Systems analysis of adaptive immunity by utilization of high-throughput technologies

Current Opinion in Biotechnology

Volumn 22, Issue 4, 2011, Pages 584-589

  Reddy, Sai T ^a   Georgiou, George ^a,b  

^a The University of Texas at Austin   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTIVE IMMUNE RESPONSE; ADAPTIVE IMMUNITY; DISEASE STATE; DNA SEQUENCING; EXPERIMENTAL SYSTEM; HIGH-THROUGHPUT; HIGH-THROUGHPUT TECHNOLOGIES; IMMUNE CELLS; INFORMATION DEPTH; LYMPHOCYTE POPULATION; MICROFLUIDIC ASSAYS; PATHOGENIC INFECTIONS; PROTEIN MICROARRAY; RAPID EXPANSION; T CELLS;

BIOASSAY; BIOCHIPS; GENE ENCODING; IMMUNOLOGY; SYSTEMS ANALYSIS;

THROUGHPUT;

HUMAN IMMUNODEFICIENCY VIRUS VACCINE; LYMPHOCYTE RECEPTOR; TETANUS ANTIBODY; TETANUS TOXOID;

ADAPTIVE IMMUNITY; B LYMPHOCYTE; CELL ACTIVATION; CELL CLONING; CELLULAR DISTRIBUTION; DNA SEQUENCE; HIGH THROUGHPUT SEQUENCING; HUMAN; MICROFLUIDICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN MICROARRAY; PROTEIN PROTEIN INTERACTION; PROTEOMICS; REVIEW; SINGLE CELL ANALYSIS; SYSTEM ANALYSIS; T LYMPHOCYTE; TETANUS; VACCINATION;

ADAPTIVE IMMUNITY; ANIMALS; B-LYMPHOCYTES; CYTOLOGICAL TECHNIQUES; HUMANS; IMMUNITY, ACTIVE; MICROFLUIDICS; PROTEOMICS; T-LYMPHOCYTES;

EID: 79960940363     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2011.04.015     Document Type: Review

References (49)

1. Janeway C. Immunobiology 2005, Garland Pub.
2. Janetzki S., Schaed S., Blachere N.E.B., Ben-Porat L., Houghton A.N., Panageas K.S. Evaluation of elispot assays: influence of method and operator on variability of results. J Immunol Methods 2004, 291:175-183.
3. Papagno L., Almeida J.R., Nemes E., Autran B., Appay V. Cell permeabilization for the assessment of T lymphocyte polyfunctional capacity. J Immunol Methods 2007, 328:182-188.
4. Gnjatic S., Ritter E., Büchler M.W., Giese N.A., Brors B., Frei C., Murray A., Halama N., Zörnig I., Chen Y.-T., et al. Seromic profiling of ovarian and pancreatic cancer. Proc Natl Acad Sci U S A 2010, 107:5088-5093.
5. Law M., Maruyama T., Lewis J., Giang E., Tarr A.W., Stamataki Z., Gastaminza P., Chisari F.V., Jones I.M., Fox R.I., et al. Broadly neutralizing antibodies protect against hepatitis C virus quasispecies challenge. Nat Med 2008, 14:25-27.
6. Yu X., Tsibane T., McGraw P.A., House F.S., Keefer C.J., Hicar M.D., Tumpey T.M., Pappas C., Perrone L.A., Martinez O., et al. Neutralizing antibodies derived from the B cells of 1918 influenza pandemic survivors. Nature 2008, 455:532-536.
7. Germain R.N., Meier-Schellersheim M., Nita-Lazar A., Fraser I.D.C. Systems biology in immunology: a computational modeling perspective. Annu Rev Immunol 2010, 29:527-585.
8. Querec T.D., Akondy R.S., Lee E.K., Cao W., Nakaya H.I., Teuwen D., Pirani A., Gernert K., Deng J., Marzolf B., et al. Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans. Nat Immunol 2009, 10:116-125.
9. Becker P.D., Legrand N., van Geelen C.M.M., Noerder M., Huntington N.D., Lim A., Yasuda E., Diehl S.A., Scheeren F.A., Ott M., et al. Generation of human antigen-specific monoclonal IgM antibodies using vaccinated 'human immune system' mice. PLoS ONE 2010, 5:e13137.
10. Kwakkenbos M.J., Diehl S.A., Yasuda E., Bakker A.Q., van Geelen C.M.M., Lukens M.V., van Bleek G.M., Widjojoatmodjo M.N., Bogers W.M.J.M., Mei H., et al. Generation of stable monoclonal antibody-producing B cell receptor-positive human memory B cells by genetic programming. Nat Med 2009, 16:123-128.
11. Lanzavecchia A., Sallusto F. Human B cell memory. Curr Opin Immunol 2009, 21:298-304.
12. Tiller T., Meffre E., Yurasov S., Tsuiji M., Nussenzweig M.C., Wardemann H. Efficient generation of monoclonal antibodies from single human B cells by single cell RT-PCR and expression vector cloning. J Immunol Methods 2008, 329:112-124.
13. Smith K., Garman L., Wrammert J., Zheng N.-Y., Capra J.D., Ahmed R., Wilson P.C. Rapid generation of fully human monoclonal antibodies specific to a vaccinating antigen. Nat Protoc 2009, 4:372-384.
14. Wrammert J., Smith K., Miller J., Langley W.A., Kokko K., Larsen C., Zheng N.-Y., Mays I., Garman L., Helms C., et al. Rapid cloning of high-affinity human monoclonal antibodies against influenza virus. Nature 2008, 453:667-671.
15. Meijer P.-J., Andersen P.S., Haahr Hansen M., Steinaa L., Jensen A., Lantto J., Oleksiewicz M.B., Tengbjerg K., Poulsen T.R., Coljee V.W., et al. Isolation of human antibody repertoires with preservation of the natural heavy and light chain pairing. J Mol Biol 2006, 358:764-772.
16. Poulsen T.R., Meijer P.-J., Jensen A., Nielsen L.S., Andersen P.S. Kinetic, affinity, and diversity limits of human polyclonal antibody responses against tetanus toxoid. J Immunol (Baltimore, MD) 2007, 179:3841-3850.
17. Wiberg F.C., Rasmussen S.K., Frandsen T.P., Rasmussen L.K., Tengbjerg K., Coljee V.W., Sharon J., Yang C.Y., Bregenholt S., Nielsen L.S., et al. Production of target-specific recombinant human polyclonal antibodies in mammalian cells. Biotechnol Bioeng 2006, 94:396-405.
18. Tajiri K., Kishi H., Tokimitsu Y., Kondo S., Ozawa T., Kinoshita K., Jin A., Kadowaki S., Sugiyama T., Muraguchi A. Cell-microarray analysis of antigen-specific B-cells: single cell analysis of antigen receptor expression and specificity. Cytometry 2007, 71:961-967.
19. Tokimitsu Y., Kishi H., Kondo S., Honda R., Tajiri K., Motoki K., Ozawa T., Kadowaki S., Obata T., Fujiki S., et al. Single lymphocyte analysis with a microwell array chip. Cytometry 2007, 71:1003-1010.
20. Jin A., Ozawa T., Tajiri K., Obata T., Kondo S., Kinoshita K., Kadowaki S., Takahashi K., Sugiyama T., Kishi H., et al. A rapid and efficient single-cell manipulation method for screening antigen-specific antibody-secreting cells from human peripheral blood. Nat Med 2009, 15:1088-1092.
21. Love J.C., Ronan J.L., Grotenbreg G.M., van der Veen A.G., Ploegh H.L. A microengraving method for rapid selection of single cells producing antigen-specific antibodies. Nat Biotechnol 2006, 24:703-707.
22. Ogunniyi A.O., Story C.M., Papa E., Guillen E., Love J.C. Screening individual hybridomas by microengraving to discover monoclonal antibodies. Nat Protoc 2009, 4:767-782.
23. Story C.M., Papa E., Hu C-CA, Ronan J.L., Herlihy K., Ploegh H.L., Love J.C. Profiling antibody responses by multiparametric analysis of primary B cells. Proc Natl Acad Sci U S A 2008, 105:17902-17907.
24. Song Q., Han Q., Bradshaw E.M., Kent S.C., Raddassi K., Nilsson B., Nepom G.T., Hafler D.A., Love J.C. On-chip activation and subsequent detection of individual antigen-specific T cells. Anal Chem 2010, 82:473-477.
25. Han Q., Bradshaw E.M., Nilsson B., Hafler D.A., Love J.C. Multidimensional analysis of the frequencies and rates of cytokine secretion from single cells by quantitative microengraving. Lab Chip 2010, 10:1391-1400.
26. Flatz L., Roychoudhuri R., Honda M., Filali-Mouhim A., Goulet J.-P., Kettaf N., Lin M., Roederer M., Haddad E.K., Sékaly R.P., et al. Single-cell gene-expression profiling reveals qualitatively distinct CD8 T cells elicited by different gene-based vaccines. Proc Natl Acad Sci U S A 2011, 108:5724-5729.
27. Kwong G.A., Radu C.G., Hwang K., Shu C.J., Ma C., Koya R.C., Comin-Anduix B., Hadrup S.R., Bailey R.C., Witte O.N., et al. Modular nucleic acid assembled p/MHC microarrays for multiplexed sorting of antigen-specific T cells. J Am Chem Soc 2009, 131:9695-9703.
28. Michaud G.A., Salcius M., Zhou F., Bangham R., Bonin J., Guo H., Snyder M., Predki P.F., Schweitzer B.I. Analyzing antibody specificity with whole proteome microarrays. Nat Biotechnol 2003, 21:1509-1512.
29. Prechl J., Papp K., Erdei A. Antigen microarrays: descriptive chemistry or functional immunomics?. Trends Immunol 2010, 31:133-137.
30. Kingsmore S.F. Multiplexed protein measurement: technologies and applications of protein and antibody arrays. Nat Rev Drug Discov 2006, 5:310-320.
31. Davies D.H., Liang X., Hernandez J.E., Randall A., Hirst S., Mu Y., Romero K.M., Nguyen T.T., Kalantari-Dehaghi M., Crotty S., et al. Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery. Proc Natl Acad Sci U S A 2005, 102:547-552.
32. Felgner P.L., Kayala M.A., Vigil A., Burk C., Nakajima-Sasaki R., Pablo J., Molina D.M., Hirst S., Chew J.S.W., Wang D., et al. A Burkholderia pseudomallei protein microarray reveals serodiagnostic and cross-reactive antigens. Proc Natl Acad Sci U S A 2009, 106:13499-13504.
33. Kunnath-Velayudhan S., Salamon H., Wang H.-Y., Davidow A.L., Molina D.M., Huynh V.T., Cirillo D.M., Michel G., Talbot E.A., Perkins M.D., et al. Dynamic antibody responses to the Mycobacterium tuberculosis proteome. Proc Natl Acad Sci U S A 2010, 107:14703-14708.
34. Robinson W.H., DiGennaro C., Hueber W., Haab B.B., Kamachi M., Dean E.J., Fournel S., Fong D., Genovese M.C., de Vegvar H.E.N., et al. Autoantigen microarrays for multiplex characterization of autoantibody responses. Nat Med 2002, 8:295-301.
35. Gnjatic S., Wheeler C., Ebner M., Ritter E., Murray A., Altorki N.K., Ferrara C.A., Hepburne-Scott H., Joyce S., Koopman J., et al. Seromic analysis of antibody responses in non-small cell lung cancer patients and healthy donors using conformational protein arrays. J Immunol Methods 2009, 341:50-58.
36. Reddy M.M., Wilson R., Wilson J., Connell S., Gocke A., Hynan L., German D., Kodadek T. Identification of candidate IgG biomarkers for Alzheimer's disease via combinatorial library screening. Cell 2011, 144:132-142.
37. Legutki J.B., Magee D.M., Stafford P., Johnston S.A. A general method for characterization of humoral immunity induced by a vaccine or infection. Vaccine 2010, 28:4529-4537.
38. Fischer N. Sequencing antibody repertoires: the next generation. mAbs 2011, 3:17-20.
39. Weinstein J.A., Jiang N., White R.A., Fisher D.S., Quake S.R. High-throughput sequencing of the zebrafish antibody repertoire. Science (New York, NY) 2009, 324:807-810.
40. Jiang N., Weinstein J.A., Penland L., White R.A., Fisher D.S., Quake S.R. Determinism and stochasticity during maturation of the zebrafish antibody repertoire. Proc Natl Acad Sci U S A 2011.
41. Boyd S.D., Marshall E.L., Merker J.D., Maniar J.M., Zhang L.N., Sahaf B., Jones C.D., Simen B.B., Hanczaruk B., Nguyen K.D., et al. Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci Trans Med 2009, 1:12ra23.
42. Freeman J.D., Warren R.L., Webb J.R., Nelson B.H., Holt R.A. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res 2009, 19:1817-1824.
43. Robins H.S., Campregher P.V., Srivastava S.K., Wacher A., Turtle C.J., Kahsai O., Riddell S.R., Warren E.H., Carlson C.S. Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells. Blood 2009, 114:4099-4107.
44. Robins H.S., Srivastava S.K., Campregher P.V., Turtle C.J., Andriesen J., Riddell S.R., Carlson C.S., Warren E.H. Overlap and effective size of the human CD8+ T cell receptor repertoire. Sci Transl Med 2010, 2:47ra64.
45. Warren RL, Freeman JD, Zeng T, Choe G, Munro S, Moore R, Webb JR, Holt RA: Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes. Genome Res. Advanced Online Publication.
46. Glanville J., Zhai W., Berka J., Telman D., Huerta G., Mehta G.R., Ni I., Mei L., Sundar P.D., Day G.M.R., et al. Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire. Proc Natl Acad Sci U S A 2009, 106:20216-20221.
47. Ge X., Mazor Y., Hunicke-Smith S.P., Ellington A.D., Georgiou G. Rapid construction and characterization of synthetic antibody libraries without DNA amplification. Biotechnol Bioeng 2010, 106:347-357.
48. Ravn U., Gueneau F., Baerlocher L., Osteras M., Desmurs M., Malinge P., Magistrelli G., Farinelli L., Kosco-Vilbois M.H., Fischer N. By-passing in vitro screening-next generation sequencing technologies applied to antibody display and in silico candidate selection. Nucleic Acids Res 2010, 38:e193.
49. Reddy S.T., Ge X., Miklos A.E., Hughes R.A., Kang S.H., Hoi K.H., Chrysostomou C., Hunicke-Smith S.P., Iverson B.L., Tucker P.W., et al. Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells. Nat Biotechnol 2010, 28:965-969.