Identification of common blood gene signatures for the diagnosis of renal and cardiac acute allograft rejection

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Li, Li ^a   Khush, Kiran ^a   Hsieh, Szu Chuan ^a,b   Ying, Lihua ^a   Luikart, Helen ^a   Sigdel, Tara ^a,b   Roedder, Silke ^a,b   Yang, Andrew ^a   Valantine, Hannah ^a   Sarwal, Minnie M ^a,b  

^a STANFORD UNIVERSITY   (United States)

^b CALIFORNIA PACIFIC MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACUTE GRAFT REJECTION; ADULT; ARTICLE; BLOOD SAMPLING; CARDIAC ALLOGRAFT VASCULOPATHY; CARDIAC GRAFT REJECTION; CONTROLLED STUDY; CYTOMEGALOVIRUS INFECTION; DIAGNOSTIC ACCURACY; DISEASE ASSOCIATION; FEMALE; GENE; GENE EXPRESSION; GENE IDENTIFICATION; GENE SIGNATURE; GENETIC MARKER; HEART MUSCLE BIOPSY; HEART TRANSPLANTATION; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; KIDNEY BIOPSY; KIDNEY GRAFT REJECTION; KIDNEY TRANSPLANTATION; MAJOR CLINICAL STUDY; MALE; OUTCOME ASSESSMENT; POLYMERASE CHAIN REACTION; PREDICTION; QUANTITATIVE ANALYSIS; SCORING SYSTEM; SENSITIVITY AND SPECIFICITY; SYNDROME DELINEATION;

ADULT; AGED; ALLOGRAFTS; BIOLOGICAL MARKERS; CYTOMEGALOVIRUS INFECTIONS; FEMALE; GENE EXPRESSION; GRAFT REJECTION; HEART TRANSPLANTATION; HUMANS; KIDNEY TRANSPLANTATION; MALE; MIDDLE AGED;

EID: 84893005048     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0082153     Document Type: Article

References (54)

1. Taylor DO, Stehlik J, Edwards LB, Aurora P, Christie JD, et al. (2009) Registry of the International Society for Heart and Lung Transplantation: Twenty-sixth Official Adult Heart Transplant Report-2009. J Heart Lung Transplant 28: 1007-1022.
2. Raichlin E, Edwards BS, Kremers WK, Clavell AL, Rodeheffer RJ, et al. (2009) Acute cellular rejection and the subsequent development of allograft vasculopathy after cardiac transplantation. J Heart Lung Transplant 28: 320-327.
3. Deng MC, Eisen HJ, Mehra MR, Billingham M, Marboe CC, et al. (2006) Noninvasive discrimination of rejection in cardiac allograft recipients using gene expression profiling. Am J Transplant 6: 150-160.
4. Wong BW, Rahmani M, Rezai N, McManus BM (2005) Progress in heart transplantation. Cardiovasc Pathol 14: 176-180.
5. Baraldi-Junkins C, Levin HR, Kasper EK, Rayburn BK, Herskowitz A, et al. (1993) Complications of endomyocardial biopsy in heart transplant patients. J Heart Lung Transplant 12: 63-67.
6. Deckers JW, Hare JM, Baughman KL (1992) Complications of transvenous right ventricular endomyocardial biopsy in adult patients with cardiomyopathy: a seven-year survey of 546 consecutive diagnostic procedures in a tertiary referral center. J Am Coll Cardiol 19: 43-47.
7. Navia JL, Atik FA, Vega PR, Garcia M, Starling RC, et al. (2005) Tricuspid valve repair for biopsy-induced regurgitation in a heart transplant recipient. J Heart Valve Dis 14: 264-267.
8. Evans RW, Williams GE, Baron HM, Deng MC, Eisen HJ, et al. (2005) The economic implications of noninvasive molecular testing for cardiac allograft rejection. Am J Transplant 5: 1553-1558.
9. Mehra MR, Feller E, Rosenberg S (2006) The promise of protein-based and gene-based clinical markers in heart transplantation: from bench to bedside. Nat Clin Pract Cardiovasc Med 3: 136-143.
10. Kienzl K, Sarg B, Golderer G, Obrist P, Werner ER, et al. (2009) Proteomic profiling of acute cardiac allograft rejection. Transplantation 88: 553-560.
11. Li L, Khatri P, Sigdel TK, Tran T, Ying L, et al. (2012) A peripheral blood diagnostic test for acute rejection in renal transplantation. Am J Transplant 12: 2710-2718.
12. Sarwal MM, Ettenger RB, Dharnidharka V, Benfield M, Mathias R, et al. (2012) Complete Steroid Avoidance Is Effective and Safe in Children With Renal Transplants: A Multicenter Randomized Trial With Three-Year Follow-Up. Am J Transplant 12: 2719-2729.
13. Naesens M, Salvatierra O, Benfield M, Ettenger RB, Dharnidharka V, et al. (2012) Subclinical Inflammation and Chronic Renal Allograft Injury in a Randomized Trial on Steroid Avoidance in Pediatric Kidney Transplantation. Am J Transplant 12: 2730-2743.
14. Wang E, Worschech A, Marincola FM (2008) The immunologic constant of rejection. Trends Immunol 29: 256-262.
15. Chen R, Sigdel TK, Li L, Kambham N, Dudley JT, et al. (2010) Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions. PLoS Comput Biol 6.
16. Bromberg JS, Ikle D (2012) Is the time ripe for genomic diagnosis and prediction of rejection? Am J Transplant 12: 2573-2574.
17. Purvesh Khatri SR, Kimura N, De Vusser K, Morgan AA, Gong Y,et al. (2013) A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation. JEM.
18. Billingham ME, Cary NR, Hammond ME, Kemnitz J, Marboe C, et al. (1990) A working formulation for the standardization of nomenclature in the diagnosis of heart and lung rejection: Heart Rejection Study Group. The International Society for Heart Transplantation. The Journal of heart transplantation 9: 587-593.
19. St Goar FG, Pinto FJ, Alderman EL, Valantine HA, Schroeder JS, et al. (1992) Intracoronary ultrasound in cardiac transplant recipients. In vivo evidence of "angiographically silent" intimal thickening. Circulation 85: 979-987.
20. Schmittgen TD, Livak KJ (2008) Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc 3: 1101-1108.
21. Sahai H, Khurshid A (1995) A note on confidence intervals for the hypergeometric parameter in analyzing biomedical data. Comput Biol Med 25: 35-38.
22. Ferreira JA (2007) The Benjamini-Hochberg method in the case of discrete test statistics. Int J Biostat 3: Article 11.
23. Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, et al. (2010) Cell type-specific gene expression differences in complex tissues. Nat Methods 7: 287-289.
24. Alpert S, Lewis NP, Ross H, Fowler M, Valantine HA (1995) The relationship of granzyme A and perforin expression to cardiac allograft rejection and dysfunction. Transplantation 60: 1478-1485.
25. Baan CC, van Emmerik NE, Balk AH, Quint WG, Mochtar B, et al. (1994) Cytokine mRNA expression in endomyocardial biopsies during acute rejection from human heart transplants. Clin Exp Immunol 97: 293-298.
26. de Groot-Kruseman HA, Baan CC, Hagman EM, Mol WM, Niesters HG, et al. (2002) Intragraft interleukin 2 mRNA expression during acute cellular rejection and left ventricular total wall thickness after heart transplantation. Heart 87: 363-367.
27. Shulzhenko N, Morgun A, Zheng XX, Diniz RV, Almeida DR, et al. (2001) Intragraft activation of genes encoding cytotoxic T lymphocyte effector molecules precedes the histological evidence of rejection in human cardiac transplantation. Transplantation 72: 1705-1708.
28. Shulzhenko N, Morgun A, Rampim GF, Franco M, Almeida DR, et al. (2001) Monitoring of intragraft and peripheral blood TIRC7 expression as a diagnostic tool for acute cardiac rejection in humans. Hum Immunol 62: 342-347.
29. Shulzhenko N, Morgun A, Franco M, Souza MM, Almeida DR, et al. (2001) Expression of CD40 ligand, interferon-gamma and Fas ligand genes in endomyocardial biopsies of human cardiac allografts: correlation with acute rejection. Braz J Med Biol Res 34: 779-784.
30. van Emmerik N, Baan C, Vaessen L, Jutte N, Quint W, et al. (1994) Cytokine gene expression profiles in human endomyocardial biopsy (EMB) derived lymphocyte cultures and in EMB tissue. Transpl Int 7 Suppl 1: S623-626.
31. Kimball PM, Radovancevic B, Isom T, Spickard A, Frazier OH (1996) The paradox of cytokine monitoring-predictor of immunologic activity as well as immunologic silence following cardiac transplantation. Transplantation 61: 909-915.
32. Lagoo AS, George JF, Naftel DC, Griffin AK, Kirklin JK, et al. (1996) Semiquantitative measurement of cytokine messenger RNA in endomyocardium and peripheral blood mononuclear cells from human heart transplant recipients. J Heart Lung Transplant 15: 206-217.
33. Morgun A, Shulzhenko N, Diniz RV, Almeida DR, Carvalho AC, et al. (2001) Cytokine and TIRC7 mRNA expression during acute rejection in cardiac allograft recipients. Transplant Proc 33: 1610-1611.
34. Sarwal M, Chua MS, Kambham N, Hsieh SC, Satterwhite T, et al. (2003) Molecular heterogeneity in acute renal allograft rejection identified by DNA microarray profiling. N Engl J Med 349: 125-138.
35. Khatri P, Sarwal MM (2009) Using gene arrays in diagnosis of rejection. Curr Opin Organ Transplant 14: 34-39.
36. Horwitz PA, Tsai EJ, Putt ME, Gilmore JM, Lepore JJ, et al. (2004) Detection of cardiac allograft rejection and response to immunosuppressive therapy with peripheral blood gene expression. Circulation 110: 3815-3821.
37. Pham MX, Teuteberg JJ, Kfoury AG, Starling RC, Deng MC, et al. (2010) Gene-expression profiling for rejection surveillance after cardiac transplantation. N Engl J Med 362: 1890-1900.
38. Solez K, Axelsen RA, Benediktsson H, Burdick JF, Cohen AH, et al. (1993) International standardization of criteria for the histologic diagnosis of renal allograft rejection: the Banff working classification of kidney transplant pathology. Kidney Int 44: 411-422.
39. Stewart S, Fishbein MC, Snell GI, Berry GJ, Boehler A, et al. (2007) Revision of the 1996 working formulation for the standardization of nomenclature in the diagnosis of lung rejection. J Heart Lung Transplant 26: 1229-1242.
40. Wu T, Abu-Elmagd K, Bond G, Nalesnik MA, Randhawa P, et al. (2003) A schema for histologic grading of small intestine allograft acute rejection. Transplantation 75: 1241-1248.
41. Delgado DH, Luu L, Edwards J, Cardella C, Rao V, et al. (2002) Should moderate acute rejection of a cardiac transplant graft be treated? Clin Transplant 16: 217-221.
42. Fishbein MC, Bell G, Lones MA, Czer LS, Miller JM, et al. (1994) Grade 2 cellular heart rejection: does it exist? J Heart Lung Transplant 13: 1051-1057.
43. Nielsen H, Sorensen FB, Nielsen B, Bagger JP, Thayssen P, et al. (1993) Reproducibility of the acute rejection diagnosis in human cardiac allografts. The Stanford Classification and the International Grading System. J Heart Lung Transplant 12: 239-243.
44. Winters GL, McManus BM (1996) Consistencies and controversies in the application of the International Society for Heart and Lung Transplantation working formulation for heart transplant biopsy specimens. Rapamycin Cardiac Rejection Treatment Trial Pathologists. J Heart Lung Transplant 15: 728-735.
45. Yeoh TK, Frist WH, Eastburn TE, Atkinson J (1992) Clinical significance of mild rejection of the cardiac allograft. Circulation 86: II267-271.
46. Stewart S, Winters GL, Fishbein MC, Tazelaar HD, Kobashigawa J, et al. (2005) Revision of the 1990 working formulation for the standardization of nomenclature in the diagnosis of heart rejection. J Heart Lung Transplant 24: 1710-1720.
47. Laguens RP, Meckert PM, Martino JS, Perrone S, Favaloro R (1996) Identification of programmed cell death (apoptosis) in situ by means of specific labeling of nuclear DNA fragments in heart biopsy samples during acute rejection episodes. J Heart Lung Transplant 15: 911-918.
48. Bernstein D, Williams GE, Eisen H, Mital S, Wohlgemuth JG, et al. (2007) Gene expression profiling distinguishes a molecular signature for grade 1B mild acute cellular rejection in cardiac allograft recipients. J Heart Lung Transplant 26: 1270-1280.
49. Holweg CT, Potena L, Luikart H, Yu T, Berry GJ, et al. (2011) Identification and classification of acute cardiac rejection by intragraft transcriptional profiling. Circulation 123: 2236-2243.
50. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98: 5116-5121.
51. Russell ME, Fujita M, Masek MA, Rowan RA, Billingham ME (1993) Cardiac graft vascular disease. Nonselective involvement of large and small vessels. Transplantation 56: 1599-1601.
52. Stoica SC, Cafferty F, Pauriah M, Taylor CJ, Sharples LD, et al. (2006) The cumulative effect of acute rejection on development of cardiac allograft vasculopathy. J Heart Lung Transplant 25: 420-425.
53. Hornick P, Smith J, Pomerance A, Mitchell A, Banner N, et al. (1997) Influence of acute rejection episodes, HLA matching, and donor/recipient phenotype on the development of 'early' transplant-associated coronary artery disease. Circulation 96: II-148-153.
54. Yamani MH, Taylor DO, Rodriguez ER, Cook DJ, Zhou L, et al. (2007) Transplant vasculopathy is associated with increased AlloMap gene expression score. J Heart Lung Transplant 26: 403-406.