Efficient Identification of Murine M2 Macrophage Peptide Targeting Ligands by Phage Display and Next-Generation Sequencing

Bioconjugate Chemistry

Volumn 26, Issue 8, 2015, Pages 1811-1817

  Liu, Gary W ^a   Livesay, Brynn R ^a   Kacherovsky, Nataly A ^a   Cieslewicz, Maryelise ^a   Lutz, Emi ^a   Waalkes, Adam ^b   Jensen, Michael C ^a,c   Salipante, Stephen J ^b   Pun, Suzie H ^a  

^a University of Washington   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c SEATTLE CHILDREN S RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIGANDS; PEPTIDES; THROUGHPUT;

BINDING MOTIF; BINDING SEQUENCE; HIGH THROUGHPUT SCREENING; NEXT-GENERATION SEQUENCING; PARASITICS; PEPTIDE LIGAND; PHAGE-DISPLAY; SEQUENCE SPACE; TARGET BINDING; TARGETING LIGANDS;

MACROPHAGES;

M2 MACROPHAGE PEPTIDE; PEPTIDE; UNCLASSIFIED DRUG; LIGAND; PEPTIDE FRAGMENT; PEPTIDE LIBRARY;

ALGORITHM; AMINO ACID SEQUENCE; ANIMAL CELL; ARTICLE; MACROPHAGE; NEXT GENERATION SEQUENCING; NONHUMAN; PROTEIN BINDING; SANGER SEQUENCING; ANIMAL; BACTERIOPHAGE; CELL CULTURE; CHEMISTRY; CYTOLOGY; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; MOUSE; PEPTIDE LIBRARY; PROCEDURES;

MURINAE;

ALGORITHMS; ANIMALS; BACTERIOPHAGES; CELLS, CULTURED; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LIGANDS; MACROPHAGES; MICE; PEPTIDE FRAGMENTS; PEPTIDE LIBRARY;

EID: 84939629389     PISSN: 10431802     EISSN: 15204812     Source Type: Journal    
DOI: 10.1021/acs.bioconjchem.5b00344     Document Type: Article

References (22)

1. Gaertner, F., Kessler, H., Wester, H.-J., Schwaiger, M., and Beer, A. (2012) Radiolabelled RGD peptides for imaging and therapy Eur. J. Nucl. Med. Mol. Imaging 39, 126-138 10.1007/s00259-011-2028-1
2. Putzer, D., Kroiss, A., Waitz, D., Gabriel, M., Traub-Weidinger, T., Uprimny, C., von Guggenberg, E., Decristoforo, C., Warwitz, B., and Widmann, G. (2013) Somatostatin receptor PET in neuroendocrine tumours: 68Ga-DOTA0, Tyr3-octreotide versus 68Ga-DOTA0-lanreotide Eur. J. Nucl. Med. Mol. Imaging 40, 364-372 10.1007/s00259-012-2286-6
3. Vymazal, J., Spuentrup, E., Cardenas-Molina, G., Wiethoff, A. J., Hartmann, M. G., Caravan, P., and Parsons, E. C., Jr (2009) Thrombus imaging with fibrin-specific gadolinium-based MR contrast agent EP-2104R: results of a phase II clinical study of feasibility Invest. Radiol. 44, 697-704 10.1097/RLI.0b013e3181b092a7
4. Smith, G. P. (1985) Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface Science 228, 1315-1317 10.1126/science.4001944
5. Hammers, C. M. and Stanley, J. R. (2014) Antibody phage display: technique and applications J. Invest. Dermatol. 134, e17 10.1038/jid.2013.521
6. Dantas-Barbosa, C., de Macedo Brigido, M., and Maranhao, A. Q. (2012) Antibody phage display libraries: contributions to oncology Int. J. Mol. Sci. 13, 5420-5440 10.3390/ijms13055420
7. Matochko, W. L., Cory, Li. S., Tang, S. K., and Derda, R. (2014) Prospective identification of parasitic sequences in phage display screens Nucleic Acids Res. 42, 1784-1798 10.1093/nar/gkt1104
8. 't Hoen, P. A., Jirka, S. M., Ten Broeke, B. R., Schultes, E. A., Aguilera, B., Pang, K. H., Heemskerk, H., Aartsma-Rus, A., van Ommen, G. J., and den Dunnen, J. T. (2012) Phage display screening without repetitious selection rounds Anal. Biochem. 421, 622-631 10.1016/j.ab.2011.11.005
9. Ngubane, N. A., Gresh, L., Ioerger, T. R., Sacchettini, J. C., Zhang, Y. J., Rubin, E. J., Pym, A., and Khati, M. (2013) High-throughput sequencing enhanced phage display identifies peptides that bind mycobacteria PLoS One 8, e77844 10.1371/journal.pone.0077844
10. Rentero Rebollo, I., Sabisz, M., Baeriswyl, V., and Heinis, C. (2014) Identification of target-binding peptide motifs by high-throughput sequencing of phage-selected peptides Nucleic Acids Res. 42, e169 10.1093/nar/gku940
11. Cieslewicz, M., Tang, J., Yu, J. L., Cao, H., Zavaljevski, M., Motoyama, K., Lieber, A., Raines, E. W., and Pun, S. H. (2013) Targeted delivery of proapoptotic peptides to tumor-associated macrophages improves survival Proc. Natl. Acad. Sci. U. S. A. 110, 15919-15924 10.1073/pnas.1312197110
12. Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., and Soding, J. et al. 2014, Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega Mol. Syst. Biol. 7, 539 10.1038/msb.2011.75
13. Vodnik, M., Zager, U., Strukelj, B., and Lunder, M. (2011) Phage display: selecting straws instead of a needle from a haystack Molecules 16, 790-817 10.3390/molecules16010790
14. Bailey, T. L. and Elkan, C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28-36
15. Bailey, T. L., Williams, N., Misleh, C., and Li, W. W. (2006) MEME: discovering and analyzing DNA and protein sequence motifs Nucleic Acids Res. 34, W369-373 10.1093/nar/gkl198
16. Dias-Neto, E., Nunes, D. N., Giordano, R. J., Sun, J., Botz, G. H., Yang, K., Setubal, J. C., Pasqualini, R., and Arap, W. (2009) Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis PLoS One 4, e8338 10.1371/journal.pone.0008338
17. Lam, H. Y., Clark, M. J., Chen, R., Natsoulis, G., O'Huallachain, M., Dewey, F. E., Habegger, L., Ashley, E. A., Gerstein, M. B., and Butte, A. J. et al. 2012, Performance comparison of whole-genome sequencing platforms Nat. Biotechnol. 30, 78-82 10.1038/nbt.2065
18. Loman, N. J., Misra, R. V., Dallman, T. J., Constantinidou, C., Gharbia, S. E., Wain, J., and Pallen, M. J. (2012) Performance comparison of benchtop high-throughput sequencing platforms Nat. Biotechnol. 30, 434-439 10.1038/nbt.2198
19. Salipante, S. J., Kawashima, T., Rosenthal, C., Hoogestraat, D. R., Cummings, L. A., Sengupta, D. J., Harkins, T. T., Cookson, B. T., and Hoffman, N. G. (2014) Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling Appl. Environ. Microbiol. 80, 7583-7591 10.1128/AEM.02206-14
20. Huang, J., Ru, B., Zhu, P., Nie, F., Yang, J., Wang, X., Dai, P., Lin, H., Guo, F. B., and Rao, N. (2012) MimoDB 2.0: a mimotope database and beyond Nucleic Acids Res. 40, D271-277 10.1093/nar/gkr922
21. Huang, J., Ru, B., Li, S., Lin, H., and Guo, F. B. (2010) SAROTUP: scanner and reporter of target-unrelated peptides J. Biomed. Biotechnol. 2010, 1-7 10.1155/2010/101932
22. Duchrow, T., Shtatland, T., Guettler, D., Pivovarov, M., Kramer, S., and Weissleder, R. (2009) Enhancing navigation in biomedical databases by community voting and database-driven text classification BMC Bioinf. 10, 317 10.1186/1471-2105-10-317