Links of Sleep Duration with Biomarkers of Accelerated Aging: the Baltimore Longitudinal Study of Aging

Sleep disorders and sleep deprivation have been linked to markers of biological aging, including methylation change and increases in white blood cell and neutrophil counts. However, little is known regarding the association of sleep duration with biological markers of aging. We investigated links of self-reported sleep duration with biological aging markers in 615 participants in the Baltimore Longitudinal Study of Aging (BLSA) aged ≥50 years (mean = 71.0 ± 11.2, 49.6% women, 68.8% white) with data on self-reported sleep duration in hours (i.e., ≤6 (n=131), >6 to 7 (n=234), >7 (n=250)), demographics, and genetic and methylation data (mDNA). Our aging biomarker outcomes were four epigenetic clocks (Horvath, Hannum, PhenoAge, and GrimAge), mDNA-estimated PAI1, and estimated granulocyte count. After adjustment for age, sex, and race, compared to those sleeping ≤6 hours, those reporting >7 hours of sleep had faster biological aging according to Hannum age-acceleration, PhenoAge, GrimAge, mDNA-estimated PAI1, and granulocyte count. In addition, sleep duration interacted with age, such that compared to individuals reporting ≤6 hours of sleep, individuals reporting >6 to 7 hours showed lower GrimAge with increasing age, and with sex, such that males with longer sleep duration (>6 to 7 and >7 hours) showed a lower granulocyte count compared to females. Findings suggest that both short and long sleep duration are associated with and may contribute to accelerated aging. Prospective studies in larger samples are needed to examine whether changes in sleep duration precede changes in aging biomarkers.

Impact of BMI and waist circumference on epigenome-wide DNA methylation and identification of epigenetic biomarkers in blood: an EWAS in multi-ethnic Asian individuals

Background The prevalence of obesity and its related chronic diseases have been increasing especially in Asian countries. Obesity-related genetic variants have been identified, but these explain little of the variation in BMI. Recent studies reported associations between DNA methylation and obesity, mostly in non-Asian populations. Methods We performed an epigenome-wide association study (EWAS) on general adiposity (body mass index, BMI) and abdominal adiposity (waist circumference, WC) in 409 multi-ethnic Asian individuals and replicated BMI and waist-associated DNA methylation CpGs identified in other populations. The cross-lagged panel model and Mendelian randomization were used to assess the temporal relationship between methylation and BMI. The temporal relationship between the identified CpGs and inflammation and metabolic markers was also examined. Results EWAS identified 116 DNA methylation CpGs independently associated with BMI and eight independently associated with WC at false discovery rate PFDR < 0.05 in 409 Asian samples. We replicated 110 BMI-associated CpGs previously reported in Europeans and identified six novel BMI-associated CpGs and two novel WC-associated CpGs. We observed high consistency in association direction of effect compared to studies in other populations. Causal relationship analyses indicated that BMI was more likely to be the cause of DNA methylation alteration, rather than the consequence. The causal analyses using BMI-associated methylation risk score also suggested that higher levels of the inflammation marker IL-6 were likely the consequence of methylation change. Conclusion Our study provides evidence of an association between obesity and DNA methylation in multi-ethnic Asians and suggests that obesity can drive methylation change. The results also suggested possible causal influence that obesity-related methylation changes might have on inflammation and lipoprotein levels.

An Integrative Transcriptomic and Methylation Approach for Identifying Differentially Expressed Circular RNAs Associated with DNA Methylation Change

Recently, accumulating evidence has supported that circular RNA (circRNA) plays important roles in tumorigenesis by regulating gene expression at transcriptional and post-transcriptional levels. Expression of circRNAs can be epigenetically silenced by DNA methylation; however, the underlying regulatory mechanisms of circRNAs by DNA methylation remains largely unknown. We explored this regulation in hepatocellular carcinoma (HCC) using genome-wide DNA methylation and RNA sequencing data of the primary tumor and matched adjacent normal tissues from 20 HCC patients. Our pipeline identified 1012 upregulated and 747 downregulated circRNAs (collectively referred to as differentially expressed circRNAs, or DE circRNAs) from HCC RNA-seq data. Among them, 329 DE circRNAs covered differentially methylated sites (adjusted p-value < 0.05, |ΔM| > 0.5) in circRNAs’ interior and/or flanking regions. Interestingly, the corresponding parental genes of 46 upregulated and 31 downregulated circRNAs did not show significant expression change in the HCC tumor versus normal samples. Importantly, 34 of the 77 DE circRNAs (44.2%) had significant correlation with DNA methylation change in HCC (Spearman’s rank-order correlation, p-value < 0.05), suggesting that aberrant DNA methylation might regulate circular RNA expression in HCC. Our study revealed genome-wide differential circRNA expression in HCC. The significant correlation with DNA methylation change suggested that epigenetic regulation might act on both mRNA and circRNA expression. The specific regulation in HCC and general view in other cancer or disease requires further investigation.

Epigenomic analysis of biliary tract cancer identifies subtypes with different immune characteristics and clinical outcomes.

e16153 Background: Biliary tract cancer (BTC) is an aggressive malignancy with poor prognosis and limited treatment options. The epigenome-associated multi-dimensional studies for BTC are limited. Here, we proposed a DNA methylation-based classification scheme and investigated the associations between methylation and multi-dimensional data including clinicopathological features, genetic aberrations, and prognosis. Methods: Multi-dimensional data concerning mutation, DNA methylation, and clinical data from 105 BTC patients who received surgical resection (gallbladder cancer [GBC], n=48, cholangiocarcinoma [CCA], n=57) were analyzed. Differentially methylated blocks (DMBs) in GBCs and CCAs were identified by comparing tumors and adjacent tissues. Methylation-based subtyping was performed via non-supervised consensus clustering. Results: The differentially methylated blocks (DMBs) in GBCs and CCAs are highly overlapping. Based on the common DMBs of GBCs and CCAs, the classifier yielded high sensitivity of 95.2% and specificity of 96.0%. Hypomethylated genes were enriched in pathways of transmemberane receptor and ion binding, while hypermethylation occurred in genes concerning DNA binding transcription activity. By non-supervised clustering of common DMBs, 6 clusters with different degrees of methylation change were identified. Higher methylation alteration (cluster risk-high) was associated with more copy number variation and shorter OS. By LASSO regression, a 12-gene prognostic model was trained and validated (Table). As for immune characteristics, the methylation of CD8A gene was lower in the cluster risk-high group, and this association was validated in the TCGA-cholangiocarcinoma cohort. In addition, lower methylation change was associated with higher BCR/TCR diversity, immune cell infiltration, and PD-L1 and CTLA4 mRNA expression. Conclusions: In BTC, methylation patterns may serve as a robust indicator of immune-related features and prognosis. Our integrative analysis highlights the association between genomic and epigenomic features, and provides insights into the molecular heterogeneity, and the potential therapeutic significance in biliary tract malignancies. Included methylation sites in the LASSO model.[Table: see text]

DNA methylation predicts age and provides insight into exceptional longevity of bats

Exceptionally long-lived species, including many bats, rarely show overt signs of aging, making it difficult to determine why species differ in lifespan. Here, we use DNA methylation (DNAm) profiles from 712 known-age bats, representing 26 species, to identify epigenetic changes associated with age and longevity. We demonstrate that DNAm accurately predicts chronological age. Across species, longevity is negatively associated with the rate of DNAm change at age-associated sites. Furthermore, analysis of several bat genomes reveals that hypermethylated age- and longevity-associated sites are disproportionately located in promoter regions of key transcription factors (TF) and enriched for histone and chromatin features associated with transcriptional regulation. Predicted TF binding site motifs and enrichment analyses indicate that age-related methylation change is influenced by developmental processes, while longevity-related DNAm change is associated with innate immunity or tumorigenesis genes, suggesting that bat longevity results from augmented immune response and cancer suppression.

Genome Methylation Predicts Age and Longevity of Bats

Exceptionally long-lived species, including many bats, rarely show overt signs of aging, making it difficult to determine why species differ in lifespan. Here, we use DNA methylation (DNAm) profiles from 712 known-age bats, representing 26 species, to identify epigenetic changes associated with age and longevity. We demonstrate that DNAm accurately predicts chronological age. Across species, longevity is negatively associated with the rate of DNAm change at age-associated sites. Furthermore, analysis of several bat genomes reveals that hypermethylated age- and longevity-associated sites are disproportionately located in promoter regions of key transcription factors (TF) and enriched for histone and chromatin features associated with transcriptional regulation. Predicted TF binding site motifs and enrichment analyses indicate that age-related methylation change is influenced by developmental processes, while longevity-related DNAm change is associated with innate immunity or tumorigenesis genes, suggesting that bat longevity results from augmented immune response and cancer suppression.

S17. GLOBAL DNA METHYLATION IN CURRENT AND EMERGENT SUICIDAL IDEATION: ANALYSIS IN SCHIZOPHRENIA

Background Several lines of evidence have shown that epigenetic mechanisms influence suicidal behavior, but do not indicate specific susceptibility variants. In a recent study, analysis of global methylation levels found that psychiatric patients with a history of suicide attempt (SA) had significantly higher levels of 5-methyl cytosine (5mC), suggesting that patients with a history of SA have global hypermethylation of their genome. However, there is no study investigated the link between global DNA methylation and suicidal ideation (SI) in schizophrenia. In this study, we analyzed global DNA methylation in suicide ideators and non-ideators in a sample of schizophrenia patients to find if global DNA methylation can predict SI in schizophrenia. Methods There are several methods of detecting total 5-methylcytosine content in the genome. We used Cell Biolabs’ Global DNA Methylation ELISA Kit, which is a competitive enzyme immunoassay developed for rapid detection and quantitation of 5’-methyl-2’-deoxycytidine (5MedCyd) in DNA extracted from white blood cells (WBC). We digested the genomic DNA, extracted from WBC, into single nucleotides and the quantity of 5MedCyd was determined by comparing its absorbance with that of a known 5MedCyd standard curve. We measured global DNA methylation in predicting current and emergent suicidal ideation. Results In the analysis of current SI in our schizophrenia patients, the average quantity of 5MedCyd was 7.56 ± 0.77 ng 5mC/µg DNA for suicide ideators and 8.72 ± 1.97 ng 5mC/µg DNA for non-ideators. There was no evidence of a significant difference between these two groups in our analysis (p=0.176). Also, we did not find a significant difference between global DNA methylation change (global DNA methylation change between baseline and three-month follow-up visits) in patients with and without emergent SI (p=0.121). Discussion This preliminary analysis did not find a predictive role of global DNA methylation in SI in patients with schizophrenia. The small sample size, used in this pilot study, is probably responsible for the fact that the results found here did not support those of previous research, showing that methylation levels are higher in patients with a history of a suicide attempt.