Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Resident Macrophages are Locally Programmed for Silent Clearance of Apoptotic Cells

ABSTRACT: Although apoptotic cells (ACs) contain nucleic acids that can be recognized by Toll-like receptors (TLRs), engulfment of ACs does not initiate inflammation in healthy organisms. To better understand this phenomenon, we identified and characterized macrophage populations that continually engulf ACs in several distinct tissues. These macrophages share characteristics compatible with immunologically silent clearance of ACs, including high expression of AC recognition receptors, low expression of TLR9, and reduced TLR responsiveness to nucleic acids. When removed from tissues, these macrophages lose many of these characteristics and generate inflammatory responses to AC-derived nucleic acids, suggesting that cues from the tissue microenvironment are required to program macrophages for silent AC clearance. We show that KLF2 and KLF4 control expression of many genes within this AC clearance program. Coordinated expression of AC receptors with genes that limit responses to nucleic acids may represent a central feature of tissue macrophages that ensures maintenance of homeostasis.

ORGANISM(S): Mus musculus

PROVIDER: GSE93820 | GEO | 2017/11/15

SECONDARY ACCESSION(S): PRJNA362496

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Molecular and functional features of synucleinopathy-associated astrocytes

Project description:Astrocyte (AC) involvement is a common neuropathological feature in human synucleinopathy-associated neurodegeneration. However, our understanding of the in vivo characteristics of reactive ACs in synucleinopathy remained limited. Here we report the transcriptomic and functional features of a unique synucleinopathy-associated AC (SAA) subtype in a mouse model. SAAs share a convergent transcriptomic state across synucleinopathy-laden brain regions, and are at least partially reliant on microglia for their phenotypic maintenance in vivo. Intravital imaging revealed that an upregulation of the excitatory amino acid transporter 2 (EAAT2) in synucleinopathy-affected ACs is associated with depressed neuronal activities. This is potentially mediated via increased AC glutamate uptake, as pharmacological induction of EAAT2 reproduced the same effect. With cross-species comparative analysis, we showed that the core SAA transcriptomic features are present in human aged and synucleinopathy-affected midbrain ACs, while important distinct characteristics also exist. Collectively, our results uncovered complex reactive AC changes that likely play important adaptive roles in synucleinopathy.

2023-06-30 | GSE205511 | GEO

miRNA expression signatures in human alveolar macrophages after toll-like receptor activation

Project description:We have employed miRNA microarray expression profiling to identify miRNAs that are differentially regulated by toll-like receptor activation in alveolar macrophages. Macrophages are strategically distributed all over the body and represent the first line of defense to invading pathogens. In response to bacterial or viral infections, these phagocytic cells engulf and destroy the infectious agent. Macrophages recognize a variety of microbial products, such as bacterial cell wall components and nucleic acids, via pathogen recognition receptors (PRRs), such as toll-like receptors (TLRs). TLR4 represents the receptor for bacterial lipopolysaccharide (LPS). The extracellular TLR1/2 heterodimer recognizes bacterial triacetylated lipopeptides and their mimic, the synthetic compound Pam3CSK4. In contrast, intracellular TLR3 detects double-stranded RNA, i.e., an intermediate in viral replication, as well as its synthetic analogon polyinosinic:polycytidylic acid (Poly(I:C)). TLRs differentially activate transcription factors due to the varying involvement of the adapter molecules. However, little is known about TLR-mediated miRNA induction in macrophages. In this study, several microRNAs were identified that were specifically associated with a certain treatment scheme, suggesting that macrophage responses highly depend on the nature of the stimulus.

2018-12-13 | GSE123756 | GEO

Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization

Project description:To investigate how exogenous DNA concatemerizes to form episomal artificial chromosomes (ACs), acquire equal segregation ability and maintain stable holocentromeres, we injected DNA sequences with different features, including sequences that are repetitive or complex, and sequences with different AT-contents, into the gonad of Caenorhabditis elegans to form ACs in embryos, and monitored AC mitotic segregation. We demonstrated that AT-poor sequences (26% AT-content) delayed the acquisition of segregation competency of newly formed ACs. We also co-injected fragmented Saccharomyces cerevisiae genomic DNA, differentially expressed fluorescent markers and ubiquitously expressed selectable marker to construct a less repetitive, more complex AC. We sequenced the whole genome of a strain which propagates this AC through multiple generations, and de novo assembled the AC sequences. We discovered CENP-AHCP-3 domains/peaks are distributed along the AC, as in endogenous chromosomes, suggesting a holocentric architecture. We found that CENP-AHCP-3 binds to the unexpressed marker genes and many fragmented yeast sequences, but is excluded in the yeast extremely high-AT-content centromeric and mitochondrial DNA (> 83% AT-content) on the AC. We identified A-rich motifs in CENP-AHCP-3 domains/peaks on the AC and on endogenous chromosomes, which have some similarity with each other and similarity to some non-germline transcription factor binding sites.

2021-08-22 | GSE145600 | GEO

Mus musculus

Project description:Resident Macrophages are Locally Programmed for Silent Clearance of Apoptotic Cells

| PRJNA362496 | ENA

Identification of novel candidate target genes at 3q26.2-q29 in squamous cell carcinoma of the lung

Project description:High-resolution array-CGH was performed to identify differences in the patterns of genomic imbalances between SCC and AC of non-small cell lung cancer (NSCLC). On a genome-wide profile, SCCs showed higher frequency of gains than ACs (p = 0.067). More specifically, statistically significant differences were observed across the histologic subtypes for gains at 2q14.2, 3q26.2-q29, 12p13.2-p13.33, and 19p13.3, as well as losses at 3p26.2-p26.3, 16p13.11, and 17p11.2 in SCC, and gains at 7q22.1 and losses at 15q22.2-q25.2 occurred in AC (P < 0.05). The most striking difference between SCC and AC was gains at 3q26.2-q29, occurring in 86% (19/22) of SCCs, but in only 21% (3/14) of ACs.

2009-06-19 | GSE16597 | GEO

Mouse retinal cell atlas: molecular identification of sixty-three amacrine cell types

Project description:Amacrine cells (ACs) are a diverse class of interneurons that modulate input from photoreceptors to retinal ganglion cells (RGCs), rendering each RGC type selectively sensitive to particular visual features, which are then relayed to the brain. While many AC types have been identified morphologically and physiologically, they have not been comprehensively classified or molecularly characterized. We used high-throughput single-cell RNA sequencing (scRNA-seq) to profile >32,000 ACs from mice of both sexes, and applied computational methods to identify 63 AC types. We identified molecular markers for each type, and used them to characterize the morphology of multiple types. We show that they include nearly all previously known AC types as well as many that had not been described. Consistent with previous studies, most of the AC types expressed markers for the canonical inhibitory neurotransmitters GABA or glycine, but several expressed neither or both. In addition, many expressed one or more neuropeptides, and two express glutamatergic markers. We also explored transcriptomic relationships among AC types and identified transcription factors expressed by individual or multiple closely related types. Noteworthy among these were Meis2 and Tcf4, expressed by most GABAergic and most glycinergic types, respectively. Together, these results provide a foundation for developmental and functional studies of ACs, as well as means for genetically accessing them. Along with previous molecular, physiological and morphological analyses, they establish the existence of at least 130 neuronal types and nearly 140 cell types in mouse retina.

2020-06-22 | GSE149715 | GEO

Human CD11b+ macrophages - Aging of hematopoietic stem cells is driven by regional specialization of marrow macrophages

Project description:The human aged hematopoietic system is prone to dysfunction and clonal selection. Aged hematopoietic stem cells (HSCs) have well-defined characteristics, but the contribution of the bone marrow microenvironment (BMME) to HSC ageing is unclear. We identify age-dependent changes in bone-associated (BA) and marrow-associated (MA) cell populations in murine and human marrow, where only aged MA cells induce aged HSC characteristics. MA aged macrophages (Mφs) could impart aged characteristics to both HSC and BMME populations, and demonstrated decreased ability to engulf senescent neutrophils. Moreover, removal of Mφs from young mice rapidly induced aged HSC characteristics. Interleukin-1β (IL-1β), a cytokine that is restrained when Mφs engulf apoptotic cells, was a key mediator of microenvironmental HSC aging. These data define a previously unknown role for aged MA Mφs to orchestrate BMME and HSC changes. Mφs and IL-1β may therefore represent novel targets for preventing or reversing hematopoietic defects due to advanced age.

2019-06-10 | GSE100905 | GEO

Mouse CD11b+ macrophages - Aging of hematopoietic stem cells is driven by regional specialization of marrow macrophages

2019-06-10 | GSE98249 | GEO

Mouse lt-hsc single cells - Aging of hematopoietic stem cells is driven by regional specialization of marrow macrophages

2019-06-10 | GSE100906 | GEO

Transcriptome sequencing at early stage infection of the wheat pathogen Zymoseptoria tritici reveals chromosomal differences in transcription patterns and host specific gene expression.

Project description:We have applied whole transcriptome profiling to infer genetic determinants of pathogenicity and host specialization in Z. tritici. Our data includes RNAseq data from early infection stages of a compatible (wheat) and a non-compatible host (Brachypodium distachyon). Overall transcription of AC genes is remarkably lower than genes on core chromosomes (CC) and only 40% of the genes are transcribed. We identify 31 AC and 1069 CC genes showing plant specific expression. In addition 21 CC genes are only upregulated in wheat supporting functional relevance in host specificity. We further explore the genomic composition and distribution of unique and paralogous genes in Z. tritici focusing on the evolutionary origin of AC genes. In contrast to previous studies we show that ACs mainly encode unique genes. Phylogenetic analyses suggest that rare duplication events in the Z. tritici genome precede diversification of Zymoseptoria species and demonstrate that ACs have been maintained in the genome of Zymoseptoria over long evolutionary times.

2014-06-30 | GSE54874 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data