Integrated pseudotime analysis of human pre-implantation embryo single-cell transcriptomes reveals the dynamics of lineage specification

doi:10.1016/j.stem.2021.04.027

. 2021 Sep 2;28(9):1625-1640.e6.

doi: 10.1016/j.stem.2021.04.027. Epub 2021 May 17.

Integrated pseudotime analysis of human pre-implantation embryo single-cell transcriptomes reveals the dynamics of lineage specification

Dimitri Meistermann¹, Alexandre Bruneau², Sophie Loubersac³, Arnaud Reignier³, Julie Firmin³, Valentin François-Campion², Stéphanie Kilens², Yohann Lelièvre⁴, Jenna Lammers⁵, Magalie Feyeux⁶, Phillipe Hulin⁷, Steven Nedellec⁷, Betty Bretin², Gaël Castel², Nicolas Allègre⁸, Simon Covin², Audrey Bihouée⁹, Magali Soumillon¹⁰, Tarjei Mikkelsen¹⁰, Paul Barrière³, Claire Chazaud⁸, Joel Chappell¹¹, Vincent Pasque¹¹, Jérémie Bourdon⁴, Thomas Fréour¹², Laurent David¹³

Affiliations

¹ Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; LS2N, UNIV Nantes, CNRS, Nantes, France.
² Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France.
³ Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; CHU Nantes, Université de Nantes, Service de Biologie de la Reproduction, 44000 Nantes, France.
⁴ LS2N, UNIV Nantes, CNRS, Nantes, France.
⁵ CHU Nantes, Université de Nantes, Service de Biologie de la Reproduction, 44000 Nantes, France.
⁶ Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; Université de Nantes, CHU Nantes, INSERM, CNRS, SFR Santé, FED 4203, INSERM UMS 016, CNRS UMS 3556, Nantes, France.
⁷ Université de Nantes, CHU Nantes, INSERM, CNRS, SFR Santé, FED 4203, INSERM UMS 016, CNRS UMS 3556, Nantes, France.
⁸ GReD Laboratory, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, CRBC, 63000 Clermont-Ferrand, France.
⁹ Université de Nantes, CHU Nantes, INSERM, CNRS, SFR Santé, FED 4203, INSERM UMS 016, CNRS UMS 3556, Nantes, France; Institut du Thorax, UNIV Nantes, INSERM, CNRS, Nantes, France.
¹⁰ Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
¹¹ KU Leuven - University of Leuven, Department of Development and Regeneration, Institute for Single Cell Omics, Leuven Stem Cell Institute, Herestraat 49, 3000 Leuven, Belgium.
¹² Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; CHU Nantes, Université de Nantes, Service de Biologie de la Reproduction, 44000 Nantes, France. Electronic address: thomas.freour@chu-nantes.fr.
¹³ Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; Université de Nantes, CHU Nantes, INSERM, CNRS, SFR Santé, FED 4203, INSERM UMS 016, CNRS UMS 3556, Nantes, France. Electronic address: laurent.david@univ-nantes.fr.

PMID: 34004179
DOI: 10.1016/j.stem.2021.04.027

Free article

Integrated pseudotime analysis of human pre-implantation embryo single-cell transcriptomes reveals the dynamics of lineage specification

Dimitri Meistermann et al. Cell Stem Cell. 2021.

Free article

. 2021 Sep 2;28(9):1625-1640.e6.

doi: 10.1016/j.stem.2021.04.027. Epub 2021 May 17.

Authors

Affiliations

¹ Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; LS2N, UNIV Nantes, CNRS, Nantes, France.
² Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France.
³ Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; CHU Nantes, Université de Nantes, Service de Biologie de la Reproduction, 44000 Nantes, France.
⁴ LS2N, UNIV Nantes, CNRS, Nantes, France.
⁵ CHU Nantes, Université de Nantes, Service de Biologie de la Reproduction, 44000 Nantes, France.
⁶ Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; Université de Nantes, CHU Nantes, INSERM, CNRS, SFR Santé, FED 4203, INSERM UMS 016, CNRS UMS 3556, Nantes, France.
⁷ Université de Nantes, CHU Nantes, INSERM, CNRS, SFR Santé, FED 4203, INSERM UMS 016, CNRS UMS 3556, Nantes, France.
⁸ GReD Laboratory, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, CRBC, 63000 Clermont-Ferrand, France.
⁹ Université de Nantes, CHU Nantes, INSERM, CNRS, SFR Santé, FED 4203, INSERM UMS 016, CNRS UMS 3556, Nantes, France; Institut du Thorax, UNIV Nantes, INSERM, CNRS, Nantes, France.
¹⁰ Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
¹¹ KU Leuven - University of Leuven, Department of Development and Regeneration, Institute for Single Cell Omics, Leuven Stem Cell Institute, Herestraat 49, 3000 Leuven, Belgium.
¹² Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; CHU Nantes, Université de Nantes, Service de Biologie de la Reproduction, 44000 Nantes, France. Electronic address: thomas.freour@chu-nantes.fr.
¹³ Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; Université de Nantes, CHU Nantes, INSERM, CNRS, SFR Santé, FED 4203, INSERM UMS 016, CNRS UMS 3556, Nantes, France. Electronic address: laurent.david@univ-nantes.fr.

PMID: 34004179
DOI: 10.1016/j.stem.2021.04.027

Abstract

Understanding lineage specification during human pre-implantation development is a gateway to improving assisted reproductive technologies and stem cell research. Here we employ pseudotime analysis of single-cell RNA sequencing (scRNA-seq) data to reconstruct early mouse and human embryo development. Using time-lapse imaging of annotated embryos, we provide an integrated, ordered, and continuous analysis of transcriptomics changes throughout human development. We reveal that human trophectoderm/inner cell mass transcriptomes diverge at the transition from the B2 to the B3 blastocyst stage, just before blastocyst expansion. We explore the dynamics of the fate markers IFI16 and GATA4 and show that they gradually become mutually exclusive upon establishment of epiblast and primitive endoderm fates, respectively. We also provide evidence that NR2F2 marks trophectoderm maturation, initiating from the polar side, and subsequently spreads to all cells after implantation. Our study pinpoints the precise timing of lineage specification events in the human embryo and identifies transcriptomics hallmarks and cell fate markers.

Keywords: blastocyst; cell fate; epiblast; human embryo; lineage specification; pluripotency; preimplantation development; pseudotime; scRNA-seq; trophectoderm.

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Conflict of interest statement

Declaration of interests The authors declare no competing interests.

Comment in

Refined transcriptional blueprint of human preimplantation embryos.
Weltner J, Lanner F. Weltner J, et al. Cell Stem Cell. 2021 Sep 2;28(9):1503-1504. doi: 10.1016/j.stem.2021.08.011. Cell Stem Cell. 2021. PMID: 34478626

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Integrated pseudotime analysis of human pre-implantation embryo single-cell transcriptomes reveals the dynamics of lineage specification

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Integrated pseudotime analysis of human pre-implantation embryo single-cell transcriptomes reveals the dynamics of lineage specification

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