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Human A549 CD38, part 2 - Decreased NAD Activates STAT3 and Integrin Pathways to Drive Epithelial-Mesenchymal Transition

ABSTRACT: SILAC-Labeled proteomic analysis of A549 CD38 human lung cancer cell

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung

SUBMITTER: weixuan wang

LAB HEAD: haiteng deng

PROVIDER: PXD007123 | Pride | 2018-07-11

REPOSITORIES: Pride

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			Action	DRS
	MS161743_A-1.pep.xml	Pepxml
	MS161743_A-1.prot.xml	Xml
	MS161743_A10_170115074502.raw	Raw
	MS161743_A11_170115100155.raw	Raw
	MS161743_A12_170115121847.raw	Raw

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Decreased NAD Activates STAT3 and Integrin Pathways to Drive Epithelial-Mesenchymal Transition.

Wang Weixuan W Hu Yadong Y Yang Changmei C Zhu Songbiao S Wang Xiaofei X Zhang Zhenyu Z Deng Haiteng H

Molecular & cellular proteomics : MCP 20180706 10

Nicotinamide adenine dinucleotide (NAD) plays an essential role in all aspects of human life. NAD levels decrease as humans age, and supplementation with NAD precursors plays a protective role against aging and associated disease. Less is known about the effects of decreased NAD on cellular processes, which is the basis for understanding the relationship between cellular NAD levels and aging-associated disease. In the present study, cellular NAD levels were decreased by overexpression of CD38, a ...[more]

PMID: 29980616

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Human A549 CD38, part 1 - Decreased NAD Activates STAT3 and Integrin Pathways to Drive Epithelial-Mesenchymal Transition

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2018-07-10 | PXD007122 | Pride

A549 CD38 proteomic analysis, part 1

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A549 CD38 proteomic analysis, part 2

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A549 CD38 phosphoproteomics analysis

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Identification and quantification of KPNA2 phosphorylation and interactome in response to hydrogen peroxide-induced oxidative stress

Project description:Karyopherin α 2 (KPNA2, importin α1) is involved in the nuclear import of proteins and participates in cellular processes and accumulates in the nucleus under cellular stresses including hydrogen peroxide-indeced oxidative stress via unknown mechanisms. We performed the immunoprecipitation assay and SILAC-based quantitative proteomic analysis in HeLa cells to reveal that hydrogen peroxide decreased the phosphorylation of KPNA2 at serine 62 (S62) and increased its interaction with nucleophosmin 1 (NPM1). Specifically, a reduction in phosphorylated S62 on KPNA2 was observed in the cytoplasmic fraction, but this phosphorylated KPNA2 was not detected in the nuclear fraction. We also identified fifty-four KPNA2-interacting proteins in the nuclear fraction. Among them, NPM1, RPLP0, and MYH9 interacted with KPNA2 in cells exposed to hydrogen peroxide but not in unstressed control cells. Furthermore, the subcellular fractionation, immunoprecipitation, western blotting, immunofluorescence assay, and qRT-PCR analyses were used to support a novel finding that S62 phosphorylation maintains KPNA2 in the cytoplasm, and hydrogen peroxide reduces the phosphorylation of KPNA2 S62 to promote KPNA2-NPM1 complex nuclear entry for gene regulation.

2024-10-17 | PXD051121 | Pride

Real-Time Search Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics

Project description:In the young field of single-cell proteomics (scMS), there is a great need for improved global proteome characterization, both in terms of proteins quantified per cell and quantitative performance thereof. The recently introduced real-time search (RTS) on the Orbitrap Eclipse Tribrid mass spectrometer in combination with SPS-MS3 acquisition has been shown to be beneficial for the measurement of samples that are multiplexed using isobaric tags. Multiplexed single-cell proteomics requires high ion injection times and high-resolution spectra to quantify the single-cell signal, however the carrier channel facilitates peptide identification and thus offers the opportunity for fast on-the-fly precursor filtering before committing to the time intensive quantification scan. Here, we compared classical MS2 acquisition against RTS-SPS-MS3, both using the Orbitrap Eclipse Tribrid MS with the FAIMS Pro ion mobility interface and we present a new acquisition strategy termed RETICLE (RTS Enhanced Quant of Single Cell Spectra) that makes use of fast real-time searched linear ion trap scans to preselect MS1 peptide precursors for quantitative MS2 Orbitrap acquisition. Here we show that classical MS2 acquisition is outperformed by both RTS-SPS-MS3 through increased quantitative accuracy at similar proteome coverage, and RETICLE through higher proteome coverage, with the latter enabling the quantification of over 1000 proteins per cell at a MS2 injection time of 750ms using a 2h gradient.

2022-03-14 | PXD029320 | Pride

PRMT7 substrates

Project description:Protein arginine methyltransferases (PRMTs) regulate diverse biological processes and are increasingly being recognized for their potential as drug targets. Here we report the discovery of a potent, selective and cell active chemical probe for PRMT7. SGC3027 is a cell permeable prodrug, which in cells, is converted to SGC8158, a potent, SAM-competitive PRMT7 inhibitor. Inhibition or knockout of cellular PRMT7 resulted in drastically reduced levels of monomethylation of HSP70 family members and other stress-associated proteins. Structural and biochemical analysis revealed that PRMT7-driven in vitro methylation of HSP70 at R469 requires an ATP-bound, open conformation of HSP70. In cells, SGC3027 inhibited methylation of both, constitutive and inducible forms of HSP70, and led to decreased tolerance for perturbations in proteostasis. These results demonstrate a role for PRMT7 in stress response. SGC3027 is the first chemical probe for PRMT7 and together with its inactive control SGC3027N, will be valuable chemical tools to further investigate the role of PRMT7 in human health and disease.

2022-02-23 | PXD012119 | Pride

Haloferax volcanii SILAC study of Oxidative stress

Project description:SILAC was used to monitor proteome changes to Haloferax volcanii after treatment with oxidizing agent NaOCl. SILAC amino acids used were Lysine(+8) and Arginine(+6). For treatment and control groups 4 replicates were used. In replicates 1 and 3, the control group had supplementation of both light lysine and argninie to the medium and the treatment group was supplemented with both heavy lysine(+8) and arginine(+6). In replicates 2 and 4, the labeling was switched, with the control containing heavy lysine(+8) and arginine(+6) and the treatement was supplemented with light lysine and arginine. After treatment, cells were mixed at a 1:1 ratio (control:treatment) and proteins were extracted and digested with trypsin. For the incorporation test, cells were grown in meduim containing heavy lysine(+8) and argnine(+6) and allowed to grow for 24 hours, then subcultured twice, sequentially after 24 h of growth. To test for incorporation of the heavy amino acids, cells were harvested, proteins extracted, and digested with trypsin.

2018-01-09 | PXD006877 | Pride

Improving the identification and coverage of plant transmembrane proteins in Medicago using bottom-up proteomics

Project description:Plant transmembrane proteins (TMPs) are essential for normal cellular homeostasis, nutrient exchange and responses to environmental cues. Commonly used bottom-up proteomic approaches fail to identify a broad coverage of peptide fragments derived from TMPs. Here, we used mass spectrometry (MS) to compare the effectiveness of two solubilisation and protein cleavage methods to identify shoot-derived TMPs from the legume Medicago. We compared a urea solubilisation, trypsin Lys-C (UR-TLC) cleavage method to a formic acid solubilisation, cyanogen bromide and trypsin Lys-C (FA-CTLC) cleavage method. We assessed the effectiveness of these methods by (i) comparing total protein identifications, (ii) determining how many TMPs were identified, and (iii) defining how many peptides incorporate all, or part, of transmembrane domains (TMD) sequences. The results show that the FA-CTLC method identified nine-fold more TMDs, and enriched more TMPs than the UR-TLC method. FA-CTLC identified more TMPs, particularly transporters, whereas, UR-TLC preferentially identified TMPs with one TMD, particularly signalling proteins. The results suggest that combining plant membrane purification techniques with both the FA-CTLC and UR-TLC methods will achieve a more complete identification and coverage of TMPs.

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Transfer of Alarmins from Neutrophils to Platelets after Acute Myocardial Infarction

Project description:Platelets are central to the pathophysiology of myocardial infarction (MI). How the platelet proteome is altered during MI is unknown. We sought to describe changes in the platelet proteome at the time of MI and identify potential mechanisms. Platelets from patients experiencing ST-elevation myocardial infarction (STEMI) before and 3 days after treatment (n= 30), and a matched cohort of patients with severe stable coronary artery disease (CAD) prior to and 3 days after coronary artery bypass grafting (CABG, n=25) underwent quantitative proteomic analysis. Elevations of the alarmins S100A8 and S100A9 were detected at the time of STEMI compared with stable CAD (S100A8, FC = 2.00, FDR = 0.05; S100A9, FC = 2.28, FDR = 0.005). During STEMI, S100A8 mRNA and protein levels were correlated in platelets (R = 0.46, p = 0.012). To determine if protein synthesis occurs, activated platelets were incubated with 13C-labelled amino acids for 24 hours and analyzed by mass spectrometry. No incorporation was detected, consistent with the notion that protein synthesis in platelets is not a major contributor to the platelet proteome. Platelet abundance of S100A8 and A9 was strongly correlated with neutrophil abundance at the time of STEMI. When isolated platelets and neutrophils were co-incubated under quiescent and TRAP-6 activated conditions, release of S100A8 from neutrophils resulted in uptake of S100A8 by platelets. Leukocyte-to-platelet protein transfer, rather than protein synthesis, may occur in a thromboinflammatory environment such as STEMI, representing a potential new contributor in the innate immune pathogenesis of STEMI.

2023-11-15 | PXD024159 | Pride

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