TY - JOUR
T1 - Longitudinal DNA methylation dynamics as a practical indicator in clinical epigenetics
AU - Komaki, Shohei
AU - Ohmomo, Hideki
AU - Hachiya, Tsuyoshi
AU - Sutoh, Yoichi
AU - Ono, Kanako
AU - Furukawa, Ryohei
AU - Umekage, So
AU - Otsuka-Yamasaki, Yayoi
AU - Tanno, Kozo
AU - Sasaki, Makoto
AU - Shimizu, Atsushi
N1 - Funding Information:
This study was supported by the Tohoku Medical Megabank Project (Special Account for the Reconstruction from the Great East Japan Earthquake) from the Japan Agency for Medical Research and Development (AMED; https://www.amed.go.jp/en/ ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Publisher Copyright:
© 2021, The Author(s).
PY - 2021/12
Y1 - 2021/12
N2 - Background: One of the fundamental assumptions of DNA methylation in clinical epigenetics is that DNA methylation status can change over time with or without interplay with environmental and clinical conditions. However, little is known about how DNA methylation status changes over time under ordinary environmental and clinical conditions. In this study, we revisited the high frequency longitudinal DNA methylation data of two Japanese males (24 time-points within three months) and characterized the longitudinal dynamics. Results: The results showed that the majority of CpGs on Illumina HumanMethylation450 BeadChip probe set were longitudinally stable over the time period of three months. Focusing on dynamic and stable CpGs extracted from datasets, dynamic CpGs were more likely to be reported as epigenome-wide association study (EWAS) markers of various traits, especially those of immune- and inflammatory-related traits; meanwhile, the stable CpGs were enriched in metabolism-related genes and were less likely to be EWAS markers, indicating that the stable CpGs are stable both in the short-term within individuals and under various environmental and clinical conditions. Conclusions: This study indicates that CpGs with different stabilities are involved in different functions and traits, and thus, they are potential indicators that can be applied for clinical epigenetic studies to outline underlying mechanisms.
AB - Background: One of the fundamental assumptions of DNA methylation in clinical epigenetics is that DNA methylation status can change over time with or without interplay with environmental and clinical conditions. However, little is known about how DNA methylation status changes over time under ordinary environmental and clinical conditions. In this study, we revisited the high frequency longitudinal DNA methylation data of two Japanese males (24 time-points within three months) and characterized the longitudinal dynamics. Results: The results showed that the majority of CpGs on Illumina HumanMethylation450 BeadChip probe set were longitudinally stable over the time period of three months. Focusing on dynamic and stable CpGs extracted from datasets, dynamic CpGs were more likely to be reported as epigenome-wide association study (EWAS) markers of various traits, especially those of immune- and inflammatory-related traits; meanwhile, the stable CpGs were enriched in metabolism-related genes and were less likely to be EWAS markers, indicating that the stable CpGs are stable both in the short-term within individuals and under various environmental and clinical conditions. Conclusions: This study indicates that CpGs with different stabilities are involved in different functions and traits, and thus, they are potential indicators that can be applied for clinical epigenetic studies to outline underlying mechanisms.
KW - Blood DNA methylation
KW - EWAS marker likelihood
KW - Illumina 450 K beadchip
KW - Temporal stability
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U2 - 10.1186/s13148-021-01202-6
DO - 10.1186/s13148-021-01202-6
M3 - Article
C2 - 34903243
AN - SCOPUS:85121299772
VL - 13
JO - Clinical Epigenetics
JF - Clinical Epigenetics
SN - 1868-7075
IS - 1
M1 - 219
ER -