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Development of a new macrophage-specific TRAP mouse (MacTRAP) and the definition of the renal macrophage translational signature

ABSTRACT: Development of a new macrophage-specific TRAP mouse (MacTRAP) and the definition of the renal macrophage translational signature

PROVIDER: PRJNA561785 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10027326.fastq.gz	Fastqsanger.gz
	SRR10027327.fastq.gz	Fastqsanger.gz
	SRR10027328.fastq.gz	Fastqsanger.gz
	SRR10027329.fastq.gz	Fastqsanger.gz
	SRR10027330.fastq.gz	Fastqsanger.gz

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Development of a new macrophage-specific TRAP mouse (MacTRAP) and the definition of the renal macrophage translational signature

Project description:We generated a new macrophage-specific mouse line for the application of Translating Ribosome Affinity Purification (MacTRAP). MacTRAP mice express an eGFP-tagged ribosomal protein (L10a) under the control of the macrophage-specific c-fms promoter (driver of Csf1r). The TRAP line was characterized and expression of the transgene confirmed in kidney and other tissues. Validation included testing the responsiveness of the transgene under pro-inflammatory challenge in the kidney. Using TRAP, we successfully extracted macrophage-specific polysomal RNA from MacTRAP kidneys and conducted RNA-Seq following bioinformatic analyses to establish a comprehensive in vivo gene expression and pathway signature of resident renal macrophages, which may be of use to investigators studying the gene expression profile of these cells. Overall, this new in vivo tool may be of great value for the study of macrophage biology in different organs and various models of injury and disease.

2020-05-13 | GSE136265 | GEO

Development of a new macrophage-specific TRAP mouse (Mac<sup>TRAP</sup>) and definition of the renal macrophage translational signature.

Project description:Tissue macrophages play an important role in organ homeostasis, immunity and the pathogenesis of various inflammation-driven diseases. One major challenge has been to selectively study resident macrophages in highly heterogeneous organs such as kidney. To address this problem, we adopted a Translational Ribosome Affinity Purification (TRAP)- approach and designed a transgene that expresses an eGFP-tagged ribosomal protein (L10a) under the control of the macrophage-specific c-fms promoter to generate c-fms-eGFP-L10a transgenic mice (MacTRAP). Rigorous characterization found no gross abnormalities in MacTRAP mice and confirmed transgene expression across various organs. Immunohistological analyses of MacTRAP kidneys identified eGFP-L10a expressing cells in the tubulointerstitial compartment which stained positive for macrophage marker F4/80. Inflammatory challenge led to robust eGFP-L10a upregulation in kidney, confirming MacTRAP responsiveness in vivo. We successfully extracted macrophage-specific polysomal RNA from MacTRAP kidneys and conducted RNA sequencing followed by bioinformatical analyses, hereby establishing a comprehensive and unique in vivo gene expression and pathway signature of resident renal macrophages. In summary, we created, validated and applied a new, responsive macrophage-specific TRAP mouse line, defining the translational profile of renal macrophages and dendritic cells. This new tool may be of great value for the study of macrophage biology in different organs and various models of injury and disease.

| S-EPMC7200716 | biostudies-literature

Prenociceptin TRAP

Project description:Prenociceptin TRAP

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Translational regulation of specific mRNAs controls feedback inhibition and survival during macrophage activation [array]

Project description:When macrophages encounter pathogens, they transiently induce an orchestrated cascade of pro- and anti-inflammatory genes. We systematically analyzed the contribution of translational regulation to the early phase of macrophage activation. While the expression of most cytokines is regulated by changes in mRNA levels, de-repression of translation was found to permit expression of many feedback inhibitors of the inflammatory response. This includes NF-kB inhibitors (IkBd, IkBz, Nr4a1, Ier3), a p38 MAPK antagonist (Dusp1) and post-transcriptional suppressors of cytokine expression (TTP and Zc3h12a). Ier3 is tightly co-regulated with TNF at the level of mRNA abundance and translation. Macrophages lacking Ier3 show reduced survival upon activation, indicating that induction of Ier3 is required to protect macrophages from lipopolysaccharide-induced cell death. Our analysis reveals an important role of translational regulation in the resolution of inflammation and macrophage survival. RNA was purified from cytoplasmic lysate or polysome fractionation before and 1 h after stimulation of RAW264.7 macrophages with LPS. Fractions were pooled into four samples per condition: Free RNA (F), 40S-associated RNA (S), light (L) and heavy polysomes (H). The experiment was performed in three biological replicates, and RNA was quantified with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix).

2014-06-19 | E-GEOD-52449 | biostudies-arrayexpress

RNAseq from macrophages and osteoclasts from wild-type and TRAP deficient bone cell reporter mice

Project description:Osteoclasts are multinucleated giant cells generated by the fusion of precursors in response to stimulation with macrophage colony stimulating factor (MCSF) and receptor activator of NF-kB ligand (RANKL). These cells are the only cells capable of resorbing bone. Tartarate-resistant acid phosphatase is an enzyme secreted by osteoclasts that acts in bone resorption. Mice that are deficient for TRAP have shorter bones and their osteoclasts have decreased resorption capacity. In this project, we will isolate bone marrow macrophages from wild type and TRAP deficient mice, and differentiate the cells in osteoclasts in vitro. RNA will be extracted from macrophages and from macrophages stimulated with RANKL for both mouse lines (n=3/group) yielding 4 groups: Group 1 – macrophages from wild type mice, Group 2 – osteoclasts from wild type mice, Group 3 – macrophages from TRAP deficient mice, Group 4 – osteoclasts from TRAP deficient mice. The differential gene expression will be analyzed by RNAseq.

2024-02-02 | E-MTAB-11403 | biostudies-arrayexpress

VEGF Trap in Treating Patients With Previously Treated Metastatic Colorectal Cancer

Project description:This phase II trial is studying how well VEGF Trap works in treating patients with previously treated metastatic colorectal cancer. VEGF Trap may stop the growth of colorectal cancer by blocking blood flow to the tumor.

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TRAP-seq of mouse astrocytes involved in central nervous system remyelination

Project description:Remyelination failure contributes to axonal dysfunction in neurodegenerative disorders. But whether astrocytes, the most abundant glial cell type in demyelinated lesions, support or impede remyelination is controversial. Following focal demyelinated lesions of the mouse corpus callosum induced with the myelin toxin lysolecithin, we used TRAP (translational ribosome affinity purification) sequencing to isolate and sequence ribosome-associated mRNAs which are being actively translated in astrocytes, and studied how the responses and molecular mechanisms in astrocytes are linked to remyelination.

2023-05-17 | E-MTAB-9270 | biostudies-arrayexpress

Transcriptional profiling of pyramidal neurons in the cerebral cortex of Glt25d2-TRAP (DU9) mice administered either saline or cocaine [TRAP-seq]

Project description:TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain. Using this technique we obtained RNA-Seq data from actively translating transcripts present in pyramidal neurons in the cerebral cortex of adult Glt25d2-EGFP/Rpl10a (DU9) mice that were administered either saline or cocaine.

2019-12-16 | GSE141337 | GEO

Translational regulation of specific mRNAs controls feedback inhibition and survival during macrophage activation [array]

2014-06-19 | GSE52449 | GEO

Transcriptional profiling of neurons in the midbrain of a Stard8-TRAP (ES2342) mouse line

Project description:TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain. Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the thalamus of adult Stard8-EGFP/Rpl10a (ES2342) mice.

2019-09-10 | GSE137079 | GEO

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