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Savvides S. Anaplastic lymphoma kinases and ligands: structure, mechanism and antagonism in cancer and metabolism. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322096346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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DeBouver N, Cao L, Coventry B, Bera A, Yang W, Bernard S, Stewart L, Wilson I, Ruohola-Baker H, Schlessinger J, Lee S, Savvides S, Garcia KC. Protein-binding proteins designed from target structural information. Acta Crystallogr A Found Adv 2022. [DOI: 10.1107/s2053273322097182] [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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Savvides S, Kumar S, Stephen JJ, Eugster P. C3PO:
C
loud-based
C
onfidentiality-preserving
C
ontinuous Query
P
r
o
cessing. ACM Trans Priv Secur 2022. [DOI: 10.1145/3472717] [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] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
With the advent of the Internet of things (IoT), billions of devices are expected to continuously collect and process sensitive data (e.g., location, personal health factors). Due to the limited computational capacity available on IoT devices, the current de facto model for building IoT applications is to send the gathered data to the cloud for computation. While building private cloud infrastructures for handling large amounts of data streams can be expensive, using low-cost public (untrusted) cloud infrastructures for processing continuous queries including sensitive data leads to strong concerns over data confidentiality.
This article presents C3PO, a confidentiality-preserving, continuous query processing engine, that leverages the public cloud. The key idea is to intelligently utilize partially homomorphic and property-preserving encryption to perform as many computationally intensive operations as possible—without revealing plaintext—in the untrusted cloud. C3PO provides simple abstractions to the developer to hide the complexities of applying complex cryptographic primitives, reasoning about the performance of such primitives, deciding which computations can be executed in an untrusted tier, and optimizing cloud resource usage. An empirical evaluation with several benchmarks and case studies shows the feasibility of our approach. We consider different classes of IoT devices that differ in their computational and memory resources (from a Raspberry Pi 3 to a very small device with a Cortex-M3 microprocessor) and through the use of optimizations, we demonstrate the feasibility of using partially homomorphic and property-preserving encryption on IoT devices.
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Affiliation(s)
- Savvas Savvides
- Fortanix Inc. USA , and Purdue University, Mountain View, CA, USA
| | | | | | - Patrick Eugster
- Università della Svizzera italiana, Switzerland, Purdue University USA, TU Darmstadt Germany, and SensorHound Inc., USA
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Maes B, Smole U, Vanderkerken M, Deswarte K, Van Moorleghem J, Vergote K, Vanheerswynghels M, De Wolf C, De Prijck S, Debeuf N, Pavie B, Toussaint W, Janssens S, Savvides S, Lambrecht BN, Hammad H. The STE20 kinase TAOK3 controls the development house dust mite-induced asthma in mice. J Allergy Clin Immunol 2021; 149:1413-1427.e2. [PMID: 34506849 DOI: 10.1016/j.jaci.2021.08.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/14/2021] [Accepted: 08/03/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND The most common endotype of asthma is type 2-high asthma, which is sometimes driven by adaptive allergen-specific TH2 lymphocytes that react to allergens presented by dendritic cells (DCs), or sometimes by an innate immune response dominated by type 2 innate lymphocytes (ILC2s). Understanding the underlying pathophysiology of asthma is essential to improve patient-tailored therapy. The STE20 kinase thousand-and-one kinase 3 (TAOK3) controls key features in the biology of DCs and lymphocytes, but to our knowledge, its potential usefulness as a target for asthma therapy has not yet been addressed. OBJECTIVE We examined if and how loss of Taok3 affects the development of house dust mite (HDM)-driven allergic asthma in an in vivo mouse model. METHODS Wild-type Taok3+/+ and gene-deficient Taok3-/- mice were sensitized and challenged with HDM, and bronchoalveolar lavage fluid composition, mediastinal lymph node cytokine production, lung histology, and bronchial hyperreactivity measured. Conditional Taok3fl/fl mice were crossed to tissue- and cell-specific specific deletor Cre mice to understand how Taok3 acted on asthma susceptibility. Kinase-dead (KD) Taok3KD mice were generated to probe for the druggability of this pathway. Activation of HDM-specific T cells was measured in adoptively transferred HDM-specific T-cell receptor-transgenic CD4+ T cells. ILC2 biology was assessed by in vivo and in vitro IL-33 stimulation assays in Taok3-/- and Taok3+/+, Taok3KD, and Red5-Cre Taok3fl/fl mice. RESULTS Taok3-/- mice failed to mount salient features of asthma, including airway eosinophilia, TH2 cytokine production, IgE secretion, airway goblet cell metaplasia, and bronchial hyperreactivity compared to controls. This was due to intrinsic loss of Taok3 in hematopoietic and not epithelial cells. Loss of Taok3 resulted in hampered HDM-induced lung DC migration to the draining lymph nodes and defective priming of HDM-specific TH2 cells. Strikingly, HDM and IL-33-induced ILC2 proliferation and function were also severely affected in Taok3-deficient and Taok3KD mice. CONCLUSIONS Absence of Taok3 or loss of its kinase activity protects from HDM-driven allergic asthma as a result of defects in both adaptive DC-mediated TH2 activation and innate ILC2 function. This identifies Taok3 as an interesting drug target, justifying further testing as a new treatment for type 2-high asthma.
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Affiliation(s)
- Bastiaan Maes
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium; Laboratory of ER Stress and Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Ursula Smole
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Matthias Vanderkerken
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Kim Deswarte
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Justine Van Moorleghem
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Karl Vergote
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Manon Vanheerswynghels
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Caroline De Wolf
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Sofie De Prijck
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Nincy Debeuf
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Benjamin Pavie
- VIB Bioimaging Core, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Wendy Toussaint
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Sophie Janssens
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium; Laboratory of ER Stress and Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Savvas Savvides
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent, Belgium
| | - Bart N Lambrecht
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium; Department of Pulmonary Medicine, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Hamida Hammad
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.
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Semwal S, Boukherroub R, Savvides S, Bouckaert J. Natural antibodies: Protecting role of IgM in glioblastoma and brain tumours. Curr Pharm Des 2021; 27:4515-4529. [PMID: 34323181 DOI: 10.2174/1381612827666210728103524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 06/07/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Glioblastoma is a grade IV astrocytoma with an average survival span for patients of 18 months after initial diagnosis and no standard treatment protocol. There is a need to look at novel approaches to target glioblastoma. OBJECTIVES This review intends to capture the role of immunoglobulin-M in cancer, more specifically in glioblastoma multiforme (GBM), and to compile the latest developments and immunological pathways relevant to glioblastoma Methods: Information on glioblastoma, cancer microenvironment, cancer therapeutics and how to improve the scenario was obtained from scientific literature databases such as Pubmed, Medline, Google Scholar, Science Direct, Springer, Wiley online library and some data was harvested from regulatory and compliance databases such as clinicaltrials.gov, FDA database, WHO Globocan. RESULTS AND CONCLUSIONS Currently, only a limited number of therapies are approved for GBM, and no standard of care is in place in case of disease relapse, necessitating a possible broader perspective in looking at the disease and its underlying mechanisms.
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Affiliation(s)
- Shubham Semwal
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 from the CNRS and the University of Lille, 50 Avenue Halley, 59650 Villeneuve d'Ascq, France
| | - Rabah Boukherroub
- Univ. Lille, CNRS, Centrale Lille, Univ. Polytechnique Hauts-de-France, UMR 8520 - IEMN, F-59000 Lille, France
| | - Savvas Savvides
- Unit for Structural Biology, VIB - UGent Center for Inflammation Research, Department of Biochemistry and Microbiology, Ghent University, Technologiepark 71, 9052 Ghent. Belgium
| | - Julie Bouckaert
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 from the CNRS and the University of Lille, 50 Avenue Halley, 59650 Villeneuve d'Ascq, France
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Felix J, Moharana K, Demunck S, Pannecoucke E, Elegheert J, Verstraete K, Shkumatov A, Svergun D, Gutsche I, Savvides S. Plasticity and cooperativity of cytokine-receptor assemblies at the cell surface. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314095941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Hybrid approaches in structural biology have had a tremendous impact on our ability to tackle complex biological problems including large and flexible protein-protein assemblies. We have been employing creative combinations of X-ray crystallography, Small-angle X-ray Scattering (SAXS) and electron microscopy in conjunction with molecular interaction studies and cellular interrogation of the systems under study to elucidate the structural and mechanistic principles underlying diverse cytokine-receptor assemblies. Our studies have revealed the unexpected structural diversity of such assemblies, and have established that structural plasticity and molecular cooperativity both at the level of the cytokines and the receptors play critical roles in the assembly of signaling complexes. My presentation will provide a coherent overview of how we have tackled cytokine-receptor signalling complexes in a hypothesis-driven manner with the help of hybrid approaches in structural biology.
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Dondelinger Y, Declercq W, Montessuit S, Roelandt R, Goncalves A, Bruggeman I, Hulpiau P, Weber K, Sehon CA, Marquis RW, Bertin J, Gough PJ, Savvides S, Martinou JC, Bertrand MJM, Vandenabeele P. MLKL compromises plasma membrane integrity by binding to phosphatidylinositol phosphates. Cell Rep 2014; 7:971-81. [PMID: 24813885 DOI: 10.1016/j.celrep.2014.04.026] [Citation(s) in RCA: 697] [Impact Index Per Article: 69.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/09/2014] [Accepted: 04/18/2014] [Indexed: 10/25/2022] Open
Abstract
Although mixed lineage kinase domain-like (MLKL) protein has emerged as a specific and crucial protein for necroptosis induction, how MLKL transduces the death signal remains poorly understood. Here, we demonstrate that the full four-helical bundle domain (4HBD) in the N-terminal region of MLKL is required and sufficient to induce its oligomerization and trigger cell death. Moreover, we found that a patch of positively charged amino acids on the surface of the 4HBD binds to phosphatidylinositol phosphates (PIPs) and allows recruitment of MLKL to the plasma membrane. Importantly, we found that recombinant MLKL, but not a mutant lacking these positive charges, induces leakage of PIP-containing liposomes as potently as BAX, supporting a model in which MLKL induces necroptosis by directly permeabilizing the plasma membrane. Accordingly, we found that inhibiting the formation of PI(5)P and PI(4,5)P2 specifically inhibits tumor necrosis factor (TNF)-mediated necroptosis but not apoptosis.
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Affiliation(s)
- Yves Dondelinger
- VIB Inflammation Research Center, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium
| | - Wim Declercq
- VIB Inflammation Research Center, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium
| | - Sylvie Montessuit
- Department of Cell Biology, University of Geneva, 1211 Geneva 4, Switzerland
| | - Ria Roelandt
- VIB Inflammation Research Center, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium
| | - Amanda Goncalves
- Microscopy Core Facility, VIB Inflammation Research Center, VIB/Ghent University, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium
| | - Inge Bruggeman
- VIB Inflammation Research Center, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium
| | - Paco Hulpiau
- VIB Inflammation Research Center, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium
| | - Kathrin Weber
- VIB Inflammation Research Center, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium
| | - Clark A Sehon
- Pattern Recognition Receptor Discovery Performance Unit, Immuno-Inflammation Therapeutic Area, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - Robert W Marquis
- Pattern Recognition Receptor Discovery Performance Unit, Immuno-Inflammation Therapeutic Area, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - John Bertin
- Pattern Recognition Receptor Discovery Performance Unit, Immuno-Inflammation Therapeutic Area, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - Peter J Gough
- Pattern Recognition Receptor Discovery Performance Unit, Immuno-Inflammation Therapeutic Area, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - Savvas Savvides
- Unit for Structural Biology and Biophysics, Laboratory for Protein Biochemistry and Biomolecular Engineering, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | | | - Mathieu J M Bertrand
- VIB Inflammation Research Center, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium
| | - Peter Vandenabeele
- VIB Inflammation Research Center, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium; Methusalem Program, Ghent University, Technologiepark 927, 9052 Zwijnaarde-Ghent, Belgium.
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Yeo HJ, Savvides S, Lanka E, Waksman G. Crystal structure of the hexameric traffic ATPase of the Helicobacter pyloritype IV secretion system: insights into function and mode of action. Acta Crystallogr A 2002. [DOI: 10.1107/s0108767302097088] [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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Ponasik JA, Strickland C, Faerman C, Savvides S, Karplus PA, Ganem B. Kukoamine A and other hydrophobic acylpolyamines: potent and selective inhibitors of Crithidia fasciculata trypanothione reductase. Biochem J 1995; 311 ( Pt 2):371-5. [PMID: 7487870 PMCID: PMC1136010 DOI: 10.1042/bj3110371] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The enzyme trypanothione reductase (TR), together with its substrate, the glutathione-spermidine conjugate trypanothione, plays an essential role in protecting parasitic trypanosomatids against oxidative stress and is a target for drug design. Here we show that a naturally occurring spermine derivative, the antihypertensive agent kukoamine A [N1N12-bis(dihydrocaffeoyl)-spermine] inhibits TR as a mixed inhibitor (Ki = 1.8 microM, Kii = 13 microM). Kukoamine shows no significant inhibition of human glutathione reductase (Ki > 10 mM) and thus provides a novel selective drug lead. The corresponding N1N8-bis(dihydrocaffeoyl)spermidine derivative was synthesized and acted as a purely competitive inhibitor with Ki = 7.5 microM. A series of mono- and di-acylated spermines and spermidines were synthesized to gain an insight into the effect of polyamine chain length, the nature and position of the acyl substituent and the importance of conformational mobility. These compounds inhibited TR with Ki values ranging from 11 to 607 microM.
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Affiliation(s)
- J A Ponasik
- Department of Chemistry, Baker Laboratory, Cornell University, Ithaca, NY 14853-1301, USA
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