Systemic Age-Associated DNA Hypermethylation of ELOVL2 Gene: In Vivo and In Vitro Evidences of a Cell Replication Process

Abstract

Epigenetic remodeling is one of the major features of the aging process. We recently demonstrated that DNA methylation of ELOVL2 and FHL2 CpG islands is highly correlated with age in whole blood. Here we investigated several aspects of age-associated hypermethylation of ELOVL2 and FHL2. We showed that ELOVL2 methylation is significantly different in primary dermal fibroblast cultures from donors of different ages. Using epigenomic data from public resources, we demonstrated that most of the tissues show ELOVL2 and FHL2 hypermethylation with age. Interestingly, ELOVL2 hypermethylation was not found in tissues with very low replication rate. We demonstrated that ELOVL2 hypermethylation is associated with in vitro cell replication rather than with senescence. We confirmed intra-individual hypermethylation of ELOVL2 and FHL2 in longitudinally assessed participants from the Doetinchem Cohort Study. Finally we showed that, although the methylation of the two loci is not associated with longevity/mortality in the Leiden Longevity Study, ELOVL2 methylation is associated with cytomegalovirus status in nonagenarians, which could be informative of a higher number of replication events in a fraction of whole-blood cells. Collectively, these results indicate that ELOVL2 methylation is a marker of cell divisions occurring during human aging.

Keywords: Biomarker; Epigenetics; FHL2; Methylation.

Figure 1.

ELOVL2 and FHL2 DNA methylation profiles in dermal fibroblasts from young, middle-aged, and centenarian donors. Mean methylation values and standard deviations of the CpG sites assessed by the EpiTyper assay are reported.

Figure 2.

Age-dependent hypermethylation of ELOVL2 cg16867657 in 30 normal tissues analyzed using the Infinium 450k platform (1: whole blood; 2: peripheral blood mononuclear cells; 3: neutrophils; 4: CD4 T cells; 5: CD8 T cells: 6: monocytes; 7: subcutaneous adipose tissue abdominal; 8: subcutaneous adipose tissue gluteal; 9: hip cartilage; 10: bone; 11: prefrontal cortex; 12: temporal cortex; 13: cerebellum; 14: frontal lobe white matter; 15: caudate nucleus; 16: cingulate gyrus; 17: frontal cortex; 18: hippocampus; 19: midbrain; 20: motor cortex; 21: occipital cortex; 22: parietal cortex; 23: sensory cortex; 24: visual cortex; 25: skeletal muscle; 26: liver; 27: aortic tissue; 28: dermis; 29: epidermis; 30: mesenchymal stem cells). For each tissue, linear regression between age and DNA methylation is plotted.

Figure 3.

(A) ELOVL2 and FHL2 DNA methylation profiles in dermal fibroblasts (DFs) from middle-aged donor 1 (DF1) at replicative Passages 3, 13, and 22. (B) ELOVL2 and FHL2 DNA methylation profiles in F1 fetal lung fibroblasts at early passages, after 8 weeks in senescence (senescent LF1) and after 16 weeks in senescence (deeply senescent LF1).

Figure 4.

Regression lines between DNA methylation of ELOVL2 CpG_11.12.13.14 or FHL2 CpG_9.10 and age of 19 participants longitudinally assessed at five intervals of 5 years.

Figure 5.

Scatterplot of age and methylation level for CpG unit CpG_11.12.13.14 in ELOVL2 and CpG_9.10 in FHL2 in the Leiden Longevity Study. Black circles (blue circles online) indicate male nonagenarians, gray circles (orange circles online) indicate female nonagenarians, gray diamonds (green diamonds online) indicate male offspring, black diamonds (purple diamonds online) indicate female offspring, gray squares (blue squares online) indicate male spouses, and black squares (red squares online) indicate female spouses.