Papers - Furukawa, Ryohei

PREDICTION OF THE PROCESS FOR THE IMMUNE SYSTEM MATURATION IN THE SEA STAR, <i>PATIRIA PECTINIFERA</i>

Taguchi, M; Minakata, K; Sato, H; Tame, A; Furukawa, R

DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 148 2023.11

ISSN  0145-305X

Sex-inducing effects toward planarians widely present among parasitic flatworms

Sekii K., Miyashita S., Yamaguchi K., Saito I., Saito Y., Manta S., Ishikawa M., Narita M., Watanabe T., Ito R., Taguchi M., Furukawa R., Ikeuchi A., Matsuo K., Kurita G., Kumagai T., Shirakashi S., Ogawa K., Sakamoto K., Koyanagi R., Satoh N., Sasaki M., Maezawa T., Ichikawa-Seki M., Kobayashi K.

iScience (iScience)  26 ( 1 ) 105776 2023.01

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Various parasitic flatworms infect vertebrates for sexual reproduction, often causing devastating diseases in their hosts. Consequently, flatworms are of great socioeconomic and biomedical importance. Although the cessation of parasitic flatworm sexual reproduction is a major target of anti-parasitic drug design, little is known regarding bioactive compounds controlling flatworm sexual maturation. Using the planarian Dugesia ryukyuensis, we observed that sex-inducing substances found in planarians are also widespread in parasitic flatworms, such as monogeneans and flukes (but not in tapeworms). Reverse-phase HPLC analysis revealed the sex-inducing substance(s) eluting around the tryptophan retention time in the fluke Calicophoron calicophorum, consistent with previous studies on the planarian Bipalium nobile, suggesting that the substance(s) is likely conserved among flatworms. Moreover, six of the 18 ovary-inducing substances identified via transcriptome and metabolome analyses are involved in purine metabolism. Our findings provide a basis for understanding and modifying the life cycles of various parasitic flatworms.

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Establishment of the immunological self in juvenile Patiria pectinifera post-metamorphosis

Taguchi M., Minakata K., Tame A., Furukawa R.

Frontiers in Immunology (Frontiers in Immunology)  13   1056027 2022.12

ISSN  1664-3224

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Ontogeny of the immune system is a fundamental immunology issue. One indicator of immune system maturation is the establishment of the immunological self, which describes the ability of the immune system to distinguish allogeneic individuals (allorecognition ability). However, the timing of immune system maturation during invertebrate ontogeny is poorly understood. In the sea star Patiria pectinifera, cells that have dissociated from the embryos and larvae are able to reconstruct larvae. This reconstruction phenomenon is possible because of a lack of allorecognition capability in the larval immune system, which facilitates the formation of an allogeneic chimera. In this study, we revealed that the adult immune cells of P. pectinifera (coelomocytes) have allorecognition ability. Based on a hypothesis that allorecognition ability is acquired before and after metamorphosis, we conducted detailed morphological observations and survival time analysis of metamorphosis-induced chimeric larvae. The results showed that all allogeneic chimeras died within approximately two weeks to one month of reaching the juvenile stage. In these chimeras, the majority of the epidermal cell layer was lost and the mesenchymal region expanded, but cell death appeared enhanced in the digestive tract. These results indicate that the immunological self of P. pectinifera is established post-metamorphosis during the juvenile stage. This is the first study to identify the timing of immune system maturation during echinodermal ontogenesis. As well as establishing P. pectinifera as an excellent model for studies on self- and non-self-recognition, this study enhances our understanding of the ontogeny of the immune system in invertebrates.

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Evaluation of short-term epigenetic age fluctuation

Komaki S., Ohmomo H., Hachiya T., Sutoh Y., Ono K., Furukawa R., Umekage S., Otsuka-Yamasaki Y., Minabe S., Takashima A., Tanno K., Sasaki M., Shimizu A.

Clinical Epigenetics (Clinical Epigenetics)  14 ( 1 ) 76 2022.12

ISSN  18687075

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Considerable effort has been spent on lowering and maintaining the epigenetic age. However, the extent to which epigenetic age fluctuates under normal conditions is poorly understood. Therefore, we analyzed methylation data from monocytes and peripheral blood mononuclear cells collected from two Japanese men. The ranges of the Pan-tissue, Skin and blood, and DNAm PhenoAge epigenetic age during 3 months were ≥ 5.62, ≥ 3.04, and ≥ 8.23 years, and the maximum daily changes were 5.21, 3.20, and 6.53 years, respectively. These fluctuations were not suppressed by correcting for cell-type composition. Although the underlying biological mechanism remains unclear, there was a nonnegligible degree of age fluctuation which should inform personalized clinical applications.

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Longitudinal DNA methylation dynamics as a practical indicator in clinical epigenetics.

Komaki, S., Ohmomo, H., Hachiya, T., Sutoh Y., Ono, K., Furukawa, R., Umekage, S., Otsuka-Yamasaki, Y., Tanno, K., Sasaki, M., Shimizu. A.

Clinical Epigenetics (Clinical Epigenetics)  13 ( 1 ) 219 2021.12

Joint Work, Accepted,  ISSN  18687075

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Background: One of the fundamental assumptions of DNA methylation in clinical epigenetics is that DNA methylation status can change over time with or without interplay with environmental and clinical conditions. However, little is known about how DNA methylation status changes over time under ordinary environmental and clinical conditions. In this study, we revisited the high frequency longitudinal DNA methylation data of two Japanese males (24 time-points within three months) and characterized the longitudinal dynamics. Results: The results showed that the majority of CpGs on Illumina HumanMethylation450 BeadChip probe set were longitudinally stable over the time period of three months. Focusing on dynamic and stable CpGs extracted from datasets, dynamic CpGs were more likely to be reported as epigenome-wide association study (EWAS) markers of various traits, especially those of immune- and inflammatory-related traits; meanwhile, the stable CpGs were enriched in metabolism-related genes and were less likely to be EWAS markers, indicating that the stable CpGs are stable both in the short-term within individuals and under various environmental and clinical conditions. Conclusions: This study indicates that CpGs with different stabilities are involved in different functions and traits, and thus, they are potential indicators that can be applied for clinical epigenetic studies to outline underlying mechanisms.

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dbTMM: an integrated database of large-scale cohort, genome and clinical data for the Tohoku Medical Megabank Project

Ogishima S., Nagaie S., Mizuno S., Ishiwata R., Iida K., Shimokawa K., Takai-Igarashi T., Nakamura N., Nagase S., Nakamura T., Tsuchiya N., Nakaya N., Murakami K., Ueno F., Onuma T., Ishikuro M., Obara T., Mugikura S., Tomita H., Uruno A., Kobayashi T., Tsuboi A., Tadaka S., Katsuoka F., Narita A., Sakurai M., Makino S., Tamiya G., Aoki Y., Shimizu R., Motoike I.N., Koshiba S., Minegishi N., Kumada K., Nobukuni T., Suzuki K., Danjoh I., Nagami F., Tanno K., Ohmomo H., Asahi K., Shimizu A., Hozawa A., Kuriyama S., Yamamoto M., Abe M., Aizawa Y., Aoki Y., Chida K., Egawa S., Eto A., Funayama T., Fuse N., Hamanaka Y., Harada Y., Hashizume H., Higuchi S., Hirano S., Hirata T., Hiratsuka M., Hozawa A., Igarashi K., Inoue J., Ishida N., Ishii N., Ishii T., Ishikuro M., Ito K., Ito S., Kageyama M., Katsuoka F., Kawame H., Kawashima J., Kikuya M., Kinoshita K., Kitatani K., Kiyama T., Kiyomoto H., Kobayashi T., Kodama E., Kogure M., Kojima K., Koreeda S., Koshiba S., Koyama S., Kudo H., Kumada K., Kure S., Kuriki M., Kuriyama S., Kuroki Y., Maikusa N., Makino S., Matsubara H., Matsui H., Metoki H., Mimori T., Misawa K.

Human Genome Variation (Human Genome Variation)  8 ( 1 )  2021.12

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To reveal gene-environment interactions underlying common diseases and estimate the risk for common diseases, the Tohoku Medical Megabank (TMM) project has conducted prospective cohort studies and genomic and multiomics analyses. To establish an integrated biobank, we developed an integrated database called “dbTMM” that incorporates both the individual cohort/clinical data and the genome/multiomics data of 157,191 participants in the Tohoku Medical Megabank project. To our knowledge, dbTMM is the first database to store individual whole-genome data on a variant-by-variant basis as well as cohort/clinical data for over one hundred thousand participants in a prospective cohort study. dbTMM enables us to stratify our cohort by both genome-wide genetic factors and environmental factors, and it provides a research and development platform that enables prospective analysis of large-scale data from genome cohorts.

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D-Tryptophan enhances the reproductive organ-specific expression of the amino acid transporter homolog Dr-SLC38A9 involved in the sexual induction of the planarian Dugesia ryukyuensis.

15. Maezawa, T., Ishikawam M., Sekii, K., Nagamatsu, G., Furukawa, R., Kobayashi, K.

Zoological Letters (Zoological Letters)  7 ( 4 ) 4 2021.03

Research paper (scientific journal), Joint Work, Accepted,  ISSN  2056-306X

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Background: Many animals switch between asexual and sexual reproduction in nature. We previously established a system for the sexual induction of planarian Dugesia ryukyuensis by feeding asexual planarians with minced sexual planarians. We identified dl-tryptophan (Trp) as one of the sex-inducing substances. dl-Trp can induce ovarian development, the first and essential step of sexual induction. d-Trp must act as a principal bioactive compound in terms of ovarian development, because the ovary-inducing activity of d-Trp was 500 times more potent than that of l-Trp. However, how Trp controls sexual induction is still unknown. Results: In this study, qRT-PCR analyses suggested that the putative amino acid transporter gene Dr-SLC38A9 is highly expressed in sexual worms, especially in the yolk glands. In situ hybridization analyses showed that Dr-SLC38A9 is expressed in the ovarian primordia of asexual worms and in the mature ovaries, testes, and yolk glands of sexual worms. In addition, Dr-SLC38A9 RNA interference during sexual induction resulted in the suppression of the development of reproductive organs. These results suggest that Dr-SLC38A9 is involved in the development of these organs. Moreover, we demonstrated that the reproductive organ-specific expression of Dr-SLC38A9 is enhanced by the addition of d-Trp. Conclusion: We propose that d-Trp activates the expression of Dr-SLC38A9 to promote sexual induction in the planarian D. ryukyuensis.

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Development of an online platform that can simulate the biological course of field training

SHITO Takumi, FUNAKOSHI Haruka, TOTSUKA Nozomu, KOGURE Yuki, FURUKAWA Ryohei, KURAISHI Ritsu, OKA Kotaro, HOTTA Kohji

Proceedings of the Annual Meeting of Japan Society for Science Education (Japan Society for Science Education)  45 ( 0 ) 621 - 624 2021

ISSN  21863628

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<p>現下のコロナ禍において，オンライン授業は大学教育の大きな割合を占めている．しかし生徒の主体的な体験を求める実習型授業をオンライン授業下で行うことは難しく，授業効果の減少や教材整備にかかる教員側の大幅なコスト増加が見込まれる．著者らは沿岸海洋生物の採集・観察を通じて生物教育をおこなう野外実習の一種である臨海実習に着目して，生物採集や観察をオンライン上で主体的に体験する「バーチャル臨海実習」プラットフォームVRinkaiを試験的に開発した．VRinkaiは慶應義塾大学の過去の臨海実習で蓄積された千を越える海洋生物の写真・動画データに基づいており，偶発的な生物採集や種同定，発生過程の観察など様々なプロセスをオンライン上で疑似体験することによる分類学の理解や基礎的な研究手法の習得を目的とする．本稿では開発中のプラットフォームの概要及び，実際の授業における使用方法や応用可能性の検討について報告する．</p>

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Construction and introduction of interactive WEB teaching materials that enable simulated experience of microscopic observation for biological education

FUNAKOSHI Haruka, SHITO Takumi, OKA Kotaro, FURUKAWA Ryohei, KURAISHI Ritsu, HOTTA Kohji

Proceedings of the Annual Meeting of Japan Society for Science Education (Japan Society for Science Education)  45 ( 0 ) 625 - 628 2021

ISSN  21863628

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<p>新型コロナウイルス感染拡大の影響で授業のオンライン化が喫緊の課題となる一方，生物学教育に不可欠な実体験型の授業を行うことは困難である．そこで，このような授業の疑似体験が可能なオンライン教材の構築を目指した１つの取り組みとして，発生学のモデル生物としてよく用いられるホヤの任意の発生段階や部位の顕微鏡画像の観察が可能なデジタルホヤ図鑑EducAnatO「のぞいてみようホヤの発生と解剖学」を紹介する．本教材はカタユウレイボヤの共焦点顕微鏡画像やタイムラプス画像を含んだホヤ発生学・解剖学オントロジーデータベースTunicAnatO (Hotta et al.， 2020)を理系・文系を問わず大学生向けの生物学教材として利用しやすいように再構築した画像データベースである．実際に本教材を用いたオンライン授業に対する学生のフィードバックを調査し，オンライン授業におけるWEB教材の有用性について検討した．</p>

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pmar1/phb homeobox genes and the evolution of the doublenegative gate for endomesoderm specification in echinoderms

Yamazaki A., Morino Y., Urata M., Yamaguchi M., Minokawa T., Furukawa R., Kondo M., Wada H.

Development (Cambridge) (Development (Cambridge))  147 ( 4 )  2020

Joint Work, Accepted,  ISSN  09501991

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© 2020 Published by The Company of Biologists Ltd. In several model animals, the earliest phases of embryogenesis are regulated by lineage-specific genes, such as Drosophila bicoid. Sea urchin (echinoid) embryogenesis is initiated by zygotic expression of pmar1, a paired-class homeobox gene that has been considered to be present only in the lineage of modern urchins (euechinoids). In euechinoids, Pmar1 promotes endomesoderm specification by repressing the hairy and enhancer of split C (hesC) gene. Here, we have identified the basal echinoid (cidaroid) pmar1 gene, which also promotes endomesoderm specification but not by repressing hesC. A further search for related genes demonstrated that other echinoderms have pmar1-related genes named phb. Functional analyses of starfish Phb proteins indicated that, similar to cidaroid Pmar1, they promote activation of endomesoderm regulatory gene orthologs via an unknown repressor that is not HesC. Based on these results, we propose that Pmar1 may have recapitulated the regulatory function of Phb during the early diversification of echinoids and that the additional repressor HesC was placed under the control of Pmar1 in the euechinoid lineage. This case provides an exceptional model for understanding how early developmental processes diverge.

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transcriptomic analysis reveals differences in the regulation of amino acid metabolism in asexual and sexual planarians

Kiyono Sekii, Shunta Yoritomo, Hikaru Okamoto, Takanobu Maezawa, Yasuhisa Matsui, Katsushi Yamaguchi, Ryohei Furukawa, Shuji Shigenobu, Kazuya Kobayashi

Scientific Reports (Nature Publishing Group)  9 ( 1 ) 6132 2019.04

Research paper (scientific journal), Joint Work, Accepted

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© 2019, The Author(s). Many flatworms can alternate between asexual and sexual reproduction. This is a powerful reproductive strategy enabling them to benefit from the features of the two reproductive modes, namely, rapid multiplication and genetic shuffling. The two reproductive modes are enabled by the presence of pluripotent adult stem cells (neoblasts), by generating any type of tissue in the asexual mode, and producing and maintaining germ cells in the sexual mode. In the current study, RNA sequencing (RNA-seq) was used to compare the transcriptomes of two phenotypes of the planarian Dugesia ryukyuensis: an asexual OH strain and an experimentally sexualized OH strain. Pathway enrichment analysis revealed striking differences in amino acid metabolism in the two worm types. Further, the analysis identified serotonin as a new bioactive substance that induced the planarian ovary de novo in a postembryonic manner. These findings suggest that different metabolic states and physiological conditions evoked by sex-inducing substances likely modulate stem cell behavior, depending on their different function in the asexual and sexual reproductive modes. The combination of RNA-seq and a feeding assay in D. ryukyuensis is a powerful tool for studying the alternation of reproductive modes, disentangling the relationship between gene expression and chemical signaling molecules.

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iMETHYL: an integrative database of human DNA methylation, gene expression, and genomic variation.

Komaki, S., Shiwa, Y., Furukawa, Ryohei, Hachiya, T., Ohmomo, H., Otomo, R., Satoh, M., Hitomi, J., Sobue, K., Sasaki, M., Shimizu, A.

Human Genome Variation (Human Genome Variation)  5   18008 2018

Research paper (scientific journal), Joint Work, Accepted

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© 2018 Nature Publishing Group. All rights reserved. We launched an integrative multi-omics database, iMETHYL (http://imethyl.iwate-megabank.org). iMETHYL provides whole-DNA methylation (∼24 million autosomal CpG sites), whole-genome (∼9 million single-nucleotide variants), and whole-Transcriptome (>14 000 genes) data for CD4 + T-lymphocytes, monocytes, and neutrophils collected from approximately 100 subjects. These data were obtained from whole-genome bisulfite sequencing, whole-genome sequencing, and whole-Transcriptome sequencing, making iMETHYL a comprehensive database.

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Characterization of TRPA channels in the starfish Patiria pectinifera: involvement of thermally activated TRPA1 in thermotaxis in marine planktonic larvae.

Saito, S., Hamanaka, G., Kawai, N., Furukawa, R., Gojobori, J., Tominaga, M., Kaneko, H., Satta, Y.

SCIENTIFIC REPORTS 7   315 - 321 2017.05

Research paper (scientific journal),  ISSN  2045-2322

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Genetic Predisposition to Ischemic Stroke: A Polygenic Risk Score.

Hachiya, T., Kamatani, Y., Takahashi, A., Hata, J., Furukawa, R., Shiwa, Y., Yamaji, T., Hara, M., Tanno, K., Ohmomo, H., Ono, K., Takashima, N., Matsuda, K., Wakai, K., Sawada, N., Iwasaki, M., Yamagishi, K., Ago, T., Ninomiya, T., Fukushima, A., Hozawa, A., Minegishi, N., Satoh, M., Endo, R., Sasaki, M., Sakata, K., Kobayashi, S., Ogasawara, K., Nakamura, M., Hitomi, J., Kita, Y., Tanaka, K., Iso, H., Kitazono, T., Kubo, M., Tanaka, H., Tsugane, S., Kiyohara, Y., Yamamoto, M., Sobue, K., Shimizu, A.

STROKE 48 ( 2 ) 253 - 258 2017.02

Research paper (scientific journal),  ISSN  0039-2499

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An epigenome-wide association study based on cell type-specific whole-genome bisulfite sequencing: Screening for DNA methylation signatures associated with bone mass.

Komaki, S., Ohmomo, H., Hachiya, T., Furukawa, R, Shiwa, Y., Satoh, M., Endo, R., Doita, M., Sasaki, M., Shimizu, A.

Integrative Molocular Medicine 4 ( 5 ) 1 - 7 2017

Research paper (scientific journal), Joint Work, Accepted

Genome-wide identification of inter-individually variable DNA methylation sites improves the efficacy of epigenetic association studies.

Hachiya, T., Furukawa, R., Shiwa, Y., Ohmomo, H., Ono, K., Katsuoka, F., Nagasaki, M., Yasuda, J., Fuse, N., Kinoshita, K., Yamamoto, M., Tanno, K., Satoh, M., Endo, R., Sasaki, M., Sakata, K., Kobayashi, S., Ogasawara, K., Hitomi, J., Sobue, K., Shimizu, A.

npj Genomic Medicine 2   11 2017

Research paper (scientific journal), Joint Work

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Intraindividual dynamics of transcriptome and genome-wide stability of DNA methylation.

Furukawa, R., Hachiya T., Ohmomo H., Shiwa Y., Ono K., Suzuki S., Satoh M., Hitomi J., Sobue K., Shimizu A.

SCIENTIFIC REPORTS 6 2016.05

Research paper (scientific journal),  ISSN  2045-2322

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Two macrophage migration inhibitory factors regulate starfish larval immune cell chemotaxis.

Furukawa, R., Tamaki, K., Kaneko, H.

IMMUNOLOGY AND CELL BIOLOGY 94 ( 4 ) 315 - 321 2016.04

Research paper (scientific journal),  ISSN  0818-9641

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Adjustment of Cell-Type Composition Minimizes Systematic Bias in Blood DNA Methylation Profiles Derived by DNA Collection Protocols.

Shiwa, Y., Hachiya, T., Furukawa, R., Ohmomo, H., Ono, K., Kudo, H., Hata, J., Hozawa, A., Iwasaki, M., Matsuda, K., Minegishi, N., Satoh, M., Tanno, K., Yamaji, T., Wakai, K., Hitomi, J., Kiyohara, Y., Kubo, M., Tanaka, H., Tsugane, S., Yamamoto, M., Sobue, K., Shimizu, A.

PLOS ONE 11 ( 1 )  2016.01

Research paper (scientific journal),  ISSN  1932-6203

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Reduction of Systematic Bias in Transcriptome Data from Human Peripheral Blood Mononuclear Cells for Transportation and Biobanking.

Ohmomo, H., Hachiya, T., Shiwa, Y., Furukawa, R., Ono, K, Ito, S., Ishida, Y., Satoh, M., Hitomi, J., Sobue, K., Shimizu, A.

PLOS ONE 9 ( 8 )  2014.08

Research paper (scientific journal),  ISSN  1932-6203

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