Single cell insights into development of the bovine placenta
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA981588 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24880360.fastq.gz | Fastqsanger.gz | |||
| SRR24880361.fastq.gz | Fastqsanger.gz | |||
| SRR24880362.fastq.gz | Fastqsanger.gz | |||
| SRR24880363.fastq.gz | Fastqsanger.gz | |||
| SRR24880364.fastq.gz | Fastqsanger.gz |
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Project description:A central determinant of pregnancy success is proper development of the conceptus (embryo/fetus and associated extraembryonic membranes including the placenta). Although the gross morphology and histology of the bovine placenta has been well studied, the cellular and molecular mechanisms regulating placenta development and trophoblast differentiation and function remain essentially undefined. Here single cell RNA-seq analysis was performed on the day 17 bovine conceptus and chorion of day 24, 30 and 50 conceptuses (n = 3-4 samples per day) using the 10X Genomics platform. Bioinformatic analyses identified cell types and their ontogeny including trophoblast, mesenchyme, and immune cells. Loss of IFNT-expressing trophoblast uninucleate cells (UNC) occurred between days 17 and 30, whereas binucleate cells (BNC), identified based on expression of placental lactogen (CSH2) and pregnancy-associated glycoproteins (PAGs) marker genes, first appeared on day 24. Several different types of UNC were present in day 24, 30 and 50 samples, but only one (day 24) or two types of BNC (days 30 and 50). Cell trajectory analyses provided a conceptual framework for UNC development and BNC differentiation, and upstream transcription factor binding enrichment analyses identified candidate transcription factors governing differentiation and function of the trophoblasts. The digital atlas of cell types in the developing bovine conceptus reported here serves as a resource to discover key genes and biological pathways regulating its development during the critical periods of implantation and placentation.
2023-11-08 | GSE234524 | GEO
Project description:Ruminants have a semi-invasive placenta, which possess highly vascularized placentomes formed by maternal endometrial caruncles and fetal placental cotyledons and required for fetal development to term. The synepitheliochorial placenta of cattle contains at least two trophoblast cell populations, including uninucleate (UNC) and binucleate (BNC) cells that are most abundant in the cotyledonary chorion of the placentomes. The interplacentomal placenta is more epitheliochorial in nature with the chorion developing specialized areolae over the openings of uterine glands. Of note, the cell types in the placenta and cellular and molecular mechanisms governing trophoblast differentiation and function are little understood in ruminants. To fill this knowledge gap, the cotyledonary and intercotyledonary areas of the mature day 195 bovine placenta were analyzed by single nuclei analysis. Single-nuclei RNA-seq analysis found substantial differences in cell type composition and transcriptional profiles between the two distinct regions of the placenta. Based on clustering and cell marker gene expression, five different trophoblast cell types were identified in the chorion, including proliferating and differentiating UNC and two different types of BNC in the cotyledon. Cell trajectory analyses provided a framework for understanding the differentiation of trophoblast UNC into BNC. The upstream transcription factor binding analysis of differentially expressed genes identified a candidate set of regulator factors and genes regulating trophoblast differentiation. This foundational information is useful to discover essential biological pathways underpinning the development and function of the bovine placenta.
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Project description:Gene expression patterns of bovine placenta from initial to late stage of pregnancy were investigated by using the our custom designed utero-placental cDNA microarray. Keywords: Time course
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Project description:Supporting healthy pregnancy outcomes requires a comprehensive understanding of the cellular hierarchy and underlying molecular mechanisms during peri-implantation development. Here, we presented a single-cell transcriptome-wide view of the bovine peri-implantation embryo development at day 12, 14, 16 and 18, when most of the pregnancy failure occurs. We defined the development and dynamic progression of cellular composition and gene expression of embryonic disc, hypoblast, and trophoblast lineages during bovine peri-implantation development. Notably, the comprehensive transcriptomic mapping of trophoblast development revealed a previous unrecognized primitive trophoblast cell lineage that are responsible for pregnancy maintenance in bovine prior to the time when binucleate cell emerges. We analyzed novel markers for the cell lineage development during bovine early development. We also identified cell-cell communication signaling underling embryonic and extraembryonic cells interact to ensure proper early development in bovine. Collectively, our work provides foundational information to discover essential biological pathways underpinning bovine peri-implantation development and the molecular causes of the early pregnancy failure during this critical period.
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Project description:Single-cell trascriptiponal landscapes of bovine peri-implantation development
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Project description:The germ cell lineage ensures the creation of new individuals perpetuating the genetic information across generations. Primordial germ cells (PGCs) are pioneers of gametes and exist transiently during development until they differentiate into oogonia in females, or spermatogonia in males. Little is known about the molecular characteristics of PGCs in cattle. By performing single-cell RNA-sequencing of bovine fetal gonads we evaluated the molecular signatures of bovine germ cells and their niche at 50 days of development. Our results indicate that PGCs and somatic cells were in very early stages of development, and that bovine and human germ cells share expression of transcriptional regulators of germline specification, and several genes coding for membrane-bound proteins. Additionally, the expression of members of Notch, Nodal/Activin, and BMP signaling cascades in the bovine fetal ovary, suggests that these pathways are involved in the interaction between germ cells and their niche. Results of this study provide insights into the mechanisms involved in the development of bovine PGCs and put in evidence similarities between the bovine and human germline.
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Project description:KRAS is required for placenta development
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Project description:In our study, we performed single-cell sequencing of the E12.5 mouse placenta to explore the cellular diversity and gene expression dynamics during placental development. This approach allowed us to delineate the complex landscape of cell types and states present at this critical stage of gestation. By analyzing the transcriptomic data, we identified several distinct trophoblast subpopulations, each characterized by unique gene expression patterns that suggest different functional roles in placental structure and function. Additionally, our data provided insights into the potential regulatory pathways involved in cell differentiation.
2024-10-31 | GSE273446 | GEO
Project description:During mammalian pre-implantation embryonic development dramatic and orchestrated changes occur in gene transcription. The identification of the complete changes has not been possible until the development of the Next Generation Sequencing Technology. Here we report the first transcriptome dynamics of single matured bovine oocytes and all stages of pre-implantation embryos developed in vivo. Surprisingly, nearly half of the bovine genome, 11,488 to 12,729 genes involved in more than 100 pathways, is expressed in oocytes and early embryos. Despite the similarity in the total numbers of genes expressed across stages, the nature of the expressed genes is dramatically different. A total of 2,845 genes were differentially expressed among different stages, of which the largest change was observed between the 4- and 8-cell stages, demonstrating that the bovine embryonic genome activation occurs at this transition. Additionally, 774 genes were identified as only expressed/highly enriched in particular stages of development. Using weighted gene co-expression network analysis, we found 12 stage-specific modules of co-expressed genes that can be used to represent the corresponding stage of development. Furthermore, we identified conserved key members (or hub genes) of the bovine expressed gene networks. Their vast association with other embryonic genes suggests that they may have important regulatory roles in embryogenesis; yet, the majority of the hub genes are relatively unknown/under-studied in embryos. We also conducted the first embryonic expression profile comparison across three mammalian species, human, mouse and bovine, for which RNA-seq data are available. We found that the three species share more maternally deposited genes than embryonic genome activated genes. More importantly, there are more similarities in embryonic transcriptomes between bovine and humans than between humans and mice, demonstrating that bovine embryos are better models for human embryonic development. This study provides the first comprehensive examination for gene activities in bovine embryos and identified little-known potential master regulators of pre-implantation development. RNA-Seq profiles from single in vivo matured oocytes and in vivo developed embryos from the 2-cell to the blastocyst stages generated using Solid RNA-seq platform.
2014-09-10 | E-GEOD-59186 | biostudies-arrayexpress
Project description:The mechanisms regulating early stages of placentation and trophectoderm differentiation in the ruminant conceptus remain poorly understood. Here we present a model of trophectoderm (TE) differentiation in vitro from outgrowths of individual in vitro derived embryos. Cell outgrowths expressed markers of mononucleate (MNC) and binucleate (BNC) TE cells. The percentage of BNC ranged from 14-39% in individual outgrowths as determined by flow cytometry. Pregnancy-associated glycoproteins (PAGs), produced by BNC, were measured in culture media on days 35 to 54. Continuous secretion of PAGs was observed and indicative of BNC functionality. Gene expression was evaluated in 20 embryo cell outgrowths derived from two different sires. Expression of HAND1, which is involved in TE differentiation, and CSH2, a BNC-specific gene, was altered in cell outgrowths between the two sires tested. Single-cell RNA-seq analysis of day 40 TE cell outgrowths revealed 11 distinct cell populations, with specific clusters genes involved in TE lineage specification, proliferation, and differentiation. In addition, whole -RNAseq analysis was performed in day 35 and 40 TE cell outgrowths and confirmed sustained expression of genes expressed by BNC, such as CSH2 and some PAGs. The developed in vitro bovine embryo outgrowth culture found evidence for MNC and BNC differentiation and continuous production of PAGs, recapitulating key features of early bovine placenta development. This model can be used to understand the developmental biology of TE cells, provide insights into paternal influences on TE differentiation, and impact our understanding of early pregnancy loss in cattle.
2023-04-03 | GSE200216 | GEO