Epigenetic influences on aging: a longitudinal genome-wide methylation study in old Swedish twins

ABSTRACT

Age-related changes in DNA methylation were observed in cross-sectional studies, but longitudinal evidence is still limited. Here, we aimed to characterize longitudinal age-related methylation patterns using 1011 blood samples collected from 385 Swedish twins (age at entry: mean 69 and standard deviation 9.7, 73 monozygotic and 96 dizygotic pairs) up to five times (mean 2.6) over 20 years (mean 8.7). We identified 1316 age-associated methylation sites (P<1.3×10⁻⁷) using a longitudinal epigenome-wide association study design. We measured how estimated cellular compositions changed with age and how much they confounded the age effect. We validated the results in two independent longitudinal cohorts, where 118 CpGs were replicated in Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS, 390 samples) (P<3.9×10⁻⁵), 594 in Lothian Birth Cohort (LBC, 3018 samples) (P<5.1×10⁻⁵) and 63 in both. Functional annotation of age-associated CpGs showed enrichment in CCCTC-binding factor (CTCF) and other transcription factor binding sites. We further investigated genetic influences on methylation and found no interaction between age and genetic effects in the 1316 age-associated CpGs. Moreover, in the same CpGs, methylation differences within twin pairs increased with 6.4% over 10 years, where monozygotic twins had smaller intra-pair differences than dizygotic twins. In conclusion, we show that age-related methylation changes persist in a longitudinal perspective, and are fairly stable across cohorts. The changes are under genetic influence, although this effect is independent of age. Moreover, methylation variability increase over time, especially in age-associated CpGs, indicating the increase of environmental contributions on DNA methylation with age.

KEYWORDS:

• DNA methylation
• aging
• longitudinal study
• meQTL
• twin-pair analysis

Ethics approval and consent to participate

All participants in SATSA, PIVUS and LBC have provided written informed consents. This study was approved by the ethics committee at Karolinska Institutet with Dnr 2015/1729-31/5.

Availability of data and material

The methylation array data have been submitted to the Array Express database of EMBL-EBL (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-7309.

Acknowledgement

Lothian Birth Cohort methylation typing was supported by Centre for Cognitive Ageing and Cognitive Epidemiology (Pilot Fund award), Age UK, The Wellcome Trust Institutional Strategic Support Fund, The University of Edinburgh, and The University of Queensland. REM, IJD, and PMV are members of the University of Edinburgh Centre for Cognitive Ageing and Cognitive Epidemiology (CCACE), which is supported by funding from the BBSRC, the Medical Research Council (MRC), and the University of Edinburgh as part of the cross-council Lifelong Health and Wellbeing initiative [MR/K026992/1].

Competing interests

EI is a scientific advisor for Precision Wellness, Cellink and Olink Proteomics for work unrelated to the present project.

Supplementary material

Supplementary data for this article can be accessed here

Additional information

Funding

The SATSA study was supported by NIH grants R01 [AG04563, AG10175, AG028555], the MacArthur Foundation Research Network on Successful Aging, the European Union's Horizon 2020 research and innovation programme [No. 634821], the Swedish Council for Working Life and Social Research (FAS/FORTE) [97:0147:1B, 2009-0795, 2013-2292], the Swedish Research Council [825-2007-7460, 825-2009-6141, 521-2013-8689, 2015-03255], Karolinska Institutet delfinansiering (KID) grant for doctoral students (YW), the KI Foundation, and by Erik Rönnbergs donation for scientific studies in aging and age-related diseases.