DNA methylation profiling in mummified human remains from the eighteenth-century

Abstract Reconstruction of ancient epigenomes by DNA methylation (DNAm) can shed light into the composition of cell types, disease states, and age at death. However, such analysis is hampered by impaired DNA quality and little is known how decomposition affects DNAm. In this study, we determined if...

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Main Authors:	Marco Schmidt, Frank Maixner, Gerhard Hotz, Ildikó Pap, Ildikó Szikossy, György Pálfi, Albert Zink, Wolfgang Wagner
Format:	Article
Language:	English
Published:	Nature Publishing Group 2021-07-01
Series:	Scientific Reports
Online Access:	https://doi.org/10.1038/s41598-021-95021-7

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spelling	doaj-bee5fab012094b68a2b309edebaed1302021-08-01T11:24:32ZengNature Publishing GroupScientific Reports2045-23222021-07-011111710.1038/s41598-021-95021-7DNA methylation profiling in mummified human remains from the eighteenth-centuryMarco Schmidt0Frank Maixner1Gerhard Hotz2Ildikó Pap3Ildikó Szikossy4György Pálfi5Albert Zink6Wolfgang Wagner7Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical SchoolInstitute for Mummy Studies, Eurac ResearchAnthropological Collection, Natural History Museum of BaselDepartment of Biological Anthropology, Faculty of Science and Informatics, University of SzegedDepartment of Biological Anthropology, Faculty of Science and Informatics, University of SzegedDepartment of Biological Anthropology, Faculty of Science and Informatics, University of SzegedInstitute for Mummy Studies, Eurac ResearchHelmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical SchoolAbstract Reconstruction of ancient epigenomes by DNA methylation (DNAm) can shed light into the composition of cell types, disease states, and age at death. However, such analysis is hampered by impaired DNA quality and little is known how decomposition affects DNAm. In this study, we determined if EPIC Illumina BeadChip technology is applicable for specimens from mummies of the eighteenth century CE. Overall, the signal intensity on the microarray was extremely low, but for one of two samples we were able to detect characteristic DNAm signals in a subset of CG dinucleotides (CpGs), which were selected with a stringent processing pipeline. Using only these CpGs we could train epigenetic signatures with reference DNAm profiles of multiple tissues and our predictions matched the fact that the specimen was lung tissue from a 28-year-old woman. Thus, we provide proof of principle that Illumina BeadChips are applicable for DNAm profiling in ancient samples.https://doi.org/10.1038/s41598-021-95021-7
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Marco Schmidt Frank Maixner Gerhard Hotz Ildikó Pap Ildikó Szikossy György Pálfi Albert Zink Wolfgang Wagner
spellingShingle	Marco Schmidt Frank Maixner Gerhard Hotz Ildikó Pap Ildikó Szikossy György Pálfi Albert Zink Wolfgang Wagner DNA methylation profiling in mummified human remains from the eighteenth-century Scientific Reports
author_facet	Marco Schmidt Frank Maixner Gerhard Hotz Ildikó Pap Ildikó Szikossy György Pálfi Albert Zink Wolfgang Wagner
author_sort	Marco Schmidt
title	DNA methylation profiling in mummified human remains from the eighteenth-century
title_short	DNA methylation profiling in mummified human remains from the eighteenth-century
title_full	DNA methylation profiling in mummified human remains from the eighteenth-century
title_fullStr	DNA methylation profiling in mummified human remains from the eighteenth-century
title_full_unstemmed	DNA methylation profiling in mummified human remains from the eighteenth-century
title_sort	dna methylation profiling in mummified human remains from the eighteenth-century
publisher	Nature Publishing Group
series	Scientific Reports
issn	2045-2322
publishDate	2021-07-01
description	Abstract Reconstruction of ancient epigenomes by DNA methylation (DNAm) can shed light into the composition of cell types, disease states, and age at death. However, such analysis is hampered by impaired DNA quality and little is known how decomposition affects DNAm. In this study, we determined if EPIC Illumina BeadChip technology is applicable for specimens from mummies of the eighteenth century CE. Overall, the signal intensity on the microarray was extremely low, but for one of two samples we were able to detect characteristic DNAm signals in a subset of CG dinucleotides (CpGs), which were selected with a stringent processing pipeline. Using only these CpGs we could train epigenetic signatures with reference DNAm profiles of multiple tissues and our predictions matched the fact that the specimen was lung tissue from a 28-year-old woman. Thus, we provide proof of principle that Illumina BeadChips are applicable for DNAm profiling in ancient samples.
url	https://doi.org/10.1038/s41598-021-95021-7
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DNA methylation profiling in mummified human remains from the eighteenth-century

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