Defining the three cell lineages of the human blastocyst by single-cell RNA-seq.
Paul Blakeley, Norah M E Fogarty, Ignacio del Valle, Sissy E Wamaitha, Tim Xiaoming Hu, Kay Elder, Philip Snell, Leila Christie, Paul Robson, Kathy K Niakan
Author Information
Paul Blakeley: Human Embryology and Stem Cell Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, UK.
Norah M E Fogarty: Human Embryology and Stem Cell Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, UK.
Ignacio del Valle: Human Embryology and Stem Cell Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, UK.
Sissy E Wamaitha: Human Embryology and Stem Cell Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, UK.
Tim Xiaoming Hu: Genome Institute of Singapore, A-STAR, Singapore 138672, Singapore MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK.
Kay Elder: Bourn Hall Clinic, Bourn, Cambridge CB23 2TN, UK.
Philip Snell: Bourn Hall Clinic, Bourn, Cambridge CB23 2TN, UK.
Leila Christie: Bourn Hall Clinic, Bourn, Cambridge CB23 2TN, UK.
Paul Robson: Genome Institute of Singapore, A-STAR, Singapore 138672, Singapore The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA.
Kathy K Niakan: Human Embryology and Stem Cell Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, UK kathy.niakan@crick.ac.uk.
Here, we provide fundamental insights into early human development by single-cell RNA-sequencing of human and mouse preimplantation embryos. We elucidate conserved transcriptional programs along with those that are human specific. Importantly, we validate our RNA-sequencing findings at the protein level, which further reveals differences in human and mouse embryo gene expression. For example, we identify several genes exclusively expressed in the human pluripotent epiblast, including the transcription factor KLF17. Key components of the TGF-β signalling pathway, including NODAL, GDF3, TGFBR1/ALK5, LEFTY1, SMAD2, SMAD4 and TDGF1, are also enriched in the human epiblast. Intriguingly, inhibition of TGF-β signalling abrogates NANOG expression in human epiblast cells, consistent with a requirement for this pathway in pluripotency. Although the key trophectoderm factors Id2, Elf5 and Eomes are exclusively localized to this lineage in the mouse, the human orthologues are either absent or expressed in alternative lineages. Importantly, we also identify genes with conserved expression dynamics, including Foxa2/FOXA2, which we show is restricted to the primitive endoderm in both human and mouse embryos. Comparison of the human epiblast to existing embryonic stem cells (hESCs) reveals conservation of pluripotency but also additional pathways more enriched in hESCs. Our analysis highlights significant differences in human preimplantation development compared with mouse and provides a molecular blueprint to understand human embryogenesis and its relationship to stem cells.
