Arap, W. et al. Steps toward mapping the human vasculature by phage display. Nat. Med. 8, 121-127

Department of Genito-Urinary Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA.
Nature Medicine (Impact Factor: 27.36). 03/2002; 8(2):121-7. DOI: 10.1038/nm0202-121
Source: PubMed


The molecular diversity of receptors in human blood vessels remains largely unexplored. We developed a selection method in which peptides that home to specific vascular beds are identified after administration of a peptide library. Here we report the first in vivo screening of a peptide library in a patient. We surveyed 47,160 motifs that localized to different organs. This large-scale screening indicates that the tissue distribution of circulating peptides is nonrandom. High-throughput analysis of the motifs revealed similarities to ligands for differentially expressed cell-surface proteins, and a candidate ligand-receptor pair was validated. These data represent a step toward the construction of a molecular map of human vasculature and may have broad implications for the development of targeted therapies.

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Available from: Ricardo J Giordano, Sep 30, 2015
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    • "Different vascular beds exhibit extensive internal regional variations in gene expression in vivo [5], [39], [40], and a variety of gene promoters have been described that can affect gene expression patterns in ECs [41]. For human von Willebrand factor (vWF), a DNA sequence between -843 and -620 is necessary for its expression in capillaries, whereas the first intron is required for its expression in large blood vessels of the heart and skeletal muscle as well as in capillaries [42], indicating that a combination of particular DNA modules regulates the vascular bed-specific expression of vWF. "
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    ABSTRACT: Vascular endothelial cells often change their phenotype to adapt to their local microenvironment. Here we report that the vascular endothelial adhesion molecule nepmucin/CD300LG, which is implicated in lymphocyte binding and transmigration, shows unique expression patterns in the microvascular endothelial cells of different tissues. Under physiological conditions, nepmucin/CD300LG was constitutively and selectively expressed at the luminal surface of the small arterioles, venules, and capillaries of most tissues, but it was only weakly expressed in the microvessels of the splenic red pulp and thymic medulla. Furthermore, it was barely detectable in immunologically privileged sites such as the brain, testis, and uterus. The nepmucin/CD300LG expression rapidly decreased in lymph nodes receiving acute inflammatory signals, and this loss was mediated at least in part by TNF-α. It was also down-regulated in tumors and tumor-draining lymph nodes, indicating that nepmucin/CD300LG expression is negatively regulated by locally produced signals under these circumstances. In contrast, nepmucin/CD300LG was induced in the high endothelial venule-like blood vessels of chronically inflamed pancreatic islets in an animal model of non-obese diabetes. Interestingly, the activated CD4(+) T cells infiltrating the inflamed pancreas expressed high levels of the nepmucin/CD300LG ligand(s), supporting the idea that nepmucin/CD300LG and its ligand interactions are locally involved in pathological T cell trafficking. Taken together, these observations indicate that the nepmucin/CD300LG expression in microvascular endothelial cells is influenced by factor(s) that are locally produced in tissues, and that its expression is closely correlated with the level of leukocyte infiltration in certain tissues.
    PLoS ONE 12/2013; 8(12):e83681. DOI:10.1371/journal.pone.0083681 · 3.23 Impact Factor
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    • "In standard phage display, the Pan operator is a complex product of all manipulation steps (binding, amplification, dilutions, etc.). If a screen uses no amplification and uses deep-sequencing [9, 16], or large-scale Sanger sequencing [36, 37] to analyze the enrichment, it might be possible to define the panning process as a simple product of two operators as follows: "
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    ABSTRACT: Next-generation sequencing techniques empower selection of ligands from phage-display libraries because they can detect low abundant clones and quantify changes in the copy numbers of clones without excessive selection rounds. Identification of errors in deep sequencing data is the most critical step in this process because these techniques have error rates >1%. Mechanisms that yield errors in Illumina and other techniques have been proposed, but no reports to date describe error analysis in phage libraries. Our paper focuses on error analysis of 7-mer peptide libraries sequenced by Illumina method. Low theoretical complexity of this phage library, as compared to complexity of long genetic reads and genomes, allowed us to describe this library using convenient linear vector and operator framework. We describe a phage library as N × 1 frequency vector n = ||ni||, where ni is the copy number of the ith sequence and N is the theoretical diversity, that is, the total number of all possible sequences. Any manipulation to the library is an operator acting on n. Selection, amplification, or sequencing could be described as a product of a N × N matrix and a stochastic sampling operator (Sa). The latter is a random diagonal matrix that describes sampling of a library. In this paper, we focus on the properties of Sa and use them to define the sequencing operator (Seq). Sequencing without any bias and errors is Seq = Sa IN, where IN is a N × N unity matrix. Any bias in sequencing changes IN to a nonunity matrix. We identified a diagonal censorship matrix (CEN), which describes elimination or statistically significant downsampling, of specific reads during the sequencing process.
    Computational and Mathematical Methods in Medicine 12/2013; 2013(4967):491612. DOI:10.1155/2013/491612 · 0.77 Impact Factor
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    • "Collapse of the naïve library to a collection of a few sequences indicates that selection narrowed onto clones that bind to a target (Figure 1A). While most screens exhibit convergence to one sequence motif, screens against the surfaces of cells or tissues (10–12), mixtures of antibodies (13–16) or other proteins, could converge on multiple binding epitopes. The screens against such ‘multisite targets’ could yield information about multiple ligands for multiple receptors on the cell (10,11). "
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    ABSTRACT: Phage display empowered the development of proteins with new function and ligands for clinically relevant targets. In this report, we use next-generation sequencing to analyze phage-displayed libraries and uncover a strong bias induced by amplification preferences of phage in bacteria. This bias favors fast-growing sequences that collectively constitute <0.01% of the available diversity. Specifically, a library of 10(9) random 7-mer peptides (Ph.D.-7) includes a few thousand sequences that grow quickly (the 'parasites'), which are the sequences that are typically identified in phage display screens published to date. A similar collapse was observed in other libraries. Using Illumina and Ion Torrent sequencing and multiple biological replicates of amplification of Ph.D.-7 library, we identified a focused population of 770 'parasites'. In all, 197 sequences from this population have been identified in literature reports that used Ph.D.-7 library. Many of these enriched sequences have confirmed function (e.g. target binding capacity). The bias in the literature, thus, can be viewed as a selection with two different selection pressures: (i) target-binding selection, and (ii) amplification-induced selection. Enrichment of parasitic sequences could be minimized if amplification bias is removed. Here, we demonstrate that emulsion amplification in libraries of ∼10(6) diverse clones prevents the biased selection of parasitic clones.
    Nucleic Acids Research 11/2013; 42(3). DOI:10.1093/nar/gkt1104 · 9.11 Impact Factor
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