ChIP-seq of EGR1 in human primary unstimulated monocytes and in unstimulated human monocytes from three CMML patients
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ABSTRACT: Identification of EGR1 chromatin localization in human primary monocytes (2 donors), in human primary monocytes from 2 CMML patients with TET2 truncating mutations (high VAF) and in human primary monocytes from 1 CMML patients with TET2 truncating mutations with low VAF.
Project description:Identification of nuclear CSF-1R, H3K4me1 and H3K4me3 localization on chromatin in human primary monocytes and modification of this localization during monocyte differentiation into macrophage induced by 100ng/mL CSF-1 during 6 hours (1 donor) or 72h (3 donors). Identification of EGR1 chromatin localization in human primary monocytes (3 donors) Comparison of nuclear CSF-1R chromatin localization in monocytes from 1 healthy donor and 2 chronic myelomonocytic leukemia patients.
Project description:CSF-1R is recruited on EGR1 motifs in monocytes where it colocalizes with EGR1. To address if EGR1 required for CSF-1R recruitment on chromatin, THP-1 monocytic cell line has been deleted for EGR1 by CRISPR-Cas9 approach. 3 clones were generated by single cell cloning and CSF-1R localization on chromatin was compared to two unmodified THP-1 clones by ChIP-sequencing. Since the read number was strongly decreased in the EGR1-deleted clones, the three clones were pooled for the comparison with wild-type clones. ChIPseq of CSF-1R (Nter Antibody) in monocytes of two CMML patients (CMML2130 and CMML2609)
Project description:Somatic mutation in TET2 gene is one of the most common clonal genetic events detected in age-related clonal hematopoiesis as well as in chronic myelomonocytic leukemia (CMML). In addition to being a pre-malignant state, TET2 mutated clones are associated with an increased risk of death from cardiovascular disease, which could involve cytokine/chemokine overproduction by monocytic cells. Here, we show in mice and in human cells that, in the absence of any inflammatory challenge, TET2 down-regulation promotes the production of MIF (macrophage migration inhibitory factor), a pivotal mediator of atherosclerotic lesion formation. In healthy monocytes, TET2 is recruited to MIF promoter and interacts with the transcription factor EGR1 and histone deacetylases. Disruption of these interactions as a consequence of TET2-decreased expression favors EGR1-driven transcription of MIF gene and its secretion. MIF favors monocytic differentiation of myeloid progenitors. These results designate MIF as a chronically overproduced chemokine and a potential therapeutic target in patients with clonal TET2 down-regulation in myeloid cells.
Project description:Chronic myelomonocytic leukemia (CMML) is a myelodysplastic/myeloproliferative overlap neoplasm with few treatment options and generally poor prognosis. A defining feature is expansion of classical monocytes, which are responsible for various clinical sequelae and thus represent viable therapeutic targets. Given the near-ubiquity of mutations involving epigenetic regulators, we profiled the epigenome (open chromatin configuration; H3K4-monomethylation; H3K27-acetylation; H3K27/H3K4-trimethylation) and transcriptome of primary CD14+ monocytes from CMML patients and age-matched healthy controls. Compared with healthy monocytes, CMML monocytes displayed heterogeneous but distinct epigenetic and transcriptome signatures. Most epigenetic changes mapped to distal elements, suggesting generalized enhancer dysregulation. We observed strong epigenetic (but not transcriptional) suppression of the NF-κB pathway, suggesting poised potential to repress downstream targets and modulate inflammatory responses. RNA-seq revealed up-regulation of genes involved in the oxidative phosphorylation (OxPhos) machinery, with significantly heightened OxPhos activity of primary CMML monocytes validated in mitochondrial stress tests, highlighting a potentially tractable therapeutic vulnerability. In line with the observed metabolic phenotype of CMML monocytes, unpolarized CMML monocyte-derived macrophages exhibited transcriptional bias towards an M2 (“anti-inflammatory”) phenotype, reflected by an increased Th2/Th1 ratio in comparison with control monocytes. These observations may be germane to the observed clinical heterogeneity and prominent immune dysfunction characteristic of CMML.
Project description:Chronic myelomonocytic leukemia (CMML) is a myelodysplastic/myeloproliferative overlap neoplasm with few treatment options and generally poor prognosis. A defining feature is expansion of classical monocytes, which are responsible for various clinical sequelae and thus represent viable therapeutic targets. Given the near-ubiquity of mutations involving epigenetic regulators, we profiled the epigenome (open chromatin configuration; H3K4-monomethylation; H3K27-acetylation; H3K27/H3K4-trimethylation) and transcriptome of primary CD14+ monocytes from CMML patients and age-matched healthy controls. Compared with healthy monocytes, CMML monocytes displayed heterogeneous but distinct epigenetic and transcriptome signatures. Most epigenetic changes mapped to distal elements, suggesting generalized enhancer dysregulation. We observed strong epigenetic (but not transcriptional) suppression of the NF-κB pathway, suggesting poised potential to repress downstream targets and modulate inflammatory responses. RNA-seq revealed up-regulation of genes involved in the oxidative phosphorylation (OxPhos) machinery, with significantly heightened OxPhos activity of primary CMML monocytes validated in mitochondrial stress tests, highlighting a potentially tractable therapeutic vulnerability. In line with the observed metabolic phenotype of CMML monocytes, unpolarized CMML monocyte-derived macrophages exhibited transcriptional bias towards an M2 (“anti-inflammatory”) phenotype, reflected by an increased Th2/Th1 ratio in comparison with control monocytes. These observations may be germane to the observed clinical heterogeneity and prominent immune dysfunction characteristic of CMML.
Project description:Chronic myelomonocytic leukemia (CMML) is a myelodysplastic/myeloproliferative overlap neoplasm with few treatment options and generally poor prognosis. A defining feature is expansion of classical monocytes, which are responsible for various clinical sequelae and thus represent viable therapeutic targets. Given the near-ubiquity of mutations involving epigenetic regulators, we profiled the epigenome (open chromatin configuration; H3K4-monomethylation; H3K27-acetylation; H3K27/H3K4-trimethylation) and transcriptome of primary CD14+ monocytes from CMML patients and age-matched healthy controls. Compared with healthy monocytes, CMML monocytes displayed heterogeneous but distinct epigenetic and transcriptome signatures. Most epigenetic changes mapped to distal elements, suggesting generalized enhancer dysregulation. We observed strong epigenetic (but not transcriptional) suppression of the NF-κB pathway, suggesting poised potential to repress downstream targets and modulate inflammatory responses. RNA-seq revealed up-regulation of genes involved in the oxidative phosphorylation (OxPhos) machinery, with significantly heightened OxPhos activity of primary CMML monocytes validated in mitochondrial stress tests, highlighting a potentially tractable therapeutic vulnerability. In line with the observed metabolic phenotype of CMML monocytes, unpolarized CMML monocyte-derived macrophages exhibited transcriptional bias towards an M2 (“anti-inflammatory”) phenotype, reflected by an increased Th2/Th1 ratio in comparison with control monocytes. These observations may be germane to the observed clinical heterogeneity and prominent immune dysfunction characteristic of CMML.
Project description:Chronic myelomonocytic leukemia (CMML) is an aggressive myeloid neoplasm of older individuals characterized by persistent monocytosis. Somatic mutations in CMML are heterogeneous and only partially explain the variability in clinical outcomes. Recent data suggest that cardiovascular morbidity is increased in CMML and contributes to reduced survival. Clonal hematopoiesis of indeterminate potential (CHIP), the presence of mutated blood cells in hematologically normal individuals, is a precursor of age-related myeloid neoplasms and associated with increased cardiovascular risk. To isolate CMML-specific alterations from those related to aging, we performed RNA sequencing and DNA methylation profiling on purified monocytes from CMML patients and from age-matched (old) and young healthy controls. We found that the transcriptional signature of CMML monocytes is highly pro-inflammatory, with upregulation of multiple inflammatory pathways, including tumor necrosis factor, IL-6 and IL-17 signaling, while age per se does not significantly contribute to this pattern. We observed no consistent correlations between aberrant gene expression and CpG island methylation, suggesting that pro-inflammatory signaling in CMML monocytes is governed by multiple and complex regulatory mechanisms. We propose that pro-inflammatory monocytes may contribute to cardiovascular morbidity in CMML patients, and promote progression by selection of mutated cell clones. Our data raise questions whether asymptomatic CMML patients may benefit from monocyte-depleting or anti-inflammatory therapies.