Target Discovery and Validation Reviews and Protocols

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Overview of Immune System 317 74. Dybwad, A., Bogen, A., Natvig, J. B., Førre, Ø., and Sioud, M. (1995) Peptide phage libraries can be an efficient tool for identifying antibody ligands for polyclonal antisera. Clin. Exp. Immunol. 102, 438–442. 75. Hansen, M. H., Østenstad, B., and Sioud, M. (2001) Antigen-specific IgG antibodies in stage IV long-term survival breast cancer patients. Mol. Med. 7, 230–239. 76. Sioud, M. and Hansen, M. H. (2001) Profiling the immune response in patients with breast cancer by phage-displayed cDNA libraries. Eur. J. Immunol. 31, 716–725. 77. Boublik, Y., Di Bonito, P., and Jones, I. M. (1995) Eukaryotic virus display: engineering the major surface glycoprotein of the Autographa californica nuclear polyhedrosis virus (AcNPV) for the presentation of foreign proteins on the virus surface. Biotechnology 13, 1079–1084. 78. Russel, S. J., Hawkins, R. E., and Winter, G. (1993) Retroviral vectors displaying functional antibody fragments. Nucleic Acids Res. 21, 1081–1085. 79. Boder, E. T. and Wittrup, K. D. (1997) Yeast surface display for screening combinatorial polypeptide libraries. Nat. Biotechnol. 15, 553–557. 80. Wadle, A., Mischo, A., Imig, J., et al. (2005) Serological identification of breast cancer-related antigens from a Saccharomyces cerevisiae surface display library. Int. J. Cancer 117, 104–113. 81. Velculescu, V. E., Zhang, L., Vogelstein, B., and Kinzler, K. W. (1995) Serial analysis of gene expression. Science 270, 484–487. 82. Lash, A. E., Tolstoshev, C. M., Wagner, L., et al. (2000) SAGEmap; a public gene expression resource. Genome Res. 10, 1051–1060. 83. Boon, K., Osorio, E. C., Greenhut, S. F., et al. (2002) An anatomy of normal and malignant gene expression. Proc Natl. Acad. Sci. USA 99, 11,287–11,292. 83a. Loging, W.T. et al. (2000) Identifying potential tumor markers and antigens by database mining and rapid expression screening. Genome Res. 10, 1393–1402. 84. Segal, E., Fiedman, N., Kaminski, N., Regev, A., and Koller, D. (2005) From signatures to models: understanding cancer using microarrays. Nat. Genet. 37, S38–S45. 85. Leirdal, M., Shadidy, M., Røsok, Ø., and Sioud, M. (2004) Identification of genes differentially expressed in breast cancer cell line SKBR3: Potential identification of new prognostic biomarkers. Int. J. Mol. Med. 14, 217–222. 86. de Hoog, C. L. and Mann, M. (2004) Proteomics. Annu. Rev. Genomics Hum. Genet. 5, 267–293. 87. Sioud, A. and Sørensen, D. (2003) Generation of an effective anti-tumor immunity after immunization with xenogeneic antigens. Eur. J. Immunol. 33, 38–45. 88. Davis, I. D., Jefford, M., Parente, P., and Cebon, J. (2003) Rational approaches to human cancer immunotherapy. J. Leukoc. Biol. 73, 3–29. 89. Zou, W. (2005) Immunosuppressive networks in the tumour environment and their therapeutic relevance. Nat. Rev. 5, 263–274. 90. Sioud, M. (2004) Therapeutic siRNAs. Trends Pharmacol. Sci. 25, 22–28.
318 Sioud 91. Golgher, D., Jones, E., Powrie, F., Elliot, T., and Gallimore, A. (2002) Depletion of CD25 regulatory cells uncovers immune responses to shared murine tumour rejection antigens. Eur. J. Immunol. 32, 3267–3275. 92. Dudley, M. E., Wunderlich, J. R., Robbins, P. F., et al. (2002) Cancer regression and autoimmunity in patients after clonal repopulation with antitumor lymphocytes. Science 298, 850–854. 93. Wiernik, P. H. (1976) Spontaneous regression of hematologic cancers. Natl. Cancer Inst. Monogr. 44, 35–38. 94. Sioud, M. (2002) How does autoimmunity cause tumor regression? A potential mechanism involving cross-reaction through epitope mimicry. Mol. Med. 8, 115–119. 95. Banchereau, J. and Steinman, R. M. (1998) Dendritic cells and the control of immunity. Nature 392, 245–252. 96. Langenkamp, A., Messi, M., Lanzavecchia, A., and Sallusto, F. (2000) Kinetics of dendritic cell activation: impact on priming of TH1, TH2 and nonpolarized T cells. Nat. Immunol. 1, 311–316. 97. Steinman, R. M., Hawiger, D., and Nussenzweig, M. C. (2003) Tolerogenic dendritic cells. Annu. Rev. Immunol. 21, 685–711. 98. Sioud, M. (2005) Induction of inflammatory cytokines and interferon responses by double-stranded and single-stranded siRNAs is sequence-dependent and requires endosomal localization. J. Mol. Biol. 348, 1079–1090.
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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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216 Vijayaraj, Söhl, and Magin of
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222 Vijayaraj, Söhl, and Magin 1.2
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226 Vijayaraj, Söhl, and Magin gen
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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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Page 292 and 293: Overview of Immune System 279 diffe
Page 294 and 295: Overview of Immune System 281 Fig.
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Page 322 and 323: Overview of Immune System 309 sera
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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 346 and 347: Immunoproteomics 333 3. 2D-PAGE is
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Page 350 and 351: Protein Arrays 337 Table 1 Classifi
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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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