Minako Ueda

Development of novel research strategy that integrates low dimensionalized bioinformation with multilevel modeling

Research Director

Minako Ueda

Collaborator

Satoru Tsugawa	Assistant Professor Faculty of Systems Science and Technology Akita Prefectural University
Takumi Higaki	Professor Faculty of Advanced Science and Technology Kumamoto University
Koichi Fujimoto	Professor Graduate School of Integrated Sciences for Life Hiroshima University

Outline

High dimensional and hierarchical natures of living systems have been elementary obstacles to understanding the whole molecular mechanisms of which genes control which events to contribute to which rules. In this project, we will quantitatively generate multilevel mathematical models that recapitulate the spatiotemporal dynamics of living systems. By combining these models with low dimensionalized omics and imaging data, we aim to develop a novel strategy to comprehensively identify the molecular underpinnings and the control principle of the complex living systems.

Koji Okamoto

Quantitative reconstruction of spatial organization of refractory cancers via integrative analyses of single-cell and spatial multiomics

Research Director

Koji Okamoto

Collaborator

Ryuji Hamamoto	Chief Research Institute National Cancer Center
Yasushi Yatabe	Department Director National Cancer Center Hospital National Cancer Center

Outline

It has been reported that chemoresistance of clinical cancers is intricately associated with intercellular networks within tumor ecosystem. In this project, we will combine integrative analyses of single-cell and spatial multiomics with various mathematical models and investigate spatial organization and intercellular interaction in clinical cancers and mouse tumor xengrafts. Through our approach, we will visualize cell-cell interactions within tumor microenvironment and thereby reveal a global picture of intercellular networks that are responsible for sustaining chemoresistance of refractory cancers.

Shinya Kuroda

Spatio-temporal trans-omics analysis of metabolic control mechanisms of multi-cellular organ systems

Research Director

Shinya Kuroda

Collaborator

Yuka Inaba	Associate Professor Institute for Frontier Science Initiative Kanazawa University
Tomoyoshi Soga	Professor Institute for Advanced Biosciences Keio University

Outline

Metabolic homeostasis in the mammals is regulated at the molecular level by trans-omics networks across the multi-omic layers of DNA, RNA, proteins, and metabolites; at the cellular level by the optimal spatial arrangement (zonation) of metabolic cells within organs; and at the organ level by crosstalk between the endocrine and autonomic nervous systems. In this study, we investigate the molecular and autonomic regulation of the endocrine and autonomic nervous systems. We will integrate molecular, cellular, and organ levels using spatio-temporal transomic analysis to elucidate the mechanism of metabolic homeostasis.

Hirofumi Shintaku

Annotating multicellular fate dynamics via RNA movie

Research Director

Hirofumi Shintaku

Collaborator

Takahiro Kuchimaru	Associate Professor Graduate Scholl of Medicine Jichi Medical University
Asako Sakaue-Sawano	Research Scientist Center for Brain Science RIKEN
Hidekazu Nishikii	Associate Professor Faculty of Medicine University of Tsukuba

Outline

Omics approaches are powerful but mostly endpoint measurements, limiting our understanding of regulatory networks of genetic interaction. Our project will devise an approach, RNA movie, that visualizes spatial-temporal transcriptional dynamics and the regulatory network by exploiting RNA-sampling from living multicellular systems via nanoelectroporation. We will utilize our approach to explore the fate dynamics of multicellular systems in various contexts of diseases and development.