Multiplexed color-coded probe-based gene expression assessment for clinical molecular diagnostics in formalin-fixed paraffin-embedded human renal allograft tissue

Clinical Transplantation

Volumn 30, Issue 3, 2016, Pages 295-305

  Adam, Benjamin ^a   Afzali, Bahman ^a,b   Dominy, Katherine M ^c   Chapman, Erin ^a   Gill, Reeda ^a   Hidalgo, Luis G ^a   Roufosse, Candice ^c,d   Sis, Banu ^a   Mengel, Michael ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

^b UNIVERSITY OF DUISBURG ESSEN   (Germany)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

^d HAMMERSMITH HOSPITAL   (United Kingdom)

Author keywords

Allograft; Gene expression; Molecular; NanoString ; Transplantation

Indexed keywords

BETA ACTIN; CADHERIN 13; CAVEOLIN 1; CD31 ANTIGEN; CD34 ANTIGEN; CHEMOKINE RECEPTOR CX3CR1; CXCL11 CHEMOKINE; ENDOTHELIAL LEUKOCYTE ADHESION MOLECULE 1; GAMMA INTERFERON; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; GRANULYSIN; KRUPPEL LIKE FACTOR 4; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2; PALMDELPHIN; PHOSPHOLIPASE A1; PROTEIN S6; PROTEIN TYROSINE KINASE; RAS HOMOLOG FAMILY MEMBER J; REAGENT; RNA; THROMBOMODULIN; TISSUE PLASMINOGEN ACTIVATOR; TRANSCRIPTION FACTOR GATA 3; TRANSCRIPTION FACTOR SOX7; TRANSCRIPTION FACTOR T BET; TRIBBLES PSEUDOKINASE 1; TUMOR NECROSIS FACTOR; UNCLASSIFIED DRUG; UNINDEXED DRUG; VASCULAR ENDOTHELIAL CADHERIN; VON WILLEBRAND FACTOR; BIOLOGICAL MARKER; FLUORESCENT DYE; FORMALDEHYDE; MESSENGER RNA; NUCLEIC ACID PROBE; ORGANIC COMPOUND; PARAFFIN; SYBR GREEN I;

ANTIBODY MEDIATED REJECTION; ANTIGEN ANTIBODY REACTION; ARTICLE; BK VIRUS NEPHROPATHY; CLINICAL ASSESSMENT; CONTROLLED STUDY; EMBEDDING; ENDOTHELIUM CELL; FORMALIN FIXED PARAFFIN EMBEDDED PROCESSING; GENE EXPRESSION; GLOMERULONEPHRITIS; HUMAN; HUMAN TISSUE; INFLAMMATION; INTERSTITIAL FIBROSIS AND TUBULAR ATROPHY; KIDNEY ALLOGRAFT; KIDNEY BIOPSY; KIDNEY DISEASE; KIDNEY PARENCHYMA; KIDNEY TRANSPLANTATION; KIDNEY TUBULE DAMAGE; MICROARRAY ANALYSIS; MOLECULAR DIAGNOSIS; NATURAL KILLER CELL; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REPRODUCIBILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ISOLATION; T CELL MEDIATED REJECTION; ALLOGRAFT; FOLLOW UP; GENE EXPRESSION PROFILING; GENETIC PROCEDURES; GENETICS; GRAFT REJECTION; MOLECULAR PATHOLOGY; NANOTECHNOLOGY; NUCLEIC ACID PROBE; PROCEDURES; RETROSPECTIVE STUDY; TISSUE FIXATION;

ALLOGRAFTS; BIOMARKERS; FLUORESCENT DYES; FOLLOW-UP STUDIES; FORMALDEHYDE; GENE EXPRESSION PROFILING; GRAFT REJECTION; HUMANS; KIDNEY TRANSPLANTATION; MOLECULAR PROBE TECHNIQUES; NANOTECHNOLOGY; NUCLEIC ACID PROBES; ORGANIC CHEMICALS; PARAFFIN EMBEDDING; PATHOLOGY, MOLECULAR; RETROSPECTIVE STUDIES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; TISSUE FIXATION;

EID: 84959527620     PISSN: 09020063     EISSN: 13990012     Source Type: Journal    
DOI: 10.1111/ctr.12689     Document Type: Article

References (34)

1. Broecker V, Mengel M. The significance of histological diagnosis in renal allograft biopsies in 2014. Transpl Int 2015: 28: 136.
2. Mengel M, Sis B, Halloran PF. SWOT analysis of Banff: strengths, weaknesses, opportunities and threats of the international Banff consensus process and classification system for renal allograft pathology. Am J Transplant 2007: 7: 2221.
3. Mirnezami R, Nicholson J, Darzi A. Preparing for precision medicine. N Engl J Med 2012: 366: 489.
4. Mengel M, Campbell PM, Gebel H et al. Precision diagnostics in transplantation: from bench to bedside. Am J Transplant 2013: 13: 562.
5. Halloran PF, Einecke G. Microarrays and transcriptome analysis in renal transplantation. Nat Clin Pract Nephrol 2006: 2: 2.
6. Akalin E, Hendrix RC, Polavarapu RG et al. Gene expression analysis in human renal allograft biopsy samples using high-density oligoarray technology. Transplantation 2001: 72: 948.
7. Stegall MD, Park WD, Kim D, Kremers W. Gene expression during acute allograft rejection: novel statistical analysis of microarray data. Am J Transplant 2002: 2: 913.
8. Scherer A, Krause A, Walker JR, Korn A, Niese D, Raulf F. Early prognosis of the development of renal chronic allograft rejection by gene expression profiling of human protocol biopsies. Transplantation 2003: 75: 1323.
9. Sarwal M, Chua MS, Kambham N et al. Molecular heterogeneity in acute renal allograft rejection identified by DNA microarray profiling. N Engl J Med 2003: 349: 125.
10. Hoffmann SC, Hale DA, Kleiner DE et al. Functionally significant renal allograft rejection is defined by transcriptional criteria. Am J Transplant 2005: 5: 573.
11. Halloran PF, de Freitas DG, Einecke G et al. The molecular phenotype of kidney transplants. Am J Transplant 2010: 10: 2215.
12. Traitanon O, Poggio E, Fairchild R. Molecular monitoring of alloimmune-mediated injury in kidney transplant patients. Curr Opin Nephrol Hypertens 2014: 23: 625.
13. Reeve J, Einecke G, Mengel M et al. Diagnosing rejection in renal transplants: a comparison of molecular- and histopathology-based approaches. Am J Transplant 2009: 9: 1802.
14. Reeve J, Sellarés J, Mengel M et al. Molecular diagnosis of T cell-mediated rejection in human kidney transplant biopsies. Am J Transplant 2013: 13: 645.
15. Sis B, Jhangri GS, Bunnag S, Allanach K, Kaplan B, Halloran PF. Endothelial gene expression in kidney transplants with alloantibody indicates antibody-mediated damage despite lack of C4d staining. Am J Transplant 2009: 9: 2312.
16. Hidalgo LG, Sis B, Sellares J et al. NK cell transcripts and NK cells in kidney biopsies from patients with donor-specific antibodies: evidence for NK cell involvement in antibody-mediated rejection. Am J Transplant 2010: 10: 1812.
17. Hidalgo LG, Sellares J, Sis B, Mengel M, Chang J, Halloran PF. Interpreting NK cell transcripts versus T cell transcripts in renal transplant biopsies. Am J Transplant 2012: 12: 1180.
18. Lepin EJ, Zhang Q, Zhang X et al. Phosphorylated S6 ribosomal protein: a novel biomarker of antibody-mediated rejection in heart allografts. Am J Transplant 2006: 6: 1560.
19. Valenzuela NM, Hong L, Shen XD et al. Blockade of p-selectin is sufficient to reduce MHC I antibody-elicited monocyte recruitment in vitro and in vivo. Am J Transplant 2013: 13: 299.
20. Sellarés J, Reeve J, Loupy A et al. Molecular diagnosis of antibody-mediated rejection in human kidney transplants. Am J Transplant 2013: 13: 971.
21. Halloran PF, Pereira AB, Chang J et al. Microarray diagnosis of antibody-mediated rejection in kidney transplant biopsies: an international prospective study (INTERCOM). Am J Transplant 2013: 13: 2865.
22. Dean PG, Park WD, Cornell LD, Gloor JM, Stegall MD. Intragraft gene expression in positive crossmatch kidney allografts: ongoing inflammation mediates chronic antibody-mediated injury. Am J Transplant 2012: 12: 1551.
23. Hayde N, Bao Y, Pullman J et al. The clinical and genomic significance of donor-specific antibody-positive/C4d-negative and donor-specific antibody-negative/C4d-negative transplant glomerulopathy. Clin J Am Soc Nephrol 2013: 8: 2141.
24. Hayde N, Broin PÓ, Bao Y et al. Increased intragraft rejection-associated gene transcripts in patients with donor-specific antibodies and normal biopsies. Kidney Int 2014: 86: 600.
25. Dominy KM, Roufosse C, de Kort H et al. Use of quantitative real time polymerase chain reaction to assess gene transcripts associated with antibody-mediated rejection of kidney transplants. Transplantation 2015: 99: 1981.
26. Haas M, Sis B, Racusen LC et al. Banff 2013 meeting report: inclusion of C4d-negative antibody-mediated rejection and antibody-associated arterial lesions. Am J Transplant 2014: 14: 272.
27. Mengel M, Bock O, Priess M, Haller H, Kreipe H, Gwinner W. Expression of pro- and antifibrotic genes in protocol biopsies from renal allografts with interstitial fibrosis and tubular atrophy. Clin Nephrol 2008: 69: 408.
28. Allanach K, Mengel M, Einecke G et al. Comparing microarray versus RT-PCR assessment of renal allograft biopsies: similar performance despite different dynamic ranges. Am J Transplant 2008: 8: 1006.
29. Geiss GK, Bumgarner RE, Birditt B et al. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 2008: 26: 317.
30. Reis PP, Waldron L, Goswami RS et al. mRNA transcript quantification in archival samples using multiplexed, color-coded probes. BMC Biotechnol 2011: 11: 46.
31. Simon R, Lam A, Li MC, Ngan M, Menenzes S, Zhao Y. Analysis of gene expression data using BRB-ArrayTools. Cancer Inform 2007: 3: 11.
32. von Ahlfen S, Missel A, Bendrat K, Schlumpberger M. Determinants of RNA quality from FFPE samples. PLoS One 2007: 2: e1261.
33. Nielsen T, Wallden B, Schaper C et al. Analytical validation of the PAM50-based Prosigna Breast Cancer Prognostic Gene Signature Assay and nCounter Analysis System using formalin-fixed paraffin-embedded breast tumor specimens. BMC Cancer 2014: 14: 177.
34. Bustin S, Dhillon HS, Kirvell S et al. Variability of the reverse transcription step: practical implications. Clin Chem 2015: 61: 202.