Applications in high-content functional protein microarrays

Current Opinion in Chemical Biology

Volumn 30, Issue , 2016, Pages 21-27

  Moore, Cedric D ^a,b   Ajala, Olutobi Z ^a,b   Zhu, Heng ^a,b  

^a Department of Pharmacology and Molecular Sciences ^*  (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; DNA; PROTEIN; RNA;

ANTIBODY SPECIFICITY; ARTICLE; BASIC RESEARCH; CLINICAL RESEARCH; FUNCTIONAL PROTEIN MICROARRAY; HIGH THROUGHPUT SCREENING; HUMAN; NONHUMAN; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN MICROARRAY; PROTEIN NUCLEIC ACID INTERACTION; PROTEIN PROCESSING; CLINICAL PROTOCOL; METABOLISM; PROCEDURES;

CLINICAL PROTOCOLS; DNA; HUMANS; PROTEIN ARRAY ANALYSIS; PROTEINS; RNA;

EID: 84947474766     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2015.10.013     Document Type: Review

References (59)

1. Zhu H., Bilgin M., Bangham R., Hall D., Casamayor A., Bertone P., Lan N., Jansen R., Bidlingmaier S., Houfek T., et al. Global analysis of protein activities using proteome chips. Science 2001, 293:2101-2105.
2. Haab B.B., Dunham M.J., Brown P.O. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol 2001, 2. RESEARCH0004.
3. Paweletz C.P., Charboneau L., Bichsel V.E., Simone N.L., Chen T., Gillespie J.W., Emmert-Buck M.R., Roth M.J., Petricoin I.E., Liotta L.A. Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene 2001, 20:1981-1989.
4. Sutandy F.X., Qian J., Chen C.S., Zhu H. Overview of protein microarrays. Curr Protoc Protein Sci 2013, (Chapter 27:Unit 27.1).
5. Liang W., Wang S., Festa F., Wiktor P., Wang W., Magee M., LaBaer J., Tao N. Measurement of small molecule binding kinetics on a protein microarray by plasmonic-based electrochemical impedance imaging. Anal Chem 2014, 86:9860-9865.
6. Landry J.P., Sun Y.S., Guo X.W., Zhu X.D. Protein reactions with surface-bound molecular targets detected by oblique-incidence reflectivity difference microscopes. Appl Opt 2008, 47:3275-3288.
7. Liu S., Zhang H., Dai J., Hu S., Pino I., Eichinger D.J., Lyu H., Zhu H. Characterization of monoclonal antibody's binding kinetics using oblique-incidence reflectivity difference approach. MAbs 2015, 7:110-119.
8. Evans-Nguyen K.M., Tao S.C., Zhu H., Cotter R.J. Protein arrays on patterned porous gold substrates interrogated with mass spectrometry: detection of peptides in plasma. Anal Chem 2008, 80:1448-1458.
9. Zhang X., Zhu S., Deng C., Zhang X. An aptamer based on-plate microarray for high-throughput insulin detection by MALDI-TOF MS. Chem Commun (Camb) 2012, 48:2689-2691.
10. Shtenberg G., Massad-Ivanir N., Moscovitz O., Engin S., Sharon M., Fruk L., Segal E. Picking up the pieces: a generic porous Si biosensor for probing the proteolytic products of enzymes. Anal Chem 2013, 85:1951-1956.
11. Lee M.R., Fauchet P.M. Two-dimensional silicon photonic crystal based biosensing platform for protein detection. Opt Express 2007, 15:4530-4535.
12. Zhang J.T., Cai Z., Kwak D.H., Liu X., Asher S.A. Two-dimensional photonic crystal sensors for visual detection of lectin concanavalin A. Anal Chem 2014, 86:9036-9041.
13. Tusher V.G., Tibshirani R., Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 2001, 98:5116-5121. (PMID 16398926).
14. Diaz-Uriarte R., Alvarez de Andres S. Gene selection and classification of microarray data using random forest. BMC Bioinformatics 2006, 7:3. (PMID 16398926).
15. Zhu X., Gerstein M., Snyder M. ProCAT: a data analysis approach for protein microarrays. Genome Biol 2006, 7:R110. (PMID 17109749).
16. Kellis M., Wold B., Snyder M.P., Bernstein B.E., Kundaje A., Marinov G.K., Ward L.D., Birney E., Crawford G.E., Dekker J., et al. Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A 2014, 111:6131-6138.
17. Xie Z., Hu S., Blackshaw S., Zhu H., Qian J. hPDI: a database of experimental human protein-DNA interactions. Bioinformatics 2010, 26:287-289.
18. Hu S., Wan J., Su Y., Song Q., Zeng Y., Nguyen H.N., Shin J., Cox E., Rho H.S., Woodard C., et al. DNA methylation presents distinct binding sites for human transcription factors. Elife 2013, 2:e00726.
19. Siprashvili Z., Webster D.E., Kretz M., Johnston D., Rinn J.L., Chang H.Y., Khavari P.A. Identification of proteins binding coding and non-coding human RNAs using protein microarrays. BMC Genomics 2012, 13:633.
20. Newman R.H., Zhang J., Zhu H. Toward a systems-level view of dynamic phosphorylation networks. Front Genet 2014, 5:263.
21. Hu J., Rho H.S., Newman R.H., Zhang J., Zhu H., Qian J. PhosphoNetworks: a database for human phosphorylation networks. Bioinformatics 2014, 30:141-142.
22. Lin Y.Y., Lu J.Y., Zhang J., Walter W., Dang W., Wan J., Tao S.C., Qian J., Zhao Y., Boeke J.D., et al. Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis. Cell 2009, 136:1073-1084.
23. Newman R.H., Hu J., Rho H.S., Xie Z., Woodard C., Neiswinger J., Cooper C., Shirley M., Clark H.M., Hu S., et al. Construction of human activity-based phosphorylation networks. Mol Syst Biol 2013, 9:655.
24. Li Y., Tao S.C., Bova G.S., Liu A.Y., Chan D.W., Zhu H., Zhang H. Detection and verification of glycosylation patterns of glycoproteins from clinical specimens using lectin microarrays and lectin-based immunosorbent assays. Anal Chem 2011, 83:8509-8516.
25. Dias W.B., Cheung W.D., Hart G.W. O-GlcNAcylation of kinases. Biochem Biophys Res Commun 2012, 422:224-228.
26. Lu J.Y., Lin Y.Y., Qian J., Tao S.C., Zhu J., Pickart C., Zhu H. Functional dissection of a HECT ubiquitin E3 ligase. Mol Cell Proteomics 2008, 7:35-45.
27. Li R., Wang L., Liao G., Guzzo C.M., Matunis M.J., Zhu H., Hayward S.D. SUMO binding by the Epstein-Barr virus protein kinase BGLF4 is crucial for BGLF4 function. J Virol 2012, 86:5412-5421.
28. Zhu J., Liao G., Shan L., Zhang J., Chen M.R., Hayward G.S., Hayward S.D., Desai P., Zhu H. Protein array identification of substrates of the Epstein-Barr virus protein kinase BGLF4. J Virol 2009, 83:5219-5231.
29. Desbien A.L., Van Hoeven N., Reed S.J., Casey A.C., Laurance J.D., Baldwin S.L., Duthie M.S., Reed S.G., Carter D. Development of a high density hemagglutinin protein microarray to determine the breadth of influenza antibody responses. Biotechniques 2013, 54:345-348.
30. Deng J., Bi L., Zhou L., Guo S.J., Fleming J., Jiang H.W., Zhou Y., Gu J., Zhong Q., Wang Z.X., et al. Mycobacterium tuberculosis proteome microarray for global studies of protein function and immunogenicity. Cell Rep 2014, 9:2317-2329.
31. Liang L., Juarez S., Nga T.V., Dunstan S., Nakajima-Sasaki R., Davies D.H., McSorley S., Baker S., Felgner P.L. Immune profiling with a Salmonella Typhi antigen microarray identifies new diagnostic biomarkers of human typhoid. Sci Rep 2013, 3:1043.
32. Kalantari-Dehaghi M., Chun S., Chentoufi A.A., Pablo J., Liang L., Dasgupta G., Molina D.M., Jasinskas A., Nakajima-Sasaki R., Felgner J., et al. Discovery of potential diagnostic and vaccine antigens in herpes simplex virus 1 and 2 by proteome-wide antibody profiling. J Virol 2012, 86:4328-4339.
33. Liang L., Felgner P.L. A systems biology approach for diagnostic and vaccine antigen discovery in tropical infectious diseases. Curr Opin Infect Dis 2015, 28:438-445.
34. Gaze S., Driguez P., Pearson M.S., Mendes T., Doolan D.L., Trieu A., McManus D.P., Gobert G.N., Periago M.V., Correa Oliveira R., et al. An immunomics approach to schistosome antigen discovery: antibody signatures of naturally resistant and chronically infected individuals from endemic areas. PLoS Pathog 2014, 10:e1004033.
35. Dotsey E.Y., Gorlani A., Ingale S., Achenbach C.J., Forthal D.N., Felgner P.L., Gach J.S. A high throughput protein microarray approach to classify HIV monoclonal antibodies and variant antigens. PLOS ONE 2015, 10:e0125581.
36. Reusken C., Mou H., Godeke G.J., van der Hoek L., Meyer B., Muller M.A., Haagmans B., de Sousa R., Schuurman N., Dittmer U., et al. Specific serology for emerging human coronaviruses by protein microarray. Euro Surveill 2013, 18:20441.
37. Helb D.A., Tetteh K.K., Felgner P.L., Skinner J., Hubbard A., Arinaitwe E., Mayanja-Kizza H., Ssewanyana I., Kamya M.R., Beeson J.G., et al. Novel serologic biomarkers provide accurate estimates of recent Plasmodium falciparum exposure for individuals and communities. Proc Natl Acad Sci U S A 2015, 112:E4438-E4447.
38. Santacatterina F., Chamorro M., de Arenas C.N., Navarro C., Martin M.A., Cuezva J.M., Sanchez-Arago M. Quantitative analysis of proteins of metabolism by reverse phase protein microarrays identifies potential biomarkers of rare neuromuscular diseases. J Transl Med 2015, 13:65.
39. Hu B., Niu X., Cheng L., Yang L.N., Li Q., Wang Y., Tao S.C., Zhou S.M. Discovering cancer biomarkers from clinical samples by protein microarrays. Proteomics Clin Appl 2015, 9:98-110.
40. Hudson M.E., Pozdnyakova I., Haines K., Mor G., Snyder M. Identification of differentially expressed proteins in ovarian cancer using high-density protein microarrays. Proc Natl Acad Sci U S A 2007, 104:17494-17499.
41. Song Q., Liu G., Hu S., Zhang Y., Tao Y., Han Y., Zeng H., Huang W., Li F., Chen P., et al. Novel autoimmune hepatitis-specific autoantigens identified using protein microarray technology. J Proteome Res 2010, 9:30-39.
42. Hu C.J., Song G., Huang W., Liu G.Z., Deng C.W., Zeng H.P., Wang L., Zhang F.C., Zhang X., Jeong J.S., et al. Identification of new autoantigens for primary biliary cirrhosis using human proteome microarrays. Mol Cell Proteomics 2012, 11:669-680.
43. Chen R., Mias G.I., Li-Pook-Than J., Jiang L., Lam H.Y., Chen R., Miriami E., Karczewski K.J., Hariharan M., Dewey F.E., et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 2012, 148:1293-1307.
44. Fagerberg L., Jonasson K., von Heijne G., Uhlen M., Berglund L. Prediction of the human membrane proteome. Proteomics 2010, 10:1141-1149.
45. Hu S., Feng Y., Henson B., Wang B., Huang X., Li M., Desai P., Zhu H. VirD: a virion display array for profiling functional membrane proteins. Anal Chem 2013, 85:8046-8054.
46. Woodard C.L., Goodwin C.R., Wan J., Xia S., Newman R., Hu J., Zhang J., Hayward S.D., Qian J., Laterra J., et al. Profiling the dynamics of a human phosphorylome reveals new components in HGF/c-Met signaling. PLoS ONE 2013, 8:e72671.
47. Tarrant M.K., Rho H.S., Xie Z., Jiang Y.L., Gross C., Culhane J.C., Yan G., Qian J., Ichikawa Y., Matsuoka T., et al. Regulation of CK2 by phosphorylation and O-GlcNAcylation revealed by semisynthesis. Nat Chem Biol 2012, 8:262-269.
48. Jeong J.S., Jiang L., Albino E., Marrero J., Rho H.S., Hu J., Hu S., Vera C., Bayron-Poueymiroy D., Rivera-Pacheco Z.A., et al. Rapid identification of monospecific monoclonal antibodies using a human proteome microarray. Mol Cell Proteomics 2012, 11. O111.016253.
49. Stafford P., Halperin R., Legutki J.B., Magee D.M., Galgiani J., Johnston S.A. Physical characterization of the "immunosignaturing effect". Mol Cell Proteomics 2012, 11. M111.011593.
50. Uhlen M., Bjorling E., Agaton C., Szigyarto C.A., Amini B., Andersen E., Andersson A.C., Angelidou P., Asplund A., Asplund C., et al. A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol Cell Proteomics 2005, 4:1920-1932.
51. Sjoberg R., Sundberg M., Gundberg A., Sivertsson A., Schwenk J.M., Uhlen M., Nilsson P. Validation of affinity reagents using antigen microarrays. N Biotechnol 2012, 29:555-563.
52. Buus S., Rockberg J., Forsstrom B., Nilsson P., Uhlen M., Schafer-Nielsen C. High-resolution mapping of linear antibody epitopes using ultrahigh-density peptide microarrays. Mol Cell Proteomics 2012, 11:1790-1800.
53. Popescu S.C., Popescu G.V., Bachan S., Zhang Z., Seay M., Gerstein M., Snyder M., Dinesh-Kumar S.P. Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays. Proc Natl Acad Sci U S A 2007, 104:4730-4735.
54. Manohar M., Tian M., Moreau M., Park S.W., Choi H.W., Fei Z., Friso G., Asif M., Manosalva P., von Dahl C.C., et al. Identification of multiple salicylic acid-binding proteins using two high throughput screens. Front Plant Sci 2014, 5:777.
55. Lee H.Y., Bowen C.H., Popescu G.V., Kang H.G., Kato N., Ma S., Dinesh-Kumar S., Snyder M., Popescu S.C. Arabidopsis RTNLB1 and RTNLB2 Reticulon-like proteins regulate intracellular trafficking and activity of the FLS2 immune receptor. Plant Cell 2011, 23:3374-3391.
56. Takulapalli B.R., Qiu J., Magee D.M., Kahn P., Brunner A., Barker K., Means S., Miersch S., Bian X., Mendoza A., et al. High density diffusion-free nanowell arrays. J Proteome Res 2012, 11:4382-4391.
57. Miersch S., Bian X., Wallstrom G., Sibani S., Logvinenko T., Wasserfall C.H., Schatz D., Atkinson M., Qiu J., LaBaer J. Serological autoantibody profiling of type 1 diabetes by protein arrays. J Proteomics 2013, 94:486-496.
58. Yu X., Wallstrom G., Magee D.M., Qiu J., Mendoza D.E., Wang J., Bian X., Graves M., LaBaer J. Quantifying antibody binding on protein microarrays using microarray nonlinear calibration. Biotechniques 2013, 54:257-264.
59. Chen C.S., Korobkova E., Chen H., Zhu J., Jian X., Tao S.C., He C., Zhu H. A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli. Nat Methods 2008, 5:69-74.