Single-cell time-resolved multi-omics reveal macrophage heterogeneity during foam cell formation
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ABSTRACT:
PROVIDER: PRJNA898297 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22190525_1.fastq.gz | Fastqsanger.gz | |||
| SRR22190525_2.fastq.gz | Fastqsanger.gz |
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Project description:Macrophage-derived foam cell plays a pivotal role in the plaque formation and rupture during the progression of atherosclerosis. Foam cells are destined to divergent cell fate and functions in response to external stimuli based on their internal states, which however is hidden in the traditional studies based on population of cells. Herein, we used time-resolved and single-cell multi-omics to investigate the macrophage heterogeneity along foam cell formation. Dynamic metabolome and lipidome outlined the dual regulating axis of inflammation and ferroptosis. Single cell metabolomics and lipidomics further demonstrated a macrophage continuum featuring a differed susceptibility to apoptosis and ferroptosis. Using single-cell transcriptomic profiling, we verified the divergent cell fate toward apoptosis or ferroptosis. Therefore, the molecular choreography underlying the divergent cell fate during foam cell formation was revealed, which is of high significance for the understanding of the pathogenesis of atherosclerosis and development of new drug targets.
2024-08-10 | GSE240820 | GEO
Project description:<p>Macrophage-derived foam cell plays a pivotal role in the plaque formation and rupture during the progression of atherosclerosis. Foam cells are destined to divergent cell fate and functions in response to external stimuli based on their internal states, which however is hidden in the traditional studies based on population of cells. Herein, we used time-resolved and single-cell multi-omics to investigate the macrophage heterogeneity along foam cell formation. Dynamic metabolome and lipidome outlined the dual regulating axis of inflammation and ferroptosis. Single cell metabolomics and lipidomics further demonstrated a macrophage continuum featuring a differed susceptibility to apoptosis and ferroptosis. Using single-cell transcriptomic profiling, we verified the divergent cell fate toward apoptosis or ferroptosis. Therefore, the molecular choreography underlying the divergent cell fate during foam cell formation was revealed, which is of high significance for the understanding of the pathogenesis of atherosclerosis and development of new drug targets.</p>
2023-09-08 | MTBLS6366 | MetaboLights
Project description:The study aims to investigate the macrophage heterogeneity during foam cell formation.
2023-12-01 | GSE217251 | GEO
Project description:Single-cell time-resolved multi-omics reveal apoptotic and ferroptotic heterogeneity during foam cell formation
| PRJNA1005309 | ENA
Project description:Background: Cardiovascular diseases remain the leading cause of morbidity and mortality worldwide, most of which are caused by atherosclerosis. Discerning processes that participate in macrophage-to-foam cell formation are critical for understanding the basic mechanisms underlying atherosclerosis. To explore the molecular mechanisms of foam cell formation, the differentially expressed proteins were identified. Methods: In this paper, human monocytes, macrophage colony-stimulating factor induced macrophages, and oxidized low-density lipoprotein induced foam cells were cultured, and tandem mass tag (TMT) labeling combined with mass spectrometry (MS) were performed to find associations between foam cell transformation and proteome profiles. Results: Totally, 5146 quantifiable proteins were identified, among which 1515 and 182 differentially expressed proteins (DEPs) were found in macrophage/monocyte and foam cell/macrophage, respectively, using a cutoff of 1.5-fold change. Subcellular localization analysis revealed that downregulated DEPs of macrophages/monocytes were mostly located in the nucleus and upregulated DEPs of foam cells/macrophages mostly located in the plasma membrane and extracellular. Functional analysis of DEPs demonstrated that cholesterol metabolism related proteins were upregulated in foam cells, whereas the immune response-related proteins were downregulated in foam cells. The protein-interaction network showed that the DEPs with the highest interaction intensity between macrophages and foam cells were mainly concentrated in lysosomes and the endoplasmic reticulum. Conclusions: This study for the first time to perform quantitative proteomic investigation by TMT labeling and LC-MS/MS to identify differentially expressed proteins in human monocyte, macrophage, and foam cell. The results confirmed cholesterol metabolism was upregulated in foam cells, while immune response was suppressed, which suggested that foam cells were not the population that promote inflammation. In addition, KEGG enrichment analysis and protein-protein interaction indicated that the differentially expressed proteins locating in the endoplasmic reticulum and lysosomes may be key targets to regulate foam cell formation. These data provide a basis for identifying the potential proteins associated with the molecular mechanism involved in the transformation of macrophages to foam cells.
2022-02-15 | PXD028363 | Pride
Project description:Macrophages participate in plaque formation and development through the process of foam cell formation, and mitochondria play a crucial role in macrophage phenotype transformation. However, the mitochondrial metabolic characteristics of macrophages during foam cell formation have not been systematically studied. In this work, we investigated the mechanism of mitochondrial metabolic reprogramming during macrophage foam cell formation using proteomics, metabolomics and lipidomics. Multi-omics integrative analysis highlighted key metabolic pathway changes, including the tricarboxylic acid cycle fragmentation, and the recombination of mitochondria protein complexes and mitochondria membrane lipids.
2024-11-26 | PXD058260 |
Project description:Macrophage death in advanced atherosclerotic lesions is a key event in the conversion of benign lesions to vulnerable plaques. One fundamental transcription factor that has been shown to play a pivotal role in cell death/survival is nuclear factor kB (NF-kB). Still, the relevance of this key transcription factor for macrophage-derived foam cell survival has not been unequivocally resolved at the molecular level. THP-1 monocytic cell lines were generated in which NF-kB activation is specifically inhibited by overexpression of a trans-dominant, non-degradable form of IkBa (IkBa (32A/36A)) under control of the macrophage-specific SR-A promoter. A diminished lipid loading during NF-κB inhibition during foam cell formation was accompanied by increased cell death. A genome-wide expression profile of NF-kB-dependent genes during foam cell formation was established showing a widespread effect on the macrophage transcriptome. The three largest functional gene clusters identified and validated by independent techniques, were those involved in lipid metabolism, apoptosis and oxidative stress. The net result of these complex gene expression changes invoked by inhibition of NF-κB activation during lipid loading is a reduction of foam cell survival through caspase-dependent apoptosis. Thus, the NF-kB-dependent gene repertoire seems essential for sustained macrophage survival during the process of pathological lipid loading. Keywords: genetic modification, lipid loading, timecourse
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Project description:Macrophage death in advanced atherosclerotic lesions is a key event in the conversion of benign lesions to vulnerable plaques. One fundamental transcription factor that has been shown to play a pivotal role in cell death/survival is nuclear factor kB (NF-kB). Still, the relevance of this key transcription factor for macrophage-derived foam cell survival has not been unequivocally resolved at the molecular level. THP-1 monocytic cell lines were generated in which NF-kB activation is specifically inhibited by overexpression of a trans-dominant, non-degradable form of IkBa (IkBa (32A/36A)) under control of the macrophage-specific SR-A promoter. A diminished lipid loading during NF-κB inhibition during foam cell formation was accompanied by increased cell death. A genome-wide expression profile of NF-kB-dependent genes during foam cell formation was established showing a widespread effect on the macrophage transcriptome. The three largest functional gene clusters identified and validated by independent techniques, were those involved in lipid metabolism, apoptosis and oxidative stress. The net result of these complex gene expression changes invoked by inhibition of NF-κB activation during lipid loading is a reduction of foam cell survival through caspase-dependent apoptosis. Thus, the NF-kB-dependent gene repertoire seems essential for sustained macrophage survival during the process of pathological lipid loading. Keywords: genetic modification, lipid loading, timecourse THP-1 cells and two different THP-1 IkB mutants (A3 and A12) were exposed to PMA to induce macrophage differentiation and subsequently loaded with oxidized LDL or vehicle for 5 or 8 days. One replicate per array, a total of 15 arrays. A common reference pool, composed of an equimolar mixture of all samples, was labeled with Cy3 and hybridized against the Cy5-labeled experimental sample.
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