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Comparison of the DNA methylation profiles of CD14+ monocytes from human peripheral blood with DCs and MACs obtained by exposure with GM-CSF/IL-4 and GM-CSF, respectively, and with mature DCs and MACs after LPS exposure

ABSTRACT: Comparison of the DNA methylation profiles of CD14+ monocytes from human peripheral blood with derived dendritic cells (DCs) and macrophages (MACs) obtained by exposure with GM-CSF/IL-4 and GM-CSF, respectively, and with mature DCs and MACs after lipopolysaccharide (LPS) exposure The methylation profiles of bisulfite-modified DNA of human CD14+ monocytes were compared with derived immature dendritic cells (iDCs) and macrophages (iMACs) following GM-CSF/IL-4 and GM-CSF incubation, and then activation/maturation with lypopolysaccharyde (LPS) using the Infinium HumanMethylation450 BeadChips (Illumina, Inc., San Diego, CA,). This platform allows the interrogation of >485,000 methylation sites per sample at single-nucleotide resolution, and comprises an average of 17 CpG sites per gene in the 99% of RefSeq genes. 96% of CpG islands are covered, with additional coverage in CpG island shores and the regions flanking them. The samples were hybridized in the array following the manufacturer’s instructions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE71837 | GEO | 2015/12/11

SECONDARY ACCESSION(S): PRJNA292302

REPOSITORIES: GEO

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Comparison of the DNA methylation profiles of CD14+ monocytes from human peripheral blood with DCs and MACs obtained by exposure with GM-CSF/IL-4 and GM-CSF, respectively, and with mature DCs and MACs after LPS exposure

Project description:Comparison of the DNA methylation profiles of CD14+ monocytes from human peripheral blood with derived dendritic cells (DCs) and macrophages (MACs) obtained by exposure with GM-CSF/IL-4 and GM-CSF, respectively, and with mature DCs and MACs after lipopolysaccharide (LPS) exposure The methylation profiles of bisulfite-modified DNA of human CD14+ monocytes were compared with derived immature dendritic cells (iDCs) and macrophages (iMACs) following GM-CSF/IL-4 and GM-CSF incubation, and then activation/maturation with lypopolysaccharyde (LPS) using the Infinium HumanMethylation450 BeadChips (Illumina, Inc., San Diego, CA,). This platform allows the interrogation of >485,000 methylation sites per sample at single-nucleotide resolution, and comprises an average of 17 CpG sites per gene in the 99% of RefSeq genes. 96% of CpG islands are covered, with additional coverage in CpG island shores and the regions flanking them. The samples were hybridized in the array following the manufacturerâs instructions. Total DNA isolated by standard procedures from CD14+ cells (total monocytes, MOs) corresponding to three sets of samples of monocytes (MOs), derived immature DCs and MACs (iDCS and iMACS) and activated/mature DCs and MACs following incubation with LPS (mDCS and mMACs)

2015-12-11 | E-GEOD-71837 | biostudies-arrayexpress

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Project description:Comparison of the DNA methylation profiles of CD14+ monocytes from human peripheral blood with derived dendritic cells (DCs) and macrophages (MACs) obtained by exposure with GM-CSF/IL-4 and GM-CSF, respectively. Effects on the methylation profiles of DCs and MACs of JAK3 inhibitor PF-956980 The methylation profiles of bisulfite-modified DNA of human CD14+ monocytes were compared with derived dendritic cells (DCs), macrophages (MACs) following GM-CSF/IL-4 and GM-CSF incubation, and DC and MAC samples incubated with JAK3 inhibitor PF-956980 using the Infinium HumanMethylation450 BeadChips (Illumina, Inc., San Diego, CA,). This platform allows the interrogation of >485,000 methylation sites per sample at single-nucleotide resolution, and comprises an average of 17 CpG sites per gene in the 99% of RefSeq genes. 96% of CpG islands are covered, with additional coverage in CpG island shores and the regions flanking them. The samples were hybridized in the array following the manufacturerÃ¢ÂÂs instructions. Total DNA isolated by standard procedures from CD14+ cells (total monocytes, MOs) corresponding to three sets of samples of monocytes (MOs), derived DCs and MACs (DCs and iMACs; DMSO as these samples were differentiated in the absence of JAK3 inhibitors) and DCs and MACs differentiated in the presence of JAK3 inhibitor PF-956980.

2015-12-12 | E-GEOD-75937 | biostudies-arrayexpress

Human CD14+CD16- and CD16+ monocyte-derived macrophages primed by GM-CSF or M-CSF

Project description:Identification of genes differentially expressed between human CD14+CD16- and CD16+ monocyte-derived macrophages generated in the presence of either GM-CSF (termed GM14 and GM16, respectively) or M-CSF (termed M14 and M16, respectively) Human peripheral CD14+CD16- and CD16+ blood monocytes from three independent healthy donors (D1, D2 and D3) were isolated by positive selection from peripheral blood mononuclear cells (PBMC) using magnetic separation systems (MACS, Miltenyi Biotec). Briefly, PBMC were first incubated with MACS anti-CD56 antibody conjugated to paramagnetic microbeads in order to eliminate the NK (CD16+) cell fraction. NK-depleted PBMC were further incubated with MACS anti-CD16 antibody to isolate CD16+ monocytes. CD56-CD16- PBMC were finally incubated with MACS anti-CD14 antibody to obtain the CD14+CD16- monocyte fraction. Monocytes were cultured for 7 days in medium containing either GM-CSF or M-CSF. Total RNA from each condition was extracted using the RNeasy kit (Qiagen) and hybridized to an Agilent Human Whole Genome (4x44) Oligo Microarray. All experimental procedures were performed following manufacturer instructions.

2015-04-21 | E-GEOD-68061 | biostudies-arrayexpress

Methylation data and effect of JAK3 inhibition on human MO-to-DC and MO-to-MAC differentiation

Project description:Comparison of the DNA methylation profiles of CD14+ monocytes from human peripheral blood with derived dendritic cells (DCs) and macrophages (MACs) obtained by exposure with GM-CSF/IL-4 and GM-CSF, respectively. Effects on the methylation profiles of DCs and MACs of JAK3 inhibitor PF-956980 The methylation profiles of bisulfite-modified DNA of human CD14+ monocytes were compared with derived dendritic cells (DCs), macrophages (MACs) following GM-CSF/IL-4 and GM-CSF incubation, and DC and MAC samples incubated with JAK3 inhibitor PF-956980 using the Infinium HumanMethylation450 BeadChips (Illumina, Inc., San Diego, CA,). This platform allows the interrogation of >485,000 methylation sites per sample at single-nucleotide resolution, and comprises an average of 17 CpG sites per gene in the 99% of RefSeq genes. 96% of CpG islands are covered, with additional coverage in CpG island shores and the regions flanking them. The samples were hybridized in the array following the manufacturer’s instructions.

2015-12-12 | GSE75937 | GEO

Comparison of the RNA expression profiles of CD14+ monocytes from human peripheral blood with derived dendritic cells (DCs) and myeloid-derived suppressor cells (MDSCs) obtained by exposure with GM-CSF/IL4 and GM-CSF/IL4/PGE2, respectively, during 6 days

Project description:The expression profiles of RNA of human CD14+ monocytes were compared with derived dendritic cells (DCs) and myeloid-derived suppressor cells (MDSCs) following GM-CSF/IL4 and GM-CSF/IL4/PGE2 incubation for 6 days using the Agilent Human GE v3 8x60K array (Agilent Technologies, CA, USA). The samples were hybridized in the array following the manufacturer’s instructions.

2017-09-11 | GSE103210 | GEO

Guanabenz effect on activated GM-CSF DCs

Project description:Guanabenz is an FDA approved drug for hypertension. It has been shown also to be an inhibitor of GADD34, the stress-inducible cofactor of PP1. GADD34 has been shown to play a key role in controlling cytokine production in MEFs and dendritic cells. A microarray-based mRNA transcription analysis was used to compare the transcriptional response of GM-CSF DCs, activated with poly I:C or Proteus mirabilis, in presence or absence of 50µM Guanabenz.

2017-08-15 | GSE90831 | GEO

Expression data on human MO-to-DC and MO-to-MAC differentiation

Project description:Comparison of the RNA expression profiles of CD14+ monocytes from human peripheral blood with derived dendritic cells (DCs) and macrophages (MACs) obtained by exposure with GM-CSF/IL-4 and GM-CSF, respectively, and with mature DCs and MACs after lipopolysaccharide (LPS) exposure The expression profiles of RNA of human CD14+ monocytes were compared with derived immature dendritic cells (iDCs) and macrophages (iMACs) following GM-CSF/IL-4 and GM-CSF incubation, and then activation/maturation with lypopolysaccharyde (LPS) using the Affymetrix PrimeView Human Gene Expression array (Affymetrix, Santa Clara, CA). This platform allows the interrogation of >36,000 transcrits and variants per sample. The samples were hybridized in the array following the manufacturerâ??s instructions. Total RNA isolated by standard procedures from CD14+ cells (total monocytes, MOs) corresponding to three sets of samples of monocytes (MOs), derived immature DCs and MACs (iDCS and iMACS) and activated/mature DCs and MACs following incubation with LPS (mDCS and mMACs)

2015-12-12 | E-GEOD-75938 | biostudies-arrayexpress

Simultaneous inhibition of PPAR-γ and mTORC1 enables GM-CSF to induce the differentiation of monocytes into highly immunogenic dendritic cells

Project description:Monocytes can differentiate into macrophages or dendritic cells. When treated with granulocyte-macrophage colony-stimulating factor (GM-CSF) monocytes differentiate into macrophage-like cells. Here, we report that pharmacological blockade of the nuclear receptor PPARγ in monocytes turns GM-CSF into a potent inducer of dendritic cell (Mo-DC) differentiation. Remarkably, simultaneous blockade of PPARγ and mTORC1 in the presence of GM-CSF promoted the differentiation of Mo-DCs with a stronger phenotypic stability and immunogenic profile when compared with canonical Mo-DCs differentiated by treatment with GM-CSF and IL-4. Moreover, and in contrast with the observations made with GM-CSF and IL-4, blockade of PPARγ and mTORC1 was shown to be able to induce the differentiation of monocyte-derived macrophages (Mo-Macs) into Mo-DCs. Transcriptional profiling performed at either early time points, as well as at the end of the differentiation process, revealed marked differences in the gene expression signature between Mo-DCs induced by GM-CSF and IL-4 and Mo-DCs induced by GM-CSF in the presence of PPARγ and/or mTORC1 inhibitors, thus suggesting diverging differentiation pathways. Our observations might contribute, not only to a better understanding of the mechanisms involved in Mo-DCs differentiation but also to improving the efficacy of both, DC vaccines and therapies focusing on the modulation of myeloid cell functions.

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Expression data on human MO-to-DC and MO-to-MAC differentiation

2015-12-12 | GSE75938 | GEO

Single-cell RNA-sequencing of GM-CSF derived macrophages

Project description:We obtained single-cell RNA-sequencing (scRNA-seq) profiles of GM-CSF derived macrophages from CD14+ monocytes isolated from human peripheral blood with 6 days of GM-CSF stimulatio across multiple donors.

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