DNA methylation profiles unique to Kalahari KhoeSan individuals

ABSTRACT

Genomes of KhoeSan individuals of the Kalahari Desert provide the greatest understanding of single nucleotide diversity in the human genome. Compared with individuals in industrialized environments, the KhoeSan have a unique foraging and hunting lifestyle. Given these dramatic environmental differences, and the responsiveness of the methylome to environmental exposures of many types, we hypothesized that DNA methylation patterns would differ between KhoeSan and neighbouring agropastoral and/or industrial Bantu. We analysed Illumina HumanMethylation 450 k array data generated from blood samples from 38 KhoeSan and 42 Bantu, and 6 Europeans. After removing CpG positions associated with annotated and novel polymorphisms and controlling for white blood cell composition, sex, age and technical variation we identified 816 differentially methylated CpG loci, out of which 133 had an absolute beta-value difference of at least 0.05. Notably SLC39A4/ZIP4, which plays a role in zinc transport, was one of the most differentially methylated loci. Although the chronological ages of the KhoeSan are not formally recorded, we compared historically estimated ages to methylation-based calculations. This study demonstrates that the epigenetic profile of KhoeSan individuals reveals differences from other populations, and along with extensive genetic diversity, this community brings increased accessibility and understanding to the diversity of the human genome.

KEYWORDS:

• Methylation
• epigenome
• Illumina methylation array
• methylation probes
• single nucleotide variants
• Khoesan

Acknowledgements

The authors would like to thank all the study participants and every day local Namibians and South Africans, who over the last decade have made this study possible. Specifically, we acknowledge the late Professor Chris F. Heyns (1949–2014) from the University of Stellenbosch and retired Professor Philip Venter from the University of Limpopo, South Africa, and more recently Dr. Hagen E.A. Förtsch from Windhoek Central Hospital, Namibia, for technical and administrative assistance with recruitments. We thank Kristin Harper and Mia DeFino for constructive and technical input and providing medical writing and editing support. Marypat Jones and Ursula Harper ran the Illumina arrays at the National Human Genome Research Genomics Core.

Authors’ contributions

V.M.H and M.S.R.B collected and prepared DNA for the Southern African sample source, providing critical insights into lifestyle relevant data. V.M.H and W.J. generated and provided the Southern African genome validation data (manuscript in preparation); L.E. and V.M.H conceived of the study; B.L. implemented code for the U-test based analysis and wrote the first draft, S.T. contributed computational and statistical data analyses; A.G. implemented linear regression-based differential methylation analysis, leukocyte composition and batch effect normalization, and revised the manuscript; L.E. supervised and led the analysis; H.P. managed the Illumina array samples. All authors participated in writing or revising the draft.

Disclosure statement

No potential conflict of interest was reported by the authors.

Declarations

Ethics approval

granted through the Ministry of Health and Social Services in Namibia, with additional approvals from local community leaders, as well as approvals granted by independent academic and national Human Research Ethics Committee’s (HRECs) in South Africa.

Consent for publication

No personal data are included. All samples were deidentified.

Consent to participate

All subjects were consented and deidentified. No personal data are included.

Availability of data and materials

Data from KhoeSan sample data will not be publicly released because of sensitivity to KhoeSan data control requests. KhoeSan sequence or methylation data are available upon request to V.M.H.

Supplementary material

Supplemental data for this article can be accessed here.

Additional information

Funding

Intramural Program of the National Human Genome Research Institute to L.E. This work was also supported by an Australian Research Council Discovery Project grant awarded to V.M.H. (DP170103071) and sampling contributed by the Cancer Association of South Africa to M.S.R.B. and V.M.H. V.M.H. is supported by the University of Sydney Foundation in a Petre Foundation chair position.