MiRNA profiling of FACS sorted human leukocyte cell types
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: R van Eijsden
PROVIDER: E-GEOD-19183 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Affymetrix miRNA arrays were used to generate miRNA profiles of peripheral blood leukocytes and FACS sorted neutrophils, monocytes, B-cells, T-cells, CD4+ T-cells, and CD8+ T-cells, being the major leukocyte cell types in human. The study allowed for the determination of the miRNAs that were expressed in each leukocyte cell subtype. Two-way hierarchical clustering on the miRNAs and samples illustrated that miRNA expression profiles of B- and T-cells were very much alike, and that there there were a number of miRNAs which appeared to have an expression profile specific to certain leukocyte cell subtypes. This study will facilitate the identification of microRNAs associated with and contributing to single leukocyte cell subtypes.
2009-11-26 | GSE19183 | GEO
Project description:Peripheral blood leukocytes are the most commonly used surrogates to study epigenome-induced risk and epigenomic response to disease related stress. We considered the hypothesis that the TET enzyme catalyzed hydroxymethylation of 5mC to 5hmC might vary among peripheral blood leukocytes and reflect their responsiveness to environment. Reduction in TET1 and/or TET2 activity leads to the over-proliferation of various leukocyte precursors in bone marrow and acute leukemia, yet, the role of 5mC hydroxymethylation in peripheral blood is less well studied. We developed simplified protocols to rapidly and reiteratively isolate mostly non-overlapping leukocyte populations from a single small sample of fresh or frozen whole blood. Among peripheral leukocyte types we found extreme variation in the levels of transcripts encoding proteins involved in cytosine methylation (DNMT1, 3A, 3B) and turnover by de-methylation (TET1, 2, 3) and DNA repair (GADD45a, b, g) and in the gene-region-specific levels of DNA 5hmC (CD4 T cells >> CD14 monocytes > CD16 neutrophils > CD19 B cells > CD56 NK cells > Siglec 8 eosinophils > CD8 T cells). Taken together our results suggest a hierarchy of responsiveness among classes of leukocytes with CD4+ and CD8+ T cells and CD14 monocytes being the most distinctly potentiated for a rapid methylome response to physiological stress and disease. TAB-seq data on 5-hydroxymehtylcytosine (Yu, M. et al. 2012. Cell 149, 1368-1380.) was collected from seven leukocyte types (CD4+ T cells, CD8+ T cells, CD14+ monocytes, CD16+ neutrophils, CD19+ B cells, CD56+ natural killer cells, and Siglec-8+ eosinophils) reiteratively isolated from peripheral blood collected from a healthy male.
2016-07-05 | E-GEOD-70519 | biostudies-arrayexpress
Project description:Blood consists of different cell populations with distinct functions and correspondingly, distinct gene expression profiles. In this study, global miRNA expression profiling was performed across a panel of nine human immune cell subsets (neutrophils, eosinophils, monocytes, B cells, NK cells, CD4 T cells, CD8 T cells, mDCs and pDCs) to identify cell-type specific miRNAs. mRNA expression profiling was performed on the same samples, to determine if miRNAs specific to certain cell types down-regulated expression levels of their target genes. Six cell-type specific miRNAs (miR-143; neutrophil specific, miR-125; T cells and neutrophil specific, miR-500; monocytes and pDC specific, miR-150; lymphoid cells specific, miR-652 and miR-223; both myeloid cells specific) were negatively correlated with expression of their predicted target genes. These results were further validated using an independent cohort where similar immune cell subsets were isolated and profiled for both miRNA and mRNA expression. miRNAs negatively correlated with target gene expression in both cohorts were identified as candidates for miRNA-mRNA regulatory pairs and were used to construct a cell-type specific regulatory network. miRNA-mRNA pairs formed two distinct clusters in the network corresponding to myeloid (nine miRNAs) and lymphoid lineages (two miRNAs). Several myeloid specific miRNAs targeted common genes including ABL2, EIF4A2, EPC1 and INO80D; these common targets were enriched for genes involved in the regulation of gene expression (p < 9.0E-7). Those miRNA might therefore have significant further effect on gene expression by repressing the expression of genes involved in transcriptional regulation. The miRNA and mRNA expression profiles reported in this study form a comprehensive transcriptome database of various human blood cells and serve as a valuable resource for elucidating the role of miRNA mediated regulation in the establishment of immune cell identity. Nine cell subsets (CD16+CD66b+ Neutrophils, CD16-CD66b+ Eosinophils, CD14+ Monocytes, CD4+ T cells, CD8+ T cells, CD56+ NK cells, CD19+ B cells, CD123+ pDCs and CD11c+ mDCs) were isolated from healthy human blood and assessed for cell type purity by flow cytometry. Cell types were isolated from 5 pools of 5 healthy donors each, with the exception for monocytes, where 10 pools were used. RNA obtained from these purified populations were subsequently used for miRNA and mRNA expression profiling by Affymetrix GeneChip miRNA and HG-U133Plus2.0 microarrays.
2012-01-31 | E-GEOD-28487 | biostudies-arrayexpress
Project description:Blood consists of different cell populations with distinct functions and correspondingly, distinct gene expression profiles. In this study, global miRNA expression profiling was performed across a panel of nine human immune cell subsets (neutrophils, eosinophils, monocytes, B cells, NK cells, CD4 T cells, CD8 T cells, mDCs and pDCs) to identify cell-type specific miRNAs. mRNA expression profiling was performed on the same samples, to determine if miRNAs specific to certain cell types down-regulated expression levels of their target genes. Six cell-type specific miRNAs (miR-143; neutrophil specific, miR-125; T cells and neutrophil specific, miR-500; monocytes and pDC specific, miR-150; lymphoid cells specific, miR-652 and miR-223; both myeloid cells specific) were negatively correlated with expression of their predicted target genes. These results were further validated using an independent cohort where similar immune cell subsets were isolated and profiled for both miRNA and mRNA expression. miRNAs negatively correlated with target gene expression in both cohorts were identified as candidates for miRNA-mRNA regulatory pairs and were used to construct a cell-type specific regulatory network. miRNA-mRNA pairs formed two distinct clusters in the network corresponding to myeloid (nine miRNAs) and lymphoid lineages (two miRNAs). Several myeloid specific miRNAs targeted common genes including ABL2, EIF4A2, EPC1 and INO80D; these common targets were enriched for genes involved in the regulation of gene expression (p < 9.0E-7). Those miRNA might therefore have significant further effect on gene expression by repressing the expression of genes involved in transcriptional regulation. The miRNA and mRNA expression profiles reported in this study form a comprehensive transcriptome database of various human blood cells and serve as a valuable resource for elucidating the role of miRNA mediated regulation in the establishment of immune cell identity. Nine cell subsets (CD16+CD66b+ Neutrophils, CD16-CD66b+ Eosinophils, CD14+ Monocytes, CD4+ T cells, CD8+ T cells, CD56+ NK cells, CD19+ B cells, CD123+ pDCs and CD11c+ mDCs) were isolated from healthy human blood and assessed for cell type purity by flow cytometry. Cell types were isolated from 5 pools of 5 healthy donors each, with the exception for monocytes, where 10 pools were used. RNA obtained from these purified populations were subsequently used for miRNA and mRNA expression profiling by Affymetrix GeneChip miRNA and HG-U133Plus2.0 microarrays.
2012-01-31 | E-GEOD-28489 | biostudies-arrayexpress
Project description:Diversity of biological molecules in newborn and adult immune cells contributes to differences in cell function and atopic properties. Micro RNAs (miRNAs) are reported involve in the regulation of immune system. Therefore, determining the miRNA expression profile of leukocyte sub-populations is important for understanding immune system regulation. In order to explore the unique microRNA profiling that contribute to altered immune in neonates, we comprehensively analyzed the functional miRNA signatures of eight leukocyte subsets (polymorphonuclear cells, monocytes, CD4+ T cells, CD8+ T cells, natural killer cells, B cells, plasmacytoid dendritic cells (pDCs), and myeloid dendritic cells (mDCs)) from both neonatal and adult umbilical cord and peripheral blood samples, respectively. We observed distinct miRNA profiles between adult and neonatal blood leukocyte subsets, including unique miRNA signatures for each cell lineage. Leukocyte miRNA signatures were altered after stimulation. Adult peripheral leukocytes had higher let-7b-5p expression levels compared to neonatal cord leukocytes across multiple subsets, irrespective of stimulation. Transfecting neonatal monocytes with a let-7b-5p mimic resulted in a reduction of LPS-induced IL-6 and TNF-a production, while transfection of a let-7b-5p inhibitor into adult monocytes enhanced IL-6 and TNF-a production. With this functional approach, we provide intact differential microRNA expression profiling of specific immune cell subsets between neonates and adults. These studies serve as a basis to further understand the altered immune response observed in neonates and advance the development of therapeutic strategies
2016-11-16 | GSE89853 | GEO
Project description:Peripheral blood leukocytes are the most commonly used surrogates to study epigenome-induced risk and epigenomic response to disease related stress. We considered the hypothesis that the TET enzyme catalyzed hydroxymethylation of 5mC to 5hmC might vary among peripheral blood leukocytes and reflect their responsiveness to environment. Reduction in TET1 and/or TET2 activity leads to the over-proliferation of various leukocyte precursors in bone marrow and acute leukemia, yet, the role of 5mC hydroxymethylation in peripheral blood is less well studied. We developed simplified protocols to rapidly and reiteratively isolate mostly non-overlapping leukocyte populations from a single small sample of fresh or frozen whole blood. Among peripheral leukocyte types we found extreme variation in the levels of transcripts encoding proteins involved in cytosine methylation (DNMT1, 3A, 3B) and turnover by de-methylation (TET1, 2, 3) and DNA repair (GADD45a, b, g) and in the gene-region-specific levels of DNA 5hmC (CD4 T cells >> CD14 monocytes > CD16 neutrophils > CD19 B cells > CD56 NK cells > Siglec 8 eosinophils > CD8 T cells). Taken together our results suggest a hierarchy of responsiveness among classes of leukocytes with CD4+ and CD8+ T cells and CD14 monocytes being the most distinctly potentiated for a rapid methylome response to physiological stress and disease.
2016-07-05 | GSE70519 | GEO
Project description:Gene expression microarray profiling was performed on peripheral blood leukocyte subsets (CD4+ T cells, CD14+ monocytes, and CD16+ neutrophils) from healthy controls and patients with flaring autoimmune disease.
2014-08-31 | E-MTAB-2452 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE28487: miRNA expression profiling of human immune cell subsets (Roche) GSE28489: miRNA expression profiling of human immune cell subsets (HUG) GSE28490: mRNA expression profiling of human immune cell subset (Roche) GSE28491: mRNA expression profiling of human immune cell subsets (HUG) Blood consists of different cell populations with distinct functions and correspondingly, distinct gene expression profiles. In this study, global miRNA expression profiling was performed across a panel of nine human immune cell subsets (neutrophils, eosinophils, monocytes, B cells, NK cells, CD4 T cells, CD8 T cells, mDCs and pDCs) to identify cell-type specific miRNAs. mRNA expression profiling was performed on the same samples, to determine if miRNAs specific to certain cell types down-regulated expression levels of their target genes. Six cell-type specific miRNAs (miR-143; neutrophil specific, miR-125; T cells and neutrophil specific, miR-500; monocytes and pDC specific, miR-150; lymphoid cells specific, miR-652 and miR-223; both myeloid cells specific) were negatively correlated with expression of their predicted target genes. These results were further validated using an independent cohort where similar immune cell subsets were isolated and profiled for both miRNA and mRNA expression. miRNAs negatively correlated with target gene expression in both cohorts were identified as candidates for miRNA-mRNA regulatory pairs and were used to construct a cell-type specific regulatory network. miRNA-mRNA pairs formed two distinct clusters in the network corresponding to myeloid (nine miRNAs) and lymphoid lineages (two miRNAs). Several myeloid specific miRNAs targeted common genes including ABL2, EIF4A2, EPC1 and INO80D; these common targets were enriched for genes involved in the regulation of gene expression (p < 9.0E-7). Those miRNA might therefore have significant further effect on gene expression by repressing the expression of genes involved in transcriptional regulation. The miRNA and mRNA expression profiles reported in this study form a comprehensive transcriptome database of various human blood cells and serve as a valuable resource for elucidating the role of miRNA mediated regulation in the establishment of immune cell identity. Refer to individual Series
2012-01-23 | E-GEOD-28492 | biostudies-arrayexpress
Project description:Circulating miRNAs are an emerging class of biomarkers correlating their specific expression patterns to disease states. A considerable proportion of hematopoietically-derived miRNAs are present in plasma with the ability to confound the signature of true circulating miRNA species. We use microarray analysis to catalogue a list of 313 haemotopoetic miRNAs and analyze expression profiles of cell-free miRNAs in individual plasma fractions after calibrating for cellular miRNA signals. Comprehensive global maps of bona fide circulating miRNA species are presented, and inter-individual variability and gender-specific expression is explored in populations of healthy individuals. Healthy Caucasian individuals were used to segregate blood into 8 subfractions: white blood cells (WBC)/buffy coat, leukocytes, red blood cells (red blood cells (RBC)), cloudy supernatant (CS), supernatant 1 (S1), supernatant 2 (S2), pellet 1 (P1) and pellet 2 (P2) through differential centrifugation to understand the proportion of cellular miRNAs in each category.
2011-06-17 | E-GEOD-27230 | biostudies-arrayexpress
Project description:Neutrophils form the most abundant leukocyte subset and are central to many disease processes. Technical challenges in transcriptomic profiling have prohibited genetical genomic approaches to date. Here, we map expression quantitative trait loci (eQTL) in peripheral blood CD16+ neutrophils from 101 healthy European adults. This dataset includes expression data from neutrophils. The genotypes and expression data from monocytes can be found in E-MTAB-2232 - Genetics of gene expression across innate immune stimulation in primary monocytes.
2015-05-04 | E-MTAB-3536 | biostudies-arrayexpress