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A pan-family screen of Nuclear Receptors in immunocytes reveals ligand-dependent inflammasome control [scRNA-seq]

ABSTRACT: To examine more closely the varied effects of RA receptor deletions on peritoneal MFs, and determine whether inactivation of RXRα and RARγ elicited superimposable effects on different LPM clusters (as predicted if they operate as a heterodimer, a known propensity of RXR proteins), we performed single-cell RNA sequencing (scRNAseq) analyses on total CD11b+CD115+ peritoneal cells from BMC mice edited for several RA receptors, 17 days after reconstitution.

ORGANISM(S): Mus musculus

PROVIDER: GSE254572 | GEO | 2024/12/16

REPOSITORIES: GEO

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A pan-family screen of Nuclear Receptors in immunocytes reveals ligand-dependent inflammasome control [RNA-seq 2]

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A pan-family screen of Nuclear Receptors in immunocytes reveals ligand-dependent inflammasome control [ChIPmentation]

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Two distinct subsets are identified from the peritoneal myeloid mononuclear cells expressing both CD11c and CD115

Project description:The peritoneal cavity is home to various immune cells. Previous studies have investigated the heterogenous nature of peritoneal myeloid mononuclear cells. However, up to this date, there are no clear criteria to distinguish peritoneal macrophages and dendritic cells (DCs). In the present study, we delineate the subsets of myeloid mononuclear cells in the mouse peritoneal cavity. Considering phenotypical, functional, and ontogenic features, peritoneal myeloid mononuclear cells are divided into 5 subsets: large peritoneal macrophages (LPMs), small peritoneal macrophages (SPMs), DCs, and 2 MHCII+CD11c+CD115+ subpopulations (i.e., MHCII+CD11c+CD115+CD14-CD206- and MHCII+CD11c+CD115+CD14+CD206+). Among them, 2 subsets of competent antigen presenting cells are demonstrated with distinct functional characteristics, one being DCs and the other being MHCII+CD11c+CD115+CD14-CD206- cells. DCs are able to promote fully activated T cells and superior in expanding cytokine producing inflammatory T cells, whereas MHCII+CD11c+CD115+CD14-CD206- cells generate partially activated T cells and possess a greater ability to induce regulatory T cells under TGF-β and retinoic acid conditions. While the development of DCs and MHCII+CD11c+CD115+CD14-CD206- cells are responsive to the treatment of FLT3L and GM-CSF, the numbers of LPMs, SPMs, and MHCII+CD11c+CD115+CD14+CD206+ cells are only influenced by the injection of GM-CSF. In addition, the analysis of transcriptomes reveals that the gene expression profile of MHCII+CD11c+CD115+CD14+CD206+ cells share high similarity with that of SPMs. Collectively, our study identifies 2 distinct subpopulations of MHCII+CD11c+CD115+ cells, (i) MHCII+CD11c+CD115+CD14-CD206- cells closely related to DCs and (ii) MHCII+CD11c+CD115+CD14+CD206+ cells to SPMs.

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A pan-family screen of Nuclear Receptors in immunocytes reveals ligand-dependent inflammasome control [RNA-seq 1]

Project description:We profiled the transcriptional effects of NR deficiencies on peritoneal macrophages.

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RA-dependent proximal and distal enhancers’ architecture promotes RA-induced early ESC differentiation

Project description:Retinoic acid (RA) plays a pivotal role in different biological processes including inducing differentiation of embryonic stem cells (ESCs). We first knocked out one or both of RA receptors- Rarα and Rxrα to partially abolish the RA signaling, and then overexpressed one of them separately to hyper activation of RA signaling pathway. By transcriptome analysis, we show that RA signaling effects multi-lineage differentiation, particularly the endoderm, and identify RA signaling target genes, interesting, there are two family cluster genes- Hoxb and Cyp26. Chromosome immunoprecipitation (ChIP-seq) shows that RA induces novel proximal and distal enhancers around the cluster target genes and these enhancers are dependent of RA receptors(Rarα/Rxrα). 4C-seq reveals enhancer-enhancer and enhancer-promoter interactions in their regions and shows a decrease in the relative frequency of contact relative to WT after Rarα/Rxrα-knockout, suggesting Rarα/Rxrα participate in mediating chromatin interaction. We also identify that enhancers significantly maintain expression of RA-induced Hoxb and Cyp26 family genes and regulate multi-lineage marker genes. At the same time, we reveal that disrupting RA-response elements (RAREs) in the enhancer affects the expression of the target gene. Our study provides mechanistic insight into RA-induced early ESC differentiation to endoderm and potential regular regulation of downstream target genes.

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RNA-seq gene expression profiles of primary murine peritoneal mesothelial cells.

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2020-08-01 | GSE129391 | GEO

Gene expression induced by LPS, two amyloidogenic peptides, Tau 623-628 and Amylin 28-33, in peritoneal macrophages and B1a cells

Project description:Amyloidogenic peptides are therapeutic in EAE, reducing systemic levels of IL6, TNF, and INFg. The fibrils are bound and endocytosed in peritoneal MFs and B1a cells. Differential gene expression was used to further understand the process. Groups of three female C57BL/6 mice were injected with 10ug of Tau 623-628, Amylin 28-33, LPS, or PBS. 30-40 minutes post injection, the peritoneal cavity was lavaged, CD11b high (MFs) and CD5+CD19+ (B1a lymphocytes) were purified by flow cytometry directly into Trizol. RNA was extracted from the aqueous phase using the Qiagen RNeasy microkits. RNA quality was assessed using the Agilent 2100 bioanalyzer and the RNA 6000 nano reagents kit. One color microarray, Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray, was performed at the human immune monitoring center. All samples were processed and run at the same time.

2015-09-15 | E-GEOD-73026 | biostudies-arrayexpress

Gene expression induced by LPS, two amyloidogenic peptides, Tau 623-628 and Amylin 28-33, in peritoneal macrophages and B1a cells

2015-09-15 | GSE73026 | GEO

Retinoic acid induces Snai1 in stem cells of the preimplantation blastocyst to initiate differentiation

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2015-01-12 | GSE57854 | GEO

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