Methods for the identification of vascular markers in health and disease: From the bench to the clinic

Several diseases are characterized by changes in the molecular composition of vascular structures, thus offering the opportunity to use specific ligands (e.g., monoclonal antibodies) for imaging and therapy application. This novel pharmaceutical strategy, often referred to as “vascular targeting”, promises to facilitate the discovery and development of selective biopharmaceuticals for the management of angiogenesis-related diseases. This article reviews novel biomedical applications based on vascular targeting strategies, as well as methodologies which have been used for the discovery of vascular markers of pathology.     

Chemical proteomic and bioinformatic strategies for the identification and quantification of vascular antigens in cancer

One avenue towards the development of more selective anti-cancer drugs consists in the targeted delivery of bioactive molecules to the tumor environment by means of binding molecules specific to tumor-associated markers. In this context, the targeted delivery of therapeutic agents to newly-formed blood vessels (“vascular targeting”) is particularly attractive, because of the dependence of tumors on new blood vessels to sustain growth and invasion, and because of the accessibility of neo-vascular structures for therapeutic agents injected intravenously. Ligand-based vascular targeting strategies crucially rely on good-quality vascular tumor markers. Here we describe a number of established technologies for the enrichment of accessible vascular proteins based on the isolation of glycoproteins, the in vivo coating of accessible cell surfaces with colloidal silica and the in vivo perfusion with reactive ester derivatives of biotin. Label-free as well as isotopic labeling based strategies for the subsequent MS-based protein quantification are outlined. Finally, bioinformatic workflows for protein quantification are depicted aiming at assisting in the evaluation of appropriate strategies for individual projects. This review gives an overview of current chemical proteomic strategies for the enrichment and quantification of the accessible vascular proteome and helps in selecting bioinformatic strategies for data analysis and validation.     

A comparison of different biotinylation reagents, tryptic digestion procedures, and mass spectrometric techniques for 2-D peptide mapping of membrane proteins

2-D peptide mapping is a novel technique for the relative quantification of membrane proteins (Scheurer S. et al., Proteomics 2005, in press). Using closely related metastatic and nonmetastatic teratocarcinoma cell lines as a model system, we have performed a comparative analysis of different biotinylation reagents, tryptic digestion procedures, and mass spectrometric techniques, with the aim to increase the number of proteins identified by 2-D peptide mapping. Our experience indicates that the LC-MALDI TOF/TOF technique is superior to LC-ESI MS/MS in terms of the number of proteins identified and confidence in protein identification. Furthermore, the best results were obtained by tryptic digestion of proteins eluted from a streptavidin column using a cleavable biotin derivative.     

Recent advances in proteomically subtyping pancreatic ductal adenocarcinomas and their potential clinical impact

Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with a median overall survival of 6 months. Late diagnosis due to the absence of specific symptoms during disease development, in addition to extensive metastatic potential and resistance to chemotherapy and radiotherapy, are the most important reasons for short survival. Research efforts have therefore been focused on the development of early disease detection. However, the only US FDA-approved clinical biomarker, CA19–9, is considered inapplicable for screening and/or early detection of PDAC. The following editorial provides the reader with a short introduction to the topic of PDAC and gives focus to the current state of proteomic research in the field of PDAC biomarker discovery. This editorial also highlights the efforts made to subdivide this tumor entity and the potential clinical impact of patient stratification. Finally, the author provides opinions on the impact of proteomics to PDAC subtype stratification over the next 5 years.     

MALDI‐TOF and nESI Orbitrap MS/MS identify orthogonal parts of the phosphoproteome

Phosphorylation is a reversible posttranslational protein modification which plays a pivotal role in intracellular signaling. Despite extensive efforts, phosphorylation site mapping of proteomes is still incomplete motivating the exploration of alternative methods that complement existing workflows. In this study, we compared tandem mass spectrometry (MS/MS) on matrix assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) and nano‐electrospray ionization (nESI) Orbitrap instruments with respect to their ability to identify phosphopeptides from complex proteome digests. Phosphopeptides were enriched from tryptic digests of cell lines using Fe‐IMAC column chromatography and subjected to LC‐MS/MS analysis. We found that the two analytical workflows exhibited considerable orthogonality. For instance, MALDI‐TOF MS/MS favored the identification of phosphopeptides encompassing clear motif signatures for acidic residue directed kinases. The extent of orthogonality of the two LC‐MS/MS systems was comparable to that of using alternative proteases such as Asp‐N, Arg‐C, chymotrypsin, Glu‐C and Lys‐C on just one LC‐MS/MS instrument. Notably, MALDI‐TOF MS/MS identified an unexpectedly high number and percentage of phosphotyrosine sites (～20% of all sites), possibly as a direct consequence of more efficient ionization. The data clearly show that LC‐MALDI MS/MS can be a useful complement to LC‐nESI MS/MS for phosphoproteome mapping and particularly so for acidic and phosphotyrosine containing peptides.     

Male vocalization and female choice in the hybridogenetic Rana lessonae/Rana esculenta complex

In many species, females can improve their fitness by preferring particular males over others. In Palaearctic water frogs of the Rana lessonae/R. esculenta complex the consequences of such mate choice are particularly pronounced. To produce viable offspring, the hybrid R. esculenta (genotype RL) must mate with the parental species R. lessonae (LL); but R. lessonae should avoid mating with R. esculenta, because the resulting hybrid offspring will eliminate the L genome from the germline (hybridogenesis). Hence, there exists a conflict between the sexual parasite (RL) and its sexual host (LL) over the best mating partner. Previous studies have shown a preference for LL males in LL and RL females; but they have also shown that females cannot usually realize their choice when in close proximity to males, because the males forcefully and indiscriminately amplex them. We tested whether females use male vocalizations as a long-distance signal to increase their chances of mating with the preferred LL males. We exposed female R. lessonae and R. esculenta to playbacks of single LL and RL mating calls (experiment 1) and to choruses with a 3:1 excess of LL and RL calls, respectively (experiment 2). In experiment 1, both female types were attracted more by the LL than by the RL calls. In experiment 2, no discrimination between LL- and RL-dominated choruses was observed. The results suggest that females do not use distant male vocalization to approach preferentially ponds or arenas within a pond that hold an excess of LL males. But once they have arrived in a chorus, mating calls from nearby males can direct them to the preferred LL mates. We discuss possible reasons for the failure to discriminate between choruses and the chances for successful choice between individuals within choruses. Copyright 2000 The Association for the Study of Animal Behaviour.     

The accessible cerebral vascular proteome in a mouse model of cerebral β-amyloidosis

Assessing protein changes in the cerebral vasculature of brain disorders may increase our understanding of disease pathogenesis and facilitate diagnostic and therapeutic intervention. By combining perfusion of mice with a charged reactive biotin derivative and subsequent quantification of the biotinylated proteins, the proteome accessible from the vasculature in an APPPS1 transgenic mouse model of cerebral β-amyloidosis was identified and compared to that in non-transgenic control mice. Our results provide proof-of-concept of this technology for the identification of new targets for antibody-based therapy or pharmacodelivery, and for neuroimaging in neurodegenerative diseases.     

A chemical proteomics approach for the identification of accessible antigens expressed in human kidney cancer

A promising avenue toward the development of more selective anticancer drugs consists in the targeted delivery of bioactive molecules to the tumor environment by means of binding molecules specific to tumor-associated markers. We have used a chemical proteomics approach based on the ex vivo perfusion and biotinylation of accessible structures within surgically resected human kidneys with tumor to gain information about accessible and abundant antigens that are overexpressed in human cancer. This procedure led to the selective labeling with biotin of vascular structures. Biotinylated proteins were purified on streptavidin resin and identified using mass spectrometric methodologies, revealing 637 proteins, 184 of which were only found in tumor specimens and 223 of which were only found in portions of normal kidneys. Immunohistochemical and PCR analysis confirmed that several of the putative cancer antigens identified in this study are indeed preferentially expressed in tumors. In conclusion, we have developed a methodology that allows the identification of accessible biomarkers in human tissues. The tumor-associated antigens identified in this study may be suitable targets for antibody-based anticancer therapies. The experimental approach described here should be applicable to other surgical specimens and to other pathologies as well as to the study of basic physiological and immunological processes.     

DeepQuanTR: MALDI‐MS‐based label‐free quantification of proteins in complex biological samples

The quantification of changes in protein abundance in complex biological specimens is essential for proteomic studies in basic and applied research. Here we report on the development and validation of the DeepQuanTR software for identification and quantification of differentially expressed proteins using LC‐MALDI‐MS. Following enzymatic digestion, HPLC peptide separation and normalization of MALDI‐MS signal intensities to the ones of internal standards, the software extracts peptide features, adjusts differences in HPLC retention times and performs a relative quantification of features. The annotation of multiple peptides to the corresponding parent protein allows the definition of a Protein Quant Value, which is related to protein abundance and which allows inter‐sample comparisons. The performance of DeepQuanTR was evaluated by analyzing 24 samples deriving from human serum spiked with different amounts of four proteins and eight complex samples of vascular proteins, derived from surgically resected human kidneys with cancer following ex vivo perfusion with a reactive ester biotin derivative. The identification and experimental validation of proteins, which were differentially regulated in cancerous lesions as compared with normal kidney, was used to demonstrate the power of DeepQuanTR. This software, which can easily be used with established proteomic methodologies, facilitates the relative quantification of proteins derived from a wide variety of different samples.     

Stored-product insects associated with a retail pet store chain in Kansas

The types and numbers of insect species associated with eight Kansas retail stores belonging to a pet store chain were surveyed during February to August 2001. Insects were monitored at 1-3-wk intervals using food- and pheromone-baited pitfall traps for beetles and pheromone-baited sticky traps for moths. Thirty traps of each type were placed within a store. Thirty insect species belonging to 20 families in four orders were recorded from the eight stores. The weevils, Sitophilus spp.; Indianmeal moth, Plodia interpunctella (Hübner); and merchant grain beetle, Oryzaephilus mercator (Fauvel), were the most common and abundant species in all stores, whereas the red-legged ham beetle, Necrobia rufipes (Degeer), and red flour beetle, Tribolium castaneum (Herbst), were abundant only in one store. The numbers of each insect species captured varied from store to store. In each of the stores, a total of 12-19 stored-product species were captured in traps, and seven of the eight stores had relatively high species diversity. With the exception of one store, the different types of insect species found among the remaining seven stores were essentially similar. The mean density of insects in infested bulk-stored and bagged pet food products removed from a store ranged from 65 to 656 adults/kg. The types and numbers of insect species captured in traps indicated that infestations were well established in the surveyed stores. Early detection and management of these infestations is critical for maintaining quality and integrity of food products sold in the pet stores.