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High resolution 3D chromatin maps of human primary monocytes [ChIP-Seq]

ABSTRACT: Although the Hi-C maps in cultured immune cell has been reported, there still lacks 3D landscape of human primary monocytes. The peripheral blood from two health people and two SLE patients was collected and CD14+ monocytes were selected to perform Hi-C, RNA-seq, ATAC-seq and ChIP-seq. The raw data of THP1 cell Hi-C library was also used in comparison. We firstly presented the 3D genome structure heterogeneity in human primary monocytes. Significantly diversity of chromatin interaction in HLA complex region might regulates many immunologic processes. The chromatin loop regulation around CD16 and its relevant expression pattern indicated the CD16 associated monocyte functions are dominated regulated by this variable TAD boundary.

ORGANISM(S): Homo sapiens

PROVIDER: GSE157970 | GEO | 2022/01/01

REPOSITORIES: GEO

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High resolution 3D chromatin maps of human primary monocytes [RNA-Seq]

Project description:Although the Hi-C maps in cultured immune cell has been reported, there still lacks 3D landscape of human primary monocytes. The peripheral blood from two health people and two SLE patients was collected and CD14+ monocytes were selected to perform Hi-C, RNA-seq, ATAC-seq and ChIP-seq. The raw data of THP1 cell Hi-C library was also used in comparison. We firstly presented the 3D genome structure heterogeneity in human primary monocytes. Significantly diversity of chromatin interaction in HLA complex region might regulates many immunologic processes. The chromatin loop regulation around CD16 and its relevant expression pattern indicated the CD16 associated monocyte functions are dominated regulated by this variable TAD boundary.

2022-01-01 | GSE157978 | GEO

High resolution 3D chromatin maps of human primary monocytes [Hi-C]

2022-01-01 | GSE157971 | GEO

High resolution 3D chromatin maps of human primary monocytes [ATAC-Seq]

2022-01-01 | GSE157969 | GEO

High resolution 3D chromatin maps of human primary monocytes [Hi-C]

Project description:High resolution 3D chromatin maps of human primary monocytes [Hi-C]

| PRJNA663570 | ENA

Transcription profiling of human CD14+ CD16- and CD14low CD16+ monocytes from patients with Sjogrens syndrome and normal controls

Project description:Sjogren's syndrome is an autoimmune disease, characterized by complaints such as xerostomia and keratoconjunctivitis sicca. In other autoimmune diseases such as diabetes and SLE, monocyte abberancies have been described. Therefore, this study aimed at studying the monocyte compartment in Sjogren's Syndrome, by transcription profiling of CD14+CD16- and CD14lowCD16+ monocytes in patients and controls.

2008-08-04 | E-MEXP-1242 | biostudies-arrayexpress

Gene expression profile of primary human monocyte subsets

Project description:Human primary monocytes are composed of a minor, more mature CD16+(CD14low/neg) population and a major CD16neg(CD14+) subset. The specific functions of CD16+ vs. CD16neg monocytes in steady state or inflammation remain poorly understood. In previous work we found that IL-12 is selectively produced by the CD16+ subset in response to the protozoan pathogen, Toxoplasma gondii. Here we demonstrated that this differential responsiveness correlates with the presence of an IFN-induced transcriptional signature in CD16+ monocytes already at baseline. Consistent with this observation, we found that in vitro IFN-γ-priming overcomes the defect in IL-12 response of the CD16neg subset. We have anayzed the gene expression profile of primary human CD16+ and CD16neg monocyte subsets cultured for without or with IFN-gamma

2021-01-07 | GSE164346 | GEO

In human CD16+ monocytes NK1R signaling upregulates inflammatory pathways and negatively regulates apoptosis

Project description:The neurokinin-1 receptor (NK1R) pathway has immunomodulatory properties and is implicated in the pathophysiology of neurodegenerative, infectious and inflammatory diseases. Monocytes are important cells in inflammation and they consist of subsets with distinct phenotypes and biological functions. NK1R signaling is elevated in conditions that alter the balance of monocyte subsets, such as in HIV infection. In order to understand the pro-inflammatory mechanism of NK1R signaling in monocyte subsets, a transcriptome study was performed using RNA sequencing. Human primary peripheral monocytes were treated with the NK1R cognate ligand, substance P (SP), prior to being sorted into CD16- and CD16+ subsets. SP treatment led to the differential expression of 38 genes in CD16- monocytes and 12 genes in CD16+ monocytes. The canonical NF-κB pathway was activated in both subsets, as indicated by the upregulation of transcripts including IL1α, IL1β, IL6, CCL3 and CCL4. In the CD16+ monocytes, NK1R signaling led to priming of the NLRP3 inflammasome and upregulated transcripts including NLRP3 and CARD16. Alternative splicing analysis showed that NK1R signaling resulted in differential exon usage of CASP1 and CARD16 in CD16+ monocytes. SP treatment altered the properties of both CD16- and CD16+ monocytes, leading to an inflammatory response with activation of the canonical NF-κB pathway in both monocyte subsets, and priming of the NLRP3 inflammasome in the CD16+ subset.

2022-01-30 | GSE109635 | GEO

Expression data from intermediate monocytes from healthy donors and autoimmune uveitis patients

Project description:Human peripheral monocytes have been categorized into three subsets based on differential expression levels of CD14 and CD16. However, the factors that influence the distribution of monocyte subsets and the roles which each subset plays in autoimmunity are not well studied. To compare the gene expression profiling 1) on intermediate monocytes CD14++CD16+ monocytes between healthy donors and autoimmune uveitis patients and 2) among 3 monocyte subsets in health donors, here we purified circulating intermediate CD14++CD16+ monocytes from 5 patients with autoimmune uveitis (labeled as P1-5) and 4 healthy donors (labeled as HD1-4) by flow cytometry and isolated total RNA to proceed microarray assay. In addition, we also purified CD14+CD16++ (non-classical monocytes) and CD14++CD16- (classical monocytes) from 4 healthy donors to do microarray. We demonstrate that CD14++CD16+ monocytes from patients and healthy control donors share a similar gene expression profile. The CD14+CD16++ cells (non-classical monocytes) display the most distinctive gene expression profiling when compared to intermediate CD14++CD16+ monocytes and classical CD14++CD16- monocytes.

2015-03-17 | GSE66936 | GEO

SuperSAGE evidence for CD14++CD16+ monocytes as a third monocyte subset

Project description:Monocytes are a heterogeneous cell population with subset-specific functions and phenotypes. The differential expression of CD14 and CD16 distinguishes classical CD14++CD16-, intermediate CD14++CD16+ and non-classical CD14+CD16++ monocytes. However, CD14++CD16+ monocytes remain the most poorly characterized subset so far. Therefore we analyzed the transcriptomes of the three monocyte subsets using SuperSAGE in combination with high-throughput sequencing. Analysis of 5,487,603 tags revealed unique identifiers of CD14++CD16+ monocytes, delineating these cells from the two other monocyte subsets. CD14++CD16+ monocytes were linked to antigen processing and presentation (e.g. CD74, HLA-DR, IFI30, CTSB), to inflammation and monocyte activation (e.g. TGFB1, AIF1, PTPN6), and to angiogenesis (e.g. TIE2, CD105). Therefore we provide genetic evidence for a distinct role of CD14++CD16+ monocytes in human immunity.

2011-07-24 | GSE30811 | GEO

Proteomics of human dendritic cell subsets

Project description:We exploited label-free quantitative mass spectrometry to compare primary human blood Dendritic cells (DCs) subsets protein expression to identify new markers. Subsets distinguished are: Plasmacytoid DCs (pDC) and BDCA3+ and CD1c+ myeloid DCs and CD16+ monocytes. The dendritic cells were analyzed by LC-MS/MS and processed by MaxQuant for identification and LFQ quantification.

2016-09-27 | PXD004678 | Pride

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