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Reinke PYA, Schubert R, Oberthür D, Galchenkova M, Rahmani Mashhour A, Günther S, Chretien A, Round A, Seychell BC, Norton-Baker B, Kim C, Schmidt C, Koua FHM, Tolstikova A, Ewert W, Peña Murillo GE, Mills G, Kirkwood H, Brognaro H, Han H, Koliyadu J, Schulz J, Bielecki J, Lieske J, Maracke J, Knoska J, Lorenzen K, Brings L, Sikorski M, Kloos M, Vakili M, Vagovic P, Middendorf P, de Wijn R, Bean R, Letrun R, Han S, Falke S, Geng T, Sato T, Srinivasan V, Kim Y, Yefanov OM, Gelisio L, Beck T, Doré AS, Mancuso AP, Betzel C, Bajt S, Redecke L, Chapman HN, Meents A, Turk D, Hinrichs W, Lane TJ. SARS-CoV-2 M pro responds to oxidation by forming disulfide and NOS/SONOS bonds. Nat Commun 2024; 15:3827. [PMID: 38714735 PMCID: PMC11076503 DOI: 10.1038/s41467-024-48109-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 04/19/2024] [Indexed: 05/10/2024] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is critical for viral function and a key drug target. Mpro is only active when reduced; turnover ceases upon oxidation but is restored by re-reduction. This suggests the system has evolved to survive periods in an oxidative environment, but the mechanism of this protection has not been confirmed. Here, we report a crystal structure of oxidized Mpro showing a disulfide bond between the active site cysteine, C145, and a distal cysteine, C117. Previous work proposed this disulfide provides the mechanism of protection from irreversible oxidation. Mpro forms an obligate homodimer, and the C117-C145 structure shows disruption of interactions bridging the dimer interface, implying a correlation between oxidation and dimerization. We confirm dimer stability is weakened in solution upon oxidation. Finally, we observe the protein's crystallization behavior is linked to its redox state. Oxidized Mpro spontaneously forms a distinct, more loosely packed lattice. Seeding with crystals of this lattice yields a structure with an oxidation pattern incorporating one cysteine-lysine-cysteine (SONOS) and two lysine-cysteine (NOS) bridges. These structures further our understanding of the oxidative regulation of Mpro and the crystallization conditions necessary to study this structurally.
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Affiliation(s)
- Patrick Y A Reinke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Aida Rahmani Mashhour
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Sebastian Günther
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Anaïs Chretien
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Adam Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Brandon Charles Seychell
- Institute of Physical Chemistry, Department of Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Brenna Norton-Baker
- Max Plank Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Chemistry, University of California at Irvine, Irvine, CA, 92697-2025, USA
| | - Chan Kim
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Faisal H M Koua
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Wiebke Ewert
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Gisel Esperanza Peña Murillo
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Grant Mills
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Henry Kirkwood
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Hévila Brognaro
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, Universität Hamburg, Build. 22a, c/o DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Huijong Han
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Johan Bielecki
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Julia Lieske
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Julia Maracke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | | | - Lea Brings
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marcin Sikorski
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marco Kloos
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Mohammad Vakili
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Patrik Vagovic
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Philipp Middendorf
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Raphael de Wijn
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Richard Bean
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Seonghyun Han
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Sven Falke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Tian Geng
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, CB21 6DG, Cambridge, UK
| | - Tokushi Sato
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Vasundara Srinivasan
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, Universität Hamburg, Build. 22a, c/o DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Yoonhee Kim
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Oleksandr M Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Luca Gelisio
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tobias Beck
- Institute of Physical Chemistry, Department of Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Andrew S Doré
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, CB21 6DG, Cambridge, UK
- CHARM Therapeutics Ltd., B900 Babraham Research Campus, CB22 3AT, Cambridge, UK
| | - Adrian P Mancuso
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- La Trobe Institute for Molecular Science, Department of Chemistry and Physics, La Trobe University, Melbourne, VIC, 3086, Australia
- Diamond Light Source, Harwell Science and Innovation Campus, OX11 0DE, Didcot, UK
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, Universität Hamburg, Build. 22a, c/o DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Saša Bajt
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Lars Redecke
- Institute of Biochemistry, Universität zu Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Dušan Turk
- Jožef Stefan Institute, Jamova cesta 39, 1000, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins Jamova 39, 1000, Ljubljana, Slovenia
| | - Winfried Hinrichs
- Universität Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Thomas J Lane
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany.
- CHARM Therapeutics Ltd., B900 Babraham Research Campus, CB22 3AT, Cambridge, UK.
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2
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Chretien A, Nagel MF, Botha S, de Wijn R, Brings L, Dörner K, Han H, Koliyadu JCP, Letrun R, Round A, Sato T, Schmidt C, Secareanu RC, von Stetten D, Vakili M, Wrona A, Bean R, Mancuso A, Schulz J, Pearson AR, Kottke T, Lorenzen K, Schubert R. Light-induced Trp in/Met out Switching During BLUF Domain Activation in ATP-bound Photoactivatable Adenylate Cyclase OaPAC. J Mol Biol 2024; 436:168439. [PMID: 38185322 DOI: 10.1016/j.jmb.2024.168439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/28/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
The understanding of signal transduction mechanisms in photoreceptor proteins is essential for elucidating how living organisms respond to light as environmental stimuli. In this study, we investigated the ATP binding, photoactivation and signal transduction process in the photoactivatable adenylate cyclase from Oscillatoria acuminata (OaPAC) upon blue light excitation. Structural models with ATP bound in the active site of native OaPAC at cryogenic as well as room temperature are presented. ATP is found in one conformation at cryogenic- and in two conformations at ambient-temperature, and is bound in an energetically unfavorable conformation for the conversion to cAMP. However, FTIR spectroscopic experiments confirm that this conformation is the native binding mode in dark state OaPAC and that transition to a productive conformation for ATP turnover only occurs after light activation. A combination of time-resolved crystallography experiments at synchrotron and X-ray Free Electron Lasers sheds light on the early events around the Flavin Adenine Dinucleotide (FAD) chromophore in the light-sensitive BLUF domain of OaPAC. Early changes involve the highly conserved amino acids Tyr6, Gln48 and Met92. Crucially, the Gln48 side chain performs a 180° rotation during activation, leading to the stabilization of the FAD chromophore. Cryo-trapping experiments allowed us to investigate a late light-activated state of the reaction and revealed significant conformational changes in the BLUF domain around the FAD chromophore. In particular, a Trpin/Metout transition upon illumination is observed for the first time in the BLUF domain and its role in signal transmission via α-helix 3 and 4 in the linker region between sensor and effector domain is discussed.
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Affiliation(s)
- Anaïs Chretien
- European XFEL GmbH, Schenefeld, Germany; Department of Chemistry, Universität Hamburg, Hamburg, Germany
| | - Marius F Nagel
- Department of Chemistry and Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA; Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | | | | | | | | | | | | | | | | | | | | | - David von Stetten
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | | | | | | | | | | | - Arwen R Pearson
- Institute for Nanostructure and Solid-State Physics, Universität Hamburg, Hamburg, Germany
| | - Tilman Kottke
- Department of Chemistry and Medical School OWL, Bielefeld University, Bielefeld, Germany
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3
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Perrett S, Fadini A, Hutchison CDM, Bhattacharya S, Morrison C, Turkot O, Jakobsen MB, Größler M, Licón-Saláiz J, Griese F, Flewett S, Valerio J, Schulz J, Biednov M, Jiang Y, Han H, Yousef H, Khakhulin D, Milne C, Barty A, van Thor JJ. Kilohertz droplet-on-demand serial femtosecond crystallography at the European XFEL station FXE. Struct Dyn 2024; 11:024310. [PMID: 38638699 PMCID: PMC11026113 DOI: 10.1063/4.0000248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/03/2024] [Indexed: 04/20/2024]
Abstract
X-ray Free Electron Lasers (XFELs) allow the collection of high-quality serial femtosecond crystallography data. The next generation of megahertz superconducting FELs promises to drastically reduce data collection times, enabling the capture of more structures with higher signal-to-noise ratios and facilitating more complex experiments. Currently, gas dynamic virtual nozzles (GDVNs) stand as the sole delivery method capable of best utilizing the repetition rate of megahertz sources for crystallography. However, their substantial sample consumption renders their use impractical for many protein targets in serial crystallography experiments. Here, we present a novel application of a droplet-on-demand injection method, which allowed operation at 47 kHz at the European XFEL (EuXFEL) by tailoring a multi-droplet injection scheme for each macro-pulse. We demonstrate a collection rate of 150 000 indexed patterns per hour. We show that the performance and effective data collection rate are comparable to GDVN, with a sample consumption reduction of two orders of magnitude. We present lysozyme crystallographic data using the Large Pixel Detector at the femtosecond x-ray experiment endstation. Significant improvement of the crystallographic statistics was made by correcting for a systematic drift of the photon energy in the EuXFEL macro-pulse train, which was characterized from indexing the individual frames in the pulse train. This is the highest resolution protein structure collected and reported at the EuXFEL at 1.38 Å resolution.
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Affiliation(s)
- Samuel Perrett
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Alisia Fadini
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Sayantan Bhattacharya
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Cade Morrison
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Mads Bregenholt Jakobsen
- Center for Data and Computing in Natural Sciences (CDCS), Notkestrasse 10, D-22607 Hamburg, Germany
| | - Michael Größler
- Center for Data and Computing in Natural Sciences (CDCS), Notkestrasse 10, D-22607 Hamburg, Germany
| | - José Licón-Saláiz
- Center for Data and Computing in Natural Sciences (CDCS), Notkestrasse 10, D-22607 Hamburg, Germany
| | | | - Samuel Flewett
- Center for Data and Computing in Natural Sciences (CDCS), Notkestrasse 10, D-22607 Hamburg, Germany
| | - Joana Valerio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | - Yifeng Jiang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Huijong Han
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Hazem Yousef
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | - Anton Barty
- Center for Data and Computing in Natural Sciences (CDCS), Notkestrasse 10, D-22607 Hamburg, Germany
| | - Jasper J. van Thor
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
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Huang YX, Zou XP, Zhang ZL, Ning K, Luo X, Xiong LB, Peng YL, Zhou ZH, Dong P, Guo SJ, Han H, Zhou FJ. [Relation factor analysis for the short-term preservation of ipsilateral renal function after partial nephrectomy]. Zhonghua Wai Ke Za Zhi 2023; 61:1099-1103. [PMID: 37932147 DOI: 10.3760/cma.j.cn112139-20230228-00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Objectives: To analyze the factors relative to the short-term preservation of ipsilateral renal function after partial nephrectomy. Methods: The clinical data of 83 patients who were treated with partial nephrectomy from December 2014 to December 2019 in the Department of Urology, Sun Yat-sen University Cancer Center were retrospectively analyzed. There were 54 males and 29 females, aging (M (IQR)) 49 (17) years (range: 27 to 74 years). The ischemia time in operation was 25 (18) minutes (range: 10 to 67 minutes). Emission computed tomography scan and CT scan were performed before (within 1 month) and after (3 to 12 months) surgery. The volume of the ipsilateral and contralateral kidney was measured on the basis of preoperative and postoperative CT scans. The glomerular filtration rate (GFR) specifically in each kidney was estimated by emission computed tomography. Recovery from ischemia is determined by the formula: GFR preservation/volume saved×100%. Linear regression was used to explore the factors ralative to the short-term preservation of ipsilateral renal function after partial nephrectomy. Results: The GFR preservation of the ipsilateral kidney was 80.9 (25.2) % (range: 31.0% to 109.4%). The volume loss of the kidney resulted in a decrease of 12.0% (5.8 ml/(min×1.96 m2)) of GFR, while the ischemic injury resulted in a decrease of 6.5% (2.5 ml/(min×1.96 m2)) of GFR. The volume saved from the ipsilateral kidney was 87.1 (12.9) % (range: 27.0% to 131.7%). Recovery from ischemia was 93.5 (17.5) % (range:44.3% to 178.3%). In multivariate analysis, GFR preservation of the ipsilateral kidney was significantly correlated with the volume saved of the ipsilateral kidney (β=0.383, 95%CI: 0.144 to 0.622, P=0.002). It was not related to the ischemia time (β=0.046, 95%CI:-0.383 to 0.475, P=0.831). Conclusion: In the condition of limited ischemic time, in the short term ipsilateral renal function after partial nephrectomy is mainly determined by the loss of kidney volume, while ischemic injury only plays a minor role.
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Affiliation(s)
- Y X Huang
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - X P Zou
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Z L Zhang
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - K Ning
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - X Luo
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - L B Xiong
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Y L Peng
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Z H Zhou
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - P Dong
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - S J Guo
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - H Han
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - F J Zhou
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
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5
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Zou XP, Ning K, Zhang ZL, Zou L, Xiong LB, Peng YL, Zhou ZH, Liu HM, Yu CP, Dong P, Guo SJ, Han H, Zhou FJ. [Long-term survival analysis of 1 367 patients treated with radical nephrectomy from a single center]. Zhonghua Zhong Liu Za Zhi 2023; 45:981-987. [PMID: 37968085 DOI: 10.3760/cma.j.cn112152-20220614-00420] [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] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
Objective: To report the long-term survival of renal cell carcinoma (RCC) patients treated with radical nephrectomy in Sun Yat-sen University Cancer Center. Methods: We retrospectively analyzed the clinical, pathological and follow-up records of 1 367 non-metastatic RCC patients treated with radical nephrectomy from 1999 to 2020 in this center. The primary endpoint of this study was overall survival rate. Survival curves were estimated using the Kaplan-Meier method, and group differences were compared through Log-rank test. Univariate and multivariate Cox analysis were fit to determine the clinical and pathological features associated with overall survival rate. Results: A total of 1 367 patients treated with radical nephrectomy with complete follow-up data were included in the study. The median follow-up time was 52.6 months, and 1 100 patients survived and 267 died, with the median time to overall survival not yet reached. The 5-year and 10-year overall survival rates were 82.8% and 74.9%, respectively. The 5-year and 10-year overall survival rates of Leibovich low-risk patients were 93.3% and 88.2%, respectively; of Leibovich intermediate-risk patients were 82.2% and 72.3%, respectively; and of Leibovich high-risk patients were 50.5% and 30.2%, respectively. There were significant differences in the long-term survival among the three groups (P<0.001). The 10-year overall survival rates for patients with pT1, pT2, pT3 and pT4 RCC were 83.2%, 73.6%, 55.0% and 31.4%, respectively. There were significant differences among pT1, pT2, pT3 and pT4 patients(P<0.001). The 5-year and 10-year overall survival rates of patients with lymph node metastasis were 48.5% and 35.6%, respectively, and those of patients without lymph node metastasis were 85.1% and 77.5%, respectively. There was significant difference in the long-term survival between patients with lymph node metastasis and without lymph node metastasis. The 10-year overall survival rate was 96.2% for nuclear Grade 1, 81.6% for nuclear Grade 2, 60.5% for nuclear Grade 3, and 43.4% for nuclear Grade 4 patients. The difference was statistically significant. There was no significant difference in the long-term survival between patients with localized renal cancer (pT1-2N0M0) who underwent open surgery and minimally invasive surgery (10-year overall survival rate 80.5% vs 85.6%, P=0.160). Multivariate Cox analysis showed that age≥55 years (HR=2.11, 95% CI: 1.50-2.96, P<0.001), T stage(T3+ T4 vs T1a: HR=2.37, 95% CI: 1.26-4.46, P=0.008), local lymph node metastasis (HR=3.04, 95%CI: 1.81-5.09, P<0.001), nuclear grade (G3-G4 vs G1: HR=4.21, 95%CI: 1.51-11.75, P=0.006), tumor necrosis (HR=1.66, 95% CI: 1.17-2.37, P=0.005), sarcomatoid differentiation (HR=2.39, 95% CI: 1.31-4.35, P=0.005) and BMI≥24kg/m(2) (HR=0.56, 95%CI: 0.39-0.80, P=0.001) were independent factors affecting long-term survival after radical nephrectomy. Conclusions: The long-term survival of radical nephrectomy in patients with renal cell carcinoma is satisfactory. Advanced age, higher pathological stage and grade, tumor necrosis and sarcomatoid differentiation were the main adverse factors affecting the prognosis of patients. Higher body mass index was a protective factor for the prognosis of patients.
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Affiliation(s)
- X P Zou
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - K Ning
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Z L Zhang
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - L Zou
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - L B Xiong
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Y L Peng
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Z H Zhou
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - H M Liu
- Department of Imaging, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - C P Yu
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - P Dong
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - S J Guo
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - H Han
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - F J Zhou
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
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6
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Lima FA, Otte F, Vakili M, Ardana-Lamas F, Biednov M, Dall’Antonia F, Frankenberger P, Gawelda W, Gelisio L, Han H, Huang X, Jiang Y, Kloos M, Kluyver T, Knoll M, Kubicek K, Bermudez Macias IJ, Schulz J, Turkot O, Uemura Y, Valerio J, Wang H, Yousef H, Zalden P, Khakhulin D, Bressler C, Milne C. Experimental capabilities for liquid jet samples at sub-MHz rates at the FXE Instrument at European XFEL. J Synchrotron Radiat 2023; 30:1168-1182. [PMID: 37860937 PMCID: PMC10624029 DOI: 10.1107/s1600577523008159] [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] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023]
Abstract
The Femtosecond X-ray Experiments (FXE) instrument at the European X-ray Free-Electron Laser (EuXFEL) provides an optimized platform for investigations of ultrafast physical, chemical and biological processes. It operates in the energy range 4.7-20 keV accommodating flexible and versatile environments for a wide range of samples using diverse ultrafast X-ray spectroscopic, scattering and diffraction techniques. FXE is particularly suitable for experiments taking advantage of the sub-MHz repetition rates provided by the EuXFEL. In this paper a dedicated setup for studies on ultrafast biological and chemical dynamics in solution phase at sub-MHz rates at FXE is presented. Particular emphasis on the different liquid jet sample delivery options and their performance is given. Our portfolio of high-speed jets compatible with sub-MHz experiments includes cylindrical jets, gas dynamic virtual nozzles and flat jets. The capability to perform multi-color X-ray emission spectroscopy (XES) experiments is illustrated by a set of measurements using the dispersive X-ray spectrometer in von Hamos geometry. Static XES data collected using a multi-crystal scanning Johann-type spectrometer are also presented. A few examples of experimental results on ultrafast time-resolved X-ray emission spectroscopy and wide-angle X-ray scattering at sub-MHz pulse repetition rates are given.
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Affiliation(s)
- F. A. Lima
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - F. Otte
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Fakultät für Physik, Technical University Dortmund, Dortmund, Germany
| | - M. Vakili
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - M. Biednov
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | - W. Gawelda
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Faculty of Physics, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - L. Gelisio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - H. Han
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - X. Huang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Y. Jiang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - M. Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - T. Kluyver
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - M. Knoll
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - K. Kubicek
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- The Hamburg Centre for Ultrafast Imaging, 22761 Hamburg, Germany
- Institut für Experimentalphysik, Universität Hamburg, 22607 Hamburg, Germany
| | | | - J. Schulz
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - O. Turkot
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Y. Uemura
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - J. Valerio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - H. Wang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - H. Yousef
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - P. Zalden
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - D. Khakhulin
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - C. Bressler
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- The Hamburg Centre for Ultrafast Imaging, 22761 Hamburg, Germany
- Institut für Experimentalphysik, Universität Hamburg, 22607 Hamburg, Germany
| | - C. Milne
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
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7
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Son HJ, Bae S, Cho K, Park I, Kim J, Han H, Kim EO, Jung J, Kim SH, Lee SO. Impact of carbapenem-targeted antimicrobial stewardship interventions: an interrupted time-series analysis. J Hosp Infect 2023; 140:132-138. [PMID: 37544365 DOI: 10.1016/j.jhin.2023.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 08/08/2023]
Abstract
BACKGROUND The development of carbapenem-resistant Gram-negative bacilli (CR-GNB) is largely favoured by indiscriminate and prolonged carbapenem use, which is a significant contributing factor. AIM To evaluate the impact of two carbapenem antibiotic stewardship programme interventions on both carbapenem prescriptions and the clinical isolation rates of CR-GNBs, using interrupted time-series analysis. METHODS A time-series analysis was performed using data for carbapenem usage from a tertiary hospital in South Korea from January 2017 to July 2022. Two carbapenem antibiotic stewardship programme interventions were implemented sequentially: (i) a prospective audit and feedback (PAF) from November 2018 to April 2020 (intervention 1), and (ii) preauthorization from May 2020 to August 2020 (intervention 2). Monthly carbapenem usage and incidence of CR-GNB before and after each intervention were compared using an autoregressive integrated moving average model. FINDINGS Implementation of PAF resulted in a significant reduction in carbapenem consumption, followed by an additional decrease after the preauthorization was implemented. The incidence of carbapenem-resistant Escherichia coli and Klebsiella pneumoniae increased after intervention 1, but there was a significant change from an increasing trend to a stationary trend after intervention 2. The incidence of carbapenem-resistant Pseudomonas aeruginosa, which had increased during the baseline period, became stationary after intervention 1. A significant decrease was observed in the incidence of carbapenem-resistant Acinetobacter baumannii during the implementation of intervention 1 and 2. CONCLUSION This study emphasizes the importance of adopting comprehensive antibiotic management and rigorous infection control to prevent infections caused by antibiotic-resistant bacteria.
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Affiliation(s)
- H-J Son
- Department of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea; Department of Infectious Diseases, Uijeongbu Eulji Medical Center, Eulji University School of Medicine, Uijeongbu, South Korea
| | - S Bae
- Department of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea; Antibiotic Support Team, Asan Medical Center, Seoul, South Korea
| | - K Cho
- Department of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea; Antibiotic Support Team, Asan Medical Center, Seoul, South Korea
| | - I Park
- Department of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea; Antibiotic Support Team, Asan Medical Center, Seoul, South Korea
| | - J Kim
- Department of Pharmacy, Asan Medical Center, Seoul, South Korea
| | - H Han
- Department of Pharmacy, Asan Medical Center, Seoul, South Korea
| | - E O Kim
- Office for Infection Control, Asan Medical Center, Seoul, South Korea
| | - J Jung
- Department of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea; Office for Infection Control, Asan Medical Center, Seoul, South Korea
| | - S-H Kim
- Department of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea; Office for Infection Control, Asan Medical Center, Seoul, South Korea
| | - S-O Lee
- Department of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea; Antibiotic Support Team, Asan Medical Center, Seoul, South Korea.
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8
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Wang J, Wei WS, Jiang LJ, Zhang ZL, Guo SJ, Han H, Zhou FJ, Dong P. [Efficacy and safety evaluation of immunotherapy combined with targeted therapy as second-line treatment in patients with metastatic non-clear cell renal cell carcinoma]. Zhonghua Zhong Liu Za Zhi 2023; 45:704-708. [PMID: 37580277 DOI: 10.3760/cma.j.cn112152-20220330-00220] [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] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Objective: This study aimed to evaluate the efficacy and safety of programmed death-1 (PD-1) inhibitor combined tyrosine kinase inhibitor (TKI) therapy versus TKI monotherapy as the second-line regimen for patients with metastatic non-clear cell renal carcinoma (nccRCC) who failed first-line TKI therapy. Methods: The clinicopathological data of 67 patients with metastatic nccRCC who failed first-line TKI therapy between October 2011 and September 2020 were retrospectively analyzed, including 22 patients who received TKI monotherapy and 45 patients who received TKI plus PD-1 inhibitor as the second-line therapy. The efficacy was assessed according to Response Evaluation Criteria in Solid Tumors version 1.0/1.1 (RECIST 1.0/1.1), the Kaplan-Meier method was used to plot the survival curves, and the Log rank test was used to analyze the differences in the survival between the two groups. Treatment-related adverse events (AEs) after treatment were observed in both groups. Results: The overall objective response rate (ORR) and disease control rate (DCR) were 37.3% (25/67) and 56.7% (38/67), respectively. The overall second-line progression-free survival (PFS) was 7.7 months and Overall Survival (OS) was 25.2 months. The ORR and DCR of patients in the combination therapy group were 48.9% (22/45) and 71.1% (32/45), respectively, which were significantly improved compared with the TKI monotherapy group [13.6% (3/22) and 27.3% (6/22), respectively] (P=0.007 and P=0.001, respectively). The median PFS of 9.2 months for second-line treatment was longer in patients in the combination therapy group than in the TKI monotherapy group (5.2 months, P=0.001), but the median OS was not statistically different between the two groups (28.2 months vs 20.8 months, P=0.068). Common treatment-related AEs included hypertension, diarrhea, fatigue, stomatitis, hand-foot syndrome, and hypothyroidism. The incidence of hypothyroidism was higher in the combination therapy group [40.0% (18/45)] than in the TKI monotherapy group [22.7% (5/22), P=0.044]; the incidence of other treatment-related AEs between the two groups were not statistically significant (all P>0.05). Conclusion: Immune-targeted combination therapy was more effective than TKI monotherapy alone and was well tolerated in the treatment of metastatic nccRCC patients who failed first-line TKIs.
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Affiliation(s)
- J Wang
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - W S Wei
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - L J Jiang
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Z L Zhang
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - S J Guo
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - H Han
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - F J Zhou
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - P Dong
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
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9
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Xiong LB, Zou XP, Ning K, Luo X, Peng YL, Zhou ZH, Wang J, Li Z, Yu CP, Dong P, Guo SJ, Han H, Zhou FJ, Zhang ZL. [Establishment and validation of a novel nomogram to predict overall survival after radical nephrectomy]. Zhonghua Zhong Liu Za Zhi 2023; 45:681-689. [PMID: 37580273 DOI: 10.3760/cma.j.cn112152-20221027-00722] [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] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Objective: To establish a nomogram prognostic model for predicting the 5-, 10-, and 15-year overall survival (OS) of non-metastatic renal cell carcinoma patients managed with radical nephrectomy (RN), compare the modelled results with the results of pure pathologic staging, the Karakiewicz nomogram and the Mayo Clinic Stage, Size, Grade, and Necrosis (SSIGN) score commonly used in foreign countries, and stratify the patients into different prognostic risk subgroups. Methods: A total of 1 246 non-metastatic renal cell carcinoma patients managed with RN in Sun Yat-sen University Cancer Center (SYSUCC) from 1999 to 2020 were retrospectively analyzed. Multivariate Cox regression analysis was used to screen the variables that influence the prognosis for nomogram establishment, and the bootstrap random sampling was used for internal validation. The time-receiver operating characteristic curve (ROC), the calibration curve and the clinical decision curve analysis (DCA) were applied to evaluate the nomogram. The prediction efficacy of the nomogram and that of the pure pathologic staging, the Karakiewicz nomogram and the SSIGN score was compared through the area under the curve (AUC). Finally, patients were stratified into different risk subgroups according to our nomogram scores. Results: A total of 1 246 patients managed with RN were enrolled in this study. Multivariate Cox regression analysis showed that age, smoking history, pathological nuclear grade, sarcomatoid differentiation, tumor necrosis and pathological T and N stages were independent prognostic factors for RN patients (all P<0.05). A nomogram model named SYSUCC based on these factors was built to predict the 5-, 10-, and 15-year survival rate of the participating patients. In the bootstrap random sampling with 1 000 iterations, all these factors occurred for more than 800 times as independent predictors. The Harrell's concordance index (C-index) of SYSUCC was higher compared with pure pathological staging [0.770 (95% CI: 0.716-0.823) vs 0.674 (95% CI: 0.621-0.728)]. The calibration curve showed that the survival rate as predicted by the SYSUCC model simulated the actual rate, while the clinical DCA showed that the SYSUCC nomogram has a benefit in certain probability ranges. In the ROC analysis that included 857 patients with detailed pathological nuclear stages, the nomogram had a larger AUC (5-/10-year AUC: 0.823/0.804) and better discriminating ability than pure pathological staging (5-/10-year AUC: 0.701/0.658), Karakiewicz nomogram (5-/10-year AUC: 0.772/0.734) and SSIGN score (5-/10-year AUC: 0.792/0.750) in predicting the 5-/10-year OS of RN patients (all P<0.05). In addition, the AUC of the SYSUCC nomogram for predicting the 15-year OS (0.820) was larger than that of the SSIGN score (0.709), and there was no statistical difference (P<0.05) between the SYSUCC nomogram, pure pathological staging (0.773) and the Karakiewicz nomogram (0.826). The calibration curve was close to the standard curve, which indicated that the model has good predictive performance. Finally, patients were stratified into low-, intermediate-, and high-risk subgroups (738, 379 and 129, respectively) according to the SYSUCC nomogram scores, among whom patients in intermediate- and high-risk subgroups had a worse OS than patients in the low-risk subgroup (intermediate-risk group vs. low-risk group: HR=4.33, 95% CI: 3.22-5.81, P<0.001; high-risk group vs low-risk group: HR=11.95, 95% CI: 8.29-17.24, P<0.001), and the high-risk subgroup had a worse OS than the intermediate-risk group (HR=2.63, 95% CI: 1.88-3.68, P<0.001). Conclusions: Age, smoking history, pathological nuclear grade, sarcomatoid differentiation, tumor necrosis and pathological stage were independent prognostic factors for non-metastasis renal cell carcinoma patients after RN. The SYSUCC nomogram based on these independent prognostic factors can better predict the 5-, 10-, and 15-year OS than pure pathological staging, the Karakiewicz nomogram and the SSIGN score of patients after RN. In addition, the SYSUCC nomogram has good discrimination, agreement, risk stratification and clinical application potential.
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Affiliation(s)
- L B Xiong
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - X P Zou
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - K Ning
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - X Luo
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Y L Peng
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Z H Zhou
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - J Wang
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Z Li
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - C P Yu
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - P Dong
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - S J Guo
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - H Han
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - F J Zhou
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Z L Zhang
- Department of Urology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
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10
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Aleksich M, Paley DW, Schriber EA, Linthicum W, Oklejas V, Mittan-Moreau DW, Kelly RP, Kotei PA, Ghodsi A, Sierra RG, Aquila A, Poitevin F, Blaschke JP, Vakili M, Milne CJ, Dall'Antonia F, Khakhulin D, Ardana-Lamas F, Lima F, Valerio J, Han H, Gallo T, Yousef H, Turkot O, Bermudez Macias IJ, Kluyver T, Schmidt P, Gelisio L, Round AR, Jiang Y, Vinci D, Uemura Y, Kloos M, Hunter M, Mancuso AP, Huey BD, Parent LR, Sauter NK, Brewster AS, Hohman JN. XFEL Microcrystallography of Self-Assembling Silver n-Alkanethiolates. J Am Chem Soc 2023; 145:17042-17055. [PMID: 37524069 DOI: 10.1021/jacs.3c02183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
New synthetic hybrid materials and their increasing complexity have placed growing demands on crystal growth for single-crystal X-ray diffraction analysis. Unfortunately, not all chemical systems are conducive to the isolation of single crystals for traditional characterization. Here, small-molecule serial femtosecond crystallography (smSFX) at atomic resolution (0.833 Å) is employed to characterize microcrystalline silver n-alkanethiolates with various alkyl chain lengths at X-ray free electron laser facilities, resolving long-standing controversies regarding the atomic connectivity and odd-even effects of layer stacking. smSFX provides high-quality crystal structures directly from the powder of the true unknowns, a capability that is particularly useful for systems having notoriously small or defective crystals. We present crystal structures of silver n-butanethiolate (C4), silver n-hexanethiolate (C6), and silver n-nonanethiolate (C9). We show that an odd-even effect originates from the orientation of the terminal methyl group and its role in packing efficiency. We also propose a secondary odd-even effect involving multiple mosaic blocks in the crystals containing even-numbered chains, identified by selected-area electron diffraction measurements. We conclude with a discussion of the merits of the synthetic preparation for the preparation of microdiffraction specimens and compare the long-range order in these crystals to that of self-assembled monolayers.
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Affiliation(s)
- Mariya Aleksich
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Daniel W Paley
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Elyse A Schriber
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Will Linthicum
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Vanessa Oklejas
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - David W Mittan-Moreau
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ryan P Kelly
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Patience A Kotei
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Anita Ghodsi
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Frédéric Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Johannes P Blaschke
- National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | | | | | | | | | | | | | - Joana Valerio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Huijong Han
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Tamires Gallo
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- MAX IV Laboratory, Lund University, Box 118, SE-22100 Lund, Sweden
| | - Hazem Yousef
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | | | | | - Luca Gelisio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Adam R Round
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Yifeng Jiang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Doriana Vinci
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Yohei Uemura
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Marco Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Mark Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe University, Melbourne 3086, Australia
- Diamond Light Source, Harwell Science & Innovation Campus, Oxfordshire OX11 0DE, U.K
| | - Bryan D Huey
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Materials Science and Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Lucas R Parent
- Innovation Partnership Building, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - J Nathan Hohman
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
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11
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Vakili M, Han H, Schmidt C, Wrona A, Kloos M, de Diego I, Dörner K, Geng T, Kim C, Koua FHM, Melo DVM, Rappas M, Round A, Round E, Sikorski M, Valerio J, Zhou T, Lorenzen K, Schulz J. Mix-and-extrude: high-viscosity sample injection towards time-resolved protein crystallography. J Appl Crystallogr 2023; 56:1038-1045. [PMID: 37555221 PMCID: PMC10405586 DOI: 10.1107/s1600576723004405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/21/2023] [Indexed: 08/10/2023] Open
Abstract
Time-resolved crystallography enables the visualization of protein molecular motion during a reaction. Although light is often used to initiate reactions in time-resolved crystallography, only a small number of proteins can be activated by light. However, many biological reactions can be triggered by the interaction between proteins and ligands. The sample delivery method presented here uses a mix-and-extrude approach based on 3D-printed microchannels in conjunction with a micronozzle. The diffusive mixing enables the study of the dynamics of samples in viscous media. The device design allows mixing of the ligands and protein crystals in 2 to 20 s. The device characterization using a model system (fluorescence quenching of iq-mEmerald proteins by copper ions) demonstrated that ligand and protein crystals, each within lipidic cubic phase, can be mixed efficiently. The potential of this approach for time-resolved membrane protein crystallography to support the development of new drugs is discussed.
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Affiliation(s)
| | - Huijong Han
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | | | | | - Marco Kloos
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | - Iñaki de Diego
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | | | - Tian Geng
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Chan Kim
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | | | | | - Mathieu Rappas
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Adam Round
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | | | | | - Joana Valerio
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | - Tiankun Zhou
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom
| | | | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
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12
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Kalkan Ö, Kantamneni S, Brings L, Han H, Bean R, Mancuso AP, Koua FHM. Heterologous expression, purification and structural features of native Dictyostelium discoideum dye-decolorizing peroxidase bound to a natively incorporated heme. Front Chem 2023; 11:1220543. [PMID: 37593106 PMCID: PMC10427876 DOI: 10.3389/fchem.2023.1220543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/20/2023] [Indexed: 08/19/2023] Open
Abstract
The Dictyostelium discoideum dye-decolorizing peroxidase (DdDyP) is a newly discovered peroxidase, which belongs to a unique class of heme peroxidase family that lacks homology to the known members of plant peroxidase superfamily. DdDyP catalyzes the H2O2-dependent oxidation of a wide-spectrum of substrates ranging from polycyclic dyes to lignin biomass, holding promise for potential industrial and biotechnological applications. To study the molecular mechanism of DdDyP, highly pure and functional protein with a natively incorporated heme is required, however, obtaining a functional DyP-type peroxidase with a natively bound heme is challenging and often requires addition of expensive biosynthesis precursors. Alternatively, a heme in vitro reconstitution approach followed by a chromatographic purification step to remove the excess heme is often used. Here, we show that expressing the DdDyP peroxidase in ×2 YT enriched medium at low temperature (20°C), without adding heme supplement or biosynthetic precursors, allows for a correct native incorporation of heme into the apo-protein, giving rise to a stable protein with a strong Soret peak at 402 nm. Further, we crystallized and determined the native structure of DdDyP at a resolution of 1.95 Å, which verifies the correct heme binding and its geometry. The structural analysis also reveals a binding of two water molecules at the distal site of heme plane bridging the catalytic residues (Arg239 and Asp149) of the GXXDG motif to the heme-Fe(III) via hydrogen bonds. Our results provide new insights into the geometry of native DdDyP active site and its implication on DyP catalysis.
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Affiliation(s)
- Özlem Kalkan
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul, Türkiye
| | | | - Lea Brings
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
| | - Huijong Han
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
| | - Richard Bean
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
| | - Adrian P. Mancuso
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, United Kingdom
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13
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Shang S, He Z, Hou W, Chen X, Zhao X, Han H, Chen S, Yang S, Tai F. Molecular cloning, expression analysis and functional characterization of chicken cytochrome P450 27A1: A novel mitochondrial vitamin D 3 25-hydroxylase. Poult Sci 2023; 102:102747. [PMID: 37276702 PMCID: PMC10258509 DOI: 10.1016/j.psj.2023.102747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/05/2023] [Accepted: 04/19/2023] [Indexed: 06/07/2023] Open
Abstract
Vitamin D3 is hydroxylated by cytochrome P450 (CYP) before exerting biological effects. The chicken CYP involved in vitamin D3 25-hydroxylation has yet to be cloned, and little is known about its functional characteristics, tissue distribution, and cellular expression. We identified a novel, full-length CYP27A1 gene cloned from chicken hepatocyte cDNA that encodes a putative protein of 518 amino acids. Swiss modeling revealed that chicken CYP27A1 has a classic open-fold form. Multisequence homology alignment determined that CYP27A1 contains conserved motifs for substrate recognition and binding. Quantitative real-time PCR analysis in 2-mo-old Partridge Shank broilers demonstrated that CYP27A1 mRNA levels were highest in the liver, followed by the thigh muscles, the breast muscles, and kidneys. The transcripts of CYP27A1 in breast muscles were significantly higher in males than in females. A subcellular localization analysis demonstrated that CYP27A1 was mainly expressed in the mitochondria. In vitro enzyme assays suggested that recombinant CYP27A1 hydroxylates vitamin D3 at the C-25 position to form 25-hydroxyvitamin D3 (25(OH)D3). The Km and Vmax values for CYP27A1-dependent vitamin D3 25-hydroxylation were estimated to be 4.929 μM and 0.389 mol min-1 mg-1 protein, respectively. In summary, these results suggest that CYP27A1 encodes a mitochondrial CYP that plays an important physiologic role in the 25-hydroxylation of vitamin D3 in chickens, providing novel insights into vitamin D3 metabolism in this species.
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Affiliation(s)
- S Shang
- Shaanxi Province Key Laboratory of Bio-Resources, Shaanxi University of Technology, Hanzhong, China; Institute of Brain and Behavioral Sciences, College of Life Sciences, Shaanxi Normal University, Xi'an, China; Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), Hanzhong, China; Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, China
| | - Z He
- Institute of Brain and Behavioral Sciences, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - W Hou
- Institute of Brain and Behavioral Sciences, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - X Chen
- Shaanxi Province Key Laboratory of Bio-Resources, Shaanxi University of Technology, Hanzhong, China
| | - X Zhao
- Hanzhong Central Hospital, Hanzhong, China
| | - H Han
- Shaanxi Province Key Laboratory of Bio-Resources, Shaanxi University of Technology, Hanzhong, China
| | - S Chen
- Shaanxi Province Key Laboratory of Bio-Resources, Shaanxi University of Technology, Hanzhong, China
| | - S Yang
- Shaanxi Province Key Laboratory of Bio-Resources, Shaanxi University of Technology, Hanzhong, China
| | - F Tai
- Institute of Brain and Behavioral Sciences, College of Life Sciences, Shaanxi Normal University, Xi'an, China.
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14
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Zhang X, Feng G, Han H, Dong B, Yang Y, Zhu H, Fan S, Tang H. 39P Preliminary clinical investigations and mechanism exploration of furmonertinib in NSCLC with EGFR exon 20 insertion. J Thorac Oncol 2023. [DOI: 10.1016/s1556-0864(23)00293-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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15
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Zou XP, Ning K, Zhang ZL, Xiong LB, Peng YL, Zhou ZH, Huang YX, Luo X, Li JB, Dong P, Guo SJ, Han H, Zhou FJ. [Efficacy of partial nephrectomy in patients with localized renal carcinoma: a 20-year experience of 2 046 patients in a single center]. Zhonghua Wai Ke Za Zhi 2023; 61:395-402. [PMID: 36987674 DOI: 10.3760/cma.j.cn112139-20221002-00416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Objectives: To analyze the long-term survival of patients with localized renal cell carcinoma after partical nephrectomy. Methods: The clinicopathological records and survival follow-up data of 2 046 patients with localized renal cell carcinoma, who were treated with partial nephrectomy from August 2001 to February 2021 in the Department of Urology, Sun Yat-sen University Cancer Center, were retrospectively analyzed. There were 1 402 males and 644 females, aged (M(IQR)) 51 (19) years (range: 6 to 86 years). The primary end point of this study was cancer-specific survival. Survival curves were estimated using the Kaplan-Meier method, and the difference test was performed by Log-rank test. Univariate and multivariate Cox analysis were fitted to determine factors associated with cancer-specific survival. Results: The follow-up time was 49.2 (48.0) months (range: 1 to 229 months), with 1 974 patients surviving and 72 dying. The median cancer-specific survival time has not yet been reached. The 5- and 10-year cancer specific survival rates were 97.0% and 91.2%, respectively. The 10-year cancer-specific survival rates for stage pT1a (n=1 447), pT1b (n=523) and pT2 (n=58) were 95.3%, 81.8%, and 81.7%, respectively. The 10-year cancer-specific survival rates of patients with nuclear grade 1 (n=226), 2 (n=1 244) and 3 to 4 (n=278) were 96.6%, 89.4%, and 85.5%, respectively. There were no significant differences in 5-year cancer-specific survival rates among patients underwent open, laparoscopic, or robotic surgery (96.7% vs. 97.1% vs. 97.5%, P=0.600). Multivariate analysis showed that age≥50 years (HR=3.93, 95%CI: 1.82 to 8.47, P<0.01), T stage (T1b vs. T1a: HR=3.31, 95%CI: 1.83 to 5.99, P<0.01; T2+T3 vs. T1a: HR=2.88, 95%CI: 1.00 to 8.28, P=0.049) and nuclear grade (G3 to 4 vs. G1: HR=2.81, 95%CI: 1.01 to 7.82, P=0.048) were independent prognostic factors of localized renal cell carcinoma after partial nephrectomy. Conclusions: The long-term cancer-specific survival rates of patients with localized renal cancer after partial nephrectomy are satisfactory. The type of operation (open, laparoscopic, or robotic) has no significant effect on survival. However, patients with older age, higher nuclear grade, and higher T stage have a lower cancer-specific survival rate. Grasping surgical indications, attaching importance to preoperative evaluation, perioperative management, and postoperative follow-up, could benefit achieving satisfactory long-term survival.
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Affiliation(s)
- X P Zou
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - K Ning
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Z L Zhang
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - L B Xiong
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Y L Peng
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Z H Zhou
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Y X Huang
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - X Luo
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - J B Li
- Department of Clinical Research, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - P Dong
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - S J Guo
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - H Han
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - F J Zhou
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
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Han H, Yu JG, Yan H. [Research progress on signaling pathways related to drug research in proliferative vitreoretinopathy]. Zhonghua Yan Ke Za Zhi 2023; 59:225-230. [PMID: 36860112 DOI: 10.3760/cma.j.cn112142-20221117-00589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Proliferative vitreoretinopathy (PVR) is an avascular fibroproliferative disease that occurs in the retina. The main pathological changes are the proliferation and traction of retinal pigment epithelial cells (RPE) and glial cells on the vitreous and retina. Basic research has confirmed that the formation of PVR is related to multiple signaling pathways, including NK-κB signaling pathway, MAPK and its downstream signaling pathways, JAK/STAT signaling pathway, PI3K/Akt signaling pathway, thrombin and its receptor pathway, TGF-β and downstream signaling pathway, North signaling pathway and Wnt/β-catenin signaling pathway, etc. This review summarizes the research progress of the main signaling pathways in the formation mechanism of PVR, and provides the basis and support for the research of PVR drug therapy.
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Affiliation(s)
- H Han
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin Key Laboratory of Ocular Trauma, Tianjin 300052, China
| | - J G Yu
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin Key Laboratory of Ocular Trauma, Tianjin 300052, China
| | - H Yan
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin Key Laboratory of Ocular Trauma, Tianjin 300052, China
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Li Z, Xue T, Jietian J, Xiong L, Wei L, Guo S, Han H. Infiltrating pattern and prognostic value of tertiary lymphoid structures, and predicting the efficacy of anti-PD-1 combination therapy in patients with penile cancer. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00675-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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18
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Zhang X, Feng G, Han H, Dong B, Yang Y, Zhu H, Fan S, Tang H. 48P Efficacy analysis and mechanism exploration of furmonertinib for advanced NSCLC with EGFR exon 20 insertion mutation. ESMO Open 2023. [DOI: 10.1016/j.esmoop.2023.100906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
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19
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Li Y, Han H, Fu M, Zhou X, Ye J, Xu F, Zhang W, Liao Y, Yang X. Genome-wide identification and expression analysis of NAC family genes in Ginkgo biloba L. Plant Biol (Stuttg) 2023; 25:107-118. [PMID: 36377299 DOI: 10.1111/plb.13486] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
NAC (NAM, ATAF, CUC2) transcription factors constitute one of the largest families of plant-specific transcription factors with important roles in plant growth and development and in biotic and abiotic stresses. The physicochemical properties, gene structure, cis-acting elements and expression patterns of NAC transcription factors in Ginkgo biloba were analysed using bioinformatics, and expression of this gene family was analysed via quantitative reverse transcription PCR. The family of G. biloba NAC transcription factors had 50 members, distributed on 12 chromosomes and divided into 11 groups. Members in the same group share a similar gene structure and motif distribution. Transcriptome data analysis of G. biloba showed that 35 genes were expressed in eight tissues. Correlation analysis suggested that GbNAC007 and GNAC008 might be involved in flavonoid biosynthesis. Expression levels of 12 GbNACs under cold, het, and salt stresses were analysed. Results indicate that NAC transcription factors play an important role in response to abiotic stresses. This study provides a reference for the functional analysis of the G. biloba family of NAC transcription factors, as well as a resource for studies on the involvement of this family in responses to abiotic stresses and flavonoid biosynthesis.
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Affiliation(s)
- Y Li
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - H Han
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - M Fu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - X Zhou
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - J Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - F Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - W Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Y Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - X Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
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20
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Sonker M, Doppler D, Egatz-Gomez A, Zaare S, Rabbani MT, Manna A, Cruz Villarreal J, Nelson G, Ketawala GK, Karpos K, Alvarez RC, Nazari R, Thifault D, Jernigan R, Oberthür D, Han H, Sierra R, Hunter MS, Batyuk A, Kupitz CJ, Sublett RE, Poitevin F, Lisova S, Mariani V, Tolstikova A, Boutet S, Messerschmidt M, Meza-Aguilar JD, Fromme R, Martin-Garcia JM, Botha S, Fromme P, Grant TD, Kirian RA, Ros A. Electrically stimulated droplet injector for reduced sample consumption in serial crystallography. Biophys Rep (N Y) 2022; 2:100081. [PMID: 36425668 PMCID: PMC9680787 DOI: 10.1016/j.bpr.2022.100081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
With advances in X-ray free-electron lasers (XFELs), serial femtosecond crystallography (SFX) has enabled the static and dynamic structure determination for challenging proteins such as membrane protein complexes. In SFX with XFELs, the crystals are typically destroyed after interacting with a single XFEL pulse. Therefore, thousands of new crystals must be sequentially introduced into the X-ray beam to collect full data sets. Because of the serial nature of any SFX experiment, up to 99% of the sample delivered to the X-ray beam during its "off-time" between X-ray pulses is wasted due to the intrinsic pulsed nature of all current XFELs. To solve this major problem of large and often limiting sample consumption, we report on improvements of a revolutionary sample-saving method that is compatible with all current XFELs. We previously reported 3D-printed injection devices coupled with gas dynamic virtual nozzles (GDVNs) capable of generating samples containing droplets segmented by an immiscible oil phase for jetting crystal-laden droplets into the path of an XFEL. Here, we have further improved the device design by including metal electrodes inducing electrowetting effects for improved control over droplet generation frequency to stimulate the droplet release to matching the XFEL repetition rate by employing an electrical feedback mechanism. We report the improvements in this electrically triggered segmented flow approach for sample conservation in comparison with a continuous GDVN injection using the microcrystals of lysozyme and 3-deoxy-D-manno-octulosonate 8-phosphate synthase and report the segmented flow approach for sample injection applied at the Macromolecular Femtosecond Crystallography instrument at the Linear Coherent Light Source for the first time.
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Affiliation(s)
- Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Diandra Doppler
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Sahba Zaare
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Mohammad T. Rabbani
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Abhik Manna
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Gihan K. Ketawala
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Konstantinos Karpos
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Roberto C. Alvarez
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Reza Nazari
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Darren Thifault
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Rebecca Jernigan
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | | | - Raymond Sierra
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Mark S. Hunter
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Alexander Batyuk
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Christopher J. Kupitz
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Robert E. Sublett
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Frederic Poitevin
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Stella Lisova
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Valerio Mariani
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - Sebastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Marc Messerschmidt
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - J. Domingo Meza-Aguilar
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Jose M. Martin-Garcia
- Institute Physical-Chemistry Rocasolano, Spanish National Research Council, Madrid, Spain
| | - Sabine Botha
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Thomas D. Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York
| | - Richard A. Kirian
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
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Yan R, Guo SJ, An X, Jiang LJ, Liu TY, Xue T, Ma HL, Yao K, Shi YX, Han H. [Efficacy and safety of neoadjuvant toripalimab combined with nimotuzumab and chemotherapy in patients with unresectable stage Ⅳ squamous cell carcinoma of penis]. Zhonghua Wai Ke Za Zhi 2022; 60:1093-1099. [PMID: 36480877 DOI: 10.3760/cma.j.cn112139-20220509-00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Objective: To compare the efficacy and safety of neoadjuvant chemotherapy alone or combined with toripalimab and nimotuzumab in patients with unresectable locally advanced or metastatic squamous cell carcinoma of penis. Methods: A total of 33 patients with unresectable squamous cell carcinoma of penis undergoing neoadjuvant chemotherapy alone or combined with toripalimab and nimotuzumab at Sun Yat-sen University Cancer Center from May 2015 to June 2021 were enrolled retrospectively. All the patients were male, with a median age (M(IQR))of 49.0 (13.5) years (range: 30 to 70 years). According to the therapy protocols, patients were divided into the chemotherapy group (16 cases) and the triple combination group (17 cases). Log-rank test was used to compare the progression-free survival and overall survival. χ2 test or Fisher exact method was used to compare the objective response rate, pathological down-stage rate and adverse events between these two groups. Results: The follow-up time was 28.1(19.2) months (range: 1.5 to 33.4 months). Patients of triple combination group were observed significantly longer progression-free survival (30.0 months vs. 8.2 months, χ²=3.998, P=0.046) than those of chemotherapy group. The median overall survival of the triple combination group and chemotherapy group were not reached and 15.2 months (χ²=3.298, P=0.069), respectively. Although there was no significant difference in the subsequent surgical resection rate between these two groups (12/17 vs.11/16, P=1), the objective response rate and the pathological complete response rate in triple combination group were significantly higher than in chemotherapy group (13/17 vs. 6/16, χ²=5.125, P=0.024; 6/7 vs. 0, P=0.001). The main common grade 1 to 2 adverse events in the triple combination group were alopecia (16 cases), anemia (15 cases), and nausea (14 cases). The main common grade 1 to 2 adverse events in the chemotherapy group were anemia (14 cases), alopecia (12 cases), decreased appetite (12 cases), and nausea (11 cases). The incidence of adverse events ≥grade 3 was similar in the triple combination group and chemotherapy group (8/17 vs. 6/16, χ²=0.308, P=0.579). There was no grade 3 adverse event in both groups. Conclusion: Compared with traditional chemotherapy alone, chemotherapy combined with toripalimab and nimotuzumab provides longer progression-free survival and similar toxicity for unresectable stage Ⅳ squamous cell carcinoma of penis.
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Affiliation(s)
- R Yan
- Department of Urology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - S J Guo
- Department of Urology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - X An
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - L J Jiang
- Department of Urology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - T Y Liu
- Department of Experimental Research, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - T Xue
- Department of Urology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - H L Ma
- Department of Radiology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - K Yao
- Department of Urology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Y X Shi
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - H Han
- Department of Urology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
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Guo SJ, Wei LC, Zhuo SQ, Wang YJ, Yang XY, Zhang ZL, Dong P, Zhou FJ, Han H. [Clinical analysis of three-dimensional surgical planning system for guiding robot-assisted selective artery clamping partial nephrectomy in completely endophytic renal tumor]. Zhonghua Wai Ke Za Zhi 2022; 60:992-998. [PMID: 36323581 DOI: 10.3760/cma.j.cn112139-20211216-00608] [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: 06/16/2023]
Abstract
Objective: To examine the safety and feasibility of three-dimensional (3D) surgical planning system for guiding robot-assisted selective artery clamping partial nephrectomy (RASPN) in completely endophytic renal tumor. Methods: Clinical data of 32 patients who suffered from completely endophytic renal tumor and underwent RASPN associated with 3D surgical planning system in Department of Urology, Sun Yat-Sen University Cancer Center from November 2018 to August 2021 were analyzed retrospectively. There were 21 males and 11 females, with the age (M (IQR)] of 45.0 (17.5) years (range: 30 to 68 years). Fifteen tumors were located on the left and 17 on the right. Maximum tumor diameter, R.E.N.A.L. Score and preoperative estimated glomerular filtration rate (eGFR) were 27.5 (13.0) mm (range: 14 to 50 mm), 10.0 (1.8) (range: 7 to 11), and 105.5 (15.7) ml·min-1·(1.73 m2)-1 (range: 71.1 to 124.8 ml·min-1·(1.73 m2)-1), respectively. The 3D reconstruction before RASPN was performed in all patients to formulate surgical planning, mainly including stereo localization of renal mass, confirmation of tumor feeding artery, and injury prediction of collecting system or vessel via "2 mm distance method" defined as probable damage of renal pelvis/calyx and artery/vein when these tissues were less than 2 mm away from tumor. Results: Totally 32 patients successfully underwent RASPN guided by 3D surgical planning system, without conversion to open operation or radical nephrectomy. Rapid location of tumor and selective clamping of artery were achieved in all cases and no one encountered global ischemia, with branch occlusion time of 24.5 (15.4) min (range: 12 to 60 min) and coincidence rate of 95.0% (57/60) between planned and actual clamping vessels. The sensitivity and specificity of 2 mm distance method for predicting the injury of collecting system were 13/15 and 17/17, respectively. The operating time of 185 (48) minuetes (range: 76 to 295 minutes) and estimated blood loss of 200 (350) ml (range: 20 to 800 ml) were observed, without intraoperative transfusion case. There was one patient performed with renal vein repair. Clavien-Dindo postoperative grade Ⅱ and Ⅲa bleeding complications occurred in 2 cases, and no postoperative urinary fistula was found. The length of hospitalization was 3 (0) days (range: 2 to 10 days). The pathological diagnosis demonstrated 4 chromophobe cell carcinomas and 2 angiomyolipomas, besides 26 clear cell carcinomas including one positive surgical margin. The postoperative latest eGFR was 103.9(18.5) ml·min-1·(1.73 m2)-1 (range: 75.8 to 122.3 ml·min-1·(1.73 m2)-1) and no tumor recurrence or metastasis was detected during the follow-up time of 15.4 (13.9) months (range: 3 to 35 months). Conclusion: For RASPN in completely endophytic renal tumor, 3D surgical planning system is contributed to determining mass position, defining tumor feeding artery, and predicting collecting system/vessel injury, which benefited precise tumor resection, postoperative renal function preservation, and perioperative urinary fistula and bleeding complication decrease.
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Affiliation(s)
- S J Guo
- Department of Urology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - L C Wei
- Department of Urology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - S Q Zhuo
- Department of Radiology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Y J Wang
- Department of Urology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - X Y Yang
- Department of Urology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Z L Zhang
- Department of Urology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - P Dong
- Department of Urology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - F J Zhou
- Department of Urology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - H Han
- Department of Urology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
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Rischin D, Brungs D, Day F, Christie H, Patel V, Adams G, Jackson J, Schurmann M, Kirtbaya D, Shin T, Hart C, Stankevich E, Li S, Lowy I, Han H, Fury M, Porceddu S. C-POST Protocol Update: A Phase 3, Randomized, Double-Blind Study of Adjuvant Cemiplimab vs. Placebo Post Surgery and Radiation Therapy in Patients with High-Risk Cutaneous Squamous Cell Carcinoma. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.1822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Jhaveri K, Han H, Dotan E, Oh DY, Ferrario C, Tolcher A, Lee KW, Liao CY, Kang YK, Kim Y, Hamilton E, Spira A, Patel N, Karapetis C, Rha S, Boyken L, Woolery J, Bedard P. 460MO Preliminary results from a phase I study using the bispecific, human epidermal growth factor 2 (HER2)-targeting antibody-drug conjugate (ADC) zanidatamab zovodotin (ZW49) in solid cancers. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Gross N, Miller D, Khushanlani N, Divi V, Ruiz E, Lipson E, Meier F, Su Y, Swiecicki P, Atlas J, Geiger J, Hauschild A, Choe J, Hughes B, Yoo SY, Fenech K, Mathias M, Han H, Fury M, Rischin D. 789O Neoadjuvant cemiplimab in patients (pts) with stage II–IV (M0) cutaneous squamous cell carcinoma (CSCC): Primary analysis of a phase II study. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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26
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Jindal T, Han H, Deshmukh P, De Kouchkovsky I, Kwon D, Borno H, Koshkin V, Desai A, Bose R, Chou J, Friedlander T, Small E, Angelidakis A, Johnson M, Feng S, Patnaik A, Fong L, Alumkal J, Aggarwal R. 1404P A phase II study of ZEN-3694 (ZEN), enzalutamide (ENZ), and pembrolizumab (P) in metastatic castration resistant prostate cancer (mCRPC): Interim safety results. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Han H, Brings L, Chretien A, De Diego I, Round E, Schmidt C, Schubert R, Schulz J, Lorenzen K. Protein crystallization and characterization for serial femtosecond crystallography at the European XFEL. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322089926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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28
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De Wijn R, Mills G, Bean R, Bielecki J, Han H, Koua F, Kantamneni S, Kim C, Koliyadu J, Letrun R, Melo D, Round A, Sato T, Schubert R, Vakili M, Wrona A, Mancuso A, Mancuso A. On-the-fly crystallization for nucleation studies by serial femtosecond crystallography at the European X-ray Free-Electron Laser. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322093299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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29
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Srinivasan V, Brognaro H, Prabhu PR, de Souza EE, Günther S, Reinke PYA, Lane TJ, Ginn H, Han H, Ewert W, Sprenger J, Koua FHM, Falke S, Werner N, Andaleeb H, Ullah N, Franca BA, Wang M, Barra ALC, Perbandt M, Schwinzer M, Schmidt C, Brings L, Lorenzen K, Schubert R, Machado RRG, Candido ED, Oliveira DBL, Durigon EL, Niebling S, Garcia AS, Yefanov O, Lieske J, Gelisio L, Domaracky M, Middendorf P, Groessler M, Trost F, Galchenkova M, Mashhour AR, Saouane S, Hakanpää J, Wolf M, Alai MG, Turk D, Pearson AR, Chapman HN, Hinrichs W, Wrenger C, Meents A, Betzel C. Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease. Commun Biol 2022; 5:805. [PMID: 35953531 PMCID: PMC9366811 DOI: 10.1038/s42003-022-03737-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
Abstract
SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, facilitating cleavage of the viral polypeptide chain, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to support coronaviruses in evading the host's innate immune responses. We identified three phenolic compounds bound to PLpro, preventing essential molecular interactions to ISG15 by screening a natural compound library. The compounds identified by X-ray screening and complexed to PLpro demonstrate clear inhibition of PLpro in a deISGylation activity assay. Two compounds exhibit distinct antiviral activity in Vero cell line assays and one inhibited a cytopathic effect in non-cytotoxic concentration ranges. In the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.
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Affiliation(s)
- Vasundara Srinivasan
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.
| | - Hévila Brognaro
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Prince R Prabhu
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Edmarcia Elisa de Souza
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Sebastian Günther
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Patrick Y A Reinke
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Thomas J Lane
- Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Helen Ginn
- Diamond Light Source Ltd. Diamond House, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Huijong Han
- European XFEL GmbH. Holzkoppel 4, 22869, Schenefeld, Germany
| | - Wiebke Ewert
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Janina Sprenger
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Faisal H M Koua
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Sven Falke
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Nadine Werner
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Hina Andaleeb
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Department of Biochemistry, Bahauddin Zakariya University Multan-, 60800, Punjab, Pakistan
| | - Najeeb Ullah
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Department of Biochemistry, Bahauddin Zakariya University Multan-, 60800, Punjab, Pakistan
| | - Bruno Alves Franca
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Mengying Wang
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Angélica Luana C Barra
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Pólo TerRa, São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Markus Perbandt
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Martin Schwinzer
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | | | - Lea Brings
- European XFEL GmbH. Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Robin Schubert
- European XFEL GmbH. Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Erika Donizette Candido
- Department of Microbiology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Danielle Bruna Leal Oliveira
- Department of Microbiology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.,Clinical Laboratory, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Edison Luiz Durigon
- Department of Microbiology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.,Scientific Platform Pasteur USP, São Paulo, Brazil
| | - Stephan Niebling
- European Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Angelica Struve Garcia
- European Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Julia Lieske
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Luca Gelisio
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Martin Domaracky
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Philipp Middendorf
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Michael Groessler
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Fabian Trost
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Aida Rahmani Mashhour
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Sofiane Saouane
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607, Hamburg, Germany
| | - Johanna Hakanpää
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607, Hamburg, Germany
| | - Markus Wolf
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee114, 22525, Hamburg, Germany
| | - Maria Garcia Alai
- European Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Dusan Turk
- Department of Biochemistry & Molecular & Structural Biology, Jozef Stefan Institute, Jamova 39, 1 000, Ljubljana, Slovenia.,Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKEBIP), Jamova 39, 1 000, Ljubljana, Slovenia
| | - Arwen R Pearson
- Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Institut für Nanostruktur- und Festkörperphysik, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Henry N Chapman
- Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Winfried Hinrichs
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Alke Meents
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Christian Betzel
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany. .,Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
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Bi XJ, Lv YQ, Yang XH, Ge Y, Han H, Feng JS, Zhang M, Chen L, Xu MZ, Guan FY. A New Berberine Preparation Protects Pancreatic Islet Cells from Apoptosis Mediated by Inhibition of Phospholipase A2/p38 MAPK Pathway. Bull Exp Biol Med 2022; 173:346-353. [DOI: 10.1007/s10517-022-05547-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Indexed: 11/30/2022]
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Han H, Swaisgood RR, Qiu L, Chen Y, Zhang Z. Down‐listing pandas and upgrading conservation: China setting an example to preserve wildlife worldwide. Anim Conserv 2022. [DOI: 10.1111/acv.12803] [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: 11/29/2022]
Affiliation(s)
- H. Han
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province Science and Technology Department of Sichuan Province Chengdu China
| | - R. R. Swaisgood
- Institute for Conservation Research San Diego Zoo Global Escondido Escondido CA USA
| | - L. Qiu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province Science and Technology Department of Sichuan Province Chengdu China
| | - Y. Chen
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province Science and Technology Department of Sichuan Province Chengdu China
| | - Z. Zhang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province Science and Technology Department of Sichuan Province Chengdu China
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Park Y, Jung K, Sohn J, Lee K, Kim J, Yang Y, Baek E, Han H, Im SA. 176P Poziotinib for HER2-positive metastatic breast cancer (MBC): Final clinical efficacy and safety results for long-term follow-up of the phase II NOV120101-203 trial. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.03.195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Ewert W, Günther S, Miglioli F, Falke S, Reinke PYA, Niebling S, Günther C, Han H, Srinivasan V, Brognaro H, Lieske J, Lorenzen K, Garcia-Alai MM, Betzel C, Carcelli M, Hinrichs W, Rogolino D, Meents A. Hydrazones and Thiosemicarbazones Targeting Protein-Protein-Interactions of SARS-CoV-2 Papain-like Protease. Front Chem 2022; 10:832431. [PMID: 35480391 PMCID: PMC9038201 DOI: 10.3389/fchem.2022.832431] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/28/2022] [Indexed: 12/14/2022] Open
Abstract
The papain-like protease (PLpro) of SARS-CoV-2 is essential for viral propagation and, additionally, dysregulation of the host innate immune system. Using a library of 40 potential metal-chelating compounds we performed an X-ray crystallographic screening against PLpro. As outcome we identified six compounds binding to the target protein. Here we describe the interaction of one hydrazone (H1) and five thiosemicarbazone (T1-T5) compounds with the two distinct natural substrate binding sites of PLpro for ubiquitin and ISG15. H1 binds to a polar groove at the S1 binding site by forming several hydrogen bonds with PLpro. T1-T5 bind into a deep pocket close to the polyubiquitin and ISG15 binding site S2. Their interactions are mainly mediated by multiple hydrogen bonds and further hydrophobic interactions. In particular compound H1 interferes with natural substrate binding by sterical hindrance and induces conformational changes in protein residues involved in substrate binding, while compounds T1-T5 could have a more indirect effect. Fluorescence based enzyme activity assay and complementary thermal stability analysis reveal only weak inhibition properties in the high micromolar range thereby indicating the need for compound optimization. Nevertheless, the unique binding properties involving strong hydrogen bonding and the various options for structural optimization make the compounds ideal lead structures. In combination with the inexpensive and undemanding synthesis, the reported hydrazone and thiosemicarbazones represent an attractive scaffold for further structure-based development of novel PLpro inhibitors by interrupting protein-protein interactions at the S1 and S2 site.
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Affiliation(s)
- Wiebke Ewert
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Sebastian Günther
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Francesca Miglioli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sven Falke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Patrick Y. A. Reinke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Stephan Niebling
- European Molecular Biology Laboratory Hamburg, DESY, Hamburg, Germany
| | - Christian Günther
- European Molecular Biology Laboratory Hamburg, DESY, Hamburg, Germany
| | | | - Vasundara Srinivasan
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, University Hamburg, Hamburg, Germany
| | - Hévila Brognaro
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, University Hamburg, Hamburg, Germany
| | - Julia Lieske
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | | | | | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, University Hamburg, Hamburg, Germany
| | - Mauro Carcelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Winfried Hinrichs
- Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Dominga Rogolino
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Alke Meents
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
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Vakili M, Bielecki J, Knoška J, Otte F, Han H, Kloos M, Schubert R, Delmas E, Mills G, de Wijn R, Letrun R, Dold S, Bean R, Round A, Kim Y, Lima FA, Dörner K, Valerio J, Heymann M, Mancuso AP, Schulz J. 3D printed devices and infrastructure for liquid sample delivery at the European XFEL. J Synchrotron Radiat 2022; 29:331-346. [PMID: 35254295 PMCID: PMC8900844 DOI: 10.1107/s1600577521013370] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
The Sample Environment and Characterization (SEC) group of the European X-ray Free-Electron Laser (EuXFEL) develops sample delivery systems for the various scientific instruments, including systems for the injection of liquid samples that enable serial femtosecond X-ray crystallography (SFX) and single-particle imaging (SPI) experiments, among others. For rapid prototyping of various device types and materials, sub-micrometre precision 3D printers are used to address the specific experimental conditions of SFX and SPI by providing a large number of devices with reliable performance. This work presents the current pool of 3D printed liquid sample delivery devices, based on the two-photon polymerization (2PP) technique. These devices encompass gas dynamic virtual nozzles (GDVNs), mixing-GDVNs, high-viscosity extruders (HVEs) and electrospray conical capillary tips (CCTs) with highly reproducible geometric features that are suitable for time-resolved SFX and SPI experiments at XFEL facilities. Liquid sample injection setups and infrastructure on the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument are described, this being the instrument which is designated for biological structure determination at the EuXFEL.
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Affiliation(s)
| | | | - Juraj Knoška
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Florian Otte
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Physics, TU Dortmund, Otto-Hahn-Straße 4, 44221 Dortmund, Germany
| | - Huijong Han
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Marco Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Elisa Delmas
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Grant Mills
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Romain Letrun
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Simon Dold
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Richard Bean
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Adam Round
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- School of Chemical and Physical Sciences, Keele University, Staffordshire ST5 5AZ, United Kingdom
| | - Yoonhee Kim
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | - Joana Valerio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Michael Heymann
- Institute for Biomaterials and Biomolecular Systems (IBBS), University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Adrian P. Mancuso
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne 3086, Australia
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35
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Yang K, Han H, Li Y, Ye J, Xu F. Significance of miRNA in enhancement of flavonoid biosynthesis. Plant Biol (Stuttg) 2022; 24:217-226. [PMID: 34806280 DOI: 10.1111/plb.13361] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 10/15/2021] [Indexed: 05/20/2023]
Abstract
Flavonoid metabolism shows very strong plasticity in plant development and coping with the changing environment. Flavonoid biosynthesis is regulated by many metabolic pathways, including transcriptional regulation, post-transcriptional control, post-translational regulationand epigenetic regulation. miRNA is a form of endogenous noncoding single-strand small molecule RNA that primarily regulates the expression of target genes horizontally after transcription through splicing and translational suppression. It also plays an important role in regulating plant growth and development, secondary metabolism and biotic and abiotic stress. miRNA can regulate the formation of flavonoids by acting on structural genes or indirectly by using an MBW transcription complex comprising MYB-bHLH-WD40. This study summarizes the biosynthesis and mechanisms of miRNA, and provides a summary of the mechanisms of miRNAs involved in production of flavonoids, in order to elucidate the biosynthesis pathway and complex regulatory network of plant flavonoids. We aim to provide new insights into improving the content of flavonoid active ingredients in plants.
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Affiliation(s)
- K Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - H Han
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Y Li
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - J Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - F Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
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36
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Han H, Park C, Cho N, Lee J, Han W, Ham W, Choi Y. BRCA1/2 and ATM mutated metastatic prostate cancers may present with low serum PSA. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)00596-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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37
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Li Z, Wu C, Han H, Li X, Zhou F. Glasgow prognostic score is a pre-surgical prognostic marker of inguinal lymph node metastasis extranodal extension in penile cancer. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)00770-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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38
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Liu W, Liu J, Zhou Y, Cao D, Lei Q, Han H, Wang J, Li D, Gao J, Li H, Li F. Genome-Wide Association Study of Abdominal Fat in Wenshang Barred Chicken Based on the Slaf-Seq Technology. Braz J Poult Sci 2022. [DOI: 10.1590/1806-9061-2021-1612] [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] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- W Liu
- Shandong Academy of Agricultural Sciences, P. R. China; Poultry Breeding Engineering Technology Center of Shandong Province, China
| | - J Liu
- Shandong Academy of Agricultural Sciences, P. R. China; Poultry Breeding Engineering Technology Center of Shandong Province, China
| | - Y Zhou
- Shandong Academy of Agricultural Sciences, P. R. China; Poultry Breeding Engineering Technology Center of Shandong Province, China
| | - D Cao
- Shandong Academy of Agricultural Sciences, P. R. China; Poultry Breeding Engineering Technology Center of Shandong Province, China
| | - Q Lei
- Shandong Academy of Agricultural Sciences, P. R. China; Poultry Breeding Engineering Technology Center of Shandong Province, China
| | - H Han
- Shandong Academy of Agricultural Sciences, P. R. China; Poultry Breeding Engineering Technology Center of Shandong Province, China
| | - J Wang
- Shandong Academy of Agricultural Sciences, P. R. China; Poultry Breeding Engineering Technology Center of Shandong Province, China
| | - D Li
- Shandong Academy of Agricultural Sciences, P. R. China; Poultry Breeding Engineering Technology Center of Shandong Province, China
| | - J Gao
- Shandong Academy of Agricultural Sciences, P. R. China; Poultry Breeding Engineering Technology Center of Shandong Province, China
| | - H Li
- Shandong Academy of Agricultural Sciences, P. R. China
| | - F Li
- Shandong Academy of Agricultural Sciences, P. R. China; Poultry Breeding Engineering Technology Center of Shandong Province, China
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39
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Li S, Tang K, Khodadadi-Jamayran A, Jen J, Han H, Guidry K, Chen T, Hao Y, Fedele C, Zebala J, Maeda D, Christensen J, Olson P, Athanas A, Wong K, Neel B. OA12.03 Combined Inhibition of SHP2 and CXCR1/2 Promotes Anti-Tumor T Cell Response in NSCLC. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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40
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Fu Z, Yang H, Han H, Jia D, Xu L, Su G, Wang Z. Effect of whole-grain rice on pellet quality, geese performance, and economic benefits. J APPL POULTRY RES 2021. [DOI: 10.1016/j.japr.2021.100176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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41
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Kim B, Bae H, Kwon J, Han H, Kim H. PO-1911 Low-dose irradiation could mitigate osteoarthritis progression by modulating mitochondrial function. Radiother Oncol 2021. [DOI: 10.1016/s0167-8140(21)08362-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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42
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Shi Y, An X, Yan R, Yao K, Xue C, Guo S, Liu T, Li J, Ma H, Tian L, Zhou F, Shi Y, Han H. A phase II study to evaluate safety and efficacy of PD-1 blockade plus anti-EGFR target therapy plus chemotherapy in patients with advanced penile squamous cell carcinoma. Eur Urol 2021. [DOI: 10.1016/s0302-2838(21)01057-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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43
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Wu C, Han H, Wang Y, Zhuo S, Guo S. Better specificity and less ischemia: High-precision three-dimensional Reconstruction is superior to routine CT angiography in navigation of Robot assisted partial nephrectomy with selective clamping. Eur Urol 2021. [DOI: 10.1016/s0302-2838(21)00966-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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44
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Günther S, Reinke PYA, Fernández-García Y, Lieske J, Lane TJ, Ginn HM, Koua FHM, Ehrt C, Ewert W, Oberthuer D, Yefanov O, Meier S, Lorenzen K, Krichel B, Kopicki JD, Gelisio L, Brehm W, Dunkel I, Seychell B, Gieseler H, Norton-Baker B, Escudero-Pérez B, Domaracky M, Saouane S, Tolstikova A, White TA, Hänle A, Groessler M, Fleckenstein H, Trost F, Galchenkova M, Gevorkov Y, Li C, Awel S, Peck A, Barthelmess M, Schlünzen F, Lourdu Xavier P, Werner N, Andaleeb H, Ullah N, Falke S, Srinivasan V, França BA, Schwinzer M, Brognaro H, Rogers C, Melo D, Zaitseva-Doyle JJ, Knoska J, Peña-Murillo GE, Mashhour AR, Hennicke V, Fischer P, Hakanpää J, Meyer J, Gribbon P, Ellinger B, Kuzikov M, Wolf M, Beccari AR, Bourenkov G, von Stetten D, Pompidor G, Bento I, Panneerselvam S, Karpics I, Schneider TR, Garcia-Alai MM, Niebling S, Günther C, Schmidt C, Schubert R, Han H, Boger J, Monteiro DCF, Zhang L, Sun X, Pletzer-Zelgert J, Wollenhaupt J, Feiler CG, Weiss MS, Schulz EC, Mehrabi P, Karničar K, Usenik A, Loboda J, Tidow H, Chari A, Hilgenfeld R, Uetrecht C, Cox R, Zaliani A, Beck T, Rarey M, Günther S, Turk D, Hinrichs W, Chapman HN, Pearson AR, Betzel C, Meents A. X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science 2021; 372:642-646. [PMID: 33811162 PMCID: PMC8224385 DOI: 10.1126/science.abf7945] [Citation(s) in RCA: 203] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/29/2021] [Indexed: 12/17/2022]
Abstract
The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput x-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast to commonly applied x-ray fragment screening experiments with molecules of low complexity, our screen tested already-approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to Mpro In subsequent cell-based viral reduction assays, one peptidomimetic and six nonpeptidic compounds showed antiviral activity at nontoxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.
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Affiliation(s)
- Sebastian Günther
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
| | - Patrick Y A Reinke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Yaiza Fernández-García
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany
| | - Julia Lieske
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Thomas J Lane
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Helen M Ginn
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Faisal H M Koua
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Christiane Ehrt
- Universität Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany
| | - Wiebke Ewert
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Susanne Meier
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | | | - Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, 20251 Hamburg, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, 20251 Hamburg, Germany
| | - Luca Gelisio
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Ilona Dunkel
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Brandon Seychell
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
| | - Henry Gieseler
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Brenna Norton-Baker
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Chemistry, UC Irvine, Irvine, CA 92697-2025, USA
| | - Beatriz Escudero-Pérez
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany
| | - Martin Domaracky
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Sofiane Saouane
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Anna Hänle
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Michael Groessler
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Fabian Trost
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Vision Systems, Hamburg University of Technology, 21071 Hamburg, Germany
| | - Chufeng Li
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Ariana Peck
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Miriam Barthelmess
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Frank Schlünzen
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - P Lourdu Xavier
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Nadine Werner
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Hina Andaleeb
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Najeeb Ullah
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Sven Falke
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Vasundara Srinivasan
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Bruno Alves França
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Martin Schwinzer
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Hévila Brognaro
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Cromarte Rogers
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Diogo Melo
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Joanna J Zaitseva-Doyle
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Gisel E Peña-Murillo
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Aida Rahmani Mashhour
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Vincent Hennicke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Pontus Fischer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Johanna Hakanpää
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Jan Meyer
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Markus Wolf
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | | | - Gleb Bourenkov
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - David von Stetten
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Isabel Bento
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Ivars Karpics
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | | | - Stephan Niebling
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Christian Günther
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Huijong Han
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Juliane Boger
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Diana C F Monteiro
- Hauptmann Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Linlin Zhang
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany
| | - Xinyuanyuan Sun
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany
| | | | - Jan Wollenhaupt
- Helmholtz Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Christian G Feiler
- Helmholtz Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Manfred S Weiss
- Helmholtz Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Eike-Christian Schulz
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Pedram Mehrabi
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Katarina Karničar
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Aleksandra Usenik
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Jure Loboda
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Henning Tidow
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Ashwin Chari
- Research Group for Structural Biochemistry and Mechanisms, Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, 20251 Hamburg, Germany
| | - Russell Cox
- Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Tobias Beck
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany
| | - Dusan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Winfried Hinrichs
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
- Universität Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Physics, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Arwen R Pearson
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Christian Betzel
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
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Spring L, Han H, Hamilton E, Irie H, Santa-Maria C, Reeves J, Pan P, Shan M, Tang Y, Graham J, Hazard S, Ellisen L, Isakoff S. Neoadjuvant niraparib in patients with HER2-negative, BRCA-mutated resectable breast cancer. Breast 2021. [DOI: 10.1016/s0960-9776(21)00183-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Han H, Round E, Schubert R, Gül Y, Makroczyová J, Meza D, Heuser P, Aepfelbacher M, Barák I, Betzel C, Fromme P, Kursula I, Nissen P, Tereschenko E, Schulz J, Uetrecht C, Ulicný J, Wilmanns M, Hajdu J, Lamzin VS, Lorenzen K. The XBI BioLab for life science experiments at the European XFEL. J Appl Crystallogr 2021; 54:7-21. [PMID: 33833637 PMCID: PMC7941304 DOI: 10.1107/s1600576720013989] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/19/2020] [Indexed: 11/26/2022] Open
Abstract
The science of X-ray free-electron lasers (XFELs) critically depends on the performance of the X-ray laser and on the quality of the samples placed into the X-ray beam. The stability of biological samples is limited and key biomolecular transformations occur on short timescales. Experiments in biology require a support laboratory in the immediate vicinity of the beamlines. The XBI BioLab of the European XFEL (XBI denotes XFEL Biology Infrastructure) is an integrated user facility connected to the beamlines for supporting a wide range of biological experiments. The laboratory was financed and built by a collaboration between the European XFEL and the XBI User Consortium, whose members come from Finland, Germany, the Slovak Republic, Sweden and the USA, with observers from Denmark and the Russian Federation. Arranged around a central wet laboratory, the XBI BioLab provides facilities for sample preparation and scoring, laboratories for growing prokaryotic and eukaryotic cells, a Bio Safety Level 2 laboratory, sample purification and characterization facilities, a crystallization laboratory, an anaerobic laboratory, an aerosol laboratory, a vacuum laboratory for injector tests, and laboratories for optical microscopy, atomic force microscopy and electron microscopy. Here, an overview of the XBI facility is given and some of the results of the first user experiments are highlighted.
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Affiliation(s)
- Huijong Han
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
| | - Ekaterina Round
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Yasmin Gül
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jana Makroczyová
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovak Republic
| | - Domingo Meza
- Biodesign Center for Applied Structural Discovery and School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Philipp Heuser
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Imrich Barák
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovak Republic
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery and School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Inari Kursula
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Poul Nissen
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Department of Molecular Biology and Genetics, Gustav Wieds Vej 10C, DK – 8000 Aarhus C, Denmark
| | - Elena Tereschenko
- Institute of Crystallography, Russian Academy of Sciences, 59 Leninsky prospekt, Moscow, 117333, Russian Federation
| | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Charlotte Uetrecht
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany
| | - Jozef Ulicný
- Department of Biophysics, Institute of Physics, Faculty of Science, P. J. Šafárik University, Jesenná 5, 04154 Košice, Slovak Republic
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Janos Hajdu
- The European Extreme Light Infrastructure, Institute of Physics, Academy of Sciences of the Czech Republic, Za Radnici 835, 25241 Dolní Břežany, Czech Republic
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Victor S. Lamzin
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
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Kim CH, Yeom YS, Petoussi-Henss N, Zankl M, Bolch WE, Lee C, Choi C, Nguyen TT, Eckerman K, Kim HS, Han MC, Qiu R, Chung BS, Han H, Shin B. ICRP Publication 145: Adult Mesh-Type Reference Computational Phantoms. Ann ICRP 2020; 49:13-201. [PMID: 33231095 DOI: 10.1177/0146645319893605] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
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Kaufman B, Han H, Arun B, Wildiers H, Friedlander M, Ayoub JP, Puhalla S, Maag D, Feng D, Fages S, Dieras V. 325P Characteristics of patients with HER2-negative advanced/metastatic gBRCA-associated breast cancer who achieved durable response in the phase III BROCADE3 study. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Kim B, Han H. PIN55 TREND in Medical Utilization and Treatment Status of CHB-Treated Patients in South Korea. Value Health Reg Issues 2020. [DOI: 10.1016/j.vhri.2020.07.302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Cortés J, Diab S, Basho R, Oliveira M, Pluard T, Alemany C, Brown-Glaberman U, Meisel J, Boni V, Sinha R, Estevez LG, Ettl J, Kuemmel S, Sanchez LM, Moon Y, Vazquez RV, Wuerstlein R, Wang Y, Wang Z, Han H. 357TiP SGNLVA-002: Single arm, open-label, phase Ib/II study of ladiratuzumab vedotin (LV) in combination with pembrolizumab for first-line treatment of triple-negative breast cancer. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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