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Transcriptome sequencing for cancer stem cell properties in MCF-7 cells with knocked down CD24

ABSTRACT: CD24 is the one of cell surface protein that anchored via glycosyl phosphatidylinositol that links to cell surface and modulates growth and differentiation signal many of cell types. A small population of cells, namely ‘Cancer Stem Cells (CSCs)’, charges highly aggressive and metastatic character of cancer cells and shows conformational change of ‘epithelial to mesenchymal transition (EMT). To understand the role of CD24 in CSC and EMT, CD24 was knocked down using siRNA in the MCF7 cell line (MCF-7 hCD24 KD) and analyzed transcriptome profiles by mRNA-sequencing. Corresponding author: Chul Geun Kim, Department of Life Science, Hanyang University, Seoul 133-791, Korea (e-mail, cgkim@hanyang.ac.kr).

ORGANISM(S): Homo sapiens

PROVIDER: GSE61917 | GEO | 2014/10/15

SECONDARY ACCESSION(S): PRJNA262675

REPOSITORIES: GEO

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Transcriptome sequencing for cancer stem cell properties in MCF-7 cells with knocked down CD24

Project description:CD24 is the one of cell surface protein that anchored via glycosyl phosphatidylinositol that links to cell surface and modulates growth and differentiation signal many of cell types. A small population of cells, namely M-bM-^@M-^XCancer Stem Cells (CSCs)M-bM-^@M-^Y, charges highly aggressive and metastatic character of cancer cells and shows conformational change of M-bM-^@M-^Xepithelial to mesenchymal transition (EMT). To understand the role of CD24 in CSC and EMT, CD24 was knocked down using siRNA in the MCF7 cell line (MCF-7 hCD24 KD) and analyzed transcriptome profiles by mRNA-sequencing. Corresponding author: Chul Geun Kim, Department of Life Science, Hanyang University, Seoul 133-791, Korea (e-mail, cgkim@hanyang.ac.kr). mRNA profiles of MCF-7 hCD24 KD cells [M-bM-^@M-^Xmonolayer (m) cultured MCF7 wild type (WT) and mMCF7 CD24KDM-bM-^@M-^Y and M-bM-^@M-^Xsphere-forming (s) MCF7 WT and sMCF7 CD24KDM-bM-^@M-^Y] were generated by deep sequencing using Illumina GAIIx.

2014-10-15 | E-GEOD-61917 | biostudies-arrayexpress

Transcriptomic analyses for the CSC-like properties under monolayer and sphere culture conditions in 293T and MCF-7 cells

Project description:In order to verify the CSC-like properties in 3D spheres of 293T cells as compared to monolayer, MCF-7 breast cancer cells under monolayer and sphere culture conditions were used as a control. Corresponding author: Chul Geun Kim, Department of Life Science, Hanyang University, Seoul 133-791, Korea (e-mail, cgkim@hanyang.ac.kr).

2016-10-12 | GSE86896 | GEO

Analysis of gastric microbiota by pyrosequencing in Korea

Project description:Sequencing of 16S ribosomal RNA (rRNA) gene, which has improved the characterization of microbial community, has made it possible to detect a low level Helicobacter pylori (HP) sequences even in HP-negative subjects which were determined by a combination of conventional methods. This study was conducted to obtain a cutoff value for HP colonization in gastric mucosa biopsies and gastric juices by the pyrosequencing method. Corresponding author: Nayoung Kim, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoungnam, Gyeonggi-do, Korea; Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea (Tel., +82-31-787-7008; e-mail, nayoungkim49@empas.com).

2014-09-18 | GSE61493 | GEO

Analysis of gastric microbiota by pyrosequencing in Korea

Project description:Sequencing of 16S ribosomal RNA (rRNA) gene, which has improved the characterization of microbial community, has made it possible to detect a low level Helicobacter pylori (HP) sequences even in HP-negative subjects which were determined by a combination of conventional methods. This study was conducted to obtain a cutoff value for HP colonization in gastric mucosa biopsies and gastric juices by the pyrosequencing method. Corresponding author: Department of Internal Medicine, Seoul National University Bundang Hospital, Seoungnam, Gyeonggi-do, Korea; Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea (Tel., +82-31-787-7008; e-mail, nayoungkim49@empas.com). Microbial DNA from gastric mucosal samples [gastric antrum (n=63, mucosal biopsy), follow-up sample on gastric antrum (n=16, mucosal biopsy), and gastric body (n=18, mucosal biopsy)] and gastric juices (n=4, not mucosal biopsy) was amplified by nested PCR using universal bacterial primers, and the 16S rRNA genes were pyrosequenced.

2014-09-18 | E-GEOD-61493 | biostudies-arrayexpress

microRNA expressions in gastric cancer

Project description:The study was undertaken to identify microRNAs differently expressed by intestinal type of gastric cancer using miRNA microarray. The miRNA expression in the intestinal type of gastric cancer depending on H. pylori infection suggest that different gastric cancer pathogenesis could be exist between H. pylori-positive and -negative gastric cancer. Total RNA was extracted from cancerous region and non-cancerous regions in formalin fixed paraffin embedded tissues of intestinal type gastric cancer patients who were H. pylori-positive (n=8) or -negative (n=8). Corresponding author: Nayoung Kim, M.D., Department of Internal Medicine, Seoul National University Bundang Hospital (Tel., +82-31-787-7008; e-mail, nayoungkim49@empas.com).

2014-01-25 | E-GEOD-54397 | biostudies-arrayexpress

The CD24 receptor induces changes to the surface protein composition of B cell microvesicles with variable effects on their RNA and protein cargo

Project description:The CD24 cell surface receptor promotes apoptosis in developing B cells, and we recently found that it induces B cells to release plasma membrane-derived, CD24-bearing microvesicles (MVs). Here we have performed a systematic characterization of B cell MVs released from WEHI-231 B lymphoma cells in response to CD24 stimulation. We found that B cells constitutively release MVs of approximately 120 nm, and that CD24 induces an increase in phosphatidylserine-positive MV release. RNA cargo was predominantly comprised of 5S rRNA, regardless of stimulation; however, CD24 caused a decrease in the incorporation of protein coding transcripts. The MV proteome was enriched with mitochondrial and metabolism-related proteins after CD24 stimulation; however, these changes were variable and could not be fully validated by western blotting. CD24-bearing MVs carried Siglec-2, CD63, IgM, and, unexpectedly, Ter-119, but not Siglec-G or MHC-II despite their presence on the cell surface. CD24 stimulation also induced changes in CD63 and IgM expression on MVs not mirrored by the changes in cell surface expression. Overall, the composition of these MVs suggests that they may be involved in releasing mitochondrial components in response to pro-apoptotic stress with changes to the surface receptors potentially altering the cell type(s) that interact with the MVs.

2017-09-01 | PXD005919 | Pride

CD24+ and CD24- myeloma-derived cancer stem cell lines

Project description:Expression profiling of CD24+ and CD24- population cells from myeloma cell lines. Results provide insight into the role of CD24+ cells in myeloma development. Keywords: multiple myeloma, cancer stem cell, CD24

2020-10-31 | GSE109650 | GEO

CD24+ and CD24- myeloma-derived cancer stem cell lines

Project description:CD24+ and CD24- myeloma-derived cancer stem cell lines

| PRJNA431593 | ENA

Ontogeny of CD24 expression in the human fetal kidney

Project description:CD24, or heat stable antigen, is a cell surface sialoglycoprotein expressed on immature cells that disappears after the cells have reached their final differentiation stage. CD24 may be important in human embryonic kidney epithelial cell differentiation. In mice, CD24 expression is up-regulated in the early metanephros and localized to developing epithelial structures but the role and expression of CD24 in the developing human kidney has not been well described. In normal human fetal kidneys from 8 to 38 weeks gestation, CD24 expression was up-regulated and restricted to the early epithelial aggregates of the metanephric blastema and to the committed proliferating tubular epithelia of the S-shape nephron; however individual CD24+ cells were identified in the interstitium of later gestation and postnatal kidneys. In freshly isolated cells, FACS analysis demonstrated distinct CD24+ and CD24+133+ cell populations, constituting up to 16% and 14% respectively of the total cells analyzed. Isolated and expanded CD24+ clones displayed features of an epithelial progenitor cell line. Early fetal urinary tract obstruction resulted in an upregulation of CD24 expression, both in developing epithelial structures of early gestation kidneys and in the cells of the injured tubular epithelium of the later gestation kidneys. These results highlight the cell specific expression of CD24 in the developing human kidney and dysregulation in fetal urinary tract obstruction. We used microarrays to define the differences in global gene expression between obstructed and normal human fetal kidneys.

2009-11-11 | GSE18969 | GEO

Expression data of CD24-CD44+ and ALDH+ cells

Project description:It has been suggested that breast cancers are driven and maintained by a cellular subpopulation with stem cell properties. These breast cancer stem cells (BCSCs) mediate metastasis and by virtue of their resistance to radiation and chemotherapy, contribute to relapse. Although several BCSC markers have been described, it is unclear whether these markers identify the same or independent BCSC populations. Based on established breast cancer cell lines, as well as primary tumor xenografts, we show that BCSCs exist in distinct mesenchymal-like (epithelial-mesenchymal transition, EMT) and epithelial-like (mesenchymal-epithelial transition, MET) states characterized by expression of distinct markers, proliferative capacity and invasive characteristics. The gene expression profiles of mesenchymal-like and epithelial-like BCSCs are remarkably similar across the different molecular subtypes of breast cancer and resemble those of distinct basal and luminal stem cells found in the normal breast. We propose that the plasticity of BCSCs allowing them to transition between EMT- and MET-like states endows these cells with the capacity for tissue invasion, dissemination and growth at metastatic sites. Breast cancer cell lines, primary xenografts and normal breast cells from patient were sorted using flow cytometry to select for cells that were CD24-,CD44+ and ALDH+. Gene expression profiles of CD24-CD44+ cells were compared with non-CD24-CD44+ cells. Gene expression profiles of ALDH+ cells were compared with ALDH- cells.

2013-11-13 | E-GEOD-52262 | biostudies-arrayexpress

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