Cited by 196Epigenetics and DNA MethylationDementia and Cognitive Impairment ResearchAlzheimer's disease research and treatments

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Elevated DNA methylation across a 48‐kb region spanning the HOXA gene cluster is associated with Alzheimer's disease neuropathology

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Smith, Rebecca G., Hannon, Eilis, De Jager, Philip L., Chibnik, Lori, Lott, Simon J., Condliffe, Daniel, Smith, Adam R., Haroutunian, Vahram, Troakes, Claire, Al‐Sarraj, Safa, Bennett, David A., Powell, John, Lovestone, Simon, Schalkwyk, Leonard, Mill, Jonathan, Lunnon, Katie·2018·Alzheimer's & Dementia

DOI 10.1016/j.jalz.2018.01.017PMC PMC6438205

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Abstract

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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Additional file 6 of Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer’s disease and implicate its dynamic role in disease progression
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Additional file 3 of Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer’s disease and implicate its dynamic role in disease progression
Wang, Q., Chen, Y., Readhead, B. P., Chen, K., Su, Y., Reiman, E. M., & Dudley, J. T. (2020) · Figshare · doi:10.6084/m9.figshare.13357532
Additional file 7 of Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer’s disease and implicate its dynamic role in disease progression
Wang, Q., Chen, Y., Readhead, B. P., Chen, K., Su, Y., Reiman, E. M., & Dudley, J. T. (2020) · Figshare · doi:10.6084/m9.figshare.13357544
Additional file 2 of Epigenome-wide association study of Alzheimer’s disease replicates 22 differentially methylated positions and 30 differentially methylated regions
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Additional file 1 of Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer’s disease and implicate its dynamic role in disease progression
Wang, Q., Chen, Y., Readhead, B. P., Chen, K., Su, Y., Reiman, E. M., & Dudley, J. T. (2020) · Figshare · doi:10.6084/m9.figshare.13357526
Additional file 5 of Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer’s disease and implicate its dynamic role in disease progression
Wang, Q., Chen, Y., Readhead, B. P., Chen, K., Su, Y., Reiman, E. M., & Dudley, J. T. (2020) · Figshare · doi:10.6084/m9.figshare.13357538
Additional file 4 of Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer’s disease and implicate its dynamic role in disease progression
Wang, Q., Chen, Y., Readhead, B. P., Chen, K., Su, Y., Reiman, E. M., & Dudley, J. T. (2020) · Figshare · doi:10.6084/m9.figshare.13357535
Additional file 2 of Distinct sex-specific DNA methylation differences in Alzheimer’s disease
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Additional file 2 of Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer’s disease and implicate its dynamic role in disease progression
Wang, Q., Chen, Y., Readhead, B. P., Chen, K., Su, Y., Reiman, E. M., & Dudley, J. T. (2020) · Figshare · doi:10.6084/m9.figshare.13357529
Additional file 8 of Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer’s disease and implicate its dynamic role in disease progression
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Additional file 2 of Sex-specific DNA methylation differences in Alzheimer’s disease pathology
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Additional file 3 of Epigenetic modulation of AREL1 and increased HLA expression in brains of multiple system atrophy patients
Rydbirk, R., Folke, J., Busato, F., Roché, E., Chauhan, A. S., Løkkegaard, A., Hejl, A.-M., Bode, M., Blaabjerg, M., Møller, M. L., et al. (2020) · Figshare · doi:10.6084/m9.figshare.11960322
Additional file 1 of Sex-specific DNA methylation differences in Alzheimer’s disease pathology
Zhang, L., Young, J. I., Gomez, L., Silva, T. C., Schmidt, M. A., Cai, J., Chen, X., Martin, E. R., & Wang, L. (2021) · Figshare · doi:10.6084/m9.figshare.14490461
Additional file 2 of Quantifying the proportion of different cell types in the human cortex using DNA methylation profiles
Hannon, E. J., Dempster, E. L., Davies, J. P., Chioza, B. A., Blake, G. E. T., Burrage, J., Policicchio, S. S. S., Franklin, A., Walker, E., Bamford, R. A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26672745
Self-citation
Additional file 1 of Distinct sex-specific DNA methylation differences in Alzheimer’s disease
C. Silva, T., Zhang, W., Young, J. I., Gomez, L., Schmidt, M. A., Varma, A., Chen, X. S., Martin, E. R., & Wang, L. (2022) · Figshare · doi:10.6084/m9.figshare.21129953
Additional file 1 of Association of peripheral blood DNA methylation level with Alzheimer’s disease progression
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Additional file 1 of DNA methylation analysis on purified neurons and glia dissects age and Alzheimer’s disease-specific changes in the human cortex
Gasparoni, G., Bultmann, S., Lutsik, P., Kraus, T. F. J., Sordon, S., Vlcek, J., Dietinger, V., Steinmaurer, M., Haider, M., Mulholland, C. B., et al. (2018) · Figshare · doi:10.6084/m9.figshare.6864296
Additional file 9 of Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer’s disease and implicate its dynamic role in disease progression
Wang, Q., Chen, Y., Readhead, B., Chen, K., Su, Y., Reiman, E. M., & Dudley, J. T. (2020) · Figshare · doi:10.6084/m9.figshare.13357550
Additional file 1 of LncRNA HOXA-AS2 regulates microglial polarization via recruitment of PRC2 and epigenetic modification of PGC-1α expression
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Additional file 2 of Epigenetic modulation of AREL1 and increased HLA expression in brains of multiple system atrophy patients
Rydbirk, R., Folke, J., Busato, F., Roché, E., Chauhan, A. S., Løkkegaard, A., Hejl, A.-M., Bode, M., Blaabjerg, M., Møller, M. L., et al. (2020) · Figshare · doi:10.6084/m9.figshare.11960316
Additional file 1 of Epigenome-wide association study of Alzheimer’s disease replicates 22 differentially methylated positions and 30 differentially methylated regions
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Additional file 1 of Entorhinal cortex epigenome-wide association study highlights four novel loci showing differential methylation in Alzheimer’s disease
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Additional file 1 of Quantifying the proportion of different cell types in the human cortex using DNA methylation profiles
Hannon, E. J., Dempster, E. L., Davies, J. P., Chioza, B. A., Blake, G. E. T., Burrage, J., Policicchio, S. S. S., Franklin, A., Walker, E., Bamford, R. A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26672742
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Miao, G., Gao, C., Yu, L., Yang, J., Li, Y., Grodstein, F., Schneider, J. A., Barnes Lisa, L., Jager, P. L. D., Yao, B., et al. (2026) · Nature Aging · doi:10.1038/s43587-026-01243-7
Self-citation

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: Smith, Rebecca G.
Hannon, Eilis
Chibnik, Lori
Smith, Adam R.
Haroutunian, Vahram
Troakes, Claire
Al‐Sarraj, Safa
Bennett, David A.
Powell, John
Lovestone, Simon
Schalkwyk, Leonard
Mill, Jonathan
Lunnon, Katie
Venue: Alzheimer's & Dementia
Publisher: Wiley
Published: 2018-03-14
Volume: 14
Issue: 12
Pages: 1580-1588
ISSN: 1552-5260 (ISSN-L)
1552-5279
DOI: 10.1016/j.jalz.2018.01.017
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: cc-by-nc-nd
onlinelibrary.wiley.com/termsAndConditions#vor (vor)
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
Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › 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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Elevated DNA methylation across a 48‐kb region spanning the HOXA gene cluster is associated with Alzheimer's disease neuropathology

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