Cell-specific characterization of the placental methylome.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33407091", "kind": "science-record", "revision": 6, "content_hash": "sha256:56c6111756e1e8319cd2f68361311b7feadd6e34ba36b35597807f8b930c8d2b", "created_at": "2026-11-01T15:41:21Z", "updated_at": "2026-11-01T21:24:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Cell-specific characterization of the placental methylome.", "doi": "10.1186/s12864-020-07186-6", "pmid": "33407091", "authors": ["Victor Yuan", "Desmond Hui", "Yifan Yin", "Maria S Peñaherrera", "Alexander G Beristain", "Wendy P Robinson"], "journal": "BMC genomics", "year": 2021, "abstract": "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.\nRESULTS: 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.\nCONCLUSIONS: 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.", "claims": [{"id": "claim-method", "statement": "RPC cellular deconvolution was applied to our 7 first trimester and 19 term CV samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33407091", "locator": "sections[8] \"Assessing cell composition in chorionic villi\" paragraph 5", "quote": "RPC cellular deconvolution was applied to our 7 first trimester and 19 term CV samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Cell DNAm data and supporting sample-specific information is available on GEO dataset accession number (GSE159526). Cell-specific reference CpGs for cellular deconvolution can be found in Table S5, and also online using the R package planet [60] (github.com/wvictor14/planet). Cell DNAm data can be explored interactively using the R shiny app Placental Methylome Browser [61] (https://robinsonlab.shinyapps.io/Placental_Methylome_Browser/). The hg19 and hg18 genomic coordinates were used from UCSC genome browser [62] (https://genome.ucsc.edu/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33407091", "locator": "sections[28] \"notes\" paragraph 1", "quote": "Cell DNAm data and supporting sample-specific information is available on GEO dataset accession number (GSE159526). Cell-specific reference CpGs for cellular deconvolution can be found in Table S5, and also online using the R package planet [60] (github.com/wvictor14/planet). Cell DNAm data can be explored interactively using the R shiny app Placental Methylome Browser [61] (https://robinsonlab.shinyapps.io/Placental_Methylome_Browser/). The hg19 and hg18 genomic coordinates were used from UCSC genome browser [62] (https://genome.ucsc.edu/)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:33407091"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE159526"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE159526"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33407091", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12864-020-07186-6", "sha256": "sha256:9692f88f9d321224f971fcb3f142279887a16926aab66371e29801366fd3daa3", "bytes": 73902, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12864-020-07186-6", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7788826", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE159526", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159526", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE159526", "version": null, "note": "Cell DNAm data and supporting sample-specific information is available on GEO dataset accession number (GSE159526). Cell-specific reference CpGs for cellular deconvolution can be found in Table S5, and also online using the R package planet [60] (github.com/wvictor14/planet). Cell DNAm data can be explored interactively using the R shiny app Placental Methylome Browser [61] (https://robinsonlab.shinyapps.io/Placental_Methylome_Browser/). The hg19 and hg18 genomic coordinates were used from UCSC genome browser [62] (https://genome.ucsc.edu/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Cell DNAm data and supporting sample-specific information is available on GEO dataset accession number (GSE159526). Cell-specific reference CpGs for cellular deconvolution can be found in Table S5, and also online using the R package planet [60] (github.com/wvictor14/planet). Cell DNAm data can be explored interactively using the R shiny app Placental Methylome Browser [61] (https://robinsonlab.shinyapps.io/Placental_Methylome_Browser/). 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Enrichment for preeclampsia-associated CpGs was statistically significant for each term cell-specific set of CpGs at a Bonferroni-adjusted p < 0.01", "structure": {"pmcid": "PMC7788826", "section_index": 4, "section_title": "Cell-specific DNAm occurs at highly functionally-relevant genes", "row_count": 5, "column_count": 5}, "table": {"label": "Table 2", "caption": "Number of preeclampsia-associated CpGs from Wilson et al. 2018 that are cell-specific DMCs for term samples. 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Standard deviation is shown in parentheses", "structure": {"pmcid": "PMC7788826", "section_index": 8, "section_title": "Assessing cell composition in chorionic villi", "row_count": 7, "column_count": 3}, "table": {"label": "Table 3", "caption": "Mean of cell composition estimates (%) for first trimester and term CV samples using RPC cellular deconvolution. 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