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, 18 (5), e12995

Epigenetic Signatures of Werner Syndrome Occur Early in Life and Are Distinct From Normal Epigenetic Aging Processes

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Epigenetic Signatures of Werner Syndrome Occur Early in Life and Are Distinct From Normal Epigenetic Aging Processes

Anna Maierhofer et al. Aging Cell.

Abstract

Werner Syndrome (WS) is an adult-onset segmental progeroid syndrome. Bisulfite pyrosequencing of repetitive DNA families revealed comparable blood DNA methylation levels between classical (18 WRN-mutant) or atypical WS (3 LMNA-mutant and 3 POLD1-mutant) patients and age- and sex-matched controls. WS was not associated with either age-related accelerated global losses of ALU, LINE1, and α-satellite DNA methylations or gains of rDNA methylation. Single CpG methylation was analyzed with Infinium MethylationEPIC arrays. In a correspondence analysis, atypical WS samples clustered together with the controls and were clearly separated from classical WS, consistent with distinct epigenetic pathologies. In classical WS, we identified 659 differentially methylated regions (DMRs) comprising 3,656 CpG sites and 613 RefSeq genes. The top DMR was located in the HOXA4 promoter. Additional DMR genes included LMNA, POLD1, and 132 genes which have been reported to be differentially expressed in WRN-mutant/depleted cells. DMRs were enriched in genes with molecular functions linked to transcription factor activity and sequence-specific DNA binding to promoters transcribed by RNA polymerase II. We propose that transcriptional misregulation of downstream genes by the absence of WRN protein contributes to the variable premature aging phenotypes of WS. There were no CpG sites showing significant differences in DNA methylation changes with age between WS patients and controls. Genes with both WS- and age-related methylation changes exhibited a constant offset of methylation between WRN-mutant patients and controls across the entire analyzed age range. WS-specific epigenetic signatures occur early in life and do not simply reflect an acceleration of normal epigenetic aging processes.

Keywords: (classical and atypical) Werner syndrome; bisulfite pyrosequencing; methylation array; premature aging; segmental progeria; transcription deficiency.

Conflict of interest statement

None declared.

Figures

Figure 1
Figure 1
Correspondence analysis of the 10,000 most variable CpG sites over all 48 blood samples. Clear separation of classical WS from the remaining samples on the second axis explains 4.8% of the variance. The samples from LMNA‐ and POLD1‐mutant patients cluster with the controls
Figure 2
Figure 2
Venn diagrams showing the overlaps of genome‐wide significant CpG sites (a, b) and DMR‐containing genes (c, d) between WRN‐, LMNA‐, and POLD1‐mutant patients (a, c) as well as between WS‐ and age‐related changes (b, d)
Figure 3
Figure 3
Top promoter DMRs in WRN‐mutant (a), LMNA‐mutant (b), and POLD1‐mutant (c) patients. Thick colored lines represent the methylation profile of the analyzed DMR in controls (blue), WRN‐mutant (mauve), LMNA‐mutant (red), and POLD1‐mutant (green) patients. The genomic region is indicated on the x‐axis and individual CpG sites within the DMR on the top. The y‐axis indicates the methylation level at a given genomic position. Thin colored lines represent methylation profiles of individual samples, while the solid line indicates the mean methylation level per group. HOXA4 (a) is hypermethylated in classical WS patients; LMNA‐ and POLD1‐mutant patients behave similar to controls. The CARNS1 promoter (b) is hypermethylated in LMNA‐mutant patients and the FUCA1 promoter (c) in POLD1‐mutant patients
Figure 4
Figure 4
Age effect on HOXA4, ZIC1, ZIC4, and PPP1R18 methylations in WRN‐mutant patients (red dots) and controls (blue dots). Each dot represents an individual sample; regression lines (standard errors are shaded in red and blue) indicate the methylation gains (HOXA4, ZIC1, and ZIC4) or losses (PPP1R18) of the analyzed DMR with age. Note that the methylation differences between WRN‐mutant patients and controls remain constant over the entire analyzed age range

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  • Lessons for aging from Werner syndrome epigenetics.
    Martin GM, Poot M, Haaf T. Martin GM, et al. Aging (Albany NY). 2020 Feb 5;12(3):2022-2023. doi: 10.18632/aging.102829. Epub 2020 Feb 5. Aging (Albany NY). 2020. PMID: 32023552 Free PMC article. No abstract available.

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