Establishment of a PF2D-MS/MS platform for rapid profiling and semiquantitative analysis of membrane protein biomarkers

Identification of a Novel ITGαvβ6-Binding Peptide Using Protein Separation and Phage Display

Purpose: Targeted therapies are regarded as promising approaches to increase 5-year survival rate of head and neck squamous cell carcinoma (HNSCC) patients.Experimental design: For the selection of carcinoma-specific peptides membrane proteome of HNO97 tumor cells fractionated by the ProteomeLab PF2D system and corresponding HNO97 cells were deployed for an alternating biopanning using a sunflower trypsin inhibitor1-based phage display (SFTI8Ph) library. Stability, binding properties and affinity of novel candidates were assessed in vitro using radio-HPLC, binding experiments and surface plasmon resonance assay (SPR), respectively. Subsequently, the affinity of the peptide was verified in situ by using peptide histochemistry, in vitro using flow cytometry, and in vivo by positron emissions tomography (PET/CT).Results: We identified a novel ITGα_vβ₆ binding peptide (SFITGv6) containing the amino acid sequence FRGDLMQL. SFITGv6 provides stability over a period of 24 hours and demonstrates high affinity (K_D = 14.8 nmol/L) for ITGα_vβ₆ In HNO97 cells, a maximal uptake and internalization of up to 37.3% and 37.5%, respectively, was measured. Small-animal PET imaging and biodistribution studies of HNO97 xenografted Balb/c nu/nu mice showed tumor-specific accumulation of ⁶⁸Ga- and ¹⁷⁷Lu-labeled DOTA-SFITGv6, respectively, 30 to 60 minutes after injection. Moreover, peptide histochemistry revealed a strong and homogenous binding of biotin-labeled SFITGv6 to HNSCC tumors and breast- and lung cancer-derived brain metastases. Finally, first PET/CT scans of HNSCC and NSCLC patients displayed SFITGv6 accumulation specifically in tumors, but not in inflammatory lesions.Conclusions: Thus, SFITGv6 represents a novel powerful tracer for imaging and possibly for endoradiotherapy of ITGα_vβ₆-positive carcinoma. Clin Cancer Res; 23(15); 4170-80. ©2017 AACR.

Transition from identity to bioactivity-guided proteomics for biomarker discovery with focus on the PF2D platform

Proteomic strategies provide a valuable tool kit to identify proteins involved in diseases. With recent progress in MS technology, high throughput proteomics has accelerated protein identification for potential biomarkers. Numerous biomarker candidates have been identified in several diseases, and many are common among pathologies. An overall strategy that could complement and strengthen the search for biomarkers is combining protein identity with biological outcomes. This review describes an emerging framework of bridging bioactivity to protein identity, exploring the possibility that some biomarkers will have a mechanistic role in the disease process. A review of pulmonary, cardiovascular, and CNS biomarkers will be discussed to demonstrate the utility of combining bioactivity with identification as a means to not only find meaningful biomarkers, but also to uncover functional mediators of disease.

NSBP-1 mediates the effects of cholesterol on insulin/IGF-1 signaling in Caenorhabditis elegans

Nematode sterol-binding protein 1 (NSBP-1) is a homolog of nucleosome assembly protein 1 in mammals that is expressed widely in Caenorhabditis elegans. NSBP-1 mutants are biologically lethal, demonstrating the significance of the gene in growth and development. We investigated how cholesterol influences the insulin signaling pathway through this novel sterol-binding protein in C. elegans. Here we report that NSBP-1 influences many biological processes mediated by insulin signaling, such as longevity, dauer formation, fat storage, and resistance to oxidative stress. We found that NSBP-1 is phosphorylated by AKT-1 downstream of insulin signaling. In the absence of insulin signaling, NSBP-1 is translocated to the nucleus and binds to DAF-16, a FOXO transcription factor, in a cholesterol-dependent manner. Moreover, NSBP-1 and DAF-16 regulate a common set of genes that can directly modulate fat storage, longevity, and resistance to stress. Together, our results present a new steroid-binding molecule that can connect sterol signaling to insulin signaling through direct interaction with FOXO.

GenomewidePDB, a proteomic database exploring the comprehensive protein parts list and transcriptome landscape in human chromosomes

In an effort to map the human proteome, the Chromosome-centric Human Proteome Project (C-HPP) was recently initiated. As a member of the international consortium working on this project, our laboratory developed a gene-centric proteomic database called GenomewidePDB, which integrates proteomic data for proteins encoded by chromosomes with transcriptomic data and other information from public databases. As an example case, we chose chromosome 13, which is the largest acrocentric human chromosome with the lowest gene density and contains 326 predicted proteins. All proteins stored in GenomewidePDB are linked to other resources, including neXtProt and Ensembl for protein and gene information, respectively. The Global Proteome Machine database (GPMdb) and the PeptideAtlas are also accessed for observed mass spectrometry (MS) information, while Human Protein Atlas is used for information regarding antibody availability and tissue expression, respectively. Gene ontology disease information is also included. As a pilot work, we constructed this GenomewidePDB with the identified 3615 proteins including 53 chromosome 13-origin proteins that are present in normal human placenta tissue. Thus, developing a comprehensive database containing actual experimental proteomics data will provide a valuable resource for cross chromosomal comparison in the C-HPP community.

[Current methods of cytochrome p450 analysis]

Current review describes recent approaches of cytochrome P450 concentration and activity evaluation. Special attention paid to modem methods of proteomic analysis such as electrophoresis and chromato-mass-spectrometry. Methods of targeted proteomic applicable for quantitative and qualitative study of P450s in biological samples as well as methods for the enzyme activity measurements are reviewed. Finally, data on correlation between certain P450 isoform content and its specific enzymatic activities were described and discussed in the review.

Improved recovery and identification of membrane proteins from rat hepatic cells using a centrifugal proteomic reactor

Despite their importance in many biological processes, membrane proteins are underrepresented in proteomic analysis because of their poor solubility (hydrophobicity) and often low abundance. We describe a novel approach for the identification of plasma membrane proteins and intracellular microsomal proteins that combines membrane fractionation, a centrifugal proteomic reactor for streamlined protein extraction, protein digestion and fractionation by centrifugation, and high performance liquid chromatography-electrospray ionization-tandem MS. The performance of this approach was illustrated for the study of the proteome of ER and Golgi microsomal membranes in rat hepatic cells. The centrifugal proteomic reactor identified 945 plasma membrane proteins and 955 microsomal membrane proteins, of which 63 and 47% were predicted as bona fide membrane proteins, respectively. Among these proteins, >800 proteins were undetectable by the conventional in-gel digestion approach. The majority of the membrane proteins only identified by the centrifugal proteomic reactor were proteins with ≥ 2 transmembrane segments or proteins with high molecular mass (e.g. >150 kDa) and hydrophobicity. The improved proteomic reactor allowed the detection of a group of endocytic and/or signaling receptor proteins on the plasma membrane, as well as apolipoproteins and glycerolipid synthesis enzymes that play a role in the assembly and secretion of apolipoprotein B100-containing very low density lipoproteins. Thus, the centrifugal proteomic reactor offers a new analytical tool for structure and function studies of membrane proteins involved in lipid and lipoprotein metabolism.

A new versatile peptide-based size exclusion chromatography platform for global profiling and quantitation of candidate biomarkers in hepatocellular carcinoma specimens

Disease biomarkers are predicted to be in low abundance; thus, the most crucial step of biomarker discovery is the efficient fractionation of clinical samples into protein sets that define disease stages and/or predict disease development. For this purpose, we developed a new platform that uses peptide-based size exclusion chromatography (pep-SEC) to quantify disease biomarker candidates. This new platform has many advantages over previously described biomarker profiling platforms, including short run time, high resolution, and good reproducibility, which make it suitable for large-scale analysis. We combined this platform with isotope labeling and label-free methods to identify and quantitate differentially expressed proteins in hepatocellular carcinoma (HCC) tissues. When we combined pep-SEC with a gas phase fractionation method, which broadens precursor ion selection, the protein coverage was significantly increased, which is critical for the global profiling of HCC specimens. Furthermore, pep-SEC-LC-MS/MS analysis enhanced the detection of low-abundance proteins (e.g. insulin receptor substrate 2 and carboxylesterase 1) and glycopeptides in HCC plasma. Thus, our pep-SEC platform is an efficient and versatile pre-fractionation system for the large-scale profiling and quantitation of candidate biomarkers in complex disease proteomes.

Visual indicator for surfactant abundance in MS-based membrane and general proteomics applications

The existence of surfactants in proteomics samples can severely reduce enzymatic digestion efficiency, liquid chromatography (LC) separation efficiency, column lifetime, and mass spectrometry (MS) sensitivity. Although various techniques are able to remove surfactants, surfactants may occasionally be retained in samples due to variations in sample preparation method or personal skill. Evaluation of surfactant residue in a sample, however, usually requires an additional instrument and is time-consuming. In this study, a simple and rapid visual indicator for surfactant abundance (VISA) was developed. With the detection of a visible surfactant pellet in the solution, this assay was able to detect surfactant residue in aqueous solutions within 5 min. Without the need of additional equipment such as a mass spectrometer, every user can perform a quick test on their bench before sending the sample to the MS facility. The detection limit for the commonly used surfactants, Triton X-114 and SDS, was about 0.0005% and 0.0002%, respectively. The VISA was successfully applied to evaluate the efficiency of removal of surfactants in Triton X-114 extracted membrane proteins using tube-gel. With the combination of Triton X-114 extraction and tube-gel protocol, a study of spermatozoa membrane proteome identified about 252 proteins of which about 67.5% were classified as membrane proteins. The coexistence of protein and surfactant did not affect the VISA sensitivity, suggesting that this indicator is suitable for proteomics applications. The VISA also has potential for the detection of other surfactants and can be applied to other surfactant removing protocols.

Rapid T cell-based identification of human tumor tissue antigens by automated two-dimensional protein fractionation

Identifying the antigens that have the potential to trigger endogenous antitumor responses in an individual cancer patient is likely to enhance the efficacy of cancer immunotherapy, but current methodologies do not efficiently identify such antigens. This study describes what we believe to be a new method of comprehensively identifying candidate tissue antigens that spontaneously cause T cell responses in disease situations. We used the newly developed automated, two-dimensional chromatography system PF2D to fractionate the proteome of human tumor tissues and tested protein fractions for recognition by preexisting tumor-specific CD4+ Th cells and CTLs. Applying this method using mice transgenic for a TCR that recognizes an OVA peptide presented by MHC class I, we demonstrated efficient separation, processing, and cross-presentation to CD8+ T cells by DCs of OVA expressed by the OVA-transfected mouse lymphoma RMA-OVA. Applying this method to human tumor tissues, we identified MUC1 and EGFR as tumor-associated antigens selectively recognized by T cells in patients with head and neck cancer. Finally, in an exemplary patient with a malignant brain tumor, we detected CD4+ and CD8+ T cell responses against two novel antigens, transthyretin and calgranulin B/S100A9, which were expressed in tumor and endothelial cells. The immunogenicity of these antigens was confirmed in 4 of 10 other brain tumor patients. This fast and inexpensive method therefore appears suitable for identifying candidate T cell antigens in various disease situations, such as autoimmune and malignant diseases, without being restricted to expression by a certain cell type or HLA allele.

Application of slicing of one-dimensional gels with subsequent slice-by-slice mass spectrometry for the proteomic profiling of human liver cytochromes P450

Sequential thin slicing of one-dimensional electrophoresis gels followed by slice-by-slice mass spectrometry to allow protein identification was used to produce a proteomic map for cytochromes P450. Parallel MALDI-TOF-MS and LC-MS/MS analyses were performed. Combination of the two MS methods increased the quality of protein identification. We have proposed an efficient approach to obtain a comprehensive profile of drug-metabolizing enzymes in the liver that can be used to differentiate between polymorphic variants of cytochromes P450.

Regulation of Dauer formation by O-GlcNAcylation in Caenorhabditis elegans

Modification of proteins at serine or threonine residues with N-acetylglucosamine, termed O-GlcNAcylation, plays an important role in most eukaryotic cells. To understand the molecular mechanism by which O-GlcNAcylation regulates the entry of Caenorhabditis elegans into the non-aging dauer state, we performed proteomic studies using two mutant strains: the O-GlcNAc transferase-deficient ogt-1(ok430) strain and the O-GlcNAcase-defective oga-1(ok1207) strain. In the presence of the dauer pheromone daumone, ogt-1 showed suppression of dauer formation, whereas oga-1 exhibited enhancement of dauer formation. Consistent with these findings, treatment of wild-type N2 worms with low concentrations of daumone and the O-GlcNAcase inhibitor O-(2-acetamido-2-deoxy-d-glucopyranosylidene)amino-N-phenylcarbamate (PUGNAc) enhanced dauer formation, which was dependent on intact O-GlcNAcylation metabolism. We also found that the treatment of daumone enhanced O-GlcNAcylation in vivo. Seven proteins, identified by coupled two-dimensional electrophoresis/liquid chromatography-mass spectroscopy (LC-MS) analysis, were differentially expressed in oga-1(ok1207) worms compared with wild-type N2 worms. The identities of these proteins suggest that O- GlcNAcylation influences stress resistance, protein folding, and mitochondrial function. Using O-GlcNAc labeling with fluorescent dye combined with two-dimensional electrophoresis/LC-MS analysis, we also identified five proteins that were differentially O-GlcNAcylated during dauer formation. Analysis of these candidate O-GlcNAcylated proteins suggests that O-GlcNAcylation may regulate cytoskeleton modifications and protein turnover during dauer formation.

The AOHUPO Membrane Proteomics Initiative, Fourth Workshop 22 June 2008, Cairns, Australia

The Fourth Asia Oceania Human Proteome Organisation Membrane Proteomics Initiative (AOHUPO MPI) Workshop took place on 22 June 2008 in Cairns, Australia, with approximately 90 attendees from academia and industry. Participants from ten of the seventeen collaborating centres presented workshop papers. This was part of the pre-conference programme of the Joint Fourth Asian Oceania Human Proteome Organisation Conference and the Second Pacific Rim International Conference on Protein Structure.

Application of a peptide-based PF2D platform for quantitative proteomics in disease biomarker discovery

A peptide-based 2-D liquid phase fractionation (PF2D) system was used in a quantitative proteomic analysis of hepatocellular carcinoma. 2-D liquid maps of peptide specimens showed better resolution than those of proteins, leading to the identification of differentially expressed proteins. Peptide-based PF2D gave well-matched theoretical and experimental pI values and was proven to be a very efficient and versatile analytical tool for both large-scale profiling and quantification of phosphoproteins in disease biomarker discovery.