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ATG7KO SILAC Secretome_Proteome

ABSTRACT: human lung fibroblasts WT and ATG7KO (two clones) were used for unbiased SILAC/AHA-based secretome and proteome measurements.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung, Fibroblast

DISEASE(S): Disease Free

SUBMITTER: Julian Nüchel

LAB HEAD: Markus Plomann

PROVIDER: PXD025001 | Pride | 2021-09-10

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	1204.7z	Other
	1429.7z	Other
	Oxidation__M_Sites_1_.txt	Txt
	allPeptides_1_.txt	Txt
	checksum.txt	Txt

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1 - 5 of 16

Publications

TGFβ promotes fibrosis by MYST1-dependent epigenetic regulation of autophagy.

Zehender Ariella A Li Yi-Nan YN Lin Neng-Yu NY Stefanica Adrian A Nüchel Julian J Chen Chih-Wei CW Hsu Hsiao-Han HH Zhu Honglin H Ding Xiao X Huang Jingang J Shen Lichong L Györfi Andrea-Hermina AH Soare Alina A Rauber Simon S Bergmann Christina C Ramming Andreas A Plomann Markus M Eckes Beate B Schett Georg G Distler Jörg H W JHW

Nature communications 20210720 1

Activation of fibroblasts is essential for physiological tissue repair. Uncontrolled activation of fibroblasts, however, may lead to tissue fibrosis with organ dysfunction. Although several pathways capable of promoting fibroblast activation and tissue repair have been identified, their interplay in the context of chronic fibrotic diseases remains incompletely understood. Here, we provide evidence that transforming growth factor-β (TGFβ) activates autophagy by an epigenetic mechanism to amplify ...[more]

PMID: 34285225

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Transcriptomic and proteomic profiling of KEAP1 disrupted and sulforaphane treated human breast epithelial cells

Project description:Sulforaphane (SFN), an isothiocyanate found in cruciferous vegetables, is a potent inhibitor of experimental mammary carcinogenesis and may be an effective, safe chemopreventive agent for use in humans. SFN acts in part on the Keap1/Nrf2 pathway to regulate a battery of cytoprotective genes. In this study transcriptomic and proteomic changes in the estrogen receptor negative, non tumorigenic human breast epithelial MCF10A cell line were analyzed following SFN treatment or KEAP1 knockdown with siRNA using microarray and stable isotopic labeling with amino acids in culture (SILAC), respectively. Changes in selected transcripts and proteins were confirmed by PCR and Western blot in MCF10A and MCF12A cells. There was strong correlation between the transcriptomic and proteomic responses in both the SFN treatment (R=0.679, P<0.05) and KEAP1 knockdown (R=0.853, P<0.05) experiments. Common pathways for SFN treatment and KEAP1 knockdown were xenobiotic metabolism and antioxidants, glutathione metabolism, carbohydrate metabolism and NADH/NADPH regeneration. Moreover, these pathways were most prominent in both the transcriptomic and proteomic analyses. The aldo-keto reductase family members, AKR1B10, AKR1C1, AKR1C2 and AKR1C3, as well as NQO1 and ALDH3A1, were highly upregulated at both the transcriptomic and proteomic level. Collectively, these studies served to identify potential biomarkers that can be used in clinical trials to investigate the initial pharmacodynamic action of SFN in the breast. MCF10A cells were treated with SFN or had KEAP1 knocked down by siRNA.

2011-04-22 | E-GEOD-28813 | biostudies-arrayexpress

Positional proteomics reveals differences in N-terminal proteoform stability.

Project description:To understand the impact of alternative translation initiation on a proteome, we performed the first large-scale study of protein turnover rates in which we distinguish between N-terminal proteoforms pointing to translation initiation events. Using pulsed SILAC combined with N-terminal COFRADIC we monitored the stability of 1,941human N-terminal proteoforms, including 147 proteoform pairs with heterogeneous N-termini originating from the same gene that result from alternative translation initiation and incomplete processing of the initiator methionine. N-terminally truncated proteoforms were on average less abundant than canonical proteoforms, many had different stabilities and exhibited both faster and slower turnover rates compared to their canonical counterparts. These differences in stability did not depend on the length of truncation but on individual protein characteristics. In silico simulation of N-terminal proteoforms in macromolecular complexes revealed possible consequences for complex integrity such as replacement of unstable canonical subunits. The extent of intrinsic disorder in N-terminal protein structures correlated with turnover times, indicating that a change in the structural flexibility of protein N-termini in truncated proteoforms might impact proteoform stability. Interestingly, removal of the initiator methionine by methionine aminopeptidases reduced the stability of processed proteoforms while susceptibility for N-terminal acetylation, another common co-translational modification, did not seem to impact on turnover rates. Taken together, our findings reveal differences in protein stability between N-terminal proteoforms and point to a role for alternative translation initiation and co-translational initiator methionine removal in the overall regulation of proteome homeostasis.

2013-03-14 | PXD002091 | Pride

Transcriptome comparison of Streptococcus suis wildytpe and a ccpA knock-out strain in exponential growth phase

Project description:Transcriptome comparison of Streptococcus suis wildytpe and a ccpA knock-out strain in exponential growth phase.

2010-12-31 | E-MEXP-2946 | biostudies-arrayexpress

mTORC1 regulates GRASP55-dependent unconventional secretion in response to stress

Project description:In cells, several cargoes are delivered to the cell surface or the extracellular space via unconventional secretion routes. GRASP55 is a Golgi protein that regulates unconventional secretion of distinct proteins and controls the assembly and membrane stacking of Golgi cisternae. Recent work suggested that the role of GRASP55 in unconventional secretion may involve its relocalization to other organelles. However, the stimuli that drive GRASP55-dependent unconventional secretion, the signaling events that regulate GRASP55 function, the subcellular locations where GRASP55 acts, and the cargoes that follow this route for secretion remain unclear. Here, we show that mTORC1 directly phosphorylates GRASP55 at multiple sites to maintain its Golgi localization. Cellular stresses or drugs that inhibit mTORC1 cause GRASP55 dephosphorylation and relocalization to autophagosomal / MVB structures. Using secretome and surfactome analyses in GRASP55-null cells, we identify for the first time numerous -previously unknown- cargoes that rely on this unconventional secretory pathway.

2021-09-09 | PXD020331 | Pride

Primary myeloid cell proteomics and transcriptomics: importance of β-tubulin isotypes for osteoclast function

Project description:Among hematopoietic cells, osteoclasts (Oc) and immature dendritic cells (Dc) are closely related myeloid cells with distinct functions; Oc participate skeleton maintenance while Dc sample the environment for foreign antigens. Such specificities rely on profound modifications of gene and protein expression during Oc and Dc differentiation. We provide global proteomic and transcriptomic analyses of primary mouse Oc and Dc, based on original SILAC and RNAseq data. We established specific signatures for Oc and Dc including genes and proteins of unknown functions. In particular, we showed that Oc and Dc have the same alpha and beta tubulin isotypes repertoire but that Oc express much more beta tubulin isotype Tubb6 (also known as Tubulin beta class V). In both mouse and human Oc, we demonstrate that elevated expression of Tubb6 in Oc is necessary for correct podosomes organization and thus for the structure of the sealing zone, which sustains the bone resorption apparatus. Hence, lowering Tubb6 expression hindered Oc resorption activity. Overall, we highlight here potential new regulators of Oc and Dc biology and illustrate the functional importance of the tubulin isotype repertoire in the biology of differentiated cells.

2020-09-16 | PXD018832 | Pride

CDS composition drives differential regulation of mRNA fate by the Ccr4-Not complex

Project description:Regulation of protein output at the level of translation allows for a swift response to dynamic changes in the requirements of the cell. This is achieved by a complex set of biochemical processes that regulate protein synthesis and mRNA stability. A major factor coordinating this regulation is the Ccr4-Not complex. Despite playing a role in most stages of the mRNA life cycle, no attempt has been made to take a global integrated view of how the Ccr4-Not complex affects gene expression. Bioreplicate one for this paper is available at the Proteome xchange identifier: PXD014764

2021-10-11 | PXD020305 | Pride

Chemical genetic validation of CSNK2 substrates using an inhibitor-resistant mutant in combination with triple SILAC quantitative phosphoproteomics

Project description:Casein Kinase 2 (CSNK2) is an extremely pleiotropic, ubiquitously expressed protein kinase involved in the regulation of numerous key biological processes. Mapping the CSNK2-dependent phosphoproteome is necessary for better characterization of its fundamental role in cellular signalling. While ATP-competitive inhibitors have enabled the identification of many putative kinase substrates, compounds targeting the highly conserved ATP-binding pocket often exhibit off-target effects limiting their utility for definitive kinase-substrate assignment. To overcome this limitation, we devised a strategy combining chemical genetics and quantitative phosphoproteomics to identify and validate physiological CSNK2 substrates. We engineered U2OS cells expressing exogenous wild type CSNK2A1 (WT) or a triple mutant (TM, V66A/H160D/I174A) with substitutions at residues important for inhibitor binding. These cells were treated with CX-4945, a clinical-stage inhibitor of CSNK2, and analyzed using large-scale triple SILAC (Stable Isotope Labelling of Amino Acids in Cell Culture) quantitative phosphoproteomics. In contrast to wild-type CSNK2A1, CSNK2A1-TM retained activity in the presence of CX-4945 enabling identification and validation of several physiological CSNK2 substrates on the basis of their increased phosphorylation in cells expressing CSNK2A1-TM. Based on high conservation within the kinase family, we expect that this strategy can be broadly adapted for identification of other kinase-substrate relationships.

2022-07-14 | PXD033523 | Pride

Efficiency of isotopic labbeling in whole Drosophila body

Project description:We used isotopic (heavy) labelling to delineate between female and male proteins interacting in the female reproductive tract. Here, we test the efficiency of the labelling protocols on the whole body of males and females.

2021-09-22 | PXD025072 | Pride

TIAR and FMRP shape pro-survival nascent proteome of leukemia cells in the bone marrow microenvironment

Project description:Chronic myeloid leukemia (CML) cells circulate between blood and bone marrow niche, representing different microenvironments. We studied the role of the two RNA binding proteins, T-cell-restricted intracellular antigen (TIAR) and the fragile X mental retardation protein (FMRP) in the regulation of protein translation in CML cells residing in settings mimicking peripheral blood microenvironment (PBM) and bone marrow microenvironment (BMM). We studied how conditions shaped the translation process through TIAR and FMRP activity, considering its relevance in therapy resistance. The QuaNCAT mass-spectrometric approach revealed that TIAR and FMRP have a discrete modulatory effect on protein synthesis and thus affect distinct aspects of leukemic cells functioning in the hypoxic niche. We demonstrate that TIAR substantially supports the resistance of CML cells to translation inhibition by homoharringtonine in the BMM. Overall, our results show that targeting post-transcriptional control should be considered when designing anti-leukemia therapeutic solutions.

2023-05-10 | PXD032332 | Pride

Ascorbic acid enhances Tet-mediated 5-methylcytosine oxidation and promotes DNA demethylation in mammals.

Project description:DNA demethylation occurs in multiple cellular processes but its regulation is poorly understood. Here we report that a vital nutrient factor ascorbic acid (AA), or vitamin C (Vc), induces DNA demethylation in mammalian cells. The levels of active 5mC oxidation products, 5-formylcytosine and 5-carboxylcytosine, increase by more than one magnitude of order in mouse ES cells when cultured in the presence of AA. In cells deleted of Tet1 and Tet2 dioxygenase genes, AA does not facilitate 5mC oxidation. The AA effect is however restored when Tet2 was re-expressed in the mutant cells. The enhancing effect of AA on 5mC oxidation and DNA demethylation was also observed in a mouse model deficient in AA synthesis. Our results thus reveal a role of AA in the regulation of DNA modification, which might mediate a plethora of functions of AA. Examination of 5hmC levels with or without AA in mouse ES cells

2015-01-01 | E-GEOD-43262 | biostudies-arrayexpress

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