Bulk RNAseq analysis reveals distinct differentiation traits of COMMD10-deficient Ly6Chi monocytes in the injured liver
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ABSTRACT:
PROVIDER: PRJNA761080 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15729226.fastq.gz | Fastqsanger.gz | |||
| SRR15729227.fastq.gz | Fastqsanger.gz | |||
| SRR15729228.fastq.gz | Fastqsanger.gz | |||
| SRR15729229.fastq.gz | Fastqsanger.gz | |||
| SRR15729230.fastq.gz | Fastqsanger.gz |
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Project description:Hepatic macrophages play a central role in the initiation, progression and resolution of various liver diseases. Specifically, infiltrating Ly6Chi monocytes and their-derived macrophage (MoMFs) descendants prevail in acute or chronic liver injury, display marked transcriptional variance and provide crucial functional plasticity. A specific example of MoMFs are lipid associated macrophages (LAMs) involved in progression of metabolic liver disease (Remmerie et al., 2020). Recent studies have uncovered binary developmental trajectories of monocytes in the BM with Neutrophil-like (NeuMo) and dendritic cell (DC)-like (DCMo) monocytes (Weinreb et al., 2020; Yanez et al., 2017), hence further challenging our current comprehension of macrophage heterogeneity in the diseased liver. Yet, the molecular factors regulating their inflammatory versus restorative activity remains enigmatic. The COMMD (copper metabolism MURR1 domain) family includes 10 evolutionarily conserved proteins. Functions of COMMD proteins are still being defined, but they seem to play non-redundant roles in regulating transcription and protein trafficking. Utilizing conditional COMMD10 knockout mice we uncovered a role for COMMD10 in limiting inflammasome activation in Ly6Chi monocytes during experimental sepsis and colitis (Mouhadeb et al., 2018), and in supporting phagolysosomal biogenesis and maturation in KCs and BM-derived macrophages infected with Staphylococcus aureus (Ben Shlomo et al., 2019). Hence, these studies mark COMMD10 as a candidate mediator of monocyte and macrophage fate and immune responses. Here we studeis the effect of COMMD10-deficiency on Ly6Chi monocyte differentiation and inflammatory behaviour in the injured liver, using an acute model of acetaminophen-induced liver injury (AILI). Single cell RNAseq analysis of sorted Ly6Chi monocytes, comparing between COMMD10+ and COMMD10-deficient cells, revealed increased differentiation bias of Ly6Chi monocytes towards NeuMo and LAM differentiation fates. Collectively, COMMD10 appears as an important regulator of Ly6Chi monocyte fate decisions and reparative behavior in the diseased liver.
2021-10-05 | GSE183367 | GEO
Project description:Hepatic macrophages play a central role in the initiation, progression and resolution of various liver diseases. Specifically, infiltrating Ly6Chi monocytes and their-derived macrophage (MoMFs) descendants prevail in acute or chronic liver injury, display marked transcriptional variance and provide crucial functional plasticity. A specific example of MoMFs are lipid associated macrophages (LAMs) involved in progression of metabolic liver disease (Remmerie et al., 2020). Recent studies have uncovered binary developmental trajectories of monocytes in the BM with Neutrophil-like (NeuMo) and dendritic cell (DC)-like (DCMo) monocytes (Weinreb et al., 2020; Yanez et al., 2017), hence further challenging our current comprehension of macrophage heterogeneity in the diseased liver. Yet, the molecular factors regulating their inflammatory versus restorative activity remains enigmatic. The COMMD (copper metabolism MURR1 domain) family includes 10 evolutionarily conserved proteins. Functions of COMMD proteins are still being defined, but they seem to play non-redundant roles in regulating transcription and protein trafficking. Utilizing conditional COMMD10 knockout mice we uncovered a role for COMMD10 in limiting inflammasome activation in Ly6Chi monocytes during experimental sepsis and colitis (Mouhadeb et al., 2018), and in supporting phagolysosomal biogenesis and maturation in KCs and BM-derived macrophages infected with Staphylococcus aureus (Ben Shlomo et al., 2019). Hence, these studies mark COMMD10 as a candidate mediator of monocyte and macrophage fate and immune responses. Here we studeid the effect of COMMD10-deficiency on Ly6Chi monocyte differentiation and inflammatory behaviour in the injured liver, using an acute model of acetaminophen-induced liver injury (AILI). Bulk RNAseq analysis of sorted Ly6Chi monocytes, comparing between COMMD10+ and COMMD10-deficient cells, revealed an increased differentiation bias of Ly6Chi monocytes towards NeuMo and LAM differentiation fates. Collectively, COMMD10 appears as an important regulator of Ly6Chi monocyte fate decisions and reparative behavior in the diseased liver.
2021-10-05 | GSE183494 | GEO
Project description:Single cell RNAseq reveals distinct differentiation traits of COMMD10-deficient Ly6Chi monocytes in the injured liver
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Project description:Monocytes are circulating myeloid immune precursor cells that are generated in the bone marrow (BM). Upon their release into the circulation, monocytes are recruited to inflammatory sites, where they differentiate into monocyte-derived effector cells. In absence of overt inflammation, monocytes also extravasate into selected tissues, where they complement tissue-resident macrophage compartments. Recent studies have uncovered binary developmental trajectories of monocytes in the BM with Neutrophil-like (NeuMo) and dendritic cell (DC)-like (DCMo) monocytes differentiating downstream of granulocyte-macrophage progenitors (GMP) and macrophage-dendritic cell progenitors (MDP), respectively (Weinreb et al., 2020; Yanez et al., 2017). Yet, the molecular cues that dictate BM monocyte differentiation remain incompletely understood. The COMMD (copper metabolism MURR1 domain) family includes 10 evolutionarily conserved proteins. Functions of COMMD proteins are still being defined, but they seem to play non-redundant roles in regulating transcription and protein trafficking. Utilizing conditional COMMD10 knockout mice we uncovered a role for COMMD10 in limiting inflammasome activation in Ly6Chi monocytes during experimental sepsis and colitis (Mouhadeb et al., 2018), and in supporting phagolysosomal biogenesis and maturation in KCs and BM-derived macrophages infected with Staphylococcus aureus (Ben Shlomo et al., 2019). Hence, these studies mark COMMD10 as a candidate mediator of monocyte and macrophage fate and immune responses. Here we studied the effect of COMMD10-deficiency on Ly6Chi monocyte differentiation. We show that COMMD10-deficiency in steady state Ly6Chi monocytes promotes a differentiation bias towards NeuMo fate.
2021-10-05 | GSE183495 | GEO
Project description:COMMD10-deficiency promotes 'neutrophil like' differentiation fate of bone marrow Ly6Chi monocytes
| PRJNA761081 | ENA
Project description:mRNA expression profiles between Ym1+Ly6Chi monocytes and Ym1-Ly6Chi monocytes from LPS-treated mice were analyzed by RNA-sequencing
2021-07-02 | GSE118032 | GEO
Project description:Gene expression analysis of neutrophils, Ym1+Ly6Chi monocytes and Ym1-Ly6Chi monocytes
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Project description:Most tissue-resident macrophages are established prenatally and self-maintain independently of bone marrow (BM) monocytes. Instructed by local cues, these cells adopt unique transcriptional modules that impart tissue-specific functional identity (Varol et al., 2015). In the liver, Kupffer cells (KCs) dominate the homeostatic macrophage pool. They reside in the sinusoidal vessels and in the space of Disse, interacting with hepatic stellate cells (HSC) and hepatocytes (Bonnardel et al., 2019), where they act as sentinels and perform specialized accessory functions involving iron and lipid metabolism (Scott and Guilliams, 2018). Yet, the molecular cues governing KC differentiation and maintanence remain largly elusive. Embryonic lethality of COMMD10 deficiency has hampered the study of its function. Yet, utilizing conditional COMMD10 knockout mice we recently uncovered a role for COMMD10 in supporting phagolysosomal biogenesis and maturation in KCs and BM-derived macrophages infected with Staphylococcus aureus (Ben Shlomo et al., 2019). Here we show that COMMD10-deficient KCs adopt liver-specific identity. Strikingly, COMMD10-deficiency in KCs and in other tissue resident macrophages impedes their homeostatic survival, leading to their continuous replacement by Ly6Chi monocytes. Transcriptional analysis of COMMD10-deficiet KCs reveales a notable reduction in genes encoding for translation initiation- and ribosomal complex proteins, for ubiquitin and the proteasome protein complex, and for key proteins of the mitochondrial respiration chain. These transcriptional alterations allude to protein stress and mitochondrial dysfunction, and hint at the reason of their premature death.
2021-10-05 | GSE183493 | GEO
Project description:COMMD10 is critical for Kupffer cell survival and controls Ly6Chi monocyte differentiation and inflammation in the injured liver
| PRJNA761971 | ENA
Project description:Monocytes comprise two major subsets, Ly6Chi classical monocytes and Ly6Clo non-classical monocytes. Notch2 signaling in Ly6Chi monocytes triggers transition to Ly6Clo monocytes, which require Nr4a1, Bcl6, Irf2 and Cebpb. By comparison, less is known about transcriptional requirements for Ly6Chi monocytes. We find transcription factor CCAAT/enhancer-binding protein alpha (C/EBPα) is highly expressed in Ly6Chi monocytes, but down-regulated in Ly6Clo monocytes. A few previous studies described the requirement of C/EBPα in the development of neutrophils and eosinophils. However, role of C/EBPα for in vivo monocyte development has not been understood. We deleted the Cebpa +37 kb enhancer in mice, eliminating hematopoietic expression of C/EBPα, reproducing the expected neutrophil defect. Surprisingly, we also discovered a severe and selective loss of Ly6Chi monocytes, while preserving Ly6Clo monocytes. We find that BM progenitors from Cebpa +37–/– mice rapidly progress through the cMoP stage to develop directly into Ly6Clo monocytes even in the absence of Notch2 signaling. These results identify a previously unrecognized role for C/EBPα in maintaining Ly6Chi monocyte identity.
2024-03-18 | GSE254202 | GEO