Monitoring Pharmacologically Induced Immunosuppression by Immune Repertoire Sequencing to Detect Acute Allograft Rejection in Heart Transplant Patients: A Proof-of-Concept Diagnostic Accuracy Study

PLoS Medicine

Volumn 12, Issue 10, 2015, Pages

  Vollmers, Christopher ^a,b   De Vlaminck, Iwijn ^a,b,c   Valantine, Hannah A ^d   Penland, Lolita ^a,b   Luikart, Helen ^d   Strehl, Calvin ^d   Cohen, Garrett ^d   Khush, Kiran K ^d   Quake, Stephen R ^a,b,c  

^a Stanford University   (United States)

^b STANFORD UNIVERSITY   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^d STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN A; IMMUNOGLOBULIN D; IMMUNOGLOBULIN G; IMMUNOGLOBULIN M; METHYLPREDNISOLONE; PREDNISONE; TACROLIMUS; IMMUNOSUPPRESSIVE AGENT;

ACUTE GRAFT REJECTION; ADULT; ARTICLE; B LYMPHOCYTE; BIOPSY; CLINICAL ARTICLE; CLINICAL TRIAL (TOPIC); CONTROLLED STUDY; DIAGNOSTIC ACCURACY; DIAGNOSTIC TEST ACCURACY STUDY; DISEASE SEVERITY; HEART TRANSPLANTATION; HUMAN; HUMAN TISSUE; IMMUNE DEFICIENCY; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; ALLOGRAFT; FEMALE; GRAFT REJECTION; IMMUNOLOGICAL MONITORING; IMMUNOLOGY; IMMUNOSUPPRESSIVE TREATMENT; MALE; PROCEDURES; PROSPECTIVE STUDY;

ALLOGRAFTS; B-LYMPHOCYTES; FEMALE; GRAFT REJECTION; HEART TRANSPLANTATION; HUMANS; IMMUNOSUPPRESSION; IMMUNOSUPPRESSIVE AGENTS; MALE; MONITORING, IMMUNOLOGIC; PROSPECTIVE STUDIES; SENSITIVITY AND SPECIFICITY;

EID: 84946034563     PISSN: 15491277     EISSN: 15491676     Source Type: Journal    
DOI: 10.1371/journal.pmed.1001890     Document Type: Article

References (31)

1. Plosker GL, Foster RH, Tacrolimus: a further update of its pharmacology and therapeutic use in the management of organ transplantation. Drugs. 2000;59:323–389. 10730553
2. Liu J, Farmer JD, Lane WS, Friedman J, Weissman I, Schreiber SL, Calcineurin is a common target of cyclophilin-cyclosporin A and FKBP-FK506 complexes. Cell. 1991;66:807–815. 1715244
3. Heidt S, Roelen DL, Eijsink C, Eikmans M, Van Kooten C, Claas FHJ, et al. Calcineurin inhibitors affect B cell antibody responses indirectly by interfering with T cell help. Clin Exp Immunol. 2010;159:199–207. doi: 10.1111/j.1365-2249.2009.04051.x 19922499
4. Perez-Andres M, Paiva B, Nieto WG, Caraux A, Schmitz A, Almeida J, et al. Human peripheral blood B-cell compartments: a crossroad in B-cell traffic. Cytometry B Clin Cytom. 2010;78 (Suppl 1):S47–S60. doi: 10.1002/cyto.b.20547 20839338
5. Newell KA, Asare A, Kirk AD, Gisler TD, Bourcier K, Suthanthiran M, et al. Identification of a B cell signature associated with renal transplant tolerance in humans. J Clin Invest. 2010;120:1836–1847. doi: 10.1172/JCI39933 20501946
6. Glanville J, Kuo TC, von Budingen H-C, Guey L, Berka J, Sundar PD, et al. Naive antibody gene-segment frequencies are heritable and unaltered by chronic lymphocyte ablation. Proc Natl Acad Sci U S A. 2011;108:20066–20071. doi: 10.1073/pnas.1107498108 22123975
7. Vollmers C, Sit RV, Weinstein JA, Dekker CL, Quake SR, Genetic measurement of memory B-cell recall using antibody repertoire sequencing. Proc Natl Acad Sci U S A. 2013;110:13463–13468. doi: 10.1073/pnas.1312146110 23898164
8. Boyd SD, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, et al. Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci Transl Med. 2009;1:12ra23. 20161664
9. Georgiou G, Ippolito GC, Beausang J, Busse CE, Wardemann H, Quake SR, The promise and challenge of high-throughput sequencing of the antibody repertoire. Nat Biotechnol. 2014;32:158–168. doi: 10.1038/nbt.2782 24441474
10. Jiang N, He J, Weinstein JA, Penland L, Sasaki S, He X-S, et al. Lineage structure of the human antibody repertoire in response to influenza vaccination. Sci Transl Med. 2013;5:171ra19. doi: 10.1126/scitranslmed.3004794 23390249
11. Logan AC, Gao H, Wang C, Sahaf B, Jones CD, Marshall EL, et al. High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment. Proc Natl Acad Sci U S A. 2011:108:21194–21199. doi: 10.1073/pnas.1118357109 22160699
12. De Vlaminck I, Khush KK, Strehl C, Kohli B, Luikart H, Neff NF, et al. Temporal response of the human virome to immunosuppression and antiviral therapy. Cell. 2013;155:1178–1187. doi: 10.1016/j.cell.2013.10.034 24267896
13. De Vlaminck I, Valantine HA, Snyder TM, Strehl C, Cohen G, Luikart H, et al. Circulating cell-free DNA enables noninvasive diagnosis of heart transplant rejection. Sci Transl Med. 2014;6:241ra77. doi: 10.1126/scitranslmed.3007803 24944192
14. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, Basic local alignment search tool. J Mol Biol. 1990;215:403–410. 2231712
15. Hunter JD, Matplotlib: a 2D graphics environment. Comput Sci Eng. 2007;9:90–95.
16. SciPy Developers. SciPy [computer program]. http://www.scipy.org/. Accessed 10 September 2015.
17. Oliphant TE, Python for scientific computing. Comput Sci Eng. 2007;9:10–20.
18. Van der Walt S, Colbert SC, Varoquaux G, The NumPy array: a structure for efficient numerical computation. Comput Sci Eng. 2011;13:22–30.
19. Xia LC, Cram JA, Chen T, Fuhrman JA, Sun F, Accurate genome relative abundance estimation based on shotgun metagenomic reads. PLoS ONE. 2011;6:e27992. doi: 10.1371/journal.pone.0027992 22162995
20. Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, et al. Scikit-learn: machine learning in Python. J Mach Learn Res. 2011;12:2825–2830.
21. Wilson EB, Probable inference, the law of succession, and statistical inference. J Am Stat Assoc. 1927;22:209.
22. Julious SA, Two-sided confidence intervals for the single proportion: comparison of seven methods by Robert G. Newcombe, Statistics in Medicine 1998; 17:857–872. Stat Med. 2005;24:3383–3384. 16206245
23. Nair N, Newell EW, Vollmers C, Quake SR, Morton JM, Davis MM, et al. High-dimensional immune profiling of total and rotavirus VP6-specific intestinal and circulating B cells by mass cytometry. Mucosal Immunol. 2015 Apr 22. 25899688
24. Tayebi H, Lapierre V, Saas P, Lienard A, Sutton L, Milpied N, et al. Enhanced activation of B cells in a granulocyte colony-stimulating factor-mobilized peripheral blood stem cell graft. Br J Haematol. 2001;114:698–700. 11553000
25. Jensen GS, Poppema S, Mant MJ, Pilarski LM, Transition in CD45 isoform expression during differentiation of normal and abnormal B cells. Int Immunol. 1989;1:229–236. 2535062
26. Hoffman FM, Outcomes and complications after heart transplantation: a review. J Cardiovasc Nurs. 2005;20:S31–S42. 16160582
27. Giese T, Zeier M, Meuer S, Analysis of NFAT-regulated gene expression in vivo: a novel perspective for optimal individualized doses of calcineurin inhibitors. Nephrol Dial Transplant. 2004;19 (Suppl 4):iv55–iv60. 15240851
28. Wieland E, Olbricht CJ, Süsal C, Gurragchaa P, Böhler T, Israeli M, et al. Biomarkers as a tool for management of immunosuppression in transplant patients. Ther Drug Monit. 2010;32:560–572. doi: 10.1097/FTD.0b013e3181efb3d2 20814352
29. Rossano JW, Denfield SW, Kim JJ, Price JF, Jefferies JL, Decker JA, et al. Assessment of the Cylex ImmuKnow cell function assay in pediatric heart transplant patients. J Hear Lung Transplant. 2009;28:26–31.
30. Pham MX, Teuteberg JJ, Kfoury AG, Starling RC, Deng MC, Cappola TP, et al. Gene-expression profiling for rejection surveillance after cardiac transplantation. N Engl J Med. 2010;362:1890–1900. doi: 10.1056/NEJMoa0912965 20413602
31. Deng MC, Eisen HJ, Mehra MR, Billingham M, Marboe CC, Berry G, et al. Noninvasive discrimination of rejection in cardiac allograft recipients using gene expression profiling. Am J Transplant. 2006;6:150–160. 16433769