Proteomics Profiling of Autologous Blood and Semen Exosomes from HIV-infected and Uninfected Individuals Reveals Compositional and Functional Variabilities

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Highlights

• •SMPP enabled analysis of autologous blood and semen proteomes of HIV- and HIV+ participants.
• •Common and distinct exProteins from autologous semen and blood are associated with exosomes.
• •HIV-induced perturbations were less frequent in semen compared to blood.
• •Semen but not blood exosomes is enriched in nucleic acids and protein binding factors.

     

Temporal Quantitative Proteomics of mGluR-induced Protein Translation and Phosphorylation in Neurons

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Highlights

• •Integrated phosphoproteomics and analyses of newly synthesized proteins in neurons.
• •Resource of temporal mGluR-induced signaling pathways upon DHPG stimulation.
• •Validation of PKC, MAPK1, CAMKIIa, and CDK2 in mGluR-activation and signaling.
• •Validation of Intersectin-1 in DHPG-induced AMPAR internalization.

     

The Proteome of the Dentate Terminal Zone of the Perforant Path Indicates Presynaptic Impairment in Alzheimer Disease

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Highlights

• •Laser microdissection of highly vulnerable hippocampal region.
• •Proteomic analysis of postmortem human brain tissue of AD and control cases.
• •Decreased levels of presynaptic proteins, but not postsynaptic proteins, in AD.
• •Immunohistochemistry verifies decreased levels of selected presynaptic proteins.

     

Characterizing Patients with Recurrent Urinary Tract Infections in Vesicoureteral Reflux: A Pilot Study of the Urinary Proteome

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Highlights

• •Urinary proteomes of patients with recurrent UTI, renal scarring, and VUR.
• •80 proteins differentially expressed, compared to healthy controls.
• •62 proteins may be indicative of susceptibility for UTI.
• •Altered acute phase response, extracellular matrix and carbohydrate metabolism.

     

Concentration Determination of >200 Proteins in Dried Blood Spots for Biomarker Discovery and Validation

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Highlights

• •Repeatable quantification of 200 proteins in dried blood spots.
• •Determined lower limit of quantification, repeatability, parallelism and stability.
• •Protein stability in DBS stored at ambient temperatures for up to 2 months.
• •Concentration ranges for 200 proteins in 20 healthy individuals.

     

Organellar Maps Through Proteomic Profiling – A Conceptual Guide

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Highlights

• •Organelle profiling maps capture localizations of 1000s of proteins in one experiment.
• •Comparing maps +/− perturbation reveals disease mechanisms & cellular responses.
• •A conceptual guide to planning and interpreting organellar profiling experiments.
• •A cross-study consensus set of human organellar marker proteins.

     

An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics

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Highlights

• •Higher AGC significantly improves quantitation quality in single-cell analysis.
• •The boosting-to-sample ratio should be carefully evaluated and optimized.
• •iBASIL allows for precise quantitation of 1,500 proteins from 104 AML single cells.
• •iBASIL recapitulates major biological differences in different AML single cells.

     

Phenotypic Adaption of Pseudomonas aeruginosa by Hacking Siderophores Produced by Other Microorganisms

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Highlights

• •P. aeruginosa grown with exosiderophores and analyzed by proteomic and RT-qPCR.
• •Catechol-type exosiderophores strongly induce the expression of their transporters.
• •Repression of the endogenous iron uptake pathways.
• •Complex phenotypic plasticity in the expression of the various iron-uptake pathways.

     

Changes in the Oligodendrocyte Progenitor Cell Proteome with Ageing

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Highlights

• •Quantitative proteome of neonatal, young, and aged OPCs.
• •50% of the proteome is differentially expressed between neonatal and adult OPCs.
• •Myelin proteins are increased, and cholesterol synthesis proteins decreased with age.
• •Proteins associated with other neurodegenerative diseases are increased in aged OPCs.

     

Immediate Adaptation Analysis Implicates BCL6 as an EGFR-TKI Combination Therapy Target in NSCLC

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Highlights

• •EGFR-TKI molecular response profiling covering 10138 proteins and 13486 mRNAs.
• •EGFR-TKI combination therapy screen using a library of 528 compounds.
• •Several new candidate EGFR-TKI escape mechanisms and combination therapy targets.
• •Combined targeting of the oncogene BCL6 and EGFR results in synergy in NSCLC cells.

     

Proteaphagy in Mammalian Cells Can Function Independent of ATG5/ATG7

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Highlights

• •Quantitative proteomics of isolated lysosomes, autophagosomes and proteasomes.
• •Pharmacological inhibition of proteasomes leads to their accumulation within lysosomes.
• •Inhibition of classical autophagy pathways cannot completely block this process.
• •Known autophagy adaptor proteins are not involved.

     

Molecular Dynamics Simulation-assisted Ionic Liquid Screening for Deep Coverage Proteome Analysis

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Highlights

• •Mechanistic insights into ionic liquids and proteins at molecular level.
• •Extractants prescreen for proteome analysis with MD simulation system.
• •A loss-less sample preparation method developed for in-depth proteome profiling.
• •Over 3,300 proteins were confidently identified from 1,000 HeLa cells in a 1 h run.
• •Label-free quantitative proteome analysis of human liver cancer tissues.

     

Quantitative Profiling of the Human Substantia Nigra Proteome from Laser-capture Microdissected FFPE Tissue

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Highlights

• •A detailed investigation of the protein extraction step from FFPE tissue is shown.
• •Acidification during peptide wash increased peptide recovery of the SP3 method.
• •LCM of substantia nigra enriched neuron-specific proteins including TH.
• •>5,600 proteins were quantified using 3000 cells per sample from substantia nigra.

     

A Comprehensive Gender-related Secretome of Plasmodium berghei Sexual Stages

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Highlights

• •Quantitative analysis of Plasmodium sexual stage egress secretome.
• •Activated gametocytes release gender-related proteins.
• •Gametocyte egress process involves different types of vesicles.

     

Multi-omic Characterization of the Mode of Action of a Potent New Antimalarial Compound,JPC-3210, Against Plasmodium falciparum

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Highlights

• •Multi-omics analysis on mode of action of novel antimalarial, JPC-3210
• •JPC-3210 has rapid parasite killing kinetics.
• •Metabolomics and peptidomics demonstrated JPC-3210 inhibits hemoglobin digestion.
• •Proteomics demonstrated JPC-3210 enriches for translation regulation proteins.

     

The DNA Sensor cGAS is Decorated by Acetylation and Phosphorylation Modifications in the Context of Immune Signaling

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Highlights

• •cGAS acetylations and phosphorylations under basal and immune-stimulated states.
• •K384 and K414 acetylations and S305 phosphorylation inhibit cGAS-mediated apoptosis.
• •Acetylation at K198 stimulates cGAS-dependent interferon signaling.
• •K198 acetylation is decreased upon herpesvirus infection.

     

Upregulation of CD73 Confers Acquired Radioresistance and is Required for Maintaining Irradiation-selected Pancreatic Cancer Cells in a Mesenchymal State

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Highlights

• •CD73 is one of the most upregulated proteins in the radioresistant cells.
• •CD73 upregulation confers radioresistance and irradiation-induced apoptosis.
• •CD73 confers radioresistance potentially through inactivating protein BAD.
• •Elevated CD73 is required for maintaining the resistant cells in a mesenchymal state.

     

Data,Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing

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Highlights

• •In-depth proteomes of 4 SARS-CoV-2 cell line models (Vero E6, Calu-3, Caco-2, A549).
• •Proteomic evidence for thousands of Chlorocebus sabaeus proteins.
• •Proteomic response of Vero E6 cells to SARS-CoV-2 infection.
• •Synthetic peptides, spectral libraries, and targeted assays for SARS-CoV-2 proteins.

     

The Capture of a Disabled Proteasome Identifies Erg25 as a Substrate for Endoplasmic Reticulum Associated Degradation

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Highlights

• •Epitope-tagging of a proteasome subunit allows for facile immuno-isolation.
• •An engineered yeast strain permits capture of proteasome-associated substrates.
• •MS/MS identified all 33 resident proteasome subunits in the 20S and 19S particles.
• •Analysis of associated proteins and characterization of newly identified ERAD substrate.

     

ProAlanase is an Effective Alternative to Trypsin for Proteomics Applications and Disulfide Bond Mapping

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Highlights

• •ProAlanase is a powerful protease for efficient low pH disulfide bond mapping.
• •High suitability for analysis of histone family members and their PTMs.
• •Accurate phosphorylation profiling in proline-rich proteins.
• •Sequence coverage increase and full de novo sequencing in combination with trypsin.