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SILAC phosphoproteome analysis upon transient Abl1/2 or DDR1 knockdown in human U-2 OS cells

ABSTRACT: Analysis of changes in the phosphoproteome upon transient siRNA-mediated knockdown of ABL1/ABL2 or DDR1 for 48 hours. CILAC phosphoproteome analysis was conducted after 48hrs using human U-2 OS cells.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): U2-os Cell

SUBMITTER: Nicolas Nalpas

LAB HEAD: Prof. Dr. Tassula Proikas-Cezanne

PROVIDER: PXD023146 | Pride | 2023-10-24

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	20180702_CO_0810TaPC_Mix2_R4R5_phospho_1.raw	Raw
	20180702_CO_0810TaPC_Mix2_R4R5_phospho_10.raw	Raw
	20180702_CO_0810TaPC_Mix2_R4R5_phospho_2.raw	Raw
	20180702_CO_0810TaPC_Mix2_R4R5_phospho_3.raw	Raw
	20180702_CO_0810TaPC_Mix2_R4R5_phospho_4.raw	Raw

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1 - 5 of 24

Publications

The ABL-MYC axis controls WIPI1-enhanced autophagy in lifespan extension.

Sporbeck Katharina K Haas Maximilian L ML Pastor-Maldonado Carmen J CJ Schüssele David S DS Hunter Catherine C Takacs Zsuzsanna Z Diogo de Oliveira Ana L AL Franz-Wachtel Mirita M Charsou Chara C Pfisterer Simon G SG Gubas Andrea A Haller Patricia K PK Knorr Roland L RL Kaulich Manuel M Macek Boris B Eskelinen Eeva-Liisa EL Simonsen Anne A Proikas-Cezanne Tassula T

Communications biology 20230824 1

Human WIPI β-propellers function as PI3P effectors in autophagy, with WIPI4 and WIPI3 being able to link autophagy control by AMPK and TORC1 to the formation of autophagosomes. WIPI1, instead, assists WIPI2 in efficiently recruiting the ATG16L1 complex at the nascent autophagosome, which in turn promotes lipidation of LC3/GABARAP and autophagosome maturation. However, the specific role of WIPI1 and its regulation are unknown. Here, we discovered the ABL-ERK-MYC signalling axis controlling WIPI1. ...[more]

PMID: 37620393

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USP32 regulates late endosomal transport and recycling through deubiquitylation of Rab7

Project description:The endosomal system is a highly dynamic multifunctional organelle, whose complexity is regulated in part by reversible ubiquitylation. Despite the wide-ranging influence of ubiquitin in endosomal processes, relatively few enzymes utilizing ubiquitin have been described to control endosome integrity and function. Here we reveal the deubiquitylating enzyme (DUB) ubiquitin-specific protease 32 (USP32) as a powerful new player in this context. Loss of USP32 inhibits late endosome (LE) transport and recycling of LE cargos to the TGN, resulting in dispersion and swelling of the late compartment. Using SILAC-based ubiquitome profiling we identify the small GTPase Rab7—the logistical centerpiece of LE biology—as a substrate of USP32. Mechanistic studies reveal that LE transport effector RILP prefers ubiquitylation-deficient Rab7, while retromer-mediated LE recycling benefits from an intact cycle of Rab7 ubiquitylation. Collectively, our observations suggest that reversible ubiquitylation helps switch Rab7 between its various functions, thereby maintaining global spatiotemporal order in the endosomal system.

2019-03-20 | PXD011899 | Pride

Linking post-translational modifications and protein turnover by site-resolved protein turnover (SPOT) profiling

Project description:Proteome-wide measurements of protein turnover have largely ignored the impact of post-translational modifications (PTMs). To address this gap, we employ stable isotope labelling and mass spectrometry to measure the turnover of >120,000 peptidoforms including >33,000 phosphorylated, acetylated and ubiquitinated peptides for >9,000 native proteins. This site-resolved protein turnover (SPOT) profiling discloses global and site-specific differences in turnover associated with the presence or absence of PTMs. While causal relationships may not always be immediately apparent, we hypothesize that PTMs with diverging turnover may distinguish states of differential protein stability, structure, localization, enzymatic activity, or protein-protein interactions. We exemplify how the turnover data may facilitate insights into unknown functions of PTMs and provide a web-tool for the scientific community that allows interrogation and visualisation of all turnover data. Since the methodology is applicable to many cell types and modifications, it has substantial potential to prioritize PTMs for functional investigation in the future.

2021-11-10 | PXD023218 | Pride

Global ubiquitinome profiling identify Nedd4 as aregulator of Profilin 1 and actin remodeling in neural crest cells

Project description:We utilized quantitative analyses of the proteome, transcriptome, and ubiquitinome to study how ubiquitination and NEDD4 control neural crest cell survival and stem-cell-like properties. We report 276 novel NEDD4 targets in neural crest cells and show that loss of NEDD4 leads to a striking global reduction in specific ubiquitin lysine linkages.

2022-02-08 | PXD024103 | Pride

EBprot: Bayesian Analysis of Labelling-based Quantitative Proteomics Data

Project description:Labelling-based proteomics is a powerful method for detection of differentially expressed proteins (DEPs) between biological samples. The current data analysis platform relies on protein-level ratios, where peptide-level ratios are averaged to yield a single summary ratio for each protein. In shotgun proteomics, however, some proteins are quantified with more peptides than others, and this reproducibility information is incorporated into the differential expression (DE) analysis. Here we propose a novel probabilistic framework EBprot that directly models the peptide-to-protein hierarchy and rewards the proteins with reproducible quantification over multiple peptides. To evaluate its performance with known DE states, we first verified that the peptide-level analysis of EBprot provides more accurate estimation of the false discovery rates and better receiver-operating characteristic than other protein ratio analyses using simulation datasets, and confirmed the superior classification performance in a UPS1 mixture spike-in dataset. To illustrate the performance of EBprot in realistic applications, we applied EBprot to a SILAC dataset for lung cancer subtype analysis and an iTRAQ dataset for time course phosphoproteome analysis of EGF-stimulated HeLa cells, each featuring a different experimental design. Through these various examples, we show that the peptide-level analysis of EBprot provides a competitive advantage over alternative methods for the DE analysis of labelling-based quantitative datasets.

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Phosphorylation dynamics in neuronal cells

Project description:We performed global phosphorylation quantitative proteomics analysis of neuronal HT-22 cells in response to iron deficiency. Our data applied SILAC-based quantitative analysis with replicates and studied the phosphorylation dynamics under acute, chronic iron deficiency as well as acute hypoxia.

2021-09-09 | PXD023294 | Pride

SILAC APMS analysis of SHQ1 interactome in HEK-293 cells

Project description:The conserved box H/ACA RNPs consist of one box H/ACA RNA and 4 core proteins: Dyskerin, NHP2, NOP10 and GAR1. The assembly of the H/ACA RNPs is a stepwise process which requires several assembly factors: SHQ1, NAF1, the Survival of Motor Neuron complex SMN, and the R2TP complex. It implicates the co-transcriptional assembly of a pre-particle containing the nascent RNAs, Dyskerin, NOP10, NHP2 and NAF1. The latest keeps the H/ACA RNP inactive, and needs to be replaced by GAR1 to produce mature and functional H/ACA RNPs in the Cajal bodies. In this study, we explore in details the molecular mechanism leading to the assembly of mature box H/ACA RNPs. MS analysis of purified GAR1 revealed new sites of arginine methylations in the two GAR domains of GAR1, and showed that most of these methylated arginines exist both in mono-methylated and di-methylated forms in cells. By different methods, we showed that unmethylated GAR1 is correctly incorporated in H/ACA RNPs. We performed extensive analysis of GAR1, NHP2 and NAF1 proteomes by quantitative stable isotope labeling by amino acids in cell culture proteomic analyses (SILAC), and revealed new assembly intermediates: 1) an early protein-only pre-H/ACA RNP complex containing the core proteins DKC1, NOP10 and NHP2, and the assembly factors SHQ1 and NAF1, and 2) a late assembly intermediates containing the RNA, the core proteins and NAF1. We showed that the SMN complex is associated with late forming H/ACA pre-RNP complexes containing GAR1. Moreover, our study identifies new proteins highly and specifically associated with GAR1, NHP2 and NAF1, suggesting their importance in box H/ACA assembly or function, such as the PRMT1 and PRMT5 arginine methylases.

2023-05-10 | PXD035330 | Pride

SILAC APMS analysis of NAF1 interactome in HEK-293 cells

2022-02-17 | PXD026747 | Pride

Global Lysine Acetylome Analysis of LPS-Stimulated HepG2 Cells Identifies Hyperacetylation of PKM2 as a Metabolic Reg-ulator in Sepsis

Project description:Sepsis-induced liver dysfunction is a frequent event and is strongly associated with mortality. Establishing a causative link between protein post-translational modification (PTM) and diseases is challenging. We studied the relationship among the lysine acetylation (Kac), the sirtuin (SIRTs), and their interactors carefully selected in sepsis-induced liver dysfunction (SILD), per-formed on LPS-stimulated HepG2 cells. Protein hyperacetylation was observed according to SIRTs reduction after LPS treatment for 24 h. We identified 1,449 Kac sites based on comparative acetylome analysis, and quantified 1,086 Kac sites on 410 proteins for acetylation. Interestingly, the up-regulated Kac proteins are enriched in glycolysis/gluconeogenesis pathways in the KEGG category. Among the proteins in the glycolysis pathway, hyperacetylation, a key regulator of lactate level in sepsis, was observed in three pyruvate kinase M2 (PKM2) sites. Hyperacetylation of PKM2 induced an increase in its activity, increasing the lactate concentration as a result. In conclusion, this study is the first to conduct global profiling of Kac, suggesting the Kac mecha-nism of PKM2 in glycolysis of sepsis. Moreover, it helps further understand the systematical in-formation of hyperacetylation during the sepsis process.

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Project description:Identification of proteins that associate with chromatin (fraction) upon heat shock by SILAC-based quantitative proteomics

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