Standardization and quality control for high-dimensional mass cytometry studies of human samples

Cytometry Part A

Volumn 89, Issue 10, 2016, Pages 903-913

  Kleinsteuber, Katja ^a,b,c   Corleis, Björn ^a   Rashidi, Narges ^a   Nchinda, Nzuekoh ^a,b   Lisanti, Antonella ^a   Cho, Josalyn L ^d   Medoff, Benjamin D ^d   Kwon, Douglas ^a,d   Walker, Bruce D ^a,b,d  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^c LEIBNIZ INSTITUTE FOR EXPERIMENTAL VIROLOGY   (Germany)

^d MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

clinical studies; CyTOF; HIV; human immunology; Mass cytometry

Indexed keywords

ANTIBODY; CYTOKINE;

CD8+ T LYMPHOCYTE; CYTOLOGY; FLOW CYTOMETRY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNOPHENOTYPING; LUNG LAVAGE; MASS SPECTROMETRY; METABOLISM; MONONUCLEAR CELL; PROCEDURES; QUALITY CONTROL; REPRODUCIBILITY; STANDARD;

ANTIBODIES; BRONCHOALVEOLAR LAVAGE; CD8-POSITIVE T-LYMPHOCYTES; CYTOKINES; FLOW CYTOMETRY; HIV INFECTIONS; HUMANS; IMMUNOPHENOTYPING; LEUKOCYTES, MONONUCLEAR; MASS SPECTROMETRY; QUALITY CONTROL; REFERENCE STANDARDS; REPRODUCIBILITY OF RESULTS;

EID: 84992126905     PISSN: 15524922     EISSN: 15524930     Source Type: Journal    
DOI: 10.1002/cyto.a.22935     Document Type: Article

References (28)

1. Bandura DR, Baranov VI, Ornatsky OI, Antonov A, Kinach R, Lou X, Pavlov S, Vorobiev S, Dick JE, Tanner SD. Mass cytometry: Technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry. Anal Chem 2009;81:6813–6822.
2. Ornatsky O, Baranov VI, Bandura DR, Tanner SD, Dick J. Multiple cellular antigen detection by ICP-MS. J Immunol Methods 2006;308:68–76.
3. Bendall SC, Nolan GP, Roederer M, Chattopadhyay PK. A deep profiler's guide to cytometry. Trends Immunol 2012;33:323–332.
4. Zunder ER, Finck R, Behbehani GK, Amir E-AD, Krishnaswamy S, Gonzalez VD, Lorang CG, Bjornson Z, Spitzer MH, Bodenmiller B, et al. Palladium-based mass tag cell barcoding witha doublet-filtering scheme and single-celldeconvolution algorithm. Nat Protoc 2015;10:316–333.
5. Bendall SC, Simonds EF, Qiu P, Amir EAD, Krutzik PO, Finck R, Bruggner RV, Melamed R, Trejo A, Ornatsky OI, et al. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science 2011;332:687–696.
6. Chattopadhyay PK, Gierahn TM, Roederer M, Love JC. Single-cell technologies for monitoring immune systems. Nature Immunology 2014;15:128–135.
7. Catena R, Özcan A, Zivanovic N, Bodenmiller B. Enhanced multiplexing in mass cytometry using osmium and ruthenium tetroxide species. Cytometry A 2016;89A:491–497.
8. Chattopadhyay PK, Roederer M. A mine is a terrible thing to waste: High content, single cell technologies for comprehensive immune analysis. Am J Transplant 2015;15:1155–1161.
9. Perfetto SP, Chattopadhyay PK, Roederer M. Seventeen-colour flow cytometry: Unravelling the immune system. Nat Rev Immunol 2004;4:648–655.
10. Simonds EF, Bendall SC, Gibbs KD, Bruggner RV, Linderman MD, Sachs K, Nolan GP, Plevritis SK, Qiu P. Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE. Nat Biotechnol 2011;29:886–891.
11. Amir E-AD, Davis KL, Tadmor MD, Simonds EF, Levine JH, Bendall SC, Shenfeld DK, Krishnaswamy S, Nolan GP, Pe'er D. viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. Nat Biotechnol 2013;31:545–552.
12. Finck R, Simonds EF, Jager A, Krishnaswamy S, Sachs K, Fantl W, Pe'er D, Nolan GP, Bendall SC. Normalization of mass cytometry data with bead standards. Cytometry A 2013;83A:483–494.
13. Mei HE, Leipold MD, Schulz AR, Chester C, Maecker HT. Barcoding of live human peripheral blood mononuclear cells for multiplexed mass cytometry. J Immunol 2015;194:2022–2031.
14. Day CL, Kaufmann DE, Kiepiela P, Brown JA, Moodley ES, Reddy S, Mackey EW, Miller JD, Leslie AJ, DePierres C, et al. PD-1 expression on HIV-specific T cells is associated with T-cell exhaustion and disease progression. Nature 2006;443:350–354.
15. Trautmann L, Janbazian L, Chomont N, Said EA, Gimmig S, Bessette B, Boulassel MR, Delwart E, Sepulveda H, Balderas RS, et al. Upregulation of PD-1 expression on HIV-specific CD8+ T cells leads to reversible immune dysfunction. Nat Med 2006;12:1198–1202.
16. Yamamoto T, Price DA, Casazza JP, Ferrari G, Nason M, Chattopadhyay PK, Roederer M, Gostick E, Katsikis PD, Douek DC, et al. Surface expression patterns of negative regulatory molecules identify determinants of virus-specific CD8+ T-cell exhaustion in HIV infection. Blood 2011;117:4805–4815.
17. Peretz Y, He Z, Shi Y, Yassine-Diab B, Goulet J-P, Bordi R, Filali-Mouhim A, Loubert J-B, El-Far M, Dupuy FP, et al. CD160 and PD-1 Co-expression on HIV-specific CD8 T cells defines a subset with advanced dysfunction. PLoS Pathog 2012;8:e1002840.
18. Viganò S, Bellutti Enders F, Miconnet I, Cellerai C, Savoye A-L, Rozot V, Perreau M, Faouzi M, Ohmiti K, Cavassini M, et al. Rapid perturbation in viremia levels drives increases in functional avidity of HIV-specific CD8 T cells. PLoS Pathog 2013;9:e1003423.
19. Porichis F, Kwon DS, Zupkosky J, Tighe DP, McMullen A, Brockman MA, Pavlik DF, Rodriguez-Garcia M, Pereyra F, Freeman GJ, et al. Responsiveness of HIV-specific CD4 T cells to PD-1 blockade. Blood 2011;118:965–974.
20. Cordone I, Matutes E, Catovsky D. Characterisation of normal peripheral blood cells in cycle identified by monoclonal antibody Ki-67. J Clin Pathol 1992;45:201–205.
21. Li X, Miao H, Henn A, Topham DJ, Wu H, Zand MS, Mosmann TR. Ki-67 expression reveals strong, transient influenza specific CD4 T cell responses after adult vaccination. Vaccine 2012;30:4581–4584.
22. Bendall SC, Davis KL, Amir E-AD, Tadmor MD, Simonds EF, Chen TJ, Shenfeld DK, Nolan GP, Pe'er D. Single-cell trajectory detectionuncovers progression and regulatory coordination in human B cell development. Cell 2014;157:714–725.
23. Newell EW, Sigal N, Bendall SC, Nolan GP, Davis MM. Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes. Immunity 2012;36:142–152.
24. Becher B, Schlitzer A, Chen J, Mair F, Sumatoh HR, Teng KWW, Low D, Ruedl C, Riccardi-Castagnoli P, Poidinger M, et al. High-dimensional analysis of the murine myeloid cell system. Nature Immunology 2014;15:1181–1189.
25. Kozera B, Rapacz M. Reference genes in real-time PCR. J Appl Genet 2013;54:391–406.
26. Neff CP, Chain JL, MaWhinney S, Martin AK, Linderman DJ, Flores SC, Campbell TB, Palmer BE, Fontenot AP. Lymphocytic alveolitis is associated with the accumulation of functionally impaired HIV-specific T cells in the lung of antiretroviral therapy—Naive subjects. Am J Respir Crit Care Med 2015;191:464–473.
27. Mitchell AJ, Pradel LC, Chasson L, Van Rooijen N, Grau GE, Hunt NH, Chimini G. Technical advance: Autofluorescence as a tool for myeloid cell analysis. J Leuk Biol 2010;88:597–603.
28. Tricot S, Meyrand M, Sammicheli C, Elhmouzi-Younes J, Corneau A, Bertholet S, Malissen M.L, Grand R, Nuti S, Luche H, et al. Evaluating the efficiency of isotope transmission for improved panel design and a comparison of the detection sensitivities of mass cytometer instruments. Cytometry A 2015;87A:357–368.