Publicly Offered Research Projects

A01 

Inflammation Cell Society in cardiac homeostasis and pathobiology

Ichiro Manabe, MD, PhD
Department of Disease Biology and Molecular Medicine, Chiba University

We have reported that macrophages and fibroblasts play divergent and essential roles in the maintenance of homeostasis as well as pathobiology. In particular, macrophages can assume diverse phenotypes and functions in response to environmental cues. We and others have found that the changes of macrophages depend on the dynamic regulation of epigenome. In this study, we aim to analyze the dynamic changes in the transcriptome and epigenome at a single cell level in macrophages and fibroblasts in the heart. We will analyze the communication among the cells to elucidate the dynamism of the inflammation cellular society in stress response and heart failure.

Inflammation cellular sociology from the points of RNA function

Motoyuki Otsuka
Department of Gastroenterology, The University of Tokyo Hospital

In digestive organs, chronic inflammation often induces inflammation-associated tumors, such as hepatocellular carcinoma, gastric cancer, and inflammation-associated colon cancers, irrespective of the original causes. To prevent these inflammation-associated tumors, we need to clarify the pathogenesis regarding inflammation-associated tumors, and we need to develop interventional approaches based on the molecular mechanisms. We previously reported that chronic inflammation impairs global microRNA function, which leads to the tumorigenesis. However, at that stage, we did not examine how such functional impairment of microRNAs occurs at the cellular levels from the point of views of inflammation cellular sociology.
In this study, we will look into the microRNA functional changes at cellular levels in the inflammatory sites and try to integrate the results of microRNA function and gene expression at cellular levels. For this purpose, we will establish a reporter mouse which indicates the microRNA function and by putting these mice under chronic inflammatory states we will examine the microRNA function to clarify the microRNA functional changes in every cell in the inflammatory tissues.
In addition, to discover preventive methods against inflammation-associated tumors, we will establish the idea “oncogenic processes by the inflammatory cellular sociology from the points of views of non-coding RNA function”. For this purpose, we will integrate the information about microRNA function and transcriptome at the cellular levels to discover the multilayer geneexpression regulation.
Based on the obtained results, we will develop preventive methods against inflammation and inflammation-associated tumors. Finally, we will try to discover therapeutics to maintain the silent status, in which no apparent diseases occur, throughout the chronic inflammation.

Identification of the major cellular origin in the damaged intestine and related inflammatory network society

Toshiaki Ohteki, Ph.D.
Professor, Department of Biodefense Research, Medical Research Institute, Tokyo Medical and Dental University

Once apoptosis is induced in the intestinal stem cells (ISCs) by anti-cancer drug or total body radiation (TBI), a variety of surviving radio-resistant cells proliferate or de-differentiate massively to replenish the lost ISC pool and ISC-derived epithelial cells. However, it remains unclear to what degree each population contributes to the overall epithelial regeneration.
Using a combination of genetic lineage tracing and single-cell gene expression profiling, we will elucidate the complete picture and major source of the “cell-of-origin” for epithelial regeneration and the inflammatory molecule(s) likely required for the proliferation of the “cell-of-origin” in the damaged intestine. To identify the major cellular origin for irradiation-induced epithelial regeneration, we first perform lineage-tracing of ISCs and secretory progenitors. Based on the results of lineage-tracing analysis, we next isolate the cells including the major cellular origin from the damaged intestinal crypt and perform single cell RNA sequencing (scRNA seq). By performing hierarchical clustering and principle component (PC) analysis of the scRNA seq data, we will identify the candidate of major cellular origin. We will next extract the surface molecule(s) expressed on the candidate population and try to isolate the cells. Using organoid-formation assay, the potential of ISC recovery and epithelial regeneration of the isolated cells will be evaluated. Finally, we will extract the inflammatory molecule(s) critical for the proliferation of major cellular origin. Using organoid-formation assay combined with or without the inflammatory molecule(s), the responsible molecule will be determined. Our findings, i.e. the identification of the major cellular origin in the damaged intestine, might be applicable to the study of IBD and colon cancer.

 

Involvement of microglial activation in the pathogenesis of autism spectrum disorders

Yoshiaki Kubota, M.D., Ph.D.
Professor, Department of Anatomy, Keio University School of Medicine

Autism spectrum disorder (ASD) refers to a complex developmental disorder that impairs social interaction, communication, and behavioral flexibility. Although ASD is highly heritable, its etiology is complex and involves multiple cellular and molecular mechanisms. So far, we found that aberrant activation of microglia, cells responsible for innate immunity in the central nervous system, caused by conventional or myeloid-specific deletion of a newly identified gene in mice leads to severe ASD-like behavioral abnormalities. Mechanistically, massively secreted inflammatory cytokines due to constitutive activation of TLR3 in microglia of the mutant mice are thought to persistently damage brain neurons. In this study, we further investigate into the detailed mechanism for this phenotype. Moreover, genomic analysis of human samples found novel SNPs specific to ASD patients. We’re now in the process of generating knock-in mice recapitulating such mutations to examine the significance of those mutations in behavioral abnormalities. Taken together, our results may propose that the disruption of “a cellular society of inflammation” is highly associated with human ASD pathology and immune modulatory drugs could ameliorate a population of human ASD.

Identification of critical factor for development of fibrosis in non-immune system

Takashi Satoh
Assistant Professor, Research Institute for Microbial Diseases, Osaka University

Macrophages that have been discovered more than 100 years ago have been considered to be only one type in the body until recently, unlike other immune system cells such as T cells and dendritic cells. However, in recent years, some studies indicated that monocytes and macrophages ca be categorized into several distinct phenotypes and their respective differentiation mechanisms are known. We also reported that the Jmjd3 is critical for the macrophage subtype activated by allergic stimuli (Satoh, T. et al. Nat. Immunol. 2010; 11: 936 -944) and that the tissue resident macrophage subtype in adipose tissue, which is controlled by Trib1, is responsible for maintaining homeostasis of peripheral tissues such as adipocyte (Satoh, T. et al. NATURE 2013; 495: 524-528). Thus, it is considered that various macrophage subtypes exist for each disease.

Furthermore, in order to investigate the relationship between macrophage subtype and disease, we focused on fibrosis as the next target disease. Fibrosis is a life-threatening disease of unknown aetiology. Its pathogenesis is poorly understood, and there are few effective therapies. Previously we found that a new macrophage subtype, which their markers are Msr1+Ceacam1+Ly6CMac1+F4/80monocyte and share granulocyte characteristics, involved in development of fibrosis was accumulated in the affected area in the lungs at the beginning of fibrosis. We termed the monocyte/ macrophage subtype segregated-nucleus-containing atypical monocytes (SatM) (Satoh, T. et al. Nature. 2017; 541: 96-101). However, the mechanism by which they migrate to fibrotic areas at the start of fibrosis has not been elucidated. In this study, we aim to clarify the mechanism of migration / accumulation of the macrophage subtype SatM. In order to solve this problem, we utilize pulmonary fibrosis model using bleomycin (BLM). Administration of BLM induces the destruction of lung tissue (nonimmune system), and an endogenous ligand released from damaged tissue. Therefore, examination of nonimmune cells during fibrotic lung is indispensable for elucidating the mechanism of the migration / activation of immune system cells such as SatM.

Control of the Intestinal Immune System through Innate Immune Receptors and Its Effects on the Systemic Immune System

Representative
Yoichiro Iwakura, D. Sc.
Professor and Director, Center for Experimental Animal Models, Research Institute for Biomedical Sciences, Tokyo University of Science

Our intestinal tract is colonized by many types of microbiota. The number and diversity of these microbes are always changing in any given moment throughout our life, and the majority of these organisms are not harmful invaders but cohabitants living with us as their one-and-only home. Indeed, our metabolic and immune functions are largely dependent on our intestinal microflora. By activating host antimicrobial innate immune mechanisms and by directing the development of adequate adaptive immune cells of the mucosal and systemic immune system, commensal microbes contribute to the host defense against pathogens and host immune homeostasis.
Recent studies have revealed the importance of pattern recognition receptors (PRRs), which recognize pathogen- associated molecular patterns, in the host defense against pathogens and intestinal immune homeostasis. C-type lectin receptors (CLRs) is a group of such PRRs and bind carbohydrate structures on pathogens, such as fungi and mycobacteria, in a Ca2+-dependent manner, providing an important mechanism for the protection against these pathogens. Dectin-1 is one of type II CLRs that contains a carbohydrate recognition domain in its extracellular carboxyl terminus and an immunoreceptor tyrosine-based activation motif in its intracellular amino terminus, and highly expressed in dendritic cells, macrophages (Mfs), and neutrophils. Previously, the group of Gordon Brown and we showed that Dectin-1 is the receptor for β-1, 3- linked glucans with β-1, 6-linked branches (β-glucans) and plays an important role for the host defense against fungi by producing Th17 cytokines and reactive oxygen species (Saijo et al., Nat. Immunol., 2007). We have also shown that Dectin-2 is the receptor for α-mannans and important for the host defense against fungal infection (Saijo et al., Immunity, 2010). Because Dectin-1 and Dectin-2 are expressed in the colonic lamina propria (cLP) and Peyer’s patches in the small intestine and β-glucans and α-mannans are contained in many foods such as mushrooms, yeasts, and seaweeds, we investigated the role of these CLRs in the intestinal immune system.
Recently, we reported that Dectin-1 deficiency causes an increase of a specific lactobacillus species (Lactobacillus murinus) in the colon because of a decrease of a group of anti-microbial proteins, and suppresses the development of colitis by promoting regulatory T-cell (Treg) expansion in a lactobacillus-dependent manner (Tang et al., Cell Host & Microbe, 2015). Furthermore, we found that IL-17F is preferentially induced by Dectin-1 signaling (Kamiya et al., Mucosal Immunol., 2018), and induces antimicrobial proteins such as phospholipase A2 and suppresses growth of Treg-inducing bacteria, Clostridium cluster XIVa as well as L. murinus. Thus, inhibition of IL-17F, but not IL-17A, signaling induce Treg cell expansion in the colon resulting in the suppression of colitis (Tang et al., Nat. Immunol., 2018). In this project, we will analyze the roles of C-type lectins in the regulation of systemic immune system and in the development of tumors.

Intercellular network analysis using mice spontaneously developing pulmonary fibrosis

Yasutaka Motomura
Researcher, Laboratory for Innate Immune Systems, RIKEN Center for Integrative Medical Sciences (IMS)

Idiopathic interstitial pneumonias (IIPs) are interstitial lung diseases with unknown etiology that is designated as a refractory disease. Idiopathic pulmonary fibrosis (IPF), which accounts for half of IIPs cases, has a poor prognosis and patients with this disease have an average life expectancy of 3 to 5 years. The pathophysiological mechanism for IPF is unknown, however, and there are currently no curative drugs. One major limitation in the clarification of the pathology of IPF is the lack of an IPF animal model that replicates human pathology. Since the most commonly used bleomycin-induced pulmonary fibrosis mouse model is drug-dependent, the progression of the disease state is transient and can be reversed by stopping administration of the drug. This model does not adequately reflect human IPF which is a chronic pathological condition and establishment of a new IPF animal model that mimics human pathology is required.
Group2 innate lymphoid cells (ILC2), which were discovered in our laboratory in 2010, were found to produce the type 2 cytokines IL-5 and IL-13 in response to IL-25 and IL-33 from epithelial cells, leading to the pathogenesis of allergic disorders. We found that mice lacking ILC2 inhibitory mechanisms spontaneously develop pulmonary fibrosis. The fibrosis seen in these mice replicates the pathology of IPF, including spontaneous development, pathological progression from the pleural side and abnormal deposition of collagen and periostin. Therefore, these mice may be a useful model for IPF research since it was recently reported that ILC2 increase in the bronchoalveolar lavage fluid of IPF patients, strongly suggesting that activation of ILC2 is involved in the pathogenesis of IPF.
In our research, we will clarify the onset and progression of pulmonary fibrosis using our mouse model of fibrosis. Furthermore, we will comprehensively analyze the intercellular network in the lung tissue using single cell RNAseq analysis. By observing dynamic changes in the lung prior to the appearance of symptoms, we aim to establish diagnostic and preventive methods for IPF by searching for candidate biomarkers that can detect the early onset of IPF.

Integrated description of the effect of cancer cell-dependent inflammation on the whole body

Kanae Yumimoto, PhD
Research Assistant Professor, Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University

Inflammatory response is one of defense mechanism against tissue injury and microbial infection. However, it has become clear that inflammatory response is involved in the promotion of cancer development and malignancy. Cytokines and growth factors produced from inflammatory cells promote carcinogenesis. Cancer cells also “take over” the inflammatory response, which is a biological response originally intended to eliminate cancer cells themselves. Cancer cells recruit inflammatory cells around themselves to form “cancer niche” for their malignancy. In addition, humoral factors such as inflammatory cytokines produced from the primary cancer affect the whole body through the bloodstream, and prepare the environment (= ”premetastatic niche”) so that it is easy to survive and grow at the metastatic site. We have previously reported that various cytokine fluctuations occur in peripheral blood when tumors are transplanted, and this fluctuation affects metastatic niche formation of inflammatory cells [Yumimoto et al., J. Clin. Invest. (2015); Yumimoto & Nakayama, Oncoimmunology (2015)].
Although primary cancer cells promote premetastatic niche formation through systemic inflammation via blood flow, organs where cancer metastasis occurs are limited, and their tendency varies depending on cancer cells. In this study, we are searching for “signals” of cancer niche formation emitted by cancer cells. We also attempt to elucidate how the organ directionality of cancer metastasis is determined by comparing how the metastatic organs (=premetastatic niches formation) or non-metastatic organs (= no premetastatic niche formation) are affected by the “signals”. We also aim to lead to early detection and eventual prevention of cancer metastasis by constructing a system to visualize premetastatic niche.

Spatiotemporal identification and elucidation of the cellular society of inflammation based on cell death imaging

Yusuke Imagawa, PhD
Chief Scientist, Department of Molecular and Cellular Biology, Osaka International Cancer Institute

It is thought that “homeostatic inflammation” that is non-infectious inflammation is initiated by autologous ligands (intrinsic ligands) that is released from plasma membrane-disrupted necrotic cells. However, it is not cleared how the necrotic cell initiates, expands and prolongs inflammatory signals in vivo.
In this project, I will analyze the spatiotemporal relation between cell death and inflammation by using a newly developed imaging technique for necrosis in mouse body. Moreover, I will elucidate mechanisms of controlling necrosis-induced inflammation by comparing the inflammation-inducibility of a variety of necrotic programmed cell death.

A02 

Regulation of inflammation cellular sociology by lipids toward better understanding of allergic diseases

Professor
Makoto Murakami, PhD
Laboratory of Microenvironmental Metabolic Health Sciences Center for Disease Biology and Integrative Medicine Graduate School of Medicine The University of Tokyo

Transepidermal invasion of environmental factors, such as bacterial toxins and harmful antigens, due to skin barrier dysfunction can trigger excessive activation of type 2 immunity, leading to development of atopic dermatitis, a refractory chronic skin disease, and even rhinitis and asthma in distal organs, known as a process of “allergic march”. Therefore, appropriate control of the skin barrier is an urgent task in considering the prevention of allergic diseases. Quantitative and qualitative changes in lipids have great influences on the inflammatory cell society. The purpose of this study is to unveil the molecular mechanism underlying the process of transitioning from skin homeostasis (undiseased) to its failure (prolonged) and further to chronic allergic condition (irreversible) with lipid as a keyword, and accordingly, to create a new concept concerning the molecular preventive control of allergy based on the maintenance of lipid microenvironment. By taking advantages of a series of gene-manipulated mice for various phospholipase A2s in combination with comprehensive lipidomics, we herein aim to clarify the roles of particular lipid pathways in the regulation of allergy, especially focusing on immune responses of epidermal origin and controls of mast cell microenvironment.

  1. 村上誠、武富芳隆. 脂質によるマスト細胞の制御とアレルギー. 医学のあゆみ. 265 (9), 773-778, 2018
  2. 村上誠、佐藤弘泰、武富芳隆、平林哲也. ホスホリパーゼA2ファミリーによるリポクオリティ制御. 実験医学. 36 (10), 1623-1630, 2018
  3. 村上誠,木原章雄. 脂質による皮膚バリア形成と疾患制御. 実験医学. 36 (10), 1730-1737, 2018

Elucidation of mechanism of chronic intestinal inflammation at single-cell level using optogenetic technique

Kazuo Takayama, PhD
Assistant Professor, Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University

Chronic inflammation have a risk to cause organ fibrosis and to promote cancer progression. Recently, mechanism of chronic inflammation is becoming apparent using single-cell analysis. Although many researchers have trying to elucidate the mechanism of chronic inflammation using single-cell genomic, epigenomic, and transcriptomic analyses, it is difficult to induce genomic, epigenomic, and transcriptomic error at the single-cell level.We have previously generated a technology for spatiotemporally controllable gene expression regulation (ACS Chem Biol. 2018 Feb 16;13(2):449-454.). We introduced optogenetic and CRISPR/Cas9 techniques into a recombinant adenovirus (Ad) vector to generate an illumination-dependent spatiotemporally controllable gene regulation system. In this study, we will try to induce genomic and transcriptomic error at the single-cell level in chronic intestinal inflammation. In addition, we attempt to identify the genomic and transcriptomic error which can be utilized for prediction and treatment of colorectal cancer.

Elucidation of the mechanism of inflammation induced by ischemic stress and its control

Akira Shibuya
Professor, Life Science center of survival dynamics and faculty of Medicine, University of Tsukuba

Death due to cerebrovascular disease in our country is the fourth in all causes of death (9%), of which the number of cerebral infarctions is 66,058 and that medical expenses will rise to 1,7 82.1 billion yen per year. The social and economic loss caused by it is immeasurable. When blood flow in brain tissue is interrupted by thrombus or embolism and ischemia begins, cell death of astrocyte and infiltration of inflammatory cells accompanying it occur in 1 to 3 hours of onset, and when the onset exceeds 6 hours, death begins. That is, at the onset of cerebral ischemia, it is not diseased and its pathology is reversible. However, when astrocyte deaths and inflammatory response of prolonged, irreversible neuronal cell death is established. Ultimately, reactive astrocytes become fibrous astrocytes and form fibrotic gliosis in surrounding tissues of the injured nerve. Among these event cascades, it is speculated that the inflammatory response induced by DAMPs (Damage-associated molecular pattern) derived from dead cells re-amplifies the event cascade and further enhances the irreversibility of neuropathy. Therefore, if it is possible to control the inflammation induced by DAMPs by promoting the removal of dead cells in the premorbid period, it would be possible to reversibly restore the pathological condition or to delay irreversibility of neuropathy. However, the pathology of a series of event cascades leading to this neuropathy and its molecular mechanism have not been sufficiently elucidated.
In this study, we elucidate the molecular mechanisms of initiation, amplification and proliferation of inflammatory pathologies caused by DAMPs released from dead cells induced by ischemic stress. In addition, we clarified the function of the inhibitory immunoreceptor CD300a, which is a receptor of phosphatidylserein exposed on the plasma membrane of apoptotic cells, in the ischemic pathology and cerebral ischemic disease. Based on the results, we will develop the foundation of preventive and therapeutic methods.

Epigenetic regulation of cytokine gene expression underlying chronic inflammatory and allergic diseases

Representative
Takashi Moriguchi, MD, PhD
Professor, Tohoku Medical Pharmaceutical University

Group member

  • Satoshi Uemura, PhD
    Assistant Professor, Tohoku Medical Pharmaceutical University
  • Jun Takai, PhD
    Assistant Professor, Tohoku Medical Pharmaceutical University

Epigenetic regulation of inflammatory cytokine gene loci plays fundamental roles for etiological basis of inflammatory diseases. Zinc finger transcription factor GATA2 activates expression of a series of inflammatory cytokine genes and promotes progression of inflammatory diseases. In this project, we try to address regulatory mechanism of the GATA-factor-mediated inflammatory cytokine gene induction, and challenge to develop anti-inflammatory therapeutics utilizing GATA-inhibitors.

GATA factor target genes and transcription complexes; Target genes and components of transcription factor complexes of GATA2/3 will be comprehensively addressed. This information will be quite essential for thorough clarification of underlying mechanism for prolonged inflammatory cytokine gene expression.

Dynamics of epigenetic regulation of inflammatory cytokine genes; We have generated Hdc (Histidine Decarboxylase) BAC-directed GFP reporter transgenic mice, which enables sorting of histamine-producing cells and other inflammatory cells. Dynamics of epigenetic changes around the inflammatory cytokine gene loci will be analyzed utilizing this sorting strategy.

in vivo monitoring of inflammatory and allergic diseases; To address disease status of model animals, we generated a luciferase reporter transgenic mouse line, exploiting human IL6 BAC DNA clone. Applying multiple types of disease models to this reporter mouse, we will establish in vivo monitoring system for inflammatory status.

GATA3 function in metabolic syndrome; Adipose tissue inflammation plays a central role for the etiology of metabolic syndrome. We will clarify possible involvement of GATA3 transcription factor in pathogenesis of metabolic syndrome, exploiting a newly developed hematopoietic lineage-specific Gata3 deficient mice.

Mechanism of postmenopausal NASH-HCC development and its preventive strategies based on the “Inflammation Cellular Sociology”

Yoshihiro Ogawa
Professor, Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University
Professor, Department of Molecular and Cellular Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University

The metabolic syndrome is a cluster of visceral fat obesity, impaired glucose metabolism, atherogenic dyslipidemia, and blood pressure elevation, which all increase independently a risk of atherosclerotic diseases Nonalcoholic fatty liver disease (NAFLD) is defined as excessive lipid accumulation in the liver and considered as the hepatic manifestation of the metabolic syndrome. It includes a spectrum of liver conditions ranging from nonalcoholic fatty liver (NAFL) to nonalcoholic steatohepatitis (NASH) with advanced fibrosis and cirrhosis, which may occasionally cause hepatocellular carcinoma (HCC). Currently, NAFLD is an increasingly important cause of chronic liver disease in western countries, affecting more than 30% of the general population. The risk of NAFLD is gradually increased in men before the age of menopause, while in women, it increases abruptly after menopause, with increased risk of HCC in postmenopausal women.
Using melanocortin-4 receptor (MC4R)-deficient mice fed western diet (WD), we have developed a mouse model for human NASH, which exhibit obesity, liver steatosis, steatohepatitis, hepatic fibrosis, and eventually hepatocellular carcinoma. We found the unique histological features, which we have called hepatic crown-like structures (hCLS), in the NASH-like liver, where dead hepatocytes with large lipid droplet are surrounded by macrophages, and suggested that hCLS serves as an origin of hepatic inflammation and fibrosis during the progression from NAFL to NASH (Am. J. Pathol. 179: 2454-2463, 2011; PLoS ONE 8: e82163, 2013; JCI Insight 2: e92902, 2017). On the other hand, estrogen is known to suppress hepatic inflammation and fibrosis in the liver. However, how estrogen deficiency is involved in the development of NASH-HCC in postmenopausal women has not been fully elucidated.
In this study, using the ovariectomized MC4R-KO mice fed WD, we develop “postmenopausal NASH-HCC mice” and examine how hepatic inflammation and fibrosis occurs as a result of complex interaction among parenchymal hepatocytes and stromal cells such as macrophages within hCLS during estrogen deficiency. Accordingly, we aim to elucidate the entire picture of “Inflammation Cellular Sociology”, from the reversible pre-symptomatic state (NAFL), beyond the so-called “point of no return” state, to the irreversible diseased state (NASH-HCC) during the postmenopausal period.

Understanding of the mechanism for chronic inflammation in senescence

Yoshikazu Johmura
Assistant Professor, Division of Cancer cell Biology, Institute of Medical Science, University of Tokyo

The most important problem to be solved of modern science in Japan is to extend healthy lifespan. Reorganization of the medical system and improvement of lifestyle and diet is clearly important to prolong our healthy lifespan. However, comprehensive understanding of the mechanism for aging and development of new technology for preventing age-associated disorders and deterioration of tissues and organs is necessary for the drastic improvement of healthy lifespan. Recent reports indicate that accumulation of senescent cells (p16-positive cells) in body accelerates age-related changes such as arteriosclerosis and kidney injury and limits healthy lifespan using genetically engineered mouse models. An important hallmark of senescent cells is the inability to proliferate in response to physiological mitotic stimuli, which can limit the ability of stem cells to renew tissues and organs. Another hallmark of senescence is the appearance senescence-associated secretory phenotypes (SASP), such as robust secretion of numerous growth factors, cytokines, proteases and other proteins, which can cause deleterious effects on the tissue microenvironment. What extent these two hallmarks contribute to aging and the related disorders remains elusive. Moreover, how senescent cells affect the gene expression patterns and epigenome of surrounding cells in vivo remains largely unknown. This study develops new mouse models for senescent cells-specific knockout and high-sensitive senescent detection based on our previous finding, and applies these mouse models to comprehensive single-cell gene expression analysis for the understanding of the mechanisms by which senescence-induced inflammation contributes to aging and the related disorders. Therefore, this study will be expected to contribute to the main purpose of ‘Inflammation Cellular Society’ and develop the preventions for aging and the related disorders.

Metabolic and epigenetic regulation of the cellular society of chronic inflammation

Representative
Masakatsu Yamashita, PhD
Professor, Department of Immunology, Graduate School of Medicine, Ehime University

Group member

  • Makoto Kuwahara, PhD
    (Assistant Professor, Department of Immunology, Graduate School of Medicine, Ehime University)
  • Nobuaki Takemori, PhD
    (Lecturer, Advanced Research Support Center, Ehime University)

Asthma and chronic obstructive pulmonary disease (COPD) are usually clinically distinct and have different causal mechanisms. In some elderly patients, there are features of both diseases, and this has been termed asthma-COPD overlap syndrome (ACOS). While nationwide aging has been advancing rapidly in Japan, the number of ACOS patient may rapidly increase. However, an effective treating method has not been established, and the molecular mechanisms of ACOS onset remain to be elucidated.
Recently, we found that T cell-specific Bach2-deficient mice spontaneous developed ACOS-like chronic lung inflammation accompanying infiltration of eosinophils, neutrophils and lymphocytes. Increased innate-type Th2 cell response in Bach2-deficient lung CD4 T cells plays an important role in the onset of ACOS-like lung inflammation. Augmented activation of IL-7- and IL-33-mediated signals by Bach2 deficiency seem to be involved in the activation of innate-type Th2 cell response (Figure 1). Furthermore, we found that IL-7-dependet reprograming of cellular energy metabolism and subsequent epigenetic changes are required for the acquisition of innate-type Th2 function of CD4 T cells.
In this research project, we try to reveal the metabolic and epigenetic regulation of the ACOS to clarify the regulatory mechanism of the cellular society of chronic lung inflammation.

Decreased Bach2 expression confers innate
Th2 function to CD4 T cells

A03 

Network Analysis Model and Efficient Methods for Single Cell Sequence Data

Representative
Yasuhito Asano, PhD
Associate Professor, Graduate School of Informatics, Kyoto University

Group Member

  • Atsushi Ogura, PhD
    (Associate Professor,
    Nagahama
    Institute of Bio-science and Technology) 

Early-stage preventive interventions are considered important to deal with chronic inflammatory diseases. One of the effective ways is probably to focus on “pre-disease” state before abnormalities of cell organisms are colonized as the inflammatory memory, although the pre-disease state has not been elucidated sufficiently. In order to elucidate the mechanism of the pre-disease, it would be desired to model information about gene mutation, epigenome alteration, and cell interaction as a “cellular society network” among cells, genes and molecules. We expect to establish a method for analyzing the propagation process of the inflammatory memory based on this model. However, conventional network model for comparing two states is not sufficient for analyzing a mechanism including three states, that is, normal, pre-disease, and inflammatory. Therefore, we will try the following two tasks:

  • (1) Establishing a model of information propagation on a cellular society network containing the three states.
  • (2) Developing efficient analysis methods for large-scale networks generated from single cell sequence data.

Analysis of migration dynamics of inflammatory cells by bio-imaging and development of its simulation method

Representative
Hideo Matsuda, PhD
Professor, Osaka University, Graduate School of Information Science and Technology

Group member

  • Masaru Ishii, MD PhD
    (Professor, Osaka University, Graduate School of Frontier Biosciences)

In this study, we perform an integrated analysis between migration dynamics and single-cell transcriptome of a large number of immune cells. In the migration dynamics analysis, immune cells are fluorescently labeled, responses by inflammatory stimuli are observed by a two-photon excitation microscope, and by detecting the dynamics by an image processing method. We intend to quantitatively compare and classify the immune cells by their chemotaxis. In the single-cell transcriptome analysis, we develop a method of estimating the temporal state on the stimulus response, which is determined by the gene expressions of each cell obtained by single-cell sequencing.

As an image processing method for analyzing the migration dynamics of immune cells, we use a method called Deep Matching. Deep Matching is an object-tracking method that was developed in the computer vision field. By applying the method to cell images, we detect the migration cell trajectories from time-lapse microscopy images. For the single-cell transcriptome analysis, we analyze the heterogeneity of each cell in the cell population by their gene expression profiles with a statistical model called ‘topic model’. We estimate topics as potential factors that determines the expression levels of genes. By using latent Dirichlet allocation (LDA) as a topic model, we classify cells by the proportion of individual topics present. Moreover, we study on mathematical modeling and development of a simulation method of migration dynamics by correlating analysis of the dynamics of cells in the inflammatory state with the analysis of single-cell gene expression profiles.