Research & Members

Through detailed comparative analyses of pluripotent stem cells and cells from in vivo embryos of humans and model organisms, our goal is to establish a novel culture system for pluripotent stem cells that closely replicates the properties of the in vivo embryonic epiblast. Using these newly developed pluripotent stem cells as a starting point, we will work to refine in vitro embryo models and attain a deeper understanding of the emergence of life.

While research on human cells is vital to our understanding of human embryonic development, ethical restrictions limit studies using human embryos or interspecific chimera with animal embryos. In this project, we will leverage novel culture systems developed by our project to rigorously assess the developmental potential of pluripotent stem cells from model animals. By studying various animal species, we aim to uncover both species-specific differences and conserved mechanisms involved in maintaining pluripotency, thereby approaching the fundamental principles of life's emergence.

The peri-implantation stage is a critical window during which the early mammalian embryo undergoes dynamic morphological changes leading to organogenesis. In humans, however, this process occurs within the uterus, thus making direct observations extremely challenging. Furthermore, many aspects of human implantation mechanisms remain poorly understood due to ethical constraints. In this study, by building upon our previous work on the generation of stem cell-based human blastocyst model (blastoids) and imaging of both embryonic and extraembryonic tissues, we aim to visualize the developmental processes occurring during human implantation and to elucidate the mechanisms regulating morphological changes in the peri-implantation embryo. Through this work, we seek to deepen our understanding of human embryogenesis and the fundamental mechanisms underlying the emergence of life.

Organogenesis is a critical step in establishing the basic body plan. While organogenesis has been extensively analyzed using model animals, human organogenesis has been less explored due to ethical issues. Advances in stem cell culture technologies now enable the in vitro reconstruction of early human embryo-like structures. However, no current model accurately recapitulates the organogenesis stage. In this study, we aim to uncover the mechanisms of organogenesis in humans by reconstructing the developmental processes from peri-implantation to organogenesis stages in vitro using organoid culture techniques, microfluidic devices, and genome editing techniques.

Three lineages—epiblast, trophectoderm, and primitive endoderm—compose the blastocyst, giving rise to the embryo, placenta, and yolk sac, respectively. Although ES, TS, and PrES cells have been established from these lineages and could conceptually reconstitute a blastocyst, no one has yet to succeed in generating a functional embryo solely from stem cells. This project aims to reconstruct embryo-like models with developmental capacity by precisely capturing the properties of each cell type and reestablishing intercellular interactions among the three lineages.

Based on single-cell analyses of early embryonic cells, we will construct intercellular interaction networks among epiblast, trophectoderm, and primitive endoderm in the blastocyst. We will compare these to networks formed by stem cell lines established in vitro. For newly established lines with high similarity to the blastocyst network, we will evaluate their potential for chimera contribution by injection into blastocysts. Our work will clarify essential interactions required for developmental potential in artificial embryos derived from stem cells.

Life begins when a sperm and an egg meet and fuse to form a fertilized egg, which contains maternal and paternal factors derived from each gamete. However, how sperm and eggs acquire paternal and maternal factors during gametogenesis and how they contribute to successful embryonic development remains unclear. While, as if by default, most naturally fertilized mouse eggs successfully develop, many in vitro-produced oocytes fail to do so, likely due to imbalanced expression of maternal factors during oocyte growth. This study aims to elucidate the gene networks allowing oocytes to acquire the precise amount of necessary maternal factors during the growth stage and to determine the roles of these factors in fertilization and development, thereby revealing the mechanisms that ensure successful embryonic development.

Paternal factors conferred during spermatogenesis have been reported in recent years to influence post-fertilization embryo development and offspring phenotype, but the underlying mechanisms remain largely unknown. We have established nearly 100 genetically modified mouse strains exhibiting male infertility due to spermatogenesis defects and sperm dysfunction. In this study, we aim to clarify the effects of paternal factors on subsequent generations by analyzing wild-type and mutant sperm.

Transcriptional programs, such as zygotic genome activation, are essential for embryogenesis. Since embryonic development progresses rapidly, RNAs and proteins synthesized during early stages often play critical roles at later stages. While stem cell-derived embryo models have been developed recently, they bypass certain in vivo developmental processes, which may underlie their limited developmental potential. This study aims to elucidate the regulatory mechanisms of early embryonic transcriptional programs and the functions of downstream RNAs and proteins. Through this work, we hope to enhance the understanding of embryogenesis and help advance embryo model research.

Epigenomes are crucial for proper gene regulation during development and differentiation and undergo dramatic changes during gametogenesis, fertilization, and preimplantation development. For example, oocytes form unique epigenomic structures partially erased or retained after fertilization, contributing to the next generation. During preimplantation, somatic-type epigenomes are newly formed. However, mechanisms regulating these dynamic changes and their biological significance are poorly understood. This study aims to unveil these aspects of epigenome dynamics during oogenesis and preimplantation development, thereby elucidating in vivo developmental robustness ensuring successful embryogenesis and improving in vitro embryo models.

Somatic cell nuclear transfer (SCNT) embryos are created by replacing the nucleus of an oocyte with that of a somatic cell and possess a genome identical to that of a fertilized embryo. However, most SCNT embryos arrest development during early stages, particularly immediately after implantation. Notably, a similar developmental arrest also occurs in stem cell-derived embryo models, thus indicating that these failures may result from shared epigenetic abnormalities. This study aims to identify novel epigenetic defects underlying these failures and to elucidate the developmental robustness required for normal development, thereby contributing to research on the emergence of life using embryo models.

In Japan, one in every 5–6 couples experiences infertility, and one in ten babies is born via assisted reproductive technologies (ART), such as in vitro fertilization. However, the lack of sufficient animal experiments has been a long-standing concern. Although fertilization is generally believed to reset genetic information completely, our mouse studies have shown that ART-derived individuals can exhibit abnormalities across generations. The long-term and transgenerational effects of ART in humans remain unknown due to the long reproductive cycle. We aim to compare individuals conceived naturally and via ART using mouse models to uncover the molecular mechanisms governing healthy inheritance.

To compare naturally fertilized and ART-conceived individuals, we must comprehensively and accurately assess their phenotypes. As part of the International Mouse Phenotyping Consortium (IMPC), we have established a globally standardized phenotype analysis pipeline with over 700 items (hematology, morphology, behavior, etc.). Using this platform, we will analyze the phenotypes of ART-derived individuals and subsequent-generation their offspring and further conduct detailed secondary analyses with newly developed methods to clarify molecular mechanisms ensuring proper transgenerational developmental robustness.

Embryonic development is a remarkable process in which a single fertilized egg gives rise to a fully formed organism, involving resetting and reorganizing epigenomic states, differentiating into various cell types, and self-organization. Through these complex events, a functional living system is built. To understand this process, it is not enough to study individual molecular mechanisms or pathways. We must also grasp how the entire system works in a coordinated manner. Furthermore, to artificially engineer aspects of the emergence of life, we need to have a rational strategy for designing complex bioengineering processes to manipulate stem cell-based embryos. This research project aims to gain new insights into the emergence of life by constructing an “in silico digital embryo.” In addition to our efforts to obtain novel datasets, we will develop simulations capable of predicting embryonic development by integrating diverse data and knowledge from researchers involved in this initiative. These digital models will help uncover the principles underlying the emergence of life and robust mechanisms ensuring proper development.

The rapid and robust generation of in vitro embryo models and their multimodal analysis is crucial for advancing the development of digital embryo models to understand the mechanisms of early development. This project aims to overcome these challenges by integrating genetic barcoding with optical barcoding in stem cell-derived embryo models, enabling high-precision tracing and detailed visualization and quantification of spatiotemporal developmental processes. In conjunction with multiplexed phenotypic analysis, our approach will enhance the construction reproducibility of embryo models and aid the development of digital embryo models. Ultimately, this work will provide deeper insights into the fundamental principles of early development and the mechanisms underlying developmental disruptions.