Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA312371 | ENA |
REPOSITORIES: ENA
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Project description:Introduction: Extracellular vesicles (EVs) are a heterogeneous group of membrane-enclosed vesicles released by cells. They play important roles in intercellular communication and contribute to several physiological and pathological processes. Cells release subpopulations of EVs with distinct biogenesis and functions, however, we currently have few markers to differentiate them. This study therefore aimed to determine proteomic and lipidomic differences among four EV subpopulations of varying sizes and densities. Methods: Large and small EVs (L-EVs and S-EVs) were isolated from two immune cell lines by differential ultracentrifugation at 16,500 × g and 118,000 × g, respectively. The crude EVs were then further separated by density cushion centrifugation. EVs were isolated from the interphase between 1.079-1.146 and 1.146-1.185 g/ml, hereafter referred to as low density (LD) and high density (HD), respectively. This resulted in four subpopulations of EVs, namely, L-EV LD, L-EV HD, S-EV LD, and S-EV HD. The purity, morphology, size, and yield of EVs were determined by nanoparticle tracking analysis, electron microscopy, and western blot. The proteome and lipidome of the four subpopulations of EVs were determined with mass spectrometry. Results: A total of 5364 proteins were quantified in the dataset. L-EV and S-EVs as well as LD and HD were well separated. Briefly, L-EVs LD were enriched in mitochondrial proteins such as the TIMM/TOMM complex, MICOS, and ATP5 proteins, while L-EVs HD were enriched in proteins associated with the cytoskeleton, such as KIF proteins. Furthermore, S-EVs LD were enriched in tetraspanins and ESCRT machinery proteins, while S-EVs HD were enriched in histones, CCT proteins, and proteins from the complement pathway. While proteins such as flotillins, RABs, annexins, and integrins were enriched in two or several subpopulations. Our study quantified 108 lipids, and the most abundant lipids in EVs were phosphatidylcholine (PC), sphingomyelin, and phosphatidylethanolamine (PE). The most profound difference was that PE was less abundant in L-EVs LD as compared to the other EV subtypes and ceramides were enriched in L-EVs as compared to S-EVs. Conclusion: This study demonstrates that the proteome strongly differs in EV subpopulations separated at different densities. Furthermore, it validates several protein groups that have previously been suggested to be enriched in either S-EVs or L-EVs.
2026-03-16 | PXD063334 | Pride
Project description:Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated two distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, snoRNA, and snRNA with little or no evidence of full-length 18S and 28S rRNA. The LD exRNA was enriched in mitochondrial rRNA, mitochondrial tRNA, tRNA, piRNA, Y RNA, and full-length 18S and 28S rRNA. The proteomes of the HD and LD exRNA-containing fractions were determined with LC-MS/MS and analysed with Gene Ontology term finder, which showed that both proteomes were associated with extracellular vesicles. Additionally, the proteins in the HD fractions tended to be associated with the nucleus and ribosomes, whereas the LD fraction proteome tended to be associated with the mitochondrion. We show that the two exRNA signatures released by a single cell type can be separated by floatation on a density gradient. These results show that cells can release multiple types of exRNA with substantial differences in RNA species content. This is important for any future studies determining the nature and function of exRNA released from different cells under different conditions.
2018-10-26 | PXD004931 | Pride
Project description:The extracellular matrix has been shown to control breast epithelial cell morphogenesis, proliferation and signalling. Here we compared changes in gene expression between 4T1 murine mammary carcinoma cells grown in a low or high density collagen matrix
2019-02-16 | GSE78022 | GEO
Project description:Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated two distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, snoRNA, and snRNA with little or no evidence of full-length 18S and 28S rRNA. The LD exRNA was enriched in mitochondrial rRNA, mitochondrial tRNA, tRNA, piRNA, Y RNA, and full-length 18S and 28S rRNA. The proteomes of the HD and LD exRNA-containing fractions were determined with LC-MS/MS and analysed with Gene Ontology term finder, which showed that both proteomes were associated with the term extracellular vesicles and electron microscopy suggests that at least a part of the exRNA is associated with exosome-like extracellular vesicles. Additionally, the proteins in the HD fractions tended to be associated with the nucleus and ribosomes, whereas the LD fraction proteome tended to be associated with the mitochondrion. We show that the two exRNA signatures released by a single cell type can be separated by floatation on a density gradient. These results show that cells can release multiple types of exRNA with substantial differences in RNA species content. This is important for any future studies determining the nature and function of exRNA released from different cells under different conditions.
2016-10-31 | GSE88753 | GEO
Project description:Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated two distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, snoRNA, and snRNA with little or no evidence of full-length 18S and 28S rRNA. The LD exRNA was enriched in mitochondrial rRNA, mitochondrial tRNA, tRNA, piRNA, Y RNA, and full-length 18S and 28S rRNA. The proteomes of the HD and LD exRNA-containing fractions were determined with LC-MS/MS and analysed with Gene Ontology term finder, which showed that both proteomes were associated with the term extracellular vesicles and electron microscopy suggests that at least a part of the exRNA is associated with exosome-like extracellular vesicles. Additionally, the proteins in the HD fractions tended to be associated with the nucleus and ribosomes, whereas the LD fraction proteome tended to be associated with the mitochondrion. We show that the two exRNA signatures released by a single cell type can be separated by floatation on a density gradient. These results show that cells can release multiple types of exRNA with substantial differences in RNA species content. This is important for any future studies determining the nature and function of exRNA released from different cells under different conditions.
2016-10-31 | GSE88754 | GEO
Project description:Stress represents a major factor negatively affecting fish welfare in aquaculture. The objective of the present study was to identify and evaluate informative indicators for the welfare and particular health status of maraena whitefish (Coregonus maraena) farmed at four different stocking densities. Transcriptome profiling revealed that numerous stress-related signaling pathways were activated in liver and kidney under ED and HD conditions, such as ERK/MAPK, mTOR, glucocorticoid receptor, SAPK/JNK and JAK/Stat signalling, as well as p38 and p53 signalling. Moreover, several stress-relevant effector pathways were found to be overexpressed including glycolysis and glycogen degradation. Strikingly, a high number of upregulated genes in kidney and in liver of fish kept at HD (compared to MD fish) were related to immunological processes, such as Acute-phase response signalling, B cell receptor signaling, CD28 signaling in T helper cells, and Interleukin-6 signaling. Four stocking density conditions were investigated: an uncrowded âmoderateâ density (MD: 33 kg trout/m³) , an elevated density (ED: 60 kg/m³ ), a low density (LD: 10 kg/m³ ), and high density (HD: 100 kg/m³). The experiment was performed twice, randomly assigned to identical glass tanks with MD (100 individuals), ED (180 individuals), LD (30 individuals), and HD (300 individuals). Trout were sampled 8 d after experimental onset.
2016-01-06 | E-GEOD-76543 | biostudies-arrayexpress
Project description:Murine erythroleukemia (MEL) cells are differentiated by dimethyl sulfoxide (DMSO）, hexamethylene bisacetamide (HMBA） or trichostatin A (TSA） treatment. We selsected high differentiation-inducible (HD) and low differentiation-inducible (LD)-MEL cells by recloning of original MEL cells. We screened erythroid differentiation related-genes to compare transcriptome of HD and LD-MEL cells.
2013-04-23 | GSE40754 | GEO
Project description:Gene expression profiling of the rat lung following intratracheal instillation with C60 fullerene particles was employed to gain insights into these molecular events. Groups of nine-week-old male Wistar rats (n= 4-6 per group/ time point) were intratracheally instilled with C60 fullerene suspended in 0.4 ml distilled water including 0.8% Tween-80 as a single injection (0.1 mg, 0.2 mg (LD: low doses) and 1.0 mg (HD: high dose) C60 fullerene/ rat). Control groups received 0.8 % Tween-80 (vehicle control). After intratracheal instillation treatment, rats were housed within polycarbonate cages at a controlled temperature of 22 °C with a chow diet ad libitum, and dissected at 3 days, 1 week, 1 month, 3 month, and 6 month post-instillation. Right lungs of anesthetized rats were perfused with physiological saline, excised, and used for DNA microarray analysis.
2009-08-26 | E-GEOD-17747 | biostudies-arrayexpress
Project description:Murine erythroleukemia (MEL) cells are differentiated by dimethyl sulfoxide (DMSOM-oM-<M-^I, hexamethylene bisacetamide (HMBAM-oM-<M-^I or trichostatin A (TSAM-oM-<M-^I treatment. We selsected high differentiation-inducible (HD) and low differentiation-inducible (LD)-MEL cells by recloning of original MEL cells. We screened erythroid differentiation related-genes to compare transcriptome of HD and LD-MEL cells. HD-MEL cells and LD-MEL cells were cultured 6, 12, 24, or 36 hours with 1.0% DMSO, 3.0 mM HMBA, or 15 nM TSA. The RNA of HD-MEL cells and LD-MEL cells were compare same time points of each drug treatment. The expression ratio (HD/LD) was calculated by average of technical quadruplicate microarray experiments includes two dye-swaps.
2013-04-23 | E-GEOD-40754 | biostudies-arrayexpress
Project description:Peripubertal endocrine disruption has immediate and lifelong consequences on health, cognition, and lifespan. Disruption comes from dietary, environmental, and pharmaceutical sources. The plasticizer Bisphenol A (BPA) is one such endocrine disrupting chemical (EDC). However, it’s unclear if peripubertal BPA exposure incites long-lasting physiological, neuro-cognitive, and/or longevity-related metabolic impairments. Catabolism of cysteine via transsulfuration enzymes produces hydrogen sulfide (H2S), a redox-modulating gasotransmitter causative to endocrine and metabolic homeostasis and improved cognitive function with age. As thyroid hormone (TH) regulates hepatic H2S production and BPA is a TH receptor antagonist, we hypothesized BPA exposure during peripubertal development impairs metabolic and neuro-cognitive/behavioral endpoints in aged mice, in part, due to altered peripheral H2S production. Results: To test this, male C57BL/6J mice at 5 weeks of age were orally exposed for 5 weeks to 250 ug BPA/kg defined as low dose group (LD BPA), or 250 mg BPA/kg defined as high dose group (HD BPA). Both LD and HD BPA exposure decreased lean mass and increased fat mass. These changes were accompanied by decreased serum total TH. Additionally, LD BPA had an anxiogenic effect while HD BPA caused cognitive deficits. Notably, HD BPA attenuated renal H2S production both acutely and during aging, which correlated with spatial memory deficits. Innovation and Conclusion: These findings provide a potential mechanism of action for the acute and long-term health impacts of BPA-induced peripubertal endocrine disruption and bolster the need for improved monitoring and limitation of adolescent BPA exposure.
2021-05-25 | PXD025746 | Pride