Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteome analysis of BMPR2 mutation PASMCs

ABSTRACT: Proteome analysis of BMPR2 mutation PASMCs with or without PERK knockout under hypoxia.

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: Takashi Shimizu

PROVIDER: PXD020182 | JPOST Repository | Sat Jul 03 00:00:00 BST 2021

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	F07PASMC_PERKpp.mzid	Mzid
	F07PASMC_PERKpp_10ul.raw	Raw
	F07PASMC_PERKpp_10ul_CID_%5BNode_03%5D.mgf	Mgf
	F62PASMC_PERKcko_hypoxia.mzid	Mzid
	F62PASMC_PERKcko_hypoxia_7ul1.raw	Raw

Items per page:

1 - 5 of 18

Publications

PERK inhibition attenuates vascular remodeling in pulmonary arterial hypertension caused by <i>BMPR2</i> mutation.

Shimizu Takashi T Higashijima Yoshiki Y Kanki Yasuharu Y Nakaki Ryo R Kawamura Takeshi T Urade Yoshihiro Y Wada Youichiro Y

Science signaling 20210126 667

Pulmonary arterial hypertension (PAH) is a fatal disease characterized by excessive pulmonary vascular remodeling. However, despite advances in therapeutic strategies, patients with PAH bearing mutations in the bone morphogenetic protein receptor type 2 (<i>BMPR2</i>)-encoding gene present severe phenotypes and outcomes. We sought to investigate the effect of PER-like kinase (PERK), which participates in one of three major pathways associated with the unfolded protein response (UPR), on PAH path ...[more]

PMID: 33500333

Similar Datasets

Spatial Environment Affects HNF4A Mutation-Specific Proteome Signatures and Cellular Morphology in hiPSC-Derived β-Like Cells

Project description:Studies of monogenic diabetes are particularly useful as we can gain insight into the molecular events of pancreatic β-cell failure. Maturity-onset diabetes of the young 1 (MODY1) is a monogenic diabetes form, caused by a mutation in the HNF4A gene. Human induced pluripotent stem cells (hiPSC) provide an excellent tool for disease modelling by subsequent directed differentiation toward desired pancreatic islet cells, but cellular phenotypes in terminally differentiated cells are notoriously difficult to detect. Re-creating a spatial (3D) environment may facilitate phenotype detection. In this study, we studied MODY1 using hiPSC-derived pancreatic β-like patient and isogenic control cell lines in two different 3D contexts. Using size-adjusted cell aggregates and alginate capsules we showed that the 3D context was critical to facilitate the detection of mutation-specific phenotypes. In 3D cell aggregates we identified irregular cell clusters and lower levels of structural proteins by proteome analysis, whereas in 3D alginate capsules we identified altered levels of glycolytic proteins in the glucose sensing apparatus by proteome analysis. Our study provides novel knowledge on normal and abnormal function of HNF4A paving the way for translational studies of new drug targets that can be used in precision diabetes medicine of MODY.

2022-04-04 | GSE188827 | GEO

RNA-seq in SNRPD3 G96V mutation knock-in cell clones.

Project description:Aberrant RNA splicing may contribute to carcinogenesis. Here, we focused on the G96V mutation in SNRPD3, one of the splicing factors. We found that RNA splicing is altered under hypoxia in cell lines in which the gene mutation is knocked-in.

2022-08-06 | GSE210185 | GEO

RNA-seq analysis on SW480 cells treated with or without YH-620 under hypoxia

Project description:To globally assess the role of alternatively translated 63 kDa NKRF, we performed and report on RNA-seq analysis on SW480 cells treated with or without novel small molecule HIF antagonist YH-620 under hypoxia. This study provides a framework for understanding the effect of novel small molecule HIF antagonist YH-620 on downstream targets. In addition, we also performed RNA-seq analysis on SW480 cells treated with or without specific small molecule CBP/catenin antagonist ICG-001 under hypoxia.

2021-06-30 | GSE160661 | GEO

Directed shotgun proteomics guided by RNA-Seq identifies a complete expressed prokaryotic proteome

Project description:Prokaryotes are, due to their moderate complexity, particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and proteins extracted from matched samples. Saturated transcriptome profiling by RNA-seq provided an endpoint estimate of the protein-coding genes expressed under two conditions which mimic the interaction of Bartonella henselae with its mammalian host. Directed shotgun proteomics experiments were carried out on four subcellular fractions. By specifically targeting proteins which are short, basic, low abundant and membrane localized, we could eliminate their initial under-representation compared to the estimated endpoint. A total of 1,250 proteins were identified with an estimated false discovery rate below 1%. This represents 85% of all distinct annotated proteins and around 90% of the expressed protein-coding genes. Genes, whose transcripts were detected, but not their corresponding protein products, were found highly enriched in several genomic islands. Additionally, genes that lacked an ortholog and a functional annotation were not detected at the protein level, and possibly include over-predicted genes in genome annotations. Furthermore, a dramatic membrane proteome re-organization was observed including differential regulation of autotransporters, adhesins and hemin binding proteins. Particularly noteworthy was the complete membrane proteome coverage which included expression of all members of the VirB/D4 type IV secretion system, a key virulence factor. Transcriptome and proteome analysis of B.henselae in two conditions and duplicates: uninduced and induced for host invasion.

2013-04-23 | E-GEOD-44564 | biostudies-arrayexpress

Genome-wide transcriptome and proteome analysis of the global GATA transcription factors AreA and AreB in Fusarium fujikuroi

Project description:We performed genome-wide transcriptome and proteome analyses of the Fusarium fujikuroi wild type and ΔAREA and ΔAREB mutants under nitrogen limitation and excess. Microarray analysis revealed that each transcription factor regulates a total set of about 4200 genes under nitrogen limiting conditions with an enrichment of genes belonging to functional classes of primary/secondary metabolism, transporters, cell defense/virulence and transcription. Under nitrogen excess, AreA is not active as a transcriptional regulator, while AreB affects expression of about 4400 genes. Both transcription factors regulate a common set of about 2100 genes and most of the time work together either as positive or as negative regulators. Our proteomics analysis identified 446 AreA-regulated and 386 AreB-regulated proteins at nitrogen limitation and 138 AreA-regulated and 447 AreB-regulated proteins at nitrogen excess, respectively. Comparison of the proteome and transcriptome data indicates that many post-transcriptional regulations are facilitated by both GATA-factors, for example on enzymes involved in the TCA and glyoxylate cycle and the main glutamate/glutamine cycling.

2017-05-10 | GSE80480 | GEO

Heart fibroblasts from Siah-knockout mice in hypoxia

Project description:Heart fibroblasts from wildtype mice and Siah2-/- knockout mice were isolated and cultured. The cells were either left untreated or incubated for 6 hs under hypoxic conditions. One experiment consists of wildtype cells (normoxia/hypoxia) and Siah2 knockout cells (normoxia/hypoxia) = 4 samples. To allow statistical analysis of the data set the experiment was repeated once under identical conditions.

2021-07-01 | GSE154667 | GEO

Clinical trial of Human BRAF Gene V600E Mutation Diagnostic kit (Fluorescence PCR Analysis)

Project description:Interventions: Gold Standard:Fluorescence PCR Analysis;Index test:Human BRAF Gene V600E Mutation Diagnostic kit (Fluorescence PCR Analysis) Primary outcome(s): colorectal cancer;cancerous goiter Study Design: Diagnostic test for accuracy

| 2676654 | ecrin-mdr-crc

Proteome-wide effects of single gene perturbations in a eukaryotic cell

Project description:Eukaryotic gene expression is controlled at the transcriptional, translational and protein degradation level and its principles are starting to emerge. While transcriptional outcomes, which are commonly also used as a proxy for protein abundance, have been investigated on a larger scale, the study of translational output requires large-scale proteomics data. However, data for proteome alterations by systematic assessment of knockouts genome-wide is not available yet. We here determined the individual proteome changes for 3,308 non-essential genes in the yeast S. pombe (www.butterlab.org/SpProtQuant). We observed that genes with high proteome remodeling are predominantly involved in gene expression regulation, in particular acting as translational regulators. Focusing on those knockout strains with a large number of altered proteins, we performed paired transcriptome/proteome measurements to uncover translational regulators and features of translational regulation. Furthermore, by similarity clustering of these proteome changes, we infer gene functionality that can be extended to other species such as human or baker’s yeast.

2022-09-20 | GSE167543 | GEO

Retapamulin-assisted Ribo-seq reveals the alternative bacterial proteome

Project description:Unorthodox rules of extracting genetic information enable proteome expansion without increasing the genome size. The use of alternative translation initiation sites achieves this goal by allowing production of more than one protein from a single gene. Although several such examples have been serendipitously found in bacteria, genome-wide experimental mapping of alternative translation start sites has been unattainable. We found that the antibiotic retapamulin specifically arrests initiating ribosomes at start codons of the genes. Retapamulin treatment followed by Ribo-seq analysis (Ribo-RET) not only allowed mapping of conventional initiation sites at the beginning of the annotated Escherichia coli genes but, strikingly, it also revealed putative alternative internal start sites in a number of genes. Experimental evidence demonstrated that the internal start codons can be recognized by the ribosomes and direct translation initiation in vitro and in vivo. Proteins, whose translation is initiated at an internal in-frame and out-of-frame start sites, can be functionally important and contribute to the ‘alternative’ bacterial proteome. In addition to proteome expansion, the internal start sites may play regulatory role in gene expression.

2019-03-04 | GSE122129 | GEO