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Series GSE93798 Query DataSets for GSE93798
Status Public on Jul 03, 2017
Title Transcriptomic and proteomic profiling reveal insights of mesangial cell function in patients with IgA Nephropathy
Organism Homo sapiens
Experiment type Expression profiling by array
Summary IgA nephropathy (IgAN) is the most common glomerulonephritis in the world. The disease is characterized by galactose deficient IgA (gd-IgA) in the circulation forming immune complexes. The complexes are deposited in the glomerular mesangium leading to inflammation and loss of renal function, but the pathophysiology of the disease is still not fully understood. Using an integrated global transcriptomic and proteomic profiling approach we investigated the role of the mesangium in the onset and progression of IgAN. Global gene expression was investigated by microarray analysis of the glomerular compartment of renal biopsies from patients with IgAN. The influence of galactose deficient IgA (gd-IgA) on mesangial cells was investigated by proteomic profiling. By utilizing the previous published literature curated glomerular cell type-specific genes, we found that mesangial cells and their positive standard genes play a more dominant role in IgAN comparing to the podocyte standard genes. Additionally, the patient clinical parameters (serum creatinine values and estimated glomerular filtration rate - eGFR) significantly correlate with z-scores derived from expression profile of mesangial cell positive standard genes. 22 common pathways were identified both from in vivo microarray data and in vitro mesangial cell mass spectrometry data and the main part was inflammatory pathways. The correlation between clinical data and mesangial standard genes allows for a better understanding of the onset of IgAN. The genes, proteins and their corresponding pathways identified in this paper give us novel insights into the pathophysiological mechanisms leading to progression of IgAN.
 
Overall design RNA from glomerular compartment was extracted and processed for hybridization on Affymetrix microarrays.
 
Contributor(s) Liu P, Lassén E, Nair V, Berthier CC, Katayama M, Sihlbom C, Kretzler M, Betsholtz C, Haraldsson B, Ju W, Ebefors K, Nyström J
Citation(s) 28646076
Submission date Jan 18, 2017
Last update date Oct 13, 2017
Contact name Celine C Berthier
Organization name University of Michigan
Street address 1150 W. Medical Center Dr, MSRB2
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platforms (1)
GPL22945 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray HGU133Plus2_Hs_ENTREZG_v19]
Samples (42)
GSM2462533 Glomerular compartment from control human kidney H11_F_27_1_Con_L
GSM2462534 Glomerular compartment from control human kidney H12_M_67_1_Con_L
GSM2462535 Glomerular compartment from control human kidney H13_M_53_1_Con_L
Relations
BioProject PRJNA362368

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE93798_RAW.tar 200.3 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
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