Targeting mammalian organelles with internalizing phage (iPhage) libraries

Nature Protocols

Volumn 8, Issue 10, 2013, Pages 1916-1939

  Rangel, Roberto ^a,d   Dobroff, Andrey S ^a   Guzman Rojas, Liliana ^a,d   Salmeron, Carolina C ^a   Gelovani, Juri G ^b   Sidman, Richard L ^c   Pasqualini, Renata ^a   Arap, Wadih ^a  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^b Wayne State University   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d HOUSTON METHODIST RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL RECEPTOR; VIRUS PROTEIN; VIRUS RECEPTOR; VIRUS VECTOR;

AFFINITY CHROMATOGRAPHY; ANIMAL CELL; ARTICLE; CELL COMPARTMENTALIZATION; CELL FUNCTION; CELL ORGANELLE; CLINICAL PROTOCOL; ESCHERICHIA COLI; EUKARYOTIC CELL; EXPERIMENTAL DESIGN; FLUORESCENCE MICROSCOPY; IN VITRO STUDY; INTERNALIZATION; INTERNALIZING PHAGE LIBRARY; MEDICAL PARAMETERS; MITOCHONDRION; MOLECULAR CLONING; MOLECULAR DYNAMICS; MOLECULAR LIBRARY; NONHUMAN; NUCLEAR LOCALIZATION SIGNAL; PARTICLE SIZE; PEPTIDE LIBRARY; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN DETERMINATION; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PURIFICATION; RAPID PHAGE QUANTIFICATION; REACTION TIME; SCREENING TEST; SIGNAL TRANSDUCTION; TARGET CELL; VALIDATION PROCESS;

ANIMALS; CELL SURFACE DISPLAY TECHNIQUES; CLONING, MOLECULAR; MAMMALS; PEPTIDE LIBRARY;

EID: 84884996236     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2013.119     Document Type: Article

References (68)

1. Pasqualini, R. & Ruoslahti, E. Organ targeting in vivo using phage display peptide libraries. Nature 380, 364-366 (1996
2. Arap, W., Pasqualini, R. & Ruoslahti, E. Cancer treatment by targeted drug delivery to tumor vasculature in a mouse model. Science 279, 377-380 (1998
3. Pasqualini, R., Arap, W., Rajotte, D. & Ruoslahti, E. in Phage display: A laboratory manual. (eds. Barbas, C.F., Burton, D.R., Scott, J.K. & Silverman, G.J.) 1-24 (Cold Spring Harbor Laboratory Press, 2001
4. Pasqualini, R. et al. Aminopeptidase N is a receptor for tumor-homing peptides and a target for inhibiting angiogenesis. Cancer Res. 60, 722-727 (2000
5. Arap, W. et al. Steps toward mapping the human vasculature by phage display. Nat. Med. 8, 121-127 (2002
6. Laakkonen, P., Porkka, K., Hoffman, J.A. & Ruoslahti, E. A tumor-homing peptide with a targeting specificity related to lymphatic vessels. Nat. Med. 8, 751-755 (2002
7. Mintz, P.J. et al. Fingerprinting the circulating repertoire of antibodies from cancer patients. Nat. Biotechnol. 21, 57-63 (2003
8. Higgins, L.M. et al. In vivo phage display to identify M cell-targeting ligands. Pharm. Res. 21, 695-705 (2004
9. Kolonin, M.G., Saha, P.K., Chan, L., Pasqualini, R. & Arap, W. Reversal of obesity by targeted ablation of adipose tissue. Nat. Med. 10, 625-632 (2004
10. Ballard, V.L., Holm, J.M. & Edelberg, J.M. Quantitative PCR-based approach for rapid phage display analysis: A foundation for high throughput vascular proteomic profiling. Physiol. Genomics 26, 202-208 (2006
11. Kolonin, M.G. et al. Synchronous selection of homing peptides for multiple tissues by in vivo phage display. FASEB J. 20, 979-981 (2006
12. Zhang, L., Giraudo, E., Hoffman, J.A., Hanahan, D. & Ruoslahti, E. Lymphatic zip codes in premalignant lesions and tumors. Cancer Res. 66, 5696-5706 (2006
13. Hardy, B., Battler, A., Weiss, C., Kudasi, O. & Raiter, A. Therapeutic angiogenesis of mouse hind limb ischemia by novel peptide activating GRP78 receptor on endothelial cells. Biochem. Pharmacol. 75, 891-899 (2008
14. Mintz, P.J. et al. An unrecognized extracellular function for an intracellular adapter protein released from the cytoplasm into the tumor microenvironment. Proc. Natl. Acad. Sci. USA 106, 2182-2187 (2009
15. Staquicini, F.I. et al. Vascular ligand-receptor mapping by direct combinatorial selection in cancer patients. Proc. Natl. Acad. Sci. USA 108, 18637-18642 (2011
16. Joliot, A., Pernelle, C., Deagostini-Bazin, H. & Prochiantz, A. Antennapedia homeobox peptide regulates neural morphogenesis. Proc. Natl. Acad. Sci. USA 88, 1864-1868 (1991
17. Derossi, D., Joliot, A.H., Chassaing, G. & Prochiantz, A. The third helix of the Antennapedia homeodomain translocates through biological membranes. J. Biol. Chem. 269, 10444-10450 (1994
18. Derossi, D. et al. Cell internalization of the third helix of the Antennapedia homeodomain is receptor-independent. J. Biol. Chem. 271, 18188-18193 (1996
19. Théodore, L. et al. Intraneuronal delivery of protein kinase C pseudosubstrate leads to growth cone collapse. J. Neurosci. 15, 7158-7167 (1995
20. Chen, Y.N. et al. Selective killing of transformed cells by cyclin/cyclin-dependent kinase 2 antagonists. Proc. Natl. Acad. Sci. USA 96, 4325-4329 (1999
21. Mi, Z., Mai, J., Lu, X. & Robbins, P.D. Characterization of a class of cationic peptides able to facilitate efficient protein transduction in vitro and in vivo. Mol. Ther. 2, 339-347 (2000
22. Cardó-Vila, M., Arap, W. & Pasqualini, R. Mol. Cell 11, 1151-1162 (2003
23. Davidson, T.J. et al. Highly efficient small interfering RNA delivery to primary mammalian neurons induces MicroRNA-like effects before mRNA degradation. J. Neurosci. 24, 10040-10046 (2004
24. Muratovska, A. & Eccles, M.R. Conjugate for efficient delivery of short interfering RNA (siRNA) into mammalian cells. FEBS Lett. 558, 63-68 (2004
25. Apostolopoulos, V. et al. Delivery of tumor associated antigens to antigen presenting cells using penetratin induces potent immune responses. Vaccine 24, 3191-3202 (2006
26. Fabani, M.M. & Gait, M.J. miR-122 targeting with LNA/2′-O- methyl oligonucleotide mixmers, peptide nucleic acids (PNA), and PNA-peptide conjugates. RNA 14, 336-346 (2008
27. Blobel, G. & Sabatini, D.D. Controlled proteolysis of nascent polypeptides in rat liver cell fractions. I. Location of the polypeptides within ribosomes. J. Cell Biol. 45, 130-145 (1970
28. Blobel, G. & Dobberstein, B. Transfer of proteins across membranes. I. Presence of proteolytically processed and unprocessed nascent immunoglobulin light chains on membrane-bound ribosomes of murine myeloma. J. Cell Biol. 67, 835-851 (1975
29. Blobel, G. Intracellular protein topogenesis. Proc. Natl. Acad. Sci. USA 77, 1496-1500 (1980
30. Walter, P. & Blobel, G. Purification of a membrane-Associated protein complex required for protein translocation across the endoplasmic reticulum. Proc. Natl. Acad Sci. USA 77, 7112-7116 (1980
31. Pain, D., Murakami, H. & Blobel, G. Identification of a receptor for protein import into mitochondria. Nature 347, 444-449 (1990
32. Rangel, R. et al. Combinatorial targeting and discovery of ligand-receptors in organelles of mammalian cells. Nat. Commun. 3, 788 (2012
33. Barnhart, K.F. et al. A peptidomimetic targeting white fat causes weight loss and improved insulin resistance in obese monkeys. Sci. Transl. Med. 3, 108-112 (2011
34. Zurita, A.J. et al. Combinatorial screenings in patients: The interleukin-11 receptor as a candidate target in the progression of human prostate cancer. Cancer Res. 64, 435-439 (2004
35. Lewis, V.O. et al. The interleukin-11 receptor as a candidate ligand-directed target in osteosarcoma: Consistent data from cell lines, orthotopic models, and human tumor samples. Cancer Res. 69, 1995-1999 (2009
36. Cardó-Vila, M. et al. From combinatorial peptide selection to drug prototype (II): Targeting the epidermal growth factor receptor pathway. Proc. Natl. Acad. Sci. USA 107, 5118-5123 (2010
37. Giordano, R.J. et al. From combinatorial peptide selection to drug prototype (I): Targeting the vascular endothelial growth factor receptor pathway. Proc. Natl. Acad. Sci. USA 107, 5112-5117 (2010
38. Marchiò, S. et al. Aminopeptidase A is a functional target in angiogenic blood vessels. Cancer Cell 5, 151-162 (2004
39. Hajitou, A. et al. A hybrid vector for ligand-directed tumor targeting and molecular imaging. Cell 125, 385-398 (2006
40. Hajitou, A. et al. Design and construction of targeted AAVP vectors for mammalian cell transduction. Nat. Protoc. 2, 523-531 (2007
41. Hajitou, A. et al. A preclinical model for predicting drug response in soft-tissue sarcoma with targeted AAVP molecular imaging. Proc. Natl. Acad. Sci. USA 105, 4471-4476 (2008
42. Soghomonyan, S. et al. Molecular PET imaging of HSV1-tk reporter gene expression using [18F]FEAU. Nat. Protoc. 2, 416-423 (2007
43. Paoloni, M.C. et al. Launching a novel preclinical infrastructure: Comparative oncology trials consortium directed therapeutic targeting of TNF to cancer vasculature. PLoS ONE 4, e4972 (2009
44. Tandle, A et al. Tumor vasculature-targeted delivery of tumor necrosis factor-Cancer 115, 128-139 (2009
45. Staquicini, F.I. et al. Systemic combinatorial peptide selection yields a non-canonical iron-mimicry mechanism for targeting tumors in a mouse model of human glioblastoma. J. Clin. Invest. 121, 161-173 (2011
46. Xu, X. et al. Dominant effector genetics in mammalian cells. Nat. Genet. 27, 23-29 (2001
47. Schlabach, M.R. et al. Cancer proliferation gene discovery through functional genomics. Science 319, 620-624 (2008
48. Silva, J.M. et al. Profiling essential genes in human mammary cells by multiplex RNAi screening. Science 319, 617-620 (2008
49. Peelle, B. et al. Intracellular protein scaffold-mediated display of random peptide libraries for phenotypic screens in mammalian cells. Chem. Biol. 8, 521-534 (2001
50. Norman, T.C. et al. Genetic selection of peptide inhibitors of biological pathways. Science 285, 591-595 (1999
51. Zhong, J., Zhang, H., Stanyon, C.A., Tromp, G. & Finley, R.L. A strategy for constructing large protein interaction maps using the yeast two-hybrid system: Regulated expression arrays and two-phase mating. Genome Res. 13, 2691-2699 (2003
52. Staquicini, F.I., Sidman, R.L., Arap, W. & Pasqualini, R. Phage display technology for stem cell delivery and systemic therapy. Adv. Drug Deliv. Rev. 62, 1213-1216 (2010
53. Smith, G.P. & Scott, J.K. Libraries of peptides and proteins displayed on filamentous phage. Methods Enzymol. 217, 228-257 (1993
54. Herndier, B.G. et al. Characterization of a human Kaposi's sarcoma cell line that induces angiogenic tumors in animals. AIDS 8, 575-581 (1994
55. Claude, A. Fractionation of mammalian liver cells by differential centrifugation: I. problems, methods, and preparation of extract. J. Exp. Med. 84, 51-59 (1946
56. Castle, J.D. Purification of organelles from mammalian cells. Curr. Protoc. Immunol. 56, 8.1B.1-8.1B.57 (2003
57. de Araùjo, M.E., Huber, L.A. & Stasyk, T. Isolation of endocitic organelles by density gradient centrifugation. Methods Mol. Biol. 424, 317-331 (2008
58. Huber, L.A., Pfaller, K. & Vietor, I. Organelle proteomics: Implications for subcellular fractionation in proteomics. Circ. Res. 92, 962-968 (2003
59. Cox, B. & Emili, A. Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomics. Nat. Protoc. 1, 1872-1878 (2006
60. Hoffmann, K. et al. New application of a subcellular fractionation method to kidney and testis for the determination of conjugated linoleic acid in selected cell organelles of healthy and cancerous human tissues. Anal. Bioanal. Chem. 381, 1138-1144 (2005
61. Spann, T.P. in Cells: A laboratory manual, Vol. 1: Culture and Biochemical Analysis of Cells (eds. Spector, D.L., Goldman, R.D. & Leinwand, L.A.) 2136 (Cold Spring Harbor Laboratory Press, 1998
62. Huang, D.W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nat. Protoc. 4, 44-57 (2009
63. Franceschini, A. et al. STRING v9.1: Protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41, D808-D815 (2013
64. Dias-Neto, E. et al. Next-generation phage display: Integrating and comparing available molecular tools to enable cost-effective high-throughput analysis. PLoS ONE 4, e8338 (2009
65. Parmley, S.F. & Smith, G.P. Antibody-selectable filamentous fd phage vectors: Affinity purification of target genes. Gene 73, 305-318 (1988
66. Sambrook, J.J. & Russell, D.W. Molecular Cloning: A Laboratory Manual Vol. 1, 3rd edn. (Cold Spring Harbor Laboratory Press, 2001
67. Sambrook, J., Fritsch, E.F. & Maniatis, T. Molecular Cloning: A Laboratory Manual Vol. 3, 2nd edn. (Cold Spring Harbor Laboratory Press, 1989
68. Kalderon, D., Roberts, B.L., Richardson, W.D. & Smith, A.E. A short amino acid sequence able to specify nuclear location. Cell 39, 499-509 (1984