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RNA-Seq for primary rat Kupffer cells and monocytes treated with hepatic stellate cell-derived small extracellular vesicles

ABSTRACT: RNA-Seq for primary rat Kupffer cells and monocytes treated with hepatic stellate cell-derived small extracellular vesicles

PROVIDER: PRJEB60496 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR10980957.fastq.gz	Fastqsanger.gz
	ERR10980958.fastq.gz	Fastqsanger.gz
	ERR10980959.fastq.gz	Fastqsanger.gz
	ERR10980960.fastq.gz	Fastqsanger.gz
	ERR10980961.fastq.gz	Fastqsanger.gz

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RNA-Seq for primary rat Kupffer cells and monocytes treated with hepatic stellate cell-derived small extracellular vesicles

Project description:Aim: To find out the effects of small extracellular vesicles (sEVs) from short-term activated and long-term activated hepatic stellate cells (HSCs) on Kupffer cells (KCs) and bone marrow-derived monocytes (MOs). Methods: For the isolation of HSC-derived sEVs, culture media (CMs) from Day 0 to Day 3 and Day 7 to Day 14 were collected. The sEVs from Day 0 to Day 3 HSC CMs were referred to as short-term activated HSC-sEVs (3dHSC-sEVs), and those from Day 7 to Day 14 HSC CMs were referred to as long-term activated HSC-sEVs (14dHSC-sEVs). Purified primary rat KCs and MOs were cocultured with 3dHSC- or 14dHSC-sEVs for 48 h. HSC-sEVs cocultured KCs or MOs were lysed in TRIzol (Life Technologies) for RNA sample preparation at the indicated time points.

2024-08-29 | E-MTAB-12754 | biostudies-arrayexpress

Stellate cells, hepatocytes and endothelial cells imprint the Kupffer cell identity on monocytes colonizing the liver macrophage niche (microarray)

Project description:Macrophages are strongly adapted to their tissue of residence. Yet, we know little about the cell-cell interactions that imprint the tissue-specific identities of macrophages in their respective niches. Using conditional depletion of liver Kupffer cells, we traced the developmental stages of monocytes differentiating into Kupffer cells and mapped the cellular interactions imprinting the Kupffer cell identity. Kupffer cell loss induced the tumor necrosis factor (TNF) and interleukin-1 (IL-1) receptor-dependent activation of stellate cells and endothelial cells, resulting in the transient production of chemokines and adhesion molecules orchestrating monocyte engraftment. Engrafted circulating monocytes transmigrated into the perisinusoidal space, and acquired the liver-associated transcription factors ID3 and LXRα. Coordinated interactions with hepatocytes induced ID3 expression, while endothelial cells and stellate cells induced LXRα via a synergistic NOTCH-BMP pathway. This study shows that the Kupffer cell niche is composed of stellate cells, hepatocytes and endothelial cells that together imprint the liver-specific macrophage identity.

2019-08-14 | GSE135788 | GEO

Stellate cells, hepatocytes and endothelial cells imprint the Kupffer cell identity on monocytes colonizing the liver macrophage niche (RNA-Seq)

2019-08-14 | GSE135789 | GEO

Small RNA-Seq for primary rat hepatic stellate cells and hepatic stellate cell-derived small extracellular vesicles

Project description:Aims: To obtain small non-coding RNA expression profiles of short-term activated and long-term activated hepatic stellate cells (HSCs). To obtain small non-coding RNA expression profiles of small extracellular vesicles (sEVs) from short-term activated and long-term activated HSCs. Methods: Primary rat HSCs were isolated and cultured in vitro. To isolate HSC-derived sEVs, culture media (CMs) from Day 0 to Day 3 and Day 7 to Day 14 were collected. The sEVs from Day 0 to Day 3 HSC CMs were referred to as short-term activated HSC-sEVs (3dHSC-sEVs), and those from Day 7 to Day 14 HSC CMs were referred to as long-term activated HSC-sEVs (14dHSC-sEVs). Day 3 HSCs, Day 14 HSCs, and HSC-sEVs were collected and lysed in TRIzol (Life Technologies) for RNA sample preparation at the indicated time points.

2024-08-29 | E-MTAB-12764 | biostudies-arrayexpress

Human hepatic stellate cell-derived extracellular vesicles LC-MSMS

Project description:Activation and migration of hepatic stellate cells (HSCs) followed by matrix deposition are characteristics of liver fibrosis. Several studies have shown the importance of hepatocyte and endothelial cell-derived extracellular vesicles (EVs) in liver pathobiology. However, less is known about the role of HSC-derived EVs in liver diseases. In this study, we investigated the molecules released through HSC-derived EVs and whether these can promote fibrosis.

2018-10-18 | PXD007258 | Pride

Small RNA-Seq for primary rat hepatic stellate cells and hepatic stellate cell-derived small extracellular vesicles

Project description:Small RNA-Seq for primary rat hepatic stellate cells and hepatic stellate cell-derived small extracellular vesicles

| PRJEB60610 | ENA

Gene expression changes in hepatic stellate cells in response to fibrogenic agents.

Project description:Gene expression of hepatic stellate cells exposed to fetal bovine serum (FBS) (cultured alone and in the presence of Kupffer cells) activated and CCl4 exposure and Bile-duct ligation is characterized. Affymetrix Mouse 430 2.0 gene expression measurements were used to characterize the transcriptomic basis of the effects of the above treatments and genotypes on firbrogenesis. Gene expression of mouse hepatic stellate cells was characterized under the following conditions: A. Quiescent (n=5). B. Activated by FBS (n=3). C. Cocultured with Kupffer cells and activated by FBS (n=3). D. Activate by bile-duct ligation (n=3). E. Activated by CCl4 (n=3).

2014-12-19 | E-GEOD-34640 | biostudies-arrayexpress

Transcriptome reprogramming of CD11b+ bone marrow cells by pancreatic cancer extracellular vesicles

Project description:Pancreatic cancers (PC) are highly metastatic with poor prognosis, mainly due to delayed detection. We previously showed that PC-derived extracellular vesicles (EVs) act on macrophages residing in the liver, preparing pre-metastatic niches that support metastasis to this organ. This process involves the binding of PC-EVs to Kupffer cells, followed by TGFβ secretion and upregulation of fibronectin production by hepatic stellate cells, which supports hepatic accumulation of CD11b+ bone marrow (BM) cells and PC liver metastasis. We here show that PC-EVs preferentially bind to CD11b+ BM cells and induce the expansion of this cell population. Transcriptomic characterization shows that PC-EVs upregulate IgG and IgA genes, which have been linked to the presence of monocytes/macrophages in tumor microenvironments. We also report here the transcription downregulation of genes linked to monocytes/macrophages activation, trafficking and expression of inflammatory molecules. Together, these results demonstrate the existence of a PC-BM communication axis mediated by EVs with a potential role in PC tumor microenvironments.

2020-10-19 | GSE156071 | GEO

COMPARATIVE ANALYSIS OF THE PROTEOME OF KUPFFER CELLS AND MONOCYTES

Project description:Macrophage population in most mammalian organs consists of cells of different origin, with the exception of the central nervous system and the liver, where macrophages of monocytic origin are almost completely absent. The reasons for such distribution and the phenomenon of coexistence of the two separate macrophage lineages with different origin in mammals remain poorly understood. In present study we compared Kupffer cells and monocytes by the immunophenotype, gene expression profile, proteome and pool of mircoRNA. Observed differences do not allow to consider the resident liver macrophages as purely M2 macrophages or monocytes have purely M1 features. Two populations of macrophages of monocytic origin and resident macrophages have fundamentally different roles in maintaining homeostasis. Monocytic macrophages are involved in the regulation of inflammation, and resident macrophages are involved in the regulation of specific organ functions (nitrogen metabolism, complement system protein synthesis). However, if other indicators would be considered as markers of macrophage activity, it is worth noting that Kupffer cells possess some features of M2 macrophages. This is indicated by their expression profile of let-7b/c/d/e miRNAs, a high content of proteins associated with oxidative phosphorylation, as well as an increased level of synthesis of Arg1, IL10.

2021-09-09 | PXD018586 | Pride

Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells

Project description:Self-renewing tissue-resident macrophages are thought to be exclusively derived from embryonic progenitors. However, whether circulating monocytes can also give rise to such macrophages has not been formally investigated. Here we use a new model of diphtheria toxin-mediated depletion of liver-resident Kupffer cells to generate niche availability and show that circulating monocytes engrafted in the liver, gradually adopt the transcriptional profile of their depleted counterparts and become long-lived self-renewing cells. Underlining the physiological relevance of our findings, circulating monocytes also contribute to the expanding pool of macrophages in the liver shortly after birth, when macrophage niches become available during normal organ growth. Thus, like embryonic precursors, monocytes can and do give rise to self-renewing tissue-resident macrophages if the niche is available to them. Clec4F+ Kupffer cells were isolated and sorted from livers from adult WT mice or KC-DTR or KC-DTR littermate control mice +/- 50ng DT at indicated timepoints. 19 samples (arrays) in total. RNA was isolated, amplified with Nugene pico kit, converted to cDNA and then hybridised on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays.

2015-11-21 | E-GEOD-75225 | biostudies-arrayexpress

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