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Fujinami-Yokokawa Y, Joo K, Liu X, Tsunoda K, Kondo M, Ahn SJ, Robson AG, Naka I, Ohashi J, Li H, Yang L, Arno G, Pontikos N, Park KH, Michaelides M, Tachimori H, Miyata H, Sui R, Woo SJ, Fujinami K. Distinct Clinical Effects of Two RP1L1 Hotspots in East Asian Patients With Occult Macular Dystrophy (Miyake Disease): EAOMD Report 4. Invest Ophthalmol Vis Sci 2024; 65:41. [PMID: 38265784 PMCID: PMC10810149 DOI: 10.1167/iovs.65.1.41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024] Open
Abstract
Purpose To characterize the clinical effects of two RP1L1 hotspots in patients with East Asian occult macular dystrophy (OMD). Methods Fifty-one patients diagnosed with OMD harboring monoallelic pathogenic RP1L1 variants (Miyake disease) from Japan, South Korea, and China were enrolled. Patients were classified into two genotype groups: group A, p.R45W, and group B, missense variants located between amino acids (aa) 1196 and 1201. The clinical parameters of the two genotypes were compared, and deep learning based on spectral-domain optical coherence tomographic (SD-OCT) images was used to distinguish the morphologic differences. Results Groups A and B included 29 and 22 patients, respectively. The median age of onset in groups A and B was 14.0 and 40.0 years, respectively. The median logMAR visual acuity of groups A and B was 0.70 and 0.51, respectively, and the survival curve analysis revealed a 15-year difference in vision loss (logMAR 0.22). A statistically significant difference was observed in the visual field classification, but no significant difference was found in the multifocal electroretinographic classification. High accuracy (75.4%) was achieved in classifying genotype groups based on SD-OCT images using machine learning. Conclusions Distinct clinical severities and morphologic phenotypes supported by artificial intelligence-based classification were derived from the two investigated RP1L1 hotspots: a more severe phenotype (p.R45W) and a milder phenotype (1196-1201 aa). This newly identified genotype-phenotype association will be valuable for medical care and the design of therapeutic trials.
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Affiliation(s)
- Yu Fujinami-Yokokawa
- Department of Health Policy and Management, Keio University School of Medicine, Tokyo, Japan
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo, Japan
- UCL Institute of Ophthalmology, London, United Kingdom
- Division of Public Health, Yokokawa Clinic, Suita, Japan
| | - Kwangsic Joo
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Xiao Liu
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo, Japan
- Southwest Hospital, Army Medical University, Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Kazushige Tsunoda
- Division of Vision Research, National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo, Japan
| | - Mineo Kondo
- Department of Ophthalmology, Mie University Graduate School of Medicine, Mie, Japan
| | - Seong Joon Ahn
- Department of Ophthalmology, Hanyang University Hospital, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Anthony G. Robson
- UCL Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hui Li
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Lizhu Yang
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Gavin Arno
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo, Japan
- UCL Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Nikolas Pontikos
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo, Japan
- UCL Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Kyu Hyung Park
- Department of Ophthalmology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Michel Michaelides
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo, Japan
- UCL Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Hisateru Tachimori
- Endowed Course for Health System Innovation, Keio University School of Medicine, Tokyo, Japan
| | - Hiroaki Miyata
- Department of Health Policy and Management, Keio University School of Medicine, Tokyo, Japan
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Se Joon Woo
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Kaoru Fujinami
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo, Japan
- UCL Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - for the East Asia Inherited Retinal Disease Society Study Group*
- Department of Health Policy and Management, Keio University School of Medicine, Tokyo, Japan
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo, Japan
- UCL Institute of Ophthalmology, London, United Kingdom
- Division of Public Health, Yokokawa Clinic, Suita, Japan
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
- Southwest Hospital, Army Medical University, Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
- Division of Vision Research, National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo, Japan
- Department of Ophthalmology, Mie University Graduate School of Medicine, Mie, Japan
- Department of Ophthalmology, Hanyang University Hospital, Hanyang University College of Medicine, Seoul, Republic of Korea
- Moorfields Eye Hospital, London, United Kingdom
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Department of Ophthalmology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Endowed Course for Health System Innovation, Keio University School of Medicine, Tokyo, Japan
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Dhanji SD, Ohashi J, Song J. Chronomobility of international students under COVID-19 Australia. Front Sociol 2023; 8:1159600. [PMID: 38156311 PMCID: PMC10753181 DOI: 10.3389/fsoc.2023.1159600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 10/31/2023] [Indexed: 12/30/2023]
Abstract
This article investigates the chronomobility of international students in Australia going through COVID-19. Existing literature on international students approaches them largely in two manners: a market or victims. Using Shanti Robertson's chronomobility, the study focuses on international students' coping mechanisms and strategies for their next moves. Drawing from 15 in-depth interviews with international students formally enrolled in Australian institutions in Melbourne, the longest lockdown city during the pandemic, the authors find various ways of short-term coping mechanisms through meditation, physical exercises, virtual escapism and counselling. Furthermore, despite pandemic immobility, students presented a high level of resilience in making future decisions for post-pandemic mobilities. We conclude that family support and social networks are key to realise full potentials of international students as skilled migrants and valued members of society. Our manuscript contributes to the field of migration and mobility by enriching Robertson's concept of chrono-mobility and adding the empirical case study from international students in Australia during the latest pandemic in 2020-2021.
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Affiliation(s)
- Surjeet D. Dhanji
- Asia Institute, Faculty of Arts, The University of Melbourne, Parkville, VIC, Australia
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Hadate T, Kawamura R, Tabara Y, Maruyama K, Takakado M, Ikeda Y, Ohashi J, Takata Y, Saito I, Osawa H. Positive association between serum resistin and smoking was strongest in homozygotes of the G-A haplotype at c.-420 C>G and c.-358 G>A in RETN promoter: the Toon Genome Study. J Hum Genet 2023; 68:745-750. [PMID: 37423942 DOI: 10.1038/s10038-023-01176-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 06/01/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023]
Abstract
Resistin is mainly expressed in human monocytes/macrophages and is associated with insulin resistance, inflammation, and atherosclerosis. Serum resistin is strongly correlated with the G-A haplotype defined by single nucleotide polymorphisms (SNPs) c.-420 C>G (SNP-420) (rs1862513) and c.-358 G>A (SNP-358) (rs3219175) in the promoter region of the human resistin gene (RETN). Smoking is also associated with insulin resistance. We investigated the association between smoking and serum resistin and the effect of the G-A haplotype on this association. Participants were recruited under the Toon Genome Study (an observational epidemiology research in the Japanese population). Of these, 1975 subjects genotyped for both SNP-420 and SNP-358 were analyzed for serum resistin by grouping them based on smoking status and G-A haplotype status. RETN mRNA, isolated from whole blood cells, was evaluated in smokers (n = 7) and age-, sex-, and BMI-matched non-smokers (n = 7) with the G-A haplotype homozygotes. Serum resistin tended to be higher in current smokers who smoked more cigarettes per day (P for trend < 0.0001). The positive association between serum resistin and smoking was strongest in the G-A haplotype homozygotes, followed by heterozygotes and non-carriers (interaction P < 0.0001). This positive association was stronger in the G-A homozygotes than the C-G homozygotes (interaction P < 0.0001). RETN mRNA was 1.40-fold higher in smokers than non-smokers with the G-A homozygotes (P = 0.022). Therefore, the positive association between serum resistin and smoking was strongest in the G-A haplotype homozygotes defined by RETN SNP-420 and SNP-358.
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Affiliation(s)
- Toshimi Hadate
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Ryoichi Kawamura
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Yasuharu Tabara
- Graduate School of Public Health, Shizuoka Graduate University of Public Health, Shizuoka, Japan
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Koutatsu Maruyama
- Department of Bioscience, Graduate School of Agriculture, Ehime University, Ehime, Japan
| | - Misaki Takakado
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Yosuke Ikeda
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Yasunori Takata
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Isao Saito
- Department of Public Health and Epidemiology, Faculty of Medicine, Oita University, Oita, Japan
| | - Haruhiko Osawa
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Ehime, Japan.
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Watanabe Y, Ohashi J. Modern Japanese ancestry-derived variants reveal the formation process of the current Japanese regional gradations. iScience 2023; 26:106130. [PMID: 36879818 PMCID: PMC9984562 DOI: 10.1016/j.isci.2023.106130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/02/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Modern Japanese people have two major ancestral populations: indigenous Jomon hunter-gatherers and continental East Asian farmers. To determine the formation process of the current Japanese population, we developed a detection method for variants derived from ancestral populations using a summary statistic, the ancestry marker index (AMI). We applied AMI to modern Japanese population samples and identified 208,648 single nucleotide polymorphisms (SNPs) that were likely derived from the Jomon people (Jomon-derived variants). Analysis of Jomon-derived variants in 10,842 modern Japanese individuals recruited from all over Japan revealed that the admixture proportions of the Jomon people varied between prefectures, probably owing to the prehistoric population size difference. The estimated allele frequencies of genome-wide SNPs in the ancestral populations of the modern Japanese suggested their adaptive phenotypic characteristics to their respective livelihoods. Based on our findings, we propose a formation model for the genotypic and phenotypic gradations of the current Japanese archipelago populations.
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Affiliation(s)
- Yusuke Watanabe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.,Genome Medical Science Project Toyama Project, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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Ikeda Y, Kawamura R, Takata Y, Tabara Y, Maruyama K, Takakado M, Hadate T, Ohashi J, Saito I, Ogawa Y, Osawa H. Resistin G-A haplotype at SNP-420/-358 is associated with the latent sarcopenic obesity index in the toon genome study. J Diabetes Investig 2023; 14:686-694. [PMID: 36897532 PMCID: PMC10119914 DOI: 10.1111/jdi.13998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 01/24/2023] [Accepted: 02/08/2023] [Indexed: 03/11/2023] Open
Abstract
AIM/INTRODUCTION Resistin, which induces insulin resistance, is mainly expressed in monocytes/macrophages in humans. We reported previously that serum resistin was highest in the G-A haplotype defined by resistin single nucleotide polymorphisms (SNPs) at -420 (rs1862513) and - 358 (rs3219175). As sarcopenic obesity is associated with insulin resistance, we aimed to examine whether serum resistin and its haplotypes were associated with sarcopenic obesity at a latent stage. MATERIALS AND METHODS We cross-sectionally analyzed 567 community-dwelling Japanese participants attending annual medical check-ups in which the sarcopenic obesity index was evaluated. The age- and gender-matched normal glucose tolerance subjects with G-A homozygotes and those with C-G homozygotes were examined via RNA-sequencing and pathway analysis (each n = 3), and RT-PCR (each n = 8). RESULTS In multivariate logistic regression analyses, the fourth quartile (Q4) of serum resistin and G-A homozygotes were both associated with the latent sarcopenic obesity index defined by a visceral fat area of ≥ 100 cm2 and grip strength Q1 after adjustment for age and gender, with or without other confounding factors. RNA sequencing and pathway analysis showed that tumor necrosis factor (TNF) was involved in the top five pathways in the whole blood cells of G-A homozygotes compared with C-G homozygotes. RT-PCR revealed that TNF mRNA was higher in G-A homozygotes than in C-G homozygotes. CONCLUSIONS The G-A haplotype was associated with the latent sarcopenic obesity index defined by grip strength in the Japanese cohort, could be mediated by TNF-α.
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Affiliation(s)
- Yosuke Ikeda
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Ryoichi Kawamura
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Yasunori Takata
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Yasuharu Tabara
- Graduate School of Public Health, Shizuoka Graduate University of Public Health, Shizuoka, Japan.,Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Koutatsu Maruyama
- Department of Bioscience, Graduate School of Agriculture, Ehime University, Ehime, Japan
| | - Misaki Takakado
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Toshimi Hadate
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Isao Saito
- Department of Public Health and Epidemiology, Faculty of Medicine, Oita University, Oita, Japan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Haruhiko Osawa
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Ehime, Japan
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Nishida N, Ohashi J, Suda G, Chiyoda T, Tamaki N, Tomiyama T, Ogasawara S, Sugiyama M, Kawai Y, Khor SS, Nagasaki M, Fujimoto A, Tsuchiura T, Ishikawa M, Matsuda K, Yano H, Yoshizumi T, Izumi N, Hasegawa K, Sakamoto N, Mizokami M, Tokunaga K. Prediction Model with HLA-A*33:03 Reveals Number of Days to Develop Liver Cancer from Blood Test. Int J Mol Sci 2023; 24:ijms24054761. [PMID: 36902191 PMCID: PMC10003621 DOI: 10.3390/ijms24054761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
The development of liver cancer in patients with hepatitis B is a major problem, and several models have been reported to predict the development of liver cancer. However, no predictive model involving human genetic factors has been reported to date. For the items incorporated in the prediction model reported so far, we selected items that were significant in predicting liver carcinogenesis in Japanese patients with hepatitis B and constructed a prediction model of liver carcinogenesis by the Cox proportional hazard model with the addition of Human Leukocyte Antigen (HLA) genotypes. The model, which included four items-sex, age at the time of examination, alpha-fetoprotein level (log10AFP) and presence or absence of HLA-A*33:03-revealed an area under the receiver operating characteristic curve (AUROC) of 0.862 for HCC prediction within 1 year and an AUROC of 0.863 within 3 years. A 1000 repeated validation test resulted in a C-index of 0.75 or higher, or sensitivity of 0.70 or higher, indicating that this predictive model can distinguish those at high risk of developing liver cancer within a few years with high accuracy. The prediction model constructed in this study, which can distinguish between chronic hepatitis B patients who develop hepatocellular carcinoma (HCC) early and those who develop HCC late or not, is clinically meaningful.
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Affiliation(s)
- Nao Nishida
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa 272-8516, Japan
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
- Correspondence: ; Tel.: +81-473723501
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Goki Suda
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Hokkaido University, North 15, West 7, Kita-ku, Sapporo 060-8638, Japan
| | - Takehiro Chiyoda
- Hepato-Biliary-Pancreatic Division, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Nobuharu Tamaki
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Musashino 180-8610, Japan
| | - Takahiro Tomiyama
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Sachiko Ogasawara
- Department of Pathology, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Masaya Sugiyama
- Department of Viral Pathogenesis and Controls, National Center for Global Health and Medicine, Ichikawa 272-8516, Japan
| | - Yosuke Kawai
- Genome Medical Science Project-Toyama, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Seik-Soon Khor
- Genome Medical Science Project-Toyama, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Masao Nagasaki
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto 606-8507, Japan
| | - Akihiro Fujimoto
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0003, Japan
| | - Takayo Tsuchiura
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa 272-8516, Japan
| | - Miyuki Ishikawa
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa 272-8516, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Hirohisa Yano
- Department of Pathology, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Tomoharu Yoshizumi
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Namiki Izumi
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Musashino 180-8610, Japan
| | - Kiyoshi Hasegawa
- Hepato-Biliary-Pancreatic Division, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Naoya Sakamoto
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Hokkaido University, North 15, West 7, Kita-ku, Sapporo 060-8638, Japan
| | - Masashi Mizokami
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa 272-8516, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project-Toyama, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
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Nii-Trebi NI, Matsuoka S, Kawana-Tachikawa A, Bonney EY, Abana CZ, Ofori SB, Mizutani T, Ishizaka A, Shiino T, Ohashi J, Naruse TK, Kimura A, Kiyono H, Ishikawa K, Ampofo WK, Matano T. Super high-resolution single-molecule sequence-based typing of HLA class I alleles in HIV-1 infected individuals in Ghana. PLoS One 2022; 17:e0269390. [PMID: 35653364 PMCID: PMC9162337 DOI: 10.1371/journal.pone.0269390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 05/19/2022] [Indexed: 11/18/2022] Open
Abstract
Polymorphisms in human leukocyte antigen (HLA) class I loci are known to have a great impact on disease progression in HIV-1 infection. Prevailing HIV-1 subtypes and HLA genotype distribution are different all over the world, and the HIV-1 and host HLA interaction could be specific to individual areas. Data on the HIV-1 and HLA interaction have been accumulated in HIV-1 subtype B- and C-predominant populations but not fully obtained in West Africa where HIV-1 subtype CRF02_AG is predominant. In the present study, to obtain accurate HLA typing data for analysis of HLA association with disease progression in HIV-1 infection in West African populations, HLA class I (HLA-A, -B, and -C) four-digit allele typing was performed in treatment-naïve HIV-1 infected individuals in Ghana (n = 324) by a super high-resolution single-molecule sequence-based typing (SS-SBT) using next-generation sequencing. Comparison of the SS-SBT-based data with those obtained by a conventional sequencing-based typing (SBT) revealed incorrect assignment of several alleles by SBT. Indeed, HLA-A*23:17, HLA-B*07:06, HLA-C*07:18, and HLA-C*18:02 whose allele frequencies were 2.5%, 0.9%, 4.3%, and 3.7%, respectively, were not determined by SBT. Several HLA alleles were associated with clinical markers, viral load and CD4+ T-cell count. Of note, the impact of HLA-B*57:03 and HLA-B*58:01, known as protective alleles against HIV-1 subtype B and C infection, on clinical markers was not observed in our cohort. This study for the first time presents SS-SBT-based four-digit typing data on HLA-A, -B, and -C alleles in Ghana, describing impact of HLA on viral load and CD4 count in HIV-1 infection. Accumulation of these data would facilitate high-resolution HLA genotyping, contributing to our understanding of the HIV-1 and host HLA interaction in Ghana, West Africa.
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Affiliation(s)
- Nicholas I. Nii-Trebi
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | - Saori Matsuoka
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Evelyn Y. Bonney
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Christopher Z. Abana
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Sampson B. Ofori
- Department of Medicine, Koforidua Government Hospital, Eastern Region, Ghana
| | | | - Aya Ishizaka
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Teiichiro Shiino
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Sciences, University of Tokyo, Tokyo, Japan
| | - Taeko K. Naruse
- Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akinori Kimura
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Institute of Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroshi Kiyono
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Future Medicine Education and Research Organization, Chiba University, Chiba, Japan
- CU-UCSD Center for Mucosal Immunology, Allergy and Vaccines, Department of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Koichi Ishikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - William K. Ampofo
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- * E-mail: (WKA); (TM)
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- * E-mail: (WKA); (TM)
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8
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Nishida N, Sugiyama M, Kawai Y, Naka I, Iwamoto N, Suzuki T, Suzuki M, Miyazato Y, Suzuki S, Izumi S, Hojo M, Tsuchiura T, Ishikawa M, Ohashi J, Ohmagari N, Tokunaga K, Mizokami M. Genetic association of IL17 and the importance of ABO blood group antigens in saliva to COVID-19. Sci Rep 2022; 12:3854. [PMID: 35264675 PMCID: PMC8907215 DOI: 10.1038/s41598-022-07856-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 02/25/2022] [Indexed: 12/14/2022] Open
Abstract
The outbreak of COVID-19 caused by infection with SARS-CoV-2 virus has become a worldwide pandemic, and the number of patients presenting with respiratory failure is rapidly increasing in Japan. An international meta-analysis has been conducted to identify genetic factors associated with the onset and severity of COVID-19, but these factors have yet to be fully clarified. Here, we carried out genomic analysis based on a genome-wide association study (GWAS) in Japanese COVID-19 patients to determine whether genetic factors reported to be associated with the onset or severity of COVID-19 in the international meta-GWAS are replicated in the Japanese population, and whether new genetic factors exist. Although no significant genome-wide association was detected in the Japanese GWAS, an integrated analysis with the international meta-GWAS identified for the first time the involvement of the IL17A/IL17F gene in the severity of COVID-19. Among nine genes reported in the international meta-GWAS as genes involved in the onset of COVID-19, the association of FOXP4-AS1, ABO, and IFNAR2 genes was replicated in the Japanese population. Moreover, combined analysis of ABO and FUT2 genotypes revealed that the presence of oral AB antigens was significantly associated with the onset of COVID-19. FOXP4-AS1 and IFNAR2 were also significantly associated in the integrated analysis of the Japanese GWAS and international meta-GWAS when compared with severe COVID-19 cases and the general population. This made it clear that these two genes were also involved in not only the onset but also the severity of COVID-19. In particular, FOXP4-AS1 was not found to be associated with the severity of COVID-19 in the international meta-GWAS, but an integrated analysis with the Japanese GWAS revealed an association with severity. Individuals with the SNP risk allele found between IL17A and IL17F had significantly lower mRNA expression levels of IL17F, suggesting that activation of the innate immune response by IL17F may play an important role in the severity of SARS-CoV-2 infection.
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Affiliation(s)
- Nao Nishida
- Genome Medical Science Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Chiba, Ichikawa, 272-8516, Japan.
| | - Masaya Sugiyama
- Genome Medical Science Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Chiba, Ichikawa, 272-8516, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Noriko Iwamoto
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Tetsuya Suzuki
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Michiyo Suzuki
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Yusuke Miyazato
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Satoshi Suzuki
- Biobank, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Shinyu Izumi
- Department of Respiratory Medicine, National Center for Global Health and Medicine Hospital, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Masayuki Hojo
- Department of Respiratory Medicine, National Center for Global Health and Medicine Hospital, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Takayo Tsuchiura
- Genome Medical Science Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Chiba, Ichikawa, 272-8516, Japan
| | - Miyuki Ishikawa
- Genome Medical Science Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Chiba, Ichikawa, 272-8516, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Masashi Mizokami
- Genome Medical Science Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Chiba, Ichikawa, 272-8516, Japan
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9
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Kawamura R, Miyao S, Onuma H, Uchigata Y, Kawasaki E, Ohashi J, Shiraishi S, Nishida W, Yokomoto-Umakoshi M, Takata Y, Osawa H, Makino H. Recurrent Hypoglycemia Due to a High Titer of Insulin Antibody in Response to Exogenous Insulin Administration in Two Cases of Type 1 Diabetes. Intern Med 2022; 61:687-695. [PMID: 34471020 PMCID: PMC8943391 DOI: 10.2169/internalmedicine.7647-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the first case, a 60-year-old man who was using continuous subcutaneous insulin infusion (CSII), developed recurrent hypoglycemia due to insulin antibodies. This is the first report of such a case using CSII. In the second case, a 70-year-old man was follow-up case who developed hypoglycemia while using human insulin. In both cases, the hypoglycemia subsided after switching to multiple daily insulin injection and/or insulin preparation. The results of Scatchard analyses of the two cases were similar to those of cases of insulin autoimmune syndrome (IAS) that improved after recovery from hypoglycemia.The clinical characteristics and Scatchard analysis data were essentially the same as those for IAS, except for the presence of insulin administration.
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Affiliation(s)
- Ryoichi Kawamura
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Japan
| | | | - Hiroshi Onuma
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Japan
- Department of Diabetes, Endocrine and Metabolic Disease, Tokyo Women's Medical University Yachiyo Medical Center, Japan
| | | | - Eiji Kawasaki
- Department of Diabetes and Endocrinology, Shin-Koga Hospital, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan
| | | | - Wataru Nishida
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Japan
| | - Maki Yokomoto-Umakoshi
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Japan
| | - Yasunori Takata
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Japan
| | - Haruhiko Osawa
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Japan
| | - Hideichi Makino
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Japan
- Shiraishi Hospital Diabetes Center, Japan
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10
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Koga M, Senkoji T, Kubota M, Ishizaka A, Mizutani T, Sedohara A, Ikeuchi K, Kikuchi T, Adachi E, Saito M, Koibuchi T, Hosomichi K, Ohashi J, Kawana-Tachikawa A, Matano T, Tsutsumi T, Yotsuyanagi H. Predictors associated with a better response to the Japanese aluminum-free hepatitis A vaccine, Aimmugen ® , for people living with HIV. Hepatol Res 2022; 52:227-234. [PMID: 34825436 DOI: 10.1111/hepr.13736] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/14/2021] [Accepted: 11/23/2021] [Indexed: 12/13/2022]
Abstract
AIM After the hepatitis A virus (HAV) outbreak among men who have sex with men (MSM) around 2018, the importance of HAV vaccination was emphasized, especially for MSM-living with human immunodeficiency virus (MSM-LWHIV). Aimmugen® is licensed and distributed exclusively in Japan. While administration of three doses is recommended, 85% of recipients in the general population were reported to acquire seroprotection after the second dose. In this study, we evaluated the efficacy of two or three vaccine doses along with predictors associated with the response to Aimmugen® in MSM-LWHIV. METHODS We retrospectively examined anti-HA-IgG titers of MSM-LWHIV vaccinated with Aimmugen® in our hospital. Patients' data were collected from medical records. RESULTS Between January 2018 and October 2019, 141 subjects whose median age was 46 years old, were examined. All the subjects were on antiretroviral therapy (ART) and the median CD4 count was 615/μL. The acquisition rate of protectable anti-HA-IgG titers after the second and third dose was 71.1% and 98.6%, respectively. In 114 subjects whose anti-HA-IgG titers were tested after the second-dose, factors significantly associated with better response were prolonged ART duration and higher CD4 count. The titers of anti-HA-IgG after the third dose were higher in those who became seropositive after the second-dose than those who did not. CONCLUSIONS Three-dose of Aimmugen® for MSM-LWHIV was effective while two-dose was less effective compared to non-HIV-infected people. People-LWHIV with shorter duration of ART and lesser CD4 cell count achieved lower titers of anti-HA-IgG and might require an additional vaccination.
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Affiliation(s)
- Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Tomoe Senkoji
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Megumi Kubota
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Aya Ishizaka
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Taketoshi Mizutani
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Ayako Sedohara
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Kazuhiko Ikeuchi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Tadashi Kikuchi
- Department of Infectious Diseases and Applied Immunology, Hospital of the Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Eisuke Adachi
- Department of Infectious Diseases and Applied Immunology, Hospital of the Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Makoto Saito
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Tomohiko Koibuchi
- Department of Infectious Diseases and Applied Immunology, Hospital of the Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | | | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Department of Infectious Diseases and Applied Immunology, Hospital of the Institute of Medical Science, University of Tokyo, Tokyo, Japan
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11
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Maharani N, Soetadji A, Utari A, Naka I, Ohashi J, Mexitalia M. Cytochrome b-245 Alpha Chain Gene Variants and Arterial Function in Indonesian Short Stature Children. Cardiol Res 2022; 12:351-357. [PMID: 34970365 PMCID: PMC8683098 DOI: 10.14740/cr1314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/05/2021] [Indexed: 11/11/2022] Open
Abstract
Background The association between short stature, undernutrition and the risk to cardiovascular disease has been clinically established. Genetic factor, particularly the variants in cytochrome b-245 alpha chain (CYBA) gene, which alter the formation of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase level, might affect arterial function. This study aimed to observe the association between single nucleotide variants (SNVs) of the CYBA gene and the arterial function of short stature children to understand the reason why some people with short stature develop cardiovascular disease. Methods A total of 142 genomic deoxyribonucleic acid (DNA) samples have been collected from short stature children in Brebes, Central Java, Indonesia. Four common single-nucleotide polymorphisms (SNPs): C242T (rs4673), A640G (rs1049255), -930A>G (rs9932581) and *49A>G (rs7195830) in the CYBA gene were examined using TaqMan allelic discrimination assay. The arterial function was measured using transthoracic echocardiography and described as aortic stiffness and distensibility index. Statistical analysis was done to find a significant difference in arterial function between genotypes of each SNV. Results A P-value of < 0.05 was considered significant. In rs9932581 (-930A>G) of CYBA gene, the subjects with GG genotype were found to have significantly lower arterial stiffness and higher distensibility compared to AA and AG genotypes. No significant difference was found in the other SNVs. Conclusion The GG genotype in rs9932581 of the CYBA gene might have a protective effect on cardiovascular disease in short stature children.
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Affiliation(s)
- Nani Maharani
- Center for Biomedical Research, Faculty of Medicine, Universitas Diponegoro, Semarang, Indonesia.,Department of Pharmacology and Therapy, Faculty of Medicine, Universitas Diponegoro, Semarang, Indonesia
| | - Anindita Soetadji
- Department of Pediatrics, Faculty of Medicine, Universitas Diponegoro/Dr Kariadi Hospital, Semarang, Indonesia
| | - Agustini Utari
- Center for Biomedical Research, Faculty of Medicine, Universitas Diponegoro, Semarang, Indonesia.,Department of Pediatrics, Faculty of Medicine, Universitas Diponegoro/Dr Kariadi Hospital, Semarang, Indonesia
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Maria Mexitalia
- Department of Pediatrics, Faculty of Medicine, Universitas Diponegoro/Dr Kariadi Hospital, Semarang, Indonesia
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12
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Isshiki M, Naka I, Kimura R, Nishida N, Furusawa T, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Inaoka T, Matsumura Y, Ohtsuka R, Ohashi J. Admixture with indigenous people helps local adaptation: admixture-enabled selection in Polynesians. BMC Ecol Evol 2021; 21:179. [PMID: 34551727 PMCID: PMC8456657 DOI: 10.1186/s12862-021-01900-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 08/25/2021] [Indexed: 01/08/2023] Open
Abstract
Background Homo sapiens have experienced admixture many times in the last few thousand years. To examine how admixture affects local adaptation, we investigated genomes of modern Polynesians, who are shaped through admixture between Austronesian-speaking people from Southeast Asia (Asian-related ancestors) and indigenous people in Near Oceania (Papuan-related ancestors). Methods In this study local ancestry was estimated across the genome in Polynesians (23 Tongan subjects) to find the candidate regions of admixture-enabled selection contributed by Papuan-related ancestors. Results The mean proportion of Papuan-related ancestry across the Polynesian genome was estimated as 24.6% (SD = 8.63%), and two genomic regions, the extended major histocompatibility complex (xMHC) region on chromosome 6 and the ATP-binding cassette transporter sub-family C member 11 (ABCC11) gene on chromosome 16, showed proportions of Papuan-related ancestry more than 5 SD greater than the mean (> 67.8%). The coalescent simulation under the assumption of selective neutrality suggested that such signals of Papuan-related ancestry enrichment were caused by positive selection after admixture (false discovery rate = 0.045). The ABCC11 harbors a nonsynonymous SNP, rs17822931, which affects apocrine secretory cell function. The approximate Bayesian computation indicated that, in Polynesian ancestors, a strong positive selection (s = 0.0217) acted on the ancestral allele of rs17822931 derived from Papuan-related ancestors. Conclusions Our results suggest that admixture with Papuan-related ancestors contributed to the rapid local adaptation of Polynesian ancestors. Considering frequent admixture events in human evolution history, the acceleration of local adaptation through admixture should be a common event in humans. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01900-y.
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Affiliation(s)
- Mariko Isshiki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, 903-0125, Japan
| | - Nao Nishida
- Genome Medical Science Project, Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, 272-8516, Japan
| | - Takuro Furusawa
- Graduate School of Asian and African Area Studies, Kyoto University, Kyoto, 606-8501, Japan
| | - Kazumi Natsuhara
- Department of International Health and Nursing, Faculty of Nursing, Toho University, Tokyo, 143-0015, Japan
| | - Taro Yamauchi
- Faculty of Health Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Minato Nakazawa
- Graduate School of Health Sciences, Kobe University, Kobe, 654-0142, Japan
| | - Takafumi Ishida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Tsukasa Inaoka
- Department of Human Ecology, Faculty of Agriculture, Saga University, Saga, 840-8502, Japan
| | - Yasuhiro Matsumura
- Faculty of Health and Nutrition, Bunkyo University, Chigasaki, 253-8550, Japan
| | | | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
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13
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Kim J, Jeon S, Choi JP, Blazyte A, Jeon Y, Kim JI, Ohashi J, Tokunaga K, Sugano S, Fucharoen S, Al-Mulla F, Bhak J. The Origin and Composition of Korean Ethnicity Analyzed by Ancient and Present-Day Genome Sequences. Genome Biol Evol 2021; 12:553-565. [PMID: 32219389 PMCID: PMC7250502 DOI: 10.1093/gbe/evaa062] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2020] [Indexed: 01/08/2023] Open
Abstract
Koreans are thought to be an ethnic group of admixed northern and southern subgroups. However, the exact genetic origins of these two remain unclear. In addition, the past admixture is presumed to have taken place on the Korean peninsula, but there is no genomic scale analysis exploring the origin, composition, admixture, or the past migration of Koreans. Here, 88 Korean genomes compared with 91 other present-day populations showed two major genetic components of East Siberia and Southeast Asia. Additional paleogenomic analysis with 115 ancient genomes from Pleistocene hunter-gatherers to Iron Age farmers showed a gradual admixture of Tianyuan (40 ka) and Devil’s gate (8 ka) ancestries throughout East Asia and East Siberia up until the Neolithic era. Afterward, the current genetic foundation of Koreans may have been established through a rapid admixture with ancient Southern Chinese populations associated with Iron Age Cambodians. We speculate that this admixing trend initially occurred mostly outside the Korean peninsula followed by continuous spread and localization in Korea, corresponding to the general admixture trend of East Asia. Over 70% of extant Korean genetic diversity is explained to be derived from such a recent population expansion and admixture from the South.
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Affiliation(s)
- Jungeun Kim
- Personal Genomics Institute (PGI), Genome Research Foundation, Osong, Republic of Korea
| | - Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Jae-Pil Choi
- Personal Genomics Institute (PGI), Genome Research Foundation, Osong, Republic of Korea
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Yeonsu Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Jong-Il Kim
- Department of Archaeology and Art History, Seoul National University, Republic of Korea
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Medicine, The University of Tokyo, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Japan
| | - Suthat Fucharoen
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakorn Pathom, Thailand
| | - Fahd Al-Mulla
- Center of Genomic Medicine, Kuwait University, Kuwait
| | - Jong Bhak
- Personal Genomics Institute (PGI), Genome Research Foundation, Osong, Republic of Korea.,Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.,Clinomics Inc, Ulsan, Republic of Korea
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14
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Anzurez A, Naka I, Miki S, Nakayama-Hosoya K, Isshiki M, Watanabe Y, Nakamura-Hoshi M, Seki S, Matsumura T, Takano T, Onodera T, Adachi Y, Moriyama S, Terahara K, Tachikawa N, Yoshimura Y, Sasaki H, Horiuchi H, Miyata N, Miyazaki K, Koga M, Ikeuchi K, Nagai H, Saito M, Adachi E, Yotsuyanagi H, Kutsuna S, Kawashima A, Miyazato Y, Kinoshita N, Kouno C, Tanaka K, Takahashi Y, Suzuki T, Matano T, Ohashi J, Kawana-Tachikawa A. Association of HLA-DRB1*09:01 with severe COVID-19. HLA 2021; 98:37-42. [PMID: 33734601 PMCID: PMC8251239 DOI: 10.1111/tan.14256] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/17/2021] [Accepted: 03/09/2021] [Indexed: 01/06/2023]
Abstract
HLA‐A, ‐C, ‐B, and ‐DRB1 genotypes were analyzed in 178 Japanese COVID‐19 patients to investigate the association of HLA with severe COVID‐19. Analysis of 32 common HLA alleles at four loci revealed a significant association between HLA‐DRB1*09:01 and severe COVID‐19 (odds ratio [OR], 3.62; 95% CI, 1.57–8.35; p = 0.00251 [permutation p value = 0.0418]) when age, sex, and other common HLA alleles at the DRB1 locus were adjusted. The DRB1*09:01 allele was more significantly associated with risk for severe COVID‐19 compared to preexisting medical conditions such as hypertension, diabetes, and cardiovascular diseases. These results indicate a potential role for HLA in predisposition to severe COVID‐19.
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Affiliation(s)
- Alitzel Anzurez
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan.,Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Shoji Miki
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Mariko Isshiki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Yusuke Watanabe
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | | | - Sayuri Seki
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takayuki Matsumura
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomohiro Takano
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Taishi Onodera
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yu Adachi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Saya Moriyama
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazutaka Terahara
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Natsuo Tachikawa
- Department of Infectious Diseases, Yokohama Municipal Citizens' Hospital, Kanagawa, Japan
| | - Yoshihiro Yoshimura
- Department of Infectious Diseases, Yokohama Municipal Citizens' Hospital, Kanagawa, Japan
| | - Hiroaki Sasaki
- Department of Infectious Diseases, Yokohama Municipal Citizens' Hospital, Kanagawa, Japan
| | - Hiroshi Horiuchi
- Department of Infectious Diseases, Yokohama Municipal Citizens' Hospital, Kanagawa, Japan
| | - Nobuyuki Miyata
- Department of Infectious Diseases, Yokohama Municipal Citizens' Hospital, Kanagawa, Japan
| | - Kazuhito Miyazaki
- Department of Infectious Diseases, Yokohama Municipal Citizens' Hospital, Kanagawa, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Kazuhiko Ikeuchi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Hiroyuki Nagai
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Makoto Saito
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Eisuke Adachi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Satoshi Kutsuna
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Akira Kawashima
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yusuke Miyazato
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Noriko Kinoshita
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | | | | | - Yoshimasa Takahashi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan.,Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Department of AIDS Vaccine Development, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan.,Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Department of AIDS Vaccine Development, Institute of Medical Science, University of Tokyo, Tokyo, Japan
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15
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Nishida N, Sugiyama M, Ohashi J, Kawai Y, Khor SS, Nishina S, Yamasaki K, Yazaki H, Okudera K, Tamori A, Eguchi Y, Sakai A, Kakisaka K, Sawai H, Tsuchiura T, Ishikawa M, Hino K, Sumazaki R, Takikawa Y, Kanda T, Yokosuka O, Yatsuhashi H, Tokunaga K, Mizokami M. Importance of HBsAg recognition by HLA molecules as revealed by responsiveness to different hepatitis B vaccines. Sci Rep 2021; 11:3703. [PMID: 33654122 PMCID: PMC7925550 DOI: 10.1038/s41598-021-82986-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/25/2021] [Indexed: 12/17/2022] Open
Abstract
Hepatitis B (HB) vaccines (Heptavax-II and Bimmugen) designed based on HBV genotypes A and C are mainly used for vaccination against HB in Japan. To determine whether there are differences in the genetic background associated with vaccine responsiveness, genome-wide association studies were performed on 555 Heptavax-II and 1193 Bimmugen recipients. Further HLA imputation and detailed analysis of the association with HLA genes showed that two haplotypes, DRB1*13:02-DQB1*06:04 and DRB1*04:05-DQB1*04:01, were significantly associated in comparison with high-responders (HBsAb > 100 mIU/mL) for the two HB vaccines. In particular, HLA-DRB1*13:02-DQB1*06:04 haplotype is of great interest in the sense that it could only be detected by direct analysis of the high-responders in vaccination with Heptavax-II or Bimmugen. Compared with healthy controls, DRB1*13:02-DQB1*06:04 was significantly less frequent in high-responders when vaccinated with Heptavax-II, indicating that high antibody titers were less likely to be obtained with Heptavax-II. As Bimmugen and Heptavax-II tended to have high and low vaccine responses to DRB1*13:02, 15 residues were found in the Heptavax-II-derived antigenic peptide predicted to have the most unstable HLA-peptide binding. Further functional analysis of selected hepatitis B patients with HLA haplotypes identified in this study is expected to lead to an understanding of the mechanisms underlying liver disease.
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Affiliation(s)
- Nao Nishida
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa, 272-8516, Japan.
| | - Masaya Sugiyama
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa, 272-8516, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, 113-0033, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa, 272-8516, Japan
| | - Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa, 272-8516, Japan
| | - Sohji Nishina
- Department of Hepatology and Pancreatology, Kawasaki Medical School, Okayama, 701-0192, Japan
| | - Kazumi Yamasaki
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, 856-8562, Japan
| | - Hirohisa Yazaki
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa, 272-8516, Japan
| | - Kaori Okudera
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa, 272-8516, Japan
| | - Akihiro Tamori
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka, 558-8585, Japan
| | - Yuichiro Eguchi
- Division of Hepatology, Saga Medical School, Saga, 840-8502, Japan
| | - Aiko Sakai
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa, 272-8516, Japan.,Department of Child Health, Faculty of Medicine, University of Tsukuba, Tsukuba, 305-8577, Japan
| | - Keisuke Kakisaka
- Division of Hepatology, Department of Internal Medicine, Iwate Medical University, Yahaba-cho, 028-3694, Japan
| | - Hiromi Sawai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, 113-0033, Japan
| | - Takayo Tsuchiura
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa, 272-8516, Japan
| | - Miyuki Ishikawa
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa, 272-8516, Japan
| | - Keisuke Hino
- Department of Hepatology and Pancreatology, Kawasaki Medical School, Okayama, 701-0192, Japan
| | - Ryo Sumazaki
- Department of Child Health, Faculty of Medicine, University of Tsukuba, Tsukuba, 305-8577, Japan
| | - Yasuhiro Takikawa
- Division of Hepatology, Department of Internal Medicine, Iwate Medical University, Yahaba-cho, 028-3694, Japan
| | - Tatsuo Kanda
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Itabashi-ku, 173-8610, Japan
| | - Osamu Yokosuka
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Japan Community Health Care Organization Funabashi Central Hospital, Funabashi, 273-8556, Japan
| | - Hiroshi Yatsuhashi
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, 856-8562, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa, 272-8516, Japan
| | - Masashi Mizokami
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa, 272-8516, Japan
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16
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Hirayasu K, Sun J, Hasegawa G, Hashikawa Y, Hosomichi K, Tajima A, Tokunaga K, Ohashi J, Hanayama R. Characterization of LILRB3 and LILRA6 allelic variants in the Japanese population. J Hum Genet 2021; 66:739-748. [PMID: 33526815 DOI: 10.1038/s10038-021-00906-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/16/2021] [Accepted: 01/17/2021] [Indexed: 11/09/2022]
Abstract
Leukocyte immunoglobulin (Ig)-like receptors (LILRs) are encoded by members of a human multigene family, comprising 11 protein-coding genes and two pseudogenes. Among the LILRs, LILRB3 and LILRA6 show the highest homology with each other, along with high allelic and copy number variations. Therefore, it has been difficult to discriminate between them, both genetically and functionally, precluding disease association studies of LILRB3 and LILRA6. In this study, we carefully performed variant screening of LILRB3 and LILRA6 by cDNA cloning from Japanese individuals and identified four allelic lineages showing significantly high non-synonymous-to-synonymous ratios in pairwise comparisons. Furthermore, the extracellular domains of the LILRB3*JP6 and LILRA6*JP1 alleles were identical at the DNA level, suggesting that gene conversion-like events diversified LILRB3 and LILRA6. To determine the four allelic lineages from genomic DNA, we established a lineage typing method that accurately estimated the four allelic lineages in addition to specific common alleles from genomic DNA. Analysis of LILRA6 copy number variation revealed one, two, and three copies of LILRA6 in the Japanese-in-Tokyo (JPT) population. Flow cytometric analysis showed that an anti-LILRB3 antibody did not recognize the second most common lineage in the Japanese population, indicating significant amino acid differences across the allelic lineages. Taken together, our findings indicate that our lineage typing is useful for classifying the lineage-specific functions of LILRB3 and LILRA6, serving as the basis for disease association studies.
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Affiliation(s)
- Kouyuki Hirayasu
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Ishikawa, Japan. .,Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan.
| | - Jinwen Sun
- Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Gen Hasegawa
- Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Yuko Hashikawa
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Ishikawa, Japan
| | - Kazuyoshi Hosomichi
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Ishikawa, Japan.,Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Atsushi Tajima
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Ishikawa, Japan.,Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Rikinari Hanayama
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Ishikawa, Japan.,Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan.,WPI Nano Life Science Institute (NanoLSI), Kanazawa University, Kakuma, Kanazawa, Ishikawa, Japan
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17
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Mizuno F, Naka I, Ueda S, Ohashi J, Kurosaki K. The number of SNPs required for distinguishing Japanese from other East Asians. Leg Med (Tokyo) 2021; 49:101849. [PMID: 33485062 DOI: 10.1016/j.legalmed.2021.101849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 09/16/2020] [Accepted: 01/10/2021] [Indexed: 11/25/2022]
Abstract
In some cases, it is necessary to estimate the national origin of an unknown subject in forensic medicine. The use of single nucleotide polymorphism (SNP) markers appears to be very effective for this purpose, since genome-wide SNP genotype data of many human populations are publicly available. In this study, we examined the number of SNPs that could objectively and accurately distinguish Japanese subjects (1KG-JPT) from the other East Asians (1KG-CDX, -CHB, -CHS, and -KHV) using the combination of principal component analysis and hierarchical cluster analysis. A computer simulation showed that approximately 3000 randomly selected SNPs were enough for the discrimination. Our results suggest that at least a 0.024% coverage is needed in the next generation sequencing experiment to objectively determine whether an unknown person is Japanese or not if the amount of DNA sample from him/her is insufficient or the quality is low.
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Affiliation(s)
- Fuzuki Mizuno
- Department of Legal Medicine, Toho University School of Medicine, Japan
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan
| | - Shintaroh Ueda
- Department of Legal Medicine, Toho University School of Medicine, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan.
| | - Kunihiko Kurosaki
- Department of Legal Medicine, Toho University School of Medicine, Japan.
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18
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Miotto O, Sekihara M, Tachibana SI, Yamauchi M, Pearson RD, Amato R, Gonçalves S, Mehra S, Noviyanti R, Marfurt J, Auburn S, Price RN, Mueller I, Ikeda M, Mori T, Hirai M, Tavul L, Hetzel MW, Laman M, Barry AE, Ringwald P, Ohashi J, Hombhanje F, Kwiatkowski DP, Mita T. Emergence of artemisinin-resistant Plasmodium falciparum with kelch13 C580Y mutations on the island of New Guinea. PLoS Pathog 2020; 16:e1009133. [PMID: 33320907 PMCID: PMC7771869 DOI: 10.1371/journal.ppat.1009133] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 12/29/2020] [Accepted: 11/05/2020] [Indexed: 12/22/2022] Open
Abstract
The rapid and aggressive spread of artemisinin-resistant Plasmodium falciparum carrying the C580Y mutation in the kelch13 gene is a growing threat to malaria elimination in Southeast Asia, but there is no evidence of their spread to other regions. We conducted cross-sectional surveys in 2016 and 2017 at two clinics in Wewak, Papua New Guinea (PNG) where we identified three infections caused by C580Y mutants among 239 genotyped clinical samples. One of these mutants exhibited the highest survival rate (6.8%) among all parasites surveyed in ring-stage survival assays (RSA) for artemisinin. Analyses of kelch13 flanking regions, and comparisons of deep sequencing data from 389 clinical samples from PNG, Indonesian Papua and Western Cambodia, suggested an independent origin of the Wewak C580Y mutation, showing that the mutants possess several distinctive genetic features. Identity by descent (IBD) showed that multiple portions of the mutants’ genomes share a common origin with parasites found in Indonesian Papua, comprising several mutations within genes previously associated with drug resistance, such as mdr1, ferredoxin, atg18 and pnp. These findings suggest that a P. falciparum lineage circulating on the island of New Guinea has gradually acquired a complex ensemble of variants, including kelch13 C580Y, which have affected the parasites’ drug sensitivity. This worrying development reinforces the need for increased surveillance of the evolving parasite populations on the island, to contain the spread of resistance. Artemisinin is the most widely used drug against Plasmodium falciparum malaria. In southeast Asia, parasites have evolved genetic changes making them resistant to artemisinin. The elimination of resistant strains is a global priority, since their global spread could result in massive loss of lives. In Papua New Guinea, we found three patients infected with parasites carrying the most widespread resistant variant in southeast Asia, and they were confirmed to be artemisinin resistant. We established that the mutations were not imported from southeast Asia, and found other drug resistance variants in their genetic background, including some shared with parasites in Indonesia. This indicates that artemisinin resistance has emerged in New Guinea separately from southeast Asia, not by a chance event, but by a gradual process of evolution which may still be ongoing undetected on the island. These resistant strains could undermine malaria local control efforts, and constitute a global threat.
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Affiliation(s)
- Olivo Miotto
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- * E-mail: (OM); (TM)
| | - Makoto Sekihara
- Department of Tropical Medicine and Parasitology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Shin-Ichiro Tachibana
- Department of Tropical Medicine and Parasitology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Masato Yamauchi
- Department of Tropical Medicine and Parasitology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Richard D. Pearson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | | | - Somya Mehra
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | | | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Sarah Auburn
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Ric N. Price
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Ivo Mueller
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Mie Ikeda
- Department of Tropical Medicine and Parasitology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Toshiyuki Mori
- Department of Tropical Medicine and Parasitology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Makoto Hirai
- Department of Tropical Medicine and Parasitology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Manuel W. Hetzel
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Moses Laman
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Alyssa E. Barry
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, Australia
- Burnet Institute, Melbourne, Australia
| | | | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Francis Hombhanje
- Centre for Health Research & Diagnostics, Divine Word University, Madang, Papua New Guinea
| | - Dominic P. Kwiatkowski
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Toshihiro Mita
- Department of Tropical Medicine and Parasitology, Juntendo University Faculty of Medicine, Tokyo, Japan
- * E-mail: (OM); (TM)
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19
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Arayasongsak U, Naka I, Ohashi J, Patarapotikul J, Nuchnoi P, Kalambaheti T, Sa-Ngasang A, Chanama S, Chaorattanakawee S. Genetic association study of interferon lambda 3, CD27, and human leukocyte antigen-DPB1 with dengue severity in Thailand. BMC Infect Dis 2020; 20:948. [PMID: 33308178 PMCID: PMC7731073 DOI: 10.1186/s12879-020-05636-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Dengue patients develop different disease severity ranging from mild (dengue fever [DF]) to severe forms (dengue hemorrhagic fever [DHF] and the fatal dengue shock syndrome [DSS]). Host genetics are considered to be one factor responsible for the severity of dengue outcomes. To identify genes associated with dengue severity that have not been studied yet, we performed genetic association analyses of interferon lambda 3 (IFNL3), CD27, and human leukocyte antigen-DPB1 (HLA-DPB1) genes in Thai dengue patients. METHODS A case-control association study was performed in 877 children (age ≤ 15 years) with dengue infection (DF, n = 386; DHF, n = 416; DSS, n = 75). A candidate single nucleotide polymorphism of each of IFNL3, CD27, and HLA-DPB1 was selected to be analyzed. Genotyping was performed by TaqMan real-time PCR assay, and the association with dengue severity was examined. RESULTS The rs9277534 variant of HLA-DPB1 was weakly associated with DHF. The genotype GG and G allele conferred protection against DHF (p = 0.04, odds ratio 0.74 for GG genotype, p = 0.03, odds ratio 0.79 for G allele). The association became borderline significant after adjusting for confounders (p = 0.05, odds ratio 0.82). No association was detected for IFNL3 or CD27. CONCLUSIONS The present study demonstrated the weak association of the rs9277534 variant of HLA-DPB1 with protection against DHF. This variant is in the 3' untranslated region and affects HLA-DPB1 surface protein expression. Our finding suggests that HLA-DPB1 may be involved in DHF pathogenesis.
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Affiliation(s)
- Unchana Arayasongsak
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Bangkok, 10400, Thailand
| | - Izumi Naka
- Laboratory of Human Genome Diversity, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Jun Ohashi
- Laboratory of Human Genome Diversity, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Jintana Patarapotikul
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Bangkok, 10400, Thailand
| | - Pornlada Nuchnoi
- Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Thareerat Kalambaheti
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Bangkok, 10400, Thailand
| | - Areerat Sa-Ngasang
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Sumalee Chanama
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Suwanna Chaorattanakawee
- Department of Parasitology and Entomology, Faculty of Public Health, Mahidol University, Ratchawithi Road, Bangkok, 10400, Thailand.
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20
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Watanabe Y, Isshiki M, Ohashi J. Prefecture-level population structure of the Japanese based on SNP genotypes of 11,069 individuals. J Hum Genet 2020; 66:431-437. [PMID: 33051579 DOI: 10.1038/s10038-020-00847-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 11/09/2022]
Abstract
We analyzed genome-wide single-nucleotide polymorphism data of 11,069 Japanese individuals recruited from all 47 prefectures of Japan to clarify their genetic structure. The principal component analysis at the prefectural level enabled us to study the relationship between geographical location and genetic differentiation. The results revealed that the mainland Japanese were not genetically homogeneous, and the genetic structure could be explained mainly by the degree of Jomon ancestry and the geographical location. One of the interesting findings was that individuals in the Shikoku region (i.e., Tokushima Prefecture, Kagawa Prefecture, Ehime Prefecture, and Kochi Prefecture) were genetically close to Han Chinese. Therefore, the genetic components of immigrants from continental East Asia in the Yayoi period may have been well maintained in Shikoku. The present results will be useful for understanding the peopling of Japan, and also provide suggestions for recruiting subjects in genetic association studies.
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Affiliation(s)
- Yusuke Watanabe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.,Genome Medical Science Project Toyama Project, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Mariko Isshiki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
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21
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Liu X, Kosugi S, Koide R, Kawamura Y, Ito J, Miura H, Matoba N, Matsuzaki M, Fujita M, Kamada AJ, Nakagawa H, Tamiya G, Matsuda K, Murakami Y, Kubo M, Aswad A, Sato K, Momozawa Y, Ohashi J, Terao C, Yoshikawa T, Parrish NF, Kamatani Y. Endogenization and excision of human herpesvirus 6 in human genomes. PLoS Genet 2020; 16:e1008915. [PMID: 32776928 PMCID: PMC7444522 DOI: 10.1371/journal.pgen.1008915] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/20/2020] [Accepted: 06/07/2020] [Indexed: 12/12/2022] Open
Abstract
Sequences homologous to human herpesvirus 6 (HHV-6) are integrated within the nuclear genome of about 1% of humans, but it is not clear how this came about. It is also uncertain whether integrated HHV-6 can reactivate into an infectious virus. HHV-6 integrates into telomeres, and this has recently been associated with polymorphisms affecting MOV10L1. MOV10L1 is located on the subtelomere of chromosome 22q (chr22q) and is required to make PIWI-interacting RNAs (piRNAs). As piRNAs block germline integration of transposons, piRNA-mediated repression of HHV-6 integration has been proposed to explain this association. In vitro, recombination of the HHV-6 genome along its terminal direct repeats (DRs) leads to excision from the telomere and viral reactivation, but the expected "solo-DR scar" has not been described in vivo. Here we screened for integrated HHV-6 in 7,485 Japanese subjects using whole-genome sequencing (WGS). Integrated HHV-6 was associated with polymorphisms on chr22q. However, in contrast to prior work, we find that the reported MOV10L1 polymorphism is physically linked to an ancient endogenous HHV-6A variant integrated into the telomere of chr22q in East Asians. Unexpectedly, an HHV-6B variant has also endogenized in chr22q; two endogenous HHV-6 variants at this locus thus account for 72% of all integrated HHV-6 in Japan. We also report human genomes carrying only one portion of the HHV-6B genome, a solo-DR, supporting in vivo excision and possible viral reactivation. Together these results explain the recently-reported association between integrated HHV-6 and MOV10L1/piRNAs, suggest potential exaptation of HHV-6 in its coevolution with human chr22q, and clarify the evolution and risk of reactivation of the only intact (non-retro)viral genome known to be present in human germlines.
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Affiliation(s)
- Xiaoxi Liu
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research and RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shunichi Kosugi
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Rie Koide
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research and RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroki Miura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Nana Matoba
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Motomichi Matsuzaki
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Anselmo Jiro Kamada
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research and RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Gen Tamiya
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Koichi Matsuda
- Laboratory of Molecular Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Laboratory for Clinical Genome Sequencing, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Amr Aswad
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Nicholas F. Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research and RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- * E-mail:
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Complex Trait Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Japan
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22
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Okamura K, Abe Y, Naka I, Ohashi J, Yagami A, Matsunaga K, Kobayashi Y, Fukai K, Tanemura A, Katayama I, Masui Y, Ito A, Yamashita T, Nagai H, Nishigori C, Oiso N, Aoyama Y, Araki Y, Saito T, Hayashi M, Hozumi Y, Suzuki T. Genome-wide association study identifies CDH13 as a susceptibility gene for rhododendrol-induced leukoderma. Pigment Cell Melanoma Res 2020; 33:826-833. [PMID: 32558222 DOI: 10.1111/pcmr.12904] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/30/2020] [Accepted: 06/09/2020] [Indexed: 11/28/2022]
Abstract
Racemic RS-4-(4-hydroxyphenyl)-2-butanol (rhododendrol; trade name: Rhododenol [RD]), which is used in topical skin-lightening cosmetics, was unexpectedly reported in Japan to induce leukoderma or vitiligo called RD-induced leukoderma (RIL) after repeated application. To our knowledge, no studies have investigated chemical-induced vitiligo pathogenesis on a genome-wide scale. Here, we conducted a genome-wide association study (GWAS) for 147 cases and 112 controls. CDH13, encoding a glycosylphosphatidylinositol-anchored protein called T-cadherin (T-cad), was identified as the strongest RIL susceptibility gene. RD sensitivity was remarkably increased by T-cad knockdown in cultured normal human melanocytes. Furthermore, we confirmed tyrosinase upregulation and downregulation of the anti-apoptotic molecules (BCL-2 and BCL-XL), suggesting that T-cad is associated with RD via tyrosinase or apoptotic pathway regulation. Finally, monobenzyl ether of hydroquinone sensitivity also tended to increase with T-cad knockdown, suggesting that the T-cad could be a candidate susceptibility gene for RIL and other chemical-induced vitiligo forms. This is the first GWAS for chemical-induced vitiligo, and it could be a useful model for studying the disease's genetic aspects.
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Affiliation(s)
- Ken Okamura
- Department of Dermatology, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Yuko Abe
- Department of Dermatology, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Akiko Yagami
- Department of Dermatology, Fujita Health University School of Medicine, Aichi, Japan.,Department of Allergology, Fujita Health University School of Medicine, Aichi, Japan
| | - Kayoko Matsunaga
- Department of Dermatology, Fujita Health University School of Medicine, Aichi, Japan.,Department of Integrative Medical Science for Allergic Disease, Fujita Health University School of Medicine, Aichi, Japan
| | - Yui Kobayashi
- Department of Dermatology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Kazuyoshi Fukai
- Department of Dermatology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Atsushi Tanemura
- Department of Dermatology, Course of Integrated Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Ichiro Katayama
- Department of Dermatology, Course of Integrated Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan.,Department of Pigmentation Research and Therapeutics, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Yukiko Masui
- Division of Dermatology, Nagata Clinic, Niigata, Japan.,Department of Dermatology, Niigata University Graduate School of Medicine and Dental Sciences, Niigata, Japan
| | - Akiko Ito
- Division of Dermatology, Nagata Clinic, Niigata, Japan.,Department of Dermatology, Niigata University Graduate School of Medicine and Dental Sciences, Niigata, Japan
| | - Toshiharu Yamashita
- Department of Dermatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroshi Nagai
- Division of Dermatology, Department of Internal Related, Graduate School of Medicine, Kobe University, Hyogo, Japan
| | - Chikako Nishigori
- Division of Dermatology, Department of Internal Related, Graduate School of Medicine, Kobe University, Hyogo, Japan
| | - Naoki Oiso
- Department of Dermatology, Faculty of Medicine, Kinki University, Osaka, Japan
| | - Yumi Aoyama
- Department of Dermatology, Kawasaki Medical School, Okayama, Japan
| | - Yuta Araki
- Department of Dermatology, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Toru Saito
- Department of Dermatology, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Masahiro Hayashi
- Department of Dermatology, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Yutaka Hozumi
- Department of Dermatology, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Tamio Suzuki
- Department of Dermatology, Faculty of Medicine, Yamagata University, Yamagata, Japan
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23
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Isshiki M, Naka I, Watanabe Y, Nishida N, Kimura R, Furusawa T, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Eddie R, Ohtsuka R, Ohashi J. Admixture and natural selection shaped genomes of an Austronesian-speaking population in the Solomon Islands. Sci Rep 2020; 10:6872. [PMID: 32327716 PMCID: PMC7181741 DOI: 10.1038/s41598-020-62866-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/16/2020] [Indexed: 11/24/2022] Open
Abstract
People in the Solomon Islands today are considered to have derived from Asian- and Papuan-related ancestors. Papuan-related ancestors colonized Near Oceania about 47,000 years ago, and Asian-related ancestors were Austronesian (AN)-speaking population, called Lapita, who migrated from Southeast Asia about 3,500 years ago. These two ancestral populations admixed in Near Oceania before the expansion of Lapita people into Remote Oceania. To understand the impact of the admixture on the adaptation of AN-speaking Melanesians in Near Oceania, we performed the genome-wide single nucleotide polymorphism (SNP) analysis of 21 individuals from Munda, the main town of the New Georgia Islands in the western Solomon Islands. Population samples from Munda were genetically similar to other Solomon Island population samples. The analysis of genetic contribution from the two different ancestries to the Munda genome revealed significantly higher proportions of Asian- and Papuan-related ancestries in the region containing the annexin A1 (ANXA1) gene (Asian component > 82.6%) and in the human leukocyte antigen (HLA) class II region (Papuan component > 85.4%), respectively. These regions were suspected to have undergone natural selection since the time of admixture. Our results suggest that admixture had affected adaptation of AN-speaking Melanesians in the Solomon Islands.
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Affiliation(s)
- Mariko Isshiki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yusuke Watanabe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Nao Nishida
- Genome Medical Science Project, Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, 272-8516, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, 903-0125, Japan
| | - Takuro Furusawa
- Graduate School of Asian and African Area Studies, Kyoto University, Kyoto, 606-8501, Japan
| | - Kazumi Natsuhara
- Department of International Health and Nursing, Faculty of Nursing, Toho University, Tokyo, 143-8540, Japan
| | - Taro Yamauchi
- Faculty of Health Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Minato Nakazawa
- Graduate School of Health Sciences, Kobe University, Kobe, 654-0142, Japan
| | - Takafumi Ishida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Ricky Eddie
- National Gizo Hospital, Ministry of Health and Medical Services, P.O. Box 36, Gizo, Solomon Islands
| | | | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
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24
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Arayasongsak U, Naka I, Ohashi J, Patarapotikul J, Nuchnoi P, Kalambaheti T, Sa-Ngasang A, Chanama S, Chaorattanakawee S. Interferon lambda 1 is associated with dengue severity in Thailand. Int J Infect Dis 2020; 93:121-125. [PMID: 31981768 DOI: 10.1016/j.ijid.2020.01.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/07/2020] [Accepted: 01/14/2020] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVES Patients with dengue exhibit a range of symptoms from an acute febrile illness (dengue fever, DF), to dengue hemorrhagic fever (DHF), and to the most severe outcome, dengue shock syndrome (DSS). This study was performed to determine the host genetic factors responsible for dengue severity. Two single nucleotide polymorphisms (SNPs) of the interferon lambda 1 (IFNL1) gene (rs30461 and rs7247086) were analyzed for their association with dengue severity in a Thai population. METHODS This was a case-control association study involving 877 patients under the age of 15 years (DF, n = 386; DHF, n = 416; DSS, n = 75). Genotyping was performed by TaqMan real-time PCR assay. RESULTS It was found that the rs7247086 variant of IFNL1 was associated with DHF, but not DSS. Genotypes CT and TT and the T allele were protective against DHF (p = 0.03, odds ratio 0.62 for CT, odds ratio 0.13 for TT; and p = 0.01, odds ratio 0.54 for the T allele). The other SNP tested was not associated with DHF or DSS. CONCLUSIONS The rs7247086 variant of IFNL1 (the T allele) was found to be protective against DHF, suggesting that IFNL1 may play a role in the pathogenesis of DHF.
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Affiliation(s)
- Unchana Arayasongsak
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Bangkok 10400, Thailand
| | - Izumi Naka
- Laboratory of Human Genome Diversity, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Jun Ohashi
- Laboratory of Human Genome Diversity, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Jintana Patarapotikul
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Bangkok 10400, Thailand
| | - Pornlada Nuchnoi
- Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Thareerat Kalambaheti
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Bangkok 10400, Thailand
| | - Areerat Sa-Ngasang
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Sumalee Chanama
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Suwanna Chaorattanakawee
- Department of Parasitology and Entomology, Faculty of Public Health, Mahidol University, Ratchawithi Road, Bangkok 10400, Thailand.
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25
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Onuma H, Kawamura R, Tabara Y, Yamashita M, Ohashi J, Kawasaki E, Imagawa A, Yamada Y, Chujo D, Takahashi K, Suehiro T, Takata Y, Osawa H, Makino H. Variants in the BACH2 and CLEC16A gene might be associated with susceptibility to insulin-triggered type 1 diabetes. J Diabetes Investig 2019; 10:1447-1453. [PMID: 30970177 PMCID: PMC6825945 DOI: 10.1111/jdi.13057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/18/2019] [Accepted: 04/04/2019] [Indexed: 01/25/2023] Open
Abstract
AIM/INTRODUCTION Insulin administration was found to trigger type 1 diabetes in six Japanese type 2 diabetes patients with type 1 diabetes high-risk human leukocyte antigen class II and the class I allele of the insulin gene variable number tandem repeat genotype. The objective of the present study was to assess the contribution of non-human leukocyte antigen single-nucleotide polymorphisms (SNPs) to the risk of developing insulin-triggered type 1 diabetes. MATERIALS AND METHODS We genotyped 13 type 1 diabetes susceptible SNPs in six patients and compared them with those in Japanese controls (Hap Map3-JPT). The SNPs that showed statistically significant results were further analyzed using non-diabetic control participants and participants with type 2 diabetes at the Ehime University Hospital. RESULTS The risk allele frequency of BACH2 rs3757247 in the six patients was significantly more frequent than that in 86 Japanese controls (P = 0.038). No significant difference in the allele frequency was observed in the other SNPs. This result was confirmed by the findings that the risk allele frequency of BACH2 in the six patients was significantly higher than that in the non-diabetic control participants (n = 179) and type 2 diabetes with or without insulin treatment (n = 154 or n = 152; P = 0.035, 0.034 or 0.037, respectively). Despite being statistically not significant, the six patients were all homozygous for the CLEC16A rs12708716 risk allele and five were homozygous for the CLEC16A rs2903692 risk allele. CONCLUSIONS In addition to type 1 diabetes high-risk human leukocyte antigen class II and the class I allele of the insulin gene variable number tandem repeat genotype, the possibility that the risk variants of BACH2 and CLEC16A could contribute to the development of insulin-triggered type 1 diabetes cannot be excluded.
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Affiliation(s)
- Hiroshi Onuma
- Department of Diabetes and Molecular GeneticsEhime University Graduate School of MedicineTo‐onEhimeJapan
- Department of Diabetes, Endocrine and Metabolic DiseaseTokyo Women's Medical University Yachiyo Medical CenterYachiyoChibaJapan
| | - Ryoichi Kawamura
- Department of Diabetes and Molecular GeneticsEhime University Graduate School of MedicineTo‐onEhimeJapan
| | - Yasuharu Tabara
- Center for Genomic MedicineKyoto University Graduate School of MedicineKyotoJapan
| | - Masakatsu Yamashita
- Department of ImmunologyEhime University Graduate School of MedicineTo‐onEhimeJapan
| | - Jun Ohashi
- Department of Biological SciencesGraduate School of ScienceThe University of TokyoTokyoJapan
| | - Eiji Kawasaki
- Department of Diabetes and EndocrinologyShin‐Koga HospitalKurumeFukuokaJapan
| | - Akihisa Imagawa
- Department of Internal Medicine (I)Osaka Medical CollegeTakatsukiOsakaJapan
| | - Yuya Yamada
- Department of Endocrinology and MetabolismSumitomo HospitalOsakaJapan
| | - Daisuke Chujo
- Department of Diabetes, Endocrinology and MetabolismNational Center for Global Health and MedicineTokyoJapan
| | - Kenji Takahashi
- Department of Internal MedicineDiabetes DivisionKurashiki Central HospitalKurashikiOkayamaJapan
| | | | - Yasunori Takata
- Department of Diabetes and Molecular GeneticsEhime University Graduate School of MedicineTo‐onEhimeJapan
| | - Haruhiko Osawa
- Department of Diabetes and Molecular GeneticsEhime University Graduate School of MedicineTo‐onEhimeJapan
| | - Hideichi Makino
- Department of Diabetes and Molecular GeneticsEhime University Graduate School of MedicineTo‐onEhimeJapan
- Shiraishi Hospital Diabetes CenterImabariEhimeJapan
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26
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Cameron N, Yamauchi T, Ohashi J. Human Biology of Japan. Ann Hum Biol 2019; 46:285-286. [PMID: 31650872 DOI: 10.1080/03014460.2019.1671675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
| | - Taro Yamauchi
- Faculty of Health Sciences, Hokkaido University , Sapporo , Japan.,Research Institute for Humanity and Nature , Kyoto , Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo , Tokyo , Japan
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27
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Watanabe Y, Naka I, Khor SS, Sawai H, Hitomi Y, Tokunaga K, Ohashi J. Analysis of whole Y-chromosome sequences reveals the Japanese population history in the Jomon period. Sci Rep 2019; 9:8556. [PMID: 31209235 PMCID: PMC6572846 DOI: 10.1038/s41598-019-44473-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 05/17/2019] [Indexed: 01/06/2023] Open
Abstract
The Jomon and the Yayoi are considered to be the two major ancestral populations of the modern mainland Japanese. The Jomon people, who inhabited mainland Japan, admixed with Yayoi immigrants from the Asian continent. To investigate the population history in the Jomon period (14,500–2,300 years before present [YBP]), we analyzed whole Y-chromosome sequences of 345 Japanese males living in mainland Japan. A phylogenetic analysis of East Asian Y chromosomes identified a major clade (35.4% of mainland Japanese) consisting of only Japanese Y chromosomes, which seem to have originated from indigenous Jomon people. A Monte Carlo simulation indicated that ~70% of Jomon males had Y chromosomes in this clade. The Bayesian skyline plots of 122 Japanese Y chromosomes in the clade detected a marked decrease followed by a subsequent increase in the male population size from around the end of the Jomon period to the beginning of the Yayoi period (2,300 YBP). The colder climate in the Late to Final Jomon period may have resulted in critical shortages of food for the Jomon people, who were hunter-gatherers, and the rice farming introduced by Yayoi immigrants may have helped the population size of the Jomon people to recover.
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Affiliation(s)
- Yusuke Watanabe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Seik-Soon Khor
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiromi Sawai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
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28
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Ikeda M, Kaneko M, Tachibana SI, Balikagala B, Sakurai-Yatsushiro M, Yatsushiro S, Takahashi N, Yamauchi M, Sekihara M, Hashimoto M, Katuro OT, Olia A, Obwoya PS, Auma MA, Anywar DA, Odongo-Aginya EI, Okello-Onen J, Hirai M, Ohashi J, Palacpac NMQ, Kataoka M, Tsuboi T, Kimura E, Horii T, Mita T. Artemisinin-Resistant Plasmodium falciparum with High Survival Rates, Uganda, 2014-2016. Emerg Infect Dis 2019; 24:718-726. [PMID: 29553316 PMCID: PMC5875287 DOI: 10.3201/eid2404.170141] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Because ≈90% of malaria cases occur in Africa, emergence of artemisinin-resistant Plasmodium falciparum in Africa poses a serious public health threat. To assess emergence of artemisinin-resistant parasites in Uganda during 2014–2016, we used the recently developed ex vivo ring-stage survival assay, which estimates ring-stage–specific P. falciparum susceptibility to artemisinin. We conducted 4 cross-sectional surveys to assess artemisinin sensitivity in Gulu, Uganda. Among 194 isolates, survival rates (ratio of viable drug-exposed parasites to drug-nonexposed controls) were high (>10%) for 4 isolates. Similar rates have been closely associated with delayed parasite clearance after drug treatment and are considered to be a proxy for the artemisinin-resistant phenotype. Of these, the PfKelch13 mutation was observed in only 1 isolate, A675V. Population genetics analysis suggested that these possibly artemisinin-resistant isolates originated in Africa. Large-scale surveillance of possibly artemisinin-resistant parasites in Africa would provide useful information about treatment outcomes and help regional malaria control.
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29
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Wah ST, Hananantachai H, Patarapotikul J, Ohashi J, Naka I, Nuchnoi P. microRNA-27a and microRNA-146a SNP in cerebral malaria. Mol Genet Genomic Med 2019; 7:e00529. [PMID: 30599464 PMCID: PMC6393659 DOI: 10.1002/mgg3.529] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 10/06/2018] [Accepted: 10/25/2018] [Indexed: 12/19/2022] Open
Abstract
Background During Plasmodium falciparum infection, microRNA expression alters in brain tissue of mice with cerebral malaria compared to noninfected controls. MicroRNA regulates gene expression post‐transcriptionally to influence biological processes. Cerebral malaria pathology caused mainly by the immunological disorder. We hypothesize that single‐nucleotide polymorphism in a microRNA influences microRNA biogenesis or target gene recognition and altering susceptibility to cerebral malaria. Methods We performed a literature search based on immunological mechanism and applied microRNA‐related single‐nucleotide polymorphisms database to examine candidate microRNA SNPs possibly responsible for cerebral malaria. MicroRNA‐27a and microRNA‐146a are supposed to involve in cerebral malaria pathology. To assess the relationship of microRNA SNP to cerebral malaria outcome, we performed TaqMan Genotyping Assays in 110 cerebral malaria and 207 uncomplicated malaria cases for three candidate microRNA SNPs (rs895819 of microRNA‐27a, rs57095329 and rs2910164 of microRNA‐146a). Results Our study detected no significant difference in genotype and allele frequency of individual microRNA SNPs as well as in haplotypes of microRNA‐146a between these two groups of malaria patients in Thailand. Hardy–Weinberg disequilibrium of rs57095329 in the cerebral malaria group showed a heterozygous excess which might be due to natural selection. Conclusion Our data supported that the candidate microRNA SNPs have no major role to develop cerebral malaria.
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Affiliation(s)
- Saw Thu Wah
- Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand.,Department of Medical Laboratory Technology, University of Medical Technology, Yangon, Myanmar
| | | | | | - Jun Ohashi
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Izumi Naka
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Pornlada Nuchnoi
- Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand.,Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
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30
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Ohashi J, Naka I, Furusawa T, Kimura R, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Inaoka T, Matsumura Y, Ohtsuka R. Association study of CREBRF missense variant (rs373863828:G > A; p.Arg457Gln) with levels of serum lipid profile in the Pacific populations. Ann Hum Biol 2018; 45:215-219. [PMID: 29877158 DOI: 10.1080/03014460.2018.1461928] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
BACKGROUND A missense variant (rs373863828:G > A; p.Arg457Gln) of the CREBRF gene is strongly associated with a higher body mass index (BMI; kg/m2) in Polynesian populations. This variant has also been reported to be associated with lower total cholesterol in Samoans. AIM The aim of this study is to examine the association of rs373863828:G > A with levels of serum lipids in four Pacific populations. METHODS A total of 613 adult subjects were recruited from Tonga (Polynesians) and the Solomon Islands (Melanesians and Micronesians). Multiple regression analyses adjusted for age and sex were performed to examine the association of rs373863828 with levels of serum lipids in each population. RESULTS A significant association of rs373863828:G > A with lower level of HDL-cholesterol was detected in the Tonga population (β = -3.32 and p-value = 0.030). The expected change in HDL-cholesterol with respect to a single copy of the rs373863828-A allele was 3.32 mg/dL. However, the association between rs373863828-A and lower levels of HDL-cholesterol was not significant after further adjustment for BMI in the Tonga population (β = -2.32 and p-value = 0.13). CONCLUSIONS The rs373863828-A allele may not directly affect the level of serum HDL-cholesterol independent of BMI. To confirm the present findings, association studies with large sample sizes and functional analyses are required.
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Affiliation(s)
- Jun Ohashi
- a Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Tokyo , Japan
| | - Izumi Naka
- a Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Tokyo , Japan
| | - Takuro Furusawa
- b Graduate School of Asian and African Area Studies , Kyoto University , Kyoto , Japan
| | - Ryosuke Kimura
- c Department of Human Biology and Anatomy, Graduate School of Medicine , University of the Ryukyus , Nishihara , Japan
| | - Kazumi Natsuhara
- d Faculty of Nursing , The Japanese Red Cross Akita College of Nursing , Akita , Japan
| | - Taro Yamauchi
- e Faculty of Health Science , Hokkaido University , Sapporo , Japan
| | - Minato Nakazawa
- f Graduate School of Health Sciences , Kobe University , Kobe , Japan
| | - Takafumi Ishida
- a Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Tokyo , Japan
| | - Tsukasa Inaoka
- g Department of Human Ecology, Faculty of Agriculture , Saga University , Saga , Japan
| | - Yasuhiro Matsumura
- h Faculty of Health and Nutrition , Bunkyo University , Chigasaki , Japan
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31
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Nishida N, Sugiyama M, Sawai H, Nishina S, Sakai A, Ohashi J, Khor S, Kakisaka K, Tsuchiura T, Hino K, Sumazaki R, Takikawa Y, Murata K, Kanda T, Yokosuka O, Tokunaga K, Mizokami M. Key HLA-DRB1-DQB1 haplotypes and role of the BTNL2 gene for response to a hepatitis B vaccine. Hepatology 2018; 68. [PMID: 29534301 PMCID: PMC6175380 DOI: 10.1002/hep.29876] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Approximately 5-10% of individuals who are vaccinated with a hepatitis B (HB) vaccine designed based on the hepatitis B virus (HBV) genotype C fail to acquire protective levels of antibodies. Here, host genetic factors behind low immune response to this HB vaccine were investigated by a genome-wide association study (GWAS) and Human Leukocyte Antigen (HLA) association tests. The GWAS and HLA association tests were carried out using a total of 1,193 Japanese individuals including 107 low responders, 351 intermediate responders, and 735 high responders. Classical HLA class II alleles were statistically imputed using the genome-wide SNP typing data. The GWAS identified independent associations of HLA-DRB1-DQB1, HLA-DPB1 and BTNL2 genes with immune response to a HB vaccine designed based on the HBV genotype C. Five HLA-DRB1-DQB1 haplotypes and two DPB1 alleles showed significant associations with response to the HB vaccine in a comparison of three groups of 1,193 HB vaccinated individuals. When frequencies of DRB1-DQB1 haplotypes and DPB1 alleles were compared between low immune responders and HBV patients, significant associations were identified for three DRB1-DQB1 haplotypes, and no association was identified for any of the DPB1 alleles. In contrast, no association was identified for DRB1-DQB1 haplotypes and DPB1 alleles in a comparison between high immune responders and healthy individuals. Conclusion: The findings in this study clearly show the importance of HLA-DR-DQ (i.e., recognition of a vaccine related HB surface antigen (HBsAg) by specific DR-DQ haplotypes) and BTNL2 molecules (i.e., high immune response to HB vaccine) for response to a HB vaccine designed based on the HBV genotype C. (Hepatology 2018).
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Affiliation(s)
- Nao Nishida
- Genome Medical Science ProjectNational Center for Global Health and MedicineIchikawaJapan,Department of Human Genetics, Graduate School of MedicineThe University of TokyoBunkyo‐kuJapan
| | - Masaya Sugiyama
- Genome Medical Science ProjectNational Center for Global Health and MedicineIchikawaJapan
| | - Hiromi Sawai
- Department of Human Genetics, Graduate School of MedicineThe University of TokyoBunkyo‐kuJapan
| | - Sohji Nishina
- Department of Hepatology and PancreatologyKawasaki Medical SchoolOkayamaJapan
| | - Aiko Sakai
- Department of Child Health, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoBunkyo‐kuJapan
| | - Seik‐Soon Khor
- Department of Human Genetics, Graduate School of MedicineThe University of TokyoBunkyo‐kuJapan
| | - Keisuke Kakisaka
- Division of Hepatology, Department of Internal MedicineIwate Medical UniversityMoriokaJapan
| | - Takayo Tsuchiura
- Genome Medical Science ProjectNational Center for Global Health and MedicineIchikawaJapan
| | - Keisuke Hino
- Department of Hepatology and PancreatologyKawasaki Medical SchoolOkayamaJapan
| | - Ryo Sumazaki
- Department of Child Health, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Yasuhiro Takikawa
- Division of Hepatology, Department of Internal MedicineIwate Medical UniversityMoriokaJapan
| | - Kazumoto Murata
- Genome Medical Science ProjectNational Center for Global Health and MedicineIchikawaJapan,Department of GastroenterologyInternational University of Health and Welfare, Graduate School of Medical SciencesChibaJapan
| | - Tatsuo Kanda
- Department of Gastroenterology and Nephrology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Osamu Yokosuka
- Department of Gastroenterology and Nephrology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of MedicineThe University of TokyoBunkyo‐kuJapan
| | - Masashi Mizokami
- Genome Medical Science ProjectNational Center for Global Health and MedicineIchikawaJapan
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Chaorattanakawee S, Nuchnoi P, Hananantachai H, Tumkosit U, Saunders D, Naka I, Ohashi J, Patarapotikul J. Correction: Sequence variation in Plasmodium falciparum merozoite surface protein-2 is associated with virulence causing severe and cerebral malaria. PLoS One 2018; 13:e0196694. [PMID: 29694418 PMCID: PMC5919017 DOI: 10.1371/journal.pone.0196694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0190418.].
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Mita T, Hombhanje F, Takahashi N, Sekihara M, Yamauchi M, Tsukahara T, Kaneko A, Endo H, Ohashi J. Rapid selection of sulphadoxine-resistant Plasmodium falciparum and its effect on within-population genetic diversity in Papua New Guinea. Sci Rep 2018; 8:5565. [PMID: 29615786 PMCID: PMC5882878 DOI: 10.1038/s41598-018-23811-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/21/2018] [Indexed: 11/18/2022] Open
Abstract
The ability of the human malarial parasite Plasmodium falciparum to adapt to environmental changes depends considerably on its ability to maintain within-population genetic variation. Strong selection, consequent to widespread antimalarial drug usage, occasionally elicits a rapid expansion of drug-resistant isolates, which can act as founders. To investigate whether this phenomenon induces a loss of within-population genetic variation, we performed a population genetic analysis on 302 P. falciparum cases detected during two cross-sectional surveys in 2002/2003, just after the official introduction of sulphadoxine/pyrimethamine as a first-line treatment, and again in 2010/2011, in highly endemic areas in Papua New Guinea. We found that a single-origin sulphadoxine-resistant parasite isolate rapidly increased from 0% in 2002/2003 to 54% in 2010 and 84% in 2011. However, a considerable number of pairs exhibited random associations among 10 neutral microsatellite markers located in various chromosomes, suggesting that outcrossing effectively reduced non-random associations, albeit at a low average multiplicity of infection (1.35–1.52). Within-population genetic diversity was maintained throughout the study period. This indicates that the parasites maintained within-population variation, even after a clonal expansion of drug-resistant parasites. Outcrossing played a role in the preservation of within-population genetic diversity despite low levels of multiplicity of infection.
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Affiliation(s)
- Toshihiro Mita
- Department of Tropical Medicine and Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan.
| | - Francis Hombhanje
- Centre for Health Research & Diagnostics, Divine Word University, Nabasa Road, P.O. Box 483, Madang, Papua New Guinea
| | - Nobuyuki Takahashi
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan
| | - Makoto Sekihara
- Department of Tropical Medicine and Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan
| | - Masato Yamauchi
- Department of Tropical Medicine and Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan
| | - Takahiro Tsukahara
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan
| | - Akira Kaneko
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden.,Department of Parasitology, Osaka City University Graduate School of Medicine, Asahi-cho 1-4-3, Abeno-ku, Osaka, 545-8585, Japan
| | - Hiroyoshi Endo
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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Wah S, Hananantachai H, Patarapotikul J, Ohashi J, Naka I, Nuchnoi P. Interferon-induced protein with tetratricopeptide repeats 1 (IFIT1) polymorphism as a genetic marker of cerebral malaria in Thai population. ASIAN PAC J TROP MED 2018. [DOI: 10.4103/1995-7645.234765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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35
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Issiki M, Naka I, Kimura R, Furusawa T, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Ohtsuka R, Ohashi J. Mitochondrial DNA variations in Austronesian-speaking populations living in the New Georgia Islands, the Western Province of the Solomon Islands. J Hum Genet 2017; 63:101-104. [DOI: 10.1038/s10038-017-0372-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/15/2017] [Accepted: 09/15/2017] [Indexed: 01/11/2023]
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36
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Eriguchi Y, Kuwabara H, Inai A, Kawakubo Y, Nishimura F, Kakiuchi C, Tochigi M, Ohashi J, Aoki N, Kato K, Ishiura H, Mitsui J, Tsuji S, Doi K, Yoshimura J, Morishita S, Shimada T, Furukawa M, Umekage T, Sasaki T, Kasai K, KanoMD PhD Y. Identification of candidate genes involved in the etiology of sporadic Tourette syndrome by exome sequencing. Am J Med Genet B Neuropsychiatr Genet 2017; 174:712-723. [PMID: 28608572 DOI: 10.1002/ajmg.b.32559] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 05/15/2017] [Indexed: 01/01/2023]
Abstract
Tourette Syndrome (TS) is a neurodevelopmental disorder characterized by chronic motor and vocal tics. Although there is a large genetic contribution, the genetic architecture of TS remains unclear. Exome sequencing has successfully revealed the contribution of de novo mutations in sporadic cases with neuropsychiatric disorders such as autism and schizophrenia. Here, using exome sequencing, we investigated de novo mutations in individuals with sporadic TS to identify novel risk loci and elucidate the genetic background of TS. Exome analysis was conducted for sporadic TS cases: nine trio families and one quartet family with concordant twins were investigated. Missense mutations were evaluated using functional prediction algorithms, and their population frequencies were calculated based on three public databases. Gene expression patterns in the brain were analyzed using the BrainSpan Developmental Transcriptome. Thirty de novo mutations, including four synonymous and four missense mutations, were identified. Among the missense mutations, one in the rapamycin-insensitive companion of mammalian target of rapamycin (RICTOR)-coding gene (rs140964083: G > A, found in one proband) was predicted to be hazardous. In the three public databases analyzed, variants in the same SNP locus were absent, and variants in the same gene were either absent or present at an extremely low frequency (3/5,008), indicating the rarity of hazardous RICTOR mutations in the general population. The de novo variant of RICTOR may be implicated in the development of sporadic TS, and RICTOR is a novel candidate factor for TS etiology.
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Affiliation(s)
- Yosuke Eriguchi
- Department of Child Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Neuropsychiatry, Sakura Hospital, Aomori, Japan
| | - Hitoshi Kuwabara
- Department of Child Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Disability Services Office, The University of Tokyo, Tokyo, Japan
| | - Aya Inai
- Department of Child Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuki Kawakubo
- Department of Child Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Fumichika Nishimura
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Chihiro Kakiuchi
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mamoru Tochigi
- Department of Neuropsychiatry, Teikyo University School of Medicine, Tokyo, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Naoto Aoki
- Department of Neuropsychiatry, Sakura Hospital, Aomori, Japan
| | - Kayoko Kato
- Department of Physical and Health Education, Graduate School of Education, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun Mitsui
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Medical Genome Center, The University of Tokyo Hospital, The University of Tokyo, Tokyo, Japan
| | - Koichiro Doi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Takafumi Shimada
- Division for Counseling and Support, The University of Tokyo, Tokyo, Japan
| | - Masaomi Furukawa
- Department of Child Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tadashi Umekage
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tsukasa Sasaki
- Department of Physical and Health Education, Graduate School of Education, The University of Tokyo, Tokyo, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yukiko KanoMD PhD
- Department of Child Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Furusawa T, Naka I, Yamauchi T, Natsuhara K, Eddie R, Kimura R, Nakazawa M, Ishida T, Ohtsuka R, Ohashi J. Polymorphisms associated with a tropical climate and root crop diet induce susceptibility to metabolic and cardiovascular diseases in Solomon Islands. PLoS One 2017; 12:e0172676. [PMID: 28253292 PMCID: PMC5333831 DOI: 10.1371/journal.pone.0172676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/08/2017] [Indexed: 01/19/2023] Open
Abstract
The people of the Solomon Islands represent an Austronesian (AN)-speaking population's adaptation to a humid tropical environment and subsistence of tuberous crops. Genome-wide association studies (GWASs) of other populations (e.g. the Human Genome Diversity Project [HGDP]) have suggested the existence of genotypes adaptive to ecoregion, diet, and subsistence, and that those genotypes are also associated with metabolic and cardiovascular diseases. Recently, the incidence of non-communicable diseases has been increasing in the Solomon Islands. In the present study, we explored the association of genotypes adaptive to a tropical environment and tuberous crop diet with metabolic and cardiovascular conditions in rural and urban AN-speaking Melanesian and Micronesian populations of the Solomon Islands. A total of 561 participants were genotyped for single nucleotide polymorphisms (SNPs) potentially associated with a tropical environment (rs174570 and rs2237892) and a tuberous crop diet (rs162036, rs185819, and rs2722425). The results showed that the allele frequencies of the Solomon Islands populations adopted patterns similar to those in populations from other hot, tropical areas with a tuberous crop diet in previous studies. Furthermore, rs162036, rs185819, rs2237892, and rs2722425 were all strongly associated with one or more metabolic and cardiovascular conditions. The derived allele of rs2722425 (i.e. rs2722425-G) was significantly associated with an elevated LDL level (P = 0.000264) even after the significance level was adjusted for multiple testing (i.e., α = 0.0005). Our results suggest that the inhabitants of the Solomon Islands exhibit the effects of the tropical environment and tuberous crop diet on their allele frequencies, and that their susceptibility to metabolic and cardiovascular diseases is therefore considered to be associated with their environment and diet.
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Affiliation(s)
- Takuro Furusawa
- Graduate School of Asian and African Area Studies, Kyoto University, Kyoto, Japan
| | - Izumi Naka
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Taro Yamauchi
- Graduate School of Health Sciences, Hokkaido University, Hokkaido, Japan
| | | | - Ricky Eddie
- National Gizo Hospital, Ministry of Health and Medical Services, Gizo, Solomon Islands
| | - Ryosuke Kimura
- Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Minato Nakazawa
- Department of International Health, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - Takafumi Ishida
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | | | - Jun Ohashi
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
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38
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Onuma H, Tabara Y, Kawamura R, Ohashi J, Nishida W, Takata Y, Ochi M, Nishimiya T, Ohyagi Y, Kawamoto R, Kohara K, Miki T, Osawa H. Dual Effects of a RETN Single Nucleotide Polymorphism (SNP) at -420 on Plasma Resistin: Genotype and DNA Methylation. J Clin Endocrinol Metab 2017; 102:884-892. [PMID: 27929711 DOI: 10.1210/jc.2016-2417] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 12/07/2016] [Indexed: 02/03/2023]
Abstract
CONTEXT We previously reported that single nucleotide polymorphism (SNP)-420 C>G (rs1862513) in the promoter region of RETN was associated with type 2 diabetes. Plasma resistin was tightly correlated with SNP-420 genotypes. SNP-420 is a CpG-SNP affecting the sequence of cytosine-phosphate-guanine dinucleotides. OBJECTIVE To examine whether methylation at SNP-420 affects plasma resistin, we analyzed plasma resistin and methylation at RETN SNP-420. DESIGN AND METHODS Genomic DNA was extracted from peripheral white blood cells in 2078 Japanese subjects. Quantification of the methylation was performed by pyrosequencing after DNA bisulfite conversion. RESULTS Methylation at SNP-420 was highest in the C/C genotype (36.9 ± 5.7%), followed by C/G (21.4 ± 3.5%) and G/G (2.9 ± 1.4%; P < 0.001). When assessed in each genotype, methylation at SNP-420 was inversely associated with plasma resistin in the C/C (β = -0.134, P < 0.001) or C/G (β = -0.227, P < 0.001) genotype. In THP-1 human monocytes intrinsically having the C/C genotype, a demethylating reagent, 5-aza-dC, decreased the methylation at SNP-420 and increased RETN messenger RNA. SNP+1263 (rs3745369), located in the 3' untranslated region of RETN, was also associated with methylation at SNP-420. In addition, highly sensitive C-reactive protein was inversely associated with methylation at SNP-420 in the C/C genotype, whereas body mass index was positively associated. CONCLUSIONS Plasma resistin was inversely associated with the extent of methylation at SNP-420 mainly dependent on the SNP-420 genotype. The association can also be explained partially independent of SNP-420 genotypes. SNP-420 could have dual, genetic and epigenetic effects on plasma resistin.
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Affiliation(s)
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan; and
| | | | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-8654, Japan
| | | | | | | | | | | | - Ryuichi Kawamoto
- Community Medicine, Ehime University Graduate School of Medicine, Ehime 791-0295, Japan
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Yasukochi Y, Naka I, Patarapotikul J, Hananantachai H, Ohashi J. Evolution of Fseg/Cseg dimorphism in region III of the Plasmodium falciparum eba-175 gene. Infect Genet Evol 2017; 49:251-255. [PMID: 28137625 DOI: 10.1016/j.meegid.2017.01.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Revised: 01/23/2017] [Accepted: 01/25/2017] [Indexed: 11/27/2022]
Abstract
The 175-kDa erythrocyte binding antigen (EBA-175) of the malaria parasite Plasmodium falciparum is important for its invasion into human erythrocytes. The primary structure of eba-175 is divided into seven regions, namely I to VII. Region III contains highly divergent dimorphic segments, termed Fseg and Cseg. The allele frequencies of segmental dimorphism within a P. falciparum population have been extensively examined; however, the molecular evolution of segmental dimorphism is not well understood. A comprehensive comparison of nucleotide sequences among 32 P. falciparum eba-175 alleles identified in our previous study, two Plasmodium reichenowi, and one P. gaboni orthologous alleles obtained from the GenBank database was conducted to uncover the origin and evolutionary processes of segmental dimorphism in P. falciparum eba-175. In the eba-175 nucleotide sequence derived from a P. reichenowi CDC strain, both Fseg and Cseg were found in region III, which implies that the original eba-175 gene had both segments, and deletions of F- and C-segments generated Cseg and Fseg alleles, respectively. We also confirmed the presence of allele with Fseg and Cseg in another P. reichenowi strain (SY57), by re-mapping short reads obtained from the GenBank database. On the other hand, the segmental sequence of eba-175 ortholog in P. gaboni was quite diverged from those of the other species, suggesting that the original eba-175 dimorphism of P. falciparum can be traced back to the stem linage of P. falciparum and P. reichenowi. Our findings suggest that Fseg and Cseg alleles are derived from a single eba-175 allele containing both segments in the ancestral population of P. falciparum and P. reichenowi, and that the allelic dimorphism of eba-175 was shaped by the independent emergence of similar dimorphic lineage in different species that has never been observed in any evolutionary mode of allelic dimorphism at other loci in malaria genomes.
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Affiliation(s)
- Yoshiki Yasukochi
- Department of Human Functional Genomics, Advanced Science Research Promotion Center, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan.
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Jintana Patarapotikul
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Hathairad Hananantachai
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
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Yasukochi Y, Ohashi J. Elucidating the origin of HLA-B*73 allelic lineage: Did modern humans benefit by archaic introgression? Immunogenetics 2016; 69:63-67. [PMID: 27695917 PMCID: PMC5203853 DOI: 10.1007/s00251-016-0952-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/16/2016] [Indexed: 12/01/2022]
Abstract
A previous study reported that some of the human leukocyte antigen (HLA) alleles and haplotypes in present-day humans were acquired by admixture with archaic humans; specifically, an exceptionally diverged HLA-B*73 allele was proposed to be transmitted from Denisovans, although the DNA sequence of HLA-B*73 has not been detected in the Denisovan genome. Here, we argue against the hypothesis that HLA-B*73 introgressed from Denisovans into early modern humans. A phylogenetic analysis revealed that HLA-B*73:01 formed a monophyletic group with a chimpanzee MHC-B allele, strongly suggesting that the HLA-B*73 allelic lineage has been maintained in humans as well as in chimpanzees since the divergence of humans and chimpanzees. The global distribution of HLA-B*73 allele showed that the population frequency of HLA-B*73 in west Asia (0.24 %)—a possible site of admixture with Denisovans—is lower than that in Europe (0.72 %) and in south Asia (0.69 %). Furthermore, HLA-B*73 is not observed in Melanesia even though the Melanesian genome contains the highest proportion of Denisovan ancestry in present-day human populations. Single nucleotide polymorphisms in HLA-A*11-HLA-C*12:02 or HLA-A*11-C*15 haplotypes, one of which was assumed to be transmitted together with HLA-B*73 from Denisovans by the study of Abi-Rached and colleagues, were not differentiated from those in other HLA-A-C haplotypes in modern humans. These results do not support the introgression hypothesis. Thus, we conclude that it is highly likely that HLA-B*73 allelic lineage has been maintained in the direct ancestors of modern humans.
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Affiliation(s)
- Yoshiki Yasukochi
- Department of Human Functional Genomics, Life Science Research Center, Mie University, 1577 Kurima-machiya, Tsu, Mie, 514-8507, Japan.
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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Kawamura R, Tabara Y, Tsukada A, Igase M, Ohashi J, Yamada R, Takata Y, Kawamoto R, Saito I, Onuma H, Tanigawa T, Yamada K, Kato N, Ohyagi Y, Miki T, Kohara K, Osawa H. Genome-wide association study of plasma resistin levels identified rs1423096 and rs10401670 as possible functional variants in the Japanese population. Physiol Genomics 2016; 48:874-881. [PMID: 27664181 DOI: 10.1152/physiolgenomics.00040.2016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/22/2016] [Indexed: 01/06/2023] Open
Abstract
Resistin is a cytokine inducing insulin resistance in mice. We previously identified single nucleotide polymorphisms (SNPs) at -420 (rs1862513) and -358 (rs3219175) located in the human resistin gene (RETN) promoter as strong determinants for circulating resistin in the Japanese population. The objective was to identify additional functional variants for circulating resistin. We conducted a genome-wide association study in 448 Japanese subjects. A peak association signal was found on chromosome 19 where RETN is located. The top-hit SNP was SNP -358 G>A, followed by rs1423096 C>T, SNP -420 C>G, and rs10401670 C>T (P = 5.39×10-47, 1.81×10-22, 2.09×10-16, and 9.25×10-15, respectively). Meta-analysis including another two independent general Japanese populations showed that circulating resistin was most strongly associated with SNP-358, followed by SNP-420, rs1423096, and rs10401670. Rs1423096 and rs10401670 were located in the 3'-region of RETN and were in strong linkage disequilibrium. Although these SNPs were also in linkage disequilibrium with the promoter SNPs, conditional and haplotype association analyses identified rs1423096 and rs10401670 as independent determinants for circulating resistin. Functionally, nuclear proteins specifically recognized T but not C at rs10401670 as evidenced by an electrophoretic mobility shift assay. The promoter activity of a luciferase reporter with T at either rs1423096 or rs10401670 was lower than that with C in THP-1 human monocytes. Therefore, rs1423096 and rs10401670, in addition to SNP-420 and SNP-358, were identified as possible functional variants affecting circulating resistin by the genome-wide search in the Japanese population.
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Affiliation(s)
- Ryoichi Kawamura
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Akiko Tsukada
- Matsumoto University Graduate School of Health Science, Nagano, Japan
| | - Michiya Igase
- Department of Geriatric Medicine & Neurology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ryo Yamada
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yasunori Takata
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Ryuichi Kawamoto
- Department of Community Medicine, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Isao Saito
- Department of Community Health Systems Nursing, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Hiroshi Onuma
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Takeshi Tanigawa
- Department of Public Health, Juntendo University School of Medicine, Tokyo, Japan; and
| | - Kazuya Yamada
- Matsumoto University Graduate School of Health Science, Nagano, Japan
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yasumasa Ohyagi
- Department of Geriatric Medicine & Neurology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Tetsuro Miki
- Department of Geriatric Medicine & Neurology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Katsuhiko Kohara
- Department of Geriatric Medicine & Neurology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Haruhiko Osawa
- Department of Diabetes and Molecular Genetics, Ehime University Graduate School of Medicine, Ehime, Japan;
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Dang TN, Naka I, Sa-Ngasang A, Anantapreecha S, Wichukchinda N, Sawanpanyalert P, Patarapotikul J, Tsuchiya N, Ohashi J. Association of BAK1 single nucleotide polymorphism with a risk for dengue hemorrhagic fever. BMC Med Genet 2016; 17:43. [PMID: 27401010 PMCID: PMC4940700 DOI: 10.1186/s12881-016-0305-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 06/22/2016] [Indexed: 11/10/2022]
Abstract
BACKGROUND Dengue hemorrhagic fever (DHF) is a severe life-threatening form of dengue infection. Low platelet count is one of the characteristic clinical manifestations in patients with severe dengue. However, little is known about genetic factors in the host that cause low platelet count in patients with dengue. METHODS A previous genome-wide association study of hematological and biochemical traits identified single nucleotide polymorphisms (SNPs) associated with low platelet count in healthy subjects. To examine the possible association of these SNPs with DHF, 918 Thai patients with dengue [509 patients with DHF and 409 with dengue fever (DF)] were genotyped for five SNPs: rs5745568 in BAK1, rs6141 in THPO, rs6065 in GP1BA, rs739496 in SH2B3, and rs385893 in RCL1. In addition, rs4804803 in CD209, that has been reported to be associated with dengue infection, was also genotyped to examine if rs4804803 affects the association detected in this study. RESULTS The allele frequencies of each SNP were compared between the DHF and DF groups. Among the five SNPs, the G allele of rs5745568 in BAK1 was significantly associated with a risk for DHF [P = 0.006 and crude odd ratio (95 % confidence interval) = 1.32 (1.09-1.60)]. The association of this allele with DHF was also significant in a logistic regression analysis adjusted for age, sex, hospital (i.e., geographic region), immune status (i.e., primary or secondary infection), and virus serotype [P = 0.016 and adjusted odd ratio (95 % confidence interval) = 1.29 (1.05-1.58)]. The result was not influenced by rs4804803 [P = 0.0167 and adjusted OR (95 % CI) = 1.29 (1.05-1.58)]. No other SNPs including rs4804803 showed significant association. CONCLUSIONS The low-level constitutive production of platelets caused by the G allele of rs5745568 seems to increase the risk of bleeding in dengue infection. Our results suggest that BCL-2 homologous antagonist/killer (BAK) protein, encoded by BAK1, plays a crucial role in the pathogenesis of DHF.
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Affiliation(s)
- Tran Ngoc Dang
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan.,Faculty of Public Health, University of Medicine and Pharmacy at Ho Chi Minh city, Ho Chi Minh City, Viet Nam
| | - Izumi Naka
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan.,Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Areerat Sa-Ngasang
- Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | | | | | | | | | - Naoyuki Tsuchiya
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan.,Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Jun Ohashi
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan. .,Faculty of Medicine, University of Tsukuba, Tsukuba, Japan. .,Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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43
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Kamori D, Hasan Z, Ohashi J, Kawana-Tachikawa A, Gatanaga H, Oka S, Ueno T. Identification of two unique naturally occurring Vpr sequence polymorphisms associated with clinical parameters in HIV-1 chronic infection. J Med Virol 2016; 89:123-129. [PMID: 27328918 DOI: 10.1002/jmv.24612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2016] [Indexed: 01/08/2023]
Abstract
HIV-1 viral protein R (Vpr) plays important roles in HIV-1 replication. Despite the identification of a number of HLA class I-associated immune escape mutations; it is yet known whether immune-driven Vpr polymorphisms are associated with disease outcome. Hereby, we comprehensively analyzed Vpr sequence polymorphisms and their association with disease outcome and host HLA genotypes, by using plasma viral RNA isolated from 444 HLA-typed, treatment-naïve, chronically HIV-1 infected individuals. Vpr amino acid residues at positions 13, 37, 45, 55, 63, 77, 84, 85, 86, and 93 were significantly associated with patients' plasma viral load and/or CD4 count. Further analysis revealed Ala at position 55 was significantly associated with lower plasma viral load; and Thr at position 63 was significantly associated with lower plasma viral load and higher CD4 count. Also, the number of amino acid residues at the two positions, located in a functionally important α-helical domain, correlated inversely with plasma viral load and positively with CD4 count. Moreover, a phylogenetically corrected method revealed residues at positions 55 and 63 are associated with patients' HLA genotypes. Taken together, our results suggest that Vpr polymorphisms at functionally important and immune-reactive sites may contribute, at least in part, to viral replication and disease outcome in vivo. J. Med. Virol. 89:123-129, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Doreen Kamori
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Zafrul Hasan
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan.,Institute of Medical Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan.,AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan.,AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Takamasa Ueno
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan. .,International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan.
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Ohashi J, Naka I, Hananantachai H, Patarapotikul J. Association of PECAM1/CD31 polymorphisms with cerebral malaria. Int J Mol Epidemiol Genet 2016; 7:87-94. [PMID: 27335627 PMCID: PMC4913224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 04/30/2016] [Indexed: 06/06/2023]
Abstract
Platelet/endothelial cell adhesion molecule-1 (PECAM1/CD31), a receptor recognized by P. falciparum-infected red blood cells (iRBCs), on the vascular endothelium has been implicated in mediating cytoadherence in patients with P. falciparum malaria. To examine associations of PECAM1 polymorphisms with cerebral malaria, 11 tag single nucleotide polymorphisms (SNPs) of PECAM1 were analysed for 312 Thai patients with P. falciparum malaria (109 with cerebral malaria and 203 with mild malaria). The rs1122800-C allele was significantly associated with protection from cerebral malaria (P = 0.017), and the rs9912957-A significantly increased the risk for cerebral malaria (P = 0.0065) in malaria patients. Fine-scale mapping using genotyped and imputed SNPs and linkage disequilibrium (LD) analysis revealed that rs1122800 and rs9912957 were located in two distinct LD blocks and were independently associated with cerebral malaria. The rs1122800-C allele was significantly associated with lower expression level of PECAM1 in EBV-transformed lymphoblastoid cell lines (P = 0.045). The present results suggest that PECAM1-mediated cytoadherence of iRBCs to brain endothelium plays a crucial role in the pathogenesis of cerebral malaria.
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Affiliation(s)
- Jun Ohashi
- Graduate School of Science, The University of TokyoTokyo, Japan
- Faculty of Medicine, University of TsukubaIbaraki, Japan
| | - Izumi Naka
- Graduate School of Science, The University of TokyoTokyo, Japan
- Faculty of Medicine, University of TsukubaIbaraki, Japan
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Liu X, Homma A, Sayadi J, Yang S, Ohashi J, Takumi T. Sequence features associated with the cleavage efficiency of CRISPR/Cas9 system. Sci Rep 2016; 6:19675. [PMID: 26813419 PMCID: PMC4728555 DOI: 10.1038/srep19675] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/16/2015] [Indexed: 12/26/2022] Open
Abstract
The CRISPR-Cas9 system has recently emerged as a versatile tool for biological and medical research. In this system, a single guide RNA (sgRNA) directs the endonuclease Cas9 to a targeted DNA sequence for site-specific manipulation. In addition to this targeting function, the sgRNA has also been shown to play a role in activating the endonuclease activity of Cas9. This dual function of the sgRNA likely underlies observations that different sgRNAs have varying on-target activities. Currently, our understanding of the relationship between sequence features of sgRNAs and their on-target cleavage efficiencies remains limited, largely due to difficulties in assessing the cleavage capacity of a large number of sgRNAs. In this study, we evaluated the cleavage activities of 218 sgRNAs using in vitro Surveyor assays. We found that nucleotides at both PAM-distal and PAM-proximal regions of the sgRNA are significantly correlated with on-target efficiency. Furthermore, we also demonstrated that the genomic context of the targeted DNA, the GC percentage, and the secondary structure of sgRNA are critical factors contributing to cleavage efficiency. In summary, our study reveals important parameters for the design of sgRNAs with high on-target efficiencies, especially in the context of high throughput applications.
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Affiliation(s)
- Xiaoxi Liu
- RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Ayaka Homma
- RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Jamasb Sayadi
- RIKEN Brain Science Institute, Wako, Saitama, Japan
- Harvard College, Cambridge, Massachusetts 02138, United States
| | - Shu Yang
- Department of Computer Science, University of British Columbia, Vancouver, Canada
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo, Tokyo, Japan
| | - Toru Takumi
- RIKEN Brain Science Institute, Wako, Saitama, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan.
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Affiliation(s)
- Naoyuki Tsuchiya
- Molecular and Genetic Epidemiology Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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47
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Hamada J, Onuma H, Ochi F, Hirai H, Takemoto K, Miyoshi A, Matsushita M, Kadota Y, Ohashi J, Kawamura R, Takata Y, Nishida W, Hashida S, Ishii E, Osawa H. Endoplasmic reticulum stress induced by tunicamycin increases resistin messenger ribonucleic acid through the pancreatic endoplasmic reticulum eukaryotic initiation factor 2α kinase-activating transcription factor 4-CAAT/enhancer binding protein-α homologous protein pathway in THP-1 human monocytes. J Diabetes Investig 2015; 7:312-23. [PMID: 27330716 PMCID: PMC4847884 DOI: 10.1111/jdi.12434] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 09/09/2015] [Accepted: 09/23/2015] [Indexed: 01/06/2023] Open
Abstract
AIMS/INTRODUCTION Resistin, secreted from adipocytes, causes insulin resistance in mice. In humans, the resistin gene is mainly expressed in monocytes and macrophages. Tunicamycin is known to induce endoplasmic reticulum (ER) stress, and reduce resistin gene expression in 3T3-L1 mouse adipocytes. The aim of the present study was to examine whether ER stress affects resistin gene expression in human monocytes. MATERIALS AND METHODS The relationship between resistin messenger ribonucleic acid (mRNA) and ER stress markers mRNA was analyzed by reverse transcription polymerase chain reaction in isolated monocytes of 30 healthy volunteers. The effect of endotoxin/lipopolysaccharides or tunicamycin on resistin gene expression was analyzed in THP-1 human monocytes. Signaling pathways leading to resistin mRNA were assessed by the knockdown using small interfering RNA or overexpression of key molecules involved in unfolded protein response. RESULTS Resistin mRNA was positively associated with immunoglobulin heavy chain-binding protein (BiP) or CAAT/enhancer binding protein-α homologous protein (CHOP) mRNA in human isolated monocytes. In THP-1 cells, lipopolysaccharides increased mRNA of BiP, pancreatic endoplasmic reticulum eukaryotic initiation factor 2α kinase (PERK) and CHOP, as well as resistin. Tunicamycin also increased resistin mRNA. This induction appeared to be dose- and time-dependent. Tunicamycin-induced resistin mRNA was inhibited by chemical chaperone, 4-phenylbutyric acid. The knockdown of either PERK, activating transcription factor 4 (ATF4) or CHOP reduced tunicamycin-induced resistin mRNA. Conversely, overexpression of ATF4 or CHOP increased resistin mRNA. CONCLUSIONS Endoplasmic reticulum stress induced by tunicamycin increased resistin mRNA through the PERK-ATF4-CHOP pathway in THP-1 human monocytes. ER stress could lead to insulin resistance through enhanced resistin gene expression in human monocytes.
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Affiliation(s)
- Junpei Hamada
- Department of Pediatrics Ehime University Graduate School of Medicine Ehime Japan
| | - Hiroshi Onuma
- Department of Diabetes and Molecular Genetics Ehime University Graduate School of Medicine Ehime Japan
| | - Fumihiro Ochi
- Department of Pediatrics Ehime University Graduate School of Medicine Ehime Japan
| | - Hiroki Hirai
- Department of Pediatrics Ehime University Graduate School of Medicine Ehime Japan
| | - Koji Takemoto
- Department of Pediatrics Ehime University Graduate School of Medicine Ehime Japan
| | - Akiko Miyoshi
- Department of Diabetes and Molecular Genetics Ehime University Graduate School of Medicine Ehime Japan
| | - Manami Matsushita
- Department of Diabetes and Molecular Genetics Ehime University Graduate School of Medicine Ehime Japan
| | - Yuko Kadota
- Department of Diabetes and Molecular Genetics Ehime University Graduate School of Medicine Ehime Japan
| | - Jun Ohashi
- Department of Biological Sciences Tokyo University Graduate School of Science Tokyo Japan
| | - Ryoichi Kawamura
- Department of Diabetes and Molecular Genetics Ehime University Graduate School of Medicine Ehime Japan
| | - Yasunori Takata
- Department of Diabetes and Molecular Genetics Ehime University Graduate School of Medicine Ehime Japan
| | - Wataru Nishida
- Department of Diabetes and Molecular Genetics Ehime University Graduate School of Medicine Ehime Japan
| | - Seiichi Hashida
- Institute for Health Sciences Tokushima Bunri University Tokushima Japan
| | - Eiichi Ishii
- Department of Pediatrics Ehime University Graduate School of Medicine Ehime Japan
| | - Haruhiko Osawa
- Department of Diabetes and Molecular Genetics Ehime University Graduate School of Medicine Ehime Japan
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Nishida N, Ohashi J, Sugiyama M, Tsuchiura T, Yamamoto K, Hino K, Honda M, Kaneko S, Yatsuhashi H, Koike K, Yokosuka O, Tanaka E, Taketomi A, Kurosaki M, Izumi N, Sakamoto N, Eguchi Y, Sasazuki T, Tokunaga K, Mizokami M. Effects of HLA-DPB1 genotypes on chronic hepatitis B infection in Japanese individuals. ACTA ACUST UNITED AC 2015; 86:406-12. [PMID: 26449183 DOI: 10.1111/tan.12684] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/04/2015] [Accepted: 09/15/2015] [Indexed: 01/26/2023]
Abstract
Significant associations of HLA-DP alleles with chronic hepatitis B (CHB) infection are evident in Asian and Arabian populations, including Japanese, Han Chinese, Korean, and Saudi Arabian populations. Here, significant associations between CHB infection and five DPB1 alleles (two susceptibility alleles, DPB1(*) 05:01 and (*) 09:01, and three protective alleles, DPB1(*) 02:01, (*) 04:01, and (*) 04:02) were confirmed in a population comprising of 2582 Japanese individuals. Furthermore, odds ratios for CHB were higher for those with both DPB1 susceptibility alleles than for those with only one susceptibility allele; therefore, effects of susceptibility alleles were additive for risk of CHB infection. Similarly, protective alleles showed an additive effect on protection from CHB infection. Moreover, heterozygotes of any protective allele showed stronger association with CHB than did homozygotes, suggesting that heterozygotes may bind a greater variety of hepatitis B-derived peptides, and thus present these peptides more efficiently to T-cell receptors than homozygotes. Notably, compound heterozygote of the protective allele (any one of DPB1*02:01, *04:01, and *04:02) and the susceptible allele DPB1*05:01 was significantly associated with protection against CHB infection, which indicates that one protective HLA-DPB1 molecule can provide dominant protection. Identification of the HLA-DPB1 genotypes associated with susceptibility to and protection from CHB infection is essential for future analysis of the mechanisms responsible for immune recognition of hepatitis B virus antigens by HLA-DPB1 molecules.
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Affiliation(s)
- N Nishida
- Department of Hepatic Disease, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, Japan.,Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - J Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - M Sugiyama
- Department of Hepatic Disease, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, Japan
| | - T Tsuchiura
- Department of Hepatic Disease, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, Japan
| | - K Yamamoto
- Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Japan
| | - K Hino
- Department of Hepatology and Pancreatology, Kawasaki Medical School, Kurashiki, Japan
| | - M Honda
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - S Kaneko
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - H Yatsuhashi
- Clinical Research Center, National Nagasaki Medical Center, Nagasaki, Japan
| | - K Koike
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - O Yokosuka
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - E Tanaka
- Department of Medicine, Shinshu University School of Medicine, Matsumoto, Japan
| | - A Taketomi
- Department of Gastroenterological Surgery I, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - M Kurosaki
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo, Japan
| | - N Izumi
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo, Japan
| | - N Sakamoto
- Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Y Eguchi
- Division of Hepatology, Saga Medical School, Saga, Japan
| | - T Sasazuki
- Institute for Advanced Study, Kyushu University, Fukuoka, Japan
| | - K Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - M Mizokami
- Department of Hepatic Disease, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, Japan
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Yasukochi Y, Naka I, Patarapotikul J, Hananantachai H, Ohashi J. Genetic evidence for contribution of human dispersal to the genetic diversity of EBA-175 in Plasmodium falciparum. Malar J 2015; 14:293. [PMID: 26231699 PMCID: PMC4522064 DOI: 10.1186/s12936-015-0820-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/21/2015] [Indexed: 01/06/2023] Open
Abstract
Background The 175-kDa erythrocyte binding antigen (EBA-175) of Plasmodium falciparum plays a crucial role in merozoite invasion into human erythrocytes. EBA-175 is believed to have been under diversifying selection; however, there have been no studies investigating the effect of dispersal of humans out of Africa on the genetic variation of EBA-175 in P. falciparum. Methods The PCR-direct sequencing was performed for a part of the eba-175 gene (regions II and III) using DNA samples obtained from Thai patients infected with P. falciparum. The divergence times for the P. falciparum eba-175 alleles were estimated assuming that P. falciparum/Plasmodium reichenowi divergence occurred 6 million years ago (MYA). To examine the possibility of diversifying selection, nonsynonymous and synonymous substitution rates for Plasmodium species were also estimated. Results A total of 32 eba-175 alleles were identified from 131 Thai P. falciparum isolates. Their estimated divergence time was 0.13–0.14 MYA, before the exodus of humans from Africa. A phylogenetic tree for a large sequence dataset of P. falciparumeba-175 alleles from across the world showed the presence of a basal Asian-specific cluster for all P. falciparum sequences. A markedly more nonsynonymous substitutions than synonymous substitutions in region II in P. falciparum was also detected, but not within Plasmodium species parasitizing African apes, suggesting that diversifying selection has acted specifically on P. falciparumeba-175. Conclusions Plasmodium falciparumeba-175 genetic diversity appeared to increase following the exodus of Asian ancestors from Africa. Diversifying selection may have played an important role in the diversification of eba-175 allelic lineages. The present results suggest that the dispersals of humans out of Africa influenced significantly the molecular evolution of P. falciparum EBA-175. Electronic supplementary material The online version of this article (doi:10.1186/s12936-015-0820-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yoshiki Yasukochi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. .,Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Jintana Patarapotikul
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Hathairad Hananantachai
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. .,Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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50
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Miyadera H, Ohashi J, Lernmark Å, Kitamura T, Tokunaga K. Cell-surface MHC density profiling reveals instability of autoimmunity-associated HLA. J Clin Invest 2014; 125:275-91. [PMID: 25485681 DOI: 10.1172/jci74961] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 11/06/2014] [Indexed: 12/17/2022] Open
Abstract
Polymorphisms within HLA gene loci are strongly associated with susceptibility to autoimmune disorders; however, it is not clear how genetic variations in these loci confer a disease risk. Here, we devised a cell-surface MHC expression assay to detect allelic differences in the intrinsic stability of HLA-DQ proteins. We found extreme variation in cell-surface MHC density among HLA-DQ alleles, indicating a dynamic allelic hierarchy in the intrinsic stability of HLA-DQ proteins. Using the case-control data for type 1 diabetes (T1D) for the Swedish and Japanese populations, we determined that T1D risk-associated HLA-DQ haplotypes, which also increase risk for autoimmune endocrinopathies and other autoimmune disorders, encode unstable proteins, whereas the T1D-protective haplotypes encode the most stable HLA-DQ proteins. Among the amino acid variants of HLA-DQ, alterations in 47α, the residue that is located on the outside of the peptide-binding groove and acts as a key stability regulator, showed strong association with T1D. Evolutionary analysis suggested that 47α variants have been the target of positive diversifying selection. Our study demonstrates a steep allelic hierarchy in the intrinsic stability of HLA-DQ that is associated with T1D risk and protection, suggesting that HLA instability mediates the development of autoimmune disorders.
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