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Prolyl endopeptidase-mediated transcriptional regulation in quiescent and activated bone marrow-derived macrophages (Bulk RNA-seq)

ABSTRACT: Prolyl endopeptidase-mediated transcriptional regulation in quiescent and activated bone marrow-derived macrophages (Bulk RNA-seq)

PROVIDER: PRJNA878835 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21508127_1.fastq.gz	Fastqsanger.gz
	SRR21508127_2.fastq.gz	Fastqsanger.gz
	SRR21508128_1.fastq.gz	Fastqsanger.gz
	SRR21508128_2.fastq.gz	Fastqsanger.gz
	SRR21508129_1.fastq.gz	Fastqsanger.gz

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Prolyl endopeptidase-mediated transcriptional regulation in quiescent and activated bone marrow-derived macrophages

Project description:Prolyl endopeptidase-mediated transcriptional regulation in quiescent and activated bone marrow-derived macrophages

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Prolyl endopeptidase-mediated transcriptional regulation in quiescent and activated bone marrow-derived macrophages (CUT&Tag)

Project description:Prolyl endopeptidase-mediated transcriptional regulation in quiescent and activated bone marrow-derived macrophages (CUT&Tag)

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Prolyl endopeptidase-mediated transcriptional regulation in quiescent and activated bone marrow-derived macrophages (Bulk RNA-seq)

Project description:Liver fibrosis, a pathogical change commonly existing in various chronic liver diseases, can ultimately develop into life-threatening liver cirrhosis, but effective antifibrotic therapy is absent due to limited understanding of fibrogenic process. The characteristic fibrotic scar in fibrosis is stiff and disorganized extracellular matrix (ECM) yielded by ECM remodeling, a pathogenic process with vigorous participation of aberrantly activated macrophages. Prolyl endopeptidase (PREP) is a dipeptidyl peptidase that possess both proteolytic and non-proteolytic functions. Using Prep knockout mouse, we found aggravated liver fibrosis in a NASH-related fibrosis murine model, as well as significantly altered transcriptome by in vitro M1/M2 polarization in primary macrophages after PREP ablation. Most importantly, a PREP-mediated direct transcriptional regulation to active cis-regulatory genomic regions was identified for the first time as a novel non-proteolytic function of PREP, based on significant nuclear localization of PREP and CUT&Tag-seq results. Among the PREP-downstream genes, Ctsb and Ctsd, genes encoding ECM remodeling-related profibrogenic cathepsin B and D respectively, were excessively expressed in PREP-ablated macrophages in vitro and in vivo. Our results indicates that PREP is a newly found transcriptional regulator in macrophage, and is a promising therapeutic target for fibrosis-related aberrant macrophage activation.

2023-08-09 | GSE213050 | GEO

Prolyl endopeptidase-mediated transcriptional regulation in quiescent and activated bone marrow-derived macrophages (CUT&Tag)

2023-08-09 | GSE213049 | GEO

Prolyl endopeptidase-mediated transcriptional regulation in quiescent and activated bone marrow-derived macrophages

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-08-09 | GSE213051 | GEO

Quiescent vs. Activated Endothelial Cell-Derived Extracellular Vesicles

Project description:Proteomics was performed on extracellular vesicles derived from in vitro cultures of activated and quiescent human endothelial cells.

2024-01-04 | PXD038914 | Pride

Induced-fit mechanism for prolyl endopeptidase.

Project description:Prolyl peptidases cleave proteins at proline residues and are of importance for cancer, neurological function, and type II diabetes. Prolyl endopeptidase (PEP) cleaves neuropeptides and is a drug target for neuropsychiatric diseases such as post-traumatic stress disorder, depression, and schizophrenia. Previous structural analyses showing little differences between native and substrate-bound structures have suggested a lock-and-key catalytic mechanism. We now directly demonstrate from seven structures of Aeromonus punctata PEP that the mechanism is instead induced fit: the native enzyme exists in a conformationally flexible opened state with a large interdomain opening between the beta-propeller and alpha/beta-hydrolase domains; addition of substrate to preformed native crystals induces a large scale conformational change into a closed state with induced-fit adjustments of the active site, and inhibition of this conformational change prevents substrate binding. Absolute sequence conservation among 28 orthologs of residues at the active site and critical residues at the interdomain interface indicates that this mechanism is conserved in all PEPs. This finding has immediate implications for the use of conformationally targeted drug design to improve specificity of inhibition against this family of proline-specific serine proteases.

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DL-endopeptidase changes in CD

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Quiescent and non-quiescent deletion-mutant strains

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2010-05-29 | E-GEOD-8624 | biostudies-arrayexpress

Peptidomics of prolyl endopeptidase in the central nervous system.

Project description:Prolyl endopeptidase (Prep) is a member of the prolyl peptidase family and is of interest because of its unique biochemistry and connections to cognitive function. Using an unbiased mass spectrometry (MS)-based peptidomics platform, we identified Prep-regulated peptides in the central nervous system (CNS) of mice by measuring changes in the peptidome as a function of Prep activity. This approach was validated by the identification of known Prep substrates, such as the neuropeptide substance P and thymosin-beta4, the precursor to the bioactive peptide Ac-SDKP. In addition to these known substrates, we also discovered that Prep regulates many additional peptides, including additional bioactive peptides and proline rich peptides (PRPs). Biochemical experiments confirmed that some of these Prep-regulated peptides are indeed substrates of the enzyme. Moreover, these experiments also supported the known preference of Prep for shorter peptides while revealing a previously unknown cleavage site specificity of Prep when processing certain multi-proline-containing peptides, including PRPs. The discovery of Prep-regulated peptides implicates Prep in new biological pathways and provides insights into the biochemistry of this enzyme.

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