Metabolic,Anti-apoptotic and Immune Evasion Strategies of Primary Human Myeloma Cells Indicate Adaptations to Hypoxia*

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Highlights

• •In-depth proteome profiling of primary human myeloma cells
• •Characteristics of myeloma cells are related to hypoxic bone marrow conditions
• •Myeloma cells show specific immune evasion strategies
• •Metabolic adaptations involve tumor and stroma cells

     

Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays,

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Highlights

• •R-10G is a mono-sulfated glycan antigen of human iPS and ES cells on podocalyxin.
• •R-10G and nonsulfated i are reciprocal antigens on type 2 glycan backbones.
• •TRA-1–60 and -81 and FC10.2 are antigens expressed on unsulfated type 1 backbones.
• •These assignments open the way to probing their roles in podocalyxin-signaling.

     

A Combined N-terminomics and Shotgun Proteomics Approach to Investigate the Responses of Human Cells to Rapamycin and Zinc at the Mitochondrial Level

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Highlights

• •Rapamycin and zinc induce moderate but significant mitochondrial proteome changes.
• •The mitochondrial proteins processing system is robust under subtoxic conditions.
• •Rapamycin and zinc perturb the mitochondrial proteins processing system.
• •Rapamycin and zinc perturb the mitochondrial proteins homeostasis.

     

Chromobodies to Quantify Changes of Endogenous Protein Concentration in Living Cells

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Highlights

• •Chromobodies are stabilized by antigen binding in live cells.
• •Monitoring changes of endogenous protein levels in living cells with chromobodies.
• •Broadly applicable system to generate turnover-accelerated chromobodies.
• •Quantification of time- and dose-dependent compound effects.

     

Functional Proteomics and Deep Network Interrogation Reveal a Complex Mechanism of Action of Midostaurin in Lung Cancer Cells

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Highlights

• •Anticancer activity of midostaurin but not other PKC inhibitors in NSCLC cells.
• •Mechanism of action by network-based integration of chemo- and phosphoproteomics.
• •Midostaurin polypharmacology by simultaneous inhibition of TBK1, PDPK1 and AURKA.
• •Design of synergistic drug combination with PLK1 inhibitor by pathway validation.

     

Mass Spectrometry-based Absolute Quantification of 20S Proteasome Status for Controlled Ex-vivo Expansion of Human Adipose-derived Mesenchymal Stromal/Stem Cells

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Highlights

• •Design of an MRM assay to determine the absolute quantity and stoichiometry of ubiquitous and tissue-specific human 20S proteasome subtypes.
• •Use of purified isotopically labelled 20S proteasome as internal standard for accurate quantification.
• •Variation in the expression of immunoproteasome in adipocyte-derived stem cells (ADSCs) grown under different O₂ levels might be causal for change in cells differentiation capacity.
• •The status of 20S proteasome during ADSCs expansion might constitute an additional relevant quality control parameter to contribute to predict, among other quality markers, their therapeutic capacity.

     

Spatiotemporal Changes of the Phagosomal Proteome in Dendritic Cells in Response to LPS Stimulation*

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Highlights

• •Characterization of the phagosomal proteome comparing resting and LPS-treated BMDCs.
• •Label-free quantification determined 2843 phagosomal proteins.
• •Reduced recruitment of hydrolases and V-ATPase to phagosomes of LPS-treated cells.
• •Increased recruitment of antigen cross-presentation molecules to these phagosomes.

     

Metabolic Cross-talk Between Human Bronchial Epithelial Cells and Internalized Staphylococcus aureus as a Driver for Infection*

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Highlights

• •Interplay of epithelial cells and internalized S. aureus was dissected over 96 h.
• •Surviving host cells contain nonreplicating bacteria that persists in the cytoplasm.
• •Competition over resources triggers temporal metabolic changes.
• •Metabolic adaptation of host and bacteria determines the outcome of infection.

     

Temporal Proteomic Analysis of Pancreatic β-Cells in Response to Lipotoxicity and Glucolipotoxicity

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Highlights

• •Temporal proteome profiling of lipotoxicity and glucolipotoxicity in β-cells
• •Palmitate induced cholesterol metabolism earlier than fatty acid metabolism
• •Setd8 promotes palmitate + glucose-stimulated INS-1 cell proliferation
• •PA induced apoptosis partially via upregulation of Rhob in INS-1 cells

     

Proteomics Analysis of Extracellular Matrix Remodeling During Zebrafish Heart Regeneration

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Highlights

• •We have developed a decellularization protocol for ECM protein enrichment.
• •We have characterized the proteome of adult zebrafish heart ECM.
• •We describe dynamic changes in heart ECM proteome during regeneration.
• •We describe changes in heart ECM stiffness during regeneration.

     

Exploring Regulation of Protein O-Glycosylation in Isogenic Human HEK293 Cells by Differential O-Glycoproteomics

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Highlights

• •A panel of HEK293 isogenic cell lines with knockout of GALNT genes.
• •Identification of nonredundant O-glycosylation sites regulated by specific GalNAc-T isoforms.
• •GalNAc-T7 and T10 contribute to follow-up activity in regions of high density O-glycosylation.
• •GalNAc-T11 specifically controls O-glycosylation of specific linker regions in the low-density lipoprotein receptor related proteins.

     

Decreased Antibiotic Susceptibility Driven by Global Remodeling of the Klebsiella pneumoniae Proteome

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Highlights

• •Global proteomic remodeling alters antibiotic susceptibility in K. pneumoniae.
• •Drug specific transport, sugar utilization, central metabolism, capsule synthesis.
• •Common pathways of reactive oxygen scavenging, turnover of misfolded proteins.
• •Integrated adjustments and unique drug-specific features for drug combinations.

     

Comparative Secretome Analyses of Primary Murine White and Brown Adipocytes Reveal Novel Adipokines

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Highlights

• •First comparative proteomic analysis of white and brown adipocyte secretomes.
• •100 novel adipokines differentially secreted from white versus brown adipocytes.
• •Functionally enriched protein class changes in white and brown adipocytes.
• •200 novel, NE-responsive adipokines from brown adipocytes.

     

BioID Performed on Golgi Enriched Fractions Identify C10orf76 as a GBF1 Binding Protein Essential for Golgi Maintenance and Secretion

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Highlights

• •BioID with Golgi fractions identified C10orf76 as proximal to GBF1.
• •Tagged C10orf76 overlaps with Golgi markers.
• •C10orf76 binds GBF1 and exchanges rapidly between free and bound forms.
• •C10orf76 is essential for maintenance of the Golgi and for secretion.

     

Complexome Profiling Reveals Association of PPR Proteins with Ribosomes in the Mitochondria of Plants

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Highlights

• •Plant mitoribosomes contain several pentatricopeptide repeat proteins.
• •The small mitoribosomal subunit is of an exceptionally large size.
• •Protein units not directly related to translation may be attached to plant mitoribosomes to confer additional functions to these molecular machines.