Elevated DNA methylation across a 48‐kb region spanning the HOXA gene cluster is associated with Alzheimer's disease neuropathology
Open accessAbstract
Introduction: Alzheimer's disease is a neurodegenerative disorder that is hypothesized to involve epigenetic dysregulation of gene expression in the brain. Methods: We performed an epigenome‐wide association study to identify differential DNA methylation associated with neuropathology in prefrontal cortex and superior temporal gyrus samples from 147 individuals, replicating our findings in two independent data sets (N = 117 and 740). Results: We identify elevated DNA methylation associated with neuropathology across a 48‐kb region spanning 208 CpG sites within the HOXA gene cluster. A meta‐analysis of the top‐ranked probe within the HOXA3 gene (cg22962123) highlighted significant hypermethylation across all three cohorts (P = 3.11 × 10−18). Discussion: We present robust evidence for elevated DNA methylation associated with Alzheimer's disease neuropathology spanning the HOXA gene cluster on chromosome 7. These data add to the growing evidence highlighting a role for epigenetic variation in Alzheimer's disease, implicating the HOX gene family as a target for future investigation.
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Alterations in DNA methylation levels are involved in many diseases, including AD.
“Alterations of DNA methylation levels have been shown to be involved in many diseases, including AD [19–24].”
From Distinct sex-specific DNA methylation differences in Alzheimer’s disease (2022) · cites this paper as [23]
The Introduction and Discussion (page numbers unavailable) report altered DNA methylation associated with AD neuropathology. The paper also mentions differential methylation in Down syndrome, but it does not establish the broader claim that methylation alterations are involved in many diseases; its AD finding is an association, not proof of causation. (LLM, conf=0.83)
Experimental — accuracy not yet measuredDNA methylation is an important epigenetic modification that regulates gene transcription and is involved in Alzheimer's disease.
“DNA methylation is an important epigenetic modification that regulates gene transcription and is known to be involved in AD”
From Sex-specific DNA methylation differences in Alzheimer’s disease pathology (2021) · cites this paper as [20]
The Introduction and Discussion report that altered DNA methylation is associated with AD neuropathology, supporting the AD-related part of the claim. The paper does not establish that DNA methylation regulates gene transcription; the Discussion says gene-expression analyses are still needed to interpret the methylation differences observed in HOXA. (LLM, conf=0.84)
Experimental — accuracy not yet measuredAlterations of DNA methylation levels have been implicated in multiple neurological disorders including AD.
“Importantly, alterations of DNA methylation levels have also been implicated in multiple neurological disorders including AD [18–22]”
From Sex-specific DNA methylation differences in Alzheimer’s disease pathology (2021) · cites this paper as [20]
The Introduction and Discussion report altered DNA methylation associated with AD neuropathology, supporting the AD portion of the claim. The paper mentions differential methylation in Down syndrome, but does not establish DNA methylation alterations across multiple neurological disorders as the sentence states. (LLM, conf=0.85)
Experimental — accuracy not yet measuredNone of the 14 CpGs detected in our interaction analysis was identified in previous large-scale DNA methylation studies.
“Notably, none of the 14 CpGs detected in our interaction analysis was identified in previous large-scale DNA methylation studies [18–22]”
From Sex-specific DNA methylation differences in Alzheimer’s disease pathology (2021) · cites this paper as [20]
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Feature Selection of OMIC Data by Ensemble Swarm Intelligence Based Approaches
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The contribution of DNA methylation to the (dys)function of oligodendroglia in neurodegeneration
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- Authors
- Smith, R. G., Hannon, E., De Jager, P. L., Chibnik, L., Lott, S. J., Condliffe, D., Smith, A. R., Haroutunian, V., Troakes, C., Al‐Sarraj, S., Bennett, D. A., Powell, J., Lovestone, S., Schalkwyk, L., Mill, J., & Lunnon, K.
- Affiliations
- University of Exeter (GB)
- Program in Translational NeuroPsychiatric Genomics Departments of Neurology and Psychiatry Institute for the Neurosciences Brigham and Women's Hospital Boston MA USA
- Brigham and Women's Hospital (US)
- King's College London (GB)
- Queen Mary University of London (GB)
- James J. Peters VA Medical Center (US)
- Rush University Medical Center (US)
- Warneford Hospital (GB)
- University of Essex (GB)
- Corresponding author
- Mill, Jonathan
- Lunnon, Katie
- ORCID
- Venue
- Alzheimer's & Dementia
- Publisher
- Wiley
- Published
- 2018-03-14
- Volume
- 14
- Issue
- 12
- Pages
- 1580-1588
- ISSN
- 1552-5260 (ISSN-L)
- 1552-5279
- PMC
- PMC6438205
- OpenAlex
- W2789414284
- Cited by
- 184
- References
- 26
- Citations by year
- 2026: 13 · 2025: 20 · 2024: 22 · 2023: 28 · 2022: 26 · 2021: 27 · 2020: 26 · 2019: 15 · 2018: 7
- FWCI
- 7.56
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Alzheimer s & Dementia (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion, cc-by-nc-nd)
- Open Access at Essex (University of Essex) (acceptedVersion)
- Figshare (submittedVersion, cc-by-nc-nd)
- Research Portal (King's College London) (submittedVersion, other-oa)
- Open Research Exeter (University of Exeter) (submittedVersion, cc-by-nc-nd)
- Royal Devon and Exeter Research Repository (Royal Devon and Exeter) (submittedVersion)
- Funders
- National Institutes of Health (R01 AG036039, AG02219, AG05138, MH064673, R01 AG036042, R01AG036836, R01 AG17917, R01 AG15819, R01 AG032990, R01 AG18023, RC2 AG036547, P30 AG10161, P50 AG016574, U01 ES017155, KL2 RR024151, K25 AG041906‐01)
- Alzheimer's Society (AS‐PG‐14‐038)
- Alzheimer's Association (NIRG‐14‐320878)
- BRACE
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
- Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
- Keywords
- Alzheimer's disease, DNA methylation
- MeSH terms
- Alzheimer Disease, Multigene Family, Temporal Lobe, Prefrontal Cortex, Homeodomain Proteins, CpG Islands, DNA Methylation, Genetic Predisposition to Disease, Epigenesis, Genetic, Genome-Wide Association Study
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