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Associations between epigenome-wide DNA methylation and height-related traits among Sub-Saharan Africans: the RODAM study

Published online by Cambridge University Press:  04 December 2023

Galatea Swart*
Affiliation:
Department of Human Genetics, Department of Human Genetics, Genome Diagnostic Laboratory, Amsterdam Reproduction and Development, Research Institute, Amsterdam University Medical Centers, Amsterdam, The Netherlands
Karlijn Meeks
Affiliation:
Department of Public and Occupational Health, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institute of Health, Bethesda, MD, USA Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, The John Hopkins University School of Medicine, Baltimore, MD, USA
Felix Chilunga
Affiliation:
Department of Public and Occupational Health, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
Andrea Venema
Affiliation:
Department of Human Genetics, Department of Human Genetics, Genome Diagnostic Laboratory, Amsterdam Reproduction and Development, Research Institute, Amsterdam University Medical Centers, Amsterdam, The Netherlands
Charles Agyemang
Affiliation:
Department of Public and Occupational Health, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, The John Hopkins University School of Medicine, Baltimore, MD, USA
Eva van der Linden
Affiliation:
Department of Public and Occupational Health, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands Department of Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
Peter Henneman
Affiliation:
Department of Human Genetics, Department of Human Genetics, Genome Diagnostic Laboratory, Amsterdam Reproduction and Development, Research Institute, Amsterdam University Medical Centers, Amsterdam, The Netherlands
*
Corresponding author: G. Swart; Email: galateaswart@gmail.com
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Abstract

Human height and related traits are highly complex, and extensively research has shown that these traits are determined by both genetic and environmental factors. Such factors may partially affect these traits through epigenetic programing. Epigenetic programing is dynamic and plays an important role in controlling gene expression and cell differentiation during (early) development. DNA methylation (DNAm) is the most commonly studied epigenetic feature. In this study we conducted an epigenome-wide DNAm association analysis on height-related traits in a Sub-Saharan African population, in order to detect DNAm biomarkers across four height-related traits. DNAm profiles were acquired in whole blood samples of 704 Ghanaians, sourced from the Research on Obesity and Diabetes among African Migrants study, using the Illumina Infinium HumanMethylation450 BeadChip. Linear models were fitted to detect differentially methylated positions (DMPs) and regions (DMRs) associated with height, leg-to-height ratio (LHR), leg length, and sitting height. No epigenome-wide significant DMPs were recorded. However we did observe among our top DMPs five informative probes associated with the height-related traits: cg26905768 (leg length), cg13268132 (leg length), cg19776793 (height), cg23072383 (LHR), and cg24625894 (sitting height). All five DMPs are annotated to genes whose functions were linked to bone cell regulation and development. DMR analysis identified overlapping DMRs within the gene body of HLA-DPB1 gene, and the HOXA gene cluster. In this first epigenome-wide association studies of these traits, our findings suggest DNAm associations with height-related heights, and might influence development and maintenance of these traits. Further studies are needed to replicate our findings, and to elucidate the molecular mechanism underlying human height-related traits.

Information

Type
Original Article
Creative Commons
Creative Common License - CCCreative Common License - BY
This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited.
Copyright
© The Author(s), 2023. Published by Cambridge University Press in association with The International Society for Developmental Origins of Health and Disease (DOHaD)
Figure 0

Figure 1. Conceptual framework diagram. The diagram demonstrates this study’s exploration of DNA methylation profiles associated with height-related traits due to these traits being influenced by both genetics and environmental factors.

Figure 1

Figure 2. QQ plots visualizing the fit of the linear regression models used in DMP analysis for height (A), LHR (B), leg length (C), and sitting height (D).

Figure 2

Table 1. Characteristics of RODAM study including participants demographic information, lifestyle factors, height-related traits, and distribution of the cell types observed

Figure 3

Table 2. Differentially methylated regions (DMRs) for height, sitting height, and leg length identified using two methods (DMRcate and bumphunter). DMRs with FWER > 0.2 or Stouffer coefficient > 0.05

Figure 4

Figure 3. Manhattan plot of epigenome-wide p-values for height (A), LHR (B), leg length (C), and sitting height (D).

Figure 5

Figure 4. Comet plot of the differentially methylated region identified HLA-DPB1 gene based on the sitting height trait results. Plot show a differentially methylated region in chromosome 6, 33.646943 and 33.051125 megabases (mb) obtained via DMRcate. The red box highlights the probes annotated to the DMR. Correlations are measured using the spearman rambling coefficient.

Figure 6

Figure 5. Comet plot of the differentially methylated region identified HOXA cluster gene based on the sitting height trait results. Plot show a differentially methylated region in chromosome 7, 27.167207 and 27.173529 megabases (mb) obtained via DMRcate. The red box highlights the probes annotated to the DMR. Correlations are measured using the spearman rambling coefficient.

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