Publicly Offered Research (2021-2022)

A01

Ca2+-mediated singularity phenomenon in influenza virus infection


Name Yoichiro Fujioka
Affiliation Department of Cell Physiology, Faculty of Medicine, Hokkaido University
Major Cell Biology
Purpose The outbreak of SARS-CoV-2 continues to pose a threat to society. Viral infection is one of the important themes in the life sciences. We established infection assay with tightly controls the number of influenza virus particles and found that host cellsrespond differently depending on the number of virus particles. Exposure of cells to 20 virus particles triggers calcium elevation and accelerates the infection. 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.

Networked analysis of adherent singularity cells


Name Sadao Ota
Affiliation Research Center for Advanced Science and Technology, University of Tokyo
Major Optics, fluidics, genetic engineering, cell analysis
Purpose Adherent cells are important in the seek of singularity phenomenon that changes morphologies and dynamics of multicellular systems. In contrast, although the world is moving to the development of spatial transcriptomics technology, to the best of our knowledge, multimodal measurement with live imaging of adherent cells is still challenging. In this study, we aim to develop a technology of multimodal cell analysis for observing and identifying singularity phenomena and cells in the adherent state by live imaging and capture the intrinsic state of singularity cells by sequencing technology.

Characterization of singularity cells in stem cell cultures


Name Daisuke Nanba
Affiliation Tokyo Medical and Dental University
Major StemCell 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. In this study, we try to find the moment of the emergence of this singularity cells by using DeepACT that we developed for automated cell tracking, and clarify how the singularity cells are generated in the stem cell colony.

Development of optical manipulation technology with multitasking and high-throughput properties


Name Kiwamu Takemoto
Affiliation Department of Biochemistry, Mie University GraduatevSchool of Medicine
Major Neurochemistry, Neurophysiology
Purpose In order to capture the singularity phenomenon, trans-scale imaging techniques are indispensable. On the other hand, to elucidate the physiological significance and causality of singularity phenomena, it is necessary to develop light manipulation methods that can perturb molecules expressed in singularity cells and surrounding cells locally and at arbitrary timing. Therefore, for the future development of singularity biology, it is essential to have a new technology that can rapidly develop photo manipulation methods for various molecules and can manipulate multiple molecules at any time and place. In this study, we aim to develop a new photo-manipulation method that enables high-throughput and multi-tasking manipulation based on the light-induced molecular inactivation (CALI) method, which we have studied as an elemental technology.

Development of Dual-Responsive Probes for Evaluation of Cancer Stem Cell Malignancy


Name Koji Miki
Affiliation Graduate Scholl of Engineering, Kyoto University
Major Molecular Imaging
Purpose Cancer stem cells (CSCs) are known to be responsible for tumor initiation, progression, metastasis, chemo-and radiotherapy resistance, and tumor recurrence. We have recently developed turn-on fluorescence probes, which respond to aldehyde dehydrogenase 1A1 (ALDH1A1) overexpressed in CSCs, and applied them to in vitroand in vivoCSC imaging as well as CSC isolation. In this research, we will try to synthesize dual-responsive fluorescence probes for evaluation of CSC malignancy. We will also develop not only single-input probes but dual-responsive probes for detection of singularity cells and phenomena.

Spatio-temporal dynamics of self-reactive “Singularity” T cells


Name Shinya Tanaka
Affiliation Division of Immunology and Genome Biology, Medical Institute of Bioregulation, Kyushu University
Major Immunology
Purpose An activation of self-reactive T cells is one of the direct causes of induction of autoimmune diseases. That means the body always carries the risk that the dysregulation of self-reactive T cells, which are extremely rate in peripheral lymphoid organs, results in a crisis of an individual life. Therefore, it is necessary to understand how they are regulated. However, it has remain unclear mainly because the method to identify the self-reactive T cells has not been established. In the study, I aim to elucidate their dynamics in autoimmune reaction by constructing a novel sensor that detects T cell activation in our murine autoimmune disease model.

Development of supramolecular 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 furimazineas a novel bioluminescence platform, NanoLucshowed the highest level of luminescence brightness and enabled imaging at the organelle level. However, Long-term bioluminescence imaging with furimazineis 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 furimazinederivatives with improved water solubility, stability and retention in blood by supramolecular complexation.

Photoacoustic imaging For the Detection of Singularityin 3D space


Name Miya Ishihara
Affiliation Dept. of Medical Engineering, National Defense Medical College
Major Imaging
Purpose We aim to detect very rare events which act as singularity by novel photoacoustic imaging techniques. Photoacoustic (PA) imaging has the advantage of extension in 2D space to 3D space imaging. We will promote effective use endogenous photoacoustic signals.

A02

Development of spatial transcriptomics for singularity cells and its peripheral cells


Name Akihito Harada
Affiliation Medical Institute of Bioregulation, Kyushu University
Major Omicsbiology
Purpose To characterize singularity cells, which are thought to exist as rare cells in tissues, it is important to compare them with its peripheral cells. Therefore, spatial information is necessary to analyze the cells. In this research, we will develop a spatial transcriptomics technique using cell barcoding, which can distinguish individual cells from singularity cells and peripheral cells by applying the photo isolation chemistry method.

A03

REM sleep regulating cells as a starting point for the singularity of the brain physiology and evolution


Name Yu Hayashi
Affiliation University of Tsukuba
Major Neuroscience, sleep medicine
Purpose During REM sleep, the brain and the body are in a state largely different from that during wakefulness or non-REM sleep, and vivid dreams often occur. REM sleep is abundant during the neonatal period and declines rapidly thereafter, suggesting its involvement in brain maturation. In this study, we aim to (1) elucidate the mechanism by which the group of neurons in the brain involved in inducing REM sleep, which we have identified, can rapidly induce changes in the whole body state during REM sleep, and to (2) verify the possibility that the birth of these cells in the process of evolution was a “singularity” that produced REM sleep and brought about a major turning point in the evolution of subsequent cerebral development in vertebrates.

Tissue homeostasis and regeneration governed by rare de-differentiating progenitor cells


Name Mio Nakanishi
Affiliation Graduate School of Medicine, Chiba University
Major Stem Cell Biology
Purpose Stem and progenitor cells change their individual roles in tissue homeostasis drastically according to the tissue status. In hematopoietic system for example, multipotent progenitors and stem cells are majorly contributing to in steady-state-and regenerative homeostasis, respectively. Nevertheless, mechanisms underlying the balancing between stem cells and progenitors are largely unknown. RecentlyI found a progenitor-like subset in human ESC cultures that regulates the stem vs progenitor balance in the culture through its de-differentiation to the stem cell. Keeping these findings in mind, and using hematopoietic stem-and progenitor cells (HSPC) as amodel, I will unveil previously-unknown mechanisms underlying tissue homeostasis governed by rare multipotent progenitors de-differentiating to the stem cells.

Analysis of digital viral replication


Name Yuhei Maruzuru
Affiliation The Institute of Medical Science, The University of Tokyo
Major Virology
Purpose After entry into the host cell, the virus expresses proteins required for viral assembly. These proteins assemble within the host cell to form viral particles, with the number of intracellular viral particles possibly depending on the concentration of viral proteins. The amount of infectious virus particles in infected cells was found to increase drastically when the intracellular concentration of viral proteins exceeded a certain value (singularity). In other words, infected cells could distinguish between “ON” and “OFF” viral production. Therefore, the process of viral proliferation could be reinterpreted as an increase in the number of cells with viral production turned “ON”. In this study, we introduce this concept as “digital viral replication” and plan to perform detailed investigations into this mechanism using omics-based analysis and imaging technology.

Elucidation of the singularity that determines the progression of brain tumor


Name Naofumi Uesaka
Affiliation Tokyo Medical and Dental University
Major Neurophysiology, Brain tumor
Purpose Brain tumor cells are generated by the alteration of one or a few normal cells that have been mutated, and they irreversibly cause serious damage to the animal. A small number of brain tumor cells are singularity cells, and the singularity phenomenonshould exist in the process of their progression. Recently, the formation of direct and indirect networks between tumor cellsand normal cells in the brain and the possibility that these networks influence tumor progression have been reported. In thisstudy, we will test the hypothesis that the networks formed by brain tumor cells and normal cells changes, and that the change becomes a singularity that determines tumor progression.

Physiological significance of algal phototaxis as revealed by the behavior of perverse cells


Name Ken-ichi Wakabayashi
Affiliation Tokyo Institute of Technology
Major Cell Biology
Purpose The model unicellular green algaChlamydomonas reinhardtiireverses its phototactic signs (positive and negative phototaxis: toward or away from the light source, respectively) in response to changes in intracellular reactive oxygen species (ROS) accumulation. However, ROS is a hazardous byproduct of photosynthesis, and the regulation of positive phototaxis (more ROS produced) when ROS is accumulated seems to be suicidal. We would like to clarify the physiological significance of this behavior in two studies. (1) To clarify the relationship between the sign change shown by the majority of cells with light exposure time and the amount of intracellular ROS accumulation. (2) To analyze the phenotype and causative genes of mutant strains that, unlike wild type, exhibit positive phototaxis when ROS accumulation is low and negative phototaxis when ROS accumulation is high.

Deciphering evolutional dynamics of resistance/recurrence-initiating singularity cells by RNA-expressed barcoding technology


Name Shinichiro Kato
Affiliation Molecular Immunology and Center for 5D Cell Dynamics, Graduate School of Medicine, Nagoya University
Major Cancer Biology
Purpose Therapeutic resistance and recurrence are cancer evolutional dynamics that would be caused by an emergence of genetically and/or phenotypically distinct rare cancer cells. However, it has been totally unclear the molecular mechanism behind these singularity points of cancer malignant development. Here, we apply a novel RNA-expressed barcode technology, which allows simultaneous lineage-tracing and transcriptome analysis at single cell resolution, and will develop a retrospective phenotype tracking method. We will pursue spatio-temporal phenotypic trajectories of every single cancer cell within tumor tissue undergoing to malignant development (therapeutic resistance, recurrence or metastasis) by using this method and eventually identify a singularity cancer cell(s) as a main cell pool that leads or instigates to therapeutic resistance and recurrence.

Circadian clock related singularity neuronal circuits in mice


Name Daisuke Ono
Affiliation Research Institute of Environmental Medicine, Nagoya University
Major Neuroscience, Physiology, Chronobiolog
Purpose Mice show a hibernation-like state called daily torpor when they are exposed to cold temperature with food deprivation. During daily torpor, mice show hypometabolismto save energy expenditure. This hypometablismis known to be regulated by three factors, low ambient temperature, food availability, and the circadian clock. However, it is not clearly understood howthese factors integrated to regulate daily torpor. In this research, we define neurons overlapped with three factors as singularity cells, and try to identify which types of neurons are critical for the regulation of timing of daily torpor in mice.By using optogeneticsand newly developed bioluminescence calcium probe, we will find the circadian clock related neuronal circuits that regulate daily torpor.

Elucidation singularity cells in tissue repair


Name Masato Enomoto
Affiliation Graduate School of Biostudies, Kyoto University
Major Genetics, Cell Biology
Purpose Tissue remodeling is a dynamic process that spatiotemporally coordinates cell proliferation, cytoskeletal rearrangement, and inflammation. However, the mechanism by which damaged tissue is reconstructed via spatiotemporal coordination of multiple biological processes in vivo is poorly understood. In Drosophila epithelium, we recently found a small number of cells that are essential for tissue repair and regeneration. Interestingly, these cells express a specific transcriptional factor that is silenced in normal epithelia. In this study, we aim to elucidate the mechanism of how the “singularity cells” are generated in damaged tissues, and reveal the roles of these cells in tissue repair.

Motility profiles generating singularity in sperm collective dynamics


Name Tsuyoshi Hirashima
Affiliation The HakubiCenter/Graduate School of Biostudies, Kyoto University
Major Biophysics, Developmental Biology
Purpose Mammalian sperm acquire motility by passing through the epididymal duct. Although this process involves a very important singularity phenomenon, it remains largely unexplored how the sperms acquire their motility. Previously, I have found that a characteristic collective sperm flow is generated in the epididymal duct of mice. In this project, I aim to clarify the generation mechanism of collective sperm flow that leads to the acquisition of reproductive functions using fluorescence live imaging and mathematical modeling.

Elucidation of the developmental clock singularity phenomena


Name Masayuki Oginuma
Affiliation Research Institute for Microbial Diseases, Osaka University
Major Developmental biology/Endocrinology & Metabolism
Purpose During an animal embryogenesis, biological clock accurately measure developmental velocity and they allow the correct timing of developmental processes, however molecular mechanism of these clock machinery is still unknown. Recently I discovered a velocity control factor that is a secretory factor which integrates the rate of embryogenesis in small fish embryos. In this study, I elucidate the synchronization mechanism of developmental processes to identify the control center which secrete the velocity control factor using a small fish model in which the embryo is transparent, and we can simultaneously observe from the molecular behavior in the cell, tissue formation and the whole body. This control center might allow synchronization of development called as a “developmental clock singularity phenomenon”

Investigation of the singular land/fresh-water invasion with “pioneers”


Name Tatsuya Sakamoto
Affiliation UshimadoMarine Institute, Okayama University
Major Marine Biology
Purpose We will elucidate the singularity of “vasopressin/vasotocin.kidney” to make the singular land/fresh-water invasion during evolution, using intertidal planarians as“pioneers”. Several groups including my own have been trying, over the past decade since the discovery of nematocinfrom Nematoda(Science 2012; 338, 540.543; Science 2012; 338, 543.545), to identify the origin of such neuroendocrine system by using a wide variety of genomic/transcriptome information from many earlier invertebrates including freshwater planarians/Schistosomes. Using intertidal planarians, which are not common model organisms, we have now been able to demonstrate the existence of what we believe to be the definitive ancestor of the vasopressin/vasotocin.oxytocin system from Platyhelminthes, and name it the “platytocin” system. Despite a search, we have not been able to find this molecule either in other flatworms or in cnidarians. We have worked to emphasize the antidiuretic hormone (vasopressin/vasotocin)-like action of platytocin. This, we believe, strengthens our proposal that platytocinis an ancestral osmoregulatoryhormone (vasopressin/vasotocin) though animal kingdom and therefore demonstrates a hitherto unrecognized evolutionary origin of antidiuresis/osmoregulation.

Singularity phenomenon by immune response in the development of neuropsychiatric disorders


Name Minako Ito
Affiliation Division of Allergy and Immunology, Medical Institute of Bioregulation, Kyushu University
Major Neuroimmunology
Purpose Alzheimer’s disease is a singular phenomenon in which singular cells with aggregates of Amyloid beta and phosphorylated Tau emerge and expand upon some stimulus. It has become clear that a wide variety of immune cells are involved in various central nervous system diseases. T-cell infiltration is enhanced in the brains of mouse models of Alzheimer’s disease, suggesting the involvement of immune responses in the development of neurological diseases. Inflammatory bowel disease also worsens the pathology of Alzheimer’s disease. In humans, inflammatory bowel disease has been reported to be a risk factor for dementia, but the mechanism remains unclear. In this study, we aim to elucidate the immune response that regulates the expansion of singular cells, which is a key factor in the development of neurodegenerative diseases.

Elucidation of Singularity events by analysing spaciotemporal dynamimcsof T-cells using a new technology


Name Masahiro Ono
Affiliation Kumamoto University, Imperial College London
Major Immunology
Purpose T-cells react to antigens and thereby induce immune response. Due to the random recombination of T cell receptor genes, individual T-cells have their own unique TCR sequences. Thus T-cells specific to each antigen are very rare. However, once T-cells get activated, such a small number of T-cells can initiate a significant immune response. Here we hypothesisethat rare activated T-cells coordinate and lead the T-cell response as “Singularity cells”, aiming to identify and characterize their features through spaciotemporal analysis using our new tools.

Analysis of the singularity phenomenon in the evolution of the eye


Name Mitsumasa Koyanagi
Affiliation Graduate School of Science, Osaka City University
Major Photobiology, Molecular Evolution
Purpose Animal eyes are one of the most complex and elaborate organs, with a wide variety of shapes and mechanisms depending on the animal. The evolutionary process by which these complex phenotypes arise is an important issue in evolutionary biology, but remains largely unknown due to the difficulty of experimental investigation. In this study, we consider photoreceptor cells, which are the basic elements of the eye, as the singularity cells in the evolution of the eye. The aim of this project is to reproduce the evolutionary process from the acquisition of photoreceptor cells to the evolution of the eye, that is, to analyze an evolutionary process to a more advanced photoreceptor organ by giving the eye-spot (photosensory system) to C. elegans, which lacks eyes, through the application of optogenetics, followed by artificial selection on the photo-responsiveness.

Analysis of the singularity phenomenon to causeneuroinflammation using disease-specific iPScells


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

Organoid-based modeling of symmetry breaking in morphogenesis


Name Kent Imaizumi
Affiliation Keio University
Major Neurodevelopmental biology, Stem cell biology
Purpose The organs are generated from homogenous cell populations. During development, these homogenous populations acquire axial polarity, which is established by a small number of specialized cells, called organizers, and this polarity contributestothe complex organ structure. We previously found that this spontaneous polarity establishment can be recapitulated in organoid cultures. In our culture system, organizer cells were initially randomly distributed, but these specialized cells were eventually localized to a single place, giving rise to spontaneous symmetry breaking. In this project, we aim to elucidate how the organizer cells are spontaneously assembled, and this study will highlight robust mechanisms of self-organized patterning of morphogenesis.

Singularity in the development of autoimmune diseases


Name Shunsuke Chikuma
Affiliation Keio University
Major Immunology (Autoimmunity, anti-tumor Immunity)
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 define the number of initial immune reaction that sets a “point of no return” for the establishment of autoimmune symptoms as a final phenotype.

Quantitative analysis of ascidian metamorphosis


Name Kohji Hotta
Affiliation Department of Biosciences and Informatics,Faculty of Science and Technology, Keio University
Major Developmental biology
Purpose In various life phenomena, the singularity that mediates between different phases has a mechanism that triggers the transition to the next phase by a “two-step” signal. For example, two-step model of carcinogenesis initiation and promotion, two-step caspase activation during apoptosis induction, two-step response of MAPK to plant immune response, and stepwise activation of ion channels at neural junctions in muscle contraction, etc. Animal metamorphosis is also regarded as one of the singularity phenomena in ontogeny, but it is unclear what kind of internal system mediates the external input that triggers metamorphosis. However, ingeneral, it is difficult to predict when and where the singularity will occur, and since it is non-linear, it is difficult to construct an analysis system. I discovered that ascidian Ciona intestinalis type A induce metamorphosis by mechanical stimulation and constructed an experimental system that can quantitatively analyze how metamorphosis occurs from the stimulation at the cellular level (Wakaiet al., 2021). To elucidate the two-step signal transduction mechanism located at the singularity of this metamorphosis, I will visualize and quantify the molecular / cell dynamics that contribute to the metamorphosis.

Singularity at emergence of cancer cells in normal stroma


Name Shunsuke Kon
Affiliation Tokyo University of Science
Major Cancer Cell Biology
Purpose Cancercellsgeneratedwithinepitheliainvade intostromaltissues, anddeveloptumor microenvironment(TME) whichisa specialized, complexcompartmentto promotebothsurvivalandproliferationofcancercells. However, itremainsenigmaticwhathappensatemergenceofcancercellsin stroma, wherenormal stromalcellsare confrontedwithcancercellsatthefirsttime. Ourgrouphasrecentlyrevealedthatnormal fibroblastscountervailtheexpansionoflow-grade cancercells, whilehigh-grade cancercellstransformnormal stromaintoTME. In thisstudy, weaimto revealthenatureofcancersingularityattheinitialstageofTME formationbycombiningexvivo imagingandomicsapproaches.

Construction and control of the singularity synapses


Name Kosei Takeuchi
Affiliation Aichi Medical University
Major Neuroscience, Cell biology, Regenerative medicine
Purpose We attempt to establish the super-recovery from spinal cord injury(SCI) by inducing artificial synapse connect and providing extra cellular matrix suitable for regeneration. We reported that synthetic synapse connector have outstanding property of restoring neurological function in SCI(Suzuki et.al. Science. 2020). As the second strategy for amelioration, we regulate the microenvironment of extracellular matrix to induce axon regeneration (Takeuchi et.al. Nature commun.) The combination of these models will allow us to dissect the neural basis of adaptive circuits during neuronal recovery and treatments.

Identification and elucidation of a leader cell that controls nephron development in the kidney


Name Minoru Takasato
Affiliation RIKEN BDR
Major Developmental Biology
Purpose During kidney development, nephron progenitor cells develop into the nephron, a functional unit of the kidney, via mesenchymal-epithelial transition (MET). We have 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-Wntsignaling. Interestingly, we further demonstrated that those MET events occur constantly and singularly within a uniform nephron progenitor population. Currently, we established a reporter hiPSC-line to detect the earliest evidence of MET in kidney organoids through live imaging. Here, in this research project, we aim to elucidate the mechanism that controls such rare MET events using the reporter hiPSC-line and our developed in vitro MET occurrence system.

Investigating mechanisms of tau protein phase transition caused by neuron-glia crosstalk failure


Name Naruhiko Sahara
Affiliation National Institute for Quantum and radiological Science and Technology
Major Neurochemistry, neurodegenerative disorders
Purpose Causal mechanisms of pathological tau aggregation associated with neurodegeneration are still unknown. We will search a singularity point of tau protein phase transition and neuroinflammation.