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.

     

Identification of Novel Natural Substrates of Fibroblast Activation Protein-alpha by Differential Degradomics and Proteomics

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Highlights

• •Natural substrates of FAP were identified using degradomic and proteomic techniques and FAP gene knockout mouse derived embryonic fibroblasts stably transduced with enzymatically active or inactive FAP.
• •Terminal amine isotopic labelling of substrates (TAILS) based degradomics identified cleavage sites in collagens, and many other extracellular matrix (ECM) and associated proteins.
• •Cleavages of lysyl oxidase-like-1, CXCL-5, CSF-1 and C1qT6 by FAP were confirmed in vitro.
• •Differential metabolic labelling coupled with quantitative proteomic analysis implicated FAP in regulating proteins that are associated with ECM, ECM-cell interactions, coagulation, metabolism and wound healing.

     

Quantitative Early Auxin Root Proteomics Identifies GAUT10, a Galacturonosyltransferase,as a Novel Regulator of Root Meristem Maintenance

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Highlights

• •Auxin responsive proteins in Arabidopsis roots were identified from 3,514 detected proteins.
• •All six auxin receptors are stable in response to hormone via novel MRM assays.
• •The >100 differentially expressed proteins exhibit dynamic and transient responses to auxin.
• •Phenotypic screening of the top responsive proteins uncovered several novel root mutants.

     

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.

     

Comparative Secretome Analyses of Human and Zoonotic Staphylococcus aureus Isolates CC8, CC22, and CC398

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Highlights

• •Proteogenomics and secretome comparison of human and zoonotic Staphylococcus aureus lineages.
• •869 secreted proteins identified in eight S. aureus isolates of CC8, CC22 and CC398.
• •CC398 lower secretion of surface proteins and higher secretion of hemolysins and exoenzymes.
• •Regulatory differences in the secretomes could be linked to lower SigB activity in CC398.

     

Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers,

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Highlights

• •Shotgun identification of neopeptides released from osteoarthritic cartilage.
• •Specific endogenous peptides from the cartilage ECM are measured by MRM.
• •Identification of neopeptides differentially generated from diseased tissue.
• •The peptide DSNKIETIPN shows the best metrics as biomarker of OA cartilage.

     

The Proteome of Pig Spermatozoa Is Remodeled During Ejaculation

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Highlights

• •Proteome of mature boar spermatozoa from cauda epididymal and ejaculated sources were analyzed by iTRAQ-based LC-MS/MS.
• •1,723 sperm proteins identified (974 of Sus scrofa taxonomy).
• •1,602 sperm proteins quantified (960 of Sus scrofa taxonomy).
• •32 Sus scrofa sperm proteins were differentially expressed among sperm sources.
• •The proteome of boar spermatozoa is remodelled during ejaculation.

     

Identification of Salivary Biomarkers for Oral Cancer Detection with Untargeted and Targeted Quantitative Proteomics Approaches

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Highlights

• •iTRAQ-based analysis of saliva samples from oral cancer patients.
• •Proteome profiling of saliva samples from patients with oral premalignant lesions.
• •Verification of salivary biomarker candidates with MRM-MS and immunoassays.
• •Identification of salivary proteins as potential biomarkers of oral cancer.

     

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.

     

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.

     

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.

     

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.

     

DECA,A Comprehensive,Automatic Post-processing Program for HDX-MS Data*

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Highlights

• •Open source software for comprehensive HDX-MS data analysis.
• •Automatic back-exchange correction options.
• •Rigorous statistical analysis of the significance of uptake differences.
• •High quality visualization tools.

     

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.

     

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.

     

Mapping Spatiotemporal Microproteomics Landscape in Experimental Model of Traumatic Brain Injury Unveils a link to Parkinson's Disease,

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Highlights

• •Spatiotemporal microproteomics analysis of TBI.
• •Injury site microproteomics reveal distinct phases in 10-day frame post TBI.
• •Uninjured proteomic profile is restored in TBI at 10 days post injury.
• •Substantia nigra protein post 3 days suggest link to Parkinson's disease.

     

Proteomics of Asrij Perturbation in Drosophila Lymph Glands for Identification of New Regulators of Hematopoiesis

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Highlights

• •First report on the quantitative proteomic profiling of Drosophila lymph glands.
• •Comparative proteomic analysis under conditions of perturbed blood cell homeostasis.
• •Resource for identifying new regulators of insect and vertebrate hematopoiesis.

     

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.