Pancreatic Cancer 87 19. Argani, P., Rosty, C., Reiter, R. E., et al. (2001) <strong>Discovery</strong> of new markers of cancer through serial analysis of gene expression: prostate stem cell antigen is overexpressed in pancreatic adenocarcinoma. Cancer Res. 61, 4320–4324. 20. Argani, P., Iacobuzio-Donahue. C., Ryu. B., et al. (2001) Mesothelin is overexpressed in the vast majority of ductal adenocarcinomas of the pancreas: identification of a new pancreatic cancer marker by serial analysis of gene expression (SAGE). Clin. Cancer Res. 7, 3862–3868. 21. Rosty, C., Christa, L., Kuzdzal, S., et al. (2002) Identification of hepatocarcinoma-intestine-pancreas/pancreatitis-associated protein I as a biomarker for pancreatic ductal adenocarcinoma by protein biochip technology. Cancer Res. 62, 1868–1875. 22. Koopmann, J., Fedarko, N. S., Jain, A., et al. (2004) Evaluation of osteopontin as biomarker for pancreatic adenocarcinoma. Cancer Epidemiol. Biomarkers Prev. 13, 487–491. 23. Shalon, D., Smith, S. J., <strong>and</strong> Brown, P. O. (1996) A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6, 639–645. 24. Velculescu, V. E., Zhang, L., Vogelstein, B., <strong>and</strong> Kinzler, K. W. (1995) Serial analysis of gene expression. Science 270, 484–487. 25. P<strong>and</strong>ey, A. <strong>and</strong> Mann, M. (2000) Proteomics to study genes <strong>and</strong> genomes. Nature 405, 837–846. 26. Schena, M., Shalon, D., Davis, R. W., <strong>and</strong> Brown, P. O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470. 27. DeRisi, J., Penl<strong>and</strong>, L., Brown, P. O., et al. (1996) Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat. Genet. 14, 457–460. 28. Pollack, J. R. (2002) Comparative genomic hybridization using cDNA microarrays. In: DNA microarrays: A Molecular Cloning Manual, Sambrook, J., ed. Cold Spring Harbor Press, pp. 363–369. 29. Van Gelder, R. N., von Zastrow, M. E., Yool, A., Dement, W. C., Barchas, J. D., <strong>and</strong> Eberwine, J. H. (1990) Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc. Natl. Acad. Sci. USA 87, 1663–1667. 30. Polyak, K. <strong>and</strong> Riggins, G. J. (2001) Gene discovery using the serial analysis of gene expression technique: implications for cancer research. J. Clin. Oncol. 19, 2948–2958. 31. Kenzelmann, M. <strong>and</strong> Muhlemann, K. (1999) Substantially enhanced cloning efficiency of SAGE (serial analysis of gene expression) by adding a heating step to the original protocol. Nucleic Acids Res. 27, 917–918. 32. Angelastro, J. M., Klimaschewski, L. P., <strong>and</strong> Vitolo, O. V. (2000) Improved NlaIII digestion of PAGE-purified 102 bp ditags by addition of a single purification step in both the SAGE <strong>and</strong> microSAGE protocols. Nucleic Acids Res. 28, e62. 33. Datson, N. A., van der Perk-de Jong, J., van den Berg, M. P., de Kloet, E. R., <strong>and</strong> Vreugdenhil, E. (1999) MicroSAGE: a modified procedure for serial analysis of gene expression in limited amounts of tissue. Nucleic Acids Res. 27, 1300–1377.
88 Beaty et al. 34. Peters, D. G., Kassam, A. B.,Yonas, H., O’Hare, E. H., Ferrell, R. E., <strong>and</strong> Brufsky, A. M. (1999) Comprehensive transcript analysis in small quantities of mRNA by SAGE-lite. Nucleic Acids Res. 27, e39. 35. Foss, C. A., Maitra, A., Iacobuzio-Donahue, C., Kern, S., snf Pomper, M. G. (2004) [125I]anti-Claudin 4 <strong>and</strong> [125I]anti-PSCA monoclonal antibodies as novel imaging agents for human pancreatic cancer in xenograft-bearing mice, In Proceedings of the Third Annual Meeting of the Society for Molecular Imaging, St. Louis, MO. 36. Hassan, R., Bera, T., <strong>and</strong> Pastan, I. (2004) Mesothelin: a new target for immunotherapy. Clin. Cancer Res. 10, 3937–3942. 37. Thomas, A. M., Santarsiero, L. M., Lutz, E. R., et al. (2004) Mesothelinspecific CD8(+) T cell responses provide evidence of in vivo cross-priming by antigen-presenting cells in vaccinated pancreatic cancer patients. J. Exp. Med. 200, 297–306. 38. Rosty, C. <strong>and</strong> Goggins, M. (2002) Early detection of pancreatic carcinoma. Hematol. Oncol. Clin. North Am. 16, 37–52. 39. Nichols, L. S., Ashfaq, R., <strong>and</strong> Iacobuzio-Donahue, C. A. (2004) Claudin 4 protein expression in primary <strong>and</strong> metastatic pancreatic cancer: support for use as a therapeutic target. Am. J. Clin. Pathol. 121, 226–230. 40. Michl, P., Buchholz, M., Rolke, M., et al. (2001) Claudin-4: a new target for pancreatic cancer treatment using Clostridium perfringens enterotoxin. Gastroenterology 121, 678–684. 41. Offner, S., Hekele, A., Teichmann, U., et al. (2005) Epithelial tight junction proteins as potential antibody targets for pancarcinoma therapy. Cancer Immunol. Immunother. 54, 431–445. 42. Tuteja, R. <strong>and</strong> Tuteja, N. (2004) Serial analysis of gene expression (SAGE): unraveling the bioinformatics tools. Bioessays 26, 916–922. 43. Lash, A. E., Tolstoshev, C. M., Wagner, L., et al. (2000) SAGEmap: a public gene expression resource. Genome Res. 10, 1051–1060. 44. Lal, A., Lash, A. E., Altschul, S. F., et al. (1999) A public database for gene expression in human cancers. Cancer Res. 59, 5403–5407. 45. Wolters, D. A., Washburn, M. P., <strong>and</strong> Yates, J. R., 3rd. (2001) An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73, 5683–5690. 46. Washburn, M. P., Wolters, D., <strong>and</strong> Yates, J. R., 3rd. (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242–247. 47. Switzer, R. C., 3rd, Merril, C. R., <strong>and</strong> Shifrin, S. (1979) A highly sensitive silver stain for detecting proteins <strong>and</strong> peptides in polyacrylamide gels. Anal. Biochem. 98, 231–237. 48. Neuhoff, V., Arold, N., Taube, D., <strong>and</strong> Ehrhardt, W. (1988) Improved staining of proteins in polyacrylamide gels including isoelectric focusing gels with clear background at nanogram sensitivity using Coomassie Brilliant Blue G-250 <strong>and</strong> R-250. Electrophoresis 9, 255–262.
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METHODS IN MOLECULAR BIOLOGY 360 T
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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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Harnessing the Human Genome 15 The
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34 Imoto et al. (4,5), and Bayesian
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144 Fig. 1. The ribozyme-expression
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148 Sano and Taira ribozymes may cl
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9 Production of siRNA- and cDNA-Tra
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Tumor Antigen Discovery 321 develop
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Tumor Antigen Discovery 323 panel b
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16 Identification of Tumor Antigens
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Immunoproteomics 329 by “shot gun
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17 Protein Arrays A Versatile Toolb
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Protein Arrays 337 Table 1 Classifi
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Protein Arrays 339 fractions from c
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Protein Arrays 343 The ideal proteo
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Protein Arrays 347 49. Yuko Kawahas
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Index 349 Index A Acetyl-CoA carbox
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Index 351 conditional by using FRT
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Index 353 Recombinant tumor antigen