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LncRNA Uc003xsl.1 Activates of NF-κB/IL8 Axis to Promotes Triple-negative Breast Cancer Progression via A Decoy Role to NKRF [lnc231]

ABSTRACT: To discover the potential drivers of TNBC metastasis, we established an in vivo model by injecting MDA-MB-231cells into the tail veins of mice. Then, the breast tumor cells that successfully grew into metastatic lung tumors were collected and expanded in vitro, followed by re-injected into the tail veins of mice for lung metastasis. After three rounds of selection, a highly metastatic subline, MDA-MB-231-P3, was established, and more frequent micro-metastasis was detected in MDA-MB-231-P3 groups than that of MDA-MB-231 groups when the lungs of mice were stained with hematoxylin and eosin (HE). The lncRNA profiles of MDA-MB-231 or MDA-MB-231-P3 cells were analyzed by lncRNA sequencing. A total of 267 lncRNAs in MDA-MB-231-P3 cells were upregulated more than 2-fold in comparison to the MDA-MB-231 cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE163900 | GEO | 2021/11/29

REPOSITORIES: GEO

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LncRNA Uc003xsl.1 Activates of NF-κB/IL8 Axis to Promotes Triple-negative Breast Cancer Progression via A Decoy Role to NKRF [ChIP-Seq]

Project description:We explore the NF-κB responsive transcription that was regulated by Uc003xsl.1/NKRF complex. The chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) was performed for NKRF in MDA-MB-231-P3 cells treated with si-Uc003xsl.1 or control siRNA. The ChIP-seq data displayed 3604 peak calls in MDA-MB-231-P3 cells against control siRNA and were primarily identified as NF-κB targeting genes.

2021-11-29 | GSE163897 | GEO

LncRNA Uc003xsl.1 Activates of NF-κB/IL8 Axis to Promotes Triple-negative Breast Cancer Progression via A Decoy Role to NKRF [RNA-Seq]

Project description:The RNA-seq analysis was also performed on MDA-MB-231-P3 cells transfected with control or Uc003xsl.1 siRNA. A gene signature with highly significant expression changes post-Uc003xsl.1 siRNA treatment was observed

2021-11-29 | GSE163898 | GEO

lncRNA/mRNA expression profiling of miR-200c-overexpressing MDA-MB-231 cells

Project description:MiR-200c is a well-studied miRNA that is involved in stemness, the epithelial-mesenchymal transition, chemoresistance, radioresistance, and invasion/metastasis of various cancer cells. To obtain an overview of the lncRNA/mRNA regulated by miR-200c signaling in breast-cancer cell lines, we performed global lncRNA/mRNA-expression profiling on MDA-MB-231-pGIPZ and MDA-MB-231-miR-200c cells.

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Human Adipocytes Regulate Gene Expression in Triple-negative Breast Cancer Assessed by NGS Sequencing

Project description:Adipocyte was found play a pivotal role in tumorgenesis, progression and metastasis in breast cancer. However, affection of adipocyte on gene expression profile in triple-negative breast cancer (TNBC) is still not clear. In the present study, firstly we reported the gene expression profiles of TNBC regulated by human adipocytes using NGS. TNBC cell MDA-MB-231 was used in this study. MDA-MB-231 cells were treated with medium derived from adipocytes culture supernatants. Using two different RNA libraries, we sequenced the complete transcriptome(including mRNA, lncRNA, circleRNA and small RNA) of MDA-MB-231 treated with medium derived from adipocytes culture supernatants.

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RNAseq analysis of genes differentially expressed in MDA-MB-231 and 231-BR

Project description:We used RNA sequencing to analyze gene expression profiles of MDA-MB-231 and its brain metastasis variant (231-BR). The goal of this study is to explore genes that are differentially expressed in 231-BR and MDA-MB-231.

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NBAT1 overexpression effect on breast cancer cell line MDA-MB-231

Project description:Analysis of MDA-MB-231 breast cancer cells overexpressing lncRNA neuroblastoma associated transcript 1 (NBAT1). Results provide insight into the function of NBAT1 in breast cancer. NBAT1 overexpressed in breast cancer cells MDA-MB-231 compared to control (empty vector alone). Three replicates of each treatment were analyzed.

2015-04-21 | E-GEOD-68034 | biostudies-arrayexpress

Expression data from CD44-knockdown MDA-MB-231 human breast cancer cells.

Project description:CD44, an adhesion molecule that binds to extracellular matrix, primarily to hyaluronan (HA), has been implicated in cancer cell migration, invasion, and metastasis. CD44 has also recently been recognized as a marker for stem cells of several types of cancer. However, the roles of CD44 in the development of bone metastasis still remain unclear. To explore this issue, we established the MDA-MB-231 human breast cancer cells stably expressing short hairpin RNA against CD44. The CD44-knockdown MDA-MB-231 cells (MDA-MB-231 shCD44-2 and shCD44-3) were analyzed. As control, MDA-MB-231 cells stably expressing shRNA against firefly luciferase (shLuc) were used. Total of three samples. No replicates.

2013-04-24 | E-GEOD-45613 | biostudies-arrayexpress

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.

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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.

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