High throughput cellular screens to interrogate the human T and B cell repertoires

Current Opinion in Immunology

Volumn 23, Issue 3, 2011, Pages 430-435

  Corti, Davide ^a   Sallusto, Federica ^a   Lanzavecchia, Antonio ^a  

^a INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

MONOCLONAL ANTIBODY; NEUTRALIZING ANTIBODY;

B LYMPHOCYTE; CELL CULTURE; CELL FUNCTION; CELL IMMORTALIZATION; CELL ISOLATION; CELL SPECIFICITY; DRUG DESIGN; EFFECTOR CELL; FLOW CYTOMETRY; FLUORESCENCE ANALYSIS; HIGH THROUGHPUT SCREENING; HOST PATHOGEN INTERACTION; HUMAN; MEMORY CELL; MEMORY T LYMPHOCYTE; PLASMA CELL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; T LYMPHOCYTE;

ADAPTIVE IMMUNITY; B-LYMPHOCYTES; CELL CULTURE TECHNIQUES; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; IMMUNOLOGIC MEMORY; T-LYMPHOCYTES;

EID: 79957686113     PISSN: 09527915     EISSN: 18790372     Source Type: Journal    
DOI: 10.1016/j.coi.2011.04.006     Document Type: Review

References (62)

1. Chaussabel D., Quinn C., Shen J., Patel P., Glaser C., Baldwin N., Stichweh D., Blankenship D., Li L., Munagala I., et al. A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus. Immunity 2008, 29:150-164.
2. Berry M.P., Graham C.M., McNab F.W., Xu Z., Bloch S.A., Oni T., Wilkinson K.A., Banchereau R., Skinner J., Wilkinson R.J., et al. An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature 2010, 466:973-977.
3. 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.
4. Schneider D.S., Ayres J.S. Two ways to survive infection: what resistance and tolerance can teach us about treating infectious diseases. Nat Rev Immunol 2008, 8:889-895.
5. Jamieson A.M., Yu S., Annicelli C.H., Medzhitov R. Influenza virus-induced glucocorticoids compromise innate host defense against a secondary bacterial infection. Cell Host Microbe 2010, 7:103-114.
6. Chtanova T., Newton R., Liu S.M., Weininger L., Young T.R., Silva D.G., Bertoni F., Rinaldi A., Chappaz S., Sallusto F., et al. Identification of T cell-restricted genes, and signatures for different T cell responses, using a comprehensive collection of microarray datasets. J Immunol 2005, 175:7837-7847.
7. Kaech S.M., Hemby S., Kersh E., Ahmed R. Molecular and functional profiling of memory CD8 T cell differentiation. Cell 2002, 111:837-851.
8. Kasturi S.P., Skountzou I., Albrecht R.A., Koutsonanos D., Hua T., Nakaya H.I., Ravindran R., Stewart S., Alam M., Kwissa M., et al. Programming the magnitude and persistence of antibody responses with innate immunity. Nature 2011, 470:543-547.
9. Wirth T.C., Xue H.H., Rai D., Sabel J.T., Bair T., Harty J.T., Badovinac V.P. Repetitive antigen stimulation induces stepwise transcriptome diversification but preserves a core signature of memory CD8(+) T cell differentiation. Immunity 2010, 33:128-140.
10. Hertoghs K.M., Moerland P.D., van Stijn A., Remmerswaal E.B., Yong S.L., van de Berg P.J., van Ham S.M., Baas F., ten Berge I.J., van Lier R.A. Molecular profiling of cytomegalovirus-induced human CD8+ T cell differentiation. J Clin Invest 2010, 120:4077-4090.
11. Riou C., Yassine-Diab B., Van grevenynghe J., Somogyi R., Greller L.D., Gagnon D., Gimmig S., Wilkinson P., Shi Y., Cameron M.J., et al. Convergence of TCR and cytokine signaling leads to FOXO3a phosphorylation and drives the survival of CD4+ central memory T cells. J Exp Med 2007, 204:79-91.
12. Araki K., Turner A.P., Shaffer V.O., Gangappa S., Keller S.A., Bachmann M.F., Larsen C.P., Ahmed R. mTOR regulates memory CD8 T-cell differentiation. Nature 2009, 460:108-112.
13. Venturi V., Quigley M.F., Greenaway H.Y., Ng P.C., Ende Z.S., McIntosh T., Asher T.E., Almeida J.R., Levy S., Price D.A., et al. A mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing. J Immunol 2011, 186:4285-4294.
14. Wu Y.C., Kipling D., Leong H.S., Martin V., Ademokun A.A., Dunn-Walters D.K. High-throughput immunoglobulin repertoire analysis distinguishes between human IgM memory and switched memory B-cell populations. Blood 2010, 116:1070-1078.
15. Seifert M., Kuppers R. Molecular footprints of a germinal center derivation of human IgM+(IgD+)CD27+ B cells and the dynamics of memory B cell generation. J Exp Med 2009, 206:2659-2669.
16. 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 Transl Med 2009, 1:12ra23.
17. Nguyen P., Ma J., Pei D., Obert C., Cheng C., Geiger T.L. Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire. BMC Genomics 2011, 12:106.
18. Burton D.R. Antibodies, viruses and vaccines. Nat Rev Immunol 2002, 2:706-713.
19. Steel J., Lowen A.C., Wang T.T., Yondola M., Gao Q., Haye K., Garcia-Sastre A., Palese P. Influenza virus vaccine based on the conserved hemagglutinin stalk domain. MBio 2010, 1. e00018-10.
20. Stamatatos L., Morris L., Burton D.R., Mascola J.R. Neutralizing antibodies generated during natural HIV-1 infection: good news for an HIV-1 vaccine?. Nat Med 2009, 15:866-870.
21. Lyons A.B., Parish C.R. Determination of lymphocyte division by flow cytometry. J Immunol Methods 1994, 171:131-137.
22. Traggiai E., Becker S., Subbarao K., Kolesnikova L., Uematsu Y., Gismondo M.R., Murphy B.R., Rappuoli R., Lanzavecchia A. An efficient method to make human monoclonal antibodies from memory B cells: potent neutralization of SARS coronavirus. Nat Med 2004, 10:871-875.
23. Altman J.D., Davis M.M. MHC-peptide tetramers to visualize antigen-specific T cells. Curr Protoc Immunol 2003, (Chapter 17: Unit 17 13).
24. Leyendeckers H., Odendahl M., Lohndorf A., Irsch J., Spangfort M., Miltenyi S., Hunzelmann N., Assenmacher M., Radbruch A., Schmitz J. Correlation analysis between frequencies of circulating antigen-specific IgG-bearing memory B cells and serum titers of antigen-specific IgG. Eur J Immunol 1999, 29:1406-1417.
25. Moon J.J., Chu H.H., Pepper M., McSorley S.J., Jameson S.C., Kedl R.M., Jenkins M.K. Naive CD4(+) T cell frequency varies for different epitopes and predicts repertoire diversity and response magnitude. Immunity 2007, 27:203-213.
26. Chu H.H., Moon J.J., Takada K., Pepper M., Molitor J.A., Schacker T.W., Hogquist K.A., Jameson S.C., Jenkins M.K. Positive selection optimizes the number and function of MHCII-restricted CD4+ T cell clones in the naive polyclonal repertoire. Proc Natl Acad Sci U S A 2009, 106:11241-11245.
27. Jenkins M.K., Chu H.H., McLachlan J.B., Moon J.J. On the composition of the preimmune repertoire of T cells specific for peptide-major histocompatibility complex ligands. Annu Rev Immunol 2010, 28:275-294.
28. Rodenko B., Toebes M., Hadrup S.R., van Esch W.J., Molenaar A.M., Schumacher T.N., Ovaa H. Generation of peptide-MHC class I complexes through UV-mediated ligand exchange. Nat Protoc 2006, 1:1120-1132.
29. Newell E.W., Klein L.O., Yu W., Davis M.M. Simultaneous detection of many T-cell specificities using combinatorial tetramer staining. Nat Methods 2009, 6:497-499.
30. Geiger R., Duhen T., Lanzavecchia A., Sallusto F. Human naive and memory CD4+ T cell repertoires specific for naturally processed antigens analyzed using libraries of amplified T cells. J Exp Med 2009, 206:1525-1534.
31. Hinrichs C.S., Borman Z.A., Gattinoni L., Yu Z., Burns W.R., Huang J., Klebanoff C.A., Johnson L.A., Kerkar S.P., Yang S., et al. Human effector CD8+ T cells derived from naive rather than memory subsets possess superior traits for adoptive immunotherapy. Blood 2011, 117:808-814.
32. Hawkins R.E., Gilham D.E., Debets R., Eshhar Z., Taylor N., Abken H., Schumacher T.N., Consortium A. Development of adoptive cell therapy for cancer: a clinical perspective. Hum Gene Ther 2010, 21:665-672.
33. Sallusto F., Lanzavecchia A., Araki K., Ahmed R. From vaccines to memory and back. Immunity 2010, 33:451-463.
34. Stemberger C., Huster K.M., Koffler M., Anderl F., Schiemann M., Wagner H., Busch D.H. A single naive CD8+ T cell precursor can develop into diverse effector and memory subsets. Immunity 2007, 27:985-997.
35. Seder R.A., Darrah P.A., Roederer M. T-cell quality in memory and protection: implications for vaccine design. Nat Rev Immunol 2008, 8:247-258.
36. Roederer M., Tarnok A. OMIPs-orchestrating multiplexity in polychromatic science. Cytometry A 2010, 77:811-812.
37. Krutzik P.O., Trejo A., Schulz K.R., Nolan G.P. Phospho flow cytometry methods for the analysis of kinase signaling in cell lines and primary human blood samples. Methods Mol Biol 2011, 699:179-202.
38. Darrah P.A., Hegde S.T., Patel D.T., Lindsay R.W., Chen L., Roederer M., Seder R.A. IL-10 production differentially influences the magnitude, quality, and protective capacity of Th1 responses depending on the vaccine platform. J Exp Med 2010, 207:1421-1433.
39. Klebanoff C.A., Gattinoni L., Torabi-Parizi P., Kerstann K., Cardones A.R., Finkelstein S.E., Palmer D.C., Antony P.A., Hwang S.T., Rosenberg S.A., et al. Central memory self/tumor-reactive CD8+ T cells confer superior antitumor immunity compared with effector memory T cells. Proc Natl Acad Sci U S A 2005, 102:9571-9576.
40. Harari A., Bart P.A., Stohr W., Tapia G., Garcia M., Medjitna-Rais E., Burnet S., Cellerai C., Erlwein O., Barber T., et al. An HIV-1 clade C DNA prime, NYVAC boost vaccine regimen induces reliable, polyfunctional, and long-lasting T cell responses. J Exp Med 2008, 205:63-77.
41. Gaucher D., Therrien R., Kettaf N., Angermann B.R., Boucher G., Filali-Mouhim A., Moser J.M., Mehta R.S., Drake D.R., Castro E., et al. Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses. J Exp Med 2008, 205:3119-3131.
42. Zielinski C.E., Corti D., Mele F., Pinto D., Lanzavecchia A., Sallusto F. Dissecting the human immunologic memory for pathogens. Immunol Rev 2011, 240:40-51.
43. Amanna I.J., Carlson N.E., Slifka M.K. Duration of humoral immunity to common viral and vaccine antigens. N Engl J Med 2007, 357:1903-1915.
44. 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.
45. Scheid J.F., Mouquet H., Feldhahn N., Seaman M.S., Velinzon K., Pietzsch J., Ott R.G., Anthony R.M., Zebroski H., Hurley A., et al. Broad diversity of neutralizing antibodies isolated from memory B cells in HIV-infected individuals. Nature 2009, 458:636-640.
46. Mouquet H., Scheid J.F., Zoller M.J., Krogsgaard M., Ott R.G., Shukair S., Artyomov M.N., Pietzsch J., Connors M., Pereyra F., et al. Polyreactivity increases the apparent affinity of anti-HIV antibodies by heteroligation. Nature 2010, 467:591-595.
47. Wu X., Yang Z.Y., Li Y., Hogerkorp C.M., Schief W.R., Seaman M.S., Zhou T., Schmidt S.D., Wu L., Xu L., et al. Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to HIV-1. Science 2010, 329:856-861.
48. Zhou T., Georgiev I., Wu X., Yang Z.Y., Dai K., Finzi A., Do Kwon Y., Scheid J.F., Shi W., Xu L., et al. Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01. Science 2010, 329:811-817.
49. Macagno A., Bernasconi N.L., Vanzetta F., Dander E., Sarasini A., Revello M.G., Gerna G., Sallusto F., Lanzavecchia A. Isolation of human monoclonal antibodies that potently neutralize human cytomegalovirus infection by targeting different epitopes on the gH/gL/UL128-131A complex. J Virol 2010, 84:1005-1013.
50. Simmons C.P., Bernasconi N.L., Suguitan A.L., Mills K., Ward J.M., Chau N.V., Hien T.T., Sallusto F., Ha do Q., Farrar J., et al. Prophylactic and therapeutic efficacy of human monoclonal antibodies against H5N1 influenza. PLoS Med 2007, 4:e178.
51. Beltramello M., Williams K.L., Simmons C.P., Macagno A., Simonelli L., Quyen N.T., Sukupolvi-Petty S., Navarro-Sanchez E., Young P.R., de Silva A.M., et al. The human immune response to Dengue virus is dominated by highly cross-reactive antibodies endowed with neutralizing and enhancing activity. Cell Host Microbe 2010, 8:271-283.
52. Corti D., Suguitan A.L., Pinna D., Silacci C., Fernandez-Rodriguez B.M., Vanzetta F., Santos C., Luke C.J., Torres-Velez F.J., Temperton N.J., et al. Heterosubtypic neutralizing antibodies are produced by individuals immunized with a seasonal influenza vaccine. J Clin Invest 2010, 120:1663-1673.
53. Collarini E.J., Lee F.E., Foord O., Park M., Sperinde G., Wu H., Harriman W.D., Carroll S.F., Ellsworth S.L., Anderson L.J., et al. Potent high-affinity antibodies for treatment and prophylaxis of respiratory syncytial virus derived from B cells of infected patients. J Immunol 2009, 183:6338-6345.
54. Walker L.M., Phogat S.K., Chan-Hui P.Y., Wagner D., Phung P., Goss J.L., Wrin T., Simek M.D., Fling S., Mitcham J.L., et al. Broad and potent neutralizing antibodies from an African donor reveal a new HIV-1 vaccine target. Science 2009, 326:285-289.
55. Bernasconi N.L., Traggiai E., Lanzavecchia A. Maintenance of serological memory by polyclonal activation of human memory B cells. Science 2002, 298:2199-2202.
56. Pinna D., Corti D., Jarrossay D., Sallusto F., Lanzavecchia A. Clonal dissection of the human memory B-cell repertoire following infection and vaccination. Eur J Immunol 2009, 39:1260-1270.
57. Amanna I.J., Slifka M.K. Quantitation of rare memory B cell populations by two independent and complementary approaches. J Immunol Methods 2006, 317:175-185.
58. Radbruch A., Muehlinghaus G., Luger E.O., Inamine A., Smith K.G., Dorner T., Hiepe F. Competence and competition: the challenge of becoming a long-lived plasma cell. Nat Rev Immunol 2006, 6:741-750.
59. 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.
60. 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.
61. Wrammert J., Koutsonanos D., Li G.M., Edupuganti S., Sui J., Morrissey M., McCausland M., Skountzou I., Hornig M., Lipkin W.I., et al. Broadly cross-reactive antibodies dominate the human B cell response against 2009 pandemic H1N1 influenza virus infection. J Exp Med 2011, 208:181-193.
62. Fazekas de St G., Webster R.G. Disquisitions of original antigenic sin. I. Evidence in man. J Exp Med 1966, 124:331-345.