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.

     

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

     

Virulence Factors Produced by Staphylococcus aureus Biofilms Have a Moonlighting Function Contributing to Biofilm Integrity

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Highlights

• •Establishment of a flow system allowing multi-omics analysis of S. aureus biofilms.
• •Biofilm proteome profiling (intracellular and ECM) plus metabolic footprint analysis.
• •Virulence factors and ribosomal proteins stabilize the ECM as moonlighting proteins.
• •They act as electrostatic bridges between anionic cell surfaces, eDNA and metabolites.

     

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.

     

Proteomic Profiling of Human Prostate Cancer-associated Fibroblasts (CAF) Reveals LOXL2-dependent Regulation of the Tumor Microenvironment

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Highlights

• •Quantitative (phoshpo)proteome of primary cell cultures of patient-matched prostate CAF and NPF.
• •Key CAF-associated proteins validated using orthogonal methodologies.
• •LOXL2 inhibitors D-penicillamine and PXS-S2A impaired CAF migration and ECM alignment.
• •Pre-treatment with LOXL2 inhibitors impaired migratory capacity of RWPE-2 cells in co-culture.

     

Global Proteome and Ubiquitinome Changes in the Soluble and Insoluble Fractions of Q175 Huntington Mice Brains

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Highlights

• •Quantitative changes in global proteome and ubiquitinome in Huntington's disease.
• •Differential ubiquitination of wild-type and mutant Htt in mice brain.
• •Enriched pathways include vesicle transport and mRNA processing.
• •Correlation between protein and diGly site fold changes.

     

A New Tool to Reveal Bacterial Signaling Mechanisms in Antibiotic Treatment and Resistance

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Highlights

• •Quantitative (phospho)proteome analysis of antibiotic treatment in E. coli.
• •Largest bacterial phosphorylation catalogue.
• •Specific phosphorylation motifs changes during resistance development.
• •Phosphorylation mediated signaling could be a potential target for drug design.

     

Reductive Stress Selectively Disrupts Collagen Homeostasis and Modifies Growth Factor-independent Signaling Through the MAPK/Akt Pathway in Human Dermal Fibroblasts

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Highlights

• •Changes to the proteome of skin fibroblasts subjected to reductive stress have been quantitated.
• •Only a small set of proteins is selectively diminished upon exposure to reductants.
• •Collagens (COL1A2 and COL6A2) emerge as sentinels of reductive stress.
• •Reductive stress triggers receptor-independent Akt phosphorylation at Ser473.

     

Proteomic Analysis of Vocal Fold Fibroblasts Exposed to Cigarette Smoke Extract: Exploring the Pathophysiology of Reinke's Edema,

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Highlights

• •First global study on laryngeal cells cultured with cigarette smoke enriched medium.
• •Vocal fold fibroblasts increased production of ECM component hyaluronan.
• •Expression of several fibrillar collagens was reduced.

     

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

     

In-depth Proteome of the Hypopharyngeal Glands of Honeybee Workers Reveals Highly Activated Protein and Energy Metabolism in Priming the Secretion of Royal Jelly

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Highlights

• •In-depth proteome underpins the gland ontogeny and age-specific activity of the HGs.
• •The well-developed acini in the HGs of NBs promote the RJ secretary activities.
• •The enhanced protein and energy metabolism in the HGs boost the stronger RJ secretion of RJBs.

     

Associations of the Fecal Microbial Proteome Composition and Proneness to Diet-induced Obesity

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Highlights

• •Feeding mice a western-style obesogenic diet resulted in dramatic changes in fecal microbial proteome.
• •Basal fecal microbial proteome, but not microbiome, composition was associated with extent of diet-induced obesity.
• •A major feature of fecal microbial proteome of high-responder mice was enriched motility-related proteins.

     

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.

     

Nonparametric Analysis of Thermal Proteome Profiles Reveals Novel Drug-binding Proteins*

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Highlights

• •Method for the analysis of response curves from thermal proteome profiling (TPP).
• •NPARC uses nonparametric statistics and provides false discovery-rate (FDR) control.
• •Increased proteome coverage and sensitivity to identify drug-binding proteins.

     

Proteomics,Glycomics, and Glycoproteomics of Matrisome Molecules

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Highlights

• •Highly glycosylated matrisome proteins and their binding partners comprise extracellular networks that mediate tissue-specific cellular microenvironments.
• •Elucidation of roles of matrisome molecules in disease mechanisms requires detailed mapping of matrisome glycosylation and other post-translational modifications.
• •We review tissue workup methods for matrisome proteomics, glycomics and glycoproteomics.
• •The combination of proteomics, glycomics and glycoproteomics profiles matrisome protein modifications distinct from those studied by immunohistochemistry.

     

Small-protein Enrichment Assay Enables the Rapid,Unbiased Analysis of Over 100 Low Abundance Factors from Human Plasma

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Highlights

• •Development of a method for low-abundance small protein analysis in human plasma.
• •Deep proteome profiling demonstrated unbiased identification of diverse factors.
• •Method enabled identification of a novel human plasma protein C5ORF46.
• •Analysis of intermittent fasting response showed changes in iron regulation.

     

Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance,

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Highlights

• •Bayesian Beta-Binomial model integrates ion statistics with peptide ratio agreement.
• •Model appropriately interprets information from low signal peptides.
• •Confidence can be assigned even without replicates.
• •Model adds sensitivity to detection of small changes.

     

Comprehensive Analysis of Individual Variation in the Urinary Proteome Revealed Significant Gender Differences

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Highlights

• •Comprehensive analysis of inter-individual variation of normal urinary proteome.
• •Significant gender differences were observed.
• •Proteins increased in female urine are enriched in immunological pathways.
• •Estimated reference intervals of proteins as the baseline for biomarker discovery.

     

Development of a Gill Assay Library for Ecological Proteomics of Threespine Sticklebacks (Gasterosteus aculeatus)

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Highlights

• •Construction of threespine stickleback gill assay library using DDA proteomics
• •Population-specific gill proteome signatures of four ecotypes identified by DIA
• •HSP47 and extracellular matrix proteins highly elevated in warm-adapted sticklebacks
• •Inflammasome and proteolytic proteins highly elevated in freshwater sticklebacks