Omics Perspective on Cell Fate Determination Mechanisms

Background Introduction

During early mammalian embryo development, a totipotent zygote undergoes several cell divisions and two rounds of cell fate determination, ultimately forming a mature blastocyst. In this process, as the embryo compresses, the establishment of apicobasal cell polarity breaks the symmetry of the embryo and guides subsequent cell fate choices. The lineage separation of the inner cell mass (ICM) and trophectoderm (TE) is the first sign of cell differentiation, but some molecules have been shown to bias early cell fate through inter-cellular variations at earlier stages (such as 2-cell and 4-cell stages).

Revealing the mechanisms of early cell fate determination has become an important research topic. In this review, we summarize the molecular events that occur during early embryogenesis and their regulatory roles in cell fate determination. Additionally, single-cell omics technology, as a powerful tool for early embryogenesis research, has been applied to pre-implantation embryos in mice and humans, contributing to the discovery of cell fate regulators.

Paper Source

This article was written by Lin-Fang Ju, Heng-Ji Xu, Yun-Gui Yang, and Ying Yang from the University of Chinese Academy of Sciences, Beijing Institute of Genomics, and CAS Center for Excellence in Precision Medicine and Genomics Innovation. The paper was published in the journal “Genomics Proteomics Bioinformatics” in 2023.

Research Process

Preliminary Research

The research first focused on molecular events during early mammalian embryogenesis. Prior to implantation, the fertilized egg goes through 2-cell, 4-cell, 8-cell, and morula (16 to 32 cell embryo) stages, eventually forming a hollow spherical blastocyst. A series of events occur during this process, including zygote genome activation (ZGA), embryo compression, and two rounds of cell fate determination.

Molecular Mechanisms

To better understand the molecular mechanisms behind early cell fate determination, the study explored the roles of several key transcription factors and signaling pathways.

1. First Cell Fate Determination:

   • The first cell fate determination separates cells into TE and ICM lineages. Representative transcription factors such as SOX2, OCT4, and NANOG are activated in ICM, while CDX2 is expressed in TE. SOX2 and OCT4 are highly expressed in morula and blastocyst stages and can be detected at 2-cell and 4-cell stages.
   • Hippo and Notch signaling pathways also play important roles in the first cell fate determination. The Hippo pathway is activated in ICM cells through changes in TEAD4 and YAP states, while inactive in TE cells. Unphosphorylated YAP translocates from the cytoplasm to the nucleus, interacting with TEAD4 to promote the expression of TE lineage-specific genes CDX2 and GATA3.
   • The Notch signaling pathway works in concert with YAP and TEAD4 to control the first cell fate determination. In TE cells, the NICD–RBPJ complex of the Hippo and Notch pathways enters the nucleus, upregulating the expression of TE-specific genes such as CDX2.

2. Second Cell Fate Determination:

   • The second cell fate determination further differentiates ICM cells into EPI and PE cells. Specific marker transcription factors such as NANOG and GATA6 identify EPI and PE lineages, respectively. NANOG and OCT4 cooperatively upregulate FGF4 expression and inhibit GATA6 expression. FGF4 binds specifically to FGFR, activating the FGF/MAPK signaling cascade, increasing GATA6 expression and inhibiting NANOG, thereby promoting PE lineage formation.

Establishment of Cell Polarity

When compaction begins, the embryo’s blastomeres break the symmetry of cell morphology, dividing into polar and non-polar cells. Polar cells are in the outer region, while non-polar cells are in the central region. The apical cortex of polar cells establishes an F-actin ring containing apical polarity proteins, and this cell polarity interacts with the Hippo signaling pathway to regulate cell fate allocation.

Cell Heterogeneity

During early cell fate determination, cells exhibit significant heterogeneity in RNA transcription, histone modifications, and transcription factor dynamics. These cellular differences influence subsequent cell fate determination by affecting the function of specific transcription factors. For example, CARM1 and its methylated histone H3 show significant differences between cells in 4-cell stage embryos, driving cell fate determination.

Research Results

1. First Cell Fate Determination

• In the first cell fate determination, ICM and TE cell lineages are achieved through the activation of transcription factors such as SOX2, OCT4, and NANOG, with significant differences in the activity of Hippo and Notch signaling pathways between different lineages.

1. Second Cell Fate Determination

• The second cell fate determination further differentiates ICM cells into EPI and PE cells, with the FGF signaling pathway playing a key role.

1. Cell Polarity

• In the establishment of cell polarity, the symmetry of cell morphology is broken, polar cells gradually form, and apical polarity proteins and their F-actin rings accumulate in the outer region, participating in the regulation of cell fate.

1. Cell Heterogeneity

• Cells in early embryos show significant heterogeneity, which influences cell fate determination by affecting the dynamic behavior of transcription factors such as SOX2, NANOG, and CDX2.

Conclusions and Significance

Research Conclusions

This article summarizes the molecular events during early mammalian embryo development and their roles in cell fate determination, pointing out the powerful application potential of single-cell omics technology in such research. The study found that transcription factors, signaling pathways, cell polarity, and cell heterogeneity together form a complex network that accurately determines cell fate through multi-level regulation.

Scientific Value

These studies are of great significance for understanding the mechanisms of early mammalian embryonic development, not only providing strong theoretical support for basic biological research but also having broad application prospects in medical fields, especially in reproductive medicine and stem cell research.

Future Outlook

Although much progress has been made, many mysteries remain unsolved. For example, are there other important regulatory layers, such as RNA translation, that are asymmetrically distributed in the 2-4 cell stage or earlier and related to early cell fate separation? Are there other types of histone modifications, such as histone acetylation, that determine different regulatory axes of cell fate? What is the origin of heterogeneity between cells? The answers to these questions will provide a clearer picture of the detailed mechanisms of early cell fate regulation.

The development of single-cell omics/multi-omics technologies has made genomic and epigenomic profiling possible and will help comprehensively understand the process of early embryonic development. With continuous innovation and application of technology, these questions will be further answered in future research.