Target Discovery and Validation Reviews and Protocols

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Immunoproteomics 333 3. 2D-PAGE is usually performed in reducing conditions, which may be an issue for detection of certain antigens for which epitope(s) involving disulfide bonds would be lost. References 1. Happ, S. S. (1997) A Commotion in the Blood: Life, Death, and the Immune System. The Spoon Technology Series. Henry Holt and Company Inc., NY, NY. 2. Jager, E., Chen, Y. T., Drijfhout, J. W., et al. (1998) Simultaneous humoral and cellular immune response against cancer-testis antigen NY-ESO-1: definition of human histocompatibility leukocyte antigen (HLA)-A2-binding peptide epitopes. J. Exp. Med. 187, 265–270. 3. Jager, D., Jager, E., and Knuth, A. (2001) Vaccination for malignant melanoma: recent developments. Oncology 60, 1–7. 4. Nakatsura, T., Senju, S., Ito, M., Nishimura, Y., and Itoh, K. (2002) Cellular and humoral immune responses to a human pancreatic cancer antigen, coactosinlike protein, originally defined by the SEREX method. Eur. J. Immunol. 32, 826–836. 5. van der Bruggen, P., Traversari, C., Chomez, P., et al. (1991) A gene encoding an antigen recognized by cytolytic T lymphocytes on a human melanoma. Science 254, 1643–1647. 6. Renkvist, N., Castelli, C., Robbins, P. F., and Parmiani, G. (2001) A listing of human tumor antigens recognized by T cells. Cancer Immunol. Immunother. 50, 3–15. 7. Sahin, U., Türeci, O., Schmitt, H., et al. (1995) Human neoplasms elicit multiple specific immune responses in the autologous host. Proc. Natl. Acad. Sci. USA 92, 11,810–11,813. 8. Old, L. J. and Chen, Y. T. (1998) New paths in human cancer serology. J. Exp. Med. 187, 1163–1167. 9. Türeci, O., Sahin, U., Zwick, C., Neumann, F., and Pfreundschuh M. (1999) Exploitation of the antibody repertoire of cancer patients for the identification of human tumor antigens. Hybridoma 18, 23–28. 10. Chen, Y. T. (2000) Cancer vaccine: identification of human tumor antigens by SEREX. Cancer J. Sci. Am. 6, s208–s217. 11. Nishikawa, H., Tanida, K., Ikeda, H., et al. (2001) Role of SEREX-defined immunogenic wild-type cellular molecules in the development of tumor-specific immunity. Proc. Natl. Acad. Sci. USA 98, 14,571–14,576. 12. Patterson, S. D. and Aebersold, R. H. (2003) Proteomics: the first decade and beyond. Nat. Genet. 33, Suppl, 311–323. 13. Gharahdaghi, F., Weinberg, C. R., Meagher, D. A., Imai, B. S., and Mische, S. M. (1999) Mass spectrometric identification of proteins from silver-stained polyacrylamide gel: a method for the removal of silver ions to enhance sensitivity. Electrophoresis 20, 601–605. 14. Shevchenko, A., Wilm, M., Vorm, O., and Mann, M. (1996) Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal. Chem. 68, 850–858.
334 Le Naour 15. Le Naour, F., Misek, D. E., Krause, M. C., et al. (2001) Proteomics-based identification of RS/DJ-1 as a novel circulating tumor antigen in breast cancer. Clin. Cancer Res. 11, 3328–3335. 16. Brichory, F. M., Misek, D. E., Yim, A. M., et al. (2001) An immune response manifested by the common occurrence of annexins I and II autoantibodies and high circulating levels of IL-6 in lung cancer. Proc. Natl. Acad. Sci. USA 98, 9824–9829. 17. Le Naour, F., Brichory, F., Misek, D. E., Bréchot, C., Hanash, S. M., and Beretta L. (2001) A distinct repertoire of autoantibodies in hepatocellular carcinoma identified by proteomic analysis. Mol. Cell Proteomics 1, 197–203. 18. Klade, C. S., Voss, T., Krystek, E., et al. (2001) Identification of tumor antigens in renal cell carcinoma by serological proteome analysis. Proteomics 1, 890–898. 19. Lichtenfels, R., Kellner, R., Bukur, J., et al. (2002) Heat shock protein expression and anti-heat shock protein reactivity in renal cell carcinoma. Proteomics 2, 561–570. 20. Prasannan, L., Misek, D. E., Hinderer, R., Michon, J., Geiger, J. D., and Hanash, S. M. (2000) Identification of β-tubulin isoforms as tumor antigens in neuroblastoma. Clin. Cancer Res. 6, 3949–3956. 21. Brichory, F., Beer D., Le Naour, F., Giordano, T., and Hanash, S. M. (2001) Proteomics-based identification of PGP 9.5 as a tumor antigen that induces a humoral immune response in lung cancer. Cancer Res. 61, 7908–7912. 22. Le Naour, F. (2001) Contribution of proteomics to tumor immunology. Proteomics 1, 1295–1302. 23. Hanash, S., Brichory, F., and Beer, D. (2001) A proteomic approach to the identification of lung cancer markers. Dis. Markers 17, 295–300. 24. Shalhoub, P., Kern, S., Girard, S., and Beretta, L. (2001) Proteomic-based approach for the identification of tumor markers associated with hepatocellular carcinoma. Dis. Markers 17, 217–223. 25. Hong, S. H., Misek, D. E., Wang, H., et al. (2004) An autoantibody-mediated immune response to calreticulin isoforms in pancreatic cancer. Cancer Res. 64, 5504–5510. 26. Rauch, J., Ahlemann, M., Schaffrik, M., et al. (2004) Allogenic antibodymediated identification of head and neck cancer antigens. Biochem. Biophys. Res. Commun. 323, 156–162. 27. Gires, O., Munz, M., Schaffrik, M., et al. (2004) Profile identification of diseaseassociated humoral antigens using AMIDA, a novel proteomics-based technology. Cell Mol. Life Sci. 61, 1198–1207. 28. Henash, S. M. (2003) The emerging field of protein microarrays. Proteomics 3 (special issue), 2075. 29. Imafuku, Y., Omenn, G. S., and Hanash, S. (2004) Proteomics approaches to identify tumor antigen directed autoantibodies as cancer biomarkers. Dis. Markers 20, 149–153. 30. Qiu, J., Madoz-Gurpide, J., Misek, D. E., et al. (2004) Development of natural protein microarrays for diagnosing cancer based on an antibody response to tumor antigens. J. Proteome Res. 3, 261–267.
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METHODS IN MOLECULAR BIOLOGY 360 T
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M E T H O D S I N M O L E C U L A R
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© 2007 Humana Press Inc. 999 River
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vi Preface get. Approaches to targe
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viii Contents 10 Transgenic Animal
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x Contributors SAHOHIME MATSUMOTO
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xii Contents of Volume 2 12 Validat
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2 Sioud disease pathogenesis and pe
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4 Sioud A more fruitful approach fo
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6 Sioud both transient and permanen
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8 Sioud serum biomarkers. This syne
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10 Sioud Fig. 2. Schematic of targe
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12 Sioud 13. Magin, T. M. (1998) Le
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Harnessing the Human Genome 15 The
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Harnessing the Human Genome 17 Fig.
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Harnessing the Human Genome 23 The
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Harnessing the Human Genome 27 repr
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Harnessing the Human Genome 29 14.
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Harnessing the Human Genome 31 45.
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34 Imoto et al. (4,5), and Bayesian
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36 Imoto et al. 2. Materials Two ty
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38 Imoto et al. Fig. 3. Graphical v
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40 Imoto et al. Fig. 5. Result of t
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42 Imoto et al. p(D |G) = ∫ p(D,
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44 Imoto et al. β k (k = 1,…,q j
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46 Imoto et al. Fig. 7. Partial res
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48 Imoto et al. Fig. 8. Strategy to
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50 Imoto et al. Fig. 9. (continued)
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52 Imoto et al. Table 3 List of Roo
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54 Imoto et al. 5. De Hoon, M. J. L
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56 Imoto et al. 39. Kamimura, T., S
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58 Beaty et al. cytotoxic drugs and
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60 Beaty et al. Fig. 1. Principles
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62 Beaty et al. oligonucleotide mic
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64 Beaty et al. 3. The 12% polyacry
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66 Beaty et al. 2.3.3. Protein Stai
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68 Beaty et al. 3.1.3. Labeling of
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70 Beaty et al. 1 µL of the anneal
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72 Beaty et al. 4. Phenol:cholorfor
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74 Beaty et al. 19. Wash twice with
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76 Beaty et al. The Following Volum
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78 Beaty et al. using a protein ass
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80 Beaty et al. 6. Shake the gel fo
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82 Beaty et al. Fig. 2. Preparation
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84 Beaty et al. search in. A widely
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86 Beaty et al. 3. Kern, S. E., Hru
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88 Beaty et al. 34. Peters, D. G.,
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5 Molecular Classification of Breas
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Molecular Profiling of Breast Cance
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Fig. 2. (Continued) the right ident
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6 Discovery of Differentially Expre
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Gene Target Discovery 117 In the fi
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Gene Target Discovery 119 sequences
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Gene Target Discovery 121 There is
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Gene Target Discovery 123 digestion
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Gene Target Discovery 125 Fig. 1. P
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Gene Target Discovery 127 5. Sargen
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Gene Target Discovery 129 41. Berry
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132 Matsumoto, Miyagishi, and Taira
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144 Fig. 1. The ribozyme-expression
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146 Sano and Taira 5. 10X L (low-sa
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148 Sano and Taira ribozymes may cl
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150 Fig. 3. A system for the identi
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152 Sano and Taira 4. Notes 1. We r
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9 Production of siRNA- and cDNA-Tra
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Transfected Cell Arrays 157 Fig. 1.
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Transfected Cell Arrays 159 2. The
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Transfected Cell Arrays 161 5. Simp
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164 Houdebine Fig. 1. Different met
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166 Houdebine concentrations become
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168 Houdebine Fig. 2. Major methods
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170 Houdebine integrate into the me
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172 Houdebine 2.2.3. Knock-In Into
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174 Houdebine as insulators. The co
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176 Houdebine Fig. 5. Different met
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178 Houdebine systems. Moreover, st
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180 Houdebine contribute to generat
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182 Houdebine Fig.7. Example of a v
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184 Houdebine more extensively. Tra
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186 Houdebine and stroma. Several o
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188 Houdebine explained at the mole
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190 Houdebine of the intestinal epi
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192 Houdebine interference of the g
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194 Houdebine 17. Whitelaw, C. B. A
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196 Houdebine 51. Bell, A. C., West
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198 Houdebine 86. Carmichael, G. G.
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200 Houdebine 121. Pailhoux, E., Vi
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202 Houdebine 156. Auerbach, A. B.,
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204 Vijayaraj, Söhl, and Magin 1.
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206 Vijayaraj, Söhl, and Magin Fig
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208 Vijayaraj, Söhl, and Magin fil
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210 Table 1 Orthologous Human and M
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212 Table 2 Orthologous Human and M
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214 Vijayaraj, Söhl, and Magin ulc
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216 Vijayaraj, Söhl, and Magin of
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218 Vijayaraj, Söhl, and Magin sug
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220 Vijayaraj, Söhl, and Magin abs
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222 Vijayaraj, Söhl, and Magin 1.2
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224 Vijayaraj, Söhl, and Magin Fig
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226 Vijayaraj, Söhl, and Magin gen
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228 Vijayaraj, Söhl, and Magin the
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230 Vijayaraj, Söhl, and Magin f.
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234 Vijayaraj, Söhl, and Magin b.
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240 Vijayaraj, Söhl, and Magin alt
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242 Table 3 Time Schedule For Aggre
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250 Vijayaraj, Söhl, and Magin 101
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12 The HUVEC/Matrigel Assay An In V
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256 Skovseth, Küchler, and Haralds
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270 Iversen and Sørensen witnessed
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272 Iversen and Sørensen Fig. 1. P
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274 Iversen and Sørensen the core
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14 An Overview of the Immune System
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Overview of Immune System 279 diffe
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Overview of Immune System 281 Fig.
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Page 332 and 333: 15 Potential Target Antigens for Im
Page 334 and 335: Tumor Antigen Discovery 321 develop
Page 336 and 337: Tumor Antigen Discovery 323 panel b
Page 338 and 339: Tumor Antigen Discovery 325 16. Joc
Page 340 and 341: 16 Identification of Tumor Antigens
Page 342 and 343: Immunoproteomics 329 by “shot gun
Page 344 and 345: Immunoproteomics 331 isoelectric fo
Page 348 and 349: 17 Protein Arrays A Versatile Toolb
Page 350 and 351: Protein Arrays 337 Table 1 Classifi
Page 352 and 353: Protein Arrays 339 fractions from c
Page 354 and 355: Protein Arrays 341 combinatorial sc
Page 356 and 357: Protein Arrays 343 The ideal proteo
Page 358 and 359: Protein Arrays 345 18. Cekaite, H.
Page 360 and 361: Protein Arrays 347 49. Yuko Kawahas
Page 362 and 363: Index 349 Index A Acetyl-CoA carbox
Page 364 and 365: Index 351 conditional by using FRT
Page 366 and 367: Index 353 Recombinant tumor antigen
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