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Fukasawa Y, Driguez P, Bougouffa S, Carty K, Putra A, Cheung MS, Ermini L. Plasticity of repetitive sequences demonstrated by the complete mitochondrial genome of Eucalyptus camaldulensis. Front Plant Sci 2024; 15:1339594. [PMID: 38601302 PMCID: PMC11005031 DOI: 10.3389/fpls.2024.1339594] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/07/2024] [Indexed: 04/12/2024]
Abstract
The tree Eucalyptus camaldulensis is a ubiquitous member of the Eucalyptus genus, which includes several hundred species. Despite the extensive sequencing and assembly of nuclear genomes from various eucalypts, the genus has only one fully annotated and complete mitochondrial genome (mitogenome). Plant mitochondria are characterized by dynamic genomic rearrangements, facilitated by repeat content, a feature that has hindered the assembly of plant mitogenomes. This complexity is evident in the paucity of available mitogenomes. This study, to the best of our knowledge, presents the first E. camaldulensis mitogenome. Our findings suggest the presence of multiple isomeric forms of the E. camaldulensis mitogenome and provide novel insights into minor rearrangements triggered by nested repeat sequences. A comparative sequence analysis of the E. camaldulensis and E. grandis mitogenomes unveils evolutionary changes between the two genomes. A significant divergence is the evolution of a large repeat sequence, which may have contributed to the differences observed between the two genomes. The largest repeat sequences in the E. camaldulensis mitogenome align well with significant yet unexplained structural variations in the E. grandis mitogenome, highlighting the adaptability of repeat sequences in plant mitogenomes.
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Affiliation(s)
- Yoshinori Fukasawa
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
| | - Patrick Driguez
- Core Labs, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Salim Bougouffa
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Karen Carty
- Core Labs, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexander Putra
- Core Labs, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ming-Sin Cheung
- Core Labs, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Luca Ermini
- NORLUX NeuroOncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
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2
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AlAbdi L, Shamseldin HE, Khouj E, Helaby R, Aljamal B, Alqahtani M, Almulhim A, Hamid H, Hashem MO, Abdulwahab F, Abouyousef O, Jaafar A, Alshidi T, Al-Owain M, Alhashem A, Al Tala S, Khan AO, Mardawi E, Alkuraya H, Faqeih E, Afqi M, Alkhalifi S, Rahbeeni Z, Hagos ST, Al-Ahmadi W, Nadeef S, Maddirevula S, Khabar KSA, Putra A, Angelov A, Park C, Reyes-Ramos AM, Umer H, Ullah I, Driguez P, Fukasawa Y, Cheung MS, Gallouzi IE, Alkuraya FS. Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases. Genome Med 2023; 15:114. [PMID: 38098057 PMCID: PMC10720148 DOI: 10.1186/s13073-023-01270-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Long-read whole genome sequencing (lrWGS) has the potential to address the technical limitations of exome sequencing in ways not possible by short-read WGS. However, its utility in autosomal recessive Mendelian diseases is largely unknown. METHODS In a cohort of 34 families in which the suspected autosomal recessive diseases remained undiagnosed by exome sequencing, lrWGS was performed on the Pacific Bioscience Sequel IIe platform. RESULTS Likely causal variants were identified in 13 (38%) of the cohort. These include (1) a homozygous splicing SV in TYMS as a novel candidate gene for lethal neonatal lactic acidosis, (2) a homozygous non-coding SV that we propose impacts STK25 expression and causes a novel neurodevelopmental disorder, (3) a compound heterozygous SV in RP1L1 with complex inheritance pattern in a family with inherited retinal disease, (4) homozygous deep intronic variants in LEMD2 and SNAP91 as novel candidate genes for neurodevelopmental disorders in two families, and (5) a promoter SNV in SLC4A4 causing non-syndromic band keratopathy. Surprisingly, we also encountered causal variants that could have been identified by short-read exome sequencing in 7 families. The latter highlight scenarios that are especially challenging at the interpretation level. CONCLUSIONS Our data highlight the continued need to address the interpretation challenges in parallel with efforts to improve the sequencing technology itself. We propose a path forward for the implementation of lrWGS sequencing in the setting of autosomal recessive diseases in a way that maximizes its utility.
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Affiliation(s)
- Lama AlAbdi
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ebtissal Khouj
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana Helaby
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Bayan Aljamal
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Aisha Almulhim
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Halima Hamid
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Omar Abouyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amal Jaafar
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa Alshidi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohammed Al-Owain
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Collage of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Collage of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Pediatric Department, Division of Genetic and Metabolic Medicine, Prince Sultan Medical Military City, Riyadh, Saudi Arabia
| | - Saeed Al Tala
- Pediatric Department, Neonatal Unit, Armed Forces Hospital, Khamis Mushayt, Saudi Arabia
| | - Arif O Khan
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Elham Mardawi
- Maternal Fetal Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia
| | - Hisham Alkuraya
- Vitreoretinal Surgery and Ocular Genetics, Global Eye Care/Specialized Medical Center Hospital, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Section of Medical Genetics, King Fahad Medical City, Children's Specialist Hospital, Riyadh, Saudi Arabia
| | - Manal Afqi
- Metabolic and Genetic Center, King Salman Bin Abdulaziz Medical City, Almadinah Almunwarah, Saudi Arabia
| | - Salwa Alkhalifi
- Newborn Screening, Ministry of Health, Eastern Province, Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Samya T Hagos
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Wijdan Al-Ahmadi
- Department of Molecular Biomedicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Seba Nadeef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Khalid S A Khabar
- Department of Molecular Biomedicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Alexander Putra
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Angel Angelov
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Changsook Park
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ana M Reyes-Ramos
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Husen Umer
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ikram Ullah
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Patrick Driguez
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Yoshinori Fukasawa
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ming Sin Cheung
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Imed Eddine Gallouzi
- KAUST Smart-Health Initiative King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- KAUST Smart-Health Initiative King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Alfares A, Alsubaie L, Aloraini T, Alaskar A, Althagafi A, Alahmad A, Rashid M, Alswaid A, Alothaim A, Eyaid W, Ababneh F, Albalwi M, Alotaibi R, Almutairi M, Altharawi N, Alsamer A, Abdelhakim M, Kafkas S, Mineta K, Cheung N, Abdallah AM, Büchmann-Møller S, Fukasawa Y, Zhao X, Rajan I, Hoehndorf R, Al Mutairi F, Gojobori T, Alfadhel M. What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations. BMC Med Genomics 2020; 13:103. [PMID: 32680510 PMCID: PMC7368798 DOI: 10.1186/s12920-020-00743-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/19/2020] [Indexed: 02/04/2023] Open
Abstract
Background Testing strategies is crucial for genetics clinics and testing laboratories. In this study, we tried to compare the hit rate between solo and trio and trio plus testing and between trio and sibship testing. Finally, we studied the impact of extended family analysis, mainly in complex and unsolved cases. Methods Three cohorts were used for this analysis: one cohort to assess the hit rate between solo, trio and trio plus testing, another cohort to examine the impact of the testing strategy of sibship genome vs trio-based analysis, and a third cohort to test the impact of an extended family analysis of up to eight family members to lower the number of candidate variants. Results The hit rates in solo, trio and trio plus testing were 39, 40, and 41%, respectively. The total number of candidate variants in the sibship testing strategy was 117 variants compared to 59 variants in the trio-based analysis. We noticed that the average number of coding candidate variants in trio-based analysis was 1192 variants and 26,454 noncoding variants, and this number was lowered by 50–75% after adding additional family members, with up to two coding and 66 noncoding homozygous variants only, in families with eight family members. Conclusion There was no difference in the hit rate between solo and extended family members. Trio-based analysis was a better approach than sibship testing, even in a consanguineous population. Finally, each additional family member helped to narrow down the number of variants by 50–75%. Our findings could help clinicians, researchers and testing laboratories select the most cost-effective and appropriate sequencing approach for their patients. Furthermore, using extended family analysis is a very useful tool for complex cases with novel genes.
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Affiliation(s)
- Ahmed Alfares
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia. .,Department of Pediatrics, College of Medicine, Qassim University, Qassim, Saudi Arabia. .,Qassim University, Department of Pediatrics, Almulyda, Saudi Arabia.
| | - Lamia Alsubaie
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Taghrid Aloraini
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Aljoharah Alaskar
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Azza Althagafi
- Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Ahmed Alahmad
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Mamoon Rashid
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Abdulrahman Alswaid
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Ali Alothaim
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Wafaa Eyaid
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Faroug Ababneh
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Mohammed Albalwi
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Raniah Alotaibi
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia.,Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Mashael Almutairi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Nouf Altharawi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Alhanouf Alsamer
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Marwa Abdelhakim
- Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Senay Kafkas
- Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Katsuhiko Mineta
- Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Nicole Cheung
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, 23955-6900, Saudi Arabia
| | - Abdallah M Abdallah
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Stine Büchmann-Møller
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, 23955-6900, Saudi Arabia
| | - Yoshinori Fukasawa
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, 23955-6900, Saudi Arabia
| | - Xiang Zhao
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, 23955-6900, Saudi Arabia
| | - Issaac Rajan
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, 23955-6900, Saudi Arabia
| | - Robert Hoehndorf
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, 23955-6900, Saudi Arabia
| | - Fuad Al Mutairi
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Takashi Gojobori
- Biological and Environmental Science and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Majid Alfadhel
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
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4
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Nakamura T, Oda T, Fukasawa Y, Tomii K. Template-based quaternary structure prediction of proteins using enhanced profile-profile alignments. Proteins 2017; 86 Suppl 1:274-282. [PMID: 29178285 PMCID: PMC5836938 DOI: 10.1002/prot.25432] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 11/11/2017] [Accepted: 11/22/2017] [Indexed: 12/26/2022]
Abstract
Proteins often exist as their multimeric forms when they function as so‐called biological assemblies consisting of the specific number and arrangement of protein subunits. Consequently, elucidating biological assemblies is necessary to improve understanding of protein function. Template‐Based Modeling (TBM), based on known protein structures, has been used widely for protein structure prediction. Actually, TBM has become an increasingly useful approach in recent years because of the increased amounts of information related to protein amino acid sequences and three‐dimensional structures. An apparently similar situation exists for biological assembly structure prediction as protein complex structures in the PDB increase, although the inference of biological assemblies is not a trivial task. Many methods using TBM, including ours, have been developed for protein structure prediction. Using enhanced profile–profile alignments, we participated in the 12th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP12), as the FONT team (Group # 480). Herein, we present experimental procedures and results of retrospective analyses using our approach for the Quaternary Structure Prediction category of CASP12. We performed profile–profile alignments of several types, based on FORTE, our profile–profile alignment algorithm, to identify suitable templates. Results show that these alignment results enable us to find templates in almost all possible cases. Moreover, we have come to understand the necessity of developing a model selection method that provides improved accuracy. Results also demonstrate that, to some extent, finding templates of protein complexes is useful even for MEDIUM and HARD assembly prediction.
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Affiliation(s)
- Tsukasa Nakamura
- Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8562, Japan
| | - Toshiyuki Oda
- Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Yoshinori Fukasawa
- Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kentaro Tomii
- Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8562, Japan.,Biotechnology Research Institute for Drug Discovery (BRD), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,AIST-Tokyo Tech Real World Big-Data Computation Open Innovation Laboratory (RWBC-OIL), 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
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Abstract
Protein transport systems are fundamentally important for maintaining mitochondrial function. Nevertheless, mitochondrial protein translocases such as the kinetoplastid ATOM complex have recently been shown to vary in eukaryotic lineages. Various evolutionary hypotheses have been formulated to explain this diversity. To resolve any contradiction, estimating the primitive state and clarifying changes from that state are necessary. Here, we present more likely primitive models of mitochondrial translocases, specifically the translocase of the outer membrane (TOM) and translocase of the inner membrane (TIM) complexes, using scrutinized phylogenetic profiles. We then analyzed the translocases’ evolution in eukaryotic lineages. Based on those results, we propose a novel evolutionary scenario for diversification of the mitochondrial transport system. Our results indicate that presequence transport machinery was mostly established in the last eukaryotic common ancestor, and that primitive translocases already had a pathway for transporting presequence-containing proteins. Moreover, secondary changes including convergent and migrational gains of a presequence receptor in TOM and TIM complexes, respectively, likely resulted from constrained evolution. The nature of a targeting signal can constrain alteration to the protein transport complex.
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Affiliation(s)
- Yoshinori Fukasawa
- Artificial Intelligence Research Center, National Institute of Advanced Science and Technology (AIST), Tokyo, Japan
| | - Toshiyuki Oda
- Artificial Intelligence Research Center, National Institute of Advanced Science and Technology (AIST), Tokyo, Japan
| | - Kentaro Tomii
- Artificial Intelligence Research Center, National Institute of Advanced Science and Technology (AIST), Tokyo, Japan.,Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Science and Technology (AIST), Tokyo, Japan
| | - Kenichiro Imai
- Artificial Intelligence Research Center, National Institute of Advanced Science and Technology (AIST), Tokyo, Japan.,Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Science and Technology (AIST), Tokyo, Japan
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Yamada KD, Kunishima N, Matsuura Y, Nakai K, Naitow H, Fukasawa Y, Tomii K. Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on the crystal-packing propensity of amino acids. Acta Crystallogr D Struct Biol 2017; 73:757-766. [PMID: 28876239 PMCID: PMC5586248 DOI: 10.1107/s2059798317010932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 07/25/2017] [Indexed: 11/13/2023] Open
Abstract
An alternative rational approach to improve protein crystals by using single-site mutation of surface residues is proposed based on the results of a statistical analysis using a compiled data set of 918 independent crystal structures, thereby reflecting not only the entropic effect but also other effects upon protein crystallization. This analysis reveals a clear difference in the crystal-packing propensity of amino acids depending on the secondary-structural class. To verify this result, a systematic crystallization experiment was performed with the biotin carboxyl carrier protein from Pyrococcus horikoshii OT3 (PhBCCP). Six single-site mutations were examined: Ala138 on the surface of a β-sheet was mutated to Ile, Tyr, Arg, Gln, Val and Lys. In agreement with prediction, it was observed that the two mutants (A138I and A138Y) harbouring the residues with the highest crystal-packing propensities for β-sheet at position 138 provided better crystallization scores relative to those of other constructs, including the wild type, and that the crystal-packing propensity for β-sheet provided the best correlation with the ratio of obtaining crystals. Two new crystal forms of these mutants were obtained that diffracted to high resolution, generating novel packing interfaces with the mutated residues (Ile/Tyr). The mutations introduced did not affect the overall structures, indicating that a β-sheet can accommodate a successful mutation if it is carefully selected so as to avoid intramolecular steric hindrance. A significant negative correlation between the ratio of obtaining amorphous precipitate and the crystal-packing propensity was also found.
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Affiliation(s)
- Kazunori D. Yamada
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Naoki Kunishima
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshinori Matsuura
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Koshiro Nakai
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hisashi Naitow
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshinori Fukasawa
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Kentaro Tomii
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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7
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Santos HJ, Imai K, Hanadate Y, Fukasawa Y, Oda T, Mi-Ichi F, Nozaki T. Screening and discovery of lineage-specific mitosomal membrane proteins in Entamoeba histolytica. Mol Biochem Parasitol 2016; 209:10-17. [PMID: 26792249 DOI: 10.1016/j.molbiopara.2016.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 10/10/2015] [Revised: 01/05/2016] [Accepted: 01/06/2016] [Indexed: 11/17/2022]
Abstract
Entamoeba histolytica, an anaerobic intestinal parasite causing dysentery and extra-intestinal abscesses in humans, possesses highly reduced and divergent mitochondrion-related organelles (MROs) called mitosomes. This organelle lacks many features associated with canonical aerobic mitochondria and even other MROs such as hydrogenosomes. The Entamoeba mitosome has been found to have a compartmentalized sulfate activation pathway, which was recently implicated to have a role in amebic stage conversion. It also features a unique shuttle system via Tom60, which delivers proteins from the cytosol to the mitosome. In addition, only Entamoeba mitosomes possess a novel subclass of β-barrel outer membrane protein called MBOMP30. With the discoveries of such unique features of mitosomes of Entamoeba, there still remain a number of significant unanswered issues pertaining to this organelle. Particularly, the present understanding of the inner mitosomal membrane of Entamoeba is extremely limited. So far, only a few homologs for transporters of various substrates have been confirmed, while the components of the protein translocation complexes appear to be absent or are yet to be discovered. Employing a similar strategy as in our previous work, we collaborated to screen and discover mitosomal membrane proteins. Using a specialized prediction pipeline, we searched for proteins possessing α-helical transmembrane domains, which are unique to E. histolytica mitosomes. From the prediction algorithm, 25 proteins emerged as candidates, two of which were initially observed to be localized to the mitosomes. Further screening and analysis of the predicted proteins may provide clues to answer key questions on mitosomal evolution, biogenesis, dynamics, and biochemical processes.
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Affiliation(s)
- Herbert J Santos
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Kenichiro Imai
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Yuki Hanadate
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Yoshinori Fukasawa
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Toshiyuki Oda
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Fumika Mi-Ichi
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan; Division of Molecular and Cellular Immunoscience, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Tomoyoshi Nozaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
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Shiota T, Imai K, Qiu J, Hewitt VL, Tan K, Shen HH, Sakiyama N, Fukasawa Y, Hayat S, Kamiya M, Elofsson A, Tomii K, Horton P, Wiedemann N, Pfanner N, Lithgow T, Endo T. Molecular architecture of the active mitochondrial protein gate. Science 2015; 349:1544-8. [DOI: 10.1126/science.aac6428] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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9
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Kikuchi K, Moriuchi R, Inokuma D, Ito T, Kawashima K, Yoshida T, Nozaki A, Horiuchi K, Nakayama C, Itami H, Yanai M, Fukasawa Y, Kimura T, Shimizu S. Immunohistochemical analysis of extramammary Paget's disease with Bowenoid features: case report and review of the literature. J Eur Acad Dermatol Venereol 2015; 30:1404-5. [PMID: 26289934 DOI: 10.1111/jdv.13251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K Kikuchi
- Department of Dermatology, Sapporo City General Hospital, North 11, West 13, Chuo-ku, Sapporo, 060-8604, Japan
| | - R Moriuchi
- Department of Dermatology, Sapporo City General Hospital, North 11, West 13, Chuo-ku, Sapporo, 060-8604, Japan
| | - D Inokuma
- Department of Dermatology, Sapporo City General Hospital, North 11, West 13, Chuo-ku, Sapporo, 060-8604, Japan
| | - T Ito
- Department of Dermatology, Sapporo City General Hospital, North 11, West 13, Chuo-ku, Sapporo, 060-8604, Japan
| | - K Kawashima
- Department of Plastic Surgery, Sapporo City General Hospital, North 11, West 13, Chuo-ku, Sapporo, 060-8604, Japan
| | - T Yoshida
- Department of Plastic Surgery, Sapporo City General Hospital, North 11, West 13, Chuo-ku, Sapporo, 060-8604, Japan
| | - A Nozaki
- Department of Plastic Surgery, Sapporo City General Hospital, North 11, West 13, Chuo-ku, Sapporo, 060-8604, Japan
| | - K Horiuchi
- Department of Plastic Surgery, Sapporo City General Hospital, North 11, West 13, Chuo-ku, Sapporo, 060-8604, Japan
| | - C Nakayama
- Department of Pathology, Sapporo City General Hospital, North 11, West 13, Chuo-ku, Sapporo, 060-8604, Japan
| | - H Itami
- Department of Pathology, Sapporo City General Hospital, North 11, West 13, Chuo-ku, Sapporo, 060-8604, Japan
| | - M Yanai
- Department of Pathology, Sapporo City General Hospital, North 11, West 13, Chuo-ku, Sapporo, 060-8604, Japan
| | - Y Fukasawa
- Department of Pathology, Sapporo City General Hospital, North 11, West 13, Chuo-ku, Sapporo, 060-8604, Japan
| | - T Kimura
- Sapporo Dermatopathology Institute, North 18, West 3, Kita-ku, Sapporo, 001-0018, Japan
| | - S Shimizu
- Department of Dermatology, Sapporo City General Hospital, North 11, West 13, Chuo-ku, Sapporo, 060-8604, Japan
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Fukasawa Y, Tsuji J, Fu SC, Tomii K, Horton P, Imai K. MitoFates: improved prediction of mitochondrial targeting sequences and their cleavage sites. Mol Cell Proteomics 2015; 14:1113-26. [PMID: 25670805 PMCID: PMC4390256 DOI: 10.1074/mcp.m114.043083] [Citation(s) in RCA: 359] [Impact Index Per Article: 39.9] [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: 08/05/2014] [Indexed: 01/25/2023] Open
Abstract
Mitochondria provide numerous essential functions for cells and their dysfunction leads to a variety of diseases. Thus, obtaining a complete mitochondrial proteome should be a crucial step toward understanding the roles of mitochondria. Many mitochondrial proteins have been identified experimentally but a complete list is not yet available. To fill this gap, methods to computationally predict mitochondrial proteins from amino acid sequence have been developed and are widely used, but unfortunately, their accuracy is far from perfect. Here we describe MitoFates, an improved prediction method for cleavable N-terminal mitochondrial targeting signals (presequences) and their cleavage sites. MitoFates introduces novel sequence features including positively charged amphiphilicity, presequence motifs, and position weight matrices modeling the presequence cleavage sites. These features are combined with classical ones such as amino acid composition and physico-chemical properties as input to a standard support vector machine classifier. On independent test data, MitoFates attains better performance than existing predictors in both detection of presequences and in predicting their cleavage sites. We used MitoFates to look for undiscovered mitochondrial proteins from 42,217 human proteins (including isoforms such as alternative splicing or translation initiation variants). MitoFates predicts 1167 genes to have at least one isoform with a presequence. Five-hundred and eighty of these genes were not annotated as mitochondrial in either UniProt or Gene Ontology. Interestingly, these include candidate regulators of parkin translocation to damaged mitochondria, and also many genes with known disease mutations, suggesting that careful investigation of MitoFates predictions may be helpful in elucidating the role of mitochondria in health and disease. MitoFates is open source with a convenient web server publicly available.
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Affiliation(s)
- Yoshinori Fukasawa
- From the ‡Department of Computational Biology, Graduate School of Frontier Sciences, The University Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Junko Tsuji
- From the ‡Department of Computational Biology, Graduate School of Frontier Sciences, The University Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Szu-Chin Fu
- From the ‡Department of Computational Biology, Graduate School of Frontier Sciences, The University Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Kentaro Tomii
- From the ‡Department of Computational Biology, Graduate School of Frontier Sciences, The University Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan; §Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Paul Horton
- From the ‡Department of Computational Biology, Graduate School of Frontier Sciences, The University Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan; §Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Kenichiro Imai
- §Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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Kono M, Yasuda S, Kato M, Kanetsuka Y, Kurita T, Fujieda Y, Otomo K, Horita T, Oba K, Kondo M, Mukai M, Yanai M, Fukasawa Y, Atsumi T. Long-term outcome in Japanese patients with lupus nephritis. Lupus 2014; 23:1124-32. [PMID: 24860121 DOI: 10.1177/0961203314536246] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The objective of this study was to clarify the long-term outcome in patients with lupus nephritis (LN) according to the International Society of Nephrology and Renal Pathology Society classification. This retrospective analysis comprised 186 Japanese patients given a diagnosis of LN by renal specimen with a mean observation period of 12 years. Primary end point was defined as death or end-stage renal disease, and standardized mortality ratios were calculated. Five patients presented with histopathological class I, 62 with II, 21 with III or III+V, 73 with IV or IV+V and 25 with V. Fourteen deaths occurred, corresponding to an overall standardized mortality ratio of 3.59 (95% confidence interval 2.02-5.81, p < 0.0001). Kaplan-Meier analysis revealed a 10-year overall survival of 95.7%. Nephrotic proteinuria (≥3.5 g/day) at baseline was identified as an independent poor prognostic factor for overall survival in Cox regression analysis. Kaplan-Meier analysis revealed a 10-year renal survival as 94.3%. Male gender and nephrotic proteinuria at baseline were identified as independent poor prognostic factors for renal survival in Cox regression analysis. In conclusion, LN was associated with a 3.59-fold increase in mortality compared with the general population. Male gender and nephrotic proteinuria were predictive for poor renal outcome.
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Affiliation(s)
- M Kono
- Division of Rheumatology, Endocrinology and Nephrology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - S Yasuda
- Division of Rheumatology, Endocrinology and Nephrology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - M Kato
- Division of Rheumatology, Endocrinology and Nephrology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Y Kanetsuka
- Division of Rheumatology, Endocrinology and Nephrology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - T Kurita
- Division of Rheumatology, Endocrinology and Nephrology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Y Fujieda
- Division of Rheumatology, Endocrinology and Nephrology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - K Otomo
- Division of Rheumatology, Endocrinology and Nephrology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - T Horita
- Division of Rheumatology, Endocrinology and Nephrology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - K Oba
- Translational Research and Clinical Trial Center, Hokkaido University Hospital, Sapporo, Japan
| | - M Kondo
- Department of Rheumatology, Sapporo City General Hospital, Sapporo, Japan
| | - M Mukai
- Department of Rheumatology, Sapporo City General Hospital, Sapporo, Japan
| | - M Yanai
- Department of Pathology, Sapporo City General Hospital, Sapporo, Japan
| | - Y Fukasawa
- Department of Pathology, Sapporo City General Hospital, Sapporo, Japan
| | - T Atsumi
- Division of Rheumatology, Endocrinology and Nephrology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
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12
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Fukasawa Y, Leung RKK, Tsui SKW, Horton P. Plus ça change - evolutionary sequence divergence predicts protein subcellular localization signals. BMC Genomics 2014; 15:46. [PMID: 24438075 PMCID: PMC3906766 DOI: 10.1186/1471-2164-15-46] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [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: 07/31/2013] [Accepted: 01/06/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Protein subcellular localization is a central problem in understanding cell biology and has been the focus of intense research. In order to predict localization from amino acid sequence a myriad of features have been tried: including amino acid composition, sequence similarity, the presence of certain motifs or domains, and many others. Surprisingly, sequence conservation of sorting motifs has not yet been employed, despite its extensive use for tasks such as the prediction of transcription factor binding sites. RESULTS Here, we flip the problem around, and present a proof of concept for the idea that the lack of sequence conservation can be a novel feature for localization prediction. We show that for yeast, mammal and plant datasets, evolutionary sequence divergence alone has significant power to identify sequences with N-terminal sorting sequences. Moreover sequence divergence is nearly as effective when computed on automatically defined ortholog sets as on hand curated ones. Unfortunately, sequence divergence did not necessarily increase classification performance when combined with some traditional sequence features such as amino acid composition. However a post-hoc analysis of the proteins in which sequence divergence changes the prediction yielded some proteins with atypical (i.e. not MPP-cleaved) matrix targeting signals as well as a few misannotations. CONCLUSION We report the results of the first quantitative study of the effectiveness of evolutionary sequence divergence as a feature for protein subcellular localization prediction. We show that divergence is indeed useful for prediction, but it is not trivial to improve overall accuracy simply by adding this feature to classical sequence features. Nevertheless we argue that sequence divergence is a promising feature and show anecdotal examples in which it succeeds where other features fail.
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Affiliation(s)
- Yoshinori Fukasawa
- Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
- Japan Society for the Promotion of Science, Tokyo Chiyoda, Japan
| | - Ross KK Leung
- Hong Kong Bioinformatics Centre and School of Biomedical Sciences, Chinese University of Hong Kong, Shatin, China
| | - Stephen KW Tsui
- Hong Kong Bioinformatics Centre and School of Biomedical Sciences, Chinese University of Hong Kong, Shatin, China
| | - Paul Horton
- Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
- Computational Biology Research Center, Advanced Industrial Science and Technology, Tokyo, Japan
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13
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14
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15
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Tosaka M, Fukasawa Y, Takahashi A, Sasaki A, Saito N. Incidentally detected parafalcine chondrosarcoma. Acta Neurochir (Wien) 2005; 147:795-9; discussion 799. [PMID: 15864410 DOI: 10.1007/s00701-005-0530-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2004] [Accepted: 02/23/2005] [Indexed: 10/25/2022]
Abstract
Parafalcine chondrosarcoma is extremely rare, and may be difficult to differentiate preoperatively from falx meningioma. An 18-year-old woman presented with a parafalcine chondrosarcoma incidentally detected as a small lesion 2 years before admission, suggesting falx meningioma. Brain computed tomography and magnetic resonance imaging just before admission revealed the parafalcine lesion had increased by about nine times in volume during the last 2 years. Single-photon emission computed tomography (SPECT) after intravenous administration of both thallium-201 chloride ((201)TlCl) and N-isopropyl-p-[(123)I]iodoamphetamine ((123)I-IMP) demonstrated no abnormal uptake of either tracer. Histological examination revealed classic low-grade chondrosarcoma. Parafalcine chondrosarcoma should be considered at this site if relatively rapid growth is observed. SPECT using (201)TlCl and (123)I-IMP may be useful to discriminate parafalcine low-grade chondrosarcoma from meningioma or other tumours originating in this region.
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Affiliation(s)
- M Tosaka
- Department of Neurosurgery, Gunma University Graduate School of Medicine, Gunma, Japan.
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Ishiwata H, Nishijima M, Fukasawa Y. Estimation of preservative concentrations in foods and their daily intake based on official inspection results in Japan in fiscal year 1998. Shokuhin Eiseigaku Zasshi 2001; 42:404-12. [PMID: 11875827 DOI: 10.3358/shokueishi.42.404] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The mean concentration and daily intake of five preservatives were estimated based on the results of an analysis of 89,927 samples of food obtained in official inspections by Japanese local governments in fiscal year 1998. The mean concentration of benzoic acid was 9.5% of the allowable limit, and those of dehydroacetic acid, p-hydroxybenzoic acid, propionic acid, and sorbic acid were 1.5%, 5.7%, 1.7%, and 23.9%, respectively. Daily intake levels of these preservatives per person estimated from the concentration and daily consumption of foods were 6.23 mg, 0.0303 mg, 1.02 mg, 8.10 mg, and 25.0 mg, respectively, and assuming a body weight of 50 kg, the amounts of benzoic acid, p-hydroxybenzoic acid, and sorbic acid consumed were 2.5%, 0.2%, and 2.0% of their acceptable daily intakes, respectively. These values were similar to those obtained based on the results of the official inspections in fiscal years 1994 and 1996.
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Affiliation(s)
- H Ishiwata
- National Institute of Health Sciences: 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
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17
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Yanagida O, Kanai Y, Chairoungdua A, Kim DK, Segawa H, Nii T, Cha SH, Matsuo H, Fukushima J, Fukasawa Y, Tani Y, Taketani Y, Uchino H, Kim JY, Inatomi J, Okayasu I, Miyamoto K, Takeda E, Goya T, Endou H. Human L-type amino acid transporter 1 (LAT1): characterization of function and expression in tumor cell lines. Biochim Biophys Acta 2001; 1514:291-302. [PMID: 11557028 DOI: 10.1016/s0005-2736(01)00384-4] [Citation(s) in RCA: 551] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
System L is a major nutrient transport system responsible for the transport of large neutral amino acids including several essential amino acids. We previously identified a transporter (L-type amino acid transporter 1: LAT1) subserving system L in C6 rat glioma cells and demonstrated that LAT1 requires 4F2 heavy chain (4F2hc) for its functional expression. Since its oncofetal expression was suggested in the rat liver, it has been proposed that LAT1 plays a critical role in cell growth and proliferation. In the present study, we have examined the function of human LAT1 (hLAT1) and its expression in human tissues and tumor cell lines. When expressed in Xenopus oocytes with human 4F2hc (h4F2hc), hLAT1 transports large neutral amino acids with high affinity (K(m)= approximately 15- approximately 50 microM) and L-glutamine and L-asparagine with low affinity (K(m)= approximately 1.5- approximately 2 mM). hLAT1 also transports D-amino acids such as D-leucine and D-phenylalanine. In addition, we show that hLAT1 accepts an amino acid-related anti-cancer agent melphalan. When loaded intracellularly, L-leucine and L-glutamine but not L-alanine are effluxed by extracellular substrates, confirming that hLAT1 mediates an amino acid exchange. hLAT1 mRNA is highly expressed in the human fetal liver, bone marrow, placenta, testis and brain. We have found that, while all the tumor cell lines examined express hLAT1 messages, the expression of h4F2hc is varied particularly in leukemia cell lines. In Western blot analysis, hLAT1 and h4F2hc have been confirmed to be linked to each other via a disulfide bond in T24 human bladder carcinoma cells. Finally, in in vitro translation, we show that hLAT1 is not a glycosylated protein even though an N-glycosylation site has been predicted in its extracellular loop, consistent with the property of the classical 4F2 light chain. The properties of the hLAT1/h4F2hc complex would support the roles of this transporter in providing cells with essential amino acids for cell growth and cellular responses, and in distributing amino acid-related compounds.
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MESH Headings
- Amino Acid Transport Systems
- Amino Acids, Essential/metabolism
- Animals
- Antigens, CD/biosynthesis
- Antigens, CD/genetics
- Carrier Proteins/biosynthesis
- Carrier Proteins/chemistry
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- DNA Probes
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- Fetus/metabolism
- Fusion Regulatory Protein-1
- Humans
- Molecular Sequence Data
- Oocytes/metabolism
- Protein Biosynthesis
- RNA, Complementary/genetics
- RNA, Complementary/isolation & purification
- RNA, Messenger/analysis
- RNA, Messenger/biosynthesis
- Substrate Specificity
- Tumor Cells, Cultured
- Xenopus
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Affiliation(s)
- O Yanagida
- Second Department of Surgery, Kyorin University School of Medicine, Mitaka, Tokyo, Japan
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Kanai Y, Fukasawa Y, Cha SH, Segawa H, Chairoungdua A, Kim DK, Matsuo H, Kim JY, Miyamoto K, Takeda E, Endou H. Transport properties of a system y+L neutral and basic amino acid transporter. Insights into the mechanisms of substrate recognition. J Biol Chem 2000; 275:20787-93. [PMID: 10777485 DOI: 10.1074/jbc.m000634200] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The properties of system y(+)L-mediated transport were investigated on rat system y(+)L transporter, ry(+)LAT1, coexpressed with the heavy chain of cell surface antigen 4F2 in Xenopus oocytes. ry(+)LAT1-mediated transport of basic amino acids was Na(+)-independent, whereas that of neutral amino acids, although not completely, was dependent on Na(+), as is typical of system y(+)L-mediated transport. In the absence of Na(+), lowering of pH increased leucine transport, without affecting lysine transport. Therefore, it is proposed that H(+), besides Na(+) and Li(+), is capable of supporting neutral amino acid transport. Na(+) and H(+) augmented leucine transport by decreasing the apparent K(m) values, without affecting the V(max) values. We demonstrate that although ry(+)LAT1-mediated transport of [(14)C]l-leucine was accompanied by the cotransport of (22)Na(+), that of [(14)C]l-lysine was not. The Na(+) to leucine coupling ratio was determined to be 1:1 in the presence of high concentrations of Na(+). ry(+)LAT1-mediated leucine transport, but not lysine transport, induced intracellular acidification in Chinese hamster ovary cells coexpressing ry(+)LAT1 and 4F2 heavy chain in the absence of Na(+), but not in the presence of physiological concentrations of Na(+), indicating that cotransport of H(+) with leucine occurred in the absence of Na(+). Therefore, for the substrate recognition by ry(+)LAT1, the positive charge on basic amino acid side chains or that conferred by inorganic monovalent cations such as Na(+) and H(+), which are cotransported with neutral amino acids, is presumed to be required. We further demonstrate that ry(+)LAT1, due to its peculiar cation dependence, mediates a heteroexchange, wherein the influx of substrate amino acids is accompanied by the efflux of basic amino acids.
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Affiliation(s)
- Y Kanai
- Department of Pharmacology and Toxicology, Kyorin University School of Medicine, Mitaka, Tokyo 181-8611, Japan.
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Saito H, Fukasawa Y, Otsubo Y, Yamada K, Sezaki H, Yamashita S. Carrier-mediated transport of macrolide antimicrobial agents across Caco-2 cell monolayers. Pharm Res 2000; 17:761-5. [PMID: 10955854 DOI: 10.1023/a:1007550820196] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- H Saito
- Taisho Pharmceutical Co, Ltd, Saitama, Japan
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20
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Fukasawa Y, Segawa H, Kim JY, Chairoungdua A, Kim DK, Matsuo H, Cha SH, Endou H, Kanai Y. Identification and characterization of a Na(+)-independent neutral amino acid transporter that associates with the 4F2 heavy chain and exhibits substrate selectivity for small neutral D- and L-amino acids. J Biol Chem 2000; 275:9690-8. [PMID: 10734121 DOI: 10.1074/jbc.275.13.9690] [Citation(s) in RCA: 226] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A cDNA was isolated from the mouse brain that encodes a novel Na(+)-independent neutral amino acid transporter. The encoded protein, designated as Asc-1 (asc-type amino acid transporter 1), was found to be structurally related to recently identified mammalian amino acid transporters for the transport systems L, y(+)L, x(C)(-), and b(0,+), which are linked, via a disulfide bond, to the type II membrane glycoproteins, 4F2 heavy chain (4F2hc), or rBAT (related to b(0,+) amino acid transporter). Asc-1 required 4F2hc for its functional expression. In Western blot analysis in the nonreducing condition, a 118-kDa band, which seems to correspond to the heterodimeric complex of Asc-1 and 4F2hc, was detected in the mouse brain. The band shifted to 33 kDa in the reducing condition, confirming that Asc-1 and 4F2hc are linked via a disulfide bond. Asc-1-mediated transport was not dependent on the presence of Na(+) or Cl(-). Although Asc-1 showed a high sequence homology (66% identity at the amino acid level) to the Na(+)-independent broad scope neutral amino acid transporter LAT2 (Segawa, H., Fukasawa, Y., Miyamoto, K., Takeda, E., Endou, H., and Kanai, Y. (1999) J. Biol. Chem. 274, 19745-19751), Asc-1 also exhibited distinctive substrate selectivity and transport properties. Asc-1 preferred small neutral amino acids such as Gly, L-Ala, L-Ser, L-Thr, and L-Cys, and alpha-aminoisobutyric acid as substrates. Asc-1 also transported D-isomers of the small neutral amino acids, in particular D-Ser, a putative endogenous modulator of N-methyl-D-aspartate-type glutamate receptors, with high affinity. Asc-1 operated preferentially, although not exclusively, in an exchange mode. Asc-1 mRNA was detected in the brain, lung, small intestine, and placenta. The functional properties of Asc-1 seem to be consistent with those of a transporter subserving the Na(+)-independent small neutral amino acid transport system asc.
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Affiliation(s)
- Y Fukasawa
- Department of Pharmacology and Toxicology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo 181-8611, Japan
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Segawa H, Fukasawa Y, Miyamoto K, Takeda E, Endou H, Kanai Y. Identification and functional characterization of a Na+-independent neutral amino acid transporter with broad substrate selectivity. J Biol Chem 1999; 274:19745-51. [PMID: 10391916 DOI: 10.1074/jbc.274.28.19745] [Citation(s) in RCA: 385] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have isolated a cDNA from rat small intestine that encodes a novel Na+-independent neutral amino acid transporter with distinctive characteristics in substrate selectivity and transport property. The encoded protein, designated L-type amino acid transporter-2 (LAT-2), shows amino acid sequence similarity to the system L Na+-independent neutral amino acid transporter LAT-1 (Kanai, Y., Segawa, H., Miyamoto, K., Uchino, H., Takeda, E., and Endou, H. (1998) J. Biol. Chem. 273, 23629-23632) (50% identity) and the system y+L transporters y+LAT-1 (47%) and KIAA0245/y+LAT-2 (45%) (Torrents, D., Estevez, R., Pineda, M., Fernandez, E., Lloberas, J., Shi, Y.-B., Zorzano, A., and Palacin, M. (1998) J. Biol. Chem. 273, 32437-32445). LAT-2 is a nonglycosylated membrane protein. It requires 4F2 heavy chain, a type II membrane glycoprotein, for its functional expression in Xenopus oocytes. LAT-2-mediated transport is not dependent on Na+ or Cl- and is inhibited by a system L-specific inhibitor, 2-aminobicyclo-(2,2,1)-heptane-2-carboxylic acid (BCH), indicating that LAT-2 is a second isoform of the system L transporter. Compared with LAT-1, which prefers large neutral amino acids with branched or aromatic side chains, LAT-2 exhibits remarkably broad substrate selectivity. It transports all of the L-isomers of neutral alpha-amino acids. LAT-2 exhibits higher affinity (Km = 30-50 microM) to Tyr, Phe, Trp, Thr, Asn, Ile, Cys, Ser, Leu, Val, and Gln and relatively lower affinity (Km = 180-300 microM) to His, Ala, Met, and Gly. In addition, LAT-2 mediates facilitated diffusion of substrate amino acids, as distinct from LAT-1, which mediates amino acid exchange. LAT-2-mediated transport is increased by lowering the pH level, with peak activity at pH 6.25, because of the decrease in the Km value without changing the Vmax value. Because of these functional properties and a high level of expression of LAT-2 in the small intestine, kidney, placenta, and brain, it is suggested that the heterodimeric complex of LAT-2 and 4F2 heavy chain is involved in the trans-cellular transport of neutral amino acids in epithelia and blood-tissue barriers.
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Affiliation(s)
- H Segawa
- Department of Pharmacology and Toxicology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo 181-8611, Japan
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Ohta K, Fukasawa Y, Yamaguchi J, Kohno Y, Fukushima K, Suwa T, Awazu S. Retention mechanism of imidazoles in connective tissue. IV. Identification of a nucleophilic imidazolone metabolite in rats. Biol Pharm Bull 1998; 21:1334-7. [PMID: 9881649 DOI: 10.1248/bpb.21.1334] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Formation of a nucleophilic 4(5H)(or 5(4H))-imidazolone structure has been postulated from in vitro studies to be one of the causative elements involved in the retention of drugs with imidazole moiety in connective tissue. To confirm this, we searched for the imidazolone-related metabolite in rats after intravenous dosing of 2-methylimidazole (2MI; 14C-labeled and unlabeled form, 3 and 300 micromol/kg body weight) as a model compound. The excreted urine, the major route of elimination of the compound, was collected and analyzed using the HPLC/MS system with a counterion effect for metabolite separation. 2-Methyl-4(5H)(or 5(4H))-imidazolone (2MIone) was identified as a urinary metabolite by chromatographic and mass-spectral inspection with the corresponding authentic standard. Pretreatment of rats with either SKF-525A (50 mg/kg, i.p.) or cimetidine (200 mg/kg, i.p.) significantly increased the excreted amount of 2MIone in urine and the irreversible binding of 2MI equivalents in the aortic tissue, whereas both factors were reduced by pretreatment with triethylenetetramine dihydrochloride (150 mg/kg/d for 5 d, s.c.). These results support the aforementioned deduction, and also raise the possibility that a cytochrome P450-independent, copper-related metabolic reaction might be involved in the imidazolone formation in vivo.
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Affiliation(s)
- K Ohta
- Department of Drug Metabolism, Taisho Pharmaceutical Research Center, Ohmiya, Saitama, Japan
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23
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Ohta K, Fukasawa Y, Yamaguchi J, Akimoto M, Kohno Y, Fukushima K, Suwa T, Awazu S. Retention mechanism of imidazoles in connective tissue. III. Aldehyde adduct formation of a 4(5H)(or5(4H))-imidazolone product in vitro. Biol Pharm Bull 1998; 21:958-63. [PMID: 9781847 DOI: 10.1248/bpb.21.958] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
2-Methylimidazole (2MI), as well as imidazole, has been thought to undergo cupro-ascorbate (Cu-VC)-catalyzed oxidative transformation in vitro to become a reactive species capable of combining with aldehydes intrinsic to connective-tissue proteins. We attempted to seize the essence of the above reaction through obtaining the structural information of an aldehyde-bonding species. As major products from 2MI in the in vitro Cu-VC system, 2-hydroxymethylimidazole (2(OH)MI) and 2-methyl-4(5H)(or 5(4H))-imidazolone (2MIone) were identified by mass-spectral and chromatographic comparison with the corresponding authentic standards synthesized. The in situ addition of acetaldehyde or propionaldehyde as a simple protein-aldehyde model to the system resulted in the deducible formation of an aldol condensate, 2-methyl-4(or 5)-ethylidene-4(5H)(or 5(4H))-imidazolone (2MEIone) or its possible analogue with a propylidene moiety, respectively. The authentic compound of 2MIone directly reacted with acetaldehyde and easily afforded the products assignable to the isomers of 2MEIone through the ethylidene moiety at physiological pH and temperature, whereas neither 2MI or 2(OH)MI reacted at all. These results suggest that a 4(5H)(or 5(4H))-imidazolone product, although simply a monooxygenated form, is sufficiently reactive to give aldol condensation-typed covalent adducts with aldehydes, even under physiological conditions, probably having an activated methylene moiety in the ring structure. Based on the present results, we discussed the mechanism of the retention of imidazole-containing drugs in connective tissue.
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Affiliation(s)
- K Ohta
- Department of Drug Metabolism, Taisho Pharmaceutical Research Center, Ohmiya, Saitama, Japan
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Hirano K, Takahashi M, Kazumi Y, Fukasawa Y, Abe C. Mutation in pncA is a major mechanism of pyrazinamide resistance in Mycobacterium tuberculosis. Tuber Lung Dis 1998; 78:117-22. [PMID: 9692180 DOI: 10.1016/s0962-8479(98)80004-x] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE To characterize the correlation of the mutations in the pncA gene encoding pyrazinamidase (PZase) of Mycobacterium tuberculosis to a loss of PZase activity and development of pyrazinamide (PZA) resistance. DESIGN The association of PZase activity, minimum inhibitory concentrations (MICs), and mutations in the pncA gene of M. tuberculosis isolated in mostly Asian countries was investigated. RESULTS One hundred thirty-five out of 168 isolates were PZase positive, and 33 were negative. The MICs of PZA at pH 6.0 were over 400 micrograms/ml for all 33 PZase-negative isolates, while those of PZase-positive isolates were equal to or less than 200 micrograms/ml. Among 33 PZase-negative isolates sequenced, 32 (97%) had mutations within the pncA gene. A mutation was seen in various regions throughout the pncA gene. It was surprising that all three strains of in vitro selected PZA resistant mutants were PZase-positive and showed no change in the pncA gene. These results indicate that additional mechanisms may be involved in PZA resistance. No mutations were observed in all of 135 PZase-positive M. tuberculosis isolates tested, indicating that mutations in the pncA gene could be involved in the loss of PZase activity. CONCLUSIONS Sequencing analysis of the pncA gene should provide rapid diagnosis of PZA resistant clinical isolates of M. tuberculosis.
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Affiliation(s)
- K Hirano
- Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
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Fukasawa Y, Takada A, Tateno M, Sato H, Koizumi M, Tanaka A, Sato T. Solitary fibrous tumor of the pleura causing recurrent hypoglycemia by secretion of insulin-like growth factor II. Pathol Int 1998; 48:47-52. [PMID: 9589464 DOI: 10.1111/j.1440-1827.1998.tb03827.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A case of malignant solitary fibrous tumor (SFT) is reported, occurring in a 61-year-old man with frequent hypoglycemia. Endocrinological analyses showed high serum levels of insulin-like growth factor II (IGF-II) and suppressed secretion of insulin. After the removal of a pleural tumor, which weighed 3150 g, serum IGF-II levels returned to normal and hypoglycemic attacks ceased. The tumor was composed of uniform spindle cells arranged in bundles, and fascicles with varying amounts of collagen and reticulin fibers. Mitotic figures at the rate of 6/10 high-power fields, and frequent foci of necrosis and hemorrhage were seen. Almost all of the tumor cells were immunohistochemically positive for vimentin and CD34. Electron microscopy revealed the immature mesenchymal or myofibroblastic nature of the tumor cells. These findings are consistent with malignant SFT of the pleura. Moreover, the tumor produced IGF-II mRNA as demonstrated by northern blot analysis. Thus, hypoglycemia of this patient was induced by SFT through the production and secretion of IGF-II.
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Affiliation(s)
- Y Fukasawa
- Department of Pathology, Sapporo City General Hospital, Japan.
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Sato S, Koshiro A, Kakemi M, Fukasawa Y, Katayama K, Koizumi T. Pharmacokinetic and pharmacodynamic studies of centrally acting drugs in rat: effect of pentobarbital and chlorpromazine on electroencephalogram in rat. Biol Pharm Bull 1995; 18:1094-103. [PMID: 8535403 DOI: 10.1248/bpb.18.1094] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Electroencephalogram (EEG) alterations in rat after the i.v. administration of pentobarbital (PTB) and chlorpromazine (CPZ) were measured by power spectral analysis. The time courses of PTB concentrations in plasma, cerebrospinal fluid (CSF) and brain were determined after the i.v. administration of PTB (20, 40 mg/kg) by GC-MS. The PTB concentrations in plasma, CSF and brain could be described by a biexponential equation, a CSF model and a blood flow limited model, respectively. The relationship between the alteration of EEG and the PTB concentrations in the CSF or brain or the effect compartment were analyzed using the sigmoid Emax model. The alteration of EEG after PTB administration could be described by the PTB concentration in these compartments using the sigmoid Emax model. These results indicated that the site of action for the alteration of EEG after PTB administration is in instantaneous equilibrium with the CSF, the brain and the effect compartment. Thus, alterations in EEG after PTB administration can be predicted by monitoring the total PTB concentration in plasma. The alteration of EEG after i.v. administration of CPZ (4 mg/kg) showed a two-phase variation. Although the relationship between the alteration of EEG and the CPZ concentrations in CSF or the striatum or the effect compartment (total and free drug) were analyzed using the linear model, the Emax model or the sigmoid Emax model, the two-phase alteration of EEG after CPZ administration could not be described by any of these models. These results indicated that the pharmacokinetic and pharmacodynamic modeling of CPZ during the alteration of EEG may be complicated due to several pharmacokinetic and pharmacodynamic factors, such as an alteration of the free fraction of CPZ in the striatum, the formation of active metabolites, and two different intrinsic effects of CPZ on the EEG (one in an increase and the other in a decrease of the brain's electrical activity.
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Affiliation(s)
- S Sato
- Department of Pharmaceutics, Niigata College of Pharmacy, Japan
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27
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Fukasawa Y, Ishikura H, Takada A, Yokoyama S, Imamura M, Yoshiki T, Sato H. Massive apoptosis in infantile myofibromatosis. A putative mechanism of tumor regression. Am J Pathol 1994; 144:480-5. [PMID: 8129033 PMCID: PMC1887082] [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] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Two cases of solitary infantile myofibromatosis (IM) are presented. Solitary IM are tumors prone to spontaneous regression. Histopathologically, several tumor lobules in our IM cases had central areas of massive cell death, with nuclear pyknosis, cytoplasmic hyalinization and nuclear fragmentation but without lymphoid or neutrophilic cell infiltration. These central cell death areas consisted of about 40% in case 2 and 50% in case 1 of the entire tumor tissues, respectively. Electron microscopy revealed that the condensed nuclei and cytoplasm were fragmented into "apoptotic bodies", with or without phagocytosis by histiocytes. DNA fragmentation, as evidenced by the terminal deoxy transferase-mediated uptake of biotinylated dUTP, was identified at massive cell death areas on paraffin sections from both cases. A characteristic 180- to 190-bp nucleosomal ladder was detected in DNA obtained from the tumor cells in case 1. The collective evidence suggested that these tumors underwent a central, massive apoptosis. As massive cell death similar to that seen in the present cases has been described in other documented cases of IM, we propose that the spontaneous regression that frequently occurs with this type of tumor may be mediated by massive apoptotic cell death.
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Affiliation(s)
- Y Fukasawa
- Department of Pathology, Sapporo City General Hospital, Japan
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28
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Abe C, Hirano K, Wada M, Kazumi Y, Takahashi M, Fukasawa Y, Yoshimura T, Miyagi C, Goto S. Detection of Mycobacterium tuberculosis in clinical specimens by polymerase chain reaction and Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test. J Clin Microbiol 1993; 31:3270-4. [PMID: 8308121 PMCID: PMC266398 DOI: 10.1128/jcm.31.12.3270-3274.1993] [Citation(s) in RCA: 146] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The polymerase chain reaction (PCR) using oligonucleotides based on the repetitive sequence (IS986) of Mycobacterium tuberculosis as a primer and the Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test (MTD), which combines an M. tuberculosis rRNA amplification method with the hybridization protection assay format, were evaluated for detection of M. tuberculosis in clinical samples. The detection limits of these two assay systems based on nucleic acid amplification for cultured M. tuberculosis were less than 10 cells per reaction. A total of 135 sputum specimens were examined by the two assay systems. The PCR and the MTD systems for detection of M. tuberculosis gave overall positivity rates of 84.2% (32 of 38) and 91.9% (34 of 37), respectively, as compared with 71.9% (23 of 32) by smear and 96.9% (31 of 32) by culture in the liquid medium MB-Check. Procedures for sample preparation used in the two methods were different. Although the sensitivities of the PCR and MTD appeared to be similar to that of culture with the MB-Check system, the two methods based on nucleic acid amplification should be very useful for rapid detection of M. tuberculosis infections without the long time required for culture of M. tuberculosis.
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Affiliation(s)
- C Abe
- Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo
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29
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Fukasawa Y, Kano S. [Anti-type II collagen antibodies in collagen disease]. Rinsho Byori 1993; 41:876-81. [PMID: 8371503] [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] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Using enzyme-linked immunosorbent assay (ELISA), we determined the incidence of serum IgG antibodies to native type II collagen in patients with collagen diseases such as rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), progressive systemic sclerosis (PSS) and overlap syndrome (OL). Raised serum IgG anti-type II collagen antibody levels were present in 11% of patients with RA, 30% with SLE, 44% with PSS and 42% with OL. There was, however, no correlation with clinical manifestations or other laboratory data.
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Takahashi M, Kazumi Y, Fukasawa Y, Hirano K, Mori T, Dale JW, Abe C. Restriction fragment length polymorphism analysis of epidemiologically related Mycobacterium tuberculosis isolates. Microbiol Immunol 1993; 37:289-94. [PMID: 8102472 DOI: 10.1111/j.1348-0421.1993.tb03212.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Restriction fragment length polymorphism (RFLP) analysis of a large number of Japanese isolates of Mycobacterium tuberculosis, containing isolates from small outbreaks of M. tuberculosis infection, and clinical isolates of M. bovis BCG, was carried out using a DNA probe derived from the insertion sequence IS986. Clinical isolates of M. tuberculosis had a high degree of RFLP. The occurrences of the IS element varied from 1 to 19, the majority of isolates having 8 to 15 copies. Very similar fingerprints, however, were seen among strains isolated in the Kanto district. In particular, 3 strains were of the same pattern with or without an additional band. Similarity of the banding patterns of strains isolated in the same district was observed in other areas. Six groups of strains, each group arising from a suspected common source of infection, were analyzed. Of these, 5 showed identical fingerprints within each group, but one showed different fingerprints. RFLP patterns of three strains isolated from individuals with lymphadenitis developed about two months after BCG vaccination, and one strain isolated from a bladder cancer patient with BCG instillation therapy were identical to those of BCG-Tokyo which had been used for the vaccination and therapy. These results confirm that RFLP analysis using IS986 is a suitable tool for epidemiology of tuberculosis.
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Affiliation(s)
- M Takahashi
- Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo
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31
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Abe C, Hosojima S, Fukasawa Y, Kazumi Y, Takahashi M, Hirano K, Mori T. Comparison of MB-Check, BACTEC, and egg-based media for recovery of mycobacteria. J Clin Microbiol 1992; 30:878-81. [PMID: 1572974 PMCID: PMC265178 DOI: 10.1128/jcm.30.4.878-881.1992] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The rate of recovery and time to the detection of mycobacteria from clinical specimens were measured for biphasic (MB-Check; Nippon Roche Co., Ltd., Tokyo, Japan) and radiometric (BACTEC; Nippon Becton Dickinson Co., Ltd., Tokyo, Japan) liquid-based culture systems and egg-based media (3% Ogawa and Ogawa K). From the 245 sputum specimens processed, a total of 86 (35.1%) mycobacterial isolates were detected. Of these, 81 (94.2%) and 80 (93.0%) isolates were detected with the MB-Check and BACTEC systems, respectively, and 65 (75.6%) isolates were detected with the 3% Ogawa egg method. The difference in the percentages of positive cultures between the two systems based on liquid media and the 3% Ogawa egg method was significant (P less than 0.01). This difference was even greater among smear-negative specimens. The detection time was shorter with the liquid-based systems. The mean times to the detection of the Mycobacterium tuberculosis complex were 19.1 days with the MB-Check system, 13.4 days with the BACTEC system, and 21.7 days with the 3% Ogawa egg method. These results indicate that both the MB-Check and the BACTEC systems, based on liquid media, are efficient for the recovery of mycobacteria.
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Affiliation(s)
- C Abe
- Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo
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32
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Yamaguchi R, Matsuo K, Yamazaki A, Takahashi M, Fukasawa Y, Wada M, Abe C. Cloning and expression of the gene for the Avi-3 antigen of Mycobacterium avium and mapping of its epitopes. Infect Immun 1992; 60:1210-6. [PMID: 1371765 PMCID: PMC257614 DOI: 10.1128/iai.60.3.1210-1216.1992] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Avi-3 antigen, which is found only in Mycobacterium avium culture sonic extracts, is species specific and results in strong skin test activity in guinea pigs sensitized with heat-killed M. avium. Its gene was cloned by using a previously developed single-probe method and was sequenced. The gene encoded a 194-amino-acid polypeptide with a molecular weight of 21,500. A recombinant Avi-3 antigen expressed in Escherichia coli reacted with monoclonal and polyclonal antibodies raised against the native Avi-3 antigen. To identify epitopes on this protein for immunodiagnostic purposes, various parts of the Avi-3 antigen were expressed as beta-galactosidase fusion proteins, using pUR and pURS expression vectors. The clones screened by both antibody reactivity and T-cell proliferative activity defined fragments with coexisting B- and T-cell epitopes. A B-cell epitope (Asn-176 to Ala-186) and two T-cell epitopes (Glu-75 to Ile-86 and Arg-155 to Leu-164) were thus defined. The synthetic polymerized peptides of the T-cell epitopes were proven to elicit a delayed cutaneous hypersensitivity reaction in guinea pigs. This mapping method would be useful in the development of a subunit vaccine consisting of an immunodominant B-cell epitope linked to a T-cell epitope in the vicinity.
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Affiliation(s)
- R Yamaguchi
- Central Research Laboratories, Ajinomoto Co., Inc., Kawasaki, Japan
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33
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Abe C, Saito H, Tomioka H, Fukasawa Y. Production of a monoclonal antibody specific for Mycobacterium avium and immunological activity of the affinity-purified antigen. Infect Immun 1989; 57:1095-9. [PMID: 2925241 PMCID: PMC313235 DOI: 10.1128/iai.57.4.1095-1099.1989] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Three hybridomas which secrete antibodies to Mycobacterium avium were obtained by the fusion of p3u1 myeloma cells with spleen cells of mice immunized with M. avium culture sonicate. The reactivity of these monoclonal antibodies was determined in 16 species of mycobacteria by an enzyme-linked immunosorbent assay. An antibody, designated Avi-3, reacted only with M. avium and not with the reference strains of the other 15 species of mycobacteria tested, including M. intracellulare, M. paratuberculosis, and M. lepraemurium. Specificity of the antibody was confirmed by assay, using a specific DNA probe of M. avium complex in 29 M. avium complex isolates. An antigen was purified from M. avium culture sonicate on a monoclonal antibody Avi-3-coupled affinity column. The purified antigen gave a single band (molecular size, about 27 kilodaltons) upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The antigen Avi-3 showed strong skin test activity in guinea pig preimmunized with heat-killed M. avium but not in those sensitized with heat-killed M. intracellulare or M. bovis BCG. Purified protein derivative elicited positive skin reactions in all the immunized guinea pigs. When heat-killed M. avium was used as the immunogen, strong lymphoproliferative responses were observed in cultures stimulated with the antigen Avi-3. These results suggest that M. avium-specific antigen Avi-3 may facilitate the diagnosis of mycobacterial infections.
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Affiliation(s)
- C Abe
- Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo
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34
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Kojima H, Fukasawa Y, Ishikawa N, Tajima Y, Wakisaka A, Aizawa M. Detection of a novel HLA-DQ specificity. II. Cellular analysis by cytotoxic T-cell clones. Immunogenetics 1988; 27:145-7. [PMID: 3257198 DOI: 10.1007/bf00351090] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- H Kojima
- Department of Pathology, Hokkaido University School of Medicine, Sapporo, Japan
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Ishikawa N, Kojima H, Nakayama T, Kunikane H, Hawkin S, Fukasawa Y, Ikeda H, Ogasawara K, Kasahara M, Tajima Y. Detection of a novel HLA-DQ specificity: serological and immunochemical analyses by a monoclonal antibody. Immunogenetics 1987; 26:143-9. [PMID: 3497872 DOI: 10.1007/bf00365903] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A monoclonal antibody (mAb) with a novel human B-cell allospecificity was produced by immunizing a C3H/He mouse with the human B lymphoblastoid cell line EBV-Wa (HLA-DR4/Dw15/DQblank homozygous). The mAb, termed HU-46, reacted with B cells from not only DR4/Dw15-positive individuals but also certain DRw8/Dw8-positive ones whose DQ phenotypes had not yet been defined. Two-dimensional gel analyses indicated that the mAb recognized class II antigens which were encoded by the HLA-DQ locus. Furthermore, in genetic analysis, the gene encoding the class II antigen detected by HU-46 met the Hardy-Weinberg condition as a fourth allele of the DQ locus. We provisionally labeled this novel DQ specificity DQWa.
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Nakayama T, Ogasawara K, Ikeda H, Kunikane H, Kasahara M, Ishikawa N, Fukasawa Y, Hawkin S, Kojima H, Wakisaka A. A cytotoxic monoclonal antibody (HU-39) that detects DRw8 + DRw12. Hum Immunol 1987; 19:117-26. [PMID: 3497138 DOI: 10.1016/0198-8859(87)90099-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A monoclonal antibody, HU-39, was produced by immunizing BALB/c mice with a cultured human B lymphoblastoid cell line, Shi-C3 (HLA-A24, A31, B51, Bw52, DR2, DRw12, DQw1, DQw3). Utilizing the complement-dependent cytotoxicity test, HU-39 was found to detect a polymorphic determinant common to HLA-DRw8 and HLA-DRw12, a split antigen of HLA-DR5. Although HU-39 reacted with the cells from all of nine DRw12 positive individuals, the cells from only 18 out of 21 DRw8 positive individuals reacted with HU-39 and the remaining three were negative for HU-39. The cytotoxicity of the antibody was reduced after the surface HLA-DR molecules of two cell lines, GI and EBV-Sh, typed as DRw8 and DRw12, respectively, were masked with F(ab')2, of anti-HLA-DR monoclonal antibody. The results of the sequential coprecipitation test and the two-dimensional gel electrophoresis by using EBV-Sh also indicated that HU-39 preferentially recognizes an epitope borne on the DR molecules, but not on the DQ molecules. Thus, HU-39 appeared to be of great value as a tissue typing reagent to define DRw8 and DRw12, the latter of which had been difficult to assign because of the lack of monospecific alloantisera.
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Fukasawa Y. [Human cytotoxic T cell clones that recognize HLA-DQw3 antigens]. Hokkaido Igaku Zasshi 1986; 61:682-9. [PMID: 3023217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Human cytotoxic T cell (CTL) clones generated against a DQw3-positive EBV-transformed B cell line were analyzed in terms of immunological characteristics. The cytolytic activities of clones 1-18 and 3-34 were inhibited by anti-DQw3 monoclonal antibodies (HU-18 and HU-23), but they were not affected by anti-DR (HU-4 and HU-20) and anti-HLA-A, B, C (W6/32) monoclonal antibodies. In contrast to that the clone 1-18 cytolyzed all the human B cell lines typed as DQw3, the clone 3-34 reacted only with DR4/Dw4 and DR5-positive cells that were positive for HU-23 and typed as TA10. In addition, the clone 3-34 were cross-reactive to DQw2-typed cells. These results show that there are two epitopes that CTL recognize on the same DQw3 molecules; one is the public epitope among DQw3 antigens, and the other is the private epitope that HU-23 recognizes. This is the further evidence for CTL recognition of HLA-DQ antigens.
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Ogasawara K, Kojima H, Ikeda H, Ishikawa N, Kasahara M, Fukasawa Y, Natori T, Wakisaka A, Kikuchi Y, Aizawa M. A study on class II antigens involved in the T cell proliferative responses to PPD using cross-reacting monoclonal antibodies in human and murine system. Immunobiology 1986; 171:112-24. [PMID: 3086213 DOI: 10.1016/s0171-2985(86)80021-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Two monoclonal antibodies (MoAb) 1E4 and ISCR3, which detect class II antigens across species barriers, were studied for their inhibitory effects on human and murine T cell proliferative responses to purified protein derivative of tuberculin (PPD). The 1E4 detected at least a polymorphic determinant on I-A molecules from mice carrying the H-2b haplotype, and the ISCR3 detected the Ia.7 determinant on I-E molecules. Nevertheless, both 1E4 and ISCR3 recognized monomorphic determinants on HLA-DR antigens (human I-E equivalent molecules), but not on HLA-DQ antigens (human I-A equivalent molecules). It was demonstrated that 1E4 significantly inhibited PPD-specific responses of T cells from Ib-bearing mice. In contrast, ISCR3 showed marginal effects on the responses of mice bearing Ia.7. However, in the human system both 1E4 and ISCR3 reduced proliferative responses to PPD. These results suggest that a functional difference exists between humans and mice in the I subregion products involved in the T cell proliferative responses to PPD.
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Abstract
A patient with primary gastric adenocarcinoma with extremely high serum alpha-fetoprotein (AFP) levels (12,000 ng/ml) is described. Histologically, foci strongly resembling hepatocellular carcinoma with hyaline globules were noted. Within tumor cells, AFP was identified with both light and electron microscopy, showing the production of AFP by tumor cells themselves. Furthermore, 88% of serum AFP combined with Concanavalin A (ConA), revealing that it was hepatic-type AFP and not germ-cell-type. Localization of alpha-1-antitrypsin within tumor cells was also noted. Ultrastructural study showed that there were two types of structures corresponding to periodic acid-Schiff (PAS)-positive globules, one of which, the proteinaceous material in intracytoplasmic lumina, was found to contain AFP. Among gastric adenocarcinomas with a high serum AFP level (several thousand or more ng/ml of AFP), foci resembling hepatocellular carcinomas have been reported by several investigators. Those gastric carcinomas, together with the current case, may constitute a clinicopathologic entity, hepatoid adenocarcinoma of the stomach.
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Abstract
A patient with primary gastric adenocarcinoma with extremely high serum alpha-fetoprotein (AFP) levels (12,000 ng/ml) is described. Histologically, foci strongly resembling hepatocellular carcinoma with hyaline globules were noted. Within tumor cells, AFP was identified with both light and electron microscopy, showing the production of AFP by tumor cells themselves. Furthermore, 88% of serum AFP combined with Concanavalin A (ConA), revealing that it was hepatic-type AFP and not germ-cell-type. Localization of alpha-1-antitrypsin within tumor cells was also noted. Ultrastructural study showed that there were two types of structures corresponding to periodic acid-Schiff (PAS)-positive globules, one of which, the proteinaceous material in intracytoplasmic lumina, was found to contain AFP. Among gastric adenocarcinomas with a high serum AFP level (several thousand or more ng/ml of AFP), foci resembling hepatocellular carcinomas have been reported by several investigators. Those gastric carcinomas, together with the current case, may constitute a clinicopathologic entity, hepatoid adenocarcinoma of the stomach.
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Ishikura H, Fukasawa Y, Ogasawara K, Natori T, Tsukada Y, Aizawa M. An AFP-producing gastric carcinoma with features of hepatic differentiation. A case report. Cancer 1985. [PMID: 2410093 DOI: 10.1002/1097-0142.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A patient with primary gastric adenocarcinoma with extremely high serum alpha-fetoprotein (AFP) levels (12,000 ng/ml) is described. Histologically, foci strongly resembling hepatocellular carcinoma with hyaline globules were noted. Within tumor cells, AFP was identified with both light and electron microscopy, showing the production of AFP by tumor cells themselves. Furthermore, 88% of serum AFP combined with Concanavalin A (ConA), revealing that it was hepatic-type AFP and not germ-cell-type. Localization of alpha-1-antitrypsin within tumor cells was also noted. Ultrastructural study showed that there were two types of structures corresponding to periodic acid-Schiff (PAS)-positive globules, one of which, the proteinaceous material in intracytoplasmic lumina, was found to contain AFP. Among gastric adenocarcinomas with a high serum AFP level (several thousand or more ng/ml of AFP), foci resembling hepatocellular carcinomas have been reported by several investigators. Those gastric carcinomas, together with the current case, may constitute a clinicopathologic entity, hepatoid adenocarcinoma of the stomach.
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Abstract
A patient with primary gastric adenocarcinoma with extremely high serum alpha-fetoprotein (AFP) levels (12,000 ng/ml) is described. Histologically, foci strongly resembling hepatocellular carcinoma with hyaline globules were noted. Within tumor cells, AFP was identified with both light and electron microscopy, showing the production of AFP by tumor cells themselves. Furthermore, 88% of serum AFP combined with Concanavalin A (ConA), revealing that it was hepatic-type AFP and not germ-cell-type. Localization of alpha-1-antitrypsin within tumor cells was also noted. Ultrastructural study showed that there were two types of structures corresponding to periodic acid-Schiff (PAS)-positive globules, one of which, the proteinaceous material in intracytoplasmic lumina, was found to contain AFP. Among gastric adenocarcinomas with a high serum AFP level (several thousand or more ng/ml of AFP), foci resembling hepatocellular carcinomas have been reported by several investigators. Those gastric carcinomas, together with the current case, may constitute a clinicopathologic entity, hepatoid adenocarcinoma of the stomach.
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Kasahara M, Ikeda H, Ogasawara K, Ishikawa N, Okuyama T, Fukasawa Y, Kojima H, Kunikane H, Hawkin S, Ohhashi T. Inhibition of autologous mixed lymphocyte reaction by monoclonal antibodies specific for the beta chain of HLA-DR antigens. Immunology 1984; 53:79-86. [PMID: 6205985 PMCID: PMC1454738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Recent studies using rabbit antisera to the separated HLA-DR alpha and beta subunits have suggested that alpha chain-specific, but not beta chain-specific, antisera inhibit T cell proliferative responses in primary and secondary human autologous mixed lymphocyte reaction (AMLR). In the present study, with the aid of sequential co-precipitation assays and Western blotting methods, a monoclonal rat alloantibody 1E4, specific for the beta chain of rat class II molecules carrying an Ia determinant Ba-2.7, was characterized to recognize a monomorphic determinant located on the beta chain of DR antigens. This antibody and a murine monoclonal antibody HU-4, also specific for the beta chain of DR antigens, strongly inhibited both primary and secondary AMLR through a mechanism distinct from an antibody-dependent cell-mediated cytotoxicity reaction. These results indicate that the inhibition of AMLR is not a unique feature of DR alpha-specific antibodies.
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Abstract
In order to better define the frequency and patterns of metastasis to the female genital tract, all cases of nonhematopoietic metastases to the adnexa, uterus, vagina, and vulva encountered in patients treated at Barnes Hospital between 1950 and 1981 were reviewed. Three hundred twenty-five metastatic cancers from 269 patients were recovered. One hundred forty-nine cases were from extragenital primaries; the remaining tumors were intragenital metastases. Ovary and vagina were the most frequent metastatic sites for both extragenital and genital primaries. The majority of the extragenital metastases were adenocarcinomas from the gastrointestinal tract, but a variety of other primaries did spread, on occasion, to the genital tract. Twenty-seven percent of the metastases presented as possible primary gynecologic lesions, and 75% of these tumors had an extragenital origin. It is shown that despite certain trends in the distribution of metastases, all sites in the female genital tract are at risk for the occurrence of metastases.
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Fukasawa Y, Yoshimura M, Kuroki M, Nemoto I. [Agglutination test using S-type Mycobacterium tuberculosis cultured in the Ogawa media containing Tween-80. 2. Comparison with the Middlebrook-Dubos reaction and its clinical application]. Iryo 1966; 20:268-73. [PMID: 4960740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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