Abstract
Phosphate addition is a posttranslational modification of proteins, and this modification can affect the activity and other properties of intracellular proteins. Different animal species can be used to generate phosphosite-specific antibodies as either polyclonals or monoclonals, and each approach offers its own benefits and disadvantages. The validation of phosphosite-specific antibodies requires multiple techniques and tactics to demonstrate their specificity. These antibodies can be used in arrays, flow cytometry, and imaging platforms. The specificity of phosphosite-specific antibodies is vital for their use in proteomics and profiling of disease.
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References
Ubersax JA, Ferrell JE Jr (2007) Mechanisms of specificity in protein phosphorylation. Nat Rev Mol Cell Biol 8:530–541
Manning G, Whyte DB, Martinez R et al (2002) The protein kinase complement of the human genome. Science 298:1912–1934
Tarrant MK, Cole PA (2009) The chemical biology of protein phosphorylation. Annu Rev Biochem 78:797–825
Alonso A, Sasin J, Bottini N et al (2004) Protein phosphatases in the human genome. Cell 117:699–711
Hunter T (2009) Tyrosine phosphorylation: thirty years and counting. Curr Opin Cell Biol 21:140–146
Boyle WJ, van der Geer P, Hunter T (1991) Phosphopeptide mapping and phosphoamino acid analysis by two-dimensional separation on thin-layer cellulose plates. Methods Enzymol 201:201–240
Ross AH, Baltimore D, Eisen HN (1981) Phosphotyrosine-containing proteins isolated by affinity chromatography with antibodies to a synthetic hapten. Nature 294:654–656
Nairn AC, Detre JA, Casnellie JE et al (1982) Serum antibodies that distinguish between the phospho- and dephospho-forms of a phosphoprotein. Nature 299:734–736
Glenney JR Jr, Zokas L, Kamps MP (1988) Monoclonal antibodies to phosphotyrosine. J Immunol Methods 109:277–285
Kanakura Y, Druker B, Cannistra SA et al (1990) Signal transduction of the human granulocyte-macrophage colony-stimulating factor and interleukin-3 receptors involves tyrosine phosphorylation of a common set of cytoplasmic proteins. Blood 76:706–715
Okamoto M, Karasik A, White MF et al (1990) Epidermal growth factor stimulated phosphorylation of a 120-kilodalton endogenous substrate protein in rat hepatocytes. Biochemistry 29:9489–9494
Glenney JR Jr (1989) Tyrosine phosphorylation of a 22-kDa protein is correlated with transformation by Rous sarcoma virus. J Biol Chem 264:20163–20166
Kanner SB, Reynolds AB, Vines RR et al (1990) Monoclonal antibodies to individual tyrosine-phosphorylated protein substrates of oncogene-encoded tyrosine kinases. Proc Natl Acad Sci U S A 87:3328–3332
Towbin H, Staehelin T, Gordon J (1979) Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications. Proc Natl Acad Sci U S A 76:4350–4354
Glenney JR Jr (1992) Tyrosine phosphorylated proteins: mediators of signal transduction from the tyrosine kinases. Biochim Biophys Acta 1134:113–127
Sefton BM (1982) Phosphorylation and metabolism of the transforming protein of Rous sarcoma virus. J Virol 41:813–820
Shankaran H, Ippolito DL, Chrisler WB et al (2009) Rapid and sustained nuclear-cytoplasmic ERK oscillations induced by epidermal growth factor. Mol Syst Biol 5:1–13
Lemeer S, Heck AJ (2009) The phosphoproteomics data explosion. Curr Opin Chem Biol 13:414–420
Kehoe JW, Velappan N, Walbolt M et al (2006) Using phage display to select antibodies recognizing post-translational modifications independently of sequence context. Mol Cell Proteomics 5:2350–2363
Harlow E, Lane D (1988) Antibodies: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
Weng Q-P, Kozlowski M, Belham C et al (1995) Regulation of the p70 S6 kinase by phosphorylation in vivo. J Biol Chem 273:16621–16629
Yung Y, Dolginov Y, Zao Z et al (1997) Detection of ERK activation by a novel monoclonal antibody. FEBS Lett 408:292–296
Campos-Gonzalez R, Glenney JR Jr (1991) Immunodetection of the ligand-activated receptor for epidermal growth factor. Growth Factors 4:305–316
Sternberger LA, Sternberger NH (1983) Monoclonal antibodies distinguish phosphorylated and nonphosphorylated forms of neurofilaments in situ. Proc Natl Acad Sci U S A 80:6126–6130
Heffetz D, Fridkin M, Zick Y (1991) Generation and use of antibodies to phosphothreonine. Methods Enzymol 201:44–52
Wang JY (1991) Generation and use of anti-phosphotyrosine antibodies raised against bacterially expressed abl protein. Methods Enzymol 201:53–65
Briand JP, Muller S, Van Regenmortel MHV (1985) Synthetic peptides as antigens: pitfalls of conjugation methods. J Immunol Methods 78:59–69
Epstein RJ, Druker BJ, Roberts TM et al (1992) Synthetic phosphopeptide immunogens yield activation-specific antibodies to the c-erbB-2 receptor. Proc Natl Acad Sci U S A 89:10435–10439
Edbauer D, Cheng D, Batterton MN et al (2009) Identification and characterization of neuronal mitogen-activated protein kinase substrates using a specific phosphomotif antibody. Mol Cell Proteomics 8:681–695
Shi Y, Dodson GE, Mukhopadhyay PS et al (2007) Identification of carboxyl-terminal MCM3 phosphorylation sites using polyreactive phosphospecific antibodies. J Biol Chem 282:9236–9243
Tam JP, Zavala F (1989) Multiple antigen peptide: a novel approach to increase detection sensitivity of synthetic peptides in solid-phase immunoassays. J Immunol Methods 124:53–61
Spieker-Polet H, Sethupathi P, Yam PC et al (1995) Rabbit monoclonal antibodies: generating a fusion partner to produce rabbit-rabbit hybridomas. Proc Natl Acad Sci U S A 92:9348–9352
Ruff-Jamison S, Campos-Gonzalez R, Glenney JR Jr (1991) Heavy and light variable region sequences and antibody properties of anti-phosphotyrosine antibodies reveal both common and distinct features. J Biol Chem 266:6607–6613
Ruff-Jamison S, Glenney JR Jr (1993) Requirements for both H and L chain V regions, VH and VK joining amino acids, and the unique H chain D region for the high affinity binding of an anti-phosphotyrosine antibody. J Immunol 150:3389–3396
Ruff-Jamison S, Glenner JR Jr (1993) Molecular modeling and site-directed mutagenesis of an anti-phosphotyrosine antibody predicts the combining site and allows the detection of higher affinity interactions. Protein Eng 6:661–668
Tuckey CD, Noren CJ (2002) Selection for mutants improving expression of an anti-MAP kinase monoclonal antibody by filamentous phage display. J Immunol Methods 270:247–257
Campos-Gonzalez R, Glenney JR Jr (1991) Temperature-dependent tyrosine phosphorylation of microtubule-associated protein kinase in epidermal growth factor-stimulated human fibroblasts. Cell Regul 2:663–673
Vaughan MH, Xia X, Wang X et al (2007) Generation and characterization of a novel phospho-specific monoclonal antibody to p120-catenin serine 879. Hybridoma 26:407–415
Borrebaeck CAK, Malmborg AC, Furebring C et al (1992) Kinetic analysis of recombinant antibody-antigen interactions: relation between structural domains and antigen binding. Nat Biotechnol 10:697–698
Michalewski MP, Kaczmarski W, Golabek A et al (2002) Immunoblotting with anti-phosphoamino acid antibodies: importance of the blocking solution. Anal Biochem 276:254–257
Song KS, Tang Z, Lisanti MP (1997) Mutational analysis of the properties of caveolin-1. A novel role for the C-terminal domain in mediating homo-typic caveolin-caveolin interactions. J Biol Chem 271:4398–4403
Heinrich MC, Griffith DJ, Druker BJ et al (2000) Inhibition of c-kit receptor tyrosine kinase kinase activity by STI571, a selective tyrosine kinase inhibitor. Blood 96:925–932
Nelson EA, Walker SR, Kepich A et al (2008) Nifuroxazide inhibits survival of multiple myeloma cells by directly inhibiting STAT3. Blood 112:5095–5102
Hardie DG, Haystead TAJ, Sim ATR (2001) Use of okadaic acid to inhibit protein phosphatases in intact cells. Methods Enzymol 201:531–538
Gordon JA (2001) Use of vanadate as protein-phosphotyrosine phosphatase inhibitor. Methods Enzymol 201:581–586
Evans GA, Garcia GG, Erwin R et al (1994) Pervanadate stimulates the effects of interleukin-2 (IL-2) in human T cells and provides evidence for the activation of two distinct tyrosine kinase pathways by IL-2. J Biol Chem 269:23407–23412
Ruff SJ, Chen K, Cohen S (1997) Peroxovanadate induces tyrosine phosphorylation of multiple signaling proteins in mouse liver and kidney. J Biol Chem 272:1263–1267
Yang TT, Yu RY, Agadir A et al (2008) Integration of protein kinases mTOR and extracellular signal-regulated kinase 5 in regulating nucleocytoplasmic localization of NFATc4. Mol Cell Biol 28:3489–3501
Espina V, Edmiston KH, Heiby M et al (2008) A portrait of tissue phosphoprotein stability in the clinical tissue procurement process. Mol Cell Proteomics 7:1998–2018
Gilbert C, Rollet-Labelle E, Con AC, Naccache PH (2002) Immunoblotting and sequential lysis protocols for the analysis of tyrosine phosphorylation-dependent signaling. J Immnol Methods 271:185–201
Skolnik EY, Lee CH, Batzer A et al (1993) The SH2/SH3 domain-containing protein GRB2 interacts with tyrosine-phosphorylated IRS1 and Sch: implications for insulin control of ras signaling. EMBO J 12:1929–1936
Barbareschi M, Girlando S, Mauri FM et al (1994) Quantitative growth fraction evaluation with MIB1 and Ki67 antibodies in breast carcinomas. Am J Clin Pathol 102:171–175
Mandell JW (2003) Phosphorylation state-specific antibodies. Applications in investigative and diagnostic pathology. Am J Pathol 163:1687–1698
Bordeaux J, Welsh AW, Agarwal S et al (2010) Antibody validation. Biotechniques 48:197–209
Mandell JW (2008) Immunohistochemical assessment of protein phosphorylation state: the dream and the reality. Histochem Cell Biol 130:465–471
Kalyuzhny AE (2009) The dark side of the immunohistochemical moon: industry. J Histochem Cytochem 57:1099–1101
Krutzik PO, Irish JM, Nolan GP et al (2004) Analysis of protein phosphorylation and cellular signaling events by flow cytometry: techniques and clinical applications. Clin Immunol 110:206–221
Perez OD, Mitchell D, Campos R et al (2005) Multiparameter analysis of intracellular phosphoepitopes in immunophenotyped cell populations by flow cytometry. Curr Protoc Cytom 6:1–22
Chow S, Patel H, Hedley DW (2001) Measurement of MAP kinase activation by flow cytometry using phospho-specific antibodies to MEK and ERK: potential for pharmacodynamic monitoring of signal transduction inhibitors. Cytometry 46:72–78
Lombardi Givan A (2001) Flow cytometry. First principles, 2nd edn. Wiley-Liss Press, New York
Smith CL, Debouk C, Rosenberg M et al (1988) Phosphorylation of ferine residue 89 of human adenovirus E1A proteins is responsible for their characteristic electrophoretic mobility shits, and its mutation affects biological function. J Virol 63:1569–1577
Wegener AD, Jones LR (1984) Phosphorylation-induced mobility shift in phospholamban in sodium dodecyl sulfate-polyacrylamide gels. Evidence for a protein structure consisting of multiple identical phosphorylatable subunits. J Biol Chem 259:1834–1841
Jorgensen CS, Jagd M, Sorensen BK et al (2004) Efficacy and compatibility with mass spectrometry of methods for elution of proteins from sodium dodecyl sulfate-polyacrylamide gels and polyvinyldifluoride membranes. Anal Biochem 330:87–97
Forrer P, Tamaskovic R, Jaussi R (1998) Enzyme-linked immunosorbent assay for measurement of JNK, ERK and p38 kinase activities. Biol Chem 379:1101–1111
Suzuki S, Tamai K, Yoshida S (2002) Enzyme-linked immunosorbent assay for distinct cyclin-dependent kinase activities using phosphorylation-site-specific anti pRB monoclonal antibodies. Anal Biochem 301:65–74
Offterdinger M, Bastiaens PI (2008) Prolonged EGFR signaling by ERBB2-mediated sequestration at the plasma membrane. Traffic 9:147–155
Loos T, Mortier A, Gouwy M et al (2008) Citrullination of CXCL10 and CXCL11 by peptidylarginine deiminase: a naturally occurring posttranslational modification of chemokines and new dimension of immunoregulation. Blood 112:2648–2656
Ramos JW (2008) The regulation of extracellular signal-regulated kinase (ERK) in mammalian cells. Int J Biochem Cell Biol 40:2707–2719
Gonzalez E, McGraw TE (2009) The AKT kinases: isoform specificity in metabolism and cancer. Cell Cycle 8:2502–2508
Ribeiro-Oliveira A Jr, Franchi G, Kola B et al (2008) Protein western array analysis in human pituitary tumors: insights and limitations. Endocr Relat Cancer 15:1099–1114
Pelech S, Sutter C, Zhang H (2003) Kinetworks protein kinase multiblot analysis. Methods Mol Biol 218:99–111
Ciaccio MF, Wagner JP, Chuu C-P et al (2010) Systems analysis of EGF receptor signaling dynamics with microwestern arrays. Nat Methods 7:148–155
Rikova K, Guo A, Zeng Q et al (2007) Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 131:1190–1203
Mayya V, Lundgren DH, Hwang S-I et al (2009) Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. Sci Signal 2:ra46, 1–16
Fan A, Deb-Basu D, Orban MW et al (2009) Nanofluidic proteomic assay for serial analysis of oncoprotein activation in clinical samples. Nat Med 15:566–571
Hughes TR, Shoemaker DD (2001) DNA microarrays for expression profiling. Curr Opin Chem Biol 5:21–25
Andersson O, Kozlowski M, Garachtchenko T et al (2005) Determination of relative protein abundance by internally normalized ratio algorithm with antibody arrays. J Proteome Res 4:758–767
Pelech S, Jelinkova L, Susor A et al (2008) Antibody microarray analyses of signal transduction protein expression and phosphorylation during porcine oocyte maturation. J Proteome Res 7:2860–2871
MacBeath G (2002) Protein microarrays and proteomics. Nat Genet 32:526–532
Russo G, Zegar C, Giordano A (2003) Advantages and limitations of microarray technology in human cancer. Oncogene 22:6497–6507
Nielsen UB, Cardone MH, Sinskey AJ et al (2003) Profiling receptor kinase activation by using ab microarrays. Proc Natl Acad Sci U S A 100:9330–9335
Liu X, Kim P, Kirkland R et al (2009) Prevalence of activated & total p95HER2 and other receptor tyrosine kinases in breast cancer. AACR San Antonio Breast Cancer Symposium Abstract # 3053
Paweletz CP, Charboneau L, Bichsel VE 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
Espina V, Woodhouse EC, Wulfkuhle J et al (2004) Protein microarray detection strategies: focus on direct detection technologies. J Immunol Methods 290:121–133
Spurrier B, Ramalingam S, Nishizuka S (2008) Reverse-phase protein lysate microarrays for cell signaling analysis. Nat Protoc 3:1796–1808
Chan SM, Ermann J, Su L et al (2004) Protein microarrays for multiplex analysis of signal transduction pathways. Nat Med 10:1390–1396
Natarajan Mendes K, Nicorici D, Cogdell D et al (2007) Analysis of signaling pathways in 90 cancer cell lines by protein lysate array. J Proteome Res 6:2753–2767
Schweitzer B, Roberts S, Grimwade B et al (2002) Multiplex protein profiling on microarrays by rolling-circle amplification. Nat Biotechnol 20:359–365
Dahut WL, Scripture C, Posadas E et al (2008) A phase II clinical trial of sorafenib in androgen-independent prostate cancer. Clin Cancer Res 14:209–214
Tan CSH, Bodenmiller B, Pascualescu A et al (2009) Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Sci Signal 2:ra39, 1–13
Drucker BJ (2009) Perspectives on the development of imatinib and the future of cancer research. Nat Med 10:1149–1152
Jilani I, Kanttarjian H, Gorre M et al (2008) Phosphorylation levels of BCR-ABL, CrkL, AKT, and STAT5 in imatinib-resistant chronic myeloid leukemia cells implicate alternative pathway usage as a survival strategy. Leuk Res 32:643–649
Irish JM, Kotecha N, Nolan GP (2006) Mapping normal and cancer cell signaling networks: towards single-cell proteomics. Nat Rev Cancer 6:146–155
Juan G, Gruenwald S, Darzynkiewicz (1998) Phosphorylation of retinoblastoma susceptibility gene protein assayed in individual lymphocytes during their mitogenic stimulation. Exp Cell Res 239:104–110
Juan G, Traganos F, Darzynkiewicz Z (1999) Histone H3 phosphorylation in human monocytes and during HL-60 cell differentiation. Exp Cell Res 246:212–220
Zell T, Khoruts A, Ingulli E et al (2001) Single-cell analysis of signal transduction in CD4 T cells stimulated by antigen in vivo. Proc Natl Acad Sci U S A 98:10805–10810
Krutzik PO, Hale MB, Nolan GP (2005) Characterization of the murine immunological signaling network with phosphospecific flow cytometry. J Immunol 175:2366–2373
Lu XP, Alpdogan O, Lin J et al (2008) STAT-3 and ERK1/2 phosphorylation are critical for T-cell activation and graft-versus-host disease. Blood 112:5254–5258
Perez OD, Nolan GP (2002) Simultaneous measurement of multiple active kinase states using polychromatic flow cytometry. Nat Biotechnol 20:155–162
Shachaf CM, Elchuri SV, Koh AL et al (2009) A novel method for detection of phosphorylation in single cells by surface enhanced Raman scattering (SERS) using composite organic-inorganic nanoparticles. PLoS One 4:e5206, 1–12
Irish JM, Hovland R, Krutzik PO et al (2004) Single cell profiling of potentiated phospho-protein networks in cancer cells. Cell 118:217–228
Hale MB, Krutzik PO, Samra SS et al (2009) Stage dependent aberrant regulation of cytokine-STAT signaling in murine systemic lupus erythematosus. PLoS One 4:e6756, 1–10
Krutzik PO, Nolan GP (2006) Fluorescent cell barcoding in flow cytometry allows high-throughput drug screening and signaling profiling. Nat Methods 3:361–368
Pritchard JR, Cosgrove BD, Hemann MT et al (2009) Three-kinase inhibitor combination recreates multipathway effects of a geldanamycin analogue on hepatocellular carcinoma cell death. Mol Cancer Ther 8:2183–2192
Morgan E, Varro R, Sepulveda H et al (2004) Cytometric bead array: a multiplexed assay platform with applications in various areas of biology. Clin Immunol 110:252–266
Chen L, Huynh L, Apgar J et al (2008) ZA-70 enhances IgM signaling independent of its kinase activity in chronic lymphocytic leukemia. Blood 111:2685–2692
Massarelli E, Liu DD, Lee JJ et al (2005) Akt activation correlates with adverse outcome in tongue cancer. Cancer 104:2430–2436
Smitz KJ, Otterbach F, Callies R et al (2004) Prognostic relevance of activated Akt kinase in node-negative breast cancer: a clinicopathological study of 99 cases. Mod Pathol 17:15–21
Okamoto I, Kenyon LC, Emlet DR et al (2003) Expression of activated EGFRvIII in small cell lung cancer. Cancer Sci 94:50–56
D’Andrea MR, Mel JM, Tuman RW et al (2005) Validation of in vivo pharmacodynamic activity of a novel PDGF receptor tyrosine kinase inhibitor using immunohistochemistry and quantitative image analysis. Mol Cancer Ther 4:1198–1204
Kong A, Leboucher P, Leek R et al (2006) Prognostic value of an activation state marker for epidermal growth factor receptor in tissue microarrays of head and neck cancer. Cancer Res 66:2834–2843
VanMeter AJ, Rodriguez AS, Bowman ED et al (2008) Laser capture microdissection and protein microarray analysis of human non-small cell lung cancer. Mol Cell Proteomics 7:1902–1924
Nagai Y, Miyasaki M, Akoi R et al (2000) A fluorescent indicator for visualizing cAMP-induced phosphorylation in vivo. Nat Biotechnol 18:313–316
Ng T, Squire A, Hansra G et al (1999) Imaging protein kinase C alpha activation in cells. Science 283:2085–2089
Tomida T, Takekawa M, O’Grady P et al (2009) Stimulus-specific distinctions in spatial and temporal dynamics of stress-activated protein kinase kinase kinases revealed by a fluorescence resonance energy transfer biosensor. Mol Cell Biol 29:6117–6127
Ting AY, Kain KH, Klemke RL et al (2001) Genetically encoded fluorescent reporters of protein tyrosine kinase activities in living cells. Proc Natl Acad Sci U S A 98:15003–15008
Kelleher MT, Fruhwirth G, Patel G et al (2009) The potential of optical proteomic technologies to individualize prognosis and guide rational treatment for cancer patients. Target Oncol 4:235–252
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Brumbaugh, K., Liao, WC., Houchins, J.P., Cooper, J., Stoesz, S. (2017). Phosphosite-Specific Antibodies: A Brief Update on Generation and Applications. In: Kalyuzhny, A. (eds) Signal Transduction Immunohistochemistry. Methods in Molecular Biology, vol 1554. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6759-9_1
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