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  1. Article ; Online: Stabilized mosaic single-cell data integration using unshared features.

    Ghazanfar, Shila / Guibentif, Carolina / Marioni, John C

    Nature biotechnology

    2023  Volume 42, Issue 2, Page(s) 284–292

    Abstract: Currently available single-cell omics technologies capture many unique features with different biological information content. Data integration aims to place cells, captured with different technologies, onto a common embedding to facilitate downstream ... ...

    Abstract Currently available single-cell omics technologies capture many unique features with different biological information content. Data integration aims to place cells, captured with different technologies, onto a common embedding to facilitate downstream analytical tasks. Current horizontal data integration techniques use a set of common features, thereby ignoring non-overlapping features and losing information. Here we introduce StabMap, a mosaic data integration technique that stabilizes mapping of single-cell data by exploiting the non-overlapping features. StabMap first infers a mosaic data topology based on shared features, then projects all cells onto supervised or unsupervised reference coordinates by traversing shortest paths along the topology. We show that StabMap performs well in various simulation contexts, facilitates 'multi-hop' mosaic data integration where some datasets do not share any features and enables the use of spatial gene expression features for mapping dissociated single-cell data onto a spatial transcriptomic reference.
    MeSH term(s) Software ; Computer Simulation ; Gene Expression Profiling ; Technology ; Transcriptome
    Language English
    Publishing date 2023-05-25
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1311932-1
    ISSN 1546-1696 ; 1087-0156
    ISSN (online) 1546-1696
    ISSN 1087-0156
    DOI 10.1038/s41587-023-01766-z
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  2. Article ; Online: Single cell genomics and developmental biology: moving beyond the generation of cell type catalogues.

    Ton, Mai-Linh N / Guibentif, Carolina / Göttgens, Berthold

    Current opinion in genetics & development

    2020  Volume 64, Page(s) 66–71

    Abstract: Major developmental processes such as gastrulation and early embryogenesis rely on a complex network of cell-cell interactions, chromatin remodeling, and transcriptional regulators. This makes it challenging to study early development when using bulk ... ...

    Abstract Major developmental processes such as gastrulation and early embryogenesis rely on a complex network of cell-cell interactions, chromatin remodeling, and transcriptional regulators. This makes it challenging to study early development when using bulk populations of cells. Recent advances in single-cell technologies have allowed researchers to better understand the interactions between different molecular modalities and the heterogeneities within classically defined cell types. As new single-cell technologies mature, they have the potential of providing a step-change in our understanding of embryogenesis. In this review, we summarize recent advances in single-cell technologies with particular focus on those that lend insight into early organogenesis. We then discuss current pitfalls and implications for future research.
    MeSH term(s) Animals ; Developmental Biology ; Embryonic Development ; Gene Expression Regulation, Developmental ; Genome ; Genomics/methods ; Humans ; Single-Cell Analysis/methods
    Language English
    Publishing date 2020-07-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1077312-5
    ISSN 1879-0380 ; 0959-437X
    ISSN (online) 1879-0380
    ISSN 0959-437X
    DOI 10.1016/j.gde.2020.05.033
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  3. Article ; Online: Blood: Education for stem cells.

    Guibentif, Carolina / Göttgens, Berthold

    Nature

    2017  Volume 545, Issue 7655, Page(s) 415–417

    MeSH term(s) Blood Banks ; Fetal Blood ; Hematopoietic Stem Cells ; Humans ; Stem Cells
    Language English
    Publishing date 2017-05-17
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/nature22496
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  4. Article ; Online: Single-cell transcriptional profiling: a window into embryonic cell-type specification.

    Pijuan-Sala, Blanca / Guibentif, Carolina / Göttgens, Berthold

    Nature reviews. Molecular cell biology

    2018  Volume 19, Issue 6, Page(s) 399–412

    Abstract: During mammalian embryonic development, a single fertilized egg cell will proliferate and differentiate into all the cell lineages and cell types that eventually form the adult organism. Cell lineage diversification involves repeated cell fate choices ... ...

    Abstract During mammalian embryonic development, a single fertilized egg cell will proliferate and differentiate into all the cell lineages and cell types that eventually form the adult organism. Cell lineage diversification involves repeated cell fate choices that ultimately occur at the level of the individual cell rather than at the cell-population level. Improvements in single-cell technologies are transforming our understanding of mammalian development, not only by overcoming the limitations presented by the extremely low cell numbers of early embryos but also by enabling the study of cell fate specification in greater detail. In this Review, we first discuss recent advances in single-cell transcriptomics and imaging and provide a brief outline of current bioinformatics methods available to analyse the resulting data. We then discuss how these techniques have contributed to our understanding of pre-implantation and early post-implantation development and of in vitro pluripotency. Finally, we overview the current challenges facing single-cell research and highlight the latest advances and potential future avenues.
    MeSH term(s) Animals ; Cell Differentiation/genetics ; Cell Differentiation/physiology ; Embryo, Mammalian/physiology ; Embryonic Development/genetics ; Embryonic Development/physiology ; Humans ; Transcription, Genetic/genetics ; Transcription, Genetic/physiology ; Transcriptome/genetics ; Transcriptome/physiology
    Language English
    Publishing date 2018-04-17
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2031313-5
    ISSN 1471-0080 ; 1471-0072
    ISSN (online) 1471-0080
    ISSN 1471-0072
    DOI 10.1038/s41580-018-0002-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation

    Barile, Melania / Imaz-Rosshandler, Ivan / Inzani, Isabella / Ghazanfar, Shila / Nichols, Jennifer / Marioni, John C. / Guibentif, Carolina / Göttgens, Berthold

    Genome biology. 2021 Dec., v. 22, no. 1

    2021  

    Abstract: BACKGROUND: Single-cell technologies are transforming biomedical research, including the recent demonstration that unspliced pre-mRNA present in single-cell RNA-Seq permits prediction of future expression states. Here we apply this RNA velocity concept ... ...

    Abstract BACKGROUND: Single-cell technologies are transforming biomedical research, including the recent demonstration that unspliced pre-mRNA present in single-cell RNA-Seq permits prediction of future expression states. Here we apply this RNA velocity concept to an extended timecourse dataset covering mouse gastrulation and early organogenesis. RESULTS: Intriguingly, RNA velocity correctly identifies epiblast cells as the starting point, but several trajectory predictions at later stages are inconsistent with both real-time ordering and existing knowledge. The most striking discrepancy concerns red blood cell maturation, with velocity-inferred trajectories opposing the true differentiation path. Investigating the underlying causes reveals a group of genes with a coordinated step-change in transcription, thus violating the assumptions behind current velocity analysis suites, which do not accommodate time-dependent changes in expression dynamics. Using scRNA-Seq analysis of chimeric mouse embryos lacking the major erythroid regulator Gata1, we show that genes with the step-changes in expression dynamics during erythroid differentiation fail to be upregulated in the mutant cells, thus underscoring the coordination of modulating transcription rate along a differentiation trajectory. In addition to the expected block in erythroid maturation, the Gata1-chimera dataset reveals induction of PU.1 and expansion of megakaryocyte progenitors. Finally, we show that erythropoiesis in human fetal liver is similarly characterized by a coordinated step-change in gene expression. CONCLUSIONS: By identifying a limitation of the current velocity framework coupled with in vivo analysis of mutant cells, we reveal a coordinated step-change in gene expression kinetics during erythropoiesis, with likely implications for many other differentiation processes.
    Keywords GATA transcription factors ; RNA ; biomedical research ; data collection ; embryonic germ layers ; erythrocytes ; erythropoiesis ; gastrulation ; gene expression ; humans ; liver ; mice ; mutants ; organogenesis ; prediction ; sequence analysis
    Language English
    Dates of publication 2021-12
    Size p. 197.
    Publishing place BioMed Central
    Document type Article
    ZDB-ID 2040529-7
    ISSN 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-021-02414-y
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: Tracking early mammalian organogenesis - prediction and validation of differentiation trajectories at whole organism scale.

    Imaz-Rosshandler, Ivan / Rode, Christina / Guibentif, Carolina / Harland, Luke T G / Ton, Mai-Linh N / Dhapola, Parashar / Keitley, Daniel / Argelaguet, Ricard / Calero-Nieto, Fernando J / Nichols, Jennifer / Marioni, John C / de Bruijn, Marella F T R / Göttgens, Berthold

    Development (Cambridge, England)

    2024  Volume 151, Issue 3

    Abstract: Early organogenesis represents a key step in animal development, during which pluripotent cells diversify to initiate organ formation. Here, we sampled 300,000 single-cell transcriptomes from mouse embryos between E8.5 and E9.5 in 6-h intervals and ... ...

    Abstract Early organogenesis represents a key step in animal development, during which pluripotent cells diversify to initiate organ formation. Here, we sampled 300,000 single-cell transcriptomes from mouse embryos between E8.5 and E9.5 in 6-h intervals and combined this new dataset with our previous atlas (E6.5-E8.5) to produce a densely sampled timecourse of >400,000 cells from early gastrulation to organogenesis. Computational lineage reconstruction identified complex waves of blood and endothelial development, including a new programme for somite-derived endothelium. We also dissected the E7.5 primitive streak into four adjacent regions, performed scRNA-seq and predicted cell fates computationally. Finally, we defined developmental state/fate relationships by combining orthotopic grafting, microscopic analysis and scRNA-seq to transcriptionally determine cell fates of grafted primitive streak regions after 24 h of in vitro embryo culture. Experimentally determined fate outcomes were in good agreement with computationally predicted fates, demonstrating how classical grafting experiments can be revisited to establish high-resolution cell state/fate relationships. Such interdisciplinary approaches will benefit future studies in developmental biology and guide the in vitro production of cells for organ regeneration and repair.
    MeSH term(s) Mice ; Animals ; Cell Differentiation ; Gastrulation ; Organogenesis/genetics ; Primitive Streak ; Endothelium ; Embryo, Mammalian ; Mammals
    Language English
    Publishing date 2024-01-31
    Publishing country England
    Document type Journal Article
    ZDB-ID 90607-4
    ISSN 1477-9129 ; 0950-1991
    ISSN (online) 1477-9129
    ISSN 0950-1991
    DOI 10.1242/dev.201867
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  7. Article ; Online: Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation.

    Barile, Melania / Imaz-Rosshandler, Ivan / Inzani, Isabella / Ghazanfar, Shila / Nichols, Jennifer / Marioni, John C / Guibentif, Carolina / Göttgens, Berthold

    Genome biology

    2021  Volume 22, Issue 1, Page(s) 197

    Abstract: Background: Single-cell technologies are transforming biomedical research, including the recent demonstration that unspliced pre-mRNA present in single-cell RNA-Seq permits prediction of future expression states. Here we apply this RNA velocity concept ... ...

    Abstract Background: Single-cell technologies are transforming biomedical research, including the recent demonstration that unspliced pre-mRNA present in single-cell RNA-Seq permits prediction of future expression states. Here we apply this RNA velocity concept to an extended timecourse dataset covering mouse gastrulation and early organogenesis.
    Results: Intriguingly, RNA velocity correctly identifies epiblast cells as the starting point, but several trajectory predictions at later stages are inconsistent with both real-time ordering and existing knowledge. The most striking discrepancy concerns red blood cell maturation, with velocity-inferred trajectories opposing the true differentiation path. Investigating the underlying causes reveals a group of genes with a coordinated step-change in transcription, thus violating the assumptions behind current velocity analysis suites, which do not accommodate time-dependent changes in expression dynamics. Using scRNA-Seq analysis of chimeric mouse embryos lacking the major erythroid regulator Gata1, we show that genes with the step-changes in expression dynamics during erythroid differentiation fail to be upregulated in the mutant cells, thus underscoring the coordination of modulating transcription rate along a differentiation trajectory. In addition to the expected block in erythroid maturation, the Gata1-chimera dataset reveals induction of PU.1 and expansion of megakaryocyte progenitors. Finally, we show that erythropoiesis in human fetal liver is similarly characterized by a coordinated step-change in gene expression.
    Conclusions: By identifying a limitation of the current velocity framework coupled with in vivo analysis of mutant cells, we reveal a coordinated step-change in gene expression kinetics during erythropoiesis, with likely implications for many other differentiation processes.
    MeSH term(s) Animals ; Cell Differentiation ; Datasets as Topic ; Embryo, Mammalian ; Erythroid Cells/cytology ; Erythroid Cells/metabolism ; Erythropoiesis/genetics ; Fetus ; GATA1 Transcription Factor/deficiency ; GATA1 Transcription Factor/genetics ; Gastrula/growth & development ; Gastrula/metabolism ; Gene Expression Regulation, Developmental ; Humans ; Kinetics ; Liver/cytology ; Liver/growth & development ; Liver/metabolism ; Mice ; Organogenesis/genetics ; Proto-Oncogene Proteins/genetics ; Proto-Oncogene Proteins/metabolism ; Single-Cell Analysis ; Trans-Activators/genetics ; Trans-Activators/metabolism ; Transcriptional Activation
    Chemical Substances GATA1 Transcription Factor ; Gata1 protein, mouse ; Proto-Oncogene Proteins ; Trans-Activators ; proto-oncogene protein Spi-1
    Language English
    Publishing date 2021-07-05
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1474-760X
    ISSN (online) 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-021-02414-y
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  8. Article ; Online: Pyruvate metabolism guides definitive lineage specification during hematopoietic emergence.

    Oburoglu, Leal / Mansell, Els / Canals, Isaac / Sigurdsson, Valgardur / Guibentif, Carolina / Soneji, Shamit / Woods, Niels-Bjarne

    EMBO reports

    2021  Volume 23, Issue 2, Page(s) e54384

    Abstract: During embryonic development, hematopoiesis occurs through primitive and definitive waves, giving rise to distinct blood lineages. Hematopoietic stem cells (HSCs) emerge from hemogenic endothelial (HE) cells, through endothelial-to-hematopoietic ... ...

    Abstract During embryonic development, hematopoiesis occurs through primitive and definitive waves, giving rise to distinct blood lineages. Hematopoietic stem cells (HSCs) emerge from hemogenic endothelial (HE) cells, through endothelial-to-hematopoietic transition (EHT). In the adult, HSC quiescence, maintenance, and differentiation are closely linked to changes in metabolism. However, metabolic processes underlying the emergence of HSCs from HE cells remain unclear. Here, we show that the emergence of blood is regulated by multiple metabolic pathways that induce or modulate the differentiation toward specific hematopoietic lineages during human EHT. In both in vitro and in vivo settings, steering pyruvate use toward glycolysis or OXPHOS differentially skews the hematopoietic output of HE cells toward either an erythroid fate with primitive phenotype, or a definitive lymphoid fate, respectively. We demonstrate that glycolysis-mediated differentiation of HE toward primitive erythroid hematopoiesis is dependent on the epigenetic regulator LSD1. In contrast, OXPHOS-mediated differentiation of HE toward definitive hematopoiesis is dependent on cholesterol metabolism. Our findings reveal that during EHT, metabolism is a major regulator of primitive versus definitive hematopoietic differentiation.
    MeSH term(s) Cell Differentiation ; Cell Lineage/genetics ; Female ; Hemangioblasts/metabolism ; Hematopoiesis/genetics ; Hematopoietic Stem Cells/metabolism ; Humans ; Pregnancy ; Pyruvates/metabolism
    Chemical Substances Pyruvates
    Language English
    Publishing date 2021-12-16
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020896-0
    ISSN 1469-3178 ; 1469-221X
    ISSN (online) 1469-3178
    ISSN 1469-221X
    DOI 10.15252/embr.202154384
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  9. Article ; Online: An atlas of rabbit development as a model for single-cell comparative genomics.

    Ton, Mai-Linh Nu / Keitley, Daniel / Theeuwes, Bart / Guibentif, Carolina / Ahnfelt-Rønne, Jonas / Andreassen, Thomas Kjærgaard / Calero-Nieto, Fernando J / Imaz-Rosshandler, Ivan / Pijuan-Sala, Blanca / Nichols, Jennifer / Benito-Gutiérrez, Èlia / Marioni, John C / Göttgens, Berthold

    Nature cell biology

    2023  Volume 25, Issue 7, Page(s) 1061–1072

    Abstract: Traditionally, the mouse has been the favoured vertebrate model for biomedical research, due to its experimental and genetic tractability. However, non-rodent embryological studies highlight that many aspects of early mouse development, such as its egg- ... ...

    Abstract Traditionally, the mouse has been the favoured vertebrate model for biomedical research, due to its experimental and genetic tractability. However, non-rodent embryological studies highlight that many aspects of early mouse development, such as its egg-cylinder gastrulation and method of implantation, diverge from other mammals, thus complicating inferences about human development. Like the human embryo, rabbits develop as a flat-bilaminar disc. Here we constructed a morphological and molecular atlas of rabbit development. We report transcriptional and chromatin accessibility profiles for over 180,000 single cells and high-resolution histology sections from embryos spanning gastrulation, implantation, amniogenesis and early organogenesis. Using a neighbourhood comparison pipeline, we compare the transcriptional landscape of rabbit and mouse at the scale of the entire organism. We characterize the gene regulatory programmes underlying trophoblast differentiation and identify signalling interactions involving the yolk sac mesothelium during haematopoiesis. We demonstrate how the combination of both rabbit and mouse atlases can be leveraged to extract new biological insights from sparse macaque and human data. The datasets and computational pipelines reported here set a framework for a broader cross-species approach to decipher early mammalian development, and are readily adaptable to deploy single-cell comparative genomics more broadly across biomedical research.
    MeSH term(s) Rabbits ; Humans ; Animals ; Mice ; Gastrulation/genetics ; Organogenesis/genetics ; Embryo Implantation/genetics ; Embryo, Mammalian ; Cell Differentiation ; Embryonic Development/genetics ; Mammals
    Language English
    Publishing date 2023-06-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 1474722-4
    ISSN 1476-4679 ; 1465-7392
    ISSN (online) 1476-4679
    ISSN 1465-7392
    DOI 10.1038/s41556-023-01174-0
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  10. Article ; Online: Reactive Oxygen Species Impair the Function of CD90

    Rönn, Roger E / Guibentif, Carolina / Saxena, Shobhit / Woods, Niels-Bjarne

    Stem cells (Dayton, Ohio)

    2017  Volume 35, Issue 1, Page(s) 197–206

    Abstract: Cell stressors, such as elevated levels of reactive oxygen species (ROS), adversely affect hematopoietic stem cell (HSC) reconstituting ability. However, the effects of ROS have not been evaluated in the context of hematopoietic development from human ... ...

    Abstract Cell stressors, such as elevated levels of reactive oxygen species (ROS), adversely affect hematopoietic stem cell (HSC) reconstituting ability. However, the effects of ROS have not been evaluated in the context of hematopoietic development from human pluripotent stem cells (hPSCs). Using our previously described in vitro system for efficient derivation of hematopoietic cells from hPSCs, we show that the vast majority of generated hematopoietic cells display supraphysiological levels of ROS compared to fresh cord blood cells. Elevated ROS resulted in DNA damage of the CD34
    Language English
    Publishing date 2017-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1143556-2
    ISSN 1549-4918 ; 1066-5099
    ISSN (online) 1549-4918
    ISSN 1066-5099
    DOI 10.1002/stem.2503
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