Publicly Offered Research


Development of fluorescent probes for visualizing the pH-based singularity inside bodies

Name Kenjiro Hanaoka
Affiliation Graduate School of Pharmaceutical Sciences, The University of Tokyo
Major Chemical Biology
Purpose In this study, we will try to develop fluorescent probes, which enable the wide-field and long-term observation of pH-based singularity inside bodies. In the biological system, pH is strictly controlled in tissues, while the singular regions such as tumors show weakly acidic condition due to the active cell proliferation. So, the pH observation can potentially detect the singularity of various biological phenomena. Fluorescent probes should possess the near-infrared fluorescence from 650 nm to 900 nm, which is suitable for the whole-body imaging, and can be applied to the ratiometric fluorescence imaging for correcting the biodistribution of the probes.

Development of the non-invasive method for detection of transformed cells in human stem cell cultures

Name Daisuke Nanba
Affiliation Medical Research Institute, Tokyo Medical and Dental University
Major Stem Cell Biology
Purpose Human epidermal stem cells self-new themselves and form the stem cell colonies. However, the stem cells sometimes give rise to a growth-arrested transformed cell within the colony. The appearance of a transformed cell (= a singularity cell) results in the growth arrest of the stem cell colony itself. Although the mechanisms of the appearance of transformed cells are largely unknown, the transformed cells decrease their migration activity. In this study, we try to develop a noninvasive method for detecting the transformed cells based on their motility, and clarify how the transformed cells are generated in the stem cell colony.

Development of polymer caged luciferin enabling spatiotemporal trans-scale imaging

Name Yuki Hiruta
Affiliation Department of Applied Chemistry, Faculty of Science and Technology,Keio University
Major Analytical chemistry
Purpose In order to realize spatiotemporal trans-scale imaging, it is essential to develop a bright, and long-term observable luminescent probe enabling long-term imaging. In this research, we focus on the bioluminescent substrate furimazine, and aim to establish a highly bright, and long-term observable bioluminescence imaging technology. With furimazine as a novel bioluminescence platform, NanoLuc showed the highest level of luminescence brightness and enabled imaging at the organelle level. However, Long-term bioluminescence imaging with furimazine is limited by poor oxidative stability, non-specific luminescence in animals, short half-life time in blood, and lower water solubility. In this study, we develop furimazine derivatives with improved water solubility, stability and retention in blood by introduction of polymer chains.

Finding and Understanding Singularity Phenomena Using 4D Photoacoustic Imaging

Name Miya Ishihara
Affiliation Dept. of Medical Engineering, National Defense Medical College
Major Biomedical optical engineering
Purpose Photoacoustic (PA) imaging based on optical absorption and ultrasonic detection has the advantage of imaging that can penetrate deeply without compromising on visualization depth or imaging resolution. This study targets the spatiotemporal dynamics of singularity cell using PA imaging technology. We will establish cross-organ 4D PA spectroscopic imaging in order to find singularity cell as discontinuous change.


Mechanistic Modeling of Crowds Led by Cells of Singularity

Name Yuichi Togashi
Affiliation Graduate School of Integrated Sciences for Life, Hiroshima University
Major Computational Biology
Purpose What leads to cells of “singularity”, and what does the “singularity” bring about? Our goal is to show possible answers to these questions in a theoretical and universal way. We particularly focus on mechanical interactions between cells and the environment. Recently, we have modeled crowds of molecular machines and studied possible interplay between their internal states and surroundings. In this project, by extending this modeling framework, we aim to construct mechanistic models of cell crowds that can reproduce and predict how cells of “singularity” arise from and make an impact on the crowds.

Development of single cell multi-omics tecnique for identification of singularity cells

Name Akihito Harada
Affiliation Division of Transcriptomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation Kyushu University
Major Biochemistry
Purpose Singularity cells exist as rare cells during process of sequential cell change in tissues. Although single cell RNA-seq (scRNA-seq) is a technique for detecting rare cells, it is difficult to clarify whether the quantified transcript is reflected the result as during transcription or as the end of transcription in the cell (the loss of time scale). Then, in order to identify singularity cells, it is necessary to predict next change. This research will develop technology that can identify and predict the function of singularity cells by simultaneously obtaining both of transcripts and the chromatin structural changes which reflected cell states in a single cell.

Detection of singularity neurons during neural network formation

Name Kotaro Oka
Affiliation Department of Biosciences and Informatics, Keio University
Major Neuroscience/Biophysics
Purpose We will detect and investigate the generation of singularity neurons which govern network behavior in the random neural network consisted of about 10~100 neurons. After application of perturbation on neural activity by optogenetics and/or ITO electrode, we will induce the re-wiring in the network. And the changes of network characteristics will be evaluated by several imaging techniques: neural activities, synaptic vesicle release, and kinase activities. We will reveal how to generate the specific singularity neurons during re-wiring the neural networks.

Identifying singular cells based on quantification of unpredictabiliy through spatio-temporal modeling

Name Yohei Kondo
Affiliation Exploratory Research Center on Life and Living Systems
Major Theoretical biology
Purpose We will develop a statisical technique to identify singler cells based on “unpredictability” of their behaviors. Our strategy is to infer a dynamical systems model from live-imaging data on a tissue, and to quantify how the model fails to predict the dynamics of each cell by error analysis. As a proof-of-concept, we will apply the method to wound healing of cultured cell sheet where spatio-temporal MAPK signaling drives collective cell migration, and thereby reveal the role of singular cells in this popular model system.


Singularity in influenza virus infection

Name Yusuke Ohba
Affiliation Department of Cell Physiology, Faculty of Medicine, Hokkaido University
Major Cell Biology
Purpose Even with recent advances in medicine, viral infection is one of the leading cause of death worldwide. We performed infection assay with tightly controlling the number of virus particles, and found that host cells display different responses in a manner dependent on the number of virus particles (more than 20 and less than 20 particels per cell). In this study, we define such 20 particles/cell as “singularity,” and the changes in cellular response as “singularity phenomena in viral infection.” We will elucidate a role of singularity cells and the mode of infection in the real world.

Cancer-promoting singularity cells in pancreatic cancer

Name Masahiro Sonoshita
Affiliation Division of Biomedical Oncology, Hokkaido University Institute for Genetic Medicine
Major Oncology, Pharmaceutical Sciences
Purpose Cancer is the top leading cause of death in advanced countries including Japan. Especially pancreatic cancer is frequently resistant to therapies, making it one of the cancer types with the worst prognosis.
In this study, we aim to test a hypothesis that there exist cancer-promoting singularity cells among transformed cells in the pancreas promoting carcinogenesis. To this end, we will generate an efficient research platform by combining cell culture, mouse and Drosophila pancreatic cancer models with AMATERAS, the high-resolution and real-time monitoring system. This effort would contribute to identifying the disease mechanisms and novel therapeutics for this devastating disorder.

Elucidation of the principle of ploidy reversal in tumorigenesis


Name Ryota Uehara
Affiliation Hokkaido University, Faculty of Advanced Life Science
Major Cell Biology
Purpose Whole genome duplication and subsequent chromosome loss (ploidy reversal), which drastically change cellular phenotypes, are hallmarks of cancer. However, as ploidy reversal happens at extremely low frequency both in cell cultures and tissues, it is difficult to specify cellular conditions that evoke the event and to trace its long-term consequences in the process of tumorigenesis. In this study, using a new imaging system that enables simultaneous high spatiotemporal imaging and long-term cell lineage tracing, we will identify rare cellular states that cause ploidy reversal and elucidate its principle and pathological contribution in tumorigenesis.

Imaging of synapse elimination in the developing brain


Name Masanobu Kano
Affiliation The University of Tokyo
Major Meurophysiology
Purpose Postnatal development of the climbing fiber (CF) to Purkinje cell (PC) synapse is a representative model of synapse elimination. In this process, a single CF is selectively strengthened (‘winner’CF) and remains into adulthood, while the other CFs (‘loser’ CFs) are eventually eliminated. This is a typical singularity phenomenon because it occurs during a limited critical period, and once a winner and losers are determined, the fate is usually irreversible. Here we will investigate how a winner and losers are determined and how neural activity is involved in CF synapse elimination.

Singularity in the collectives state transition in Dictyostelium movement


Name Satoshi Sawai
Affiliation University of Tokyo
Major Physical Biology
Purpose Cell movments in Dictyostelium aggregates are directed not just by the well-known chemotaxis to extracellular cAMP but also by contact-dependent signal. The directed cell movements are responsible for large scale cell rearrangements in the aggregates. The project will focus on a few minority cells that exhibit irregular cell movements in the aggregates to understanding how cellular rearrangements takes place by a delicate balance of ordered and disordered tissue-level dynamics. The work will combine a new fluorescent tagging approach and high-throughput cell migration assays and elucidate the multi-level relationship between polariy ordering and synchrony in the reaction-diffusion chemoattractant dynamics.

Life and death decisions on encephalitis

Name Jun Arii
Affiliation Divison of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine
Major Virology
Purpose Viral encephalitis occurs sporadically and often follows a fatal course. Herpesviruses involve a wide variety of diseases including encephalitis in human. They also establish life-long latent infections in the host. Although most humans are infected with herpesviruses, they rarely cause encephalitis. Thus, it is not clear how they reactivate to cause encephalitis. The goal of this project is to identify and characterize cells which trigger the onset of viral encephalitis. This project might promote better understanding of pathogenesis of viral encephalitis and contribute intervention for it.

Mathematical modeling of outlier immune cells using extreme statistics

Name Naotoshi Nakamura
Affiliation Center for Mathematical Modeling and Data Science, Osaka University
Major Mathematical cell biology
Purpose Recent developments in bioimaging studies have revealed an unexpected degree of functional variability among the same cellular species. We have devised a method of analysis to uncover cell-to-cell variability from the dynamics of cells and elucidate the axes that govern intercellular differences. Based on this method, here we aim to identify outlier immune cells from a set of mouse imaging data. We then analyze their spatiotemporal dynamics in detail and reveal their functional significance using extreme value statistics.

Identification of singularity cells that masculinize a primary organizer in response to environmental stimuli

Name Yasuhiko Kato
Affiliation Graduate School of Engineering, Osaka University
Major Environmental Molecular Biology
Purpose In sex determination of the crustacean Daphnia magna, decline of environmental qualities is detected by mothers and is transmitted to offspring via juvenile hormone (JH) signaling, which results in transition from female to male sex during early embryogenesis. In this process, we previously found that transcription factor Dsx1 masculinizes a presumptive primary organizer of the gastrula to trigger male differentiation. Before this singularity phenomenon, we also found JH-dependent expression of the other transcription factors. In this study, to identify the singularity cells, live imaging and perturbation of cells expressing the transcription factors including Dsx1 are planned.

Elucidation of singularity events during immune reactions by Time-dependent Immunology and single cell analysis

Name Masahiro Ono
Affiliation The International Research Center for Medical Sciences (IRCMS) , Kumamoto University; Imperial College London
Major Immunology, Genomics
Purpose T cells play central roles in regulating immune responses. However, it is almost unknown when the bifurcation of cellular fates occurs in individual cells. The project will aim to identify and analyse the rare and unique cells that are at the bifurcation point, which we define as the ‘singularity’ of T cell activation and differentiation. Firstly, we will analyse single cell RNA-seq data and thereby identify the ‘singularity’ cells. Next, we will aim to develop a new reporter system for analysing these cells. Subsequently, we will use our immunological genome analysis methods, which analyse single cell dynamics, and our Tocky technology, which analyses temporal dynamics of molecular events in T cells, in order to identify the singularity cells, and elucidate their single cell transcriptomes, and reveal the features of these cells by microscopic analysis.

Identification and functional analysis of singularity cells on intratumoral heterogeneity

Name Tomoya Yamaguchi
Affiliation Department of Cancer Biology, Graduate School of Medical Sciences, Kumamoto University
Major Tumor Biology
Purpose A lung adenocarcinoma arising from a peripheral lung, the most frequently occurring histological type, exhibits a high degree of heterogeneity. However, the molecular and cellular mechanisms that underlie tumor heterogeneity remain central questions in the field of cancer biology research. In the present study, we show that lung adenocarcinoma subtype classifiers are expressed across individual cells within a tumor, and identify the potential singularity cells of such intratumoral heterogeneity. Accurate identification of singularity cells allows for earlier detection of malignancy and may ultimately lead to development of novel preventive therapies for individuals at high risk for cancer.

Analysis of the singularity phenomenon by mosaicism using disease-specific iPS cells

Name Etsuro Ohta
Affiliation Kitasato University School of Allied Health Sciences
Major Neuroscience
Purpose Tau is related to cognitive dysfunction that is one of non-motor symptoms of Parkinson’s disease (PD). In this study, to elucidate the propagation of oligomer-Tau and its degradation mechanism by singularity phenomenon, we analyze disease-specific iPS cells (iPSC) from familial PD patient with LRRK2 mutation. Furthermore, to investigate whether singularity cells with oligomer-Tau are caused by mosaicism of mutant LRRK2 allele, we analyze iPSC-derived neurons under in vitro and in vivo conditions.

Singularity determining development of autoimmune diseases

Name Shunsuke Chikuma
Affiliation Keio University School of Medicine
Major Cellular and Molecular Immunology
Purpose Autoimmune diseases are initiated by lymphocytes attacking limited number of autoantigen, which causes activation of more lymphocytes against more antigens, and progress to antigen non-specific inflammation. We will observe “epitope spreading” after initiating the autoimmune reaction with known antigen specificity. We aim to difine the number of initial immune reaction that sets a “point of no return” for the establishment of autoimmune symptoms as a final phenotype.

Evocation of singularity at emergence of cancer cells in normal stroma

Name Kon Shunsuke
Affiliation Tokyo University of Science, Research Institute for Biomedical Sciences, Division of Development and Aging
Major Cancer Biology
Purpose Tumor microenvironment (TME) is a specialized, complex compartment comprising of tumor-educated stromal cells, which promotes both survival and proliferation of cancer cells. However, it remains enigmatic what happens at emergence of cancer cells in stroma, where normal stromal cells face to cancer cells at the first time. Our preliminary results suggest that normal stroma countervails the expansion of low-grade cancer cells, while high-grade cancer cells are able to transform normal storma into TME. In this study, we aim to reveal the nature of singularity at the initial stage of TME formation by combined ex vivo imaging and omics approaches.

Analysis and control of singularity structures triggering epileptic seizure

Name Keiko Muguruma
Affiliation Faculty of Medicine, Kansai Medical University
Major Neuroscience, Developmental Biology, Stem Cell Biology
Purpose Epilepsy is a neurological disorder that is characterized by epileptic seizure due to abnormally excessive neuronal activity. In this study, we aim to understand and control epileptic seizure as a singular transition of neuronal activity from normal stable state to abnormal hyper-excitable state. We first develop a culture system that recapitulates the seizure by applying iPS cell differentiation technology. We further investigate the mechanism that triggers the seizure by precise real-time measurement and quantitative analysis of the neuronal activity. We finally search for effective methods to predict, prevent and stop the seizure.

Search and functional analysis of singularity synapses

Name Hideji Murakoshi
Affiliation National Institute for Physiological Sciences
Major Neuroscience, Biophysics
Purpose Hippocampal and neocortical neurons have thousands of excitatory synapses (spines). A single neuron receives multiple synaptic inputs from many presynaptic neurons. If the sum of these inputs is strong enough, it evokes an action potential. Recently, we found that the reactivity of individual spines is variable, and there are spines that have large reactivity for an input stimulation. The aim of this research is to identify the singularity spines (that efficiently convert a certain input to large outputs such as action potentials) using the cutting-edge optical microscopy in combination of electrophysiology.

Investigation of emvironmental factors causing singular MET events using a realtime evaluation system

Name Minoru Takasato
Affiliation RIKEN Center for Biosystems Dynamics Research
Major Stem Cell Biology
Purpose During kidney development, nephron progenitor cells develop into the nephron, a functional unit of the kidney, via mesenchymal-epithelial transition (EMT). We previously established an in vitro system in which METs can be artificially induced to human iPSCs-derived nephron progenitor cells by the stimulation of canonical-Wnt signalling. Interestingly, we further demonstrated that those MET events occur constantly and singularly within a uniform nephron progenitor population. Here, in this research project, we aim to elucidate the singularity of environmental factors that control such rare MET events using our developed in vitro MET occurrence system.

Investigating phase transition mechanisms of tau protein using in vivo multimodal imaging systems

Name Naruhiko Sahara
Affiliation National Institutes for Quantum and Radiological Sciences and Technology
Major Neurochemistry, Dementia
Purpose Accumulation of intracellular neurofibrillary tangles (NFTs) consisting of microtubule-associated protein tau is a major hallmark of tauopathy. NFTs are closely associated with the severity of brain function loss and neuronal death. At present, we don’t know causal mechanisms of tau neuropathology. We hypothesize that tau protein phase transition induces neurotoxicity and cell death in the brain. The aim of this study is to identify the checkpoint of tau protein transition in tauopathy mouse models using in vivo multimodal imaging techniques.

Regulatory mechanism of sponge stem cells

Name Noriko Funayama
Affiliation Department of Biophysics, Graduate School of Science, Kyoto University
Major Complex systems
Purpose Demosponges have totipotent stem cells. Some species, especially freshwater sponges, can undergo asexual reproduction in which an individual juvenile sponge develops from thousands of totipotent stem cells alone. Initially, for asexual reproduction, sponges form small structures known as gemmules, in which quiescent totipotent stem cells are surrounded by a collagenous coat so as to be resistant to cold and other harsh external environments. In this study, we focused on the “early stage of gemmule formation, in which exclusively totipotent stem cells rapidly form aggregates in the body of a sponge in which a large number of different types of cells are actively moving. We aim to investigate “when” “where” and “how” totipotent stem cells initiate aggregation. Furthermore, we will analyze their comprehensive gene expression to identify the cells that are the core of cell aggregation during this singularity and to elucidate the molecular basis thereof.