Skip to main content

Advertisement

Antibody-based tissue profiling as a tool for clinical proteomics

Article metrics

Abstract

Here, we show a strategy for high-throughput antibody-based tissue profiling with the aim to create an atlas of protein expression patterns in normal human tissues and cancer tissues representing the 20 most prevalent cancer types. A set of standardized tissue microarrays (TMAs) was produced to allow for rapid screening of a multitude of different cells and tissues using immunohistochemistry. Eight TMA blocks were produced containing 48 different normal human tissues in triplicate and cancer tissue from 216 individually different tumors in duplicate. Sections from these blocks were immunohistochemically stained using five commercial and five in-house generated antibodies. Digital images for annotation of expression profiles were generated using a semiautomated approach. Five hundred seventy-six images and annotation data corresponding to a total of 30 Gbytes of data were collected for each antibody. The data presented here suggest that antibody-based profiling of protein expression in tissues can be used as a valuable tool in clinical proteomics.

References

  1. 1.

    Miettinen, M. (1993). Immunohistochemistry in tumour diagnosis. Ann. Med. 25:221–233.

  2. 2.

    Gown, A. (2002). Genogenic immunohistochemistry: a new era in diagnostic immunohistochemistry. Curr. Diagn. Pathol. 8:193–200.

  3. 3.

    Chu, P.G., Chang, K.L., Arber, D.A., and Weiss, L.M. (1999). Practical applications of immunohistochemistry in hematolymphoid neoplasms. Ann. Diagn. Pathol. 3:104–133.

  4. 4.

    Abbondanzo, S.L. (1999). Paraffin immunohistochemistry as an adjunct to hematopathology. Ann. Diagn. Pathol. 3:318–327.

  5. 5.

    Dabbs, D.J. (2002). Diagnostic Immunohistochemistry, Churchill Livingstone, Philadelphia, PA.

  6. 6.

    Backvall, H., Stromberg, S., Gustafsson, A., Asplund, A., Sivertsson, A., Lundeberg, J., et al. (2004). Mutation spectra of epidermal p53 clones adjacent to basal sell carcinoma and squamous cell carcinoma. Exp. Dermatol. 13:643–650.

  7. 7.

    Warford, A., Howat, W., and McCafferty, J. (2004). Expression profiling by high-throughput immunohistochemistry. J. Immunol. Methods 290:81–92.

  8. 8.

    Agaton, C., Galli, J., Hoiden Guthenberg, I., Janzon, L., Hansson, M., Asplund, A., et al. (2003). Affinity proteomics for systematic protein profiling of chromosome 21 gene products in human tissues. Mol. Cell. Proteomics 2:405–414.

  9. 9.

    Agaton, C., Falk, R., Hoiden Guthenberg, I., Gostring, L., Uhlen, M., and Hober, S. (2004). Selective enrichment of monospecific polyclonal antibodies for antibody-based proteomics efforts. J. Chromatogr. A 1043:33–40.

  10. 10.

    Simon, R., Mirlacher, M., and Sauter, G. (2003). Tissue microarrays in cancer diagnosis. Expert Rev. Mol. Diagn. 3:421–430.

  11. 11.

    Kraaz, W., Risberg, B., and Hussein, A. (1988). Multiblock: an aid in diagnostic immunohistochemistry. J. Clin. Pathol. 41:1337.

  12. 12.

    Battifora, H. (1986). The multitumor (sausage) tissue block: novel method for immunohistochemical antibody testing. Lab. Invest. 55:244–248.

  13. 13.

    Wan, W.H., Fortuna, M.B., and Furmanski, P. (1987). A rapid and efficient method for testing immunohistochemical reactivity of monoclonal antibodies against multiple tissue samples simultaneously. J. Immunol. Methods 103:121–129.

  14. 14.

    Kononen, J., Bubendorf, L., Kallioniemi, A., Barlund, M., Schraml, P., Leighton, S., et al. (1998). Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat. Med. 4:844–847.

  15. 15.

    Kallioniemi, O.P., Wagner, U., Kononen, J., and Sauter, G. (2001). Tissue microarray technology for high-throughput molecular profiling of cancer. Hum. Mol. Genet. 10:657–662.

  16. 16.

    Wester, K., Asplund, A., Backvall, H., Micke, P., Derveniece, A., Hartmane, I., et al. (2003). Zinc-based fixative improves preservation of genomic DNA and proteins in histoprocessing of human tissues. Lab. Invest. 83:889–899.

  17. 17.

    Rimm, D.L., Camp, R.L., Charette, L.A., Costa, J., Olsen, D.A., and Reiss, M. (2001). Tissue microarray: a new technology for amplification of tissue resources. Cancer J. 7:24–31.

  18. 18.

    Shi, S.R., Cote, R.J., and Taylor, C.R. (2001). Antigen retrieval techniques: current perspectives. J. Histochem. Cytochem. 49:931–937.

  19. 19.

    Becich, M.J. (2001). The role of the pathologist as tissue refiner and data miner: the impact of functional genomics on the modern pathology laboratory and the critical roles of pathology informatics and bioinformatics. Mol. Diagn. 5:287–299.

  20. 20.

    Camp, R.L., Chung, G.G., and Rimm, D.L. (2002). Automated subcellular localization and quantification of protein expression in tissue microarrays. Nat. Med. 8:1323–1327.

  21. 21.

    Wester, K., Andersson, A.C., Ranefall, P., Bengtsson, E., Malmstrom, P.U., and Busch, C. (2000). Cultured human fibroblasts in agarose gel as a multi-functional control for immunohistochemistry. Standardization Of Ki67 (MIB1) assessment in routinely processed urinary bladder carcinoma tissue. J. Pathol. 190:503–511.

  22. 22.

    Quackenbush, J. (2001). Computational analysis of microarray data. Nat. Rev. Genet. 2:418–427.

  23. 23.

    Sorlie, T., Tibshirani, R., Parker, J., Hastie, T., Marron, J.S., Nobel, A., et al. (2003). Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc. Natl. Acad. Sci. USA 100:8418–8423.

  24. 24.

    Cleator, S. and Ashworth, A. (2004). Molecular profiling of breast cancer: clinical implications. Br. J. Cancer 90:1120–1124.

  25. 25.

    Braunschweig, T., Chung, J.Y., and Hewitt S.M. (2004). Perspectives in tissue microarrays. Comb. Chem. High Throughput Screen. 7:575–585.

Download references

Author information

Correspondence to Caroline Kampf.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Kampf, C., Andersson, A., Wester, K. et al. Antibody-based tissue profiling as a tool for clinical proteomics. Clin Proteom 1, 285–299 (2004) doi:10.1385/CP:1:3-4:285

Download citation

Key words

  • Protein epitope signature tags
  • tissue microarray
  • protein atlas
  • antibody-based proteomics
  • monospecific antibodies