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Table 11 Transcriptomics studies in kidney diseases

From: Genomic approaches in the search for molecular biomarkers in chronic kidney disease

PMID Author Year Sample Patients Ethnics Methodology Main findings
29642064 Zhou 2018 Gene expression microarray datasets retrieved from GEO repository 18 DKD/40 HC, 
26 HTN/44 HC, 
68 IgAN/44 HC, 
36 MGN/44 HC, 
35 FSGS/62 HC
Integrative bioinformatics analysis
Affymetrix U133 Plus 2.0 Affymetrix U133 A
Glomeruli: 176 genes were differentially expressed among all diseases, 104 upregulated (e.g., FCN1, CX3CR1) and 72 downregulated (e.g., APOM, SLC13A1). Gene Ontology analysis showed mainly cellular components associated with diseased glomeruli, as integral components of the plasma membrane, extracellular space, and within the MHC class II protein complex. Pathway enrichment analysis showed dysregulation of several metabolic, immune response, and signalling pathways (e.g., lipids/lipoproteins and amino acids metabolism, SLC-mediated transmembrane transport, and IFN-γ pathway). Protein interaction network identified a cluster mainly associated with platelet dysfunction, abnormal interleukin signalling, and extracellular matrix organization
Tubules: 50 genes were differentially expressed among all diseases, nine upregulated (e.g., COL3A1, MARCKS) and 41 downregulated (e.g., GDF15, RGS3). Gene Ontology analysis showed association mainly with molecule binding and transcription factor activity. Pathway enrichment analysis showed dysregulation of several signalling pathways (e.g., cholecystokinin receptor (CCKR), apoptosis, PI3 K-Akt, MAPK, and TGF-β signalling pathways). Protein interaction network identified a cluster mainly associated with SMAD2/SMAD3/SMAD4 heterotrimer-regulated transcription, TGF-β receptor complex signalling, and interleukin signalling
Nine genes were significantly differentially expressed both in diseased glomeruli and tubules (IFI16, COL3A1, ZFP36, NR4A3, DUSP1, FOSB, HBB, FN1, PTPRC)
28158872 Zhao 2017 CD4 + T Cells 15 SLE
15 HC
United States qRT-PCR TNFAIP3 expression has been found downregulated in CD4 + T cells from SLE
26986150 Zhai 2016 B lymphocytes 166 IgAN
77 HC
China qRT-PCR Increased TNFSF13 expression is accompanied by upregulation of its receptors in B-lymphocytes from IgAN patients, inducing Gd-IgA1 overproduction
26631632 Ju 2015 Biopsy 55 CKD United States Microarray
(Affymetrix GeneChip and TaqMan Low Density Arrays)
Urine levels of EGF correlated with tissue EGF transcript expression and predicted eGFR
26490557 Leal 2015 Peripheral
Blood mononuclear
20 CKD
20 HD
11 HC
Brazil qRT-PCR NFE2L2 mRNA was positively correlated with NF-κB mRNA expression in CKD patients (r = 0.52, p = 0.02) and healthy individuals
26116588 Perlman 2015 Blood 20 T2DM + DKD, 
20 HC
United States qRT-PCR transcripts levels differentially expressed in T2DM with nephropathy
elevated expression occurred in early stage 1-2, before a significant decline in eGFR
Interest in MCP-1, FGF-2, VEGF and EGF
23921255 Hara 2013 Leukocytes 40 CKD
20 HC
Japan qRT-PCR S100A12 expression was significantly higher in CKD patients compared to healthy controls
24347824 Yadav 2013 CD4+CD28null peripheral mononuclear cells 25 CKD
8 HC
India qRT-PCR Basal expression of IFN-γ, perforin, and granzyme B in CD4+CD28null cells was increased in CKD
23061738 Chen 2012 Urine 35 CKD
12 HC
China qRT-PCR CTGF and NOV genes were overexpressed in CKD
21906921 Spoto 2012 Plasma 75 CKD
33 HC
Italy qRT-PCR Upregulation of TNF-α was inversely correlated with eGFR
Increase of plasma IL-6 in early stages of CKD, without showing any further increase at more severe stages
23024773 Rudnicki 2012 Biopsy 3 DKD
19 IgAN
10 MCD
2 LN
16 Other
Switzerland Microarray analysis Correlation of versican isoforms V0 and V1 with creatinine levels
22969957 Tachaudomdach 2012 Biopsy 39 LN Thailand qRT-PCR TGF-β1 and collagen I were correlated with CTGF expression
Baseline eGFR and Renal CTGF mRNA expression were inversely correlated
20650904 Brabcova 2011 Biopsy 51 IgAN Czech Republic qRT-PCR Higher TGF-β1 expression associated with IgAN progression
21640098 Chon 2011 Leukocytes 20 CKD
10 HC
Netherlands qRT-PCR Inverse correlation of leukocyte angiotensin II AT1 receptor mRNA expression with renal function
Leukocyte angiotensin II AT1 receptor expression is higher in CKD
21040163 Lepenies 2010 Biopsy 64 CKD UK qRT-PCR Inverse correlation of mRNA expression of peroxisome proliferator-activated receptor gamma (PPARγ) with renal function
19698090 Granata 2009 Peripheral blood mononuclear cells 9 CKD II-III,
17 HD, 
8 HC
Helsinki Microarray analysis COX6C, COX7C, ATP5ME, and UQCRH were all significantly higher in CKD IV-V compared to CKD II-III and HC
18758661 Ibrahim 2008 Biopsy 20 T2DM, 
4 normal tissue from renal tumor patients
Egyptian qRT-PCR Increased PKC alpha gene expression in diabetic patients with CKD
PKC alpha gene concentrations and proteinuria had significant correlation in diabetic patients. 
18784644 Zehnder 2008 Urine 174 CKD 81.6% white, 10.9% Asian, 6.9% Afro-Caribbean qRT-PCR MCP-1 expression was increased in those with acute renal inflammation
16564935 Szeto 2006 Urine 131 CKD China qRT-PCR Urinary HGF expression remained an independent predictor of the primary end point, it was increased in those at risk of end point.
15561743 Szeto 2005 Urine 29 CKD
10 HC
China qRT-PCR Overexpression of TGF-β and MCP-1 was associated with glomerulosclerosis
Overexpression of collagen IV was associated with CKD
  1. Akt: Protein kinase B, also known as Akt; APOM: apolipoprotein M; AT1: angiotensin II Type 1 receptor; ATP5ME: ATP synthase membrane subunit e; CCKR: cholecystokinin receptor; CD4: cluster of differentiation 4; CD28: cluster of differentiation 28; CKD: chronic kidney disease; COL3A1: collagen type III alpha 1 chain; COX6C: cytochrome c oxidase subunit 6C; COX7C: cytochrome c oxidase subunit 7C; CTGF: connective tissue growth factor; CX3CR1: C-X3-C motif chemokine receptor 1; DKD: diabetic kidney disease; DUSP1: dual specificity phosphatase 1; EGF: epidermal growth factor; eGFR: estimated glomerular filtration rate; FCN1: ficolin 1; FGF: fibroblast growth factor; FN1: fibronectin 1; FOSB: FosB proto-oncogene; AP-1 transcription factor subunit; FSGS: focal segmental glomerulosclerosis; Gd-IgA1: galactose-deficient hinge region O-glycans; GDF15: growth differentiation factor 15; GEO: gene expression omnibus;, HBB: hemoglobin subunit beta; HC: healthy controls; HD: hemodialysis; HGF hepatocyte growth factor; HTN: hypertension; IFI16: interferon gamma inducible protein 16; IFN-γ: interferon gamma; IgAN: IgA nephropathy; IL-6: interleukin 6; LN: lupus nephritis; MAPK: Mitogen-activated protein kinases; MARCKS: myristoylated alanine rich protein kinase C substrate; MCD: minimal change disease; MHC: major histocompatibility complex; MCP-1: monocyte Chemoattractant Protein-1; MGN: membranous nephropathy; MPGN: membranoproliferative glomerulonephritis; mRNA: messenger ribonucleic acid; NF-κB: NF-kappa B complex subunits; NFE2L2: nuclear factor, erythroid 2 like 2; NOV: nephroblastoma overexpressed; NR4A3: nuclear receptor subfamily 4 group A member 3; PKC: protein kinase C; PPARγ: peroxisome proliferator-activated receptor gamma; PTPRC: protein tyrosine phosphatase, receptor type C; PI3K: phosphatidylinositol-3-kinases; qRT-PCR: quantitative reverse transcription polymerase chain reaction; RGS3: regulator of G protein signalling 3; RPGN: rapidly progressive glomerulonephritis; S100A12: S100 calcium binding protein A12; SLC: human solute carrier gene superfamily; SLC13A1: solute carrier family 13 member 1; SLE: systematic lupus erythematosus; SMAD2: SMAD family member 2; SMAD3: SMAD family member 3; SMAD4: SMAD family member 4; T1DM: type 1 diabetes mellitus; T2DM: type 2 diabetes mellitus; TNF: tumour necrosis factor superfamily; TGF-β1: transforming growth factor beta 1; TNF-α: tumour necrosis factor alpha; TNFAIP3: TNF alpha induced protein 3; TNFSF13: TNF superfamily member 13; TGF-β: transforming growth factor beta; UK: United Kingdom; UQCRH: ubiquinol-cytochrome c reductase hinge protein; VEGF: vascular endothelial growth factor; ZFP36: ZFP36 ring finger protein