Novel Proteome Extraction Method Illustrates a Conserved Immunological Signature of MSI-H Colorectal Tumors

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Highlights

• •TOP: robust, bio-friendly FFPE proteome extraction method with less fixation bias.
• •Proteome of MSI-H colorectal cancer identifies immunobiology key elements.
• •MSI-H tumor displays an “INFg-STAT1 centric signature”.
• •Long-term IFNg induction In-vitro mimicks MSI-H signature.

     

Identification of Tumor Antigens in the HLA Peptidome of Patient-derived Xenograft Tumors in Mouse

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Highlights

• •Sufficient tumor tissues are often unavailable large HLA peptidome discovery.
• •Using patient derived xenograft (PDX) tumors can overcome this limitation.
• •The large PDX HLA peptidomes expand significantly those of the original biopsies.
• •The HLA peptidomes of the PDX tumors included many tumor antigens.

     

Robust Summarization and Inference in Proteome-wide Label-free Quantification

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Highlights

• •In depth performance assessment of leading tools for differential protein abundance.
• •Novel fast modular framework MSqRobSum for robust protein summarization and inference.
• •MsqRobSum outperforms leading protein summarization-based tools.
• •MSqRobSum is on par with top-performing peptide based tool MSqRob.

     

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.

     

Site-specific N-glycan Analysis of Antibody-binding Fc γ Receptors from Primary Human Monocytes

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Highlights

• •Monocytes are isolated from single donors after apheresis.
• •Monocytes process CD16a and CD32a N-glycosylation differently by site and donor.
• •CD16a with hybrid and oligomannose type N-glycans bind IgG1 Fc with stronger affinity than complex type.

     

Flow-induced Reorganization of Laminin-integrin Networks Within the Endothelial Basement Membrane Uncovered by Proteomics

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Highlights

• •Proteomics uncovers the flow-induced remodeling of the endothelial basement membrane.
• •Flow alters the composition and localization of the laminin-integrin network.
• •Flow induces proteolytic processing of LAMA4, resulting in shedding of LG4–5 region.
• •TNFα- and flow-exposure induce a distinct proteomic signature with limited interplay.

     

Characterization of Prenylated C-terminal Peptides Using a Thiopropyl-based Capture Technique and LC-MS/MS

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Highlights

• •Brain membrane protein extraction.
• •Protein prenylation.
• •Prenyl peptide capture and characterization by LC-MS/MS.
• •HCD and EThcD peptide fragmentation.

     

An Interaction Network of RNA-Binding Proteins Involved in Drosophila Oogenesis

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Highlights

• •Label-free and dimethyl labeling MS analysis of 6 RBPs from Drosophila ovaries.
• •Functionally related RBPs show overlapping proteomes.
• •Selective co-purification of splicing factors and translational regulators.
• •Validation of 26 novel interactions by co-immunoprecipitation.

     

Genetic Profile and Functional Proteomics of Anal Squamous Cell Carcinoma: Proposal for a Molecular Classification

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Highlights

• •Two molecular groups in anal squamous carcinoma according proteomic profile.
• •Differences in possible targeted processes such as metabolism or immune response.
• •Different percentage of tumor lymphocyte infiltration.
• •Difference in the frequency of ATM variants, related to PPAR inhibitors.

     

Developments and Applications of Functional Protein Microarrays

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Highlights

• •Summarize the development of functional protein microarray.
• •Application of functional proteome microarray in basic research.
• •Application of functional proteome microarray in translational research.
• •Fabrication of functional membrane protein array using virion display method.

     

MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics

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Highlights

• •Highly parallelizable 4D feature detection in ion mobility enhanced shotgun proteomics.
• •Multidimensional non-linear mass, retention time and ion mobility recalibration.
• •Collision cross section aware matching between runs.
• •Label-free quantification of ion mobility MS data.

     

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.

     

Identification of a Multiplex Biomarker Panel for Hypertrophic Cardiomyopathy Using Quantitative Proteomics and Machine Learning

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Highlights

• •Quantitative proteomics and machine learning to study plasma biomarkers in HCM.
• •Six peptides are increased in plasma of LVH+ HCM compared to controls.
• •Peptide biomarkers correlate with imaging markers of phenotype severity.
• •Peptide biomarkers correlate with the estimated sudden cardiac death risk.

     

The Challenge of Classifying Metastatic Cell Properties by Molecular Profiling Exemplified with Cutaneous Melanoma Cells and Their Cerebral Metastasis from Patient Derived Mouse Xenografts

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Highlights

• •Comprehensive molecular profiling of cutaneous and cerebellar metastasis variants.
• •Identification of differentially regulated metastasis-associated molecules.
• •Evidence for individually distinct patterns of metastasis-associated molecules.
• •Highlighting the evident need for establishing meta-analyses strategies.

     

Global Proteome and Phosphoproteome Characterization of Sepsis-induced Kidney Injury

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Highlights

• •Cecal Ligation Puncture (CLP) mouse model to study sepsis-induced kidney disease.
• •Quantitative global proteome and phosphoproteome profiling of mouse kidneys.
• •Highly significant candidate markers for onset and progression of AKI to CKD.
• •Mechanistic insights into sepsis-associated kidney injuries.

     

Profiling Cell Signaling Networks at Single-cell Resolution

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Highlights

• •Signaling networks can be highly heterogeneous across cells in a tissue.
• •Various technologies allow analyzing signaling networks at single-cell resolution.
• •The advantages and limitations of each single-cell approach are summarized.
• •Confounding factors in single-cell signaling network analysis are discussed.

     

Glutathionylation Decreases Methyltransferase Activity of PRMT5 and Inhibits Cell Proliferation

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Highlights

• •PRMT5 glutathionylation is increased in aged mice or under oxidative stress.
• •Deglutathionylation of PRMT5 is catalyzed by glutaredoxin-1.
• •PRMT5 glutathionylation decreases its methyltransferase activity.
• •PRMT5 glutathionylation results in G2/M arrest and inhibits cell proliferation.

     

Next-generation Interactomics: Considerations for the Use of Co-elution to Measure Protein Interaction Networks

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Highlights

• •Co-elution stands out as a global interactome mapping method.
• •Benefits include all-to-all protein analysis and measurement of interactome perturbations.
• •Different separation, quantification and bioinformatic strategies are available.
• •Design considerations depend largely on system under study.

     

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.

     

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.