Cited by 160Epigenetics and DNA MethylationGenetic Associations and EpidemiologyGenomics and Chromatin Dynamics

Buccals are likely to be a more informative surrogate tissue than blood for epigenome-wide association studies

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Lowe, Robert, Gemma, Carolina, Beyan, Huriya, Hawa, Mohammed I., Bazeos, Alexandra, Leslie, R. David, Montpetit, Alexandre, Rakyan, Vardhman K. +1 more·2013·Epigenetics

Abstract

There is increasing evidence that interindividual epigenetic variation is an etiological factor in common human diseases. Such epigenetic variation could be genetic or non-genetic in origin, and epigenome-wide association studies (EWASs) are underway for a wide variety of diseases/phenotypes. However, performing an EWAS is associated with a range of issues not typically encountered in genome-wide association studies (GWASs), such as the tissue to be analyzed. In many EWASs, it is not possible to analyze the target tissue in large numbers of live humans, and consequently surrogate tissues are employed, most commonly blood. But there is as yet no evidence demonstrating that blood is more informative than buccal cells, the other easily accessible tissue. To assess the potential of buccal cells for use in EWASs, we performed a comprehensive analysis of a buccal cell methylome using whole-genome bisulfite sequencing. Strikingly, a buccal vs. blood comparison reveals>6X as many hypomethylated regions in buccal. These tissue-specific differentially methylated regions (tDMRs) are strongly enriched for DNaseI hotspots. Almost 75% of these tDMRs are not captured by commonly used DNA methylome profiling platforms such as Reduced Representational Bisulfite Sequencing and the Illumina Infinium HumanMethylation450 BeadChip, and they also display distinct genomic properties. Buccal hypo-tDMRs show a statistically significant enrichment near SNPs associated to disease identified through GWASs. Finally, we find that, compared with blood, buccal hypo-tDMRs show significantly greater overlap with hypomethylated regions in other tissues. We propose that for non-blood based diseases/phenotypes, buccal will be a more informative tissue for EWASs.

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  • DNA methylation patterns in saliva may be closer to that of brain tissue than DNA methylation in blood or buccal cells.

    “it has been suggested that DNA methylation patterns in saliva may be closer to that of brain tissue than DNA methylation in blood or buccal cells (Braun et al., 2019;Lowe et al., 2013;Smith et al., 2015).”

    From The applied implications of epigenetics in anxiety, affective and stress-related disorders - A review and synthesis on psychosocial stress, psychotherapy and prevention (2020) · cites this paper as Lowe et al., 2013

    In “Generation of a human buccal cell DNA methylome” (page not available), the paper reports that buccal methylation profiles are closer than blood profiles to other non-blood tissues, including brain. It explicitly says it profiled brushed buccal cells, not saliva, and provides no comparison showing saliva is closer to brain than either blood or buccal cells. (LLM, conf=0.84)

    Experimental — accuracy not yet measured
  • Overlap in DNA methylation levels measured in saliva, buccal cells and blood is limited.

    “overlap in DNA methylation levels measured in saliva, buccal cells and blood is limited”

    From The applied implications of epigenetics in anxiety, affective and stress-related disorders - A review and synthesis on psychosocial stress, psychotherapy and prevention (2020) · cites this paper as Lowe et al., 2013

    The 'Generation of a human buccal cell DNA methylome' section reports substantial methylation differences between buccal cells and blood. It explicitly says the researchers profiled brushed buccal cells, not saliva, so it does not establish limited overlap across all three sample types. Page numbers are unavailable in our copy. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

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Authors
Lowe, R., Gemma, C., Beyan, H., Hawa, M. I., Bazeos, A., Leslie, R. D., Montpetit, A., Rakyan, V. K., & Ramagopalan, S. V.
Affiliations
  • Queen Mary University of London (GB)
  • McGill University and Génome Québec Innovation Centre (CA)
Corresponding author
  • Lowe, Robert
  • Rakyan, Vardhman K.
  • Ramagopalan, Sreeram V.
Venue
Epigenetics
Published
2013-04
Volume
8
Issue
4
Pages
445-454
ISSN
  • 1559-2294 (ISSN-L)
  • 1559-2308
OpenAlex
W2118382560
Cited by
160
References
40
Citations by year
2026: 9 · 2025: 7 · 2024: 5 · 2023: 7 · 2022: 10 · 2021: 12 · 2020: 19 · 2019: 13 · 2018: 18 · 2017: 17 · 2016: 17 · 2015: 13 · 2014: 10 · 2013: 1 · 2012: 1
FWCI
6.13
Type
journal article
Language
en
Open access
Locations
  • Epigenetics (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • Juvenile Diabetes Research Foundation International
  • Diabetes UK (10/0004107)
  • Multiple Sclerosis Society
  • European Foundation for the Study of Diabetes
  • Novo Nordisk
  • Medical Research Council (G0801976)
  • Biotechnology and Biological Sciences Research Council (BB/H012494/1)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
buccal epithelial cells, blood, DNA methylation, epigenome-wide association study, hypomethylated regions, surrogate tissue
MeSH terms
Adult, Aged, DNA, Humans, Middle Aged, Mouth Mucosa, Genome, Human, Sequence Analysis, DNA, DNA Methylation, Polymorphism, Single Nucleotide, Epigenesis, Genetic, Genome-Wide Association Study, Young Adult

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