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Table 5 Methylation studies in chronic kidney disease

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

PMID Author Year Sample Patients (n) Controls (n) Ethnicity Methodology Main findings
28609449 Bailie 2017 Blood CKD (n = 255) No evidence of CKD (n = 152) Caucasian 450 K array
485,577 CpG sites: UMOD1, UMOL1 and UMODL1-AS1 genes
Differential methylation of three CpG sites in UMOD. The most significant was cg03140788 (p = 3.7∙10−10)
Eight associated CpG sites in UMODL1 and UMODL1-AS1 genes, with genome wide significance. The most significant for non-diabetic ESRD was cg16624482 (p = 2.9∙10−32)
28755807 Zinellu 2017 Blood CKD (n = 30) Healthy (n = 30) Age- and sex-matched controls Italy Percentage of methylated to total cytosine Lower DNA methylation in CKD
(4.06 ± 0.20% vs. 4.27 ± 0.17%; p = 0.0001
Cholesterol lowering treatment significantly increased DNA methylcytosine concentrations in all patients (4.06 ± 0.04% at baseline; 4.12 ± 0.03% at 4 months; 4.17 ± 0.03% at 8 months; and 4.20 ± 0.02% at 12 months; p = 0.0001 for trend)
The combined 10/40 mg/day ezetimibe/simvastatin treatment showed a trend for a greater effect on DNA methylation (+5.2% after one year treatment)
27018948 Zawada 2016 Differentiated
intermediate monocytes from haematopoietic stem cells, isolated from healthy donors
ESRD (n = 5) RRT Healthy (n = 5) Age- and sex-matched controls Germany
Primary culture (Treatment with serum from CKD patients (uraemic) or control patients)
Methyl-Seq 813,267 Genomic loci Patients had higher counts of intermediate (p < 0.05) and nonclassical (p < 0.01) monocytes
Upon stimulation with uremic serum, more intermediate monocytes were generated as compared to control conditions (p < 0.001)
Monocytes generated under uremic conditions were closer related to circulating intermediate monocytes than monocytes generated under control conditions
Five of the top 50 DMRs included in the comparison between “CKD” and “control” monocytes had been found involved with CKD by other authors
24363223 Ghattas 2014 Blood ESRD (n = 96) Healthy (n = 96) Egyptian Methylation-specific PCR
MTHFR gene
The frequency of MTHFR methylation was significantly higher in ESRD patients (p = 0.003)
eGFR was significantly lower when MTHFR promoter was methylated (p = 0.026)
24253112 Smyth 2014 Blood CKD (n = 255) No evidence of CKD (n = 152) Caucasian 450 K array
485,577 CpG sites
More than one significantly affected CpG in 23 unique genes after adjustment (p < 10−8)
RNA-seq data also supported a functional role for DM in ELMO1 and PRKAG2, as they saw altered expression in the expected manner, even if change in PRKAG2 expression was not statistically significant
CUX1, ELMO1, FKBP5, INHBA-AS1, PTPRN2, and PRKAG2 genes proposed as biological candidates for kidney disease
24516231 Wing 2014 Blood “Rapid Progression” CKD (n = 20) eGFR 20–70 ml/min/1.73 m2
“Highest Rate of Decline”
CRIC cohort
“Stable Kidney Function” CKD (n = 20)
eGFR 20–70 ml/min/1.73 m2
“Slowest Rate of Decline”
Caucasian (50%)
African American/Black (40%)
Oher (10%)
450 K array
485,577 CpG sites
No gene reached significance after FDR
Of the 15 genes most strongly associated with rapid progression, 14 of them were more heavily affected in the slow progression group
UMODL1 among several others, proposed as “top candidates”
24224012 Chen 2013 Renal biopsy/PBMC CKD (n = 47) Renal cell carcinoma (Renal biopsy, n = 47)
Healthy (PBMC, n = 46)
China Pyrosequencing: 6 CpGs assessed in Klotho (KL) Gene KL gene was hypermethylated in 68% tissue and 70% PMBC samples from CKD patients when compared to controls, significance reached across all CpG sites (p < 0.001)
Methylation of PBMC KL positively correlated with renal KL methylation (p < 0.001)
eGFR inverse correlation with renal and PBMC levels of KL promoter methylation (both p < 0.001)
18287179 Nanayakkara 2008 Genomic DNA extracted from Leukocytes CKD 2–4 (n = 78)
(eGFR 15-70 ml/min/1.73 m2)
ATIC study
109 healthy volunteers The Netherlands LC–MS No association was found between DNA methylation and renal function
18067454 Geisel 2007 PBMC ESRD (n = 22) all receiving RRT (22 HT, 20 DM and 14 CVD) Healthy (n = 26).
Age- and sex-matched
Germany Pyrosequencing: LINE-1
(nCpG = 7)
p66Shc Promoter (nCpG = 3)
Methylation of p66Shc promoter significantly reduced in ESRD patients (p < 0.01).
LINE-1 (used as surrogate marker of global methylation) significantly hypermethylated in ESRD patients (p < 0.01)
17444888 Stenvinkel 2007 Peripheral blood leukocytes 4 Groups:
Group 1: Non-Inflamed (CRP < 10mgL-1) stage 3 or 4 (7 GN, 1 DKD, 4 PCKD, 5 = nephrosclerosis, 5 = other, 6 = unknown)
Group 2A: stage 5 + RRT + Non-inflamed (n = 56)
Group 2B: stage 5 + RRT + Inflamed (n = 42).
Group 3: stage 5 + RRT + Constant Inflammation (weekly CRP measurements for 3 months) (n = 20)
Group 4: Healthy controls randomly selected from the population (n = 36) Sweden LUMA
HpaII/MspI ratio
No association found between DNA methylation and eGFR
No differences found between diabetic and non-diabetic patients
Association of global hypermethylation with CVD (p < 0.01)
Inflammation associated with global hypermethylation (p = 0.0001)
In essence, the association was with inflammation, not CKD
  1. ATIC: Anti-Oxidant Therapy In Chronic Renal Insufficiency study; CKD: chronic kidney disease; CpGs: CpG islands or CG islands (5′—C—phosphate—G—3′: cytosine and guanine separated by only one phosphate group); CRP: C-reactive protein; CRIC: Chronic Renal Insufficiency Cohort; CUX1: cut like homeobox 1; CVD: cardiovascular disease; DM: diabetes mellitus; DKD: diabetic kidney disease; DMR: differentially methylated regions; DNA: deoxyribonucleic acid; eGFR: estimated glomerular filtration rate; ELMO1:engulfment and cell motility 1; ESRD: end-stage renal disease; FDR: false discovery rate; FKBP5: FK506 binding protein 5; HT: hypertension; INHBA-AS1: INHBA antisense RNA 1; KL: klotho; LC–MS: liquid chromatography-tandem mass spectrometry; LINE-1: Long interspersed nuclear element 1; LUMA: luminometric methylation assay; MTHFR: methylenetetrahydrofolate reductase; p66Shc: p66 isoform of the SHC-transforming protein 1; PBMC: peripheral blood mononuclear cells; PCKD: polycystic kidney disease; PRKAG2: protein kinase AMP-activated non-catalytic subunit gamma 2; PTPRN2: protein tyrosine phosphatase, receptor type N2; RRT: renal replacement therapy; UMOD: uromodulin; UMODL1: uromodulin like 1; UMODL1-AS1: UMODL1 antisense RNA 1