Protein biomarker validation via proximity ligation assays

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1844, Issue 5, 2014, Pages 933-939

  Blokzijl, A ^a   Nong, R ^a   Darmanis, S ^a   Hertz, E ^a   Landegren, U ^a   Kamali Moghaddam, M ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

Biomarkers; Diagnostic; Protein detection; Proximity ligation assay

Indexed keywords

BIOMARKERS; DIAGNOSTIC; PROTEIN DETECTION; PROXIMITY LIGATION ASSAY;

ANIMALS; BIOLOGICAL ASSAY; BIOLOGICAL MARKERS; HUMANS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; VALIDATION STUDIES AS TOPIC;

EID: 84898835915     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2013.07.016     Document Type: Review

References (48)

1. P.E. Garrett, and S.R. Kurtz Clinical utility of oncofetal proteins and hormones as tumor markers Med. Clin. North Am. 70 1986 1295 1306 (Pubitemid 17213978)
2. S. Tsimikas, J.T. Willerson, and P.M. Ridker C-reactive protein and other emerging blood biomarkers to optimize risk stratification of vulnerable patients J. Am. Coll. Cardiol. 47 2006 C19 C31
3. C.P. Wen, J. Lin, Y.C. Yang, M.K. Tsai, C.K. Tsao, C. Etzel, M. Huang, C.Y. Hsu, Y. Ye, L. Mishra, E. Hawk, and X. Wu Hepatocellular carcinoma risk prediction model for the general population: the predictive power of transaminases J. Natl. Cancer Inst. 104 2012 1599 1611
4. M.S. Sabatine, D.A. Morrow, J.A. de Lemos, C.M. Gibson, S.A. Murphy, N. Rifai, C. McCabe, E.M. Antman, C.P. Cannon, and E. Braunwald Multimarker approach to risk stratification in non-ST elevation acute coronary syndromes: simultaneous assessment of troponin I, C-reactive protein, and B-type natriuretic peptide Circulation 105 2002 1760 1763 (Pubitemid 34408881)
5. M. Onsrud Tumour markers in gynaecologic oncology Scand. J. Clin. Lab. Investig. Suppl. 206 1991 60 70
6. N.L. Anderson The clinical plasma proteome: a survey of clinical assays for proteins in plasma and serum Clin. Chem. 56 2010 177 185
7. N.L. Anderson The clinical plasma proteome: a survey of clinical assays for proteins in plasma and serum Clin. Chem. 56 2010 177 185
8. M.H. Starmans, M. Pintilie, T. John, S.D. Der, F.A. Shepherd, I. Jurisica, P. Lambin, M.S. Tsao, and P.C. Boutros Exploiting the noise: improving biomarkers with ensembles of data analysis methodologies Genome Med. 4 2012 84
9. T.A. Addona, X. Shi, H. Keshishian, D.R. Mani, M. Burgess, M.A. Gillette, K.R. Clauser, D. Shen, G.D. Lewis, L.A. Farrell, M.A. Fifer, M.S. Sabatine, R.E. Gerszten, and S.A. Carr A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease Nat. Biotechnol. 29 2011 635 643
10. J.R. Whiteaker, C. Lin, J. Kennedy, L. Hou, M. Trute, I. Sokal, P. Yan, R.M. Schoenherr, L. Zhao, U.J. Voytovich, K.S. Kelly-Spratt, A. Krasnoselsky, P.R. Gafken, J.M. Hogan, L.A. Jones, P. Wang, L. Amon, L.A. Chodosh, P.S. Nelson, M.W. McIntosh, C.J. Kemp, and A.G. Paulovich A targeted proteomics-based pipeline for verification of biomarkers in plasma Nat. Biotechnol. 29 2011 625 634
11. N.L. Anderson, and N.G. Anderson The human plasma proteome: history, character, and diagnostic prospects Mol. Cell Proteomics 1 2002 845 867
12. U. Landegren, J. Vanelid, M. Hammond, R.Y. Nong, D. Wu, E. Ulleras, and M. Kamali-Moghaddam Opportunities for sensitive plasma proteome analysis Anal. Chem. 84 2012 1824 1830
13. M.P. Pavlou, and E.P. Diamandis The cancer cell secretome: a good source for discovering biomarkers? J. Proteomics. 73 2010 1896 1906
14. J. Lovgren, C. Valtonen-Andre, K. Marsal, H. Lilja, and A. Lundwall Measurement of prostate-specific antigen and human glandular kallikrein 2 in different body fluids J. Androl. 20 1999 348 355 (Pubitemid 29289094)
15. G. De Angelis, H.G. Rittenhouse, S.D. Mikolajczyk, L. Blair Shamel, and A. Semjonow Twenty years of PSA: from prostate antigen to tumor marker Rev. Urol. 9 2007 113 123
16. P.A. Abrahamsson, H. Lilja, and J.E. Oesterling Molecular forms of serum prostate-specific antigen. the clinical value of percent free prostate-specific antigen Urol. Clin. North Am. 24 1997 353 365 (Pubitemid 27169260)
17. P. Picotti, and R. Aebersold Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions Nat. Methods 9 2012 555 566
18. S. Darmanis, R.Y. Nong, J. Vanelid, A. Siegbahn, O. Ericsson, S. Fredriksson, C. Backlin, M. Gut, S. Heath, I.G. Gut, L. Wallentin, M.G. Gustafsson, M. Kamali-Moghaddam, and U. Landegren ProteinSeq: high-performance proteomic analyses by proximity ligation and next generation sequencing PLoS One 6 2011 e25583
19. D.M. Rissin, C.W. Kan, T.G. Campbell, S.C. Howes, D.R. Fournier, L. Song, T. Piech, P.P. Patel, L. Chang, A.J. Rivnak, E.P. Ferrell, J.D. Randall, G.K. Provuncher, D.R. Walt, and D.C. Duffy Single-molecule enzyme-linked immunosorbent assay detects serum proteins at subfemtomolar concentrations Nat. Biotechnol. 28 2010 595 599
20. J. Todd, B. Freese, A. Lu, D. Held, J. Morey, R. Livingston, and P. Goix Ultrasensitive flow-based immunoassays using single-molecule counting Clin. Chem. 53 2007 1990 1995 (Pubitemid 350036054)
21. M. Lundberg, A. Eriksson, B. Tran, E. Assarsson, and S. Fredriksson Homogeneous antibody-based proximity extension assays provide sensitive and specific detection of low-abundant proteins in human blood Nucleic Acids Res. 39 2011 e102
22. S. Fredriksson, M. Gullberg, J. Jarvius, C. Olsson, K. Pietras, S.M. Gustafsdottir, A. Ostman, and U. Landegren Protein detection using proximity-dependent DNA ligation assays Nat. Biotechnol. 20 2002 473 477 (Pubitemid 34495933)
23. M. Gullberg, S.M. Gustafsdottir, E. Schallmeiner, J. Jarvius, M. Bjarnegard, C. Betsholtz, U. Landegren, and S. Fredriksson Cytokine detection by antibody-based proximity ligation Proc. Natl. Acad. Sci. U. S. A. 101 2004 8420 8424 (Pubitemid 38736590)
24. S.M. Gustafsdottir, A. Nordengrahn, S. Fredriksson, P. Wallgren, E. Rivera, E. Schallmeiner, M. Merza, and U. Landegren Detection of individual microbial pathogens by proximity ligation Clin. Chem. 52 2006 1152 1160 (Pubitemid 43794429)
25. S. Darmanis, R.Y. Nong, M. Hammond, J. Gu, A. Alderborn, J. Vanelid, A. Siegbahn, S. Gustafsdottir, O. Ericsson, U. Landegren, and M. Kamali-Moghaddam Sensitive plasma protein analysis by microparticle-based proximity ligation assays Mol. Cell Proteomics 9 2010 327 335
26. M. Kamali-Moghaddam, F.E. Pettersson, D. Wu, H. Englund, S. Darmanis, A. Lord, G. Tavoosidana, D. Sehlin, S. Gustafsdottir, L.N. Nilsson, L. Lannfelt, and U. Landegren Sensitive detection of Abeta protofibrils by proximity ligation - relevance for Alzheimer's disease BMC Neurosci. 11 2010 124
27. U. Wallin, B. Glimelius, K. Jirstrom, S. Darmanis, R.Y. Nong, F. Ponten, C. Johansson, L. Pahlman, and H. Birgisson Growth differentiation factor 15: a prognostic marker for recurrence in colorectal cancer Br. J. Cancer 104 2011 1619 1627
28. S. Cheng, F. Shi, X. Jiang, L. Wang, W. Chen, and C. Zhu Sensitive detection of small molecules by competitive immunomagnetic-proximity ligation assay Anal. Chem. 84 2012 2129 2132
29. M. Lundberg, S.B. Thorsen, E. Assarsson, A. Villablanca, B. Tran, N. Gee, M. Knowles, B.S. Nielsen, E. Gonzalez Couto, R. Martin, O. Nilsson, C. Fermer, J. Schlingemann, I.J. Christensen, H.J. Nielsen, B. Ekstrom, C. Andersson, M. Gustafsson, N. Brunner, J. Stenvang, and S. Fredriksson Multiplexed homogeneous proximity ligation assays for high-throughput protein biomarker research in serological material Mol. Cell Proteomics 10 2011 M110 (004978)
30. E. Schallmeiner, E. Oksanen, O. Ericsson, L. Spangberg, S. Eriksson, U.H. Stenman, K. Pettersson, and U. Landegren Sensitive protein detection via triple-binder proximity ligation assays Nat. Methods 4 2007 135 137 (Pubitemid 46454681)
31. G. Tavoosidana, G. Ronquist, S. Darmanis, J. Yan, L. Carlsson, D. Wu, T. Conze, P. Ek, A. Semjonow, E. Eltze, A. Larsson, U.D. Landegren, and M. Kamali-Moghaddam Multiple recognition assay reveals prostasomes as promising plasma biomarkers for prostate cancer Proc. Natl. Acad. Sci. U. S. A. 108 2011 8809 8814
32. O. Soderberg, M. Gullberg, M. Jarvius, K. Ridderstrale, K.J. Leuchowius, J. Jarvius, K. Wester, P. Hydbring, F. Bahram, L.G. Larsson, and U. Landegren Direct observation of individual endogenous protein complexes in situ by proximity ligation Nat. Methods 3 2006 995 1000 (Pubitemid 44782698)
33. M. Jarvius, J. Paulsson, I. Weibrecht, K.J. Leuchowius, A.C. Andersson, C. Wahlby, M. Gullberg, J. Botling, T. Sjoblom, B. Markova, A. Ostman, U. Landegren, and O. Soderberg In situ detection of phosphorylated platelet-derived growth factor receptor beta using a generalized proximity ligation method Mol. Cell Proteomics 6 2007 1500 1509 (Pubitemid 47506163)
34. I. Weibrecht, M. Gavrilovic, L. Lindbom, U. Landegren, C. Wahlby, and O. Soderberg Visualising individual sequence-specific protein-DNA interactions in situ Nat. Biotechnol. 29 2012 589 598
35. J. Jung, A.W. Lifland, C. Zurla, E.J. Alonas, and P.J. Santangelo Quantifying RNA-protein interactions in situ using modified-MTRIPs and proximity ligation Nucleic Acids Res. 41 2013 e12
36. C.M. Clausson, A. Allalou, I. Weibrecht, S. Mahmoudi, M. Farnebo, U. Landegren, C. Wahlby, and O. Soderberg Increasing the dynamic range of in situ PLA Nat. Methods 8 2011 892 893
37. K.J. Leuchowius, C.M. Clausson, K. Grannas, Y. Erbilgin, J. Botling, A. Zieba, U. Landegren, and O. Soderberg Parallel visualization of multiple protein complexes in individual cells in tumor tissue Mol. Cell Proteomics 12 2013 1563 1571
38. M. Hammond, R.Y. Nong, O. Ericsson, K. Pardali, and U. Landegren Profiling cellular protein complexes by proximity ligation with dual tag microarray readout PLoS One 7 2012 e40405
39. J. Jarvius, J. Melin, J. Goransson, J. Stenberg, S. Fredriksson, C. Gonzalez-Rey, S. Bertilsson, and M. Nilsson Digital quantification using amplified single-molecule detection Nat. Methods 3 2006 725 727 (Pubitemid 44275741)
40. J. Goransson, R. Ke, R.Y. Nong, W.M. Howell, A. Karman, J. Grawe, J. Stenberg, M. Granberg, M. Elgh, D. Herthnek, P. Wikstrom, J. Jarvius, and M. Nilsson Rapid identification of bio-molecules applied for detection of biosecurity agents using rolling circle amplification PLoS One 7 2012 e31068
41. T.Z. Gomez de la Torre, R. Ke, A. Mezger, P. Svedlindh, M. Stromme, and M. Nilsson Sensitive detection of spores using volume-amplified magnetic nanobeads Small 8 2012 2174 2177
42. G.J. Gu, M. Friedman, C. Jost, K. Johnsson, M. Kamali-Moghaddam, A. Pluckthun, U. Landegren, and O. Soderberg Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation Nat. Biotechnol. 30 2013 144 152
43. G. Sahlen, A. Ahlander, A. Frost, G. Ronquist, B.J. Norlen, and B.O. Nilsson Prostasomes are secreted from poorly differentiated cells of prostate cancer metastases Prostate 61 2004 291 297 (Pubitemid 39350452)
44. H. Peinado, M. Aleckovic, S. Lavotshkin, I. Matei, B. Costa-Silva, G. Moreno-Bueno, M. Hergueta-Redondo, C. Williams, G. Garcia-Santos, C. Ghajar, A. Nitadori-Hoshino, C. Hoffman, K. Badal, B.A. Garcia, M.K. Callahan, J. Yuan, V.R. Martins, J. Skog, R.N. Kaplan, M.S. Brady, J.D. Wolchok, P.B. Chapman, Y. Kang, J. Bromberg, and D. Lyden Melanoma exosomes educate bone marrow progenitor cells toward a pro-metastatic phenotype through MET Nat. Med. 18 2012 883 891
45. M. Lundberg, A. Eriksson, B. Tran, E. Assarsson, and S. Fredriksson Homogeneous antibody-based proximity extension assays provide sensitive and specific detection of low-abundant proteins in human blood Nucleic Acids Res. 39 2011 e102
46. J.R. Whiteaker, L. Zhao, L. Anderson, and A.G. Paulovich An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers Mol. Cell Proteomics 9 2010 184 196
47. I. Cima, R. Schiess, P. Wild, M. Kaelin, P. Schuffler, V. Lange, P. Picotti, R. Ossola, A. Templeton, O. Schubert, T. Fuchs, T. Leippold, S. Wyler, J. Zehetner, W. Jochum, J. Buhmann, T. Cerny, H. Moch, S. Gillessen, R. Aebersold, and W. Krek Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer Proc. Natl. Acad. Sci. U. S. A. 108 2011 3342 3347
48. B. Houser Bio-Rad's Bio-Plex(R) suspension array system, xMAP technology overview Arch. Physiol. Biochem. 118 2012 192 196