Cardiac . For each 10X Genomics Visium sequencing data, we used Space Ranger Software Suite (v.1.2.1) to align to the GRCh38 human reference genome (official Cell Ranger reference, v.2020-A) and quantify gene counts. All samples were karyotypically normal. Bottom shows UMAP projections of cell lineages (colour) in the human male scRNA-seq (n=133,811), human male scATAC-seq (n=52,285) and mouse male scRNA-seq (n=32,889) datasets. the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Left, 12PCW testis and ovary stained for CD68 (yellow, macrophages), F13A1 (red, tissue-repair macrophages) and NR2F2 (cyan, mesenchymal) (n=2). Colour proportional to scaled log-transformed expression. Gosselin, D. et al. Nat. Hayman, A. R. et al. Figure 1 Diagram of ovarian and tubal anatomy depicting the coelomic and Mllerian models of ovarian cancer development. Curr. The first wave of pregranulosa (preGC-I) is restricted to the medulla as the ovary develops. Scale bars = 100m (left) and 10m in magnified regions (right). 9ik). 11, 499524 (2016). b, Dot plots show the variance-scaled, log-transformed expression of genes (x-axis) characteristic of the first wave of somatic cells (y-axis) in humans and mice. 15, 615622 (2019). We also found this population at a similar location in mice (Extended Data Fig. In both humans and mice, expression of the transcription factors (TFs) GATA4, LHX9 and ARX is a hallmark of the gonadal coelomic epithelium and mesenchymal cells, whereas GATA2 expression is restricted to the mesonephros and other extragonadal tissue (Extended Data Fig. 9g,h, Extended Data Fig. Coelomic epithelium refers to the epithelium that lines the surface of the body wall and abdominal organs. 7h). Knoblaugh, S. E., True, L., Tretiakova, M. & Hukkanen, R. R. in Comparative Anatomy and Histology (eds. We used several single-cell genomics methods: (1) single-cell RNA sequencing (scRNA-seq); (2) single-cell accessible chromatin sequencing (scATAC-seq) and (3) combined single-nucleus RNA and ATAC sequencing (snRNA-seq/scATAC-seq) to profile 347,709, 96,174 and 40,742 cells, respectively (Fig. Gigascience 9, giaa151 (2020). https://doi.org/10.1038/s41586-022-04918-4, DOI: https://doi.org/10.1038/s41586-022-04918-4. Scale bars = 100m and 10m in magnified regions. Sancho, C., Hoo, R. & Vento-Tormo, R. Human embryonic gonad dissociation with Collagenase & Trypsin v3. Nat. The resulting clustered manifold was preliminary annotated by transferring labels from a publicly available dataset of human fetal liver haematopoiesis31. Cell 161, 14531467 (2015). Khan, A. et al. by Prof. Stephen Gallik | Nov 12, 2022 | Tissues There are three main layers that make up the coelomic epithelium: the mesothelium, the endoderm, and the ectoderm. The ovarian coelomic epithelium covers the ovary as a layer of squamous or cuboidal cells. . The white dashed line outlines the ovary; the white dashed rectangle highlights the enlarged gonadal region. Li et al.s annotations were visualized onto the male and female UMAPs, respectively. 2ac, Extended Data Fig. 60, 533 (1996). 22, 14361446 (2020). Conservation heatmap (right) highlights significant overexpression (log2-fold change>0 and FDR<0.05) in each species. PreGC-IIa coappear in space (outer cortex) and time (mid-8PCW) with OSE (UPK3B+, LHX2+, IRX3+), and express the retinoic acid inhibitor CYP26B1 (meiosis inhibitor) as well as low amounts of FOXL2. If material is not included in the articles Creative Commons license 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. Estimated cell abundance (colour intensity) for OSE, preGC-I, preGC-IIa, preGC-IIb and developing granulosa cells (colour) in each Visium spot shown over the haematoxylin and eosin (H&E) images. b, UMAP (uniform manifold approximation and projection) of female (top) and male (bottom) human scATAC-seq datasets labelled by donor and post-conceptional weeks (PCW). Roser Vento-Tormo. During embryonic development, the coelomic epithelium covering the intermediate mesoderm thickens and gives rise to the urogenital ridges, the precursors of the urogenital system (Fig. Rev. Top. Proc. b, Heatmap reporting label transfer scores from human scRNA-seq to scATAC-seq germ cell data of matched individuals. and O.A.B. h, Dot plot showing the variance-scaled, log-transformed expression of microglia markers in the cluster of TREM2+ ftM in both sexes reveals that the few female cells that belong to this cluster do not express the key markers. and V.K. Before training the model, human cell types were downsampled to the cell type with the lowest number of cells to obtain a balanced dataset. 13, 206218 (2013). (right) Dot plots showing the scaled log-transformed expression of genes coding for cognate ligand or receptor proteins in the supporting epithelial, endothelial and germ cells. After converting the expression space to log(CPM/100+1), the object was transposed to gene space to identify cell cycling genes in a data-driven manner, as described31,32. Pachkov, M., Erb, I., Molina, N. & van Nimwegen, E. SwissRegulon: a database of genome-wide annotations of regulatory sites. & Saint-Jeannet, J.-P. Zic1 controls placode progenitor formation non-cell autonomously by regulating retinoic acid production and transport. PubMed Pathology Outlines - Embryology In other animals, such as molluscs, it remains undifferentiated. Coelomic Cavity Development - Embryology Clusters for mesothelial, supporting and gonadal mesenchymal LHX9+ cells were defined in an independent per-lineage reanalysis and projected onto this dataset (Fig. Most cases are associated with fusion genes. Article Nuclei were released by Dounce homogenization as described in detail in the protocols.io (ref. 10c), suggesting a role in promoting mesonephric endothelial cell migration36, a transient process required for testis cord formation (roughly 814PCW). Zhao, Z.-H. et al. Lineages unique to developing ovaries and testes are highlighted with "*". d, (left) UMAP projections of the predicted probability of ESGC from our dataset onto Guo et al., 2021 somatic cells manifold using a Support Vector Machine (SVM) classifier. In mouse ovaries, the coelomic epithelium differentiates into the ovarian surface epithelium and initiates a second wave of cortical pregranulosa cells, independent of RSPO1/WNT4-catenin signalling5,21. 10 Macrophages smFISH panels. Rastetter, R. H. et al. Mice were housed in specific pathogen-free conditions at the UK Home Office-approved facility at the University of Cambridge. We used trajectory reconstruction methods to trace the differentiation of human PGCs into prespermatogonia and oocytes (Extended Data Fig. 5d and Extended Data Fig. This publication is part of the Human Cell Atlas. CAS a, Schematic representation of the computational workflow used to analyse scRNA-seq data. Natl Acad. Top UMAPs depict two human (7 post-conceptional weeks, PCW testis; 7.5PCW ovary) gonadal samples while bottom UMAPs depict two mouse (E11.5 testis and E12.5 ovary) gonadal samples, analysed independently. Chronic eosinophilic leukemia is a form of cancer in which too many eosinophils are found in the bone marrow, blood, and other tissues. 6h). 2017 scRNA-seq analysis of human gonads on our human scRNA-seq dataset. After being rinsed with deionized water, slides were dipped in Mayers haematoxylin solution for 90s. Slides were completely rinsed in 45 washes of deionized water, which also served to blue the haematoxylin. Sci. Finally, we used the function run_palantir (with num_waypoints=500) to estimate the pseudotime of each cell from the root cell. 4a) and forming a gradient from the outer (preGC-IIa) to the inner cortex (preGC-IIb; Fig. On this treatment, no endogenous fluorescence from the Oct4PE-GFP transgene was observed. Conservation heatmap (right) highlights significant overexpression (log2 fold change>0 and FDR<0.05) in each species. Coming into focus: The nonovarian origins of ovarian cancer Contrib. For the scRNA-seq experiments, cells were loaded according to the manufacturers protocol for the Chromium Single Cell 5 Kit v.1.0, v.1.1 and v.2 (10X Genomics) to attain between 2,000 and 10,000 cells per reaction. It is recommended that serological testing should be offered to any children or adults . Despite the similar spatiotemporal patterns in humans and mice, we show that certain regulatory programmes differ; for example, LGR5, characteristic of second-wave pregranulosa cells in mice5,38, is restricted to ESGCs in humans. CoelEpi = coelomic epithelium; E = embryonic day; ESGC = early supporting gonadal cells; Gi = gonadal interstitial; P = postnatal day; PCW = post-conceptional week; preGC = pre-granulosa cells; sPAX8 = supporting PAX8; Ti = testicular interstitial. We set the number of terminal states to four, letting CellRank determine the number of initial states. During development, the coelomic epithelium is a highly active cell layer, which locally is able to supply mesenchymal cells that contribute to the mesodermal elements of many organs and provide signals which are necessary for their development. 2 Analysis of the chromatin accessibility landscape of the human developing ovaries and testes. We used the scmap tool57 to project the Li et al. White dashed rectangles highlight the magnified regions from the following organs: testis (top), skin (middle), spinal cord (labelled as CNS = central nervous system) (bottom); n=1 e, High-resolution imaging of representative gonadal sections of two fetal testes (12 and 14PCW), with intensity proportional to smFISH signal to SOX9 (cyan, Sertoli cells), CD68 (red, macrophages), P2RY12 (yellow, TREM2+ ftM); n=5. ftM = fetal testicular macrophages; PCW = post-conceptional week; prob_ = probability. Cool, S. Teichmann, T. Hagai, S. Williams, A. Greenfield, D. Alvarez-Errico and the VenTo team for helpful discussions; A. Garca, scientific illustrator from Bio-Graphics and Z. Marekov for graphical images; A. Maartens for proofreading; S. Pritchard and K. Tudor for smFISH experiments; A. Oszlanczi, A. Knights and T. Porter for help with library preparation; M. Prete for web portal support and R. Tesloianu for adding interactions in CellPhoneDB. CAS Interacting partners (CellPhoneDB) are indicated with a matching symbol. The intra-embryonic coelom ( coelomic cavity) forms within the lateral plate mesoderm early in embryonic development (week 3-4 ( GA 5-6). The detailed protocol is available at https://www.protocols.io/view/tissue-freezing-in-cryostor-solution-processing-bgsnjwde. 9, 4292 (2018). OSE activates the primate-specific TF LHX2, which is kept active in preGC-IIa (Fig. To study the transcriptomic similarity of a given cell type across species, we compared the estimated probabilities between humanmouse matching cell types and visualized them with boxplots. Kracht, L. et al. RNA velocity of single cells. Single-cell RNA-seq analysis maps development of human germline cells and gonadal niche interactions. Extended Data Fig. The HDBR is regulated by the UK Human Tissue Authority (www.hta.gov.uk) and operates in accordance with the relevant Human Tissue Authority Codes of Practice. Nucleic Acids Res. b, Diagram summarizing the stage and sex composition of our sample cohort along with main events occurring during gonadogenesis. Coelomic epithelium-derived cells in visceral morphogenesis j, UMAP (uniform manifold approximation and projection) of the multi-organ integrated fetal myeloid dataset labelled by tissue and donor. The space then undergoes complex morphological changes of folding and partitioning during the development of the 3 major body cavities . We then trained an SVM classifier (sklearn.svm.SVC) on human data and projected the cell type annotations onto the mouse datasets. Previously, WT1 and NR5A1 were used to identify an equivalent population in mice2, but we show that these markers are broadly expressed by other gonadal somatic cells. The cell of origin of ovarian epithelial tumours - ScienceDirect To compare the differentiation of human germ cells with that of other mammals, we integrated our human and mouse gonadal germ cells with more scRNA-seq gonadal germ cells datasets from mouse and macaque5,10,11 (Extended Data Fig. Cold Spring Harbor Laboratory https://doi.org/10.1101/2020.11.15.378125 (2020). PubMed Central USA 117, 2001520026 (2020). Hanley, N. A. et al. We included six males and three females at E10.5, six males and two females at E11.5, and three males and three females at E12.5. SIGLEC15+ ftMs also express the remodelling molecule MMP9 and their numbers decrease in later stages of development (Extended Data Fig. At roughly 17 PCW, preGC-IIb cells differentiate into developing granulosa cells, which surround the oocyte to mediate follicle formation and/or regulate oocyte survival.