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Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics - whole genome sequencing

ABSTRACT: To explore the interactions between the range of maternal and fetal placental cell types present, we profiled the transcriptomes of more than 50,000 single cells from matched first trimester samples of maternal blood and decidua, as well as fetal cells from the placenta itself. Demuxlet was used to discern between cells of fetal and maternal origin, from SNPs inferred from genotyping.

INSTRUMENT(S): HiSeq X Ten

ORGANISM(S): Homo sapiens

SUBMITTER: Mirjana Efremova

PROVIDER: E-MTAB-7304 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Single-cell reconstruction of the early maternal-fetal interface in humans.

Vento-Tormo Roser R Efremova Mirjana M Botting Rachel A RA Turco Margherita Y MY Vento-Tormo Miquel M Meyer Kerstin B KB Park Jong-Eun JE Stephenson Emily E Polański Krzysztof K Goncalves Angela A Gardner Lucy L Holmqvist Staffan S Henriksson Johan J Zou Angela A Sharkey Andrew M AM Millar Ben B Innes Barbara B Wood Laura L Wilbrey-Clark Anna A Payne Rebecca P RP Ivarsson Martin A MA Lisgo Steve S Filby Andrew A Rowitch David H DH Bulmer Judith N JN Wright Gavin J GJ Stubbington Michael J T MJT Haniffa Muzlifah M Moffett Ashley A Teichmann Sarah A SA

Nature 20181114 7731

During early human pregnancy the uterine mucosa transforms into the decidua, into which the fetal placenta implants and where placental trophoblast cells intermingle and communicate with maternal cells. Trophoblast-decidual interactions underlie common diseases of pregnancy, including pre-eclampsia and stillbirth. Here we profile the transcriptomes of about 70,000 single cells from first-trimester placentas with matched maternal blood and decidual cells. The cellular composition of human decidua ...[more]

PMID: 30429548

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Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics - 10x data

Project description:To explore the interactions between the range of maternal and fetal placental cell types present, we profiled the transcriptomes of more than 50,000 single cells from matched first trimester samples of maternal blood and decidua, as well as fetal cells from the placenta itself. RNA-seq was done using the standard 10x chromium v2 chemistry.

2018-10-02 | E-MTAB-6701 | biostudies-arrayexpress

Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics - Smartseq 2 data

Project description:To explore the interactions between the range of maternal and fetal placental cell types present, we profiled the transcriptomes of more than 50,000 single cells from matched first trimester samples of maternal blood and decidua, as well as fetal cells from the placenta itself. This part contains RNA-seq of Decidua cells using Smartseq 2

2019-08-21 | E-MTAB-6678 | biostudies-arrayexpress

scRNAseq/snucRNAseq of human implantation sites, placenta and decidua.

Project description:These samples are part of a study to provide a spatially resolved single-cell multiomics map of human trophoblast differentiation in early pregnancy. Here we profiled three human implantation sites (between 6 and 9 post-conceptional weeks, PCW) with snucRNAseq; five decidual and three placental samples from 8-13 PCW by scRNA-seq/snRNA-seq.

2023-02-09 | E-MTAB-12421 | biostudies-arrayexpress

Prospective surface marker-based isolation and expansion of fetal endothelial colony-forming cells from human term placenta.

Project description:The term placenta is a highly vascularized tissue and is usually discarded upon birth. Our objective was to isolate clinically relevant quantities of fetal endothelial colony-forming cells (ECFCs) from human term placenta and to compare them to the well-established donor-matched umbilical cord blood (UCB)-derived ECFCs. A sorting strategy was devised to enrich for CD45-CD34+CD31Lo cells prior to primary plating to obtain pure placental ECFCs (PL-ECFCs) upon culture. UCB-ECFCs were derived using a well-described assay. PL-ECFCs were fetal in origin and expressed the same cell surface markers as UCB-ECFCs. Most importantly, a single term placenta could yield as many ECFCs as 27 UCB donors. PL-ECFCs and UCB-ECFCs had similar in vitro and in vivo vessel forming capacities and restored mouse hind limb ischemia in similar proportions. Gene expression profiles were only minimally divergent between PL-ECFCs and UCB-ECFCs, probably reflecting a vascular source versus a circulating source. Finally, PL-ECFCs and UCB-ECFCs displayed similar hierarchies between high and low proliferative colonies. We report a robust strategy to isolate ECFCs from human term placentas based on their cell surface expression. This yielded much larger quantities of ECFCs than UCB, but the cells were comparable in immunophenotype, gene expression, and in vivo functional ability. We conclude that PL-ECFCs have significant bio-banking and clinical translatability potential. Data has been integrated into the Stemformatics web resource http://www.stemformatics.org/datasets/view/6306

2015-03-02 | E-MTAB-3277 | biostudies-arrayexpress

A systematic proteogenomic approach to deciphering of the missing proteins: the example of newly uncovered NHERF1 function associated with human reproductive disorder

Project description:We propose and demonstrate a systematic approach designed to combine stringent criteria for claims of missing protein (MP) identification with extensive annotation as critical components of the discovery and functional validation of MPs.

2018-01-05 | PXD004723 | Pride

Transcription profiling by array of decidual CD8+ CCR7-CD45RA- Effector-Memory T cells

Project description:To understand the regulation of cytotoxicity by decidual CD8+ T cells (CD8+ dT) at the maternal-fetal interface, gene expression analysis of CCR7-CD45RA- effector-memory CD8+ T cells isolated from peripheral blood of unrelated healthy controls and decidual tissue from first trimester (6-12 weeks) and term (>37 weeks) pregnancy was performed. Furthermore, first trimester decidual effector-memory CD8+ T cells were stimulated with anti-CD3/CD28 in the presence of IL-2 for 12 hours or 72 hours. RNA was isolated and gene expression profiles were generated by employing Affymetrix HG_U133_Plus 2 arrays on the Affymetrix Geneatlas system.

2017-12-19 | E-MTAB-5890 | biostudies-arrayexpress

Gene expression analysis of rat glomerular parietal epithelial cells

Project description:Very little is known about the function of glomerular parietal epithelial cells (PECs). In this study, we performed genome-wide expression analysis on PEC-enriched capsulated vs. PEC-deprived decapsulated rat glomeruli to determine the transcriptional state of PECs under normal conditions. We identified hundreds of differentially expressed genes that mapped to distinct biologic modules including development, tight junction, ion transport, and metabolic processes. Since developmental programs were highly enriched in PECs, we characterized several of their candidate members at the protein level. Collectively, our findings confirm that PECs are multifaceted cells and help define their diverse functional repertoire. We developed a sequential sieving methodology to selectively isolate capsulated (PEC-enriched) glomeruli from un-capsulated (PEC-deprived) glomeruli in rats. Three samples were obtained for each preparation. Total RNA was isolated and its integrity confirmed via Bioanalyzer 2100. Each sample (n =6) was hybridized to an Affymetrix Rat GeneChip 1.0ST microarray.

2014-08-01 | E-GEOD-54085 | biostudies-arrayexpress

scRNA-seq and snucRNA-seq of human primary trophoblast organoids (PTO) and trophoblast stem cells (TSCs) differentiation into extravillous trophoblast organoids (EVTs)

Project description:This study aims to compare in vivo human trophoblast differentiation into EVTs to different in vitro trophoblast organoids using single-cell and single-nuclei RNA sequencing. The study includes two type of systems: human primary trophoblast organoids (PTO) and trophoblast stem cells (TSCs). Trophoblast stem cell (TSC) lines BTS5 and BTS11 derived by Okae and colleagues were grown as described previously (Okae et al. 2018) and together with EVT media. Primary trophoblast organoids (PTO) were grown and differentiated into EVT as previously described by Turco & Sheridan (Turco et al 2018; Sheridan et al 2020). This study shows that the main regulatory programs mediating EVT invasion in vivo are preserved in in vitro models of EVT differentiation from primary trophoblast organoids and trophoblast stem cells.

2023-02-09 | E-MTAB-12650 | biostudies-arrayexpress

Development of decidual cell polyploidy and bi-nucleation necessitates mitochondrial activity

Project description:In the present study, to better define the aspects of decidual cell polyploidy, we isolated pure polyploid and non-polyploid decidual cell populations from the in vivo decidual bed. Three independent RNA pools prepared for each population were then subjected to the Affymetrix gene chip analysis for the whole mouse genome transcripts. Our data revealed up-regulation of 1015 genes and down-regulation of 1207 genes in the polyploid populations, as compared to the non-polyploid group. We analyzed whole gnenome transcription from non-polyploid and polyploid cell populations using the Affymetrix GeneChip® Mouse Gene 1.0 ST Array . 3 replicates were performed.

2011-04-29 | E-GEOD-28917 | biostudies-arrayexpress

Micro array gene expression analysis of three types of HLA-G+ EVT

Project description:Three types of HLA-G+ EVT were purified from placental tissues. To investigate transcriptional differences RNA was isolated and gene expression profiles were generated by employing Affymetrix HG_U133_Plus 2 arrays on the Affymetrix Geneatlas system.

2020-06-16 | E-MTAB-8639 | biostudies-arrayexpress

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