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Heterogeneity in White Blood Cells Has Potential to Confound DNA Methylation Measurements
Epigenetic studies are commonly conducted on DNA from tissue samples. However, tissues are ensembles of cells that may each have their own epigenetic profile, and therefore inter-individual cellular heterogeneity may compromise these studies. Here, we explore the potential for such confounding on DN...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465258/ https://www.ncbi.nlm.nih.gov/pubmed/23071618 http://dx.doi.org/10.1371/journal.pone.0046705 |
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author | Adalsteinsson, Bjorn T. Gudnason, Haukur Aspelund, Thor Harris, Tamara B. Launer, Lenore J. Eiriksdottir, Gudny Smith, Albert V. Gudnason, Vilmundur |
author_facet | Adalsteinsson, Bjorn T. Gudnason, Haukur Aspelund, Thor Harris, Tamara B. Launer, Lenore J. Eiriksdottir, Gudny Smith, Albert V. Gudnason, Vilmundur |
author_sort | Adalsteinsson, Bjorn T. |
collection | PubMed |
description | Epigenetic studies are commonly conducted on DNA from tissue samples. However, tissues are ensembles of cells that may each have their own epigenetic profile, and therefore inter-individual cellular heterogeneity may compromise these studies. Here, we explore the potential for such confounding on DNA methylation measurement outcomes when using DNA from whole blood. DNA methylation was measured using pyrosequencing-based methodology in whole blood (n = 50–179) and in two white blood cell fractions (n = 20), isolated using density gradient centrifugation, in four CGIs (CpG Islands) located in genes HHEX (10 CpG sites assayed), KCNJ11 (8 CpGs), KCNQ1 (4 CpGs) and PM20D1 (7 CpGs). Cellular heterogeneity (variation in proportional white blood cell counts of neutrophils, lymphocytes, monocytes, eosinophils and basophils, counted by an automated cell counter) explained up to 40% (p<0.0001) of the inter-individual variation in whole blood DNA methylation levels in the HHEX CGI, but not a significant proportion of the variation in the other three CGIs tested. DNA methylation levels in the two cell fractions, polymorphonuclear and mononuclear cells, differed significantly in the HHEX CGI; specifically the average absolute difference ranged between 3.4–15.7 percentage points per CpG site. In the other three CGIs tested, methylation levels in the two fractions did not differ significantly, and/or the difference was more moderate. In the examined CGIs, methylation levels were highly correlated between cell fractions. In summary, our analysis detects region-specific differential DNA methylation between white blood cell subtypes, which can confound the outcome of whole blood DNA methylation measurements. Finally, by demonstrating the high correlation between methylation levels in cell fractions, our results suggest a possibility to use a proportional number of a single white blood cell type to correct for this confounding effect in analyses. |
format | Online Article Text |
id | pubmed-3465258 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-34652582012-10-15 Heterogeneity in White Blood Cells Has Potential to Confound DNA Methylation Measurements Adalsteinsson, Bjorn T. Gudnason, Haukur Aspelund, Thor Harris, Tamara B. Launer, Lenore J. Eiriksdottir, Gudny Smith, Albert V. Gudnason, Vilmundur PLoS One Research Article Epigenetic studies are commonly conducted on DNA from tissue samples. However, tissues are ensembles of cells that may each have their own epigenetic profile, and therefore inter-individual cellular heterogeneity may compromise these studies. Here, we explore the potential for such confounding on DNA methylation measurement outcomes when using DNA from whole blood. DNA methylation was measured using pyrosequencing-based methodology in whole blood (n = 50–179) and in two white blood cell fractions (n = 20), isolated using density gradient centrifugation, in four CGIs (CpG Islands) located in genes HHEX (10 CpG sites assayed), KCNJ11 (8 CpGs), KCNQ1 (4 CpGs) and PM20D1 (7 CpGs). Cellular heterogeneity (variation in proportional white blood cell counts of neutrophils, lymphocytes, monocytes, eosinophils and basophils, counted by an automated cell counter) explained up to 40% (p<0.0001) of the inter-individual variation in whole blood DNA methylation levels in the HHEX CGI, but not a significant proportion of the variation in the other three CGIs tested. DNA methylation levels in the two cell fractions, polymorphonuclear and mononuclear cells, differed significantly in the HHEX CGI; specifically the average absolute difference ranged between 3.4–15.7 percentage points per CpG site. In the other three CGIs tested, methylation levels in the two fractions did not differ significantly, and/or the difference was more moderate. In the examined CGIs, methylation levels were highly correlated between cell fractions. In summary, our analysis detects region-specific differential DNA methylation between white blood cell subtypes, which can confound the outcome of whole blood DNA methylation measurements. Finally, by demonstrating the high correlation between methylation levels in cell fractions, our results suggest a possibility to use a proportional number of a single white blood cell type to correct for this confounding effect in analyses. Public Library of Science 2012-10-05 /pmc/articles/PMC3465258/ /pubmed/23071618 http://dx.doi.org/10.1371/journal.pone.0046705 Text en © 2012 Adalsteinsson et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Adalsteinsson, Bjorn T. Gudnason, Haukur Aspelund, Thor Harris, Tamara B. Launer, Lenore J. Eiriksdottir, Gudny Smith, Albert V. Gudnason, Vilmundur Heterogeneity in White Blood Cells Has Potential to Confound DNA Methylation Measurements |
title | Heterogeneity in White Blood Cells Has Potential to Confound DNA Methylation Measurements |
title_full | Heterogeneity in White Blood Cells Has Potential to Confound DNA Methylation Measurements |
title_fullStr | Heterogeneity in White Blood Cells Has Potential to Confound DNA Methylation Measurements |
title_full_unstemmed | Heterogeneity in White Blood Cells Has Potential to Confound DNA Methylation Measurements |
title_short | Heterogeneity in White Blood Cells Has Potential to Confound DNA Methylation Measurements |
title_sort | heterogeneity in white blood cells has potential to confound dna methylation measurements |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465258/ https://www.ncbi.nlm.nih.gov/pubmed/23071618 http://dx.doi.org/10.1371/journal.pone.0046705 |
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