iTRAQ is a useful method to screen for membrane-bound proteins differentially expressed in human natural killer cell types

Journal of Proteome Research

Volumn 6, Issue 2, 2007, Pages 644-653

  Lund, Troy C ^a,c   Anderson, Lorraine B ^b   McCullar, Valarie ^a   Higgins, LeeAnn ^b   Yun, Gong H ^a   Grzywacz, Bartek ^b   Verneris, Michael R ^b   Miller, Jeffrey S ^a  

^a UNIVERSITY OF MINNESOTA MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

^c Mayo Mail Code 609   (United States)

Author keywords

iTRAQ; Liquid chromatography; Membrane bound; Natural killer cell; Tandem mass spectrometry; Umbilical cord blood

Indexed keywords

ALLOGRAFT INFLAMMATORY FACTOR 1; ALPHA 2 MACROGLOBULIN; CD9 ANTIGEN; MEMBRANE PROTEIN; PROTEIN BASP1; UNCLASSIFIED DRUG;

ARTICLE; CELL FUNCTION; CELL MEMBRANE; CONTROLLED STUDY; FLUORESCENCE ACTIVATED CELL SORTING; HUMAN; HUMAN CELL; HUMAN TISSUE; LYSOSOME; NATURAL KILLER CELL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DETERMINATION; PROTEIN EXPRESSION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; UMBILICAL CORD BLOOD; WESTERN BLOTTING;

ADULT; CELL CULTURE TECHNIQUES; CELL MEMBRANE; DNA PRIMERS; FETAL BLOOD; FLOW CYTOMETRY; GRANZYMES; HUMANS; INFANT, NEWBORN; KILLER CELLS, NATURAL; MEMBRANE PROTEINS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA; UMBILICAL VEINS;

EID: 33847371618     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr0603912     Document Type: Article

References (40)

1. Miller, J. S.; McCullar, V. Human natural killer cells with polyclonal lectin and immunoglobulinlike receptors develop from single hematopoietic stem cells with preferential expression of NKG2A and KIR2DL2/L3/S2. Blood 2001, 98 (3), 705-13.
2. Miller, J. S.; Oelkers, S.; Verfaillie, C.; McGlave, P. Role of monocytes in the expansion of human activated natural killer cells. Blood 1992, 80 (9), 2221-9.
3. Miller, J. S.; McCullar, V.; Punzel, M.; Lemischka, I. R.; Moore, K. A. Single adult human CD34(+)/Lin-/CD38(-) progenitors give rise to natural killer cells, B-lineage cells, dendritic cells, and myeloid cells. Blood 1999, 93 (1), 96-106.
4. Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17 (10), 994-9.
5. Choe, L. H.; Aggarwal, K.; Franck, Z.; Lee, K. H. A comparison of the consistency of proteome quantitation using two-dimensional electrophoresis and shotgun isobaric tagging in Escherichia coli cells. Electrophoresis 2005, 26 (12), 2437-49.
6. DeSouza, L.; Diehl, G.; Rodrigues, M. J.; Guo, J.; Romaschin, A. D.; Colgan, T. J.; Siu, K. W. Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cICAT with multidimensional liquid chromatography and tandem mass spectrometry. J. Proteome Res. 2005, 4 (2), 377-86.
7. Pierson, B. A.; McGlave, P. B.; Hu, W. S.; Miller, J. S. Natural killer cell proliferation is dependent on human serum and markedly increased utilizing an enriched supplemented basal medium. J. Hematother. 1995, 4 (3), 149-58.
8. Nelsestuen, G. L.; Zhang, Y.; Martinez, M. B.; Key, N. S.; Jilma, B.; Verneris, M.; Sinaiko, A.; Kasthuri, R. S. Plasma protein profiling: unique and stable features of individuals. Proteomics 2005, 5 (15), 4012-24.
9. Tang, W. H.; Halpern, B. R.; Shilov, I. V.; Seymour, S. L.; Keating, S. P.; Loboda, A.; Patel, A. A.; Schaeffer, D. A.; Nuwaysir, L. M. Discovering known and unanticipated protein modifications using MS/MS database searching. Anal. Chem. 2005, 77 (13), 3931-46.
10. Unwin, R. D.; Smith, D. L.; Blinco, D.; Wilson, C. L.; Miller, C. J.; Evans, C. A.; Jaworska, E.; Baldwin, S. A.; Barnes, K.; Pierce, A.; Spooncer, E.; Whetton, A. D. Quantitative proteomics reveals posttranslational control as a regulatory factor in primary hematopoietic stem cells. Blood 2006, 107 (12), 4687-94.
11. Zhang, Y.; Wolf-Yadlin, A.; Ross, P. L.; Pappin, D. J.; Rush, J.; Lauffenburger, D. A.; White, F. M. Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol. Cell. Proteomics 2005, 4 (9), 1240-50.
12. Hardt, M.; Witkowska, H. E.; Webb, S.; Thomas, L. R.; Dixon, S. E.; Hall, S. C.; Fisher, S. J. Assessing the effects of diurnal variation on the composition of human parotid saliva: quantitative analysis of native peptides using iTRAQ reagents. Anal. Chem. 2005, 77 (15), 4947-54.
13. Chen, X.; Walker, A. K.; Strahler, J. R.; Simon, E. S.; Tomanicek-Volk, S. L.; Nelson, B. B.; Hurley, M. C.; Ernst, S. A.; Williams, J. A.; Andrews, P. C. Organellar proteomics: Analysis of pancreatic zymogen granule membranes. Mol. Cell. Proteomics 2005.
14. Miller, J. S.; Alley, K. A.; McGlave, P. Differentiation of natural killer (NK) cells from human primitive marrow progenitors in a stroma-based long-term culture system: identification of a CD34+7+ NK progenitor. Blood 1994, 83 (9), 2594-601.
15. Man, P.; Novak, P.; Cebecauer, M.; Horvath, O.; Fiserova, A.; Havlicek, V.; Bezouska, K. Mass spectrometric analysis of the glycosphingolipid-enriched microdomains of rat natural killer cells. Proteomics 2005, 5 (1), 113-22.
16. Schena, M.; Shalon, D.; Heller, R.; Chai, A.; Brown, P. O.; Davis, R. W. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl. Acad. Sci. U.S.A. 1996, 93 (20), 10614-9.
17. Schena, M.; Shalon, D.; Davis, R. W.; Brown, P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270 (5235), 467-70.
18. Liu, H.; Sadygov, R. G.; Yates, J. R., 3rd. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76 (14), 4193-201.
19. Adkins, J. N.; Varnum, S. M.; Auberry, K. J.; Moore, R. J.; Angell, N. H.; Smith, R. D.; Springer, D. L.; Pounds, J. G. Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol. Cell. Proteomics 2002, 1 (12), 947-55.
20. Veenstra, T. D.; Conrads, T. P.; Issaq, H. J. What to do with "one-hit wonders"? Electrophoresis 2004, 25 (9), 1278-9.
21. Kelemen, S. E.; Autieri, M. V. Expression of allograft inflammatory factor-1 in T lymphocytes: a role in T-lymphocyte activation and proliferative arteriopathies. Am. J. Pathol. 2005, 167 (2), 619-26.
22. Tian, Y.; Kelemen, S. E.; Autieri, M. V. Inhibition of AIF-1 Expression by Constitutive siRNA Expression Reduces Macrophage Migration, Proliferation and Signal Transduction initiated by Atherogenic Stimuli. Am. J. Physiol. Cell Physiol. 2005.
23. Eriksson, M.; Meadows, S. K.; Wira, C. R.; Sentman, C. L. Unique phenotype of human uterine NK cells and their regulation by endogenous TGF-beta. J. Leukocyte Biol. 2004, 76 (3), 667-75.
24. Koopman, L. A.; Kopcow, H. D.; Rybalov, B.; Boyson, J. E.; Orange, J. S.; Schatz, F.; Masch, R.; Lockwood, C. J.; Schachter, A. D.; Park, P. J.; Strominger, J. L. Human decidual natural killer cells are a unique NK cell subset with immunomodulatory potential. J. Exp. Med. 2003, 198 (8), 1201-12.
25. Yashiro-Ohtani, Y.; Zhou, X. Y.; Toyo-Oka, K.; Tai, X. G.; Park, C. S.; Hamaoka, T.; Abe, R.; Miyake, K.; Fujiwara, H. Non-CD28 costimulatory molecules present in T cell rafts induce T cell costimulation by enhancing the association of TCR with rafts. J. Immunol. 2000, 164 (3), 1251-9.
26. Mori, S.; Jewett, A.; Cavalcanti, M.; Murakami-Mori, K.; Nakamura, S.; Bonavida, B.; Vaz, F.; Hoffman, R.; Almeida-Porada, G.; Ascensao, J. L.; Gaddy, J.; Broxmeyer, H. E. Differential regulation of human NK cell-associated gene expression following activation by IL-2, IFN-alpha and PMA/ionomycin Definition of early progenitors and functional maturation of human natural killer cells: requirements for cytocidal activity Cord blood CD16+56-cells with low lytic activity are possible precursors of mature natural killer cells. Int. J. Oncol. 1998, 12 (5), 1165-70.
27. Vaz, F.; Hoffman, R.; Almeida-Porada, G.; Ascensao, J. L. Definition of early progenitors and functional maturation of human natural killer cells: requirements for cytocidal activity. Pathobiology 1998, 66 (1), 41-8.
28. Gaddy, J.; Broxmeyer, H. E. Cord blood CD16+56- cells with low lytic activity are possible precursors of mature natural killer cells. Cell. Immunol. 1997, 180 (2), 132-42.
29. Inaba, T.; Shimazaki, C.; Sumikuma, T.; Ochiai, N.; Okano, A.; Hatsuse, M.; Ashihara, E.; Kobayashi, Y.; Rin, K.; Murakami, S.; Haruyama, H.; Fujita, N.; Nakagawa, M. Clinicopathological features of myeloid/natural killer (NK) cell precursor acute leukemia. Leukocyte Res. 2001, 25 (2), 109-13.
30. Lee, P. S.; Lin, C. N.; Liu, C.; Huang, C. T.; Hwang, W. S. Acute leukemia with myeloid, B-, and natural killer cell differentiation. Arch. Pathol. Lab. Med. 2003, 127 (2), E93-5.
31. Rutella, S.; Bonanno, G.; Marone, M.; De Ritis, D.; Mariotti, A.; Voso, M. T.; Scambia, G.; Mancuso, S.; Leone, G.; Pierelli, L. Identification of a novel subpopulation of human cord blood CD34-CD133-CD7-CD45+lineage- cells capable of lymphoid/NK cell differentiation after in vitro exposure to IL-15. J. Immunol. 2003, 171 (6), 2977-88.
32. Armstrong, P. B.; Quigley, J. P. Alpha2-macroglobulin: an evolutionarily conserved arm of the innate immune system. Dev. Comp. Immunol. 1999, 23 (4-5), 375-90.
33. Chaudhuri, L. Human alpha 2-macroglobulin and its biological significance. Indian J. Exp. Biol. 1993, 31 (9), 723-7.
34. Feige, J. J.; Negoescu, A.; Keramidas, M.; Souchelnitskiy, S.; Chambaz, E. M. Alpha 2-macroglobulin: a binding protein for transforming growth factor-beta and various cytokines. Horm. Res. 1996, 45 (3-5), 227-32.
35. Mather, J. P. Follistatins and alpha 2-macroglobulin are soluble binding proteins for inhibin and activin. Horm. Res. 1996, 45 (3-5), 207-10.
36. Croy, B. A.; Esadeg, S.; Chantakru, S.; van den Heuvel, M.; Paffaro, V. A.; He, H.; Black, G. P.; Ashkar, A. A.; Kiso, Y.; Zhang, J. Update on pathways regulating the activation of uterine Natural Killer cells, their interactions with decidual spiral arteries and homing of their precursors to the uterus. J. Reprod. Immunol. 2003, 59 (2), 175-91.
37. Kovacs, D. M. alpha2-macroglobulin in late-onset Alzheimer's disease. Exp. Gerontol. 2000, 35 (4), 473-9.
38. Morris, J. S.; Stein, T.; Pringle, M. A.; Davies, C. R.; Weber-Hall, S.; Ferrier, R. K.; Bell, A. K.; Heath, V. J.; Gusterson, B. A. Involvement of axonal guidance proteins and their signaling partners in the developing mouse mammary gland. J. Cell. Physiol. 2006, 206 (1), 16-24.
39. Iino, S.; Taguchi, K.; Maekawa, S.; Nojyo, Y. Motor, sensory and autonomic nerve terminals containing NAP-22 immunoreactivity in the rat muscle. Brain Res. 2004, 1002 (1-2), 142-50.
40. Pompach, P.; Man, P.; Novak, P.; Havlicek, V.; Fiserova, A.; Bezouska, K. Mass spectrometry is a powerful tool for identification of proteins associated with lipid rafts of Jurkat T-cell line. Biochem. Soc. Trans. 2004, 32 (Pt 5), 777-9.