Browse
Submit Data
Databases
API
Help

Dataset Information

223 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Regulatory T cells in hepatic circadian rhythm

ABSTRACT: Regulatory T cells (Treg cells) are important to maintain self-tolerance. In tissues, Treg cells can perform non-classical functions, for example, they are implicated in regulating metabolic processes in the adipose tissue. Their function in the liver is less well understood. We found here that Treg cells are important to secure the peripheral hepatic circadian rhythm of core-clock regulators and clock-controlled genes. Undisturbed metabolism in the liver required the presence of Treg cells and was especially important in the early postnatal phase, a distinct time period at around day 10, when the liver had not fully matured and Treg cells proliferated and accumulated in the liver-tissue. Our findings highlight a critical role for Treg cells to establish and maintain liver homeostasis.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Hepatocyte, Liver

SUBMITTER: Sophia Foehr

LAB HEAD: Jeroen Krijgsveld

PROVIDER: PXD005047 | Pride | 2018-08-29

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	150904_SF_1_1.msf	Msf
	150904_SF_1_1.raw	Raw
	150904_SF_1_2.msf	Msf
	150904_SF_1_2.raw	Raw
	150904_SF_1_3.msf	Msf

Items per page:

1 - 5 of 34

Similar Datasets

Human oocyte proteome and secretome

2016-06-01 | PXD004142 | Pride

Human oocyte proteome and secretome

Project description:The proteome and secretome of human oocytes was studied by shotgun LCMSMS, starting from pools of 100 cells. Exploiting SP3, a novel technology for proteomic sample preparation using magnetic beads, we scaled down proteome analysis to single cells. Despite the low protein content of only ~100ng per cell, we consistently identified ~450 proteins from individual oocytes. When comparing proteomes of individual oocytes at the germinal vesicle (GV) and metaphase II (MII) stage by label-free quantification, we found several proteins preferentially expressed in matuare and immature cells. This study demonstrates that an innovative proteomics workflow facilitates analysis of single human oocytes to investigate human oocyte biology and pre-implantation development. The approach presented here paves the way for quantitative proteomics in other quantity-limited tissues and cell types.

2016-05-26 | PXD003691 | Pride

Investigating the target and off-target landscape of PLK1 small molecule inhibitor volasertib

Project description:In this study we aimed to identify off-targets of polo-like kinase 1 (Plk1) small molecule inhibitor volasertib. Plk1 is an important cell cycle kinase and an attractive target for anticancer treatment. Volasertib is ATP-competitive small molecules that may also block the ATP-pocket of other proteins. Despite the fatal infections and negative survival in a phase III trial on volasertib in acute myeloid leukemia volasertib has been a promising treatment option in children with rhabdomyosarcoma. Therefore, there is a need to understand the nature of adverse effects that possibly originate from the off-target proteins. We used thermal proteome profiling (TPP) to identify proteins that have a change in the thermal stability after treatment with volasertib. The temperature of aggregation of several proteins involved in prostaglandin and phosphatidyl-inositol phosphate metabolism increased after treatment with volasertib. PIP4K2A and ZADH2 were stabilized both by treatment in living cells and cell lysate. Functional disruption of these proteins affects the immune response and fatty acid metabolism. In addition, volasertib was found to affect transcriptional coactivators, normal and alternative RNA splicing regulators and proteins involved in the intracellular transport regulation. Our data suggests that the identified proteins may contribute more to the understanding of anti-tumor effect of volasertib.

2021-08-23 | PXD024040 | Pride

Clinical proteomics data contains uniquely identifiable, personally sensitive and incidental findings

Project description:The goal of clinical proteomics is to identify, quantify, and characterize proteins in body fluids or tissue to assist diagnosis, prognosis, and treatment of patients. In this way, it is similar to more mature omics technologies, such as genomics, that are increasingly applied in biomedicine. We argue that, similar to those fields, proteomics also faces ethical issues related to the kinds of information that is inherently obtained through sample measurement, although their acquisition was not the primary purpose. Specifically, we show that individuals can be identified both by their characteristic, individual-specific protein levels and by variant peptides reporting on coding single nucleotide polymorphisms. Furthermore, it is in the nature of blood plasma proteomics profiling that it broadly reports on the health status of an individual – beyond the disease under investigation. Finally, we show that private and potentially sensitive information, such as ethnicity and pregnancy status, can increasingly be derived from proteomics data. Although this is potentially valuable not only to the individual, but also for biomedical research, it raises ethical questions similar to the incidental findings obtained through other omics technologies. We here introduce the necessity of - and argue for the desirability for - ethical and human rights-related issues to be discussed within the proteomics community. Those thoughts are more fully developed in our accompanying manuscript. Appreciation and discussion of ethical aspects of proteomic research will allow for deeper, better-informed, more diverse, and, most importantly, wiser guidelines for clinical proteomics.

2020-12-21 | PXD021677 | Pride

Harnessing PROTAC technology to combat stress hormone receptor activation

Project description:We want to quantify the proteome alteration following PROTAC mediated Glucocorticoid receptor depletion in vitro.

2023-12-11 | PXD046949 | Pride

Multi-layered chromatin proteomics identifies cell vulnerabilities in DNA repair

Project description:DNA damage response (DDR) is instrumental for maintaining genome stability and its deregulation predisposes to carcinogenesis, while revealing attractive targets for innovative therapies. Chromatin governs the DNA repair process via the interplay among different layers consisting of DNA, histones post-translational modifications (hPTMs), and chromatin-associated proteins. Here we employ multi-layered proteomics to follow, during double-strand break repair, chromatin-mediated interactions of repair proteins, signatures of hPTMs, and the DNA-bound proteome. In particular, we functionally attribute novel chromatin-associated proteins to non-homologous end-joining or homologous recombination (HR) repair, we reveal susceptibility to PARP inhibitor treatment upon knockdown of ATAD2, TPX2 and EHMT2, and we profile hPTMs at γH2AX-mononucleosomes. Moreover, through the integration of these multiple chromatin layers we identify a potential role for EHMT2-mediated monomethylation of H3K56 in HR. Collectively, our results provide an innovative chromatin-centered view of the DDR process, while representing a valuable resource for the use of PARP inhibitors in cancer.

2023-02-20 | PXD027421 | Pride

IgE antibodies increase honeybee venom responsiveness and detoxification efficiency of mast cells

Project description:In contrast to their clearly defined roles in allergic diseases, the physiologic functions of Immunoglobulin E antibodies (IgEs) and mast cells (MCs) remain enigmatic. Recent research supports the toxin hypothesis, showing that MCs and IgE-related type 2 immune responses can enhance host defense against certain noxious substances, including honeybee venom (BV). However, the mechanisms by which MCs can interfere with BV toxicity are unknown. In this study, we assessed the role of IgE and certain MC products in MC-mediated BV detoxification. We applied in vitro and in vivo fluorescence microscopy imaging, and flow cytometry, fibroblast-based toxicity assays and mass spectrometry to investigate IgE-mediated detoxification of BV cytotoxicity by mouse and human MCs in vitro. Pharmacologic strategies to interfere with MC-derived heparin and proteases helped to define the importance of specific detoxification mechanisms. Venom-specific IgE increased the degranulation and cytokine responses of MCs to BV in vitro. Passive serum sensitization enhanced MC degranulation in vivo. IgE-activated mouse or human MCs exhibited enhanced potential for detoxifying BV by both proteolytic degradation and heparin-related interference with toxicity. Mediators released by IgE-activated human MCs efficiently degraded multiple BV toxins. Our results both reveal that IgE sensitization enhances the MC’s ability to detoxify BV and also assign efficient toxin-neutralizing activity to MC-derived heparin and proteases. Our study thus highlights the potential importance of IgE, MCs, and particular MC products in defense against BV.

2021-11-25 | PXD023851 | Pride

A synthetically methylotrophic Escherichia coli as a chassis for bioproduction

Project description:Proteome characterization of three E. coli strains: a methanol-dependent strain (MEvo1-0) and two synthetically methylotrophic strains (MEcoli_ref_1, MEcoli_ref_2)

2024-02-08 | PXD046243 | Pride

Par3A and Par3B interactome IMCDs

Project description:We assessed the functional role of the cell polarity proteins Par3A and B in inner medullary collecting duct cells (IMCD). Here, we did an interactome analysis from IMCDs after transiently transfecting Par3A or Par3B with a flag tag.

2022-07-07 | PXD018637 | Pride

Drosophila nephrocytes Par3A and B rescue

Project description:We assessed the functional role of the cell polarity proteins Par3A and B in Bazooka Knockdown nephrocytes. Here, we did a proteomics anaylsis of isolated garland nephrocytes from 3rd instar larvae. Analysis of the data identified differentially regulated proteins.

2022-07-07 | PXD018636 | Pride

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