Genome-wide methylation profiling of ADPKD identified epigenetically regulated genes associated with renal cyst development

Yu Mi Woo, Jae Bum Bae, Yeon Hee Oh, Young Gun Lee, Min Joo Lee, Eun Young Park, Jung Kyoon Choi, Sunyoung Lee, Yubin Shin, Jaemyun Lyu, Hye Yoon Jung, Yeon Su Lee, Young Hwan Hwang, Young-Joon Kim, Jong Hoon Park

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Autosomal dominant polycystic kidney disease (ADPKD) is a common human genetic disease characterized by the formation of multiple fluid-filled cysts in bilateral kidneys. Although mutations in polycystic kidney disease 1 (PKD1) are predominantly responsible for ADPKD, the focal and sporadic property of individual cystogenesis suggests another molecular mechanism such as epigenetic alterations. To determine the epigenomic alterations in ADPKD and their functional relevance, ADPKD and non-ADPKD individuals were analyzed by unbiased methylation profiling genome-wide and compared with their expression data. Intriguingly, PKD1 and other genes related to ion transport and cell adhesion were hypermethylated in gene-body regions, and their expressions were downregulated in ADPKD, implicating epigenetic silencing as the key mechanism underlying cystogenesis. Especially, in patients with ADPKD, PKD1 was hypermethylated in gene-body region and it was associated with recruitment of methyl-CpG-binding domain 2 proteins. Moreover, treatment with DNA methylation inhibitors retarded cyst formation of Madin-Darby Canine Kidney cells, accompanied with the upregulation of Pkd1 expression. These results are consistent with previous studies that knock-down of PKD1 was sufficient for cystogenesis. Therefore, our results reveal a critical role for hypermethylation of PKD1 and cystogenesis-related regulatory genes in cyst development, suggesting epigenetic therapy as a potential treatment for ADPKD.

Original languageEnglish
Pages (from-to)281-297
Number of pages17
JournalHuman Genetics
Volume133
Issue number3
DOIs
Publication statusPublished - 2014 Mar 1

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Autosomal Dominant Polycystic Kidney
Polycystic Kidney Diseases
Methylation
Cysts
Genome
Kidney
Epigenomics
Genes
Body Regions
Cyst Fluid
Inborn Genetic Diseases
Madin Darby Canine Kidney Cells
Ion Transport
Medical Genetics
DNA Methylation
Regulator Genes
Cell Adhesion
Up-Regulation
Therapeutics
Down-Regulation

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

Woo, Yu Mi ; Bae, Jae Bum ; Oh, Yeon Hee ; Lee, Young Gun ; Lee, Min Joo ; Park, Eun Young ; Choi, Jung Kyoon ; Lee, Sunyoung ; Shin, Yubin ; Lyu, Jaemyun ; Jung, Hye Yoon ; Lee, Yeon Su ; Hwang, Young Hwan ; Kim, Young-Joon ; Park, Jong Hoon. / Genome-wide methylation profiling of ADPKD identified epigenetically regulated genes associated with renal cyst development. In: Human Genetics. 2014 ; Vol. 133, No. 3. pp. 281-297.
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abstract = "Autosomal dominant polycystic kidney disease (ADPKD) is a common human genetic disease characterized by the formation of multiple fluid-filled cysts in bilateral kidneys. Although mutations in polycystic kidney disease 1 (PKD1) are predominantly responsible for ADPKD, the focal and sporadic property of individual cystogenesis suggests another molecular mechanism such as epigenetic alterations. To determine the epigenomic alterations in ADPKD and their functional relevance, ADPKD and non-ADPKD individuals were analyzed by unbiased methylation profiling genome-wide and compared with their expression data. Intriguingly, PKD1 and other genes related to ion transport and cell adhesion were hypermethylated in gene-body regions, and their expressions were downregulated in ADPKD, implicating epigenetic silencing as the key mechanism underlying cystogenesis. Especially, in patients with ADPKD, PKD1 was hypermethylated in gene-body region and it was associated with recruitment of methyl-CpG-binding domain 2 proteins. Moreover, treatment with DNA methylation inhibitors retarded cyst formation of Madin-Darby Canine Kidney cells, accompanied with the upregulation of Pkd1 expression. These results are consistent with previous studies that knock-down of PKD1 was sufficient for cystogenesis. Therefore, our results reveal a critical role for hypermethylation of PKD1 and cystogenesis-related regulatory genes in cyst development, suggesting epigenetic therapy as a potential treatment for ADPKD.",
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Woo, YM, Bae, JB, Oh, YH, Lee, YG, Lee, MJ, Park, EY, Choi, JK, Lee, S, Shin, Y, Lyu, J, Jung, HY, Lee, YS, Hwang, YH, Kim, Y-J & Park, JH 2014, 'Genome-wide methylation profiling of ADPKD identified epigenetically regulated genes associated with renal cyst development', Human Genetics, vol. 133, no. 3, pp. 281-297. https://doi.org/10.1007/s00439-013-1378-0

Genome-wide methylation profiling of ADPKD identified epigenetically regulated genes associated with renal cyst development. / Woo, Yu Mi; Bae, Jae Bum; Oh, Yeon Hee; Lee, Young Gun; Lee, Min Joo; Park, Eun Young; Choi, Jung Kyoon; Lee, Sunyoung; Shin, Yubin; Lyu, Jaemyun; Jung, Hye Yoon; Lee, Yeon Su; Hwang, Young Hwan; Kim, Young-Joon; Park, Jong Hoon.

In: Human Genetics, Vol. 133, No. 3, 01.03.2014, p. 281-297.

Research output: Contribution to journalArticle

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T1 - Genome-wide methylation profiling of ADPKD identified epigenetically regulated genes associated with renal cyst development

AU - Woo, Yu Mi

AU - Bae, Jae Bum

AU - Oh, Yeon Hee

AU - Lee, Young Gun

AU - Lee, Min Joo

AU - Park, Eun Young

AU - Choi, Jung Kyoon

AU - Lee, Sunyoung

AU - Shin, Yubin

AU - Lyu, Jaemyun

AU - Jung, Hye Yoon

AU - Lee, Yeon Su

AU - Hwang, Young Hwan

AU - Kim, Young-Joon

AU - Park, Jong Hoon

PY - 2014/3/1

Y1 - 2014/3/1

N2 - Autosomal dominant polycystic kidney disease (ADPKD) is a common human genetic disease characterized by the formation of multiple fluid-filled cysts in bilateral kidneys. Although mutations in polycystic kidney disease 1 (PKD1) are predominantly responsible for ADPKD, the focal and sporadic property of individual cystogenesis suggests another molecular mechanism such as epigenetic alterations. To determine the epigenomic alterations in ADPKD and their functional relevance, ADPKD and non-ADPKD individuals were analyzed by unbiased methylation profiling genome-wide and compared with their expression data. Intriguingly, PKD1 and other genes related to ion transport and cell adhesion were hypermethylated in gene-body regions, and their expressions were downregulated in ADPKD, implicating epigenetic silencing as the key mechanism underlying cystogenesis. Especially, in patients with ADPKD, PKD1 was hypermethylated in gene-body region and it was associated with recruitment of methyl-CpG-binding domain 2 proteins. Moreover, treatment with DNA methylation inhibitors retarded cyst formation of Madin-Darby Canine Kidney cells, accompanied with the upregulation of Pkd1 expression. These results are consistent with previous studies that knock-down of PKD1 was sufficient for cystogenesis. Therefore, our results reveal a critical role for hypermethylation of PKD1 and cystogenesis-related regulatory genes in cyst development, suggesting epigenetic therapy as a potential treatment for ADPKD.

AB - Autosomal dominant polycystic kidney disease (ADPKD) is a common human genetic disease characterized by the formation of multiple fluid-filled cysts in bilateral kidneys. Although mutations in polycystic kidney disease 1 (PKD1) are predominantly responsible for ADPKD, the focal and sporadic property of individual cystogenesis suggests another molecular mechanism such as epigenetic alterations. To determine the epigenomic alterations in ADPKD and their functional relevance, ADPKD and non-ADPKD individuals were analyzed by unbiased methylation profiling genome-wide and compared with their expression data. Intriguingly, PKD1 and other genes related to ion transport and cell adhesion were hypermethylated in gene-body regions, and their expressions were downregulated in ADPKD, implicating epigenetic silencing as the key mechanism underlying cystogenesis. Especially, in patients with ADPKD, PKD1 was hypermethylated in gene-body region and it was associated with recruitment of methyl-CpG-binding domain 2 proteins. Moreover, treatment with DNA methylation inhibitors retarded cyst formation of Madin-Darby Canine Kidney cells, accompanied with the upregulation of Pkd1 expression. These results are consistent with previous studies that knock-down of PKD1 was sufficient for cystogenesis. Therefore, our results reveal a critical role for hypermethylation of PKD1 and cystogenesis-related regulatory genes in cyst development, suggesting epigenetic therapy as a potential treatment for ADPKD.

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