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Hazawa M, Ikliptikawati DK, Iwashima Y, Lin DC, Jiang Y, Qiu Y, Makiyama K, Matsumoto K, Kobayashi A, Nishide G, Keesiang L, Yoshino H, Minamoto T, Suzuki T, Kobayashi I, Meguro-Horike M, Jiang YY, Nishiuchi T, Konno H, Koeffler HP, Hosomichi K, Tajima A, Horike SI, Wong RW. Super-enhancer trapping by the nuclear pore via intrinsically disordered regions of proteins in squamous cell carcinoma cells. Cell Chem Biol 2024; 31:792-804.e7. [PMID: 37924814 DOI: 10.1016/j.chembiol.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/07/2023] [Accepted: 10/10/2023] [Indexed: 11/06/2023]
Abstract
Master transcription factors such as TP63 establish super-enhancers (SEs) to drive core transcriptional networks in cancer cells, yet the spatiotemporal regulation of SEs within the nucleus remains unknown. The nuclear pore complex (NPC) may tether SEs to the nuclear pore where RNA export rates are maximal. Here, we report that NUP153, a component of the NPC, anchors SEs to the NPC and enhances TP63 expression by maximizing mRNA export. This anchoring is mediated through protein-protein interaction between the intrinsically disordered regions (IDRs) of NUP153 and the coactivator BRD4. Silencing of NUP153 excludes SEs from the nuclear periphery, decreases TP63 expression, impairs cellular growth, and induces epidermal differentiation of squamous cell carcinoma. Overall, this work reveals the critical roles of NUP153 IDRs in the regulation of SE localization, thus providing insights into a new layer of gene regulation at the epigenomic and spatial level.
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Affiliation(s)
- Masaharu Hazawa
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; Laboratory of molecular cell biology, School of Natural System, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan.
| | - Dini Kurnia Ikliptikawati
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Yuki Iwashima
- Laboratory of molecular cell biology, School of Natural System, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - De-Chen Lin
- Herman Ostrow School of Dentistry, Center for Craniofacial Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, Los Angeles, CA, USA
| | - Yuan Jiang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, P.R.China; University of Science and Technology of China, Hefei 230026, P.R.China
| | - Yujia Qiu
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Kei Makiyama
- Division of Transdisciplinary Sciences, Graduate School of Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Koki Matsumoto
- Division of Transdisciplinary Sciences, Graduate School of Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Akiko Kobayashi
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Goro Nishide
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Lim Keesiang
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Hironori Yoshino
- Department of Radiation Science, Hirosaki University Graduate School of Health Sciences, Hirosaki, Aomori 036-8564, Japan
| | - Toshinari Minamoto
- Division of Translational and Clinical Oncology, Cancer Research Institute, Kanazawa University, Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Takeshi Suzuki
- Division of Functional Genomics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Isao Kobayashi
- Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Makiko Meguro-Horike
- Advanced Science Research Center, Institute for Gene Research, Kanazawa University, Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Yan-Yi Jiang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, P.R.China; University of Science and Technology of China, Hefei 230026, P.R.China
| | - Takumi Nishiuchi
- Division of Integrated Omics research, Bioscience Core Facility Research Center for Experimental Modeling of Human Disease, Kanazawa University 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Hiroki Konno
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - H Phillip Koeffler
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kazuyoshi Hosomichi
- Laboratory of Computational Genomics, School of Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Shin-Ichi Horike
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; Advanced Science Research Center, Institute for Gene Research, Kanazawa University, Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Richard W Wong
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; Laboratory of molecular cell biology, School of Natural System, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan.
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Romero VI, Sáenz S, Arias-Almeida B, DiCapua D, Hosomichi K. AARS and CACNA1A mutations: diagnostic insights into a case report of uncommon epileptic encephalopathy phenotypes in two siblings. Front Neurol 2024; 15:1376643. [PMID: 38689878 PMCID: PMC11059961 DOI: 10.3389/fneur.2024.1376643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/04/2024] [Indexed: 05/02/2024] Open
Abstract
Epilepsy, characterized by recurrent seizures, impacts 70-80% of patients, leading to cognitive deficits. The intricate relationship between seizure control and cognitive impairment remains complex. Epileptic encephalopathy (EE), an intensified form often rooted in genetic factors, is detectable through next-generation sequencing, aiding in precise diagnoses, family counseling, and potential treatment strategies. We present a case involving two sisters with refractory generalized seizures evolving into dysarthria, dysphagia, ataxia, and cognitive decline. Despite normal physical exams, abnormal electroencephalogram results consistent with epilepsy were noted. Whole Exome Sequencing identified heterozygous variants in the alanyl-tRNA synthetase (AARS) and Calcium Voltage-Gated Channel Subunit Alpha 1 (CACNA1A) genes. The AARS variant (c.C2083T, p.R695*) was maternal, while the CACNA1A variant (c.G7400C, p.R2467P) was paternal. Patients A and B exhibited a unique blend of neurological and psychiatric conditions, distinct from common disorders that begin adolescence, like Juvenile Myoclonic Epilepsy. Whole Exome Sequencing uncovered an AARS gene and CACNA1A gene, linked to various autosomal dominant phenotypes. Presence in both parents, coupled with familial reports of migraines and seizures, provides insight into accelerated symptom progression. This study underscores the importance of genetic testing in decoding complex phenotypes and emphasizes the value of documenting family history for anticipating related symptoms and future health risks.
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Affiliation(s)
- Vanessa I. Romero
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - Samantha Sáenz
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Daniela DiCapua
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
- Neurology Service, Hospital de Especialidades Eugenio Espejo, Quito, Ecuador
| | - Kazuyoshi Hosomichi
- Laboratory of Computational Genomics, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
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Saenz Hinojosa S, Adrian Jinam T, Hosomichi K, Romero VI. HLA allelic diversity in the Waorani population of Ecuador: Its significance to their ancestry and migration. Hum Immunol 2024:110771. [PMID: 38443236 DOI: 10.1016/j.humimm.2024.110771] [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: 07/31/2023] [Revised: 02/09/2024] [Accepted: 02/28/2024] [Indexed: 03/07/2024]
Abstract
The Waorani, an isolated indigenous tribe in Ecuador, have long been characterized by limited genetic diversity, with few studies delving into their genetic background. Human Leukocyte Antigen (HLA) genes which are located in the human major histocompatibility complex (MHC) provides valuable insights into population evolution due to its highly polymorphic nature. However, little is known about the HLA diversity and ancestry of the Waorani population. In this study, we sequenced eight HLA genes using Next Generation Sequencing (NGS) from 134 Waorani individuals and obtained up to four-field HLA allele resolution. Cluster and phylogenetic analysis show that the Waorani are genetically distant from other Ecuador populations, but instead show genetic affinities with the Puyanawa and Terena tribes from Brazil, as well as the Mixe tribe from Mexico. The identification of alleles common within the Waorani population, previously linked to specific health conditions, notably paves the way for future association analyses. This extensive study, employing Next-Generation Sequencing (NGS) technology, significantly enriches the sparse and segmented understanding of HLA diversity in the South American region. Our findings enhance the global comprehension of human genetic diversity and underscore the value of studying indigenous populations. Such research is vital for deepening our insights into human migration patterns and evolutionary processes.
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Affiliation(s)
| | - Timothy Adrian Jinam
- Department of Para-Clinical Sciences, Faculty of Medicine & Health Sciences, University Malaysia Sarawak, Malaysia
| | - Kazuyoshi Hosomichi
- Laboratory of Computational Genomics, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Vanessa I Romero
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador.
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Yamamoto H, Miyashita Y, Minamiguchi H, Hosomichi K, Yoshida S, Kioka H, Shinomiya H, Nagata H, Onoue K, Kawasaki M, Kuramoto Y, Nomura A, Toma Y, Watanabe T, Yamada T, Ishihara Y, Nagata M, Kato H, Hakui H, Saito Y, Asano Y, Sakata Y. Human leukocyte antigen-DQ risk heterodimeric haplotypes of left ventricular dysfunction in cardiac sarcoidosis: an autoimmune view of its role. Sci Rep 2023; 13:19767. [PMID: 37957180 PMCID: PMC10643531 DOI: 10.1038/s41598-023-46915-1] [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: 12/13/2022] [Accepted: 11/07/2023] [Indexed: 11/15/2023] Open
Abstract
Cardiac sarcoidosis (CS) is the scarring of heart muscles by autoimmunity, leading to heart abnormalities and patients with sarcoidosis with cardiac involvements have poor prognoses. Due to the small number of patients, it is difficult to stratify all patients of CS by human leukocyte antigen (HLA) analysis. We focused on the structure of antigen-recognizing pockets in heterodimeric HLA-class II, in addition to DNA sequences, and extracted high-affinity combinations of antigenic epitopes from candidate autoantigen proteins and HLA. Four HLA heterodimer-haplotypes (DQA1*05:03/05:05/05:06/05:08-DQB1*03:01) were identified in 10 of 68 cases. Nine of the 10 patients had low left ventricular ejection fraction (< 50%). Fourteen amino-acid sequences constituting four HLA anchor pockets encoded by the HLA haplotypes were all common, suggesting DQA1*05:0X-DQB1*03:01 exhibit one group of heterodimeric haplotypes. The heterodimeric haplotypes recognized eight epitopes from different proteins. Assuming that autoimmune mechanisms might be activated by molecular mimicry, we searched for bacterial species having peptide sequences homologous to the eight epitopes. Within the peptide epitopes form the SLC25A4 and DSG2, high-homology sequences were found in Cutibacterium acnes and Mycobacterium tuberculosis, respectively. In this study, we detected the risk heterodimeric haplotypes of ventricular dysfunction in CS by searching for high-affinity HLA-class II and antigenic epitopes from candidate cardiac proteins.
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Affiliation(s)
- Hironori Yamamoto
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yohei Miyashita
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Department of Legal Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan.
| | - Hitoshi Minamiguchi
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kazuyoshi Hosomichi
- Laboratory of Computational Genomics, School of Life Science, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
| | - Shohei Yoshida
- Department of Cardiovascular Medicine, Kanazawa University Hospital, Kanazawa, Ishikawa, 920-8641, Japan
| | - Hidetaka Kioka
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Haruki Shinomiya
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Haruno Nagata
- Department of Cardiovascular Medicine, University of the Ryukyus Graduate School of Medicine, Nakagami, Okinawa, 903-0215, Japan
| | - Kenji Onoue
- Department of Cardiovascular Medicine, Nara Medical University, Kashihara, Nara, 634-8522, Japan
| | - Masato Kawasaki
- Department of Cardiology, Osaka General Medical Center, Osaka, Osaka, 558-8558, Japan
| | - Yuki Kuramoto
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Akihiro Nomura
- Innovative Research Center, Kanazawa University School of Medicine, Kanazawa, Ishikawa, 920-8641, Japan
| | - Yuichiro Toma
- Department of Cardiovascular Medicine, University of the Ryukyus Graduate School of Medicine, Nakagami, Okinawa, 903-0215, Japan
| | - Tetsuya Watanabe
- Department of Cardiology, Osaka General Medical Center, Osaka, Osaka, 558-8558, Japan
| | - Takahisa Yamada
- Department of Cardiology, Osaka General Medical Center, Osaka, Osaka, 558-8558, Japan
| | - Yasuki Ishihara
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- The 1st Department of Oral and Maxillofacial Surgery, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Miho Nagata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Department of Medical Ethics and Medical Genetics, Kyoto University Graduate School of Medicine, Kyoto, Kyoto, 606-8501, Japan
| | - Hisakazu Kato
- Department of Medical Biochemistry, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Hideyuki Hakui
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshihiko Saito
- Department of Cardiovascular Medicine, Nara Prefecture Seiwa Medical Center, Nara, Nara, 636-0802, Japan
| | - Yoshihiro Asano
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Department of Genomic Medicine, National Cerebral and Cardiovascular Center, Suita, Osaka, 564-8565, Japan.
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Mizumaki H, Tran DC, Hosokawa K, Hosomichi K, Zaimoku Y, Takamatsu H, Yamazaki H, Ishiyama K, Yamazaki R, Fujiwara H, Tajima A, Nakao S. Minor GPI(-) granulocyte populations in aplastic anemia and healthy individuals derived from a few PIGA-mutated hematopoietic stem progenitor cells. Blood Cancer J 2023; 13:165. [PMID: 37938545 PMCID: PMC10632376 DOI: 10.1038/s41408-023-00932-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/08/2023] [Accepted: 09/15/2023] [Indexed: 11/09/2023] Open
Affiliation(s)
- Hiroki Mizumaki
- Department of Hematology, Faculty of Medicine, Institute of Medical Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Dung Cao Tran
- Department of Hematology, Faculty of Medicine, Institute of Medical Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Kohei Hosokawa
- Department of Hematology, Faculty of Medicine, Institute of Medical Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Yoshitaka Zaimoku
- Department of Hematology, Faculty of Medicine, Institute of Medical Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroyuki Takamatsu
- Department of Hematology, Faculty of Medicine, Institute of Medical Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Hirohito Yamazaki
- Division of Transfusion Medicine, Kanazawa University Hospital, Kanazawa, Japan
| | - Ken Ishiyama
- Department of Hematology, Faculty of Medicine, Institute of Medical Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Rena Yamazaki
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroshi Fujiwara
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Shinji Nakao
- Department of Hematology, Faculty of Medicine, Institute of Medical Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan.
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Muromachi K, Hosomichi K, Park H, Yamaguchi T, Tani-Ishii N. Identification of Candidate Genes of Familial Multiple Idiopathic Cervical Root Resorption. J Endod 2023; 49:1537-1547. [PMID: 37742719 DOI: 10.1016/j.joen.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/12/2023] [Accepted: 09/17/2023] [Indexed: 09/26/2023]
Abstract
INTRODUCTION Multiple idiopathic cervical root resorption (MICRR) is a disease with an unknown etiology that causes invasive cervical root resorption in multiple teeth. Although previous MICRR genomic studies have identified candidate gene variants, the etiology of the condition remains poorly understood. In the present study, we investigated the genetic causality of MICRR to explore candidate variants. METHODS Saliva samples from a family containing 2 affected and two unaffected subjects with the dominant transmission of MICRR were subjected to whole-exome sequencing. RESULTS As a result, we identified novel candidate variants of 10 genes. Each variant was confirmed by Sanger sequencing. Among them, the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines classified doublecortin domain containing 1 (c.1099 C > T) and β-defensin 114 (c.189 T > G) as "pathogenic," and solute carrier family 45 member 2 (c.152_153del) as "likely pathogenic." CONCLUSIONS These results provide new insight to help clarify the pathogenesis of MICRR, and the variants could be applied for further investigation to understand invasive cervical root resorption.
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Affiliation(s)
- Koichiro Muromachi
- Department of Endodontics, Graduate School of Dentistry, Kanagawa Dental University, Yokosuka, Kanagawa, Japan.
| | - Kazuyoshi Hosomichi
- Laboratory of Computational Genomics, School of Life Science, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Heetae Park
- Department of Orthodontics, Graduate School of Dentistry, Kanagawa Dental University, Yokosuka, Kanagawa, Japan
| | - Tetsutaro Yamaguchi
- Department of Orthodontics, Graduate School of Dentistry, Kanagawa Dental University, Yokosuka, Kanagawa, Japan.
| | - Nobuyuki Tani-Ishii
- Department of Endodontics, Graduate School of Dentistry, Kanagawa Dental University, Yokosuka, Kanagawa, Japan
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Cho J, Horikawa Y, Oiwa Y, Hosomichi K, Yabe D, Imai T. Glucokinase Variant Proteins Are Resistant to Fasting-Induced Uridine Diphosphate Glucose-Dependent Degradation in Maturity-Onset Diabetes of the Young Type 2 Patients. Int J Mol Sci 2023; 24:15842. [PMID: 37958824 PMCID: PMC10649437 DOI: 10.3390/ijms242115842] [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: 09/21/2023] [Revised: 10/27/2023] [Accepted: 10/29/2023] [Indexed: 11/15/2023] Open
Abstract
We previously reported that glucokinase undergoes ubiquitination and subsequent degradation, a process mediated by cereblon, particularly in the presence of uridine diphosphate glucose (UDP-glucose). In this context, we hereby present evidence showcasing the resilience of variant glucokinase proteins of maturity-onset diabetes of the young type 2 (MODY2) against degradation and, concomitantly, their influence on insulin secretion, both in cell lines and in the afflicted MODY2 patient. Hence, glucose-1-phodphate promotes UDP-glucose production by UDP-glucose pyrophosphorylase 2; consequently, UDP-glucose-dependent glucokinase degradation may occur during fasting. Next, we analyzed glucokinase variant proteins from MODY2 or persistent hyperinsulinemic hypoglycemia in infancy (PHHI). Among the eleven MODY2 glucokinase-mutated proteins tested, those with a lower glucose-binding affinity exhibited resistance to UDP-glucose-dependent degradation. Conversely, the glucokinaseA456V-mutated protein from PHHI had a higher glucose affinity and was sensitive to UDP-glucose-dependent degradation. Furthermore, in vitro studies involving UDP-glucose-dependent glucokinase variant proteins and insulin secretion during fasting in Japanese MODY2 patients revealed a strong correlation and a higher coefficient of determination. This suggests that UDP-glucose-dependent glucokinase degradation plays a significant role in the pathogenesis of glucose-homeostasis-related hereditary diseases, such as MODY2 and PHHI.
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Affiliation(s)
- Jaeyong Cho
- Department of Chemical Biology, National Center for Geriatrics and Gerontology, Obu 474-8511, Japan; (J.C.); (Y.O.)
| | - Yukio Horikawa
- Departments of Diabetes, Endocrinology and Metabolism, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (Y.H.); (D.Y.)
| | - Yuki Oiwa
- Department of Chemical Biology, National Center for Geriatrics and Gerontology, Obu 474-8511, Japan; (J.C.); (Y.O.)
| | - Kazuyoshi Hosomichi
- Laboratory of Computational Genomics, School of Life Science, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan;
| | - Daisuke Yabe
- Departments of Diabetes, Endocrinology and Metabolism, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (Y.H.); (D.Y.)
- Department of Rheumatology and Clinical Immunology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Takeshi Imai
- Department of Chemical Biology, National Center for Geriatrics and Gerontology, Obu 474-8511, Japan; (J.C.); (Y.O.)
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Kurayoshi K, Takase Y, Ueno M, Ohta K, Fuse K, Ikeda S, Watanabe T, Nishida Y, Horike SI, Hosomichi K, Ishikawa Y, Tadokoro Y, Kobayashi M, Kasahara A, Jing Y, Shoulkamy MI, Meguro-Horike M, Kojima K, Kiyoi H, Sugiyama H, Nagase H, Tajima A, Hirao A. Targeting cis-regulatory elements of FOXO family is a novel therapeutic strategy for induction of leukemia cell differentiation. Cell Death Dis 2023; 14:642. [PMID: 37773170 PMCID: PMC10541907 DOI: 10.1038/s41419-023-06168-2] [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: 04/20/2023] [Revised: 09/10/2023] [Accepted: 09/21/2023] [Indexed: 10/01/2023]
Abstract
Differentiation therapy has been proposed as a promising therapeutic strategy for acute myeloid leukemia (AML); thus, the development of more versatile methodologies that are applicable to a wide range of AML subtypes is desired. Although the FOXOs transcription factor represents a promising drug target for differentiation therapy, the efficacy of FOXO inhibitors is limited in vivo. Here, we show that pharmacological inhibition of a common cis-regulatory element of forkhead box O (FOXO) family members successfully induced cell differentiation in various AML cell lines. Through gene expression profiling and differentiation marker-based CRISPR/Cas9 screening, we identified TRIB1, a complement of the COP1 ubiquitin ligase complex, as a functional FOXO downstream gene maintaining an undifferentiated status. TRIB1 is direct target of FOXO3 and the FOXO-binding cis-regulatory element in the TRIB1 promoter, referred to as the FOXO-responsive element in the TRIB1 promoter (FRE-T), played a critical role in differentiation blockade. Thus, we designed a DNA-binding pharmacological inhibitor of the FOXO-FRE-T interface using pyrrole-imidazole polyamides (PIPs) that specifically bind to FRE-T (FRE-PIPs). The FRE-PIPs conjugated to chlorambucil (FRE-chb) inhibited transcription of TRIB1, causing differentiation in various AML cell lines. FRE-chb suppressed the formation of colonies derived from AML cell lines but not from normal counterparts. Administration of FRE-chb inhibited tumor progression in vivo without remarkable adverse effects. In conclusion, targeting cis-regulatory elements of the FOXO family is a promising therapeutic strategy that induces AML cell differentiation.
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Affiliation(s)
- Kenta Kurayoshi
- Division of Molecular Genetics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Yusuke Takase
- Division of Molecular Genetics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Masaya Ueno
- Division of Molecular Genetics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
- Division of Molecular Genetics, WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Kumiko Ohta
- Division of Molecular Genetics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
- Department of Pharmacy, University of the Ryukyus Hospital, 207 Uehara, Nishihara, Nakagami District, Okinawa, 903-0215, Japan
| | - Kyoko Fuse
- Division of Molecular Genetics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
- Department of Hematopoietic Cell Transplantation, Niigata University Medical and Dental Hospital, 1-757 Asahimachi-dori Chuoh-ku, Niigata, 951-8510, Japan
| | - Shuji Ikeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Takayoshi Watanabe
- Department of Molecular Carcinogenesis, Chiba Cancer Center Research Institute, Chuo-ku, Chiba, 260-8717, Japan
| | - Yuki Nishida
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Shin-Ichi Horike
- Division of Integrated Omics Research, Research Center for Experimental Modeling of Human Disease Kanazawa University, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-0934, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan
- Laboratory of Computational Genomics, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Yuichi Ishikawa
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Yuko Tadokoro
- Division of Molecular Genetics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
- Division of Molecular Genetics, WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Masahiko Kobayashi
- Division of Molecular Genetics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
- Division of Molecular Genetics, WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Atsuko Kasahara
- Division of Molecular Genetics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
- Division of Molecular Genetics, WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
- Division of Molecular Genetics, Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Yongwei Jing
- Division of Molecular Genetics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Mahmoud I Shoulkamy
- Division of Molecular Genetics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
- Division of Molecular Genetics, WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
- Zoology Department, Faculty of Science, Minia University, El-Minia, 61519, Egypt
| | - Makiko Meguro-Horike
- Division of Integrated Omics Research, Research Center for Experimental Modeling of Human Disease Kanazawa University, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-0934, Japan
| | - Kensuke Kojima
- Department of Hematology, Kochi Medical School Hospital, Kochi University, Okocho Kohasu, Nankoku, Kochi, 783-8505, Japan
| | - Hitoshi Kiyoi
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroki Nagase
- Intractable Disease Research Center, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan
| | - Atsushi Hirao
- Division of Molecular Genetics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.
- Division of Molecular Genetics, WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.
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9
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Imi T, Mizumaki H, Hosomichi K, Nannya Y, Zaimoku Y, Yoroidaka T, Katagiri T, Ishiyama K, Yamazaki H, Ogawa R, Kuroiwa M, Tajima A, Ogawa S, Nakao S. Familial immune-mediated aplastic anaemia in six different families. EJHaem 2023; 4:714-718. [PMID: 37601868 PMCID: PMC10435714 DOI: 10.1002/jha2.722] [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] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/16/2023] [Accepted: 05/15/2023] [Indexed: 08/22/2023]
Abstract
We studied the pathophysiology of aplastic anaemia (AA) in six different pairs of relatives without a family history of hematologic disorders or congenital AA. Five and four of the six pairs shared the HLA-DRB1*15:01 and B*40:02 alleles, respectively. Glycosylphosphatidylinositol-anchored protein-deficient blood cells were detected in eight of the 10 patients evaluated. In a mother-daughter pair from one family, flow cytometry detected leukocytes lacking HLA-A2 due to loss of heterogeneity in chromosome 6p. Whole-exome sequencing of the family pair revealed a missense mutation in MYSM1. These results suggest that genetic inheritance of immune traits might underlie familial AA in some patients.
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Affiliation(s)
- Tatsuya Imi
- Department of HematologyGraduate School of Medical SciencesKanazawa UniversityKanazawaJapan
| | - Hiroki Mizumaki
- Department of HematologyGraduate School of Medical SciencesKanazawa UniversityKanazawaJapan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and GenomicsGraduate School of Advanced Preventive Medical SciencesKanazawa UniversityKanazawaJapan
| | - Yasuhito Nannya
- Pathology and Tumor BiologyGraduate School of MedicineKyoto UniversityKyotoJapan
- Division of Hematopoietic Disease ControlInstitute of Medical SciecenThe University of TokyoTokyoJapan
| | - Yoshitaka Zaimoku
- Department of HematologyGraduate School of Medical SciencesKanazawa UniversityKanazawaJapan
| | - Takeshi Yoroidaka
- Department of HematologyGraduate School of Medical SciencesKanazawa UniversityKanazawaJapan
| | - Takamasa Katagiri
- Department of Clinical Laboratory SciencesGraduate School of Medical SciencesKanazawa UniversityKanazawaJapan
| | - Ken Ishiyama
- Department of HematologyGraduate School of Medical SciencesKanazawa UniversityKanazawaJapan
| | - Hirohito Yamazaki
- Department of HematologyGraduate School of Medical SciencesKanazawa UniversityKanazawaJapan
| | - Ryosuke Ogawa
- Department of Hematology and OncologyJapan Community Health Care Organization Kyushu HospitalFukuokaJapan
| | - Mika Kuroiwa
- Department of Hematology and OncologyNational Hospital Organization Fukuoka Higashi Medical CenterFukuokaJapan
| | - Atsushi Tajima
- Department of Bioinformatics and GenomicsGraduate School of Advanced Preventive Medical SciencesKanazawa UniversityKanazawaJapan
| | - Seishi Ogawa
- Pathology and Tumor BiologyGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Shinji Nakao
- Department of HematologyGraduate School of Medical SciencesKanazawa UniversityKanazawaJapan
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10
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Hattori T, Cherepanov SM, Sakaga R, Roboon J, Nguyen DT, Ishii H, Takarada-Iemata M, Nishiuchi T, Kannon T, Hosomichi K, Tajima A, Yamamoto Y, Okamoto H, Sugawara A, Higashida H, Hori O. Postnatal expression of CD38 in astrocytes regulates synapse formation and adult social memory. EMBO J 2023:e111247. [PMID: 37357972 PMCID: PMC10390870 DOI: 10.15252/embj.2022111247] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/23/2023] [Accepted: 05/31/2023] [Indexed: 06/27/2023] Open
Abstract
Social behavior is essential for health, survival, and reproduction of animals; however, the role of astrocytes in social behavior remains largely unknown. The transmembrane protein CD38, which acts both as a receptor and ADP-ribosyl cyclase to produce cyclic ADP-ribose (cADPR) regulates social behaviors by promoting oxytocin release from hypothalamic neurons. CD38 is also abundantly expressed in astrocytes in the postnatal brain and is important for astroglial development. Here, we demonstrate that the astroglial-expressed CD38 plays an important role in social behavior during development. Selective deletion of CD38 in postnatal astrocytes, but not in adult astrocytes, impairs social memory without any other behavioral abnormalities. Morphological analysis shows that depletion of astroglial CD38 in the postnatal brain interferes with synapse formation in the medial prefrontal cortex (mPFC) and hippocampus. Moreover, astroglial CD38 expression promotes synaptogenesis of excitatory neurons by increasing the level of extracellular SPARCL1 (also known as Hevin), a synaptogenic protein. The release of SPARCL1 from astrocytes is regulated by CD38/cADPR/calcium signaling. These data demonstrate a novel developmental role of astrocytes in neural circuit formation and regulation of social behavior in adults.
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Grants
- 21K06407 Ministry of Education, Science, Technology, Sports and Culture of Japan
- 18KK0435 Ministry of Education, Science, Technology, Sports and Culture of Japan
- 18KK0255 Ministry of Education, Science, Technology, Sports and Culture of Japan
- 18K06500 Ministry of Education, Science, Technology, Sports and Culture of Japan
- 20K09343 Ministry of Education, Science, Technology, Sports and Culture of Japan
- 21K06406 Ministry of Education, Science, Technology, Sports and Culture of Japan
- 18K06463 Ministry of Education, Science, Technology, Sports and Culture of Japan
- Kanazawa University
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Affiliation(s)
- Tsuyoshi Hattori
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | | | - Ryo Sakaga
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Jureepon Roboon
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Dinh Thi Nguyen
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroshi Ishii
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Mika Takarada-Iemata
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Takumi Nishiuchi
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Takayuki Kannon
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Yasuhiko Yamamoto
- Department of Biochemistry and Molecular Vascular Biology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroshi Okamoto
- Department of Biochemistry and Molecular Vascular Biology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Akira Sugawara
- Department of Molecular Endocrinology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Haruhiro Higashida
- Research Center for Child Mental Development, Kanazawa University, Kanazawa, Japan
| | - Osamu Hori
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
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11
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Peñaloza D, Paredes D, Arias-Almeida B, Hosomichi K, Reyes C, Romero VI. Novel ribosomal protein L26 variant and modeling in a patient with Diamond-Blackfan anemia: Case report. Pediatr Blood Cancer 2023:e30368. [PMID: 37073646 DOI: 10.1002/pbc.30368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/20/2023]
Affiliation(s)
- Diana Peñaloza
- Colegio de la Salud, Escuela de Medicina, Universidad San Francisco de Quito, Quito, Ecuador
| | - Diana Paredes
- Colegio de la Salud, Escuela de Medicina, Universidad San Francisco de Quito, Quito, Ecuador
| | - Benjamín Arias-Almeida
- Colegio de la Salud, Escuela de Medicina, Universidad San Francisco de Quito, Quito, Ecuador
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Carlos Reyes
- Department of Genetics, Hospital de Especialidades Eugenio Espejo, Quito, Ecuador
| | - Vanessa Isabel Romero
- Colegio de la Salud, Escuela de Medicina, Universidad San Francisco de Quito, Quito, Ecuador
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12
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Cui S, Hayashi K, Kobayashi I, Hosomichi K, Nomura A, Teramoto R, Usuda K, Okada H, Deng Y, Kobayashi-Sun J, Nishikawa T, Furusho H, Saito T, Hirase H, Ohta K, Fujimoto M, Horita Y, Kusayama T, Tsuda T, Tada H, Kato T, Usui S, Sakata K, Fujino N, Tajima A, Yamagishi M, Takamura M. The utility of zebrafish cardiac arrhythmia model to predict the pathogenicity of KCNQ1 variants. J Mol Cell Cardiol 2023; 177:50-61. [PMID: 36898499 DOI: 10.1016/j.yjmcc.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/11/2023]
Abstract
Genetic testing for inherited arrhythmias and discriminating pathogenic or benign variants from variants of unknown significance (VUS) is essential for gene-based medicine. KCNQ1 is a causative gene of type 1 long QT syndrome (LQTS), and approximately 30% of the variants found in type 1 LQTS are classified as VUS. We studied the role of zebrafish cardiac arrhythmia model in determining the clinical significance of KCNQ1 variants. We generated homozygous kcnq1 deletion zebrafish (kcnq1del/del) using the CRISPR/Cas9 and expressed human Kv7.1/MinK channels in kcnq1del/del embryos. We dissected the hearts from the thorax at 48 h post-fertilization and measured the transmembrane potential of the ventricle in the zebrafish heart. Action potential duration was calculated as the time interval between peak maximum upstroke velocity and 90% repolarization (APD90). The APD90 of kcnq1del/del embryos was 280 ± 47 ms, which was significantly shortened by injecting KCNQ1 wild-type (WT) cRNA and KCNE1 cRNA (168 ± 26 ms, P < 0.01 vs. kcnq1del/del). A study of two pathogenic variants (S277L and T587M) and one VUS (R451Q) associated with clinically definite LQTS showed that the APD90 of kcnq1del/del embryos with these mutant Kv7.1/MinK channels was significantly longer than that of Kv7.1 WT/MinK channels. Given the functional results of the zebrafish model, R451Q could be reevaluated physiologically from VUS to likely pathogenic. In conclusion, functional analysis using in vivo zebrafish cardiac arrhythmia model can be useful for determining the pathogenicity of loss-of-function variants in patients with LQTS.
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Affiliation(s)
- Shihe Cui
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Kenshi Hayashi
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan; School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan.
| | - Isao Kobayashi
- Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - Kazuyoshi Hosomichi
- Laboratory of Computational Genomics, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Akihiro Nomura
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Ryota Teramoto
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Keisuke Usuda
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Hirofumi Okada
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Yaowen Deng
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Jingjing Kobayashi-Sun
- Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan; Department of Clinical Engineering, Faculty of Health Sciences, Komatsu University, Komatsu, Japan
| | - Tetsuo Nishikawa
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Hiroshi Furusho
- Department of Cardiology, Ishikawa Prefectural Central Hospital, Kanazawa, Japan
| | - Takekatsu Saito
- Department of Pediatrics, Minamigaoka Hospital, Kanazawa, Japan
| | - Hiroaki Hirase
- Department of Cardiology, Takaoka Minami Heart Center, Takaoka, Japan
| | - Kunio Ohta
- Department of Pediatrics, School of Medicine, Institute of Medical, Pharmaceutical, and Health Sciences, Kanazawa University, Kanazawa, Japan; Medical Education Research Center, Graduate School of Medical Sciences, Kanazawa University, Japan
| | - Manabu Fujimoto
- Department of Cardiology, Kouseiren Takaoka Hospital, Takaoka, Japan
| | - Yuki Horita
- Department of Cardiology, Kanazawa Cardiovascular Hospital, Kanazawa, Japan
| | - Takashi Kusayama
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Toyonobu Tsuda
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Hayato Tada
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Takeshi Kato
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Soichiro Usui
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Kenji Sakata
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Noboru Fujino
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan; School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | | | - Masayuki Takamura
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
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13
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Yamamoto R, Takeshita Y, Tsujiguchi H, Kannon T, Sato T, Hosomichi K, Suzuki K, Kita Y, Tanaka T, Goto H, Nakano Y, Yamashita T, Kaneko S, Tajima A, Nakamura H, Takamura T. Nutrigenetic interaction between apolipoprotein C3 polymorphism and fat intake in people with non-alcoholic fatty liver disease. Curr Dev Nutr 2023. [DOI: 10.1016/j.cdnut.2023.100051] [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: 03/05/2023] Open
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14
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Nayema Z, Sato T, Kannon T, Tsujiguchi H, Hosomichi K, Nakamura H, Tajima A. Genetic factors associated with serum amylase in a Japanese population: combined analysis of copy-number and single-nucleotide variants. J Hum Genet 2023; 68:313-319. [PMID: 36599956 PMCID: PMC10125868 DOI: 10.1038/s10038-022-01111-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/02/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023]
Abstract
Amylase activity and levels in humans are heritable quantitative traits. Although many studies exist on the effects of copy-number variants (CNVs) in amylase genes (AMY) on human phenotypes, such as body mass index (BMI), the genetic factors controlling interindividual variation in amylase levels remain poorly understood. Here, we conducted a genome-wide association study (GWAS) of serum amylase levels (SAL) in 814 Japanese individuals to identify associated single-nucleotide variants (SNVs), after adjusting for non-genetic factors. Diploid copy numbers (CN) of AMY (AMY1, AMY2A, and AMY2B) were measured using droplet digital PCR to examine the association between each diploid CN and SAL. We further assessed the relative contribution of the GWAS-lead SNV and AMY CNVs to SAL. GWAS identified 14 significant SNVs (p < 5 × 10-8) within a linkage disequilibrium block near the AMY cluster on chromosome 1. The association analyses of AMY CNVs and SAL showed a significant association between AMY1 diploid CN and SAL (p = 1.89 × 10-19), while no significant association with SAL was found for AMY2A CN (p = 0.54) or AMY2B CN (p = 0.15). In a joint association analysis with SAL using the GWAS-lead SNV and AMY1 diploid CN, AMY1 CN remained significant (p = 5.4 ×10-13), while the association of the lead SNV was marginal (p = 0.08). We also found no association between AMY1 diploid CN and BMI (p = 0.14). Our results indicate that AMY1 CNV is the major genetic factor for Japanese SAL, with no significant association with BMI.
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Affiliation(s)
- Zannatun Nayema
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Takayuki Kannon
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan.,Department of Biomedical Data Science, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hiromasa Tsujiguchi
- Department of Hygiene and Public Health, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan.,Laboratory of Computational Genomics, School of Life Science, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Hiroyuki Nakamura
- Department of Hygiene and Public Health, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan.
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15
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Goto RM, Warden CD, Shiina T, Hosomichi K, Zhang J, Kang TH, Wu X, Glass MC, Delany ME, Miller MM. The Gallus gallus RJF reference genome reveals an MHCY haplotype organized in gene blocks that contain 107 loci including 45 specialized, polymorphic MHC class I loci, 41 C-type lectin-like loci, and other loci amid hundreds of transposable elements. G3 (Bethesda) 2022; 12:jkac218. [PMID: 35997588 PMCID: PMC9635633 DOI: 10.1093/g3journal/jkac218] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
MHCY is a second major histocompatibility complex-like gene region in chickens originally identified by the presence of major histocompatibility complex class I-like and class II-like gene sequences. Up to now, the MHCY gene region has been poorly represented in genomic sequence data. A high density of repetitive sequence and multiple members of several gene families prevented the accurate assembly of short-read sequence data for MHCY. Identified here by single-molecule real-time sequencing sequencing of BAC clones for the Gallus gallus Red Jungle Fowl reference genome are 107 MHCY region genes (45 major histocompatibility complex class I-like, 41 c-type-lectin-like, 8 major histocompatibility complex class IIβ, 8 LENG9-like, 4 zinc finger protein loci, and a single only zinc finger-like locus) located amid hundreds of retroelements within 4 contigs representing the region. Sequences obtained for nearby ribosomal RNA genes have allowed MHCY to be precisely mapped with respect to the nucleolar organizer region. Gene sequences provide insights into the unusual structure of the MHCY class I molecules. The MHCY class I loci are polymorphic and group into 22 types based on predicted amino acid sequences. Some MHCY class I loci are full-length major histocompatibility complex class I genes. Others with altered gene structure are considered gene candidates. The amino acid side chains at many of the polymorphic positions in MHCY class I are directed away rather than into the antigen-binding groove as is typical of peptide-binding major histocompatibility complex class I molecules. Identical and nearly identical blocks of genomic sequence contribute to the observed multiplicity of identical MHCY genes and the large size (>639 kb) of the Red Jungle Fowl MHCY haplotype. Multiple points of hybridization observed in fluorescence in situ hybridization suggest that the Red Jungle Fowl MHCY haplotype is made up of linked, but physically separated genomic segments. The unusual gene content, the evidence of highly similar duplicated segments, and additional evidence of variation in haplotype size distinguish polymorphic MHCY from classical polymorphic major histocompatibility complex regions.
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Affiliation(s)
| | | | | | | | | | - Tae Hyuk Kang
- Integrative Genomics Core Facility, Beckman Research Institute, City of Hope, Duarte, CA 91010-3000, USA
| | - Xiwei Wu
- Integrative Genomics Core Facility, Beckman Research Institute, City of Hope, Duarte, CA 91010-3000, USA
| | | | | | - Marcia M Miller
- Corresponding author: Center for RNA Biology and Therapeutics, Beckman Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010-3000, USA.
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16
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Yamaguchi T, Hosomichi K, Shirota T, Miyamoto Y, Ono W, Ono N. Primary failure of tooth eruption: Etiology and management. Jpn Dent Sci Rev 2022; 58:258-267. [PMID: 36159186 PMCID: PMC9489741 DOI: 10.1016/j.jdsr.2022.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 07/01/2022] [Accepted: 08/21/2022] [Indexed: 11/16/2022] Open
Abstract
Primary failure of eruption (PFE) is a rare disorder defined as incomplete tooth eruption despite the presence of a clear eruption pathway. PFE is known to be caused by rare variants in the parathyroid hormone 1 receptor gene (PTH1R). Although several PTH1R variants have been reported, the etiology of PFE remains unclear. However, important studies that help elucidate the pathology of PFE have recently been published. The purpose of this review is to summarize current treatment options, clinical symptoms or phenotypes for diagnosis, genetic information including solid evidence in mouse disease models and disease-specific induced pluripotent stem cells, thus approaching the etiology of PFE from the perspective of the latest research.
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Affiliation(s)
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Tatsuo Shirota
- Department of Oral and Maxillofacial Surgery, Showa University School of Dentistry, Tokyo, Japan
| | - Yoichi Miyamoto
- Department of Biochemistry, Showa University School of Dentistry, Tokyo, Japan
| | - Wanida Ono
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA
| | - Noriaki Ono
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA
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17
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Roboon J, Hattori T, Nguyen DT, Ishii H, Takarada-Iemata M, Kannon T, Hosomichi K, Maejima T, Saito K, Shinmyo Y, Mieda M, Tajima A, Kawasaki H, Hori O. Isolation of ferret astrocytes reveals their morphological, transcriptional, and functional differences from mouse astrocytes. Front Cell Neurosci 2022; 16:877131. [PMID: 36274991 PMCID: PMC9584309 DOI: 10.3389/fncel.2022.877131] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Astrocytes play key roles in supporting the central nervous system structure, regulating synaptic functions, and maintaining brain homeostasis. The number of astrocytes in the cerebrum has markedly increased through evolution. However, the manner by which astrocytes change their features during evolution remains unknown. Compared with the rodent brain, the brain of the ferret, a carnivorous animal, has a folded cerebral cortex and higher white to gray matter ratio, which are common features of the human brain. To further clarify the features of ferret astrocytes, we isolated astrocytes from ferret neonatal brains, cultured these cells, and compared their morphology, gene expression, calcium response, and proliferating ability with those of mouse astrocytes. The morphology of cultured ferret astrocytes differed from that of mouse astrocytes. Ferret astrocytes had longer and more branched processes, smaller cell bodies, and different calcium responses to glutamate, as well as had a greater ability to proliferate, compared to mouse astrocytes. RNA sequencing analysis revealed novel ferret astrocyte-specific genes, including several genes that were the same as those in humans. Astrocytes in the ferret brains had larger cell size, longer primary processes in larger numbers, and a higher proliferation rate compared to mouse astrocytes. Our study shows that cultured ferret astrocytes have different features from rodent astrocytes and similar features to human astrocytes, suggesting that they are useful in studying the roles of astrocytes in brain evolution and cognitive functions in higher animals.
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Affiliation(s)
- Jureepon Roboon
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Tsuyoshi Hattori
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
- *Correspondence: Tsuyoshi Hattori,
| | - Dinh Thi Nguyen
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroshi Ishii
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Mika Takarada-Iemata
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Takayuki Kannon
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Takashi Maejima
- Department of Integrative Neurophysiology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kengo Saito
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Yohei Shinmyo
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Michihiro Mieda
- Department of Integrative Neurophysiology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroshi Kawasaki
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Osamu Hori
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
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18
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Kawashima S, Yuno A, Sano S, Nakamura A, Ishiwata K, Kawasaki T, Hosomichi K, Nakabayashi K, Akutsu H, Saitsu H, Fukami M, Usui T, Ogata T, Kagami M. Familial Pseudohypoparathyroidism Type IB Associated with an SVA Retrotransposon Insertion in the GNAS Locus. J Bone Miner Res 2022; 37:1850-1859. [PMID: 35859320 DOI: 10.1002/jbmr.4652] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 11/09/2022]
Abstract
Loss of methylation (LOM) at GNAS-A/B:TSS-differentially methylated regions (DMRs) in the GNAS locus is observed in pseudohypoparathyroidism type 1B (PHP1B). Many PHP1B cases are sporadic, but autosomal dominant-PHP1B has a deletion involving NESP55 expressed from the maternal allele or STX16 located upstream of the GNAS locus on the maternal allele. We report the possible first familial PHP1B cases with retrotransposon insertion in the GNAS locus on the maternal allele. To our knowledge, they are the possible first cases with imprinting disorders caused by retrotransposon insertion. The two sibling cases experienced tetany and/or cramps from school age and had hypocalcemia and an increased serum intact parathyroid hormone (PTH) level together with overweight, round face, and normal intellectual levels. Methylation analysis for DMRs in the GNAS locus showed only LOM of the GNAS-A/B:TSS-DMR. Copy number abnormalities at STX16 and the GNAS locus were not detected by array comparative genomic hybridization. Whole-genome sequencing and Sanger sequencing revealed an approximately 1000-bp SVA retrotransposon insertion upstream of the first exon of A/B on the GNAS locus in these siblings. Whole-genome methylome analysis by Enzymatic Methyl-Seq in the siblings showed normal methylation status in the region surrounding the insertion site and mild LOM of the GNAS-A/B:TSS-DMR. We conducted transcriptome analysis using mRNA from skin fibroblasts and induced pluripotent stem cells (iPSCs) derived from the siblings and detected no aberrant NESP55 transcripts. Quantitative reverse-transcriptase PCR (qRT-PCR) analysis in skin fibroblasts showed increased A/B expression in the patients and no NESP55 expression, even in a control. qRT-PCR analysis in iPSCs showed decreased NESP55 expression with normal methylation status of the GNAS-NESP:TSS-DMR in the patients. The retrotransposon insertion in the siblings likely caused decreased NESP55 expression that could lead to increased A/B expression via LOM of the GNAS-A/B:TSS-DMR, subsequent reduced Gsα expression, and finally, PHP1B development. © 2022 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Sayaka Kawashima
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Akiko Yuno
- Department of Endocrinology and Metabolism, Kin-ikyo Chuo Hospital, Sapporo, Japan
| | - Shinichiro Sano
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Endocrinology and Metabolism, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Akie Nakamura
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, Hokkaido University School of Medicine, Sapporo, Japan
| | - Keisuke Ishiwata
- Department of Maternal Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tomoyuki Kawasaki
- Department of Reproductive Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hidenori Akutsu
- Department of Reproductive Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Takeshi Usui
- Research Support Center, Shizuoka General Hospital, Shizuoka, Japan.,Shizuoka Graduate University of Public Health, Shizuoka, Japan
| | - Tsutomu Ogata
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Pediatrics, Hamamatsu Medical Center, Hamamatsu, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
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19
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Tsuboi H, Matsunaga M, Tsujiguchi H, Kannon T, Hosomichi K, Sato T, Tajima A, Yoshida N, Hara A, Nakamura H. Elevated ratio of serum anandamide to arachidonic acid intake in community-dwelling women with high depressive symptoms. Neuro Endocrinol Lett 2022; 43:145-153. [PMID: 36179725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/08/2022] [Indexed: 01/02/2023]
Abstract
OBJECTIVES The purpose of the present study was to investigate the serum levels of endocannabinoids (eCBs; anandamide: AEA and 2-arachidonoylglycerol: 2-AG) and daily intake of polyunsaturated fatty acids (PUFAs; arachidonic acid: ARA, docosahexaenoic acid: DHA, and eicosapentaenoic acid: EPA) among subjects with high and low depressive symptoms. METHODS The participants comprised female community-dwellers aged 40 years or older in Japan. Among 208 females, fourteen participants with high depressive symptoms and ten participants with low depressive symptoms were selected for this study. The depressive symptoms were measured by the Japanese version of the Centre for Epidemiologic Studies Depression Scale (CES-D). The daily intake of PUFAs were assessed utilising the brief-type self-administered diet history questionnaire. The blood samples were analysed for AEA, 2-AG, and the CB receptor 1 gene (CNR1) single nucleotide polymorphism (SNP) rs806377. RESULTS The ratio of AEA serum level to ARA intake (AEA/ARA) in high depressive participants was significantly higher compared with those in low depressive participants even after controlling for confounders, whereas there were no significant differences in the serum concentrations of eCBs, daily intake of PUFAs, as well as the CNR1 SNP (rs806377) between the high and low CES-D scored groups. CONCLUSION The elevated level of AEA/ARA among high depressive participants suggests that the conversion rate of ARA to AEA may be accelerated in depressive individuals.
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Affiliation(s)
- Hirohito Tsuboi
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Masahiro Matsunaga
- Department of Health and Psychosocial Medicine, Aichi Medical University School of Medicine, Nagakute 480-1195, Japan
| | - Hiromasa Tsujiguchi
- Department Hygiene and of Public Health, Graduate School of Medicine, Kanazawa University, Kanazawa 920-8640, Japan
| | - Takayuki Kannon
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa 920-8640, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa 920-8640, Japan
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa 920-8640, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa 920-8640, Japan
| | - Naoko Yoshida
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Akinori Hara
- Department of Health and Psychosocial Medicine, Aichi Medical University School of Medicine, Nagakute 480-1195, Japan
| | - Hiroyuki Nakamura
- Department of Health and Psychosocial Medicine, Aichi Medical University School of Medicine, Nagakute 480-1195, Japan
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20
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Pham LT, Peng H, Ueno M, Kohno S, Kasada A, Hosomichi K, Sato T, Kurayoshi K, Kobayashi M, Tadokoro Y, Kasahara A, Shoulkamy MI, Xiao B, Worley PF, Takahashi C, Tajima A, Hirao A. RHEB is a potential therapeutic target in T cell acute lymphoblastic leukemia. Biochem Biophys Res Commun 2022; 621:74-79. [PMID: 35810594 DOI: 10.1016/j.bbrc.2022.06.089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 06/06/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 11/02/2022]
Abstract
T cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy of immature T lymphocytes. Although various therapeutic approaches have been developed, refractoriness of chemotherapy and relapse cause a poor prognosis of the disease and further therapeutic strategies are required. Here, we report that Ras homolog enriched in brain (RHEB), a critical regulator of mTOR complex 1 activity, is a potential target for T-ALL therapy. In this study, we established an sgRNA library that comprehensively targeted mTOR upstream and downstream pathways, including autophagy. CRISPR/Cas9 dropout screening revealed critical roles of mTOR-related molecules in T-ALL cell survival. Among the regulators, we focused on RHEB because we previously found that it is dispensable for normal hematopoiesis in mice. Transcriptome and metabolic analyses revealed that RHEB deficiency suppressed de novo nucleotide biosynthesis, leading to human T-ALL cell death. Importantly, RHEB deficiency suppressed tumor growth in both mouse and xenograft models. Our data provide a potential strategy for efficient therapy of T-ALL by RHEB-specific inhibition.
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Affiliation(s)
- Loc Thi Pham
- Division of Molecular Genetics, Cancer and Stem Cell Research Program, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Hui Peng
- Division of Molecular Genetics, Cancer and Stem Cell Research Program, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Masaya Ueno
- Division of Molecular Genetics, Cancer and Stem Cell Research Program, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan; WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Susumu Kohno
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Atuso Kasada
- Division of Molecular Genetics, Cancer and Stem Cell Research Program, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan
| | - Kenta Kurayoshi
- Division of Molecular Genetics, Cancer and Stem Cell Research Program, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Masahiko Kobayashi
- Division of Molecular Genetics, Cancer and Stem Cell Research Program, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Yuko Tadokoro
- Division of Molecular Genetics, Cancer and Stem Cell Research Program, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan; WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Atsuko Kasahara
- Division of Molecular Genetics, Cancer and Stem Cell Research Program, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan; WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan; Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Mahmoud I Shoulkamy
- Division of Molecular Genetics, Cancer and Stem Cell Research Program, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan; WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan; Zoology Department, Faculty of Science, Minia University, El-Minia, 61519, Egypt
| | - Bo Xiao
- Department of Biology, School of Life Sciences, Brain Research Center, Southern University of Science and Technology, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Shenzhen, 518055, PR China
| | - Paul F Worley
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Chiaki Takahashi
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan
| | - Atsushi Hirao
- Division of Molecular Genetics, Cancer and Stem Cell Research Program, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan; WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan.
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21
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Castillo MI, Freire E, Romero VI, Arias-Almeida B, Reyes C, Hosomichi K. Novel Variation in Acyl-CoA Synthetase Long Chain Family Member 6 (ACSL6) Results in Protein Structural Modification and Multiple Non-Related Neoplasia in a 46-Year-Old: Case Report. Front Oncol 2022; 12:899579. [PMID: 35756649 PMCID: PMC9215171 DOI: 10.3389/fonc.2022.899579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
Multiple non-related neoplasia does not have an established approach or benefits for performing whole-exome sequencing (WES) analysis. We report on a 46-year-old woman who developed astrocytoma, thyroid, and breast cancer within 10 years. The WES analysis found a novel missense variant in the ACSL6 gene, and the protein modeling showed altered secondary and tertiary structures, which modify the binding to cofactors and substrates. ACSL6 is involved in lipid metabolism, expressed in the brain, thyroid, and breast tissues, and is associated with diverse types of cancer. Our study demonstrates the benefit of WES analysis compared with commercial panels in patients with non-related neoplasia.
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Affiliation(s)
| | - Erick Freire
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - Vanessa I Romero
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - Benjamín Arias-Almeida
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Carlos Reyes
- Departamento de Genetica, Hospital de Especialidades Eugenio Espejo, Quito, Ecuador
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Kanazawa University, Kanazawa, Japan
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22
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Yamanaka MP, Saito S, Hara Y, Matsuura R, Takeshima SN, Hosomichi K, Matsumoto Y, Furuta RA, Takei M, Aida Y. No evidence of bovine leukemia virus proviral DNA and antibodies in human specimens from Japan. Retrovirology 2022; 19:7. [PMID: 35585539 PMCID: PMC9116711 DOI: 10.1186/s12977-022-00592-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/13/2022] [Indexed: 11/30/2022] Open
Abstract
Background The potential risk and association of bovine leukemia virus (BLV) with human remains controversial as it has been reported to be both positive and negative in human breast cancer and blood samples. Therefore, establishing the presence of BLV in comprehensive human clinical samples in different geographical locations is essential. Result In this study, we examined the presence of BLV proviral DNA in human blood and breast cancer tissue specimens from Japan. PCR analysis of BLV provirus in 97 Japanese human blood samples and 23 breast cancer tissues showed negative result for all samples tested using long-fragment PCR and highly-sensitive short-fragment PCR amplification. No IgG and IgM antibodies were detected in any of the 97 human serum samples using BLV gp51 and p24 indirect ELISA test. Western blot analysis also showed negative result for IgG and IgM antibodies in all tested human serum samples. Conclusion Our results indicate that Japanese human specimens including 97 human blood, 23 breast cancer tissues, and 97 serum samples were negative for BLV. Supplementary Information The online version contains supplementary material available at 10.1186/s12977-022-00592-6.
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Affiliation(s)
- Meripet Polat Yamanaka
- Laboratory of Global Infectious Diseases Control Science, Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Viral Infectious Diseases Unit, RIKEN, Saitama, 351-0198, Japan.,Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Susumu Saito
- Viral Infectious Diseases Unit, RIKEN, Saitama, 351-0198, Japan.,Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Yukiko Hara
- Division of Department of Breast and Endocrine Surgery, Department of Surgery, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Ryosuke Matsuura
- Laboratory of Global Infectious Diseases Control Science, Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Viral Infectious Diseases Unit, RIKEN, Saitama, 351-0198, Japan.,Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Shin-Nosuke Takeshima
- Viral Infectious Diseases Unit, RIKEN, Saitama, 351-0198, Japan.,Department of Food and Nutrition, Jumonji University, Saitama, 352-8510, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, 920-8640, Japan
| | - Yasunobu Matsumoto
- Laboratory of Global Infectious Diseases Control Science, Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Laboratory of Global Animal Resource Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Rika A Furuta
- Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, 135-8521, Japan
| | - Masami Takei
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Yoko Aida
- Laboratory of Global Infectious Diseases Control Science, Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan. .,Viral Infectious Diseases Unit, RIKEN, Saitama, 351-0198, Japan. .,Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, Tokyo, 173-8610, Japan.
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23
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Nanjo S, Wu W, Karachaliou N, Blakely CM, Suzuki J, Chou YT, Ali SM, Kerr DL, Olivas VR, Shue J, Rotow J, Mayekar MK, Haderk F, Chatterjee N, Urisman A, Yeo JC, Skanderup AJ, Tan AC, Tam WL, Arrieta O, Hosomichi K, Nishiyama A, Yano S, Kirichok Y, Tan DS, Rosell R, Okimoto RA, Bivona TG. Deficiency of the splicing factor RBM10 limits EGFR inhibitor response in EGFR mutant lung cancer. J Clin Invest 2022; 132:145099. [PMID: 35579943 PMCID: PMC9246391 DOI: 10.1172/jci145099] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 10/19/2020] [Accepted: 05/13/2022] [Indexed: 11/18/2022] Open
Abstract
Molecularly targeted cancer therapy has improved outcomes for patients with cancer with targetable oncoproteins, such as mutant EGFR in lung cancer. Yet, the long-term survival of these patients remains limited, because treatment responses are typically incomplete. One potential explanation for the lack of complete and durable responses is that oncogene-driven cancers with activating mutations of EGFR often harbor additional co-occurring genetic alterations. This hypothesis remains untested for most genetic alterations that co-occur with mutant EGFR. Here, we report the functional impact of inactivating genetic alterations of the mRNA splicing factor RNA-binding motif 10 (RBM10) that co-occur with mutant EGFR. RBM10 deficiency decreased EGFR inhibitor efficacy in patient-derived EGFR-mutant tumor models. RBM10 modulated mRNA alternative splicing of the mitochondrial apoptotic regulator Bcl-x to regulate tumor cell apoptosis during treatment. Genetic inactivation of RBM10 diminished EGFR inhibitor–mediated apoptosis by decreasing the ratio of (proapoptotic) Bcl-xS to (antiapoptotic) Bcl-xL isoforms of Bcl-x. RBM10 deficiency was a biomarker of poor response to EGFR inhibitor treatment in clinical samples. Coinhibition of Bcl-xL and mutant EGFR overcame the resistance induced by RBM10 deficiency. This study sheds light on the role of co-occurring genetic alterations and on the effect of splicing factor deficiency on the modulation of sensitivity to targeted kinase inhibitor cancer therapy.
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Affiliation(s)
- Shigeki Nanjo
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Niki Karachaliou
- Cancer Biology and Precision Medicine Program, Germans Trias i Pujol Research Institute and Hospital, Badalona, Spain
| | - Collin M Blakely
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Junji Suzuki
- Department of Physiology, University of California, San Francisco, San Francisco, United States of America
| | - Yu-Ting Chou
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Siraj M Ali
- Foundation Medicine, Inc., Foundation Medicine, Inc., Cambridge, United States of America
| | - D Lucas Kerr
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Victor R Olivas
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Jonathan Shue
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Julia Rotow
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Manasi K Mayekar
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Franziska Haderk
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Nilanjana Chatterjee
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Anatoly Urisman
- Department of Pathology, University of California, San Francisco, San Francisco, United States of America
| | - Jia Chi Yeo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Anders J Skanderup
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Aaron C Tan
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Oscar Arrieta
- Thoracic Oncology Unit, National Cancer Center Institute (INCan), México City, Mexico
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomic, Kanazawa Universuty, Kanazawa, Japan
| | - Akihiro Nishiyama
- Division of Medical Oncology, Kanazawa University Cancer Research Institute, Kanazawa, Japan
| | - Seiji Yano
- Kanazawa University Cancer Research Institute, Kanazawa, Japan
| | - Yuriy Kirichok
- Department of Physiology, University of California, San Francisco, San Francisco, United States of America
| | - Daniel Sw Tan
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Rafael Rosell
- Cancer Biology and Precision Medicine Program, Germans Trias i Pujol Research Institute and Hospital, Badalona, Spain
| | - Ross A Okimoto
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Trever G Bivona
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, United States of America
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24
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Pham KO, Hara A, Tsujiguchi H, Suzuki K, Suzuki F, Miyagi S, Kannon T, Sato T, Hosomichi K, Tsuboi H, Nguyen TTT, Shimizu Y, Kambayashi Y, Nakamura M, Takazawa C, Nakamura H, Hamagishi T, Shibata A, Konoshita T, Tajima A, Nakamura H. Association between Vitamin Intake and Chronic Kidney Disease According to a Variant Located Upstream of the PTGS1 Gene: A Cross-Sectional Analysis of Shika Study. Nutrients 2022; 14:2082. [PMID: 35631221 PMCID: PMC9143472 DOI: 10.3390/nu14102082] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/02/2022] [Accepted: 05/14/2022] [Indexed: 11/22/2022] Open
Abstract
Chronic kidney disease (CKD) patients have been advised to take vitamins; however, the effects have been controversial. The individual differences in developing CKD might involve genetic variants of inflammation, including variant rs883484 located upstream of the prostaglandin-endoperoxide synthase 1 (PTGS1) gene. We aimed to identify whether the 12 dietary vitamin intake interacts with genotypes of the rs883484 on developing CKD. The population-based, cross-sectional study had 684 Japanese participants (≥40 years old). The study used a validated, brief, self-administered diet history questionnaire to estimate the intake of the dietary vitamins. CKD was defined as estimated glomerular filtration < 60 mL/min/1.73 m2. The study participants had an average age of 62.1 ± 10.8 years with 15.4% minor homozygotes of rs883484, and 114 subjects had CKD. In the fully adjusted model, the higher intake of vitamins, namely niacin (odds ratio (OR) = 0.74, 95% confidence interval (CI): 0.57−0.96, p = 0.024), α-tocopherol (OR = 0.49, 95% CI: 0.26−0.95, p = 0.034), and vitamin C (OR = 0.97, 95% CI: 0.95−1.00, p = 0.037), was independently associated with lower CKD tendency in the minor homozygotes of rs883484. The results suggested the importance of dietary vitamin intake in the prevention of CKD in middle-aged to older-aged Japanese with minor homozygous of rs883484 gene variant.
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Affiliation(s)
- Kim-Oanh Pham
- Information Management Department, Asia Center for Air Pollution Research, Niigata City 950-2144, Japan
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City 920-8640, Japan; (A.H.); (H.T.); (K.S.); (F.S.); (M.N.); (C.T.); (H.N.); (T.H.); (A.S.); (H.N.)
| | - Akinori Hara
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City 920-8640, Japan; (A.H.); (H.T.); (K.S.); (F.S.); (M.N.); (C.T.); (H.N.); (T.H.); (A.S.); (H.N.)
| | - Hiromasa Tsujiguchi
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City 920-8640, Japan; (A.H.); (H.T.); (K.S.); (F.S.); (M.N.); (C.T.); (H.N.); (T.H.); (A.S.); (H.N.)
| | - Keita Suzuki
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City 920-8640, Japan; (A.H.); (H.T.); (K.S.); (F.S.); (M.N.); (C.T.); (H.N.); (T.H.); (A.S.); (H.N.)
| | - Fumihiko Suzuki
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City 920-8640, Japan; (A.H.); (H.T.); (K.S.); (F.S.); (M.N.); (C.T.); (H.N.); (T.H.); (A.S.); (H.N.)
- Community Medicine Support Dentistry, Faculty of Dentist, Ohu University Hospital, Koriyama 963-8611, Japan
| | - Sakae Miyagi
- Innovative Clinical Research Center, Takaramachi Campus, Kanazawa University, Kanazawa City 920-8640, Japan;
| | - Takayuki Kannon
- Department of Bioinformatics and Genomics, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City 920-8640, Japan; (T.K.); (T.S.); (K.H.); (A.T.)
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City 920-8640, Japan; (T.K.); (T.S.); (K.H.); (A.T.)
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City 920-8640, Japan; (T.K.); (T.S.); (K.H.); (A.T.)
| | - Hirohito Tsuboi
- Institute of Medical, Pharmaceutical and Health Sciences, Kakuma Campus, Kanazawa University, Kanazawa City 920-1192, Japan;
| | - Thao Thi Thu Nguyen
- Department of Epidemiology, Faculty of Public Health, Haiphong University of Medicine and Pharmacy, Hai Phong 180000, Vietnam;
| | - Yukari Shimizu
- Department of Nursing, Faculty of Health Sciences, Komatsu University, Komatsu City 923-0961, Japan;
| | - Yasuhiro Kambayashi
- Department of Public Health, Faculty of Veterinary Medicine, Okayama University of Science, Imabari 794-8555, Japan;
| | - Masaharu Nakamura
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City 920-8640, Japan; (A.H.); (H.T.); (K.S.); (F.S.); (M.N.); (C.T.); (H.N.); (T.H.); (A.S.); (H.N.)
| | - Chie Takazawa
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City 920-8640, Japan; (A.H.); (H.T.); (K.S.); (F.S.); (M.N.); (C.T.); (H.N.); (T.H.); (A.S.); (H.N.)
| | - Haruki Nakamura
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City 920-8640, Japan; (A.H.); (H.T.); (K.S.); (F.S.); (M.N.); (C.T.); (H.N.); (T.H.); (A.S.); (H.N.)
| | - Toshio Hamagishi
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City 920-8640, Japan; (A.H.); (H.T.); (K.S.); (F.S.); (M.N.); (C.T.); (H.N.); (T.H.); (A.S.); (H.N.)
| | - Aki Shibata
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City 920-8640, Japan; (A.H.); (H.T.); (K.S.); (F.S.); (M.N.); (C.T.); (H.N.); (T.H.); (A.S.); (H.N.)
| | - Tadashi Konoshita
- Third Department of Internal Medicine, Faculty of Medical Sciences, University of Fukui, Tsuruga 914-0055, Japan;
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City 920-8640, Japan; (T.K.); (T.S.); (K.H.); (A.T.)
| | - Hiroyuki Nakamura
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City 920-8640, Japan; (A.H.); (H.T.); (K.S.); (F.S.); (M.N.); (C.T.); (H.N.); (T.H.); (A.S.); (H.N.)
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25
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Suzuki K, Tsujiguchi H, Hara A, Pham OK, Miyagi S, Nguyen TTT, Nakamura H, Suzuki F, Kasahara T, Shimizu Y, Yamada Y, Kambayashi Y, Tsuboi H, Sato T, Kannon T, Hosomichi K, Tajima A, Takamura T, Nakamura H. Association Between Serum 25-Hydroxyvitamin D Concentrations, CDX2 Polymorphism in Promoter Region of Vitamin D Receptor Gene, and Chronic Pain in Rural Japanese Residents. J Pain Res 2022; 15:1475-1485. [PMID: 35633918 PMCID: PMC9139339 DOI: 10.2147/jpr.s356630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/17/2022] [Indexed: 11/23/2022] Open
Abstract
Background Previous studies examined the association between chronic pain (CP) and serum 25-hydroxyvitamin D (25(OH)D) concentrations; however, the findings obtained were inconsistent. Single nucleotide polymorphisms (SNP) associated with the transcriptional activity of the vitamin D receptor (VDR) gene may influence the association of 25(OH)D levels with CP. We aimed to clarify the association between CP, serum 25(OH)D concentration, and SNPs. Methods In the Shika study, we performed a cross-sectional analysis of 551 participants older than 40 years who were asked whether they had been having persistent pain lasting for at least 3 months in any part of the body on a self-administered questionnaire. Serum 25(OH)D concentrations were assessed as a biomarker of the vitamin D status using a radioimmunoassay. rs731236, rs7975232, rs1544410, rs2228570, and rs11568820 were identified using peripheral blood samples, and participants were assigned to those with or without the minor allele for each SNP. Results The prevalence of CP was 37.2%. We observed a tendency for lower 25(OH)D levels in participants with CP than in those without CP in the hetero/minor group of rs11568820, which is a polymorphism within the CDX2-binding site in the 1e promoter region of the VDR gene. Furthermore, a logistic regression analysis revealed that lower serum 25(OH)D concentrations were significantly associated with CP in the hetero/minor group, but not in the major group. Conclusion These results suggest that sufficient serum 25(OH)D concentration reduces the risk of CP in individuals with the minor allele of the CDX2 polymorphism.
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Affiliation(s)
- Keita Suzuki
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
- Correspondence: Keita Suzuki, Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan, Tel +81 76 265 2218, Fax +81 76 234 4233, Email
| | - Hiromasa Tsujiguchi
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
- Department of Public Health, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
- Kanazawa University Advanced Preventive Medical Sciences Research Center, Kanazawa, Ishikawa, Japan
| | - Akinori Hara
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
- Department of Public Health, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
- Kanazawa University Advanced Preventive Medical Sciences Research Center, Kanazawa, Ishikawa, Japan
| | - Oanh Kim Pham
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Sakae Miyagi
- Kanazawa University Advanced Preventive Medical Sciences Research Center, Kanazawa, Ishikawa, Japan
- Innovative Clinical Research Center, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Thao Thi Thu Nguyen
- Department of Epidemiology, Faculty of Public Health, Haiphong University of Medicine and Pharmacy, Hai Phong, Vietnam
| | - Haruki Nakamura
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Fumihiko Suzuki
- Department of Public Health, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
- Community Medicine Support Dentistry, Ohu University Hospital, Koriyama, Fukushima, Japan
| | - Tomoko Kasahara
- Department of Public Health, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Yukari Shimizu
- Department of Nursing, Faculty of Health Sciences, Komatsu University, Komatsu, Ishikawa, Japan
| | - Yohei Yamada
- Department of Public Health, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Yasuhiro Kambayashi
- Department of Public Health, Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Ehime, Japan
| | - Hirohito Tsuboi
- Institute of Medical, Pharmaceutical, and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Takehiro Sato
- Kanazawa University Advanced Preventive Medical Sciences Research Center, Kanazawa, Ishikawa, Japan
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Takayuki Kannon
- Kanazawa University Advanced Preventive Medical Sciences Research Center, Kanazawa, Ishikawa, Japan
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kazuyoshi Hosomichi
- Kanazawa University Advanced Preventive Medical Sciences Research Center, Kanazawa, Ishikawa, Japan
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Atsushi Tajima
- Kanazawa University Advanced Preventive Medical Sciences Research Center, Kanazawa, Ishikawa, Japan
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Toshinari Takamura
- Department of Endocrinology and Metabolism, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Ishikawa, Japan
| | - Hiroyuki Nakamura
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
- Department of Public Health, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
- Kanazawa University Advanced Preventive Medical Sciences Research Center, Kanazawa, Ishikawa, Japan
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26
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Nomura N, Iizuka K, Goshima E, Hosomichi K, Tajima A, Kubota S, Liu Y, Takao K, Kato T, Mizuno M, Hirota T, Suwa T, Horikawa Y, Yabe D. Glucokinase-maturity onset diabetes mellitus in the young suggested by factory-calibrated glucose monitoring data: a case report. Endocr J 2022; 69:473-477. [PMID: 34803122 DOI: 10.1507/endocrj.ej21-0526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Glucokinase has an important role in regulating glycolysis as a glucose sensor in liver and pancreatic β cells. Glucokinase-maturity onset diabetes in young (GCK-MODY also known as MODY2) is caused by autosomal dominant gene mutation of the GCK gene; it is characterized by mild fasting hyperglycemia and small 2-h glucose increment during 75 g-oral glucose tolerance test (OGTT) as well as near-normal postprandial glucose variabilities. A 10-year-old girl with family history of diabetes visited her physician after being found positive for urinary glucose by school medical checkup. She received a diagnosis of diabetes based on the laboratory data: 75 g-OGTT (mild fasting hyperglycemia and small 2-h glucose increment) and factory-calibrated glucose monitoring (mild elevation of average glucose level and near-normal glycemic variability), which raised suspicion of GCK-MODY. She was then referred to our institution for genetic examination, which revealed a GCK heterozygous mutation (NM_000162: exon10: c.1324G>T: p.E442X) in the proband as well as in her mother and maternal grandmother, who had been receiving anti-diabetes medications without knowing that they had GCK-MODY specifically. GCK-MODY cases show incidence of microvascular and macrovascular diseases similar to that of normal subjects, and their glucose levels are adequately controlled without anti-diabetes drug use. Thus, early and definitive diagnosis of MODY2 by genetic testing is important to avoid unnecessary medication.
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Affiliation(s)
- Nao Nomura
- Department of Diabetes, Endocrinology and Metabolism/Department of Rheumatology and Clinical Immunology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Katsumi Iizuka
- Department of Diabetes, Endocrinology and Metabolism/Department of Rheumatology and Clinical Immunology, Gifu University Graduate School of Medicine, Gifu, Japan
- Department of Clinical Nutrition, School of Medicine, Fujita Health University, Aichi, Japan
- Yutaka Seino Distinguished Center for Diabetes Research, Kansai Electric Power Medical Research Institution, Hyogo, Japan
| | | | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Sodai Kubota
- Department of Diabetes, Endocrinology and Metabolism/Department of Rheumatology and Clinical Immunology, Gifu University Graduate School of Medicine, Gifu, Japan
- Yutaka Seino Distinguished Center for Diabetes Research, Kansai Electric Power Medical Research Institution, Hyogo, Japan
| | - Yanyan Liu
- Department of Diabetes, Endocrinology and Metabolism/Department of Rheumatology and Clinical Immunology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Ken Takao
- Department of Diabetes, Endocrinology and Metabolism/Department of Rheumatology and Clinical Immunology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Takehiro Kato
- Department of Diabetes, Endocrinology and Metabolism/Department of Rheumatology and Clinical Immunology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Masami Mizuno
- Department of Diabetes, Endocrinology and Metabolism/Department of Rheumatology and Clinical Immunology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Takuo Hirota
- Department of Diabetes, Endocrinology and Metabolism/Department of Rheumatology and Clinical Immunology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Tetsuya Suwa
- Department of Diabetes, Endocrinology and Metabolism/Department of Rheumatology and Clinical Immunology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yukio Horikawa
- Department of Diabetes, Endocrinology and Metabolism/Department of Rheumatology and Clinical Immunology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Daisuke Yabe
- Department of Diabetes, Endocrinology and Metabolism/Department of Rheumatology and Clinical Immunology, Gifu University Graduate School of Medicine, Gifu, Japan
- Yutaka Seino Distinguished Center for Diabetes Research, Kansai Electric Power Medical Research Institution, Hyogo, Japan
- Division of Molecular and Metabolic Medicine, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Hyogo, Japan
- Center for Healthcare Information Technology, Tokai National Higher Education and Research System, Aichi, Japan
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27
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Hara A, Nguyen PM, Tsujiguchi H, Nakamura M, Yamada Y, Suzuki K, Suzuki F, Kasahara T, Pham OK, Nakamura H, Kambayashi Y, Shimizu Y, Nguyen TTT, Miyagi S, Kannon T, Sato T, Hosomichi K, Tajima A, Nakamura H. Effect of β3‐adrenergic receptor gene polymorphism and lifestyle on overweight Japanese rural residents: A cross‐sectional study. Obes Sci Pract 2022; 8:199-207. [PMID: 35388349 PMCID: PMC8976547 DOI: 10.1002/osp4.560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 12/22/2022] Open
Abstract
Objectives The β3‐adrenergic receptor (ADRB3) gene polymorphism has been implicated in obesity. Therefore, the contribution of ADRB3 Trp64Arg polymorphism to obesity‐related indicators was investigated, taking into account the lifestyle‐related factors in a Japanese rural population. Methods A total of 600 Japanese adults aged ≥40 years in a population‐based cohort study were analyzed. The ADRB3 polymorphism was determined using peripheral blood samples. Associations between genotype and body mass index (BMI), waist circumference (WC), and body fat (BF) percentage were examined, adjusting for lifestyle‐related factors, including daily nutrient intake. Results The frequency of Arg64 allele carriers was 36%. There was no significant difference in BMI, WC, or BF between the groups with or without the Trp64Arg polymorphism. Multivariable logistic regression analysis showed that the Trp64Arg polymorphism was not associated with these three indicators, but lifestyle factors including physical inactivity, higher energy and sodium consumption, and less animal protein intake were significantly related to increased WC and BF percentages. Conclusions The Trp64Arg polymorphism of ADRB3 gene did not contribute to increased BMI, WC, or BF. However, lifestyle‐related factors impacted these indicators in middle‐aged and older Japanese individuals living in rural areas.
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Affiliation(s)
- Akinori Hara
- Department of Hygiene and Public Health Faculty of Medicine Institute of Medical, Pharmaceutical and Health Sciences Kanazawa University Kanazawa Ishikawa Japan
| | - Phat Minh Nguyen
- Department of Hygiene and Public Health Faculty of Medicine Institute of Medical, Pharmaceutical and Health Sciences Kanazawa University Kanazawa Ishikawa Japan
| | - Hiromasa Tsujiguchi
- Department of Hygiene and Public Health Faculty of Medicine Institute of Medical, Pharmaceutical and Health Sciences Kanazawa University Kanazawa Ishikawa Japan
| | - Masaharu Nakamura
- Department of Hygiene and Public Health Faculty of Medicine Institute of Medical, Pharmaceutical and Health Sciences Kanazawa University Kanazawa Ishikawa Japan
| | - Yohei Yamada
- Department of Hygiene and Public Health Faculty of Medicine Institute of Medical, Pharmaceutical and Health Sciences Kanazawa University Kanazawa Ishikawa Japan
| | - Keita Suzuki
- Department of Hygiene and Public Health Faculty of Medicine Institute of Medical, Pharmaceutical and Health Sciences Kanazawa University Kanazawa Ishikawa Japan
| | - Fumihiko Suzuki
- Department of Hygiene and Public Health Faculty of Medicine Institute of Medical, Pharmaceutical and Health Sciences Kanazawa University Kanazawa Ishikawa Japan
- Community Medicine Support Dentistry Ohu University Hospital Koriyama Fukushima Japan
| | - Tomoko Kasahara
- Department of Hygiene and Public Health Faculty of Medicine Institute of Medical, Pharmaceutical and Health Sciences Kanazawa University Kanazawa Ishikawa Japan
| | - Oanh Kim Pham
- Department of Hygiene and Public Health Faculty of Medicine Institute of Medical, Pharmaceutical and Health Sciences Kanazawa University Kanazawa Ishikawa Japan
| | - Haruki Nakamura
- Department of Hygiene and Public Health Faculty of Medicine Institute of Medical, Pharmaceutical and Health Sciences Kanazawa University Kanazawa Ishikawa Japan
| | - Yasuhiro Kambayashi
- Department of Public Health Faculty of Veterinary Medicine Okayama University of Science Imabari Ehime Japan
| | - Yukari Shimizu
- Department of Nursing Faculty of Health Sciences Komatsu University Komatsu Ishikawa Japan
| | - Thao Thi Thu Nguyen
- Department of Epidemiology Faculty of Public Health Haiphong University of Medicine and Pharmacy Hai Phong Vietnam
| | - Sakae Miyagi
- Division of Biostatistics Innovative Clinical Research Center Kanazawa University Kanazawa Ishikawa Japan
| | - Takayuki Kannon
- Department of Bioinformatics and Genomics Faculty of Medicine Institute of Medical, Pharmaceutical and Health Sciences Kanazawa University Kanazawa Ishikawa Japan
| | - Takehiro Sato
- Department of Bioinformatics and Genomics Faculty of Medicine Institute of Medical, Pharmaceutical and Health Sciences Kanazawa University Kanazawa Ishikawa Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics Faculty of Medicine Institute of Medical, Pharmaceutical and Health Sciences Kanazawa University Kanazawa Ishikawa Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics Faculty of Medicine Institute of Medical, Pharmaceutical and Health Sciences Kanazawa University Kanazawa Ishikawa Japan
| | - Hiroyuki Nakamura
- Department of Hygiene and Public Health Faculty of Medicine Institute of Medical, Pharmaceutical and Health Sciences Kanazawa University Kanazawa Ishikawa Japan
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28
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Sakai K, Ishida C, Hayashi K, Tsuji N, Kannon T, Hosomichi K, Takei N, Kakita A, Tajima A, Yamada M. Familial idiopathic basal ganglia calcification with a heterozygous missense variant (c.902C>T/p.P307L) in SLC20A2 showing widespread cerebrovascular lesions. Neuropathology 2022; 42:126-133. [PMID: 35026865 DOI: 10.1111/neup.12781] [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: 06/01/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 12/01/2022]
Abstract
We describe a postmortem case of familial idiopathic basal ganglia calcification (FIBGC) in a 72-year-old Japanese man. The patient showed progressive cognitive impairment with a seven-year clinical course and calcification of the basal ganglia, thalami, and cerebellar dentate nuclei. A novel heterozygous missense variant in SLC20A2 (c.920C>T/p.P307L), a type III sodium-dependent phosphate transporter (PiT-2), was subsequently identified, in addition to typical neuropathological findings of FIBGC, such as capillary calcification of the occipital gray matter, confluent calcification of the basal ganglia and cerebellar white matter, widespread occurrence of vasculopathic changes, cerebrovascular lesions, and vascular smooth muscle cell depletion. Immunohistochemistry for PiT-2 protein revealed no apparent staining in endothelial cells in the basal ganglia and insular cortex; however, the immunoreactivity in endothelial cells of the cerebellum was preserved. Moreover, Western blot analysis identified preserved PiT-2 immunoreactivity signals in the frontal cortex and cerebellum. The variant identified in the present patient could be associated with development of FIBGC and is known to be located at the large intracytoplasmic part of the PiT-2 protein, which has potential phosphorylation sites with importance in the regulation of inorganic phosphate transport activity. The present case is an important example to prove that FIGBC could stem from a missense variant in the large intracytoplasmic loop of the PiT-2 protein. Abnormal clearance of inorganic phosphate in the brain could be related to the development of vascular smooth muscle damage, the formation of cerebrovascular lesions, and subsequent brain calcification in patients with FIBGC with SLC20A2 variants.
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Affiliation(s)
- Kenji Sakai
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Chiho Ishida
- Department of Neurology, National Hospital Organization Iou National Hospital, Kanazawa, Japan
| | - Koji Hayashi
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
- Department of Neurology, National Hospital Organization Iou National Hospital, Kanazawa, Japan
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Naotaka Tsuji
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Takayuki Kannon
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Nobuyuki Takei
- Department of Brain Tumor Biology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Masahito Yamada
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
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Shinmyo Y, Saito K, Hamabe-Horiike T, Kameya N, Ando A, Kawasaki K, Duong TAD, Sakashita M, Roboon J, Hattori T, Kannon T, Hosomichi K, Slezak M, Holt MG, Tajima A, Hori O, Kawasaki H. Localized astrogenesis regulates gyrification of the cerebral cortex. Sci Adv 2022; 8:eabi5209. [PMID: 35275722 PMCID: PMC8916738 DOI: 10.1126/sciadv.abi5209] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 03/16/2021] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
The development and evolution of mammalian higher cognition are represented by gyrification of the laminar cerebral cortex and astrocyte development, but their mechanisms and interrelationships remain unknown. Here, we show that localized astrogenesis plays an important role in gyri formation in the gyrencephalic cerebral cortex. In functional genetic experiments, we show that reducing astrocyte number prevents gyri formation in the ferret cortex, while increasing astrocyte number in mice, which do not have cortical folds, can induce gyrus-like protrusions. Morphometric analyses demonstrate that the vertical expansion of deep pallial regions achieved by localized astrogenesis is crucial for gyri formation. Furthermore, our findings suggest that localized astrogenesis by a positive feedback loop of FGF signaling is an important mechanism underlying cortical folding in gyrencephalic mammalian brains. Our findings reveal both the cellular mechanisms and the mechanical principle of gyrification in the mammalian brain.
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Affiliation(s)
- Yohei Shinmyo
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Kengo Saito
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Toshihide Hamabe-Horiike
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Narufumi Kameya
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Akitaka Ando
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Kanji Kawasaki
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Tung Anh Dinh Duong
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Masataka Sakashita
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Jureepon Roboon
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Tsuyoshi Hattori
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Takayuki Kannon
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Michal Slezak
- VIB Center for Brain and Disease Research, Herestraat 49, Leuven 3000, Belgium
- Łukasiewicz Research Network-PORT Polish Institute for Technology Development, 54-066 Wroclaw, Poland
| | - Matthew G. Holt
- VIB Center for Brain and Disease Research, Herestraat 49, Leuven 3000, Belgium
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Osamu Hori
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Hiroshi Kawasaki
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
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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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Koga M, Senkoji T, Kubota M, Ishizaka A, Mizutani T, Sedohara A, Ikeuchi K, Kikuchi T, Adachi E, Saito M, Koibuchi T, Hosomichi K, Ohashi J, Kawana-Tachikawa A, Matano T, Tsutsumi T, Yotsuyanagi H. Predictors associated with a better response to the Japanese aluminum-free hepatitis A vaccine, Aimmugen ® , for people living with HIV. Hepatol Res 2022; 52:227-234. [PMID: 34825436 DOI: 10.1111/hepr.13736] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/14/2021] [Accepted: 11/23/2021] [Indexed: 12/13/2022]
Abstract
AIM After the hepatitis A virus (HAV) outbreak among men who have sex with men (MSM) around 2018, the importance of HAV vaccination was emphasized, especially for MSM-living with human immunodeficiency virus (MSM-LWHIV). Aimmugen® is licensed and distributed exclusively in Japan. While administration of three doses is recommended, 85% of recipients in the general population were reported to acquire seroprotection after the second dose. In this study, we evaluated the efficacy of two or three vaccine doses along with predictors associated with the response to Aimmugen® in MSM-LWHIV. METHODS We retrospectively examined anti-HA-IgG titers of MSM-LWHIV vaccinated with Aimmugen® in our hospital. Patients' data were collected from medical records. RESULTS Between January 2018 and October 2019, 141 subjects whose median age was 46 years old, were examined. All the subjects were on antiretroviral therapy (ART) and the median CD4 count was 615/μL. The acquisition rate of protectable anti-HA-IgG titers after the second and third dose was 71.1% and 98.6%, respectively. In 114 subjects whose anti-HA-IgG titers were tested after the second-dose, factors significantly associated with better response were prolonged ART duration and higher CD4 count. The titers of anti-HA-IgG after the third dose were higher in those who became seropositive after the second-dose than those who did not. CONCLUSIONS Three-dose of Aimmugen® for MSM-LWHIV was effective while two-dose was less effective compared to non-HIV-infected people. People-LWHIV with shorter duration of ART and lesser CD4 cell count achieved lower titers of anti-HA-IgG and might require an additional vaccination.
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Affiliation(s)
- Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Tomoe Senkoji
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Megumi Kubota
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Aya Ishizaka
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Taketoshi Mizutani
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Ayako Sedohara
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Kazuhiko Ikeuchi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Tadashi Kikuchi
- Department of Infectious Diseases and Applied Immunology, Hospital of the Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Eisuke Adachi
- Department of Infectious Diseases and Applied Immunology, Hospital of the Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Makoto Saito
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Tomohiko Koibuchi
- Department of Infectious Diseases and Applied Immunology, Hospital of the Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | | | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Department of Infectious Diseases and Applied Immunology, Hospital of the Institute of Medical Science, University of Tokyo, Tokyo, Japan
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Nishijima H, Matsumoto M, Morimoto J, Hosomichi K, Akiyama N, Akiyama T, Oya T, Tsuneyama K, Yoshida H, Matsumoto M. Aire Controls Heterogeneity of Medullary Thymic Epithelial Cells for the Expression of Self-Antigens. J Immunol 2022; 208:303-320. [PMID: 34930780 DOI: 10.4049/jimmunol.2100692] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 11/04/2021] [Indexed: 06/14/2023]
Abstract
The deficiency of Aire, a transcriptional regulator whose defect results in the development of autoimmunity, is associated with reduced expression of tissue-restricted self-Ags (TRAs) in medullary thymic epithelial cells (mTECs). Although the mechanisms underlying Aire-dependent expression of TRAs need to be explored, the physical identification of the target(s) of Aire has been hampered by the low and promiscuous expression of TRAs. We have tackled this issue by engineering mice with augmented Aire expression. Integration of the transcriptomic data from Aire-augmented and Aire-deficient mTECs revealed that a large proportion of so-called Aire-dependent genes, including those of TRAs, may not be direct transcriptional targets downstream of Aire. Rather, Aire induces TRA expression indirectly through controlling the heterogeneity of mTECs, as revealed by single-cell analyses. In contrast, Ccl25 emerged as a canonical target of Aire, and we verified this both in vitro and in vivo. Our approach has illuminated the Aire's primary targets while distinguishing them from the secondary targets.
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Affiliation(s)
- Hitoshi Nishijima
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
| | - Minoru Matsumoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
- Department of Pathology and Laboratory Medicine, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
- Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Junko Morimoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Nobuko Akiyama
- Laboratory for Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; and
| | - Takeshi Oya
- Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Koichi Tsuneyama
- Department of Pathology and Laboratory Medicine, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Hideyuki Yoshida
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Science, Yokohama, Japan
| | - Mitsuru Matsumoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan;
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Calvache CA, Vásquez EC, Romero VI, Hosomichi K, Pozo JC. Novel SRY-box transcription factor 9 variant in campomelic dysplasia and the location of missense and nonsense variants along the protein domains: A case report. Front Pediatr 2022; 10:975947. [PMID: 36467484 PMCID: PMC9716274 DOI: 10.3389/fped.2022.975947] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/21/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Campomelic dysplasia (CD) is a rare disorder that involves the skeletal and genital systems. This condition has been associated with a diverse set of mutations in the SRY-box transcription factor 9 (SOX9) gene. CASE PRESENTATION We herein report a case involving a 4-year-old female patient with CD, female sex reversal, type 1 Arnold-Chiari malformation, and bilateral conductive hearing loss and investigate the causal mutation. Whole-exome sequencing analysis detected a novel Trp115X* variant in the SOX9 gene. We performed a literature review of the reported cases and demonstrated that the missense variants were located only in the self-dimerization domain (DIM) and high-mobility group box domains. We also reported that variants in the DIM domain do not cause sex reversal and identified that the amino acid sequences that were mutated in the patients with campomelic dysplasia are evolutionarily conserved among primates. CONCLUSIONS We suggest that missense variants cannot be located in the K2, PQA, and PQS given that these domains function critically for transcriptional activation or repression of target genes and evolve under purifying selection.
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Affiliation(s)
- Carlos A Calvache
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Vanessa I Romero
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Kanazawa University, Kanazawa, Japan
| | - Juan C Pozo
- School of Medicine, Universidad de Cuenca, Cuenca, Ecuador
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Yoshiji S, Horikawa Y, Kubota S, Enya M, Iwasaki Y, Keidai Y, Aizawa-Abe M, Iwasaki K, Honjo S, Hosomichi K, Yabe D, Hamasaki A. First Japanese Family With PDX1-MODY (MODY4): A Novel PDX1 Frameshift Mutation, Clinical Characteristics, and Implications. J Endocr Soc 2022; 6:bvab159. [PMID: 34988346 PMCID: PMC8714237 DOI: 10.1210/jendso/bvab159] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Indexed: 11/19/2022] Open
Abstract
CONTEXT The PDX1 gene encodes pancreatic and duodenal homeobox, a critical transcription factor for pancreatic β-cell differentiation and maintenance of mature β-cells. Heterozygous loss-of-function mutations cause PDX1-MODY (MODY4). CASE DESCRIPTION Our patient is an 18-year-old lean man who developed diabetes at 16 years of age. Given his early-onset age and leanness, we performed genetic testing. Targeted next-generation sequencing and subsequent Sanger sequencing detected a novel heterozygous frameshift mutation (NM_00209.4:c.218delT. NP_000200.1: p.Leu73Profs*50) in the PDX1 transactivation domain that resulted in loss-of-function and was validated by an in vitro functional study. The proband and his 56-year-old father, who had the same mutation, both showed markedly reduced insulin and gastric inhibitory polypeptide (GIP) secretion compared with the dizygotic twin sister, who was negative for the mutation and had normal glucose tolerance. The proband responded well to sitagliptin, suggesting its utility as a treatment option. Notably, the proband and his father showed intriguing phenotypic differences: the proband had been lean for his entire life but developed early-onset diabetes requiring an antihyperglycemic agent. In contrast, his father was overweight, developed diabetes much later in life, and did not require medication, suggesting the oligogenic nature of PDX1-MODY. A review of all reported cases of PDX1-MODY also showed heterogeneous phenotypes regarding onset age, obesity, and treatment, even in the presence of the same mutation. CONCLUSIONS We identified the first Japanese family with PDX1-MODY. The similarities and differences found among the cases highlight the wide phenotypic spectrum of PDX1-MODY.
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Affiliation(s)
- Satoshi Yoshiji
- Department of Diabetes and Endocrinology, Tazuke Kofukai Medical Research Institute, Kitano Hospital, Osaka 530-8480, Japan
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Department of Human Genetics, McGill University, Montréal, Québec H3A 0C7, Canada
- Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Yukio Horikawa
- Department of Diabetes, Endocrinology and Metabolism, Graduate School of Medicine, Gifu University, Gifu 501-1194, Japan
- Clinical Genetics Center, Gifu University Hospital, Gifu 501-1194, Japan
| | - Sodai Kubota
- Department of Diabetes, Endocrinology and Metabolism, Graduate School of Medicine, Gifu University, Gifu 501-1194, Japan
| | - Mayumi Enya
- Department of Diabetes, Endocrinology and Metabolism, Graduate School of Medicine, Gifu University, Gifu 501-1194, Japan
| | - Yorihiro Iwasaki
- Department of Diabetes and Endocrinology, Tazuke Kofukai Medical Research Institute, Kitano Hospital, Osaka 530-8480, Japan
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Yamato Keidai
- Department of Diabetes and Endocrinology, Tazuke Kofukai Medical Research Institute, Kitano Hospital, Osaka 530-8480, Japan
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Megumi Aizawa-Abe
- Department of Diabetes and Endocrinology, Tazuke Kofukai Medical Research Institute, Kitano Hospital, Osaka 530-8480, Japan
| | - Kanako Iwasaki
- Department of Diabetes and Endocrinology, Tazuke Kofukai Medical Research Institute, Kitano Hospital, Osaka 530-8480, Japan
| | - Sachiko Honjo
- Department of Diabetes and Endocrinology, Tazuke Kofukai Medical Research Institute, Kitano Hospital, Osaka 530-8480, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Kanazawa University, Kanazawa 920-8640, Japan
| | - Daisuke Yabe
- Department of Diabetes, Endocrinology and Metabolism, Graduate School of Medicine, Gifu University, Gifu 501-1194, Japan
| | - Akihiro Hamasaki
- Department of Diabetes and Endocrinology, Tazuke Kofukai Medical Research Institute, Kitano Hospital, Osaka 530-8480, Japan
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Hayashi K, Noguchi-Shinohara M, Sato T, Hosomichi K, Kannon T, Abe C, Domoto C, Yuki-Nozaki S, Mori A, Horimoto M, Yokogawa M, Sakai K, Iwasa K, Komai K, Ishimiya M, Nakamura H, Ishida N, Suga Y, Ishizaki J, Ishigami A, Tajima A, Yamada M. Effects of functional variants of vitamin C transporter genes on apolipoprotein E E4-associated risk of cognitive decline: The Nakajima study. PLoS One 2021; 16:e0259663. [PMID: 34780525 PMCID: PMC8592483 DOI: 10.1371/journal.pone.0259663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 10/22/2021] [Indexed: 01/28/2023] Open
Abstract
Apolipoprotein E E4 (APOE4) is a risk factor for cognitive decline. A high blood vitamin C (VC) level reduces APOE4-associated risk of developing cognitive decline in women. In the present study, we aimed to examine the effects of functional variants of VC transporter genes expressed in the brain (SLC2A1, SLC2A3, and SLC23A2) on APOE4-associated risk of developing cognitive decline. This case–control study involved 393 Japanese subjects: 252 cognitively normal and 141 cognitively impaired individuals (87 mild cognitive impairment and 54 dementia). Database searches revealed that rs1279683 of SLC23A2, and rs710218 and rs841851 of SLC2A1 are functional variants that are significantly associated with the altered expression of the respective genes and genotyped as three single nucleotide variants (SNVs). When stratified by SNV genotype, we found a significant association between APOE4 and cognitive decline in minor allele carriers of rs1279683 (odds ratio [OR] 2.02, 95% CI, 1.05–3.87, p = 0.035) but not in the homozygote carriers of the major allele. Significant associations between APOE4 and cognitive decline were also observed in participants with major allele homozygotes of rs710218 (OR 2.35, 95% CI, 1.05–5.23, p = 0.037) and rs841851 (OR 3.2, 95% CI, 1.58–6.46, p = 0.0012), but not in minor allele carriers of the respective SNVs. In contrast, the three functional SNVs showed no significant effect on cognitive decline. Our results imply that functional SNVs of VC transporter genes can affect APOE4-associated risk of developing cognitive decline via altered VC levels in the brain.
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Affiliation(s)
- Koji Hayashi
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Moeko Noguchi-Shinohara
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
- Department of Preemptive Medicine for Dementia, Kanazawa University Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Takayuki Kannon
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Chiemi Abe
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Chiaki Domoto
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Sohshi Yuki-Nozaki
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Ayaka Mori
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Mai Horimoto
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Masami Yokogawa
- Department of Physical Therapy, Division of Health Sciences, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Kenji Sakai
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Kazuo Iwasa
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
- Ishikawa Prefectural Nursing University, Kahoku, Japan
| | - Kiyonobu Komai
- Department of Neurology, Iou Hospital National Hospital Organization, Kanazawa, Japan
| | - Mai Ishimiya
- Department of Oral and Maxillofacial Surgery, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Hiroyuki Nakamura
- Department of Oral and Maxillofacial Surgery, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
- Department of Oral and Maxillofacial Surgery, Ryukyu University Hospital, Nishihara, Japan
| | - Natsuko Ishida
- Clinical Pharmacy and Healthcare Sciences, Faculty of Pharmacy, Institute of Medical, Pharmaceutical & Health Science, Kanazawa University, Kanazawa, Japan
| | - Yukio Suga
- Clinical Pharmacy and Healthcare Sciences, Faculty of Pharmacy, Institute of Medical, Pharmaceutical & Health Science, Kanazawa University, Kanazawa, Japan
| | - Junko Ishizaki
- Clinical Pharmacy and Healthcare Sciences, Faculty of Pharmacy, Institute of Medical, Pharmaceutical & Health Science, Kanazawa University, Kanazawa, Japan
| | - Akihito Ishigami
- Molecular Regulation of Aging, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
- * E-mail: (AT); (MY)
| | - Masahito Yamada
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
- * E-mail: (AT); (MY)
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Koba H, Kimura H, Yoneda T, Ogawa N, Tanimura K, Tambo Y, Sone T, Hosomichi K, Tajima A, Kasahara K. NOTCH alteration in EGFR-mutated lung adenocarcinoma leads to histological small-cell carcinoma transformation under EGFR-TKI treatment. Transl Lung Cancer Res 2021; 10:4161-4173. [PMID: 35004247 PMCID: PMC8674607 DOI: 10.21037/tlcr-21-536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/13/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Molecular targeted therapy has been developed as an innovative treatment for metastatic cancer. Epidermal growth factor receptor (EGFR) mutation is one of the most important and frequent oncogenic drivers in non-small-cell lung cancer, and EGFR-tyrosine kinase inhibitors are indispensable drugs for mutation-positive patients. Currently, the acquired resistance to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) is a problem, the mechanism of which has not been elucidated. The histological transformation from original adenocarcinoma to small-cell carcinoma is rare; however, it has been detected in many cases after EGFR-TKI treatment. This study aimed to evaluate mutational status in two different histological types and further elucidate the molecular pathogenesis. METHODS Three patients with EGFR-mutant lung cancer who underwent a histological transformation to small-cell carcinoma after growth factor receptor-TKI treatment were enrolled in this study. Two samples per patient were collected from histologically different lesions, and DNA samples were extracted from formalin-fixed, paraffin-embedded tumor tissues. The paired samples were subjected to next-generation sequencing of 160 cancer-related genes. Based on the sequencing results, the expression levels of related proteins were validated using reverse-transferase polymerase chain reaction and immunohistochemical staining. RESULTS The following five variants were common among the three cases: MTOR, JAK1, NOTCH2, CSF1R, and MAP2K2. The former four variants were additive to small-cell carcinoma, and the last variant was lost. Both TP53 and Rb1 alterations were detected in adenocarcinoma. Notch2 expression was negative in small-cell carcinoma in both reverse-transcriptase polymerase chain reaction analysis and immunohistochemical staining. ASCL1 expression increased after histological transformation detected using both methods in one case, only these samples were evaluable. CONCLUSIONS Notch and ASCL1 signaling are the master regulators of neuroendocrine differentiation in small-cell lung carcinoma. Our results suggest that the Notch-ASCL1 axis may also play an essential role in the transformation of small-cell carcinoma under TP53 and RB1 inactivation.
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Affiliation(s)
- Hayato Koba
- Cellular Transplantation Biology, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan;,Respiratory Medicine, Komatsu Municipal Hospital, Komatsu, Japan
| | - Hideharu Kimura
- Respiratory Medicine, Kanazawa University Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa, Japan
| | - Taro Yoneda
- Respiratory Medicine, Komatsu Municipal Hospital, Komatsu, Japan
| | - Naohiko Ogawa
- Cellular Transplantation Biology, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
| | - Kota Tanimura
- Cellular Transplantation Biology, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
| | - Yuichi Tambo
- Respiratory Medicine, Kanazawa University Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa, Japan
| | - Takashi Sone
- Regional Respiratory Symptomatology, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kazuo Kasahara
- Respiratory Medicine, Kanazawa University Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa, Japan
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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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Imaki S, Iizuka K, Horikawa Y, Yasuda M, Kubota S, Kato T, Liu Y, Takao K, Mizuno M, Hirota T, Suwa T, Hosomichi K, Tajima A, Fujiwara Y, Yamazaki Y, Kuwata H, Seino Y, Yabe D. A novel RFX6 heterozygous mutation (p.R652X) in maturity-onset diabetes mellitus: A case report. J Diabetes Investig 2021; 12:1914-1918. [PMID: 33721395 PMCID: PMC8504905 DOI: 10.1111/jdi.13545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/01/2021] [Accepted: 03/08/2021] [Indexed: 01/07/2023] Open
Abstract
Heterozygous RFX6 mutation has emerged as a potential cause of maturity-onset diabetes mellitus of the young (MODY). A 16-year-old female was diagnosed with diabetes by her family doctor and was referred to our institution for genetic examination. Genetic testing revealed a novel RFX6 heterozygous mutation (NM_173560: exon17: c.1954C>T: p.R652X) in the patient and in her mother and brother. She had no islet-specific autoantibodies and showed a reduced meal-induced response of insulin, glucose-dependent insulinotropic polypeptide, and glucagon-like peptide-1, which is consistent with the phenotype of MODY due to heterozygous RFX6 mutation. In conclusion, we report a case of MODY due to a novel heterozygous mutation, p.R652X.
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Affiliation(s)
| | - Katsumi Iizuka
- Department of Diabetes and EndocrinologyGifu University Graduate School of MedicineGifuJapan
| | - Yukio Horikawa
- Department of Diabetes and EndocrinologyGifu University Graduate School of MedicineGifuJapan
| | - Megumi Yasuda
- Department of Diabetes and EndocrinologyGifu University Graduate School of MedicineGifuJapan
| | - Sodai Kubota
- Department of Diabetes and EndocrinologyGifu University Graduate School of MedicineGifuJapan
- Yutaka Seino Distinguished Center for Diabetes ResearchKansai Electric Power Medical Research InstitutionKobeJapan
| | - Takehiro Kato
- Department of Diabetes and EndocrinologyGifu University Graduate School of MedicineGifuJapan
| | - Yanyan Liu
- Department of Diabetes and EndocrinologyGifu University Graduate School of MedicineGifuJapan
| | - Ken Takao
- Department of Diabetes and EndocrinologyGifu University Graduate School of MedicineGifuJapan
| | - Masami Mizuno
- Department of Diabetes and EndocrinologyGifu University Graduate School of MedicineGifuJapan
| | - Takuo Hirota
- Department of Diabetes and EndocrinologyGifu University Graduate School of MedicineGifuJapan
| | - Tetsuya Suwa
- Department of Diabetes and EndocrinologyGifu University Graduate School of MedicineGifuJapan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and GenomicsGraduate School of Advanced Preventive Medical SciencesKanazawa UniversityKanazawaJapan
| | - Atsushi Tajima
- Department of Bioinformatics and GenomicsGraduate School of Advanced Preventive Medical SciencesKanazawa UniversityKanazawaJapan
| | - Yuuka Fujiwara
- Yutaka Seino Distinguished Center for Diabetes ResearchKansai Electric Power Medical Research InstitutionKobeJapan
| | - Yuji Yamazaki
- Yutaka Seino Distinguished Center for Diabetes ResearchKansai Electric Power Medical Research InstitutionKobeJapan
- Center for Diabetes, Metabolism and EndocrinologyKansai Electric Power HospitalOsakaJapan
| | - Hitoshi Kuwata
- Yutaka Seino Distinguished Center for Diabetes ResearchKansai Electric Power Medical Research InstitutionKobeJapan
- Center for Diabetes, Metabolism and EndocrinologyKansai Electric Power HospitalOsakaJapan
| | - Yutaka Seino
- Yutaka Seino Distinguished Center for Diabetes ResearchKansai Electric Power Medical Research InstitutionKobeJapan
- Center for Diabetes, Metabolism and EndocrinologyKansai Electric Power HospitalOsakaJapan
| | - Daisuke Yabe
- Department of Diabetes and EndocrinologyGifu University Graduate School of MedicineGifuJapan
- Yutaka Seino Distinguished Center for Diabetes ResearchKansai Electric Power Medical Research InstitutionKobeJapan
- Division of Molecular and Metabolic MedicineDepartment of Physiology and Cell BiologyKobe University Graduate School of MedicineKobeJapan
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Osawa Y, Aoyama KI, Hosomichi K, Uchibori M, Tajima A, Kimura M, Ota Y. Somatic mutations in oral squamous cell carcinomas in 98 Japanese patients and their clinical implications. Cancer Treat Res Commun 2021; 29:100456. [PMID: 34563788 DOI: 10.1016/j.ctarc.2021.100456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 11/29/2022]
Abstract
INTRODUCTION The somatic mutational profile of oral squamous cell carcinoma (OSCC) among Japanese patients has been less investigated, partly because of the rarity of the tumor. Moreover, previous studies have either used formalin-fixed paraffin-embedded samples or lacked paired normal tissues. We aimed to determine somatic mutations in the exomes of 76 genes, including 50 driver genes of solid cancers and NOTCH-related genes, some of which are previously reported as frequently mutated in head and neck squamous cell carcinoma or OSCC. MATERIALS AND METHODS We used fresh-frozen tumor/normal-paired samples from 98 treatment-naïve Japanese patients with OSCC and analyzed their correlations with clinicopathological characteristics and survival. RESULTS We identified 136 exonic mutations, including 78 non-synonymous mutations, 13 synonymous mutations, 22 nonsense mutations, 2 non-frameshift deletions, 11 frameshift deletion, and 5 each of splice-site and frameshift insertions. The most frequently mutated genes were TP53 (36.7%), FAT1 (9.2%), NOTCH1 (8.2%), CDKN2A (7.1%), ZFHX4 (5.1%), CASP8 (4.1%), EP300 (4.1%), and KMT2D (4.1%). We followed up 90 of the 98 patients for 3 years. Among them, TP53 mutation was associated with significantly shorter 3-year disease-free survival. Most of the identified TP53 mutations occurred in the DNA-binding domain and were functionally deleterious. DISCUSSION Our findings and the mutation spectra can contribute to the development of a therapeutic strategy for Japanese patients with OSCC.
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Affiliation(s)
- Yuko Osawa
- Department of Oral and Maxillofacial Surgery, Tokai University School of Medicine,143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Ken-Ichi Aoyama
- Department of Oral and Maxillofacial Surgery, Tokai University School of Medicine,143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Kazuyoshi Hosomichi
- The Institute of Medical Sciences, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Masahiro Uchibori
- Department of Oral and Maxillofacial Surgery, Tokai University School of Medicine,143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, Japan
| | - Minoru Kimura
- The Institute of Medical Sciences, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Yoshihide Ota
- Department of Oral and Maxillofacial Surgery, Tokai University School of Medicine,143 Shimokasuya, Isehara, Kanagawa, Japan.
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Sato T, Adachi N, Kimura R, Hosomichi K, Yoneda M, Oota H, Tajima A, Toyoda A, Kanzawa-Kiriyama H, Matsumae H, Koganebuchi K, Shimizu KK, Shinoda KI, Hanihara T, Weber A, Kato H, Ishida H. Whole-Genome Sequencing of a 900-Year-Old Human Skeleton Supports Two Past Migration Events from the Russian Far East to Northern Japan. Genome Biol Evol 2021; 13:6355032. [PMID: 34410389 PMCID: PMC8449830 DOI: 10.1093/gbe/evab192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2021] [Indexed: 12/18/2022] Open
Abstract
Recent studies on paleogenomics have reported some Paleolithic and Neolithic genomes that have provided new insights into the human population history in East and Northeast Asia. However, there remain some cases where more recent migration events need to be examined to elucidate the detailed formation process of local populations. Although the area around northern Japan is one of the regions archaeologically suggested to have been affected by migration waves after the Neolithic period, the genetic source of these migrations are still unclear. Thus, genomic data from such past migrant populations would be highly informative to clarify the detailed formation process of local populations in this region. Here, we report the genome sequence of a 900-year-old adult female (NAT002) belonging to the prehistoric Okhotsk people, who have been considered to be the past migrants to northern Japan after the Neolithic period. We found a close relationship between NAT002 and modern Lower Amur populations and past admixture events between the Amur, Jomon, and Kamchatka ancestries. The admixture dating suggested migration of Amur-related ancestry at approximately 1,600 BP, which is compatible with the archaeological evidence regarding the settlement of the Okhotsk people. Our results also imply migration of Kamchatka-related ancestry at approximately 2,000 BP. In addition, human leukocyte antigen (HLA) typing detected the HLA-B*40 allele, which is reported to increase the risk of arthritis, suggesting the genetic vulnerability of NAT002 to hyperostosis, which was observed around her chest clavicle.
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Affiliation(s)
- Takehiro Sato
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan.,Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Noboru Adachi
- Department of Legal Medicine, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Tokyo, Japan
| | - Hiroki Oota
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | | | - Hiromi Matsumae
- Kihara Institute for Biological Research (KIBR), Yokohama City University, Yokohama, Japan.,Department of Molecular Life Science, School of Medicine, Tokai University, Isehara, Japan
| | - Kae Koganebuchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Sagamihara, Japan.,Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Kentaro K Shimizu
- Kihara Institute for Biological Research (KIBR), Yokohama City University, Yokohama, Japan.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan
| | - Tsunehiko Hanihara
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Japan
| | - Andrzej Weber
- Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada.,Research Centre "Baikal Region", Irkutsk State University, Irkutsk, Russia.,Laboratoire Méditerranéen de Préhistoire Europe Afrique (LAMPEA) - UMR 7269, Aix-Marseille Université, Aix-en-Provence, France
| | - Hirofumi Kato
- Centre for Ainu and Indigenous Studies, Hokkaido University, Sapporo, Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
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Sáenz SS, Arias B, Hosomichi K, Romero VI. The limits of clinical findings in similar phenotypes, from Carpenter to ATRX syndrome using a whole exome sequencing approach: a case review. Hum Genomics 2021; 15:49. [PMID: 34348791 PMCID: PMC8336023 DOI: 10.1186/s40246-021-00348-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The diagnostic process for uncommon disorders with similar manifestations is complicated and requires newer technology, like gene sequencing for a correct diagnosis. MAIN BODY We described two brothers clinically diagnosed with Carpenter syndrome, which is a condition characterized by the premature fusion of certain skull bones (craniosynostosis), abnormalities of the fingers and toes, and other developmental problems, for which they underwent craniotomies. However, whole exome sequencing analysis concluded a novel pathological variation in the ATRX chromatin remodeler gene and protein remodeling demonstrated structural variations that decreased the function, giving a completely different diagnosis to these patients. CONCLUSION Our study focuses on the importance of using newer technologies, such as whole exome sequencing analysis, in patients with ambiguous phenotypes.
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Affiliation(s)
- Samantha S Sáenz
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Kanazawa University, Kanazawa, Japan
| | - Vanessa I Romero
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador.
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42
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Yamada Y, Nakamura H, Tsujiguchi H, Hara A, Miyagi S, Kannon T, Sato T, Hosomichi K, Nguyen TTT, Kambayashi Y, Shimizu Y, Pham KO, Suzuki K, Suzuki F, Kasahara T, Tsuboi H, Tajima A, Nakamura H. Relationships among the β3-adrenargic receptor gene Trp64Arg polymorphism, hypertension, and insulin resistance in a Japanese population. PLoS One 2021; 16:e0255444. [PMID: 34347822 PMCID: PMC8336805 DOI: 10.1371/journal.pone.0255444] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 07/19/2021] [Indexed: 11/18/2022] Open
Abstract
A polymorphism in the ADRB3 gene (Trp64Arg) has been associated with obesity, insulin resistance, and hypertension. This cross-sectional study investigated the relationships among this polymorphism, hypertension, and insulin resistance values (HOMA-IR) in 719 Japanese subjects aged 40 years and older. The genotype frequencies of Trp64Trp (homozygous, wild), Trp64Arg (heterozygous, variant), and Arg64Arg (homozygous, variant) were 466 (65%), 233 (32%), and 20 (3%), respectively. Insulin resistance was associated with an increased risk of hypertension in a Japanese population. This relationship was dependent on the presence or absence of the Trp64Arg polymorphism (odds ratio, 2.054; confidence interval, 1.191 to 3.541; P value, 0.010). Therefore, the Trp64Arg polymorphism of ADRB3 was associated with hypertension and insulin resistance in a healthy Japanese population. This relationship, which was dependent on the polymorphism, may predict the development of hypertension and diabetes.
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Affiliation(s)
- Youhei Yamada
- Department of Environmental and Preventive Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
- Department of Public Health, Kanazawa University Graduate School of Advanced Preventive Medical Sciences, Kanazawa, Japan
- * E-mail:
| | - Haruki Nakamura
- Department of Environmental and Preventive Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Hiromasa Tsujiguchi
- Department of Environmental and Preventive Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
- Department of Public Health, Kanazawa University Graduate School of Advanced Preventive Medical Sciences, Kanazawa, Japan
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Kanazawa, Japan
| | - Akinori Hara
- Department of Environmental and Preventive Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
- Department of Public Health, Kanazawa University Graduate School of Advanced Preventive Medical Sciences, Kanazawa, Japan
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Kanazawa, Japan
| | - Sakae Miyagi
- Innovative Clinical Research Center, Kanazawa University, Kanazawa, Japan
| | - Takayuki Kannon
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Kanazawa, Japan
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Takehiro Sato
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Kanazawa, Japan
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kazuyoshi Hosomichi
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Kanazawa, Japan
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Thao Thi Thu Nguyen
- Faculty of Public Health, Haiphong University of Medicine and Pharmacy, Haiphong, Vietnam
| | - Yasuhiro Kambayashi
- Department of Public Health, Faculty of Veterinary Medicine, Okayama University of Science, Kanazawa, Japan
| | - Yukari Shimizu
- Faculty of Health Sciences, Department of Nursing, Komatsu University, Kanazawa, Japan
| | - Kim Oanh Pham
- Department of Environmental and Preventive Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Keita Suzuki
- Department of Environmental and Preventive Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
- Department of Public Health, Kanazawa University Graduate School of Advanced Preventive Medical Sciences, Kanazawa, Japan
| | - Fumihiko Suzuki
- Department of Environmental and Preventive Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Tomoko Kasahara
- Department of Environmental and Preventive Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
- Department of Public Health, Kanazawa University Graduate School of Advanced Preventive Medical Sciences, Kanazawa, Japan
| | - Hirohito Tsuboi
- Institute of Medical, Pharmaceutical, and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Atsushi Tajima
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Kanazawa, Japan
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroyuki Nakamura
- Department of Environmental and Preventive Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
- Department of Public Health, Kanazawa University Graduate School of Advanced Preventive Medical Sciences, Kanazawa, Japan
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Kanazawa, Japan
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43
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Nguyen DT, Le TM, Hattori T, Takarada-Iemata M, Ishii H, Roboon J, Tamatani T, Kannon T, Hosomichi K, Tajima A, Taniuchi S, Miyake M, Oyadomari S, Tanaka T, Kato N, Saito S, Mori K, Hori O. The ATF6β-calreticulin axis promotes neuronal survival under endoplasmic reticulum stress and excitotoxicity. Sci Rep 2021; 11:13086. [PMID: 34158584 PMCID: PMC8219835 DOI: 10.1038/s41598-021-92529-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/09/2021] [Indexed: 02/08/2023] Open
Abstract
While ATF6α plays a central role in the endoplasmic reticulum (ER) stress response, the function of its paralogue ATF6β remains elusive, especially in the central nervous system (CNS). Here, we demonstrate that ATF6β is highly expressed in the hippocampus of the brain, and specifically regulates the expression of calreticulin (CRT), a molecular chaperone in the ER with a high Ca2+-binding capacity. CRT expression was reduced to ~ 50% in the CNS of Atf6b−/− mice under both normal and ER stress conditions. Analysis using cultured hippocampal neurons revealed that ATF6β deficiency reduced Ca2+ stores in the ER and enhanced ER stress-induced death. The higher levels of death in Atf6b−/− neurons were recovered by ATF6β and CRT overexpressions, or by treatment with Ca2+-modulating reagents such as BAPTA-AM and 2-APB, and with an ER stress inhibitor salubrinal. In vivo, kainate-induced neuronal death was enhanced in the hippocampi of Atf6b−/− and Calr+/− mice, and restored by administration of 2-APB and salubrinal. These results suggest that the ATF6β-CRT axis promotes neuronal survival under ER stress and excitotoxity by improving intracellular Ca2+ homeostasis.
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Affiliation(s)
- Dinh Thi Nguyen
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-Machi, Kanazawa City, Ishikawa, 920-8640, Japan
| | - Thuong Manh Le
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-Machi, Kanazawa City, Ishikawa, 920-8640, Japan.,Department of Human Anatomy, Hanoi Medical University, Hanoi, Vietnam
| | - Tsuyoshi Hattori
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-Machi, Kanazawa City, Ishikawa, 920-8640, Japan
| | - Mika Takarada-Iemata
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-Machi, Kanazawa City, Ishikawa, 920-8640, Japan
| | - Hiroshi Ishii
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-Machi, Kanazawa City, Ishikawa, 920-8640, Japan
| | - Jureepon Roboon
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-Machi, Kanazawa City, Ishikawa, 920-8640, Japan
| | - Takashi Tamatani
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-Machi, Kanazawa City, Ishikawa, 920-8640, Japan
| | - Takayuki Kannon
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Shusuke Taniuchi
- Division of Molecular Biology, Institute for Genome Research, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Masato Miyake
- Division of Molecular Biology, Institute for Genome Research, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Seiichi Oyadomari
- Division of Molecular Biology, Institute for Genome Research, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Takashi Tanaka
- Department of Anatomy II, Kanazawa Medical University, Kahoku, Japan
| | - Nobuo Kato
- Department of Physiology I, Kanazawa Medical University, Kahoku, Japan
| | - Shunsuke Saito
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Kazutoshi Mori
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Osamu Hori
- Department of Neuroanatomy, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-Machi, Kanazawa City, Ishikawa, 920-8640, Japan.
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44
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Matsukawa H, Iida N, Kitamura K, Terashima T, Seishima J, Makino I, Kannon T, Hosomichi K, Yamashita T, Sakai Y, Honda M, Yamashita T, Mizukoshi E, Kaneko S. Dysbiotic gut microbiota in pancreatic cancer patients form correlation networks with the oral microbiota and prognostic factors. Am J Cancer Res 2021; 11:3163-3175. [PMID: 34249452 PMCID: PMC8263681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/17/2021] [Indexed: 06/13/2023] Open
Abstract
Microbiota in the gut and oral cavities of pancreatic cancer (PC) patients differ from those of healthy persons, and bacteria in PC tissues are associated with patients' prognoses. However, the species-level relationship between a dysbiotic gut, oral and cancerous microbiota, and prognostic factors remains unknown. Whole-genome sequencing was performed with fecal DNA from 24 PC patients and 18 healthy persons (HD). Microbial taxonomies, metabolic pathways, and viral presence were determined. DNA was sequenced from saliva and PC tissues, and the association between the gut, oral, and cancer microbiota and prognostic factors in PC patients was analyzed. The PC microbiota were altered from those of the healthy microbiota in terms of microbial taxonomy, pathways and viral presence. Twenty-six species differed significantly between the PC and HD microbiota. Six fecal microbes, including Klebsiella pneumoniae, were associated with an increased hazard of death. In the co-occurrence network, microbes that were abundant in PC patients were plotted close together and formed clusters with prognosis-associated microbes, including K. pneumoniae. Multiple salivary microbes were present in the co-occurrence network. Microbacterium and Stenotrophomonas were detected in the PC tissues and formed a network with the fecal and salivary microbes. The dysbiotic gut microbiota in the PC patients formed a complex network with the oral and cancerous microbiota, and gut microbes abundant in the PC patients were closely linked with poor prognostic factors in the network.
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Affiliation(s)
- Hiroki Matsukawa
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University13-1 Takara-Machi, Kanazawa, Ishikawa, Japan
| | - Noriho Iida
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University13-1 Takara-Machi, Kanazawa, Ishikawa, Japan
| | - Kazuya Kitamura
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University13-1 Takara-Machi, Kanazawa, Ishikawa, Japan
| | - Takeshi Terashima
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University13-1 Takara-Machi, Kanazawa, Ishikawa, Japan
| | - Jun Seishima
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University13-1 Takara-Machi, Kanazawa, Ishikawa, Japan
| | - Isamu Makino
- Department of Hepato-Biliary-Pancreatic Surgery and Transplantation, Graduate School of Medical Sciences, Kanazawa University13-1 Takara-Machi, Kanazawa, Ishikawa, Japan
| | - Takayuki Kannon
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University13-1 Takara-Machi, Kanazawa, Ishikawa, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University13-1 Takara-Machi, Kanazawa, Ishikawa, Japan
| | - Taro Yamashita
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University13-1 Takara-Machi, Kanazawa, Ishikawa, Japan
| | - Yoshio Sakai
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University13-1 Takara-Machi, Kanazawa, Ishikawa, Japan
| | - Masao Honda
- Department of Advanced Medical Technology, Graduate School of Health Medicine, Kanazawa University13-1 Takara-Machi, Kanazawa, Ishikawa, Japan
| | - Tatsuya Yamashita
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University13-1 Takara-Machi, Kanazawa, Ishikawa, Japan
| | - Eishiro Mizukoshi
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University13-1 Takara-Machi, Kanazawa, Ishikawa, Japan
| | - Shuichi Kaneko
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University13-1 Takara-Machi, Kanazawa, Ishikawa, Japan
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45
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Mizumaki H, Hosomichi K, Hosokawa K, Yoroidaka T, Imi T, Zaimoku Y, Katagiri T, Anh Thi Nguyen M, Cao Tran D, Ibrahim Yousef Elbadry M, Chonabayashi K, Yoshida Y, Takamatsu H, Ozawa T, Azuma F, Kishi H, Fujii Y, Ogawa S, Tajima A, Nakao S. A frequent nonsense mutation in exon 1 across certain HLA-A and -B alleles in leukocytes of patients with acquired aplastic anemia. Haematologica 2021; 106:1581-1590. [PMID: 32439725 PMCID: PMC8168509 DOI: 10.3324/haematol.2020.247809] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 02/16/2020] [Indexed: 12/24/2022] Open
Abstract
Leukocytes that lack HLA allelic expression are frequently detected in patients with acquired aplastic anemia (AA) who respond to immunosuppressive therapy (IST), although the exact mechanisms underlying the HLA loss and HLA allele repertoire likely to acquire loss-of-function mutations are unknown. We identified a common nonsense mutation at position 19 (c.19C>T, p.R7X) in exon 1 (Exon1mut) of different HLA-A and -B alleles in HLA-lacking granulocytes from AA patients. A droplet digital PCR (ddPCR) assay capable of detecting as few as 0.07% Exon1mut HLA alleles in total DNA revealed the mutation was present in 29% (101/353) of AA patients, with a median allele frequency of 0.42% (range, 0.071% to 21.3%). Exon1mut occurred in only 12 different HLA-A (n=4) and HLA-B (n=8) alleles, including B*40:02 (n=31) and A*02:06 (n=15), which correspond to 4 HLA supertypes (A02, A03, B07, and B44). The percentages of patients who possessed at least one of these 12 HLA alleles were significantly higher in the 353 AA patients (92%, P.
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Affiliation(s)
- Hiroki Mizumaki
- Department of Hematology, Kanazawa University, Kanazawa, Japan
| | - Kazuyoshi Hosomichi
- Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Japan
| | - Kohei Hosokawa
- Department of Hematology, Kanazawa University, Kanazawa, Japan
| | | | - Tatsuya Imi
- Department of Hematology, Kanazawa University, Kanazawa, Japan
| | | | - Takamasa Katagiri
- Clinical Laboratory Sciences, Kanazawa University Graduate School, Kanazawa, Japan
| | | | - Dung Cao Tran
- Department of Hematology, Kanazawa University, Kanazawa, Japan
| | | | | | - Yoshinori Yoshida
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | | | - Tatsuhiko Ozawa
- Department of Immunology, University of Toyama, Toyama, Japan
| | - Fumihiro Azuma
- HLA Laboratory, Japanese Red Cross Kanto-Koshinetsu Block Blood Center, Kotoku, Japan
| | - Hiroyuki Kishi
- Department of Immunology, University of Toyama, Toyama, Japan
| | - Yoichi Fujii
- Dept. of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Japan
| | - Seishi Ogawa
- Dept. of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Japan
| | - Atsushi Tajima
- Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Shinji Nakao
- Department of Hematology, Kanazawa University, Kanazawa, Japan
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46
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Yamamura Y, Furuichi K, Murakawa Y, Hirabayashi S, Yoshihara M, Sako K, Kitajima S, Toyama T, Iwata Y, Sakai N, Hosomichi K, Murphy PM, Tajima A, Okita K, Osafune K, Kaneko S, Wada T. Identification of candidate PAX2-regulated genes implicated in human kidney development. Sci Rep 2021; 11:9123. [PMID: 33907292 PMCID: PMC8079710 DOI: 10.1038/s41598-021-88743-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 04/16/2021] [Indexed: 02/02/2023] Open
Abstract
PAX2 is a transcription factor essential for kidney development and the main causative gene for renal coloboma syndrome (RCS). The mechanisms of PAX2 action during kidney development have been evaluated in mice but not in humans. This is a critical gap in knowledge since important differences have been reported in kidney development in the two species. In the present study, we hypothesized that key human PAX2-dependent kidney development genes are differentially expressed in nephron progenitor cells from induced pluripotent stem cells (iPSCs) in patients with RCS relative to healthy individuals. Cap analysis of gene expression revealed 189 candidate promoters and 71 candidate enhancers that were differentially activated by PAX2 in this system in three patients with RCS with PAX2 mutations. By comparing this list with the list of candidate Pax2-regulated mouse kidney development genes obtained from the Functional Annotation of the Mouse/Mammalian (FANTOM) database, we prioritized 17 genes. Furthermore, we ranked three genes-PBX1, POSTN, and ITGA9-as the top candidates based on closely aligned expression kinetics with PAX2 in the iPSC culture system and susceptibility to suppression by a Pax2 inhibitor in cultured mouse embryonic kidney explants. Identification of these genes may provide important information to clarify the pathogenesis of RCS, human kidney development, and kidney regeneration.
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Affiliation(s)
- Yuta Yamamura
- Department of Nephrology and Laboratory Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan
| | - Kengo Furuichi
- Department of Nephrology, School of Medicine, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0293, Japan.
| | - Yasuhiro Murakawa
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Kanagawa, Japan
| | - Shigeki Hirabayashi
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Kanagawa, Japan
| | - Masahito Yoshihara
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Keisuke Sako
- Department of Nephrology and Laboratory Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan
| | - Shinji Kitajima
- Department of Nephrology and Laboratory Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan
| | - Tadashi Toyama
- Department of Nephrology and Laboratory Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan
| | - Yasunori Iwata
- Department of Nephrology and Laboratory Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan
| | - Norihiko Sakai
- Department of Nephrology and Laboratory Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Philip M Murphy
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Keisuke Okita
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Kenji Osafune
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Shuichi Kaneko
- Department of System Biology, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Takashi Wada
- Department of Nephrology and Laboratory Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan.
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47
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Hirayasu K, Sun J, Hasegawa G, Hashikawa Y, Hosomichi K, Tajima A, Tokunaga K, Ohashi J, Hanayama R. Characterization of LILRB3 and LILRA6 allelic variants in the Japanese population. J Hum Genet 2021; 66:739-748. [PMID: 33526815 DOI: 10.1038/s10038-021-00906-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/16/2021] [Accepted: 01/17/2021] [Indexed: 11/09/2022]
Abstract
Leukocyte immunoglobulin (Ig)-like receptors (LILRs) are encoded by members of a human multigene family, comprising 11 protein-coding genes and two pseudogenes. Among the LILRs, LILRB3 and LILRA6 show the highest homology with each other, along with high allelic and copy number variations. Therefore, it has been difficult to discriminate between them, both genetically and functionally, precluding disease association studies of LILRB3 and LILRA6. In this study, we carefully performed variant screening of LILRB3 and LILRA6 by cDNA cloning from Japanese individuals and identified four allelic lineages showing significantly high non-synonymous-to-synonymous ratios in pairwise comparisons. Furthermore, the extracellular domains of the LILRB3*JP6 and LILRA6*JP1 alleles were identical at the DNA level, suggesting that gene conversion-like events diversified LILRB3 and LILRA6. To determine the four allelic lineages from genomic DNA, we established a lineage typing method that accurately estimated the four allelic lineages in addition to specific common alleles from genomic DNA. Analysis of LILRA6 copy number variation revealed one, two, and three copies of LILRA6 in the Japanese-in-Tokyo (JPT) population. Flow cytometric analysis showed that an anti-LILRB3 antibody did not recognize the second most common lineage in the Japanese population, indicating significant amino acid differences across the allelic lineages. Taken together, our findings indicate that our lineage typing is useful for classifying the lineage-specific functions of LILRB3 and LILRA6, serving as the basis for disease association studies.
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Affiliation(s)
- Kouyuki Hirayasu
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Ishikawa, Japan. .,Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan.
| | - Jinwen Sun
- Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Gen Hasegawa
- Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Yuko Hashikawa
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Ishikawa, Japan
| | - Kazuyoshi Hosomichi
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Ishikawa, Japan.,Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Atsushi Tajima
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Ishikawa, Japan.,Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Rikinari Hanayama
- Advanced Preventive Medical Sciences Research Center, Kanazawa University, Ishikawa, Japan.,Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan.,WPI Nano Life Science Institute (NanoLSI), Kanazawa University, Kakuma, Kanazawa, Ishikawa, Japan
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48
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Kuwabara-Ohmura Y, Iizuka K, Liu Y, Takao K, Nonomura K, Kato T, Mizuno M, Hosomichi K, Tajima A, Miyazaki T, Horikawa Y, Yabe D. A case of MODY5-like manifestations without mutations or deletions in coding and minimal promoter regions of the HNF1B gene. Endocr J 2020; 67:981-988. [PMID: 32461507 DOI: 10.1507/endocrj.ej20-0038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Pancreatic tail hypoplasia is a common manifestation of maturity onset diabetes of the young (MODY) 5 that can cause reno-genito-urinary malformations such as renal cysts and bicornuate uterus. A 69-year-old female was admitted to our hospital for consultation on her relatively high HbA1c value. At age 20, she was diagnosed with uterus bicornis. At age 68, she was diagnosed with pancreas tail hypoplasia, renal cysts and non-functioning pancreatic neuroendocrine tumor (NET) in addition to right hydronephrosis due to multiple ureteral bladder carcinomas. She received total right nephrectomy, ureterectomy and partial cystectomy for multiple ureteral bladder carcinomas [non-invasive papillary urothelial carcinoma, low grade (G1), pTa, LV10, u-rtx, RM0, and pN0 (0/8)]. She also received distal pancreatomy for pancreatic NET [NET G1]. She then was referred to our department at age 69 due to increase in her HbA1c value from 6.2 to 7.2%; 75 g oral glucose tolerance test revealed impaired glucose tolerance. Her clinical characteristics (uterus bicornis, pancreas hypoplasia, and renal cysts) closely resembled the phenotype of MODY5, in which mutations in the HNF1B gene have been reported. Our genetic testing failed to detect any mutation or microdeletion in the coding or minimal promoter regions of the HNF1B gene. Although there remains a possibility that genetic mutations in introns and regulatory regions of the HNF1B gene might cause the MODY5-like manifestations in this patient, these results might suggest involvement of genes other than HNF1B in the pathogenesis of our patient's disease.
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Affiliation(s)
- Yayoi Kuwabara-Ohmura
- Department of Diabetes and Endocrinology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Katsumi Iizuka
- Department of Diabetes and Endocrinology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Yanyan Liu
- Department of Diabetes and Endocrinology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Ken Takao
- Department of Diabetes and Endocrinology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Kenta Nonomura
- Department of Diabetes and Endocrinology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Takehiro Kato
- Department of Diabetes and Endocrinology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Masami Mizuno
- Department of Diabetes and Endocrinology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa 920-8640, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa 920-8640, Japan
| | | | - Yukio Horikawa
- Department of Diabetes and Endocrinology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Daisuke Yabe
- Department of Diabetes and Endocrinology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
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49
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Romero VI, Pozo JC, Saenz S, Llamos-Paneque A, Liehr T, Hosomichi K, Tajima A. A toddler with phylloid-type pigmentary mosaicism and ambiguous genitalia resulting from trisomy 14 induced by a der(Y)t(Y;14). Hum Genome Var 2020; 7:28. [PMID: 33062287 PMCID: PMC7519037 DOI: 10.1038/s41439-020-00113-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 11/23/2022] Open
Abstract
A 1-year-old baby with phylloid-type pigmentary mosaicism, hypotonia, ambiguous genitalia, and a positive screening test for congenital adrenal hyperplasia was referred. Previous sonograph, cytogenetics, and metabolic profile were inconclusive, therefore we performed an additional karyotype and a molecular cytogenetics studies. A mosaic karyotype 45,X/46,X,der(Y)t(Y;14) was characterized in peripheral blood. Congenital adrenal hyperplasia genes were sequenced and the results were negative. The ambiguous genitalia was the result of the special gonosomal mosaicism. The low level of trisomy 14 led to minor physical characteristics and mild mental retardation; also, Turner syndrome features can be expected rather than severe trisomy 14 stigmata.
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Affiliation(s)
- V. I. Romero
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - J. C. Pozo
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - S. Saenz
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - A. Llamos-Paneque
- Specialty Army Hospital No. 1. Medical Genetic Services, Sciences of Life Faculty, School of Dentistry, International University of Ecuador, Quito, Ecuador
| | - T. Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany
| | - K. Hosomichi
- Department of Bioinformatics and Genomics, Kanazawa University, Kanazawa, Japan
| | - A. Tajima
- Department of Bioinformatics and Genomics, Kanazawa University, Kanazawa, Japan
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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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