3,001
Views
54
CrossRef citations to date
0
Altmetric
Review

High-content affinity-based proteomics: unlocking protein biomarker discovery

, , , &
Pages 1013-1022 | Published online: 09 Jan 2014

References

  • Hood L, Heath JR, Phelps ME, Lin B. Systems biology and new technologies enable predictive and preventative medicine. Science306(5696), 640–643 (2004).
  • Bueno-de-Mesquita JM, van Harten WH, Retel VP et al. Use of 70-gene signature to predict prognosis of patients with node-negative breast cancer: a prospective community-based feasibility study (RASTER). Lancet Oncol.8(12), 1079–1087 (2007).
  • Cardoso F, Van’t Veer L, Rutgers E et al. Clinical application of the 70-gene profile: the MINDACT trial. J. Clin. Oncol.26(5), 729–735 (2008).
  • Knauer M, Mook S, Rutgers EJ et al. The predictive value of the 70-gene signature for adjuvant chemotherapy in early breast cancer. Breast Cancer Res. Treat.120(3), 655–661 (2010).
  • Mamounas EP, Tang G, Fisher B et al. Association between the 21-gene recurrence score assay and risk of locoregional recurrence in node-negative, estrogen receptor-positive breast cancer: results from NSABP B-14 and NSABP B-20. J. Clin. Oncol.28(10), 1677–1683 (2010).
  • Lo SS, Mumby PB, Norton J et al. Prospective multicenter study of the impact of the 21-gene recurrence score assay on medical oncologist and patient adjuvant breast cancer treatment selection. J. Clin. Oncol.28(10), 1671–1676 (2010).
  • Albain KS, Barlow WE, Shak S et al. Prognostic and predictive value of the 21-gene recurrence score assay in postmenopausal women with node-positive, oestrogen-receptor-positive breast cancer on chemotherapy: a retrospective analysis of a randomised trial. Lancet Oncol.11(1), 55–65 (2010).
  • Gilad S, Meiri E, Yogev Y et al. Serum microRNAs are promising novel biomarkers. PloS ONE3(9) e3148 (2008).
  • Rosenfeld N, Aharonov R, Meiri E et al. MicroRNAs accurately identify cancer tissue origin. Nat. Biotechnol.26(4), 462–469 (2008).
  • Wang J, Chen J, Chang P et al. MicroRNAs in plasma of pancreatic ductal adenocarcinoma patients as novel blood-based biomarkers of disease. Cancer Prev. Res.2(9), 807–813 (2009).
  • Paik S, Shak S, Tang G et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N. Engl. J. Med.351(27), 2817–2826 (2004).
  • Zichi D, Eaton B, Singer B, Gold L. Proteomics and diagnostics: let’s get specific, again. Curr. Opin. Chem. Biol.12(1), 78–85 (2008).
  • de Sousa Abreu R, Penalva LO, Marcotte EM, Vogel C. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Mol. Biosyst.5(12), 1512–1526 (2009).
  • Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science324(5924), 218–223 (2009).
  • Pascal LE, True LD, Campbell DS et al. Correlation of mRNA and protein levels: cell type-specific gene expression of cluster designation antigens in the prostate. BMC Genomics9, 246 (2008).
  • Guo Y, Xiao P, Lei S et al. How is mRNA expression predictive for protein expression? A correlation study on human circulating monocytes. Acta Biochim. Biophys. Sin.40(5), 426–436 (2008).
  • Lu P, Vogel C, Wang R, Yao X, Marcotte EM. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol.25(1), 117–124 (2007).
  • Baek D, Villén J, Shin C et al. The impact of microRNAs on protein output. Nature455(7209), 64–71 (2008).
  • Liu N, Olson EN. MicroRNA regulatory networks in cardiovascular development. Dev. Cell18(4), 510–525 (2010).
  • Williams AH, Valdez G, Moresi V et al. MicroRNA-206 delays ALS progression and promotes regeneration of neuromuscular synapses in mice. Science326(5959), 1549–1554 (2009).
  • Mattick JS. RNA as the substrate for epigenome–environment interactions: RNA guidance of epigenetic processes and the expansion of RNA editing in animals underpins development, phenotypic plasticity, learning, and cognition. BioEssays32(7), 548–552 (2010).
  • Selbach M, Schwanhäusser B, Thierfelder N et al. Widespread changes in protein synthesis induced by microRNAs. Nature455(7209), 58–63 (2008).
  • Roth A, Breaker RR. The structural and functional diversity of metabolite-binding riboswitches. Ann. Rev. Biochem.78, 305–334 (2009).
  • Weinberg Z, Perreault J, Meyer MM, Breaker RR. Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. Nature462(7273), 656–659 (2009).
  • Subramanian J, Simon R. Gene expression-based prognostic signatures in lung cancer: ready for clinical use? J. Natl Cancer Inst.102(7), 464–474 (2010).
  • Pass HI, Goparaju C, Ivanov S et al. hsa-miR-29c* is linked to the prognosis of malignant pleural mesothelioma. Cancer Res.70(5), 1916–1924 (2010).
  • Ferracin M, Veronese A, Negrini M. Micromarkers: miRNAs in cancer diagnosis and prognosis. Expert Rev. Mol. Diagn.10(3), 297–308 (2010).
  • Rosenwald S, Gilad S, Benjamin S et al. Validation of a microRNA-based qRT-PCR test for accurate identification of tumor tissue origin. Mod. Pathol.23(6), 814–823 (2010).
  • International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature431(7011), 931–945 (2005).
  • Morozova O, Hirst M, Marra MA. Applications of new sequencing technologies for transcriptome analysis. Annu. Rev. Genomics Hum. Genet.10, 135–151 (2009).
  • Lashkari DA, DeRisi JL, McCusker JH et al. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl Acad. Sci. USA94(24), 13057–13062 (1997).
  • Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science270(5235), 467–470 (1995).
  • Mardis ER. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet.9, 387–402 (2008).
  • Goetz T. Sergey Brin’s search for a Parkinson’s cure. Wired22, 107–113 (2010).
  • Glass DJ. A critique of the hypothesis, and a defense of the question, as a framework for experimentation. Clin. Chem.56(7), 1080–1085 (2010).
  • Nabel GJ. The coordinates of truth. Science326, 53–54 (2009).
  • Kell DB, Oliver SG. Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. BioEssays26(1), 99–105 (2004).
  • Lander AD. The edges of understanding. BMC Biol.8, 40 (2010).
  • O’Farrell PH. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem.250(10), 4007–4021 (1975).
  • Addona TA, Abbatiello SE, Schilling B et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring – based measurements of proteins in plasma. Nat. Biotechnol.27(7), 633–641 (2009).
  • Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol.24(8), 971–983 (2006).
  • Parker CE, Pearson TW, Anderson NL, Borchers CH. Mass-spectrometry-based clinical proteomics – a review and prospective. Analyst135(8), 1830–1838 (2010).
  • Oudin J. Methode d’analyze immunochimique par precipitation specifique en milieu gelifie. CR Acad. Sci. Paris222, 115–116 (1946).
  • Ouchterlony O. Antigen-antibody reactions in gels. Acta Path. Microbiol. Scand.26(4), 507–515 (1949).
  • Ouchterlony O. In vitro method for testing the toxinproducing capacity of diphtheria bacteria. Acta Pathol. Microbiol. Scand.26(4), 516–524 (1949).
  • Yalow RS, Berson SA. Immunoassay of endogenous plasma insulin in man. J. Clin. Invest.39, 1157–1175 (1960).
  • Wide L, Porath J. Radioimmunoassay of proteins with the use of Sephadex-coupled antibodies. Biochem. Biophys. Acta30, 247–260 (1966).
  • Nakane P, Pierce G. Enzyme-labeled antibodies for the light and electron microscopic localization of tissue antigens. J. Cell. Biol. (33), 307–318 (1967).
  • Avrameas S, Uriel J. Methode de marquage d’antigenes et d’anticorps avec des enzymes et son application en immunodiffusion. CR Acad. Sci. Paris262, 2543–2545 (1966).
  • VanWeeman B, Schuurs A. Immunoassay using antigen-enzyme conjugates. FEBS Lett.15(3), 232–236 (1971).
  • Engvall E, Perlmann P. Enzyme-linked immunosorbent assay (ELISA). Quantitative assay of immunoglobulin G. Immunochemistry8, 871–874 (1971).
  • Haab BB, Dunham MJ, Brown PO. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol.2(2), research0004 (2001).
  • Schröder C, Jacob A, Tonack S et al. Dual-color proteomic profiling of complex samples with a microarray of 810 cancer-related antibodies. Mol. Cell. Proteomics9(6), 1271–1280 (2010).
  • Borrebaeck CA, Wingren C. Design of high-density antibody microarrays for disease proteomics: key technological issues. J. Proteomics72(6), 928–935 (2009).
  • Borrebaeck CA, Wingren C. High-throughput proteomics using antibody microarrays: an update. Expert Rev. Mol. Diagn.7(5), 673–686 (2007).
  • Seurynck-Servoss SL, White AM, Baird CL, Rodland KD, Zangar RC. Evaluation of surface chemistries for antibody microarrays. Anal. Biochem.371(1), 105–115 (2007).
  • Schweitzer B, Roberts S, Grimwade B et al. Multiplexed protein profiling on microarrays by rolling-circle amplification. Nat. Biotechnol.20(4), 359–365 (2002).
  • Sun H, Chua M, Yang D et al. Antibody arrays identify potential diagnostic markers of hepatocellular carcinoma. Biomarker Insights3, 1–18 (2008).
  • Fredriksson S, Dixon W, Ji H et al. Multiplexed protein detection by proximity ligation for cancer biomarker validation. Nat. Methods4(4), 327–329 (2007).
  • Anderson NL. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics1(11), 845–867 (2002).
  • Domenici E, Willé DR, Tozzi F et al. Plasma protein biomarkers for depression and schizophrenia by multi analyte profiling of case–control collections. PloS ONE5(2) e9166 (2010).
  • Kim BK, Lee JW, Park PJ et al. The multiplex bead array approach to identifying serum biomarkers associated with breast cancer. Breast Cancer Res.11(2), R22 (2009).
  • Rissin DM, Kan CW, Campbell TG et al. Single-molecule enzyme-linked immunosorbent assay detects serum proteins at subfemtomolar concentrations. Nat. Biotechnol.28(6), 595–599 (2010).
  • Tuerk C, Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science249(4968), 505–510 (1990).
  • Ellington A, Szostak J. In vitro selection of RNA molecules that bind specific ligands. Nature346(6287), 818–822 (1990).
  • Gold L, Ayers D, Bertino J et al. Aptamer-based multiplexed proteomic technology for biomarker discovery. PloS ONE (2010) (In press)
  • Ostroff R, Bigbee W, Franklin W et al. Unlocking biomarker discovery: large scale application of aptamer proteomic technology for early detection of lung cancer. PloS ONE (2010) (In press).
  • Zichi D, Koga T, Greef C, Ostroff R, Petach H. Photoaptamer technology: development of multiplexed microarray protein assays. Clin. Chem.48(10) 1865–1868 (2002).
  • Smith D, Collins BD, Heil J, Koch TH. Sensitivity and specificity of photoaptamer probes. Mol. Cell. Proteomics2(1), 11–18 (2003).
  • Petach H. Dimensionality is the issue: use of photoaptamers in protein microarrays. Curr. Opin. Biotechnol.13(4), 309–314 (2002).
  • Bock C, Coleman M, Collins B et al. Photoaptamer arrays applied to multiplexed proteomic analysis. Proteomics4(3), 609–618 (2004).
  • Keeney TR, Bock C, Gold L et al. Automation of the SomaLogic proteomics assay: a platform for biomarker discovery. JALA14(6), 360–366 (2009).
  • Ostroff R, Foreman T, Keeney TR et al. The stability of the circulating human proteome to variations in sample collection and handling procedures measured with an aptamer-based proteomics array. J. Proteomics73(3), 649–666 (2010).
  • Gold L, Janjic N, Jarvis T et al. Aptamers and the RNA world, past and present. In: RNA World IV. Atkins JF, Gesteland RF, Cech T (Eds). Cold Spring Harbor Laboratory Press, NY, USA, 1–10 (2010).
  • Smith D. Sensitivity and specificity of photoaptamer probes. Mol. Cell. Proteomics2(1), 11–18 (2002).
  • Hopfield JJ, Yamane T, Yue V, Coutts SM. Direct experimental evidence for kinetic proofreading in amino acylation of tRNAIle. Proc. Natl Acad. Sci. USA73(4), 1164–1168 (1976).
  • Hopfield JJ. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc. Natl Acad. Sci. USA71(10), 4135–4139 (1974).
  • Vaught JD, Dewey T, Eaton BE. T7 RNA polymerase transcription with 5-position modified UTP derivatives. J. Am. Chem. Soc.126(36), 11231–11237 (2004).
  • Vaught JD, Bock C, Carter J et al. Expanding the chemistry of DNA for in vitro selection. J. Am. Chem. Soc.132(12), 4141–4151 (2010).
  • Huang D, Vu D, Cassiday La et al. Crystal structure of NF-κB (p50)2 complexed to a high-affinity RNA aptamer. Proc. Natl Acad. Sci. USA100(16), 9268–9273 (2003).
  • Long SB, Long MB, White RR, Sullenger BA. Crystal structure of an RNA aptamer bound to thrombin. RNA14(12), 2504–2512 (2008).
  • Vicens Q, Cech TR. Atomic level architecture of group I introns revealed. Trend. Biochem. Sci.31(1), 41–51 (2006).
  • Fredriksson S, Horecka J, Brustugun OT et al. Multiplexed proximity ligation assays to profile putative plasma biomarkers relevant to pancreatic and ovarian cancer. Clin. Chem.54(3), 582–589 (2008).
  • Gloriam DE, Orchard S, Bertinetti D et al. A community standard format for the representation of protein affinity reagents. Mol. Cell. Proteomics9(1), 1–10 (2010).
  • Kraemer S, Vaught JD, Bock C et al. From aptamer-based biomarker discovery to diagnostic and clinical applications: an aptamer-based, streamlined multiplex proteomic assay. Nature PrecedingsDOI: hdl:10101/npre2010.4642.1 (2010).
  • Venturoli D, Rippe B. Ficoll and dextran vs. globular proteins as probes for testing glomerular permselectivity: effects of molecular size, shape, charge, and deformability. Am. J. Physiol. Renal Physiol.288(4), F605–F613 (2005).
  • Vanbelleghem H, Vanholder R, Levin NW et al. The kidney disease: improving global outcomes website: comparison of guidelines as a tool for harmonization. Kidney Int.71(10), 1054–1061 (2007).
  • Kassis ES, Vaporciyan AA, Swisher SG et al. Application of the revised lung cancer staging system (IASLC Staging Project) to a cancer center population. J. Thorac. Cardiovasc. Surg.138(2), 412–418 (2009).
  • Okada M, Nishio W, Sakamoto T et al. Effect of tumor size on prognosis in patients with non-small cell lung cancer: the role of segmentectomy as a type of lesser resection. J. Thorac. Cardiovasc. Surg.129(1), 87–93 (2005).
  • Lin H, Lee E, Hestir K et al. Discovery of a cytokine and its receptor by functional screening of the extracellular proteome. Science320(5877), 807–811 (2008).

Patent

  • Gold L, Stanton M, Brody EN et al. Lung cancer biomarkers and uses thereof.US2010/0070191 (2010).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.