Epigenome-Wide Association Study in Peripheral Tissues Highlights DNA Methylation Profiles Associated with Episodic Memory Performance in Humans

Vascular-related biological stress, DNA methylation, allostatic load and domain-specific cognition: an integrated machine learning and causal inference approach

BACKGROUND

Vascular disease in aging populations spans a wide range of disorders including strokes, circulation disorders and hypertension. As individuals age, vascular disorders co-occur and hence exert combined effects. In the present study we introduce vascular-related biological stress as a novel biomarker to capture the combined effects of vascular disease burden for more precision in early detection of cognitive changes in aging.

OBJECTIVE

to determine the role of vascular-related biological Stress, DNA methylation-based biological aging and Allostatic Load in the relationship between vascular disorders and major cognitive domains including global cognition, episodic memory and executive function in a representative sample of adults across the age span.

METHODS

The present study included participants from MIDUS refresher sample. Vascular-related biological stress included: BMI, Average blood pressure, sitting, Waist-hip ratio, Blood hemoglobin A1c percent, Blood dehydroepiandrosterone (ng/mL), Blood fasting insulin levels uIU/mL, Blood serum interleukin-8 (pg/mL), Blood serum interleukin-6 (pg/mL), Blood fasting glucose levels mg/dL and Blood fibrinogen (mg/dL). DNA methylation-based biological age measures included GrimAge2 that was constructed based on DNA methylation surrogate markers for select plasma proteins and smoking-pack years. Allostatic load scores were calculated based on biomarkers commonly used in allostatic load calculations: cortisol (urine), norepinephrine (urine), epinephrine (urine), dopamine (urine), glycosylated hemoglobin (HBA1C, blood), low density lipoprotein (LDL, blood), C-reactive protein (CRP, blood) dehydroepiandrosterone sulfate (DHEAS, blood), high-density lipoprotein (HDL, blood) and systolic blood pressure (average, sitting). Least Absolute Shrinkage and Selection Operator (LASSO) and response models (item and continuous) were used to calculate vascular-related biological stress and theta scores. Four-way decomposition modeling approach was used to calculate the natural direct and indirect effects in the relationship between vascular disease and major cognitive domains.

RESULTS

550 individuals with data on biomarkers, DNA methylation and cognition assessments were included in the present study. Median age was 54 (range = 26, 78) with females representing 48% of the sample. In the relationship between vascular disease and cognition, the overall proportions mediated through vascular-related biological stress (item-response scale) were 0.60 (P = 0.01); 1.1 (P = 0.308); 0.53 (P = 0.002) for global cognition, episodic memory and executive function respectively. The overall proportions mediated through DNA methylation (GrimAge2) were 0.27 (P = 0.002); 0.39 (P = 0.102); 0.20, (P = 0.002) for global cognition, episodic memory and executive function respectively and 0.10 (P = 0.08); 0.09 (P = 0.5); 0.07 (P = 0.18) through allostatic load (sum scores).

CONCLUSIONS

Our findings suggest that vascular-related biological stress, DNA methylation and to some extent allostatic load mediate the effects of vascular disease on global cognition and executive function.

Epigenomic and clinical analyses of striatal DAT binding in healthy individuals reveal well-known loci of Parkinson's disease

Background

Striatal dopamine transporter (DAT) binding is a sensitive and specific endophenotype for detecting dopaminergic deficits across Parkinson's disease (PD) spectrum. Molecular and clinical signatures of PD in asymptomatic phases help understand the earliest pathophysiological mechanisms underlying the disease. We aimed to investigate whether blood epigenetic markers are associated with inter-individual variation of striatal DAT binding among healthy elderly individuals. We also investigated whether this potential inter-individual variation can manifest as dysfunction of particular cognitive domains. Omics studies conducted on endophenotypes of PD among healthy asymptomatic individuals can provide invaluable insights into early detection, disease mechanisms, and potential therapeutic targets for PD.

Method

We conducted a blood epigenome-wide association study of striatal DAT binding on 96 healthy individuals using the Illumina EPIC array. For functional annotation of our top results, we employed the enhancer-gene mapping strategy using a midbrain single-nucleus multimodal dataset. Finally, we conducted several investigative regression analyses on several neuropsychological tests across five cognitive domains to assess their association with striatal DAT binding among 250 healthy subjects.

Results

We identified seven suggestive (P-value<10-5) CpG probes. Specifically, three probes were colocalized with three risk loci previously identified in PD's largest Genome-Wide Association Study (GWAS). UCN5A and APOE loci were identified as suggestive DMRs associated with striatal DAT binding. Functional analyses prioritized the FDFT1 gene as the potential target gene in the previously reported CTSB GWAS locus. We also showed that delayed recall memory impairment was correlated with reduced striatal DAT binding, irrespective of age.

Conclusion

Our study suggested epigenetic and cognitive signatures of striatal DAT binding among healthy individuals, providing valuable insights for future experimental and clinical studies of early PD.

Blood-based multivariate methylation risk score for cognitive impairment and dementia

INTRODUCTION

The established link between DNA methylation and pathophysiology of dementia, along with its potential role as a molecular mediator of lifestyle and environmental influences, positions blood-derived DNA methylation as a promising tool for early dementia risk detection.

METHODS

In conjunction with an extensive array of machine learning techniques, we employed whole blood genome-wide DNA methylation data as a surrogate for 14 modifiable and non-modifiable factors in the assessment of dementia risk in independent dementia cohorts.

RESULTS

We established a multivariate methylation risk score (MMRS) for identifying mild cognitive impairment cross-sectionally, independent of age and sex (P = 2.0 × 10-3). This score significantly predicted the prospective development of cognitive impairments in independent studies of Alzheimer's disease (hazard ratio for Rey's Auditory Verbal Learning Test (RAVLT)-Learning = 2.47) and Parkinson's disease (hazard ratio for MCI/dementia = 2.59).

DISCUSSION

Our work shows the potential of employing blood-derived DNA methylation data in the assessment of dementia risk.

HIGHLIGHTS

We used whole blood DNA methylation as a surrogate for 14 dementia risk factors. Created a multivariate methylation risk score for predicting cognitive impairment. Emphasized the role of machine learning and omics data in predicting dementia. The score predicts cognitive impairment development at the population level.

Blood DNA methylomic signatures associated with CSF biomarkers of Alzheimer's disease in the EMIF-AD study

INTRODUCTION

We investigated blood DNA methylation patterns associated with 15 well-established cerebrospinal fluid (CSF) biomarkers of Alzheimer's disease (AD) pathophysiology, neuroinflammation, and neurodegeneration.

METHODS

We assessed DNA methylation in 885 blood samples from the European Medical Information Framework for Alzheimer's Disease (EMIF-AD) study using the EPIC array.

RESULTS

We identified Bonferroni-significant differential methylation associated with CSF YKL-40 (five loci) and neurofilament light chain (NfL; seven loci) levels, with two of the loci associated with CSF YKL-40 levels correlating with plasma YKL-40 levels. A co-localization analysis showed shared genetic variants underlying YKL-40 DNA methylation and CSF protein levels, with evidence that DNA methylation mediates the association between genotype and protein levels. Weighted gene correlation network analysis identified two modules of co-methylated loci correlated with several amyloid measures and enriched in pathways associated with lipoproteins and development.

DISCUSSION

We conducted the most comprehensive epigenome-wide association study (EWAS) of AD-relevant CSF biomarkers to date. Future work should explore the relationship between YKL-40 genotype, DNA methylation, and protein levels in the brain.

HIGHLIGHTS

Blood DNA methylation was assessed in the EMIF-AD MBD study. Epigenome-wide association studies (EWASs) were performed for 15 Alzheimer's disease (AD)-relevant cerebrospinal fluid (CSF) biomarker measures. Five Bonferroni-significant loci were associated with YKL-40 levels and seven with neurofilament light chain (NfL). DNA methylation in YKL-40 co-localized with previously reported genetic variation. DNA methylation potentially mediates the effect of single-nucleotide polymorphisms (SNPs) in YKL-40 on CSF protein levels.

Genome-wide QTL mapping across three tissues highlights several Alzheimer's and Parkinson's disease loci potentially acting via DNA methylation

DNA methylation (DNAm) is an epigenetic mark with essential roles in disease development and predisposition. Here, we created genome-wide maps of methylation quantitative trait loci (meQTL) in three peripheral tissues and used Mendelian randomization (MR) analyses to assess the potential causal relationships between DNAm and risk for two common neurodegenerative disorders, i.e. Alzheimer's disease (AD) and Parkinson's disease (PD). Genome-wide single nucleotide polymorphism (SNP; ~5.5M sites) and DNAm (~850K CpG sites) data were generated from whole blood (n=1,058), buccal (n=1,527) and saliva (n=837) specimens. We identified between 11 and 15 million genome-wide significant (p<10-14) SNP-CpG associations in each tissue. Combining these meQTL GWAS results with recent AD/PD GWAS summary statistics by MR strongly suggests that the previously described associations between PSMC3, PICALM, and TSPAN14 and AD may be founded on differential DNAm in or near these genes. In addition, there is strong, albeit less unequivocal, support for causal links between DNAm at PRDM7 in AD as well as at KANSL1/MAPT in AD and PD. Our study adds valuable insights on AD/PD pathogenesis by combining two high-resolution "omics" domains, and the meQTL data shared along with this publication will allow like-minded analyses in other diseases.