Publications by authors named "Seiya Imoto"

179 Publications

Application of targeted nanopore sequencing for the screening and determination of structural variants in patients with Lynch syndrome.

J Hum Genet 2021 May 6. Epub 2021 May 6.

Division of Clinical Genome Research, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.

Lynch syndrome is a hereditary disease characterized by an increased risk of colorectal and other cancers. Germline variants in the mismatch repair (MMR) genes are responsible for this disease. Previously, we screened the MMR genes in colorectal cancer patients who fulfilled modified Amsterdam II criteria, and multiplex ligation-dependent probe amplification (MPLA) identified 11 structural variants (SVs) of MLH1 and MSH2 in 17 patients. In this study, we have tested the efficacy of long read-sequencing coupled with target enrichment for the determination of SVs and their breakpoints. DNA was captured by array probes designed to hybridize with target regions including four MMR genes and then sequenced using MinION, a nanopore sequencing platform. Approximately, 1000-fold coverage was obtained in the target regions compared with other regions. Application of this system to four test cases among the 17 patients correctly mapped the breakpoints. In addition, we newly found a deletion across an 84 kb region of MSH2 in a case without the pathogenic single nucleotide variants. These data suggest that long read-sequencing combined with hybridization-based enrichment is an efficient method to identify both SVs and their breakpoints. This strategy might replace MLPA for the screening of SVs in hereditary diseases.
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http://dx.doi.org/10.1038/s10038-021-00927-9DOI Listing
May 2021

Role of Circulating Tumor DNA in Hematological Malignancy.

Cancers (Basel) 2021 Apr 25;13(9). Epub 2021 Apr 25.

Division of Molecular Therapy, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.

With the recent advances in noninvasive approaches for cancer diagnosis and surveillance, the term "liquid biopsy" has become more familiar to clinicians, including hematologists. Liquid biopsy provides a variety of clinically useful genetic data. In this era of personalized medicine, genetic information is critical to early diagnosis, aiding risk stratification, directing therapeutic options, and monitoring disease relapse. The validity of circulating tumor DNA (ctDNA)-mediated liquid biopsies has received increasing attention. This review summarizes the current knowledge of liquid biopsy ctDNA in hematological malignancies, focusing on the feasibility, limitations, and key areas of clinical application. We also highlight recent advances in the minimal residual disease monitoring of leukemia using ctDNA. This article will be useful to those involved in the clinical practice of hematopoietic oncology.
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http://dx.doi.org/10.3390/cancers13092078DOI Listing
April 2021

Comprehensive molecular analysis of genomic profiles and PD-L1 expression in lung adenocarcinoma with a high-grade fetal adenocarcinoma component.

Transl Lung Cancer Res 2021 Mar;10(3):1292-1304

Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan.

Background: Fetal adenocarcinoma of the lung is a rare variant of lung adenocarcinoma and is subcategorized into low-grade and high-grade (H-FLAC) fetal adenocarcinoma. We previously reported poor prognosis in pulmonary adenocarcinomas with an H-FLAC component; however, the genetic abnormalities involved in H-FLAC remain unclear. Therefore, this study aimed to elucidate molecular abnormalities as potential therapeutic targets for H-FLACs.

Methods: We performed immunohistochemical analysis and comprehensive genetic analyses using whole-exome sequencing in 16 lung cancer samples with an H-FLAC component. DNA was extracted from formalin-fixed paraffin-embedded tissues after macrodissection of the H-FLAC component.

Results: Cancer-related mutations were identified in (7/16 cases), (6/16 cases), (4/16 cases), (3/16 cases), (3/16 cases), (2/16 cases), and (1/16 cases). A high tumor mutation burden of ≥10 mutations per megabase was observed in 3/16 cases. A high microsatellite instability was not detected in any case. Based on the cosine similarity with the Catalogue of Somatic Mutations in Cancer mutational signatures, H-FLACs were hierarchically clustered into three types: common adenocarcinoma-like (five cases), surfactant-deficient (ten cases), and signatures 2 and 13-related (one case). All common adenocarcinoma-like cases presented thyroid transcription factor-1 (TTF-1) expression, whereas surfactant-deficient cases often presented loss of TTF-1 and surfactant protein expression and included cases with mutations in the surfactant system genes and . H-FLACs displayed low programmed death ligand-1 (PD-L1) expression (1-49% of tumor cells) in 5/16 cases, and no case displayed high PD-L1 expression (≥50% of tumor cells).

Conclusions: This study indicates that lung cancers with an H-FLAC component rarely harbor currently targetable driver gene mutations for lung cancer but display a high frequency of mutations. The microsatellite instability, tumor mutation burden, and PD-L1 expression status suggest a poor response to immune checkpoint therapy.
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http://dx.doi.org/10.21037/tlcr-20-1158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8044470PMC
March 2021

COVID-19 risk assessment at the opening ceremony of the Tokyo 2020 Olympic Games.

Microb Risk Anal 2021 Mar 21:100162. Epub 2021 Mar 21.

Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.

The 2020 Olympic/Paralympic Games have been postponed to 2021, due to the COVID-19 pandemic. We developed a model that integrated source-environment-receptor pathways to evaluate how preventive efforts can reduce the infection risk among spectators at the opening ceremony of Tokyo Olympic Games. We simulated viral loads of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emitted from infectors through talking/coughing/sneezing and modeled temporal environmental behaviors, including virus inactivation and transfer. We performed Monte Carlo simulations to estimate the expected number of newly infected individuals with and without preventive measures, yielding the crude probability of a spectator being an infector among the 60,000 people expected to attend the opening ceremony. Two indicators, i.e., the expected number of newly infected individuals and the newly infected individuals per infector entry, were proposed to demonstrate the extent of achievable infection risk reduction levels by implementing possible preventive measures. A no-prevention scenario produced 1.5-1.7 newly infected individuals per infector entry, whereas a combination of cooperative preventive measures by organizers and the spectators achieved a 99% risk reduction, corresponding to 0.009-0.012 newly infected individuals per infector entry. The expected number of newly infected individuals was calculated as 0.005 for the combination of cooperative preventive scenarios with the crude probability of a spectator being an infector of 1 × 10. Based on our estimates, a combination of cooperative preventions between organizers and spectators is required to prevent a viral spread at the Tokyo Olympic/Paralympic Games. Further, under the assumption that society accepts < 10 newly infected persons traced to events held during the entire Olympic/Paralympic Games, we propose a crude probability of infectors of < 5 × 10 as a benchmark for the suppression of the infection. This is the first study to develop a model that can assess the infection risk among spectators due to exposure pathways at a mass gathering event.
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http://dx.doi.org/10.1016/j.mran.2021.100162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7981581PMC
March 2021

Functional Restoration of Bacteriomes and Viromes by Fecal Microbiota Transplantation.

Gastroenterology 2021 May 9;160(6):2089-2102.e12. Epub 2021 Feb 9.

Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan; Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan; Division of Innate Immune Regulation, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan. Electronic address:

Background & Aims: Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridioides difficile infection (rCDI). However, the overall mechanisms underlying FMT success await comprehensive elucidation, and the safety of FMT has recently become a serious concern because of the occurrence of drug-resistant bacteremia transmitted by FMT. We investigated whether functional restoration of the bacteriomes and viromes by FMT could be an indicator of successful FMT.

Methods: The human intestinal bacteriomes and viromes from 9 patients with rCDI who had undergone successful FMT and their donors were analyzed. Prophage-based and CRISPR spacer-based host bacteria-phage associations in samples from recipients before and after FMT and in donor samples were examined. The gene functions of intestinal microorganisms affected by FMT were evaluated.

Results: Metagenomic sequencing of both the viromes and bacteriomes revealed that FMT does change the characteristics of intestinal bacteriomes and viromes in recipients after FMT compared with those before FMT. In particular, many Proteobacteria, the fecal abundance of which was high before FMT, were eliminated, and the proportion of Microviridae increased in recipients. Most temperate phages also behaved in parallel with the host bacteria that were altered by FMT. Furthermore, the identification of bacterial and viral gene functions before and after FMT revealed that some distinctive pathways, including fluorobenzoate degradation and secondary bile acid biosynthesis, were significantly represented.

Conclusions: The coordinated action of phages and their host bacteria restored the recipients' intestinal flora. These findings show that the restoration of intestinal microflora functions reflects the success of FMT.
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http://dx.doi.org/10.1053/j.gastro.2021.02.013DOI Listing
May 2021

Senolysis by glutaminolysis inhibition ameliorates various age-associated disorders.

Science 2021 01;371(6526):265-270

Division of Cancer Cell Biology, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

Removal of senescent cells (senolysis) has been proposed to be beneficial for improving age-associated pathologies, but the molecular pathways for such senolytic activity have not yet emerged. Here, we identified glutaminase 1 () as an essential gene for the survival of human senescent cells. The intracellular pH in senescent cells was lowered by lysosomal membrane damage, and this lowered pH induced kidney-type glutaminase (KGA) expression. The resulting enhanced glutaminolysis induced ammonia production, which neutralized the lower pH and improved survival of the senescent cells. Inhibition of KGA-dependent glutaminolysis in aged mice eliminated senescent cells specifically and ameliorated age-associated organ dysfunction. Our results suggest that senescent cells rely on glutaminolysis, and its inhibition offers a promising strategy for inducing senolysis in vivo.
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http://dx.doi.org/10.1126/science.abb5916DOI Listing
January 2021

Data science and precision health care.

Nutr Rev 2020 12;78(12 Suppl 2):53-57

Division of Cancer Systems Biology, Aichi Cancer Center Research Institute, Aichi, Japan.

Precision health care plays a crucial role in an elderly society by providing personalized health care plans for improving an individual's health conditions and preventing disease. To realize precision health care, data science is key; it allows for analyses of health-related big data. In this article, an actual analysis of time-series health check-up data is presented and as is a discussion of how personalized simulation models of health conditions are constructed and used to modify individual behavior. Future directions for precision health care based on the integration of genetic variations and the microbiome are also discussed.
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http://dx.doi.org/10.1093/nutrit/nuaa110DOI Listing
December 2020

Genome-wide association studies and heritability analysis reveal the involvement of host genetics in the Japanese gut microbiota.

Commun Biol 2020 Nov 18;3(1):686. Epub 2020 Nov 18.

Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.

Numerous host extrinsic and intrinsic factors affect the gut microbiota composition, but their cumulative effects do not sufficiently explain the variation in the microbiota, suggesting contributions of missing factors. The Japanese population possesses homogeneous genetic features suitable for genome-wide association study (GWAS). Here, we performed GWASs for human gut microbiota using 1068 healthy Japanese adults. To precisely evaluate genetic effects, we corrected for the impacts of numerous host extrinsic and demographic factors by introducing them as covariates, enabling us to discover five loci significantly associated with microbiome diversity measures: HS3ST4, C2CD2, 2p16.1, 10p15.1, and 18q12.2. Nevertheless, these five variants explain only a small fraction of the variation in the gut microbiota. We subsequently investigated the heritability of each of the 21 core genera and found that the abundances of six genera are heritable. We propose that the gut microbiota composition is affected by a highly polygenic architecture rather than several strongly associated variants in the Japanese population.
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http://dx.doi.org/10.1038/s42003-020-01416-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7674416PMC
November 2020

Halcyon: An Accurate Basecaller Exploiting An Encoder-Decoder Model With Monotonic Attention.

Bioinformatics 2020 Nov 9. Epub 2020 Nov 9.

Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.

Motivation: In recent years, nanopore sequencing technology has enabled inexpensive long-read sequencing, which promises reads longer than a few thousand bases. Such long-read sequences contribute to the precise detection of structural variations and accurate haplotype phasing. However, deciphering precise DNA sequences from noisy and complicated nanopore raw signals remains a crucial demand for downstream analyses based on higher-quality nanopore sequencing, although various basecallers have been introduced to date.

Results: To address this need, we developed a novel basecaller, Halcyon, that incorporates neural-network techniques frequently used in the field of machine translation. Our model employs monotonic-attention mechanisms to learn semantic correspondences between nucleotides and signal levels without any pre-segmentation against input signals. We evaluated performance with a human whole-genome sequencing dataset and demonstrated that Halcyon outperformed existing third-party basecallers and achieved competitive performance against the latest Oxford Nanopore Technologies' basecallers.

Availability: The source code (halcyon) can be found at https://github.com/relastle/halcyon.
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http://dx.doi.org/10.1093/bioinformatics/btaa953DOI Listing
November 2020

Global gene network exploration based on explainable artificial intelligence approach.

PLoS One 2020 6;15(11):e0241508. Epub 2020 Nov 6.

M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan.

In recent years, personalized gene regulatory networks have received significant attention, and interpretation of the multilayer networks has been a critical issue for a comprehensive understanding of gene regulatory systems. Although several statistical and machine learning approaches have been developed and applied to reveal sample-specific regulatory pathways, integrative understanding of the massive multilayer networks remains a challenge. To resolve this problem, we propose a novel artificial intelligence (AI) strategy for comprehensive gene regulatory network analysis. In our strategy, personalized gene networks corresponding specific clinical characteristic are constructed and the constructed network is considered as a second-order tensor. Then, an explainable AI method based on deep learning is applied to decompose the multilayer networks, thus we can reveal all-encompassing gene regulatory systems characterized by clinical features of patients. To evaluate the proposed methodology, we apply our method to the multilayer gene networks under varying conditions of an epithelial-mesenchymal transition (EMT) process. From the comprehensive analysis of multilayer networks, we identified novel markers, and the biological mechanisms of the identified genes and their reciprocal mechanisms are verified through the literature. Although any biological knowledge about the identified genes was not incorporated in our analysis, our data-driven approach based on AI approach provides biologically reliable results. Furthermore, the results provide crucial evidences to reveal biological mechanism related to various diseases, e.g., keratinocyte proliferation. The use of explainable AI method based on the tensor decomposition enables us to reveal global and novel mechanisms of gene regulatory system from the massive multiple networks, which cannot be demonstrated by existing methods. We expect that the proposed method provides a new insight into network biology and it will be a useful tool to integrative gene network analysis related complex architectures of diseases.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0241508PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7647077PMC
December 2020

Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens.

Bioinformatics 2020 09;36(18):4813-4816

Division of Health Medical Data Science, Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.

Summary: It is known that some mutant peptides, such as those resulting from missense mutations and frameshift insertions, can bind to the major histocompatibility complex and be presented to antitumor T cells on the surface of a tumor cell. These peptides are termed neoantigen, and it is important to understand this process for cancer immunotherapy. Here, we introduce an R package termed Neoantimon that can predict a list of potential neoantigens from a variety of mutations, which include not only somatic point mutations but insertions, deletions and structural variants. Beyond the existing applications, Neoantimon is capable of attaching and reflecting several additional information, e.g. wild-type binding capability, allele specific RNA expression levels, single nucleotide polymorphism information and combinations of mutations to filter out infeasible peptides as neoantigen.

Availability And Implementation: The R package is available at http://github/hase62/Neoantimon.
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http://dx.doi.org/10.1093/bioinformatics/btaa616DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7750962PMC
September 2020

Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16 Cells In Vivo.

Cell Metab 2020 11 18;32(5):814-828.e6. Epub 2020 Sep 18.

Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-0022, Japan.

Cell senescence plays a key role in age-associated organ dysfunction, but the in vivo pathogenesis is largely unclear. Here, we generated a p16-Cre-tdTomato mouse model to analyze the in vivo characteristics of p16 cells at a single-cell level. We found tdTomato-positive p16 cells detectable in all organs, which were enriched with age. We also found that these cells failed to proliferate and had half-lives ranging from 2.6 to 4.2 months, depending on the tissue examined. Single-cell transcriptomics in the liver and kidneys revealed that p16 cells were present in various cell types, though most dominant in hepatic endothelium and in renal proximal and distal tubule epithelia, and that these cells exhibited heterogeneous senescence-associated phenotypes. Further, elimination of p16 cells ameliorated nonalcoholic steatohepatitis-related hepatic lipidosis and immune cell infiltration. Our new mouse model and single-cell analysis provide a powerful resource to enable the discovery of previously unidentified senescence functions in vivo.
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http://dx.doi.org/10.1016/j.cmet.2020.09.006DOI Listing
November 2020

Metagenomic profiling of gut microbiome in early chronic kidney disease.

Nephrol Dial Transplant 2020 Sep 1. Epub 2020 Sep 1.

Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto, Japan.

Background: The relationship between chronic kidney disease (CKD) and the gut microbiome, which interact through chronic inflammation, uraemic toxin production and immune response regulation, has gained interest in the development of CKD therapies. However, reports using shotgun metagenomic analysis of the gut microbiome are scarce, especially for early CKD. Here we characterized gut microbiome differences between non-CKD participants and ones with early CKD using metagenomic sequencing.

Methods: In total, 74 non-CKD participants and 37 participants with early CKD were included based on propensity score matching, controlling for various factors including dietary intake. Stool samples were collected from participants and subjected to shotgun sequencing. Bacterial and pathway abundances were profiled at the species level with MetaPhlAn2 and HUMAnN2, respectively, and overall microbiome differences were determined using Bray-Curtis dissimilarities. Diabetic and non-diabetic populations were analysed separately.

Results: For diabetic and non-diabetic participants, the mean estimated glomerular filtration rates of the CKD group were 53.71 [standard deviation (SD) 3.87] and 53.72 (SD 4.44), whereas those of the non-CKD group were 72.63 (SD 7.72) and 76.10 (SD 9.84), respectively. Alpha and beta diversities were not significantly different between groups. Based on taxonomic analysis, butyrate-producing species Roseburia inulinivorans, Ruminococcus torques and Ruminococcus lactaris were more abundant in the non-CKD group, whereas Bacteroides caccae and Bacteroides coprocora were more abundant in the non-diabetic CKD group.

Conclusions: Although gut microbiome changes in individuals with early CKD were subtle, the results suggest that changes related to producing short-chain fatty acids can already be observed in early CKD.
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http://dx.doi.org/10.1093/ndt/gfaa122DOI Listing
September 2020

Association of single nucleotide polymorphisms in the NRF2 promoter with vascular stiffness with aging.

PLoS One 2020 11;15(8):e0236834. Epub 2020 Aug 11.

Department of Stress Response Science, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, Hirosaki, Japan.

Purpose: Pulse wave velocity (PWV), an indicator of vascular stiffness, increases with age and is increasingly recognized as an independent risk factor for cardiovascular disease (CVD). Although many mechanical and chemical factors underlie the stiffness of the elastic artery, genetic risk factors related to age-dependent increases in PWV in apparently healthy people are largely unknown. The transcription factor nuclear factor E2 (NF-E2)-related factor 2 (Nrf2), which is activated by unidirectional vascular pulsatile shear stress or oxidative stress, regulates vascular redox homeostasis. Previous reports have shown that a SNP in the NRF2 gene regulatory region (-617C>A; hereafter called SNP-617) affects NRF2 gene expression such that the minor A allele confers lower gene expression compared to the C allele, and it is associated with various diseases, including CVD. We aimed to investigate whether SNP-617 affects vascular stiffness with aging in apparently healthy people.

Methods: Analyzing wide-ranging data obtained from a public health survey performed in Japan, we evaluated whether SNP-617 affected brachial-ankle PWV (baPWV) in never-smoking healthy subjects (n = 642). We also evaluated the effects of SNP-617 on other cardiovascular and blood test measurements.

Results: We have shown that not only AA carriers (n = 55) but also CA carriers (n = 247) show arterial stiffness compared to CC carriers (n = 340). Furthermore, SNP-617 also affected blood pressure indexes such as systolic blood pressure and mean arterial pressure but not the ankle brachial pressure index, an indicator of atherosclerosis. Multivariate analysis showed that SNP-617 accelerates the incremental ratio of baPWV with age.

Conclusions: This study is the first to show that SNP-617 affects the age-dependent increase in vascular stiffness. Our results indicate that low NRF2 activity induces premature vascular aging and could be targeted for the prevention of cardiovascular diseases associated with aging.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0236834PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7418968PMC
October 2020

Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts.

Cell Host Microbe 2020 09 10;28(3):380-389.e9. Epub 2020 Jul 10.

Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan; Division of Metagenome Medicine, Human Genome Center, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan; Division of Innate Immune Regulation, International Research and Development Center for Mucosal Vaccines, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan. Electronic address:

The application of bacteriophages (phages) is proposed as a highly specific therapy for intestinal pathobiont elimination. However, the infectious associations between phages and bacteria in the human intestine, which is essential information for the development of phage therapies, have yet to be fully elucidated. Here, we report the intestinal viral microbiomes (viromes), together with bacterial microbiomes (bacteriomes), in 101 healthy Japanese individuals. Based on the genomic sequences of bacteriomes and viromes from the same fecal samples, the host bacteria-phage associations are illustrated for both temperate and virulent phages. To verify the usefulness of the comprehensive host bacteria-phage information, we screened Clostridioides difficile-specific phages and identified antibacterial enzymes whose activity is confirmed both in vitro and in vivo. These comprehensive metagenome analyses reveal not only host bacteria-phage associations in the human intestine but also provide vital information for the development of phage therapies against intestinal pathobionts.
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http://dx.doi.org/10.1016/j.chom.2020.06.005DOI Listing
September 2020

Fecal Microbiome Composition in Healthy Adults in Ghana.

Jpn J Infect Dis 2021 Jan 30;74(1):42-47. Epub 2020 Jun 30.

Joint Research Center for Human Retrovirus Infection, Kumamoto University, Japan.

Recent studies have indicated an association between gut microbiome composition and various disorders, including infectious diseases. The composition of the microbiome differs among ethnicities and countries, possibly resulting in diversified interactions between host immunity and the gut microbiome. Characterization of baseline microbiome composition in healthy people is an essential step for better understanding of the biological interactions associated with individual populations. However, data on the gut/fecal microbiome have not been accumulated for individuals in West Africa. In the present study, we examined the fecal microbiome composition in healthy adults in Ghana. Toward this, 16S rRNA gene libraries were prepared using bacterial fractions derived from 55 Ghanaian adults, which were then subjected to next-generation sequencing. The fecal microbiome of the Ghanaian adults was dominated by Firmicutes (Faecalibacterium, Subdoligranulum, and Ruminococcaceae UCG-014), Proteobacteria (Escherichia-Shigella and Klebsiella), and Bacteroidetes (Prevotella 9 and Bacteroides), consistent with previous observations in African cohorts. Further, our analysis revealed differences in microbiome composition and a lower diversity of the fecal microbiome in the Ghanaian cohort compared with those reported in non-African countries. This is the first study to describe substantial fecal microbiome data obtained using high-throughput metagenomic tools on samples derived from a cohort in Ghana. The data may provide a valuable basis for determining the association between the fecal microbiome and progression of various diseases in West African populations.
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http://dx.doi.org/10.7883/yoken.JJID.2020.469DOI Listing
January 2021

The relationship between cigarette smoking and the tongue microbiome in an East Asian population.

J Oral Microbiol 2020 25;12(1):1742527. Epub 2020 Mar 25.

Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto, Japan.

: The oral microbiome, which consists of various habitats, has been shown to be influenced by smoking. However, differences in the tongue microbiomes of current and former smokers, as well as their resultant functional consequences, have rarely been investigated in East Asian populations. : We used amplicon sequencing of tongue-coating samples obtained from East Asian subjects who were current, former, or never smokers to identify differences in their tongue microbiomes and related metagenomic functions. Two sets of participants from 2016 to 2017 (n = 657 and n = 187, respectively) were analyzed separately. : We found significant differences between the overall microbiome compositions of current versus never smokers (p = 0.0015), but not between former versus never smokers (p = 0.43) based on the weighted UniFrac distance. Twenty-nine of 43 investigated genera showed significantly different expression levels in current versus never smokers. and were less abundant, and and were more abundant in current smokers. Moreover, the abundances of metagenomic pathways, including those related to nitrate reduction and the tricarboxylic acid cycle, were significantly different between current and never smokers. : The tongue microbiomes and related metagenomic pathways of current smokers differ from those of never smokers among East Asians.
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http://dx.doi.org/10.1080/20002297.2020.1742527DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7170382PMC
March 2020

Nanopore basecalling from a perspective of instance segmentation.

BMC Bioinformatics 2020 Apr 23;21(Suppl 3):136. Epub 2020 Apr 23.

The Institute of Medical Science, The University of Tokyo, Shirokanedai 4-6-1, Minato-ku, Tokyo, 108-8639, Japan.

Background: Nanopore sequencing is a rapidly developing third-generation sequencing technology, which can generate long nucleotide reads of molecules within a portable device in real-time. Through detecting the change of ion currency signals during a DNA/RNA fragment's pass through a nanopore, genotypes are determined. Currently, the accuracy of nanopore basecalling has a higher error rate than the basecalling of short-read sequencing. Through utilizing deep neural networks, the-state-of-the art nanopore basecallers achieve basecalling accuracy in a range from 85% to 95%.

Result: In this work, we proposed a novel basecalling approach from a perspective of instance segmentation. Different from previous approaches of doing typical sequence labeling, we formulated the basecalling problem as a multi-label segmentation task. Meanwhile, we proposed a refined U-net model which we call UR-net that can model sequential dependencies for a one-dimensional segmentation task. The experiment results show that the proposed basecaller URnano achieves competitive results on the in-species data, compared to the recently proposed CTC-featured basecallers.

Conclusion: Our results show that formulating the basecalling problem as a one-dimensional segmentation task is a promising approach, which does basecalling and segmentation jointly.
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http://dx.doi.org/10.1186/s12859-020-3459-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7178565PMC
April 2020

Proton pump inhibitors enhance intestinal permeability via dysbiosis of gut microbiota under stressed conditions in mice.

Neurogastroenterol Motil 2020 07 21;32(7):e13841. Epub 2020 Apr 21.

Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan.

Background: Intestinal permeability and psychological stress are considered the key mechanism(s) in functional dyspepsia (FD). Although proton pump inhibitors (PPIs) are commonly used for the treatment of FD, the effect of PPIs on intestinal permeability has not been elucidated. This study investigated the effect of PPI on intestinal permeability under stressed conditions.

Methods: C57BL/6J mice were subjected to water avoidance stress (WAS) and administered rabeprazole (40 mg/kg) or vehicle treatment (VT). We then evaluated intestinal permeability both in vivo and ex vivo using plasma fluorescein isothiocyanate-dextran and by assessing the paracellular permeability and transepithelial electrical resistance (TEER) in an Ussing chamber, respectively. Furthermore, we evaluated the effect of PPI-treated fecal microbiota transplant (FMT) on intestinal permeability in vivo. Microbiota profiles of donor feces were assessed by 16S rRNA gene analysis using MiSeq and QIIME2.

Key Results: In the WAS treatment, PPI significantly enhanced intestinal permeability in vivo compared to that in VT. Moreover, PPI significantly increased paracellular permeability and decreased TEER in the duodenum and jejunum, respectively, compared to those in VT under stressed conditions. Moreover, both vasoactive intestinal peptide (VIP) receptor antagonist and ketotifen significantly reversed the effect of PPI on intestinal permeability. Furthermore, PPI-treated FMT significantly increased the intestinal permeability in vivo compared to that in vehicle-treated FMT. Proton pump inhibitors treatment altered the gut microbiota composition, indicating that PPI induced dysbiosis.

Conclusions And Inferences: Under stressed conditions, PPI enhances intestinal permeability via dysbiosis of gut microbiota. Vasoactive intestinal peptide and mast cells are also implicated in the underlying mechanisms.
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http://dx.doi.org/10.1111/nmo.13841DOI Listing
July 2020

Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types.

Genome Res 2020 Mar 24. Epub 2020 Mar 24.

Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 230-0045, Japan.

Microsatellites are repeats of 1- to 6-bp units, and approximately 10 million microsatellites have been identified across the human genome. Microsatellites are vulnerable to DNA mismatch errors and have thus been used to detect cancers with mismatch repair deficiency. To reveal the mutational landscape of microsatellite repeat regions at the genome level, we analyzed approximately 20.1 billion microsatellites in 2717 whole genomes of pan-cancer samples across 21 tissue types. First, we developed a new insertion and deletion caller (MIMcall) that takes into consideration the error patterns of different types of microsatellites. Among the 2717 pan-cancer samples, our analysis identified 31 samples, including colorectal, uterus, and stomach cancers, with a higher proportion of mutated microsatellite (≥0.03), which we defined as microsatellite instability (MSI) cancers of genome-wide level. Next, we found 20 highly mutated microsatellites that can be used to detect MSI cancers with high sensitivity. Third, we found that replication timing and DNA shape were significantly associated with mutation rates of microsatellites. Last, analysis of mutations in mismatch repair genes showed that somatic SNVs and short indels had larger functional impacts than germline mutations and structural variations. Our analysis provides a comprehensive picture of mutations in the microsatellite regions and reveals possible causes of mutations, as well as provides a useful marker set for MSI detection.
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http://dx.doi.org/10.1101/gr.255026.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7111525PMC
March 2020

Prediction of blood test values under different lifestyle scenarios using time-series electronic health record.

PLoS One 2020 20;15(3):e0230172. Epub 2020 Mar 20.

Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan.

Owing to increasing medical expenses, researchers have attempted to detect clinical signs and preventive measures of diseases using electronic health record (EHR). In particular, time-series EHRs collected by periodic medical check-up enable us to clarify the relevance among check-up results and individual environmental factors such as lifestyle. However, usually such time-series data have many missing observations and some results are strongly correlated to each other. These problems make the analysis difficult and there exists strong demand to detect clinical findings beyond them. We focus on blood test values in medical check-up results and apply a time-series analysis methodology using a state space model. It can infer the internal medical states emerged in blood test values and handle missing observations. The estimated models enable us to predict one's blood test values under specified condition and predict the effect of intervention, such as changes of body composition and lifestyle. We use time-series data of EHRs periodically collected in the Hirosaki cohort study in Japan and elucidate the effect of 17 environmental factors to 38 blood test values in elderly people. Using the estimated model, we then simulate and compare time-transitions of participant's blood test values under several lifestyle scenarios. It visualizes the impact of lifestyle changes for the prevention of diseases. Finally, we exemplify that prediction errors under participant's actual lifestyle can be partially explained by genetic variations, and some of their effects have not been investigated by traditional association studies.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0230172PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7083324PMC
June 2020

Metagenomic analysis of bacterial species in tongue microbiome of current and never smokers.

NPJ Biofilms Microbiomes 2020 03 13;6(1):11. Epub 2020 Mar 13.

Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan.

Cigarette smoking affects the oral microbiome, which is related to various systemic diseases. While studies that investigated the relationship between smoking and the oral microbiome by 16S rRNA amplicon sequencing have been performed, investigations involving metagenomic sequences are rare. We investigated the bacterial species composition in the tongue microbiome, as well as single-nucleotide variant (SNV) profiles and gene content of these species, in never and current smokers by utilizing metagenomic sequences. Among 234 never smokers and 52 current smokers, beta diversity, as assessed by weighted UniFrac measure, differed between never and current smokers (pseudo-F = 8.44, R = 0.028, p = 0.001). Among the 26 species that had sufficient coverage, the SNV profiles of Actinomyces graevenitzii, Megasphaera micronuciformis, Rothia mucilaginosa, Veillonella dispar, and one Veillonella sp. were significantly different between never and current smokers. Analysis of gene and pathway content revealed that genes related to the lipopolysaccharide biosynthesis pathway in Veillonella dispar were present more frequently in current smokers. We found that species-level tongue microbiome differed between never and current smokers, and 5 species from never and current smokers likely harbor different strains, as suggested by the difference in SNV frequency.
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http://dx.doi.org/10.1038/s41522-020-0121-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7069950PMC
March 2020

Discrimination of prediction models between cold-heat and deficiency-excess patterns.

Complement Ther Med 2020 Mar 20;49:102353. Epub 2020 Feb 20.

Center for Kampo Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan. Electronic address:

Objective: The purpose of this study was to extract important patient questionnaire items by creating random forest models for predicting pattern diagnosis considering an interaction between deficiency-excess and cold-heat patterns.

Design: A multi-centre prospective observational study.

Setting: Participants visiting six Kampo speciality clinics in Japan from 2012 to 2015.

Main Outcome Measure: Deficiency-excess pattern diagnosis made by board-certified Kampo experts.

Methods: We used 153 items as independent variables including, age, sex, body mass index, systolic and diastolic blood pressures, and 148 subjective symptoms recorded through a questionnaire. We sampled training data with an equal number of the different patterns from a 2 × 2 factorial combination of deficiency-excess and cold-heat patterns. We constructed the prediction models of deficiency-excess and cold-heat patterns using the random forest algorithm, extracted the top 10 essential items, and calculated the discriminant ratio using this prediction model.

Results: BMI and blood pressure, and subjective symptoms of cold or heat sensations were the most important items in the prediction models of deficiency-excess pattern and of cold-heat patterns, respectively. The discriminant ratio was not inferior compared with the result ignoring the interaction between the diagnoses.

Conclusions: We revised deficiency-excess and cold-heat pattern prediction models, based on balanced training sample data obtained from six Kampo speciality clinics in Japan. The revised important items for diagnosing a deficiency-excess pattern and cold-heat pattern were compatible with the definition in the 11 version of international classification of diseases.
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http://dx.doi.org/10.1016/j.ctim.2020.102353DOI Listing
March 2020

Classification of primary liver cancer with immunosuppression mechanisms and correlation with genomic alterations.

EBioMedicine 2020 Mar 26;53:102659. Epub 2020 Feb 26.

Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. Electronic address:

Background: The tumor microenvironment can be classified into immunologically active "inflamed" tumors and inactive "non-inflamed" tumors based on the infiltration of cytotoxic immune cells. Previous studies on liver cancer have reported a superior prognosis for inflamed tumors compared to non-inflamed tumors. However, liver cancer is highly heterogeneous immunologically and genetically, and a finer classification of the liver cancer microenvironment may improve our understanding of its immunological diversity and response to immune therapy.

Methods: We characterized the immune gene signatures of 234 primary liver cancers, mainly virus-related, from a Japanese population using RNA-Seq of tumors and matched non-tumorous hepatitis livers. We then compared them with the somatic alterations detected using the whole-genome sequencing.

Findings: Liver cancers expressed lower levels of immune marker genes than non-tumorous hepatitis livers, indicating immunosuppression in the tumor microenvironment. Several immunosuppression mechanisms functioned actively and mutually exclusively, resulting in four immune subclasses of liver cancer: tumor-associated macrophage (TAM), CTNNB1, cytolytic activity (CYT), and regulatory T cell (Treg). The CYT and Treg subclasses represented inflamed tumors, while the TAM and CTNNB1 subclasses represented non-inflamed tumors. The TAM subclass, which comprised 31% of liver cancers, showed a poor survival, expressed elevated levels of extracellular matrix genes, and was associated with somatic mutations of chromatin regulator ARID2. The results of cell line experiments suggested a functional link between ARID2 and chemokine production by liver cancer cells.

Interpretation: Primary liver cancer was classified into four subclasses based on mutually exclusive mechanisms for immunosuppression. This classification indicate the importance of immunosuppression mechanisms, such as TAM and Treg, as therapeutic targets for liver cancer.

Funding: The Japan Agency for Medical Research and Development (AMED).
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http://dx.doi.org/10.1016/j.ebiom.2020.102659DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7048625PMC
March 2020

Variant analysis of prostate cancer in Japanese patients and a new attempt to predict related biological pathways.

Oncol Rep 2020 Mar 27;43(3):943-952. Epub 2020 Jan 27.

Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Kanagawa 241‑8515, Japan.

There are regional and/or ethnic differences in tumorigenic pathways among several types of cancer, including prostate cancer (PCa). However, information on genome‑wide gene alterations and the transcriptome is currently only available for PCa patients from Western countries. In order to profile the genetic alterations in Japanese patients with PCa, new panels were created to examine nucleotide sequence variations in 71 selected PCa‑related genes (KCC71) and to detect all fusion RNA transcripts known in PCa (PCaFusion). An analysis of 21 Japanese PCa cases identified 33 different somatic variants in 24 genes in the KCC71 panel, including 2 in SPOP (F102V and F133L), 2 in BRCA2 (I1859fs and R2318ter, resulting in premature termination of the polypeptide), and 1 each in BRAF (K601E), CDH1 (E880K) and RB1 (R621S), as pathogenic alterations. Unexpectedly, the TMPRSS2‑ERG fusion transcript was detected in only 1 case, although the SLC45A3‑ELK4 and USP9Y‑TTTY15 fusion transcripts, known as transcription‑mediated chimeric RNAs, were detected in all examined cases. A new pathway analysis with The Cancer Network Galaxy (TCNG), a cancer gene regulatory network database, was also applied in an attempt to predict molecular pathways implicated in PCa in the Japanese population. Based on the 24 genes having somatic variants identified by the panel analysis as initial seed genes, a putative core network was finally established, including 5 identified genes, namely TNK2, SOX9, CDH1, FOXA1 and TP53, with high commonality from TCNG datasets. These genes are expected to be involved in tumor development, as revealed by the results of an enrichment analysis with Gene Ontology terms. This analysis must be further extended to include more cases in order to verify this method and also to elucidate the characteristics of PCa in Japanese patients.
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http://dx.doi.org/10.3892/or.2020.7481DOI Listing
March 2020

Association between breath methane concentration and visceral fat area: a population-based cross-sectional study.

J Breath Res 2020 02 25;14(2):026008. Epub 2020 Feb 25.

Department of Active Life Promotion Sciences, Graduate School of Medicine, Hirosaki University, Japan. Health Care Food Research Laboratories, Kao Corporation, Japan.

High visceral fat area (VFA) is a stronger predictor of cardiovascular disease and overall mortality, compared with body mass index (BMI) and waist circumference (WC). Recent reports demonstrate that obesity is related to breath gas, which is produced by the intestinal microflora. However, these studies define obesity using BMI, not VFA. In this population-based cross-sectional study, we investigated the relationship between breath gases (methane and hydrogen) and both VFA and BMI. A total of 1033 participants (62% women; age [mean ± standard deviation] 54.4 ± 14.9 years) in the 2015 Iwaki Health Promotion Project in Japan were enrolled in the study. Breath samples were collected using a breath bag and analyzed by gas chromatography. VFA was measured using a visceral fat meter. The proportion of methanogenic bacteria to total intestinal microbiota was measured by polymerase chain reaction and 16S rRNA gene sequencing analysis. Our analysis revealed a significant association between high VFA and low breath methane, even after adjusting for confounding factors (B = -0.024 and P = 0.004). To identify the association between breath methane and VFA in participants with methane-producing bacteria in their intestinal microflora, participants were divided into two groups based on the presence or absence of methanogenic bacteria in their stool. The Methanogen + group was further divided into two subgroups with breath methane higher (Methane-UP) or lower (Methane-LO) than the median breath methane concentration. VFA was significantly lower in the Methane-UP group than in the Methane-LO group. In participants with methanogenic bacteria, breath methane concentration might be an independent biomarker of visceral fat accumulation.
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http://dx.doi.org/10.1088/1752-7163/ab61c6DOI Listing
February 2020

Integrated exome and RNA sequencing of dedifferentiated liposarcoma.

Nat Commun 2019 12 12;10(1):5683. Epub 2019 Dec 12.

Laboratory of DNA Information Analysis, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.

The genomic characteristics of dedifferentiated liposarcoma (DDLPS) that are associated with clinical features remain to be identified. Here, we conduct integrated whole exome and RNA sequencing analysis in 115 DDLPS tumors and perform comparative genomic analysis of well-differentiated and dedifferentiated components from eight DDLPS samples. Several somatic copy-number alterations (SCNAs), including the gain of 12q15, are identified as frequent genomic alterations. CTDSP1/2-DNM3OS fusion genes are identified in a subset of DDLPS tumors. Based on the association of SCNAs with clinical features, the DDLPS tumors are clustered into three groups. This clustering can predict the clinical outcome independently. The comparative analysis between well-differentiated and dedifferentiated components identify two categories of genomic alterations: shared alterations, associated with tumorigenesis, and dedifferentiated-specific alterations, associated with malignant transformation. This large-scale genomic analysis reveals the mechanisms underlying the development and progression of DDLPS and provides insights that could contribute to the refinement of DDLPS management.
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http://dx.doi.org/10.1038/s41467-019-13286-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6908635PMC
December 2019

Association between Nutrients and Visceral Fat in Healthy Japanese Adults: A 2-Year Longitudinal Study Brief Title: Micronutrients Associated with Visceral Fat Accumulation.

Nutrients 2019 Nov 7;11(11). Epub 2019 Nov 7.

Department of Social Medicine, Graduate School of Medicine, Hirosaki University, Hirosaki 0368562, Japan.

High visceral fat area (VFA) is a stronger predictor of cardiovascular disease and overall mortality than body mass index or waist circumference. VFA may be decreased by proper dietary habits. Although previous epidemiologic studies demonstrated an association between nutritional components or foodstuffs and VFA, only the associations of a few nutrients, such as dietary fiber and calcium, are reported. We performed a comprehensive 2-year longitudinal study in more than 624 healthy people and analyzed 33 micronutrients to investigate nutrients that contribute to changes in visceral fat. Our analyses revealed that "macronutrients" and "micronutrients" were "mutual confounders". Therefore, when evaluating the association between VFA and micronutrients, associations were adjusted by macronutrients. The ingestion of 7 nutrients: soluble dietary fiber, manganese, potassium, magnesium, vitamin K, folic acid, and pantothenic acid, which are abundant components in vegetable diets, was significantly inversely correlated with a change in VFA. Additionally, a change in the ingestion of one nutrient, monounsaturated fat, was significantly positively correlated with a change in VFA. These associations were independent of body mass index and waist circumference. Thus, a predominantly vegetable diet may decrease VFA. In addition, adjusting the intake of macronutrients might help to clarify the association of micronutrients with VFA.
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http://dx.doi.org/10.3390/nu11112698DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6893766PMC
November 2019