Exhaustive expansion: A novel technique for analyzing complex data generated by higher-order polychromatic flow cytometry experiments

Journal of Translational Medicine

Volumn 8, Issue , 2010, Pages

  Siebert, Janet C ^a   Wang, Lian ^b   Haley, Daniel P ^c   Romer, Ann ^b   Zheng, Bo ^b   Munsil, Wes ^a   Gregory, Kenton W ^b   Walker, Edwin B ^c  

^a CytoAnalytics   (United States)

^b PROVIDENCE ST VINCENT MEDICAL CENTER   (United States)

^c EARLE A CHILES RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CD27 ANTIGEN; CD28 ANTIGEN; CD45RA ANTIGEN; GLYCOPROTEIN GP 100; MELANOMA VACCINE; MONOCLONAL ANTIBODY; LEUKOCYTE ANTIGEN;

ANIMAL CELL; ANTIGEN EXPRESSION; ARTICLE; CD8+ T LYMPHOCYTE; CELL KINETICS; CELL SURFACE; CLINICAL PROTOCOL; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; FLOW CYTOMETRY; GENETIC ALGORITHM; MELANOMA; MEMORY T LYMPHOCYTE; NONHUMAN; PHENOTYPE; STEM CELL MOBILIZATION; T LYMPHOCYTE SUBPOPULATION; WOUND HEALING; HUMAN; IMMUNOLOGICAL MEMORY; IMMUNOLOGY; METHODOLOGY; T LYMPHOCYTE;

ANTIBODIES, MONOCLONAL; ANTIGENS, CD; FLOW CYTOMETRY; HUMANS; IMMUNOLOGIC MEMORY; T-LYMPHOCYTES;

EID: 77958556812     PISSN: None     EISSN: 14795876     Source Type: Journal    
DOI: 10.1186/1479-5876-8-106     Document Type: Article

References (46)

1. Perfetto SP, Chattopadhyay PK, Roederer M. Seventeen-colour flow cytometry: unravelling the immune system. Nat Rev Immunol 2004, 4:648-655. 10.1038/nri1416, 15286731.
2. Pyne S, Hu X, Wang K, Rossin E, Lin T, Maier LM, Baecher-Allan C, McLachlan GJ, Tamayo P, Hafler DA, De Jager PL, Mesirov JP. Automated high-dimensional flow cytometric data analysis. Proc Natl Acad Sci USA 2009, 106:8519-8524. 10.1073/pnas.0903028106, 2682540, 19443687.
3. Lo K, Brinkman RR, Gottardo R. Automated gating of flow cytometry data via robust model-based clustering. Cytometry A 2008, 73:321-332.
4. Murphy RF. Automated identification of subpopulations in flow cytometric list mode data using cluster analysis. Cytometry 1985, 6:302-309. 10.1002/cyto.990060405, 4017796.
5. Marincola FM. In support of descriptive studies; relevance to translational research. J Transl Med 2007, 5:21. 10.1186/1479-5876-5-21, 1871566, 17474987.
6. Valet G. Cytomics as a new potential for drug discovery. Drug Discov Today 2006, 11:785-791. 10.1016/j.drudis.2006.07.003, 16935745.
7. Valet G, Leary JF, Tárnok A. Cytomics--new technologies: towards a human cytome project. Cytometry A 2004, 59:167-171. 10.1002/cyto.a.20047, 15170595.
8. Walker EB, Haley D, Petrausch U, Floyd K, Miller W, Sanjuan N, Alvord G, Fox BA, Urba WJ. Phenotype and functional characterization of long-term gp100-specific memory CD8+ T cells in disease-free melanoma patients before and after boosting immunization. Clin Cancer Res 2008, 14:5270-5283. 10.1158/1078-0432.CCR-08-0022, 2756994, 18698047.
9. Gattinoni L, Zhong X, Palmer DC, Ji Y, Hinrichs CS, Yu Z, Wrzesinski C, Boni A, Cassard L, Garvin LM, Paulos CM, Muranski P, Restifo NP. Wnt signaling arrests effector T cell differentiation and generates CD8+ memory stem cells. Nat Med 2009, 15:808-813. 10.1038/nm.1982, 2707501, 19525962.
10. Berger C, Jensen MC, Lansdorp PM, Gough M, Elliott C, Riddell SR. Adoptive transfer of effector CD8+ T cells derived from central memory cells establishes persistent T cell memory in primates. J Clin Invest 2008, 118:294-305. 10.1172/JCI32103, 2104476, 18060041.
11. Gattinoni L, Powell DJ, Rosenberg SA, Restifo NP. Adoptive immunotherapy for cancer: building on success. Nat Rev Immunol 2006, 6:383-393. 10.1038/nri1842, 1473162, 16622476.
12. Hassan HT, El-Sheemy M. Adult bone-marrow stem cells and their potential in medicine. J R Soc Med 2004, 97:465-471. 10.1258/jrsm.97.10.465, 1079613, 15459256.
13. Gourgiotis S, Villias C, Germanos S, Foukas A, Ridolfini MP. Acute limb compartment syndrome: a review. J Surg Educ 2007, 64:178-186. 10.1016/j.jsurg.2007.03.006, 17574182.
14. Ferrari G, Cusella-De Angelis G, Coletta M, Paolucci E, Stornaiuolo A, Cossu G, Mavilio F. Muscle regeneration by bone marrow-derived myogenic progenitors. Science 1998, 279:1528-1530. 10.1126/science.279.5356.1528, 9488650.
15. Fukada S, Miyagoe-Suzuki Y, Tsukihara H, Yuasa K, Higuchi S, Ono S, Tsujikawa K, Takeda S, Yamamoto H. Muscle regeneration by reconstitution with bone marrow or fetal liver cells from green fluorescent protein-gene transgenic mice. J Cell Sci 2002, 115:1285-1293.
16. Corbel SY, Lee A, Yi L, Duenas J, Brazelton TR, Blau HM, Rossi FMV. Contribution of hematopoietic stem cells to skeletal muscle. Nat Med 2003, 9:1528-1532. 10.1038/nm959, 14625543.
17. Umemura T, Nishioka K, Igarashi A, Kato Y, Ochi M, Chayama K, Yoshizumi M, Higashi Y. Autologous bone marrow mononuclear cell implantation induces angiogenesis and bone regeneration in a patient with compartment syndrome. Circ J 2006, 70:1362-1364. 10.1253/circj.70.1362, 16998273.
18. Tateishi-Yuyama E, Matsubara H, Murohara T, Ikeda U, Shintani S, Masaki H, Amano K, Kishimoto Y, Yoshimoto K, Akashi H, Shimada K, Iwasaka T, Imaizumi T. Therapeutic angiogenesis for patients with limb ischaemia by autologous transplantation of bone-marrow cells: a pilot study and a randomised controlled trial. Lancet 2002, 360:427-435. 10.1016/S0140-6736(02)09670-8, 12241713.
19. Herrera MB, Bruno S, Buttiglieri S, Tetta C, Gatti S, Deregibus MC, Bussolati B, Camussi G. Isolation and characterization of a stem cell population from adult human liver. Stem Cells 2006, 24:2840-2850. 10.1634/stemcells.2006-0114, 16945998.
20. Dicker A, Le Blanc K, Aström G, van Harmelen V, Götherström C, Blomqvist L, Arner P, Rydén M. Functional studies of mesenchymal stem cells derived from adult human adipose tissue. Exp Cell Res 2005, 308:283-290. 10.1016/j.yexcr.2005.04.029, 15925364.
21. Wilson A, Oser GM, Jaworski M, Blanco-Bose WE, Laurenti E, Adolphe C, Essers MA, Macdonald HR, Trumpp A. Dormant and self-renewing hematopoietic stem cells and their niches. Ann N Y Acad Sci 2007, 1106:64-75. 10.1196/annals.1392.021, 17442778.
22. Pitchford SC, Furze RC, Jones CP, Wengner AM, Rankin SM. Differential mobilization of subsets of progenitor cells from the bone marrow. Cell Stem Cell 2009, 4:62-72. 10.1016/j.stem.2008.10.017, 19128793.
23. Miller RJ, Banisadr G, Bhattacharyya BJ. CXCR4 signaling in the regulation of stem cell migration and development. J Neuroimmunol 2008, 198:31-38. 10.1016/j.jneuroim.2008.04.008, 18508132.
24. Zheng B, Cao B, Crisan M, Sun B, Li G, Logar A, Yap S, Pollett JB, Drowley L, Cassino T, Gharaibeh B, Deasy BM, Huard J, Péault B. Prospective identification of myogenic endothelial cells in human skeletal muscle. Nat Biotechnol 2007, 25:1025-1034. 10.1038/nbt1334, 17767154.
25. Cerletti M, Jurga S, Witczak CA, Hirshman MF, Shadrach JL, Goodyear LJ, Wagers AJ. Highly efficient, functional engraftment of skeletal muscle stem cells in dystrophic muscles. Cell 2008, 134:37-47. 10.1016/j.cell.2008.05.049, 18614009.
26. Crisan M, Yap S, Casteilla L, Chen C, Corselli M, Park TS, Andriolo G, Sun B, Zheng B, Zhang L, Norotte C, Teng P, Traas J, Schugar R, Deasy BM, Badylak S, Buhring H, Giacobino J, Lazzari L, Huard J, Péault B. A perivascular origin for mesenchymal stem cells in multiple human organs. Cell Stem Cell 2008, 3:301-313. 10.1016/j.stem.2008.07.003, 18786417.
27. Middleton J, Americh L, Gayon R, Julien D, Mansat M, Mansat P, Anract P, Cantagrel A, Cattan P, Reimund J, Aguilar L, Amalric F, Girard J. A comparative study of endothelial cell markers expressed in chronically inflamed human tissues: MECA-79, Duffy antigen receptor for chemokines, von Willebrand factor, CD31, CD34, CD105 and CD146. J Pathol 2005, 206:260-268. 10.1002/path.1788, 15887283.
28. Ingram DA, Mead LE, Tanaka H, Meade V, Fenoglio A, Mortell K, Pollok K, Ferkowicz MJ, Gilley D, Yoder MC. Identification of a novel hierarchy of endothelial progenitor cells using human peripheral and umbilical cord blood. Blood 2004, 104:2752-2760. 10.1182/blood-2004-04-1396, 15226175.
29. Garlanda C, Dejana E. Heterogeneity of endothelial cells. Specific markers. Arterioscler Thromb Vasc Biol 1997, 17:1193-1202.
30. Lugli E, Pinti M, Nasi M, Troiano L, Ferraresi R, Mussi C, Salvioli G, Patsekin V, Robinson JP, Durante C, Cocchi M, Cossarizza A. Subject classification obtained by cluster analysis and principal component analysis applied to flow cytometric data. Cytometry A 2007, 71:334-344.
31. Casazza JP, Betts MR, Price DA, Precopio ML, Ruff LE, Brenchley JM, Hill BJ, Roederer M, Douek DC, Koup RA. Acquisition of direct antiviral effector functions by CMV-specific CD4+ T lymphocytes with cellular maturation. J Exp Med 2006, 203:2865-2877. 10.1084/jem.20052246, 2118179, 17158960.
32. Betts MR, Nason MC, West SM, De Rosa SC, Migueles SA, Abraham J, Lederman MM, Benito JM, Goepfert PA, Connors M, Roederer M, Koup RA. HIV nonprogressors preferentially maintain highly functional HIV-specific CD8+ T cells. Blood 2006, 107:4781-4789. 10.1182/blood-2005-12-4818, 1895811, 16467198.
33. Smith JW, Walker EB, Fox BA, Haley D, Wisner KP, Doran T, Fisher B, Justice L, Wood W, Vetto J, Maecker H, Dols A, Meijer S, Hu H, Romero P, Alvord WG, Urba WJ. Adjuvant Immunization of HLA-A2-Positive Melanoma Patients With a Modified gp100 Peptide Induces Peptide-Specific CD8+ T-Cell Responses. J Clin Oncol 2003, 21:1562-1573. 10.1200/JCO.2003.09.020, 12697882.
34. Swindle MM. Swine in the laboratory 2007, CRC Press.
35. Romero P, Zippelius A, Kurth I, Pittet MJ, Touvrey C, Iancu EM, Corthesy P, Devevre E, Speiser DE, Rufer N. Four functionally distinct populations of human effector-memory CD8+ T lymphocytes. J Immunol 2007, 178:4112-4119.
36. Takata H, Takiguchi M. Three memory subsets of human CD8+ T cells differently expressing three cytolytic effector molecules. J Immunol 2006, 177:4330-4340.
37. Perez AL, Bachrach E, Illigens BMW, Jun SJ, Bagden E, Steffen L, Flint A, McGowan FX, Del Nido P, Montecino-Rodriguez E, Tidball JG, Kunkel LM. CXCR4 enhances engraftment of muscle progenitor cells. Muscle Nerve 2009, 40:562-572. 10.1002/mus.21317, 2749072, 19760789.
38. Palmer DC, Restifo NP. Suppressors of cytokine signaling (SOCS) in T cell differentiation, maturation, and function. Trends Immunol 2009, 30:592-602. 10.1016/j.it.2009.09.009, 19879803.
39. Geginat J, Sallusto F, Lanzavecchia A. Cytokine-driven proliferation and differentiation of human naive, central memory, and effector memory CD4(+) T cells. J Exp Med 2001, 194:1711-1719. 10.1084/jem.194.12.1711, 2193568, 11748273.
40. Klebanoff CA, Gattinoni L, Torabi-Parizi P, Kerstann K, Cardones AR, Finkelstein SE, Palmer DC, Antony PA, Hwang ST, Rosenberg SA, Waldmann TA, Restifo NP. Central memory self/tumor-reactive CD8+ T cells confer superior antitumor immunity compared with effector memory T cells. Proc Natl Acad Sci USA 2005, 102:9571-9576. 10.1073/pnas.0503726102, 1172264, 15980149.
41. da Silva Meirelles L, Chagastelles PC, Nardi NB. Mesenchymal stem cells reside in virtually all post-natal organs and tissues. J Cell Sci 2006, 119:2204-2213. 10.1242/jcs.02932, 16684817.
42. Sherwood RI, Christensen JL, Conboy IM, Conboy MJ, Rando TA, Weissman IL, Wagers AJ. Isolation of adult mouse myogenic progenitors: functional heterogeneity of cells within and engrafting skeletal muscle. Cell 2004, 119:543-554. 10.1016/j.cell.2004.10.021, 15537543.
43. Zuk PA, Zhu M, Ashjian P, De Ugarte DA, Huang JI, Mizuno H, Alfonso ZC, Fraser JK, Benhaim P, Hedrick MH. Human adipose tissue is a source of multipotent stem cells. Mol Biol Cell 2002, 13:4279-4295. 10.1091/mbc.E02-02-0105, 138633, 12475952.
44. Uezumi A, Ojima K, Fukada S, Ikemoto M, Masuda S, Miyagoe-Suzuki Y, Takeda S. Functional heterogeneity of side population cells in skeletal muscle. Biochem Biophys Res Commun 2006, 341:864-873. 10.1016/j.bbrc.2006.01.037, 16455057.
45. Illa I, Leon-Monzon M, Dalakas MC. Regenerating and denervated human muscle fibers and satellite cells express neural cell adhesion molecule recognized by monoclonal antibodies to natural killer cells. Ann Neurol 1992, 31:46-52. 10.1002/ana.410310109, 1371910.
46. Precopio ML, Betts MR, Parrino J, Price DA, Gostick E, Ambrozak DR, Asher TE, Douek DC, Harari A, Pantaleo G, Bailer R, Graham BS, Roederer M, Koup RA. Immunization with vaccinia virus induces polyfunctional and phenotypically distinctive CD8(+) T cell responses. J Exp Med 2007, 204:1405-1416. 10.1084/jem.20062363, 2118607, 17535971.