scholarly journals Deciphering the Correlation between Breast Tumor Samples and Cell Lines by Integrating Copy Number Changes and Gene Expression Profiles

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Yi Sun ◽  
Qi Liu
Keyword(s):  
Breast Cancer ◽  
Cell Lines ◽  
Cancer Cell ◽  
Breast Cancer Cell ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Breast Tumors ◽  
Cancer Cell Lines ◽  
Breast Cancer Cell Lines ◽  
Tumor Group

Breast cancer is one of the most common cancers with high incident rate and high mortality rate worldwide. Although different breast cancer cell lines were widely used in laboratory investigations, accumulated evidences have indicated that genomic differences exist between cancer cell lines and tissue samples in the past decades. The abundant molecular profiles of cancer cell lines and tumor samples deposited in the Cancer Cell Line Encyclopedia and The Cancer Genome Atlas now allow a systematical comparison of the breast cancer cell lines with breast tumors. We depicted the genomic characteristics of breast primary tumors based on the copy number variation and gene expression profiles and the breast cancer cell lines were compared to different subgroups of breast tumors. We identified that some of the breast cancer cell lines show high correlation with the tumor group that agrees with previous knowledge, while a big part of them do not, including the most used MCF7, MDA-MB-231, and T-47D. We presented a computational framework to identify cell lines that mostly resemble a certain tumor group for the breast tumor study. Our investigation presents a useful guide to bridge the gap between cell lines and tumors and helps to select the most suitable cell line models for personalized cancer studies.

Identification of circadian-related gene expression profiles in entrained breast cancer cell lines

2016 ◽  
Vol 33 (4) ◽  
pp. 392-405 ◽  
Author(s):  
Miguel A. Gutiérrez-Monreal ◽  
Victor Treviño ◽  
Jorge E. Moreno-Cuevas ◽  
Sean-Patrick Scott
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Cell Lines ◽  
Cancer Cell ◽  
Breast Cancer Cell ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cancer Cell Lines ◽  
Breast Cancer Cell Lines ◽  
Related Gene

Network Analysis of Gene Expression Profiles in Breast Cancer Cell Lines

2011 ◽  
pp. 233-242
Author(s):  
T Dewey ◽  
Katie Streicher ◽  
Stephen Ethier ◽  
T Dewey ◽  
Katie Streicher ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Network Analysis ◽  
Cell Lines ◽  
Cancer Cell ◽  
Breast Cancer Cell ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cancer Cell Lines ◽  
Breast Cancer Cell Lines

scholarly journals CD146 expression is associated with a poor prognosis in human breast tumors and with enhanced motility in breast cancer cell lines

2009 ◽  
Vol 11 (1) ◽  
Author(s):  
Gwladys Zabouo ◽  
Anne-Marie Imbert ◽  
Jocelyne Jacquemier ◽  
Pascal Finetti ◽  
Thomas Moreau ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cell Lines ◽  
Cancer Cell ◽  
Breast Cancer Cell ◽  
Poor Prognosis ◽  
Breast Tumors ◽  
Cancer Cell Lines ◽  
Breast Cancer Cell Lines ◽  
Human Breast ◽  
Cd146 Expression

A high-resolution integrated analysis of genetic and expression profiles of breast cancer cell lines

2009 ◽  
Vol 118 (3) ◽  
pp. 481-498 ◽  
Author(s):  
Alan Mackay ◽  
Narinder Tamber ◽  
Kerry Fenwick ◽  
Marjan Iravani ◽  
Anita Grigoriadis ◽  
...  
Keyword(s):  
Breast Cancer ◽  
High Resolution ◽  
Cell Lines ◽  
Cancer Cell ◽  
Breast Cancer Cell ◽  
Expression Profiles ◽  
Cancer Cell Lines ◽  
Breast Cancer Cell Lines ◽  
Integrated Analysis

scholarly journals APOBEC3B expression in breast cancer cell lines and tumors depends on the estrogen receptor status

2020 ◽  
Vol 41 (8) ◽  
pp. 1030-1037 ◽  
Author(s):  
Krizia-Ivana Udquim ◽  
Clara Zettelmeyer ◽  
A Rouf Banday ◽  
Seraph Han-Yin Lin ◽  
Ludmila Prokunina-Olsson
Keyword(s):  
Breast Cancer ◽  
Estrogen Receptor ◽  
Cell Lines ◽  
Cancer Cell ◽  
Breast Cancer Cell ◽  
Mutagenic Activity ◽  
Breast Tumors ◽  
Cancer Cell Lines ◽  
The Cancer Genome Atlas ◽  
Breast Cancer Cell Lines

Abstract Increased exposure to estrogen is associated with an elevated risk of breast cancer. Considering estrogen as a possible mutagen, we hypothesized that exposure to estrogen alone or in combination with the DNA-damaging chemotherapy drug, cisplatin, could induce expression of genes encoding enzymes involved in APOBEC-mediated mutagenesis. To test this hypothesis, we measured the expression of APOBEC3A (A3A) and APOBEC3B (A3B) genes in two breast cancer cell lines treated with estradiol, cisplatin or their combination. These cell lines, T-47D (ER+) and MDA-MB-231 (ER−), differed by the status of the estrogen receptor (ER). Expression of A3A was not detectable in any conditions tested, while A3B expression was induced by treatment with cisplatin and estradiol in ER+ cells but was not affected by estradiol in ER− cells. In The Cancer Genome Atlas, expression of A3B was significantly associated with genotypes of a regulatory germline variant rs17000526 upstream of the APOBEC3 cluster in 116 ER− breast tumors (P = 0.006) but not in 387 ER+ tumors (P = 0.48). In conclusion, we show that in breast cancer cell lines, A3B expression was induced by estradiol in ER+ cells and by cisplatin regardless of ER status. In ER+ breast tumors, the effect of estrogen may be masking the association of rs17000526 with A3B expression, which was apparent in ER− tumors. Our results provide new insights into the differential etiology of ER+ and ER− breast cancer and the possible role of A3B in this process through a mitogenic rather than the mutagenic activity of estrogen.

scholarly journals Chemically Induced Hypoxia Enhances miRNA Functions in Breast Cancer

Cancers ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 2008 ◽  
Author(s):  
Emma Gervin ◽  
Bonita Shin ◽  
Reid Opperman ◽  
Mackenzie Cullen ◽  
Riley Feser ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cell Lines ◽  
Cancer Cell ◽  
Breast Cancer Cell ◽  
Metastatic Breast ◽  
Breast Tumors ◽  
Cancer Cell Lines ◽  
Breast Cancer Cell Lines ◽  
Mcf7 Cells ◽  
Cox 2

In aggressively growing tumors, hypoxia induces HIF-1α expression promoting angiogenesis. Previously, we have shown that overexpression of oncogenic microRNAs (miRNAs, miRs) miR526b/miR655 in poorly metastatic breast cancer cell lines promotes aggressive cancer phenotypes in vitro and in vivo. Additionally, miR526b/miR655 expression is significantly higher in human breast tumors, and high miR526b/miR655 expression is associated with poor prognosis. However, the roles of miR526b/miR655 in hypoxia are unknown. To test the relationship between miR526b/miR655 and hypoxia, we used various in vitro, in silico, and in situ assays. In normoxia, miRNA-high aggressive breast cancer cell lines show higher HIF-1α expression than miRNA-low poorly metastatic breast cancer cell lines. To test direct involvement of miR526b/miR655 in hypoxia, we analyzed miRNA-high cell lines (MCF7-miR526b, MCF7-miR655, MCF7-COX2, and SKBR3-miR526b) compared to controls (MCF7 and SKBR3). CoCl2-induced hypoxia in breast cancer further promotes HIF-1α mRNA and protein expression while reducing VHL expression (a negative HIF-1α regulator), especially in miRNA-high cell lines. Hypoxia enhances oxidative stress, epithelial to mesenchymal transition, cell migration, and vascular mimicry more prominently in MCF7-miR526b/MCF7-miR655 cell lines compared to MCF7 cells. Hypoxia promotes inflammatory and angiogenesis marker (COX-2, EP4, NFκB1, VEGFA) expression in all miRNA-high cells. Hypoxia upregulates miR526b/miR655 expression in MCF7 cells, thus observed enhancement of hypoxia-induced functions in MCF7 could be attributed to miR526b/miR655 upregulation. In silico bioinformatics analysis shows miR526b/miR655 regulate PTEN (a negative regulator of HIF-1α) and NFκB1 (positive regulator of COX-2 and EP4) expression by downregulation of transcription factors NR2C2, SALL4, and ZNF207. Hypoxia-enhanced functions in miRNA-high cells are inhibited by COX-2 inhibitor (Celecoxib), EP4 antagonist (ONO-AE3-208), and irreversible PI3K/Akt inhibitor (Wortmannin). This establishes that hypoxia enhances miRNA functions following the COX-2/EP4/PI3K/Akt pathways and this pathway can serve as a therapeutic target to abrogate hypoxia and miRNA induced functions in breast cancer. In situ, HIF-1α expression is significantly higher in human breast tumors (n = 96) compared to non-cancerous control tissues (n = 20) and is positively correlated with miR526b/miR655 expression. In stratified tumor samples, HIF-1α expression was significantly higher in ER-positive, PR-positive, and HER2-negative breast tumors. Data extracted from the TCGA database also show a strong correlation between HIF-1α and miRNA-cluster expression in breast tumors. This study, for the first time, establishes the dynamic roles of miR526b/miR655 in hypoxia.

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