Gene expression analysis of human renal biopsies: Recent developments towards molecular diagnosis of kidney disease

Current Opinion in Nephrology and Hypertension

Volumn 13, Issue 3, 2004, Pages 313-318

  Henger, Anna ^a   Schmid, Holger ^a   Kretzler, Matthias ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

DNA array; European Renal cDNA Bank; Kidney; Real time reverse transcriptase polymerase chain reaction

Indexed keywords

ALPHA ACTININ; CYCLOOXYGENASE 2; FIBRONECTIN; MESSENGER RNA; NEPHRIN; PLATELET DERIVED GROWTH FACTOR; PODOCIN; RNA; TRANSFORMING GROWTH FACTOR BETA; VASCULAR CELL ADHESION MOLECULE 1;

DIAGNOSTIC PROCEDURE; DIAGNOSTIC VALUE; DNA MICROARRAY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GLOMERULOPATHY; GLOMERULOSCLEROSIS; HISTOPATHOLOGY; HUMAN; IMMUNOGLOBULIN A NEPHROPATHY; KIDNEY ALLOGRAFT; KIDNEY BIOPSY; KIDNEY DISEASE; KIDNEY TRANSPLANTATION; KIDNEY TUBULE NECROSIS; MOLECULAR BIOLOGY; NEEDLE BIOPSY; NEPHROSCLEROSIS; PRIORITY JOURNAL; PROTEOMICS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; RNA ANALYSIS; URINALYSIS;

BIOLOGICAL MARKERS; BIOPSY; GENE EXPRESSION; HUMANS; IMMUNOHISTOCHEMISTRY; KIDNEY; KIDNEY DISEASES; MICROSCOPY, ELECTRON;

EID: 2342578678     PISSN: 10624821     EISSN: None     Source Type: Journal    
DOI: 10.1097/00041552-200405000-00008     Document Type: Review

References (68)

1. Kretzler M, Cohen CD, Doran P, et al. Repuncturing the renal biopay: strategies for molecular diagnosis in nephrology. J Am Soc Nephrol 2002; 13:1961-1972.
2. Striker LJ, Striker GE. Windows on renal biopsy interpretation: does mRNA analysis represent a new gold standard? J Am Soc Nephrol 2003; 14:1096-1098. This concise summary describes the latest developments in mRNA expression analysis of renal biopsies and in the interpretation of identified molecules as prognostic markers.
3. Eikmans M, Baelde HJ, de Heer E, et al. RNA expression profiling as prognostic tool in renal patients: toward nephrogenomics. Kidney Int 2002; 62:1125-1135.
4. Iyengar SK, Schelling JR, Sedor JR. Approaches to understanding susceptibility to nephropathy: from genetics to genomics. Kidney Int 2002; 61 (Suppl 1):61-67.
5. Yu SM, Gorovsky MA. In situ dot blots: quantitation of mRNA in intact cells. Nucleic Acids Res 1986; 14:7597-7615.
6. Pape ME, Melchior GW, Marotti KR. mRNA quantitation by a simple and sensitive RNAse protection assay. Genet Anal Tech Appl 1991; 8:206-213.
7. Wang AM, Doyle MV, Mark DF. Quantitation of mRNA by the polymerase chain reaction. Proc Natl Acad Sci U S A 1989; 86:9717-9721.
8. Peten EP, Garcia-Perez A, Terada Y, et al. Age-related changes in alpha 1-and alpha 2-chain type IV collagen mRNAs in adult mouse glomeruli: competitive PCR. Am J Physiol 1992; 263 (5 Pt 2):F951-F957.
9. Heid CA, Stevens J, Livak KJ, et al. Real time quantitative PCR. Genome Res 1996; 6:986-994.
10. Gibson UE, Heid CA, Williams PM. A novel method for real time quantitative RT-PCR. Genome Res 1996; 6:995-1001.
11. Cohen CD, Frach K, Schlondorff D, et al. Quantitative gene expression analysis in renal biopsies: a novel protocol for a high-throughput multicenter application. Kidney Int 2002; 61:133-140.
12. Kretzler M, Teixeira VP, Unschuld PG, et al. Integrin-linked kinase as a candidate downstream effector in proteinuria. FASEB J 2001; 15:1843-1845.
13. Eikmans M, Baelde HJ, De Heer E, et al. Processing renal biopsies for diagnostic mRNA quantification: improvement of RNA extraction and storage conditions. J Am Soc Nephrol 2000; 11:868-873.
14. Furness PN, Philpott CM, Chorbadjian MT, et al. Protocol biopsy of the stable renal transplant a multicenter study of methods and complication rates. Transplantation 2003; 76:969-973. This study shows a very low complication rate in 'protocol' transplant biopsies in a multicenter study.
15. Schmid H, Cohen CD, Henger A, et al. Validation of endogenous controls for gene expression analysis in microdissected human renal biopsies. Kidney Int 2003; 64:356-360. This systematic evaluation of endogenous controls (housekeeper) for gene expression analysis demonstrates the necessity for careful selection of house-keeping genes to avoid differences in gene expression reflecting only the regulation of the internal controls.
16. Specht K, Richter T, Muller U, et al. Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumor tissue. Am J Pathol 2001; 158:419-429.
17. Cohen CD, Grone HJ, Grone EF, et al. Laser microdissection and gene expression analysis on formaldehyde-fixed archival tissue. Kidney Int 2002; 61:125-132.
18. Schmid H, Henger A, Cohen CD, et al. Gene expression profiles of podocyte-associated molecules as diagnostic markers in acquired proteinuric diseases. J Am Soc Nephrol 2003; 14:2958-2966. This gene expression study of podocyte-associated molecules allowed a robust separation of focal segmental glomerulosclerosis from minimal change disease and nephrosclerosis in renal biopsies, and could confirm these observations in an independent population of formaldehyde-fixed archival biopsies.
19. Imai E, Takenaka M, Nagasawa Y, et al. Application of microarray assay to nephrology. Nephrol Dial Transplant 2000; 15 (Suppl 6):78-80.
20. 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; 349:125-138. This comprehensive gene expression study on acute renal allograft rejection identifies new subtypes of acute rejection, and correlates CD20 expression with steroid-resistant rejection and poor graft outcomes.
21. van de Vijver MJ, He YD, van't Veer LJ, et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002; 347:1999-2009.
22. Takahashi M, Rhodes DR, Furge KA, et al. Gene expression profiling of clear cell renal cell carcinoma: gene identification and prognostic classification. Proc Natl Acad Sci U S A 2001; 98:9754-9759.
23. van't Veer LJ, Dai H, van de Vijver MJ, et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002; 415:530-536.
24. Henger A, Kretzler M, Doran P, et al. Gene expression fingerprints in human tubulo-interstitial inflammation and fibrosis as prognostic markers of disease progression. Kidney Int 2004; 65:904-917. Gene expression based disease categorization of human nephropathies allowed prediction of disease course of tubulo-interstital damage in a small sample set.
25. Scherer A, Krause A, Walker JR, et al. Early prognosis of the development of renal chronic allograft rejection by gene expression profiling of human protocol biopsies. Transplantation 2003; 75:1323-1330. Expression patterns in human biopsies of renal chronic allograft rejection were obtained.
26. Chabardes-Garonne D, Mejean A, Aude JC, et al. A panoramic view of gene expression in the human kidney. Proc Natl Acad Sci U S A 2003; 100:13710-13715. A serial analysis of gene expression-based transcriptome analysis of different nephron segments generated a comprehensive expression catalogue from the intact human kidney. The dataset can be searched at the Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo).
27. Schelling JR, El-Meanawy MA, Barathan S, et al. Generation of kidney transcriptomes using serial analysis of gene expression. Exp Nephrol 2002; 10:82-92.
28. Eikmans M, Baelde JJ, de Heer E, et al. ECM homeoetasis in renal diseases: a genomic approach. J Pathol 2003; 200:526-536. In this comprehensive review, regulation of extracellular matrix molecule gene expression in animal models and in human disease is discussed and is followed by an outline for integrating these findings into management of patients.
29. Eikmans M, Baelde HJ, de Heer E, et al. Effect of age and biopsy site on extracellular matrix mRNA and protein levels in human kidney biopsies. Kidney Int 2001; 60:974-981.
30. Scherer A, Krause A, Walker JR, et al. Optimized protocol for linear RNA amplification and application to gene expression profiling of human renal biopsies. Biotechniques 2003; 34:546-556. This systematic evaluation of linear amplification methodologies has resulted in the development of protocols for array-based expression profiling of renal transplant biopsies.
31. Ernst T, Hergenhahn M, Kenzelmann M, et al. Decrease and gain of gene expression are equally discriminatory markers for prostate carcinoma: a gene expression analysis on total and microdissected prostate tissue. Am J Pathol 2002; 160:2169-2180.
32. Simon R, Radmacher MD, Dobbin K, et al. Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J Natl Cancer Inst 2003; 96:14-18. This paper is highly recommended; it describes the pitfalls in DNA array-based diagnostics, with special emphasis on cluster analysis and class prediction.
33. Nadon R, Shoemaker J. Statistical issues with microarrays: processing and analysis. Trends Genet 2002; 18:265-271.
34. Boer JM, Huber WK, Sultmann H, et al. Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31,500-element cDNA array. Genome Res 2001; 11:1861-1870.
35. Komatsuda A, Wakui H, Maki N, et al. Analysis of mutations in alpha-actinin 4 and podocin genes of patients with chronic renal failure due to sporadic focal segmental glomerulosclerosis. Ren Fail 2003; 26:87-93.
36. Narita I, Goto S, Saito N, et al. Genetic polymorphism of NPHS1 modifies the cinical manifestations of IgA nephropathy. Lab Invest 2003; 83:1193-1200.
37. Boute N, Gribouval O, Roselli S, et al. NPHS2, encoding the glomerular protein podocin, is mutated in autosomal recessive steroid-resistant nephrotic syndrome. Nat Genet 2000; 24:349-364.
38. Kaplan JM, Kim SH, North KN, et al. Mutations in ACTN4, encoding alpha-actinin-4, cause familial focal segmental glomerulosclerosis. Nat Genet 2000; 24:261-266.
39. Pollak MR. The genetic basis of FSGS and steroid-resistant nephrosis. Semin Nephrol 2003; 23:141-146.
40. Koop K, Eikmans M, Baelde HJ, et al. Expression of podocyte-associated molecules in acquired human kidney diseases. J Am Soc Nephrol 2003; 14:2063-2071.
41. Eikmans M, Baelde HJ, Hagen EC, et al. Renal mRNA levels as prognostic tools in kidney diseases. J Am Soc Nephrol 2003; 14:899-907. This study evaluates the prognostic value of extracellular matrix molecule mRNA levels in patients with renal diseases by correlation of variables at time of biopsy and the rate of glomerular filtration rate decline.
42. Baboolal K, Jones GA, Janezic A, et al. Molecular and structural consequences of early renal allograft injury. Kidney Int 2002; 61:686-696.
43. Adler SG, Kang SW, Feld S, et al. Glomerular mRNAs in human type 1 diabetes: biochemical evidence for microalbuminuria as a manifestation of diabetic nephropathy. Kidney Int 2001; 60:2330-2336.
44. Arrizabalaga P, Sole M, Abellana R, et al. Tubular and interstitial expression of ICAM-1 as a marker of renal injury in IgA nephropathy. Am J Nephrol 2003; 23:121-128.
45. Solari V, Piotrowska AP, Cascio S, et al. Cyclooxygenase-2 up-regulation in reflux nephropathy. J Urol 2003; 170 (4 Pt 2):1624-1627.
46. Eitner F, Ostendorf T, Kretzler M, et al. PDGF-C expression in the developing and normal adult human kidney and in glomerular diseases. J Am Soc Nephrol 2003; 14:1145-1153.
47. Fries JW, Roth T, Dienes HP, et al. A novel evaluation method for paraffinized human renal biopsies using quantitative analysis of microdissected glomeruli and VCAM-1 as marker of inflammatory mesangial cell activation. Nephrol Dial Transplant 2003; 18:710-716.
48. Waga I, Yamamoto J, Sasai H, et al. Altered mRNA expression in renal biopsy tissue from patients with IgA nephropathy. Kidney Int 2003; 64:1253-1264. Using modified comprehensive differential display expression profiling, disease-specific regulation of 13 mRNAs was identified from native renal biopsies, allowing cluster-based categorization of patients.
49. Mitterbeuer C, Schwarz C, Hauser P, et al. Impaired tubulointerstitial expression of endothelin-1 and nitric oxide isoforms in donor kidney biopsies with postischemic acute renal failure. Transplantation 2003; 76:715-720. A comparison of five mRNAs between living-donor biopsies and cadaveric-donor biopsies identified markers of reperfusion injury.
50. Sarwal MM, Jani A, Chang S, et al. Granulysin expression is a marker for acute rejection and steroid resistance in human renal transplantation. Hum Immunol 2001; 62:21-31.
51. Sabak O, Dorak MT, Kotb M, et al. Quantitative detection of T-cell activation markers by real-time PCR in renal transplant rejection and correlation with histopathologic evaluation. Transplantation 2002; 74:701-707.
52. Eikmans M, Sijpkens YW, Baelde KJ, et al. High transforming growth factor-beta and extracellular matrix mRNA response in renal allografts during early acute rejection is associated with absence of chronic rejection. Transplantation 2002; 73:573-579.
53. Akalin E, Hendrix RC, Polavarapu RG, et al. Gene expression analysis in human renal allograft biopsy samples using high-density oligoarray technology. Transplantation 2001; 72:948-953.
54. Donauer J, Rumberger B, Klein M, et al. Expression profling on chronically rejected transplant kidneys. Transplantation 2003; 76:539-547.
55. Schmid H, Henger A, Luckow B, et al. A mRNA expression marker set for the differential diagnosis of renal allograft rejection [abstract]. J Am Soc Nephrol 2003; 14:181A.
56. Randhawa PS, Vats A, Zygmunt D, et al. Quantitation of viral DNA in renal allograft tissue from patients with BK virus nephropathy. Transplantation 2002; 74:485-488.
57. Mangel M, Marwedel M, Radermacher J, et al. Incidence of polyomavirus-nephropathy in renal allografts: influence of modern immunosuppressive drugs. Nephrol Dial Transplant 2003; 18:1190-1196.
58. Schmid H, Nitschko H, Frach K, et al. Real-time RT-PCR analysis for polyomavirus DNA and RNA in renal allograft biopsies: a screening tool for BK transplant nephropathy [abstract]. J Am Soc Nephrol 2003; 14:424A.
59. Li B, Hartono C, Ding R, et al. Renal allograft surveillance by mRNA profiling of urinary cells. Transplant Proc 2001; 33:3280-3282.
60. Dadhania D, Muthukumar T, Ding R, et al. Molecular signatures of urinary cells distinguish acute rejection of renal allografts from urinary tract infection. Transplantation 2003; 75:1752-1754.
61. Li B, Hartono C, Ding R, et al. Noninvasive diagnosis of renal-allograft rejection by measurement of messenger RNA for perforin and granzyme B in urine. N Engl J Med 2001; 344:947-954.
62. Muthukumar T, Ding R, Dadhania D, et al. Serine proteinaae inhibitor-9, an endogenous blocker of granzyme B/perforin lytic pathway, is hyperexpressed during acute rejection of renal allografts. Transplantation 2003; 75:1565-1570. This follow-up study to [61] defines a set of mRNA markers of cytotoxic attack molecules in urine for non-invasive diagnosis of acute rejection.
63. Strehlau J, Pavlakis M, Lipman M, et al. Quantitative detection of immune activation transcripts as a diagnostic tool in kidney transplantation. Proc Natl Acad Sci U S A 1997; 94:695-700.
64. Ding R, Li B, Muthukumar T, et al. CD103 mRNA levels in urinary cells predict acute rejection of renal allografts. Transplantation 2003; 75:1307-1312.
65. Medeiros M, Sharma VK, Ding R, et al. Optimization of RNA yield, purity and mRNA copy number by treatment of urine cell pellets with RNAlater. J Immunol Methods 2003; 279:135-142. A detailed protocol for RNA isolation from urinary cells is described.
66. Hampel DJ, Sansome C, Sha M, et al. Toward proteomics in uroscopy: urinary protein profiles after radiocontrast medium administration. J Am Soc Nephrol 2001; 12:1026-1035.
67. Schaub S, Rush D, Wilkins J, et al. Proteomic-based detection of urine proteins associated with acute renal allograft rejection. J Am Soc Nephrol 2004; 15:219-227.
68. Weissinger EM, Wittke S, Kaiser T, et al. Proteomic pattern in urine of patients with primary renal disease [abstract]. Nephrol Dial Transplant 2003; 18 (Suppl 4):642.