Epigenetic signatures of Werner syndrome occur early in life and are distinct from normal epigenetic aging processes

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.

CTCF Mediates Replicative Senescence Through POLD1

“…POLD1, as the catalytic subunit of DNA polymerase delta and endowed with polymerase and exonuclease activities, plays a critical role in DNA synthesis and DNA repair processes ( Cui et al, 2019 ). Our previous study found that POLD1 expression was downregulated as cell aging in human lymphocytes and preliminarily confirmed that the expression of POLD1 was essential in cell cycle regulation and DNA damage repair processes ( Wang et al, 2012 ; Song et al, 2015 ; Maierhofer et al, 2019 ). However, the mechanism of age-related downregulation of POLD1 expression has not been fully explained.…”

Amplification of the epigenetic (gestational) age acceleration signal

“…In addition, the fact that several independent eEAAs were found to be significantly associated with Down's syndrome suggests that EAA is a multi-factorial composite trait. Our method also showed similar results for data on Werner's syndrome [16,24] (GSE131752), where the associations of Werner's syndrome with standard EAAs were found to be substantially weaker than those with eEAAs resulting from our PCbased method (PB<0.05, Figures S1 and S2, Additional file 2).…”

Prevalence and Phenotypic Impact of Robertsonian Translocations

“…This is in stark contrast with the increase during aging in global genomic DNA methylation in peripheral blood lymphocytes of healthy individuals and patients with Werner syndrome [Maierhofer et al, 2017;Horvath and Raj, 2018;Wang and Lemos, 2019]. In the latter syndrome, genes linked to transcription factor activity and sequencespecific DNA binding to promoters transcribed by RNA polymerase II were affected by differential methylation, which suggests that dysregulation of mRNA transcription may contribute to this syndrome [Maierhofer et al, 2019]. In contrast, RNA polymerase I rDNA transcription rates are not affected by differential methylation or loss of rDNA copies during aging [Malinovskaya et al, 2018].…”