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 cells | 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 7 HTN 19 IgAN 10 MCD 7 FSGS 8 MGN 2 LN 2 MPGN 1 RPGN 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 |