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Cell-specific characterization of the placental methylome
BACKGROUND: DNA methylation (DNAm) profiling has emerged as a powerful tool for characterizing the placental methylome. However, previous studies have focused primarily on whole placental tissue, which is a mixture of epigenetically distinct cell populations. Here, we present the first methylome-wid...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7788826/ https://www.ncbi.nlm.nih.gov/pubmed/33407091 http://dx.doi.org/10.1186/s12864-020-07186-6 |
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author | Yuan, Victor Hui, Desmond Yin, Yifan Peñaherrera, Maria S. Beristain, Alexander G. Robinson, Wendy P. |
author_facet | Yuan, Victor Hui, Desmond Yin, Yifan Peñaherrera, Maria S. Beristain, Alexander G. Robinson, Wendy P. |
author_sort | Yuan, Victor |
collection | PubMed |
description | BACKGROUND: DNA methylation (DNAm) profiling has emerged as a powerful tool for characterizing the placental methylome. However, previous studies have focused primarily on whole placental tissue, which is a mixture of epigenetically distinct cell populations. Here, we present the first methylome-wide analysis of first trimester (n = 9) and term (n = 19) human placental samples of four cell populations: trophoblasts, Hofbauer cells, endothelial cells, and stromal cells, using the Illumina EPIC methylation array, which quantifies DNAm at > 850,000 CpGs. RESULTS: The most distinct DNAm profiles were those of placental trophoblasts, which are central to many pregnancy-essential functions, and Hofbauer cells, which are a rare fetal-derived macrophage population. Cell-specific DNAm occurs at functionally-relevant genes, including genes associated with placental development and preeclampsia. Known placental-specific methylation marks, such as those associated with genomic imprinting, repetitive element hypomethylation, and placental partially methylated domains, were found to be more pronounced in trophoblasts and often absent in Hofbauer cells. Lastly, we characterize the cell composition and cell-specific DNAm dynamics across gestation. CONCLUSIONS: Our results provide a comprehensive analysis of DNAm in human placental cell types from first trimester and term pregnancies. This data will serve as a useful DNAm reference for future placental studies, and we provide access to this data via download from GEO (GSE159526), through interactive exploration from the web browser (https://robinsonlab.shinyapps.io/Placental_Methylome_Browser/), and through the R package planet, which allows estimation of cell composition directly from placental DNAm data. SUPPLEMENTARY INFORMATION: Supplementary information accompanies this paper at 10.1186/s12864-020-07186-6. |
format | Online Article Text |
id | pubmed-7788826 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-77888262021-01-07 Cell-specific characterization of the placental methylome Yuan, Victor Hui, Desmond Yin, Yifan Peñaherrera, Maria S. Beristain, Alexander G. Robinson, Wendy P. BMC Genomics Research Article BACKGROUND: DNA methylation (DNAm) profiling has emerged as a powerful tool for characterizing the placental methylome. However, previous studies have focused primarily on whole placental tissue, which is a mixture of epigenetically distinct cell populations. Here, we present the first methylome-wide analysis of first trimester (n = 9) and term (n = 19) human placental samples of four cell populations: trophoblasts, Hofbauer cells, endothelial cells, and stromal cells, using the Illumina EPIC methylation array, which quantifies DNAm at > 850,000 CpGs. RESULTS: The most distinct DNAm profiles were those of placental trophoblasts, which are central to many pregnancy-essential functions, and Hofbauer cells, which are a rare fetal-derived macrophage population. Cell-specific DNAm occurs at functionally-relevant genes, including genes associated with placental development and preeclampsia. Known placental-specific methylation marks, such as those associated with genomic imprinting, repetitive element hypomethylation, and placental partially methylated domains, were found to be more pronounced in trophoblasts and often absent in Hofbauer cells. Lastly, we characterize the cell composition and cell-specific DNAm dynamics across gestation. CONCLUSIONS: Our results provide a comprehensive analysis of DNAm in human placental cell types from first trimester and term pregnancies. This data will serve as a useful DNAm reference for future placental studies, and we provide access to this data via download from GEO (GSE159526), through interactive exploration from the web browser (https://robinsonlab.shinyapps.io/Placental_Methylome_Browser/), and through the R package planet, which allows estimation of cell composition directly from placental DNAm data. SUPPLEMENTARY INFORMATION: Supplementary information accompanies this paper at 10.1186/s12864-020-07186-6. BioMed Central 2021-01-06 /pmc/articles/PMC7788826/ /pubmed/33407091 http://dx.doi.org/10.1186/s12864-020-07186-6 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Article Yuan, Victor Hui, Desmond Yin, Yifan Peñaherrera, Maria S. Beristain, Alexander G. Robinson, Wendy P. Cell-specific characterization of the placental methylome |
title | Cell-specific characterization of the placental methylome |
title_full | Cell-specific characterization of the placental methylome |
title_fullStr | Cell-specific characterization of the placental methylome |
title_full_unstemmed | Cell-specific characterization of the placental methylome |
title_short | Cell-specific characterization of the placental methylome |
title_sort | cell-specific characterization of the placental methylome |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7788826/ https://www.ncbi.nlm.nih.gov/pubmed/33407091 http://dx.doi.org/10.1186/s12864-020-07186-6 |
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