Abstract
Cancer is the consequence of intra- and extracellular signaling network deregulation that derives from alteration of genetic and proteomic cellular homeostasis. Mapping the individual molecular circuitry of a patient’s tumor cells is the starting point for rational personalized therapy.
While genes and RNA encode information about cellular status, proteins are considered the engine of the cellular machine, as they are the effective elements that drive cellular functions, such as proliferation, migration, differentiation, and apoptosis. Consequently, investigations of the cellular protein network are considered a fundamental tool to understand cellular functions. In the last decades, increasing interest has been focused on the improvement of new technologies for proteomic analysis. In this context, reverse-phase protein microarrays (RPMAs) have been developed to study and analyze posttranslational modifications that are responsible for principal cell functions and activities. This innovative technology allows the investigation of protein activation as a consequence of protein–protein interaction or biochemical reactions, such as phosphorylation, glycosylation, ubiquitination, protein cleavage, and conformational alterations.
Intracellular balance is carefully conserved by constant rearrangements of proteins through the activity of a series of kinases and phosphatases. Therefore, knowledge of the key cellular signaling cascades reveal information regarding the cellular processes driving a tumor’s growth (such as cellular survival, proliferation, invasion, and cell death) and response to treatment.
Alteration to cellular homeostasis, driven by elaborate intra- and extracellular interactions, has become one of the most studied fields in the era of personalized medicine and targeted therapy. RPMA technology is a valid tool that can be applied to protein analysis of several diseases for the potential to generate protein interaction and activation maps that lead to the identification of critical nodes for individualized or combinatorial target therapy.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Liotta, L. A., Espina, V., Mehta, A. I., Calvert, V., Rosenblatt, K., Geho, D. et al. (2003) Protein microarrays: meeting analytical challenges for clinical applications. Cancer Cell 3, 317–25.
Paweletz, C. P., Charboneau, L., Bichsel, V. E., Simone, N. L., Chen, T., Gillespie, J. W. et al. (2001) Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene 20, 1981–9.
Grote, T., Siwak, D. R., Fritsche, H. A., Joy, C., Mills, G. B., Simeone, D. et al. (2008) Validation of reverse phase protein array for practical screening of potential biomarkers in serum and plasma: accurate detection of CA19-9 levels in pancreatic cancer. Proteomics 8, 3051–60.
VanMeter, A. J., Rodriguez, A. S., Bowman, E. D., Jen, J., Harris, C. C., Deng, J. et al. (2008) Laser capture microdissection and protein microarray analysis of human non-small cell lung cancer: differential epidermal growth factor receptor (EGPR) phosphorylation events associated with mutated EGFR compared with wild type. Mol Cell Proteomics 7, 1902–24.
Wulfkuhle, J. D., Speer, R., Pierobon, M., Laird, J., Espina, V., Deng, J. et al. (2008) Multiplexed cell signaling analysis of human breast cancer applications for personalized therapy. J Proteome Res 7, 1508–17.
Rapkiewicz, A., Espina, V., Zujewski, J. A., Lebowitz, P. F., Filie, A., Wulfkuhle, J. et al. (2007) The needle in the haystack: application of breast fine-needle aspirate samples to quantitative protein microarray technology. Cancer 111, 173–84.
Espina, V., Mehta, A. I., Winters, M. E., Calvert, V., Wulfkuhle, J., Petricoin, E. F., 3rd et al. (2003) Protein microarrays: molecular profiling technologies for clinical specimens. Proteomics 3, 2091–100.
Davuluri, G., Espina, V., Petricoin, E. F., 3rd, Ross, M., Deng, J., Liotta, L. A. et al. (2009) Activated VEGF receptor shed into the vitreous in eyes with wet AMD: a new class of biomarkers in the vitreous with potential for predicting the treatment timing and monitoring response. Arch Ophthalmol 127, 613–21.
Longo, C., Patanarut, A., George, T., Bishop, B., Zhou, W., Fredolini, C. et al. (2009) Core-shell hydrogel particles harvest, concentrate and preserve labile low abundance biomarkers. PLoS One 4, e4763.
Mueller, C., Zhou, W., Vanmeter, A., Heiby, M., Magaki, S., Ross, M. M. et al. (2009) The Heme Degradation Pathway is a Promising Serum Biomarker Source for the Early Detection of Alzheimer’s Disease. J Alzheimers Dis
Becker, K. F., Schott, C., Hipp, S., Metzger, V., Porschewski, P., Beck, R. et al. (2007) Quantitative protein analysis from formalin-fixed tissues: implications for translational clinical research and nanoscale molecular diagnosis. J Pathol 211, 370–8.
Bobrow, M. N., Harris, T. D., Shaughnessy, K. J., Litt, G. J. (1989) Catalyzed reporter deposition, a novel method of signal amplification. Application to immunoassays. J Immunol Methods 125, 279–85.
Kornblau, S. M., Tibes, R., Qiu, Y., Chen, W., Kantarjian, H. M., Andreeff, M. et al. (2008) Functional proteomic profiling of AML predicts response and survival. Blood
Hennessy, B. T., Lu, Y., Poradosu, E., Yu, Q., Yu, S., Hall, H. et al. (2007) Pharmacodynamic markers of perifosine efficacy. Clin Cancer Res 13, 7421–31.
Belluco, C., Mammano, E., Petricoin, E., Prevedello, L., Calvert, V., Liotta, L. et al. (2005) Kinase substrate protein microarray analysis of human colon cancer and hepatic metastasis. Clin Chim Acta 357, 180–3.
Silvestri, A., Colombatti, A., Calvert, V. S., Deng, J., Mammano, E., Belluco, C. et al. (2010) Protein pathway biomarker analysis of human cancer reveals requirement for upfront cellular-enrichment processing. Lab Invest 90, 787–96.
Petricoin, E. F., 3rd, Espina, V., Araujo, R. P., Midura, B., Yeung, C., Wan, X. et al. (2007) Phosphoprotein pathway mapping: Akt/mammalian target of rapamycin activation is negatively associated with childhood rhabdomyosarcoma survival. Cancer Res 67, 3431–40.
Espina, V., Wulfkuhle, J. D., Calvert, V. S., VanMeter, A., Zhou, W., Coukos, G. et al. (2006) Laser-capture microdissection. Nat Protoc 1, 586–603.
Emmert-Buck, M. R., Bonner, R. F., Smith, P. D., Chuaqui, R. F., Zhuang, Z., Goldstein, S. R. et al. (1996) Laser capture microdissection. Science 274, 998–1001.
Laemmli, U. K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680–5.
Bonner, R. F., Emmert-Buck, M., Cole, K., Pohida, T., Chuaqui, R., Goldstein, S. et al. (1997) Laser capture microdissection: molecular analysis of tissue. Science 278, 1481,1483.
Popova, T. G., Turell, M. J., Espina, V., Kehn-Hall, K., Kidd, J., Narayanan, A. et al. (2010) Reverse-phase phosphoproteome analysis of signaling pathways induced by Rift valley fever virus in human small airway epithelial cells. PLoS One 5, e13805.
Popova, T., Espina, V., Bailey, C., Liotta, L., Petricoin, E., Popov, S. (2009) Anthrax infection inhibits the AKT signaling involved in the E-cadherin-mediated adhesion of lung epithelial cells. FEMS Immunol Med Microbiol 56, 129–42.
Agarwal, R., Gonzalez-Angulo, A. M., Myhre, S., Carey, M., Lee, J. S., Overgaard, J. et al. (2009) Integrative analysis of cyclin protein levels identifies cyclin b1 as a classifier and predictor of outcomes in breast cancer. Clin Cancer Res 15, 3654–62.
Nishizuka, S., Charboneau, L., Young, L., Major, S., Reinhold, W. C., Waltham, M. et al. (2003) Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc Natl Acad Sci U S A 100, 14229–34.
Accordi, B., Espina, V., Giordan, M., VanMeter, A., Milani, G., Galla, L. et al. (2010) Functional protein network activation mapping reveals new potential molecular drug targets for poor prognosis pediatric BCP-ALL. PLoS One 5, e13552.
Mueller, C., Liotta, L. A., Espina, V. (2010) Reverse phase protein microarrays advance to use in clinical trials. Mol Oncol 4, 461–81.
Bobrow, M. N., Shaughnessy, K. J., Litt, G. J. (1991) Catalyzed reporter deposition, a novel method of signal amplification. II. Application to membrane immunoassays. J Immunol Methods 137, 103–12.
Bobrow, M. N., Litt, G. J., Shaughnessy, K. J., Mayer, P. C., Conlon, J. (1992) The use of catalyzed reporter deposition as a means of signal amplification in a variety of formats. J Immunol Methods 150, 145–9.
Hunyady, B., Krempels, K., Harta, G., Mezey, E. (1996) Immunohistochemical signal amplification by catalyzed reporter deposition and its application in double immunostaining. J Histochem Cytochem 44, 1353–62.
King, G., Payne, S., Walker, F., Murray, G. I. (1997) A highly sensitive detection method for immunohistochemistry using biotinylated tyramine. J Pathol 183, 237–41.
Berggren, K., Steinberg, T. H., Lauber, W. M., Carroll, J. A., Lopez, M. F., Chernokalskaya, E. et al. (1999) A luminescent ruthenium complex for ultrasensitive detection of proteins immobilized on membrane supports. Anal Biochem 276, 129–43.
Berggren, K. N., Schulenberg, B., Lopez, M. F., Steinberg, T. H., Bogdanova, A., Smejkal, G. et al. (2002) An improved formulation of SYPRO Ruby protein gel stain: comparison with the original formulation and with a ruthenium II tris (bathophenanthroline disulfonate) formulation. Proteomics 2, 486–98.
Miller, W. G., Gibbs, E. L., Jay, D. W., Pratt, K. W., Rossi, B., Vojt, C. M. et al. (2006) Preparation and testing of reagent water in the clinical laboratory; Approved Guideline-Fourth Edition. 26. Clinical Laboratory Standards Institute: Wayne, PA
Stillman, B. A., Tonkinson, J. L. (2000) FAST slides: a novel surface for microarrays. Biotechniques 29, 630–5.
Tonkinson, J. L., Stillman, B. A. (2002) Nitrocellulose: a tried and true polymer finds utility as a post-genomic substrate. Front Biosci 7, c1-12.
Rossner, M., Yamada, K. M. (2004) What’s in a picture? The temptation of image manipulation. J Cell Biol 166, 11–5.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Pierobon, M., VanMeter, A.J., Moroni, N., Galdi, F., Petricoin, E.F. (2012). Reverse-Phase Protein Microarrays. In: Espina, V., Liotta, L. (eds) Molecular Profiling. Methods in Molecular Biology, vol 823. Humana Press. https://doi.org/10.1007/978-1-60327-216-2_14
Download citation
DOI: https://doi.org/10.1007/978-1-60327-216-2_14
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-60327-215-5
Online ISBN: 978-1-60327-216-2
eBook Packages: Springer Protocols