Kidney cytosine methylation changes improve renal function decline estimation in patients with diabetic kidney disease

Caroline Gluck, Chengxiang Qiu, Sang Youb Han, Matthew Palmer, Jihwan Park, Yi An Ko, Yuting Guan, Xin Sheng, Robert L. Hanson, Jing Huang, Yong Chen, Ae Seo Deok Park, Maria Concepcion Izquierdo, Ioannis Mantzaris, Amit K. Verma, James M. Pullman, Hongzhe Li, Katalin Susztak

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Epigenetic changes might provide the biological explanation for the long-lasting impact of metabolic alterations of diabetic kidney disease development. Here we examined cytosine methylation of human kidney tubules using Illumina Infinium 450 K arrays from 91 subjects with and without diabetes and varying degrees of kidney disease using a cross-sectional design. We identify cytosine methylation changes associated with kidney structural damage and build a model for kidney function decline. We find that the methylation levels of 65 probes are associated with the degree of kidney fibrosis at genome wide significance. In total 471 probes improve the model for kidney function decline. Methylation probes associated with kidney damage and functional decline enrich on kidney regulatory regions and associate with gene expression changes, including epidermal growth factor (EGF). Altogether, our work shows that kidney methylation differences can be detected in patients with diabetic kidney disease and improve kidney function decline models indicating that they are potentially functionally important.

Original languageEnglish (US)
Article number2461
JournalNature Communications
Volume10
Issue number1
DOIs
StatePublished - Dec 1 2019

Fingerprint

kidney diseases
renal function
methylation
Methylation
Cytosine
Diabetic Nephropathies
kidneys
Kidney
Nucleic Acid Regulatory Sequences
Medical problems
Epidermal Growth Factor
Gene expression
probes
Genes
Kidney Tubules
damage
fibrosis
Kidney Diseases
genome
gene expression

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Kidney cytosine methylation changes improve renal function decline estimation in patients with diabetic kidney disease. / Gluck, Caroline; Qiu, Chengxiang; Han, Sang Youb; Palmer, Matthew; Park, Jihwan; Ko, Yi An; Guan, Yuting; Sheng, Xin; Hanson, Robert L.; Huang, Jing; Chen, Yong; Park, Ae Seo Deok; Izquierdo, Maria Concepcion; Mantzaris, Ioannis; Verma, Amit K.; Pullman, James M.; Li, Hongzhe; Susztak, Katalin.

In: Nature Communications, Vol. 10, No. 1, 2461, 01.12.2019.

Research output: Contribution to journalArticle

Gluck, C, Qiu, C, Han, SY, Palmer, M, Park, J, Ko, YA, Guan, Y, Sheng, X, Hanson, RL, Huang, J, Chen, Y, Park, ASD, Izquierdo, MC, Mantzaris, I, Verma, AK, Pullman, JM, Li, H & Susztak, K 2019, 'Kidney cytosine methylation changes improve renal function decline estimation in patients with diabetic kidney disease', Nature Communications, vol. 10, no. 1, 2461. https://doi.org/10.1038/s41467-019-10378-8
Gluck, Caroline ; Qiu, Chengxiang ; Han, Sang Youb ; Palmer, Matthew ; Park, Jihwan ; Ko, Yi An ; Guan, Yuting ; Sheng, Xin ; Hanson, Robert L. ; Huang, Jing ; Chen, Yong ; Park, Ae Seo Deok ; Izquierdo, Maria Concepcion ; Mantzaris, Ioannis ; Verma, Amit K. ; Pullman, James M. ; Li, Hongzhe ; Susztak, Katalin. / Kidney cytosine methylation changes improve renal function decline estimation in patients with diabetic kidney disease. In: Nature Communications. 2019 ; Vol. 10, No. 1.
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