Genome-wide analysis of human bone marrow CD45-CD271+ cells in comparision with CD45-CD271- cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE57927 | GEO | 2015/03/17
SECONDARY ACCESSION(S): PRJNA248434
REPOSITORIES: GEO
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Project description:Bone marrow (BM) mesenchymal stem/stromal cells are non-hematopoietic (CD45-), non-endothelial (CD31-) multipotential cells capable to differentiate into osteoblastes, chondrocytes and adipocytes. In addition, different subpopulations of MSCs and some of their derivatives (early osteoblastic lineage cells) were shown to form HSC-niche. This makes a complex picture of the relationship between MSCs and HSCs. Despite growing data in mice model, few describe the human counterpart. The BM CD200+ and CD271+ fractions were previously shown to be enriched in native MSCs in human. Herein, we found heterogeneity in expression of CD200 within CD45-/CD31-/CD271+ human BM fraction. We thus selected CD200+ and CD200- cells from CD45-/CD31-/CD271+ BM samples and we analyzed their transcriptome. The differential display of gene expression between these two types of BM fractions will give new insights in the identification of native human MSCs.
2022-03-08 | GSE198049 | GEO
Project description:Human engeneered skin carrying GFP positive melanoma cells was transplanted in immunocompromised rats. 6 weeks after transplatation the engeenered skin was removed and GFP positive melanoma cells sorted for CD271 HIGH and LOW populations
2017-09-02 | GSE103382 | GEO
Project description:The extensive heterogeneity both between and within the medulloblastoma (MB) subgroups underscores a critical need for variant-specific biomarkers and therapeutic strategies. We previously identified a role for the CD271/p75 neurotrophin receptor (p75NTR) in regulating stem/progenitor cells in the SHH MB subgroup. Here, we demonstrate the utility of CD271 as a novel diagnostic and prognostic marker for SHH MB using immunohistochemical analysis as well as transcriptome data across 763 primary tumors. Characterization of CD271+ and CD271- cells by RNA sequencing revealed that these two subpopulations are molecularly distinct, co-existing cellular subsets both in vitro and in vivo. MAPK/ERK signaling is upregulated in the CD271+ population and inhibiting this pathway reduced CD271 levels, stem/progenitor cell proliferation and cell survival as well as cell migration in vitro. Importantly, the MEK inhibitor selumetinib extends survival and reduces CD271 levels in vivo. Our study demonstrates the clinical utility of CD271 as both a diagnostic and prognostic tool for SHH MB tumors and reveals a novel role for MEK inhibitors in targeting CD271+ SHH MB cells.
2019-12-31 | GSE107701 | GEO
Project description:Background: Large-scale genomic analyses of patient cohorts have revealed extensive heterogeneity between individual tumors, contributing to treatment failure and drug resistance. In malignant melanoma, heterogeneity is thought to arise as a consequence of the differentiation of melanoma-initiating cells that are defined by cell-surface markers like CD271 or CD133. Results: Here we identified the nerve growth factor receptor (CD271) as a crucial determinant of melanoma cell tumorigenicity, stem-like properties, heterogeneity and plasticity. Stable shRNA mediated knock-down of CD271 in patient-derived melanoma cells abrogated their tumor-initiating and colony-forming capacity. A genome-wide expression profiling and gene-set enrichment analysis revealed novel connections of CD271 with melanoma-associated genes like CD133 and points to a neural crest stem cell (NCSC) signature lost upon CD271 knock-down. In a meta-analysis, we found CD271 linked to the neural crest specifier SOX10 and observed a shared set of 271 differentially regulated genes. To dissect the connection of CD271 and CD133 we analyzed 10 patient-derived melanoma-cell lines for cell-surface expression of both markers compared to established cell lines MeWo and A375. We found CD271+ cells in the majority of cell lines analyzed as well as in a set of 16 different patient-derived melanoma metastases. Strikingly, only 2/12 cell lines harbored a CD133+ sub-set that in addition comprised a fraction of cells of a CD271+/CD133+ phenotype. Those cells were found in the label-retaining fraction and in vitro deduced from CD271+ but not CD271 knock-down cells. Conclusions: Our present study provides a deeper insight into the regulation of melanoma cell properties and points CD271 out as a regulator of several melanoma-associated genes. Further, our data strongly suggest CD271 is a crucial determinant of stem-like properties of melanoma cells like colony-formation and tumorigenicity. For knock-down of CD271 (NGFR), melanoma cells were transfected with 2 M-BM-5g of each shRNA plasmid; #2: 5M-bM-^@M-^Y-ACAACCTCATCCCTGTCTATT-3M-bM-^@M-^Y; #3: 5M-bM-^@M-^Y-CCCGAGCACATAGA CTCCTTT-3M-bM-^@M-^Y and #4: 5M-bM-^@M-^Y-CCGAGCACATAGACTCCTTTA-3M-bM-^@M-^Y or control shRNA (shCtl 5M-bM-^@M-^Y-GGAATCTCATTCGATGCATAC-3M-bM-^@M-^Y; all from Quiagen) using Lipofectamine2000 (Invitrogen). Cells were selected with puromycin (10M-BM-5g/ ml) over a period of two weeks. Whole genome expression profiling of CD271k.d. cells (shRNA#4) and shCtl. cells was performed with three biological replicates. Illumina raw data of BeadChip HumanHT-12V4 platform were summarized via the BeadStudio without normalization and background correction. Follow-up processing was done via the R/Bioconductor environment employing packages lumi, limma and q-value. Data were normalized with quantile normalization. Genes were termed significantly differentially expressed when the average detection p-value of at least one case was < 0.05 the ratio was outside the interval [0.75,1.33], one of the p-values from limma test, Student's t-test, Welch test and Wilcoxon test was < 0.05. At least one of the q-values corresponding to one of these tests < 0.05.
2013-11-19 | E-GEOD-52456 | biostudies-arrayexpress
Project description:Some cancers are thought to follow a cancer stem cell (CSC) model in which hierarchical and epigenetically determined relationships exist between phenotypically and functionally distinct cells within tumors. In melanoma, for example, CD271/p75/NGFR (nerve growth factor receptor) was found by some groups to be expressed in cells with enriched tumorigenic potential (Boiko et al., 2010; Civenni et al., 2011). However, these observations were not reproduced in highly efficient patient-derived xenograft (PDX) assays (Quintana et al., 2008), in which plastic, nonhierarchical relationships were proposed between CD271- and CD271+ cells (Quintana et al., 2010). Here we confirm that a CD271-based CSC model does not apply to melanoma, regardless of the PDX assay method used. In side-by-side testing of published PDX assays, no consistent differences were seen in CD271 expression or in PDX tumor formation from purified CD271- or CD271+ cells from patient melanomas. Analysis of CD271 in sixty-eight PDX tumors grown from CD271- or CD271+ cells revealed strikingly variable CD271 re-expression patterns, which were not consistent with stable hierarchical or plastic relationships between CD271-defined cell sub-populations. Genotyping of sibling PDX tumors showed extensive (28% - 48%) genomic copy number differences, which were also apparent (1.4% - 23%) between CD271- and CD271+ cells purified from each of four melanomas, revealing intra-tumoral genetic heterogeneity associated with CD271 expression. Thus, CD271 is not linked reproducibly to tumorigenic potential in melanoma, regardless of the method of melanoma cell isolation, and its expression appears driven by complex and unstable interactions between changing epigenetic and genetic states. Understanding of melanoma biology and the treatment of melanoma patients are unlikely to be advanced by applying a CD271-based CSC model to this disease.
2016-02-27 | GSE66409 | GEO
Project description:Genome-wide expression profiling of stably NGFR transfected melanoma cells was used to identify genes driven by expression of the nerve growth factor receptor CD271 (NGFR). Stable overexpression of NGFR (CD271): Generation of cell lines stably overexpressing CD271 (NGFR), melanoma cells were transfected with 2 µg of a plasmid expressing GFP-tagged human NGFR (RG207966, OriGene) and selected with G418 (100-300 µg/ml, PAA) over a period of two weeks followed by sub-cloning or FACS. Gene expression profiling: Whole genome expression profiling of T20/02 and A375 cells (NGFR) and control cells (Mock or GFP) was performed with three biological replicates. Illumina raw data of BeadChip HumanHT-12V4 platform were summarized via the BeadStudio without normalization and background correction. Follow-up processing was done via the R/Bioconductor environment employing packages lumi, limma and q-value. Data were normalized with quantile normalization. Genes were termed significantly differentially expressed when the average detection p-value of at least one case was < 0.05 the ratio was outside the interval [0.75,1.33], one of the p-values from limma test, Student's t-test, Welch test and Wilcoxon test was < 0.05. At least one of the q-values corresponding to one of these tests < 0.05.
2016-02-23 | E-GEOD-78155 | biostudies-arrayexpress