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| Status |
Public on Feb 24, 2009 |
| Title |
Analyses of heterogeneous renal allograft biopsies reveal conserved rejection signatures and molecular pathways I |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Specific early diagnosis of renal allograft rejection is gaining importance in the current trend to minimize and individualize immunosuppression. Gene expression analyses could contribute significantly by defining “molecular Banff” signatures. Several previous studies have applied transcriptomics to distinguish different classes of kidney biopsies. However, the heterogeneity of microarray platforms, clinical samples and data analysis methods complicates the identification of robust signatures for the different types and grades of rejection. To address these issues, a comparative meta-analysis was performed across five different microarray datasets of heterogeneous sample collections from two published clinical datasets and three own datasets including biopsies for clinical indications, protocol biopsies, as well as comparative samples from non-human primates (NHP). This work identified conserved gene expression signatures that can differentiate groups with different histopathological findings in both human and NHP, regardless of the technical platform used. The marker panels comprise genes that clearly support the biological changes known to be involved in allograft rejection. A characteristic dynamic expression change of genes associated with immune and kidney functions was observed across samples with different grades of CAN. In addition, differences between human and NHP rejection were essentially limited to genes reflecting interstitial fibrosis progression. This data set comprises all renal allograft biopsies for clinical indications from patients at Hôpital Tenon, Paris (February 2003 until September 2004) and few respective patients from Hôpital Bicêtre, Paris, Hôpital Pellegrin, Bordeaux, and Hôpital Dupuytren, Limoges, plus control normal kidney samples from Hôpital Tenon, Paris, France (first batch).
We used microarrays to identify different gene expression signatures of renal allograft biopsies that can classify them according to different types of allograft rejection or CAN.
Keywords: disease state analysis
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| Overall design |
47 renal allograft core biopsies for clinical indications with different histopathological diagnoses according to BANFF'97 criteria, and 13 normal kidney samples as controls.
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| Contributor(s) |
Raulf F, Saint-Mezard P, Rondeau E, Marti H |
| Citation(s) |
19017305 |
| Submission date |
Oct 31, 2007 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Friedrich Raulf |
| E-mail(s) |
friedrich.raulf@novartis.com
|
| Phone |
+41 61 324 6880
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| Fax |
+41 61 324 3576
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| Organization name |
Novartis Pharma AG
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| Department |
Novartis Institutes for BioMedical Research / ATDA
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| Lab |
Raulf
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| Street address |
WSJ-386.6.09
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| City |
Basel |
| ZIP/Postal code |
4002 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
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| Samples (60)
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| GSM240785 |
Patient TX40, renal graft bx 1.48, diagnosis AR IA |
| GSM240786 |
Patient TX22, renal graft bx 1.27, diagnosis AR IA |
| GSM240787 |
Patient TX01, renal graft bx 1.15, diagnosis AR IA |
| GSM240788 |
Patient TX25, renal graft bx 1.31, diagnosis AR IB |
| GSM240789 |
Patient TX03, renal graft bx 1.03, diagnosis AR IB |
| GSM240790 |
Patient TX20, renal graft bx 1.25, diagnosis AR IB |
| GSM240791 |
Patient TX11, renal graft bx 1.12, diagnosis AR IIA |
| GSM240792 |
Patient TX50, renal graft bx 1.58, diagnosis AR IIB |
| GSM240793 |
Patient TX53, renal graft bx 1.62, diagnosis AR+CAN |
| GSM240794 |
Patient TX58, renal graft bx 1.67, diagnosis AR+CAN |
| GSM240795 |
Patient TX11, renal graft bx 1.61, diagnosis AR+CAN |
| GSM240796 |
Patient TX10, renal graft bx 1.11, diagnosis AR+CAN |
| GSM240797 |
Patient TX10, renal graft bx 1.17, diagnosis AR+CAN |
| GSM240798 |
Patient TX56, renal graft bx 1.65, diagnosis AR+CAN |
| GSM240799 |
Patient TX54, renal graft bx 1.63, diagnosis AR+CAN |
| GSM240800 |
Patient TX06, renal graft bx 1.07, diagnosis borderline changes |
| GSM240801 |
Patient TX06, renal graft bx 1.06, diagnosis borderline changes |
| GSM240802 |
Patient TX01, renal graft bx 1.01, diagnosis borderline changes |
| GSM240803 |
Patient TX42, renal graft bx 1.50, diagnosis CAN I |
| GSM240804 |
Patient TX02, renal graft bx 1.02, diagnosis CAN I |
| GSM240805 |
Patient TX52, renal graft bx 1.60, diagnosis CAN I |
| GSM240806 |
Patient TX51, renal graft bx 1.59, diagnosis CAN I |
| GSM240807 |
Patient TX23, renal graft bx 1.29, diagnosis CAN II |
| GSM240808 |
Patient TX31, renal graft bx 1.38, diagnosis CAN II |
| GSM240809 |
Patient TX33, renal graft bx 1.40, diagnosis CAN II |
| GSM240810 |
Patient TX46, renal graft bx 1.54, diagnosis CAN II |
| GSM240811 |
Patient TX44, renal graft bx 1.52, diagnosis CAN II |
| GSM240812 |
Patient TX48, renal graft bx 1.56, diagnosis CAN II |
| GSM240813 |
Patient TX13, renal graft bx 1.16, diagnosis CAN II |
| GSM240814 |
Patient TX45, renal graft bx 1.53, diagnosis CAN II |
| GSM240815 |
Patient TX55, renal graft bx 1.64, diagnosis CAN II |
| GSM240816 |
Patient TX49, renal graft bx 1.57, diagnosis CAN II |
| GSM240817 |
Patient TX38, renal graft bx 1.46, diagnosis CAN III |
| GSM240818 |
Patient TX24, renal graft bx 1.30, diagnosis CAN III |
| GSM240819 |
Patient TX34, renal graft bx 1.42, diagnosis CAN III |
| GSM240820 |
Patient TX29, renal graft bx 1.36, diagnosis CAN III |
| GSM240821 |
Patient TX07, renal graft bx 1.08, diagnosis CAN III |
| GSM240822 |
Patient TX26, renal graft bx 1.32, diagnosis CAN III |
| GSM240823 |
Patient TX04, renal graft bx 1.04, diagnosis CAN III |
| GSM240824 |
Patient TX32, renal graft bx 1.39, diagnosis CAN III |
| GSM240825 |
Patient TX41, renal graft bx 1.49, diagnosis non-rejecting |
| GSM240826 |
Patient TX21, renal graft bx 1.26, diagnosis non-rejecting |
| GSM240827 |
Patient TX12, renal graft bx 1.13, diagnosis non-rejecting |
| GSM240828 |
Patient TX08, renal graft bx 1.09, diagnosis non-rejecting |
| GSM240829 |
Patient TX25, renal graft bx 1.33, diagnosis non-rejecting |
| GSM240830 |
Patient TX37, renal graft bx 1.45, diagnosis non-rejecting |
| GSM240831 |
Patient TX27, renal graft bx 1.34, diagnosis non-rejecting |
| GSM240832 |
Patient C01, control kidney from nephrectomy |
| GSM240833 |
Patient C03, control kidney from nephrectomy |
| GSM240834 |
Patient C04, control kidney from nephrectomy |
| GSM240835 |
Patient C05, control kidney from nephrectomy |
| GSM240836 |
Patient C06, control kidney from nephrectomy, with clamping |
| GSM240837 |
Patient C06, control kidney from nephrectomy, without clamping |
| GSM240838 |
Patient C10, control kidney from nephrectomy |
| GSM240839 |
Patient C11, control kidney from nephrectomy, cortex |
| GSM240840 |
Patient C11, control kidney from nephrectomy, cortex + medulla |
| GSM240841 |
Patient C13, control kidney from nephrectomy |
| GSM240842 |
Patient C14, control kidney from nephrectomy |
| GSM240843 |
Patient C15, control kidney from nephrectomy |
| GSM240844 |
Patient C16, control kidney from nephrectomy |
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| This SubSeries is part of SuperSeries: |
| GSE9493 |
Transcriptomic analyses of renal allograft biopsies reveal conserved rejection signatures and molecular pathways |
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| Relations |
| BioProject |
PRJNA105167 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE9489_RAW.tar |
518.4 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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