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Miyazaki Y, Nakano K, Nakayamada S, Kubo S, Iwata S, Hanami K, Fukuyo S, Miyagawa I, Yamaguchi A, Kawabe A, Kazuyoshi S, Tanaka Y. FRI0102 SERUM TNFΑ LEVELS AT 24 HOURS AFTER FIRST ADMINISTRATION OF CERTOLIZUMAB PEGOL PREDICT EFFECTIVENESS AT WEEK 12 IN PATIENTS WITH RHEUMATOID ARTHRITIS FROM TSUBAME STUDY (UMIN ID:0002381). Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.2252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:To increase the remission rate of rheumatoid arthritis (RA), it is necessary to determine the efficacy of the tumor necrosis factor (TNF) inhibitor as early as possible. Moreover, the response to certolizumab pegol (CZP) at 12 weeks has been reported to predict its long-term efficacy.Objectives:As part of a prospective single-center observational study (TSUBAME study), we prospectively enrolled patients to be treated with CZP in our institution to evaluate its effectiveness and safety starting at 24 hours after the first dose in clinical settings, while recording blood CZP concentrations and biomarkers over time to examine their correlation with clinical effects.Methods:One hundred patients with RA and inadequate response to MTX who received CZP were enrolled in the TSUBAME study. The changes in serum TNFα, IL-6, and CZP levels at 24 hours after first administration of CZP were measured, and the correlation between serum biomarkers and clinical response was determined.Results:At 24 hours after CZP initiation, significant improvement was observed in the disease activity (baseline and 24 h: 5.4 ± 1.3, 5.0 ± 1.3, respectively, p < 0.01), which was maintained until week 12. (baseline and 12 w: 5.4 ± 1.3, 3.3 ± 1.4, respectively, p < 0.01). Serum TNFα and IL-6 levels significantly decreased at 24 hours after first administration of CZP compared to baseline. No correlation was found between TNFα and IL-6 levels at baseline and the clinical response. According to univariate analysis, low serum TNFα and IL-6 levels and high CZP levels at 24 hours were associated with DAS28 (ESR) remission at 12 weeks. According to multivariate analysis, low serum TNFα levels at 24 hours were significantly associated with DAS28 (ESR) remission at 12 weeks (OR 0.05, 95%CI 0.01, 0.75, p = 0.03). Based on these findings, an ROC curve was created using remission according to the DAS28 (ESR) at week 12 as a dependent variable and TNFα concentration at 24 hours as an independent variable, resulting in a cut-off value of 0.76 pg/ml. From this result, the TNFα concentration at 24 hours was divided into 2 groups according to this cut-off, and the rates of remission according to the DAS28 (ESR) at week 12 were compared. In the group with TNFα concentration at 24 hours below the cut-off value, the rate of remission according to the DAS28 (ESR) at week 12 was significantly higher than in the group with TNFα concentration at 24 hours above the cut-off value (below the cut-off: above the cut-off = 56.3%: 21.6%, p < 0.001). Between the group that achieved remission according to the DAS28(ESR) and the group that did not achieve remission at week 12, there was almost no difference in the distribution of TNFα concentrations at baseline; however, the distribution of TNFα concentrations at 24 hours was lower in the group that achieved remission.Conclusion:CZP was effective where serum TNFα was strongly neutralized within 24 hours. These results suggest that low serum TNFα levels at 24 hours after first administration of CZP may predict the effectiveness of CZP. To increase the remission rate in RA, it is necessary to determine the effectiveness of the molecular targeted drugs used at an early point, in addition to how rapid the onset of action is. CZP is extremely fast-acting, and its effectiveness can be predicted as early as 24 hours after the first dose, suggesting that it may be possible to determine the effectiveness early.Acknowledgments:The authors thank Ms. M. Hirahara for providing excellent technical assistance.Disclosure of Interests:Yusuke Miyazaki Grant/research support from: Astellas Pharma Inc and UCB S.A., Kazuhisa Nakano: None declared, Shingo Nakayamada Grant/research support from: Mitsubishi-Tanabe, Takeda, Novartis and MSD, Speakers bureau: Bristol-Myers, Sanofi, Abbvie, Eisai, Eli Lilly, Chugai, Asahi-kasei and Pfizer, Satoshi Kubo: None declared, Shigeru Iwata: None declared, Kentaro Hanami: None declared, Shunsuke Fukuyo: None declared, Ippei Miyagawa: None declared, Ayako Yamaguchi: None declared, Akio Kawabe: None declared, SAITO KAZUYOSHI: None declared, Yoshiya Tanaka Grant/research support from: Asahi-kasei, Astellas, Mitsubishi-Tanabe, Chugai, Takeda, Sanofi, Bristol-Myers, UCB, Daiichi-Sankyo, Eisai, Pfizer, and Ono, Consultant of: Abbvie, Astellas, Bristol-Myers Squibb, Eli Lilly, Pfizer, Speakers bureau: Daiichi-Sankyo, Astellas, Chugai, Eli Lilly, Pfizer, AbbVie, YL Biologics, Bristol-Myers, Takeda, Mitsubishi-Tanabe, Novartis, Eisai, Janssen, Sanofi, UCB, and Teijin
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Claesson E, Wahlgren WY, Takala H, Pandey S, Castillon L, Kuznetsova V, Henry L, Panman M, Carrillo M, Kübel J, Nanekar R, Isaksson L, Nimmrich A, Cellini A, Morozov D, Maj M, Kurttila M, Bosman R, Nango E, Tanaka R, Tanaka T, Fangjia L, Iwata S, Owada S, Moffat K, Groenhof G, Stojković EA, Ihalainen JA, Schmidt M, Westenhoff S. The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser. eLife 2020; 9:53514. [PMID: 32228856 PMCID: PMC7164956 DOI: 10.7554/elife.53514] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/13/2020] [Indexed: 01/27/2023] Open
Abstract
Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial femtosecond X-ray crystallographic data of the chromophore-binding domains of a bacterial phytochrome at delay times of 1 ps and 10 ps after photoexcitation. The data reveal a twist of the D-ring, which leads to partial detachment of the chromophore from the protein. Unexpectedly, the conserved so-called pyrrole water is photodissociated from the chromophore, concomitant with movement of the A-ring and a key signaling aspartate. The changes are wired together by ultrafast backbone and water movements around the chromophore, channeling them into signal transduction towards the output domains. We suggest that the observed collective changes are important for the phytochrome photoresponse, explaining the earliest steps of how plants, fungi and bacteria sense red light. Plants adapt to the availability of light throughout their lives because it regulates so many aspects of their growth and reproduction. To detect the level of light, plant cells use proteins called phytochromes, which are also found in some bacteria and fungi. Phytochrome proteins change shape when they are exposed to red light, and this change alters the behaviour of the cell. The red light is absorbed by a molecule known as chromophore, which is connected to a region of the phytochrome called the PHY-tongue. This region undergoes one of the key structural changes that occur when the phytochrome protein absorbs light, turning from a flat sheet into a helix. Claesson, Wahlgren, Takala et al. studied the structure of a bacterial phytochrome protein almost immediately after shining a very brief flash of red light using a laser. The experiments revealed that the structure of the protein begins to change within a trillionth of a second: specifically, the chromophore twists, which disrupts its attachment to the protein, freeing the protein to change shape. Claesson, Wahlgren, Takala et al. note that this structure is likely a very short-lived intermediate state, which however triggers more changes in the overall shape change of the protein. One feature of the rearrangement is the disappearance of a particular water molecule. This molecule can be found at the core of many different phytochrome structures and interacts with several parts of the chromophore and the phytochrome protein. It is unclear why the water molecule is lost, but given how quickly this happens after the red light is applied it is likely that this disappearance is an integral part of the reshaping process. Together these events disrupt the interactions between the chromophore and the PHY-tongue, enabling the PHY-tongue to change shape and alter the structure of the phytochrome protein. Understanding and controlling this process could allow scientists to alter growth patterns in plants, such as crops or weeds.
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Umeda R, Satouh Y, Takemoto M, Nakada-Nakura Y, Liu K, Yokoyama T, Shirouzu M, Iwata S, Nomura N, Sato K, Ikawa M, Nishizawa T, Nureki O. Structural insights into tetraspanin CD9 function. Nat Commun 2020; 11:1606. [PMID: 32231207 PMCID: PMC7105497 DOI: 10.1038/s41467-020-15459-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 03/06/2020] [Indexed: 01/16/2023] Open
Abstract
Tetraspanins play critical roles in various physiological processes, ranging from cell adhesion to virus infection. The members of the tetraspanin family have four membrane-spanning domains and short and large extracellular loops, and associate with a broad range of other functional proteins to exert cellular functions. Here we report the crystal structure of CD9 and the cryo-electron microscopic structure of CD9 in complex with its single membrane-spanning partner protein, EWI-2. The reversed cone-like molecular shape of CD9 generates membrane curvature in the crystalline lipid layers, which explains the CD9 localization in regions with high membrane curvature and its implications in membrane remodeling. The molecular interaction between CD9 and EWI-2 is mainly mediated through the small residues in the transmembrane region and protein/lipid interactions, whereas the fertilization assay revealed the critical involvement of the LEL region in the sperm-egg fusion, indicating the different dependency of each binding domain for other partner proteins. Tetraspanins play critical roles in various physiological processes, ranging from cell adhesion to virus infection. Here authors report the crystal structure of CD9 and the cryo-electron microscopic structure of CD9 in complex with its single membrane-spanning partner protein, EWI-2.
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Wolff AM, Young ID, Sierra RG, Brewster AS, Martynowycz MW, Nango E, Sugahara M, Nakane T, Ito K, Aquila A, Bhowmick A, Biel JT, Carbajo S, Cohen AE, Cortez S, Gonzalez A, Hino T, Im D, Koralek JD, Kubo M, Lazarou TS, Nomura T, Owada S, Samelson AJ, Tanaka T, Tanaka R, Thompson EM, van den Bedem H, Woldeyes RA, Yumoto F, Zhao W, Tono K, Boutet S, Iwata S, Gonen T, Sauter NK, Fraser JS, Thompson MC. Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals. IUCRJ 2020; 7:306-323. [PMID: 32148858 PMCID: PMC7055375 DOI: 10.1107/s205225252000072x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.
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Okai T, Mizutani K, Yamaguchi T, Ogawa M, Kajio K, Ito A, Iwata S, Takahashi Y, Izumiya Y, Murakami T, Shibata T, Yoshiyama M. P107 Predictors of increased d-dimer level at follow-up period after transcatheter aortic valve implantation.Is oral anticoagulation therapy better? Eur Heart J 2020. [DOI: 10.1093/ehjci/ehz872.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Recently, there are some reports that hypo-attenuated leaflet thickening (HALT) following transcatheter aortic valve implantation (TAVI) is incidentally detected by multi-slice computed tomography. It is believed that valve thrombosis causes HALT, because oral anticoagulation therapy (OAC) is effective for HALT regression. Furthermore, it is reported that d-dimer level increases in patients with HALT, and might be a key biomarker to detect HALT.
Purpose
We sought to investigate the predictors related to increased d-dimer level at 6 months after follow-up TAVI.
Methods
We enrolled 124 consecutive patients who underwent successful TAVI between 2016 and 2018. Study patients were classified into two groups according to antithrombotic therapy resume (OAC therapy or anti-platelet therapy).We set the primary endpoint as the d-dimer levels at 6 months after TAVI. To evaluate the risks of the primary endpoint, we employed a multivariable linear regression model, setting the primary endpoint as an objective variable and patient and clinical backgrounds as explanatory variables. Furthermore, we set the secondary endpoint as one-year bleeding event.
Results
The median age of patients was 83 years old (quartile 80-87). Patients who had taken OAC at 6 months follow-up after TAVI were 29.8%. The median d-dimer level at 6 months after TAVI was 1.3 (1.0-2.2) µg/ml, and OAC group had statistically lower d-dimer level at 6 months follow-up than those in non-OAC group (p = 0.020). Uni-variable liner regression model demonstrated that increased d-dimer level at follow-up had significant relationship with large effective orifice area (EOA) (p = 0.002) and low left ventricular ejection fraction (LVEF) (p = 0.048) after TAVI. Furthermore, large EOA (p = 0.003) and OAC therapy (p = 0.027) were independently associated with increased d-dimer level in multivariate analysis. Kaplan-Meier estimates revealed that there were no significant difference regarding one-year bleeding event between OAC group and non-OAC group (long-rank p = 0.167).
Conclusions
This study suggests that large EOA after TAVI is associated with increased d-dimer levels at 6 months after TAVI, and OAC therapy might have a potential to decrease d-dimer level after TAVI without increase of bleeding events.
Abstract P107 Figure: One-year bleeding event
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Asada H, Inoue A, Ngako Kadji FM, Hirata K, Shiimura Y, Im D, Shimamura T, Nomura N, Iwanari H, Hamakubo T, Kusano-Arai O, Hisano H, Uemura T, Suno C, Aoki J, Iwata S. The Crystal Structure of Angiotensin II Type 2 Receptor with Endogenous Peptide Hormone. Structure 2019; 28:418-425.e4. [PMID: 31899086 DOI: 10.1016/j.str.2019.12.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/11/2019] [Accepted: 12/05/2019] [Indexed: 12/17/2022]
Abstract
Angiotensin II (AngII) is a peptide hormone that plays a key role in regulating blood pressure, and its interactions with the G protein-coupled receptors, AngII type-1 receptor (AT1R) and AngII type-2 receptor (AT2R), are central to its mechanism of action. We solved the crystal structure of human AT2R bound to AngII and its specific antibody at 3.2-Å resolution. AngII (full agonist) and [Sar1, Ile8]-AngII (partial agonist) interact with AT2R in a similar fashion, except at the bottom of the AT2R ligand-binding pocket. In particular, the residues including Met1283.36, which constitute the deep end of the cavity, play important roles in angiotensin receptor (ATR) activation upon AngII binding. These differences that occur upon endogenous ligand binding may contribute to a structural change in AT2R, leading to normalization of the non-canonical coordination of helix 8. Our results will inform the design of more effective ligands for ATRs.
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Katayama K, Suzuki K, Suno R, Tsujimoto H, Iwata S, Kobayashi T, Kandori H. Ligand Binding-Induced Structural Changes in the M 2 Muscarinic Acetylcholine Receptor Revealed by Vibrational Spectroscopy. J Phys Chem Lett 2019; 10:7270-7276. [PMID: 31692352 DOI: 10.1021/acs.jpclett.9b02942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
M2 muscarinic acetylcholine receptor (M2R) is a prototypical G protein-coupled receptor (GPCR) that responds to acetylcholine and mediates various cellular responses in the nervous system. Here, we used attenuated total reflection-Fourier transform infrared spectroscopy analyses on M2R reconstituted in a lipid membrane to understand the molecular mechanism behind the ligand binding-induced conformational changes. Upon agonist binding, M2R shows large spectral change of the amide-I band corresponding to backbone C═O stretch, which likely connects with the receptor activation in the lipid environment. These results pave the way to probe effects of different ligand binding on GPCRs using vibrational spectroscopy.
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Koiwai K, Tsukimoto J, Higashi T, Mafuné F, Miyajima K, Nakane T, Matsugaki N, Kato R, Sirigu S, Jakobi A, Wilmanns M, Sugahara M, Tanaka T, Tono K, Joti Y, Yabashi M, Nureki O, Mizohata E, Nakatsu T, Nango E, Iwata S, Chavas LMG, Senda T, Itoh K, Yumoto F. Improvement of Production and Isolation of Human Neuraminidase-1 in Cellulo Crystals. ACS APPLIED BIO MATERIALS 2019; 2:4941-4952. [DOI: 10.1021/acsabm.9b00686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Ishchenko A, Stauch B, Han GW, Batyuk A, Shiriaeva A, Li C, Zatsepin N, Weierstall U, Liu W, Nango E, Nakane T, Tanaka R, Tono K, Joti Y, Iwata S, Moraes I, Gati C, Cherezov V. Toward G protein-coupled receptor structure-based drug design using X-ray lasers. IUCRJ 2019; 6:1106-1119. [PMID: 31709066 PMCID: PMC6830214 DOI: 10.1107/s2052252519013137] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023]
Abstract
Rational structure-based drug design (SBDD) relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process. While SBDD has proven successful for many drug-discovery projects, its application to G protein-coupled receptors (GPCRs) has been limited owing to extreme difficulties with their crystallization. Here, a method is presented for the rapid determination of multiple co-crystal structures for a target GPCR in complex with various ligands, taking advantage of the serial femtosecond crystallography approach, which obviates the need for large crystals and requires only submilligram quantities of purified protein. The method was applied to the human β2-adrenergic receptor, resulting in eight room-temperature co-crystal structures with six different ligands, including previously unreported structures with carvedilol and propranolol. The generality of the proposed method was tested with three other receptors. This approach has the potential to enable SBDD for GPCRs and other difficult-to-crystallize membrane proteins.
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Shimazu Y, Tono K, Tanaka T, Yamanaka Y, Nakane T, Mori C, Terakado Kimura K, Fujiwara T, Sugahara M, Tanaka R, Doak RB, Shimamura T, Iwata S, Nango E, Yabashi M. High-viscosity sample-injection device for serial femtosecond crystallography at atmospheric pressure. J Appl Crystallogr 2019; 52:1280-1288. [PMID: 31798359 PMCID: PMC6878880 DOI: 10.1107/s1600576719012846] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 09/16/2019] [Indexed: 11/21/2022] Open
Abstract
A high-viscosity cartridge-type injector for serial femtosecond crystallography has been developed at SPring-8 Angstrom Compact Free-Electron Laser. A sample-injection device has been developed at SPring-8 Angstrom Compact Free-Electron Laser (SACLA) for serial femtosecond crystallography (SFX) at atmospheric pressure. Microcrystals embedded in a highly viscous carrier are stably delivered from a capillary nozzle with the aid of a coaxial gas flow and a suction device. The cartridge-type sample reservoir is easily replaceable and facilitates sample reloading or exchange. The reservoir is positioned in a cooling jacket with a temperature-regulated water flow, which is useful to prevent drastic changes in the sample temperature during data collection. This work demonstrates that the injector successfully worked in SFX of the human A2A adenosine receptor complexed with an antagonist, ZM241385, in lipidic cubic phase and for hen egg-white lysozyme microcrystals in a grease carrier. The injection device has also been applied to many kinds of proteins, not only for static structural analyses but also for dynamics studies using pump–probe techniques.
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Ogawa M, Mizutani K, Okai T, Kajio K, Ito A, Iwata S, Takahashi Y, Murakami T, Shibata T, Yoshiyama M. P3693Self-expandable transcatheter aortic valve implantation is associated with frequent periprocedural stroke detected by diffusion-weighted magnetic resonance imaging -Insight from propensity score match. Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz745.0547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Little evidence is available regarding the risk of peri-procedural stroke detected by diffusion-weighted magnetic resonance imaging (DW-MRI) after transcatheter aortic valve implantation (TAVI). Our purpose was to evaluate stroke risk after TAVI using DW-MRI by enrolling consecutive patients who underwent transfemoral TAVI and post-procedural DW-MRI.
Methods
We prospectively enrolled 113 consecutive patients who underwent transfemoral TAVI and post-procedural DW-MRI. We used balloon-expandable valves as first-line therapy and selected self-expandable valves only for patients with narrow sinotubular junctions or annuli. We set the primary endpoint as the number of high intensity areas (HIA) detected by DW-MRI regardless of the size of the area. To evaluate the risks of the primary endpoint, we employed a multivariable linear regression model, setting the primary endpoint as an objective variable and patient and clinical backgrounds as explanatory variables. In addition, the relationship between valve type and the number of HIAs on DW-MRI was also confirmed by the propensity score matching analysis to evaluate the robustness of the result, using a multivariable linear regression model with the protocol described in the previous manuscript. Shortly, the propensity score was calculated with a logistic regression model by setting the treatment as the response variable and baseline characteristics and procedural information that were significantly different between 2 groups (balloon expandable and self-expandable) as explanatory variables, which included age, estimated glomerular filtration rate, oversizing rate, and BAV before THV deployment.
Results
Median patient age was 84 years, and 36.3% were men. Ninety-three patients underwent balloon-expandable TAVI and 20 underwent self-expandable TAVI. Symptomatic stroke occurred in 6 (5.3%) whereas asymptomatic stroke occurred in 59 (52.2%) patients. The incidence of symptomatic and total stroke was higher in patients who underwent self-expandable TAVI than those who underwent balloon-expandable TAVI (30.0% vs 0.0%, p<0.001 and 90.0% vs 50.5%, p=0.001, respectively). A multivariable linear regression model demonstrated an increased primary endpoint when self-expandable TAVI was performed (p<0.001). The other covariates had no significant relationship to the primary endpoint. Akaike information criterion-based stepwise statistical model selection revealed that valve type was the only explanatory variable for the best predictive model. This result was also confirmed with the propensity score matching analysis (estimate, 2.359; 95% CI, 0.426–4.292; p=0.019) after adjustments of propensity score, in which 28 patients were matched (n=14 in each group).
Conclusions
Self-expandable valves were associated with increased numbers of HIA on DW-MRI after TAVI in patients with severe aortic stenosis.
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Kinjo T, Terai K, Horita S, Nomura N, Sumiyama K, Togashi K, Iwata S, Matsuda M. FRET-assisted photoactivation of flavoproteins for in vivo two-photon optogenetics. Nat Methods 2019; 16:1029-1036. [DOI: 10.1038/s41592-019-0541-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/26/2019] [Indexed: 12/16/2022]
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Sanchez JC, Carrillo M, Pandey S, Noda M, Aldama L, Feliz D, Claesson E, Wahlgren WY, Tracy G, Duong P, Nugent AC, Field A, Šrajer V, Kupitz C, Iwata S, Nango E, Tanaka R, Tanaka T, Fangjia L, Tono K, Owada S, Westenhoff S, Schmidt M, Stojković EA. High-resolution crystal structures of a myxobacterial phytochrome at cryo and room temperatures. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:054701. [PMID: 31559319 PMCID: PMC6748860 DOI: 10.1063/1.5120527] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/27/2019] [Indexed: 05/04/2023]
Abstract
Phytochromes (PHYs) are photoreceptor proteins first discovered in plants, where they control a variety of photomorphogenesis events. PHYs as photochromic proteins can reversibly switch between two distinct states: a red light (Pr) and a far-red light (Pfr) absorbing form. The discovery of Bacteriophytochromes (BphPs) in nonphotosynthetic bacteria has opened new frontiers in our understanding of the mechanisms by which these natural photoswitches can control single cell development, although the role of BphPs in vivo remains largely unknown. BphPs are dimeric proteins that consist of a photosensory core module (PCM) and an enzymatic domain, often a histidine kinase. The PCM is composed of three domains (PAS, GAF, and PHY). It holds a covalently bound open-chain tetrapyrrole (biliverdin, BV) chromophore. Upon absorption of light, the double bond between BV rings C and D isomerizes and reversibly switches the protein between Pr and Pfr states. We report crystal structures of the wild-type and mutant (His275Thr) forms of the canonical BphP from the nonphotosynthetic myxobacterium Stigmatella aurantiaca (SaBphP2) in the Pr state. Structures were determined at 1.65 Å and 2.2 Å (respectively), the highest resolution of any PCM construct to date. We also report the room temperature wild-type structure of the same protein determined at 2.1 Å at the SPring-8 Angstrom Compact free electron LAser (SACLA), Japan. Our results not only highlight and confirm important amino acids near the chromophore that play a role in Pr-Pfr photoconversion but also describe the signal transduction into the PHY domain which moves across tens of angstroms after the light stimulus.
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Wolff AM, Young ID, Sierra RG, Brewster AS, Martynowycz MW, Aquila A, Nango E, Nakane T, Koralek JD, Sugahara M, Tanaka R, Zhao W, Ito K, Woldeyes RA, Biel JT, Thompson EM, Samelson A, Cortez S, van den Bedem H, Yumoto F, Tono K, Gonen T, Iwata S, Boutet S, Sauter NS, Fraser JS, Thompson MC. Optimizing and evaluating protein microcrystallography experiments: strengths and weaknesses of X-rays and electrons. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s0108767319096156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Thompson MC, Wolff AM, Nango E, Kubo M, Young ID, Nakane T, Sugahara M, Tanaka R, Ito K, Brewster AS, Sierra RG, Yumoto F, Nomura T, Owada S, Hino T, Tosha T, Tanaka T, Im D, Aquila A, Carbajo S, Koralek J, Yamashita A, Luo F, Boutet S, Sauter NK, Tono K, Iwata S, Fraser JS. Turning up the heat on dynamic proteins: observing molecular motion in real time with temperature-jump X-ray crystallography. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s0108767319098349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Wickstrand C, Nogly P, Nango E, Iwata S, Standfuss J, Neutze R. Bacteriorhodopsin: Structural Insights Revealed Using X-Ray Lasers and Synchrotron Radiation. Annu Rev Biochem 2019; 88:59-83. [DOI: 10.1146/annurev-biochem-013118-111327] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Directional transport of protons across an energy transducing membrane—proton pumping—is ubiquitous in biology. Bacteriorhodopsin (bR) is a light-driven proton pump that is activated by a buried all- trans retinal chromophore being photoisomerized to a 13- cis conformation. The mechanism by which photoisomerization initiates directional proton transport against a proton concentration gradient has been studied by a myriad of biochemical, biophysical, and structural techniques. X-ray free electron lasers (XFELs) have created new opportunities to probe the structural dynamics of bR at room temperature on timescales from femtoseconds to milliseconds using time-resolved serial femtosecond crystallography (TR-SFX). Wereview these recent developments and highlight where XFEL studies reveal new details concerning the structural mechanism of retinal photoisomerization and proton pumping. We also discuss the extent to which these insights were anticipated by earlier intermediate trapping studies using synchrotron radiation. TR-SFX will open up the field for dynamical studies of other proteins that are not naturally light-sensitive.
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Jiang Y, Iwata S, Yang C, Shirakawa K, Matsuoka T. Cartilage regeneration by autologous adipose-derived mesenchymal stem cells for the treatment of osteoarthritis. Cytotherapy 2019. [DOI: 10.1016/j.jcyt.2019.03.501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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68
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Nakashima Y, Kounoura M, Malasuk C, Nakakubo K, Watanabe N, Iwata S, Morita K, Oki Y, Kuhara S, Tashiro K, Nakanishi Y. Continuous cell culture monitoring using a compact microplate reader with a silicone optical technology-based spatial filter. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:035106. [PMID: 30927768 DOI: 10.1063/1.5054824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 02/23/2019] [Indexed: 06/09/2023]
Abstract
Continuous cell monitoring is very important for the maintenance and control of cell multiplication and differentiation. This paper presents a compact microplate reader that is able to continuously measure a 24-well microplate (6 × 4 wells) using the optical absorption measurement method. The 24-channel plate reader consisted of a spatial filter, light emitting diode light source, and color sensors and was similarly sized with the cell culture microwell plates. A spatial filter was previously fabricated by our group using silicone optical technology (SOT). This SOT-based spatial filter has an excellent noise reduction effect. Light reflection at the optical path interface can be absorbed and only forward light can be transmitted; accordingly, a larger S/N ratio than that of conventional optical systems is expected. The fabricated 24-channel plate reader permits real-time cell monitoring during cultivation on the clean bench and in cell culture conditions by incorporating the SOT spatial filter. Using the device, it was possible to continuously evaluate the concentration and pH of reagents in the 24 wells in real time. Moreover, cell activity and protein production were detectable using the device. These results suggest that the newly fabricated device is a promising tool for the evaluation of cell behaviors for cell management.
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Iwata S, Yonemori K, Arakawa A, Maejima A, Nakatani F, Kobayashi E, Mori T, Sudo K, Noguchi E, Hirose T, Komatsubara S, Fujimoto H, Ogawa C, Tamura K, Kawai A. Prognostic factors for post-progression survival after trabectedin treatment in patients with advanced soft tissue sarcoma. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy443.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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70
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Nagarathinam K, Nakada-Nakura Y, Parthier C, Terada T, Juge N, Jaenecke F, Liu K, Hotta Y, Miyaji T, Omote H, Iwata S, Nomura N, Stubbs MT, Tanabe M. Outward open conformation of a Major Facilitator Superfamily multidrug/H + antiporter provides insights into switching mechanism. Nat Commun 2018; 9:4005. [PMID: 30275448 PMCID: PMC6167325 DOI: 10.1038/s41467-018-06306-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/13/2018] [Indexed: 12/14/2022] Open
Abstract
Multidrug resistance (MDR) poses a major challenge to medicine. A principle cause of MDR is through active efflux by MDR transporters situated in the bacterial membrane. Here we present the crystal structure of the major facilitator superfamily (MFS) drug/H+ antiporter MdfA from Escherichia coli in an outward open conformation. Comparison with the inward facing (drug binding) state shows that, in addition to the expected change in relative orientations of the N- and C-terminal lobes of the antiporter, the conformation of TM5 is kinked and twisted. In vitro reconstitution experiments demonstrate the importance of selected residues for transport and molecular dynamics simulations are used to gain insights into antiporter switching. With the availability of structures of alternative conformational states, we anticipate that MdfA will serve as a model system for understanding drug efflux in MFS MDR antiporters. The multidrug resistance transporter mediated efflux of antibiotics from the bacterial cytoplasm represents a major challenge to medicine. Here authors solve the X-ray crystallographic structure of the drug/H+ antiporter MdfA from Escherichia coli and shed light on the conformational switching mechanism.
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Okai T, Mizutani K, Nakao M, Kajio K, Nishimura S, Ito A, Iwata S, Takahashi Y, Murakami T, Shibata T, Yoshiyama M. P4507The impact of MS with annular calcification for worsening heart failure just after TAVR. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy563.p4507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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72
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Nogly P, Weinert T, James D, Carbajo S, Ozerov D, Furrer A, Gashi D, Borin V, Skopintsev P, Jaeger K, Nass K, Båth P, Bosman R, Koglin J, Seaberg M, Lane T, Kekilli D, Brünle S, Tanaka T, Wu W, Milne C, White T, Barty A, Weierstall U, Panneels V, Nango E, Iwata S, Hunter M, Schapiro I, Schertler G, Neutze R, Standfuss J. Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser. Science 2018; 361:science.aat0094. [PMID: 29903883 DOI: 10.1126/science.aat0094] [Citation(s) in RCA: 221] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/29/2018] [Indexed: 12/23/2022]
Abstract
Ultrafast isomerization of retinal is the primary step in photoresponsive biological functions including vision in humans and ion transport across bacterial membranes. We used an x-ray laser to study the subpicosecond structural dynamics of retinal isomerization in the light-driven proton pump bacteriorhodopsin. A series of structural snapshots with near-atomic spatial resolution and temporal resolution in the femtosecond regime show how the excited all-trans retinal samples conformational states within the protein binding pocket before passing through a twisted geometry and emerging in the 13-cis conformation. Our findings suggest ultrafast collective motions of aspartic acid residues and functional water molecules in the proximity of the retinal Schiff base as a key facet of this stereoselective and efficient photochemical reaction.
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Suzuki N, Takamuku Y, Asakawa T, Inai M, Hino T, Iwata S, Kan T, Murata T. An efficient screening method for purifying and crystallizing membrane proteins using modified clear-native PAGE. Anal Biochem 2018; 548:7-14. [DOI: 10.1016/j.ab.2018.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 01/01/2018] [Accepted: 02/08/2018] [Indexed: 10/18/2022]
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Ono M, Horita S, Sato Y, Nomura Y, Iwata S, Nomura N. Structural basis for tumor necrosis factor blockade with the therapeutic antibody golimumab. Protein Sci 2018; 27:1038-1046. [PMID: 29575262 DOI: 10.1002/pro.3407] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/09/2018] [Accepted: 03/21/2018] [Indexed: 12/29/2022]
Abstract
Tumor necrosis factor α (TNFα) is a proinflammatory cytokine, and elevated levels of TNFα in serum are associated with various autoimmune diseases, including rheumatoid arthritis (RA), ankylosing spondylitis (AS), Crohn's disease (CD), psoriasis, and systemic lupus erythaematosus. TNFα performs its pleiotropic functions by binding to two structurally distinct transmembrane receptors, TNF receptor (TNFR) 1 and TNFR2. Antibody-based therapeutic strategies that block excessive TNFα signaling have been shown to be effective in suppressing such harmful inflammatory conditions. Golimumab (Simponi®) is an FDA-approved fully human monoclonal antibody targeting TNFα that has been widely used for the treatment of RA, AS, and CD. However, the structural basis underlying the inhibitory action of golimumab remains unclear. Here, we report the crystal structure of the Fv fragment of golimumab in complex with TNFα at a resolution of 2.73 Å. The resolved structure reveals that golimumab binds to a distinct epitope on TNFα that does not overlap with the binding residues of TNFR2. Golimumab exerts its inhibitory effect by preventing binding of TNFR1 and TNFR2 to TNFα by steric hindrance. Golimumab does not induce conformational changes in TNFα that could affect receptor binding. This mode of action is specific to golimumab among the four anti-TNFα therapeutic antibodies currently approved for clinical use.
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Iwata S, Saito K, Hirata S, Ohkubo N, Nakayamada S, Nakano K, Hanami K, Kubo S, Miyagawa I, Yoshikawa M, Miyazaki Y, Yoshinari H, Tanaka Y. Efficacy and safety of anti-CD20 antibody rituximab for patients with refractory systemic lupus erythematosus. Lupus 2018; 27:802-811. [DOI: 10.1177/0961203317749047] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Objective We examined the efficacy and safety of rituximab in patients with refractory systemic lupus erythematosus (SLE). Methods The study enrolled 63 SLE patients who were treated with rituximab between 2002 and 2015. The participants underwent a battery of tests before treatment and at one year. Treatment ranged from two to four times at 500 or 1000 mg. Results Baseline characteristics were males:females = 6:57, age 33.9 years, and disease duration 87.2 months. The primary endpoint: The rate of major clinical response (MCR) was 60% while the partial clinical response (PCR) was 25%. Thirty of 36 (83%) patients with lupus nephritis (WHO II: 2, III: 5, IV: 22, V: 4, IV+V: 2, not assessed: 1) and 22 of 24 patients (92%) with neuropsychiatric SLE, who could be followed at one year, showed changes from BILAG A or B score to C or D score at one year. Multivariate analysis identified high anti-dsDNA antibody and shorter disease duration as significant determinants of MCR at one year. Repeat examination was conducted at five years. Primary failure was recorded in 8.8% and secondary failure in 32.4% (time to relapse: 24.4 months). Rituximab was well tolerated although 65 adverse events, mostly infections, were recorded within one year. Conclusion Rituximab is potentially efficacious for the treatment of patients with refractory SLE.
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