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Kanamori H, Yamada Y, Ito Y, Shirosaki K, Yamagishi S, Maeda Y, Kudo Y, Umeyama T, Takahashi N, Kato M, Hasegawa Y, Matsubara K, Shinoda M, Obara H, Irie R, Tsujikawa H, Okita H, Nguyen PT, Saigo K, Mitsunaga S, Inoue I, Kitagawa Y, Kuroda T. Noninvasive graft monitoring using donor-derived cell-free DNA in Japanese liver transplantation. Hepatol Res 2024; 54:300-314. [PMID: 37850337 DOI: 10.1111/hepr.13978] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/06/2023] [Accepted: 10/13/2023] [Indexed: 10/19/2023]
Abstract
AIM To evaluate the use of donor-derived cell-free DNA (dd-cfDNA) in diagnosing graft injuries in Japanese liver transplantation (LTx), including family-related living donors. METHODS A total of 321 samples from 10 newly operated LTx recipients were collected to monitor the early dynamics of dd-cfDNA levels after LTx. Fifty-five samples from 55 recipients were collected during protocol biopsies (PB), whereas 36 samples from 27 recipients were collected during event biopsies, consisting of 11 biopsy-proven acute rejection (AR), 20 acute dysfunctions without rejection (ADWR), and 5 chronic rejections. The levels of dd-cfDNA were quantified using a next-generation sequencer based on single nucleotide polymorphisms. RESULTS The dd-cfDNA levels were elevated significantly after LTx, followed by a rapid decline to the baseline in patients without graft injury within 30 days post-LTx. The dd-cfDNA levels were significantly higher in the 11 samples obtained during AR than those obtained during PB (p < 0.0001), which decreased promptly after treatment. The receiver operator characteristic curve analysis of diagnostic ability yielded areas under the curve of 0.975 and 0.897 for AR (rejection activity index [RAI] ≥3) versus PB and versus non-AR (ADWR + PB). The dd-cfDNA levels during AR were elevated earlier and correlated more strongly with the RAI (r = 0.740) than aspartate aminotransferase/alanine aminotransferase. The dd-cfDNA levels were neither associated with graft fibrosis based on histology nor the status of donor-specific antibodies in PB samples. CONCLUSIONS Donor-derived cell-free DNA serves as a sensitive biomarker for detecting graft injuries in LTx. Further large-scale cohort studies are warranted to optimize its use in differentiating various post-LTx etiologies.
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Affiliation(s)
- Hiroki Kanamori
- Department of Pediatric Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Yohei Yamada
- Department of Pediatric Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Yoko Ito
- Department of Pediatric Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Koji Shirosaki
- Department of Pediatric Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Satoko Yamagishi
- Department of Pediatric Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Yutaro Maeda
- Department of Pediatric Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Yumi Kudo
- Department of Pediatric Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Tomoshige Umeyama
- Department of Pediatric Surgery, St Luke's International Hospital, Tokyo, Japan
| | - Nobuhiro Takahashi
- Department of Pediatric Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Mototoshi Kato
- Department of Pediatric Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Yasushi Hasegawa
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Kentaro Matsubara
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Masahiro Shinoda
- Digestive Diseases Center, International University of Health and Welfare School of Medicine, Mita Hospital, Tokyo, Japan
| | - Hideaki Obara
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Rie Irie
- Department of Diagnostic Pathology, Nippon Koukan Hospital, Kawasaki, Japan
| | - Hanako Tsujikawa
- Division of Diagnostic Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Hajime Okita
- Division of Diagnostic Pathology, Keio University School of Medicine, Tokyo, Japan
| | | | - Kenichi Saigo
- Department of Transplantation Surgery, Japan Community Health Care Organization, Chiba Hospital, Chiba, Japan
| | - Shigeki Mitsunaga
- Human Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Tatsuo Kuroda
- Department of Pediatric Surgery, Keio University School of Medicine, Tokyo, Japan
- Kanagawa Children's Medical Center, Kanagawa, Japan
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Nishimura L, Tanino A, Ajimoto M, Katsumura T, Ogawa M, Koganebuchi K, Waku D, Kumagai M, Sugimoto R, Nakaoka H, Oota H, Inoue I. Metagenomic analyses of 7000 to 5500 years old coprolites excavated from the Torihama shell-mound site in the Japanese archipelago. PLoS One 2024; 19:e0295924. [PMID: 38265980 PMCID: PMC10807776 DOI: 10.1371/journal.pone.0295924] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 12/03/2023] [Indexed: 01/26/2024] Open
Abstract
Coprolites contain various kinds of ancient DNAs derived from gut micro-organisms, viruses, and foods, which can help to determine the gut environment of ancient peoples. Their genomic information should be helpful in elucidating the interaction between hosts and microbes for thousands of years, as well as characterizing the dietary behaviors of ancient people. We performed shotgun metagenomic sequencing on four coprolites excavated from the Torihama shell-mound site in the Japanese archipelago. The coprolites were found in the layers of the Early Jomon period, corresponding stratigraphically to 7000 to 5500 years ago. After shotgun sequencing, we found that a significant number of reads showed homology with known gut microbe, viruses, and food genomes typically found in the feces of modern humans. We detected reads derived from several types of phages and their host bacteria simultaneously, suggesting the coexistence of viruses and their hosts. The food genomes provide biological evidence for the dietary behavior of the Jomon people, consistent with previous archaeological findings. These results indicate that ancient genomic analysis of coprolites is useful for understanding the gut environment and lifestyle of ancient peoples.
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Affiliation(s)
- Luca Nishimura
- Human Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| | - Akio Tanino
- Kitasato University Graduate School of Medical Sciences, Sagamihara, Kanagawa, Japan
| | | | - Takafumi Katsumura
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Motoyuki Ogawa
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Kae Koganebuchi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Daisuke Waku
- Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Tokyo, Japan
| | - Masahiko Kumagai
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Ryota Sugimoto
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, Sasaki Institute, Tokyo, Japan
| | - Hiroki Oota
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
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Chakkarappan SR, Umadharshini KV, Dhamodharan S, Rose MM, Gopu G, Murugan AK, Inoue I, Munirajan AK. Super enhancer loci of EGFR regulate EGFR variant 8 through enhancer RNA and strongly associate with survival in HNSCCs. Mol Genet Genomics 2024; 299:3. [PMID: 38236481 DOI: 10.1007/s00438-023-02089-z] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/21/2023] [Indexed: 01/19/2024]
Abstract
Epidermal growth factor receptor (EGFR) has been shown to be overexpressed in human cancers due to mutation, amplification, and epigenetic hyperactivity, which leads to deregulated transcriptional mechanism. Among the eight different EGFR isoforms, the mechanism of regulation of full-length variant 1 is well-known, no studies have examined the function & factors regulating the expression of variant 8. This study aimed to understand the function of EGFR super-enhancer loci and its associated transcription factors regulating the expression of EGFR variant 8. Our study shows that overexpression of variant 8 and its transcription was more prevalent than variant 1 in many cancers and positively correlated with the EGFR-AS1 expression in oral cancer and HNSCC. Notably, individuals overexpressing variant 8 showed shorter overall survival and had a greater connection with other clinical traits than patients with overexpression of variant 1. In this study, TCGA enhancer RNA profiling on the constituent enhancer (CE1 and CE2) region revealed that the multiple enhancer RNAs formed from CE2 by employing CE1 as a promoter. Our bioinformatic analysis further supports the enrichment of enhancer RNA specific chromatin marks H3K27ac, H3K4me1, POL2 and H2AZ on CE2. GeneHancer and 3D chromatin capture analysis showed clustered interactions between CE1, CE2 loci and this interaction may regulates expression of both EGFR-eRNA and variant 8. Moreover, increased expression of SNAI2 and its close relationship to EGFR-AS1 and variant 8 suggest that SNAI2 could regulates variant 8 overexpression by building a MegaTrans complex with both EGFR-eRNA and EGFR-AS1. Our findings show that EGFR variant 8 and its transcriptional regulation & chromatin modification by eRNAs may provide a rationale for targeting RNA splicing in combination with targeted EGFR therapies in cancer.
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Affiliation(s)
- Sundaram Reddy Chakkarappan
- Department of Health Research, Multi Disciplinary Research Unit (DHR-MRU), Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India
| | | | - Shankar Dhamodharan
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India
| | - Mathew Maria Rose
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India
| | - Govindasamy Gopu
- Department of Surgical Oncology, Rajiv Gandhi Government General Hospital, Madras Medical College, Chennai, 600003, India
| | - Avaniyapuram Kannan Murugan
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, 11211, Riyadh, Saudi Arabia
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Arasambattu Kannan Munirajan
- Department of Health Research, Multi Disciplinary Research Unit (DHR-MRU), Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India.
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India.
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Mitsunaga S, Fujito N, Nakaoka H, Imazeki R, Nagata E, Inoue I. Detection of APP gene recombinant in human blood plasma. Sci Rep 2023; 13:21703. [PMID: 38066066 PMCID: PMC10709617 DOI: 10.1038/s41598-023-48993-7] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
The pathogenesis of Alzheimer's disease (AD) is believed to involve the accumulation of amyloid-β in the brain, which is produced by the sequential cleavage of amyloid precursor protein (APP) by β-secretase and γ-secretase. Recently, analysis of genomic DNA and mRNA from postmortem brain neurons has revealed intra-exonic recombinants of APP (gencDNA), which have been implicated in the accumulation of amyloid-β. In this study, we computationally analyzed publicly available sequence data (SRA) using probe sequences we constructed to screen APP gencDNAs. APP gencDNAs were detected in SRAs constructed from both genomic DNA and RNA obtained from the postmortem brain and in the SRA constructed from plasma cell-free mRNA (cf-mRNA). The SRA constructed from plasma cf-mRNA showed a significant difference in the number of APP gencDNA reads between SAD and NCI: the p-value from the Mann-Whitney U test was 5.14 × 10-6. The transcripts were also found in circulating nucleic acids (CNA) from our plasma samples with NGS analysis. These data indicate that transcripts of APP gencDNA can be detected in blood plasma and suggest the possibility of using them as blood biomarkers for Alzheimer's disease.
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Affiliation(s)
- Shigeki Mitsunaga
- Laboratory of Human Genetics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.
| | - Naoko Fujito
- Laboratory of Human Genetics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, 411-8540, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Ryoko Imazeki
- Department of Neurology, Tokai University School of Medicine, Isehara, Japan
| | - Eiichiro Nagata
- Department of Neurology, Tokai University School of Medicine, Isehara, Japan
| | - Ituro Inoue
- Laboratory of Human Genetics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.
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5
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Shirozu N, Ohgidani M, Hata N, Tanaka S, Inamine S, Sagata N, Kimura T, Inoue I, Arimura K, Nakamizo A, Nishimura A, Maehara N, Takagishi S, Iwaki K, Nakao T, Masuda K, Sakai Y, Mizoguchi M, Yoshimoto K, Kato TA. Angiogenic and inflammatory responses in human induced microglia-like (iMG) cells from patients with Moyamoya disease. Sci Rep 2023; 13:14842. [PMID: 37684266 PMCID: PMC10491754 DOI: 10.1038/s41598-023-41456-z] [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: 06/16/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023] Open
Abstract
Angiogenic factors associated with Moyamoya disease (MMD) are overexpressed in M2 polarized microglia in ischemic stroke, suggesting that microglia may be involved in the pathophysiology of MMD; however, existing approaches are not applicable to explore this hypothesis. Herein we applied blood induced microglial-like (iMG) cells. We recruited 25 adult patients with MMD and 24 healthy volunteers. Patients with MMD were subdivided into progressive (N = 7) or stable (N = 18) group whether novel symptoms or radiographic advancement of Suzuki stage within 1 year was observed or not. We produced 3 types of iMG cells; resting, M1-, and M2-induced cells from monocytes, then RNA sequencing followed by GO and KEGG pathway enrichment analysis and qPCR assay were performed. RNA sequencing of M2-induced iMG cells revealed that 600 genes were significantly upregulated (338) or downregulated (262) in patients with MMD. Inflammation and immune-related factors and angiogenesis-related factors were specifically associated with MMD in GO analysis. qPCR for MMP9, VEGFA, and TGFB1 expression validated these findings. This study is the first to demonstrate that M2 microglia may be involved in the angiogenic process of MMD. The iMG technique provides a promising approach to explore the bioactivity of microglia in cerebrovascular diseases.
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Affiliation(s)
- Noritoshi Shirozu
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahiro Ohgidani
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
- Department of Functional Anatomy and Neuroscience, Asahikawa Medical University, Asahikawa, Japan
| | - Nobuhiro Hata
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shunya Tanaka
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shogo Inamine
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Noriaki Sagata
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Tetsuaki Kimura
- Division of Human Genetics, National Institute of Genetics, Mishima, Japan
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Koichi Arimura
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Akira Nakamizo
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ataru Nishimura
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naoki Maehara
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Soh Takagishi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Katsuma Iwaki
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomohiro Nakao
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Keiji Masuda
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Yasunari Sakai
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takahiro A Kato
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan.
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Tamura R, Nakaoka H, Yachida N, Ueda H, Ishiguro T, Motoyama T, Inoue I, Enomoto T, Yoshihara K. Spatial genomic diversity associated with APOBEC mutagenesis in squamous cell carcinoma arising from ovarian teratoma. Cancer Sci 2023; 114:2145-2157. [PMID: 36762791 PMCID: PMC10154883 DOI: 10.1111/cas.15754] [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: 11/16/2022] [Revised: 01/28/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Although the gross and microscopic features of squamous cell carcinoma arising from ovarian mature cystic teratoma (MCT-SCC) vary from case to case, the spatial spreading of genomic alterations within the tumor remains unclear. To clarify the spatial genomic diversity in MCT-SCCs, we performed whole-exome sequencing by collecting 16 samples from histologically different parts of two MCT-SCCs. Both cases showed histological diversity within the tumors (case 1: nonkeratinizing and keratinizing SCC and case 2: nonkeratinizing SCC and anaplastic carcinoma) and had different somatic mutation profiles by histological findings. Mutation signature analysis revealed a significantly enriched apolipoprotein B mRNA editing enzyme catalytic subunit (APOBEC) signature at all sites. Intriguingly, the spread of genomic alterations within the tumor and the clonal evolution patterns from nonmalignant epithelium to cancer sites differed between cases. TP53 mutation and copy number alterations were widespread at all sites, including the nonmalignant epithelium, in case 1. Keratinizing and nonkeratinizing SCCs were differentiated by the occurrence of unique somatic mutations from a common ancestral clone. In contrast, the nonmalignant epithelium showed almost no somatic mutations in case 2. TP53 mutation and the copy number alteration similarities were observed only in nonkeratinizing SCC samples. Nonkeratinizing SCC and anaplastic carcinoma shared almost no somatic mutations, suggesting that each locally and independently arose in the MCT. We demonstrated that two MCT-SCCs with different histologic findings were highly heterogeneous tumors with clearly different clones associated with APOBEC-mediated mutagenesis, suggesting the importance of evaluating intratumor histological and genetic heterogeneity among multiple sites of MCT-SCC.
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Affiliation(s)
- Ryo Tamura
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, Sasaki Institute, Tokyo, Japan
| | - Nozomi Yachida
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Haruka Ueda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tatsuya Ishiguro
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Teiichi Motoyama
- Department of Molecular and Diagnostic Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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Toyoda Y, Nakayama A, Nakatochi M, Kawamura Y, Nakaoka H, Yamamoto K, Shimizu S, Ooyama H, Ooyama K, Shimizu T, Nagase M, Hidaka Y, Ichida K, Inoue I, Shinomiya N, Matsuo H. Genome-wide meta-analysis between renal overload type and renal underexcretion type of clinically defined gout in Japanese populations. Mol Genet Metab 2022; 136:186-189. [PMID: 35148957 DOI: 10.1016/j.ymgme.2022.01.100] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 11/23/2022]
Abstract
Despite progress in understanding of the genetic basis of gout, the precise factors affecting differences in gout susceptibility among different gout subtypes remain unclear. Using clinically diagnosed gout patients, we conducted a genome-wide meta-analysis of two distinct gout subtypes: the renal overload type and the renal underexcretion type. We provide genetic evidence at a genome-wide level of significance that supports a positive association between ABCG2 dysfunction and acquisition of the renal overload type.
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Affiliation(s)
- Yu Toyoda
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Saitama, Japan
| | - Akiyoshi Nakayama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Saitama, Japan
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Yusuke Kawamura
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Saitama, Japan
| | - Hirofumi Nakaoka
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Shizuoka, Japan; Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Tokyo, Japan
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine, Fukuoka, Japan
| | - Seiko Shimizu
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Saitama, Japan
| | | | | | - Toru Shimizu
- Midorigaoka Hospital, Osaka, Japan; Kyoto Industrial Health Association, Kyoto, Japan
| | | | | | - Kimiyoshi Ichida
- Department of Pathophysiology, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan; Division of Kidney and Hypertension, Jikei University School of Medicine, Tokyo, Japan
| | - Ituro Inoue
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Shizuoka, Japan
| | - Nariyoshi Shinomiya
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Saitama, Japan
| | - Hirotaka Matsuo
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Saitama, Japan.
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Yoshioka A, Nakaoka H, Fukumoto T, Inoue I, Nishigori C, Kunisada M. The landscape of genetic alterations of UVB-induced skin tumors in DNA repair-deficient mice. Exp Dermatol 2022; 31:1607-1617. [PMID: 35751582 DOI: 10.1111/exd.14634] [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: 04/01/2022] [Revised: 05/25/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022]
Abstract
Non-melanoma skin cancer (NMSC) is mainly caused by ultraviolet (UV)-induced somatic mutations and is characterized by UV signature modifications. Xeroderma pigmentosum group A (Xpa) knockout mice exhibit extreme UV-induced photo-skin carcinogenesis, along with a photosensitive phenotype. We performed whole-exome sequencing (WES) of squamous cell carcinoma (SCC) samples after repetitive ultraviolet B (UVB) exposure to investigate the differences in the landscape of somatic mutations between Xpa knockout and wild-type mice. Although the tumors that developed in mice harbored UV signature mutations in a similar set of cancer-related genes, the pattern of transcriptional strand asymmetry was largely different; UV signature mutations in Xpa knockout and wild-type mice preferentially occurred in transcribed and non-transcribed strands, respectively, reflecting a deficiency in transcription-coupled nucleotide excision repair in Xpa knockout mice. Serial time point analyses of WES for a tumor induced by only a single UVB exposure showed pathogenic mutations in Kras, Fat1, and Kmt2c, which may be driver genes for the initiation and promotion of SCC in Xpa knockout mice. Furthermore, the inhibitory effects on tumor production in Xpa knockout mice by the anti-inflammatory CXCL1 monoclonal antibody affected the pattern of somatic mutations, wherein the transcriptional strand asymmetry was attenuated and the activated signal transduction was shifted from the RAS/RAF/MAPK to the PIK3CA pathway.
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Affiliation(s)
- Ai Yoshioka
- Division of Dermatology, Department of Internal Related, Graduate School of Medicine, Kobe University, Kobe, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, Sasaki Institute, Tokyo, Japan.,Human Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Takeshi Fukumoto
- Division of Dermatology, Department of Internal Related, Graduate School of Medicine, Kobe University, Kobe, Japan
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Chikako Nishigori
- Division of Research on Intractable Dermatological Disease, Department of iPS cell Applications, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Makoto Kunisada
- Division of Dermatology, Department of Internal Related, Graduate School of Medicine, Kobe University, Kobe, Japan
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Nishimura L, Fujito N, Sugimoto R, Inoue I. Detection of Ancient Viruses and Long-Term Viral Evolution. Viruses 2022; 14:v14061336. [PMID: 35746807 PMCID: PMC9230872 DOI: 10.3390/v14061336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 12/22/2022] Open
Abstract
The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.
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Affiliation(s)
- Luca Nishimura
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Naoko Fujito
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Ryota Sugimoto
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Correspondence: ; Tel.: +81-55-981-6795
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10
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Sakaue S, Hosomichi K, Hirata J, Nakaoka H, Yamazaki K, Yawata M, Yawata N, Naito T, Umeno J, Kawaguchi T, Matsui T, Motoya S, Suzuki Y, Inoko H, Tajima A, Morisaki T, Matsuda K, Kamatani Y, Yamamoto K, Inoue I, Okada Y. Decoding the diversity of killer immunoglobulin-like receptors by deep sequencing and a high-resolution imputation method. Cell Genom 2022; 2:100101. [PMID: 36777335 PMCID: PMC9903714 DOI: 10.1016/j.xgen.2022.100101] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 08/07/2021] [Accepted: 02/02/2022] [Indexed: 12/12/2022]
Abstract
The killer cell immunoglobulin-like receptor (KIR) recognizes human leukocyte antigen (HLA) class I molecules and modulates the function of natural killer cells. Despite its role in immunity, the complex genomic structure has limited a deep understanding of the KIR genomic landscape. Here we conduct deep sequencing of 16 KIR genes in 1,173 individuals. We devise a bioinformatics pipeline incorporating copy number estimation and insertion or deletion (indel) calling for high-resolution KIR genotyping. We define 118 alleles in 13 genes and demonstrate a linkage disequilibrium structure within and across KIR centromeric and telomeric regions. We construct a KIR imputation reference panel (nreference = 689, imputation accuracy = 99.7%), apply it to biobank genotype (ntotal = 169,907), and perform phenome-wide association studies of 85 traits. We observe a dearth of genome-wide significant associations, even in immune traits implicated previously to be associated with KIR (the smallest p = 1.5 × 10-4). Our pipeline presents a broadly applicable framework to evaluate innate immunity in large-scale datasets.
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Affiliation(s)
- Saori Sakaue
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Center for Data Sciences, Harvard Medical School, Boston, MA 02115, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Corresponding author
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Jun Hirata
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hirofumi Nakaoka
- Human Genetics Laboratory, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Keiko Yamazaki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Department of Public Health, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Makoto Yawata
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, and National University Health System, Singapore 119228, Singapore
- NUSMed Immunology Translational Research Programme, and Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore 117609, Singapore
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 860-0811, Japan
| | - Nobuyo Yawata
- Department of Ocular Pathology and Imaging Science, Kyushu University, 812-8582, Japan
- Singapore Eye Research Institute, Singapore 169856, Singapore
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Tatsuhiko Naito
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Junji Umeno
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Takaaki Kawaguchi
- Division of Gastroenterology, Department of Medicine, Tokyo Yamate Medical Center, Tokyo 169-0073, Japan
| | - Toshiyuki Matsui
- Department of Gastroenterology, Fukuoka University Chikushi Hospital, Fukuoka 818-0067, Japan
| | - Satoshi Motoya
- Department of Gastroenterology, Sapporo-Kosei General Hospital, Sapporo 060-0033, Japan
| | - Yasuo Suzuki
- Department of Internal Medicine, Faculty of Medicine, Toho University, Chiba 274-8510, Japan
| | | | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Takayuki Morisaki
- Division of Molecular Pathology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Koichi Matsuda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita 565-0871, Japan
- Corresponding author
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11
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Yamaguchi M, Nakaoka H, Suda K, Yoshihara K, Ishiguro T, Yachida N, Saito K, Ueda H, Sugino K, Mori Y, Yamawaki K, Tamura R, Revathidevi S, Motoyama T, Tainaka K, Verhaak RGW, Inoue I, Enomoto T. Spatiotemporal dynamics of clonal selection and diversification in normal endometrial epithelium. Nat Commun 2022; 13:943. [PMID: 35177608 PMCID: PMC8854701 DOI: 10.1038/s41467-022-28568-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 05/19/2021] [Accepted: 02/02/2022] [Indexed: 12/15/2022] Open
Abstract
It has become evident that somatic mutations in cancer-associated genes accumulate in the normal endometrium, but spatiotemporal understanding of the evolution and expansion of mutant clones is limited. To elucidate the timing and mechanism of the clonal expansion of somatic mutations in cancer-associated genes in the normal endometrium, we sequence 1311 endometrial glands from 37 women. By collecting endometrial glands from different parts of the endometrium, we show that multiple glands with the same somatic mutations occupy substantial areas of the endometrium. We demonstrate that “rhizome structures”, in which the basal glands run horizontally along the muscular layer and multiple vertical glands rise from the basal gland, originate from the same ancestral clone. Moreover, mutant clones detected in the vertical glands diversify by acquiring additional mutations. These results suggest that clonal expansions through the rhizome structures are involved in the mechanism by which mutant clones extend their territories. Furthermore, we show clonal expansions and copy neutral loss-of-heterozygosity events occur early in life, suggesting such events can be tolerated many years in the normal endometrium. Our results of the evolutionary dynamics of mutant clones in the human endometrium will lead to a better understanding of the mechanisms of endometrial regeneration during the menstrual cycle and the development of therapies for the prevention and treatment of endometrium-related diseases. Through regeneration, the endometrium accumulates somatic mutations that can lead to diseases like endometriosis and cancer. Here, the authors use genomics to analyse normal endometrial glands from different patient cohorts, detect rhizome structures with common clonal ancestors and infer clonal expansion dynamics.
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Affiliation(s)
- Manako Yamaguchi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Hirofumi Nakaoka
- Human Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan. .,Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Chiyoda-ku, 101-0062, Japan.
| | - Kazuaki Suda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan.
| | - Tatsuya Ishiguro
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Nozomi Yachida
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Kyota Saito
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Haruka Ueda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Kentaro Sugino
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Yutaro Mori
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Kaoru Yamawaki
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Ryo Tamura
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | | | - Teiichi Motoyama
- Department of Molecular and Diagnostic Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Kazuki Tainaka
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan.,Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, 565-5241, Japan
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.,Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV, Amsterdam, The Netherlands
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan.
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan.
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12
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Sugimoto R, Nishimura L, Nguyen PT, Ito J, Parrish NF, Mori H, Kurokawa K, Nakaoka H, Inoue I. Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: Viruses, plasmids, and more. PLoS Comput Biol 2021; 17:e1009428. [PMID: 34673779 PMCID: PMC8530359 DOI: 10.1371/journal.pcbi.1009428] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 11/24/2020] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
Viruses are the most numerous biological entity, existing in all environments and infecting all cellular organisms. Compared with cellular life, the evolution and origin of viruses are poorly understood; viruses are enormously diverse, and most lack sequence similarity to cellular genes. To uncover viral sequences without relying on either reference viral sequences from databases or marker genes that characterize specific viral taxa, we developed an analysis pipeline for virus inference based on clustered regularly interspaced short palindromic repeats (CRISPR). CRISPR is a prokaryotic nucleic acid restriction system that stores the memory of previous exposure. Our protocol can infer CRISPR-targeted sequences, including viruses, plasmids, and previously uncharacterized elements, and predict their hosts using unassembled short-read metagenomic sequencing data. By analyzing human gut metagenomic data, we extracted 11,391 terminally redundant CRISPR-targeted sequences, which are likely complete circular genomes. The sequences included 2,154 tailed-phage genomes, together with 257 complete crAssphage genomes, 11 genomes larger than 200 kilobases, 766 genomes of Microviridae species, 56 genomes of Inoviridae species, and 95 previously uncharacterized circular small genomes that have no reliably predicted protein-coding gene. We predicted the host(s) of approximately 70% of the discovered genomes at the taxonomic level of phylum by linking protospacers to taxonomically assigned CRISPR direct repeats. These results demonstrate that our protocol is efficient for de novo inference of CRISPR-targeted sequences and their host prediction. The evolution and origins of viruses are long-standing questions in the field of biology. Viral genomes provide fundamental information to infer the evolution and origin of viruses. However, viruses are extraordinarily diverse, and there are no single genes shared across entire species. Several methods were developed to collect viral genomes from metagenome. To infer viral genomes from metagenome, previous approaches relied on reference viral genomes. We thought that such reference-based methods may not be sufficient to uncover diverse viral genomes; therefore, we developed a pipeline that utilizes CRISPR, a prokaryotic adaptive immunological memory. Using this pipeline, we discovered more than 10,000 positively complete CRISPR-targeted genomes from human gut metagenome datasets. A substantial portion of the discovered genomes encoded various types of capsid proteins, supporting the contention that these sequences are viral. Although the majority of these capsid-protein-coding sequences were previously characterized, we notably discovered Inoviridae genomes that were previously difficult to infer as being viral. Furthermore, some of the remaining unclassified sequences without a detectable capsid-protein-encoding gene had a notably low protein-coding ratio. Overall, our pipeline successfully discovered viruses and previously uncharacterized presumably mobile genetic elements targeted by CRISPR.
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Affiliation(s)
- Ryota Sugimoto
- Human Genetics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Luca Nishimura
- Human Genetics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Phuong Thanh Nguyen
- Human Genetics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 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, Minato-ku, Tokyo, Japan
| | - Nicholas F. Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, Center for Integrative Medical Sciences, RIKEN, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Hiroshi Mori
- Genome Diversity Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Ken Kurokawa
- Genome Evolution Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, Sasaki Institute, Chiyoda-ku, Tokyo, Japan
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- * E-mail:
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13
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Jinam TA, Hosomichi K, Nakaoka H, Phipps ME, Saitou N, Inoue I. Allelic and haplotypic HLA diversity in indigenous Malaysian populations explored using Next Generation Sequencing. Hum Immunol 2021; 83:17-26. [PMID: 34615609 DOI: 10.1016/j.humimm.2021.09.005] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 11/04/2022]
Abstract
The heterogenous population of Malaysia includes more than 50 indigenous groups, and characterizing their HLA diversity would not only provide insights to their ancestry, but also on the effects of natural selection on their genome. We utilized hybridization-based sequence capture and short-read sequencing on the HLA region of 172 individuals representing seven indigenous groups in Malaysia (Jehai, Kintaq, Temiar, Mah Meri, Seletar, Temuan, Bidayuh). Allele and haplotype frequencies of HLA-A, -B, -C, -DRB1, -DQA1, -DQB1, -DPA1, and -DPB1 revealed several ancestry-informative markers. Using SNP-based heterozygosity and pairwise Fst, we observed signals of natural selection, particularly in HLA-A, -C and -DPB1 genes. Consequently, we showed the impact of natural selection on phylogenetic inference using HLA and non-HLA SNPs. We demonstrate the utility of Next Generation Sequencing for generating unambiguous, high-throughput, high-resolution HLA data that adds to our knowledge of HLA diversity and natural selection in indigenous minority groups.
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Affiliation(s)
- Timothy A Jinam
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Japan; Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan.
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Chiyoda-ku, Tokyo, Japan
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Japan; Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Ituro Inoue
- Human Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
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14
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Tamura R, Yoshihara K, Matsuo K, Yachida N, Miyoshi A, Takahashi K, Sugino K, Yamaguchi M, Mori Y, Suda K, Ishiguro T, Okuda S, Motoyama T, Nakaoka H, Kikuchi A, Ueda Y, Inoue I, Enomoto T. Proposing a molecular classification associated with hypercoagulation in ovarian clear cell carcinoma. Gynecol Oncol 2021; 163:327-333. [PMID: 34452748 DOI: 10.1016/j.ygyno.2021.08.009] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/12/2021] [Accepted: 08/14/2021] [Indexed: 01/26/2023]
Abstract
BACKGROUND Although ovarian clear cell carcinoma (CCC) is associated with high incidence of thromboembolism, the clinicopathological and biological significance of hypercoagulable status in CCC remains unclear. MATERIALS AND METHODS We retrospectively analyzed pretreatment D-dimer levels, thromboembolic status, and clinical outcome of 125 CCCs in the discovery set and 143 CCCs in two other independent validation sets. Next, we performed RNA sequencing of 93 CCCs and compared coagulation-related gene profiles with 2492 pan-cancer data. We investigated differences in molecular characteristics of CCC subclasses based on coagulation status. RESULTS In the discovery dataset, D-dimer elevation above the normal range was significantly associated with shorter progression-free and overall survival, irrespective to thromboembolic status. Multivariate analysis identified D-dimer elevation and clinical stage as an independent prognostic factors. We confirmed the prognostic significance of D-dimer elevation in the validation sets. Tissue factor and IL6, which are considered key elements of cancer-induced hypercoagulation, were highly expressed in CCC than in other cancers regardless of D-dimer level. Higher activity of various oncogenic pathways was observed in CCC with compared to without D-dimer elevation. Moreover, hierarchical cluster analysis divided 57 CCCs with D-dimer elevation into immunologically hot and cold tumor subtypes. Hot tumors were characterized by enrichment of T-cell inflamed phenotype, inflammation, the epithelial-mesenchymal transition, and high serum levels of CRP, and cold tumors by enrichment of cell cycle and MYC pathways. CONCLUSIONS CCC represents hypercoagulable disease and elevate D-dimer is a prognostic factor for decreased survival in CCC. D-dimer high CCC has distinct molecular characteristics into the inflammatory-driven pathway (hot tumor) and the immune-suppressive pathway (cold tumor). Treatment implication of our proposed molecular classification merits further investigation.
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Affiliation(s)
- Ryo Tamura
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.
| | - Koji Matsuo
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, CA, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Nozomi Yachida
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ai Miyoshi
- Department of Obstetrics and Gynecology, Osaka University School of Medicine, Suita, Japan
| | - Kotaro Takahashi
- Department of Gynecology, Niigata Cancer Center Hospital, Niigata, Japan
| | - Kentaro Sugino
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Manako Yamaguchi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yutaro Mori
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kazuaki Suda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tatsuya Ishiguro
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shujiro Okuda
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, Japan; Medical AI Center, Niigata University School of Medicine, Niigata, Japan
| | - Teiichi Motoyama
- Department of Molecular and Diagnostic Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, Sasaki Institute, Tokyo, Japan
| | - Akira Kikuchi
- Department of Gynecology, Niigata Cancer Center Hospital, Niigata, Japan
| | - Yutaka Ueda
- Department of Obstetrics and Gynecology, Osaka University School of Medicine, Suita, Japan
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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15
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Otsuka T, Ueda K, Furukawa T, Koriyama C, Inoue I, Sato M. Significance of Mitochondrial DNA Haplogroup on Epidermal Growth Factor Receptor Mutation in Japanese Patients With Lung Adenocarcinoma. Anticancer Res 2021; 41:3997-4004. [PMID: 34281864 DOI: 10.21873/anticanres.15197] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM The frequency of somatic mutations of epidermal growth factor receptor (EGFR) in primary lung adenocarcinoma varies among populations and countries. The aim of the present study was to clarify whether the frequency of EGFR mutations in patients with lung adenocarcinoma depends on their mitochondrial DNA haplogroup, which reflects their maternal lineage. PATIENTS AND METHODS Using normal lung tissue specimens, the mitochondrial DNA haplogroup was determined by multiplex polymerase chain reaction in 135 Japanese patients who underwent surgery for primary lung adenocarcinoma. RESULTS The 135 patients were divided into two groups according to the two primitive haplotypes (N group, n=32; M group, n=103). The frequency of EGFR mutations in the N group was significantly higher than that in the M group (69% vs. 48%, p=0.044). The difference was prominent when the analysis was restricted to non-smokers (95% vs. 57%, p<0.01). CONCLUSION The frequency of EGFR mutations in lung adenocarcinoma patients depends on their mitochondrial lineage.
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Affiliation(s)
- Tsunayuki Otsuka
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Kazuhiro Ueda
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Tatsuhiko Furukawa
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Chihaya Koriyama
- Department of Epidemiology and Preventive Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Ituro Inoue
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Shizuoka, Japan
| | - Masami Sato
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
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16
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Toyoda Y, Kawamura Y, Nakayama A, Nakaoka H, Higashino T, Shimizu S, Ooyama H, Morimoto K, Uchida N, Shigesawa R, Takeuchi K, Inoue I, Ichida K, Suzuki H, Shinomiya N, Takada T, Matsuo H. Substantial anti-gout effect conferred by common and rare dysfunctional variants of URAT1/SLC22A12. Rheumatology (Oxford) 2021; 60:5224-5232. [PMID: 33821957 PMCID: PMC8566256 DOI: 10.1093/rheumatology/keab327] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/28/2021] [Indexed: 01/17/2023] Open
Abstract
Objectives Gout, caused by chronic elevation of serum uric acid levels, is the commonest form of inflammatory arthritis. The causative effect of common and rare variants of ATP-binding cassette transporter G2 (ABCG2/BCRP) on gout risk has been studied, but little attention has been paid to the effect of common (rs121907892, p.W258X) and rare variants of urate transporter 1 (URAT1/SLC22A12) on gout, despite dysfunctional variants of URAT1 having been identified as pathophysiological causes of renal hypouricaemia. Methods To address this important but overlooked issue, we investigated the effects of these URAT1 variants on gout susceptibility, using targeted exon sequencing on 480 clinically defined gout cases and 480 controls of Japanese males in combination with a series of functional analyses of newly identified URAT1 variants. Results Our results show that both common and rare dysfunctional variants of URAT1 markedly decrease the risk of gout (OR 0.0338, reciprocal OR 29.6, P = 7.66 × 10−8). Interestingly, we also found that the URAT1-related protective effect on gout eclipsed the ABCG2-related causative effect (OR 2.30–3.32). Our findings reveal only one dysfunctional variant of URAT1 to have a substantial anti-gout effect, even in the presence of causative variants of ABCG2, a ‘gout gene’. Conclusion Our findings provide a better understanding of gout/hyperuricaemia and its aetiology that is highly relevant to personalized health care. The substantial anti-gout effect of common and rare variants of URAT1 identified in the present study support the genetic concept of a ‘Common Disease, Multiple Common and Rare Variant’ model.
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Affiliation(s)
- Yu Toyoda
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan.,Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Yusuke Kawamura
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Akiyoshi Nakayama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Hirofumi Nakaoka
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan.,Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Tokyo, Japan
| | - Toshihide Higashino
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Seiko Shimizu
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | | | - Keito Morimoto
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Naohiro Uchida
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | | | - Kenji Takeuchi
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Ituro Inoue
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kimiyoshi Ichida
- Department of Pathophysiology, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan.,Division of Kidney and Hypertension, Jikei University School of Medicine, Tokyo, Japan
| | - Hiroshi Suzuki
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Nariyoshi Shinomiya
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Tappei Takada
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Hirotaka Matsuo
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
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17
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Revathidevi S, Murugan AK, Nakaoka H, Inoue I, Munirajan AK. APOBEC: A molecular driver in cervical cancer pathogenesis. Cancer Lett 2020; 496:104-116. [PMID: 33038491 PMCID: PMC7539941 DOI: 10.1016/j.canlet.2020.10.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [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: 06/25/2020] [Revised: 09/16/2020] [Accepted: 10/04/2020] [Indexed: 02/09/2023]
Abstract
Cervical cancer is one of the foremost common cancers in women. Human papillomavirus (HPV) infection remains a major risk factor of cervical cancer. In addition, numerous other genetic and epigenetic factors also are involved in the underlying pathogenesis of cervical cancer. Recently, it has been reported that apolipoprotein B mRNA editing enzyme catalytic polypeptide like (APOBEC), DNA-editing protein plays an important role in the molecular pathogenesis of cancer. Particularly, the APOBEC3 family was shown to induce tumor mutations by aberrant DNA editing mechanism. In general, APOBEC3 enzymes play a pivotal role in the deamination of cytidine to uridine in DNA and RNA to control diverse biological processes such as regulation of protein expression, innate immunity, and embryonic development. Innate antiviral activity of the APOBEC3 family members restrict retroviruses, endogenous retro-element, and DNA viruses including the HPV that is the leading risk factor for cervical cancer. This review briefly describes the pathogenesis of cervical cancer and discusses in detail the recent findings on the role of APOBEC in the molecular pathogenesis of cervical cancer. APOBEC enzymes deaminate cytidine to uridine and control diverse biological processes including viral restriction. APOBEC3, DNA/RNA-editing enzyme plays an important role in the molecular pathogenesis of cervical cancer. APOBEC3-mediated DNA editing leads to the accumulation of somatic mutations in tumors and HPV genome. Deregulation of APOBEC3 family genes cause genomic instability and result in drug resistance, and immune-evasion in tumors.
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Affiliation(s)
- Sundaramoorthy Revathidevi
- Department of Genetics, Dr ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, 600113, India; Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Avaniyapuram Kannan Murugan
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Hirofumi Nakaoka
- Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan; Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Chiyoda-ku, 101-0062, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Arasambattu Kannan Munirajan
- Department of Genetics, Dr ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, 600113, India.
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18
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Ito J, Kimura I, Soper A, Coudray A, Koyanagi Y, Nakaoka H, Inoue I, Turelli P, Trono D, Sato K. Endogenous retroviruses drive KRAB zinc-finger protein family expression for tumor suppression. Sci Adv 2020; 6:6/43/eabc3020. [PMID: 33087347 PMCID: PMC7577720 DOI: 10.1126/sciadv.abc3020] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/04/2020] [Indexed: 06/11/2023]
Abstract
Gene expression aberration is a hallmark of cancers, but the mechanisms underlying such aberrations remain unclear. Human endogenous retroviruses (HERVs) are genomic repetitive elements that potentially function as enhancers. Since numerous HERVs are epigenetically activated in tumors, their activation could cause global gene expression aberrations in tumors. Here, we show that HERV activation in tumors leads to the up-regulation of hundreds of transcriptional suppressors, namely, Krüppel-associated box domain-containing zinc-finger family proteins (KZFPs). KZFP genes are preferentially encoded nearby the activated HERVs in tumors and transcriptionally regulated by these adjacent HERVs. Increased HERV and KZFP expression in tumors was associated with better disease conditions. Increased KZFP expression in cancer cells altered the expression of genes related to the cell cycle and cell-matrix adhesion and suppressed cellular growth, migration, and invasion abilities. Our data suggest that HERV activation in tumors drives the synchronized elevation of KZFP expression, presumably leading to tumor suppression.
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Affiliation(s)
- 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, Minato-ku, Tokyo 1088639, Japan
| | - Izumi Kimura
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Andrew Soper
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan
| | - Alexandre Coudray
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Yoshio Koyanagi
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan
| | - Hirofumi Nakaoka
- Division of Human Genetics, National Institute of Genetics, Mishima 4118540, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Mishima 4118540, Japan
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - 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, Minato-ku, Tokyo 1088639, Japan.
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 3320012, Japan
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19
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Masuhara K, Akatsuka H, Tokusanai M, Li C, Iida Y, Okada Y, Suzuki T, Ohtsuka M, Inoue I, Kimura M, Hosokawa H, Hozumi K, Sato T. AMBRA1 controls antigen-driven activation and proliferation of naïve T cells. Int Immunol 2020; 33:107-118. [PMID: 32909612 DOI: 10.1093/intimm/dxaa063] [Citation(s) in RCA: 3] [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] [Received: 07/17/2020] [Accepted: 09/07/2020] [Indexed: 11/12/2022] Open
Abstract
AMBRA1 is a member of the BECN1 (BECLIN1) complex protein, and it plays a role in autophagy, cell death, tumorigenesis, and proliferation. We recently reported that on TCR stimulation, AMBRA1 controlled both autophagy and the cell cycle with metabolic regulation. Accumulating evidence has shown that autophagy and metabolic control are pivotal for T cell activation, clonal expansion, and effector/memory cell fate decision. However, it is unknown whether AMBRA1 is involved in T cell function under physiological conditions. We found that T cells in Ambra1-conditional knockout (cKO) mice induced exacerbated graft versus host response when they were transplanted into allogeneic BALB/c mice. Furthermore, Ambra1-deficient T cells showed increased proliferation and cytotoxic capability towards specific antigens in response to in vivo stimulation using allogeneic spleen cells. This enhanced immune response mainly contributed to naïve T cell hyperactivity. The T cell hyperactivity observed in this study were similar to those in some metabolic factor-deficient mice, but not those in other pro-autophagic factor-deficient mice. Under the static condition, however, naïve T cells were reduced in Ambra1-cKO mice, as same as in pro-autophagic factor-deficient mice. Collectively, these results suggested that AMBRA1 was involved in regulating T cell-mediated immune responses through autophagy-dependent and -independent mechanisms.
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Affiliation(s)
- Kaori Masuhara
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Hisako Akatsuka
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Mizuki Tokusanai
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Chenyang Li
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Yumi Iida
- Support Center for Medical Research and Education, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Yoshinori Okada
- Support Center for Medical Research and Education, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Takahiro Suzuki
- Department of Ophthalmology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Masato Ohtsuka
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Minoru Kimura
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Katsuto Hozumi
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Takehito Sato
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
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20
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Yachida N, Yoshihara K, Suda K, Nakaoka H, Ueda H, Sugino K, Yamaguchi M, Mori Y, Yamawaki K, Tamura R, Ishiguro T, Isobe M, Motoyama T, Inoue I, Enomoto T. ARID1A protein expression is retained in ovarian endometriosis with ARID1A loss-of-function mutations: implication for the two-hit hypothesis. Sci Rep 2020; 10:14260. [PMID: 32868822 PMCID: PMC7459315 DOI: 10.1038/s41598-020-71273-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 05/18/2020] [Accepted: 08/10/2020] [Indexed: 12/22/2022] Open
Abstract
ARID1A loss-of-function mutation accompanied by a loss of ARID1A protein expression is considered one of the most important driver events in endometriosis-associated ovarian cancer. Although our recent genomic study clarified that ARID1A loss-of-function mutations were detected in 13% of ovarian endometriosis, an association between the ARID1A mutation status and ARID1A protein expression in ovarian endometriosis remains unclear. We performed immunohistochemical staining for ARID1A in 78 ovarian endometriosis samples and 99 clear cell carcinoma samples. We revealed that not only 70 endometriosis samples without ARID1A mutations but also eight endometriosis samples with ARID1A loss-of-function mutations retained ARID1A protein expression. On the other hand, most of clear cell carcinomas with ARID1A loss-of-function mutations showed a loss of ARID1A protein expression. In particular, clear cell carcinoma samples which harbor multiple ARID1A loss-of-function mutations or both a single ARID1A loss-of-function mutation and ARID1A allelic imbalance lost ARID1A protein expression. However, ARID1A protein expression was retained in seven clear cell carcinomas with ARID1A loss-of-function mutations. These results suggest that a single ARID1A loss-of-function mutation is insufficient for ARID1A loss in ovarian endometriosis and some clear cell carcinoma. Further driver events may be needed for the malignant transformation of ovarian endometriosis with ARID1A loss-of-function mutations.
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Affiliation(s)
- Nozomi Yachida
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ward, Niigata, 951-8510, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ward, Niigata, 951-8510, Japan.
| | - Kazuaki Suda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ward, Niigata, 951-8510, Japan
| | - Hirofumi Nakaoka
- Human Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan.,Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Haruka Ueda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ward, Niigata, 951-8510, Japan
| | - Kentaro Sugino
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ward, Niigata, 951-8510, Japan
| | - Manako Yamaguchi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ward, Niigata, 951-8510, Japan
| | - Yutaro Mori
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ward, Niigata, 951-8510, Japan
| | - Kaoru Yamawaki
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ward, Niigata, 951-8510, Japan
| | - Ryo Tamura
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ward, Niigata, 951-8510, Japan
| | - Tatsuya Ishiguro
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ward, Niigata, 951-8510, Japan
| | - Masanori Isobe
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ward, Niigata, 951-8510, Japan
| | - Teiichi Motoyama
- Department of Molecular and Diagnostic Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ward, Niigata, 951-8510, Japan
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21
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Suda K, Cruz Diaz LA, Yoshihara K, Nakaoka H, Yachida N, Motoyama T, Inoue I, Enomoto T. Clonal lineage from normal endometrium to ovarian clear cell carcinoma through ovarian endometriosis. Cancer Sci 2020; 111:3000-3009. [PMID: 32473611 PMCID: PMC7419022 DOI: 10.1111/cas.14507] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 03/07/2020] [Revised: 05/14/2020] [Accepted: 05/25/2020] [Indexed: 12/20/2022] Open
Abstract
Clear cell carcinoma of the ovary is thought to arise from endometriosis. In addition, retrograde menstruation of shed endometrium is considered the origin of endometriosis. However, little evidence supports cellular continuity from uterine endometrium to clear cell carcinoma through endometriosis at the genomic level. Here, we performed multiregional whole‐exome sequencing to clarify clonal relationships among uterine endometrium, ovarian endometriosis and ovarian clear cell carcinoma in a 56‐year‐old patient. Many somatic mutations including cancer‐associated gene mutations in ARID1A, ATM, CDH4, NRAS and PIK3CA were shared among epithelium samples from uterine endometrium, endometriotic lesions distant from and adjacent to the carcinoma, and the carcinoma. The mutant allele frequencies of shared mutations increased from uterine endometrium to distant endometriosis, adjacent endometriosis, and carcinoma. Although a splice site mutation of ARID1A was shared among the four epithelium samples, a frameshift insertion in ARID1A was shared by adjacent endometriosis and carcinoma samples, suggesting that the biallelic mutations triggered malignant transformation. Somatic copy number alterations, including loss of heterozygosity events at PIK3CA and ATM, were identified only in adjacent endometriosis and carcinoma, suggesting that mutant allele‐specific imbalance is another key factor driving malignant transformation. By reconstructing a clonal evolution tree based on the somatic mutations, we showed that the epithelium samples were derived from a single ancestral clone. Although the study was limited to a single patient, the results from this illustrative case could suggest the possibility that epithelial cells of ovarian endometriosis and clear cell carcinoma were descendants of uterine endometrial epithelium.
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Affiliation(s)
- Kazuaki Suda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Luis Antonio Cruz Diaz
- Department of Genetics, School of Life Sciences, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Human Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hirofumi Nakaoka
- Department of Genetics, School of Life Sciences, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Human Genetics Laboratory, National Institute of Genetics, Mishima, Japan.,Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Chiyoda-ku, Japan
| | - Nozomi Yachida
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Teiichi Motoyama
- Department of Molecular and Diagnostic Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ituro Inoue
- Department of Genetics, School of Life Sciences, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Human Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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22
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Nakayama A, Nakatochi M, Kawamura Y, Yamamoto K, Nakaoka H, Shimizu S, Higashino T, Koyama T, Hishida A, Kuriki K, Watanabe M, Shimizu T, Ooyama K, Ooyama H, Nagase M, Hidaka Y, Matsui D, Tamura T, Nishiyama T, Shimanoe C, Katsuura-Kamano S, Takashima N, Shirai Y, Kawaguchi M, Takao M, Sugiyama R, Takada Y, Nakamura T, Nakashima H, Tsunoda M, Danjoh I, Hozawa A, Hosomichi K, Toyoda Y, Kubota Y, Takada T, Suzuki H, Stiburkova B, Major TJ, Merriman TR, Kuriyama N, Mikami H, Takezaki T, Matsuo K, Suzuki S, Hosoya T, Kamatani Y, Kubo M, Ichida K, Wakai K, Inoue I, Okada Y, Shinomiya N, Matsuo H. Subtype-specific gout susceptibility loci and enrichment of selection pressure on ABCG2 and ALDH2 identified by subtype genome-wide meta-analyses of clinically defined gout patients. Ann Rheum Dis 2020; 79:657-665. [PMID: 32238385 PMCID: PMC7213308 DOI: 10.1136/annrheumdis-2019-216644] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 11/15/2019] [Revised: 02/13/2020] [Accepted: 02/17/2020] [Indexed: 01/01/2023]
Abstract
Objectives Genome-wide meta-analyses of clinically defined gout were performed to identify subtype-specific susceptibility loci. Evaluation using selection pressure analysis with these loci was also conducted to investigate genetic risks characteristic of the Japanese population over the last 2000–3000 years. Methods Two genome-wide association studies (GWASs) of 3053 clinically defined gout cases and 4554 controls from Japanese males were performed using the Japonica Array and Illumina Array platforms. About 7.2 million single-nucleotide polymorphisms were meta-analysed after imputation. Patients were then divided into four clinical subtypes (the renal underexcretion type, renal overload type, combined type and normal type), and meta-analyses were conducted in the same manner. Selection pressure analyses using singleton density score were also performed on each subtype. Results In addition to the eight loci we reported previously, two novel loci, PIBF1 and ACSM2B, were identified at a genome-wide significance level (p<5.0×10–8) from a GWAS meta-analysis of all gout patients, and other two novel intergenic loci, CD2-PTGFRN and SLC28A3-NTRK2, from normal type gout patients. Subtype-dependent patterns of Manhattan plots were observed with subtype GWASs of gout patients, indicating that these subtype-specific loci suggest differences in pathophysiology along patients’ gout subtypes. Selection pressure analysis revealed significant enrichment of selection pressure on ABCG2 in addition to ALDH2 loci for all subtypes except for normal type gout. Conclusions Our findings on subtype GWAS meta-analyses and selection pressure analysis of gout will assist elucidation of the subtype-dependent molecular targets and evolutionary involvement among genotype, phenotype and subtype-specific tailor-made medicine/prevention of gout and hyperuricaemia.
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Affiliation(s)
- Akiyoshi Nakayama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan.,Medical Squadron, Air Base Group, Western Aircraft Control and Warning Wing, Japan Air Self-Defense Force, Kasuga, Japan
| | - Masahiro Nakatochi
- Division of Department of Nursing, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Kawamura
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan.,Department of General Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Japan
| | - Hirofumi Nakaoka
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Japan
| | - Seiko Shimizu
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Toshihide Higashino
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan.,Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan
| | - Teruhide Koyama
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Asahi Hishida
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kiyonori Kuriki
- Laboratory of Public Health, School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Miki Watanabe
- Department of Public Health, Nagoya City University Graduate School Medical Science, Nagoya, Japan
| | - Toru Shimizu
- Midorigaoka Hospital, Takatsuki, Japan.,Kyoto Industrial Health Association, Kyoto, Japan
| | | | | | | | | | - Daisuke Matsui
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takashi Tamura
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takeshi Nishiyama
- Department of Public Health, Nagoya City University Graduate School Medical Science, Nagoya, Japan
| | - Chisato Shimanoe
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan.,Clinical Research Center, Saga University Hospital, Saga, Japan
| | - Sakurako Katsuura-Kamano
- Department of Preventive Medicine, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Naoyuki Takashima
- Department of Health Science, Shiga University of Medical Science, Otsu, Japan.,Department of Public Health, Faculty of Medicine, Kindai University, Osaka-Sayama, Japan
| | - Yuya Shirai
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.,Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Makoto Kawaguchi
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan.,Department of Urology, National Defense Medical College, Tokorozawa, Japan
| | - Mikiya Takao
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan.,Department of Surgery, National Defense Medical College, Tokorozawa, Japan
| | - Ryo Sugiyama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Yuzo Takada
- Faculty of Medical Science, Teikyo University of Science, Tokyo, Japan
| | - Takahiro Nakamura
- Laboratory for Mathematics, National Defense Medical College, Tokorozawa, Japan
| | - Hiroshi Nakashima
- Department of Preventive Medicine and Public Health, National Defense Medical College, Tokorozawa, Japan
| | - Masashi Tsunoda
- Department of Preventive Medicine and Public Health, National Defense Medical College, Tokorozawa, Japan
| | - Inaho Danjoh
- Group of Privacy Controls, Tohoku Medical Megabank Organization, Sendai, Japan
| | - Atsushi Hozawa
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Yu Toyoda
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Yu Kubota
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Tappei Takada
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Hiroshi Suzuki
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Blanka Stiburkova
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic.,Institute of Rheumatology, Prague, Czech Republic
| | - Tanya J Major
- Department of Biochemisty, University of Otago, Dunedin, New Zealand
| | - Tony R Merriman
- Department of Biochemisty, University of Otago, Dunedin, New Zealand
| | - Nagato Kuriyama
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Haruo Mikami
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Toshiro Takezaki
- Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Sadao Suzuki
- Department of Public Health, Nagoya City University Graduate School Medical Science, Nagoya, Japan
| | - Tatsuo Hosoya
- Division of Kidney and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan.,Department of Pathophysiology and Therapy in Chronic Kidney Disease, Jikei University School of Medicine, Tokyo, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kimiyoshi Ichida
- Division of Kidney and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan.,Department of Pathophysiology, Tokyo University of Pharmacy and Life Science, Hachioji, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ituro Inoue
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Nariyoshi Shinomiya
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Hirotaka Matsuo
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
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23
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Tamura R, Yoshihara K, Nakaoka H, Yachida N, Yamaguchi M, Suda K, Ishiguro T, Nishino K, Ichikawa H, Homma K, Kikuchi A, Ueda Y, Takei Y, Fujiwara H, Motoyama T, Okuda S, Wakai T, Inoue I, Enomoto T. XCL1 expression correlates with CD8-positive T cells infiltration and PD-L1 expression in squamous cell carcinoma arising from mature cystic teratoma of the ovary. Oncogene 2020; 39:3541-3554. [PMID: 32115573 PMCID: PMC7176584 DOI: 10.1038/s41388-020-1237-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 11/07/2019] [Revised: 02/15/2020] [Accepted: 02/19/2020] [Indexed: 01/10/2023]
Abstract
Molecular characteristics of carcinoma arising from mature cystic teratoma of the ovary (MCT) remain unclear due to its rarity. We analyzed RNA-sequencing data of 2322 pan-cancer [1378 squamous cell carcinomas (SCC), 6 adenosquamous carcinomas (ASC), and 938 adenocarcinomas (AC)] including six carcinomas arising from MCT (four SCCs, one ASC, and one AC). Hierarchical clustering and principal component analysis showed that gene expression profiles of carcinomas arising from MCT were different between each histological type and that gene expression profiles of SCCs arising MCT (MCT-SCCs) was apparently similar to those of lung SCCs. By epidermis-associated pathways activity based on gene set enrichment analysis, 1030 SCCs were divided into two groups: epidermis-signature high (head and neck, esophagus, and skin) and low (cervix, lung, and MCT). In addition to pan-SCC transcriptome analysis, cytokeratin profiling based on immunohistochemistry in the independent samples of 21 MCT-SCCs clarified that MCT-SCC dominantly expressed CK18, suggesting the origin of MCT-SCC was columnar epithelium. Subsequently, we investigated differentially expressed genes in MCT-SCCs compared with different SCCs and identified XCL1 was specifically overexpressed in MCT-SCCs. Through immunohistochemistry analysis, we identified XCL1 expression on tumor cells in 13/24 (54%) of MCT-SCCs but not in MCTs. XCL1 expression was also significantly associated with the number of tumor-infiltrating CD8-positive T cells and PD-L1 expression on tumor cells. XCL1 produced by tumor cells may induce PD1/PD-L1 interaction and dysfunction of CD8-positive T cells in tumor microenvironment. XCL1 expression may be a novel biomarker for malignant transformation of MCT into SCC and a biomarker candidate for therapeutic response to an anti-PD1/PD-L1 therapy.
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Affiliation(s)
- Ryo Tamura
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan.
| | - Hirofumi Nakaoka
- Human Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Nozomi Yachida
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Manako Yamaguchi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Kazuaki Suda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Tatsuya Ishiguro
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Koji Nishino
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Hiroshi Ichikawa
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Keiichi Homma
- Department of Pathology, Niigata Cancer Center Hospital, Niigata, 951-8133, Japan
| | - Akira Kikuchi
- Department of Gynecology, Niigata Cancer Center Hospital, Niigata, 951-8133, Japan
| | - Yutaka Ueda
- Department of Obstetrics and Gynecology, Osaka University School of Medicine, Suita, 565-0871, Japan
| | - Yuji Takei
- Department of Obstetrics and Gynecology, Jichi Medical University, Shimotsuke, 329-0498, Japan
| | - Hiroyuki Fujiwara
- Department of Obstetrics and Gynecology, Jichi Medical University, Shimotsuke, 329-0498, Japan
| | - Teiichi Motoyama
- Department of Molecular and Diagnostic Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Shujiro Okuda
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Toshifumi Wakai
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
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24
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Tomoyasu Y, Yamaguchi T, Tajima A, Inoue I, Maki K. External apical root resorption and the interleukin-1B gene polymorphism in the Japanese population. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.odw.2009.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Yoko Tomoyasu
- Department of Orthodontics, School of Dentistry, Showa University, 2-1-1, Kitasenzoku, Ota-ku, Tokyo 145-8515, Japan
| | - Tetsutaro Yamaguchi
- Department of Orthodontics, School of Dentistry, Showa University, 2-1-1, Kitasenzoku, Ota-ku, Tokyo 145-8515, Japan
| | - Atsushi Tajima
- Department of Molecular Life Science, School of Medicine, Tokai University, Tokai, Japan
| | - Ituro Inoue
- Department of Molecular Life Science, School of Medicine, Tokai University, Tokai, Japan
| | - Koutaro Maki
- Department of Orthodontics, School of Dentistry, Showa University, 2-1-1, Kitasenzoku, Ota-ku, Tokyo 145-8515, Japan
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25
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Higashino T, Morimoto K, Nakaoka H, Toyoda Y, Kawamura Y, Shimizu S, Nakamura T, Hosomichi K, Nakayama A, Ooyama K, Ooyama H, Shimizu T, Ueno M, Ito T, Tamura T, Naito M, Nakashima H, Kawaguchi M, Takao M, Kawai Y, Osada N, Ichida K, Yamamoto K, Suzuki H, Shinomiya N, Inoue I, Takada T, Matsuo H. Dysfunctional missense variant of OAT10/SLC22A13 decreases gout risk and serum uric acid levels. Ann Rheum Dis 2019; 79:164-166. [PMID: 31780526 PMCID: PMC6937405 DOI: 10.1136/annrheumdis-2019-216044] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/13/2019] [Accepted: 09/30/2019] [Indexed: 11/17/2022]
Affiliation(s)
- Toshihide Higashino
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan.,Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan
| | - Keito Morimoto
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Hirofumi Nakaoka
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Japan
| | - Yu Toyoda
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Yusuke Kawamura
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Seiko Shimizu
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Takahiro Nakamura
- Laboratory for Mathematics, National Defense Medical College, Tokorozawa, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Akiyoshi Nakayama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | | | | | | | - Miki Ueno
- Division of Nursing, National Defense Medical College, Tokorozawa, Japan
| | - Toshimitsu Ito
- Department of Internal Medicine, Self-Defense Forces Central Hospital, Tokyo, Japan
| | - Takashi Tamura
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mariko Naito
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroshi Nakashima
- Department of Preventive Medicine and Public Health, National Defense Medical College, Tokorozawa, Japan
| | - Makoto Kawaguchi
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Mikiya Takao
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Yosuke Kawai
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine, Tokyo, Japan
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan
| | - Kimiyoshi Ichida
- Department of Pathophysiology, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Japan
| | - Hiroshi Suzuki
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Nariyoshi Shinomiya
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Ituro Inoue
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Japan
| | - Tappei Takada
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Hirotaka Matsuo
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
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26
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Suda K, Nakaoka H, Yoshihara K, Ishiguro T, Tamura R, Mori Y, Yamawaki K, Adachi S, Takahashi T, Kase H, Tanaka K, Yamamoto T, Motoyama T, Inoue I, Enomoto T. Clonal Expansion and Diversification of Cancer-Associated Mutations in Endometriosis and Normal Endometrium. Cell Rep 2019; 24:1777-1789. [PMID: 30110635 DOI: 10.1016/j.celrep.2018.07.037] [Citation(s) in RCA: 242] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 04/12/2018] [Accepted: 07/11/2018] [Indexed: 11/30/2022] Open
Abstract
Endometriosis is characterized by ectopic endometrial-like epithelium and stroma, of which molecular characteristics remain to be fully elucidated. We sequenced 107 ovarian endometriotic and 82 normal uterine endometrial epithelium samples isolated by laser microdissection. In both endometriotic and normal epithelium samples, numerous somatic mutations were identified within genes frequently mutated in endometriosis-associated ovarian cancers. KRAS is frequently mutated in endometriotic epithelium, with a higher mutant allele frequency (MAF) accompanied by arm-level allelic imbalances. Analyses of MAF, combined with multiregional sequencing, illuminated spatiotemporal evolution of the endometriosis and uterine endometrium genomes. We sequenced 109 single endometrial glands and found that each gland carried distinct cancer-associated mutations, demonstrating the heterogeneity of the genomic architecture of endometrial epithelium. Remarkable increases in MAF of mutations in cancer-associated genes in endometriotic epithelium suggest retrograde flow of endometrial cells already harboring cancer-associated mutations, with selective advantages at ectopic sites, leading to the development of endometriosis.
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Affiliation(s)
- Kazuaki Suda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Hirofumi Nakaoka
- Division of Human Genetics, National Institute of Genetics, Mishima 411-8540, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan.
| | - Tatsuya Ishiguro
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Ryo Tamura
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Yutaro Mori
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Kaoru Yamawaki
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Sosuke Adachi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Tomoko Takahashi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Hiroaki Kase
- Department of Obstetrics and Gynecology, Nagaoka Chuo General Hospital, Nagaoka 940-8653, Japan
| | - Kenichi Tanaka
- Niigata Medical Center Hospital, Niigata 950-2022, Japan
| | - Tadashi Yamamoto
- COI-s Biofluid Biomarker Center, Institute of Research Collaboration and Promotion, Niigata University, Niigata 950-2181, Japan
| | - Teiichi Motoyama
- Department of Molecular and Diagnostic Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Mishima 411-8540, Japan.
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan.
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27
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Suda K, Nakaoka H, Yoshihara K, Ishiguro T, Adachi S, Kase H, Motoyama T, Inoue I, Enomoto T. Different mutation profiles between epithelium and stroma in endometriosis and normal endometrium. Hum Reprod 2019; 34:1899-1905. [DOI: 10.1093/humrep/dez155] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 06/24/2019] [Indexed: 12/15/2022] Open
Abstract
AbstractSTUDY QUESTIONAre there common mutation profiles between epithelial and stromal cells in ovarian endometriotic tissue and the normal endometrium?SUMMARY ANSWEROur study revealed no common mutations between epithelial and stromal cells in ovarian endometriotic tissue and the normal endometrium.WHAT IS KNOWN ALREADYEpithelial cells in both ovarian endometriotic tissue and the normal endometrium harbor somatic mutations in cancer-associated genes such as phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) and KRAS proto-oncogene, GTPase (KRAS).STUDY DESIGN, SIZE, DURATIONWe performed a retrospective study to identify the mutation profiles of stromal cells in endometriotic tissue and the normal endometrium. We collected 11 endometriotic stroma samples and 10 normal endometrial stroma samples between 2013 and 2017 at a tertiary care center.PARTICIPANTS/MATERIALS, SETTING, METHODSThe laser microdissection method was used to obtain stromal cells in ovarian endometriotic and normal endometrial tissues from patients with ovarian endometriosis and/or other non-invasive gynecological diseases. Target gene sequencing was performed to assess and compare the mutation profiles of stromal cells with those of epithelial cells obtained in our previous study. For target gene sequencing, 76 genes were selected based on previous genomic analyses for ovarian endometriosis, normal endometrium, endometriosis-related ovarian cancer and endometrial cancer.MAIN RESULTS AND THE ROLE OF CHANCEStromal samples in ovarian endometrioma and normal endometrium harbor somatic mutations (18 mutations in 11 endometriosis samples and 16 mutations in 10 normal endometrial samples) but did not share any mutations with paired epithelial samples. The mutant allele frequency of stromal samples was significantly lower than that of epithelial samples in ovarian endometrioma (P = 6.0 × 10-11) and normal endometrium (P = 1.4 × 10-7).LIMITATIONS, REASONS FOR CAUTIONThe number of genes evaluated in the mutational analysis was limited. Additionally, the functional roles of somatic mutations in stromal cells remain unclear.WIDER IMPLICATIONS OF THE FINDINGSDifferent mutation profiles between paired epithelial and stromal cells in both ovarian endometrioma and normal endometrium suggest that origins of epithelial and stromal cells would be independent of each other in both normal endometrium and ovarian endometrioma; however, the theory of epithelial-mesenchymal transition is proposed in ovarian endometrioma.STUDY FUNDING/COMPETING INTEREST(S)This work was supported in part by the Japan Society for the Promotion of Science KAKENHI grant number JP15H02373 (Grant-in-Aid for Scientific Research A for I.I.), JP16H06267 (Grant-in-Aid for Young Scientists A for K.Y.), JP17K08688 (Grant-in-Aid for Scientific Research C for H.N.) and JP16H06279 (Grant-in-Aid for Scientific Research on Innovative Areas—Platforms for Advanced Technologies and Research Resources for H.N. and K.Y). There are no conflicts of interest to declare.TRIAL REGISTRATION NUMBERNot applicable.
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Affiliation(s)
- Kazuaki Suda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Hirofumi Nakaoka
- Division of Human Genetics, National Institute of Genetics, Mishima 411-8540, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Tatsuya Ishiguro
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Sosuke Adachi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Hiroaki Kase
- Department of Obstetrics and Gynecology, Nagaoka Chuo General Hospital, Nagaoka 940-8653, Japan
| | - Teiichi Motoyama
- Department of Molecular and Diagnostic Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Mishima 411-8540, Japan
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
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28
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Umemoto N, Hasegawa K, Iio Y, Inoue I, Sumi T, Sugiura T, Taniguchi T, Asai T, Yamada M, Ishii H, Murohara T, Shimizu K. P2434Digital zoom decreases radiation exposure dose up to 30% in percutaneous coronary intervention. Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz748.0766] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Interventional cardiology is gaining greater popularity worldwide with each passing year. Reduction of exposure dose is a very imminent and an important issue in cardiology procedure. Although a newer radiation reduction technique, device and procedure are very valuable and expected, we should consider about therapy technique, radiation technique, devices, and the way to protection. Digital zoom digitally enlarges images in real time by up to 2.5-fold at lower doses than those used with traditional field of view changes. In our phantom examination the average dose reduction of digital zoom was 27%.
Methods and results
This study is designated as single-center, retrospective, not-randomized, observation study. 2101 eligible cases were collected. We assigned the cases of PCI without the use of Digital zoom to the Conventional group and those involving the use of Digital zoom to the Digital zoom group. There were 806 patients in the Conventional group and 1195 in the Digital zoom group. Because we had begun using Digital zoom from January 2015 onwards, all patients in the Conventional group had undergone PCI from January 2013 to December 2014 and all patients in the Digital zoom group had undergone PCI from January 2015 to December 2016. In addition, we calculated the RAK/minute and DAP/minute for an accurate assessment. To minimize the difference of characteristics between two groups, propensity score including all baseline variables was performed. Furthermore, Predictors of radiation exposure were investigated using multivariable least square methods. Inter group differences were observed in DAP, RAK, DAP/min, and RAK/min (Digital zoom group vs conventional group: DAP, 16000 cGy cm2 [from 1st quartile to 3rd quartile; 10300–24400] vs 20700 [13400–29500], p<0.001; DAP/min, 557 cGy cm2/min [392–737] vs 782 [571–1010], p<0.01; RAK, 1590 Gy [990–2410] vs 1850 [1220–2720], p<0.01; RAK/min, 54.7 Gy/min [38.5–73.2] vs 71.2 [51.5–93.0], p<0.01). Even after propensity score matching, intergroup differences in DAP (810 cases), DAP/min (811 cases), RAK (746 cases), and RAK/min (744 cases) persisted. Furthermore, the least squares method showed that Digital zoom is an important predictor of DAP (β=0.17, p<0.01) and RAK (β=0.12, p<0.01).
Conclusion
Digital zoom is an old and cost-free technique, but one of most powerful reduction of exposure method. Propensity score adjustment and least square methods show that digital zoom is one of independent effective method.
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Affiliation(s)
- N Umemoto
- Ichinomiya Municipal Hospital, Department of Cardiology, Ichinomiya, Aichi, Japan
| | - K Hasegawa
- Ichinomiya Municipal Hospital, Department of Radiology, ichinomiya, Aichi, Japan
| | - Y Iio
- Ichinomiya Municipal Hospital, Department of Cardiology, Ichinomiya, Aichi, Japan
| | - I Inoue
- Ichinomiya Municipal Hospital, Department of Cardiology, Ichinomiya, Aichi, Japan
| | - T Sumi
- Ichinomiya Municipal Hospital, Department of Cardiology, Ichinomiya, Aichi, Japan
| | - T Sugiura
- Ichinomiya Municipal Hospital, Department of Cardiology, Ichinomiya, Aichi, Japan
| | - T Taniguchi
- Ichinomiya Municipal Hospital, Department of Cardiology, Ichinomiya, Aichi, Japan
| | - T Asai
- Ichinomiya Municipal Hospital, Department of Cardiology, Ichinomiya, Aichi, Japan
| | - M Yamada
- Ichinomiya Municipal Hospital, Department of Cardiology, Ichinomiya, Aichi, Japan
| | - H Ishii
- Nagoya University Hospital, Department of Cardiology, Nagoya, Japan
| | - T Murohara
- Nagoya University Hospital, Department of Cardiology, Nagoya, Japan
| | - K Shimizu
- Ichinomiya Municipal Hospital, Department of Cardiology, Ichinomiya, Aichi, Japan
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29
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Ogawa K, Okuno T, Hosomichi K, Hosokawa A, Hirata J, Suzuki K, Sakaue S, Kinoshita M, Asano Y, Miyamoto K, Inoue I, Kusunoki S, Okada Y, Mochizuki H. Next-generation sequencing identifies contribution of both class I and II HLA genes on susceptibility of multiple sclerosis in Japanese. J Neuroinflammation 2019; 16:162. [PMID: 31382992 PMCID: PMC6683481 DOI: 10.1186/s12974-019-1551-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 03/28/2019] [Accepted: 07/22/2019] [Indexed: 12/13/2022] Open
Abstract
Background The spectrum of classical and non-classical HLA genes related to the risk of multiple sclerosis (MS) and neuromyelitis optica spectrum disorder (NMOSD) in the Japanese population has not been studied in detail. We conducted a case-control analysis of classical and non-classical HLA genes. Methods We used next-generation sequencing (NGS)-based HLA genotyping methods for mapping risk for 45 MS patients, 31 NMOSD patients, and 429 healthy controls. We evaluated the association of the HLA variants with the risk of MS and NMOSD using logistic regression analysis and Fisher’s exact test. Results We confirmed that HLA-DRB1*15:01 showed the strongest association with MS (P = 2.1 × 10−5; odds ratio [OR] = 3.44, 95% confidence interval [95% CI] = 1.95–6.07). Stepwise conditional analysis identified HLA-DRB1*04:05, HLA-B*39:01, and HLA-B*15:01 as being associated with independent MS susceptibility (PConditional < 8.3 × 10−4). With respect to amino acid polymorphisms in HLA genes, we found that phenylalanine at HLA-DQβ1 position 9 had the strongest effect on MS susceptibility (P = 3.7 × 10−8, OR = 3.48, 95% CI = 2.23–5.43). MS risk at HLA-DQβ1 Phe9 was independent of HLA-DRB1*15:01 (PConditional = 1.5 × 10−5, OR = 2.91, 95% CI = 1.79–4.72), while HLA-DRB1*15:01 was just significant when conditioned on HLA-DQβ1 Phe9 (PConditional = 0.037). Regarding a case-control analysis for NMOSD, HLA-DQA1*05:03 had a significant association with NMOSD (P = 1.5 × 10−4, OR = 6.96, 95% CI = 2.55–19.0). Conclusions We identified HLA variants associated with the risk of MS and NMOSD. Our study contributes to the understanding of the genetic architecture of MS and NMOSD in the Japanese population. Electronic supplementary material The online version of this article (10.1186/s12974-019-1551-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kotaro Ogawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Japan.,Department of Neurology, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Tatsusada Okuno
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, 920-8640, Japan
| | - Akiko Hosokawa
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan.,Department of Neurology, Suita Municipal Hospital, Suita, 564-8567, Japan
| | - Jun Hirata
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Japan.,Pharmaceutical Discovery Research Laboratories, Teijin Pharma Limited, Hino, 191-8512, Japan
| | - Ken Suzuki
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Saori Sakaue
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Makoto Kinoshita
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Yoshihiro Asano
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Katsuichi Miyamoto
- Department of Neurology, Kindai University Faculty of Medicine, Osaka-Sayama, 589-8511, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Shizuoka, 411-8540, Japan
| | - Susumu Kusunoki
- Department of Neurology, Kindai University Faculty of Medicine, Osaka-Sayama, 589-8511, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Japan. .,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, 565-0871, Japan.
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
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Kawamura Y, Nakaoka H, Nakayama A, Okada Y, Yamamoto K, Higashino T, Sakiyama M, Shimizu T, Ooyama H, Ooyama K, Nagase M, Hidaka Y, Shirahama Y, Hosomichi K, Nishida Y, Shimoshikiryo I, Hishida A, Katsuura-Kamano S, Shimizu S, Kawaguchi M, Uemura H, Ibusuki R, Hara M, Naito M, Takao M, Nakajima M, Iwasawa S, Nakashima H, Ohnaka K, Nakamura T, Stiburkova B, Merriman TR, Nakatochi M, Ichihara S, Yokota M, Takada T, Saitoh T, Kamatani Y, Takahashi A, Arisawa K, Takezaki T, Tanaka K, Wakai K, Kubo M, Hosoya T, Ichida K, Inoue I, Shinomiya N, Matsuo H. Genome-wide association study revealed novel loci which aggravate asymptomatic hyperuricaemia into gout. Ann Rheum Dis 2019; 78:1430-1437. [PMID: 31289104 PMCID: PMC6788923 DOI: 10.1136/annrheumdis-2019-215521] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [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: 04/09/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 01/06/2023]
Abstract
Objective The first ever genome-wide association study (GWAS) of clinically defined gout cases and asymptomatic hyperuricaemia (AHUA) controls was performed to identify novel gout loci that aggravate AHUA into gout. Methods We carried out a GWAS of 945 clinically defined gout cases and 1003 AHUA controls followed by 2 replication studies. In total, 2860 gout cases and 3149 AHUA controls (all Japanese men) were analysed. We also compared the ORs for each locus in the present GWAS (gout vs AHUA) with those in the previous GWAS (gout vs normouricaemia). Results This new approach enabled us to identify two novel gout loci (rs7927466 of CNTN5 and rs9952962 of MIR302F) and one suggestive locus (rs12980365 of ZNF724) at the genome-wide significance level (p<5.0×10–8). The present study also identified the loci of ABCG2, ALDH2 and SLC2A9. One of them, rs671 of ALDH2, was identified as a gout locus by GWAS for the first time. Comparing ORs for each locus in the present versus the previous GWAS revealed three ‘gout vs AHUA GWAS’-specific loci (CNTN5, MIR302F and ZNF724) to be clearly associated with mechanisms of gout development which distinctly differ from the known gout risk loci that basically elevate serum uric acid level. Conclusions This meta-analysis is the first to reveal the loci associated with crystal-induced inflammation, the last step in gout development that aggravates AHUA into gout. Our findings should help to elucidate the molecular mechanisms of gout development and assist the prevention of gout attacks in high-risk AHUA individuals.
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Affiliation(s)
- Yusuke Kawamura
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan.,Department of General Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Hirofumi Nakaoka
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Akiyoshi Nakayama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan.,Medical Squadron, Air Base Group, Western Aircraft Control and Warning Wing, Japan Air Self-Defense Force, Kasuga, Fukuoka, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Osaka, Japan.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Osaka, Japan
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Toshihide Higashino
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Masayuki Sakiyama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan.,Department of Defense Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Toru Shimizu
- Midorigaoka Hospital, Takatsuki, Osaka, Japan.,Kyoto Industrial Health Association, Kyoto, Japan
| | | | | | | | | | - Yuko Shirahama
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Yuichiro Nishida
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Ippei Shimoshikiryo
- Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Asahi Hishida
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Sakurako Katsuura-Kamano
- Department of Preventive Medicine, Institute of Health Biosciences, the University of Tokushima Graduate School, Tokushima, Japan
| | - Seiko Shimizu
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Makoto Kawaguchi
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan.,Department of Urology, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Hirokazu Uemura
- Department of Preventive Medicine, Institute of Health Biosciences, the University of Tokushima Graduate School, Tokushima, Japan
| | - Rie Ibusuki
- Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Megumi Hara
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Mariko Naito
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.,Department of Oral Epidemiology, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
| | - Mikiya Takao
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan.,Department of Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Mayuko Nakajima
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Satoko Iwasawa
- Department of Preventive Medicine and Public Health, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Hiroshi Nakashima
- Department of Preventive Medicine and Public Health, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Keizo Ohnaka
- Department of Geriatric Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takahiro Nakamura
- Laboratory for Mathematics, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Blanka Stiburkova
- Institute of Rheumatology, Prague, Czech Republic.,Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Tony R Merriman
- Department of Biochemisty, University of Otago, Dunedin, New Zealand
| | - Masahiro Nakatochi
- Data Science Division, Data Coordinating Center, Department of Advanced Medicine, Nagoya University Hospital, Nagoya, Aichi, Japan
| | - Sahoko Ichihara
- Department of Environmental and Preventive Medicine, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, Japan
| | - Mitsuhiro Yokota
- Department of Genome Science, School of Dentistry, Aichi Gakuin University, Nagoya, Aichi, Japan
| | - Tappei Takada
- Department of Pharmacy, the University of Tokyo Hospital, Tokyo, Japan
| | - Tatsuya Saitoh
- Laboratory of Bioresponse Regulation, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.,Division of Inflammation Biology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.,Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.,Department of Genomic Medicine, Research Institute, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Kokichi Arisawa
- Department of Preventive Medicine, Institute of Health Biosciences, the University of Tokushima Graduate School, Tokushima, Japan
| | - Toshiro Takezaki
- Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Keitaro Tanaka
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Tatsuo Hosoya
- Division of Kidney and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Minato-ku, Tokyo, Japan.,Department of Pathophysiology and Therapy in Chronic Kidney Disease, Jikei University School of Medicine, Minato-ku, Tokyo, Japan
| | - Kimiyoshi Ichida
- Division of Kidney and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Minato-ku, Tokyo, Japan.,Department of Pathophysiology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Ituro Inoue
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Nariyoshi Shinomiya
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Hirotaka Matsuo
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
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Zhang S, Kohira Y, Orita H, Ishimine M, Kobayashi T, Mae Buendia Chua S, Nakaoka H, Inoue I, Hino O, Yokomizo T, Fukunaga T, Lee-Okada HC. Sensitization of Gastric Cancer Cells to Irinotecan by p53 Activation. ACTA ACUST UNITED AC 2019. [DOI: 10.1248/bpbreports.2.6_130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Shun Zhang
- Department of Gastroenterology and Minimally Invasive Surgery, Juntendo University Hospital
- Department of Gastroenterology Surgery, Shanghai East Hospital (East Hospital Affiliated to Tongji University)
| | - Yoshinori Kohira
- Department of Gastroenterology and Minimally Invasive Surgery, Juntendo University Hospital
| | - Hajime Orita
- Department of Gastroenterology and Minimally Invasive Surgery, Juntendo University Hospital
| | - Momoko Ishimine
- Department of Biochemistry, Juntendo University Graduate School of Medicine
| | - Toshiyuki Kobayashi
- Department of Molecular Pathogenesis, Juntendo University Graduate School of Medicine
| | | | | | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics
| | - Okio Hino
- Department of Molecular Pathogenesis, Juntendo University Graduate School of Medicine
| | - Takehiko Yokomizo
- Department of Biochemistry, Juntendo University Graduate School of Medicine
| | - Tetsu Fukunaga
- Department of Gastroenterology and Minimally Invasive Surgery, Juntendo University Hospital
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Abstract
Genomic duplication or loss can accelerate evolution because the number of repeats could affect molecular pathways and phenotypes. We have previously reported that the repeated region of filaggrin (FLG), a crucial component of the outer layers of mammalian skin, had high levels of nucleotide diversity with species-specific divergence and expansion and that it evolved under the birth-and-death model. We focused on hornerin (HRNR), a member of the same gene family that harbor similar tandem repeats as FLG, and examined the formation process of repeated regions and the evolutional model that best fit the HRNR repeated region in the crab-eating macaque (Macaca fascicularis), orangutan (Pongo abelii), gorilla (Gorilla gorilla), and chimpanzee (Pan troglodytes) and compared them with the human (Homo sapiens) sequence. Paar et al. (2011) and Takaishi et al. (2005) have different theories as to the formation of the repeated region of HRNR; both groups share the longest repeat length of 1,404 bp (quartic or longest unit), but they differed in the process. We identified the formation described by Paar et al. {[(“39 bp (primary) × 9” × 2 (secondary)) × 2 (tertiary)] × 5 (quartic)} to be conserved in all species except the crab-eating macaque. We detected high nucleotide diversities between the longest repeats, which fits the birth-and-death model. We concluded that the high order repeat formation of HRNR was conserved in primates except the crab-eating macaque. As previously identified in FLG, the longest repeats have high levels of nucleotide diversity, which could contribute to phenotypic differences between closely related species.
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Affiliation(s)
- Vanessa Romero
- Department of Genetics School of Life Sciences, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Hirofumi Nakaoka
- Department of Genetics School of Life Sciences, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Japan
| | - Ituro Inoue
- Department of Genetics School of Life Sciences, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, Japan
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Tamura R, Nakaoka H, Yoshihara K, Mori Y, Yachida N, Nishikawa N, Motoyama T, Okuda S, Inoue I, Enomoto T. Novel MXD4-NUTM1 fusion transcript identified in primary ovarian undifferentiated small round cell sarcoma. Genes Chromosomes Cancer 2018; 57:557-563. [PMID: 30338611 PMCID: PMC6221051 DOI: 10.1002/gcc.22668] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 06/21/2018] [Accepted: 07/04/2018] [Indexed: 12/20/2022] Open
Abstract
Primary ovarian sarcomas are extremely rare tumors, and their genomic and transcriptomic alterations remain to be elucidated. We performed whole exome sequencing of primary tumor and matched normal blood samples derived from one patient with ovarian undifferentiated small round cell sarcoma. We identified 8 nonsynonymous somatic mutations, and all mutations were missense or nonsense changes. Next, we performed RNA sequencing of the tumor sample and identified two in-frame fusion transcripts: MXD4-NUTM1 and ARL6-POT1. Most NUTM1 exons were retained in the MXD4-NUTM1 fusion transcript, and we confirmed an increase in NUTM1 mRNA and protein expression in tumor tissue. Further genomic and transcriptomic analyses might lead to the development of new therapeutic strategies based on the molecular characteristics of ovarian undifferentiated small round cell sarcoma.
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Affiliation(s)
- Ryo Tamura
- Department of Obstetrics and GynecologyNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
| | - Hirofumi Nakaoka
- Division of Human GeneticsNational Institute of GeneticsMishimaJapan
| | - Kosuke Yoshihara
- Department of Obstetrics and GynecologyNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
| | - Yutaro Mori
- Department of Obstetrics and GynecologyNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
| | - Nozomi Yachida
- Department of Obstetrics and GynecologyNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
| | - Nobumichi Nishikawa
- Department of Obstetrics and GynecologyNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
| | - Teiichi Motoyama
- Department of Molecular and Diagnostic PathologyNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
| | - Shujiro Okuda
- Department of BioinformaticsNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
| | - Ituro Inoue
- Division of Human GeneticsNational Institute of GeneticsMishimaJapan
| | - Takayuki Enomoto
- Department of Obstetrics and GynecologyNiigata University Graduate School of Medical and Dental SciencesNiigataJapan
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Takase M, Shirai M, Matsushita H, Umehara H, Wakabayashi S, Doi A, Inoue I. The severity of unilateral spatial neglect was positively correlated with that of Pusher syndrome. Ann Phys Rehabil Med 2018. [DOI: 10.1016/j.rehab.2018.05.078] [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: 10/28/2022]
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Watanabe H, Goto S, Mori H, Higashi K, Hosomichi K, Aizawa N, Takahashi N, Tsuchida M, Suzuki Y, Yamada T, Horii A, Inoue I, Kurokawa K, Narita I. Comprehensive microbiome analysis of tonsillar crypts in IgA nephropathy. Nephrol Dial Transplant 2018; 32:2072-2079. [PMID: 27683270 DOI: 10.1093/ndt/gfw343] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 08/10/2016] [Indexed: 12/29/2022] Open
Abstract
Background Immunoglobulin A nephropathy (IgAN) is the most prevalent primary chronic glomerular disease, in which the mucosal immune response elicited particularly in the tonsils or intestine has been estimated to be involved in the development of the disease. To explore the relationship between IgAN and bacterial flora in the tonsils, we conducted a comprehensive microbiome analysis. Methods We enrolled 48 IgAN patients, 21 recurrent tonsillitis (RT) patients without urine abnormalities and 30 children with tonsillar hyperplasia (TH) who had undergone tonsillectomy previously. Genomic DNA from tonsillar crypts of each patient was extracted, and V4 regions of the 16S ribosomal RNA gene were amplified and analysed using a high-throughput multiplexed sequencing approach. Differences in genus composition among the three study groups were statistically analysed by permutational multivariate analysis of variance and visualized by principal component analysis (PCA). Results Substantial diversity in bacterial composition was detected in each sample. Prevotella spp., Fusobacterium spp., Sphingomonas spp. and Treponema spp. were predominant in IgAN patients. The percentage of abundance of Prevotella spp., Haemophilus spp., Porphyromonas spp. and Treponema spp. in IgAN patients was significantly different from that in TH patients. However, there was no significant difference in the percentage of abundance of any bacterial genus between IgAN and RT patients. PCA did not distinguish IgAN from RT, although it discriminated TH. No significant differences in microbiome composition among the groups of IgAN patients according to clinicopathological parameters were observed. Conclusions Similar patterns of bacteria are present in tonsillar crypts of both IgAN and RT patients, suggesting that the host response to these bacteria might be important in the development of IgAN.
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Affiliation(s)
- Hirofumi Watanabe
- Division of Clinical Nephrology and Rheumatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shin Goto
- Division of Clinical Nephrology and Rheumatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hiroshi Mori
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan
| | - Koichi Higashi
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan
| | - Kazuyoshi Hosomichi
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Shizuoka, Japan
| | - Naotaka Aizawa
- Department of Otolaryngology Head and Neck Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Nao Takahashi
- Department of Otolaryngology Head and Neck Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Masafumi Tsuchida
- Division of Clinical Nephrology and Rheumatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yusuke Suzuki
- Division of Nephrology, Department of Internal Medicine, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Takuji Yamada
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan
| | - Arata Horii
- Department of Otolaryngology Head and Neck Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ituro Inoue
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Shizuoka, Japan
| | - Ken Kurokawa
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Ichiei Narita
- Division of Clinical Nephrology and Rheumatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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36
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Yang YX, Wei L, Zhang YJ, Hayano T, Piñeiro Pereda MDP, Nakaoka H, Li Q, Barragán Mallofret I, Lu YZ, Tamagnone L, Inoue I, Li X, Luo JY, Zheng K, You H. Long non-coding RNA p10247, high expressed in breast cancer (lncRNA-BCHE), is correlated with metastasis. Clin Exp Metastasis 2018; 35:109-121. [DOI: 10.1007/s10585-018-9901-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 05/11/2018] [Indexed: 10/14/2022]
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Kawano T, Hosomichi K, Inoue I, Shimono R, Onishi S, Nakame K, Kaji T, Matsufuji H, Ieiri S. Identification of a novel variant of the RET proto-oncogene in a novel family with Hirschsprung's disease. Pediatr Surg Int 2017; 33:1041-1046. [PMID: 28799054 DOI: 10.1007/s00383-017-4134-z] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/01/2017] [Indexed: 11/25/2022]
Abstract
PURPOSE Hirschsprung's disease (HSCR) is a congenital disorder of the enteric nervous system characterized by the absence of ganglion cells in the Auerbach's and Meissner's plexuses. Although about 7% of cases are hereditary, the causal mutations have not been completely characterized. We encountered a novel family with inherited HSCR and screened them for causal mutations. METHODS A Japanese family of five female patients and six unaffected individuals was subjected to a whole-exome analysis with a next-generation sequencer. RESULTS After exome sequencing and the annotation of mutations, we identified co-segregated mutations with sequential filtering steps via a standard protocol. Eight mutations were identified: two on chromosome 10 and six on chromosome 11. We used pathogenicity prediction tools such as Genomic Evolutionary Rate Profiling, SIFT, and PolyPhen2 to predict the impact of mutations on the protein activity. S922Y, a novel mutation of RET, was identified as a likely causal mutation. In addition, a mutation of rs2435357T, known as enhancer of RET located in intron 1 of RET, was detected in this family. CONCLUSION The coexistence of RET mutations in both the exon (S922Y) and intron1 (rs2435357T) indicated a risk of HSCR in this family.
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Affiliation(s)
- Takafumi Kawano
- Department of Pediatric Surgery, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Shizuoka, Japan
| | - Ryuichi Shimono
- Department of Pediatric Surgery, Faculty of Medicine, Kagawa University Hospital, Kita, Japan
| | - Shun Onishi
- Department of Pediatric Surgery, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Kazuhiko Nakame
- Department of Pediatric Surgery, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Tatsuru Kaji
- Department of Pediatric Surgery, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Hiroshi Matsufuji
- Department of Pediatric Surgery, St. Luke's International Hospital, Tokyo, Japan
| | - Satoshi Ieiri
- Department of Pediatric Surgery, Research Field in Medicine and Health Sciences, Medical and Dental Sciences Area, Research and Education Assembly, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan.
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Higashino T, Takada T, Nakaoka H, Toyoda Y, Stiburkova B, Miyata H, Ikebuchi Y, Nakashima H, Shimizu S, Kawaguchi M, Sakiyama M, Nakayama A, Akashi A, Tanahashi Y, Kawamura Y, Nakamura T, Wakai K, Okada R, Yamamoto K, Hosomichi K, Hosoya T, Ichida K, Ooyama H, Suzuki H, Inoue I, Merriman TR, Shinomiya N, Matsuo H. Multiple common and rare variants of ABCG2 cause gout. RMD Open 2017; 3:e000464. [PMID: 29225919 PMCID: PMC5706492 DOI: 10.1136/rmdopen-2017-000464] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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: 03/24/2017] [Revised: 06/22/2017] [Accepted: 07/12/2017] [Indexed: 12/15/2022] Open
Abstract
Objective Previous studies have suggested an association between gout susceptibility and common dysfunctional variants in ATP-binding cassette transporter subfamily G member 2/breast cancer resistance protein (ABCG2/BCRP), including rs72552713 (Q126X) and rs2231142 (Q141K). However, the association of rare ABCG2 variants with gout is unknown. Therefore, we investigated the effects of rare ABCG2 variants on gout susceptibility in this study. Methods We sequenced the exons of ABCG2 in 480 patients with gout and 480 healthy controls (Japanese males). We also performed functional analyses of non-synonymous variants of ABCG2 and analysed the correlation between urate transport function and scores from the protein prediction algorithms (Sorting Intolerant from Tolerant (SIFT) and Polymorphism Phenotyping v2 (PolyPhen-2)). Stratified association analyses and multivariate logistic regression analysis were performed to evaluate the effects of rare and common ABCG2 variants on gout susceptibility. Results We identified 3 common and 19 rare non-synonymous variants of ABCG2. SIFT scores were significantly correlated with the urate transport function, although some ABCG2 variants showed inconsistent scores. When the effects of common variants were removed by stratified association analysis, the rare variants of ABCG2 were associated with a significantly increased risk of gout (OR=3.2, p=6.4×10−3). Multivariate logistic regression analysis revealed that the size effect of these rare ABCG2 variants (OR=2.7, p=3.0×10−3) was similar to that of the common variants, Q126X (OR=3.4, p=3.2×10−6) and Q141K (OR=2.3, p=2.7×10−16). Conclusions This study revealed that multiple common and rare variants of ABCG2 are independently associated with gout. These results could support both the ‘Common Disease, Common Variant’ and ‘Common Disease, Multiple Rare Variant’ hypotheses for the association between ABCG2 and gout susceptibility.
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Affiliation(s)
- Toshihide Higashino
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Tappei Takada
- Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hirofumi Nakaoka
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Japan
| | - Yu Toyoda
- Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Blanka Stiburkova
- First Faculty of Medicine, Charles University and General University Hospital in Prague, Institute of Inherited Metabolic Disorders, Prague, Czech Republic.,Institute of Rheumatology, Prague, Czech Republic
| | - Hiroshi Miyata
- Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuki Ikebuchi
- Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Nakashima
- Department of Preventive Medicine and Public Health, National Defense Medical College, Tokorozawa, Japan
| | - Seiko Shimizu
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Makoto Kawaguchi
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Masayuki Sakiyama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Akiyoshi Nakayama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Airi Akashi
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Yuki Tanahashi
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Yusuke Kawamura
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Takahiro Nakamura
- Laboratory for Mathematics, National Defense Medical College, Tokorozawa, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Rieko Okada
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ken Yamamoto
- Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Japan
| | - Kazuyoshi Hosomichi
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Japan.,Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Tatsuo Hosoya
- Division of Kidney and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan.,Department of Pathophysiology and Therapy in Chronic Kidney Disease, Jikei University School of Medicine, Tokyo, Japan
| | - Kimiyoshi Ichida
- Division of Kidney and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan.,Department of Pathophysiology, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | | | - Hiroshi Suzuki
- Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ituro Inoue
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Japan
| | - Tony R Merriman
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Nariyoshi Shinomiya
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Hirotaka Matsuo
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
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Akatsuka H, Kuga S, Masuhara K, Davaadorj O, Okada C, Iida Y, Okada Y, Fukunishi N, Suzuki T, Hosomichi K, Ohtsuka M, Tanaka M, Inoue I, Kimura M, Sato T. AMBRA1 is involved in T cell receptor-mediated metabolic reprogramming through an ATG7-independent pathway. Biochem Biophys Res Commun 2017; 491:1098-1104. [PMID: 28789945 DOI: 10.1016/j.bbrc.2017.08.019] [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] [Received: 07/28/2017] [Accepted: 08/04/2017] [Indexed: 11/30/2022]
Abstract
Metabolic reprogramming contributes to dynamic alteration of cell functions and characteristics. In T cells, TCR-mediated signaling evokes metabolic reprogramming and autophagy. AMBRA1 is known to serve in the facilitation of autophagy and quality control of mitochondria, but the role of AMBRA1 in T cell metabolic alteration is unknown. Here, we show that AMBRA1, but not ATG7, plays a role in TCR-mediated control of glycolytic factors and mitochondrial mass, while both AMBRA1 and ATG7 are required for autolysosome formation. Our results suggested that AMBRA1 is a core factor that controls both autophagy and metabolic regulation.
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Affiliation(s)
- Hisako Akatsuka
- Department of Host Defense Mechanism, Japan; Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Japan
| | | | - Kaori Masuhara
- Department of Host Defense Mechanism, Japan; Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Japan
| | - Odontuya Davaadorj
- Department of Host Defense Mechanism, Japan; Department of Ophthalmology, Tokai University School of Medicine, Kanagawa, Japan
| | - Chisa Okada
- Support Center for Medical Research and Education, Tokai University, Kanagawa, Japan
| | - Yumi Iida
- Support Center for Medical Research and Education, Tokai University, Kanagawa, Japan
| | - Yoshinori Okada
- Support Center for Medical Research and Education, Tokai University, Kanagawa, Japan
| | - Nahoko Fukunishi
- Support Center for Medical Research and Education, Tokai University, Kanagawa, Japan
| | - Takahiro Suzuki
- Department of Ophthalmology, Tokai University School of Medicine, Kanagawa, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan; Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Japan
| | - Masafumi Tanaka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Japan
| | - Ituro Inoue
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Minoru Kimura
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Japan
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40
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Higaki T, Shiode N, Nishioka K, Takeuchi A, Harima A, Oi K, Dai K, Kawase T, Nakama Y, Suenari K, Otsuka M, Sakai K, Shimatani Y, Masaoka Y, Inoue I. P524Angiographic outcomes after the combined use of paclitaxel-coated balloon and excimer laser coronary angioplasty for drug-eluting stent in-stent restenosis. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx501.p524] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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41
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Yamaguchi T, Hosomichi K, Yano K, Kim YI, Nakaoka H, Kimura R, Otsuka H, Nonaka N, Haga S, Takahashi M, Shirota T, Kikkawa Y, Yamada A, Kamijo R, Park SB, Nakamura M, Maki K, Inoue I. Comprehensive genetic exploration of selective tooth agenesis of mandibular incisors by exome sequencing. Hum Genome Var 2017; 4:17005. [PMID: 28265457 PMCID: PMC5321669 DOI: 10.1038/hgv.2017.5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 10/04/2016] [Revised: 12/23/2016] [Accepted: 12/27/2016] [Indexed: 12/21/2022] Open
Abstract
Tooth agenesis is described as the absence of one or more teeth. It is caused by a failure in tooth development and is one of the most common human developmental anomalies. We herein report genomic analyses of selective mandibular incisor agenesis (SMIA) using exome sequencing. Two Japanese families with SMIA were subjected to exome sequencing, and family with sequence similarity 65 member A (FAM65), nuclear factor of activated T-cells 3 (NFATC3) and cadherin-related 23 gene (CDH23) were detected. In the follow-up study, 51 Japanese and 32 Korean sporadic patients with SMIA were subjected to exome analyses, and 18 reported variants in PAX9, AXIN2, EDA, EDAR, WNT10A, BMP2 and GREM2 and 27 variants of FAM65, NFATC3 and CDH23 were found in 38 patients. Our comprehensive genetic study of SMIA will pave the way for a full understanding of the genetic etiology of SMIA and provide targets for treatment.
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Affiliation(s)
- Tetsutaro Yamaguchi
- Department of Orthodontics, School of Dentistry, Showa University , Tokyo, Japan
| | - Kazuyoshi Hosomichi
- Division of Human Genetics, National Institute of Genetics, Shizuoka, Japan; Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan
| | | | - Yong-Il Kim
- Department of Orthodontics, School of Dentistry, Pusan National University , Busan, South Korea
| | - Hirofumi Nakaoka
- Division of Human Genetics, National Institute of Genetics , Shizuoka, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus , Okinawa, Japan
| | - Hirotada Otsuka
- Department of Oral Anatomy and Developmental Biology, Showa University School of Dentistry , Tokyo, Japan
| | - Naoko Nonaka
- Department of Oral Anatomy and Developmental Biology, Showa University School of Dentistry , Tokyo, Japan
| | - Shugo Haga
- Department of Orthodontics, School of Dentistry, Showa University , Tokyo, Japan
| | - Masahiro Takahashi
- Department of Orthodontics, School of Dentistry, Showa University , Tokyo, Japan
| | - Tatsuo Shirota
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Showa University , Tokyo, Japan
| | - Yoshiaki Kikkawa
- Mammalian Genetics Project, Tokyo Metropolitan Institute of Medical Science , Tokyo, Japan
| | - Atsushi Yamada
- Department of Biochemistry, School of Dentistry, Showa University , Tokyo, Japan
| | - Ryutaro Kamijo
- Department of Biochemistry, School of Dentistry, Showa University , Tokyo, Japan
| | - Soo-Byung Park
- Department of Orthodontics, School of Dentistry, Pusan National University , Busan, South Korea
| | - Masanori Nakamura
- Department of Oral Anatomy and Developmental Biology, Showa University School of Dentistry , Tokyo, Japan
| | - Koutaro Maki
- Department of Orthodontics, School of Dentistry, Showa University , Tokyo, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics , Shizuoka, Japan
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Romero V, Hosomichi K, Nakaoka H, Shibata H, Inoue I. Structure and evolution of the filaggrin gene repeated region in primates. BMC Evol Biol 2017; 17:10. [PMID: 28077068 PMCID: PMC5225520 DOI: 10.1186/s12862-016-0851-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/12/2016] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The evolutionary dynamics of repeat sequences is quite complex, with some duplicates never having differentiated from each other. Two models can explain the complex evolutionary process for repeated genes-concerted and birth-and-death, of which the latter is driven by duplications maintained by selection. Copy number variations caused by random duplications and losses in repeat regions may modulate molecular pathways and therefore affect phenotypic characteristics in a population, resulting in individuals that are able to adapt to new environments. In this study, we investigated the filaggrin gene (FLG), which codes for filaggrin-an important component of the outer layers of mammalian skin-and contains tandem repeats that exhibit copy number variation between and within species. To examine which model best fits the evolutionary pathway for the complete tandem repeats within a single exon of FLG, we determined the repeat sequences in crab-eating macaque (Macaca fascicularis), orangutan (Pongo abelii), gorilla (Gorilla gorilla), and chimpanzee (Pan troglodytes) and compared these with the sequence in human (Homo sapiens). RESULTS In this study we compared concerted and birth-and-death evolution models, commonly used for gene copies. We found that there is high nucleotide diversity between filaggrin repeat regions, which fits the birth-and-death model. Phylogenetic analyses also suggested that independent duplication events created the repeat sequences in crab-eating macaques and orangutans, while different duplication and loss events created the repeats in gorillas, chimpanzees, and humans. Comparison of the repeat sequences detected purifying selection within species and lineage-specific duplications across species. We also found variation in the length of the repeated region within species such as chimpanzee and crab-eating macaque. CONCLUSIONS We conclude that the copy number variation in the repeat sequences of FLG between primates may be a consequence of species-specific divergence and expansion.
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Affiliation(s)
- Vanessa Romero
- Department of Genetics, School of Life Sciences, Graduate University for Advanced Studies (SOKENDAI), Mishima, 411-8540, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Kazuyoshi Hosomichi
- Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan.,Present address: Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, 920-8640, Japan
| | - Hirofumi Nakaoka
- Department of Genetics, School of Life Sciences, Graduate University for Advanced Studies (SOKENDAI), Mishima, 411-8540, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Ituro Inoue
- Department of Genetics, School of Life Sciences, Graduate University for Advanced Studies (SOKENDAI), Mishima, 411-8540, Japan. .,Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan.
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43
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Nakayama A, Nakaoka H, Yamamoto K, Sakiyama M, Shaukat A, Toyoda Y, Okada Y, Kamatani Y, Nakamura T, Takada T, Inoue K, Yasujima T, Yuasa H, Shirahama Y, Nakashima H, Shimizu S, Higashino T, Kawamura Y, Ogata H, Kawaguchi M, Ohkawa Y, Danjoh I, Tokumasu A, Ooyama K, Ito T, Kondo T, Wakai K, Stiburkova B, Pavelka K, Stamp LK, Dalbeth N, Sakurai Y, Suzuki H, Hosoyamada M, Fujimori S, Yokoo T, Hosoya T, Inoue I, Takahashi A, Kubo M, Ooyama H, Shimizu T, Ichida K, Shinomiya N, Merriman TR, Matsuo H. GWAS of clinically defined gout and subtypes identifies multiple susceptibility loci that include urate transporter genes. Ann Rheum Dis 2016; 76:869-877. [PMID: 27899376 PMCID: PMC5530361 DOI: 10.1136/annrheumdis-2016-209632] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [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: 03/29/2016] [Revised: 11/04/2016] [Accepted: 11/05/2016] [Indexed: 11/05/2022]
Abstract
Objective A genome-wide association study (GWAS) of gout and its subtypes was performed to identify novel gout loci, including those that are subtype-specific. Methods Putative causal association signals from a GWAS of 945 clinically defined gout cases and 1213 controls from Japanese males were replicated with 1396 cases and 1268 controls using a custom chip of 1961 single nucleotide polymorphisms (SNPs). We also first conducted GWASs of gout subtypes. Replication with Caucasian and New Zealand Polynesian samples was done to further validate the loci identified in this study. Results In addition to the five loci we reported previously, further susceptibility loci were identified at a genome-wide significance level (p<5.0×10−8): urate transporter genes (SLC22A12 and SLC17A1) and HIST1H2BF-HIST1H4E for all gout cases, and NIPAL1 and FAM35A for the renal underexcretion gout subtype. While NIPAL1 encodes a magnesium transporter, functional analysis did not detect urate transport via NIPAL1, suggesting an indirect association with urate handling. Localisation analysis in the human kidney revealed expression of NIPAL1 and FAM35A mainly in the distal tubules, which suggests the involvement of the distal nephron in urate handling in humans. Clinically ascertained male patients with gout and controls of Caucasian and Polynesian ancestries were also genotyped, and FAM35A was associated with gout in all cases. A meta-analysis of the three populations revealed FAM35A to be associated with gout at a genome-wide level of significance (pmeta=3.58×10−8). Conclusions Our findings including novel gout risk loci provide further understanding of the molecular pathogenesis of gout and lead to a novel concept for the therapeutic target of gout/hyperuricaemia.
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Affiliation(s)
- Akiyoshi Nakayama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Hirofumi Nakaoka
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Ken Yamamoto
- Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Masayuki Sakiyama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan.,Department of Dermatology, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Amara Shaukat
- Department of Biochemisty, University of Otago, Dunedin, New Zealand
| | - Yu Toyoda
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Yukinori Okada
- Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.,Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Takahiro Nakamura
- Laboratory for Mathematics, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Tappei Takada
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Katsuhisa Inoue
- Department of Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Tomoya Yasujima
- Department of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Hiroaki Yuasa
- Department of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Yuko Shirahama
- Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Hiroshi Nakashima
- Department of Preventive Medicine and Public Health, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Seiko Shimizu
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Toshihide Higashino
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Yusuke Kawamura
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Hiraku Ogata
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Makoto Kawaguchi
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Inaho Danjoh
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | | | | | - Toshimitsu Ito
- Department of Internal Medicine, Self-Defense Forces Central Hospital, Tokyo, Japan
| | - Takaaki Kondo
- Program in Radiological and Medical Laboratory Sciences, Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Blanka Stiburkova
- First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Institute of Inherited Metabolic Disorders, Prague, Czech Republic.,Institute of Rheumatology, Prague, Czech Republic
| | | | - Lisa K Stamp
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Nicola Dalbeth
- Department of Medicine, University of Auckland, Grafton, Auckland, New Zealand
| | | | - Yutaka Sakurai
- Department of Preventive Medicine and Public Health, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Hiroshi Suzuki
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Makoto Hosoyamada
- Department of Human Physiology and Pathology, Faculty of Pharma-Sciences, Teikyo University, Tokyo, Japan
| | - Shin Fujimori
- Department of Internal Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Takashi Yokoo
- Division of Kidney and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Tatsuo Hosoya
- Division of Kidney and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan.,Department of Pathophysiology and Therapy in Chronic Kidney Disease, Jikei University School of Medicine, Tokyo, Japan
| | - Ituro Inoue
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.,Omics Research Center, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa, Japan
| | | | - Toru Shimizu
- Midorigaoka Hospital, Takatsuki, Osaka, Japan.,Kyoto Industrial Health Association, Kyoto, Japan
| | - Kimiyoshi Ichida
- Department of Pathophysiology and Therapy in Chronic Kidney Disease, Jikei University School of Medicine, Tokyo, Japan.,Department of Pathophysiology, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Nariyoshi Shinomiya
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Tony R Merriman
- Department of Biochemisty, University of Otago, Dunedin, New Zealand
| | - Hirotaka Matsuo
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
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Hayano T, Matsui H, Nakaoka H, Ohtake N, Hosomichi K, Suzuki K, Inoue I. Germline Variants of Prostate Cancer in Japanese Families. PLoS One 2016; 11:e0164233. [PMID: 27701467 PMCID: PMC5049788 DOI: 10.1371/journal.pone.0164233] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 06/01/2016] [Accepted: 09/21/2016] [Indexed: 02/02/2023] Open
Abstract
Prostate cancer (PC) is the second most common cancer in men. Family history is the major risk factor for PC. Only two susceptibility genes were identified in PC, BRCA2 and HOXB13. A comprehensive search of germline variants for patients with PC has not been reported in Japanese families. In this study, we conducted exome sequencing followed by Sanger sequencing to explore responsible germline variants in 140 Japanese patients with PC from 66 families. In addition to known susceptibility genes, BRCA2 and HOXB13, we identified TRRAP variants in a mutually exclusive manner in seven large PC families (three or four patients per family). We also found shared variants of BRCA2, HOXB13, and TRRAP from 59 additional small PC families (two patients per family). We identified two deleterious HOXB13 variants (F127C and G132E). Further exploration of the shared variants in rest of the families revealed deleterious variants of the so-called cancer genes (ATP1A1, BRIP1, FANCA, FGFR3, FLT3, HOXD11, MUTYH, PDGFRA, SMARCA4, and TCF3). The germline variant profile provides a new insight to clarify the genetic etiology and heterogeneity of PC among Japanese men.
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Affiliation(s)
- Takahide Hayano
- Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Hiroshi Matsui
- Department of Urology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Hirofumi Nakaoka
- Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Nobuaki Ohtake
- Department of Urology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Kazuhiro Suzuki
- Department of Urology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Mishima, Japan
- * E-mail:
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45
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Kanzawa-Kiriyama H, Kryukov K, Jinam TA, Hosomichi K, Saso A, Suwa G, Ueda S, Yoneda M, Tajima A, Shinoda KI, Inoue I, Saitou N. A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan. J Hum Genet 2016; 62:213-221. [PMID: 27581845 PMCID: PMC5285490 DOI: 10.1038/jhg.2016.110] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [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: 05/16/2016] [Revised: 07/22/2016] [Accepted: 07/26/2016] [Indexed: 12/11/2022]
Abstract
The Jomon period of the Japanese Archipelago, characterized by cord-marked ‘jomon' potteries, has yielded abundant human skeletal remains. However, the genetic origins of the Jomon people and their relationships with modern populations have not been clarified. We determined a total of 115 million base pair nuclear genome sequences from two Jomon individuals (male and female each) from the Sanganji Shell Mound (dated 3000 years before present) with the Jomon-characteristic mitochondrial DNA haplogroup N9b, and compared these nuclear genome sequences with those of worldwide populations. We found that the Jomon population lineage is best considered to have diverged before diversification of present-day East Eurasian populations, with no evidence of gene flow events between the Jomon and other continental populations. This suggests that the Sanganji Jomon people descended from an early phase of population dispersals in East Asia. We also estimated that the modern mainland Japanese inherited <20% of Jomon peoples' genomes. Our findings, based on the first analysis of Jomon nuclear genome sequence data, firmly demonstrate that the modern mainland Japanese resulted from genetic admixture of the indigenous Jomon people and later migrants.
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Affiliation(s)
- Hideaki Kanzawa-Kiriyama
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Kirill Kryukov
- Department of Molecular Life Science, School of Medicine, Tokai University, Isehara, Japan
| | - Timothy A Jinam
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Kazuyoshi Hosomichi
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Aiko Saso
- The University Museum, The University of Tokyo, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Gen Suwa
- The University Museum, The University of Tokyo, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Shintaroh Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Tokyo, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan
| | - Ituro Inoue
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Naruya Saitou
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Population Genetics, National Institute of Genetics, Mishima, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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46
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van 't Hof FNG, Ruigrok YM, Lee CH, Ripke S, Anderson G, de Andrade M, Baas AF, Blankensteijn JD, Böttinger EP, Bown MJ, Broderick J, Bijlenga P, Carrell DS, Crawford DC, Crosslin DR, Ebeling C, Eriksson JG, Fornage M, Foroud T, von Und Zu Fraunberg M, Friedrich CM, Gaál EI, Gottesman O, Guo DC, Harrison SC, Hernesniemi J, Hofman A, Inoue I, Jääskeläinen JE, Jones GT, Kiemeney LALM, Kivisaari R, Ko N, Koskinen S, Kubo M, Kullo IJ, Kuivaniemi H, Kurki MI, Laakso A, Lai D, Leal SM, Lehto H, LeMaire SA, Low SK, Malinowski J, McCarty CA, Milewicz DM, Mosley TH, Nakamura Y, Nakaoka H, Niemelä M, Pacheco J, Peissig PL, Pera J, Rasmussen-Torvik L, Ritchie MD, Rivadeneira F, van Rij AM, Santos-Cortez RLP, Saratzis A, Slowik A, Takahashi A, Tromp G, Uitterlinden AG, Verma SS, Vermeulen SH, Wang GT, Han B, Rinkel GJE, de Bakker PIW. Shared Genetic Risk Factors of Intracranial, Abdominal, and Thoracic Aneurysms. J Am Heart Assoc 2016; 5:JAHA.115.002603. [PMID: 27418160 PMCID: PMC5015357 DOI: 10.1161/jaha.115.002603] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [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] [Indexed: 01/22/2023]
Abstract
Background Intracranial aneurysms (IAs), abdominal aortic aneurysms (AAAs), and thoracic aortic aneurysms (TAAs) all have a familial predisposition. Given that aneurysm types are known to co‐occur, we hypothesized that there may be shared genetic risk factors for IAs, AAAs, and TAAs. Methods and Results We performed a mega‐analysis of 1000 Genomes Project‐imputed genome‐wide association study (GWAS) data of 4 previously published aneurysm cohorts: 2 IA cohorts (in total 1516 cases, 4305 controls), 1 AAA cohort (818 cases, 3004 controls), and 1 TAA cohort (760 cases, 2212 controls), and observed associations of 4 known IA, AAA, and/or TAA risk loci (9p21, 18q11, 15q21, and 2q33) with consistent effect directions in all 4 cohorts. We calculated polygenic scores based on IA‐, AAA‐, and TAA‐associated SNPs and tested these scores for association to case‐control status in the other aneurysm cohorts; this revealed no shared polygenic effects. Similarly, linkage disequilibrium–score regression analyses did not show significant correlations between any pair of aneurysm subtypes. Last, we evaluated the evidence for 14 previously published aneurysm risk single‐nucleotide polymorphisms through collaboration in extended aneurysm cohorts, with a total of 6548 cases and 16 843 controls (IA) and 4391 cases and 37 904 controls (AAA), and found nominally significant associations for IA risk locus 18q11 near RBBP8 to AAA (odds ratio [OR]=1.11; P=4.1×10−5) and for TAA risk locus 15q21 near FBN1 to AAA (OR=1.07; P=1.1×10−3). Conclusions Although there was no evidence for polygenic overlap between IAs, AAAs, and TAAs, we found nominally significant effects of two established risk loci for IAs and TAAs in AAAs. These two loci will require further replication.
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Affiliation(s)
- Femke N G van 't Hof
- Utrecht Stroke Center, Department of Neurology and Neurosurgery, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ynte M Ruigrok
- Utrecht Stroke Center, Department of Neurology and Neurosurgery, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cue Hyunkyu Lee
- Department of Convergence Medicine, University of Ulsan College of Medicine and Asan Institute for Life Sciences Asan Medical Center, Seoul, Korea Department of Neurosurgery, Helsinki University Central Hospital, Helsinki, Finland
| | - Stephan Ripke
- Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA Department of Psychiatry and Psychotherapy, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Graig Anderson
- The George Institute for International Health, University of Sydney, Australia
| | | | - Annette F Baas
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jan D Blankensteijn
- Department of Vascular Surgery, VU Medical Center, Amsterdam, The Netherlands
| | - Erwin P Böttinger
- Icahn School of Medicine Mount Sinai, The Charles Bronfman Institute for Personalized Medicine, New York, NY
| | - Matthew J Bown
- Department of Cardiovascular Sciences and the NIHR Leicester Cardiovascular Biomedical Research Unit, University of Leicester, United Kingdom
| | - Joseph Broderick
- Department of Neurology, University of Cincinnati School of Medicine, Cincinnati, OH
| | - Philippe Bijlenga
- Hôpitaux Universitaire de Genève et Faculté de médecine de Genève, Geneva, Switzerland
| | | | - Dana C Crawford
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University, Cleveland, OH Center for Human Genetics Research, Vanderbilt University, Nashville, TN
| | - David R Crosslin
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Christian Ebeling
- Fraunhofer Institut Algorithmen und Wissenschaftliches Rechnen, Sankt Augustin, Germany
| | - Johan G Eriksson
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland Folkhälsan Research Center, Helsinki, Finland Department of General Practice and Primary Health Care, and Helsinki University Hospital, University of Helsinki, Finland
| | - Myriam Fornage
- Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | | | - Christoph M Friedrich
- Department of Computer Science, University of Applied Science and Arts, Dortmund, Germany
| | - Emília I Gaál
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland Department of Neurosurgery, Helsinki University Central Hospital, Helsinki, Finland
| | - Omri Gottesman
- Icahn School of Medicine Mount Sinai, The Charles Bronfman Institute for Personalized Medicine, New York, NY
| | - Dong-Chuan Guo
- Department of Internal Medicine, The University of Texas Medical School at Houston, TX
| | - Seamus C Harrison
- Department of Cardiovascular Science, University of Leicester, United Kingdom
| | - Juha Hernesniemi
- Department of Neurosurgery, Helsinki University Central Hospital, Helsinki, Finland
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | | | - Gregory T Jones
- Surgery Department, University of Otago, Dunedin, New Zealand
| | - Lambertus A L M Kiemeney
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Riku Kivisaari
- Department of Neurosurgery, Helsinki University Central Hospital, Helsinki, Finland
| | - Nerissa Ko
- Department of Neurology, University of California, San Francisco, CA
| | - Seppo Koskinen
- Department of Health, Functional Capacity and Welfare, National Institute for Health and Welfare, Helsinki, Finland
| | - Michiaki Kubo
- Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | | | - Helena Kuivaniemi
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA Department of Surgery, Temple University School of Medicine, Philadelphia, PA Department of Biomedical Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Mitja I Kurki
- Neurosurgery of NeuroCenter, Kuopio University Hospital, Kuopio, Finland Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA Medical and Population Genetics Program, Broad Institute, Boston, MA
| | - Aki Laakso
- Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Suzanne M Leal
- Center for Statistical Genetics, Baylor College of Medicine, Houston, TX
| | - Hanna Lehto
- Department of Neurosurgery, Helsinki University Central Hospital, Helsinki, Finland
| | - Scott A LeMaire
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine and the Texas Heart Institute, Houston, TX
| | - Siew-Kee Low
- Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Jennifer Malinowski
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN Department of Surgery, Yale School of Medicine, New Haven, CT
| | | | - Dianna M Milewicz
- Department of Internal Medicine, The University of Texas Medical School at Houston, TX
| | - Thomas H Mosley
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - Yusuke Nakamura
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, IL
| | - Hirofumi Nakaoka
- Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Mika Niemelä
- Department of Neurosurgery, Helsinki University Central Hospital, Helsinki, Finland
| | - Jennifer Pacheco
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Peggy L Peissig
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI
| | - Joanna Pera
- Department of Neurology, Jagiellonian University, Krakow, Poland
| | - Laura Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Marylyn D Ritchie
- Center for Systems Genomics, The Pennsylvania State University, Pennsylvania, PA
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Andre M van Rij
- Surgery Department, University of Otago, Dunedin, New Zealand
| | | | - Athanasios Saratzis
- Department of Cardiovascular Sciences and the NIHR Leicester Cardiovascular Biomedical Research Unit, University of Leicester, United Kingdom
| | - Agnieszka Slowik
- Department of Neurology, Jagiellonian University, Krakow, Poland
| | | | - Gerard Tromp
- The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA Department of Biomedical Sciences, Stellenbosch University, Tygerberg, South Africa
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Shefali S Verma
- Center for Systems Genomics, The Pennsylvania State University, Pennsylvania, PA
| | - Sita H Vermeulen
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Gao T Wang
- Center for Statistical Genetics, Baylor College of Medicine, Houston, TX
| | | | - Buhm Han
- Department of Convergence Medicine, University of Ulsan College of Medicine and Asan Institute for Life Sciences Asan Medical Center, Seoul, Korea
| | - Gabriël J E Rinkel
- Utrecht Stroke Center, Department of Neurology and Neurosurgery, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paul I W de Bakker
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
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47
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Nakaoka H, Gurumurthy A, Hayano T, Ahmadloo S, Omer WH, Yoshihara K, Yamamoto A, Kurose K, Enomoto T, Akira S, Hosomichi K, Inoue I. Allelic Imbalance in Regulation of ANRIL through Chromatin Interaction at 9p21 Endometriosis Risk Locus. PLoS Genet 2016; 12:e1005893. [PMID: 27055116 PMCID: PMC4824487 DOI: 10.1371/journal.pgen.1005893] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [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: 07/13/2015] [Accepted: 02/02/2016] [Indexed: 12/19/2022] Open
Abstract
Genome-wide association studies (GWASs) have discovered numerous single nucleotide polymorphisms (SNPs) associated with human complex disorders. However, functional characterization of the disease-associated SNPs remains a formidable challenge. Here we explored regulatory mechanism of a SNP on chromosome 9p21 associated with endometriosis by leveraging “allele-specific” functional genomic approaches. By re-sequencing 1.29 Mb of 9p21 region and scrutinizing DNase-seq data from the ENCODE project, we prioritized rs17761446 as a candidate functional variant that was in perfect linkage disequilibrium with the original GWAS SNP (rs10965235) and located on DNase I hypersensitive site. Chromosome conformation capture followed by high-throughput sequencing revealed that the protective G allele of rs17761446 exerted stronger chromatin interaction with ANRIL promoter. We demonstrated that the protective allele exhibited preferential binding affinities to TCF7L2 and EP300 by bioinformatics and chromatin immunoprecipitation (ChIP) analyses. ChIP assays for histone H3 lysine 27 acetylation and RNA polymerase II reinforced the enhancer activity of the SNP site. The allele specific expression analysis for eutopic endometrial tissues and endometrial carcinoma cell lines showed that rs17761446 was a cis-regulatory variant where G allele was associated with increased ANRIL expression. Our work illuminates the allelic imbalances in a series of transcriptional regulation from factor binding to gene expression mediated by chromatin interaction underlie the molecular mechanism of 9p21 endometriosis risk locus. Functional genomics on common disease will unlock functional aspect of genotype-phenotype correlations in the post-GWAS stage. A large number of variants associated with human complex diseases have been discovered by genome-wide association studies (GWASs). These discoveries have been anticipated to be translated into the definitive understanding of disease pathogeneses; however, functional characterization of the disease-associated SNPs remains a formidable challenge. Here we explored regulatory mechanism of a variant on chromosome 9p21 associated with endometriosis, a common gynecological disorder. By scrutinizing linkage disequilibrium structure and DNase I hypersensitive sites across the risk locus, we prioritized rs17761446 as a candidate causal variant. The results of our “allele-specific” functional genomic approaches sheds light on regulatory mechanisms underlying 9p21 endometriosis risk locus, in which preferential bindings of TCF7L2 and its coactivator EP300 to the protective G allele of rs17761446 lead to stronger chromatin interaction with the promoter of ANRIL, which in turn activate transcription of the non-coding RNA. Motivated by the fact that TCF7L2 was a key transcription factor of Wnt signaling pathway, we postulated that the induction of Wnt signaling activated expression levels of ANRIL and cell cycle inhibitors, CDKN2A/2B. Functional genomics on common disease will unlock functional aspect of genotype-phenotype correlations in the post-GWAS stage.
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Affiliation(s)
- Hirofumi Nakaoka
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Aishwarya Gurumurthy
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Takahide Hayano
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Somayeh Ahmadloo
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Waleed H Omer
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Akihito Yamamoto
- Department of Obstetrics and Gynecology, Nippon Medical School, Bunkyo-ku, Tokyo, Japan
| | - Keisuke Kurose
- Department of Obstetrics and Gynecology, Nippon Medical School, Bunkyo-ku, Tokyo, Japan
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Shigeo Akira
- Department of Obstetrics and Gynecology, Nippon Medical School, Bunkyo-ku, Tokyo, Japan
| | - Kazuyoshi Hosomichi
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Ituro Inoue
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
- * E-mail:
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48
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Mori T, Hosomichi K, Chiga M, Mandai S, Nakaoka H, Sohara E, Okado T, Rai T, Sasaki S, Inoue I, Uchida S. Comprehensive genetic testing approach for major inherited kidney diseases, using next-generation sequencing with a custom panel. Clin Exp Nephrol 2016; 21:63-75. [PMID: 26920127 DOI: 10.1007/s10157-016-1252-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [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: 01/25/2016] [Accepted: 02/13/2016] [Indexed: 11/25/2022]
Abstract
BACKGROUND Gene identification of hereditary kidney diseases by DNA sequencing is important for precise diagnosis, treatment, and genetic consultations. However, the conventional Sanger sequencing is now practically powerless in the face of ever increasing numbers of reported causative genes of various hereditary diseases. The advent of next-generation sequencing technology has enabled large-scale, genome-wide, simultaneous sequence analyses of multiple candidate genes. METHODS We designed and verified a comprehensive diagnosis panel for approximately 100 major inherited kidney diseases, including 127 known genes. The panel was named Simple, sPEedy and Efficient Diagnosis of Inherited KIdney Diseases (SPEEDI-KID). We applied the panel to 73 individuals, clinically diagnosed with an inherited kidney disease, from 56 families. RESULTS The panel efficiently covered the candidate genes and allowed a prompt and accurate genetic diagnosis. Moreover, 18 unreported mutations suspected as the disease causes were detected. All these mutations were validated by Sanger sequencing, with 100 % concordance. CONCLUSION In conclusion, we developed a powerful diagnostic method, focusing on inherited kidney diseases, using a custom panel, SPEEDI-KID, allowing a fast, easy, and comprehensive diagnosis regardless of the disease type.
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Affiliation(s)
- Takayasu Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo, 113-8519, Japan.
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Kanazawa University, Ishikawa, Japan
| | - Motoko Chiga
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo, 113-8519, Japan
| | - Shintaro Mandai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo, 113-8519, Japan
| | - Hirofumi Nakaoka
- Division of Human Genetics, National Institute of Genetics, Shizuoka, Japan
| | - Eisei Sohara
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo, 113-8519, Japan
| | - Tomokazu Okado
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo, 113-8519, Japan
| | - Tatemitsu Rai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo, 113-8519, Japan
| | - Sei Sasaki
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo, 113-8519, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Shizuoka, Japan
| | - Shinichi Uchida
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo, 113-8519, Japan
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49
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Tamura R, Yoshihara K, Yamawaki K, Suda K, Ishiguro T, Adachi S, Okuda S, Inoue I, Verhaak RGW, Enomoto T. Novel kinase fusion transcripts found in endometrial cancer. Sci Rep 2015; 5:18657. [PMID: 26689674 PMCID: PMC4687039 DOI: 10.1038/srep18657] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [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: 07/29/2015] [Accepted: 11/20/2015] [Indexed: 11/09/2022] Open
Abstract
Recent advances in RNA-sequencing technology have enabled the discovery of gene fusion transcripts in the transcriptome of cancer cells. However, it remains difficult to differentiate the therapeutically targetable fusions from passenger events. We have analyzed RNA-sequencing data and DNA copy number data from 25 endometrial cancer cell lines to identify potential therapeutically targetable fusion transcripts, and have identified 124 high-confidence fusion transcripts, of which 69% are associated with gene amplifications. As targetable fusion candidates, we focused on three in-frame kinase fusion transcripts that retain a kinase domain (CPQ-PRKDC, CAPZA2-MET, and VGLL4-PRKG1). We detected only CPQ-PRKDC fusion transcript in three of 122 primary endometrial cancer tissues. Cell proliferation of the fusion-positive cell line was inhibited by knocking down the expression of wild-type PRKDC but not by blocking the CPQ-PRKDC fusion transcript expression. Quantitative real-time RT-PCR demonstrated that the expression of the CPQ-PRKDC fusion transcript was significantly lower than that of wild-type PRKDC, corresponding to a low transcript allele fraction of this fusion, based on RNA-sequencing read counts. In endometrial cancers, the CPQ-PRKDC fusion transcript may be a passenger aberration related to gene amplification. Our findings suggest that transcript allele fraction is a useful predictor to find bona-fide therapeutic-targetable fusion transcripts.
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Affiliation(s)
- Ryo Tamura
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kaoru Yamawaki
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kazuaki Suda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tatsuya Ishiguro
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Sosuke Adachi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shujiro Okuda
- Department of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Roel G W Verhaak
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Genome Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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Moriya H, Inoue I, Ikeuchi M, Ishii N, Motojima M. Survey of Attitudes of Japanese Women Toward Genetic/Genomic Research. J Empir Res Hum Res Ethics 2015; 9:29-38. [PMID: 26251854 DOI: 10.1177/1556264614540597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Previous surveys have suggested that elderly Japanese women have the lowest scientific interest and literacy within the Japanese population and among populations across Western countries. Because recent tremendous advances in genome analysis are likely to be incorporated into standard biomedical assessments throughout the world, we conducted surveys to investigate the attitudes toward genetic/genomic research of Japanese women aged between 55 and 65 years. Current surveys indicate that obtaining adequate informed consent from elderly Japanese women is complicated. The limitation is especially relevant to participants’ literacy in genetics and genomic studies. Results of the surveys also indicate that even after the informed consent is obtained, researchers must continue to supply updated study information to the study subjects, which enables them to obtain additional information on the use of their samples and genetic/genomic information. Failure to consider these obligations may lead to a loss of the public’s trust and thus affect research progress on medical genomics.
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