Profiling cellular protein complexes by proximity ligation with dual tag microarray readout

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  Hammond, Maria ^a   Nong, Rachel Yuan ^a   Ericsson, Olle ^a,b   Pardali, Katerina ^a,c   Landegren, Ulf ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b AGILENT TECHNOLOGIES   (United States)

^c ASTRAZENECA R AND D   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; CELL PROTEIN; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; I KAPPA B ALPHA; OLIGONUCLEOTIDE; PROTEIN P50; TRANSCRIPTION FACTOR RELA; TRANSCRIPTION FACTOR RELB;

ANTIGEN BINDING; ARTICLE; CELL LYSATE; COMPLEX FORMATION; CONTROLLED STUDY; DNA BARCODING; DNA SEQUENCE; DNA STRAND; DUAL TAG MICROARRAY; GENETIC ANALYSIS; MOLECULAR PROBE; POLYMERASE CHAIN REACTION; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN INTERACTION; PROXIMITY LIGATION ASSAY; TISSUE CULTURE CELL;

ANIMALS; CELL EXTRACTS; CELL LINE; HUMANS; PROTEIN ARRAY ANALYSIS; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEINS;

EID: 84863702896     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0040405     Document Type: Article

References (24)

1. Vidal M, Cusick ME, Barabási A-L, (2011) Interactome networks and human disease. Cell 144: 986-998 doi:10.1016/j.cell.2011.02.016.
2. Förster T, (1948) Zwischenmolekulare Energiewanderung und Fluoreszenz. Annalen der Physik 437: 55-75 doi:10.1002/andp.19484370105.
3. Stryer L, Haugland RP, (1967) Energy transfer: a spectroscopic ruler. Proc Natl Acad Sci U S A 58: 719-726.
4. Kenworthy AK, (2001) Imaging Protein-Protein Interactions Using Fluorescence Resonance Energy Transfer Microscopy. Methods 24: 289-296 doi:06/meth.2001.1189.
5. Shi Y, Huang W, Tan Y, Jin X, Dua R, et al. (2009) A Novel Proximity Assay for the Detection of Proteins and Protein Complexes: Quantitation of HER1 and HER2 Total Protein Expression and Homodimerization in Formalin-fixed, Paraffin-Embedded Cell Lines and Breast Cancer Tissue. Diagnostic Molecular Pathology 18: 11-21 doi:10.1097/PDM.0b013e31818cbdb2.
6. McGregor LM, Gorin DJ, Dumelin CE, Liu DR, (2010) Interaction-dependent PCR: identification of ligand-target pairs from libraries of ligands and libraries of targets in a single solution-phase experiment. J Am Chem Soc 132: 15522-15524 doi:10.1021/ja107677q.
7. Fredriksson S, Gullberg M, Jarvius J, Olsson C, Pietras K, et al. (2002) Protein detection using proximity-dependent DNA ligation assays. Nat Biotechnol 20: 473-477 doi:10.1038/nbt0502-473.
8. Gullberg M, Gústafsdóttir SM, Schallmeiner E, Jarvius J, Bjarnegård M, et al. (2004) Cytokine detection by antibody-based proximity ligation. Proc Natl Acad Sci USA 101: 8420-8424 doi:10.1073/pnas.0400552101.
9. Soderberg O, Gullberg M, Jarvius M, Ridderstrale K, Leuchowius K-J, et al. (2006) Direct observation of individual endogenous protein complexes in situ by proximity ligation. Nat Meth 3: 995-1000 doi:10.1038/nmeth947.
10. Schallmeiner E, Oksanen E, Ericsson O, Spångberg L, Eriksson S, et al. (2007) Sensitive protein detection via triple-binder proximity ligation assays. Nat Methods 4: 135-137 doi:10.1038/nmeth974.
11. Gustafsdottir SM, Wennström S, Fredriksson S, Schallmeiner E, Hamilton AD, et al. (2008) Use of proximity ligation to screen for inhibitors of interactions between vascular endothelial growth factor A and its receptors. Clin Chem 54: 1218-1225 doi:10.1373/clinchem.2007.099424.
12. Gustafsdottir SM, Schlingemann J, Rada-Iglesias A, Schallmeiner E, Kamali-Moghaddam M, et al. (2007) In vitro analysis of DNA-protein interactions by proximity ligation. Proc Natl Acad Sci USA 104: 3067-3072 doi:10.1073/pnas.0611229104.
13. Weibrecht I, Gavrilovic M, Lindbom L, Landegren U, Wählby C, et al. (2011) Visualising individual sequence-specific protein-DNA interactions in situ. N Biotechnol. Available:http://www.ncbi.nlm.nih.gov/pubmed/21906700. Accessed 24 January 2012.
14. Kamali-Moghaddam M, Pettersson FE, Wu D, Englund H, Darmanis S, et al. (2010) Sensitive detection of Aβ protofibrils by proximity ligation-relevance for Alzheimer's disease. BMC Neurosci 11: 124 doi:10.1186/1471-2202-11-124.
15. Jarvius M, Paulsson J, Weibrecht I, Leuchowius K-J, Andersson A-C, et al. (2007) In situ detection of phosphorylated platelet-derived growth factor receptor beta using a generalized proximity ligation method. Mol Cell Proteomics 6: 1500-1509 doi:10.1074/mcp.M700166-MCP200.
16. Conze T, Carvalho AS, Landegren U, Almeida R, Reis CA, et al. (2010) MUC2 mucin is a major carrier of the cancer-associated sialyl-Tn antigen in intestinal metaplasia and gastric carcinomas. Glycobiology 20: 199-206 doi:10.1093/glycob/cwp161.
17. Fredriksson S, Dixon W, Ji H, Koong AC, Mindrinos M, et al. (2007) Multiplexed protein detection by proximity ligation for cancer biomarker validation. Nat Methods 4: 327-329 doi:10.1038/nmeth1020.
18. Fredriksson S, Horecka J, Brustugun OT, Schlingemann J, Koong AC, et al. (2008) Multiplexed proximity ligation assays to profile putative plasma biomarkers relevant to pancreatic and ovarian cancer. Clin Chem 54: 582-589 doi:10.1373/clinchem.2007.093195.
19. Lundberg M, Thorsen SB, Assarsson E, Villablanca A, Tran B, et al. (2011) Multiplexed homogeneous proximity ligation assays for high-throughput protein biomarker research in serological material. Mol Cell Proteomics 10: M110.004978 doi:10.1074/mcp.M110.004978.
20. Darmanis S, Nong RY, Vänelid J, Siegbahn A, Ericsson O, et al. (2011) ProteinSeq: High-Performance Proteomic Analyses by Proximity Ligation and Next Generation Sequencing. PLoS ONE 6: e25583 doi:10.1371/journal.pone.0025583.
21. Ericsson O, Jarvius J, Schallmeiner E, Howell M, Nong RY, et al. (2008) A dual-tag microarray platform for high-performance nucleic acid and protein analyses. Nucl Acids Res 36: e45 doi:10.1093/nar/gkn106.
22. Schröder C, Jacob A, Tonack S, Radon TP, Sill M, et al. (2010) Dual-color proteomic profiling of complex samples with a microarray of 810 cancer-related antibodies. Mol Cell Proteomics 9: 1271-1280 doi:10.1074/mcp.M900419-MCP200.
23. Darmanis S, Nong RY, Hammond M, Gu J, Alderborn A, et al. (2010) Sensitive plasma protein analysis by microparticle-based proximity ligation assays. Mol Cell Proteomics 9: 327-335 doi:10.1074/mcp.M900248-MCP200.
24. Hoffmann A, Natoli G, Ghosh G, (2006) Transcriptional regulation via the NF-kappaB signaling module. Oncogene 25: 6706-6716 doi:10.1038/sj.onc.1209933.