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Chen K, Ernst P, Kim S, Si Y, Varadkar T, Ringel MD, Liu X“M, Zhou L. An Innovative Mitochondrial-targeted Gene Therapy for Cancer Treatment. bioRxiv 2024:2024.03.24.584499. [PMID: 38585739 PMCID: PMC10996521 DOI: 10.1101/2024.03.24.584499] [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] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Targeting cancer cell mitochondria holds great therapeutic promise, yet current strategies to specifically and effectively destroy cancer mitochondria in vivo are limited. Here, we introduce mLumiOpto, an innovative mitochondrial-targeted luminoptogenetics gene therapy designed to directly disrupt the inner mitochondrial membrane (IMM) potential and induce cancer cell death. We synthesize a blue light-gated channelrhodopsin (CoChR) in the IMM and co-express a blue bioluminescence-emitting Nanoluciferase (NLuc) in the cytosol of the same cells. The mLumiOpto genes are selectively delivered to cancer cells in vivo by using adeno-associated virus (AAV) carrying a cancer-specific promoter or cancer-targeted monoclonal antibody-tagged exosome-associated AAV. Induction with NLuc luciferin elicits robust endogenous bioluminescence, which activates mitochondrial CoChR, triggering cancer cell IMM permeability disruption, mitochondrial damage, and subsequent cell death. Importantly, mLumiOpto demonstrates remarkable efficacy in reducing tumor burden and killing tumor cells in glioblastoma or triple-negative breast cancer xenografted mouse models. These findings establish mLumiOpto as a novel and promising therapeutic strategy by targeting cancer cell mitochondria in vivo.
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Affiliation(s)
- Kai Chen
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Patrick Ernst
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Seulhee Kim
- Department of Biomedical Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Yingnan Si
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Tanvi Varadkar
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Matthew D. Ringel
- Department of Molecular Medicine and Therapeutics, The Ohio State University, Columbus, Ohio, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Xiaoguang “Margaret” Liu
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Lufang Zhou
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Biomedical Engineering, The Ohio State University, Columbus, Ohio, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
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2
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Cucuzza S, Sitnik M, Jurt S, Michel E, Dai W, Müntener T, Ernst P, Häussinger D, Plückthun A, Zerbe O. Unexpected dynamics in femtomolar complexes of binding proteins with peptides. Nat Commun 2023; 14:7823. [PMID: 38016954 PMCID: PMC10684580 DOI: 10.1038/s41467-023-43596-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023] Open
Abstract
Ultra-tight binding is usually observed for proteins associating with rigidified molecules. Previously, we demonstrated that femtomolar binders derived from the Armadillo repeat proteins (ArmRPs) can be designed to interact very tightly with fully flexible peptides. Here we show for ArmRPs with four and seven sequence-identical internal repeats that the peptide-ArmRP complexes display conformational dynamics. These dynamics stem from transient breakages of individual protein-residue contacts that are unrelated to overall unbinding. The labile contacts involve electrostatic interactions. We speculate that these dynamics allow attaining very high binding affinities, since they reduce entropic losses. Importantly, only NMR techniques can pick up these local events by directly detecting conformational exchange processes without complications from changes in solvent entropy. Furthermore, we demonstrate that the interaction surface of the repeat protein regularizes upon peptide binding to become more compatible with the peptide geometry. These results provide novel design principles for ultra-tight binders.
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Affiliation(s)
- Stefano Cucuzza
- Department of Chemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
| | - Malgorzata Sitnik
- Department of Chemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
| | - Simon Jurt
- Department of Chemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
| | - Erich Michel
- Department of Chemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
- Department of Biochemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
| | - Wenzhao Dai
- Department of Chemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
| | - Thomas Müntener
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Patrick Ernst
- Department of Biochemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
| | - Daniel Häussinger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland.
| | - Oliver Zerbe
- Department of Chemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland.
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Ernst P, Kim S, Yang Z, Liu XM, Zhou L. Characterization of the far-red fluorescent probe MitoView 633 for dynamic mitochondrial membrane potential measurement. Front Physiol 2023; 14:1257739. [PMID: 37936577 PMCID: PMC10627182 DOI: 10.3389/fphys.2023.1257739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/13/2023] [Indexed: 11/09/2023] Open
Abstract
Introduction: MitoView 633, a far-red fluorescent dye, exhibits the ability to accumulate within mitochondria in a membrane potential-dependent manner, as described by the Nernst equation. This characteristic renders it a promising candidate for bioenergetics studies, particularly as a robust indicator of mitochondrial membrane potential (DYm). Despite its great potential, its utility in live cell imaging has not been well characterized. Methods: This study seeks to characterize the spectral properties of MitoView 633 in live cells and evaluate its mitochondrial staining, resistance to photobleaching, and dynamics during DYm depolarization. The co-staining and imaging of MitoView 633 with other fluorophores such as MitoSOX Red and Fluo-4 AM were also examined in cardiomyocytes using confocal microscopy. Results and Discussion: Spectrum analysis showed that MitoView 633 emission could be detected at 660 ± 50 nm, and exhibited superior thermal stability compared to tetramethylrhodamine methyl ester (TMRM), a commonly used DYm indicator, which emits at 605 ± 25 nm. Confocal imaging unequivocally illustrated MitoView 633's specific localization within the mitochondrial matrix, corroborated by its colocalization with MitoTracker Green, a well-established mitochondrial marker. Furthermore, our investigation revealed that MitoView 633 exhibited minimal photobleaching at the recommended in vitro concentrations. Additionally, the dynamics of MitoView 633 fluoresce during carbonyl cyanide-p-trifluoromethoxyphenylhydrazone (FCCP, a mitochondrial uncoupler)-induced DYm depolarization mirrored that of TMRM. Importantly, MitoView 633 demonstrated compatibility with co-staining alongside MitoSOX Red and Fluo-4 AM, enabling concurrent monitoring of DYm, mitochondrial ROS, and cytosolic Ca2+ in intact cells. Conclusion: These findings collectively underscore MitoView 633 as a superb molecular probe for the singular or combined assessment of DYm and other indicators in live cell imaging applications.
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Affiliation(s)
- Patrick Ernst
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Seulhee Kim
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, United States
| | - Zengqiao Yang
- Department of Surgery, The Ohio State University, Columbus, OH, United States
| | - Xiaoguang Margaret Liu
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, United States
| | - Lufang Zhou
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, United States
- Department of Surgery, The Ohio State University, Columbus, OH, United States
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Ernst P, Bidwell PA, Dora M, Thomas DD, Kamdar F. Cardiac calcium regulation in human induced pluripotent stem cell cardiomyocytes: Implications for disease modeling and maturation. Front Cell Dev Biol 2023; 10:986107. [PMID: 36742199 PMCID: PMC9889838 DOI: 10.3389/fcell.2022.986107] [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: 07/04/2022] [Accepted: 12/23/2022] [Indexed: 01/19/2023] Open
Abstract
Human induced pluripotent stem cell cardiomyocytes (hiPSC-CMs) are based on ground-breaking technology that has significantly impacted cardiovascular research. They provide a renewable source of human cardiomyocytes for a variety of applications including in vitro disease modeling and drug toxicity testing. Cardiac calcium regulation plays a critical role in the cardiomyocyte and is often dysregulated in cardiovascular disease. Due to the limited availability of human cardiac tissue, calcium handling and its regulation have most commonly been studied in the context of animal models. hiPSC-CMs can provide unique insights into human physiology and pathophysiology, although a remaining limitation is the relative immaturity of these cells compared to adult cardiomyocytes Therefore, this field is rapidly developing techniques to improve the maturity of hiPSC-CMs, further establishing their place in cardiovascular research. This review briefly covers the basics of cardiomyocyte calcium cycling and hiPSC technology, and will provide a detailed description of our current understanding of calcium in hiPSC-CMs.
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Affiliation(s)
- Patrick Ernst
- Cardiovascular Division, University of Minnesota, Minneapolis, MN, United States
| | - Philip A. Bidwell
- Cardiovascular Division, University of Minnesota, Minneapolis, MN, United States
| | - Michaela Dora
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States
| | - David D. Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Forum Kamdar
- Cardiovascular Division, University of Minnesota, Minneapolis, MN, United States,*Correspondence: Forum Kamdar,
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Shedrawy J, Ernst P, Lönnroth K, Nyberg F. The burden of disease due to COVID-19 in Sweden: a disability-adjusted life years (DALY) study. Eur J Public Health 2022. [PMCID: PMC9594333 DOI: 10.1093/eurpub/ckac131.568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background Many countries have been severely affected by the COVID-19 pandemic, including Sweden, which has been in the spotlight regarding its policies and their impact on mortality and morbidity. Therefore, it is of high interest to measure the disease burden of COVID-19 in terms of disability-adjusted life years (DALYs). DALYs have two main components: the years of life lost through premature death (YLL) and the number of years lived with disability (YLD). This study aims to measure DALYs due to COVID-19 in Sweden. Methods This study used data from the nationwide multi-register observational study SCIFI-PEARL (Swedish COVID-19 Investigation for Future Insights - a Population Epidemiology Approach using Register Linkage) covering the entire Swedish population. The methodology used in the modelling and calculation of DALYs was based on the Global Burden of Disease guidelines, using Sweden-specific life tables for estimated life expectancies. Results In Sweden, 152877 DALYs were lost to COVID-19 between March 2020 and October 2021, corresponding to 1447/ 100 000, 99,3% of which was attributed to YLL. DALYs loss occurred mainly among elderly groups with 66,78 % of DALYs being attributed to individuals above 70 years old. 57,6% of the lost DALYs occurred among men that lost more DALYs compared to females in all age groups. Conclusions Similar to other countries, the burden of COVID-19 in Sweden is concentrated mainly among the elderly, which contributed to the highest DALY loss due to mortality. Yet, DALY loss remains lower for COVID-19 compared to other major non-communicable diseases such as cardiovascular diseases and neoplasms. The contribution of YLD was minimal. However, YLD due to post-Covid is not well understood and long-term disability is likely still underestimated. Key messages • The burden of COVID-19 was mainly due to premature mortality in the older age groups. • More research is needed especially on post-COVID disability to derive better estimates of YLD.
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Affiliation(s)
- J Shedrawy
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
- Contact:
| | - P Ernst
- School of Public Health and Community Medicine, University of Gothenburg, Gothenburg, Sweden
| | - K Lönnroth
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
- Centre for Epidemiology and Community Medicine, Stockholm County Council, Stockholm, Sweden
| | - F Nyberg
- School of Public Health and Community Medicine, University of Gothenburg, Gothenburg, Sweden
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Chen K, Ernst P, Liu XM, Zhou L. Optogenetic Studies of Mitochondria. Methods Mol Biol 2022; 2501:311-324. [PMID: 35857235 DOI: 10.1007/978-1-0716-2329-9_15] [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] [Indexed: 05/07/2023]
Abstract
While optogenetic approaches have been widely used for remote control of cell membrane excitability and intracellular signaling pathways, their application in mitochondrial study has been limited, largely due to the challenge of effectively and specifically expressing heterologous light-gated rhodopsin channels in the mitochondria. Here, we describe the methods for expressing functional channelrhodopsin 2 (ChR2) proteins in the mitochondrial inner membrane with an unusually long mitochondrial leading sequence and characterizing optogenetic-mediated mitochondrial membrane potential (ΔΨm) depolarization. We then illustrate how this next-generation optogenetic approach can be used to study the effect of ΔΨm on mitochondrial functions such as mitophagy, programed cell death, and preconditioning-mediated cytoprotection. We anticipate that this innovative technology will enable new insights into the mechanisms by which changes in ΔΨm differentially impacts mitochondrial and cellular functions.
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Affiliation(s)
- Kai Chen
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, USA
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Patrick Ernst
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, USA
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Xiaoguang Margaret Liu
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lufang Zhou
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, USA.
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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Friedrich N, Stiegeler E, Glögl M, Lemmin T, Hansen S, Kadelka C, Wu Y, Ernst P, Maliqi L, Foulkes C, Morin M, Eroglu M, Liechti T, Ivan B, Reinberg T, Schaefer JV, Karakus U, Ursprung S, Mann A, Rusert P, Kouyos RD, Robinson JA, Günthard HF, Plückthun A, Trkola A. Distinct conformations of the HIV-1 V3 loop crown are targetable for broad neutralization. Nat Commun 2021; 12:6705. [PMID: 34795280 PMCID: PMC8602657 DOI: 10.1038/s41467-021-27075-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 11/03/2021] [Indexed: 12/14/2022] Open
Abstract
The V3 loop of the HIV-1 envelope (Env) protein elicits a vigorous, but largely non-neutralizing antibody response directed to the V3-crown, whereas rare broadly neutralizing antibodies (bnAbs) target the V3-base. Challenging this view, we present V3-crown directed broadly neutralizing Designed Ankyrin Repeat Proteins (bnDs) matching the breadth of V3-base bnAbs. While most bnAbs target prefusion Env, V3-crown bnDs bind open Env conformations triggered by CD4 engagement. BnDs achieve breadth by focusing on highly conserved residues that are accessible in two distinct V3 conformations, one of which resembles CCR5-bound V3. We further show that these V3-crown conformations can, in principle, be attacked by antibodies. Supporting this conclusion, analysis of antibody binding activity in the Swiss 4.5 K HIV-1 cohort (n = 4,281) revealed a co-evolution of V3-crown reactivities and neutralization breadth. Our results indicate a role of V3-crown responses and its conformational preferences in bnAb development to be considered in preventive and therapeutic approaches.
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Affiliation(s)
- Nikolas Friedrich
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Emanuel Stiegeler
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.424277.0Present Address: Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Deutschland
| | - Matthias Glögl
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Thomas Lemmin
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.5801.c0000 0001 2156 2780Department of Computer Science, ETH Zurich, Zurich, Switzerland ,grid.29078.340000 0001 2203 2861Present Address: Euler Institute, Faculty of Biomedicine, Università della Svizzera italiana (USI), Lugano, Switzerland
| | - Simon Hansen
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland ,Present Address: NGM Bio, 333 Oysterpoint Blvd, South San Francisco, CA 94080 USA
| | - Claus Kadelka
- grid.34421.300000 0004 1936 7312Department of Mathematics, Iowa State University, Ames, IA USA
| | - Yufan Wu
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland ,Present Address: Innovent Biologics Inc, 168 Dongping Street, Suzhou Industrial Park, 215123 China
| | - Patrick Ernst
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland ,grid.7400.30000 0004 1937 0650Present Address: Office Research and Teaching, Medical Faculty, University of Zurich, Zurich, Switzerland
| | - Liridona Maliqi
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Caio Foulkes
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Mylène Morin
- grid.7400.30000 0004 1937 0650Department of Chemistry, University of Zurich (UZH), Zurich, Switzerland ,Present Address: BeiGene Switzerland GmbH, Aeschengraben 27, 4051 Basel, Switzerland
| | - Mustafa Eroglu
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,Present Address: Janssen Vaccines AG, Rehhagstrasse 79, 3018 Bern, Switzerland
| | - Thomas Liechti
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.419681.30000 0001 2164 9667Present Address: ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD USA
| | - Branislav Ivan
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.410567.1Present Address: Laboratory Medicine, Division of Clinical Chemistry, University Hospital Basel, Basel, Switzerland
| | - Thomas Reinberg
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Jonas V. Schaefer
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland ,grid.419481.10000 0001 1515 9979Present Address: Novartis Institutes for BioMedical Research, Chemical Biology & Therapeutics (CBT), Novartis Pharma AG, Virchow 16, 4056 Basel, Switzerland
| | - Umut Karakus
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Stephan Ursprung
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.5335.00000000121885934Present Address: University of Cambridge School of Clinical Medicine, Department of Radiology, Cambridge, CB2 0QQ UK
| | - Axel Mann
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,Present Address: Roche Innovation Center Zurich, Roche Pharmaceutical Research and Early Development (pRED), Wagistrasse 10, 8952 Schlieren, Switzerland
| | - Peter Rusert
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Roger D. Kouyos
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.412004.30000 0004 0478 9977Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - John A. Robinson
- grid.7400.30000 0004 1937 0650Department of Chemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Huldrych F. Günthard
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.412004.30000 0004 0478 9977Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Andreas Plückthun
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland.
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Si Y, Kim S, Ou J, Lu Y, Ernst P, Chen K, Whitt J, Carter AM, Markert JM, Bibb JA, Chen H, Zhou L, Jaskula-Sztul R, Liu XM. Anti-SSTR2 antibody-drug conjugate for neuroendocrine tumor therapy. Cancer Gene Ther 2021; 28:799-812. [PMID: 32684623 PMCID: PMC7854894 DOI: 10.1038/s41417-020-0196-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/18/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
Neuroendocrine (NE) tumors include a diverse spectrum of hormone-secreting neoplasms that arise from the endocrine and nervous systems. Current chemo- and radio-therapies have marginal curative benefits. The goal of this study was to develop an innovative antibody-drug conjugate (ADC) to effectively treat NE tumors (NETs). First, we confirmed that somatostatin receptor 2 (SSTR2) is an ideal cancer cell surface target by analyzing 38 patient-derived NET tissues, 33 normal organs, and three NET cell lines. Then, we developed a new monoclonal antibody (mAb, IgG1, and kappa) to target two extracellular domains of SSTR2, which showed strong and specific surface binding to NETs. The ADC was constructed by conjugating the anti-SSTR2 mAb and antimitotic monomethyl auristatin E. In vitro evaluations indicated that the ADC can effectively bind, internalize, release payload, and kill NET cells. Finally, the ADC was evaluated in vivo using a NET xenograft mouse model to assess cancer-specific targeting, tolerated dosage, pharmacokinetics, and antitumor efficacy. The anti-SSTR2 ADC exclusively targeted and killed NET cells with minimal toxicity and high stability in vivo. This study demonstrates that the anti-SSTR2 ADC has a high-therapeutic potential for NET therapy.
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Affiliation(s)
- Yingnan Si
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), 1825 University Blvd, Birmingham, AL, 35294, USA
| | - Seulhee Kim
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), 1825 University Blvd, Birmingham, AL, 35294, USA
| | - Jianfa Ou
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), 1825 University Blvd, Birmingham, AL, 35294, USA
| | - Yun Lu
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), 1825 University Blvd, Birmingham, AL, 35294, USA
| | - Patrick Ernst
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), 1825 University Blvd, Birmingham, AL, 35294, USA
| | - Kai Chen
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), 1825 University Blvd, Birmingham, AL, 35294, USA
| | - Jason Whitt
- Department of Surgery, UAB, 1808 7th Avenue South, Birmingham, AL, 35294, USA
| | - Angela M Carter
- Department of Surgery, UAB, 1808 7th Avenue South, Birmingham, AL, 35294, USA
| | - James M Markert
- Department of Neurosurgery, UAB, 510 20th Street South, Birmingham, AL, 35294, USA
- O'Neal Comprehensive Cancer Center, UAB, 1824 6th Avenue South, Birmingham, AL, 35233, USA
| | - James A Bibb
- Department of Surgery, UAB, 1808 7th Avenue South, Birmingham, AL, 35294, USA
- O'Neal Comprehensive Cancer Center, UAB, 1824 6th Avenue South, Birmingham, AL, 35233, USA
| | - Herbert Chen
- Department of Surgery, UAB, 1808 7th Avenue South, Birmingham, AL, 35294, USA
- O'Neal Comprehensive Cancer Center, UAB, 1824 6th Avenue South, Birmingham, AL, 35233, USA
| | - Lufang Zhou
- Department of Medicine, UAB, 703 19th Street South, Birmingham, AL, 35294, USA
| | - Renata Jaskula-Sztul
- Department of Surgery, UAB, 1808 7th Avenue South, Birmingham, AL, 35294, USA.
- O'Neal Comprehensive Cancer Center, UAB, 1824 6th Avenue South, Birmingham, AL, 35233, USA.
| | - Xiaoguang Margaret Liu
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), 1825 University Blvd, Birmingham, AL, 35294, USA.
- O'Neal Comprehensive Cancer Center, UAB, 1824 6th Avenue South, Birmingham, AL, 35233, USA.
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9
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Yang L, Deng J, Ma W, Qiao A, Xu S, Yu Y, Boriboun C, Kang X, Han D, Ernst P, Zhou L, Shi J, Zhang E, Li TS, Qiu H, Nakagawa S, Blackshaw S, Zhang J, Qin G. Ablation of lncRNA Miat attenuates pathological hypertrophy and heart failure. Am J Cancer Res 2021; 11:7995-8007. [PMID: 34335976 PMCID: PMC8315059 DOI: 10.7150/thno.50990] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 04/29/2021] [Indexed: 12/11/2022] Open
Abstract
Rationale: The conserved long non-coding RNA (lncRNA) myocardial infarction associate transcript (Miat) was identified for its multiple single-nucleotide polymorphisms that are strongly associated with susceptibility to MI, but its role in cardiovascular biology remains elusive. Here we investigated whether Miat regulates cardiac response to pathological hypertrophic stimuli. Methods: Both an angiotensin II (Ang II) infusion model and a transverse aortic constriction (TAC) model were used in adult WT and Miat-null knockout (Miat-KO) mice to induce pathological cardiac hypertrophy. Heart structure and function were evaluated by echocardiography and histological assessments. Gene expression in the heart was evaluated by RNA sequencing (RNA-seq), quantitative real-time RT-PCR (qRT-PCR), and Western blotting. Primary WT and Miat-KO mouse cardiomyocytes were isolated and used in Ca2+ transient and contractility measurements. Results: Continuous Ang II infusion for 4 weeks induced concentric hypertrophy in WT mice, but to a lesser extent in Miat-KO mice. Surgical TAC for 6 weeks resulted in decreased systolic function and heart failure in WT mice but not in Miat-KO mice. In both models, Miat-KO mice displayed reduced heart-weight to tibia-length ratio, cardiomyocyte cross-sectional area, cardiomyocyte apoptosis, and cardiac interstitial fibrosis and a better-preserved capillary density, as compared to WT mice. In addition, Ang II treatment led to significantly reduced mRNA and protein expression of the Ca2+ cycling genes Sarcoplasmic/endoplasmic reticulum Ca2+ ATPase 2a (SERCA2a) and ryanodine receptor 2 (RyR2) and a dramatic increase in global RNA splicing events in the left ventricle (LV) of WT mice, and these changes were largely blunted in Miat-KO mice. Consistently, cardiomyocytes isolated from Miat-KO mice demonstrated more efficient Ca2+ cycling and greater contractility. Conclusions: Ablation of Miat attenuates pathological hypertrophy and heart failure, in part, by enhancing cardiomyocyte contractility.
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Kast F, Schwill M, Stüber JC, Pfundstein S, Nagy-Davidescu G, Rodríguez JMM, Seehusen F, Richter CP, Honegger A, Hartmann KP, Weber TG, Kroener F, Ernst P, Piehler J, Plückthun A. Engineering an anti-HER2 biparatopic antibody with a multimodal mechanism of action. Nat Commun 2021; 12:3790. [PMID: 34145240 PMCID: PMC8213836 DOI: 10.1038/s41467-021-23948-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 05/25/2021] [Indexed: 02/07/2023] Open
Abstract
The receptor tyrosine kinase HER2 acts as oncogenic driver in numerous cancers. Usually, the gene is amplified, resulting in receptor overexpression, massively increased signaling and unchecked proliferation. However, tumors become frequently addicted to oncogenes and hence are druggable by targeted interventions. Here, we design an anti-HER2 biparatopic and tetravalent IgG fusion with a multimodal mechanism of action. The molecule first induces HER2 clustering into inactive complexes, evidenced by reduced mobility of surface HER2. However, in contrast to our earlier binders based on DARPins, clusters of HER2 are thereafter robustly internalized and quantitatively degraded. This multimodal mechanism of action is found only in few of the tetravalent constructs investigated, which must target specific epitopes on HER2 in a defined geometric arrangement. The inhibitory effect of our antibody as single agent surpasses the combination of trastuzumab and pertuzumab as well as its parental mAbs in vitro and it is effective in a xenograft model.
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Affiliation(s)
- Florian Kast
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Martin Schwill
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
- TOLREMO therapeutics AG, Muttenz, Switzerland
| | - Jakob C Stüber
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
- Roche Innovation Center Munich, Penzberg, Germany
| | - Svende Pfundstein
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
- Zurich Integrative Rodent Physiology (ZIRP), University of Zurich, Zurich, Switzerland
| | | | - Josep M Monné Rodríguez
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Frauke Seehusen
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Christian P Richter
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | | | | | | | | | - Patrick Ernst
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
- Dean's Office and Coordination Office of the Academic Medicine Zurich, University of Zurich, Zurich, Switzerland
| | - Jacob Piehler
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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11
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Chen K, Si Y, Ou J, Guan JS, Kim S, Ernst P, Zhang Y, Zhou L, Han X, Liu X(M. Antibody-Drug Conjugate to Treat Meningiomas. Pharmaceuticals (Basel) 2021; 14:ph14050427. [PMID: 34063284 PMCID: PMC8147502 DOI: 10.3390/ph14050427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/27/2021] [Accepted: 04/30/2021] [Indexed: 12/16/2022] Open
Abstract
Meningiomas are primary tumors of the central nervous system with high recurrence. It has been reported that somatostatin receptor 2 (SSTR2) is highly expressed in most meningiomas, but there is no effective targeted therapy approved to control meningiomas. This study aimed to develop and evaluate an anti-SSTR2 antibody–drug conjugate (ADC) to target and treat meningiomas. The meningioma targeting, circulation stability, toxicity, and anti-tumor efficacy of SSTR2 ADC were evaluated using cell lines and/or an intracranial xenograft mouse model. The flow cytometry analysis showed that the anti-SSTR2 mAb had a high binding rate of >98% to meningioma CH157-MN cells but a low binding rate of <5% to the normal arachnoidal AC07 cells. The In Vivo Imaging System (IVIS) imaging demonstrated that the Cy5.5-labeled ADC targeted and accumulated in meningioma xenograft but not in normal organs. The pharmacokinetics study and histological analysis confirmed the stability and minimal toxicity. In vitro anti-cancer cytotoxicity indicated a high potency of ADC with an IC50 value of <10 nM. In vivo anti-tumor efficacy showed that the anti-SSTR2 ADC with doses of 8 and 16 mg/kg body weight effectively inhibited tumor growth. This study demonstrated that the anti-SSTR2 ADC can target meningioma and reduce the tumor growth.
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Affiliation(s)
- Kai Chen
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), 1825 University Blvd, Birmingham, AL 35294, USA; (K.C.); (Y.S.); (J.O.); (S.K.); (Y.Z.); (L.Z.)
| | - Yingnan Si
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), 1825 University Blvd, Birmingham, AL 35294, USA; (K.C.); (Y.S.); (J.O.); (S.K.); (Y.Z.); (L.Z.)
| | - Jianfa Ou
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), 1825 University Blvd, Birmingham, AL 35294, USA; (K.C.); (Y.S.); (J.O.); (S.K.); (Y.Z.); (L.Z.)
| | - Jia-Shiung Guan
- Department of Medicine, University of Alabama at Birmingham, 703 19th Street South, Birmingham, AL 35294, USA; (J.-S.G.); (P.E.)
| | - Seulhee Kim
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), 1825 University Blvd, Birmingham, AL 35294, USA; (K.C.); (Y.S.); (J.O.); (S.K.); (Y.Z.); (L.Z.)
| | - Patrick Ernst
- Department of Medicine, University of Alabama at Birmingham, 703 19th Street South, Birmingham, AL 35294, USA; (J.-S.G.); (P.E.)
| | - Ya Zhang
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), 1825 University Blvd, Birmingham, AL 35294, USA; (K.C.); (Y.S.); (J.O.); (S.K.); (Y.Z.); (L.Z.)
| | - Lufang Zhou
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), 1825 University Blvd, Birmingham, AL 35294, USA; (K.C.); (Y.S.); (J.O.); (S.K.); (Y.Z.); (L.Z.)
- Department of Medicine, University of Alabama at Birmingham, 703 19th Street South, Birmingham, AL 35294, USA; (J.-S.G.); (P.E.)
| | - Xiaosi Han
- Department of Neurology, University of Alabama at Birmingham, 1824 6th Avenue South, Birmingham, AL 35294, USA;
| | - Xiaoguang (Margaret) Liu
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), 1825 University Blvd, Birmingham, AL 35294, USA; (K.C.); (Y.S.); (J.O.); (S.K.); (Y.Z.); (L.Z.)
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, 1824 6th Avenue South, Birmingham, AL 35233, USA
- Correspondence: ; Tel.: +1-205-996-1042; Fax: +1-205-996-4701
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12
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Ernst P, Chen K, Tang Y, Kim S, Guan J, He J, Xie M, Zhang JJ, Liu XM, Zhou L. Investigation into the difference in mitochondrial-cytosolic calcium coupling between adult cardiomyocyte and hiPSC-CM using a novel multifunctional genetic probe. Pflugers Arch 2021; 473:447-459. [PMID: 33587181 PMCID: PMC8100988 DOI: 10.1007/s00424-021-02524-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/24/2021] [Accepted: 01/26/2021] [Indexed: 10/22/2022]
Abstract
Ca2+ cycling plays a critical role in regulating cardiomyocyte (CM) function under both physiological and pathological conditions. Mitochondria have been implicated in Ca2+ handling in adult cardiomyocytes (ACMs). However, little is known about their role in the regulation of Ca2+ dynamics in human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). In the present study, we developed a multifunctional genetically encoded Ca2+ probe capable of simultaneously measuring cytosolic and mitochondrial Ca2+ in real time. Using this novel probe, we determined and compared mitochondrial Ca2+ activity and the coupling with cytosolic Ca2+ dynamics in hiPSC-CMs and ACMs. Our data showed that while ACMs displayed a highly coordinated beat-by-beat response in mitochondrial Ca2+ in sync with cytosolic Ca2+, hiPSC-CMs showed high cell-wide variability in mitochondrial Ca2+ activity that is poorly coordinated with cytosolic Ca2+. We then revealed that mitochondrial-sarcoplasmic reticulum (SR) tethering, as well as the inter-mitochondrial network connection, is underdeveloped in hiPSC-CM compared to ACM, which may underlie the observed spatiotemporal decoupling between cytosolic and mitochondrial Ca2+ dynamics. Finally, we showed that knockdown of mitofusin-2 (Mfn2), a protein tethering mitochondria and SR, led to reduced cytosolic-mitochondrial Ca2+ coupling in ACMs, albeit to a lesser degree compared to hiPSC-CMs, suggesting that Mfn2 is a potential engineering target for improving mitochondrial-cytosolic Ca2+ coupling in hiPSC-CMs. Physiological relevance: The present study will advance our understanding of the role of mitochondria in Ca2+ handling and cycling in CMs, and guide the development of hiPSC-CMs for healing injured hearts.
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Affiliation(s)
- Patrick Ernst
- Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Kai Chen
- Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Yawen Tang
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Seulhee Kim
- Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Jiashiung Guan
- Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Jin He
- Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Min Xie
- Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Jianyi Jay Zhang
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Xiaoguang Margaret Liu
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Lufang Zhou
- Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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13
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Skopinski L, Ernst P, Herder M, Kozubek R, Madauß L, Sleziona S, Maas A, Königstein N, Lebius H, Wucher A, Schleberger M. Time-of-flight mass spectrometry of particle emission during irradiation with slow, highly charged ions. Rev Sci Instrum 2021; 92:023909. [PMID: 33648083 DOI: 10.1063/5.0025812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
We describe a setup for the analysis of secondary ions and neutrals emitted from solid surfaces and two-dimensional materials during irradiation with highly charged ions. The ultrahigh vacuum setup consists of an electron beam ion source to produce bunches of ions with various charge states q (e.g., Xe1+-Xe46+) and thus potential energies, a deceleration/acceleration section to tune the kinetic energy of the ions in the range of 5 keV to 20 × q keV, a sample stage for laser-cleaning and positioning of freestanding as well as supported samples, a pulsed excimer laser for post-ionization of sputtered neutrals, and a reflectron type time-of-flight mass spectrometer, enabling us to analyze mass and velocity distributions of the emitted particles. With our setup, contributions from potential and kinetic energy deposition can be studied independently of each other. Charge dependent experiments conducted at a constant kinetic energy show a clear threshold for the emission of secondary ions from SrTiO3. Data taken with the same projectile charge state, but at a different kinetic energy, reveal a difference in the ratio of emitted particles from MoS2. In addition, first results are presented, demonstrating how velocity distributions can be measured with the new setup.
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Affiliation(s)
- L Skopinski
- Fakultät für Physik and CENIDE, Universität Duisburg-Essen, 47057 Duisburg, Germany
| | - P Ernst
- Fakultät für Physik and CENIDE, Universität Duisburg-Essen, 47057 Duisburg, Germany
| | - M Herder
- Fakultät für Physik and CENIDE, Universität Duisburg-Essen, 47057 Duisburg, Germany
| | - R Kozubek
- Fakultät für Physik and CENIDE, Universität Duisburg-Essen, 47057 Duisburg, Germany
| | - L Madauß
- Fakultät für Physik and CENIDE, Universität Duisburg-Essen, 47057 Duisburg, Germany
| | - S Sleziona
- Fakultät für Physik and CENIDE, Universität Duisburg-Essen, 47057 Duisburg, Germany
| | - A Maas
- Fakultät für Physik and CENIDE, Universität Duisburg-Essen, 47057 Duisburg, Germany
| | - N Königstein
- Fakultät für Physik and CENIDE, Universität Duisburg-Essen, 47057 Duisburg, Germany
| | - H Lebius
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
| | - A Wucher
- Fakultät für Physik and CENIDE, Universität Duisburg-Essen, 47057 Duisburg, Germany
| | - M Schleberger
- Fakultät für Physik and CENIDE, Universität Duisburg-Essen, 47057 Duisburg, Germany
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14
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Deluigi M, Klipp A, Klenk C, Merklinger L, Eberle SA, Morstein L, Heine P, Mittl PRE, Ernst P, Kamenecka TM, He Y, Vacca S, Egloff P, Honegger A, Plückthun A. Complexes of the neurotensin receptor 1 with small-molecule ligands reveal structural determinants of full, partial, and inverse agonism. Sci Adv 2021; 7:7/5/eabe5504. [PMID: 33571132 PMCID: PMC7840143 DOI: 10.1126/sciadv.abe5504] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/09/2020] [Indexed: 05/15/2023]
Abstract
Neurotensin receptor 1 (NTSR1) and related G protein-coupled receptors of the ghrelin family are clinically unexploited, and several mechanistic aspects of their activation and inactivation have remained unclear. Enabled by a new crystallization design, we present five new structures: apo-state NTSR1 as well as complexes with nonpeptide inverse agonists SR48692 and SR142948A, partial agonist RTI-3a, and the novel full agonist SRI-9829, providing structural rationales on how ligands modulate NTSR1. The inverse agonists favor a large extracellular opening of helices VI and VII, undescribed so far for NTSR1, causing a constriction of the intracellular portion. In contrast, the full and partial agonists induce a binding site contraction, and their efficacy correlates with the ability to mimic the binding mode of the endogenous agonist neurotensin. Providing evidence of helical and side-chain rearrangements modulating receptor activation, our structural and functional data expand the mechanistic understanding of NTSR1 and potentially other peptidergic receptors.
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Affiliation(s)
- Mattia Deluigi
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Alexander Klipp
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Christoph Klenk
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Lisa Merklinger
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Stefanie A Eberle
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Lena Morstein
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Philipp Heine
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Peer R E Mittl
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Patrick Ernst
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Theodore M Kamenecka
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #A2A, Jupiter, FL 33458, USA
| | - Yuanjun He
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #A2A, Jupiter, FL 33458, USA
| | - Santiago Vacca
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Pascal Egloff
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Annemarie Honegger
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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15
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Kapp JN, Schaefer JV, Verdurmen W, Nagy G, Degen R, Ernst P, Scholl C, Plückthun A. Abstract B27: A DARPin-based toolbox to understand and treat RAS-addicted cancers. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.ras18-b27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The repeating failure of small molecules as specific inhibitors of KRAS has drawn the attention to macromolecular structures, which can recognize their target with high affinity and specificity. Designed Ankyrin Repeat Proteins (DARPins) are multipurpose alternative affinity reagents that have proved to recognize targets with exceptional specificities and selectivity that often surpass those of antibodies. Due to their additional outstanding ability to act intracellularly within living cells and their recognition of structural rather than linear epitopes, DARPins have enabled a multitude of more advanced projects. In-house selections against GTP- or GDP-loaded KRAS were performed, and several hundred different DARPins could be identified. In subsequent validations, we not only analyzed their affinities, but also focused on the essential features of cross-reactivities, the recognition of various epitopes and their biologic functionalities. A number of candidates directly interfere with the RAS-Raf interaction and SOS-mediated nucleotide exchange by binding to the identical epitope on RAS as proved by crystal structures. One of these lead candidates with an affinity of 10 nM was used to elucidate whether anti-KRAS DARPins can mediate a biologic effect in model systems of human cancers. For this purpose, we chose cell lines categorized as KRAS dependent to generate stable cell lines expressing a highly active anti-KRAS DARPin under an inducible promotor, and it revealed potent antitumor activity, reducing the proliferation, colony formation and anchorage-independent growth. We could furthermore show that the observed effect resulted from reduced signaling of KRAS through its downstream MEK-ERK and PI3K-AKT pathways and the induction of apoptosis. Importantly, this anti-KRAS DARPin was shown to have no effects in the immortalized cell line HEK293T. In addition to traditional knockdown approaches, this model could be used to assess RAS dependency of human cancers. Combined with various suitable intracellular delivery techniques currently under development in our laboratory, the potential of this model will be further investigated for its potential in the treatment of solid tumors in a mouse model. In our broad effort many additional DARPins were identified that recognize different, nonoverlapping epitopes and most likely will interfere with other essential functions, such as the nanoclustering of RAS. This toolbox also allows the development of various biosensors in living cells. This large set of binders has the potential not just to help the community to gain detailed insights into the various functions and of RAS, but also might highlight novel vulnerabilities and innovative ways to finally make these key players druggable.
Citation Format: Jonas N. Kapp, Jonas V. Schaefer, Wouter Verdurmen, Gabriela Nagy, Ralph Degen, Patrick Ernst, Claudia Scholl, Andreas Plückthun. A DARPin-based toolbox to understand and treat RAS-addicted cancers [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr B27.
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16
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Kim S, Song J, Ernst P, Latimer MN, Ha CM, Goh KY, Ma W, Rajasekaran NS, Zhang J, Liu X, Prabhu SD, Qin G, Wende AR, Young ME, Zhou L. MitoQ regulates redox-related noncoding RNAs to preserve mitochondrial network integrity in pressure-overload heart failure. Am J Physiol Heart Circ Physiol 2020; 318:H682-H695. [PMID: 32004065 PMCID: PMC7099446 DOI: 10.1152/ajpheart.00617.2019] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/29/2020] [Accepted: 01/29/2020] [Indexed: 01/04/2023]
Abstract
Evidence suggests that mitochondrial network integrity is impaired in cardiomyocytes from failing hearts. While oxidative stress has been implicated in heart failure (HF)-associated mitochondrial remodeling, the effect of mitochondrial-targeted antioxidants, such as mitoquinone (MitoQ), on the mitochondrial network in a model of HF (e.g., pressure overload) has not been demonstrated. Furthermore, the mechanism of this regulation is not completely understood with an emerging role for posttranscriptional regulation via long noncoding RNAs (lncRNAs). We hypothesized that MitoQ preserves mitochondrial fusion proteins (i.e., mitofusin), likely through redox-sensitive lncRNAs, leading to improved mitochondrial network integrity in failing hearts. To test this hypothesis, 8-wk-old C57BL/6J mice were subjected to ascending aortic constriction (AAC), which caused substantial left ventricular (LV) chamber remodeling and remarkable contractile dysfunction in 1 wk. Transmission electron microscopy and immunostaining revealed defective intermitochondrial and mitochondrial-sarcoplasmic reticulum ultrastructure in AAC mice compared with sham-operated animals, which was accompanied by elevated oxidative stress and suppressed mitofusin (i.e., Mfn1 and Mfn2) expression. MitoQ (1.36 mg·day-1·mouse-1, 7 consecutive days) significantly ameliorated LV dysfunction, attenuated Mfn2 downregulation, improved interorganellar contact, and increased metabolism-related gene expression. Moreover, our data revealed that MitoQ alleviated the dysregulation of an Mfn2-associated lncRNA (i.e., Plscr4). In summary, the present study supports a unique mechanism by which MitoQ improves myocardial intermitochondrial and mitochondrial-sarcoplasmic reticulum (SR) ultrastructural remodeling in HF by maintaining Mfn2 expression via regulation by an lncRNA. These findings underscore the important role of lncRNAs in the pathogenesis of HF and the potential of targeting them for effective HF treatment.NEW & NOTEWORTHY We have shown that MitoQ improves cardiac mitochondrial network integrity and mitochondrial-SR alignment in a pressure-overload mouse heart-failure model. This may be occurring partly through preventing the dysregulation of a redox-sensitive lncRNA-microRNA pair (i.e., Plscr4-miR-214) that results in an increase in mitofusin-2 expression.
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Affiliation(s)
- Seulhee Kim
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jiajia Song
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Patrick Ernst
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama
| | - Mary N Latimer
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Chae-Myeong Ha
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Kah Yong Goh
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Wenxia Ma
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Jianhua Zhang
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Xiaoguang Liu
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama
| | - Sumanth D Prabhu
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Gangjian Qin
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama
| | - Adam R Wende
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Martin E Young
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Lufang Zhou
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama
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17
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Abstract
Peptides play an important role in intermolecular interactions and are frequent analytes in diagnostic assays, also as unstructured, linear epitopes in whole proteins. Yet, due to the many different sequence possibilities even for short peptides, classical selection of binding proteins from a library, one at a time, is not scalable to proteomes. However, moving away from selection to a rational assembly of preselected modules binding to predefined linear epitopes would split the problem into smaller parts. These modules could then be reassembled in any desired order to bind to, in principle, arbitrary sequences, thereby circumventing any new rounds of selection. Designed Armadillo repeat proteins (dArmRPs) are modular, and they do bind elongated peptides in a modular way. Their consensus sequence carries pockets that prefer arginine and lysine. In our quest to select pockets for all amino acid side chains, we had discovered that repetitive sequences can lead to register shifts and peptide flipping during selections from libraries, hindering the selection of new binding specificities. To solve this problem, we now created an orthogonal binding specificity by a combination of grafting from β-catenin, computational design and mutual optimization of the pocket and the bound peptide. We have confirmed the design and the desired interactions by X-ray structure determination. Furthermore, we could confirm the absence of sliding in solution by a single-molecule Förster resonance energy transfer. The new pocket could be moved from the N-terminus of the protein to the middle, retaining its properties, further underlining the modularity of the system.
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Affiliation(s)
- Patrick Ernst
- Department of Biochemistry, University Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Franziska Zosel
- Department of Biochemistry, University Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Christian Reichen
- Department of Biochemistry, University Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry, University Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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18
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Ou J, Bao T, Ernst P, Si Y, Prabhu SD, Wu H, Zhang J(J, Zhou L, Yang ST, Liu X(M. Intracellular metabolism analysis of Clostridium cellulovorans via modeling integrating proteomics, metabolomics and fermentation. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.10.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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19
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Mittl PR, Ernst P, Plückthun A. Chaperone-assisted structure elucidation with DARPins. Curr Opin Struct Biol 2020; 60:93-100. [PMID: 31918361 DOI: 10.1016/j.sbi.2019.12.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/16/2019] [Accepted: 12/05/2019] [Indexed: 12/14/2022]
Abstract
Designed ankyrin repeat proteins (DARPins) are artificial binding proteins that have found many uses in therapy, diagnostics and biochemical research. They substantially extend the scope of antibody-derived binders. Their high affinity and specificity, rigidity, extended paratope, and facile bacterial production make them attractive for structural biology. Complexes with simple DARPins have been crystallized for a long time, but particularly the rigid helix fusion strategy has opened new opportunities. Rigid DARPin fusions expand crystallization space, enable recruitment of targets in a host lattice and reduce the size limit for cryo-EM. Besides applications in structural biology, rigid DARPin fusions also serve as molecular probes in cells to investigate spatial restraints in targets.
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Affiliation(s)
- Peer Re Mittl
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Patrick Ernst
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
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20
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Ernst P, Honegger A, van der Valk F, Ewald C, Mittl PRE, Plückthun A. Rigid fusions of designed helical repeat binding proteins efficiently protect a binding surface from crystal contacts. Sci Rep 2019; 9:16162. [PMID: 31700118 PMCID: PMC6838082 DOI: 10.1038/s41598-019-52121-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/09/2019] [Indexed: 12/26/2022] Open
Abstract
Designed armadillo repeat proteins (dArmRPs) bind extended peptides in a modular way. The consensus version recognises alternating arginines and lysines, with one dipeptide per repeat. For generating new binding specificities, the rapid and robust analysis by crystallography is key. Yet, we have previously found that crystal contacts can strongly influence this analysis, by displacing the peptide and potentially distorting the overall geometry of the scaffold. Therefore, we now used protein design to minimise these effects and expand the previously described concept of shared helices to rigidly connect dArmRPs and designed ankyrin repeat proteins (DARPins), which serve as a crystallisation chaperone. To shield the peptide-binding surface from crystal contacts, we rigidly fused two DARPins to the N- and C-terminal repeat of the dArmRP and linked the two DARPins by a disulfide bond. In this ring-like structure, peptide binding, on the inside of the ring, is very regular and undistorted, highlighting the truly modular binding mode. Thus, protein design was utilised to construct a well crystallising scaffold that prevents interference from crystal contacts with peptide binding and maintains the equilibrium structure of the dArmRP. Rigid DARPin-dArmRPs fusions will also be useful when chimeric binding proteins with predefined geometries are required.
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Affiliation(s)
- Patrick Ernst
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Annemarie Honegger
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Floor van der Valk
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Christina Ewald
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.,Cytometry Facility, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Peer R E Mittl
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.
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21
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Ernst P, Plückthun A, Mittl PRE. Structural analysis of biological targets by host:guest crystal lattice engineering. Sci Rep 2019; 9:15199. [PMID: 31645583 PMCID: PMC6811568 DOI: 10.1038/s41598-019-51017-y] [Citation(s) in RCA: 10] [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: 08/15/2019] [Accepted: 09/23/2019] [Indexed: 11/17/2022] Open
Abstract
To overcome the laborious identification of crystallisation conditions for protein X-ray crystallography, we developed a method where the examined protein is immobilised as a guest molecule in a universal host lattice. We applied crystal engineering to create a generic crystalline host lattice under reproducible, predefined conditions and analysed the structures of target guest molecules of different size, namely two 15-mer peptides and green fluorescent protein (sfGFP). A fusion protein with an N-terminal endo-α-N-acetylgalactosaminidase (EngBF) domain and a C-terminal designed ankyrin repeat protein (DARPin) domain establishes the crystal lattice. The target is recruited into the host lattice, always in the same crystal form, through binding to the DARPin. The target structures can be determined rapidly from difference Fourier maps, whose quality depends on the size of the target and the orientation of the DARPin.
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Affiliation(s)
- Patrick Ernst
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.
| | - Peer R E Mittl
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.
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22
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Daneman N, Chateau D, Dahl M, Zhang J, Fisher A, Sketris IS, Quail J, Marra F, Ernst P, Bugden S. Fluoroquinolone use for uncomplicated urinary tract infections in women: a retrospective cohort study. Clin Microbiol Infect 2019; 26:613-618. [PMID: 31655215 DOI: 10.1016/j.cmi.2019.10.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/04/2019] [Accepted: 10/15/2019] [Indexed: 11/25/2022]
Abstract
OBJECTIVES The United States Food & Drug Administration released an advisory in 2016 that fluoroquinolones be relegated to second-line agents for uncomplicated urinary tract infections (UTIs) given reports of rare but serious side effects; similar warnings have followed from Health Canada and the European Medicines Agency. The objective was to determine whether alternative non-fluoroquinolone agents are as effective as fluoroquinolones in the treatment of UTIs. METHODS We conducted a retrospective population-based cohort study using administrative health data from six Canadian provinces. We identified women (n = 1 585 997) receiving antibiotic treatment for episodes of uncomplicated UTIs (n = 2 857 243) between January 1 2005 and December 31 2015. Clinical outcomes within 30 days from the initial antibiotic dispensation were compared among patients treated with a fluoroquinolone versus non-fluoroquinolone agents. High-dimensional propensity score adjustments were used to ensure comparable treatment groups and to minimize residual confounding. RESULTS Fluoroquinolone use for UTI declined over the study period in five of six Canadian provinces and accounted for 22.3-48.5% of treatments overall. The pooled effect across the provinces indicated that fluoroquinolones were associated with fewer return outpatient visits (OR 0.89, 95%CI 0.87-0.92), emergency department visits (OR 0.74, 95%CI 0.61-0.89), hospitalizations (OR 0.83, 95%CI 0.77-0.88), and repeat antibiotic dispensations (OR 0.77, 95%CI 0.75-0.80) within 30 days. CONCLUSIONS Fluoroquinolones are associated with improved clinical outcomes among women with uncomplicated UTIs. This benefit must be weighed against the risk of fluoroquinolone resistance and rare but serious fluoroquinolone side effects when selecting first-line treatment for these patients.
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Affiliation(s)
- N Daneman
- Institute for Clinical Evaluative Sciences, Toronto, Ontario, Canada; Sunnybrook Research Institute, Toronto, Ontario, Canada; Division of Infectious Diseases, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada; Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - D Chateau
- Manitoba Centre for Health Policy, Department of Community Health Sciences, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - M Dahl
- Manitoba Centre for Health Policy, Department of Community Health Sciences, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - J Zhang
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - A Fisher
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - I S Sketris
- College of Pharmacy, Dalhousie University, Halifax, Nova Scotia, Canada
| | - J Quail
- Health Quality Council, Saskatoon, Saskatchewan, Canada; Department of Community Health & Epidemiology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - F Marra
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - P Ernst
- Centre for Clinical Epidemiology, Lady Davis Institute - Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - S Bugden
- School of Pharmacy, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada; College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.
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23
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Dunne M, Rupf B, Tala M, Qabrati X, Ernst P, Shen Y, Sumrall E, Heeb L, Plückthun A, Loessner MJ, Kilcher S. Reprogramming Bacteriophage Host Range through Structure-Guided Design of Chimeric Receptor Binding Proteins. Cell Rep 2019; 29:1336-1350.e4. [DOI: 10.1016/j.celrep.2019.09.062] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/07/2019] [Accepted: 09/19/2019] [Indexed: 01/08/2023] Open
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24
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Ernst P, Xu N, Qu J, Chen H, Goldberg MS, Darley-Usmar V, Zhang JJ, O'Rourke B, Liu X, Zhou L. Precisely Control Mitochondria with Light to Manipulate Cell Fate Decision. Biophys J 2019; 117:631-645. [PMID: 31400914 DOI: 10.1016/j.bpj.2019.06.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/13/2019] [Accepted: 06/17/2019] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial dysfunction has been implicated in many pathological conditions and diseases. The normal functioning of mitochondria relies on maintaining the inner mitochondrial membrane potential (also known as ΔΨm) that is essential for ATP synthesis, Ca2+ homeostasis, redox balance, and regulation of other key signaling pathways such as mitophagy and apoptosis. However, the detailed mechanisms by which ΔΨm regulates cellular function remain incompletely understood, partially because of the difficulty of manipulating ΔΨm with spatiotemporal resolution, reversibility, or cell type specificity. To address this need, we have developed a next generation optogenetic-based technique for controllable mitochondrial depolarization with light. We demonstrate successful targeting of the heterologous channelrhodopsin-2 fusion protein to the inner mitochondrial membrane and formation of functional cationic channels capable of light-induced selective ΔΨm depolarization and mitochondrial autophagy. Importantly, we for the first time, to our knowledge, show that optogenetic-mediated mitochondrial depolarization can be well controlled to differentially influence the fate of cells expressing mitochondrial channelrhodopsin-2; whereas sustained moderate light illumination induces substantial apoptotic cell death, transient mild light illumination elicits cytoprotection via mitochondrial preconditioning. Finally, we show that Parkin overexpression exacerbates, instead of ameliorating, mitochondrial depolarization-mediated cell death in HeLa cells. In summary, we provide evidence that the described mitochondrial-targeted optogenetics may have a broad application for studying the role of mitochondria in regulating cell function and fate decision.
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Affiliation(s)
- Patrick Ernst
- Departments of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama; Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Ningning Xu
- Departments of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jing Qu
- Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Herbert Chen
- Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | | | | | - Jianyi J Zhang
- Departments of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama
| | - Brian O'Rourke
- Division of Cardiology, Department of Medicine, The Johns Hopkins University, Baltimore, Maryland
| | - Xiaoguang Liu
- Departments of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama
| | - Lufang Zhou
- Departments of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama; Medicine, University of Alabama at Birmingham, Birmingham, Alabama.
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25
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ElGamacy M, Coles M, Ernst P, Zhu H, Hartmann MD, Plückthun A, Lupas AN. An Interface-Driven Design Strategy Yields a Novel, Corrugated Protein Architecture. ACS Synth Biol 2018; 7:2226-2235. [PMID: 30148951 DOI: 10.1021/acssynbio.8b00224] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Designing proteins with novel folds remains a major challenge, as the biophysical properties of the target fold are not known a priori and no sequence profile exists to describe its features. Therefore, most computational design efforts so far have been directed toward creating proteins that recapitulate existing folds. Here we present a strategy centered upon the design of novel intramolecular interfaces that enables the construction of a target fold from a set of starting fragments. This strategy effectively reduces the amount of computational sampling necessary to achieve an optimal sequence, without compromising the level of topological control. The solenoid architecture has been a target of extensive protein design efforts, as it provides a highly modular platform of low topological complexity. However, none of the previous efforts have attempted to depart from the natural form, which is characterized by a uniformly handed superhelical architecture. Here we aimed to design a more complex platform, abolishing the superhelicity by introducing internally alternating handedness, resulting in a novel, corrugated architecture. We employed our interface-driven strategy, designing three proteins and confirming the design by solving the structure of two examples.
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Affiliation(s)
- Mohammad ElGamacy
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Murray Coles
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Patrick Ernst
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Hongbo Zhu
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Marcus D. Hartmann
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andrei N. Lupas
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany
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26
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Yang R, Ernst P, Song J, Liu XM, Huke S, Wang S, Zhang JJ, Zhou L. Mitochondrial-Mediated Oxidative Ca 2+/Calmodulin-Dependent Kinase II Activation Induces Early Afterdepolarizations in Guinea Pig Cardiomyocytes: An In Silico Study. J Am Heart Assoc 2018; 7:e008939. [PMID: 30371234 PMCID: PMC6201444 DOI: 10.1161/jaha.118.008939] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/07/2018] [Indexed: 12/23/2022]
Abstract
Background Oxidative stress-mediated Ca2+/calmodulin-dependent protein kinase II (Ca MKII) phosphorylation of cardiac ion channels has emerged as a critical contributor to arrhythmogenesis in cardiac pathology. However, the link between mitochondrial-derived reactive oxygen species (md ROS ) and increased Ca MKII activity in the context of cardiac arrhythmias has not been fully elucidated and is difficult to establish experimentally. Methods and Results We hypothesize that pathological md ROS can cause erratic action potentials through the oxidation-dependent Ca MKII activation pathway. We further propose that Ca MKII -dependent phosphorylation of sarcolemmal slow Na+ channels alone is sufficient to elicit early afterdepolarizations. To test the hypotheses, we expanded our well-established guinea pig cardiomyocyte excitation- contraction coupling, mitochondrial energetics, and ROS - induced- ROS - release model by incorporating oxidative Ca MKII activation and Ca MKII -dependent Na+ channel phosphorylation in silico. Simulations show that md ROS mediated-Ca MKII activation elicits early afterdepolarizations by augmenting the late Na+ currents, which can be suppressed by blocking L-type Ca2+ channels or Na+/Ca2+ exchangers. Interestingly, we found that oxidative Ca MKII activation-induced early afterdepolarizations are sustained even after md ROS has returned to its physiological levels. Moreover, mitochondrial-targeting antioxidant treatment can suppress the early afterdepolarizations, but only if given in an appropriate time window. Incorporating concurrent md ROS -induced ryanodine receptors activation further exacerbates the proarrhythmogenic effect of oxidative Ca MKII activation. Conclusions We conclude that oxidative Ca MKII activation-dependent Na channel phosphorylation is a critical pathway in mitochondria-mediated cardiac arrhythmogenesis.
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Affiliation(s)
- Ruilin Yang
- Key Laboratory for Mechanism Theory and Equipment Design of Ministry of EducationTianjin UniversityTianjinChina
- Department of MedicineUniversity of Alabama at BirminghamAL
| | - Patrick Ernst
- Department of Biomedical EngineeringUniversity of Alabama at BirminghamAL
| | - Jiajia Song
- Department of MedicineUniversity of Alabama at BirminghamAL
| | - Xiaoguang M. Liu
- Department of Biomedical EngineeringUniversity of Alabama at BirminghamAL
| | - Sabine Huke
- Department of MedicineUniversity of Alabama at BirminghamAL
| | - Shuxin Wang
- Key Laboratory for Mechanism Theory and Equipment Design of Ministry of EducationTianjin UniversityTianjinChina
| | - Jianyi Jay Zhang
- Department of Biomedical EngineeringUniversity of Alabama at BirminghamAL
| | - Lufang Zhou
- Department of MedicineUniversity of Alabama at BirminghamAL
- Department of Biomedical EngineeringUniversity of Alabama at BirminghamAL
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27
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Yang R, Ernst P, Song J, Liu XM, Zhang J, Zhou L. Abstract 519: Mitochondrial-mediated Oxidative CaMKII Activation Induces Early Afterdepolarizations in Guinea Pig Cardiomyocytes: An
in Silico
Study. Circ Res 2018. [DOI: 10.1161/res.123.suppl_1.519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background:
Oxidative stress-mediated CaMKII phosphorylation of cardiac ion channels has emerged as a critical contributor to arrhythmogenesis in cardiac pathology. However, the link between mitochondrial-derived reactive oxygen species (mdROS) and increased CaMKII activity in the context of cardiac arrhythmias has not been fully elucidated and is difficult to establish experimentally.
Methods:
We hypothesize that pathological mdROS can cause erratic action potentials through the oxidation-dependent CaMKII activation pathway. We further propose that CaMKII dependent phosphorylation of sarcolemmal slow sodium channels alone is sufficient to elicit early afterdepolarizations. To test the hypotheses, we expanded our well-established guinea pig cardiomyocyte
e
xcitation-
c
ontraction coupling,
m
itochondrial
e
nergetics and
R
OS-
i
nduced-
R
OS-
r
elease model by incorporating oxidative CaMKII activation and CaMKII-dependent Na
+
channel phosphorylation
in silico
.
Results:
Simulations show that mdROS mediated-CaMKII activation elicits early afterdepolarizations (EADs) by augmenting the late Na
+
currents (
I
Na,L
), which can be suppressed by blocking L-type Ca
2+
channels or Na
+
/Ca
2+
exchangers. Interestingly, we found that oxidative CaMKII activation-induced EADs sustain even after mdROS has returned to its physiological levels. Moreover, mitochondrial-targeting antioxidant treatment can suppress the EADs, but only if given in an appropriate time window. Incorporating concurrent mdROS-induced RyRs activation further exacerbates the proarrhythmogenic effect of oxidative CaMKII activation.
Conclusions:
We conclude that oxidative CaMKII activation-dependent Na channel phosphorylation is a critical pathway in mitochondria mediated cardiac arrhythmogenesis.
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28
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Brown A, Ernst P, Cambule A, Morrow M, Dortzbach D, Golub JE, Perry HB. Applying the Care Group model to tuberculosis control: findings from a community-based project in Mozambique. Int J Tuberc Lung Dis 2018; 21:1086-1093. [PMID: 28911350 DOI: 10.5588/ijtld.17.0179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We describe the effectiveness of an innovative community-based social mobilization approach called Care Groups to improve the effectiveness of the national tuberculosis (TB) program by increasing TB testing and improving treatment outcomes in six districts of rural Mozambique. METHODS The Care Group approach, which was implemented in a population of 218 191, enabled a facilitator to meet every 6 months with 10-12 community health volunteers (forming a Care Group) to share key TB messages and then for them to convey these messages over the subsequent 6 months to 10-12 households. Three household surveys were performed over 5 years to measure population-level changes in knowledge and behaviors. Data from village TB, laboratory, and district registers were also used to monitor activities and outcomes. RESULTS There were substantial improvements in TB-related knowledge and behaviors in the number of patients initiating treatment, in the percentage of patients receiving directly observed treatment, in treatment success, and in TB-related mortality. CONCLUSION Care Groups are uniquely suited to address some of the challenges of TB control. This project sheds light on a new strategy for engaging communities to address not only TB, but other health priorities as well.
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Affiliation(s)
- A Brown
- Johns Hopkins Schools of Nursing and Public Health, Baltimore, Maryland, USA
| | - P Ernst
- World Relief/Mozambique, Chokwe, Mozambique
| | - A Cambule
- World Relief/Mozambique, Chokwe, Mozambique
| | - M Morrow
- ICF (Maternal and Child Survival Program), Washington, DC
| | | | - J E Golub
- Department of Medicine, Johns Hopkins School of Medicine, Center for Tuberculosis Research, Baltimore, Maryland
| | - H B Perry
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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29
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Schmid M, Ernst P, Honegger A, Suomalainen M, Zimmermann M, Braun L, Stauffer S, Thom C, Dreier B, Eibauer M, Kipar A, Vogel V, Greber UF, Medalia O, Plückthun A. Adenoviral vector with shield and adapter increases tumor specificity and escapes liver and immune control. Nat Commun 2018; 9:450. [PMID: 29386504 PMCID: PMC5792622 DOI: 10.1038/s41467-017-02707-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/20/2017] [Indexed: 01/16/2023] Open
Abstract
Most systemic viral gene therapies have been limited by sequestration and degradation of virions, innate and adaptive immunity, and silencing of therapeutic genes within the target cells. Here we engineer a high-affinity protein coat, shielding the most commonly used vector in clinical gene therapy, human adenovirus type 5. Using electron microscopy and crystallography we demonstrate a massive coverage of the virion surface through the hexon-shielding scFv fragment, trimerized to exploit the hexon symmetry and gain avidity. The shield reduces virion clearance in the liver. When the shielded particles are equipped with adaptor proteins, the virions deliver their payload genes into human cancer cells expressing HER2 or EGFR. The combination of shield and adapter also increases viral gene delivery to xenografted tumors in vivo, reduces liver off-targeting and immune neutralization. Our study highlights the power of protein engineering for viral vectors overcoming the challenges of local and systemic viral gene therapies. Viral gene therapy can be limited by the efficacy of virion sequestration, immune responses and the silencing of genetic payloads. Here the authors engineer an advenovirus protein coat which shields the virion from the immune system while targeting cancer cells.
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Affiliation(s)
- Markus Schmid
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Patrick Ernst
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Annemarie Honegger
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Maarit Suomalainen
- Department of Molecular Life Science, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Martina Zimmermann
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Lukas Braun
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, 8093, Zurich, Switzerland
| | - Sarah Stauffer
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Cristian Thom
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Matthias Eibauer
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Anja Kipar
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 268, 8057, Zurich, Switzerland
| | - Viola Vogel
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, 8093, Zurich, Switzerland
| | - Urs F Greber
- Department of Molecular Life Science, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland.,Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, Beer-Sheva, 84105, Israel
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland.
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Mittl P, Wu Y, Ernst P, Batyuk A, Honegger A, Pluckthun A. Design and application of crystallization aids comprising DARPin domains. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317084881] [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: 11/10/2022] Open
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Ou J, Xu N, Ernst P, Ma C, Bush M, Goh K, Zhao J, Zhou L, Yang ST, Liu X(M. Process engineering of cellulosic n-butanol production from corn-based biomass using Clostridium cellulovorans. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.07.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Kasymjanova G, Small D, Cohen V, Jagoe RT, Batist G, Sateren W, Ernst P, Pepe C, Sakr L, Agulnik J. Lung cancer care trajectory at a Canadian centre: an evaluation of how wait times affect clinical outcomes. ACTA ACUST UNITED AC 2017; 24:302-309. [PMID: 29089797 DOI: 10.3747/co.24.3611] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Lung cancer continues to be one of the most common cancers in Canada, with approximately 28,400 new cases diagnosed each year. Although timely care can contribute substantially to quality of life for patients, it remains unclear whether it also improves patient outcomes. In this work, we used a set of quality indicators that aim to describe the quality of care in lung cancer patients. We assessed adherence with existing guidelines for timeliness of lung cancer care and concordance with existing standards of treatment, and we examined the association between timeliness of care and lung cancer survival. METHODS Patients with lung cancer diagnosed between 2010 and 2015 were identified from the Pulmonary Division Lung Cancer Registry at our centre. RESULTS We demonstrated that the interdisciplinary pulmonary oncology service successfully treated most of its patients within the recommended wait times. However, there is still work to be done to decrease variation in wait time. Our results demonstrate a significant association between wait time and survival, supporting the need for clinicians to optimize the patient care trajectory. INTERPRETATION It would be helpful for Canadian clinicians treating patients with lung cancer to have wait time guidelines for all treatment modalities, together with standard definitions for all time intervals. Any reductions in wait times should be balanced against the need for thorough investigation before initiating treatment. We believe that our unique model of care leads to an acceleration of diagnostic steps. Avoiding any delay associated with referral to a medical oncologist for treatment could be an acceptable strategy with respect to reducing wait time.
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Affiliation(s)
- G Kasymjanova
- Peter Brojde Lung Cancer Centre, Segal Cancer Centre, Sir Mortimer B. Davis Jewish General Hospital, Rossy Cancer Network, and McGill University, Montreal, QC
| | - D Small
- Peter Brojde Lung Cancer Centre, Segal Cancer Centre, Sir Mortimer B. Davis Jewish General Hospital, Rossy Cancer Network, and McGill University, Montreal, QC
| | - V Cohen
- Peter Brojde Lung Cancer Centre, Segal Cancer Centre, Sir Mortimer B. Davis Jewish General Hospital, Rossy Cancer Network, and McGill University, Montreal, QC
| | - R T Jagoe
- Peter Brojde Lung Cancer Centre, Segal Cancer Centre, Sir Mortimer B. Davis Jewish General Hospital, Rossy Cancer Network, and McGill University, Montreal, QC
| | - G Batist
- Peter Brojde Lung Cancer Centre, Segal Cancer Centre, Sir Mortimer B. Davis Jewish General Hospital, Rossy Cancer Network, and McGill University, Montreal, QC
| | | | - P Ernst
- Peter Brojde Lung Cancer Centre, Segal Cancer Centre, Sir Mortimer B. Davis Jewish General Hospital, Rossy Cancer Network, and McGill University, Montreal, QC
| | - C Pepe
- Peter Brojde Lung Cancer Centre, Segal Cancer Centre, Sir Mortimer B. Davis Jewish General Hospital, Rossy Cancer Network, and McGill University, Montreal, QC
| | - L Sakr
- Peter Brojde Lung Cancer Centre, Segal Cancer Centre, Sir Mortimer B. Davis Jewish General Hospital, Rossy Cancer Network, and McGill University, Montreal, QC
| | - J Agulnik
- Peter Brojde Lung Cancer Centre, Segal Cancer Centre, Sir Mortimer B. Davis Jewish General Hospital, Rossy Cancer Network, and McGill University, Montreal, QC
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Afroz T, Hock EM, Ernst P, Foglieni C, Jambeau M, Gilhespy LAB, Laferriere F, Maniecka Z, Plückthun A, Mittl P, Paganetti P, Allain FHT, Polymenidou M. Functional and dynamic polymerization of the ALS-linked protein TDP-43 antagonizes its pathologic aggregation. Nat Commun 2017; 8:45. [PMID: 28663553 PMCID: PMC5491494 DOI: 10.1038/s41467-017-00062-0] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/02/2017] [Indexed: 01/28/2023] Open
Abstract
TDP-43 is a primarily nuclear RNA-binding protein, whose abnormal phosphorylation and cytoplasmic aggregation characterizes affected neurons in patients with amyotrophic lateral sclerosis and frontotemporal dementia. Here, we report that physiological nuclear TDP-43 in mouse and human brain forms homo-oligomers that are resistant to cellular stress. Physiological TDP-43 oligomerization is mediated by its N-terminal domain, which can adopt dynamic, solenoid-like structures, as revealed by a 2.1 Å crystal structure in combination with nuclear magnetic resonance spectroscopy and electron microscopy. These head-to-tail TDP-43 oligomers are unique among known RNA-binding proteins and represent the functional form of the protein in vivo, since their destabilization results in loss of alternative splicing regulation of known neuronal RNA targets. Our findings indicate that N-terminal domain-driven oligomerization spatially separates the adjoining highly aggregation-prone, C-terminal low-complexity domains of consecutive TDP-43 monomers, thereby preventing low-complexity domain inter-molecular interactions and antagonizing the formation of pathologic aggregates.TDP-43 aggregation is observed in amyotrophic lateral sclerosis. Here the authors combine X-ray crystallography, nuclear magnetic resonance and electron microscopy studies and show that physiological oligomerization of TDP-43 is mediated through its N-terminal domain, which forms functional and dynamic oligomers antagonizing pathologic aggregation.
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Affiliation(s)
- Tariq Afroz
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Eva-Maria Hock
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Patrick Ernst
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Chiara Foglieni
- Laboratory for Biomedical Neurosciences, Neurocenter of Southern Switzerland, Via Tesserete 46, CH-6900, Lugano, Switzerland
| | - Melanie Jambeau
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Larissa A B Gilhespy
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Florent Laferriere
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Zuzanna Maniecka
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Peer Mittl
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Paolo Paganetti
- Laboratory for Biomedical Neurosciences, Neurocenter of Southern Switzerland, Via Tesserete 46, CH-6900, Lugano, Switzerland
| | - Frédéric H T Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093, Zurich, Switzerland
| | - Magdalini Polymenidou
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
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Ernst P, Plückthun A. Advances in the design and engineering of peptide-binding repeat proteins. Biol Chem 2017; 398:23-29. [DOI: 10.1515/hsz-2016-0233] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 08/23/2016] [Indexed: 11/15/2022]
Abstract
Abstract
The specific recognition of peptides, which we define to include unstructured regions or denatured forms of proteins, is an intrinsic part of a multitude of biochemical assays and procedures. Many cellular interactions are also based on this principle as well. While it would be highly desirable to have a stockpile of sequence-specific binders for essentially any sequence, a de novo selection of individual binders against every possible target peptide sequence would be rather difficult to reduce to practice. Modular peptide binders could overcome this problem, as preselected and/or predesigned modules could be reused for the generation of new binders and thereby revolutionize the generation of binding proteins. This minireview summarizes advances in the development of peptide binders and possible scaffolds for their design.
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Reichen C, Hansen S, Forzani C, Honegger A, Fleishman SJ, Zhou T, Parmeggiani F, Ernst P, Madhurantakam C, Ewald C, Mittl PR, Zerbe O, Baker D, Caflisch A, Plückthun A. Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition. J Mol Biol 2016; 428:4467-4489. [DOI: 10.1016/j.jmb.2016.09.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 10/21/2022]
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Mittl P, Hansen S, Ernst P, Plückthun A. Designed Armadillo repeat proteins serve as scaffolds for the rational assembly of peptide binders with picomolar affinities. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315095923] [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: 11/11/2022] Open
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Ducharme F, Lamontagne AJ, Pelaez S, Grad R, Lavoie K, Ernst P, McKinney ML, Bacon S, Guay H, Collin J, Blais L. 138: Prescribing Long-Term Asthma Controller in Poorly Controlled Children with Persistent Asthma: Reported Behaviour, Facilitators and Solutions. Paediatr Child Health 2015. [DOI: 10.1093/pch/20.5.e84a] [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: 11/15/2022] Open
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Ernst P, Siu A, Weikum G. KnowLife: a versatile approach for constructing a large knowledge graph for biomedical sciences. BMC Bioinformatics 2015; 16:157. [PMID: 25971816 PMCID: PMC4448285 DOI: 10.1186/s12859-015-0549-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 03/25/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Biomedical knowledge bases (KB's) have become important assets in life sciences. Prior work on KB construction has three major limitations. First, most biomedical KBs are manually built and curated, and cannot keep up with the rate at which new findings are published. Second, for automatic information extraction (IE), the text genre of choice has been scientific publications, neglecting sources like health portals and online communities. Third, most prior work on IE has focused on the molecular level or chemogenomics only, like protein-protein interactions or gene-drug relationships, or solely address highly specific topics such as drug effects. RESULTS We address these three limitations by a versatile and scalable approach to automatic KB construction. Using a small number of seed facts for distant supervision of pattern-based extraction, we harvest a huge number of facts in an automated manner without requiring any explicit training. We extend previous techniques for pattern-based IE with confidence statistics, and we combine this recall-oriented stage with logical reasoning for consistency constraint checking to achieve high precision. To our knowledge, this is the first method that uses consistency checking for biomedical relations. Our approach can be easily extended to incorporate additional relations and constraints. We ran extensive experiments not only for scientific publications, but also for encyclopedic health portals and online communities, creating different KB's based on different configurations. We assess the size and quality of each KB, in terms of number of facts and precision. The best configured KB, KnowLife, contains more than 500,000 facts at a precision of 93% for 13 relations covering genes, organs, diseases, symptoms, treatments, as well as environmental and lifestyle risk factors. CONCLUSION KnowLife is a large knowledge base for health and life sciences, automatically constructed from different Web sources. As a unique feature, KnowLife is harvested from different text genres such as scientific publications, health portals, and online communities. Thus, it has the potential to serve as one-stop portal for a wide range of relations and use cases. To showcase the breadth and usefulness, we make the KnowLife KB accessible through the health portal (http://knowlife.mpi-inf.mpg.de).
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Affiliation(s)
- Patrick Ernst
- Max-Planck-Institute for Informatics, Campus E1 4, Saarbrücken, 66123, Germany.
| | - Amy Siu
- Max-Planck-Institute for Informatics, Campus E1 4, Saarbrücken, 66123, Germany.
| | - Gerhard Weikum
- Max-Planck-Institute for Informatics, Campus E1 4, Saarbrücken, 66123, Germany.
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Faillie JL, Filion K, Patenaude V, Ernst P, Azoulay L. Les inhibiteurs de la DPP-4 et le risque de pneumonie communautaire chez les patients diabétiques de type 2. Rev Epidemiol Sante Publique 2015. [DOI: 10.1016/j.respe.2015.03.096] [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: 11/27/2022] Open
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Faillie JL, Filion KB, Patenaude V, Ernst P, Azoulay L. Dipeptidyl peptidase-4 inhibitors and the risk of community-acquired pneumonia in patients with type 2 diabetes. Diabetes Obes Metab 2015; 17:379-85. [PMID: 25581902 DOI: 10.1111/dom.12431] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/02/2015] [Accepted: 01/02/2015] [Indexed: 12/28/2022]
Abstract
AIMS To determine whether the use of dipeptidyl peptidase-4 (DPP-4) inhibitors is associated with an increased risk of community-acquired pneumonia. METHODS The UK Clinical Practice Research Datalink and the Hospital Episodes Statistics database were used to conduct a nested case-control analysis within a cohort of new users of antidiabetic drugs between 2007 and 2012. Incident cases of hospitalization for community-acquired pneumonia were matched with up to 20 controls on age, duration of treated diabetes, calendar year and duration of follow-up. Conditional logistic regression models were used to estimate the odds ratios (ORs) and 95% confidence intervals (CIs) for hospitalization for community-acquired pneumonia associated with current use of DPP-4 inhibitors compared with current use of two or more oral antidiabetic drugs. RESULTS The cohort included 49,653 patients, of whom 562 were hospitalized for community-acquired pneumonia during follow-up (incidence rate 5.2/1000 person-years). Compared with current use of two or more oral antidiabetic drugs, current use of DPP-4 inhibitors was not associated with an increased risk of hospitalized community-acquired pneumonia overall (adjusted OR 0.80, 95% CI 0.50-1.29) or according to duration of use (p for trend = 0.57). CONCLUSIONS The use of DPP-4 inhibitors was not associated with an increased risk of hospitalization for community-acquired pneumonia. Additional research is needed to assess the association between these drugs and other serious infections.
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Affiliation(s)
- J-L Faillie
- Centre for Clinical Epidemiology, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada; Department of Pharmacoepidemiology, INSERM U1027, Faculty of Medicine, Paul Sabatier University, Toulouse, France; Department of Medical Pharmacology and Toxicology, Pharmacovigilance Regional Center, CHRU Montpellier University Hospital, Montpellier, France
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Landgraf L, Ernst P, Hilger I, Köhler O, Schick I, Tremel W. Au@Fe3O4 Nanopartikel: Ein neuartiges Werkzeug in der Nanomedizin? ROFO-FORTSCHR RONTG 2014. [DOI: 10.1055/s-0034-1372775] [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: 10/25/2022]
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Lapi F, Wilchesky M, Kezouh A, Benisty JI, Ernst P, Suissa S. Fluoroquinolones and the Risk of Serious Arrhythmia: A Population-Based Study. Clin Infect Dis 2012; 55:1457-65. [DOI: 10.1093/cid/cis664] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Ernst P, Fieg G, Schlüter F, Green V. Pareto-Optimierung integrierter verfahrenstechnischer Prozesse mit modularen Zielfunktionen und Nebenbedingungen. CHEM-ING-TECH 2012. [DOI: 10.1002/cite.201250216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Gonzalez AV, Ernst P. Authors' response. Thorax 2011. [DOI: 10.1136/thx.2011.161463] [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: 11/03/2022]
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Chan-Yeung M, Anthonisen NR, Becklake MR, Bowie D, Sonia Buist A, Dimich-Ward H, Ernst P, Sears MR, Siersted HC, Sweet L, Van Til L, Manfreda J. Geographical variations in the prevalence of atopic sensitization in six study sites across Canada. Allergy 2010; 65:1404-13. [PMID: 20557300 DOI: 10.1111/j.1398-9995.2010.02399.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Geographical variations in atopic sensitization in Canada have not been described previously. This study used the standardized protocol of the European Community Respiratory Health Survey-1 (ECRHS-1) to investigate the distribution and predictors of atopic sensitization in six sites across Canada and to compare the results with some ECRHS-1 centers. METHODS Adults aged 20-44 years in six study sites across Canada underwent allergy skin testing using 14 allergens (Dermatophagoides pteronyssinus, Dermatophagoides farinae) cat, cockroach, grasses (Timothy grass, Kentucky grass), molds (Cladosporium herbarium, Alternaria alternata, Aspergillus fumigatus, Penicillium), trees (tree mix, birch, Olea europea), and common ragweed. RESULTS The overall prevalence of atopy (skin test over 0 mm to any allergen) was 62.7%. There was significant geographical variation in the prevalence of atopy in the six study sites (lowest 55.6% [95% C.I.51.3-59.9] in Prince Edward Island, highest 66.0 [61.7-70.3] in Montreal) and of sensitization to each of the allergens tested even after adjustment for confounders. When the first eight of the nine allergens in the ECRHS were used to estimate the prevalence of atopic sensitization, the prevalence of atopy in Canada was 57% compared with 35.2% overall for centers in the ECRHS. The prevalence of atopy in Vancouver (57% [52.3-61.8]) was close to that of Portland, Oregon (52.1% [46.2-58.0]). CONCLUSION There was a significant variation in atopic sensitization among different study sites across Canada. The prevalence of atopic sensitization is relatively high in Canada compared with sites in the ECRHS and this may, in part, account for the high prevalence of asthma and asthma symptoms in Canada.
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Affiliation(s)
- M Chan-Yeung
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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Abstract
The Mixed Lineage Leukemia (MLL) gene is disrupted by chromosomal translocations in acute leukemia, producing a fusion oncogene with altered properties relative to the wild-type gene. Murine loss-of-function studies have demonstrated an essential role for Mll in developing the haematopoietic system, yet studies using different conditional knockout models have yielded conflicting results regarding the requirement for Mll during adult steady-state haematopoiesis. Here, we employ a loxP-flanked Mll allele (MllF) and a developmentally-regulated, haematopoietic-specific VavCre transgene to re-assess the consequences of Mll loss in the haematopoietic lineage, without the need for inducers of Cre recombinase. We show that VavCre;Mll mutants exhibit phenotypically normal fetal haematopoiesis, but rarely survive past 3 weeks of age. Surviving animals are anemic, thrombocytopenic and exhibit a significant reduction in bone marrow haematopoietic stem/progenitor populations, consistent with our previous findings using the inducible Mx1Cre transgene. Furthermore, the analysis of VavCre mutants revealed additional defects in B-lymphopoiesis that could not be assessed using Mx1Cre-mediated Mll deletion. Collectively, these data support the conclusion that Mll plays an essential role in sustaining postnatal haematopoiesis.
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Affiliation(s)
- T Gan
- Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Hanover, NH 03755, USA
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Ducharme FM, Noya FJD, Rich H, Davis GM, Resendes S, Khomenko L, Ernst P. Randomized Controlled Trial of a Multi-Facetted Intervention Initiated in the Emergency Department (Ed) to Improve Asthma Control. Paediatr Child Health 2009. [DOI: 10.1093/pch/14.suppl_a.52aa] [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: 11/12/2022] Open
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