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Genome binding pattern of H3K27ac and H3K4me3 in MARCO-TST postive triple-negative breast cancer

ABSTRACT: To investigate the transcription start site of MARCO-TST in triple negative breast cancer, we performed endogenous purification of H3K27ac and H3K4me3 under ChIP conditions, followed by high throughput sequencing.

ORGANISM(S): Homo sapiens

PROVIDER: GSE214133 | GEO | 2022/09/28

REPOSITORIES: GEO

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Genome binding pattern of H3K27ac and H3K4me3 in MARCO-TST postive triple-negative breast cancer

Project description:Genome binding pattern of H3K27ac and H3K4me3 in MARCO-TST postive triple-negative breast cancer

| PRJNA884102 | ENA

Contribution of the scavenger receptor MARCO to TLR-induced activation of dendritic cells

Project description:To gain additional insight into the role of MARCO in dendritic cell activation and function, we profiled transcriptomes of mouse splenic dendritic cells obtained from MARCO deficient mice and their wild type counterparts under resting and activating conditions. Pure dendritic cells from the spleens of WT and MARCO KO mice were cultured overnight in PBS or Lipopolysaccharide (LPS). Gene expression profiling was performed using Affymetrix platform.

2014-02-18 | E-GEOD-55068 | biostudies-arrayexpress

Computational inference of H3K4me3 and H3K27ac domain length.

Project description:Background. Recent epigenomic studies have shown that the length of a DNA region covered by an epigenetic mark is not just a byproduct of the assaying technologies and has functional implications for that locus. For example, expanded regions of DNA sequences that are marked by enhancer-specific histone modifications, such as acetylation of histone H3 lysine 27 (H3K27ac) domains coincide with cell-specific enhancers, known as super or stretch enhancers. Similarly, promoters of genes critical for cell-specific functions are marked by expanded H3K4me3 domains in the cognate cell type, and these can span DNA regions from 4-5kb up to 40-50kb in length. These expanded H3K4me3 domains are known as buffer domains or super promoters. Methods. To ask what correlates with-and potentially regulates-the length of loci marked with these two important histone marks, H3K4me3 and H3K27ac, we built Random Forest regression models. With these models, we computationally identified genomic and epigenomic patterns that are predictive for the length of these marks in seven ENCODE cell lines. Results. We found that certain epigenetic marks and transcription factors explain the variability of the length of H3K4me3 and H3K27ac marks across different cell types, which implies that the lengths of these two epigenetic marks are tightly regulated in a given cell type. Our source code for the regression models and data can be found at our GitHub page: https://github.com/zubekj/broad_peaks. Discussion. Our Random Forest based regression models enabled us to estimate the individual contribution of different epigenetic marks and protein binding patterns to the length of H3K4me3 and H3K27ac deposition patterns, therefore potentially revealing genomic signatures at cell specific regulatory elements.

| S-EPMC4793332 | biostudies-literature

Contribution of the scavenger receptor MARCO to TLR-induced activation of dendritic cells

2014-02-18 | GSE55068 | GEO

Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker

Project description:Macrophages are the most common infiltrating immune cells in glioblastoma (GBM), and play a wide variety of pro-tumor and anti-tumor roles. However, the different subpopulations of macrophages and their effects on the tumor microenvironment remain poorly understood. Here, we combine new and previously-published single-cell RNA-seq data from 86,279 single cells from a total of 63 gliomas to profile 17,774 individual macrophages. Unsupervised clustering revealed an anti-inflammatory subpopulation of macrophages characterized by expression of MARCO (macrophage receptor with collagenous structure), a gene which has not been previously well-characterized in gliomas. MARCO is almost exclusively expressed in macrophages of IDH1-wildtype GBM rather than IDH1-mutated GBM or lower-grade gliomas. Previous studies have implicated MARCO as an unfavorable marker in melanoma and non-small-cell lung cancer; here, we find that bulk MARCO expression is associated with worse prognosis in TCGA glioblastomas, and associates with the mesenchymal expression subtype. Our single-cell analysis shows that this previously-reported mesenchymal signature primarily arises from MARCO-expressing macrophages. These MARCO-expressing macrophages differentially over-express gene sets related to hypoxia and the epithelial-mesenchymal transition, and under-express gene sets related to inflammation and antigen presentation. We show evidence that MARCO-expressing macrophages are recruited from the blood (as opposed to being resident microglia), and paired single-cell analysis of tumor and myeloid cells demonstrate that this recruitment may be driven by known chemoattractant factors. Furthermore, MARCO expression is significantly altered over the course of treatment with PD1 checkpoint inhibitors. These findings illustrate a novel myeloid subpopulation that drives tumor progression in glioblastomas, and suggest potential therapeutic targets to prevent their recruitment glioblastoma.

2020-12-23 | GSE141383 | GEO

MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses in the draining lymph node and limit viral dissemination

Project description:While viremia in the vertebrate host is a critical determinant of arboviral reservoir competency, transmission efficiency, and disease severity, immune mechanisms that control arboviral viremia are poorly defined. Here, we identify critical roles for the scavenger receptor MARCO in controlling viremia during arthritogenic alphavirus infections in mice. Following subcutaneous inoculation, alphavirus particles drain via the lymph and are rapidly captured by MARCO+ lymphatic endothelial cells (LECs) in the draining lymph node (dLN), limiting viral spread to the bloodstream. Upon reaching the bloodstream, MARCO-expressing Kupffer cells in the liver remove circulating alphavirus particles, limiting viremia and further viral dissemination. MARCO-mediated accumulation of alphavirus particles in the lymph node and liver has important implications as viremia and viral tissue burdens are elevated in MARCO-/- mice and disease outcomes are more severe. These findings uncover a previously unrecognized pathogen scavenging role for LECs and improve our mechanistic understanding of viremia control during arboviral infections.

2021-09-10 | GSE174667 | GEO

SMAD2/3 binding pattern in triple-negative breast cancer cell lines, Hs578T and BT549 [ChIP-seq]

Project description:SMAD2 and SMAD3 have diverse binding profiles in triple-negative breast cancer cell lines.

2017-11-15 | GSE104352 | GEO

Phagocytosis of mycobacteria by zebrafish macrophages is dependent on the scavenger receptor Marco, a key control factor of pro-inflammatory signalling

Project description:Scavenger receptors on the cell surface of macrophages play an important role in host defence through their ability to bind microbial ligands and induce phagocytosis. Concurrently, signal transduction pathways are initiated that aid in defence mechanisms against the invading microbe. Here we report on the function of scavenger receptor Marco (macrophage receptor with collagenous structure) during infection of zebrafish embryos with Mycobacterium marinum, a close relative of Mycobacterium tuberculosis. Morpholino knockdown demonstrates that Marco is required for the rapid phagocytosis of M. marinum following intravenous infection. Furthermore, gene expression analysis shows that Marco controls the initial transient pro-inflammatory response to M. marinum and remains a determining factor for the immune response signature at later stages of infection. Increased bacterial burden following marco knockdown indicates that this scavenger receptor is important for control of M. marinum growth, likely due to delayed phagocytosis and reduced pro-inflammatory signalling observed under conditions of Marco deficiency

2014-08-06 | GSE58230 | GEO

Triple therapy reduced metastasis in triple-negative breast cancer.

Project description:Triple therapy reduced metastasis in triple-negative breast cancer.

| PRJNA832953 | ENA

CpG islands under selective pressure are enriched with H3K4me3, H3K27ac and H3K36me3 histone modifications.

Project description:BACKGROUND: Histone modification is an epigenetic mechanism that influences gene regulation in eukaryotes. In particular, histone modifications in CpG islands (CGIs) are associated with different chromatin states and with transcription activity. Changes in gene expression play a crucial role in adaptation and evolution. RESULTS: In this paper, we have studied, using a computational biology approach, the relationship between histone modifications in CGIs and selective pressure in Homo sapiens. We considered three histone modifications: histone H3 lysine 4 trimethylation (H3K4me3), histone H3 lysine 27 acetylation (H3K27ac) and histone H3 lysine 36 trimethylation (H3K36me3), and we used the publicly available genomic-scale histone modification data of thirteen human cell lines. To define regions under selective pressure, we used three distinct signatures that mark selective events from different evolutionary periods. We found that CGIs under selective pressure showed significant enrichments for histone modifications. CONCLUSION: Our result suggests that, CGIs that have undergone selective events are characterized by epigenetic signatures, in particular, histone modifications that are distinct from CGIs with no evidence of selection.

| S-EPMC3711888 | biostudies-other

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