Abstract
The involvement of tumor suppressor genes (TSG) in cancer initiation and progression is well documented in several tumor types such as colon (APC, p53) and breast (BrcA1, BrcA2) cancers. Loss of heterozygosity of distinct chromosomal regions, which are thought to harbor as yet unidentified TSGs, have also been linked to many cancer types. Traditional research approaches such as positional cloning have greatly assisted in elucidation of these genetic factors, and continue to be critical in efforts to understand the nature and role of TSGs in human cancers. In parallel, molecular profiling is a new strategy for analysis of tumors that has emerged based on the information provided by the Human Genome Project and the development of several high-throughput technologies. This new research concept utilizes global measurements of mRNA and protein expression patterns in tumor cells and their normal counterparts in search of the genetic culprits responsible for tumorigenesis (1).
Keywords
- Tumor Suppressor Gene
- Tumor Suppressor Protein
- Laser Capture Microdissection
- Human Genome Project
- Proteomic Tool
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Emmert-Buck, M., Strausberg, R., Krizman, D., et al. (2000) Molecular profiling of clinical tissue specimens: feasibility and applications. Am. J. Pathol. 156, 1109–1115.
Emmert-Buck, M. R., Bonner, R. F., Smith, P. D., et al. (1996) Laser capture microdissection. Science 274, 998–1001.
Gillespie, J. W., Ahram, M., Best, C. J., et al. (2001) The role of tissue microdissection in cancer research. Cancer J. 7, 32–39.
Brown, M. R., Chuaqui, R., Vocke, C. D., et al. (1999) Allelic loss on chromosome arm 8p: analysis of sporadic epithelial ovarian tumors. Gynecol. Oncol. 74, 98–102.
Chung, T. K., Cheung, T. H., Lo, W. K., et al. (2000) Loss of heterozygosity at the short arm of chromosome 3 in microdissected cervical intraepithelial neoplasia. Cancer Lett. 154, 189–194.
Boni, R., Matt, D., Voetmeyer, A., Burg, G., and Zhuang, Z. (1998) Chromosomal allele loss in primary cutaneous melanoma is heterogeneous and correlates with proliferation. J. Invest. Dermatol. 110, 215–217.
Emmert-Buck, M. R., Lubensky, I. A., Dong, Q., et al. (1997) Localization of the multiple endocrine neoplasia type I (MEN1) gene based on tumor loss of heterozygosity analysis. Cancer Res. 57, 1855–1858.
Romagnoli, S., Roncalli, M., Graziani, D., et al. (2001) Molecular alterations of Barrett’s esophagus on microdissected endoscopic biopsies. Lab. Invest. 81, 241–247.
Shivapurkar, N., Sood, S., Wistuba, II, et al. (1999) Multiple regions of chromosome 4 demonstrating allelic losses in breast carcinomas. Cancer Res. 59, 3576–3580.
Shivapurkar, N., Virmani, A. K., Wistuba, II, et al. (1999) Deletions of chromosome 4 at multiple sites are frequent in malignant mesothelioma and small cell lung carcinoma. Clin. Cancer Res. 5, 17–23.
Tannapfel, A., Benicke, M., Katalinic, A., et al. (2000) Frequency of p16(INK4A) alterations and K-ras mutations in intrahepatic cholangiocarcinoma of the liver. Gut 47, 721–727.
Werness, B. A., Parvatiyar, P., Ramus, S. J., et al. (2000) Ovarian carcinoma in situ with germline BRCA1 mutation and loss of heterozygosity at BRCA1 and TP53. J. Natl. Cancer Inst. 92, 1088–1091.
O’Farrell, P. Z. and Goodman, H. M. (1976) Resolution of simian virus 40 proteins in whole cell extracts by two-dimensional electrophoresis: heterogeneity of the major capsid protein. Cell 9, 289–298.
Klose, J. (1975) Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 26, 231–243.
Sanchez, J. C., Rouge, V., Pisteur, M., et al. (1997) Improved and simplified in-gel sample application using reswelling of dry immobilized pH gradients. Electrophoresis 18, 324–327.
Gorg, A., Obermaier, C., Boguth, G., et al. (2000) The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 21, 1037–1053.
Wildgruber, R., Harder, A., Obermaier, C., et al. (2000) Towards higher resolution: two-dimensional electrophoresis of Saccharomyces cerevisiae proteins using overlapping narrow immobilized pH gradients. Electrophoresis 21, 2610–2616.
Rabilloud, T., Adessi, C., Giraudel, A., and Lunardi, J. (1997) Improvement of the solubi-lization of proteins in two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 18, 307–316.
Santoni, V., Rabilloud, T., Doumas, P., et al. (1999) Towards the recovery of hydrophobic proteins on two-dimensional electrophoresis gels. Electrophoresis 20, 705–711.
Chevallet, M., Santoni, V., Poinas, A., et al. (1998) New zwitterionic detergents improve the analysis of membrane proteins by two-dimensional electrophoresis. Electrophoresis 19, 1901–1909.
Berggren, K., Chernokalskaya, E., Steinberg, T. H., et al. (2000) Background-free, high sensitivity staining of proteins in one-and two-dimensional sodium dodecyl sulfate-polyacry-lamide gels using a luminescent ruthenium complex. Electrophoresis 21, 2509–2521.
Vuong, G. L., Weiss, S. M., Kammer, W., et al. (2000) Improved sensitivity proteomics by postharvest alkylation and radioactive labelling of proteins. Electrophoresis 21, 2594–2605.
Blackstock, W. P. and Weir, M. P. (1999) Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol. 17, 121–127.
Humphery-Smith, I. (1998) Proteomics: from small genes to high-throughput robotics. J. Protein Chem. 17, 524–525.
Biemann, K. (1992) Mass spectrometry of peptides and proteins. Annu. Rev. Biochem. 61, 977–1010.
Hunt, D. F., Yates, J. R., 3rd, Shabanowitz, J., Winston, S., and Hauer, C. R. (1986) Protein sequencing by tandem mass spectrometry. Proc. Natl. Acad. Sci. USA 83, 6233–6237.
Qin, J., Herring, C. J., and Zhang, X. (1998) De novo peptide sequencing in an ion trap mass spectrometer with 18O labeling. Rapid Commun. Mass Spectrom. 12, 209–216.
Jungblut, P. R., Zimny-Arndt, U., Zeindl-Eberhart, E., et al. (1999) Proteomics in human disease: cancer, heart and infectious diseases. Electrophoresis 20, 2100–2110.
Celis, J. E., Celis, P., Ostergaard, M., et al. (1999) Proteomics and immunohistochemistry define some of the steps involved in the squamous differentiation of the bladder transitional epithelium: a novel strategy for identifying metaplastic lesions. Cancer Res. 59, 3003–3009.
Celis, J. E., Rasmussen, H. H., Vorum, H., et al. (1996) Bladder squamous cell carcinomas express psoriasin and externalize it to the urine. J. Urol. 155, 2105–2112.
Alaiya, A. A., Franzen, B., Auer, G., and Linder, S. (2000) Cancer proteomics: from identification of novel markers to creation of artifical learning models for tumor classification. Electrophoresis 21, 1210–1217.
Ornstein, D. K., Gillespie, J. W., Paweletz, C. P., et al. (2000) Proteomic analysis of laser capture microdissected human prostate cancer and in vitro prostate cell lines. Electrophoresis 21, 2235–2242.
Emmert-Buck, M. R., Gillespie, J. W., Paweletz, C. P., et al. (2000) An approach to proteomic analysis of human tumors. Mol. Carcinog. 27, 158–165.
Paweletz, C. P., Ornstein, D. K., Roth, M. J., et al. (2000) Loss of annexin 1 correlates with early onset of tumorigenesis in esophageal and prostate carcinoma. Cancer Res. 60, 6293–6297.
Vercoutter-Edouart, A. S., Lemoine, J., Le Bourhis, X., et al. (2001) Proteomic analysis reveals that 14-3-3sigma is down-regulated in human breast cancer cells. Cancer Res. 61, 76–80.
Araki, N., Morimasa, T., Sakai, T., et al. (2000) Comparative analysis of brain proteins from p53-deficient mice by two-dimensional electrophoresis. Electrophoresis 21, 1880–1889.
Minowa, T., Ohtsuka, S., Sasai, H., and Kamada, M. (2000) Proteomic analysis of the small intestine and colon epithelia of adenomatous polyposis coli gene-mutant mice by two-dimensional gel electrophoresis. Electrophoresis 21, 1782–1786.
Cole, A. R., Ji, H., and Simpson, R. J. (2000) Proteomic analysis of colonic crypts from normal, multiple intestinal neoplasia and p53-null mice: a comparison with colonic polyps. Electrophoresis 21, 1772–1781.
Merchant, M. and Weinberger, S. R. (2000) Recent advancements in surface-enhanced laser desorption/ionization–time of flight-mass spectrometry. Electrophoresis 21, 1164–1177.
Paweletz, C. P., Liotta, L. A., and Petricoin, E. F., 3rd. (2001) New technologies for biomarker analysis of prostate cancer progression: Laser capture microdissection and tissue proteomics. Urology 57, 160–163.
Paweletz, C. P., Gillespie, J. W., Ornstein, D. K., et al. (2000) Rapid protein display profiling of cancer progression directly from human tissue using protein biochip. Drug Develop. Res. 49, 34–42.
Vlahou, A., Schellhammer, P. F., Mendrinos, S., et al. (2001) Development of a novel proteomic approach for the detection of transitional cell carcinoma of the bladder in urine. Am. J. Pathol. 158, 1491–1502.
Kononen, J., Bubendorf, L., Kallioniemi, A., et al. (1998) Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat. Med. 4, 844–847.
Schraml, P., Kononen, J., Bubendorf, L., et al. (1999) Tissue microarrays for gene amplification surveys in many different tumor types. Clin. Cancer Res. 5, 1966–1975.
Barlund, M., Forozan, F., Kononen, J., et al. (2000) Detecting activation of ribosomal protein S6 kinase by complementary DNA and tissue microarray analysis. J. Natl. Cancer Inst. 92, 1252–1259.
Bubendorf, L., Kononen, J., Koivisto, P., et al. (1999) Survey of gene amplifications during prostate cancer progression by high-throughout fluorescence in situ hybridization on tissue microarrays Cancer Res. 59, 803–806.
Richter, J., Wagner, U., Kononen, J., et al. (2000) High-throughput tissue microarray analysis of cyclin E gene amplification and overexpression in urinary bladder cancer. Am. J. Pathol. 157, 787–794.
Bowen, C., Bubendorf, L., Voeller, H. J., et al. (2000) Loss of NKX3.1 expression in human prostate cancers correlates with tumor progression. Cancer Res. 60, 6111–6115.
Cahill, D. J. (2001) Protein and antibody arrays and their medical applications. J. Immunol. Meth. 250, 81–91.
Kodadek, T. (2001) Protein microarrays: prospects and problems. Chem. Biol. 8, 105–115.
Emili, A. Q. and Cagney, G. (2000) Large-scale functional analysis using peptide or protein arrays. Nat. Biotechnol. 18, 393–397.
MacBeath, G. and Schreiber, S. L. (2000) Printing proteins as microarrays for high-throughput function determination. Science 289, 1760–1763.
Lueking, A., Horn, M., Eickhoff, H., Bussow, K., Lehrach, H., and Walter, G. (1999) Protein microarrays for gene expression and antibody screening. Anal. Biochem. 270, 103–111.
Bichsel, V. E., Liotta, L. A., and Petricoin, E. F., 3rd. (2001) Cancer proteomics: from biomarker discovery to signal pathway profiling. Cancer J. 7, 69–78.
Paweletz, C. P., Charboneau, L., Bichsel, V. E., et al. (2001) Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene 20, 1981–1989.
Fields, S. and Song, O. (1989) A novel genetic system to detect protein-protein interactions. Nature 340, 245–246.
Li, B. and Fields, S. (1993) Identification of mutations in p53 that affect its binding to SV40 large T antigen by using the yeast two-hybrid system. FASEB J. 7, 957–963.
Iwabuchi, K., Li, B., Bartel, P., and Fields, S. (1993) Use of the two-hybrid system to identify the domain of p53 involved in oligomerization. Oncogene 8, 1693–1696.
Kasof, G. M., Goyal, L., and White, E. (1999) Btf, a novel death-promoting transcriptional repressor that interacts with Bcl-2-related proteins. Mol. Cell. Biol. 19, 4390–4404.
Gronholm, M., Sainio, M., Zhao, F., Heiska, L., Vaheri, A., and Carpen, O. (1999) Homotypic and heterotypic interaction of the neurofibromatosis 2 tumor suppressor protein merlin and the ERM protein ezrin. J. Cell Sci. 112, 895–904.
Sharan, S. K. and Bradley, A. (1998) Functional characterization of BRCA1 and BRCA2: clues from their interacting proteins. J. Mammary Gland Biol. Neoplasia 3, 413–421.
Marston, N. J., Richards, W. J., Hughes, D., Bertwistle, D., Marshall, C. J., and Ashworth, A. (1999) Interaction between the product of the breast cancer susceptibility gene BRCA2 and DSS1, a protein functionally conserved from yeast to mammals. Mol. Cell. Biol. 19, 4633–4642.
Little, N. A., Hastie, N. D., and Davies, R. C. (2000) Identification of WTAP, a novel Wilms’ tumour 1-associating protein. Hum. Mol. Genet. 9, 2231–2239.
Wu, X., Hepner, K., Castelino-Prabhu, S., et al. (2000) Evidence for regulation of the PTEN tumor suppressor by a membrane-localized multi-PDZ domain containing scaffold protein MAGI-2. Proc. Natl. Acad. Sci. USA 97, 4233–4238.
Durfee, T., Mancini, M. A., Jones, D., Elledge, S. J., and Lee, W. H. (1994) The amino-terminal region of the retinoblastoma gene product binds a novel nuclear matrix protein that co-localizes to centers for RNA processing. J. Cell Biol. 127, 609–622.
Yang, R., Gombart, A. F., Serrano, M., and Koeffler, H. P. (1995) Mutational effects on the p16INK4a tumor suppressor protein. Cancer Res. 55, 2503–2506.
Su, L. K., Burrell, M., Hill, D. E., et al. (1995) APC binds to the novel protein EB1. Cancer Res. 55, 2972–2977.
Persson, B. (2000) Bioinformatics in protein analysis. EXS 88, 215–231.
Celis, J. E., Gromov, P., Ostergaard, M., et al. (1996) Human 2-D PAGE databases for proteome analysis in health and disease: http://biobase.dk/cgi-bin/celis. FEBS Lett. 398, 129–134.
O’Donovan, C., Apweiler, R., and Bairoch, A. (2001) The human proteomics initiative (HPI). Trends Biotechnol. 19, 178–181.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2003 Humana Press Inc.
About this protocol
Cite this protocol
Ahram, M., Emmert-Buck, M.R. (2003). Approaches to Proteomic Analysis of Human Tumors. In: El-Deiry, W.S. (eds) Tumor Suppressor Genes. Methods in Molecular Biology™, vol 222. Humana Press, Totowa, NJ. https://doi.org/10.1385/1-59259-328-3:375
Download citation
DOI: https://doi.org/10.1385/1-59259-328-3:375
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-0-89603-986-5
Online ISBN: 978-1-59259-328-6
eBook Packages: Springer Protocols