Prospective identification of parasitic sequences in phage display screens

Nucleic Acids Research

Volumn 42, Issue 3, 2014, Pages 1784-1798

  Matochko, Wadim L ^a   Cory Li, S ^b   Tang, Sindy K Y ^c   Derda, Ratmir ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c Stanford University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE;

AMINO ACID SEQUENCE; ANALYZER; ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; GENE AMPLIFICATION; GROWTH RATE; MOLECULAR CLONING; NONHUMAN; PARASITE; PARASITE DEVELOPMENT; PEPTIDE LIBRARY; PHAGE DISPLAY; PRIORITY JOURNAL; PROTEIN BINDING;

CELL SURFACE DISPLAY TECHNIQUES; DATA INTERPRETATION, STATISTICAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; PEPTIDE LIBRARY; SEQUENCE ANALYSIS, DNA;

EID: 84896691914     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1104     Document Type: Article

References (74)

1. Nelson, A.L., Dhimolea, E. and Reichert, J.M. (2010) Development trends for human monoclonal antibody therapeutics. Nat. Rev. Drug Discov., 9, 767-774.
2. Rothe, A., Hosse, R.J. and Power, B.E. (2006) In vitro display technologies reveal novel biopharmaceutics. FASEB J., 20, 1599-1610.
3. Mannocci, L., Leimbacher, M., Wichert, M., Scheuermann, J. and Neri, D. (2011) 20 years of DNA-encoded chemical libraries. Chem. Commun., 47, 12747-12753.
4. Menendez, A. and Scott, J.K. (2005) The nature of target-unrelated peptides recovered in the screening of phage-displayed random peptide libraries with antibodies. Anal. Biochem., 336, 145-157.
5. Kanan, M.W., Rozenman, M.M., Sakurai, K., Snyder, T.M. and Liu, D.R. (2004) Reaction discovery enabled by DNA-templated synthesis and in vitro selection. Nature, 431, 545-549.
6. Scott, J.K. and Smith, G.P. (1990) Searching for peptide ligands with an epitope library. Science, 249, 386-390.
7. Smith, G.P. and Petrenko, V.A. (1997) Phage display. Chem. Rev., 97, 391-410.
8. Ellington, A.D. and Szostak, J.W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature, 346, 818-822.
9. Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage-T4 DNA-polymerase. Science, 249, 505-510.
10. Arap, W., Kolonin, M.G., Trepel, M., Lahdenranta, J., Cardo-Vila, M., Giordano, R.J., Mintz, P.J., Ardelt, P.U., Yao, V.J., Vidal, C.I. et al. (2002) Steps toward mapping the human vasculature by phage display. Nat. Med., 8, 121-127.
11. Kolonin, M.G., Sun, J., Do, K.A., Vidal, C.I., Ji, Y., Baggerly, K.A., Pasqualini, R. and Arap, W. (2006) Synchronous selection of homing peptides for multiple tissues by in vivo phage display. FASEB J., 20, 979-981.
12. Derda, R., Musah, S., Orner, B.P., Klim, J.R., Li, L.Y. and Kiessling, L.L. (2010) High-throughput discovery of synthetic surfaces that support proliferation of pluripotent cells. J. Am. Chem. Soc., 132, 1289-1295.
13. Folgori, A., Tafi, R., Meola, A., Felici, F., Galfre, G., Cortese, R., Monaci, P. and Nicosia, A. (1994) A general strategy to identify mimotopes of pathological antigens using only random peptide libraries and human sera. EMBO J., 13, 2236-2243.
14. Prezzi, C., Nuzzo, M., Meola, A., Delmastro, P., Galfre, G., Cortese, R., Nicosia, A. and Monaci, P. (1996) Selection of antigenic and immunogenic mimics of hepatitis C virus using sera from patients. J. Immunol., 156, 4504-4513.
15. Irving, M.B., Pan, O. and Scott, J.K. (2001) Random-peptide libraries and antigen-fragment libraries for epitope mapping and the development of vaccines and diagnostics. Curr. Opin. Chem. Biol., 5, 314-324.
16. Fierabracci, A. (2009) Unravelling autoimmune pathogenesis by screening random peptide libraries with human sera. Immunol. Lett., 124, 35-43.
17. Ravn, U., Gueneau, F., Baerlocher, L., Osteras, M., Desmurs, M., Malinge, P., Magistrelli, G., Farinelli, L., Kosco-Vilbois, M.H. and Fischer, N. (2010) By-passing in vitro screening-next generation sequencing technologies applied to antibody display and in silico candidate selection. Nucleic Acids Res., 38, e193.
18. 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) Nextgeneration phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis. PLoS One, 4, e8338.
19. 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.
20. Zhang, H., Torkamani, A., Jones, T.M., Ruiz, D.I., Pons, J. and Lerner, R.A. (2011) Phenotype-information-phenotype cycle for deconvolution of combinatorial antibody libraries selected against complex systems. Proc. Natl Acad. Sci. USA., 108, 13456-13461.
21. Matochko, W.L., Chu, K., Jin, B., Lee, S.W., Whitesides, G.M. and Derda, R. (2012) Deep sequencing analysis of phage libraries using Illumina platform. Methods, 58, 47-55.
22. Rodi, D.J., Soares, A.S. and Makowski, L. (2002) Quantitative assessment of peptide sequence diversity in M13 combinatorial peptide phage display libraries. J. Mol. Biol., 322, 1039-1052.
23. Derda, R., Tang, S.K., Li, S.C., Ng, S., Matochko, W. and Jafari, M.R. (2011) Diversity of phage-displayed libraries of peptides during panning and amplification. Molecules, 16, 1776-1803.
24. Peters, E.A., Schatz, P.J., Johnson, S.S. and Dower, W.J. (1994) Membrane insertion defects caused by positive charges in the early mature region of protein-Piii of filamentous phage-Fd can be corrected Prla suppressors. J. Bacteriol., 176, 4296-4305.
25. Cwirla, S.E., Peters, E.A., Barrett, R.W. and Dower, W.J. (1990) Peptides on phage: a vast library of peptides for identifying ligands. Proc. Natl Acad. Sci. USA, 87, 6378-6382.
26. Devlin, J.J., Panganiban, L.C. and Devlin, P.E. (1990) Random peptide libraries: a source of specific protein-binding molecules. Science, 249, 404-406.
27. Iannolo, G., Minenkova, O., Petruzzelli, R. and Cesareni, G. (1995) Modifying filamentous phage capsid: limits in the size of the major capsid protein. J. Mol. Biol., 248, 835-844.
28. Li, Z.P., Koch, H. and Dubel, S. (2003) Mutations in the N-terminus of the major coat protein (pVIII, gp8) of filamentous bacteriophage affect infectivity. J. Mol. Microbiol. Biotechnol., 6, 57-66.
29. Malik, P., Terry, T.D., Bellintani, F. and Perham, R.N. (1998) Factors limiting display of foreign peptides on the major coat protein of filamentous bacteriophage capsids and a potential role for leader peptidase. FEBS Lett., 436, 263-266.
30. Kuzmicheva, G.A., Jayanna, P.K., Sorokulova, I.B. and Petrenko, V.A. (2009) Diversity and censoring of landscape phage libraries. Protein Eng. Des. Sel., 22, 9-18.
31. Malik, P., Tarry, T.D., Gowda, L.R., Langara, A., Petukhov, S.A., Symmons, M.F., Welsh, L.C., Marvin, D.A. and Perham, R.N. (1996) Role of capsid structure and membrane protein processing in determining the size and copy number of peptides displayed on the major coat protein of filamentous bacteriophage. J. Mol. Biol., 260, 9-21.
32. Makowski, L. and Soares, A. (2003) Estimating the diversity of peptide populations from limited sequence data. Bioinformatics, 19, 483-489.
33. Mandava, S., Makowski, L., Devarapalli, S., Uzubell, J. and Rodi, D.J. (2004) RELIC: a bioinformatics server for combinatorial peptide analysis and identification of protein-ligand interaction sites. Proteomics, 4, 1439-1460.
34. Steiner, D., Forrer, P., Stumpp, M.T. and Pluckthun, A. (2006) Signal sequences directing cotranslational translocation expand the range of proteins amenable to phage display. Nat. Biotechnol., 24, 823-831.
35. Wilson, D.R. and Finlay, B.B. (1998) Phage display: applications, innovations, and issues in phage and host biology. Can. J. Microbiol., 44, 313-329.
36. Thomas, W.D., Golomb, M. and Smith, G.P. (2010) Corruption of phage display libraries by target-unrelated clones: diagnosis and countermeasures. Anal. Biochem., 407, 237-240.
37. Brammer, L.A., Bolduc, B., Kass, J.L., Felice, K.M., Noren, C.J. and Hall, M.F. (2008) A target-unrelated peptide in an M13 phage display library traced to an advantageous mutation in the gene II ribosome-binding site. Anal. Biochem., 373, 88-98.
38. Matochko, W.L., Ng, S., Jafari, M.R., Romaniuk, J., Tang, S.K. and Derda, R. (2012) Uniform amplification of phage display libraries in monodisperse emulsions. Methods, 58, 18-27.
39. Derda, R., Tang, S.K. and Whitesides, G.M. (2010) Uniform amplification of phage with different growth characteristics in individual compartments consisting of monodisperse droplets. Angew. Chem. Int. Ed., 49, 5301-5304.
40. Ryvkin, A., Ashkenazy, H., Smelyanski, L., Kaplan, G., Penn, O., Weiss-Ottolenghi, Y., Privman, E., Ngam, P.B., Woodward, J.E., May, G.D. et al. (2012) Deep panning: steps towards probing the IgOme. PLoS One, 7, e41469.
41. McLaughlin, M.E. and Sidhu, S.S. (2013) Methods in Protein Design. Academic Press, Vol. 523. pp. 327-349.
42. Syropoulos, A. (2001) Multiset Processing: Mathematical, Computer Science, and Molecular Computing Points of View, Vol. 2235. pp. 347-358.
43. Ru, B., Huang, J., Dai, P., Li, S., Xia, Z., Ding, H., Lin, H., Guo, F.- B. and Wang, X. (2010) MimoDB: a new repository for mimotope data derived from phage display technology. Molecules, 15, 8279-8288.
44. Marioni, J.C., Mason, C.E., Mane, S.M., Stephens, M. and Gilad, Y. (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res., 18, 1509-1517.
45. Balwierz, P.J., Carninci, P., Daub, C.O., Kawai, J., Hayashizaki, Y., Van Belle, W., Beisel, C. and van Nimwegen, E. (2009) Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biol., 10, R79.
46. Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Methodol., 57, 289-300.
47. Robinson, M.D. and Oshlack, A. (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol., 11, R25.
48. Robinson, M.D. and Smyth, G.K. (2007) Moderated statistical tests for assessing differences in tag abundance. Bioinformatics, 23, 2881-2887.
49. Robinson, M.D. and Smyth, G.K. (2008) Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics, 9, 321-332.
50. Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R106.
51. 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-D277.
52. Li, M., Duc, A.-C.E., Klosi, E., Pattabiraman, S., Spaller, M.R. and Chow, C.S. (2009) Selection of peptides that target the aminoacyltRNA site of bacterial 16S ribosomal RNA. Biochemistry, 48, 8299-8311.
53. Dintilhac, A. and Bernues, J. (2002) HMGB1 interacts with many apparently unrelated proteins by recognizing short amino acid sequences. J. Biol. Chem., 277, 7021-7028.
54. Denby, L., Work, L.M., Von Seggern, D.J., Wu, E., McVey, J.H., Nicklin, S.A. and Baker, A.H. (2007) Development of renaltargeted vectors through combined in vivo phage display and capsid engineering of adenoviral fibers from serotype 19p. Mol. Ther., 15, 1647-1654.
55. Souto-Carneiro, M.M., Burkhardt, H., Muller, E.C., Hermann, R., Otto, A., Kraetsch, H.G., Sack, U., Konig, A., Heinegard, D., Muller-Hermelink, H.K. et al. (2001) Human monoclonal rheumatoid synovial B lymphocyte hybridoma with a new disease-related specificity for cartilage oligomeric matrix protein. J. Immunol., 166, 4202-4208.
56. Shin, J.S., Lin, J.S., Anderson, P.W., Insel, R.A. and Nahm, M.H. (2001) Monoclonal antibodies specific for Neisseria meningitidis group B polysaccharide and their peptide mimotopes. Infect. Immun., 69, 3335-3342.
57. Shtatland, T., Guettler, D., Kossodo, M., Pivovarov, M. and Weissleder, R. (2007) PepBank: a database of peptides based on sequence text mining and public peptide data sources. BMC Bioinformatics, 8, 280.
58. Heemskerk, J.A., Van Deutekom, J.C., Van Kuik-Romeijn, P. and Platenburg, G.J. Molecules for targeting compounds to various selected organs or tissues. US patent 08268962. 2012.
59. Kim, S.N., Kuang, Z., Slocik, J.M., Jones, S.E., Cui, Y., Farmer, B.L., McAlpine, M.C. and Naik, R.R. (2011) Preferential binding of peptides to graphene edges and planes. J. Am. Chem. Soc., 133, 14480-14483.
60. Llano-Sotelo, B., Klepacki, D. and Mankin, A.S. (2009) Selection of small peptides, inhibitors of translation. J. Mol. Biol., 391, 813-819.
61. Sawada, T. and Mihara, H. (2012) Dense surface functionalization using peptides that recognize differences in organized structures of self-Assembling nanomaterials. Mol. Biosyst., 8, 1264-1274.
62. Leclerc, D. Immunogenic affinity-conjugated antigen systems based on Papaya Mosaic Virus and uses thereof. US patent 20100047264 A1. 2010.
63. Schmitt, M.W., Kennedy, S.R., Salk, J.J., Fox, E.J., Hiatt, J.B. and Loeb, L.A. (2012) Detection of ultra-rare mutations by next-generation sequencing. Proc. Natl Acad. Sci. USA, 109, 14508-14513.
64. Nakamura, K., Oshima, T., Morimoto, T., Ikeda, S., Yoshikawa, H., Shiwa, Y., Ishikawa, S., Linak, M.C., Hirai, A., Takahashi, H. et al. (2011) Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res., 39, e90.
65. Noren, K.A. and Noren, C.J. (2001) Construction of high-complexity combinatorial phage display peptide libraries. Methods, 23, 169-178.
66. DeLano, W.L., Ultsch, M.H., de Vos, A.M. and Wells, J.A. (2000) Convergent solutions to binding at a protein-protein interface. Science, 287, 1279-1283.
67. Rodi, D.J., Makowski, L. and Kay, B.K. (2002) One from column A and two from column B: the benefits of phage display in molecular-recognition studies. Curr. Opin. Chem. Biol., 6, 92-96.
68. Lancet, D., Sadovsky, E. and Seidemann, E. (1993) Probability model for molecular recognition in biological receptor repertoires: significance to the olfactory system. Proc. Natl Acad. Sci. USA, 90, 3715-3719.
69. Breaker, R.R. and Joyce, G.F. (1994) Emergence of a replicating species from an in vitro RNA evolution reaction. Proc. Natl Acad. Sci. USA, 91, 6093-6097.
70. Zimmermann, B., Gesell, T., Chen, D., Lorenz, C. and Schroeder, R. (2010) Monitoring genomic sequences during SELEX using highthroughput sequencing: neutral SELEX. PLoS One, 5, e9169.
71. Sha, J., Wang, Y., Wang, J., Ren, L., Tu, Q., Liu, W., Wang, X., Liu, A., Wang, L. and Wang, J. (2011) Capillary-composited microfluidic device for heat shock transformation of Escherichia coli. J. Biosci. Bioeng., 112, 373-378.
72. Sha, J., Wang, Y., Wang, J., Liu, W., Tu, Q., Liu, A., Wang, L. and Wang, J. (2011) Heat-shock transformation of Escherichia coli in nanolitre droplets formed in a capillary-composited microfluidic device. Anal. Methods, 3, 1988-1994.
73. Li, W., Greener, J., Voicu, D. and Kumacheva, E. (2009) Multiple modular microfluidic (M-3) reactors for the synthesis of polymer particles. Lab Chip, 9, 2715-2721.
74. Theberge, A.B., Courtois, F., Schaerli, Y., Fischlechner, M., Abell, C., Hollfelder, F. and Huck, W.T. (2010) Microdroplets in microfluidics: an evolving platform for discoveries in chemistry and biology. Angew. Chem. Int. Ed., 49, 5846-5868.