Transcriptome changes of chronic tubulointerstitial damage in early kidney transplantation

Transplantation

Volumn 89, Issue 5, 2010, Pages 537-547

  Vitalone, Matthew J ^a   O'Connell, Philip J ^a,b   Wavamunno, Moses ^a   Fung, Caroline L S ^c   Chapman, Jeremy R ^b   Nankivell, Brian J ^b  

^a WESTMEAD HOSPITAL   (Australia)

^b UNIVERSITY OF SYDNEY   (Australia)

^c WESTMEAD HOSPITAL   (Australia)

Author keywords

Chronic allograft nephropathy; Gene expression; Interstitial fibrosis; Kidney transplantation; Microarray; Transcriptome; Tubular atrophy

Indexed keywords

COMPLEMENTARY DNA; RNA; TRANSCRIPTOME;

ADULT; ARTICLE; CELL PROLIFERATION; CELL REGENERATION; CHRONIC KIDNEY FAILURE; CLINICAL ARTICLE; CONTROLLED STUDY; DNA MICROARRAY; FEMALE; FIBROSING ALVEOLITIS; GENE EXPRESSION; HISTOLOGY; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; IMMUNITY; KIDNEY BIOPSY; KIDNEY GRAFT; KIDNEY TRANSPLANTATION; LIVER FIBROSIS; MACROPHAGE; MALE; PRIORITY JOURNAL; RENAL GRAFT DYSFUNCTION; SEQUENTIAL ANALYSIS; TRANSCRIPTOMICS; TUBULOINTERSTITIAL DAMAGE; WOUND HEALING;

ADULT; BIOPSY; DNA, COMPLEMENTARY; FEMALE; FIBROSIS; FOLLOW-UP STUDIES; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HISTOCOMPATIBILITY TESTING; HUMANS; KIDNEY TRANSPLANTATION; MALE; MIDDLE AGED; NEPHRITIS, INTERSTITIAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PATIENT SELECTION; RNA, ANTISENSE; TREATMENT FAILURE; WOUND HEALING;

EID: 77949367410     PISSN: 00411337     EISSN: None     Source Type: Journal    
DOI: 10.1097/TP.0b013e3181ca7389     Document Type: Article

References (39)

1. Nankivell BJ, Borrows RJ, Fung CL,etal. The natural history of chronic allograft nephropathy. N Engl J Med 2003; 349: 2326.
2. Nankivell BJ, Fenton-Lee CA, Kuypers DR, et al. Effect of histological damage on long-term kidney transplant outcome. Transplantation 2001; 71: 515.
3. Solez K, Colvin RB, Racusen LC, et al. Banff '05 Meeting Report: Differential diagnosis of chronic allograft injury and elimination of chronic allograft nephropathy ('CAN'). Am J Transplant 2007; 7: 518.
4. Chapman JR, O'Connell PJ, Nankivell BJ. Chronic renal allograft dysfunction. J Am Soc Nephrol 2005; 16: 3015.
5. Kuypers DR, Chapman JR, O'Connell PJ, et al. Predictors of renal transplant histology at three months. Transplantation 1999; 67: 1222.
6. Nankivell BJ, Borrows RJ, Fung CLS, et al. Natural history, risk factors, and impact of subclinical rejection in kidney transplantation. Transplantation 2004; 78: 242.
7. Mas V, Maluf D, Archer K, et al. Establishing the molecular pathways involved in chronic allograft nephropathy for testing new noninvasive diagnostic markers. Transplantation 2007; 83: 448.
8. Hotchkiss H, Chu TT, Hancock WW, et al. Differential expression of profibrotic and growth factorsinchronic allograft nephropathy.Transplantation 2006; 81: 342.
9. Hayry P, Aavik E, Sarwal M, et al. Chronic rejection: Prospects for therapeutic intervention in fibroproliferative vascular disease. Exp Clin Transplant 2003; 1: 35.
10. Flechner SM, Kurian SM, SolezK,etal.Denovo kidney transplantation without use of calcineurin inhibitors preserves renal structure and function at two years [see comment]. Am J Transplant 2004; 4: 1776.
11. Park W, Griffin M, Grande JP, et al. Molecular evidence of injury and inflammation in normal and fibrotic renal allografts one year post-transplant. Transplantation 2007; 83: 1466.
12. Baboolal K, Jones GA, Janezic A, et al. Molecular and structural consequences of early renal allograft injury. Kidney Int 2002; 61: 686.
13. Racusen LC, Colvin RB, Solez K, et al. Antibody-mediated rejection criteria\An addition to the Banff 97 classification of renal allograft rejection. Am J Transplant 2003; 3: 708.
14. Charney DA, Nadasdy T, Lo AW, et al. Plasma cell-rich acute renal allograft rejection. Transplantation 1999; 68: 791.
15. Fleige S, Pfaffl MW. RNA integrity and the effect on the real-time qRT-PCR performance. Mol Aspects Med 2006; 27: 126.
16. Schroeder A, Mueller O, Stocker S, et al. The RIN: An RNA integrity number for assigning integrity values toRNA measurements. BMC Mol Biol 2006; 7: 3.
17. Vitalone MJ, O'Connell PJ, Jimenez-Vera E, et al. Epithelial-to- mesenchymal transition in early transplant tubulointerstitial damage. J Am Soc Nephrol 2008; 19: 1571.
18. The BioConductor core team. Bio Conductor. Build 2.0-2.4. Available at: http://www.bioconductor.org.
19. R Development Core Team. The R Project for Statistical Computing. Build 2.3-2.9. Available at: http://www.r-project.org.
20. Smyth GK, Michaud J, Scott HS. Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinfor-matics 2005; 21: 2067.
21. Ritchie ME, Silver J, Holmes M, et al. A comparison of background correction methods for two-colour microarrays. Bioinformatics 2007; 23: 2700.
22. Smyth GK. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004; 3: Article 3. Epub ahead of print.
23. Smyth GK, Speed TP. Normalization of cDNA microarray data. Methods 2003; 31: 265.
24. Dennis G Jr, Sherman BT, Hosack DA, et al. DAVID: Database for annotation, visualization, and integrated discovery. Genome Biol 2003; 4: P3.
25. Diehn M, Sherlock G, Binkley G, et al. SOURCE: A unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res 2003; 31: 219.
26. Rebhan M, Chalifa-Caspi V, Prilusky J, et al. GeneCards: Encyclopedia for genes, proteins and diseases. Rehovot, Israel, Weizmann Institute of Science, Bioinformatics Unit and Genome Centre 1997.
27. Wheeler DL, Barrett T, Benson DA, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2006; 34(Database issue): D173.
28. Eisen M, Imoto S, Miyano S. Cluster 3.0: Standford University and University of Tokyo, 1998-1999. 2002.
29. Simirenko L. MapleTree, 2004. Available at: http://sourceforge.net/ projects/mapletree/. Accessed February 5, 2010.
30. SPSS Inc. SPSS v11.0 Student version for Windows. Chicago, IL, SPSS Inc. 2001.
31. Higgins JPT, Wang L, Kambham N, et al. Gene expression in the normal adult human kidney assessed by complementary DNA microarray. Mol Biol Cell 2004; 15: 649.
32. Kurian SM, Flechner SM, Kaouk J, et al. Laparoscopic donor nephrec-tomy gene expression profiling reveals upregulation of stress and ischemia associated genes compared to control kidneys. Transplantation 2005; 80: 1067.
33. Hauser P, Schwarz C, Mitterbauer C, et al. Genome-wide gene-expression patterns of donor kidney biopsies distinguish primary allograft function. Lab Invest 2004; 84: 353.
34. Kainz A, Mitterbauer C, Hauser P, et al. Alterations in gene expression in cadaveric vs. live donor kidneys suggest impaired tubular counterbalance of oxidative stress at implantation. Am J Transplant 2004; 4: 1595.
35. Naesens M, Li L, Ying L, et al. Expression of complement components differs between kidney allografts from living and deceased donors.J Am Soc Nephrol 2009; 20: 1839.
36. Donauer J,Rumberger B, KleinM, etal. Expression profiling on chronically rejected transplant kidneys. Transplantation 2003; 76: 539.
37. Scherer A, Krause A, Walker JR, et al. Early prognosis of the develop-mentof renal chronic allograft rejection by gene expression profiling of human protocol biopsies. Transplantation 2003; 75: 1323.
38. Mueller TF, EineckeG,Reeve J, etal. Microarray analysis ofrejection in human kidney transplants using pathogenesis-based transcript sets [see comment]. Am J Transplant 2007; 7: 2712.
39. Sarwal M, Chang S, Barry C, et al. Genomic analysis of renal allograft dysfunction using cDNA microarrays. Transplant Proc 2001; 33: 297.