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Epigenetic signature of human immune aging: the GESTALT study

Roshni Roy, Pei-Lun Kuo, View ORCID ProfileJulián Candia, Dimitra Sarantopoulou, View ORCID ProfileCeereena Ubaida-Mohien, Dena Hernandez, Mary Kaileh, Sampath Arepalli, View ORCID ProfileAmit Singh, Arsun Bektas, Jaekwan Kim, Ann Zenobia Moore, View ORCID ProfileToshiko Tanaka, Julia McKelvey, Linda Zukley, Cuong Nguyen, Tonya Wallace, View ORCID ProfileChristopher Dunn, William Wood, Yulan Piao, Christopher Coletta, Supriyo De, Jyoti Misra Sen, Nan-ping Weng, Ranjan Sen, View ORCID ProfileLuigi Ferrucci
doi: https://doi.org/10.1101/2023.01.23.525162
Roshni Roy
1Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD
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Pei-Lun Kuo
2Translational Gerontology Branch, National Institute on Aging, Baltimore, MD
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Julián Candia
2Translational Gerontology Branch, National Institute on Aging, Baltimore, MD
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Dimitra Sarantopoulou
1Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD
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Ceereena Ubaida-Mohien
2Translational Gerontology Branch, National Institute on Aging, Baltimore, MD
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Dena Hernandez
3Laboratory of Neurogenetics, National Institute on Aging, Baltimore, MD
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Mary Kaileh
1Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD
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Sampath Arepalli
3Laboratory of Neurogenetics, National Institute on Aging, Baltimore, MD
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Amit Singh
1Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD
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  • ORCID record for Amit Singh
Arsun Bektas
2Translational Gerontology Branch, National Institute on Aging, Baltimore, MD
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Jaekwan Kim
1Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD
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Ann Zenobia Moore
2Translational Gerontology Branch, National Institute on Aging, Baltimore, MD
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Toshiko Tanaka
2Translational Gerontology Branch, National Institute on Aging, Baltimore, MD
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Julia McKelvey
4Clinical Research Core, National Institute on Aging, Baltimore, MD
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Linda Zukley
4Clinical Research Core, National Institute on Aging, Baltimore, MD
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Cuong Nguyen
5Flow Cytometry Unit, National Institute on Aging, Baltimore, MD
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Tonya Wallace
5Flow Cytometry Unit, National Institute on Aging, Baltimore, MD
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Christopher Dunn
5Flow Cytometry Unit, National Institute on Aging, Baltimore, MD
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William Wood
6Laboratory of Genetics & Genomics, National Institute on Aging, Baltimore, MD
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Yulan Piao
6Laboratory of Genetics & Genomics, National Institute on Aging, Baltimore, MD
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Christopher Coletta
6Laboratory of Genetics & Genomics, National Institute on Aging, Baltimore, MD
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Supriyo De
6Laboratory of Genetics & Genomics, National Institute on Aging, Baltimore, MD
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Jyoti Misra Sen
7Laboratory of Clinical Investigation, National Institute on Aging, Baltimore, MD
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Nan-ping Weng
1Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD
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Ranjan Sen
1Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD
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Luigi Ferrucci
3Laboratory of Neurogenetics, National Institute on Aging, Baltimore, MD
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  • ORCID record for Luigi Ferrucci
  • For correspondence: ferruccilu@grc.nia.nih.gov
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ABSTRACT

Age-associated DNA methylation in blood cells convey information on health status. However, the mechanisms that drive these changes in circulating cells and their relationships to gene regulation are unknown. We identified age-associated DNA methylation sites in six purified blood borne immune cell types (naïve B, naïve CD4+and CD8+ T cells, granulocytes, monocytes and NK cells) collected from healthy individuals interspersed over a wide age range. Of the thousand of age-associated sites, only 350 sites were differentially methylated in the same direction in all cell types and validated in an independent longitudinal cohort. Genes close to age-associated hypomethylated sites were enriched for collagen biosynthesis and complement cascade pathways, while genes close to hypermethylated sites mapped to neuronal pathways. In-silico analyses showed that in most cell types, the age-associated hypo- and hypermethylated sites were enriched for ARNT (HIF1β) and REST transcription factor motifs respectively, which are both master regulators of hypoxia response. To conclude, despite spatial heterogeneity, there is a commonality in the putative regulatory role with respect to transcription factor motifs and histone modifications at and around these sites. These features suggest that DNA methylation changes in healthy aging may be adaptive responses to fluctuations of oxygen availability.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.
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Posted January 23, 2023.
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Epigenetic signature of human immune aging: the GESTALT study
Roshni Roy, Pei-Lun Kuo, Julián Candia, Dimitra Sarantopoulou, Ceereena Ubaida-Mohien, Dena Hernandez, Mary Kaileh, Sampath Arepalli, Amit Singh, Arsun Bektas, Jaekwan Kim, Ann Zenobia Moore, Toshiko Tanaka, Julia McKelvey, Linda Zukley, Cuong Nguyen, Tonya Wallace, Christopher Dunn, William Wood, Yulan Piao, Christopher Coletta, Supriyo De, Jyoti Misra Sen, Nan-ping Weng, Ranjan Sen, Luigi Ferrucci
bioRxiv 2023.01.23.525162; doi: https://doi.org/10.1101/2023.01.23.525162
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Epigenetic signature of human immune aging: the GESTALT study
Roshni Roy, Pei-Lun Kuo, Julián Candia, Dimitra Sarantopoulou, Ceereena Ubaida-Mohien, Dena Hernandez, Mary Kaileh, Sampath Arepalli, Amit Singh, Arsun Bektas, Jaekwan Kim, Ann Zenobia Moore, Toshiko Tanaka, Julia McKelvey, Linda Zukley, Cuong Nguyen, Tonya Wallace, Christopher Dunn, William Wood, Yulan Piao, Christopher Coletta, Supriyo De, Jyoti Misra Sen, Nan-ping Weng, Ranjan Sen, Luigi Ferrucci
bioRxiv 2023.01.23.525162; doi: https://doi.org/10.1101/2023.01.23.525162

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