Cited by 99Dementia and Cognitive Impairment ResearchEpigenetics and DNA MethylationAlzheimer's disease research and treatments

Harnessing peripheral DNA methylation differences in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) to reveal novel biomarkers of disease

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Vasanthakumar, Aparna, Davis, Justin W., Idler, Kenneth, Waring, Jeffrey F., Asque, Elizabeth, Riley-Gillis, Bridget, Grosskurth, Shaun, Srivastava, Gyan +11 more·2020·Clinical Epigenetics

Abstract

Background: Alzheimer’s disease (AD) is a chronic progressive neurodegenerative disease impacting an estimated 44 million adults worldwide. The causal pathology of AD (accumulation of amyloid-beta and tau), precedes hallmark symptoms of dementia by more than a decade, necessitating development of early diagnostic markers of disease onset, particularly for new drugs that aim to modify disease processes. To evaluate differentially methylated positions (DMPs) as novel blood-based biomarkers of AD, we used a subset of 653 individuals with peripheral blood (PB) samples in the Alzheimer’s disease Neuroimaging Initiative (ADNI) consortium. The selected cohort of AD, mild cognitive impairment (MCI), and age-matched healthy controls (CN) all had imaging, genetics, transcriptomics, cerebrospinal protein markers, and comprehensive clinical records, providing a rich resource of concurrent multi-omics and phenotypic information on a well-phenotyped subset of ADNI participants. Results: In this manuscript, we report cross-diagnosis differential peripheral DNA methylation in a cohort of AD, MCI, and age-matched CN individuals with longitudinal DNA methylation measurements. Epigenome-wide association studies (EWAS) were performed using a mixed model with repeated measures over time with a P value cutoff of 1 × 10 −5 to test contrasts of pairwise differential peripheral methylation in AD vs CN, AD vs MCI, and MCI vs CN. The most highly significant differentially methylated loci also tracked with Mini Mental State Examination (MMSE) scores. Differentially methylated loci were enriched near brain and neurodegeneration-related genes (e.g., BDNF, BIN1, APOC1 ) validated using the genotype tissue expression project portal (GTex). Conclusions: Our work shows that peripheral differential methylation between age-matched subjects with AD relative to healthy controls will provide opportunities to further investigate and validate differential methylation as a surrogate of disease. Given the inaccessibility of brain tissue, the PB-associated methylation marks may help identify the stage of disease and progression phenotype, information that would be central to bringing forward successful drugs for AD.

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  • The sex-specific meta-analysis included 1284 whole blood samples (632 females and 652 males) from ADNI and AIBL.

    “included DNA methylation data for a total of 1284 whole blood samples (632 females and 652 males).”

    From Distinct sex-specific DNA methylation differences in Alzheimer’s disease (2022) · cites this paper as [38]

    Methods > Subjects reports samples from 653 ADNI participants, and Methods > Sample identity checks says 1,707 samples were analyzed after quality control—not 1,284. Methods > Statistical analysis also distinguishes whole blood from buffy coat. The cited paper does not describe the claimed sex-specific ADNI–AIBL meta-analysis or its female–male counts. Page numbers are unavailable in our copy. (LLM, conf=0.88)

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  • The meta-analysis was expected to be underpowered given modest sex-specific sample sizes, so CpGs at P < 1×10−5 were also prioritized.

    “Based on our experiences and previous studies in the analysis of EWAS measured in blood [22, 38, 47], we expected our meta-analysis to be underpowered, given the modest sample sizes of the sex-specific analyses. Therefore, we also prioritized CpGs with suggestive significance at the pre-specified significance threshold of P-value < 1×10−5.”

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Research works printed but not linked: 1

  1. [46]Phipson B, Lee S, Majewski IJ, Alexander WS, Smyth G. Robust hyperparameter estimation protects. 2016;10:946–63. PMC5373812 28367255

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Authors
Vasanthakumar, A., Davis, J. W., Idler, K., Waring, J. F., Asque, E., Riley-Gillis, B., Grosskurth, S., Srivastava, G., Kim, S., Nho, K., Nudelman, K. N. H., Faber, K., Sun, Y., Foroud, T. M., Estrada, K., Apostolova, L. G., Li, Q. S., Saykin, A. J., & (ADNI), F. T. A. D. N. I.
Affiliations
  • AbbVie (United States) (US)
  • State University of New York at Oswego (US)
  • Indiana University School of Medicine (US)
  • Janssen (United States) (US)
  • Biogen (United States) (US)
Corresponding author
Vasanthakumar, Aparna
Venue
Clinical Epigenetics
Published
2020-06-15
Volume
12
Issue
1
Pages
84-84
ISSN
  • 1868-7075 (ISSN-L)
  • 1868-7083
OpenAlex
W3035710795
Cited by
98
References
53
Citations by year
2026: 13 · 2025: 14 · 2024: 21 · 2023: 15 · 2022: 17 · 2021: 12 · 2020: 6
FWCI
9.30
Type
journal article
Language
en
Open access
Locations
  • Clinical Epigenetics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • IUScholarWorks (Indiana University) (submittedVersion, cc-by)
Funders
  • National Institutes of Health (U01 AG024904)
  • U.S. Department of Defense (W81XWH-12-2-0012)
Topics
  • Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
Keywords
Alzheimer's disease, differentially methylated positions, blood-based biomarkers, mild cognitive impairment, early diagnosis, Mini-Mental State Examination, brain-derived neurotrophic factor, BIN1, APOC1, neurodegeneration, disease progression, epigenetic biomarkers
MeSH terms
Mental Status and Dementia Tests, Aged, Aged, 80 and over, Alzheimer Disease, Diagnosis, Differential, Female, Genotype, Humans, Longitudinal Studies, Male, Phenotype, Biomarkers, Case-Control Studies, Disease Progression, DNA Methylation, Early Diagnosis, Epigenomics, Transcriptome, Neuroimaging, Cognitive Dysfunction

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