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| Status |
Public on Jul 03, 2018 |
| Title |
RNA Expression data for early diabetic nephropathy (EDN) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
There is a temporal window from the time diabetes is diagnosed to the appearance of overt kidney disease during which time the disease progresses quietly without detection. Currently, there is no way to detect early diabetic nephropathy (EDN).
Here we performed an unbiased assessment of gene-expression analysis of postmortem human kidneys using microarrays to identify candidate genes that may contribute to EDN.
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| Overall design |
Postmortem biological samples (blood and kidney tissue) from non-diabetic and individuals with EDN were obtained from the National Disease Research Interchange (Philadelphia, PA). Except for obesity, there was no significant difference in any of the parameters between study groups. There were more obese individuals in the EDN group than among non-diabetic controls. All diabetic donors had type 2 diabetes. Diabetes status was defined as hemoglobin A1c (HgbA1c) >6.5%. Proteinuria was identified by urine dipstick performed during the terminal hospital admission. These diagnoses were confirmed by careful review of pre– and postmortem clinical health records. There were stringent inclusion and exclusion criteria. Inclusion criteria included: 1) donors be between 17 to 80 years of age, 2) diabetic status confirmed as noted above, and 3) postmortem time within 24h from cross-clamping in the operating room (OR); the only exception with respect to HgbA1c testing was if a donor had been prescribed and/or using glycemic agent(s) including but not limited to metformin and insulin, in which case repeat A1c testing was not mandatory. Exclusion criteria included active infection, malignancy, severe glomerulosclerosis as determined in frozen OR biopsy material, history of renal replacement therapy (hemodialysis or peritoneal dialysis at any time), and any known genetic renal condition such as polycystic kidney disease, etc. Pathologic staging of diabetic tissues was performed using the 2010 Renal Pathology Society classification system for diabetic kidney disease.9 From each postmortem nephrectomy sample more than 100 glomeruli were reviewed in tissue sections. Pathologic stages I-III diabetic kidney disease were considered as EDN and used in the study. Stage III kidneys were included since the renal function in these donors are preserved. mRNA was extracted exclusively from kidney cortical tissue. Total RNA from flash-frozen kidney tissue was subjected to Trizol® (Invitrogen, USA) extraction and purified using RNeasy mini kit. mRNA preparations were processed by the BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, per the standard Affymetrix® protocol using the Affymetrix® Human Transcriptome 2.0 GeneChip (Affymetrix®, Inc., USA).
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| Contributor(s) |
Libermann TA, Karumanchi SA, Thadhani RI, Sircar M |
| Citation(s) |
30253844 |
| Submission date |
Feb 26, 2018 |
| Last update date |
Apr 09, 2019 |
| Contact name |
Towia A Libermann |
| E-mail(s) |
tliberma@bidmc.harvard.edu
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| Organization name |
Beth Israel Deaconess Medical Center
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| Department |
Medicine
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| Street address |
99 Brookline Ave.
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (1) |
| GPL17586 |
[HTA-2_0] Affymetrix Human Transcriptome Array 2.0 [transcript (gene) version] |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA436020 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE111154_RAW.tar |
204.8 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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