Epigenetic analysis in rheumatoid arthritis synoviocytes

Seokjin Ham; Jae Bum Bae; Suman Lee; Bong Jo Kim; Bok Ghee Han; Seung Ki Kwok; Tae Young Roh

doi:10.1038/s12276-019-0215-5

Epigenetic analysis in rheumatoid arthritis synoviocytes

Seokjin Ham, Jae Bum Bae, Suman Lee, Bong Jo Kim, Bok Ghee Han, Seung Ki Kwok, Tae Young Roh

Department of Life Science

Research output: Contribution to journal › Article › peer-review

28 Scopus citations

Abstract

Rheumatoid arthritis (RA) is a complex chronic systematic disease with progressive destruction of the joints by invasive synoviocytes. To characterize the key regulators involved in the development of RA, we obtained multilayer epigenomics data including DNA methylation by whole-genome bisulfite sequencing, miRNA profiles, genetic variations by whole-exome sequencing, and mRNA profiles from synoviocytes of RA and osteoarthritis (OA) patients. The overall DNA methylation patterns were not much different between RA and OA, but 523 low-methylated regions (LMRs) were specific to RA. The LMRs were preferentially localized at the 5′ introns and overlapped with transcription factor binding motifs for GLI1, RUNX2, and TFAP2A/C. Single base-scale differentially methylated CpGs were linked with several networks related to wound response, tissue development, collagen fibril organization, and the TGF-β receptor signaling pathway. Further, the DNA methylation of 201 CpGs was significantly correlated with 27 expressed miRNA genes. Our interpretation of epigenomic data of the synoviocytes from RA and OA patients is an informative resource to further investigate regulatory elements and biomarkers responsible for the pathophysiology of RA and OA.

Original language	English
Article number	22
Journal	Experimental and Molecular Medicine
Volume	51
Issue number	2
DOIs	https://doi.org/10.1038/s12276-019-0215-5
State	Published - 1 Feb 2019

Bibliographical note

Funding Information:
All members of the Roh laboratory are greatly appreciated for their critical discussion and help. This work was supported by a grant (NRF-2014M3C9A3064548 and NRF-2017M3C9A6047625 to T.-Y.R.) funded by the National Research Foundation of Korea (NRF). S.H. was supported by the BK21 PLUS fellowship program (10Z20130012243) funded by the Ministry of Education, Korea. Biospecimens and data were provided by Reference Data Production of Regulation of Gene Expression (4848–308) and Korean Genome Analysis Project (4845-301) that were supported by the Korea Centers for Disease Control and Prevention, Republic of Korea.

Publisher Copyright:
© 2019, The Author(s).

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title = "Epigenetic analysis in rheumatoid arthritis synoviocytes",

abstract = "Rheumatoid arthritis (RA) is a complex chronic systematic disease with progressive destruction of the joints by invasive synoviocytes. To characterize the key regulators involved in the development of RA, we obtained multilayer epigenomics data including DNA methylation by whole-genome bisulfite sequencing, miRNA profiles, genetic variations by whole-exome sequencing, and mRNA profiles from synoviocytes of RA and osteoarthritis (OA) patients. The overall DNA methylation patterns were not much different between RA and OA, but 523 low-methylated regions (LMRs) were specific to RA. The LMRs were preferentially localized at the 5′ introns and overlapped with transcription factor binding motifs for GLI1, RUNX2, and TFAP2A/C. Single base-scale differentially methylated CpGs were linked with several networks related to wound response, tissue development, collagen fibril organization, and the TGF-β receptor signaling pathway. Further, the DNA methylation of 201 CpGs was significantly correlated with 27 expressed miRNA genes. Our interpretation of epigenomic data of the synoviocytes from RA and OA patients is an informative resource to further investigate regulatory elements and biomarkers responsible for the pathophysiology of RA and OA.",

author = "Seokjin Ham and Bae, {Jae Bum} and Suman Lee and Kim, {Bong Jo} and Han, {Bok Ghee} and Kwok, {Seung Ki} and Roh, {Tae Young}",

note = "Funding Information: All members of the Roh laboratory are greatly appreciated for their critical discussion and help. This work was supported by a grant (NRF-2014M3C9A3064548 and NRF-2017M3C9A6047625 to T.-Y.R.) funded by the National Research Foundation of Korea (NRF). S.H. was supported by the BK21 PLUS fellowship program (10Z20130012243) funded by the Ministry of Education, Korea. Biospecimens and data were provided by Reference Data Production of Regulation of Gene Expression (4848–308) and Korean Genome Analysis Project (4845-301) that were supported by the Korea Centers for Disease Control and Prevention, Republic of Korea. Publisher Copyright: {\textcopyright} 2019, The Author(s).",

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N1 - Funding Information: All members of the Roh laboratory are greatly appreciated for their critical discussion and help. This work was supported by a grant (NRF-2014M3C9A3064548 and NRF-2017M3C9A6047625 to T.-Y.R.) funded by the National Research Foundation of Korea (NRF). S.H. was supported by the BK21 PLUS fellowship program (10Z20130012243) funded by the Ministry of Education, Korea. Biospecimens and data were provided by Reference Data Production of Regulation of Gene Expression (4848–308) and Korean Genome Analysis Project (4845-301) that were supported by the Korea Centers for Disease Control and Prevention, Republic of Korea. Publisher Copyright: © 2019, The Author(s).

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N2 - Rheumatoid arthritis (RA) is a complex chronic systematic disease with progressive destruction of the joints by invasive synoviocytes. To characterize the key regulators involved in the development of RA, we obtained multilayer epigenomics data including DNA methylation by whole-genome bisulfite sequencing, miRNA profiles, genetic variations by whole-exome sequencing, and mRNA profiles from synoviocytes of RA and osteoarthritis (OA) patients. The overall DNA methylation patterns were not much different between RA and OA, but 523 low-methylated regions (LMRs) were specific to RA. The LMRs were preferentially localized at the 5′ introns and overlapped with transcription factor binding motifs for GLI1, RUNX2, and TFAP2A/C. Single base-scale differentially methylated CpGs were linked with several networks related to wound response, tissue development, collagen fibril organization, and the TGF-β receptor signaling pathway. Further, the DNA methylation of 201 CpGs was significantly correlated with 27 expressed miRNA genes. Our interpretation of epigenomic data of the synoviocytes from RA and OA patients is an informative resource to further investigate regulatory elements and biomarkers responsible for the pathophysiology of RA and OA.

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Epigenetic analysis in rheumatoid arthritis synoviocytes

Abstract

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