B-cell chronic lymphocytic leukemia side population cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE30171 | GEO | 2011/09/27
SECONDARY ACCESSION(S): PRJNA143867
REPOSITORIES: GEO
Similar Datasets
Project description:Analysis of Hoechst dye 33342-effluxing side population (SP) cells from B-CLL peripheral blood mononuclear cells. 9 biological replicates from B-CLL patients sorted into CD5+CD19+ SP and non-SP subsets. Two color comparative gene expression using Agilent microarrays.
2011-09-26 | E-GEOD-30171 | biostudies-arrayexpress
Project description:Side population (SP) cells are identified based on their capacity to efflux of the fluorescent dye Hoechst 33342, and are enriched for hematopoietic stem cells (HSCs) in mammalian bone marrow. We recently demonstrated that SP cells were present in the teleost kidney, the main hematopoietic organ in teleosts, and were enriched for HSCs. In this analysis, to identify the regulated genes in teleost HSCs, gene expression analysis of zebrafish kidney SP cells were performed using the GeneChip Zebrafish Genome Array.
2008-10-10 | GSE12955 | GEO
Project description:Analysis of Hoechst 33342 dye-effluxing side population cells (SP cells defined as glioma stem cells, GSCs) and dye-retaining main population cells (MP cells defined as non-GSCs) that were FACS-sorted from the C6 glioma cell line stably expressing EGFP (C6-eGFP). ECM-related genes, such as Col4a1 and Col4a2, and the iron carrier gene Tf are upregulated in MP cells. Results provide the insight into molecular basis underlying the maintenance of GSCs by non-GSCs.
2016-01-01 | GSE72431 | GEO
Project description:Analysis of Hoechst 33342 dye-effluxing side population cells (SP cells defined as glioma stem cells, GSCs) and dye-retaining main population cells (MP cells defined as non-GSCs) that were FACS-sorted from the C6 glioma cell line stably expressing EGFP (C6-eGFP). ECM-related genes, such as Col4a1 and Col4a2, and the iron carrier gene Tf are upregulated in MP cells. Results provide the insight into molecular basis underlying the maintenance of GSCs by non-GSCs. Gene expression profiles were compared between SP and MP cells just after FACS-sorting from the whole C6-eGFP cells based on their Hoechst-effluxing abilities.
2016-07-03 | E-GEOD-72431 | biostudies-arrayexpress
Project description:Melanoma remains the most lethal skin cancer, mainly because of high resistance to therapy. Side population (SP) cells are found in many types of cancer and are usually enriched in therapy-resistant as well as tumorigenic cells. Here, we identified a Hoechst dye-effluxing SP in a large series of human melanoma samples representing different progression phases. The SP size did not change with disease stage but was correlated with the prognostic “Breslow’s depth” in the primary (cutaneous) tumors. When injected into immunodeficient mice, the SP generated larger tumors than the bulk “main population” (MP) melanoma cells in two consecutive generations, and showed tumorigenic capacity at lower cell numbers than the MP. In addition, the SP reconstituted the heterogeneous composition of the human A375 melanoma cell line, and its clonogenic activity was 2.5-fold higher than that of the MP. Gene-expression analysis revealed upregulated expression in the melanoma SP (versus the MP) of genes associated with chemoresistance and anti-apoptosis. Consistent with these molecular characteristics, the SP increased in proportion when A375 cells were exposed to the melanoma standard chemotherapeutic agent dacarbazine, and to the aggravating condition of hypoxia. In addition, the SP showed enhanced expression of genes related to cell invasion and migration, as well as to putative (melanoma) cancer stem cells (CSC) including ABCB1 and JARID1B. ABCB1 immunoreactivity was detected in a number of tumor cells in human melanomas, and in particular in clusters at the invasive front of the primary tumors. Together, our findings support that the human melanoma SP is enriched in tumorigenic and chemoresistant capacity, considered key characteristics of CSC. The melanoma SP may therefore represent an interesting therapeutic target. Four primary melanomas (subtype SSMM) were dissociated into single cells. From each of these single cell suspensions, side population (SP) and bulk \main population\ (MP) cells were isolated based on their Hoechst-effluxing capability using fluorescence-activated cell sorting. Gene expression of SP cells is analyzed relative to the gene expression of the corresponding MP cells.
2014-05-27 | E-GEOD-48838 | biostudies-arrayexpress
Project description:Side population (SP) cells are identified based on their capacity to efflux of the fluorescent dye Hoechst 33342, and are enriched for hematopoietic stem cells (HSCs) in mammalian bone marrow. We recently demonstrated that SP cells were present in the teleost kidney, the main hematopoietic organ in teleosts, and were enriched for HSCs. In this analysis, to identify the regulated genes in teleost HSCs, gene expression analysis of zebrafish kidney SP cells were performed using the GeneChip Zebrafish Genome Array. Experiment Overall Design: Based on their Hoechst fluorescence intensity, lymphoid cells (FS-low, SS-low) from zebrafish kidney were subdivided into SP and MP populations (referred to as âzSPâ and âzMPâ). To minimize the biological variability, 20 zebrafish were used for 3 independent cell sorting experiments and lysates from these 3 experiments were pooled by cell type. Each RNA sample was split into two aliquots and used for amplification, labeling, and hybridization to independent arrays.
2008-10-26 | E-GEOD-12955 | biostudies-arrayexpress
Project description:Immature cell populations, including stem cells and progenitor cells, can be found in “side-population (SP)” cells. Although SP cells isolated from some adult tissues have been reported elsewhere, isolation and characterization of human trophoblast SP cells remained to be reported. We used microarrays to detail the global program of gene expression underlying cell differentiation and identified up-regulated genes of SP cells. HTR-8/SVneo SP cells or NSP cells were isolated using a cell sorter for RNA extraction and hybridization on Affymetrix microarrays. To obtain many SP or NSP cells, we cultured a large amount of HTR-8/SVneo cells (1×10^7 cells). The cells were labeled with 2.5µg/ml Hoechst 33342 dye (Molecular Probes, Eugene, OR) for 120 minutes at 37 ℃, either alone or in combination with 50 µmol/L verapamil (Sigma-Aldrich, ST Louis, MO). Finally, the cells were then passed through EPICS ALTRA HyPerSort (Beckman Coulter, Fullerton, CA) using dual wavelength analysis (blue, 424-444 nm; red, 675 nm) after excitation with 350 nm UV light.
2011-03-12 | E-GEOD-27909 | biostudies-arrayexpress
Project description:Subpopulations of highly tumorigenic, drug resistant cancer stem-like cells play a key role in cancer recurrence and progression. Surprisingly, these aggressive cells can arise repeatedly de novo from bulk tumor cells independently of mutational events. We investigated whether transition to and from a cancer stem-like state is associated with epigenetic alterations, such as DNA methylation and chromatin accessibility. By Hoechst dye staining and FACS analysis, side population (SP) and non-side population cells were sorted from J82 cells. AcceSssIble assay by Infinium EPIC BeadArray platform was used to identify potential epigenetic driver genes in the process of SP /NSP phenotype plasticity. Genes with differential accessible promoter regions were overlapped with genes differentially expressed by HuEx array analysis. Oncomine and Basespace were adopted to explore the clinical relevance of the target genes.
2020-01-30 | GSE123607 | GEO
Project description:Melanoma remains the most lethal skin cancer, mainly because of high resistance to therapy. Side population (SP) cells are found in many types of cancer and are usually enriched in therapy-resistant as well as tumorigenic cells. Here, we identified a Hoechst dye-effluxing SP in a large series of human melanoma samples representing different progression phases. The SP size did not change with disease stage but was correlated with the prognostic “Breslow’s depth” in the primary (cutaneous) tumors. When injected into immunodeficient mice, the SP generated larger tumors than the bulk “main population” (MP) melanoma cells in two consecutive generations, and showed tumorigenic capacity at lower cell numbers than the MP. In addition, the SP reconstituted the heterogeneous composition of the human A375 melanoma cell line, and its clonogenic activity was 2.5-fold higher than that of the MP. Gene-expression analysis revealed upregulated expression in the melanoma SP (versus the MP) of genes associated with chemoresistance and anti-apoptosis. Consistent with these molecular characteristics, the SP increased in proportion when A375 cells were exposed to the melanoma standard chemotherapeutic agent dacarbazine, and to the aggravating condition of hypoxia. In addition, the SP showed enhanced expression of genes related to cell invasion and migration, as well as to putative (melanoma) cancer stem cells (CSC) including ABCB1 and JARID1B. ABCB1 immunoreactivity was detected in a number of tumor cells in human melanomas, and in particular in clusters at the invasive front of the primary tumors. Together, our findings support that the human melanoma SP is enriched in tumorigenic and chemoresistant capacity, considered key characteristics of CSC. The melanoma SP may therefore represent an interesting therapeutic target.
2014-05-27 | GSE48838 | GEO
Project description:Background The side population (SP) phenotype, a subset of cells that extrude the nucleic acid dye Hoechst 33342, has been reported to be enriched for stem cells in several human normal tissues, cancers and cell lines, and thus may be useful for the identification and isolation of cancer stem cells. Methods We demonstrated the presence of SP fractions in all analyzed tumor cell lines ranging between 7- 20% of cells. To identify gene expression patterns that contribute to SP phenotype, microarray analysis of SP and non-SP cells was performed. We additionally confirmed regulation of some genes by qRT-PCR. Results Surprisingly, only a subset of few genes in SP cells showed altered gene expression. A total of 11 genes in A2C12, 103 genes in cRAF_cMYC and 101 genes in beta5 SP cells were regulated. Most regulated genes are involved in transcription / transcriptional regulation and transport. In addition, we found no enrichment of previously described stem cell marker like CD24a, CD90 or CD133 and also the ABC transporter ABCG2 was only slightly increased in side population fraction of two cell lines. But despite the few differences between SP and non-SP cells, the beta5 tumor cells were highly tumorigenic due to their capacity to form an original murine tumor when injected in NOD/SCID mice. Conclusion These findings stand in contrast to other observations but indicate that there are further factors responsible for the SP phenotype and that SP cells alone are not suitable as a universal stem cell marker.
2016-12-31 | GSE22275 | GEO