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.

     

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.

     

Cross-linking Proteomics Indicates Effects of Simvastatin on the TLR2 Interactome and Reveals ACTR1A as a Novel Regulator of the TLR2 Signal Cascade

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Highlights

• •An innovative co-IP crosslinking proteomics study was designed for the TLR2 interactome.
• •Proteomic profiling revealed combinatorial effects of simvastatin and Pam3CSK4 on the TLR2 interactome.
• •ACTR1A and MARCKSL1 proteins were identified as potential interactors of TLR2 during the immune response.
• •ACTR1A has important modulatory actions on the TLR2 pro-inflammatory signaling cascade.

     

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.

     

Identification of a Specific Translational Machinery via TCTP–EF1A2 Interaction Regulating NF1-associated Tumor Growth by Affinity Purification and Data-independent Mass Spectrometry Acquisition (AP-DIA),

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Highlights

• •AP-DIA/SWATH analysis to identify TCTP-interacting proteins in NF1 tumor cells.
• •A highly specific TCTP–EF1A2 interaction but rather than TCTP–EF1A1 interaction.
• •TCTP–EF1A2 interaction mediating formation of EF1A2-elogation factor complex.
• •TCTP–EF1A2 dependent translation machinery regulating NF1 tumor cell growth.

     

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

     

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.

     

Comprehensive Analysis of the Lysine Succinylome and Protein Co-modifications in Developing Rice Seeds

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Highlights

• •Nonenzymatically Ksu proteins shown different pattern from native cell Ksu proteins.
• •Motif preference of Ksu proteins was associated with different biological processes.
• •Up to 67 developing rice seeds proteins contain PTMs of Kac, Ksu, Kcr, Kmal, and Khib.
• •Some lysine residues of the key pathway enzymes are modified by succinylation.

     

MS-EmpiRe Utilizes Peptide-level Noise Distributions for Ultra-sensitive Detection of Differentially Expressed Proteins

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Highlights

• •New software to determine differentially expressed proteins in quantitative MS experiments.
• •Applicable to any modern quantitative MS setup and study type, including clinical setups.
• •Ultra-sensitive at strict FDR control, up to 1000 additional proteins in a single comparison.
• •Easy to use, fast processing and readily available package, including user friendly manual.

     

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.

     

A Platform for Extracellular Interactome Discovery Identifies Novel Functional Binding Partners for the Immune Receptors B7-H3/CD276 and PVR/CD155

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Highlights

• •New platform for high throughput detection of transient interactions between membrane proteins.
• •IL20RA is a receptor for the orphan checkpoint inhibitor B7-H3.
• •The natural killer cell protein KIR2DL5A binds the immune receptor PVR.
• •KIR2DL5 binding to PVR regulates natural killer cell cytotoxicity and inhibits tumor cell killing.
• •Elucidation of receptor interactomes to gain insights into extracellular protein biology.

     

Global Interactomics Uncovers Extensive Organellar Targeting by Zika Virus

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Highlights

• •BioID and IP-MS were conducted to generate a global ZIKV-host protein interactome
• •Interactome consists of >3000 high confidence ZIKV-host protein interactions
• •Data mining indicates that ZIKV proteins interact with multiple host cell organelles
• •An important role for peroxisomes in ZIKV infection is uncovered

     

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.

     

Online Parallel Accumulation–Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer

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Highlights

• •Online PASEF achieves greater than 100 MS/MS per second at full sensitivity.
• •Accurate label-free quantification of over 6000 proteins in 2 h.
• •High throughput demonstrated on 50 ng digests measured in 5 min.
• •High-precision determination of 100,000 peptide collisional cross sections.

     

Deciphering Protein Glycosylation by Computational Integration of On-chip Profiling,Glycan-array Data,and Mass Spectrometry

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Highlights

• •Method to probe the isomeric variants of the glycans attached to purified proteins.
• •Uses multiple rounds of glycosidase cleavage and lectin profiling.
• •Computation integration of lectin-binding, glycan-array, and mass spectrometry data.
• •Applied to microspots for compatibility with analyzing low-abundance proteins.

     

Proteome-wide Analysis of Protein Thermal Stability in the Model Higher Plant Arabidopsis thaliana

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Highlights

• •Over 1700 Arabidopsis proteins with thermal models in multiple replicates.
• •Melting temperature correlates with 1°, 2°, and 3° protein characteristics.
• •Ligand-induced thermal shifts are evident in complex protein extracts.