American Journal of Transplantation 4(11):1776-85 November 2004
De Novo Kidney Transplantation Without use of Calcineurin Inhibitors Preserves Renal Structure and Function at Two Years
Stuart M. Flechner (1), Sunil M. Kurian (2), Kim Solez (3), Daniel J. Cook (1), James T. Burke (4), Hank Rollin (1), Jennifer A. Hammond (5), Thomas Whisenant (5), Caroline M. Lanigan (5), Steven R. Head (5), and Daniel R. Salomon (2)
(1) Section of Renal Transplantation, Transplant Center, Allogen Laboratories, The Cleveland Clinic Foundation, (2) Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, (3) Department of Pathology, University of Alberta, Edmonton, Alberta, Canada, (4) Immunology/Clinical Sciences, Wyeth Laboratories, Paris, France, (5) DNA Array Core Facility, The Scripps Research Institute, La Jolla, California
Background: Despite significant improvements in short-term kidney transplant survival, comparable increases in 5 and 10-year outcomes have not been achieved. Chronic allograft nephropathy (CAN) is a major cause of late graft loss. Toxic nephropathy and inadequate long-term immunosuppression are possible factors. We performed a randomized prospective trial comparing calcineurin inhibitor (CNI)-free to CNI-based immunosuppression to determine the impact on renal function, structure, and gene expression.
Methods: Sixty-one kidney recipients received mycophenolate mofetil (MMF), and prednisone (P). Randomized patients received concentration-controlled sirolimus or cyclosporine. Two years post-transplant 55 patients underwent renal function studies, 48 (87%) underwent transplant biopsies; all classified by Banff scoring and 41 by DNA microarrays.
Findings: Comparing sirolimus/MMF/P to cyclosporine/MMF/P at two years, there was a significantly lower serum creatinine (1.35 vs. 1.81 mg/dl; p=0.008), significantly higher Cockroft-Gault glomerular filtration rate (GFR) ( 80.4 vs. 63.4 cc/min; p=0.008), iothalamate GFR (60.6 vs. 49.2 cc/min; p= 0.018), and Banff 0 (normal) biopsies (66.6 vs. 20.8%; p= 0.013). Regression analysis of calculated GFR's from 1 to 36 months yielded a positive slope for sirolimus of 3.36 ml/min/year, and a negative slope for cyclosporine of -1.58 ml/min/year (p=0.008). Gene expression profiles of kidney biopsies with higher Banff CAN scores confirmed significant up regulation of genes responsible for immune/inflammation and fibrosis/tissue remodeling.
Interpretation: At two years the sirolimus-treated patients have better renal transplant function, a diminished prevalence of CAN, and down regulated expression of genes responsible for the progression of CAN. All may provide for an alternative natural history with improved graft survival.
MIAME Checklist:
Experiment Design
- Type of Experiment: Sirolimus-treated vs. Cyclosporine-treated
- Experimental Factors: Sirolimus-treated vs. Cyclosporine-treated
- Number of Hybridizations: 41
- Type of Reference: N/A
- Hybridization Design: See table below
- Quality Control: see RPT files
- URL: http://www.scripps.edu/researchservices/dna_array/
Samples Used, Extract Preparation and Labeling
- Origin of Biological Sample: All tissues are human
- Manipulation of Biological Sample: Biopsy protocol included in paper
- Hybridization Preparation: TSRI DNA Array Core Facility RNA Extraction Protocol
- Labeling: Standard Affymetrix Protocol (Affymetrix, Inc., Santa Clara, CA)
- External Controls (Spike-ins): Standard Affymetrix Spike-in Controls (Affymetrix, Inc., Santa Clara, CA)
Hybridization Procedures and Parameters
- Hybridization, Blocking and Washing: Standard Affymetrix Protocol (Affymetrix, Inc., Santa Clara, CA)
Measurement Data and Specifications
- Image Quantitation: Affymetrix scanner to generate CEL file, RMA (PM-only model) to generate signal intensities
Array Design
- General Array Design: Affymetrix HG-U133A GeneChip (Affymetrix, Inc., Santa Clara, CA)
Sample Information:
*Patient ID links to information in the NCBI Gene Expression Omnibus
|
Treatment Group |
Patient ID |
CEL File |
Immunosuppression |
GeneChip QC Percent Present |
GeneChip QC GAPDH 3'/5' ratio |
Sirolimus group
|
GSM30418.CEL |
SRL/MMF/P |
37.0 |
2.57 |
|
GSM30419.CEL |
SRL/MMF/P |
27.9 |
2.11 |
||
GSM30420.CEL |
SRL/MMF/P |
28.9 |
3.13 |
||
GSM30421.CEL |
SRL/MMF/P |
33.6 |
1.79 |
||
GSM30422.CEL |
SRL/MMF/P |
38.2 |
2.63 |
||
GSM30423.CEL |
SRL/MMF/P |
38.3 |
1.82 |
||
GSM30424.CEL |
SRL/MMF/P |
34.9 |
1.87 |
||
GSM30425.CEL |
SRL/MMF/P |
23.5 |
3.13 |
||
GSM30426.CEL |
SRL/MMF/P |
21.2 |
4.90 |
||
GSM30427.CEL |
SRL/MMF/P |
32.9 |
2.28 |
||
GSM30428.CEL |
SRL/MMF/P |
36.5 |
1.18 |
||
GSM30429.CEL |
SRL/MMF/P |
39.8 |
1.19 |
||
GSM30430.CEL |
SRL/MMF/P |
38.2 |
1.28 |
||
GSM30431.CEL |
SRL/MMF/P |
38.4 |
1.27 |
||
GSM30432.CEL |
SRL/MMF/P |
33.4 |
0.92 |
||
GSM30433.CEL |
SRL/MMF/P |
38.1 |
1.26 |
||
GSM30434.CEL |
SRL/MMF/P |
42.6 |
1.50 |
||
GSM30435.CEL |
SRL/MMF/P |
42.7 |
1.04 |
||
GSM30436.CEL |
SRL/MMF/P |
46.8 |
1.06 |
||
|
Cyclosporine group
|
GSM30437.CEL |
CsA/MMF/P |
44.3 |
1.27 |
|
GSM30438.CEL |
CsA/MMF/P |
49.9 |
1.00 |
||
GSM30439.CEL |
CsA/MMF/P |
46.9 |
0.90 |
||
GSM30440.CEL |
CsA/MMF/P |
45.3 |
1.00 |
||
GSM30441.CEL |
CsA/MMF/P |
51.5 |
1.05 |
||
GSM30442.CEL |
CsA/MMF/P |
43.6 |
1.39 |
||
GSM30443.CEL |
CsA/MMF/P |
44.3 |
1.10 |
||
GSM30444.CEL |
CsA/MMF/P |
48.1 |
1.23 |
||
GSM30445.CEL |
CsA/MMF/P |
41.0 |
1.05 |
||
GSM30446.CEL |
CsA/MMF/P |
48.1 |
1.06 |
||
GSM30447.CEL |
CsA/MMF/P |
40.8 |
1.13 |
||
GSM30448.CEL |
CsA/MMF/P |
41.8 |
1.27 |
||
GSM30449.CEL |
CsA/MMF/P |
46.2 |
2.14 |
||
GSM30450.CEL |
CsA/MMF/P |
30.6 |
3.25 |
||
GSM30451.CEL |
CsA/MMF/P |
33.8 |
3.59 |
||
GSM30452.CEL |
CsA/MMF/P |
42.0 |
1.04 |
||
GSM30453.CEL |
CsA/MMF/P |
38.8 |
1.10 |
||
GSM30454.CEL |
CsA/MMF/P |
40.7 |
1.28 |
||
GSM30455.CEL |
CsA/MMF/P |
44.2 |
1.33 |
||
GSM30456.CEL |
CsA/MMF/P |
45.5 |
0.98 |
||
GSM30457.CEL |
CsA/MMF/P |
45.6 |
1.39 |
||
GSM30458.CEL
|
CsA/MMF/P |
45.9 |
0.98 |
||
CsA - Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; SRL - Sirolumus |
|||||
Supplemental Tables and Figures:
Class Comparison Results:
- Gene list of the class comparison between the biopsies of patients treated with cyclosporine (CsA/MMF/P) and the sirolimus (SRL/MMF/P) at alpha level <0.001
- Gene list of the class comparison between patients with Banff CAN 0 scores (normal histology) and Banff CAN 2 + 3 at alpha level <0.001
- Gene list of the class comparison between patients with Banff CAN 0 scores (normal histology) and Banff CAN 2 + 3 at alpha level <0.01
