Details of the Researcher

PHOTO

Shohei Komaki
Section
Tohoku Medical Megabank Organization
Job title
Senior Assistant Professor

Research History 7

  • 2026/01 - Present
    Tohoku University　Tohoku Medical Megabank Organization

  • 2023/04 - 2025/11
    Iwate Medical University

  • 2022/10 - 2023/03
    Iwate Medical University

  • 2018/01 - 2022/09
    Iwate Medical University　Iwate Tohoku Medical Megabank Organization

  • 2016/07 - 2017/12
    岩手医科大学 いわて東北メディカル・メガバンク機構 特別研究員

  • 2015/04 - 2016/06
    Hiroshima University

  • 2013/04 - 2015/03
    日本学術振興会特別研究員（DC2)

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Education 3

  • 広島大学大学院 理学研究科 博士課程後期

    2012/04 - 2015/03

  • 広島大学大学院 理学研究科 博士課程前期

    2010/04 - 2012/03

  • 信州大学 理学部 生物科学科

    2006/04 - 2010/03

Research Interests 6

  • Biogeography

  • Molecular phylogeny

  • Hybridization

  • Introgression

  • DNA methylation

  • Gene expression

Research Areas 4

  • Life sciences / Ecology and environmental science /

  • Life sciences / Biodiversity and systematics /

  • Life sciences / Evolutionary biology /

  • Life sciences / Genomics /

Awards 4

  1. 優秀研究賞

    2024/11　日本DNA多型学会

  2. Egami Award

    2016/03

  3. Zoological Science Award

    2013/09　Distributional change and epidemic introgression in overlapping areas of Japanese pond frog species over 30 years

  4. Fujii Award

    2013/09　Distributional change and epidemic introgression in overlapping areas of Japanese pond frog species over 30 years

Papers 62

  1. Inter-individual differentially methylated region-targeted EWAS reveals epigenetic signatures of early childhood adversity. International-journal

    Taira Mayanagi, Junko Yagi, Hideki Ohmomo, Manami Akasaka, Kentaro Fukumoto, Shusaku Chiba, Shohei Komaki, Atsushi Shimizu, Takehito Yanbe, Mare Uchide, Yasuhito Yoshioka, Kaori Ogawa, Chiho Ishikawa, Shiori Minabe, Jun Ito, Kanako Ono, Nozomi Kaneko, Kenji Sobue

    Epigenomics　1-12　2026/01/07

    DOI： 10.1080/17501911.2026.2613008 　

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    AIMS: Adverse childhood experiences (ACEs), especially in early life, can affect psychosocial development and increase lifelong risk for mental disorders. ACEs are also known to induce persistent epigenetic changes. This study aimed to explore ACE-associated DNA methylation signatures using an epigenome-wide association study (EWAS) targeting inter-individual differentially methylated regions (DMRs). METHODS: We developed a targeted capture probe system covering ~1.3 million CpG sites within inter-individual DMRs. This system was applied to salivary DNA from drug-naïve children aged 6-12 years with exposure to multiple early-life ACEs (n = 23) or who had no ACEs (n = 21). RESULTS: We identified 15 novel DMRs significantly associated with ACEs. A cluster of six CpG sites within an exon of the EIF4G2 gene showed consistently increased methylation in children with ACEs, with strong inter-site correlations. Enrichment analysis indicated that genes near these DMRs are involved in neurodevelopmental disorders, suggesting that early adversity may influence brain development through epigenetic mechanisms. CONCLUSION: Our findings suggest that early adversity may contribute to lasting epigenetic modifications in children. The identified DMRs may serve as noninvasive biomarkers for retrospective ACE assessment and provide insights into the biological embedding of early-life stress.

  2. Distribution of two Pelophylax frog species and an exploratory assessment of interspecific admixture in Iwate, Japan, through RNA-seq-derived SNP analysis Peer-reviewed

    Shohei Komaki, Nozomi Komaki, Kensuke Kobayashi, Koshiro Eto, Shonosuke Shigeta, Kohsuke Akita, Koji Tojo, Atsushi Shimizu

    Zoological Science (accepted)　2026

  3. Polygenic score for blood immunoglobulin E levels in adults explains food allergy risk in children

    Yoichi Sutoh, Tsuyoshi Hachiya, Yayoi Otsuka-Yamasaki, Shohei Komaki, Shiori Minabe, Hideki Ohmomo, Kozo Tanno, Atsushi Hozawa, Naoki Nakaya, Mami Ishikuro, Taku Obara, Shinichi Kuriyama, Makoto Sasaki, Atsushi Shimizu

    JOURNAL OF IMMUNOLOGY　214　2025/11

    DOI： 10.1093/jimmun/vkaf283.514 　

    ISSN： 0022-1767

    eISSN： 1550-6606

  4. Exploring novel blood-based DNA methylation biomarkers for alzheimer's disease via targeted sequencing of highly variable CpG sites. International-journal

    Hideki Ohmomo, Shohei Komaki, Shiori Minabe, Yoichi Sutoh, Yayoi Otsuka-Yamasaki, Makoto Sasaki, Atsushi Shimizu

    BMC research notes　18　(1)　350-350　2025/08/12

    DOI： 10.1186/s13104-025-07417-7 　

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    OBJECTIVE: Dementia, particularly Alzheimer’s disease (AD), continues to be a major public health concern due to population aging, yet minimally invasive biomarkers for early diagnosis have not been established. DNA methylation (DNAm) has recently attracted considerable attention as a promising biomarker. This study aimed to identify blood-based DNAm biomarkers for early detection of AD. RESULTS: We analysed blood-derived DNA from 48 patients with AD (from Biobank Japan) and 48 age- and sex-matched controls (from the Tohoku Medical Megabank Biobank) using Apolipoprotein ε type 4 (APOE)-associated genotype analysis and targeted-bisulfite sequencing. High-risk APOE genotypes were more frequent in AD patients (23/48, [47.9%]) than in controls (6/48, [12.5%]). A typical case-control and APOE genotype-stratified epigenome-wide association study (EWAS) did not identify any genome-wide significant CpG sites. Although the primary findings were negative, some top CpG sites appeared in both analyses, including loci on the Cell Adhesion Molecule 1 (CADM1), Tubulin alpha 1b (TUBA1B), and Exocyst complex component 2 (EXOC2) genes, which have previously been linked to AD-related pathways. The relatively early clinical stage and uncertainty of disease onset might have limited detection sensitivity. Longitudinal studies with refined staging and multi-omics integration might clarify the biomarker potential of blood DNAm in AD. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13104-025-07417-7.

  5. Genetic predisposition for immunoglobulin E production explains atopic risk in children: Tohoku Medical Megabank cohort study. International-journal

    Yoichi Sutoh, Tsuyoshi Hachiya, Yayoi Otsuka-Yamasaki, Shohei Komaki, Shiori Minabe, Hideki Ohmomo, Kozo Tanno, Atsushi Hozawa, Naoki Nakaya, Aoi Noda, Masatsugu Orui, Mami Ishikuro, Taku Obara, Shinichi Kuriyama, Makoto Sasaki, Atsushi Shimizu

    American journal of human genetics　112　(8)　1852-1863　2025/08/07

    DOI： 10.1016/j.ajhg.2025.06.015 　

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    The atopic march lacks early identification methods for high-risk children. In this study, we assessed whether the risk of atopic diseases in infants could be predicted using a polygenic score (PGS) for total immunoglobulin E (IgE) levels. The PGS estimated using the polygenic model generated by PRS-CS was significantly correlated with log-transformed IgE levels (ρ = 0.200, p < 2.2 × 10-16). Assessment of the risk from birth to 2 years of age in a Japanese birth cohort (n = 17,154) applying the estimated PGS revealed significantly elevated incidence risk ratios in the highest PGS quintile (Q5) compared with those in the reference quintiles (Q1-Q3) for food allergy (1.51-fold; 95% confidence interval: 1.30-1.76), atopic dermatitis (1.30-fold; 1.12-1.51), and both conditions (1.88-fold; 1.46-2.43). These findings address critical gaps in allergy and PGS research among non-European populations, suggesting the contribution of genetic predisposition to IgE production in early-onset allergic diseases and supporting the use of PGS in early intervention.

  6. Risk factors and prediction for pediatric obesity: current status and future perspectives.

    Shiori Minabe, Yoichi Sutoh, Yayoi Otsuka-Yamasaki, Shohei Komaki, Motoki Nakao, Hideki Ohmomo, Yutaka Hasegawa, Yasushi Ishigaki, Kozo Tanno, Makoto Sasaki, Atsushi Shimizu

    Endocrine journal　2025/04/09

    DOI： 10.1507/endocrj.EJ24-0724 　

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    Childhood obesity is a growing global health concern, contributing to numerous non-communicable diseases and long-term health complications. The prevalence of obesity in children and adolescents continues to rise, driven by complex interactions among various factors. The key risk factors include both environmental and genetic influences. Environmental factors include family elements like household conditions and lifestyle, while genetic factors refer to inherited predispositions. More recently, epigenetic factors have gained attention, focusing on chemical modifications such as DNA methylation that are influenced by the prenatal and early-life environment and may contribute to obesity risk. Unlike obesity in adults, the risk factors for obesity in children are largely dependent on their family environments rather than individual behaviors. For effective intervention, it is important to identify at-risk children and their families as early as possible after birth. Despite advances in machine learning, polygenic risk scores, and epigenomic markers-which show promise as being more accurate and comprehensive prediction methods-no risk prediction models are currently in clinical use. Achieving predictions with higher accuracy, external validation, and consideration of population-specific factors (e.g., ethnic variability) while avoiding bias or stigma in targeted interventions is needed for effective childhood obesity prevention. Herein, we summarize environmental, genetic, and epigenetic risk factors for childhood obesity and review the unique situations and regional factors in Japan, which are the focus of our study. Furthermore, we introduce the major advances in risk prediction models for childhood obesity.

  7. Reference-Based Standardization Approach Stabilizing Small Batch Risk Prediction via Polygenic Score. International-journal

    Yoichi Sutoh, Tsuyoshi Hachiya, Yayoi Otsuka-Yamasaki, Tomoharu Tokutomi, Akiko Yoshida, Yuka Kotozaki, Shohei Komaki, Shiori Minabe, Hideki Ohmomo, Kozo Tanno, Akimune Fukushima, Makoto Sasaki, Atsushi Shimizu

    Genetic epidemiology　49　(2)　e70002　2025/03

    DOI： 10.1002/gepi.70002 　

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    The polygenic score (PGS) holds promise for motivating preventive behavioral changes. However, no clinically validated standardization methodology currently exists. Here, we demonstrate the efficacy of a "reference-based" approach for standardization. This method uses the PGS distribution in the general population as a reference for normalization and percentile determination; however, it has not been validated. We investigated three potential influences on PGS computation: (1) the size of the reference population, (2) biases associated with different genotyping platforms, and (3) inclusion of kinship ties within the reference group. Our results indicate that the reference size affects the bootstrap estimate of standard error for PGS percentiles, peaking around the 50th percentile and diminishing at extreme percentiles (1st or 100th). Discrepancies between genotyping platforms, such as different microarrays and whole-genome sequencing, resulted in deviations in PGS (p < 0.05 in Kolmogorov-Smirnov test). However, these deviations were reduced to a nonsignificant level using shared genetic variants in the calculations when the ancestry of the samples and reference were matched. This approach recovered approximately 9.6% of the positive predictive value of PGS by naïve genotype. Our results provide fundamental insights for establishing clinical guidelines for implementing PGS to communicate reliable risks to individuals.

  8. Study Profile of the Iwate PGS Assessment and Risk Communication (PARC) Study

    Akiko Yoshida, Tomoharu Tokutomi, Nobuhiro Suzumori, Akimune Fukushima, Yukiko Toya, Hideki Ohmomo, Kozo Tanno, Yoichi Sutoh, Yuka Kotozaki, Tsuyoshi Hachiya, Kazuki Kumada, Hisaaki Kudo, Atsushi Hasegawa, Mika Sakurai-Yageta, Akira Narita, Yohei Hamanaka, Satoshi Nagaie, Soichi Ogishima, Fuji Nagami, Yayoi Otsuka-Yamasaki, Shohei Komaki, Shiori Minabe, Koichi Asahi, Ryujin Endo, Yasushi Ishigaki, Masayuki Yamamoto, Atsushi Shimizu, Makoto Sasaki

    Journal of Epidemiology　2025

    Publisher: Japan Epidemiological Association

    DOI： 10.2188/jea.je20250078 　

    ISSN： 0917-5040

    eISSN： 1349-9092

  9. 【宿主-腸内細菌相互作用】腸内細菌叢研究における次元削減手法の活用

    八谷 剛史, 小巻 翔平, 佐保山 友加里, 川上 英良

    臨床免疫・アレルギー科　83　(1)　46-57　2025/01

    Publisher: (有)科学評論社

    ISSN： 1881-1930

  10. Influence of physical activity on the epigenetic clock: evidence from a Japanese cross-sectional study. International-journal

    Masatoshi Nagata, Shohei Komaki, Yuichiro Nishida, Hideki Ohmomo, Megumi Hara, Keitaro Tanaka, Atsushi Shimizu

    Clinical epigenetics　16　(1)　142-142　2024/10/15

    DOI： 10.1186/s13148-024-01756-1 　

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    BACKGROUND: Biological age, especially epigenetic age derived from the epigenetic clock, is a significant measure of aging, considering the differences in aging rates among individuals. The epigenetic clock, a machine learning-based algorithm, uses DNA methylation states to estimate biological age. Previous studies have reported inconsistent associations between physical activity (PA) and the epigenetic clock, especially second-generation clocks such as PhenoAge and GrimAge. This study aimed to clarify this relationship using cross-sectional data from Japanese participants aged 40-69. METHODS: We used two datasets from the Saga J-MICC study, of which 867 samples were available for analysis. DNA methylation data from peripheral blood samples were used to calculate the epigenetic age using the epigenetic clocks PhenoAge and GrimAge. PA and sedentary time were measured using a single-axis accelerometer, while self-reported PA, sedentary time, and covariates were assessed using a self-administered questionnaire. The association between PA or sedentary time and epigenetic age acceleration was assessed using multiple linear regression. RESULTS: Pearson's correlation coefficients between accelerometer-based and self-reported PA variables ranged from 0.09 to 0.20. Multivariable regression analysis showed that accelerometer-based PA and sedentary time were associated with epigenetic age decelerations and accelerations, respectively. However, self-reported PA was not associated with the epigenetic age accelerations. CONCLUSIONS: These results indicate that reducing sedentary time and increasing PA were associated with slowing both PhenoAge and GrimAge, even in East Asian populations with different exercise habits, body shapes, and lifestyles. This study highlights the potential of objective second-generation epigenetic age acceleration as an outcome index for healthcare interventions and clinical applications.

  11. Healthy lifestyle practice correlates with decreased obesity prevalence in individuals with high polygenic risk: TMM CommCohort study. International-journal

    Yoichi Sutoh, Tsuyoshi Hachiya, Yayoi Otsuka-Yamasaki, Shohei Komaki, Shiori Minabe, Hideki Ohmomo, Makoto Sasaki, Atsushi Shimizu

    Journal of human genetics　2024/08/22

    DOI： 10.1038/s10038-024-01280-3 　

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    Obesity and overweight, fundamental components of the metabolic syndrome, predispose individuals to lifestyle-related diseases. The extent to which adopting healthy lifestyles can reduce obesity risk, even in those with a high genetic risk, remains uncertain. Our aim was to assess the extent to which lifestyle modifications can improve outcomes in individuals with a high polygenic score (PGS) for obesity. We quantified the genetic risk of obesity using PGSs. Four datasets from the Tohoku Medical Megabank Community-Based Cohort (TMM CommCohort) were employed in the study. One dataset (n = 9958) was used to select the best model for calculating PGS. The remaining datasets (total n = 69,341) were used in a meta-analysis to validate the model and to evaluate associated risks. The odds ratio (OR) for obesity risk in the intermediate (11th-90th percentiles in the dataset) and high PGS categories (91st-100th) was 2.27 [95% confidence intervals: 2.12-2.44] and 4.83 [4.45-5.25], respectively, compared to that in the low PGS category (1st-10th). Trend analysis showed that an increase in leisure-time physical activity was significantly associated with reduced obesity risk across all genetic risk categories, representing an OR of 0.9 [0.87-0.94] even among individuals in the high PGS category. Similarly, sodium intake displayed a positive association with obesity across all genetic risk categories, yielding an OR of 1.24 [1.17-1.31] in the high PGS category. The risk of obesity was linked to the adoption of healthy lifestyles, even in individuals with high PGS. Our results may provide perspectives for integrating PGSs into preventive medicine.

  12. DNA Methylation Study in DOHaD Theory: A Perspective from the Tohoku Medical Megabank (TMM) Project

    MINABE Shiori, KOMAKI Shohei, OHMOMO Hideki, SHIMIZU Atsushi

    Developmental Origins of Health and Disease Research　12　(1)　5-10　2024/06/07

    Publisher: Japan Society for Developmental Origins of Health and Disease

    DOI： 10.51067/dohad.12.1_5 　

    ISSN： 2187-2562

    eISSN： 2187-2597

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    The Tohoku Medical Megabank (TMM) project advances DOHaD research, studying how prenatal and early postnatal environmental factors influence health via DNA methylation in adulthood. A correction method for cellular composition bias in DNA methylation analysis of newborn umbilical cord blood was established based on whole epigenome analysis of nucleated red blood cells from 15 newborns. The methylation status of 92 umbilical cord blood samples, excluding perinatal disease cases, has been analyzed, supporting predictions of fetal epigenetic alterations. The analyzed cord blood epigenomic information is available in the iMETHYL database. Furthermore, ongoing research on DNA methylation in 158 three-generation families and 60 sets of identical twins within the TMM cohort could elucidate DOHaD's molecular mechanisms and environmental transgenerational impacts on health.

  13. Dimension reduction of microbiome data linked Bifidobacterium and Prevotella to allergic rhinitis. International-journal

    Shohei Komaki, Yukari Sahoyama, Tsuyoshi Hachiya, Keita Koseki, Yusuke Ogata, Fumiaki Hamazato, Manabu Shiozawa, Tohru Nakagawa, Wataru Suda, Masahira Hattori, Eiryo Kawakami

    Scientific reports　14　(1)　7983-7983　2024/04/05

    DOI： 10.1038/s41598-024-57934-x 　

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    Dimension reduction has been used to visualise the distribution of multidimensional microbiome data, but the composite variables calculated by the dimension reduction methods have not been widely used to investigate the relationship of the human gut microbiome with lifestyle and disease. In the present study, we applied several dimension reduction methods, including principal component analysis, principal coordinate analysis (PCoA), non-metric multidimensional scaling (NMDS), and non-negative matrix factorization, to a microbiome dataset from 186 subjects with symptoms of  allergic rhinitis (AR) and 106 controls. All the dimension reduction methods supported that the distribution of microbial data points appeared to be continuous rather than discrete. Comparison of the composite variables calculated from the different dimension reduction methods showed that the characteristics of the composite variables differed depending on the distance matrices and the dimension reduction methods. The first composite variables calculated from PCoA and NMDS with the UniFrac distance were strongly associated with AR (FDR adjusted P = 2.4 × 10-4 for PCoA and P = 2.8 × 10-4 for NMDS), and also with the relative abundance of Bifidobacterium and Prevotella. The abundance of Bifidobacterium was also linked to intake of several nutrients, including carbohydrate, saturated fat, and alcohol via composite variables. Notably, the association between the composite variables and AR was much stronger than the association between the relative abundance of individual genera and AR. Our results highlight the usefulness of the dimension reduction methods for investigating the association of microbial composition with lifestyle and disease in clinical research.

  14. DNA Methylation Reference Panel by Gestational Age in Umbilical Cord Blood.

    Hirotaka Hamada, Komaki Shohei, Ohmomo Hideki, Kuriyama Shinichi, Sugawara Junichi, Saito Masatoshi, Shimizu Atsushi

    REPRODUCTIVE SCIENCES　31　225A-225A　2024/03

    ISSN： 1933-7191

    eISSN： 1933-7205

  15. jMorp: Japanese Multi-Omics Reference Panel update report 2023. International-journal

    Shu Tadaka, Junko Kawashima, Eiji Hishinuma, Sakae Saito, Yasunobu Okamura, Akihito Otsuki, Kaname Kojima, Shohei Komaki, Yuichi Aoki, Takanari Kanno, Daisuke Saigusa, Jin Inoue, Matsuyuki Shirota, Jun Takayama, Fumiki Katsuoka, Atsushi Shimizu, Gen Tamiya, Ritsuko Shimizu, Masahiro Hiratsuka, Ikuko N Motoike, Seizo Koshiba, Makoto Sasaki, Masayuki Yamamoto, Kengo Kinoshita

    Nucleic acids research　2023/11/01

    DOI： 10.1093/nar/gkad978 　

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    Modern medicine is increasingly focused on personalized medicine, and multi-omics data is crucial in understanding biological phenomena and disease mechanisms. Each ethnic group has its unique genetic background with specific genomic variations influencing disease risk and drug response. Therefore, multi-omics data from specific ethnic populations are essential for the effective implementation of personalized medicine. Various prospective cohort studies, such as the UK Biobank, All of Us and Lifelines, have been conducted worldwide. The Tohoku Medical Megabank project was initiated after the Great East Japan Earthquake in 2011. It collects biological specimens and conducts genome and omics analyses to build a basis for personalized medicine. Summary statistical data from these analyses are available in the jMorp web database (https://jmorp.megabank.tohoku.ac.jp), which provides a multidimensional approach to the diversity of the Japanese population. jMorp was launched in 2015 as a public database for plasma metabolome and proteome analyses and has been continuously updated. The current update will significantly expand the scale of the data (metabolome, genome, transcriptome, and metagenome). In addition, the user interface and backend server implementations were rewritten to improve the connectivity between the items stored in jMorp. This paper provides an overview of the new version of the jMorp.

  16. Integrated analysis of human DNA methylation, gene expression, and genomic variation in iMETHYL database using kernel tensor decomposition-based unsupervised feature extraction

    Y-h. Taguchi, Shohei Komaki, Yoichi Sutoh, Hideki Ohmomo, Yayoi Otsuka-Yamasaki, Atsushi Shimizu

    PLOS ONE　18　(8)　e0289029-e0289029　2023/08/09

    Publisher: Public Library of Science (PLoS)

    DOI： 10.1371/journal.pone.0289029 　

    eISSN： 1932-6203

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    Integrating gene expression, DNA methylation, and genomic variants simultaneously without location coincidence (i.e., irrespective of distance from each other) or pairwise coincidence (i.e., direct identification of triplets of gene expression, DNA methylation, and genomic variants, and not integration of pairwise coincidences) is difficult. In this study, we integrated gene expression, DNA methylation, and genome variants from the iMETHYL database using the recently proposed kernel tensor decomposition-based unsupervised feature extraction method with limited computational resources (i.e., short CPU time and small memory requirements). Our methods do not require prior knowledge of the subjects because they are fully unsupervised in that unsupervised tensor decomposition is used. The selected genes and genomic variants were significantly targeted by transcription factors that were biologically enriched in KEGG pathway terms as well as in the intra-related regulatory network. The proposed method is promising for integrated analyses of gene expression, methylation, and genomic variants with limited computational resources.

  17. 新生児臍帯血の網羅的エピゲノム解析による妊娠初期までの喫煙経験が次世代に及ぼす影響

    美辺 詩織, 小巻 翔平, 大桃 秀樹, 高嶋 聰, 小野 加奈子, 山崎 弥生, 須藤 洋一, 田高 周, 水野 聖士, 石黒 真美, 工藤 久智, 小原 拓, 熊田 和貴, 勝岡 史城, 荻島 創一, 木下 賢吾, 菅原 準一, 栗山 進一, 清水 厚志

    DOHaD研究　11　(3)　37-37　2023/08

    Publisher: (一社)日本DOHaD学会

    ISSN： 2187-2562

    eISSN： 2187-2597

  18. 日本人に最適化した新規エピゲノムクロックの開発

    清水 厚志, 小巻 翔平, 永田 雅俊, 大友 亮, 小野 加奈子, 大桃 秀樹, 梅影 創, 篠崎 夏子, 八谷 剛史, 須藤 洋一, 山崎 弥生, 米山 暁夫, 佐々木 真理

    日本抗加齢医学会総会プログラム・抄録集　23回　210-210　2023/06

    Publisher: (一社)日本抗加齢医学会

  19. 長寿者のエピゲノム解析

    小巻 翔平, 永田 雅俊, 新井 恵吏, 大友 亮, 小野 加奈子, 阿部 由紀子, 大桃 秀樹, 梅影 創, 篠崎 夏子, 八谷 剛史, 須藤 洋一, 山崎 弥生[大塚], 新井 康通, 広瀬 信義, 米山 暁夫, 岡野 栄之, 佐々木 真理, 金井 弥栄, 清水 厚志

    日本抗加齢医学会総会プログラム・抄録集　23回　220-220　2023/06

    Publisher: (一社)日本抗加齢医学会

  20. 出生三世代コホートにおける7人家族のエピゲノム研究基盤構築

    美辺 詩織, 小巻 翔平, 大桃 秀樹, 高嶋 聰, 小野 加奈子, 山崎 弥生, 須藤 洋一, 田高 周, 水野 聖士, 石黒 真美, 工藤 久智, 小原 拓, 熊田 和貴, 勝岡 史城, 荻島 創一, 木下 賢吾, 菅原 準一, 栗山 進一, 清水 厚志

    日本抗加齢医学会総会プログラム・抄録集　23回　252-252　2023/06

    Publisher: (一社)日本抗加齢医学会

  21. Epigenetic profile of Japanese supercentenarians: a cross-sectional study

    Shohei Komaki, Masatoshi Nagata, Eri Arai, Ryo Otomo, Kanako Ono, Yukiko Abe, Hideki Ohmomo, So Umekage, Natsuko O Shinozaki, Tsuyoshi Hachiya, Yoichi Sutoh, Yayoi Otsuka-Yamasaki, Yasumichi Arai, Nobuyoshi Hirose, Akio Yoneyama, Hideyuki Okano, Makoto Sasaki, Yae Kanai, Atsushi Shimizu

    The Lancet Healthy Longevity　4　(2)　e83-e90　2023/02

    Publisher: Elsevier BV

    DOI： 10.1016/s2666-7568(23)00002-8 　

    ISSN： 2666-7568

  22. Evaluation of short-term epigenetic age fluctuation

    Shohei Komaki, Hideki Ohmomo, Tsuyoshi Hachiya, Yoichi Sutoh, Kanako Ono, Ryohei Furukawa, So Umekage, Yayoi Otsuka-Yamasaki, Shiori Minabe, Akira Takashima, Kozo Tanno, Makoto Sasaki, Atsushi Shimizu

    Clinical Epigenetics　14　(1)　2022/12

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1186/s13148-022-01293-9 　

    ISSN： 1868-7075

    eISSN： 1868-7083

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    Abstract 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.

  23. Potential DNA methylation biomarkers for the detection of clear cell renal cell carcinoma identified by a whole blood-based epigenome-wide association study

    Hideki Ohmomo, Shohei Komaki, Yoichi Sutoh, Tsuyoshi Hachiya, Kanako Ono, Eri Arai, Hiroyuki Fujimoto, Teruhiko Yoshida, Yae Kanai, Koichi Asahi, Makoto Sasaki, Atsushi Shimizu

    Epigenetics Communications　2　(1)　2022/12

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1186/s43682-022-00009-7 　

    eISSN： 2730-7034

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    Abstract Background Renal cell carcinoma (RCC) is the fourteenth most common cancer worldwide, accounting for approximately 4% of all cancers. More than 70% of RCC are clear cell RCC (ccRCC). To date, no reliable biomarkers for the detection of ccRCC have been identified. The aim of this study was to identify blood-based DNA methylation (DNAm) markers for the early detection and treatment of ccRCC. Results To identify ccRCC-associated DNAm markers, we performed targeted bisulfite sequencing (TB-seq) and an epigenome-wide association study (EWAS) using whole blood-derived DNA from 50 ccRCC patients and 50 healthy controls in the discovery phase. EWAS was performed using a linear regression model. The analysis was adjusted for age, sex, and the estimated cell-type composition. In the replication phase, the accuracy of the identified ccRCC-associated CpGs was verified in 48 independent ccRCC patients and 48 healthy controls. We identified six ccRCC-associated hypomethylated CpGs in PCBD2/MTND4P12 in the discovery phase (p &lt; 1.75 × 10−8); four were reproducible in the replication phase (p &lt; 2.96 × 10−8). The sum of the DNAm levels at the six CpGs was a valid indicator of ccRCC both in the discovery phase (area under the receiver operating characteristic curve [AUC-ROC] = 0.922) and in the replication phase (AUC-ROC = 0.871). Moreover, the results of cis-expression quantitative methylation analysis suggested that the DNAm levels of the ccRCC-associated CpGs affect the gene expression of transcription factor 7 (TCF7) and voltage-dependent anion-selective channel 1 (VDAC1), which are involved in cancer progression. Conclusions In this study, we identified six ccRCC-associated CpGs in PCBD2/MTND4P12 by EWAS using blood-based DNA. We found that the DNAm levels of the six CpGs in PCBD2/MTND4P12 may be a potential biomarker for early ccRCC detection, but the value as a biomarker needs to be investigated in future studies.

  24. Evolutionary Tuning of Transient Receptor Potential Ankyrin 1 Underlies the Variation in Heat Avoidance Behaviors among Frog Species Inhabiting Diverse Thermal Niches. International-journal

    Shigeru Saito, Claire T Saito, Takeshi Igawa, Nodoka Takeda, Shohei Komaki, Toshio Ohta, Makoto Tominaga

    Molecular biology and evolution　39　(9)　2022/09/01

    DOI： 10.1093/molbev/msac180 　

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    Environmental temperature is a critical factor for all forms of life, and thermal tolerance defines the habitats utilized by a species. Moreover, the evolutionary tuning of thermal perception can also play a key role in habitat selection. Yet, the relative importance of thermal tolerance and perception in environmental adaptation remains poorly understood. Thermal conditions experienced by anuran tadpoles differ among species due to the variation in breeding seasons and water environments selected by parental frogs. In the present study, heat tolerance and avoidance temperatures were compared in tadpoles from five anuran species that spatially and temporally inhabit different thermal niches. These two parameters were positively correlated with each other and were consistent with the thermal conditions of habitats. The species difference in avoidance temperature was 2.6 times larger than that in heat tolerance, suggesting the importance of heat avoidance responses in habitat selection. In addition, the avoidance temperature increased after warm acclimation, especially in the species frequently exposed to heat in their habitats. Characterization of the heat-sensing transient receptor potential ankyrin 1 (TRPA1) ion channel revealed an amphibian-specific alternatively spliced variant containing a single valine insertion relative to the canonical alternative spliced variant of TRPA1, and this novel variant altered the response to thermal stimuli. The two alternatively spliced variants of TRPA1 exhibited different thermal responses in a species-specific manner, which are likely to be associated with a difference in avoidance temperatures among species. Together, our findings suggest that the functional change in TRPA1 plays a crucial role in thermal adaptation processes.

  25. Environmental <scp>DNA</scp> methods for detecting two invasive alien species (American bullfrog and red swamp crayfish) in Japanese ponds

    Shigeki Ogata, Hideyuki Doi, Takeshi Igawa, Shohei Komaki, Teruhiko Takahara

    Ecological Research　2022/07/05

    Publisher: Wiley

    DOI： 10.1111/1440-1703.12341 　

    ISSN： 0912-3814

    eISSN： 1440-1703

  26. Resistance to chemical carcinogenesis induction via a dampened inflammatory response in naked mole-rats. International-journal

    Kaori Oka, Shusuke Fujioka, Yoshimi Kawamura, Yoshihiro Komohara, Takeshi Chujo, Koki Sekiguchi, Yuki Yamamura, Yuki Oiwa, Natsuko Omamiuda-Ishikawa, Shohei Komaki, Yoichi Sutoh, Satoko Sakurai, Kazuhito Tomizawa, Hidemasa Bono, Atsushi Shimizu, Kimi Araki, Takuya Yamamoto, Yasuhiro Yamada, Hiroyuki Oshiumi, Kyoko Miura

    Communications biology　5　(1)　287-287　2022/03/30

    DOI： 10.1038/s42003-022-03241-y 　

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    Naked mole-rats (NMRs) have a very low spontaneous carcinogenesis rate, which has prompted studies on the responsible mechanisms to provide clues for human cancer prevention. However, it remains unknown whether and how NMR tissues respond to experimental carcinogenesis induction. Here, we show that NMRs exhibit extraordinary resistance against potent chemical carcinogenesis induction through a dampened inflammatory response. Although carcinogenic insults damaged skin cells of both NMRs and mice, NMR skin showed markedly lower immune cell infiltration. NMRs harbour loss-of-function mutations in RIPK3 and MLKL genes, which are essential for necroptosis, a type of necrotic cell death that activates strong inflammation. In mice, disruption of Ripk3 reduced immune cell infiltration and delayed carcinogenesis. Therefore, necroptosis deficiency may serve as a cancer resistance mechanism via attenuating the inflammatory response in NMRs. Our study sheds light on the importance of a dampened inflammatory response as a non-cell-autonomous cancer resistance mechanism in NMRs.

  27. DNA Methylation Abnormalities and Altered Whole Transcriptome Profiles after Switching from Combustible Tobacco Smoking to Heated Tobacco Products. International-journal

    Hideki Ohmomo, Sei Harada, Shohei Komaki, Kanako Ono, Yoichi Sutoh, Ryo Otomo, So Umekage, Tsuyoshi Hachiya, Kota Katanoda, Toru Takebayashi, Atsushi Shimizu

    Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology　31　(1)　269-279　2022/01

    DOI： 10.1158/1055-9965.EPI-21-0444 　

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    BACKGROUND: The use of heated tobacco products (HTP) has increased exponentially in Japan since 2016; however, their effects on health remain a major concern. METHODS: Tsuruoka Metabolome Cohort Study participants (n = 11,002) were grouped on the basis of their smoking habits as never smokers (NS), past smokers (PS), combustible tobacco smokers (CS), and HTP users for <2 years. Peripheral blood mononuclear cells were collected from 52 participants per group matched to HTP users using propensity scores, and DNA and RNA were purified from the samples. DNA methylation (DNAm) analysis of the 17 smoking-associated DNAm biomarker genes (such as AHRR, F2RL3, LRRN3, and GPR15), as well as whole transcriptome analysis, was performed. RESULTS: Ten of the 17 genes were significantly hypomethylated in CS and HTP users compared with NS, among which AHRR, F2RL3, and RARA showed intermediate characteristics between CS and NS; nonetheless, AHRR expression was significantly higher in CS than in the other three groups. Conversely, LRRN3 and GPR15 were more hypomethylated in HTP users than in NS, and GPR15 expression was markedly upregulated in all the groups when compared with that in NS. CONCLUSIONS: HTP users (switched from CS <2 years) display abnormal DNAm and transcriptome profiles, albeit to a lesser extent than the CS. However, because the molecular genetic effects of long-term HTP use are still unknown, long-term molecular epidemiologic studies are needed. IMPACT: This study provides new insights into the molecular genetic effects on DNAm and transcriptome profiles in HTP users who switched from CS.

  28. Low MICA gene expression confers an increased risk of Graves’ disease: a Mendelian randomization study

    Yoichi Sutoh, Shohei Komaki, Taiki Yamaji, Shiori Suzuki, Ryoko Katagiri, Norie Sawada, Kanako Ono, Hideki Ohmomo, Tsuyoshi Hachiya, Yayoi Otsuka-Yamasaki, Akira Takashima, So Umekage, Motoki Iwasaki, Atsushi Shimizu

    Thyroid　2021/12/03

    Publisher: Mary Ann Liebert Inc

    DOI： 10.1089/thy.2021.0417 　

    ISSN： 1050-7256

    eISSN： 1557-9077

  29. Longitudinal DNA methylation dynamics as a practical indicator in clinical epigenetics International-journal

    Shohei Komaki, Hideki Ohmomo, Tsuyoshi Hachiya, Yoichi Sutoh, Kanako Ono, Ryohei Furukawa, So Umekage, Yayoi Otsuka-Yamasaki, Kozo Tanno, Makoto Sasaki, Atsushi Shimizu

    Clinical Epigenetics　13　(1)　219-219　2021/12

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1186/s13148-021-01202-6 　

    ISSN： 1868-7075

    eISSN： 1868-7083

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    <title>Abstract</title><sec> <title>Background</title> 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. </sec><sec> <title>Results</title> 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. </sec><sec> <title>Conclusions</title> 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. </sec>

  30. Transcriptomic Changes in Hot Spring Frog Tadpoles (Buergeria otai) in Response to Heat Stress

    Shohei Komaki, Masatoshi Matsunami, Jhan-Wei Lin, Ko-Huan Lee, Yen-Po Lin, Yu Lee, Si-Min Lin, Takeshi Igawa

    Frontiers in Ecology and Evolution　9　2021/10/13

    Publisher: Frontiers Media SA

    DOI： 10.3389/fevo.2021.706887 　

    eISSN： 2296-701X

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    <italic>Buergeria</italic> frog tadpoles exhibit high thermal tolerance and are occasionally found in water pools that temporarily exceed 40°C. With the aim of understanding how they can cope with the severe heat stress, we performed RNA-seq of three heat-treated (38°C) and three control (25°C) tadpoles and compared their transcriptomic profiles. We identified 382 differentially expressed transcripts. A protein-protein interaction (PPI) network analysis of these transcripts further identified hub proteins involved in protein degradation, stress granule assembly, and global suppression of DNA transcription and mRNA translation. Along with the avoidance behavior against high water temperature, these endurance mechanisms potentially support tadpoles to survive in high temperatures for short periods of time. Similar mechanisms may exist in many other amphibian species whose habitats are prone to high temperatures.

  31. Widespread misperception about a major East Asian biogeographic boundary exposed through bibliographic survey and biogeographic meta‐analysis Peer-reviewed

    Shohei Komaki

    Journal of Biogeography　2021/06/27

    Publisher: Wiley

    DOI： 10.1111/jbi.14210 　

    ISSN： 0305-0270

    eISSN： 1365-2699

  32. ハダカデバネズミの炎症応答の減弱は発がん耐性に寄与している

    藤岡 周助, 岡 香織, 河村 佳見, 菰原 義弘, 中條 岳志, 山村 祐紀, 大岩 祐基, 須藤 洋一, 小巻 翔平, 大豆生田 夏子, 櫻井 智子, 清水 厚志, 坊農 秀雅, 富澤 一仁, 山本 拓也, 山田 泰広, 押海 裕之, 三浦 恭子

    日本薬学会年会要旨集　141年会　29V08-am11S　2021/03

    Publisher: (公社)日本薬学会

    ISSN： 0918-9823

  33. Evaluation of clinical formalin‐fixed paraffin‐embedded tissue quality for targeted‐bisulfite sequencing International-journal Peer-reviewed

    Hideki Ohmomo, Shohei Komaki, Kanako Ono, Yoichi Sutoh, Tsuyoshi Hachiya, Eri Arai, Hiroyuki Fujimoto, Teruhiko Yoshida, Yae Kanai, Makoto Sasaki, Atsushi Shimizu

    Pathology International　71　(2)　135-140　2021/02

    Publisher: Wiley

    DOI： 10.1111/pin.13054 　

    ISSN： 1320-5463

    eISSN： 1440-1827

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    Formalin-fixed paraffin-embedded (FFPE) tissues are promising biological resources for genetic research. Recent improvements in DNA extraction from FFPE samples allowed the use of these tissues for multiple sequencing methods. However, fundamental research addressing the application of FFPE-derived DNA for targeted-bisulfite sequencing (TB-seq) is lacking. Here, we evaluated the suitability of FFPE-derived DNA for TB-seq. We conducted TB-seq using FFPE-derived DNA and corresponding fresh frozen (FF) tissues of patients with kidney cancer and compared the quality of DNA, libraries, and TB-seq statistics between the two preservation methods. The approximately 600-bp average fragment size of the FFPE-derived DNA was significantly shorter than that of the FF-derived DNA. The sequencing libraries constructed using FFPE-derived DNA and the mapping ratio were approximately 10 times and 10% lower, respectively, than those constructed using FF-derived DNA. In the mapped data of FFPE-derived DNA, duplicated reads accounted for > 60% of the obtained sequence reads, with lower mean on-target coverage. Therefore, the standard TB-seq protocol is inadequate for obtaining high-quality data for epigenetic analysis from FFPE-derived DNA, and technical improvements are necessary for enabling the use of archived FFPE resources.

  34. jMorp updates in 2020: large enhancement of multi-omics data resources on the general Japanese population International-journal

    Shu Tadaka, Eiji Hishinuma, Shohei Komaki, Ikuko N Motoike, Junko Kawashima, Daisuke Saigusa, Jin Inoue, Jun Takayama, Yasunobu Okamura, Yuichi Aoki, Matsuyuki Shirota, Akihito Otsuki, Fumiki Katsuoka, Atsushi Shimizu, Gen Tamiya, Seizo Koshiba, Makoto Sasaki, Masayuki Yamamoto, Kengo Kinoshita

    Nucleic Acids Research　49　(D1)　D536-D544　2021/01/08

    Publisher: Oxford University Press (OUP)

    DOI： 10.1093/nar/gkaa1034 　

    ISSN： 0305-1048

    eISSN： 1362-4962

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    <title>Abstract</title> In the Tohoku Medical Megabank project, genome and omics analyses of participants in two cohort studies were performed. A part of the data is available at the Japanese Multi Omics Reference Panel (jMorp; https://jmorp.megabank.tohoku.ac.jp) as a web-based database, as reported in our previous manuscript published in Nucleic Acid Research in 2018. At that time, jMorp mainly consisted of metabolome data; however, now genome, methylome, and transcriptome data have been integrated in addition to the enhancement of the number of samples for the metabolome data. For genomic data, jMorp provides a Japanese reference sequence obtained using de novo assembly of sequences from three Japanese individuals and allele frequencies obtained using whole-genome sequencing of 8,380 Japanese individuals. In addition, the omics data include methylome and transcriptome data from ∼300 samples and distribution of concentrations of more than 755 metabolites obtained using high-throughput nuclear magnetic resonance and high-sensitivity mass spectrometry. In summary, jMorp now provides four different kinds of omics data (genome, methylome, transcriptome, and metabolome), with a user-friendly web interface. This will be a useful scientific data resource on the general population for the discovery of disease biomarkers and personalized disease prevention and early diagnosis.

  35. ALDH2 genotype modulates the association between alcohol consumption and AST/ALT ratio among middle-aged Japanese men: a genome-wide G × E interaction analysis. International-journal Peer-reviewed

    Yoichi Sutoh, Tsuyoshi Hachiya, Yuji Suzuki, Shohei Komaki, Hideki Ohmomo, Keisuke Kakisaka, Ting Wang, Yasuhiro Takikawa, Atsushi Shimizu

    Scientific reports　10　(1)　16227-16227　2020/10/01

    DOI： 10.1038/s41598-020-73263-1 　

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    Liver tests (LT), especially to measure AST, ALT and GGT levels, are widely used to evaluate the risk of alcohol-related liver disease (ALD). In this study, we investigated the potential genetic factors that modulate the association between LTs and alcohol consumption. We conducted a genome-wide interaction meta-analysis in 7856 Japanese subjects from Tohoku Medical Megabank Community-Based Cohort (TMM CommCohort) study recruited in 2013, and identified 2 loci (12q24 and 2p16) with genome-wide significance (P > 5 × 10-8). The significant variants in the 12q24 included rs671, a variant associated with alcohol intolerance and located at a coding exon of ALDH2. We found that the amount of alcohol consumption was associated with increased level AST/ALT ratio among the subjects with the rs671 GA genotype. The elevated AST/ALT ratio among subjects with moderate-to-high levels of drinking behavior and the rs671 GA genotype was due to decreased levels of ALT, which was not accompanied with significant differences in AST levels. Although the interaction effect was significant in both men and women, the effect was much larger in men. Our results suggest that the impact of alcohol consumption on LT varies according to the ALDH2 genotype, providing an insight for the accurate screening of ALD in drinkers with the rs671 GA genotype.

  36. Hot spring frogs (Buergeria japonica) prefer cooler water to hot water International-journal Peer-reviewed

    Shohei Komaki, Yoichi Sutoh, Kensuke Kobayashi, Shigeru Saito, Claire T. Saito, Takeshi Igawa, Quintin Lau

    ECOLOGY AND EVOLUTION　10　(17)　9466-9473　2020/09

    DOI： 10.1002/ece3.6637 　

    ISSN： 2045-7758

  37. エピゲノムワイド関連解析

    小巻 翔平, 清水 厚志

    遺伝子医学　10　(2)　137-141　2020/04

    Publisher: (株)メディカルドゥ

    ISSN： 1343-0971

  38. Epigenome-Wide Association Study Identifies a Novel DNA Methylation in Patients With Severe Aortic Valve Stenosis International-journal Peer-reviewed

    Takahito Nasu, Mamoru Satoh, Hideki Ohmomo, Yuh Shiwa, Shohei Komaki, Kanako Ono, Atsushi Shimizu, Satoru Taguchi, Yuji Takahashi, Takuya Osaki, Yoshihiro Morino, Kenji Sobue, Makoto Sasaki

    CIRCULATION-GENOMIC AND PRECISION MEDICINE　13　(1)　e002649　2020/02

    DOI： 10.1161/CIRCGEN.119.002649 　

    ISSN： 2574-8300

  39. Expression Changes of MHC and Other Immune Genes in Frog Skin during Ontogeny International-journal Peer-reviewed

    Quintin Lau, Takeshi Igawa, Shohei Komaki, Yoko Satta

    ANIMALS　10　(1)　2020/01

    DOI： 10.3390/ani10010091 　

    ISSN： 2076-2615

  40. An application of PCR-RFLP species identification assay for environmental DNA detection International-journal Peer-reviewed

    Takeshi Igawa, Teruhiko Takahara, Quintin Lau, Shohei Komaki

    PEERJ　7　e7597　2019/10

    DOI： 10.7717/peerj.7597 　

    ISSN： 2167-8359

  41. DNAメチル化多様性に基づく効率的なエピゲノムマーカー探索手法の確立

    清水 厚志, 八谷 剛史, 大友 亮, 大桃 秀樹, 須藤 洋一, 小巻 翔平, 志波 優, 古川 亮平, 篠崎 夏子, 小野 加奈子, 佐々木 真理

    日本遺伝カウンセリング学会誌　40　(2)　87-87　2019/07

    Publisher: (一社)日本遺伝カウンセリング学会

    ISSN： 1347-9628

  42. 抑うつ症状の指標と関連するDNAメチル化マーカーのキャプチャ法による探索

    小野 加奈子, 大桃 秀樹, 福本 健太郎, 小巻 翔平, 事崎 由佳, 八谷 剛史, 大友 亮, 篠崎 夏子, 志波 優, 古川 亮平, 須藤 洋一, 大塚 耕太郎, 佐々木 真理, 清水 厚志

    日本遺伝カウンセリング学会誌　40　(2)　162-162　2019/07

    Publisher: 日本遺伝カウンセリング学会

    ISSN： 1347-9628

  43. マルチオミクスゲノムブラウザiMETHYLの紹介

    小巻 翔平, 志波 優, 古川 亮平, 八谷 剛史, 大桃 秀樹, 須藤 洋一, 大友 亮, 佐々木 真理, 清水 厚志

    トーゴーの日2018　1　2018/10/05

    Publisher: バイオサイエンスデータベースセンター

    DOI： 10.18908/togo2018.p048 　

  44. Genome-wide analysis of polymorphism x sodium interaction effect on blood pressure identifies a novel 3 '-BCL11B gene desert locus International-journal Peer-reviewed

    Tsuyoshi Hachiya, Akira Narita, Hideki Ohmomo, Yoichi Sutoh, Shohei Komaki, Kozo Tanno, Mamoru Satoh, Kiyomi Sakata, Jiro Hitomi, Motoyuki Nakamura, Kuniaki Ogasawara, Masayuki Yamamoto, Makoto Sasaki, Atsushi Hozawa, Atsushi Shimizu

    SCIENTIFIC REPORTS　8　(1)　14162-14162　2018/09

    DOI： 10.1038/s41598-018-32074-1 　

    ISSN： 2045-2322

  45. Acoustic differentiation and behavioral response reveals cryptic species within Buergeria treefrogs (Anura, Rhacophoridae) from Taiwan (vol 12, e0184005, 2017) International-journal Peer-reviewed

    Ying-Han Wang, Yu-Wei Hsiao, Ko-Huan Lee, Hui-Yun Tseng, Yen-Po Lin, Shohei Komaki, Si-Min Lin

    PLOS ONE　13　(2)　e0193040　2018/02

    DOI： 10.1371/journal.pone.0193040 　

    ISSN： 1932-6203

  46. Riding the Kuroshio Current: Stepping stone dispersal of the Okinawa tree lizard across the East Asian Island Arc Peer-reviewed

    Shang-Fang Yang, Shohei Komaki, Rafe M. Brown, Si-Min Lin

    JOURNAL OF BIOGEOGRAPHY　45　(1)　37-50　2018/01

    DOI： 10.1111/jbi.13111 　

    ISSN： 0305-0270

    eISSN： 1365-2699

  47. iMETHYL: an integrative database of human DNA methylation, gene expression, and genomic variation. International-journal Peer-reviewed

    Shohei Komaki, Yuh Shiwa, Ryohei Furukawa, Tsuyoshi Hachiya, Hideki Ohmomo, Ryo Otomo, Mamoru Satoh, Jiro Hitomi, Kenji Sobue, Makoto Sasaki, Atsushi Shimizu

    Human genome variation　5　18008-18008　2018

    DOI： 10.1038/hgv.2018.8 　

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    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.

  48. Genome-wide meta-analysis in Japanese populations identifies novel variants at the TMC6-TMC8 and SIX3-SIX2 loci associated with HbA(1c) International-journal Peer-reviewed

    Tsuyoshi Hachiya, Shohei Komaki, Yutaka Hasegawa, Hideki Ohmomo, Kozo Tanno, Atsushi Hozawa, Gen Tamiya, Masayuki Yamamoto, Kuniaki Ogasawara, Motoyuki Nakamura, Jiro Hitomi, Yasushi Ishigaki, Makoto Sasaki, Atsushi Shimizu

    SCIENTIFIC REPORTS　7　(1)　16147-16147　2017/11

    DOI： 10.1038/s41598-017-16493-0 　

    ISSN： 2045-2322

  49. The widespread misconception about the Japanese major biogeographic boundary, the Watase line (Tokara gap), revealed by bibliographic and beta diversity analyses

    Shohei Komaki, Takeshi Igawa

    bioRxiv　2017/09/10

    Publisher: Cold Spring Harbor Laboratory

    DOI： 10.1101/186775 　

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    <title>ABSTRACT</title>The biota of the Japanese Archipelago is divided into the Palearctic and Oriental realms by the Watase line (Tokara gap), a major biogeographic boundary of Japan. This boundary is generally placed between Akusekijima and Kodakarajima Islands of the Tokara Archipelago, and has been the subject of many biogeographic debates. However, despite being widely accepted, the position of the boundary is doubtful because of a lack of clear evidence. Here, to verify the definition and existence of the biogeographic boundary, we performed a documentary search and beta diversity analysis of multiple taxa. Our documentary search suggested that the Watase line (Tokara gap) should be put between Yakushima/Tanegashima and Amamioshima Islands, but recent references to it clearly deviate from its original definition, and that the placement of the boundary line between Akusekijima and Kodakarajima Islands is based on limited and biased evidence. Our beta diversity analyses found no common biogeographic boundary dividing the Tokara Archipelago into two realms, and showed that the beta diversity pattern of this region is explained by the areas and geographic distances of the islands in agreement with the general principles of island biogeography. The widespread misunderstanding of biogeography in this region could have been perpetuated by preconception and the citation of references without verification. Our study proposes that revision of the biogeography in the Tokara Archipelago, a gap region between the Palearctic and Oriental realms, is necessary and demonstrates the negative influence of preconception in biogeographic debate.

  50. Acoustic differentiation and behavioral response reveals cryptic species within Buergeria treefrogs (Anura, Rhacophoridae) from Taiwan International-journal Peer-reviewed

    Ying-Han Wang, Yu-Wei Hsiao, Ko-Huan Lee, Hui-Yun Tseng, Yen-Po Lin, Shohei Komaki, Si-Min Lin

    PLOS ONE　12　(9)　e0184005　2017/09

    DOI： 10.1371/journal.pone.0184005 　

    ISSN： 1932-6203

  51. Fine-scale demographic processes resulting from multiple overseas colonization events of the Japanese stream tree frog, Buergeria japonica Peer-reviewed

    Shohei Komaki, Si-Min Lin, Masafumi Nozawa, Shohei Oumi, Masayuki Sumida, Takeshi Igawa

    JOURNAL OF BIOGEOGRAPHY　44　(7)　1586-1597　2017/07

    DOI： 10.1111/jbi.12922 　

    ISSN： 0305-0270

    eISSN： 1365-2699

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

    Shohei Komaki, Hideki Ohmomo, Tsuyoshi Hachiya, Ryohei Furukawa, Yuh Shiwa, Mamoru Satoh, Ryujin Endo, Minoru Doita, Makoto Sasaki, Atsushi Shimizu

    Integrative Molecular Medicine　4　(5)　2017

    Publisher: Open Access Text Pvt, Ltd.

    DOI： 10.15761/imm.1000307 　

    eISSN： 2056-6360

  53. Species diversity of insects in Japan: Their origins and diversification processes Peer-reviewed

    Koji Tojo, Kazuki Sekine, Masaki Takenaka, Yuichi Isaka, Shohei Komaki, Tomoya Suzuki, Sean D. Schoville

    ENTOMOLOGICAL SCIENCE　20　(1)　357-381　2017/01

    DOI： 10.1111/ens.12261 　

    ISSN： 1343-8786

    eISSN： 1479-8298

  54. Characterisation of major histocompatibility complex class I genes in Japanese Ranidae frogs International-journal Peer-reviewed

    Quintin Lau, Takeshi Igawa, Shohei Komaki, Yoko Satta

    IMMUNOGENETICS　68　(10)　797-806　2016/11

    DOI： 10.1007/s00251-016-0934-x 　

    ISSN： 0093-7711

    eISSN： 1432-1211

  55. Inter- and intra-specific genetic divergence of Asian tiger frogs (genus Hoplobatrachus), with special reference to the population structure of H. tigerinus in Bangladesh Peer-reviewed

    Nasrin Sultana, Takeshi Igawa, Mohammed Mafizul Islam, Mahmudul Hasan, Mohammad Shafiqul Alam, Shohei Komaki, Kensuke Kawamura, Md. Mukhlesur Rahman Khan, Masayuki Sumida

    GENES & GENETIC SYSTEMS　91　(4)　217-227　2016/08

    DOI： 10.1266/ggs.16-00006 　

    ISSN： 1341-7568

    eISSN： 1880-5779

  56. Salinity and thermal tolerance of Japanese stream tree frog (Buergeria japonica) tadpoles from island populations Peer-reviewed

    Shohei Komaki, Takeshi Igawa, Si-Min Lin, Masayuki Sumida

    HERPETOLOGICAL JOURNAL　26　(3)　207-211　2016/07

    ISSN： 0268-0130

  57. Living in a Japanese onsen: field observations and physiological measurements of hot spring amphibian tadpoles, Buergeria japonica Peer-reviewed

    Shohei Komaki, Quintin Lau, Takeshi Igawa

    AMPHIBIA-REPTILIA　37　(3)　311-314　2016

    DOI： 10.1163/15685381-00003052 　

    ISSN： 0173-5373

    eISSN： 1568-5381

  58. Robust molecular phylogeny and palaeodistribution modelling resolve a complex evolutionary history: glacial cycling drove recurrent mtDNA introgression among Pelophylax frogs in East Asia Peer-reviewed

    Shohei Komaki, Takeshi Igawa, Si-Min Lin, Koji Tojo, Mi-Sook Min, Masayuki Sumida

    JOURNAL OF BIOGEOGRAPHY　42　(11)　2159-2171　2015/11

    DOI： 10.1111/jbi.12584 　

    ISSN： 0305-0270

    eISSN： 1365-2699

  59. Development and Validation of PCR-RFLP Assay to Identify Three Japanese Brown Frogs of the True Frog Genus Rana Peer-reviewed

    Takeshi Igawa, Shohei Komaki, Teruhiko Takahara, Masayuki Sumida

    CURRENT HERPETOLOGY　34　(1)　89-94　2015/02

    DOI： 10.5358/hsj.34.89 　

    ISSN： 1345-5834

  60. Microsatellite Marker Development by Multiplex Ion Torrent PGM Sequencing: a Case Study of the Endangered Odorrana narina Complex of Frogs Peer-reviewed

    Takeshi Igawa, Masafumi Nozawa, Mai Nagaoka, Shohei Komaki, Shohei Oumi, Tamotsu Fujii, Masayuki Sumida

    JOURNAL OF HEREDITY　106　(1)　131-137　2015/01

    DOI： 10.1093/jhered/esu071 　

    ISSN： 0022-1503

    eISSN： 1465-7333

  61. Development and characterization of 14 microsatellite markers for Buergeria japonica (Amphibia, Anura, Rhacophoridae) Peer-reviewed

    Shohei Komaki, Takeshi Igawa, Masafumi Nozawa, Si-Min Lin, Shohei Oumi, Masayuki Sumida

    GENES & GENETIC SYSTEMS　89　(1)　35-39　2014/02

    DOI： 10.1266/ggs.89.35 　

    ISSN： 1341-7568

    eISSN： 1880-5779

  62. Distributional Change and Epidemic Introgression in Overlapping Areas of Japanese Pond Frog Species over 30 Years Peer-reviewed

    Shohei Komaki, Atsushi Kurabayashi, Mohammed Mafizul Islam, Koji Tojo, Masayuki Sumida

    ZOOLOGICAL SCIENCE　29　(6)　351-358　2012/06

    DOI： 10.2108/zsj.29.351 　

    ISSN： 0289-0003

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Misc. 18

  1. DNAメチル化解析および遺伝子発現解析を用いた加熱式たばこへの切り替えによる分子遺伝学的影響の解明

    大桃秀樹, 大桃秀樹, 原田成, 小巻翔平, 小巻翔平, 小野加奈子, 美辺詩織, 美辺詩織, 須藤洋一, 須藤洋一, 山崎弥生, 山崎弥生, 武林亨, 清水厚志, 清水厚志

    日本疫学会学術総会講演集(Web)　35th　2025

  2. Feasibility study for the realization of personalized prevention through the distribution of epigenome age

    清水厚志, 清水厚志, 小巻翔平, 小巻翔平, 荒木重則, 美辺詩織, 美辺詩織, 山崎弥生, 山崎弥生, 須藤洋一, 須藤洋一, 大桃秀樹, 大桃秀樹

    日本遺伝カウンセリング学会誌　46　(2)　2025

    ISSN： 1347-9628

  3. Leveraging dimensionality reduction methods for gut microbiota research.

    八谷剛史, 小巻翔平, 佐保山友加里, 川上英良, 川上英良, 川上英良

    月刊臨床免疫・アレルギー科　83　(1)　2025

    ISSN： 1881-1930

  4. 大規模ゲノムコホートの踵骨定量的超音波測定T-score値を基盤とする多遺伝子スコアを用いた骨粗鬆症発症リスク予測モデルの構築

    山崎弥生, 須藤洋一, 八谷剛史, 小巻翔平, 美辺詩織, 大桃秀樹, 佐々木真理, 清水厚志

    日本骨粗鬆症学会雑誌　10　(Suppl.1 (CD-ROM))　2024

    ISSN： 2189-8383

  5. Personalized medicine through disclosing epigenomic age to individuals: Feasibility Study

    清水厚志, 清水厚志, 清水厚志, 小巻翔平, 小巻翔平, 小巻翔平, 荒木重則, 荒木重則, 美辺詩織, 美辺詩織, 山崎弥生, 山崎弥生, 須藤洋一, 須藤洋一, 大桃秀樹, 大桃秀樹, 大桃秀樹

    日本遺伝カウンセリング学会誌　45　(2)　2024

    ISSN： 1347-9628

  6. 日本人マイクロアレイデータをレファレンスとして用いるエピゲノム年齢推定法の開発

    清水厚志, 清水厚志, 清水厚志, 小巻翔平, 小巻翔平, 小巻翔平, 大桃秀樹, 大桃秀樹, 大桃秀樹

    日本抗加齢医学会総会プログラム・抄録集　24th　2024

  7. DNA Methylation Study in DOHaD Theory: A Perspective from the Tohoku Medical Megabank (TMM) Project

    美辺詩織, 美辺詩織, 小巻翔平, 小巻翔平, 大桃秀樹, 大桃秀樹, 清水厚志, 清水厚志

    DOHad研究(Web)　12　(1)　2024

    ISSN： 2187-2597

  8. 新生児臍帯血の網羅的エピゲノム解析による妊娠初期までの喫煙経験が次世代に及ぼす影響

    美辺詩織, 小巻翔平, 大桃秀樹, 高嶋聰, 小野加奈子, 山崎弥生, 須藤洋一, 田高周, 水野聖士, 石黒真美, 工藤久智, 小原拓, 熊田和貴, 勝岡史城, 荻島創一, 木下賢吾, 菅原準一, 栗山進一, 清水厚志, 清水厚志

    DOHad研究(Web)　11　(3)　2023

    ISSN： 2187-2597

  9. ALDH2 genotype interacts the association between alcohol consumption and AST/ALT ratio among middle-aged Japanese men

    須藤洋一, 八谷剛史, 鈴木悠地, 小巻翔平, 大桃秀樹, 柿坂啓介, WANG Ting, 滝川康裕, 清水厚志, 清水厚志

    日本分子生物学会年会プログラム・要旨集(Web)　45th　2022

  10. Identification of potential DNA methylation biomarkers for detection of clear cell renal cell carcinoma in PCBD2/MTND4P12 genes.

    大桃秀樹, 大桃秀樹, 小巻翔平, 須藤洋一, 八谷剛史, 八谷剛史, 小野加奈子, 新井恵吏, 藤元博行, 吉田輝彦, 金井弥栄, 旭浩一, 佐々木真理, 清水厚志, 清水厚志

    日本分子生物学会年会プログラム・要旨集(Web)　45th　2022

  11. 【ゲノム医療におけるデータベース-使い方とコツ】一般集団・多因子疾患関連バリアントのデータベース iMETHYL

    小巻 翔平, 清水 厚志

    遺伝子医学　12　(1)　20-23　2022/01

    Publisher: (株)メディカルドゥ

    ISSN： 1343-0971

  12. ハダカデバネズミの炎症応答の減弱は発がん耐性に寄与している

    藤岡 周助, 岡 香織, 河村 佳見, 菰原 義弘, 中條 岳志, 山村 祐紀, 大岩 祐基, 須藤 洋一, 小巻 翔平, 大豆生田 夏子, 櫻井 智子, 清水 厚志, 坊農 秀雅, 富澤 一仁, 山本 拓也, 山田 泰広, 押海 裕之, 三浦 恭子

    日本薬学会年会要旨集　141年会　29V08-am11S　2021/03

    Publisher: (公社)日本薬学会

    ISSN： 0918-9823

  13. 多因子疾患の関連解析を目的とした網羅的DNAメチル化解析法の開発

    大桃秀樹, 小野加奈子, 須藤洋一, 小巻翔平, 大友亮, 八谷剛史, 佐々木真理, 清水厚志

    日本分子生物学会年会プログラム・要旨集(Web)　42nd　2019

  14. Exploratory studies for depression indicators by DNA-methylation capture sequencing

    小野加奈子, 大桃秀樹, 福本健太郎, 小巻翔平, 事崎由佳, 八谷剛史, 大友亮, 篠崎夏子, 志波優, 古川亮平, 須藤洋一, 大塚耕太郎, 大塚耕太郎, 佐々木真理, 清水厚志

    日本遺伝子診療学会大会プログラム・抄録集　26th　2019

  15. リュウキュウカジカガエル幼生・幼体の色彩変異

    小巻翔平, 井川武, 住田正幸

    爬虫両生類学会報　2014　(1)　17-18　2014

  16. 種子島におけるヌマガエル生息の報告

    小巻翔平

    爬虫両生類学会報　2012　(1)　1-2　2012

  17. 携帯電話のカメラ機能を利用した市民参加型：生物調査の試み－松本盆地・伊那盆地におけるトノサマガエル種群の分布調査－

    東城幸治, 小巻翔平

    塩尻市立自然博物館紀要　14　59-68　2012

  18. 松本盆地・伊那盆地におけるトノサマガエル種群の分布および種間交雑の可能性について

    小巻翔平, 東城幸治

    塩尻市立自然博物館紀要　12　52-60　2010

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Books and Other Publications 3

  1. バリアントデータ検索&活用 : 変異・多型情報を使いこなす達人レシピ

    坊農, 秀雅

    羊土社　2020/10

    ISBN: 9784758122450

  2. 遺伝子医学

    株式会社メディカルドゥ　2020/04

  3. 次世代シークエンサーDRY解析教本

    清水, 厚志, 坊農, 秀雅

    学研メディカル秀潤社,学研プラス (発売)　2019/12

    ISBN: 9784780909838

Presentations 1

  1. 疫学研究におけるDNAメチル化情報の活用

    小巻翔平

    日本疫学会 第28回疫学セミナー　2021/01/27

Research Projects 9

  1. DNAメチル化経時変化に基づく健康・老化状態の理解と介入ターゲットの探索

    小巻 翔平, 清水 厚志, 大桃 秀樹

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 基盤研究(B)

    Institution: 岩手医科大学

    2025/04/01 - 2028/03/31

  2. 淡明細胞型腎細胞がんに対するDNAメチル化バイオマーカーの実用化に向けた検討

    大桃 秀樹, 小巻 翔平

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 基盤研究(C)

    Institution: 岩手医科大学

    2025/04/01 - 2028/03/31

  3. Usefulness of metabolite biomarker as a common pathway for the prevention of non-communicable diseases and frailty

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (A)

    Institution: Keio University

    2023/04/01 - 2028/03/31

  4. The process of expanding the distribution of domestically introduced species revealed by Genome-Wide Association Study

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (C)

    2022/04/01 - 2025/03/31

  5. Establishment of Biomarkers for Intellectual and Mental Developmental Delays in Children Due to Stress Exposure During the Perinatal Period

    Sobue Kenji

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: Iwate Medical University

    2021/04/01 - 2024/03/31

    More details Close

    In order to establish an objective evaluation method for Adverse Childhood Experiences (ACE), we tried to identify methylation CpG sites correlate with ACE history in saliva DNA. We recruited research participants focused particularly on ACE up to the age of 5, which is an epigenetically sensitive period. We conducted various psychological tests and surveys on upbringing and development, in addition to saliva collection. We analyzed methylation status about saliva DNA using our unique capture probe targeting approximately 1.3 million CpG sites. As a result of the Epigenome-Wide Association Study (EWAS), we identified 17 methylation CpG candidates that correlate with ACE history. We are advancing verification, and it is expected that the methyl CpG candidates would be a useful biomarker to evaluate ACE history.

  6. 岩手県におけるトノサマガエル種群の分布および交雑状況の評価

    Offer Organization: 藤原ナチュラルヒストリー振興財団

    System: 学術研究助成

    2022/04 - 2023/03

  7. Ecology and evolution of hot-spring frogs

    Komaki Shohei

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research Grant-in-Aid for Early-Career Scientists

    Category: Grant-in-Aid for Early-Career Scientists

    Institution: Iwate Medical University

    2018/04/01 - 2021/03/31

    More details Close

    In this research, I focused on Buergeria frogs, a genus with an extraordinary characteristic of inhabiting hot springs, and studied underlying mechanisms that enable them to live in harsh, high-temperature environments through observational and transcriptome studies. Behavioral observations revealed that both tadpoles and adults prefer lower water temperatures for inhabiting and breeding. Gene expression analyses showed that genes involved in suppressive functions, such as global transcription and translation suppression and protein degradation, were differentially expressed in response to heat stress. These results suggest that while they can temporarily tolerate high thermal stress, they also can avoid long-term stress by temperature-selective behavior, making it possible to survive in hot spring environments.

  8. リュウキュウカジカガエルの火山島への漂流分散と高温耐性の関連

    Offer Organization: 広島大学校友会

    System: 平成27年度研究助成金（若手研究者）

    Institution: 広島大学

    2015 - 2016

  9. リュウキュウカジカガエルの島嶼生物学的研究：分布形成機構と適応進化の追究

    小巻 翔平

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業 特別研究員奨励費

    Category: 特別研究員奨励費

    Institution: 広島大学

    2013/04/01 - 2015/03/31

    More details Close

    本年度は、マイクロサテライトマーカーを用いて、琉球列島および台湾で採集されたリュウキュウカジカガエル400個体の21座分の遺伝子型を決定した。これらのデータに基づき、本種の集団遺伝学的解析を行っている。 また奄美、沖縄、台湾で採集した個体が繁殖し、幼生が得られたため、これらを用いて塩分・高温耐性を調べた。その結果、耐塩性は内陸に生息する一般的な両生類と同程度であることが明らかになった。一方、高温耐性実験では、いずれも平均40℃以上の温水でも生存することが明らかになった。これらの耐性実験の結果は論文にまとめ、現在投稿中である。 また系統地理学的解析の結果と耐性実験の結果は、第35回菅平動物学セミナーにて発表した。

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Media Coverage 1

  1. トノサマガエルは中韓交雑し由来 Myself

    共同通信社　共同通信、産経ニュース、日本経済新聞、沖縄タイムス、北海道新聞、東京新聞など

    2016/03

    Type: Newspaper, magazine