopic xenografts (n=3) were profiled. The xenografts were compared to normal mammary fat pads. A549 human lung adenocarcinoma cells (n=2), A549 orthotopic xenografts (n=3) and normal mouse lung tissue (n = 3) were profiled.

2008-07-20 | E-GEOD-6413 | biostudies-arrayexpress

Simultaneous analysis of tumor and stromal gene expression profiles from xenograft models

Project description:Identifying the gene expression alterations that occur in both the tumor and stroma is essential to understanding tumor biology. We have developed a dual-species microarray analysis method that allows the dissection of both tumor and stromal gene expression profiles from xenograft models, based on limited interspecies cross-hybridization on Illumina gene expression beadchips. This methodology allows for simultaneous genome-wide analysis of gene expression profiles of both tumor cells and the associated stromal tissue. Data is provided regarding the crosshybridization of mouse liver RNA on human microarray, and MDA-MB-231 breast cancer cell line RNA on mouse microarray. Data is also provided for comparisons of MDA-MB-231 gene expression in vitro vs. in vivo, and mouse liver gene expression in control mice vs. stroma from MDA-MB-231 xenograft liver metastasis in tumor bearing mice A total of 18 samples were analyzed. Samples consist of 6 different types with each type in triplicate. Types are (1) MDA-MB-231 cell line grown in vitro and arrayed on mouse chips, (2) mouse liver from NOD/SCID mice arrayed on human chips, (3) MDA-MB-231 cell line grown in vitro arrayed on human chips, (4) MDA-MB-231 xenograft liver metastasis arrayed on human chips, (5) mouse liver from NOD/SCID mice arrayed on mouse chips, and (6) MDA-MB-231 xenograft liver metastasis arrayed on mouse chips. The overall design had three objectives: (1) to determine crosshybridizing probes based on sample types 1, 2, 3, and 5, (2) detect stromal and tumor expression using sample types 4 and 6, and (3) determine genes differentially expressed in tumor or metastasis compared to normal by comparing sample types 3 and 4 and comparing sample types 1 and 5.

2011-11-22 | E-GEOD-30993 | biostudies-arrayexpress

LM2 cell: infected with lentivirus to stably express Elf5 vs GFP

Project description:Elf5 induced transcriptional changes in high lung metastasis subline LM2 (MDA-MB-231 origin), control (GFP) vs ELF5

2012-09-20 | GSE32143 | GEO

MDA-MB-231 metastasis to human bone

Project description:MDA-MB-231 human breast cancer cells were injected orthotopiclly into mammary glands 4 of female NOD SCID mice 4-weeks after sub-cutaneous implantation of human femoral bone chips. Primary tumour, bone chips containing metastatic deposits and naive bone chips were isolated and mRNA analysed for gene expression to determine genetic signitures associated with breast cancer bone metastasis.

2019-09-24 | GSE137842 | GEO

Lung metastatic derivative LM2 cells with and without miR-335

Project description:the LM2 breast cancer cell line is an in vivo derived line from the MDA-MB-231 parental line. this LM2 line has been transduced either with a short hairpin control or miR-335 expression vector. Keywords: breast cancer, metastasis, miRNA

2008-01-01 | GSE9586 | GEO

Identification of circRNA Expression Signatures for breast cancer metastasis

Project description:To identify breast cancer metastasis-relevant circRNAs, we assessed the expression profiles of circRNAs in parental MDA-MB-231 (231-PAR) cells, isogenic brain metastatic cells (231-BM6), lung metastatic cells (LM2) and bone metastatic cells (1833), which were isolated from brain, lung or bone-seeking 231-PAR cells

2019-03-01 | GSE111504 | GEO

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