scholarly journals Single-cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development

2018 ◽  
Author(s):  
Thorsten Boroviak ◽  
Giuliano G Stirparo ◽  
Sabine Dietmann ◽  
Irene Hernando-Herraez ◽  
Hisham Mohammed ◽  
...  
Keyword(s):  
Single Cell ◽  
Ribosome Biogenesis ◽  
Mouse Embryos ◽  
Preimplantation Development ◽  
Primitive Endoderm ◽  
Single Cell Profiling ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
Polycomb Repressive Complexes ◽  
Genome Activation

AbstractThe mouse embryo is the canonical model for mammalian preimplantation development. Recent advances in single-cell profiling allow detailed analysis of embryogenesis in other eutherian species, including human, to distinguish conserved from divergent regulatory programs and signalling pathways in the rodent paradigm. Here, we identify and compare transcriptional features of human, marmoset and mouse embryos by single-cell RNA-seq. Zygotic genome activation correlates with the presence of Polycomb Repressive Complexes in all three species, while ribosome biogenesis emerges as a predominant attribute in primate embryos, supporting prolonged translation of maternally deposited RNAs. We find that transposable element expression signatures are species-, stage- and lineage-specific. The pluripotency network in the primate epiblast lacks certain regulators operative in mouse, but encompasses WNT components and genes associated with trophoblast specification. Sequential activation of GATA6, SOX17 and GATA4 markers of primitive endoderm identity is conserved in primates. Unexpectedly, OTX2 is also associated with primitive endoderm specification in human and nonhuman primate blastocysts. Our cross-species analysis demarcates both conserved and primate-specific features of preimplantation development and underscores the molecular adaptability of early mammalian embryogenesis.

scholarly journals Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development

Development ◽  
2018 ◽  
Vol 145 (21) ◽  
pp. dev167833 ◽  
Author(s):  
Thorsten Boroviak ◽  
Giuliano G. Stirparo ◽  
Sabine Dietmann ◽  
Irene Hernando-Herraez ◽  
Hisham Mohammed ◽  
...  
Keyword(s):  
Single Cell ◽  
Transcriptome Analysis ◽  
Mouse Embryos ◽  
Preimplantation Development ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Single-cell profiling identifies myeloid cell subsets with distinct fates during neuroinflammation

Science ◽  
2019 ◽  
Vol 363 (6425) ◽  
pp. eaat7554 ◽  
Author(s):  
Marta Joana Costa Jordão ◽  
Roman Sankowski ◽  
Stefanie M. Brendecke ◽  
Sagar ◽  
Giuseppe Locatelli ◽  
...  
Keyword(s):  
Single Cell ◽  
Immune Cell ◽  
Myeloid Cell ◽  
Innate Immune ◽  
Functional Studies ◽  
Cell Diversity ◽  
Single Cell Profiling ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

The innate immune cell compartment is highly diverse in the healthy central nervous system (CNS), including parenchymal and non-parenchymal macrophages. However, this complexity is increased in inflammatory settings by the recruitment of circulating myeloid cells. It is unclear which disease-specific myeloid subsets exist and what their transcriptional profiles and dynamics during CNS pathology are. Combining deep single-cell transcriptome analysis, fate mapping, in vivo imaging, clonal analysis, and transgenic mouse lines, we comprehensively characterized unappreciated myeloid subsets in several CNS compartments during neuroinflammation. During inflammation, CNS macrophage subsets undergo self-renewal, and random proliferation shifts toward clonal expansion. Last, functional studies demonstrated that endogenous CNS tissue macrophages are redundant for antigen presentation. Our results highlight myeloid cell diversity and provide insights into the brain’s innate immune system.

scholarly journals Single cell transcriptome atlas of mouse mammary epithelial cells across development

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Bhupinder Pal ◽  
Yunshun Chen ◽  
Michael J. G. Milevskiy ◽  
François Vaillant ◽  
Lexie Prokopuk ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Single Cell ◽  
Developmental Stages ◽  
Mammary Epithelial Cells ◽  
Expression Profiles ◽  
Single Cells ◽  
Chromatin Accessibility ◽  
Mammary Epithelial ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Abstract Background Heterogeneity within the mouse mammary epithelium and potential lineage relationships have been recently explored by single-cell RNA profiling. To further understand how cellular diversity changes during mammary ontogeny, we profiled single cells from nine different developmental stages spanning late embryogenesis, early postnatal, prepuberty, adult, mid-pregnancy, late-pregnancy, and post-involution, as well as the transcriptomes of micro-dissected terminal end buds (TEBs) and subtending ducts during puberty. Methods The single cell transcriptomes of 132,599 mammary epithelial cells from 9 different developmental stages were determined on the 10x Genomics Chromium platform, and integrative analyses were performed to compare specific time points. Results The mammary rudiment at E18.5 closely aligned with the basal lineage, while prepubertal epithelial cells exhibited lineage segregation but to a less differentiated state than their adult counterparts. Comparison of micro-dissected TEBs versus ducts showed that luminal cells within TEBs harbored intermediate expression profiles. Ductal basal cells exhibited increased chromatin accessibility of luminal genes compared to their TEB counterparts suggesting that lineage-specific chromatin is established within the subtending ducts during puberty. An integrative analysis of five stages spanning the pregnancy cycle revealed distinct stage-specific profiles and the presence of cycling basal, mixed-lineage, and 'late' alveolar intermediates in pregnancy. Moreover, a number of intermediates were uncovered along the basal-luminal progenitor cell axis, suggesting a continuum of alveolar-restricted progenitor states. Conclusions This extended single cell transcriptome atlas of mouse mammary epithelial cells provides the most complete coverage for mammary epithelial cells during morphogenesis to date. Together with chromatin accessibility analysis of TEB structures, it represents a valuable framework for understanding developmental decisions within the mouse mammary gland.

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